Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold82
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1057086
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 131930 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:482466 original size:165 final size:163
Alignment explanation
Indices: 481856--482495 Score: 628
Period size: 166 Copynumber: 3.9 Consensus size: 163
481846 TAAAAAAGTT
* * * * * *
481856 CTTGTCCACGTATCTCCTCAAAAACGAGCAATGATAGAAAGCTGAAATTTTCAGGAATGAAAAAG
1 CTTGTCCACGCATTTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTT-ACGAATGATAGA-
* * * * * *
481921 GACATGA-ATGTCTGGCCTCACGAGGAAAATAATTGTCCGGAAATTCCGAGTACGGAAGCTAACT
64 TACAT-ACAAGTCTAGCCTCACGAGGAAAATCATTGTTCGGAAATTCCGAGTACGGAAGCTAACC
481985 GGGGTCAAAATATAGGACACGTTTTAGACGAGAACTC
128 GGGGTCAAAATATAGGACACGTTTTAGACGA-AACTC
** * *
482022 CTTGTCCACGCATCCCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTTAGGAATGATAGCG
1 CTTGTCCACGCATTTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAA-TTTTACGAATGATAG-A
* * * *
482087 GAC--ACGATAGTCTAGCCTCACGAAGAAAATGATTGTCCGGAAATTCCGAGTACGGAAGCTAAC
64 TACATAC-A-AGTCTAGCCTCACGAGGAAAATCATTGTTCGGAAATTCCGAGTACGGAAGCTAAC
**
482150 TTGGGTCAAAATATAGGACACGTTTTAGACGAAAACTC
127 CGGGGTCAAAATATAGGACACGTTTTAGACG-AAACTC
* * *
482188 CTTGTCCACGCATTTCCTCAAGAACAAGCAATGATAGAAAGCTGAAATTGTT-CGAAATGATAGA
1 CTTGTCCACGCATTTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATT-TTACG-AATGATAGA
* * *
482252 TGACATGA-ACGTATAGCCTCACGAGGAAAATCATTG-TCTGGAAATTCCGAGTACGGAAGCTAG
64 T-ACAT-ACAAGTCTAGCCTCACGAGGAAAATCATTGTTC-GGAAATTCCGAGTACGGAAGCTAA
* * * * *
482315 CCAGGGTCAATATATAGGACACGTTTTCGACGAAATTT
126 CCGGGGTCAAAATATAGGACACGTTTTAGACGAAACTC
* * * * * *
482353 TTTGTCCACGCATTTCCTCAAAAATGAGTAAAGATGGAAAGCTGAAATTTTACAGATTGGTAGAA
1 CTTGTCCACGCATTTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTAC-GAATGATAG-A
* * * * * ** * * *
482418 TATATACAAATCTAGCCGCAC-AGGGTAAATTACGGTTCGGAAATTCCGAATGCGGAAGCTAGCC
64 TACATACAAGTCTAGCCTCACGA-GGAAAATCATTGTTCGGAAATTCCGAGTACGGAAGCTAACC
*
482482 GGGGTCAAGATATA
128 GGGGTCAAAATATA
482496 TAACACACTT
Statistics
Matches: 402, Mismatches: 53, Indels: 39
0.81 0.11 0.08
Matches are distributed among these distances:
163 1 0.00
164 4 0.01
165 115 0.29
166 275 0.68
167 6 0.01
169 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.23
Consensus pattern (163 bp):
CTTGTCCACGCATTTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTACGAATGATAGATA
CATACAAGTCTAGCCTCACGAGGAAAATCATTGTTCGGAAATTCCGAGTACGGAAGCTAACCGGG
GTCAAAATATAGGACACGTTTTAGACGAAACTC
Found at i:482895 original size:134 final size:134
Alignment explanation
Indices: 482648--484011 Score: 1242
Period size: 134 Copynumber: 10.3 Consensus size: 134
482638 GACACTCAAT
* * *
482648 TTTTAAATTCATAATAAAT-GTGTTATAATGACCTCAGACTAGTTTTAAAACATGATATCTAAGT
1 TTTTAAATTCA-ATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGT
** * * * * *
482712 TGCACACACAATTCTTCGTCTAATGAAATC-TTCTTCAAATTGATGGGATGAAATTTGAATTTTT
65 TGCACTTACAATTCTGCGTCTAATGACATCTTTC-TCGAATTGATTGGATGAAATTTAAATTTTT
**
482776 TGAAAA
129 CAAAAA
* * * * * *
482782 TTTTAAATTTAATTAAATCGTGTTAAAACT-TCCTGAGACTAATTTTAAAACGTGATATGTAAAT
1 TTTTAAATTCAATTAAATCGTGTTAAAA-TGACCTCAGACTAATTTTAAAACATGATATCTAAGT
* * *
482846 TGCACTTACAATTCTGCGTCAAATGACATCTTTTTCGAATTGGA-CGGATGAAATTTAAATTTTT
65 TGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATT-GATTGGATGAAATTTAAATTTTT
482910 CAAAAA
129 CAAAAA
* * * * * * * * * **
482916 ATTTAAAGTCATTTAAATTGTATTAAAATGACATTAGACCAACTTTAGTACATGATATCTAAGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
* * * * *
482981 TCACTTACAATTCTGCATCTGATGACATCTTTCTCGAATTGATTGGATGAATTTTTAATTTTTCA
66 GCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTTCA
483046 AAAA
131 AAAA
* * * ** * * *
483050 TTTTAAACTCATTTTAATCGCATTAAAATGACCTCAGACTAACTTTAAAACATGATACCTCAGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
** * *
483115 GTGCTTACAATTCTGCATCTGATGACATCTTTCTCGAATTGATTGGAT-AAATTTTAAATTTTTC
66 GCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAA-TTTAAATTTTTC
483179 AAAAA
130 AAAAA
* * * * * * * *
483184 TTTTAAACTCATTTAAATTGCGTTAAAATGACATCAGACTGATTTTAAAACATGATACCTCAGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
* * * * *
483249 G-AGCTTACAATTCTGCATCTAATGACATCTTTTTTGAATTGATTGGATGAATTTTAAATTTTTG
66 GCA-CTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTTC
*
483313 GAAAA
130 AAAAA
* * * * * * ** * * *
483318 TTCTAAAATCGATTAAATCGTGTTAAAATGAGCTGAGACTAGTTTTAAATTATAATATTTAGGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
** * * * * * * *
483383 GTGCCTAGAATTTTGCGTCTAATGACATCTTTCTCGAATTGAATAGATGAATTTTAACTTTTTCA
66 GCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTTCA
*
483448 AACA
131 AAAA
* * * * * * * *
483452 TTTTAATTTCATTTAAATCGCGTTAAAATGATCTCAAACTAATTTTCAAACATAACATCTAAGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
** * * * * **
483517 GTGCTTACAATTCCGCGTCTAATGGCATCTTTCTCGAATTGATTGGATG-ATTTTTAATTTTTTT
66 GCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTTCA
483581 AAAA
131 AAAA
* * * *
483585 TTTTAAATTTAAATAAATCGTGTTTAAATGACATCAGACTAATTTTAAAACATGATATCTAAGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
*** * * **
483650 TTGCTTACAATT-TCGCGTCTAATGACATCTTTTTCGAAATGATTGGATGATTTTTAAATTTTTG
66 GCACTTACAATTCT-GCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTT-
*
483714 GAAAAA
129 CAAAAA
** * * * * * *
483720 -TTTAAATTTGAGTAAATCGTGTTAAAATGACCTCAGGCAAATTTCAAAACATTATATGTAAGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
* * * * * *
483784 ACACTTACAATTCTGCGTCTGATGA-ATCTTCCTCGAATTGATTCGATGAATTTTATATTTTT--
66 GCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTTCA
483846 ---A
131 AAAA
* * * * *
483847 ---T---CTCATTTAAATCGCGTTAAAATGACCTCAAACTAATTTTCAAACATGATATCTAAGTT
1 TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
* * * * * *
483906 GCGCTTACAATTCTGCGTCTGATGTCATCTTTCTTGAATTGATTGGATGAATTTTAAATTCTTCA
66 GCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTTCA
483971 AAAA
131 AAAA
* *
483975 TTTT-AATCTCATTTAAATCGCGTTAAAATGACCTCAG
1 TTTTAAAT-TCAATTAAATCGTGTTAAAATGACCTCAG
484012 CCATTGTGTA
Statistics
Matches: 1008, Mismatches: 196, Indels: 52
0.80 0.16 0.04
Matches are distributed among these distances:
122 67 0.07
123 32 0.03
125 1 0.00
127 1 0.00
128 1 0.00
131 1 0.00
133 152 0.15
134 741 0.74
135 12 0.01
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.39
Consensus pattern (134 bp):
TTTTAAATTCAATTAAATCGTGTTAAAATGACCTCAGACTAATTTTAAAACATGATATCTAAGTT
GCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTTCA
AAAA
Found at i:488396 original size:2 final size:2
Alignment explanation
Indices: 488389--488442 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
488379 TACATACAGA
488389 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
488431 CT CT CT CT CT CT
1 CT CT CT CT CT CT
488443 TGTTACAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:500528 original size:12 final size:12
Alignment explanation
Indices: 500511--500535 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
500501 AATATGACTC
500511 ATTTATTAAAAT
1 ATTTATTAAAAT
500523 ATTTATTAAAAT
1 ATTTATTAAAAT
500535 A
1 A
500536 CAGAGGAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTATTAAAAT
Found at i:502455 original size:166 final size:165
Alignment explanation
Indices: 502181--502958 Score: 812
Period size: 166 Copynumber: 4.7 Consensus size: 165
502171 TAAAAACGTT
* * * *
502181 CTTGTCCACGTATCTCCTCAAAAACGAGCAATGATAGAAAGCTGAAATTTTCAGGAATGAAAAAG
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAATGATAGAG
*
502246 GACATGAATGTCTAGCCTCACGAGGAAAATCATTGTCCGGAAATTCCGAGTACGGAAGCTAACTG
66 GACATGAA-GTCTAGCCTCACGAGGAAAATCATTGTCCGGAAATTCCGAGTACGGAAGCTAACCG
*
502311 GGGTCAAAATATAGGACACGTTTTTTACGAGAACTC
130 GGGTCAAAATATAGGACACGTTTTTGACGAGAACTC
502347 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAATGATAGAG
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAATGATAGAG
* * *
502412 GACACGATAGTCTAGCCTCACGAGGAAAATGATTGTCCGGAAATTCCGAGTACGGAAGCTAACTG
66 GACATGA-AGTCTAGCCTCACGAGGAAAATCATTGTCCGGAAATTCCGAGTACGGAAGCTAACCG
* *
502477 GGGTCAAAATATAGGACACGTTTTAGACGAAAACTC
130 GGGTCAAAATATAGGACACGTTTTTGACGAGAACTC
* * * * *
502513 CTTGTCCACGCATTTCCTCAAGAACAAGCAATGATAGAAAGCTGAAATTGTTC-GAAATGATAGA
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATT-TTCAGGAATGATAGA
* * *
502577 TGACATGAACGTCTAGCCTCACGAGGAAAATCATTGTCTGGAAATTCCGAGTACGGAAGCTAGCC
65 GGACATGAA-GTCTAGCCTCACGAGGAAAATCATTGTCCGGAAATTCCGAGTACGGAAGCTAACC
* * *** *
502642 AGGGTCAATATATAGGACACGTTTTTGACGA-CTTTT
129 GGGGTCAAAATATAGGACACGTTTTTGACGAGAACTC
* * * * * * * *
502678 TTTGTCCACGCATTTCCTCAAAAATGAGTAAAGATGGAAAGCTTAAATTTTACA-GATTGGTAGA
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTT-CAGGAATGATAGA
* * * * * * * ** * * * *
502742 AGATATACAAATCTAGCCGCAC-AGGGTAAATTACGGTTCGGAAATTCCGAATGCGGAAGCTAGC
65 GGACAT-GAAGTCTAGCCTCACGA-GGAAAATCATTGTCCGGAAATTCCGAGTACGGAAGCTAAC
** * * ***
502806 CGGGGTCAAGATATATATCACAC--TTTTGATGGGTTTTC
128 CGGGGTCAA-A-ATATAGGACACGTTTTTGACGAGAACTC
* * * ** ** * **
502844 ATTGTCCACACATGTATTTTAAAGCGAAAAAAGATAGAAAGCTGAAATTTTCAGGAATGATAGAG
1 CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAATGATAGAG
* * * * *
502909 GACATGATAGACTAGCATTACGAGAAAAATCATTGTCTGGAAATTCCGAG
66 GACATGA-AGTCTAGCCTCACGAGGAAAATCATTGTCCGGAAATTCCGAG
502959 AAGGGACACT
Statistics
Matches: 509, Mismatches: 90, Indels: 26
0.81 0.14 0.04
Matches are distributed among these distances:
164 3 0.01
165 115 0.23
166 377 0.74
167 14 0.03
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (165 bp):
CTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAATGATAGAG
GACATGAAGTCTAGCCTCACGAGGAAAATCATTGTCCGGAAATTCCGAGTACGGAAGCTAACCGG
GGTCAAAATATAGGACACGTTTTTGACGAGAACTC
Found at i:502905 original size:331 final size:330
Alignment explanation
Indices: 502209--502958 Score: 820
Period size: 331 Copynumber: 2.3 Consensus size: 330
502199 CAAAAACGAG
* *
502209 CAATGATAGAAAGCTGAAATTTTCAGGAATGAAAAAGGACATGAATGTCTAGCCTCACGAGGAAA
1 CAATGATAGAAAGCTGAAATTTTCAGGAATGATAGAGGACATGAA-GTCTAGCCTCACGAGGAAA
* ** *
502274 ATCATTGTCCGGAAATTCCGAGTACGGAAGCTAACTGGGGTCAAAATATAGGACACGTTTTTTAC
65 ATCATTGTCTGGAAATTCCGAGTACGGAAGCTAACCAGGGTCAAAATATAGGACACGTTTTTGAC
502339 GAGAACTCCTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAA
130 GAGAACTCCTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAA
* * ** *
502404 TGATAGAGGACACGATAGTCTAGCCTCACGAGGAAAATGATTGTCCGGAAATTCCGAGTACGGAA
195 TGATAGAGGACACGATAATCTAGCCGCACGAGGAAAATGACGGTCCGGAAATTCCGAATACGGAA
* * * * *
502469 GCTAACTGGGGTCAAAATATAGGACACGTTTTAGACGAAAACTCCTTGTCCACGCATTTCCTCAA
260 GCTAACCGGGGTCAAAATATAGCACACGTTTTAGACGAAAACTCATTGTCCACACATTTCCTAAA
502534 GAACAA
325 GAACAA
* *
502540 GCAATGATAGAAAGCTGAAATTGTTC-GAAATGATAGATGACATGAACGTCTAGCCTCACGAGGA
1 -CAATGATAGAAAGCTGAAATT-TTCAGGAATGATAGAGGACATGAA-GTCTAGCCTCACGAGGA
* *
502604 AAATCATTGTCTGGAAATTCCGAGTACGGAAGCTAGCCAGGGTCAATATATAGGACACGTTTTTG
63 AAATCATTGTCTGGAAATTCCGAGTACGGAAGCTAACCAGGGTCAAAATATAGGACACGTTTTTG
*** ** * * * * *
502669 ACGA-CTTTTTTTGTCCACGCATTTCCTCAAAAATGAGTAAAGATGGAAAGCTTAAATTTTACA-
128 ACGAGAACTCCTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTT-CAG
* * * * * * *
502732 GATTGGTAGAAGATATAC-A-AATCTAGCCGCAC-AGGGTAAATTACGGTTCGGAAATTCCGAAT
192 GAATGATAG-AG-GACACGATAATCTAGCCGCACGA-GGAAAATGACGGTCCGGAAATTCCGAAT
* * * * *****
502794 GCGGAAGCTAGCCGGGGTCAAGATATATATCACAC-TTTT-GATGGGTTTTCATTGTCCACACAT
254 ACGGAAGCTAACCGGGGTCAA-A-ATATAGCACACGTTTTAGACGAAAACTCATTGTCCACACAT
**
502857 GTATTTTAAAGCGAA-AA
317 -T-TCCTAAA--GAACAA
* * * *
502874 -AA-GATAGAAAGCTGAAATTTTCAGGAATGATAGAGGACATGATAGACTAGCATTACGAGAAAA
1 CAATGATAGAAAGCTGAAATTTTCAGGAATGATAGAGGACATGA-AGTCTAGCCTCACGAGGAAA
502937 ATCATTGTCTGGAAATTCCGAG
65 ATCATTGTCTGGAAATTCCGAG
502959 AAGGGACACT
Statistics
Matches: 350, Mismatches: 55, Indels: 27
0.81 0.13 0.06
Matches are distributed among these distances:
330 4 0.01
331 191 0.55
332 131 0.37
333 19 0.05
334 2 0.01
335 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (330 bp):
CAATGATAGAAAGCTGAAATTTTCAGGAATGATAGAGGACATGAAGTCTAGCCTCACGAGGAAAA
TCATTGTCTGGAAATTCCGAGTACGGAAGCTAACCAGGGTCAAAATATAGGACACGTTTTTGACG
AGAACTCCTTGTCCACGCATCTCCTCAAAAACGAGCAAAGATAGAAAGCTGAAATTTTCAGGAAT
GATAGAGGACACGATAATCTAGCCGCACGAGGAAAATGACGGTCCGGAAATTCCGAATACGGAAG
CTAACCGGGGTCAAAATATAGCACACGTTTTAGACGAAAACTCATTGTCCACACATTTCCTAAAG
AACAA
Found at i:503220 original size:134 final size:133
Alignment explanation
Indices: 502969--504200 Score: 1043
Period size: 134 Copynumber: 9.3 Consensus size: 133
502959 AAGGGACACT
* * *
502969 AAATTTTAAAATTCATAA-TAAAT-GTGTTATAATGACCTCAGACTAGTTTTAAAACATAATATC
1 AAATTTT-AAATT--TAATTAAATCGTGTTAAAATGACC-CAGACTAATTTTAAAACATGATATC
** * * * * *
503032 TAAGTTGCACACACAATTCTGCGTCTAATGAAATCTTTTTCAAATTGATGGGATGAAATTTGAAT
62 TAAGTTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAAT
*
503097 TTTTTGA
127 TTTTCGA
*
503104 AAATTTTAAATTTAATTAAATCGTGTTAAAACT-TCCCGAGACTAATTTTAAAACATGATATCTA
1 AAATTTTAAATTTAATTAAATCGTGTTAAAA-TGACCC-AGACTAATTTTAAAACATGATATCTA
* * * * *
503168 AATTGCACTTACATTTCTGCGTCAAATGACATCTTTTTCGAATTGGA-CGGATGAAATTTAAATT
64 AGTTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATT-GATTGGATGAAATTTAAATT
*
503232 TTTCAA
128 TTTCGA
* * * * * ** * * **
503238 AAAATTTAAAGTCATTTAAATTGTGTTAAAATGACATAAGACCAACTTTAGTACATGATATCTAA
1 AAATTTTAAATTTAATTAAATCGTGTTAAAATGAC-CCAGACTAATTTTAAAACATGATATCTAA
* * *
503303 GTTTCACTTACAATTCTGCATCTGATGACATCTTTCTCGAATTGATTGGAT-AAATTTTAAATTT
65 GTTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAA-TTTAAATTT
*
503367 TTCAA
129 TTCGA
* * * * * * * *
503372 AAATTTTAAACTCATTTAAATTGCGTTAAAATGACATCAGACTGATTTTAAAACATGATA-CCAC
1 AAATTTTAAATTTAATTAAATCGTGTTAAAATGAC-CCAGACTAATTTTAAAACATGATATCTA-
*
503436 AGTTG-AGCTTACAATTCTGCATCTAATGACATCTTTCTCGAATTGATTGGAT-AAATTTTAAAT
64 AGTTGCA-CTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAA-TTTAAAT
*
503499 TTTTGGA
127 TTTTCGA
* ** ** * ** * * *
503506 AAATTTTAAAATCGATTAAATCGTGTTAAAATGAGCTGAGACTAGTTTTAAATTATAATATTTAC
1 AAATTTTAAATTTAATTAAATCGTGTTAAAATGA-CCCAGACTAATTTTAAAACATGATATCTAA
* ** * * * * * *
503571 TTTGTGCTTAGAATTCTGCGTCTAATGACATCTTTTTCGAATTGAATAGATGAATTTTAACTTTT
65 GTTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTT
*
503636 TCAA
130 TCGA
* * * * * * *
503640 AAATTTT-AATTTCATTTAAATCGCGTTAAAATGATCTCAAACTAATTTTCAAACATAACATCTA
1 AAATTTTAAATTT-AATTAAATCGTGTTAAAATGA-CCCAGACTAATTTTAAAACATGATATCTA
* * * ** *
503704 AGTTGCGCTTACAATTCCGCGTCTTATGACATCTTTCTCGAATTGATTGGATGATTTTTAATTTT
64 AGTTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTT
*
503769 TTTGA
129 TTCGA
* * *
503774 AAATTTTAAATTTAAATAAATCGTGTTTAAATGACATCAGACTAATTTTAAAACATGATATCTAA
1 AAATTTTAAATTTAATTAAATCGTGTTAAAATGAC-CCAGACTAATTTTAAAACATGATATCTAA
*** * * * **
503839 GTTTTGCTTACAATT-TCGTGTCTAATGACATCTTTTTCGAAATGATTGGATGATTTTTAAATTT
65 GTTGCACTTACAATTCT-GCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTT
*
503903 TTGGA
129 TTCGA
* * * * * *
503908 AAAATTTAAA-TTATAGTAAATCGTGTTAAAATGACCTCAGGCTAATTTCAAAACATTATATGTA
1 AAATTTTAAATTTA-ATTAAATCGTGTTAAAATGACC-CAGACTAATTTTAAAACATGATATCTA
* * * * * *
503972 AGTTACACTTACAATTCTGCGTCTGATGACATCTTCCTCGAATTGATTCGATGAATTTTATATTT
64 AGTTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTT
504037 TT---
129 TTCGA
* * * * *
504039 --A-TCT-CA--T--TTAAATCGCGTTAAAATGACCTCAAACTAATTTTCAAACATGATATCTAA
1 AAATTTTAAATTTAATTAAATCGTGTTAAAATGACC-CAGACTAATTTTAAAACATGATATCTAA
* * * * * *
504096 GTTGCGCTTACAATTCTGCGTCTGATGTCATCTTTCTTGAATTGATTGGATGAATTTTAAATTCT
65 GTTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTT
*
504161 TCAA
130 TCGA
* * * *
504165 AAAATTT-AATCTCATTTAAATCGCGTTAAAATGACC
1 AAATTTTAAAT-TTAATTAAATCGTGTTAAAATGACC
504201 TCAGCCATTG
Statistics
Matches: 906, Mismatches: 158, Indels: 67
0.80 0.14 0.06
Matches are distributed among these distances:
123 100 0.11
126 1 0.00
127 1 0.00
128 3 0.00
129 4 0.00
132 3 0.00
133 22 0.02
134 752 0.83
135 20 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (133 bp):
AAATTTTAAATTTAATTAAATCGTGTTAAAATGACCCAGACTAATTTTAAAACATGATATCTAAG
TTGCACTTACAATTCTGCGTCTAATGACATCTTTCTCGAATTGATTGGATGAAATTTAAATTTTT
CGA
Found at i:503750 original size:402 final size:399
Alignment explanation
Indices: 502994--504204 Score: 1331
Period size: 402 Copynumber: 3.0 Consensus size: 399
502984 TAATAAATGT
* * * * * **
502994 GTTATAATGACCTCAGACTAGTTTTAAAACATAATATCTAAGTTGCA-CACACAATTCTGCGTCT
1 GTTAAAATGACATCAGACTAATTTTAAAACATGATATCCAAGTTG-AGCTTACAATTCTGC-TCT
* * * * * *
503058 AATGAAATCTTTTTCAAATTGATGGGATGAAA-TTTGAATTTTTTGAAAATTTTAAATTTAATTA
64 AATGACATCTTTTTCGAATTGATTGGAT-AAATTTTAAATTTTTGGAAAATTTTAAATTAAATTA
* * * *
503122 AATCGTGTTAAAACT-TCCCGAGACTAATTTTAAAACATGATATCTAAATTGCACTTACATTTCT
128 AATCGTGTTAAAA-TGACCTGAGACTAATTTTAAAACATAATATCTAAATTGCACTTACAATTCT
* * ** * * **
503186 GCGTCAAATGACATCTTTTTCGAATTGGACGGATGAAATTTAAATTTTTCAAAAAATTTAAAGTC
192 GCGTCTAATGACATCTTTTTCGAATTGAATAGATG-AATTTTAATTTTTCAAAAATTTTAATCTC
* * * * * * *
503251 ATTTAAATTGTGTTAAAATGACAT-AAGACCAACTTT-AGTACATGATATCTAAGTTTCACTTAC
256 ATTTAAATCGCGTTAAAATGAC-TCAA-ACTAATTTTCA-AACATGATATCTAAGTTGCGCTTAC
* *
503314 AATTCTGCATCTGATGACATCTTTCTCGAATTGATTGGATAAATTTTAAATTTTTCAAAAATTTT
318 AATTCTGCGTCTGATGACATCTTTCTCGAATTGATTGGATGAATTTTAAATTTTTCAAAAATTTT
*
503379 AAACTCATTTAAATTGC
383 AAACTCATTTAAATCGC
*
503396 GTTAAAATGACATCAGACTGATTTTAAAACATGATA-CCACAGTTGAGCTTACAATTCTGCATCT
1 GTTAAAATGACATCAGACTAATTTTAAAACATGATATCCA-AGTTGAGCTTACAATTCTGC-TCT
* * **
503460 AATGACATCTTTCTCGAATTGATTGGATAAATTTTAAATTTTTGGAAAATTTTAAAATCGATTAA
64 AATGACATCTTTTTCGAATTGATTGGATAAATTTTAAATTTTTGGAAAATTTTAAATTAAATTAA
* * ** * ** ** *
503525 ATCGTGTTAAAATGAGCTGAGACTAGTTTTAAATTATAATATTTACTTTGTGCTTAGAATTCTGC
129 ATCGTGTTAAAATGACCTGAGACTAATTTTAAAACATAATATCTAAATTGCACTTACAATTCTGC
*
503590 GTCTAATGACATCTTTTTCGAATTGAATAGATGAATTTTAACTTTTTCAAAAATTTTAATTTCAT
194 GTCTAATGACATCTTTTTCGAATTGAATAGATGAATTTTAA-TTTTTCAAAAATTTTAATCTCAT
* *
503655 TTAAATCGCGTTAAAATGATCTCAAACTAATTTTCAAACATAACATCTAAGTTGCGCTTACAATT
258 TTAAATCGCGTTAAAATGA-CTCAAACTAATTTTCAAACATGATATCTAAGTTGCGCTTACAATT
* * * * ** *
503720 CCGCGTCTTATGACATCTTTCTCGAATTGATTGGATGATTTTTAATTTTTTTGAAAATTTTAAAT
322 CTGCGTCTGATGACATCTTTCTCGAATTGATTGGATGAATTTTAAATTTTTCAAAAATTTTAAAC
* ** *
503785 TTAAATAAATCGT
387 TCATTTAAATCGC
* * **
503798 GTTTAAATGACATCAGACTAATTTTAAAACATGATATCTAAGTTTTGCTTACAATTTCGTG-TCT
1 GTTAAAATGACATCAGACTAATTTTAAAACATGATATCCAAGTTGAGCTTACAA-TTC-TGCTCT
* * * * * *
503862 AATGACATCTTTTTCGAAATGATTGGATGATTTTTAAATTTTTGGAAAAATTTAAATTATAGTAA
64 AATGACATCTTTTTCGAATTGATTGGATAAATTTTAAATTTTTGGAAAATTTTAAATTAAATTAA
* * * * * * *
503927 ATCGTGTTAAAATGACCTCAGGCTAATTTCAAAACATTATATGTAAGTTACACTTACAATTCTGC
129 ATCGTGTTAAAATGACCTGAGACTAATTTTAAAACATAATATCTAAATTGCACTTACAATTCTGC
* ** * * *
503992 GTCTGATGACATCTTCCTCGAATTGATTCGATGAATTTT-A----T-----ATTTTTATCTCATT
194 GTCTAATGACATCTTTTTCGAATTGAATAGATGAATTTTAATTTTTCAAAAATTTTAATCTCATT
504047 TAAATCGCGTTAAAATGACCTCAAACTAATTTTCAAACATGATATCTAAGTTGCGCTTACAATTC
259 TAAATCGCGTTAAAATGA-CTCAAACTAATTTTCAAACATGATATCTAAGTTGCGCTTACAATTC
* * * * *
504112 TGCGTCTGATGTCATCTTTCTTGAATTGATTGGATGAATTTTAAATTCTTCAAAAAATTTAATCT
323 TGCGTCTGATGACATCTTTCTCGAATTGATTGGATGAATTTTAAATTTTTCAAAAATTTTAAACT
504177 CATTTAAATCGC
388 CATTTAAATCGC
*
504189 GTTAAAATGACCTCAG
1 GTTAAAATGACATCAG
504205 CCATTGTGTA
Statistics
Matches: 678, Mismatches: 120, Indels: 33
0.82 0.14 0.04
Matches are distributed among these distances:
391 149 0.22
396 1 0.00
401 15 0.02
402 502 0.74
403 9 0.01
404 2 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (399 bp):
GTTAAAATGACATCAGACTAATTTTAAAACATGATATCCAAGTTGAGCTTACAATTCTGCTCTAA
TGACATCTTTTTCGAATTGATTGGATAAATTTTAAATTTTTGGAAAATTTTAAATTAAATTAAAT
CGTGTTAAAATGACCTGAGACTAATTTTAAAACATAATATCTAAATTGCACTTACAATTCTGCGT
CTAATGACATCTTTTTCGAATTGAATAGATGAATTTTAATTTTTCAAAAATTTTAATCTCATTTA
AATCGCGTTAAAATGACTCAAACTAATTTTCAAACATGATATCTAAGTTGCGCTTACAATTCTGC
GTCTGATGACATCTTTCTCGAATTGATTGGATGAATTTTAAATTTTTCAAAAATTTTAAACTCAT
TTAAATCGC
Found at i:504148 original size:123 final size:123
Alignment explanation
Indices: 503924--504154 Score: 347
Period size: 123 Copynumber: 1.9 Consensus size: 123
503914 TAAATTATAG
* ** * *
503924 TAAATCGTGTTAAAATGACCTCAGGCTAATTTCAAAACATTATATGTAAGTTACACTTACAATTC
1 TAAATCGCGTTAAAATGACCTCAAACTAATTTCAAAACATGATATCTAAGTTACACTTACAATTC
503989 TGCGTCTGATGACATCTTCCTCGAATTGATTCGATGAATTTTATATTTTTATCTCATT
66 TGCGTCTGATGACATCTTCCTCGAATTGATTCGATGAATTTTATATTTTTATCTCATT
* *
504047 TAAATCGCGTTAAAATGACCTCAAACTAATTTTC-AAACATGATATCTAAGTTGCGCTTACAATT
1 TAAATCGCGTTAAAATGACCTCAAACTAA-TTTCAAAACATGATATCTAAGTTACACTTACAATT
* * * *
504111 CTGCGTCTGATGTCATCTTTCTTGAATTGATTGGATGAATTTTA
65 CTGCGTCTGATGACATCTTCCTCGAATTGATTCGATGAATTTTA
504155 AATTCTTCAA
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
123 92 0.96
124 4 0.04
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (123 bp):
TAAATCGCGTTAAAATGACCTCAAACTAATTTCAAAACATGATATCTAAGTTACACTTACAATTC
TGCGTCTGATGACATCTTCCTCGAATTGATTCGATGAATTTTATATTTTTATCTCATT
Found at i:507256 original size:2 final size:2
Alignment explanation
Indices: 507249--507298 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
507239 TACATACAGA
507249 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
507291 CT CT CT CT
1 CT CT CT CT
507299 TTTGTTACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:509854 original size:15 final size:15
Alignment explanation
Indices: 509817--509855 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
509807 TACTATTACA
509817 TATGATATTGCAATC
1 TATGATATTGCAATC
*
509832 TATAATATTGC-ATCC
1 TATGATATTGCAAT-C
509847 TATGATATT
1 TATGATATT
509856 ATATTGTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 2 0.10
15 19 0.90
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (15 bp):
TATGATATTGCAATC
Found at i:511194 original size:16 final size:16
Alignment explanation
Indices: 511173--511207 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
511163 TACAGGTGGT
511173 CTCATAAAAGTGATGC
1 CTCATAAAAGTGATGC
*
511189 CTCATAAAGGTGATGC
1 CTCATAAAAGTGATGC
511205 CTC
1 CTC
511208 GTCTCGGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (16 bp):
CTCATAAAAGTGATGC
Found at i:515210 original size:19 final size:20
Alignment explanation
Indices: 515164--515201 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
515154 CGCCCCCAAC
515164 AAAAGC-AAGCAAGCAAGCA
1 AAAAGCAAAGCAAGCAAGCA
515183 AAAAGCAAAGCAA-CAAGCA
1 AAAAGCAAAGCAAGCAAGCA
515202 TTAAGCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.61, C:0.21, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAGCAAAGCAAGCAAGCA
Found at i:515272 original size:22 final size:22
Alignment explanation
Indices: 515244--515300 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
515234 ATGACGTAAT
*
515244 TATGACGTCATCAACAAGCAAA
1 TATGACGTAATCAACAAGCAAA
* *
515266 TATGACGTTATCAATAAGCAAA
1 TATGACGTAATCAACAAGCAAA
515288 TATGACGTAATCA
1 TATGACGTAATCA
515301 TGCACTGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (22 bp):
TATGACGTAATCAACAAGCAAA
Found at i:516106 original size:19 final size:20
Alignment explanation
Indices: 516060--516097 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
516050 CGCCCCCAAC
516060 AAAAGC-AAGCAAGCAAGCA
1 AAAAGCAAAGCAAGCAAGCA
516079 AAAAGCAAAGCAA-CAAGCA
1 AAAAGCAAAGCAAGCAAGCA
516098 TTAAGCAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.61, C:0.21, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAGCAAAGCAAGCAAGCA
Found at i:516165 original size:22 final size:22
Alignment explanation
Indices: 516140--516196 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
516130 ATGACGTAAT
*
516140 TATGACGTCATCAACAAGCAAA
1 TATGACGTAATCAACAAGCAAA
* *
516162 TATGACGTTATCAATAAGCAAA
1 TATGACGTAATCAACAAGCAAA
516184 TATGACGTAATCA
1 TATGACGTAATCA
516197 TGCACTGGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.25
Consensus pattern (22 bp):
TATGACGTAATCAACAAGCAAA
Found at i:517345 original size:88 final size:88
Alignment explanation
Indices: 517223--517437 Score: 403
Period size: 88 Copynumber: 2.4 Consensus size: 88
517213 GTATGATACA
* *
517223 AGACTAGCCCAATAATGCTTATCATTAACGAATATATGTTAAACTAAGTTACTACTTACTTAAAA
1 AGACTATCCCAATAATTCTTATCATTAACGAATATATGTTAAACTAAGTTACTACTTACTTAAAA
517288 TGATGAATGTATGATGGTATATG
66 TGATGAATGTATGATGGTATATG
517311 AGACTATCCCAATAATTCTTATCATTAACGAATATATGTTAAACTAAGTTACTACTTACTTAAAA
1 AGACTATCCCAATAATTCTTATCATTAACGAATATATGTTAAACTAAGTTACTACTTACTTAAAA
517376 TGATGAATGTATGATGGTATATG
66 TGATGAATGTATGATGGTATATG
*
517399 AGACTTTCCCAATAATTCTTATCATTAACGAATATATGT
1 AGACTATCCCAATAATTCTTATCATTAACGAATATATGT
517438 GCGATAGGCA
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 124 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (88 bp):
AGACTATCCCAATAATTCTTATCATTAACGAATATATGTTAAACTAAGTTACTACTTACTTAAAA
TGATGAATGTATGATGGTATATG
Found at i:519931 original size:21 final size:21
Alignment explanation
Indices: 519905--519982 Score: 122
Period size: 21 Copynumber: 3.7 Consensus size: 21
519895 AGGGCCCATT
519905 TGTCTTGACTGTGGTGTAACA
1 TGTCTTGACTGTGGTGTAACA
519926 TGTCTTGACTGTGGTGTAACA
1 TGTCTTGACTGTGGTGTAACA
* *
519947 TGTCTTGGCTGAGGTGTAA-A
1 TGTCTTGACTGTGGTGTAACA
519967 TTGTCTTGACTGTGGT
1 -TGTCTTGACTGTGGT
519983 AAGACTTGCC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 1 0.02
21 51 0.98
ACGTcount: A:0.17, C:0.13, G:0.31, T:0.40
Consensus pattern (21 bp):
TGTCTTGACTGTGGTGTAACA
Found at i:519996 original size:42 final size:42
Alignment explanation
Indices: 519917--519996 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
519907 TCTTGACTGT
* *
519917 GGTGTAACATGTCTTGACTGTGGTGTAACATGTCTTGGCTGA
1 GGTGTAACATGTCTTGACTGTGGTGAAACATGCCTTGGCTGA
*
519959 GGTGTAA-ATTGTCTTGACTGTGGT-AAGACTTGCCTTGG
1 GGTGTAACA-TGTCTTGACTGTGGTGAA-ACATGCCTTGG
519997 TTGATAGGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.06
42 31 0.94
ACGTcount: A:0.19, C:0.14, G:0.31, T:0.36
Consensus pattern (42 bp):
GGTGTAACATGTCTTGACTGTGGTGAAACATGCCTTGGCTGA
Found at i:522614 original size:32 final size:32
Alignment explanation
Indices: 522573--522666 Score: 134
Period size: 32 Copynumber: 2.9 Consensus size: 32
522563 TTCAGGCAAA
522573 GGGGTCATTTTTCTACGTAGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
* * *
522605 GGGGTCATTTTTCTGCTTATAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
** *
522637 GGGGTCATAATTCTACGTAGAAAAATGACC
1 GGGGTCATTTTTCTACGTAGAATAATGACC
522667 CCCGGTCATT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.31
Consensus pattern (32 bp):
GGGGTCATTTTTCTACGTAGAATAATGACCGG
Found at i:526453 original size:2 final size:2
Alignment explanation
Indices: 526446--526509 Score: 101
Period size: 2 Copynumber: 32.0 Consensus size: 2
526436 TCCAAAAACT
526446 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
526488 GA GA AA GA GA GA CA CA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
526510 AAGACAGATA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.52, C:0.03, G:0.45, T:0.00
Consensus pattern (2 bp):
GA
Found at i:538627 original size:21 final size:21
Alignment explanation
Indices: 538602--538641 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
538592 TTTTATTCTA
*
538602 AAATGTTAATGCATCAAATAT
1 AAATGTTAAGGCATCAAATAT
538623 AAATGTTAAGGCATCAAAT
1 AAATGTTAAGGCATCAAAT
538642 GGCAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (21 bp):
AAATGTTAAGGCATCAAATAT
Found at i:545375 original size:48 final size:48
Alignment explanation
Indices: 545322--545687 Score: 268
Period size: 48 Copynumber: 7.6 Consensus size: 48
545312 TTCTTGGTAA
* * * *
545322 AGATGGGCATGACATGCAGCCACATGGAAAACCTAA-TGTATTTGGTGG
1 AGATGGACATGACATGAAGCCACATGGAAAACCAAACT-TAATTGGTGG
** *
545370 AGATGGACATGATTTGAAGCCACATGGAAAATCAAACTTAATTGGTGG
1 AGATGGACATGACATGAAGCCACATGGAAAACCAAACTTAATTGGTGG
* * * * * *
545418 AGATGGACATGATC-TAAAGCCTCATGGAAAATCAAATTTGATTGGCGG
1 AGATGGACATGA-CATGAAGCCACATGGAAAACCAAACTTAATTGGTGG
* * * *
545466 AGAT-GATCATGACTTGAAGCCACA--CAAACAGCAGATA-TTGATTGGTGG
1 AGATGGA-CATGACATGAAGCCACATGGAAA-ACCA-A-ACTTAATTGGTGG
* *
545514 AGATGGACATGATC-TAAAGCCACATGGAAAACCAAA-TCTGATTGGTGG
1 AGATGGACATGA-CATGAAGCCACATGGAAAACCAAACT-TAATTGGTGG
* * * *
545562 AGATGGACATGATC-TAAAGCCACATGTAAAATCAAA-TCTGATTGGTGG
1 AGATGGACATGA-CATGAAGCCACATGGAAAACCAAACT-TAATTGGTGG
* * ** * *
545610 AGATGGACATGACATGAAACCTCATGGAAAGTCAAA-TCTGATAGGTGG
1 AGATGGACATGACATGAAGCCACATGGAAAACCAAACT-TAATTGGTGG
* * *
545658 AGATGGACATGACTTGAAACCTCATGGAAA
1 AGATGGACATGACATGAAGCCACATGGAAA
545688 CTTTAATCCT
Statistics
Matches: 275, Mismatches: 30, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
46 3 0.01
47 9 0.03
48 252 0.92
49 8 0.03
50 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.23
Consensus pattern (48 bp):
AGATGGACATGACATGAAGCCACATGGAAAACCAAACTTAATTGGTGG
Found at i:545483 original size:96 final size:95
Alignment explanation
Indices: 545363--545687 Score: 401
Period size: 96 Copynumber: 3.4 Consensus size: 95
545353 CCTAATGTAT
* *
545363 TTGGTGGAGATGGACATGATTTGAAGCCACATGGAAAATCAAACTTAATTGGTGGAGATGGACAT
1 TTGGTGGAGATGGACATGACTTGAAGCCACATGGAAAATCAAA-TTGATTGGTGGAGATGGACAT
*
545428 GATCTAAAGCCTCATGGAAAATCAAATTTGA
65 GATCTAAAGCCTCATGGAAAATCAAATCTGA
* * *
545459 TTGGCGGAGAT-GATCATGACTTGAAGCCACA--CAAACAGCAGATATTGATTGGTGGAGATGGA
1 TTGGTGGAGATGGA-CATGACTTGAAGCCACATGGAAA-ATCA-A-ATTGATTGGTGGAGATGGA
* *
545521 CATGATCTAAAGCCACATGGAAAACCAAATCTGA
62 CATGATCTAAAGCCTCATGGAAAATCAAATCTGA
* *
545555 TTGGTGGAGATGGACATGA-TCTAAAGCCACATGTAAAATCAAATCTGATTGGTGGAGATGGACA
1 TTGGTGGAGATGGACATGACT-TGAAGCCACATGGAAAATCAAAT-TGATTGGTGGAGATGGACA
*
545619 TGA-CATGAAA-CCTCATGGAAAGTCAAATCTGA
64 TGATC-T-AAAGCCTCATGGAAAATCAAATCTGA
* * *
545651 TAGGTGGAGATGGACATGACTTGAAACCTCATGGAAA
1 TTGGTGGAGATGGACATGACTTGAAGCCACATGGAAA
545688 CTTTAATCCT
Statistics
Matches: 197, Mismatches: 20, Indels: 24
0.82 0.08 0.10
Matches are distributed among these distances:
94 3 0.02
95 9 0.05
96 172 0.87
97 10 0.05
98 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (95 bp):
TTGGTGGAGATGGACATGACTTGAAGCCACATGGAAAATCAAATTGATTGGTGGAGATGGACATG
ATCTAAAGCCTCATGGAAAATCAAATCTGA
Found at i:545582 original size:144 final size:144
Alignment explanation
Indices: 545363--545627 Score: 417
Period size: 144 Copynumber: 1.8 Consensus size: 144
545353 CCTAATGTAT
* * *
545363 TTGGTGGAGATGGACATGATTTGAAGCCACATGGAAAATCAAACTTAATTGGTGGAGATGGACAT
1 TTGGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAACTTAATTGGTGGAGATGGACAT
* * *
545428 GATCTAAAGCCTCATGGAAAATCAAATTTGATTGGCGGAGAT-GATCATGACTTGAAGCCACACA
66 GATCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGATGGA-CATGACATGAAGCCACACA
545492 AACAGCAGATATTGA
130 AACAGCAGATATTGA
*
545507 TTGGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAA-TCTGATTGGTGGAGATGGACA
1 TTGGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAACT-TAATTGGTGGAGATGGACA
* *
545571 TGATCTAAAGCCACATGTAAAATCAAATCTGATTGGTGGAGATGGACATGACATGAA
65 TGATCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGATGGACATGACATGAA
545628 ACCTCATGGA
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
143 1 0.01
144 107 0.97
145 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (144 bp):
TTGGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAACTTAATTGGTGGAGATGGACAT
GATCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGATGGACATGACATGAAGCCACACAA
ACAGCAGATATTGA
Found at i:545657 original size:144 final size:144
Alignment explanation
Indices: 545365--545669 Score: 404
Period size: 144 Copynumber: 2.1 Consensus size: 144
545355 TAATGTATTT
* * *
545365 GGTGGAGATGGACATGATTTGAAGCCACATGGAAAATCAAACTTAATTGGTGGAGATGGACATGA
1 GGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAACTTAATTGGTGGAGATGGACATGA
* * * *
545430 TCTAAAGCCTCATGGAAAATCAAATTTGATTGGCGGAGATGATCATGACTTGAAGCCACACAAAC
66 TCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGATGATCATGACATGAAACCACACAAAC
*
545495 AGCAGATATTGATT
131 AGCAGATATTGATA
*
545509 GGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAA-TCTGATTGGTGGAGATGGACATG
1 GGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAACT-TAATTGGTGGAGATGGACATG
* * * **
545573 ATCTAAAGCCACATGTAAAATCAAATCTGATTGGTGGAGATGGA-CATGACATGAAACCTCATGG
65 ATCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGAT-GATCATGACATGAAACCACA-CA
545637 AA-AGTCA-A-ATCTGATA
128 AACAG-CAGATAT-TGATA
545653 GGTGGAGATGGACATGA
1 GGTGGAGATGGACATGA
545670 CTTGAAACCT
Statistics
Matches: 142, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
143 3 0.02
144 133 0.94
145 6 0.04
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.23
Consensus pattern (144 bp):
GGTGGAGATGGACATGATCTAAAGCCACATGGAAAACCAAACTTAATTGGTGGAGATGGACATGA
TCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGATGATCATGACATGAAACCACACAAAC
AGCAGATATTGATA
Found at i:545705 original size:144 final size:140
Alignment explanation
Indices: 545365--545707 Score: 347
Period size: 144 Copynumber: 2.4 Consensus size: 140
545355 TAATGTATTT
* *
545365 GGTGGAGATGGACATGATTTGAAGCCACATGGAAAATCAAA-CTTAATTGGTGGAGATGGACATG
1 GGTGGAGATGGACATGA-TTGAAACCACATGGAAACT-AAATC-T--TTGGTGGAGATGGACATG
* * * *
545429 ATCTAAAGCCTCATGGAAAATCAAATTTGATTGGCGGAGATGATCATGACTTGAAGCCACACAAA
61 ATCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGATGATCATGACATGAAACCACACAAA
*
545494 CAGCAGATATTGATT
126 CAGCAGATATTGATA
*
545509 GGTGGAGATGGACATGATCT-AAAGCCACATGGAAAACCAAATCTGATTGGTGGAGATGGACATG
1 GGTGGAGATGGACATGAT-TGAAA-CCACATGG-AAACTAAATCT--TTGGTGGAGATGGACATG
* * * **
545573 ATCTAAAGCCACATGTAAAATCAAATCTGATTGGTGGAGATGGA-CATGACATGAAACCTCATGG
61 ATCTAAAGCCACATGGAAAATCAAATCTGATTGGCGGAGAT-GATCATGACATGAAACCACA-CA
545637 AA-AGTCA-A-ATCTGATA
124 AACAG-CAGATAT-TGATA
* *
545653 GGTGGAGATGGACATGACTTGAAACCTCATGGAAACTTTAATCCTTTGGGTGGAG
1 GGTGGAGATGGACATGA-TTGAAACCACATGGAAAC-TAAAT-CTTT-GGTGGAG
545708 GACTGCTTTT
Statistics
Matches: 169, Mismatches: 17, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
143 11 0.07
144 142 0.84
145 16 0.09
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (140 bp):
GGTGGAGATGGACATGATTGAAACCACATGGAAACTAAATCTTTGGTGGAGATGGACATGATCTA
AAGCCACATGGAAAATCAAATCTGATTGGCGGAGATGATCATGACATGAAACCACACAAACAGCA
GATATTGATA
Found at i:550411 original size:17 final size:18
Alignment explanation
Indices: 550383--550417 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
550373 AAATCAATGG
550383 AATTTTTCAAATATTCTC
1 AATTTTTCAAATATTCTC
550401 AATTTTT-AAATATTCTC
1 AATTTTTCAAATATTCTC
550418 CCCCAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTTTCAAATATTCTC
Found at i:551663 original size:180 final size:180
Alignment explanation
Indices: 551354--551722 Score: 591
Period size: 180 Copynumber: 2.0 Consensus size: 180
551344 GTGAAATGGA
* *
551354 GTACCCTATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGGTTTTTTTTCCATAA
1 GTACCCT-TATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGGTTTTTCTTCCATAA
* *
551419 CTTACCGGAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATTTGCAAAA
65 CTTACCGAAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATGTGCAAAA
551484 GAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
130 GAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
551535 GTACCCTTCATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCT-GGTATTTTCTTCACA-
1 GTACCCTT-ATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGGT-TTTTCTTC-CAT
* * *
551598 AA-TTATCGAAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATGTGCAA
63 AACTTACCGAAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATGTGCAA
* * *
551662 AAGAACAACTTCTTATTTTGAAAACTGTAGGAGGAGTTATCCGTAGAATGAGG
128 AAGAACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
551715 GTACCCTT
1 GTACCCTT
551723 TTGGCAGCCG
Statistics
Matches: 175, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
180 119 0.68
181 54 0.31
182 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (180 bp):
GTACCCTTATGCAATATTTTGCCAAAAAATGACCAAGTTCAAAAGCTGGGTTTTTCTTCCATAAC
TTACCGAAAATCAAAATCCTAGCAATATGCACACCTCTAATATAAGTACAATTGATGTGCAAAAG
AACAACTTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGG
Found at i:556035 original size:21 final size:21
Alignment explanation
Indices: 556005--556060 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
555995 CACTTTGACC
556005 ACCACCCCAGTTTCCCTGGTT
1 ACCACCCCAGTTTCCCTGGTT
* *
556026 ACCACTCCAGTTTCCTTGGTT
1 ACCACCCCAGTTTCCCTGGTT
**
556047 ACTGCCCCAGTTTC
1 ACCACCCCAGTTTC
556061 TGCCTCTGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.14, C:0.39, G:0.14, T:0.32
Consensus pattern (21 bp):
ACCACCCCAGTTTCCCTGGTT
Found at i:568487 original size:22 final size:22
Alignment explanation
Indices: 568425--568487 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
568415 GTGAAAGAAA
**
568425 ATATGTATATAGTGAATTTGCT
1 ATATGTATATAACGAATTTGCT
* *
568447 ATA-GCTATTATTACGAATTTGTT
1 ATATG-TA-TATAACGAATTTGCT
568470 ATATGTATATAACGAATT
1 ATATGTATATAACGAATT
568488 ACGGATATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
21 1 0.03
22 15 0.45
23 16 0.48
24 1 0.03
ACGTcount: A:0.35, C:0.06, G:0.14, T:0.44
Consensus pattern (22 bp):
ATATGTATATAACGAATTTGCT
Found at i:576625 original size:30 final size:30
Alignment explanation
Indices: 576589--576675 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
576579 AACTGAATTT
* *
576589 GGAACACGCA-TCTGAGGCACTGAATTTGAA
1 GGAACACGCACT-TGAGACACTGAATTTAAA
*
576619 GGAACACTCACTTGAGACACTGAATTTAAA
1 GGAACACGCACTTGAGACACTGAATTTAAA
* **
576649 GGGACATTCACTTGAGACACTGAATTT
1 GGAACACGCACTTGAGACACTGAATTT
576676 TGAGAAGCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 50 0.98
31 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (30 bp):
GGAACACGCACTTGAGACACTGAATTTAAA
Found at i:580090 original size:16 final size:16
Alignment explanation
Indices: 580069--580101 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
580059 GAATGGTCCA
580069 AGAAATGCACGATATT
1 AGAAATGCACGATATT
580085 AGAAATGCACGATATT
1 AGAAATGCACGATATT
580101 A
1 A
580102 TTACTGACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (16 bp):
AGAAATGCACGATATT
Found at i:580348 original size:8 final size:8
Alignment explanation
Indices: 580331--580366 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
580321 AAGTGGGACA
580331 GACAGACG
1 GACAGACG
*
580339 GACGGACG
1 GACAGACG
580347 GACAGACG
1 GACAGACG
*
580355 GACTGACG
1 GACAGACG
580363 GACA
1 GACA
580367 CAGAGGAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.25, G:0.39, T:0.03
Consensus pattern (8 bp):
GACAGACG
Found at i:580350 original size:16 final size:16
Alignment explanation
Indices: 580326--580366 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
580316 AACTGAAGTG
*
580326 GGACAGACAGACGGAC
1 GGACGGACAGACGGAC
580342 GGACGGACAGACGGAC
1 GGACGGACAGACGGAC
*
580358 TGACGGACA
1 GGACGGACA
580367 CAGAGGAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.34, C:0.24, G:0.39, T:0.02
Consensus pattern (16 bp):
GGACGGACAGACGGAC
Found at i:586513 original size:69 final size:69
Alignment explanation
Indices: 586432--586564 Score: 196
Period size: 69 Copynumber: 1.9 Consensus size: 69
586422 GCCTTTTAAT
* *
586432 TTTTAATTGTCAATGAGTCCATAACTAAT-TATATTAGACATGGATTCATTGACAATTAAAAATT
1 TTTTAATTGTCAATGAATCCATAACTAATATA-ATTAGACATGGACTCATTGACAATTAAAAATT
586496 AACAA
65 AACAA
** **
586501 TTTTAATTGTCAATGAATCCATGTCTAATATAATTAGTTATGGACTCATTGACAATTAAAAATT
1 TTTTAATTGTCAATGAATCCATAACTAATATAATTAGACATGGACTCATTGACAATTAAAAATT
586565 GTAATTAGTA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
69 55 0.96
70 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (69 bp):
TTTTAATTGTCAATGAATCCATAACTAATATAATTAGACATGGACTCATTGACAATTAAAAATTA
ACAA
Found at i:591605 original size:7 final size:7
Alignment explanation
Indices: 591593--591659 Score: 89
Period size: 7 Copynumber: 9.6 Consensus size: 7
591583 GAGAAGGATC
591593 ATTCGAG
1 ATTCGAG
591600 ATTCGAG
1 ATTCGAG
*
591607 ATTCGAA
1 ATTCGAG
*
591614 ATACGAG
1 ATTCGAG
*
591621 ATTCGAA
1 ATTCGAG
*
591628 ATACGAG
1 ATTCGAG
591635 ATTCGAG
1 ATTCGAG
*
591642 ATTCGAA
1 ATTCGAG
591649 ATTCGAG
1 ATTCGAG
591656 ATTC
1 ATTC
591660 AATATCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (7 bp):
ATTCGAG
Found at i:594336 original size:4 final size:4
Alignment explanation
Indices: 594329--594357 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
594319 ACTCTCTCTG
594329 TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC T
594358 CTCTCTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:594362 original size:2 final size:2
Alignment explanation
Indices: 594355--594398 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
594345 TGTCTGTCTG
594355 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
594397 TC
1 TC
594399 ATATCGACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:594908 original size:7 final size:7
Alignment explanation
Indices: 594893--594959 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
594883 TTTAGATATT
594893 GAATCTC
1 GAATCTC
*
594900 GAATTTC
1 GAATCTC
594907 GAATCTC
1 GAATCTC
594914 GAATCTC
1 GAATCTC
* *
594921 GTATTTC
1 GAATCTC
594928 GAATCTC
1 GAATCTC
** * *
594935 GTTTTTT
1 GAATCTC
594942 GAATCTC
1 GAATCTC
594949 GAATCTC
1 GAATCTC
594956 GAAT
1 GAAT
594960 GATCCTTCTC
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (7 bp):
GAATCTC
Found at i:594918 original size:21 final size:21
Alignment explanation
Indices: 594893--594959 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
594883 TTTAGATATT
594893 GAATCTCGAATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
*
594914 GAATCTCGTATTTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
** * * *
594935 GTTTTTTGAATCTCGAATCTC
1 GAATCTCGAATTTCGAATCTC
594956 GAAT
1 GAAT
594960 GATCCTTCTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (21 bp):
GAATCTCGAATTTCGAATCTC
Found at i:603896 original size:2 final size:2
Alignment explanation
Indices: 603889--603946 Score: 79
Period size: 2 Copynumber: 31.0 Consensus size: 2
603879 TAACGAGATA
*
603889 CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T TT CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
603929 CT CT CT CT -T CT C- CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
603947 NATATTAATG
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
1 4 0.08
2 47 0.92
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:605355 original size:21 final size:21
Alignment explanation
Indices: 605325--605404 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
605315 TTCGATTAAT
*
605325 TATGTGGACATGCAAGATAAA
1 TATGTTGACATGCAAGATAAA
**
605346 TATGTTGACATGCAAGATAGT
1 TATGTTGACATGCAAGATAAA
** * *
605367 TATGTCAACATGCAACATAAC
1 TATGTTGACATGCAAGATAAA
*
605388 CATGTTGACATGCAAGA
1 TATGTTGACATGCAAGA
605405 AAACTGCAAT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (21 bp):
TATGTTGACATGCAAGATAAA
Found at i:605977 original size:21 final size:21
Alignment explanation
Indices: 605947--605993 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
605937 TGCGAGAAAC
* *
605947 GTTTCGTGTAAACCTTTTAGA
1 GTTTCATGTAAACCGTTTAGA
*
605968 GTTTCATGTAAACCGTTTAGC
1 GTTTCATGTAAACCGTTTAGA
605989 GTTTC
1 GTTTC
605994 GGGCAAAGCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (21 bp):
GTTTCATGTAAACCGTTTAGA
Found at i:610171 original size:165 final size:165
Alignment explanation
Indices: 609934--610463 Score: 674
Period size: 165 Copynumber: 3.2 Consensus size: 165
609924 CGCCATCCCG
* * * * * * ***
609934 CCCTACCCACGGGGACCATCATTTGAACAAACTTGAATCTACATTATCTGAGGATGGTTACACGC
1 CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTT
* * * * * * * *
609999 CAATTTGAGCTTTCTTGGTCAAATAGTTTTTAAAAAAAATG-TTTTTAATA-A-TTTCCCTATAT
66 TAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAA-GATTTTTAA-AGATTTTCTCTATAT
* * * * * * ** *
610061 ATTCCTGT-ATAAAAATTTATCCCCCAACTGTGGCTTCA
129 ATTCCTATGGT-AAACTTGATCCCCC-TCTTTGGCCCCT
*
610099 CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATTCTTCCATTT
1 CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTT
* * *
610164 TAATTTGAGCTTTCCTGGCCTATTAGTCTTTGAGAAGAAGATTTTTAAAGATTTTCTCGATATAT
66 TAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATAT
610229 TCCTATGGTAAACTTGATCCCCCTCTTTTGGCCCCT
131 TCCTATGGTAAACTTGATCCCCCTC-TTTGGCCCCT
*
610265 CCCTACCCCCGTGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTT
1 CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTT
* *
610330 TGA-TTGAGCTTTCCTGACCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATAT
66 TAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATAT
610394 TCCTATGGTAAACTTGATCCCCCTCTCTTGGCCCCT
131 TCCTATGGTAAACTTGATCCCCCTCT-TTGGCCCCT
610430 CCCTACCCCCGGGGACCATGATTTGAACAAACTT
1 CCCTACCCCCGGGGACCATGATTTGAACAAACTT
610464 TAAAGATTTT
Statistics
Matches: 321, Mismatches: 38, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
164 3 0.01
165 218 0.68
166 99 0.31
167 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (165 bp):
CCCTACCCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTT
TAATTTGAGCTTTCCTGGCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATAT
TCCTATGGTAAACTTGATCCCCCTCTTTGGCCCCT
Found at i:610684 original size:256 final size:255
Alignment explanation
Indices: 610257--610719 Score: 750
Period size: 256 Copynumber: 1.8 Consensus size: 255
610247 CCCCCTCTTT
* * * *
610257 TGGCCCCTCCCTACCCCCGTGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGC
1 TGGCCCCACCATACCACCATGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGC
* * *
610322 TTCCATTTTGATTGAGCTTTCCTGACCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTC
66 TTCCACTTTAATTGAGCTTTCCTGACCGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTC
*** *
610387 TATATATTCCTATGGTAAACTTGATCCCCCTCTCTTGGCCCCTCCCTACCCCCGGGGACCATGAT
131 TATATATTCCTATGGTAAACTTGATCCCCAAATCTTGGCCCCACCCTACCCCCGGGGACCATGAT
610452 TTGAACAAACTTTAAAGATTTTCTCGACATTTTTCTATGTAAAAATCCATTCCCCCATTG
196 TTGAACAAACTTTAAAGATTTTCTCGACATTTTTCTATGTAAAAATCCATTCCCCCATTG
*
610512 TGGCCCCACCATACCACCATGGACTATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGC
1 TGGCCCCACCATACCACCATGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGC
* *
610577 TTCCACTTTAATTTGAGCTTTTCTGGCCGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCT
66 TTCCACTTTAA-TTGAGCTTTCCTGACCGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCT
*
610642 CTATATATTTCTAT-GTAATACTTGATCCCCAAAT-TGTGGCCCCACCCTACCCCCGGGGACCAT
130 CTATATATTCCTATGGTAA-ACTTGATCCCCAAATCT-TGGCCCCACCCTACCCCCGGGGACCAT
610705 GATTTGAACAAACTT
193 GATTTGAACAAACTT
610720 GAATCTACAC
Statistics
Matches: 190, Mismatches: 15, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
255 74 0.39
256 116 0.61
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (255 bp):
TGGCCCCACCATACCACCATGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGC
TTCCACTTTAATTGAGCTTTCCTGACCGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTC
TATATATTCCTATGGTAAACTTGATCCCCAAATCTTGGCCCCACCCTACCCCCGGGGACCATGAT
TTGAACAAACTTTAAAGATTTTCTCGACATTTTTCTATGTAAAAATCCATTCCCCCATTG
Found at i:610736 original size:166 final size:166
Alignment explanation
Indices: 610462--610796 Score: 462
Period size: 166 Copynumber: 2.0 Consensus size: 166
610452 TTGAACAAAC
* *
610462 TTTAAAGATTTTCTCGACATTTTTCTATGTAAAAATCCATTCCCCCATTGTGGCCCCACCATACC
1 TTTAAAGATTTTCTCGACATATTTCTATGTAAAAATCCATTCCCCAATTGTGGCCCCACCATACC
* * *
610527 ACCATGGACTATGATTTGAACAAACTTGAATCTACACTACCTGAGGATG-CTTC-CACTTTAA-T
66 ACCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGACTACACAC---AAGT
* *
610589 TTGAGCTTTTCTGGCCGAATAGTTTTTGAGAAGAAGATT
128 TTAAGCTTTTCAGGCCGAATAGTTTTTGAGAAGAAGATT
* * * * ** *
610628 TTTAAAGATTTTCTCTATATATTTCTATGTAATACTTGA-TCCCCAAATTGTGGCCCCACCCTAC
1 TTTAAAGATTTTCTCGACATATTTCTATGTAAAAATCCATTCCCC-AATTGTGGCCCCACCATAC
* *
610692 CCCCGGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGACTACACACAAGTTT
65 CACCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGACTACACACAAGTTT
610757 AAGCTTTTCAGGCCGAATAGTTTTTGAGAAGAAGATT
130 AAGCTTTTCAGGCCGAATAGTTTTTGAGAAGAAGATT
610794 TTT
1 TTT
610797 GAAAAATACC
Statistics
Matches: 149, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
165 7 0.05
166 136 0.91
167 3 0.02
168 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (166 bp):
TTTAAAGATTTTCTCGACATATTTCTATGTAAAAATCCATTCCCCAATTGTGGCCCCACCATACC
ACCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGAGGATGACTACACACAAGTTTA
AGCTTTTCAGGCCGAATAGTTTTTGAGAAGAAGATT
Found at i:610986 original size:12 final size:12
Alignment explanation
Indices: 610969--611008 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
610959 AAAGTTTACA
610969 ACAACGACGACG
1 ACAACGACGACG
610981 ACAACGACGACG
1 ACAACGACGACG
610993 ACAACGAC-A-G
1 ACAACGACGACG
611003 ACAACG
1 ACAACG
611009 GACAAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 7 0.25
11 1 0.04
12 20 0.71
ACGTcount: A:0.45, C:0.33, G:0.23, T:0.00
Consensus pattern (12 bp):
ACAACGACGACG
Found at i:611238 original size:24 final size:24
Alignment explanation
Indices: 611206--611299 Score: 154
Period size: 24 Copynumber: 3.9 Consensus size: 24
611196 TGACATTAGA
611206 TGATAACGAACAGTGTTCAAAAGG
1 TGATAACGAACAGTGTTCAAAAGG
*
611230 TGATAACGAACAGTGCTCAAAAGG
1 TGATAACGAACAGTGTTCAAAAGG
*
611254 TGATAACGAACAGAGTTCAAAAGG
1 TGATAACGAACAGTGTTCAAAAGG
611278 TGGA-AACGAACAGTGTTCAAAA
1 T-GATAACGAACAGTGTTCAAAA
611300 TCAAAAGTCC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
24 63 0.97
25 2 0.03
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (24 bp):
TGATAACGAACAGTGTTCAAAAGG
Found at i:622654 original size:2 final size:2
Alignment explanation
Indices: 622647--622678 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
622637 GCTTTCCTTT
622647 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
622679 TACTGTATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:639740 original size:21 final size:21
Alignment explanation
Indices: 639714--639794 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
639704 TTTTTCTATC
639714 AAATATGTCGACATGCAAGAT
1 AAATATGTCGACATGCAAGAT
* **
639735 AAATATGTTGACATGCTTGAT
1 AAATATGTCGACATGCAAGAT
** * *
639756 AGTTATGTCAACATGCAACAT
1 AAATATGTCGACATGCAAGAT
** *
639777 ATCTATGTTGACATGCAA
1 AAATATGTCGACATGCAA
639795 AAAAACTGCT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (21 bp):
AAATATGTCGACATGCAAGAT
Found at i:639904 original size:21 final size:21
Alignment explanation
Indices: 639875--640115 Score: 236
Period size: 21 Copynumber: 11.5 Consensus size: 21
639865 AAGATGCTAG
* *
639875 ATGCTACTTATTTATGTCGAC
1 ATGCAACTTATTTATGTTGAC
*
639896 ATGCAACTTATTTATGTTAAC
1 ATGCAACTTATTTATGTTGAC
* *
639917 ATGCGAGA-TGA-ATATGTTGAC
1 ATGC-A-ACTTATTTATGTTGAC
*
639938 ATGCAACTTA-TTATGTTAAC
1 ATGCAACTTATTTATGTTGAC
* * *
639958 ATGCAATTTCTTTATGTCGAC
1 ATGCAACTTATTTATGTTGAC
* *
639979 ATGCAATTTATTTATGTCGAC
1 ATGCAACTTATTTATGTTGAC
*
640000 ATGCAACTTATTTATGTAGAC
1 ATGCAACTTATTTATGTTGAC
* *
640021 ATGCAACTTAATTATGTTAAC
1 ATGCAACTTATTTATGTTGAC
* ** **
640042 ATGAAAGATAAATATGTTGAC
1 ATGCAACTTATTTATGTTGAC
* *
640063 ATGCAACGTATTTATGTCGAC
1 ATGCAACTTATTTATGTTGAC
* *
640084 ATGCAATTTAGTTATGTTGAC
1 ATGCAACTTATTTATGTTGAC
640105 ATGCAACTTAT
1 ATGCAACTTAT
640116 AAGTTGCATG
Statistics
Matches: 180, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
19 1 0.01
20 19 0.11
21 156 0.87
22 3 0.02
23 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (21 bp):
ATGCAACTTATTTATGTTGAC
Found at i:640162 original size:42 final size:42
Alignment explanation
Indices: 640142--640334 Score: 181
Period size: 42 Copynumber: 4.6 Consensus size: 42
640132 TATTTATCTC
* *
640142 GCATGTGAACATAACTAAGTTGTATGTTGACATAAATAAGTA
1 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
* ** *
640184 GCATGTGATCATAACTAAACTGCATGTCGACATAAATAAGTT
1 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
* * * *
640226 GCATGTAAACATAACCAAGTTGCATGTTGACATAAATAAGTT
1 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
* * ** ** ** * *
640268 GCATGTCAGCATATTTATCTTGCATGTTTACATAAATAATTT
1 GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
*
640310 GCATGT-AGACATAAATAAGTTGCAT
1 GCATGTGA-ACATAACTAAGTTGCAT
640335 TTAGCATCTT
Statistics
Matches: 124, Mismatches: 26, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
41 1 0.01
42 123 0.99
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (42 bp):
GCATGTGAACATAACTAAGTTGCATGTCGACATAAATAAGTA
Found at i:640168 original size:21 final size:20
Alignment explanation
Indices: 640142--640334 Score: 161
Period size: 21 Copynumber: 9.2 Consensus size: 20
640132 TATTTATCTC
*
640142 GCATGTGAACATAACTAAGTT
1 GCATGTG-ACATAAATAAGTT
* *
640163 GTATGTTGACATAAATAAGTA
1 GCATG-TGACATAAATAAGTT
* **
640184 GCATGTGATCATAACTAAACT
1 GCATGTGA-CATAAATAAGTT
640205 GCATGTCGACATAAATAAGTT
1 GCATGT-GACATAAATAAGTT
* **
640226 GCATGTAAACATAACCAAGTT
1 GCATGT-GACATAAATAAGTT
640247 GCATGTTGACATAAATAAGTT
1 GCATG-TGACATAAATAAGTT
* ** **
640268 GCATGTCAGCATATTTATCTT
1 GCATGTGA-CATAAATAAGTT
* *
640289 GCATGTTTACATAAATAATTT
1 GCATG-TGACATAAATAAGTT
640310 GCATGTAGACATAAATAAGTT
1 GCATGT-GACATAAATAAGTT
640331 GCAT
1 GCAT
640335 TTAGCATCTT
Statistics
Matches: 135, Mismatches: 30, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
20 6 0.04
21 122 0.90
22 7 0.05
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (20 bp):
GCATGTGACATAAATAAGTT
Found at i:640482 original size:42 final size:42
Alignment explanation
Indices: 640402--640482 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
640392 GACTGCAATT
* **
640402 ATCTTGCATGTCAACATAGTTATGTTGCATGTTGACATAGCC
1 ATCTTGCATGTCAACATAGTTATCTTGCATGTCAACATAGCC
* *
640444 ATCTTGCATGTCGACATATTTATCTTGCATGTCAACATA
1 ATCTTGCATGTCAACATAGTTATCTTGCATGTCAACATA
640483 TTTGATAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (42 bp):
ATCTTGCATGTCAACATAGTTATCTTGCATGTCAACATAGCC
Found at i:640485 original size:21 final size:21
Alignment explanation
Indices: 640400--640482 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
640390 TTGACTGCAA
640400 TTATCTTGCATGTCAACATAG
1 TTATCTTGCATGTCAACATAG
* **
640421 TTATGTTGCATGTTGACATAG
1 TTATCTTGCATGTCAACATAG
** * *
640442 CCATCTTGCATGTCGACATAT
1 TTATCTTGCATGTCAACATAG
640463 TTATCTTGCATGTCAACATA
1 TTATCTTGCATGTCAACATA
640483 TTTGATAGAA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (21 bp):
TTATCTTGCATGTCAACATAG
Found at i:643663 original size:2 final size:2
Alignment explanation
Indices: 643656--643736 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
643646 ATACAAACAT
643656 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
643698 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
643737 TGTCTCTTTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:668694 original size:251 final size:252
Alignment explanation
Indices: 668251--668751 Score: 889
Period size: 251 Copynumber: 2.0 Consensus size: 252
668241 TTCTAAAAAT
668251 TGAGATAAGTCCTATTCATTTACATGTACTACCACACGATAAATTAAAAATTTAAAACATAACAA
1 TGAGATAAGTCCTATTCATTTACATGTACTACCACACGATAAATTAAAAATTTAAAACATAACAA
*
668316 CAATGCGTTATCTCTGAATTCATAGGTCTAATATTGGTGCGAGATATTTATCAATGGAAGAAAGA
66 CAATGCGTTATCTCTGAATTCATAGGTCTAATATTGGTGCGAGATATTTATCAATAGAAGAAAGA
* * *
668381 TCAGCTGAGTTTCTGATGAGAGGCATTACGAAATTGATGAAGATTTTTTTTAAATCATAAATATG
131 TCAGCTGAGTTTCTGATGAGAGGCATTAAGAAATTGATGAAGATATGTTTTAAATCATAAATATG
*
668446 ACTAGTTTTGTCCGTTATAAAGTATAGAACATGTCTCATAACATTAAAA-AAATCGA
196 ACTAGTTTTGTCCGTTATAAAGTATAGAAAATGTCTCATAACATTAAAACAAATCGA
*
668502 TGAGATAAGTTCTATTCATTTACATGTACTACCACACGATAAATTAAAAATTTAAAACATAACAA
1 TGAGATAAGTCCTATTCATTTACATGTACTACCACACGATAAATTAAAAATTTAAAACATAACAA
* * *
668567 CCATGCGTTGTCTCTGATTTCATAGGTCTAATATTGGTGCGAGATATTTATCAATAGAAGAAAGA
66 CAATGCGTTATCTCTGAATTCATAGGTCTAATATTGGTGCGAGATATTTATCAATAGAAGAAAGA
668632 TCAGCTGAGTTTCTGATGAGAGGCATTAAGAAATTGATGAAGA-ATGTTTTAAAGTCATAAATAT
131 TCAGCTGAGTTTCTGATGAGAGGCATTAAGAAATTGATGAAGATATGTTTTAAA-TCATAAATAT
*
668696 GACTGGTTTTGTCCGTTATAAAGTATAGAAAATGTCTCATAACATTAAAACAAATC
195 GACTAGTTTTGTCCGTTATAAAGTATAGAAAATGTCTCATAACATTAAAACAAATC
668752 ACATGTTTGT
Statistics
Matches: 238, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
250 8 0.03
251 225 0.95
252 5 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (252 bp):
TGAGATAAGTCCTATTCATTTACATGTACTACCACACGATAAATTAAAAATTTAAAACATAACAA
CAATGCGTTATCTCTGAATTCATAGGTCTAATATTGGTGCGAGATATTTATCAATAGAAGAAAGA
TCAGCTGAGTTTCTGATGAGAGGCATTAAGAAATTGATGAAGATATGTTTTAAATCATAAATATG
ACTAGTTTTGTCCGTTATAAAGTATAGAAAATGTCTCATAACATTAAAACAAATCGA
Found at i:670796 original size:2 final size:2
Alignment explanation
Indices: 670789--670840 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
670779 AGACTGACAA
670789 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T-
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
670830 TC TC TC TC TC T
1 TC TC TC TC TC T
670841 TATGCTTTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:672177 original size:145 final size:144
Alignment explanation
Indices: 671988--672249 Score: 427
Period size: 145 Copynumber: 1.8 Consensus size: 144
671978 AGAAACAAAA
* *
671988 TGCCAACATTTATGACAAAACGTGGCTATTTGTGTAACTATTTGGTATAGTGGAAGGTTTTACTT
1 TGCCAACATTTATGACAAAACGTGGCTATTTGTGTAACTATTTGGTATAGCGGAAGCTTTTACTT
* * *
672053 TGACGCTGTTTGGTGTTTTGTTTACTTTTGATGTTGTATTTTTTATAGTAACNTCGAAATTAAAA
66 TGACGCTGTTTGGTGTTTTGTTTACTTTTGAAGTTGTACTATTTATAGTAAC-TCGAAATTAAAA
672118 TAAAAACACATGCAG
130 TAAAAACACATGCAG
*
672133 TGCCAACACTTT-TGACAAAACGTGGCTCTTTGTGTAACTATTTGGTATAGCGGAAGCTTTTACT
1 TGCCAACA-TTTATGACAAAACGTGGCTATTTGTGTAACTATTTGGTATAGCGGAAGCTTTTACT
* *
672197 TTGACGCTGTTTGGTTTTTTGTTTACTTTTGAAGTTGTGCTATTTATAGTAAC
65 TTGACGCTGTTTGGTGTTTTGTTTACTTTTGAAGTTGTACTATTTATAGTAAC
672250 ATTGGCGATT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
145 105 0.97
146 3 0.03
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (144 bp):
TGCCAACATTTATGACAAAACGTGGCTATTTGTGTAACTATTTGGTATAGCGGAAGCTTTTACTT
TGACGCTGTTTGGTGTTTTGTTTACTTTTGAAGTTGTACTATTTATAGTAACTCGAAATTAAAAT
AAAAACACATGCAG
Found at i:682225 original size:1 final size:1
Alignment explanation
Indices: 682219--682257 Score: 69
Period size: 1 Copynumber: 39.0 Consensus size: 1
682209 ATTTTATACC
*
682219 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
682258 ACAGTTTACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:685182 original size:4 final size:4
Alignment explanation
Indices: 685173--685199 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
685163 CTACTGATAA
685173 GTCT GTCT GTCT GTCT GTCT GTCT GTC
1 GTCT GTCT GTCT GTCT GTCT GTCT GTC
685200 CGTCCGTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.26, T:0.48
Consensus pattern (4 bp):
GTCT
Found at i:685495 original size:11 final size:11
Alignment explanation
Indices: 685479--685503 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
685469 TAGAGTATGC
685479 AGTGATCTTGA
1 AGTGATCTTGA
685490 AGTGATCTTGA
1 AGTGATCTTGA
685501 AGT
1 AGT
685504 TTGTAGGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (11 bp):
AGTGATCTTGA
Found at i:691703 original size:144 final size:146
Alignment explanation
Indices: 691513--691788 Score: 382
Period size: 144 Copynumber: 1.9 Consensus size: 146
691503 TGGTAAGCCA
* *
691513 TATATCATAATCCAACCGTACTGGACATGACAACATAGCACCCAACCATA-AGGGGGCTAAATGG
1 TATATCATAATCCAACCGTACTGGACATGAAAACATAGCACCCAACCATATA-GGGGCTAAACGG
* * * * *
691577 TTACCAGAAGATCCAAGCATGCTGGACA-TA-ACAACATAGCACCCAACCATA-TAGGGGCTCTT
65 CTACCAGAAGATCCAAGCATACCGGACATTACACAACATAGCACCCAA-CAAACTAGGGGCTATT
691639 TGGTAAGCCATACACATG
129 TGGTAAGCCATACACATG
*
691657 TATATCATAATCCAACCAG-ACTGGATATGAAAACATAGCACCCAACCATATAGGGGCTAAACGG
1 TATATCATAATCCAACC-GTACTGGACATGAAAACATAGCACCCAACCATATAGGGGCTAAACGG
* * * *
691721 CTACCATATGATCCAAGCATACCGGATATTACATAACATAGCACCCAACAAACTAGGGGCTATTT
65 CTACCAGAAGATCCAAGCATACCGGACATTACACAACATAGCACCCAACAAACTAGGGGCTATTT
691786 GGT
130 GGT
691789 TTACCAAGTA
Statistics
Matches: 115, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
144 79 0.69
145 7 0.06
146 29 0.25
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (146 bp):
TATATCATAATCCAACCGTACTGGACATGAAAACATAGCACCCAACCATATAGGGGCTAAACGGC
TACCAGAAGATCCAAGCATACCGGACATTACACAACATAGCACCCAACAAACTAGGGGCTATTTG
GTAAGCCATACACATG
Found at i:703771 original size:166 final size:163
Alignment explanation
Indices: 703536--704007 Score: 667
Period size: 166 Copynumber: 2.8 Consensus size: 163
703526 TATATTCCTA
*
703536 ATATTCCTATGTTAAACTTGATCCCCCAATTGTGGTCCCACCCTACCCCCGGGGACCATGATTTG
1 ATATTCCTATG-TAAACTTGAT-CCCCAACTGTGG-CCCACCCTACCCCCGGGGACCATGATTTG
* * *
703601 AACAAACCTGAATCTACACTACCTGAGAATGCTTCCATTTTAATTTGAGCTTTTCTGGCCTAATA
63 AACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCCAAATA
*
703666 GTTTTTGAGAAGAAGATTTTTAAAGATTTCCTATGT
128 GTTTTTGAGAAGAAGATTTTTAAAGATTTCCTATAT
*
703702 ATATTTCTATGTAATACTTGATCCCCAAACTGTGGCCCCACCCTACCCCCGGGGACCATGATTTG
1 ATATTCCTATGTAA-ACTTGATCCCC-AACTGTGG-CCCACCCTACCCCCGGGGACCATGATTTG
* *
703767 AACAAAATTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTTCTGGCCAAATA
63 AACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCCAAATA
*
703832 GTTTTTGAGAAGAAGATTTTTAAAGATTTCCTCTAT
128 GTTTTTGAGAAGAAGATTTTTAAAGATTTCCTATAT
** *
703868 ATATTCCTATGTAAAACTTGATCCCCCTCTTGTGGCCCTCCCTACCCCCGGGGACCATGATTTGA
1 ATATTCCTATGT-AAACTTGATCCCCAAC-TGTGGCCCACCCTACCCCCGGGGACCATGATTTGA
* * * *** * * *
703933 ACAAACTTGAATCTACACTACTTGTGGATGCCTCCA-CACAAGTTTAAGCTTTTCAGGCCGAATA
64 ACAAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAA-TTTGAGCTTTTCTGGCCAAATA
703997 GTTTTTGAGAA
128 GTTTTTGAGAA
704008 AATTTTTGAA
Statistics
Matches: 276, Mismatches: 25, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
164 2 0.01
165 98 0.36
166 174 0.63
167 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (163 bp):
ATATTCCTATGTAAACTTGATCCCCAACTGTGGCCCACCCTACCCCCGGGGACCATGATTTGAAC
AAACTTGAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCCAAATAGTT
TTTGAGAAGAAGATTTTTAAAGATTTCCTATAT
Found at i:704196 original size:15 final size:15
Alignment explanation
Indices: 704176--704215 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
704166 TGAAAAGTTT
704176 ACAACAACGACGACG
1 ACAACAACGACGACG
704191 ACAACAACGACGACG
1 ACAACAACGACGACG
704206 ACAGACAACG
1 ACA-ACAACG
704216 GACAAATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.47, C:0.33, G:0.20, T:0.00
Consensus pattern (15 bp):
ACAACAACGACGACG
Found at i:704877 original size:15 final size:15
Alignment explanation
Indices: 704857--704896 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
704847 TGAAAAGTTT
704857 ACAACAACGACGACG
1 ACAACAACGACGACG
704872 ACAACAACGACGACG
1 ACAACAACGACGACG
704887 ACAGACAACG
1 ACA-ACAACG
704897 GACAAATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.47, C:0.33, G:0.20, T:0.00
Consensus pattern (15 bp):
ACAACAACGACGACG
Found at i:705563 original size:21 final size:21
Alignment explanation
Indices: 705537--705588 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
705527 ATGTAAGCTG
* *
705537 TAGTTAACGGATCGTTAATTA
1 TAGTTAACGGACCGTTAACTA
* *
705558 TAGTTATCGAACCGTTAACTA
1 TAGTTAACGGACCGTTAACTA
*
705579 TAGTTTACGG
1 TAGTTAACGG
705589 TTTGTAACTA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (21 bp):
TAGTTAACGGACCGTTAACTA
Found at i:706717 original size:167 final size:167
Alignment explanation
Indices: 706517--706930 Score: 560
Period size: 167 Copynumber: 2.5 Consensus size: 167
706507 AAAATTTCAT
* * *
706517 CATAGAAATACACAGAAAAAATGTTTAAAAAATCGTCCTCTCAAGAACCACTGTACCAGAAATGC
1 CATAGAAATACACAGGAAAAATGTTT-AAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGC
* * * * * * *
706582 TAATATTTGCACAAAGGATCGAAAAATAGTAAAGATTCTAATTTGGATAAA-AAGTGTGACACAC
65 CAATATTTACACAAAGGATCCAAAAATAGTAAAGATTCAAAATTGGACAAACAAGTGTAACACAC
* *
706646 GGACCAAAACTGGGGCTCTAGGTTGGGTTCAAAGTTTAA
130 GGACCAAAACGGGGGCTC-AGGTTGGGTTCAAAGTTAAA
* *
706685 CATAGAAATACACAGGACAAATATTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCC
1 CATAGAAATACACAGGAAAAATGTTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCC
* *
706750 AATATTTACACAAAGGATCCAAAAATTGTAAAGATTCAAAATTGGACAAACAATTGTAACACACG
66 AATATTTACACAAAGGATCCAAAAATAGTAAAGATTCAAAATTGGACAAACAAGTGTAACACACG
*
706815 GACCAAAAGGGGGGCTCAGGTTGGGTTCAAAGTTAAA
131 GACCAAAACGGGGGCTCAGGTTGGGTTCAAAGTTAAA
* * * * * * ** * *
706852 CAAAGAATTACATAGGAAAAATGTTTATAAACCTTCTTCTCAAGAAATACTGCAGCAGAAATCCC
1 CATAGAAATACACAGGAAAAATGTTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCC
706917 AATATTTACACAAA
66 AATATTTACACAAA
706931 AGCCTGTATT
Statistics
Matches: 216, Mismatches: 29, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
167 166 0.77
168 50 0.23
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.23
Consensus pattern (167 bp):
CATAGAAATACACAGGAAAAATGTTTAAAAATCTTCCTCTCAAGAACCACTGCACCAGAAATGCC
AATATTTACACAAAGGATCCAAAAATAGTAAAGATTCAAAATTGGACAAACAAGTGTAACACACG
GACCAAAACGGGGGCTCAGGTTGGGTTCAAAGTTAAA
Found at i:714716 original size:193 final size:193
Alignment explanation
Indices: 714387--714767 Score: 744
Period size: 193 Copynumber: 2.0 Consensus size: 193
714377 TTCGGAGCTT
714387 TCAATTTTGTCCTGGGGGTCATTTAATGGCTGAAAAAGACGTTTTTTAAAAAAAAACCACTGGTT
1 TCAATTTTGTCCTGGGGGTCATTTAATGGCTGAAAAAGACGTTTTTTAAAAAAAAACCACTGGTT
714452 TCAAAAACGTCATTGTTTTGGCAGTAGCCAAATGATCTTCTAGAATATGATTGGGAGTGTCATAT
66 TCAAAAACGTCATTGTTTTGGCAGTAGCCAAATGATCTTCTAGAATATGATTGGGAGTGTCATAT
*
714517 TGAGGTGTGATCAGGTTCCAGAATTTTTATTTATTGAGGGGATCAGTGGGTTAAAAAATTTTG
131 TGAGGTGTGATCAGGTTCCAGAATTTTTATTTATTAAGGGGATCAGTGGGTTAAAAAATTTTG
*
714580 TCAATTTTGTCCTGGGGGTCATTTAATGGCTGAAAAAGACGTTTTTTAAAAAAAACCCACTGGTT
1 TCAATTTTGTCCTGGGGGTCATTTAATGGCTGAAAAAGACGTTTTTTAAAAAAAAACCACTGGTT
714645 TCAAAAACGTCATTGTTTTGGCAGTAGCCAAATGATCTTCTAGAATATGATTGGGAGTGTCATAT
66 TCAAAAACGTCATTGTTTTGGCAGTAGCCAAATGATCTTCTAGAATATGATTGGGAGTGTCATAT
714710 TGAGGTGTGATCAGGTTCCAGAATTTTTATTTATTAAGGGGATCAGTGGGTTAAAAAA
131 TGAGGTGTGATCAGGTTCCAGAATTTTTATTTATTAAGGGGATCAGTGGGTTAAAAAA
714768 AAAATGATTT
Statistics
Matches: 186, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
193 186 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (193 bp):
TCAATTTTGTCCTGGGGGTCATTTAATGGCTGAAAAAGACGTTTTTTAAAAAAAAACCACTGGTT
TCAAAAACGTCATTGTTTTGGCAGTAGCCAAATGATCTTCTAGAATATGATTGGGAGTGTCATAT
TGAGGTGTGATCAGGTTCCAGAATTTTTATTTATTAAGGGGATCAGTGGGTTAAAAAATTTTG
Found at i:715081 original size:166 final size:161
Alignment explanation
Indices: 714836--715228 Score: 459
Period size: 166 Copynumber: 2.4 Consensus size: 161
714826 AGTAGCTACG
* * * * * * *
714836 TCATCTCTTGGGATATAATTGGGGCTGTCCTATAAATGCGCAATAAGGTTTTAAAAATTTGAATT
1 TCATATCTTGGGATATAATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
* * * ** **
714901 TCATCCAGGGAGTCAAATAGTAGCAGAAAATTGACGTTTATCAC-TAAAAAACCCCCCCCATTGA
66 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGAC-ATTAACACATAAAAAA-----AACAGAGA
*
714965 TCCAAGAGCTCC-TCTTATGATTTAATGGATAGACACA
125 TCCAAGAACTCCGT-TTATGATTTAATGGATAGACACA
* * *
715002 TCATATCTTTGGATATGATAGGGACTGTTCTATAGATGTGCAGTAAGGTTTTAAAAATTTAAATT
1 TCATATCTTGGGATATAATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
* *
715067 TCATCTAGGGAGTCAAAAAGTAGCAGAAAATTGACATTAACACATAAAAAAAACAGAGATCCTAG
66 TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACATTAACACATAAAAAAAACAGAGATCCAAG
715132 AACTCCGTTTATGATTTAATGGATAGACACA
131 AACTCCGTTTATGATTTAATGGATAGACACA
* * * * * *
715163 TCATGTCTTGGGATATAATAGGAACTGTTCAATGGATGTGCATTACGGTTTTGAAAAA-TTAAAT
1 TCATATCTTGGGATATAATAGGGACTGTTCTATAGATGTGCAATAAGGTTTT-AAAAATTTAAAT
715227 TT
65 TT
715229 AACCCCGAGG
Statistics
Matches: 196, Mismatches: 28, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
161 89 0.45
162 6 0.03
165 6 0.03
166 95 0.48
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (161 bp):
TCATATCTTGGGATATAATAGGGACTGTTCTATAGATGTGCAATAAGGTTTTAAAAATTTAAATT
TCATCCAGGGAGTCAAAAAGTAGCAGAAAATTGACATTAACACATAAAAAAAACAGAGATCCAAG
AACTCCGTTTATGATTTAATGGATAGACACA
Found at i:715434 original size:135 final size:133
Alignment explanation
Indices: 715263--715553 Score: 354
Period size: 134 Copynumber: 2.2 Consensus size: 133
715253 ACCTTTGGAT
* *
715263 CAAGAATATATATGGTTAAGGGGTGGGGAACTCAACTGTTTTCAAGATATT-TGTGCACTTCCTG
1 CAAGAATATATATGGTTTA-GGGTGGGGAACTCAACTGTTTTCAAGATATTAAG-GCACTTCCTG
* * * * *
715327 TTCGAGGGGGGTCATGACCATCC-CCGGGGTCCATGACCTACATAACGTTTGATGCCCCTTGACA
64 TTCGA-GGGGGTCAGGACCA-CCTACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACA
*
715391 -CAAGGAA
127 GC-AGAAA
* * * *
715398 CAAGAATATATATGGTTGTAGGGTGGGGATCTCAACTGTTTTGAAGATATTAAGGGACTTGCTGT
1 CAAGAATATATATGGTT-TAGGGTGGGGAACTCAACTGTTTTCAAGATATTAAGGCACTTCCTGT
* * * *
715463 TTGAGGGTGTCAGGACTACCTACATGGCCCATGACCTACATAACATTTGATGCCCCTTGACAGCA
65 TCGAGGGGGTCAGGACCACCTACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACAGCA
715528 GAAA
130 GAAA
*
715532 CATGAATATATATGGTTTAGGG
1 CAAGAATATATATGGTTTAGGG
715554 ATCATGATTA
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
133 7 0.05
134 67 0.50
135 59 0.44
136 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (133 bp):
CAAGAATATATATGGTTTAGGGTGGGGAACTCAACTGTTTTCAAGATATTAAGGCACTTCCTGTT
CGAGGGGGTCAGGACCACCTACAGGGCCCATGACCTACATAACATTTGATGCCCCTTGACAGCAG
AAA
Found at i:722040 original size:29 final size:29
Alignment explanation
Indices: 722003--722062 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
721993 TTATAACAGT
*
722003 TAATTGAGTTATCTTCCCTT-GCTTCTTCA
1 TAATGGAGTTATCTT-CCTTCGCTTCTTCA
*
722032 TAATGGAGTTATCTTCCTTCGCTTGTTCA
1 TAATGGAGTTATCTTCCTTCGCTTCTTCA
722061 TA
1 TA
722063 TTTAGTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 4 0.14
29 24 0.86
ACGTcount: A:0.18, C:0.22, G:0.13, T:0.47
Consensus pattern (29 bp):
TAATGGAGTTATCTTCCTTCGCTTCTTCA
Found at i:724390 original size:21 final size:21
Alignment explanation
Indices: 724365--724456 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
724355 AGATGAGTTT
724365 CATTATATGATGATACTTCAA
1 CATTATATGATGATACTTCAA
* *
724386 CATTACAT-ACTGATACTTAAA
1 CATTATATGA-TGATACTTCAA
* * *
724407 CATTATATGCTGATATTTTAA
1 CATTATATGATGATACTTCAA
* * * **
724428 CGTTACATGCTGATACTTCCT
1 CATTATATGATGATACTTCAA
724449 CATTATAT
1 CATTATAT
724457 ACCCAAATTA
Statistics
Matches: 55, Mismatches: 14, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.98
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (21 bp):
CATTATATGATGATACTTCAA
Found at i:724411 original size:42 final size:42
Alignment explanation
Indices: 724365--724445 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
724355 AGATGAGTTT
724365 CATTATATGATGATACTTCAACATTACATACTGATACTTAAA
1 CATTATATGATGATACTTCAACATTACATACTGATACTTAAA
* * * * *
724407 CATTATATGCTGATATTTTAACGTTACATGCTGATACTT
1 CATTATATGATGATACTTCAACATTACATACTGATACTT
724446 CCTCATTATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (42 bp):
CATTATATGATGATACTTCAACATTACATACTGATACTTAAA
Found at i:724453 original size:42 final size:42
Alignment explanation
Indices: 724364--724456 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
724354 TAGATGAGTT
724364 TCATTATATGATGATACTTCAACATTACATACTGATACTTAA
1 TCATTATATGATGATACTTCAACATTACATACTGATACTTAA
* * * * * * **
724406 ACATTATATGCTGATATTTTAACGTTACATGCTGATACTTCC
1 TCATTATATGATGATACTTCAACATTACATACTGATACTTAA
724448 TCATTATAT
1 TCATTATAT
724457 ACCCAAATTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (42 bp):
TCATTATATGATGATACTTCAACATTACATACTGATACTTAA
Found at i:727674 original size:48 final size:48
Alignment explanation
Indices: 727573--727700 Score: 130
Period size: 50 Copynumber: 2.6 Consensus size: 48
727563 GAAAAAAATA
* *
727573 CACTTTGAAAAATCCTTTCAAAGTGCGTTAAAACTGGGACAAAATGAACG
1 CACTTTGAAAAA-AC-TTCAAAGTGCGTTAAAACTGGGACAAAATCAACG
** * * * *
727623 CACTTTGAAAAAACTTCAAAGTGCGTTAAATTTGTGACTAAGTCAATG
1 CACTTTGAAAAAACTTCAAAGTGCGTTAAAACTGGGACAAAATCAACG
* *
727671 CACTCTAGAAAAAAATTTCAAAGTGCGTTA
1 CACT-TTG-AAAAAACTTCAAAGTGCGTTA
727701 TGAGTGTACA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
48 31 0.47
49 3 0.05
50 32 0.48
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (48 bp):
CACTTTGAAAAAACTTCAAAGTGCGTTAAAACTGGGACAAAATCAACG
Found at i:735647 original size:161 final size:161
Alignment explanation
Indices: 735363--735680 Score: 478
Period size: 161 Copynumber: 2.0 Consensus size: 161
735353 GGGCCTCTTG
*
735363 TTTTAGGAGTGCTAAACGTCAATTATTTGCTATTATTTGACTCCCTAGATAAAATCTAAATTTTA
1 TTTTAGGAGTGATAAACGTCAATTATTTGCTATTATTTGACTCCCTAGATAAAATCTAAATTTTA
* * * **
735428 TAAACCTTATTGCACATCTACAGGACAGTCCCTATTATATCCAAAGATATGGTGTGTCTATTCAT
66 AAAACCTTATTGCACATCTAAAGGACAGTCCCTATCATATCCAAAGATATAATGTGTCTATTCAT
735493 TAAATCATAAGAGGAGCTCTGGGATCTAGGT
131 TAAATCATAAGAGGAGCTCTGGGATCTAGGT
* * * *
735524 TTTTAGGAGTGATAAACGTCAA-TATTTTGCTATTATTTGACTCCTTGGATGAAATGTAAATTTT
1 TTTTAGGAGTGATAAACGTCAATTA-TTTGCTATTATTTGACTCCCTAGATAAAATCTAAATTTT
* * *
735588 AAAAACCTTATTGCACAT-TCAAAGGACAGTCCCTATCATATCCCAATATATAATGTGTCTGTTC
65 AAAAACCTTATTGCACATCT-AAAGGACAGTCCCTATCATATCCAAAGATATAATGTGTCTATTC
*
735652 ATTAAATCATAAGAGGAGTTCTGGGATCT
129 ATTAAATCATAAGAGGAGCTCTGGGATCT
735681 TTTTTTTTTT
Statistics
Matches: 141, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
160 3 0.02
161 138 0.98
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (161 bp):
TTTTAGGAGTGATAAACGTCAATTATTTGCTATTATTTGACTCCCTAGATAAAATCTAAATTTTA
AAAACCTTATTGCACATCTAAAGGACAGTCCCTATCATATCCAAAGATATAATGTGTCTATTCAT
TAAATCATAAGAGGAGCTCTGGGATCTAGGT
Found at i:739909 original size:44 final size:39
Alignment explanation
Indices: 739782--739898 Score: 234
Period size: 39 Copynumber: 3.0 Consensus size: 39
739772 TGCAGTCTAG
739782 CAATGTAGCTACTACCAAGCAAACCAAACTATGCCATCA
1 CAATGTAGCTACTACCAAGCAAACCAAACTATGCCATCA
739821 CAATGTAGCTACTACCAAGCAAACCAAACTATGCCATCA
1 CAATGTAGCTACTACCAAGCAAACCAAACTATGCCATCA
739860 CAATGTAGCTACTACCAAGCAAACCAAACTATGCCATCA
1 CAATGTAGCTACTACCAAGCAAACCAAACTATGCCATCA
739899 TTGTAAAATG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 78 1.00
ACGTcount: A:0.41, C:0.31, G:0.10, T:0.18
Consensus pattern (39 bp):
CAATGTAGCTACTACCAAGCAAACCAAACTATGCCATCA
Found at i:743081 original size:34 final size:34
Alignment explanation
Indices: 743039--743110 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
743029 TCAACAACAC
*
743039 ACACCATAACATAACATAGCATTGAATTTTCATA
1 ACACCATAACATAACATAACATTGAATTTTCATA
* *
743073 ACACCATAACATAACATAACGTTGAGTTTTCATA
1 ACACCATAACATAACATAACATTGAATTTTCATA
743107 ACAC
1 ACAC
743111 ATCGTTGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (34 bp):
ACACCATAACATAACATAACATTGAATTTTCATA
Found at i:745272 original size:4 final size:4
Alignment explanation
Indices: 745263--745296 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
745253 GTTACCCTGT
*
745263 TCCG TCCG TCCG TCCA TCCG TCCG TCCG TCCG TC
1 TCCG TCCG TCCG TCCG TCCG TCCG TCCG TCCG TC
745297 TGTCACGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.03, C:0.50, G:0.21, T:0.26
Consensus pattern (4 bp):
TCCG
Found at i:749055 original size:16 final size:16
Alignment explanation
Indices: 749034--749068 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
749024 AAAATACCCG
*
749034 GTAATTTGTGAAACTA
1 GTAATTTATGAAACTA
749050 GTAATTTATGAAACTA
1 GTAATTTATGAAACTA
749066 GTA
1 GTA
749069 TTTTTAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (16 bp):
GTAATTTATGAAACTA
Found at i:750699 original size:3 final size:3
Alignment explanation
Indices: 750693--750724 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
750683 ATGATGAACA
*
750693 ATG ATG ATG ATG ATG GTG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
750725 CAAACATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:753065 original size:16 final size:16
Alignment explanation
Indices: 753044--753083 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
753034 TTTACAAAGG
*
753044 GACAGACGGACGGACA
1 GACAGACAGACGGACA
753060 GACAGACAGACGGACA
1 GACAGACAGACGGACA
*
753076 GACGGACA
1 GACAGACA
753084 AAATGTGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.35, T:0.00
Consensus pattern (16 bp):
GACAGACAGACGGACA
Found at i:753067 original size:8 final size:8
Alignment explanation
Indices: 753052--753083 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
753042 GGGACAGACG
753052 GACGGACA
1 GACGGACA
*
753060 GACAGACA
1 GACGGACA
753068 GACGGACA
1 GACGGACA
753076 GACGGACA
1 GACGGACA
753084 AAATGTGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.41, C:0.25, G:0.34, T:0.00
Consensus pattern (8 bp):
GACGGACA
Found at i:766222 original size:2 final size:2
Alignment explanation
Indices: 766215--766249 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
766205 NNNNNNNNNN
766215 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
766250 AGACATCCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:766427 original size:44 final size:44
Alignment explanation
Indices: 766379--766483 Score: 201
Period size: 44 Copynumber: 2.4 Consensus size: 44
766369 GCTCTCGCTC
*
766379 TCTCTCTCTCTCTCTCTCTCCATAATATGTACTTTCTCTTTGTT
1 TCTCTCTATCTCTCTCTCTCCATAATATGTACTTTCTCTTTGTT
766423 TCTCTCTATCTCTCTCTCTCCATAATATGTACTTTCTCTTTGTT
1 TCTCTCTATCTCTCTCTCTCCATAATATGTACTTTCTCTTTGTT
766467 TCTCTCTATCTCTCTCT
1 TCTCTCTATCTCTCTCT
766484 TTCAGTTTTC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 60 1.00
ACGTcount: A:0.11, C:0.32, G:0.04, T:0.52
Consensus pattern (44 bp):
TCTCTCTATCTCTCTCTCTCCATAATATGTACTTTCTCTTTGTT
Found at i:766564 original size:2 final size:2
Alignment explanation
Indices: 766557--766588 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
766547 TAAGCTCAAG
*
766557 CT CT CT CT CT CT CT CT GT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
766589 TTCAGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:766737 original size:2 final size:2
Alignment explanation
Indices: 766730--766769 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
766720 CTTGATCTTT
*
766730 TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
766770 CAAAATATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:766867 original size:2 final size:2
Alignment explanation
Indices: 766860--766902 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
766850 CTTCATTAAC
766860 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
766902 C
1 C
766903 AAACATTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:768353 original size:38 final size:38
Alignment explanation
Indices: 768302--768379 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
768292 AATTACAAAG
*
768302 TATAGCTACACAAACATAGTGATATTACATGAATACTA
1 TATAGCTACACAAACATAGTGATATTAAATGAATACTA
768340 TATAGCTACACAAACATAGTGATATTAAATGAATACTA
1 TATAGCTACACAAACATAGTGATATTAAATGAATACTA
768378 TA
1 TA
768380 CCACATAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.29
Consensus pattern (38 bp):
TATAGCTACACAAACATAGTGATATTAAATGAATACTA
Found at i:768594 original size:19 final size:19
Alignment explanation
Indices: 768581--768631 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
768571 GAAGACAAGC
768581 TAATACAGTGAAGATGAGT
1 TAATACAGTGAAGATGAGT
768600 TAATACAGTGAAGATGAGT
1 TAATACAGTGAAGATGAGT
768619 TAATACAGTGAAG
1 TAATACAGTGAAG
768632 TCTCCGATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.25
Consensus pattern (19 bp):
TAATACAGTGAAGATGAGT
Found at i:768653 original size:17 final size:17
Alignment explanation
Indices: 768631--768664 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
768621 ATACAGTGAA
768631 GTCTCCGATTCCCGGTC
1 GTCTCCGATTCCCGGTC
768648 GTCTCCGATTCCCGGTC
1 GTCTCCGATTCCCGGTC
768665 ACTCCTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.41, G:0.24, T:0.29
Consensus pattern (17 bp):
GTCTCCGATTCCCGGTC
Found at i:769392 original size:16 final size:16
Alignment explanation
Indices: 769371--769409 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
769361 TTGTCAGTAA
769371 ATGCATGTATA-TATGC
1 ATGCATGTATACT-TGC
*
769387 ATGCATATATACTTGC
1 ATGCATGTATACTTGC
769403 ATGCATG
1 ATGCATG
769410 CATTATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (16 bp):
ATGCATGTATACTTGC
Found at i:770054 original size:42 final size:42
Alignment explanation
Indices: 769995--770206 Score: 388
Period size: 42 Copynumber: 5.0 Consensus size: 42
769985 CAGCACTTTA
* * * *
769995 ACCACTGAGCTATTGAGAACTGATATGTTGACCGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
770037 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
770079 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
770121 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
770163 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
1 ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
770205 AC
1 AC
770207 ACATGTTAAC
Statistics
Matches: 166, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 166 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (42 bp):
ACCACTGAGCTATTGAGACCCGATATATTGACTGACGGTCAC
Found at i:778301 original size:2 final size:2
Alignment explanation
Indices: 778294--778366 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
778284 GGTAAAACCA
778294 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
778336 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
778367 TTTTGTTTCC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:782533 original size:2 final size:2
Alignment explanation
Indices: 782526--782602 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
782516 TATGATGCTG
782526 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
782568 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
782603 TGATTTCATT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:787125 original size:15 final size:15
Alignment explanation
Indices: 787107--787138 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
787097 CATCATAAAG
787107 TTACACATCTACTTT
1 TTACACATCTACTTT
787122 TTACACATCTACTTT
1 TTACACATCTACTTT
787137 TT
1 TT
787139 GTCTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.50
Consensus pattern (15 bp):
TTACACATCTACTTT
Found at i:788454 original size:2 final size:2
Alignment explanation
Indices: 788447--788517 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
788437 TGGCATATAA
788447 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
788489 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
788518 GGAATGTGTG
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:790977 original size:20 final size:20
Alignment explanation
Indices: 790952--790996 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
790942 GCTGTAGTAC
* *
790952 GACAAGCTATAGTATATCAT
1 GACAAGCTATAGTACACCAT
*
790972 GACAAGCTCTAGTACACCAT
1 GACAAGCTATAGTACACCAT
790992 GACAA
1 GACAA
790997 AAAGTAGTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
GACAAGCTATAGTACACCAT
Found at i:791230 original size:20 final size:20
Alignment explanation
Indices: 791205--791316 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
791195 CAATTTATAG
791205 TACATCATGACAAGCTATTA
1 TACATCATGACAAGCTATTA
**
791225 TACATCATGACAAGCTATGG
1 TACATCATGACAAGCTATTA
* *
791245 T---GC--GACAAGCTATTG
1 TACATCATGACAAGCTATTA
* * *
791260 TACACCATGGCAAGCTA-CA
1 TACATCATGACAAGCTATTA
* *
791279 GTACATCATGACAAGATATAA
1 -TACATCATGACAAGCTATTA
791300 TACATCATGACAAGCTA
1 TACATCATGACAAGCTA
791317 CAGTCCCTCA
Statistics
Matches: 72, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
15 12 0.17
17 1 0.01
18 1 0.01
20 57 0.79
21 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.24
Consensus pattern (20 bp):
TACATCATGACAAGCTATTA
Found at i:791329 original size:75 final size:75
Alignment explanation
Indices: 791203--791365 Score: 227
Period size: 75 Copynumber: 2.2 Consensus size: 75
791193 GTCAATTTAT
* * ** * * * *
791203 AGTACATCATGACAAGCTATTATACATCATGACAAGCTATGGTGCGACAAGCTATTGTACACCAT
1 AGTACATCATGACAAGATATAATACATCATGACAAGCTACAGTCCCACAAGCTATGGCACACCAT
*
791268 GGCAAGCTAC
66 GACAAGCTAC
*
791278 AGTACATCATGACAAGATATAATACATCATGACAAGCTACAGTCCCTCAAGCTATGGCACACCAT
1 AGTACATCATGACAAGATATAATACATCATGACAAGCTACAGTCCCACAAGCTATGGCACACCAT
*
791343 GATAAGCTAC
66 GACAAGCTAC
791353 AGTACATCATGAC
1 AGTACATCATGAC
791366 TACCTACAGT
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.23
Consensus pattern (75 bp):
AGTACATCATGACAAGATATAATACATCATGACAAGCTACAGTCCCACAAGCTATGGCACACCAT
GACAAGCTAC
Found at i:791452 original size:20 final size:20
Alignment explanation
Indices: 791428--791523 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
791418 GGCAAGTTAT
* *
791428 AGTACACCATGACAAGCTAT
1 AGTACATCATGACAAGCTAC
* *
791448 GGTACATAATGACAAGCTAC
1 AGTACATCATGACAAGCTAC
791468 AGTACATCATGACAAGCTAC
1 AGTACATCATGACAAGCTAC
* *
791488 AGTATATCAGTG-CTAA-CTAT
1 AGTACATCA-TGAC-AAGCTAC
*
791508 AGTACATCATAACAAG
1 AGTACATCATGACAAG
791524 TTAAAAGGCA
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
19 3 0.05
20 55 0.89
21 4 0.06
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.23
Consensus pattern (20 bp):
AGTACATCATGACAAGCTAC
Found at i:791512 original size:40 final size:40
Alignment explanation
Indices: 791346--791523 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 40
791336 ACACCATGAT
* * *
791346 AAGCTACAGTACATCATGACTACCTACAGTATATCACGT-C
1 AAGCTATAGTACATCATGACAAGCTACAGTATATCA-GTGC
* * * *
791386 AAACTATATTACATCATGACAAGCGATAG--TA-C-G-GC
1 AAGCTATAGTACATCATGACAAGCTACAGTATATCAGTGC
* * ** * *
791421 AAGTTATAGTACACCATGACAAGCTATGGTACAT-AATGAC
1 AAGCTATAGTACATCATGACAAGCTACAGTATATCAGTG-C
*
791461 AAGCTACAGTACATCATGACAAGCTACAGTATATCAGTGC
1 AAGCTATAGTACATCATGACAAGCTACAGTATATCAGTGC
*
791501 TAA-CTATAGTACATCATAACAAG
1 -AAGCTATAGTACATCATGACAAG
791524 TTAAAAGGCA
Statistics
Matches: 105, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
35 25 0.24
37 2 0.02
38 2 0.02
39 1 0.01
40 70 0.67
41 5 0.05
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.24
Consensus pattern (40 bp):
AAGCTATAGTACATCATGACAAGCTACAGTATATCAGTGC
Found at i:791512 original size:95 final size:95
Alignment explanation
Indices: 791248--791486 Score: 271
Period size: 95 Copynumber: 2.5 Consensus size: 95
791238 GCTATGGTGC
* * * *
791248 GACAAGCTATTGTACACCATGGCAAGCTACAGTACATCATGACAAGATATAATACATCATGACAA
1 GACAAGCTATAGTACATCATGACAAGCTACAGTACATCATGACAAGCTATAATACATCATGACAA
* * * *
791313 GCTACAGTCCCTCAAGCTATGGCACACCAT
66 GCTATAGTACCGCAAGCTATAGCACACCAT
* * * * * * * * *
791343 GATAAGCTACAGTACATCATGACTACCTACAGTATATCACGTCAAACTATATTACATCATGACAA
1 GACAAGCTATAGTACATCATGACAAGCTACAGTACATCATGACAAGCTATAATACATCATGACAA
* * * *
791408 GCGATAGTACGGCAAGTTATAGTACACCAT
66 GCTATAGTACCGCAAGCTATAGCACACCAT
* *
791438 GACAAGCTATGGTACATAATGACAAGCTACAGTACATCATGACAAGCTA
1 GACAAGCTATAGTACATCATGACAAGCTACAGTACATCATGACAAGCTA
791487 CAGTATATCA
Statistics
Matches: 113, Mismatches: 31, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
95 113 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (95 bp):
GACAAGCTATAGTACATCATGACAAGCTACAGTACATCATGACAAGCTATAATACATCATGACAA
GCTATAGTACCGCAAGCTATAGCACACCAT
Found at i:795377 original size:1 final size:1
Alignment explanation
Indices: 795373--795407 Score: 52
Period size: 1 Copynumber: 35.0 Consensus size: 1
795363 ATCGTTGGCC
* *
795373 AAAAAAAAAAAAACAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
795408 CATGCACTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:795392 original size:12 final size:12
Alignment explanation
Indices: 795375--795407 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
795365 CGTTGGCCAA
795375 AAAAAAAAAAAC
1 AAAAAAAAAAAC
795387 AAAAAAAAAAAC
1 AAAAAAAAAAAC
795399 AAAAAAAAA
1 AAAAAAAAA
795408 CATGCACTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:801008 original size:4 final size:4
Alignment explanation
Indices: 800999--801104 Score: 196
Period size: 4 Copynumber: 26.8 Consensus size: 4
800989 AAGTTGTCAT
*
800999 TAGA TAGA TAGA TGGA T-GA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
801046 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
1 TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA TAGA
801094 TAGA TAGA TAG
1 TAGA TAGA TAG
801105 GTGGATGGGT
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
3 3 0.03
4 97 0.97
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.25
Consensus pattern (4 bp):
TAGA
Found at i:802513 original size:3 final size:3
Alignment explanation
Indices: 802505--802589 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
802495 ATTTGTATAT
802505 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
802553 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
802590 GGGGGGGGGG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:804301 original size:17 final size:18
Alignment explanation
Indices: 804273--804313 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
804263 CTCTTGATTT
804273 AGCTATATAGCTTGAAAA
1 AGCTATATAGCTTGAAAA
* *
804291 AGCTA-ATAGCTTTATAA
1 AGCTATATAGCTTGAAAA
804308 AGCTAT
1 AGCTAT
804314 TCAAAATAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (18 bp):
AGCTATATAGCTTGAAAA
Found at i:808976 original size:166 final size:166
Alignment explanation
Indices: 808355--808984 Score: 854
Period size: 166 Copynumber: 3.8 Consensus size: 166
808345 GTCGTATTTA
*
808355 TCTCAGCAACTATTTATCGCAGATGCTTG-AATTTTTACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATA-
* * * * *
808419 TATCGTGGGATATATTTTTATACCAATCAGATGTCAACTTCCTGTTAAATGACGACTTTGTTTAT
65 T-T-GTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTCAAATAATGACTTTGTTTAT
* * * * * *
808484 TTTTAGCAAAAATTTTCAAACAACTTTTTGTTAGAGAAT
128 TTTTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
808523 TCTCAGCAACTGTTTATTGCAGATGCATGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
* * * *
808588 CGTGGGATGTATTTTTGTACCAATCGGAGGTCAAATTCCTGTCAAATAATGACTTTGTTTATTTT
66 TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTCAAATAATGACTTTGTTTATTTT
*
808653 TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT
131 TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
808689 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTAT-AGGCATGCCATA
* * *
808753 TTGTGGGATATATTTTTGTATCAATCGAACGTCAACTTCCTGTCAAATAATGACTTTGTTTATTT
65 TTGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTCAAATAATGACTTTGTTTATTT
808818 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
130 TTAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
808855 TCTCAGCAGCTATTTATCGCAGATGCTTGTAATTTTTACACAGTGTTTGT-TAAGGCATGCCATA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTAT-AGGCATGCCATA
* * * * * * *
808919 TTGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAAT-GTCGACTTTGCTTATT
65 TTGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTCAAATAAT-GACTTTGTTTATT
808983 TT
129 TT
808985 GCATATCCAC
Statistics
Matches: 414, Mismatches: 45, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
165 2 0.00
166 353 0.85
168 27 0.07
169 32 0.08
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (166 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
TGTGGGATATATTTTTGTACCAATCGGATGTCAACTTCCTGTCAAATAATGACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:813524 original size:21 final size:21
Alignment explanation
Indices: 813500--813587 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 21
813490 TTTTTGAGGT
813500 ATTTTCTGATATCAGAAAATG
1 ATTTTCTGATATCAGAAAATG
*
813521 ATTTTTTGATATCAGAAATTGAAACTG
1 ATTTTCTGATATCAG--A---AAA-TG
* *
813548 ATTTTTTGATATCAAGAATTAT-
1 ATTTTCTGATATC-AGAA-AATG
813570 ATTTTCTGATATCAGAAA
1 ATTTTCTGATATCAGAAA
813588 TTTAAAGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
21 18 0.33
22 12 0.22
23 3 0.05
24 1 0.02
26 4 0.07
27 15 0.27
28 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.42
Consensus pattern (21 bp):
ATTTTCTGATATCAGAAAATG
Found at i:814045 original size:22 final size:22
Alignment explanation
Indices: 814017--814390 Score: 266
Period size: 22 Copynumber: 17.0 Consensus size: 22
814007 TGTAAGTCTT
*
814017 ATTTTCTGATATCAAAAAATAG
1 ATTTTTTGATATCAAAAAATAG
* *
814039 ATTTTCTGATATCAGAAAATGTAAATG
1 ATTTTTTGATATCA-AAAA---ATA-G
814066 ATTTTTTGATATCAAAAAAT-G
1 ATTTTTTGATATCAAAAAATAG
* * * *
814087 ATTTTGTGATATCAAGAATTCG
1 ATTTTTTGATATCAAAAAATAG
814109 ATTTTTTGATATCAAAAAAT-G
1 ATTTTTTGATATCAAAAAATAG
* * *
814130 ATTTTCTGATATCAAGAATTCA-
1 ATTTTTTGATATCAAAAAAT-AG
814152 ATTTTTTGATATCAAAAAATCA-
1 ATTTTTTGATATCAAAAAAT-AG
**
814174 ACTTTAATTCTTGATATCAAAAAATCT
1 A--TT--TT-TTGATATCAAAAAATAG
* *
814201 ATTTTGTGATATCAGAAAATA-
1 ATTTTTTGATATCAAAAAATAG
* * *
814222 ATTTTTTGATATCAAGAATTCG
1 ATTTTTTGATATCAAAAAATAG
* *
814244 AATTTGTGATATCAAAAAAT-G
1 ATTTTTTGATATCAAAAAATAG
* *
814265 ATTTTCTGATATCACAAAATAG
1 ATTTTTTGATATCAAAAAATAG
* *
814287 ATTTTTTGATATCAAGAATTA-
1 ATTTTTTGATATCAAAAAATAG
* *
814308 A-TTTTTGATATC-AAGAAT-T
1 ATTTTTTGATATCAAAAAATAG
* *
814327 ATTTTTTGATATCAAAAATTCG
1 ATTTTTTGATATCAAAAAATAG
* * * **
814349 AATTATTGATATC-AAATATTT
1 ATTTTTTGATATCAAAAAATAG
*
814370 ATTTTTTGATATCAGAAAATA
1 ATTTTTTGATATCAAAAAATA
814391 CCTCAAAAAT
Statistics
Matches: 279, Mismatches: 52, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
19 4 0.01
20 22 0.08
21 90 0.32
22 114 0.41
23 7 0.03
24 2 0.01
25 2 0.01
26 8 0.03
27 30 0.11
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.41
Consensus pattern (22 bp):
ATTTTTTGATATCAAAAAATAG
Found at i:814068 original size:27 final size:28
Alignment explanation
Indices: 814033--814086 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
814023 TGATATCAAA
*
814033 AAATAGATTTTCTGATATCAGAAAATGT
1 AAATAGATTTTCTGATATCAAAAAATGT
*
814061 AAAT-GATTTTTTGATATCAAAAAATG
1 AAATAGATTTTCTGATATCAAAAAATG
814087 ATTTTGTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (28 bp):
AAATAGATTTTCTGATATCAAAAAATGT
Found at i:814126 original size:43 final size:43
Alignment explanation
Indices: 814017--814389 Score: 337
Period size: 43 Copynumber: 8.5 Consensus size: 43
814007 TGTAAGTCTT
* * *
814017 ATTTTCTGATATCAAAAAATAGATTTTCTGATATCAGAAAATGTAAATG
1 ATTTTTTGATATCAAAAAAT-GATTTTCTGATATCA-AGAAT-T---CG
*
814066 ATTTTTTGATATCAAAAAATGATTTTGTGATATCAAGAATTCG
1 ATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCG
*
814109 ATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCA
1 ATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCG
* * * *
814152 ATTTTTTGATATCAAAAAATCAACTTTAATTCTTGATATCAAAAAATCT
1 ATTTTTTGATATCAAAAAAT-GA--TT--TTC-TGATATCAAGAATTCG
* * * *
814201 ATTTTGTGATATCAGAAAATAATTTTTTGATATCAAGAATTCG
1 ATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCG
* * * *
814244 AATTTGTGATATCAAAAAATGATTTTCTGATATCACA-AAATAG
1 ATTTTTTGATATCAAAAAATGATTTTCTGATATCA-AGAATTCG
* * *
814287 ATTTTTTGATATCAAGAATTAATTTT-TGATATCAAGAATT--
1 ATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCG
* * *
814327 ATTTTTTGATATCAAAAATTCGAATTAT-TGATATCAA-ATATT-T
1 ATTTTTTGATATCAAAAAAT-G-ATTTTCTGATATCAAGA-ATTCG
*
814370 ATTTTTTGATATCAGAAAAT
1 ATTTTTTGATATCAAAAAAT
814390 ACCTCAAAAA
Statistics
Matches: 279, Mismatches: 33, Indels: 30
0.82 0.10 0.09
Matches are distributed among these distances:
40 19 0.07
41 2 0.01
42 27 0.10
43 149 0.53
44 4 0.01
46 5 0.02
47 4 0.01
48 19 0.07
49 50 0.18
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (43 bp):
ATTTTTTGATATCAAAAAATGATTTTCTGATATCAAGAATTCG
Found at i:814205 original size:135 final size:125
Alignment explanation
Indices: 814061--814389 Score: 360
Period size: 135 Copynumber: 2.5 Consensus size: 125
814051 CAGAAAATGT
*
814061 AAATGATTTTTTGATATCAAAAAATGATTTTGTGATATCAAGAATTCGATTTTTTGATATCAAAA
1 AAATTATTTTTTGATATCAAAAAATGATTTT-TGATATCAAGAATTCGATTTTTTGATATCAAAA
*
814126 AATGATTTTCTGATATCA-AGAATTCA-ATTTTTTGATATCAAAAAATCAACTTTAATTCTTGAT
65 AATGATTTTCTGATATCACA-AAAT-AGATTTTTTGATATC----AA-CAA--TTAATTCTTGAT
814189 ATCAAA
121 ATC-AA
* * * * *
814195 AAATCTATTTTGTGATATCAGAAAATAATTTTTTGATATCAAGAATTCGAATTTGTGATATCAAA
1 AAAT-TATTTTTTGATATCAAAAAATGA-TTTTTGATATCAAGAATTCGATTTTTTGATATCAAA
* *
814260 AAATGATTTTCTGATATCACAAAATAGATTTTTTGATATCAAGAATTAATTTTTGATATCAA
64 AAATGATTTTCTGATATCACAAAATAGATTTTTTGATATCAACAATTAATTCTTGATATCAA
* * * * *
814322 GAATTATTTTTTGATATCAAAAATTCGAATTATTGATATCAA-ATATT-TATTTTTTGATATCAG
1 AAATTATTTTTTGATATCAAAAAAT-G-ATTTTTGATATCAAGA-ATTCGATTTTTTGATATCAA
814385 AAAAT
63 AAAAT
814390 ACCTCAAAAA
Statistics
Matches: 169, Mismatches: 19, Indels: 22
0.80 0.09 0.10
Matches are distributed among these distances:
126 36 0.21
127 20 0.12
128 15 0.09
130 2 0.01
131 2 0.01
134 5 0.03
135 84 0.50
136 5 0.03
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (125 bp):
AAATTATTTTTTGATATCAAAAAATGATTTTTGATATCAAGAATTCGATTTTTTGATATCAAAAA
ATGATTTTCTGATATCACAAAATAGATTTTTTGATATCAACAATTAATTCTTGATATCAA
Found at i:825044 original size:5 final size:5
Alignment explanation
Indices: 825034--825119 Score: 72
Period size: 5 Copynumber: 17.6 Consensus size: 5
825024 CCTGTAAAGT
* * * *
825034 ACGAA ACGAA AAGATA TCG-A ACGAA ACGAA ACGAA ACCAA TCGAA ACGAA
1 ACGAA ACGAA ACGA-A ACGAA ACGAA ACGAA ACGAA ACGAA ACGAA ACGAA
* *
825084 ATC-AA ACGAA ACGAA ACCAA A--AA TCGAA ACGAA ACG
1 A-CGAA ACGAA ACGAA ACGAA ACGAA ACGAA ACGAA ACG
825120 GAATTTAAAC
Statistics
Matches: 64, Mismatches: 11, Indels: 12
0.74 0.13 0.14
Matches are distributed among these distances:
3 2 0.03
4 4 0.06
5 55 0.86
6 3 0.05
ACGTcount: A:0.57, C:0.21, G:0.16, T:0.06
Consensus pattern (5 bp):
ACGAA
Found at i:825177 original size:2 final size:2
Alignment explanation
Indices: 825170--825216 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
825160 GTGAAAATAA
825170 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
825212 AG AG A
1 AG AG A
825217 TGCCTTAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:825566 original size:3 final size:3
Alignment explanation
Indices: 825553--825596 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
825543 CCCCTTCAGT
*
825553 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
825597 ATCTCTATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:825692 original size:2 final size:2
Alignment explanation
Indices: 825685--825730 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
825675 TTTTATGGCA
825685 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
825727 TC TC
1 TC TC
825731 AAAACGTCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Done.