Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold481
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: 1334154
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 122349 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:355685 original size:67 final size:67
Alignment explanation
Indices: 355604--355833 Score: 388
Period size: 67 Copynumber: 3.4 Consensus size: 67
355594 TTACCCTCAA
* *
355604 ATAGAGTATCCTTACCCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAAAACCCTAATCCTC
1 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC
355669 CC
66 CC
*
355671 ATTGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC
1 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC
355736 CC
66 CC
*
355738 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAGATACCCTAATCCTC
1 ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC
355803 CC
66 CC
* * * *
355805 ATAGGGTACCCTAACTCTCCCATAGAGTA
1 ATAGAGTATCCTTACTCTCCCATGGAGTA
355834 TTCTCACTCT
Statistics
Matches: 154, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 154 1.00
ACGTcount: A:0.27, C:0.35, G:0.13, T:0.25
Consensus pattern (67 bp):
ATAGAGTATCCTTACTCTCCCATGGAGTACCCCAGCCTTCCCATAGAGTAAATACCCTAATCCTC
CC
Found at i:355793 original size:25 final size:25
Alignment explanation
Indices: 355698--355794 Score: 61
Period size: 25 Copynumber: 4.2 Consensus size: 25
355688 TCCCATGGAG
*
355698 TACCCCAGCCTTCCCATAGAGTAAA
1 TACCCCAGCCTTCCCATAGAGTAGA
* *
355723 TACCCTAATCC-TCCCATAGAGT--A
1 TACCC-CAGCCTTCCCATAGAGTAGA
**
355746 T-CCTTA--CTCTCCCAT-G-G-AG-
1 TACCCCAGCCT-TCCCATAGAGTAGA
355765 TACCCCAGCCTTCCCATAGAGTAGA
1 TACCCCAGCCTTCCCATAGAGTAGA
355790 TACCC
1 TACCC
355795 TAATCCTCCC
Statistics
Matches: 54, Mismatches: 6, Indels: 24
0.64 0.07 0.29
Matches are distributed among these distances:
19 3 0.06
20 4 0.07
21 13 0.24
22 5 0.09
23 3 0.06
24 2 0.04
25 21 0.39
26 3 0.06
ACGTcount: A:0.27, C:0.37, G:0.12, T:0.24
Consensus pattern (25 bp):
TACCCCAGCCTTCCCATAGAGTAGA
Found at i:360468 original size:2 final size:2
Alignment explanation
Indices: 360463--360514 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
360453 TACCAAAAAG
* *
360463 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
360505 GA GA GA GA GA
1 GA GA GA GA GA
360515 TGTCATTGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
GA
Found at i:365103 original size:51 final size:50
Alignment explanation
Indices: 365055--365450 Score: 517
Period size: 51 Copynumber: 7.7 Consensus size: 50
365045 ATTCAGAATG
** *
365055 ATGTCAAAGACCCAAACAATCTTTA-AGACTTACGACTGTAGAACCAGAACA
1 ATGTCAAAG-CCTGAACAATC-TTAGAGACTTACAACTGTAGAACCAGAACA
*
365106 ATGTCAAACGCCTGAACAATCTTAGAGACTTAAAACTGTAGAACCAGAACA
1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA
* *
365157 ATGTTAAAGGTCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA
1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA
** *
365208 ATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCCTAGAACAAGAACA
1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTAC----AACTGTAGAACCAGAACA
* *
365263 ATGTCAAAGACCCGAACAATCTTTA-AGACTTACGACTGTAGAACCAGAACA
1 ATGTCAAAG-CCTGAACAATC-TTAGAGACTTACAACTGTAGAACCAGAACA
* *
365314 ATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACTGTAGAACTAGAACA
1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA
*
365365 ATGTCAAACGCCTGAACAATCTTAGAGACTTACAACTGTAGAACTAGAACA
1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA
*
365416 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAA
1 ATGTCAAA-GCCTGAACAATCTTAGAGACTTACAA
365451 GGATGTAAAA
Statistics
Matches: 308, Mismatches: 27, Indels: 20
0.87 0.08 0.06
Matches are distributed among these distances:
50 6 0.02
51 255 0.83
52 2 0.01
54 1 0.00
55 41 0.13
56 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (50 bp):
ATGTCAAAGCCTGAACAATCTTAGAGACTTACAACTGTAGAACCAGAACA
Found at i:365293 original size:157 final size:152
Alignment explanation
Indices: 365069--365447 Score: 546
Period size: 157 Copynumber: 2.4 Consensus size: 152
365059 CAAAGACCCA
* ** *
365069 AACAATCTTTA-AGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAG
1 AACAATC-TTAGAGACTTACAACCCTAGAACAAGAACAATGTCAAA-GCCTGAACAATCTTAGAG
*
365133 ACTTAAAACTGTAGAACCAGAACAATGTTAAAGGTCTGAACAATCTTAGAGACTTACAACTGTAG
64 ACTTAAAACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACTGTAG
365198 AACCAGAACAATGTCAAACGCCTG
129 AACCAGAACAATGTCAAACGCCTG
*
365222 AACAATCTTAGAGACTTACATTGAACCCTAGAACAAGAACAATGTCAAAGACCCGAACAATCTTT
1 AACAATCTTAGAGACTTAC----AACCCTAGAACAAGAACAATGTCAAAG-CCTGAACAATC-TT
**
365287 A-AGACTTACGACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACT
60 AGAGACTTAAAACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACT
*
365351 GTAGAACTAGAACAATGTCAAACGCCTG
125 GTAGAACCAGAACAATGTCAAACGCCTG
** * *
365379 AACAATCTTAGAGACTTACAACTGTAGAACTAGAACAATGTCAAAGGCCTGGACAATCTTAGAGA
1 AACAATCTTAGAGACTTACAACCCTAGAACAAGAACAATGTCAAA-GCCTGAACAATCTTAGAGA
365444 CTTA
65 CTTA
365448 CAAGGATGTA
Statistics
Matches: 203, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
152 6 0.03
153 54 0.27
154 1 0.00
156 1 0.00
157 138 0.68
158 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (152 bp):
AACAATCTTAGAGACTTACAACCCTAGAACAAGAACAATGTCAAAGCCTGAACAATCTTAGAGAC
TTAAAACTGTAGAACCAGAACAATGTTAAAGGCCTGAACAATCTTAGAGACTTACAACTGTAGAA
CCAGAACAATGTCAAACGCCTG
Found at i:365329 original size:208 final size:208
Alignment explanation
Indices: 365055--365449 Score: 691
Period size: 208 Copynumber: 1.9 Consensus size: 208
365045 ATTCAGAATG
365055 ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG
1 ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG
* * *
365120 AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTTAAAGGTCTGAACAATCTTAGAGA
66 AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGA
365185 CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCC
131 CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCC
365250 TAGAACAAGAACA
196 TAGAACAAGAACA
* * *
365263 ATGTCAAAGACCCGAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTTAAAGGCCTG
1 ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG
* *
365328 AACAATCTTAGAGACTTACAACTGTAGAACTAGAACAATGTCAAACGCCTGAACAATCTTAGAGA
66 AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGA
* * *
365393 CTTACAACTGTAGAACTAGAACAATGTCAAAGGCCTGGACAATCTTAGAGACTTACA
131 CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACA
365450 AGGATGTAAA
Statistics
Matches: 176, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
208 176 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (208 bp):
ATGTCAAAGACCCAAACAATCTTTAAGACTTACGACTGTAGAACCAGAACAATGTCAAACGCCTG
AACAATCTTAGAGACTTAAAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGA
CTTACAACTGTAGAACCAGAACAATGTCAAACGCCTGAACAATCTTAGAGACTTACATTGAACCC
TAGAACAAGAACA
Found at i:365482 original size:37 final size:37
Alignment explanation
Indices: 365416--365599 Score: 251
Period size: 37 Copynumber: 5.0 Consensus size: 37
365406 AACTAGAACA
* * *
365416 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAAGG
1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG
* * *
365453 ATGTAAAAGACCTGAACAATCTTACAGACTGACAACG
1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG
* * *
365490 ATGTAAAGGGTCTGAAAAATCTTAGAGACTTACAACG
1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG
* * *
365527 ATGTAAAAGGTCTGAAAAATTTTAGAGACTTACAACG
1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG
*
365564 ATGTAAAAGGCCTGGACAATCTTAGAGACTTACAAC
1 ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAAC
365600 TGTAGAAGCA
Statistics
Matches: 129, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 129 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (37 bp):
ATGTAAAAGGCCTGAACAATCTTAGAGACTTACAACG
Found at i:365645 original size:51 final size:51
Alignment explanation
Indices: 365564--365735 Score: 281
Period size: 51 Copynumber: 3.4 Consensus size: 51
365554 ACTTACAACG
*
365564 ATGTAAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA
1 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA
365615 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA
1 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA
* * * **
365666 ATGTCAAAGGCCTGGGCAATCTTAGAGACTTACAACTGTAGAACCAGGATG
1 ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA
*
365717 ATGTCAAAGGCCTGAACAA
1 ATGTCAAAGGCCTGGACAA
365736 GTCCACAGCT
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 113 1.00
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (51 bp):
ATGTCAAAGGCCTGGACAATCTTAGAGACTTACAACTGTAGAAGCAGAACA
Found at i:374206 original size:157 final size:157
Alignment explanation
Indices: 373920--374224 Score: 493
Period size: 157 Copynumber: 1.9 Consensus size: 157
373910 TTTATAAATT
*
373920 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAATAGACT
1 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT
* *
373985 GAGAAATTATATTTTTGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT
66 GAGAAATTATACTTTGGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT
374050 CGATAAATTTTTGCGAATACATATCTG
131 CGATAAATTTTTGCGAATACATATCTG
374077 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT
1 CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT
********* *
374142 GAGAAATTATACTTTGGAAATTTTTTTTTTTTAAAATGATACCGTAAATCTGAAAGTGTTTATGT
66 GAGAAATTATACTTTGGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT
374207 CGATAAATTTTTGCGAAT
131 CGATAAATTTTTGCGAAT
374225 CCGAGTCATA
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
157 135 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (157 bp):
CATTATTTTAACTGATCAAATGTAAGCTGCAAGTTTTCAGTGTTTAATTTCAATTTGAACAGACT
GAGAAATTATACTTTGGAAATTTAAAAAAAAAAAAATGATACCATAAATCTGAAAGTGTTTATGT
CGATAAATTTTTGCGAATACATATCTG
Found at i:376602 original size:72 final size:72
Alignment explanation
Indices: 376518--376661 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
376508 TAGTAGATAT
376518 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT
1 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT
376583 AATCCAA
66 AATCCAA
376590 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT
1 TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT
376655 AATCCAA
66 AATCCAA
376662 AATATAAAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (72 bp):
TATTAAACTAAAATAAAATAAAATTTACTCATACCTGAGGAAAATCCTAATTGAATATTAGAATT
AATCCAA
Found at i:377325 original size:18 final size:18
Alignment explanation
Indices: 377302--377340 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
377292 TTGATTTCTG
377302 ATAATTTATTTATGCAAA
1 ATAATTTATTTATGCAAA
377320 ATAATTTATTTATGCAAA
1 ATAATTTATTTATGCAAA
377338 ATA
1 ATA
377341 TTGCATATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (18 bp):
ATAATTTATTTATGCAAA
Found at i:377641 original size:179 final size:178
Alignment explanation
Indices: 377333--377890 Score: 863
Period size: 176 Copynumber: 3.1 Consensus size: 178
377323 ATTTATTTAT
*
377333 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCTTCCTACAGTTCTCAAGATAGG
1 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG
* * *
377398 AAGTTGTTCTTTTGCAGATCAATTGTACATATATAAGAGGTGTGCATATTGCTGGGATTTTGATT
66 AAGTTGTTCTTTTGCAGATTAATTGTACATATAT-AGAGGTGTGCATATTGCTAGAATTTTGATT
* * *
377463 TCCGATAATTTATCAAAAAATACAAGCTTTTGAACTTAGTCATTTTTTG
130 TCTGATAATTTATAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG
* * *
377512 GCAAAATATTGCATATAGGGTTCCTTCATTGTACGGATAATTCCTCCTACAGTTCTCAAGATAGG
1 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG
* * * *
377577 AAGTTGTTCTTTTGCAGATTAATTGTACATATATCTGAGGTGTGTATATTTCTAGAAATTTGATT
66 AAGTTGTTCTTTTGCAGATTAATTGTACATATAT-AGAGGTGTGCATATTGCTAGAATTTTGATT
*
377642 TCTGATAATTTATGAAAGAAATACCAGCTTTTGAAC-T--T-ATTTTTTG
130 TCTGATAATTTAT-AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG
* * *
377688 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGAAAACTCCTCCTACAGTTATCAAGATAAG
1 GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG
377753 AAGTTGTTCTTTTGCAGATTAATTGTACATATAATAGAGGTGTGCATATTGCTAGAATTTTGATT
66 AAGTTGTTCTTTTGCAGATTAATTGTACATAT-ATAGAGGTGTGCATATTGCTAGAATTTTGATT
*
377818 TCTGATAATTCATGAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG
130 TCTGATAATTTAT-AAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG
*
377868 GCAAAATGTTGCATATAGGGTAC
1 GCAAAATATTGCATATAGGGTAC
377891 TCCATTTCAC
Statistics
Matches: 344, Mismatches: 29, Indels: 11
0.90 0.08 0.03
Matches are distributed among these distances:
176 159 0.46
177 4 0.01
179 132 0.38
180 49 0.14
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (178 bp):
GCAAAATATTGCATATAGGGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAGG
AAGTTGTTCTTTTGCAGATTAATTGTACATATATAGAGGTGTGCATATTGCTAGAATTTTGATTT
CTGATAATTTATAAAAAAATACCAGCTTTTGAACTTAGTCATTTTTTG
Found at i:381758 original size:24 final size:22
Alignment explanation
Indices: 381707--381793 Score: 63
Period size: 24 Copynumber: 3.9 Consensus size: 22
381697 AATCTACCAT
*
381707 ATCTAAAGTTAAAAGTAAC-CGTA
1 ATCTACAGTTAAAAGTAACAC--A
381730 TATCTACAGTTAAAAGTAACAACAA
1 -ATCTACAGTTAAAAGTAAC-AC-A
* * *
381755 ATCTACATTTCAAACT-ACAC-
1 ATCTACAGTTAAAAGTAACACA
*
381775 ATTTACAGTTAAAAGTAAC
1 ATCTACAGTTAAAAGTAAC
381794 GACATAGCGT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
20 12 0.24
21 2 0.04
22 2 0.04
23 2 0.04
24 31 0.61
25 1 0.02
26 1 0.02
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (22 bp):
ATCTACAGTTAAAAGTAACACA
Found at i:382048 original size:23 final size:24
Alignment explanation
Indices: 382022--382079 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 24
382012 AAAAATCAAT
* *
382022 AAAAGTTTGCTTGCCTCAAAGAAAA
1 AAAAGTTTGCTTGACTCAAA-CAAA
382047 AAATAGTTTGCTTGACTCAAAC-AA
1 AAA-AGTTTGCTTGACTCAAACAAA
382071 AAAAGTTTG
1 AAAAGTTTG
382080 ATCGTCTCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.20
24 5 0.17
25 3 0.10
26 16 0.53
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (24 bp):
AAAAGTTTGCTTGACTCAAACAAA
Found at i:382055 original size:26 final size:26
Alignment explanation
Indices: 382025--382074 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
382015 AATCAATAAA
* *
382025 AGTTTGCTTGCCTCAAAGAAAAAAAT
1 AGTTTGCTTGACTCAAACAAAAAAAT
382051 AGTTTGCTTGACTCAAACAAAAAA
1 AGTTTGCTTGACTCAAACAAAAAA
382075 GTTTGATCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (26 bp):
AGTTTGCTTGACTCAAACAAAAAAAT
Found at i:383023 original size:2 final size:2
Alignment explanation
Indices: 383018--383061 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
383008 TGTGTGTGTG
383018 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
383060 TC
1 TC
383062 CATCACATAA
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:394761 original size:2 final size:2
Alignment explanation
Indices: 394754--394784 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
394744 ATTATGTGAT
394754 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
394785 CAGACAGACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:394789 original size:4 final size:4
Alignment explanation
Indices: 394782--394824 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
394772 AGAGAGAGAG
*
394782 AGAC AGAC AGAC AGAC AGAC GGAC AGAC AGAC AGAC AGAC AGA
1 AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGAC AGA
394825 GAAGGAGAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.49, C:0.23, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAC
Found at i:397364 original size:2 final size:2
Alignment explanation
Indices: 397359--397437 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
397349 ATGTGTGGTG
397359 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
*
397401 GA GA GA GA AA 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 G
397438 TTTTTCAGCT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:400097 original size:2 final size:2
Alignment explanation
Indices: 400090--400183 Score: 145
Period size: 2 Copynumber: 47.0 Consensus size: 2
400080 GTGTATAATG
* * *
400090 GA GA GA GA GA GA GA GA GA GA GA GA G- GCA GA CA GA GA AA GA CA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA
400132 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
400174 GA GA GA GA GA
1 GA GA GA GA GA
400184 TTCATGATAG
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
1 1 0.01
2 82 0.98
3 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:404659 original size:11 final size:11
Alignment explanation
Indices: 404643--404667 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
404633 ACATTTTGAA
404643 AAAATACAGGT
1 AAAATACAGGT
404654 AAAATACAGGT
1 AAAATACAGGT
404665 AAA
1 AAA
404668 TTTGTGTTGG
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:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (11 bp):
AAAATACAGGT
Found at i:406891 original size:2 final size:2
Alignment explanation
Indices: 406884--406925 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
406874 CCGTTTAAAC
406884 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
406926 TTACAGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:416550 original size:20 final size:20
Alignment explanation
Indices: 416525--416565 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
416515 TTATCAAGTC
416525 CTAAGATTTTTTTATGAGTA
1 CTAAGATTTTTTTATGAGTA
416545 CTAAGATTTTTTTATGAGTA
1 CTAAGATTTTTTTATGAGTA
416565 C
1 C
416566 ATTTCAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.49
Consensus pattern (20 bp):
CTAAGATTTTTTTATGAGTA
Found at i:421958 original size:156 final size:159
Alignment explanation
Indices: 421690--422082 Score: 392
Period size: 156 Copynumber: 2.5 Consensus size: 159
421680 TATCTTCCTA
* * * * * *
421690 AGTAAAATTTCATCCCCCATTGTGGCCTCACCCTA-CCCCTGGACTATTATTTAAACAAACTTGA
1 AGTAAAAATTGATCCCCCATTGTGGCCCCACCCTACCCCCGGGACTATGATTTGAACAAACTTGA
* * * * * *
421754 ATCTATATGATCTGGAGATGCCTCCACTCAAATTTGGGCTTTCCTGGCCTAATACTT-TTGAGAA
66 ATCTACATGATCTGGAGATGCCTACACTCAAATTTGAGATTTCCTGGCCAAATACTTATT-AAAA
421818 GAAGA-CTTTT-AAAGATTTTCTC-TATA-T
130 GAA-ATCTTTTAAAAGATTTTCTCATATACT
* *
421845 A-TAAAAA-TGTATCCCCCATTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTT
1 AGTAAAAATTG-ATCCCCCATTGTGGCCCCACCCTACCCCC-GGGACTATGATTTGAACAAACTT
* ** * * *
421908 GAATCTACATTATCT-GAGGATGGTTACA-TGCCAATTTGAGATTTCTTGGCCAAATAGTTATTA
64 GAATCTACATGATCTGGA-GATGCCTACACT-CAAATTTGAGATTTCCTGGCCAAATACTTATTA
*
421971 AAAGAAATTTTTTAAAAGATTTTCTCTATATACTCTT
127 AAAGAAATCTTTTAAAAGATTTTCTC-ATATA--C-T
* *
422008 ATGTAAAAATTGATCCCCCAATTGTGGCCCCACCCTACCCCCGGGGACTATGATTTGAAGAAACG
1 A-GTAAAAATTGATCCCCC-ATTGTGGCCCCACCCTACCCCC-GGGACTATGATTTGAACAAACT
422073 TGAATCTACA
63 TGAATCTACA
422083 CTTCTTCCAT
Statistics
Matches: 194, Mismatches: 26, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
153 1 0.01
154 27 0.14
155 9 0.05
156 72 0.37
157 14 0.07
159 4 0.02
163 2 0.01
165 13 0.07
166 52 0.27
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (159 bp):
AGTAAAAATTGATCCCCCATTGTGGCCCCACCCTACCCCCGGGACTATGATTTGAACAAACTTGA
ATCTACATGATCTGGAGATGCCTACACTCAAATTTGAGATTTCCTGGCCAAATACTTATTAAAAG
AAATCTTTTAAAAGATTTTCTCATATACT
Found at i:422479 original size:166 final size:166
Alignment explanation
Indices: 422182--423099 Score: 1292
Period size: 166 Copynumber: 5.5 Consensus size: 166
422172 AACTTGTACA
* *
422182 ATTTGAACAGACTTAAATCTACACTACCTGAGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCC
1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC
* * * * **
422247 AAATAATTTTTGAGAAGAGGATTTTTAAAGATTTTCTCTATATATTCCCT-TTTAAAACACGATC
66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATT-CCTATGTAAAACTTGATC
* ** *
422311 CCCCTATTGTGGCCCCACCCTACATCTGGGGACCATG
130 CCCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG
* * * ** * *
422348 ATTTAAACAAACTTGAATCTACACTACCTGAGGATGCTTCCACTCAAAGTTGAGCTTTCCTGGCC
1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC
*
422413 TCATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
**
422478 CCCAATTGTGGCCCCATACTACCCCCGGGGACCATG
131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG
* * * * *
422514 ATTTGAACAAACTTAAATATTCACTTCCTGAGCATGCTTCCAATTTAATTTCAGCTTTTCTGGCC
1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC
* *
422579 TAATAGTTTTTGAGTAGAAGATTCTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
* *
422644 CCCAATTGTGGCCCCACCCTACCCCCAGGGATCATG
131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG
*
422680 ATTTGAACATACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC
1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC
* *
422745 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCCATATATTCCTATGTACAACTTGATCC
66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
* *
422810 CCCAATTGTGGCCCCACCCTACCCCCGGGAACTATG
131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG
* * * *
422846 ATTTGAATAAACTTGAATCTACACTACCTGAGGATGCTCCCATTTTAATTTGAGCTTTTCTGGCC
1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC
*
422911 TGATAGTTTTTGAG-A-AA-ATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
66 TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
** * *
422973 CCCTCTTGTGGCCCCTCCCTACCCCCGGGGACTATG
131 CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG
* * * * * *
423009 ATTTGAACAAACGTGAATCTACACTACCTGAGGATGCCTCCACA--CAAGTTTAAGCTTTTCCGG
1 ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCA-ATTTAA-TTTGAGCTTTTCTGG
423072 -CTGAATAGTTTTTGAGAAGAAGATTTTT
64 CCT-AATAGTTTTTGAGAAGAAGATTTTT
423100 GAAAAATACC
Statistics
Matches: 670, Mismatches: 75, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
162 4 0.01
163 138 0.21
164 3 0.00
165 6 0.01
166 519 0.77
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (166 bp):
ATTTGAACAAACTTAAATCTACACTACCTGAGGATGCTTCCAATTTAATTTGAGCTTTTCTGGCC
TAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
CCCAATTGTGGCCCCACCCTACCCCCGGGGACCATG
Found at i:424447 original size:165 final size:165
Alignment explanation
Indices: 424222--425345 Score: 1640
Period size: 166 Copynumber: 6.8 Consensus size: 165
424212 TGAATATGAT
* * * * * * * *
424222 AAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACAA
1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
* * *
424287 TATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAA
66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
* *
424352 ATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCTAA
131 ATCTTTGA-CAAAATTTGTTTGAAAATTTTGGCAAA
* * * * *
424388 AAA-AAACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCCCACAA
1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
* * * * * *
424452 TATGGCATGCCAAAACAAACAGTGTGTTAAAATTTCAAGCATCTGCGATATATAGCTGCTGAGAA
66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
* *
424517 ATCTTTGACAAAATTTGTTTCAAAATTTTGACAAA
131 ATCTTTGACAAAATTTGTTTGAAAATTTTGGCAAA
* * * *
424552 AAATAAACAAAGTCGTCATTTGACAGTAAGTTGACGTCTGATTGGTACAAAAATACATCCCACGA
1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
* * *
424617 TATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCAATAAACAGTTGCTGAGAA
66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
* * *
424682 ATCTTTGACGGAAATTTGTTTGAAAATTTTTGCTAA
131 ATCTTTGAC-AAAATTTGTTTGAAAATTTTGGCAAA
* *
424718 AAAT-AACTAAAGTCGTCATTTAACAGGAAGTTGATGTCTGATTGGTACAAAAATATATCCCACG
1 AAATAAAC-AAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
424782 ATATGGCATGCCTATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAGA
65 ATATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
*
424847 ATTCTTTGACAGAAATTTGTTTGAAAATTTTGGCAAA
130 AATCTTTGACA-AAATTTGTTTGAAAATTTTGGCAAA
* * * *
424884 AAATAAACAAAGTCGTCATTTAACAGAAAGCTGGCATCCGATTGGTACAAAAATATATCCCACGA
1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
424949 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
*
425014 TTCTTTGACAGAAATTTGTTTGAAAATTTTGGCAAA
131 ATCTTTGACA-AAATTTGTTTGAAAATTTTGGCAAA
* *
425050 AAATAAACAAAGTCGTCATTTGACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACGA
1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
* * * *
425115 TATGGCATGCCTATACAAATACCGTGTAAAAATTTCAAGCATCTGCGATAAACAATTGCTGAGAA
66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
**
425180 ATCTTTGACGAAAATTTGTTTGAAAATTTTAGTTAAA
131 ATCTTTGAC-AAAATTTGTTTGAAAATTTT-GGCAAA
*
425217 AAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
1 AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
* * * *
425282 TATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCGATTAATAGTTGCTGAGA
66 TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
425346 TTAATGCGAC
Statistics
Matches: 871, Mismatches: 80, Indels: 13
0.90 0.08 0.01
Matches are distributed among these distances:
164 26 0.03
165 242 0.28
166 477 0.55
167 126 0.14
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.29
Consensus pattern (165 bp):
AAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGA
TATGGCATGCCTAAACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAA
ATCTTTGACAAAATTTGTTTGAAAATTTTGGCAAA
Found at i:425382 original size:8 final size:8
Alignment explanation
Indices: 425369--425427 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
425359 AATTTTTGTT
425369 ACAGACGG
1 ACAGACGG
*
425377 ACAGACAG
1 ACAGACGG
425385 ACAGACGG
1 ACAGACGG
*
425393 ACGGACGG
1 ACAGACGG
* *
425401 ACGGACAG
1 ACAGACGG
*
425409 ACGGACGG
1 ACAGACGG
*
425417 ACAGACAG
1 ACAGACGG
425425 ACA
1 ACA
425428 CACAAGGGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 44 1.00
ACGTcount: A:0.39, C:0.25, G:0.36, T:0.00
Consensus pattern (8 bp):
ACAGACGG
Found at i:425385 original size:4 final size:4
Alignment explanation
Indices: 425369--425427 Score: 55
Period size: 4 Copynumber: 14.8 Consensus size: 4
425359 AATTTTTGTT
* * * * * * *
425369 ACAG ACGG ACAG ACAG ACAG ACGG ACGG ACGG ACGG ACAG ACGG ACGG
1 ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG ACAG
425417 ACAG ACAG ACA
1 ACAG ACAG ACA
425428 CACAAGGGTA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.39, C:0.25, G:0.36, T:0.00
Consensus pattern (4 bp):
ACAG
Found at i:425386 original size:12 final size:12
Alignment explanation
Indices: 425369--425422 Score: 81
Period size: 12 Copynumber: 4.5 Consensus size: 12
425359 AATTTTTGTT
*
425369 ACAGACGGACAG
1 ACAGACGGACGG
*
425381 ACAGACAGACGG
1 ACAGACGGACGG
*
425393 ACGGACGGACGG
1 ACAGACGGACGG
425405 ACAGACGGACGG
1 ACAGACGGACGG
425417 ACAGAC
1 ACAGAC
425423 AGACACACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.37, C:0.26, G:0.37, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:426405 original size:63 final size:63
Alignment explanation
Indices: 426306--426623 Score: 411
Period size: 63 Copynumber: 4.9 Consensus size: 63
426296 CTTGTTACAC
* *
426306 CAGCTCTCAGACACTTAATACTGTGATCAGTAACTACTTACTGTTCTGTGTTAGAGTAGCTCA
1 CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAGCTCA
*
426369 CAGCTCTCAGACACTGAATACTGTAATCAGTTACTACCGGTACTTACTGTTCTGTGTTAGAGTAG
1 CAGCTCTCAGACACTGAATACTGTGATCAG-T--TA-C--TACTTACTGTTCTGTGTTAGAGTAG
**
426434 CTTG
60 CTCA
* * * *
426438 CAGCTCTCAGACACTTAATACTATGATCAGTTAACTACTTACTTTTCTGTGTTAGAGTAACTCA
1 CAGCTCTCAGACACTGAATACTGTGATCAGTT-ACTACTTACTGTTCTGTGTTAGAGTAGCTCA
* * * * **
426502 CAGCTCTCAGACATTGAATACTGTGATTAGTTACAACTCACTGTTCTGTGTTAGAGTAGCTTG
1 CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAGCTCA
* * *
426565 CAGCTCTCAGACACTGAATATTGTGATCAGTAACTACTTACTGTTCTGTGTTAGCGTAG
1 CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAG
426624 ACCTCAACAT
Statistics
Matches: 219, Mismatches: 29, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
63 105 0.48
64 54 0.25
66 3 0.01
67 2 0.01
68 1 0.00
69 54 0.25
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (63 bp):
CAGCTCTCAGACACTGAATACTGTGATCAGTTACTACTTACTGTTCTGTGTTAGAGTAGCTCA
Found at i:429293 original size:21 final size:21
Alignment explanation
Indices: 429269--429309 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
429259 ATTCAGGTAA
* *
429269 ATGACACACTTCATTGTCTTC
1 ATGACACACTCCACTGTCTTC
429290 ATGACACACTCCACTGTCTT
1 ATGACACACTCCACTGTCTT
429310 GATGGTACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.32, G:0.10, T:0.34
Consensus pattern (21 bp):
ATGACACACTCCACTGTCTTC
Found at i:430782 original size:2 final size:2
Alignment explanation
Indices: 430775--430819 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
430765 GCATGACAGT
430775 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
430817 TC T
1 TC T
430820 TTTTCTGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:435692 original size:4 final size:4
Alignment explanation
Indices: 435693--435734 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
435683 CTGTCTGTCT
* *
435693 GTCC GTCC GTCC GTCC GTCC GTCC GTCT GTCT GTCC GTCC GT
1 GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GTCC GT
435735 AACAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.00, C:0.43, G:0.26, T:0.31
Consensus pattern (4 bp):
GTCC
Found at i:436306 original size:166 final size:167
Alignment explanation
Indices: 435758--436666 Score: 1266
Period size: 166 Copynumber: 5.5 Consensus size: 167
435748 GTCGCATTTA
* * *
435758 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
* *
435823 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGACG-ACTTTGCTTATT
66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGA-GTACTTTGTTTA-T
* * *
435887 TTTTAACTAAAATTTTCAAACAAATTTTCGTCAAAGATT
129 TTTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT
* *
435926 TCTCAGCAACTATCTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
**
435991 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGT-TAAATGCA-T-CTTTGTTTATT
66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATG-AGTACTTTGTTTATT
** *
436053 TTTAGCAAAAATTTTCAAACAAATTTTTGTCAAAGAAT
130 TTTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT
* * *
436091 TCTCAGCAACTGTTTATCGCAGATACTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
436156 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGT-AATGAGTACTTTGTTTATTT
66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGAGTACTTTGTTTATTT
*
436220 TTAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT
131 TTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT
* * * * *
436257 TCTCAGCAGCTATTTATCGCAGATGCTTGAAATTTTAACACACTATTTGTTTTGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
* ** *
436322 TGTGGGATATATTTTTGTACCAATCAGATGTCAACTTCCTGT-TAAATGACG-ACTTTGTTTATT
66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGA-GTACTTTGTTTATT
* *
436385 TTTAGCAAAAAATTTCAAACAAATAATT--GTCAAAGAAT
130 TTTAGCAAAAATTTTCAAACAAAT--TTCCGTCAAAGATT
* * * * *
436423 TCTCAGCAACTGTTTATCGCAGATGCTTGACATTTTTACACAGTGTTTGTATAAGCATGCTATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
**
436488 CGTGGGATGCATTTTTGTACCAATTGGACGTCAACTTCCTGTGT-AATGAGTACTTTGTTTATTT
66 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGAGTACTTTGTTTATTT
** *
436552 TTAGCCCAAATTTTCAAACCAATTTTCC-TCAAAGATT
131 TTAGCAAAAATTTTCAAA-CAAATTTCCGTCAAAGATT
* * * *
436589 TCTCAGCAGCTATTTATCGCAGATGCTTGAAA-TTTAACACACTATTTGTTTAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
*
436653 TGTGGGATATATTT
66 CGTGGGATATATTT
436667 CTACCAATCG
Statistics
Matches: 655, Mismatches: 72, Indels: 31
0.86 0.09 0.04
Matches are distributed among these distances:
164 1 0.00
165 182 0.28
166 358 0.55
167 12 0.02
168 102 0.16
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (167 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGAGTACTTTGTTTATTT
TTAGCAAAAATTTTCAAACAAATTTCCGTCAAAGATT
Found at i:436362 original size:331 final size:332
Alignment explanation
Indices: 435758--436715 Score: 1543
Period size: 332 Copynumber: 2.9 Consensus size: 332
435748 GTCGCATTTA
*
435758 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT
1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT
*
435823 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAAATGACG-ACTTTGCTTATT
66 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGT-AATGA-GTACTTTGTTTA-T
* * * * *
435887 TTTTAACTAAAATTTTCAAACAAATTTTCGTCAAAGATTTCTCAGCAACTATCTATCGCAGATGC
128 TTTTAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGC
* * * *
435952 TTGAAATTTTTACACAATATTTGTATAGGCATGCCATATCGTGGGATATATTTTTGTACCAATCA
193 TTGAAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCA
* * **
436017 GACGTCAACTTCCTGTTAAATG-C-ATCTTTGTTTATTTTTAGCAAAAATTTTCAAACAAATTTT
258 GATGTCAACTTCCTGTTAAATGACGA-CTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAAT
436080 TGTCAAAGAAT
322 TGTCAAAGAAT
* * *
436091 TCTCAGCAACTGTTTATCGCAGATACTTGAAATTTTTACACAGTATTTGTATAGGCATGCTATAT
1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT
*
436156 CGTGGGATATATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT
66 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT
436221 TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTG
131 TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTG
*
436286 AAATTTTAACACACTATTTGTTTTGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGAT
196 AAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGAT
436351 GTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAATTGTC
261 GTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAATTGTC
436416 AAAGAAT
326 AAAGAAT
*
436423 TCTCAGCAACTGTTTATCGCAGATGCTTGACATTTTTACACAGTGTTTGTATAAGCATGCTATAT
1 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT
*
436488 CGTGGGATGCATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT
66 CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT
* *
436553 TAGCCCAAATTTTCAAACCAATTTTCC-TCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTT
131 TAGCCAAAATTTTCAAA-CAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTT
* *
436617 GAAA-TTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATA--TTTCTACCAATCGGA
195 GAAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGA
* * * * *
436679 TGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
260 TGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
436716 GCATATTCAC
Statistics
Matches: 585, Mismatches: 36, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
329 45 0.08
331 185 0.32
332 242 0.41
333 113 0.19
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (332 bp):
TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACAGTGTTTGTATAAGCATGCTATAT
CGTGGGATGTATTTTTGTACCAATTGGACGTCAACTTCCTGTGTAATGAGTACTTTGTTTATTTT
TAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAGCTATTTATCGCAGATGCTTG
AAATTTTAACACACTATTTGTTTAGGCATGCCATATTGTGGGATATATTTTTGTACCAATCAGAT
GTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTTAGCAAAAAATTTCAAACAAATAATTGTC
AAAGAAT
Found at i:442746 original size:26 final size:25
Alignment explanation
Indices: 442695--442752 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
442685 ATTTGTATTT
* *
442695 AAAAAAAACCAACAACAACAACAAAA
1 AAAAAAAACCAACAA-AAAAAAAAAA
* *
442721 GAAAAAAACCACCAAAAAAAAAAAA
1 AAAAAAAACCAACAAAAAAAAAAAA
442746 AAAAAAA
1 AAAAAAA
442753 TAGAAGCTGT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.81, C:0.17, G:0.02, T:0.00
Consensus pattern (25 bp):
AAAAAAAACCAACAAAAAAAAAAAA
Found at i:446674 original size:2 final size:2
Alignment explanation
Indices: 446667--446723 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
446657 GAAAACTTTC
446667 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
446709 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
446724 TTGTGTATGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:448552 original size:2 final size:2
Alignment explanation
Indices: 448545--448585 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
448535 TCGACCTTTG
448545 GA 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 GA G
448586 GGAGGGGGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:450277 original size:12 final size:12
Alignment explanation
Indices: 450260--450287 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
450250 TAACAACTCA
450260 GAAATTCTATAG
1 GAAATTCTATAG
450272 GAAATTCTATAG
1 GAAATTCTATAG
450284 GAAA
1 GAAA
450288 CCAACTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (12 bp):
GAAATTCTATAG
Found at i:456562 original size:14 final size:12
Alignment explanation
Indices: 456545--456614 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 12
456535 CTTAAATGCC
*
456545 AAAATACAAATAA
1 AAAAAACAAA-AA
456558 AAAAAACAAAAAA
1 AAAAAAC-AAAAA
456571 CAAAAAACAAAAA
1 -AAAAAACAAAAA
456584 AAACCAAA-AAAAA
1 AAA--AAACAAAAA
*
456597 AAAAACCAAAAA
1 AAAAAACAAAAA
456609 AAAAAA
1 AAAAAA
456615 ACCCCATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
11 2 0.04
12 13 0.27
13 21 0.43
14 13 0.27
ACGTcount: A:0.86, C:0.11, G:0.00, T:0.03
Consensus pattern (12 bp):
AAAAAACAAAAA
Found at i:456568 original size:7 final size:7
Alignment explanation
Indices: 456544--456616 Score: 69
Period size: 7 Copynumber: 10.1 Consensus size: 7
456534 TCTTAAATGC
*
456544 CAAAATA
1 CAAAAAA
*
456551 CAAATAA
1 CAAAAAA
456558 -AAAAAA
1 CAAAAAA
456564 CAAAAAA
1 CAAAAAA
456571 CAAAAAA
1 CAAAAAA
456578 CAAAAAAAA
1 C--AAAAAA
456587 CCAAAAAA
1 -CAAAAAA
*
456595 AAAAAAA
1 CAAAAAA
456602 CCAAAAAA
1 -CAAAAAA
456610 -AAAAAA
1 CAAAAAA
456616 C
1 C
456617 CCCATAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
6 11 0.20
7 25 0.45
8 12 0.22
9 6 0.11
10 1 0.02
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (7 bp):
CAAAAAA
Found at i:456577 original size:16 final size:15
Alignment explanation
Indices: 456556--456615 Score: 84
Period size: 15 Copynumber: 3.9 Consensus size: 15
456546 AAATACAAAT
456556 AAAAAAAACAAAAAAC
1 AAAAAAAA-AAAAAAC
456572 AAAAAACAAAAAAAAC
1 AAAAAA-AAAAAAAAC
*
456588 CAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAAC
*
456603 CAAAAAAAAAAAA
1 AAAAAAAAAAAAA
456616 CCCCATAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
15 22 0.52
16 18 0.43
17 2 0.05
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAC
Found at i:456591 original size:24 final size:24
Alignment explanation
Indices: 456556--456615 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
456546 AAATACAAAT
*
456556 AAAAAAAACAAAAAACAAAAAA-C
1 AAAAAAAACAAAAAAAAAAAAACC
456579 AAAAAAAACCAAAAAAAAAAAAACC
1 AAAAAAAA-CAAAAAAAAAAAAACC
456604 AAAAAAAA-AAAA
1 AAAAAAAACAAAA
456616 CCCCATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 12 0.35
24 13 0.38
25 9 0.26
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (24 bp):
AAAAAAAACAAAAAAAAAAAAACC
Found at i:456626 original size:1 final size:1
Alignment explanation
Indices: 456556--456615 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
456546 AAATACAAAT
* * * ** **
456556 AAAAAAAACAAAAAACAAAAAACAAAAAAAACCAAAAAAAAAAAAACCAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
456616 CCCCATAAAA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:456626 original size:15 final size:14
Alignment explanation
Indices: 456558--456617 Score: 75
Period size: 16 Copynumber: 4.0 Consensus size: 14
456548 ATACAAATAA
*
456558 AAAAAACAAAAAACAA
1 AAAAAA-AAAAAAC-C
456574 AAAACAAAAAAAACC
1 AAAA-AAAAAAAACC
456589 AAAAAAAAAAAAACC
1 -AAAAAAAAAAAACC
456604 AAAAAAAAAAAACC
1 AAAAAAAAAAAACC
456618 CCATAAAAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
14 14 0.34
15 10 0.24
16 15 0.37
17 2 0.05
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAACC
Found at i:457592 original size:2 final size:2
Alignment explanation
Indices: 457585--457637 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
457575 TTTATTCAAT
457585 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
457627 GA GA GA GA GA G
1 GA GA GA GA GA G
457638 GTGTGTGTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:464590 original size:22 final size:23
Alignment explanation
Indices: 464543--464591 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
464533 GAATTATTTT
* *
464543 TTTTCCTTGACTGCATTTTTACA
1 TTTTCCTTGACTGCAGTTTTAAA
*
464566 TTTTCCTTTACT-CAGTTTTAAA
1 TTTTCCTTGACTGCAGTTTTAAA
464588 TTTT
1 TTTT
464592 TTTGTACCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTTCCTTGACTGCAGTTTTAAA
Found at i:464592 original size:23 final size:24
Alignment explanation
Indices: 464542--464592 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
464532 AGAATTATTT
* *
464542 TTTTTCCTTGACTGCATTTTTACA
1 TTTTTCCTTGACTGCAGTTTTAAA
*
464566 -TTTTCCTTTACT-CAGTTTTAAA
1 TTTTTCCTTGACTGCAGTTTTAAA
464588 TTTTT
1 TTTTT
464593 TTGTACCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (24 bp):
TTTTTCCTTGACTGCAGTTTTAAA
Found at i:471330 original size:19 final size:20
Alignment explanation
Indices: 471291--471338 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
471281 CACTAAATAT
471291 AAAA-ATATATTAAAAGTCA
1 AAAAGATATATTAAAAGTCA
471310 AAAAGATATATTAAAAG-CA
1 AAAAGATATATTAAAAGTCA
*
471329 AAAAGGTATA
1 AAAAGATATA
471339 GAGAATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.62, C:0.04, G:0.10, T:0.23
Consensus pattern (20 bp):
AAAAGATATATTAAAAGTCA
Found at i:482824 original size:7 final size:7
Alignment explanation
Indices: 482812--482842 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
482802 TGAACATTTG
482812 TTTGTTT
1 TTTGTTT
482819 TTTGTTT
1 TTTGTTT
482826 TTTGTTT
1 TTTGTTT
482833 TTTGTTT
1 TTTGTTT
482840 TTT
1 TTT
482843 TGCAATTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (7 bp):
TTTGTTT
Found at i:491679 original size:15 final size:15
Alignment explanation
Indices: 491659--491689 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
491649 AAATATATAG
491659 ACTTTGATTTTAAAA
1 ACTTTGATTTTAAAA
*
491674 ACTTTGCTTTTAAAA
1 ACTTTGATTTTAAAA
491689 A
1 A
491690 ATGAATGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (15 bp):
ACTTTGATTTTAAAA
Found at i:495955 original size:15 final size:15
Alignment explanation
Indices: 495935--495963 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
495925 CGATACAAGA
495935 TATTACTATTCTTAC
1 TATTACTATTCTTAC
495950 TATTACTATTCTTA
1 TATTACTATTCTTA
495964 ATTTGCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTACTATTCTTAC
Found at i:503933 original size:12 final size:12
Alignment explanation
Indices: 503918--503946 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
503908 CAATCCACCA
503918 AATCCTCCATTT
1 AATCCTCCATTT
503930 AATCCTCCATTT
1 AATCCTCCATTT
503942 AATCC
1 AATCC
503947 ACCCAATCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (12 bp):
AATCCTCCATTT
Found at i:503954 original size:21 final size:21
Alignment explanation
Indices: 503930--504018 Score: 142
Period size: 21 Copynumber: 4.2 Consensus size: 21
503920 TCCTCCATTT
**
503930 AATCCTCCATTTAATCCACCC
1 AATCCTCCGGTTAATCCACCC
503951 AATCCTCCGGTTAATCCACCC
1 AATCCTCCGGTTAATCCACCC
*
503972 AATCCTCCGGTTAATCCTCCC
1 AATCCTCCGGTTAATCCACCC
*
503993 AATCCGCCGGTTAATCCACCC
1 AATCCTCCGGTTAATCCACCC
504014 AATCC
1 AATCC
504019 ACCGAACCCT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.25, C:0.43, G:0.08, T:0.25
Consensus pattern (21 bp):
AATCCTCCGGTTAATCCACCC
Found at i:504092 original size:18 final size:18
Alignment explanation
Indices: 504065--504106 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
504055 GTTAGACCCC
* * *
504065 AATCCTCCCAAACTTCCT
1 AATCCACCCAAACCTCCA
504083 AATCCACCCAAACCTCCA
1 AATCCACCCAAACCTCCA
504101 AATCCA
1 AATCCA
504107 GTATTGTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19
Consensus pattern (18 bp):
AATCCACCCAAACCTCCA
Found at i:504651 original size:21 final size:21
Alignment explanation
Indices: 504627--504722 Score: 147
Period size: 21 Copynumber: 4.6 Consensus size: 21
504617 CACCAAATCC
* **
504627 TCCACCTAATCCTCCATTTAA
1 TCCACCCAATCCTCCGGTTAA
504648 TCCACCCAATCCTCCGGTTAA
1 TCCACCCAATCCTCCGGTTAA
504669 TCCACCCAATCCTCCGGTTAA
1 TCCACCCAATCCTCCGGTTAA
* *
504690 TCCTCCCAATCCGCCGGTTAA
1 TCCACCCAATCCTCCGGTTAA
504711 TCCACCCAATCC
1 TCCACCCAATCC
504723 ACCGAACCCT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 69 1.00
ACGTcount: A:0.24, C:0.44, G:0.07, T:0.25
Consensus pattern (21 bp):
TCCACCCAATCCTCCGGTTAA
Found at i:504796 original size:18 final size:18
Alignment explanation
Indices: 504769--504810 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
504759 GTTAGACCCC
* * *
504769 AATCCTCCCAAACTTCCT
1 AATCCACCCAAACCTCCA
504787 AATCCACCCAAACCTCCA
1 AATCCACCCAAACCTCCA
504805 AATCCA
1 AATCCA
504811 GTATTGTAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19
Consensus pattern (18 bp):
AATCCACCCAAACCTCCA
Found at i:511427 original size:18 final size:18
Alignment explanation
Indices: 511400--511441 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
511390 GTTAGACCCC
* * *
511400 AATCCTCCCAAACTTCCT
1 AATCCACCCAAACCTCCA
511418 AATCCACCCAAACCTCCA
1 AATCCACCCAAACCTCCA
511436 AATCCA
1 AATCCA
511442 GTATTGTAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.19
Consensus pattern (18 bp):
AATCCACCCAAACCTCCA
Found at i:511704 original size:33 final size:36
Alignment explanation
Indices: 511628--511704 Score: 88
Period size: 36 Copynumber: 2.2 Consensus size: 36
511618 GAGTCCAGTG
* **
511628 CCTAAACCTCCCAAGGAGCCAAGACCACTATTAAGT
1 CCTAAACCTCCCAAGGAACCAAGACCACTACCAAGT
* *
511664 CCCAAACCTCCCAAGGAACCAAG-CC-C-GCCAAGT
1 CCTAAACCTCCCAAGGAACCAAGACCACTACCAAGT
511697 CCTAAACC
1 CCTAAACC
511705 ACCACCCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
33 11 0.31
34 1 0.03
35 2 0.06
36 21 0.60
ACGTcount: A:0.35, C:0.40, G:0.13, T:0.12
Consensus pattern (36 bp):
CCTAAACCTCCCAAGGAACCAAGACCACTACCAAGT
Found at i:514273 original size:1 final size:1
Alignment explanation
Indices: 514267--514295 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
514257 CATTTCTTTC
514267 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
514296 GGTTTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:515010 original size:2 final size:2
Alignment explanation
Indices: 515003--515028 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
514993 ATACAAACAT
515003 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
515029 ACATATGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:519686 original size:2 final size:2
Alignment explanation
Indices: 519679--519763 Score: 152
Period size: 2 Copynumber: 42.5 Consensus size: 2
519669 TCTAAGTGAA
519679 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
* *
519721 TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC CC 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
519763 T
1 T
519764 GTTTACCATT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:527186 original size:12 final size:12
Alignment explanation
Indices: 527171--527195 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
527161 AAATTTTCAA
527171 ATTCCTCAACTC
1 ATTCCTCAACTC
527183 ATTCCTCAACTC
1 ATTCCTCAACTC
527195 A
1 A
527196 AATCCTTTAA
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:0.28, C:0.40, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTCCTCAACTC
Found at i:527449 original size:2 final size:2
Alignment explanation
Indices: 527442--527493 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
527432 TAATAAACCA
527442 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
527484 TC TC TC TC TC
1 TC TC TC TC TC
527494 AATGATCATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:529570 original size:32 final size:32
Alignment explanation
Indices: 529529--529605 Score: 136
Period size: 32 Copynumber: 2.4 Consensus size: 32
529519 GTAAATCACG
*
529529 GTGGCATGGTTTGAATGACTGAGAGAATTCCT
1 GTGGCATGGTTTGAATAACTGAGAGAATTCCT
529561 GTGGCATGGTTTGAATAACTGAGAGAATTCCT
1 GTGGCATGGTTTGAATAACTGAGAGAATTCCT
*
529593 TTGGCATGGTTTG
1 GTGGCATGGTTTG
529606 TGTCACAATG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.34
Consensus pattern (32 bp):
GTGGCATGGTTTGAATAACTGAGAGAATTCCT
Found at i:530845 original size:10 final size:10
Alignment explanation
Indices: 530830--530855 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
530820 TCTCTTTGGA
530830 CAAGTGTACT
1 CAAGTGTACT
530840 CAAGTGTACT
1 CAAGTGTACT
530850 CAAGTG
1 CAAGTG
530856 CATTTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (10 bp):
CAAGTGTACT
Found at i:535660 original size:41 final size:41
Alignment explanation
Indices: 535610--537183 Score: 1978
Period size: 41 Copynumber: 38.6 Consensus size: 41
535600 AGAGTATGCT
* * *
535610 ATCAAATCACCTTTTTGTAGGTCTATATACCAGGGTGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * * ** * * **
535651 ATCAGATCACTTTTTTGTAAATCTTTATACCAGAATGTAAT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
535692 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
** * **
535733 ATCACATCACCTTTCTGTATATCTATATACCAGGATGAATT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
535774 ATCACATCACCTTTCTGTAGGTCTATATACCAGGGTGTACT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * * * **
535815 AACACATCACCTTTCTATAGGTCTATATACAAGGAGGTATA
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * *
535856 ATCAAATCACCTTTCTCTAGGTCCATATACCA-GAGTGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGA-TGTACC
** * **
535897 ATCACATCACCTTTCTGTATATCTATATACCAGGATGAATT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
535938 ATCACATCACATTTCTGTAGGTCTATATACCAGGGTGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
*
535979 ATCACATCACCTTTCTGTAGGTCTATATACCAGGGTGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
536020 ATCACATCACCTTTCTGTAGGTCTATATACCAGG--G----
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* ** * * * **
536055 -T-GCATCACCTTTCTGTATATCTATGTTCCAGGATGAATT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * *
536094 AACGCATCACCTTTCCGTAGGTCTATATACCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* **
536135 ATCACATCACATTTCTGTACATCTATATACCAAGG-TGT-CC
1 ATCACATCACCTTTCTGTAGGTCTATATACC-AGGATGTACC
* *
536175 TATCACATCACCTTTCTGTAGATCTATATATCAGGATGTACC
1 -ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
*
536217 AT--CATCACCTTTCTGTAGGTCTATATATCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * *
536256 ATCACATCACCTTTCTGTAGATCTATAAATCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * *
536297 ATCACATCACCTTTCTGTAGATCTATAAATCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
536338 ATCACATCACCTTTCTGTAGGTCTATATATCAGGATGTACT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
*
536379 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATCTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * *
536420 ATCACATCACCTTTCTGTAGATCTATAAATCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * * *
536461 ATCACATCACATTTCTGTAGGTCTATATATCAGGATTTACA
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
536502 ATCACATCACCTTTTTGTAGGTCTATATATCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
*
536543 ATCACATCACCCTTCTGTAGGTCTATATACCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
536584 AT--CATCACCTTTCTGTATGTCTATATACCAGGGTGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
*
536623 ATCACATCACCTTTCTGTAGGTCTGTATACCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * *
536664 ATGACATCACCTTTCTGTTGGTCTATATACCAGAATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
*
536705 ATCACATCACCTTTCTGTAGGTCTATATACCAGAATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
536746 ATCACATCACCTTTCTGTATGTCTATATACCAGGGTGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
*
536787 ATCACATCACCTTTCTGTAGGTCTGTATACCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
536828 ATCACATCACCTTTCTGTTGGTCTATATACCAGAATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
536869 ATCACATCACCTTTCTGTAGGTCTATATACCA-GAGTGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGA-TGTACC
** * **
536910 ATCACATCACCTTTCTGTATATCTATATACCAGGGTG-ATTT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTA-CC
* * *
536951 ATCACATCACCTTTCTGAAGGTCTATATAACA-GAGTGTACT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGA-TGTACC
* * *
536992 ATCATATCACCTTCCTGTAGGTCTATATACCAAGGTAGGTGAACC
1 ATCACATCACCTTTCTGTAGGTCTATATACC-AGG-A--TGTACC
* * *
537037 ATCACATCACCTTTCTGTAGGTCTATATACCAGGGTATATC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
537078 ATTACTTCACCTTTCTGTAGGTCTATATACCAGGATGTACC
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* * * *
537119 ATCACATCACTTTTCTGTAGGTCTATATACCAGGGTGAACT
1 ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
* *
537160 ATCATATCACCTTCCTGTAGGTCT
1 ATCACATCACCTTTCTGTAGGTCT
537184 TTATGCGTAA
Statistics
Matches: 1339, Mismatches: 167, Indels: 54
0.86 0.11 0.03
Matches are distributed among these distances:
33 26 0.02
34 1 0.00
35 1 0.00
39 75 0.06
40 10 0.01
41 1177 0.88
42 10 0.01
43 1 0.00
44 4 0.00
45 34 0.03
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (41 bp):
ATCACATCACCTTTCTGTAGGTCTATATACCAGGATGTACC
Found at i:544794 original size:28 final size:28
Alignment explanation
Indices: 544752--544817 Score: 114
Period size: 28 Copynumber: 2.4 Consensus size: 28
544742 AGAAGAAATT
*
544752 TTTTTGAGATTTTATTGTTCTATATGAC
1 TTTTTGAGATGTTATTGTTCTATATGAC
544780 TTTTTGAGATGTTATTGTTCTATATGAC
1 TTTTTGAGATGTTATTGTTCTATATGAC
*
544808 TTTTTAAGAT
1 TTTTTGAGAT
544818 ATGAACAGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.23, C:0.06, G:0.15, T:0.56
Consensus pattern (28 bp):
TTTTTGAGATGTTATTGTTCTATATGAC
Found at i:548959 original size:21 final size:21
Alignment explanation
Indices: 548889--548953 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
548879 CTTTGAAATT
* * * *
548889 AAGATTTGGAATATATATTAC
1 AAGATTTTGAACATACATCAC
*
548910 AAGATTTCGAACATACATCAC
1 AAGATTTTGAACATACATCAC
548931 AAGATTTTGAACATACATCAC
1 AAGATTTTGAACATACATCAC
548952 AA
1 AA
548954 TTTTTTCAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (21 bp):
AAGATTTTGAACATACATCAC
Found at i:549429 original size:2 final size:2
Alignment explanation
Indices: 549422--549453 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
549412 TCTGAGTAGG
549422 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
549454 ATTTGCATCC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:565076 original size:38 final size:38
Alignment explanation
Indices: 565019--565149 Score: 203
Period size: 38 Copynumber: 3.5 Consensus size: 38
565009 GTCAAGCATC
* *
565019 TGAGATCTGACCTTTTCAAACATTTAAACACATGATAT
1 TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT
* *
565057 TGA-ACTCTGACCTTGTCAAACATATCAACACATGACAT
1 TGAGA-TCTGACCTTGTCAAACATTTAAACACATGACAT
565095 TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT
1 TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT
565133 TGAGA-CTGACCTTGTCA
1 TGAGATCTGACCTTGTCA
565150 CTAGCATCTG
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
37 13 0.15
38 71 0.84
39 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (38 bp):
TGAGATCTGACCTTGTCAAACATTTAAACACATGACAT
Found at i:577161 original size:32 final size:32
Alignment explanation
Indices: 577116--577918 Score: 844
Period size: 32 Copynumber: 25.3 Consensus size: 32
577106 CGTGGAGAAT
**
577116 GGCTGTAGAGGATTCCCAACCCAGTCTACCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577148 GGCAGTAGAGGATTCCCGACCCAGTCTACCTC
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577180 GGCTGTAGAGGATTTCCGG-CCATATCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTA
*
577212 GGCTGTAGAGGATTCCCGGTCCAGTCTACCTTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACC-TA
*
577245 -GCT-TA-AGGATTCCCGACCCAGTCTACCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * * * *
577274 GGCTGTGGGGGAGTCTCGACCCAGTCTACCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* *
577306 GGCTGTAGGGGATTTCCGG-CCAGGT-TACCTA
1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTA
*
577337 GGCTGTAGAGGAATCCCGGCCCAGTCTACCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577369 GGCTGAACG-GGATTCCCGACCCAGTCTTCCTA
1 GGCTGTA-GAGGATTCCCGGCCCAGTCTACCTA
* * *
577401 GGCTGTAGGGGATTCCCGACCCAGTCTTCCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577433 GGCTGTAGGGGATTCCCGACCCAGTCTTCCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* *
577465 GGCTGTAGAGGATTCCCGACCCAGTCTATCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
*
577497 CGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577529 GGTTGTAGGGGATTCCCGGCCCAGTCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
577561 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACC-TA
* *
577594 -GCT-TA-AGGATTCCCGGTCCAGTCTTCCTA
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* *
577623 GGCTGTAAAGGATTTCCGGCCCAGTCTACC-A
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * * *
577654 TTGCTATAGAGGATTCCCGGCCAAGTTTACCTA
1 -GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* *
577687 GGCTGTACAGGATTCCCGGCCCAGTCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577719 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * * *
577751 GGCTGTAGGGGATTCCCGACCCATTCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577783 GACTGTAGAGGATTCCCGG-TCAGGT-TACCTT
1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTA
** * *
577814 GGCTGTAGAGGATTTTCGGCCCAGTCTATCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
* * *
577846 GGCTGTAGAGGCTTCCCGGCCCTA-TTTACCTT
1 GGCTGTAGAGGATTCCCGGCCC-AGTCTACCTA
* * * *
577878 GGCTGTAGGGGATTCCCGACCCTGTC-ACCTTG
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACC-TA
577910 GGCTGTAGA
1 GGCTGTAGA
577919 TTATCCGGCT
Statistics
Matches: 662, Mismatches: 86, Indels: 46
0.83 0.11 0.06
Matches are distributed among these distances:
29 4 0.01
30 46 0.07
31 68 0.10
32 536 0.81
33 8 0.01
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.26
Consensus pattern (32 bp):
GGCTGTAGAGGATTCCCGGCCCAGTCTACCTA
Found at i:577966 original size:32 final size:32
Alignment explanation
Indices: 577925--578280 Score: 440
Period size: 32 Copynumber: 11.3 Consensus size: 32
577915 TAGATTATCC
* * *
577925 GGCTGTAGAGGATTCCCGACTCAGTTTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
*
577957 GGCTGTAGAGGATTCCCGGCCCAGTCTATCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
* *
577989 GGCTGTAGAGGATTCCCGGTCCAGTCTATCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
*
578021 GGCT-TA-AGGATTCTCGGCCCAGTCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
* * *
578051 GGCT-TA-AGGATTCTCGGCCCATTCAACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
* *
578081 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
* *
578113 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
578145 GGCTGTAGAGGATTCCCGG-CCAGGT-TACCTT
1 GGCTGTAGAGGATTCCCGGCCCA-GTCTACCTT
*
578176 GGCTGTAGAGGATTCCCGGCCCAGTCTATCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
* * *
578208 GGCTGTAGGGGCTTCCCGGCCCTA-TTTACCTT
1 GGCTGTAGAGGATTCCCGGCCC-AGTCTACCTT
* * *
578240 GGCTGTAGGGGATTCCCGACCCTGTC-ACCTT
1 GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
578271 GGGCTGTAGA
1 -GGCTGTAGA
578281 TTATCCGGCT
Statistics
Matches: 289, Mismatches: 27, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
30 53 0.18
31 39 0.13
32 196 0.68
33 1 0.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (32 bp):
GGCTGTAGAGGATTCCCGGCCCAGTCTACCTT
Found at i:577993 original size:79 final size:79
Alignment explanation
Indices: 577846--577997 Score: 209
Period size: 79 Copynumber: 1.9 Consensus size: 79
577836 AGTCTATCTT
* * * *
577846 GGCTGTAGAGGCTTCCCGGCCCTATTTACCTTGGCTGTAGGGGATTCCCGACCCTGTCACCTTGG
1 GGCTGTAGAGGATTCCCGACCCTATTTACCTTGGCTGTAGAGGATTCCCGACCCAGTCACCTTGG
577911 GCTGTAGATTATCC
66 GCTGTAGATTATCC
* * *
577925 GGCTGTAGAGGATTCCCGACTC-AGTTTACCTTGGCTGTAGAGGATTCCCGGCCCAGTCTATCTT
1 GGCTGTAGAGGATTCCCGACCCTA-TTTACCTTGGCTGTAGAGGATTCCCGACCCAGTC-ACCTT
577989 -GGCTGTAGA
64 GGGCTGTAGA
577998 GGATTCCCGG
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
78 1 0.02
79 59 0.92
80 4 0.06
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (79 bp):
GGCTGTAGAGGATTCCCGACCCTATTTACCTTGGCTGTAGAGGATTCCCGACCCAGTCACCTTGG
GCTGTAGATTATCC
Found at i:578190 original size:95 final size:95
Alignment explanation
Indices: 577925--578280 Score: 438
Period size: 95 Copynumber: 3.8 Consensus size: 95
577915 TAGATTATCC
* * *
577925 GGCTGTAGAGGATTCCCGACTCAGTTTACCTTGGCTGTAGAGGATTCCCGGCCCAGTCTATCTTG
1 GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGT-TACCTTG
*
577990 GCTGTAGAGGATTCCCGGTCCAGTCTATCTT
65 GCTGTAGAGGATTCCCGGCCCAGTCTATCTT
* * *
578021 GGCT-TA-AGGATTCTCGGCCCAGTCTACCTTGGCT-TA-AGGATTCTCGGCCCA-TTCAACCTT
1 GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGTT--ACCTT
* * *
578081 GGCTGTAGGGGATTCCCGACCCAGTCTACCTT
64 GGCTGTAGAGGATTCCCGGCCCAGTCTATCTT
*
578113 GGCTGTAGGGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGG-CCAGGTTACCTTG
1 GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCA-GTTACCTTG
578177 GCTGTAGAGGATTCCCGGCCCAGTCTATCTT
65 GCTGTAGAGGATTCCCGGCCCAGTCTATCTT
* * * * * * * *
578208 GGCTGTAGGGGCTTCCCGGCCCTA-TTTACCTTGGCTGTAGGGGATTCCCGACCCTGTCACCTTG
1 GGCTGTAGAGGATTCCCGACCC-AGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGTTACCTT-
578272 GGCTGTAGA
64 GGCTGTAGA
578281 TTATCCGGCT
Statistics
Matches: 225, Mismatches: 24, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
90 1 0.00
91 1 0.00
92 50 0.22
93 4 0.02
94 49 0.22
95 92 0.41
96 26 0.12
97 2 0.01
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (95 bp):
GGCTGTAGAGGATTCCCGACCCAGTCTACCTTGGCTGTAGAGGATTCCCGGCCCAGTTACCTTGG
CTGTAGAGGATTCCCGGCCCAGTCTATCTT
Found at i:580112 original size:185 final size:185
Alignment explanation
Indices: 579813--580154 Score: 524
Period size: 185 Copynumber: 1.8 Consensus size: 185
579803 ATAAATATAG
* * *
579813 GTAATAAGGAATCATTCTCTGAATATTATGTGGTTATAATTTCGGTCGGAGTGTGGTCAAATCTA
1 GTAATAAGGAATCATTCTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA
** * * * *
579878 TTTTAAAATCTTTCGGCCTTTATTGGATTTGACCACGCCCCGACCGAAATTATCACCTCATAATA
66 TCATAAAACCCTACGGCCTTTATTGGATTTGACCACGCCCCGACCGAAATTATAACCTCATAATA
*
579943 CTTAAAGAATGATTCCTTATTCCTTAATCTATAGTGTACAAAAATATAAATGCAA
131 CTCAAAGAATGATTCCTTATTCCTTAATCTATAGTGTACAAAAATATAAATGCAA
** *
579998 GTAATAAGTTATCATTTTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA
1 GTAATAAGGAATCATTCTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA
* * *
580063 TCATAAAGCCCTACGGGCTTTAATT-GATTTGACCACGCCCCGACCGAAATTATAACGTCATAAT
66 TCATAAAACCCTACGGCCTTT-ATTGGATTTGACCACGCCCCGACCGAAATTATAACCTCATAAT
580127 ACTCAAAGAATGATTCCTTATTCCTTAA
130 ACTCAAAGAATGATTCCTTATTCCTTAA
580155 ATAAAACAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
185 137 0.98
186 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (185 bp):
GTAATAAGGAATCATTCTCTGAATATTATGAGGTGATAATTTCGGTCGGAGCGTGGTCAAATCTA
TCATAAAACCCTACGGCCTTTATTGGATTTGACCACGCCCCGACCGAAATTATAACCTCATAATA
CTCAAAGAATGATTCCTTATTCCTTAATCTATAGTGTACAAAAATATAAATGCAA
Found at i:583210 original size:4 final size:4
Alignment explanation
Indices: 583201--583247 Score: 76
Period size: 4 Copynumber: 11.8 Consensus size: 4
583191 GTTTTTGTTG
* *
583201 TTGT TTGT TTGT TTGT TTGT ATGC TTGT TTGT TTGT TTGT TTGT TTG
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTG
583248 AGTTACCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.02, C:0.02, G:0.26, T:0.70
Consensus pattern (4 bp):
TTGT
Found at i:584376 original size:35 final size:35
Alignment explanation
Indices: 584337--584647 Score: 424
Period size: 35 Copynumber: 8.9 Consensus size: 35
584327 GCCTATGCTT
584337 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
* * *
584372 TTGAAAACAAGTATTTTGAATGAATGGCTCAAATC
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
* *
584407 TTGAAAACAAGTATTTTGTATGCATGCCTCAAACC
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
* * * * *
584442 CTGAAAACAAGTATTTTGCATGACTGGCTCAGATC
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
* *
584477 TTGAAAACAAGTATTTTGTATGCATGCCTCAAACC
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
* *
584512 TTGAAAACAAGTATTTTGCATGAATGTCTCAAACA
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
** *
584547 TTGAAAACAAGTATTAAGCATGAATGCCTCAAACA
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
* * * *
584582 TTGAAAACAAGTATTATGCATGAATACCCCAAACA
1 TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
*
584617 TTGAAAACAAGTATTTTGCATAAATGCCTCA
1 TTGAAAACAAGTATTTTGCATGAATGCCTCA
584648 GAACTTACAG
Statistics
Matches: 241, Mismatches: 35, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 241 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.29
Consensus pattern (35 bp):
TTGAAAACAAGTATTTTGCATGAATGCCTCAAACC
Found at i:589787 original size:2 final size:2
Alignment explanation
Indices: 589780--589812 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
589770 TCGATCGATC
589780 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 G
589813 GGATGTACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:599467 original size:20 final size:20
Alignment explanation
Indices: 599437--600961 Score: 1436
Period size: 20 Copynumber: 75.8 Consensus size: 20
599427 TTGCAAGCCA
* *
599437 TGTCAATTGGTGTGTCATGC
1 TGTCTATTGGTGTGTCATGT
* *
599457 TGTTTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
*
599477 TGTCTACTGGTGTGTCA---
1 TGTCTATTGGTGTGTCATGT
*
599494 --T-TA---GTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
599508 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
599528 TGTCTACTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
599548 TGTCTATTAGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
* * *
599568 TGTCTATTTGTTTGTTATGT
1 TGTCTATTGGTGTGTCATGT
599588 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
* *
599608 TGTCTATTGGCGTGTCATATAT
1 TGTCTATTGGTGTGTC--ATGT
* *
599630 TGTCAATTGGTGTGTCATTT
1 TGTCTATTGGTGTGTCATGT
* *
599650 TGTGTCTTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
* *
599670 TGTCTATTTGATGAGTC-T-T
1 TGTCTA-TTGGTGTGTCATGT
* *
599689 ATGTCTACTGGTGTGTTATGT
1 -TGTCTATTGGTGTGTCATGT
* * *
599710 CGTCTTTTGGTGTGTCAAGT
1 TGTCTATTGGTGTGTCATGT
* * **
599730 TGTCTATTGGCGAGTCATAA
1 TGTCTATTGGTGTGTCATGT
* *
599750 TCTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
* * * * *
599770 TATCTAATGGGGTATTATGT
1 TGTCTATTGGTGTGTCATGT
*
599790 TGTCCATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
599810 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
* * *
599830 TGTATTTTGGTGTG--GTGT
1 TGTCTATTGGTGTGTCATGT
*
599848 TGTCTATTGGCT-TATCATGT
1 TGTCTATTGG-TGTGTCATGT
* * * *
599868 TGTTTATTGATGTGCCACGT
1 TGTCTATTGGTGTGTCATGT
**
599888 TGTCTATTGGTGTGTCATAC
1 TGTCTATTGGTGTGTCATGT
* * * * *
599908 TCTATGTTGGTGTTTTATGT
1 TGTCTATTGGTGTGTCATGT
* * * *
599928 TGTCTTTTTGTGTGTTAT-A
1 TGTCTATTGGTGTGTCATGT
599947 TGTTCTATTGGTGTGTCATGT
1 TG-TCTATTGGTGTGTCATGT
*
599968 TGTCT-TTAGGTGTGTAATGT
1 TGTCTATT-GGTGTGTCATGT
*
599988 TGTTTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
* *
600008 TGTCTATTGATGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
*
600028 TGTCTATTGGTGTGTCATAT
1 TGTCTATTGGTGTGTCATGT
*
600048 TGTCTATTGGTGTATCATGT
1 TGTCTATTGGTGTGTCATGT
** *
600068 TGT-TAATTGGTGTACCATCAT
1 TGTCT-ATTGGTGTGTCAT-GT
*
600089 T-TCTATTAGTGTGTTGTGCCATTT
1 TGTCTATT-G-GTG-TGT--CATGT
* *
600113 TGTCTATTGATGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
* *
600133 TGTCTATTGATGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
*
600153 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
* *
600173 TGTCTATTGGTGTGTCCTAT
1 TGTCTATTGGTGTGTCATGT
* * *
600193 TGTCTATTGGTTTGCCATCAT
1 TGTCTATTGGTGTGTCAT-GT
* * * * *
600214 TTTAATAATGTGTTGTGCCATTT
1 TGT-CT-AT-TGGTGTGTCATGT
* *
600237 TGTCTTTTGGTGTGTCACGT
1 TGTCTATTGGTGTGTCATGT
600257 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
* * *
600277 TGTCTAGTGGTCTGTCACGT
1 TGTCTATTGGTGTGTCATGT
* *
600297 AGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
* *
600317 TGTCTATTGATGTGTCACGTT
1 TGTCTATTGGTGTGTCATG-T
* *
600338 TTTCTATTGGTGTGTCATAT
1 TGTCTATTGGTGTGTCATGT
*
600358 TGTCTATTGGTGTGTCACGT
1 TGTCTATTGGTGTGTCATGT
*
600378 TTTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
600398 TGTCGATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
600418 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
* *
600438 TGTCTATTGATGTGTCACGT
1 TGTCTATTGGTGTGTCATGT
*
600458 TTTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
600478 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
*
600498 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
*
600518 TGTCTATTGATGTGTCACAT-T
1 TGTCTATTGGTGTGT--CATGT
* *
600539 TTTCTATTGGTGTGTCATAT
1 TGTCTATTGGTGTGTCATGT
*
600559 TGTCTATTGGTGTGTCACGT
1 TGTCTATTGGTGTGTCATGT
*
600579 TTTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
600599 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
600619 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
600639 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
600659 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
** *
600679 TGTCTATTATTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
*
600699 TGTCTATTGGTGTGTCATAT
1 TGTCTATTGGTGTGTCATGT
* *
600719 TGTCAATTGGTTTGCCATCAT-T
1 TGTCTATTGGTGTG---TCATGT
* * * * *
600741 TTTTTAATGTGTTGTGCCATTT
1 TGTCT-AT-TGGTGTGTCATGT
*
600763 TGTCTATTGGTGTGTCACGT
1 TGTCTATTGGTGTGTCATGT
600783 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
600803 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
* *
600823 TGTTTATTGGTGTGTCATAT
1 TGTCTATTGGTGTGTCATGT
*
600843 TGTCTATTGGTTTGCCATCAT-T
1 TGTCTATTGGTGTG---TCATGT
* * * * *
600865 TTTTTAATGTGTTGTGCCATTT
1 TGTCT-AT-TGGTGTGTCATGT
*
600887 TGTCTATTGGTGTGTCACGT
1 TGTCTATTGGTGTGTCATGT
600907 TGTCTATTGGTGTGTCATGT
1 TGTCTATTGGTGTGTCATGT
*
600927 TGTCTATTGGTGTGCCATGT
1 TGTCTATTGGTGTGTCATGT
* *
600947 TGTTTATTTGTGTGT
1 TGTCTATTGGTGTGT
600962 TGTATGACTG
Statistics
Matches: 1221, Mismatches: 232, Indels: 104
0.78 0.15 0.07
Matches are distributed among these distances:
11 7 0.01
14 2 0.00
15 1 0.00
16 1 0.00
17 2 0.00
18 12 0.01
19 17 0.01
20 1024 0.84
21 62 0.05
22 42 0.03
23 20 0.02
24 22 0.02
25 9 0.01
ACGTcount: A:0.13, C:0.12, G:0.26, T:0.49
Consensus pattern (20 bp):
TGTCTATTGGTGTGTCATGT
Found at i:599501 original size:31 final size:31
Alignment explanation
Indices: 599466--599525 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
599456 CTGTTTATTG
599466 GTGTGCCATGTTGTCTACTGGTGTGTCATTA
1 GTGTGCCATGTTGTCTACTGGTGTGTCATTA
*
599497 GTGTGCCATGTTGTCTATTGGTGTGTCAT
1 GTGTGCCATGTTGTCTACTGGTGTGTCAT
599526 GTTGTCTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.12, C:0.15, G:0.30, T:0.43
Consensus pattern (31 bp):
GTGTGCCATGTTGTCTACTGGTGTGTCATTA
Found at i:599516 original size:51 final size:51
Alignment explanation
Indices: 599446--599545 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
599436 ATGTCAATTG
* *
599446 GTGTGTCATGCTGTTTATTGGTGTGCCATGTTGTCTACTGGTGTGTCATTA
1 GTGTGCCATGCTGTCTATTGGTGTGCCATGTTGTCTACTGGTGTGTCATTA
* *
599497 GTGTGCCATGTTGTCTATTGGTGTGTCATGTTGTCTACTGGTGTGTCAT
1 GTGTGCCATGCTGTCTATTGGTGTGCCATGTTGTCTACTGGTGTGTCAT
599546 GTTGTCTATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.11, C:0.14, G:0.30, T:0.45
Consensus pattern (51 bp):
GTGTGCCATGCTGTCTATTGGTGTGCCATGTTGTCTACTGGTGTGTCATTA
Found at i:599663 original size:10 final size:11
Alignment explanation
Indices: 599437--599667 Score: 57
Period size: 10 Copynumber: 22.5 Consensus size: 11
599427 TTGCAAGCCA
599437 TGTCAATTGGTG
1 TGTC-ATTGGTG
*
599449 TGTCA-TGCTG
1 TGTCATTGGTG
*
599459 T-TTATTGGTG
1 TGTCATTGGTG
*
599469 TGCCA-T-GT-
1 TGTCATTGGTG
*
599477 TGTCTACTGGTG
1 TGTC-ATTGGTG
*
599489 TGTCATTAGTG
1 TGTCATTGGTG
*
599500 TGCCA-T-GT-
1 TGTCATTGGTG
599508 TGTCTATTGGTG
1 TGTC-ATTGGTG
599520 TGTCA-T-GT-
1 TGTCATTGGTG
*
599528 TGTCTACTGGTG
1 TGTC-ATTGGTG
599540 TGTCA-T-GT-
1 TGTCATTGGTG
*
599548 TGTCTATTAGTG
1 TGTC-ATTGGTG
599560 TGTCA-T-GT-
1 TGTCATTGGTG
* *
599568 TGTCTATTTGTT
1 TGTC-ATTGGTG
*
599580 TGTTA-T-GT-
1 TGTCATTGGTG
599588 TGTCTATTGGTG
1 TGTC-ATTGGTG
599600 TGTCA-T-GT-
1 TGTCATTGGTG
*
599608 TGTCTATTGGCG
1 TGTC-ATTGGTG
*
599620 TGTCATAT-AT-
1 TGTCAT-TGGTG
599630 TGTCAATTGGTG
1 TGTC-ATTGGTG
*
599642 TGTCATT-TTG
1 TGTCATTGGTG
599652 TGTC-TTGGTG
1 TGTCATTGGTG
599662 TGTCAT
1 TGTCAT
599668 GTTGTCTATT
Statistics
Matches: 165, Mismatches: 18, Indels: 73
0.64 0.07 0.29
Matches are distributed among these distances:
8 25 0.15
9 25 0.15
10 41 0.25
11 38 0.23
12 36 0.22
ACGTcount: A:0.12, C:0.12, G:0.28, T:0.48
Consensus pattern (11 bp):
TGTCATTGGTG
Found at i:604815 original size:70 final size:70
Alignment explanation
Indices: 604702--604839 Score: 231
Period size: 70 Copynumber: 2.0 Consensus size: 70
604692 TTGATAGGTC
* * *
604702 ATTCCTAGTGCATAAAGAAATATGCAAAATACTTTGAAATTGTCTTATCTTAAAAAAGCCTCTTT
1 ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAATTGTCTAATCTTAAAAAACCCTCTTT
604767 GATTA
66 GATTA
* *
604772 ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAGTTGTCTAATCTTAAAATACCCTCTTT
1 ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAATTGTCTAATCTTAAAAAACCCTCTTT
604837 GAT
66 GAT
604840 AAAACATAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (70 bp):
ATTCCTAGTGCATAAAAAAATATGCAAAATACTTTGAAATTGTCTAATCTTAAAAAACCCTCTTT
GATTA
Found at i:610092 original size:14 final size:12
Alignment explanation
Indices: 610056--610094 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
610046 ATACTAGTGT
*
610056 AATTATAGTATT
1 AATTATAGTATC
610068 AATTATAGTATC
1 AATTATAGTATC
610080 AATATACTAGTATC
1 AAT-TA-TAGTATC
610094 A
1 A
610095 TTTTATTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 14 0.58
13 2 0.08
14 8 0.33
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (12 bp):
AATTATAGTATC
Found at i:610796 original size:17 final size:17
Alignment explanation
Indices: 610776--610815 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
610766 TTGTATTTTG
610776 TTTTTGTTTGGGTTGTT
1 TTTTTGTTTGGGTTGTT
* * *
610793 TTTTTGTTTTGTTTTTT
1 TTTTTGTTTGGGTTGTT
610810 TTTTTG
1 TTTTTG
610816 GGGGGGGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (17 bp):
TTTTTGTTTGGGTTGTT
Found at i:623491 original size:2 final size:2
Alignment explanation
Indices: 623486--623572 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
623476 GTAAAACACA
623486 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
623528 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
623570 CT C
1 CT C
623573 NNNNNNNNNN
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:624023 original size:2 final size:2
Alignment explanation
Indices: 624010--624081 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
624000 NNNNNACTAA
*
624010 CT CT CG 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
624052 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
624082 TATTTATATC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.00, C:0.50, G:0.01, T:0.49
Consensus pattern (2 bp):
CT
Found at i:631992 original size:17 final size:17
Alignment explanation
Indices: 631949--631992 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
631939 TTTGCAAATT
*
631949 TTTACGGTTATAACGAA
1 TTTACGGATATAACGAA
*
631966 -TT-CAGATATAACGAA
1 TTTACGGATATAACGAA
631981 TTTACGGATATA
1 TTTACGGATATA
631993 GCAAACTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
15 11 0.50
16 4 0.18
17 7 0.32
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (17 bp):
TTTACGGATATAACGAA
Found at i:638868 original size:16 final size:17
Alignment explanation
Indices: 638836--638870 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
638826 TGATTTCATA
638836 TTAATTGGAGGACAAAT
1 TTAATTGGAGGACAAAT
*
638853 TTAATT-GAGGAGAAAT
1 TTAATTGGAGGACAAAT
638869 TT
1 TT
638871 TTAAGGACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (17 bp):
TTAATTGGAGGACAAAT
Found at i:650221 original size:28 final size:28
Alignment explanation
Indices: 650153--650313 Score: 254
Period size: 28 Copynumber: 5.8 Consensus size: 28
650143 ATAGAACGTG
*
650153 TGTGATTTTACATGATGTGATCAATGTC
1 TGTGATTTTACAGGATGTGATCAATGTC
*
650181 --TGATTTTACAGGATATGATCAATGTC
1 TGTGATTTTACAGGATGTGATCAATGTC
*
650207 TGTGATTTTACAGGATTTGATCAATGTC
1 TGTGATTTTACAGGATGTGATCAATGTC
* * *
650235 TCTGATTTTACAGTATGTGATCAGTGTC
1 TGTGATTTTACAGGATGTGATCAATGTC
650263 TGTGATTTTACAGGATGTGATCAATGTC
1 TGTGATTTTACAGGATGTGATCAATGTC
650291 TGTGATTTTACAGGATGTGATCA
1 TGTGATTTTACAGGATGTGATCA
650314 GCTATGGCTG
Statistics
Matches: 121, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
26 24 0.20
28 97 0.80
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.41
Consensus pattern (28 bp):
TGTGATTTTACAGGATGTGATCAATGTC
Found at i:655061 original size:1 final size:1
Alignment explanation
Indices: 655057--655088 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
655047 NNNNNGCGTC
*
655057 GGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
655089 TAGGACCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.03, G:0.97, T:0.00
Consensus pattern (1 bp):
G
Found at i:657551 original size:42 final size:40
Alignment explanation
Indices: 657457--657573 Score: 156
Period size: 42 Copynumber: 3.0 Consensus size: 40
657447 GTATGAGGTC
657457 TACATGTTTACTAGTGGCTCCCCT-GGTATGTGG-T-T--G
1 TACATGTTTACTAGTGGCT-CCCTAGGTATGTGGTTGTACG
657493 TACATGTTTACTAGTGGCTCCCTAGGTATGTGGTTGTACCGG
1 TACATGTTTACTAGTGGCTCCCTAGGTATGTGGTTGTA-C-G
657535 TACATGTTTACTAGTGGCTCCAC-AGGTATGTGGTTGTAC
1 TACATGTTTACTAGTGGCTCC-CTAGGTATGTGGTTGTAC
657574 ATGTTAACCA
Statistics
Matches: 73, Mismatches: 0, Indels: 11
0.87 0.00 0.13
Matches are distributed among these distances:
35 4 0.05
36 28 0.38
37 1 0.01
38 1 0.01
41 1 0.01
42 37 0.51
43 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.37
Consensus pattern (40 bp):
TACATGTTTACTAGTGGCTCCCTAGGTATGTGGTTGTACG
Found at i:657592 original size:36 final size:36
Alignment explanation
Indices: 657444--657593 Score: 169
Period size: 36 Copynumber: 4.0 Consensus size: 36
657434 GCTGGTGGCC
* * *
657444 CAGGTATGAGG-TCTACATGTTTACTAGTGGCTCCC
1 CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA
*
657479 CTGGTATGTGGTTGTACATGTTTACTAGTGGCTCC-
1 CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA
657514 CTAGGTATGTGGTTGTACCGGTACATGTTTACTAGTGGCTCCA
1 C-AGGTATGTGG-T-T----GTACATGTTTACTAGTGGCTCCA
* *
657557 CAGGTATGTGGTTGTACATGTTAACCAGTGGCTCCA
1 CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA
657593 C
1 C
657594 TGTCCATGTG
Statistics
Matches: 100, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
35 10 0.10
36 53 0.53
37 1 0.01
38 1 0.01
40 1 0.01
41 1 0.01
42 32 0.32
43 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.27, T:0.34
Consensus pattern (36 bp):
CAGGTATGTGGTTGTACATGTTTACTAGTGGCTCCA
Found at i:658429 original size:77 final size:77
Alignment explanation
Indices: 658276--658418 Score: 250
Period size: 77 Copynumber: 1.9 Consensus size: 77
658266 AGATTGAGGA
* *
658276 TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGGGACATGGTAAGAAACTCGC
1 TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGAGACATGGTAAGAAACTCAC
658341 TTAGAAGGGGGG
66 TTAGAAGGGGGG
* *
658353 TTGTATTGAAGTTCTCTCCAACATATTGAATCTCACATTCTCCAGAGACATGGTAAGAAATTCAC
1 TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGAGACATGGTAAGAAACTCAC
658418 T
66 T
658419 GTGACAGGGG
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
77 62 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (77 bp):
TTGTATTGAAGTTCTCTCCAACATACTGAATCTCACATTCTCCAGAGACATGGTAAGAAACTCAC
TTAGAAGGGGGG
Found at i:661171 original size:78 final size:79
Alignment explanation
Indices: 661040--661191 Score: 218
Period size: 78 Copynumber: 1.9 Consensus size: 79
661030 TGCCTCTGAT
* * * *
661040 ATTTAACTGTTTGCCCTTGATTTTCATAGAACTCAAGAAAGCCATGAATCCGATCTTCTTTGACA
1 ATTTAAATGTGTGCCCTTGATTTTCACAGAACTCAAGAAAGCCACGAATCCGATCTTCTTTGACA
661105 TGATGGTGTCTAAC
66 TGATGGTGTCTAAC
* * *
661119 ATTTAAATGTGTGCCCTTTATTTT-ACAGAACTTAGGAAAGCCACG-ATCCCGATCTTCTTTGAC
1 ATTTAAATGTGTGCCCTTGATTTTCACAGAACTCAAGAAAGCCACGAAT-CCGATCTTCTTTGAC
661182 ATGATGGTGT
65 ATGATGGTGT
661192 GCGAATTCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
77 2 0.03
78 42 0.65
79 21 0.32
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (79 bp):
ATTTAAATGTGTGCCCTTGATTTTCACAGAACTCAAGAAAGCCACGAATCCGATCTTCTTTGACA
TGATGGTGTCTAAC
Found at i:670370 original size:44 final size:44
Alignment explanation
Indices: 670304--670570 Score: 489
Period size: 44 Copynumber: 6.1 Consensus size: 44
670294 CAGTGTATTT
670304 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
* *
670348 TGTTTAGTTAATTTTTATGTCTCAGTGGTGTGAATTGCCTTGAA
1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
*
670392 TGTTTAGTTAATCTTTACGTCTCAGTGGTATGAATTGCCTTGAA
1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
* *
670436 TGTTTAGTTAATTTTTATGTCTCAGTGGTGTGAATTGCCTTGAA
1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
670480 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
670524 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
1 TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
670568 TGT
1 TGT
670571 AGTGCTGTCA
Statistics
Matches: 213, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 213 1.00
ACGTcount: A:0.21, C:0.12, G:0.22, T:0.45
Consensus pattern (44 bp):
TGTTTAGTTAATCTTTACGTCTCAGTGGTGTGAATTGCCTTGAA
Found at i:672372 original size:12 final size:12
Alignment explanation
Indices: 672355--672383 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
672345 TGCTGAGATG
672355 TGTGTATTGGAT
1 TGTGTATTGGAT
672367 TGTGTATTGGAT
1 TGTGTATTGGAT
672379 TGTGT
1 TGTGT
672384 TTGCTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.34, T:0.52
Consensus pattern (12 bp):
TGTGTATTGGAT
Found at i:674348 original size:2 final size:2
Alignment explanation
Indices: 674343--674388 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
674333 GAGAGTGTGT
674343 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
674385 GA GA
1 GA GA
674389 ACAGCTGTTG
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:677824 original size:2 final size:2
Alignment explanation
Indices: 677817--677863 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
677807 TATATCAATG
677817 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
677859 GA GA G
1 GA GA G
677864 TTTTTAATAT
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:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:681555 original size:2 final size:2
Alignment explanation
Indices: 681548--681582 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
681538 TAATCACAAA
681548 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 T
681583 GACATTTATA
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:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:684740 original size:20 final size:20
Alignment explanation
Indices: 684723--684760 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
684713 ATGTAATACA
*
684723 ATATCATATTATACAATAAT
1 ATATCATATGATACAATAAT
*
684743 ATCTCATATGATACAATA
1 ATATCATATGATACAATA
684761 TACAAGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (20 bp):
ATATCATATGATACAATAAT
Found at i:684757 original size:35 final size:35
Alignment explanation
Indices: 684679--684761 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 35
684669 TTGAATATCG
* * * *
684679 TATGATACATTATCATGGGATACAATAATATGTTA
1 TATGATACAATATCATAGGATACAATAATATCTCA
* * **
684714 TGTAATACAATATCATATTATACAATAATATCTCA
1 TATGATACAATATCATAGGATACAATAATATCTCA
684749 TATGATACAATAT
1 TATGATACAATAT
684762 ACAAGTAATA
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.37
Consensus pattern (35 bp):
TATGATACAATATCATAGGATACAATAATATCTCA
Found at i:688549 original size:104 final size:104
Alignment explanation
Indices: 688436--688891 Score: 765
Period size: 104 Copynumber: 4.4 Consensus size: 104
688426 GCAGGTGACT
*
688436 TGTATAATACTTTTGAATTCATTAATTTCAAA-TGAATCACATTTGATAACTGTGATATTGCCTA
1 TGTATAATACTTTTGAATTCATTAATTT-AAATTGAATCACATTTGATAACTGTGATATTGCCCA
688500 TCTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA
65 TCTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA
688540 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT
1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT
*
688605 CTGTGATTTGTTGCATATTTTACAAATGTAAATATTACA
66 CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA
688644 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT
1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT
*
688709 CTGTGATTTGTTGCATATTTTACAAATGTAAATATTACA
66 CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA
* * * * *
688748 TGTATAATACTTTTGAATTCATTAATTTCAATTGAATAACATGTGATAACTGTGGTATTGCCTAT
1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT
*
688813 CTGTGATTTGTTGCATATTTTACAAATGCAAGTA--ACA
66 CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA
* * * *
688850 TGTAAAATTCTTTTGAATTCATTAAATTAAATTTAATCACAT
1 TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACAT
688892 GTACTGACTG
Statistics
Matches: 336, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
102 39 0.12
103 3 0.01
104 294 0.88
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.43
Consensus pattern (104 bp):
TGTATAATACTTTTGAATTCATTAATTTAAATTGAATCACATTTGATAACTGTGATATTGCCCAT
CTGTGATTTGTTGCATATTTTACAAATGCAAATATTACA
Found at i:690111 original size:78 final size:79
Alignment explanation
Indices: 689878--690119 Score: 378
Period size: 79 Copynumber: 3.1 Consensus size: 79
689868 TTCTGATTAT
689878 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA
1 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA
*
689943 ATTTTACCTCCTGA
66 ATTTAACCTCCTGA
* * * * *
689957 ATGGACTTTAAAATTGAGCATATTTGTTTTTCTGAAAATATTTTACTTGTATTATGTCACAATAT
1 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA
*
690022 ATTTAAACTCCTGA
66 ATTTAACCTCCTGA
* *
690036 ATGGACTTTAAAATTGAGC-TGTTTGGTTTTCTGGAAATATTTTACTCGTATGATGTCACAGTAA
1 ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA
* *
690100 ACTTAACCTCCTAA
66 ATTTAACCTCCTGA
690114 ATGGAC
1 ATGGAC
690120 GGTTTTGAAA
Statistics
Matches: 146, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
78 55 0.38
79 91 0.62
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (79 bp):
ATGGACTTTAAAATTGAGCATATTTGGTTTTCTGAAAATATTTTACTCGTATGATGTCACAGTAA
ATTTAACCTCCTGA
Found at i:693423 original size:1 final size:1
Alignment explanation
Indices: 693417--693450 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
693407 GCGGGTGGGT
693417 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
693451 TTCATGTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:698087 original size:2 final size:2
Alignment explanation
Indices: 698080--698104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
698070 GTAAATAGAT
698080 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 G
698105 TGTGTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:708849 original size:25 final size:25
Alignment explanation
Indices: 708821--708870 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
708811 ATTAATTTTG
708821 TCTTCAGCCTTAGGCAATTCAATCA
1 TCTTCAGCCTTAGGCAATTCAATCA
*
708846 TCTTTAGCCTTAGGCAATTCAATCA
1 TCTTCAGCCTTAGGCAATTCAATCA
708871 AATTTTACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (25 bp):
TCTTCAGCCTTAGGCAATTCAATCA
Found at i:722352 original size:1 final size:1
Alignment explanation
Indices: 722346--722387 Score: 75
Period size: 1 Copynumber: 42.0 Consensus size: 1
722336 TTTTAGTGCT
*
722346 CCCCCCCCCCCCCCCCCCCCCCNCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
722388 TTTTATTGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.00, C:0.98, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:725746 original size:6 final size:6
Alignment explanation
Indices: 725735--725772 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
725725 TGCTATACCC
725735 TCGGCG TCGGCGG T-GGCG TCGGCG TCGGCG TCGGCG TC
1 TCGGCG TCGGC-G TCGGCG TCGGCG TCGGCG TCGGCG TC
725773 CGGACCTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 26 0.87
7 2 0.07
ACGTcount: A:0.00, C:0.32, G:0.50, T:0.18
Consensus pattern (6 bp):
TCGGCG
Found at i:726119 original size:19 final size:19
Alignment explanation
Indices: 726097--726136 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
726087 TTTCGGATGC
* *
726097 TGGAGGAGGTTAAGGTTTT
1 TGGAGCAGGTTAAAGTTTT
726116 TGGAGCAGGTTAAAGTTTT
1 TGGAGCAGGTTAAAGTTTT
726135 TG
1 TG
726137 TTGCGGGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.38, T:0.38
Consensus pattern (19 bp):
TGGAGCAGGTTAAAGTTTT
Found at i:726127 original size:177 final size:177
Alignment explanation
Indices: 725818--726603 Score: 910
Period size: 177 Copynumber: 4.4 Consensus size: 177
725808 TCTAAGCTAT
* * * * * * * *
725818 TACTTGTCCTATCTTCACCAAACTTGCATGGATGATGCATC-T-GGACCTACTTATGGACTTGA-
1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGA--TACTGATGCACCTGAC
* * * * * *
725880 AAGACTTGGATGCTGAATCTGGGTCCTA-A-ATTTCAGATGCTGGAGGAGGTTAAGGTTGTTGGA
64 AAG-CTTGAATGCTGAATCTGAG--CTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGA
* *
725943 CCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAGTATCTTAGTTAC
126 GCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTAC
* * * * * *
725995 TGCTGGT-CTGTACTTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCTCCAGACA
1 TACTGGTCCT-AACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACA
* * *
726059 GGCTTGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAG
65 AGCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAG
* * *
726124 GTTAAAGTTTTTGTTGCGGGTGCCCAT-TGATAGCAATATCTAAGTTAC
130 GTTAAAGTTTTTGTTGCAGGTGCCC-TCTGATAGCAGTATCTTAGTTAC
* *
726172 TACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGAAAA
1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA
* *
726237 GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGG
66 GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGG
**
726302 TT-AAGTTTTTGTTGCAGGTGCCCTCTGATGATTA-TATCTTAGTTAC
131 TTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-AGCAGTATCTTAGTTAC
* * *
726348 TATTGGTCCTAACTTCACCAAACATGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA
1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA
* * * *
726413 GCTTGAATGCTGAATCTGAGCAATAGGTTTCTGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGG
66 GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGG
*** *
726478 TTAGATAAAGTTTTTGAAACAGGTGCCCTCTGAT-G-ATGATATCTTAGTTAT
131 -T---TAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCA-G-TATCTTAGTTAC
* * * * * *
726529 TACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAG
1 TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA
726594 GCTTGAATGC
66 GCTTGAATGC
726604 ATAGTCTGGT
Statistics
Matches: 528, Mismatches: 63, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
175 4 0.01
176 161 0.30
177 252 0.48
178 7 0.01
179 2 0.00
180 1 0.00
181 101 0.19
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (177 bp):
TACTGGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAA
GCTTGAATGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCAGG
TTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTAC
Found at i:726453 original size:353 final size:354
Alignment explanation
Indices: 725806--726603 Score: 943
Period size: 353 Copynumber: 2.2 Consensus size: 354
725796 GCATGTCCTG
* * * * *
725806 TATCTAAGCTATTACTTGTCCTATCTTCACCAAACTTGCATGGATGATGCATC-T-GGACCTACT
1 TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGA--TACT
* * * * * *
725869 TATGGACTTG-AAAGACTTGGATGCTGAATCTGGGTCCTAAATTTCAGATGCTGGAGGAGGTTAA
64 GATGCACCTGAAAAG-CTTGAATGCTGAATCTGAG-CCTAAATTTCAGATGCTGGAAGAGGTTAA
* * *
725933 GGTTGTTGGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTTTGATAGCAGTATCTTAGTTACTGC
127 GGTTGTTAGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTACTAC
* * * * *
725998 TGGTCTGTACTTCACCAAACTTGCATGGATGGTGTGCCTTATGATACTGATGCTCCAGACAGGCT
192 TGGTCTGAACTTCACCAAACATGCATGGATGGTGCGCCTTATGATACTGATGCACCAGACAAGCT
* * **
726063 TGAGTGCTGAATCTGAGCTATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGG-T-
257 TGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCAGGTTA
*** *
726126 TAAAGTTTTTGTTGCGGGTGCCCAT-TGAT-AGCAA
322 TAAAGTTTTTGAAACAGGTGCCC-TCTGATGAG--A
* * *
726160 TATCTAAGTTACTACTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGA
1 TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGA
* *
726225 TGCACCTGAAAAGCTTGAATGCTGAATCTGAG-CTATAGGTTTCGGATGCTGGAAGAGGTTAAGG
66 TGCACCTGAAAAGCTTGAATGCTGAATCTGAGCCTA-A-ATTTCAGATGCTGGAAGAGGTTAAGG
* * * ** *
726289 TTTTTAGAGCTGGTT-AAGTTTTTGTTGCAGGTGCCCTCTGATGATTA-TATCTTAGTTACTATT
129 TTGTTAGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGAT-AGCAGTATCTTAGTTACTACT
* * *
726352 GGTCCT-AACTTCACCAAACATGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGCT
193 GGT-CTGAACTTCACCAAACATGCATGGATGGTGCGCCTTATGATACTGATGCACCAGACAAGCT
* *
726416 TGAATGCTGAATCTGAGCAATAGGTTTCTGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTTA
257 TGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCAGGTT-
726481 GATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGA
321 -ATAAAGTTTTTGAAACAGGTGCCCTCTGATGA-GA
* * * * *
726517 TATCTTAGTTATTACTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGA
1 TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGA
* *
726582 TGCACCTGACAGGCTTGAATGC
66 TGCACCTGAAAAGCTTGAATGC
726604 ATAGTCTGGT
Statistics
Matches: 377, Mismatches: 53, Indels: 25
0.83 0.12 0.05
Matches are distributed among these distances:
352 3 0.01
353 150 0.40
354 113 0.30
355 5 0.01
356 3 0.01
357 101 0.27
358 1 0.00
359 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (354 bp):
TATCTAAGTTATTACTTGTCCTAACTTCACCAAACTTGCATGGATGGTGCGTCTTATGATACTGA
TGCACCTGAAAAGCTTGAATGCTGAATCTGAGCCTAAATTTCAGATGCTGGAAGAGGTTAAGGTT
GTTAGACCAGGTTAAAGTTTTTGTTGCAGGTGCCCTCTGATAGCAGTATCTTAGTTACTACTGGT
CTGAACTTCACCAAACATGCATGGATGGTGCGCCTTATGATACTGATGCACCAGACAAGCTTGAA
TGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCAGGTTATAAA
GTTTTTGAAACAGGTGCCCTCTGATGAGA
Found at i:727291 original size:20 final size:20
Alignment explanation
Indices: 727268--727310 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
727258 TATGATAAAG
727268 TATTGTATGATATGAAACAA
1 TATTGTATGATATGAAACAA
* *
727288 TATTGTTTGATATGATACAA
1 TATTGTATGATATGAAACAA
727308 TAT
1 TAT
727311 GATATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (20 bp):
TATTGTATGATATGAAACAA
Found at i:727582 original size:15 final size:15
Alignment explanation
Indices: 727549--727695 Score: 73
Period size: 15 Copynumber: 9.3 Consensus size: 15
727539 ATATTCTATA
* **
727549 ATATTGTATCATACA
1 ATATTGTATAATATG
727564 ATATTGTATAATATG
1 ATATTGTATAATATG
727579 ATATTGATTTCAGTAATATAG
1 ATATTG---T-A-TAATAT-G
* * *
727600 A-ATTATATCACATG
1 ATATTGTATAATATG
* *
727614 AAATTGTATTATATG
1 ATATTGTATAATATG
*
727629 ATATTGTAATATTATATA
1 ATATTGT-ATA--ATATG
* *
727647 ATATTGTATCATACG
1 ATATTGTATAATATG
*
727662 ATATTGTATGATATG
1 ATATTGTATAATATG
*
727677 ATATTGGT-TTATATG
1 ATATT-GTATAATATG
727692 ATAT
1 ATAT
727696 ATTATCATAT
Statistics
Matches: 103, Mismatches: 18, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
14 2 0.02
15 69 0.67
16 5 0.05
17 3 0.03
18 12 0.12
19 1 0.01
20 9 0.09
21 2 0.02
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (15 bp):
ATATTGTATAATATG
Found at i:727628 original size:50 final size:46
Alignment explanation
Indices: 727566--727733 Score: 156
Period size: 50 Copynumber: 3.4 Consensus size: 46
727556 ATCATACAAT
*
727566 ATTGTATAATATGATATTGATTTCAGTAATATAGAATTATATCACATGAA
1 ATTGTATTATATGATATTG-TTT-A-TAATATA-AATTATATCACATGAA
* * * * * *
727616 ATTGTATTATATGATATTGTAATATTATATAATATTGTATCATACGAT
1 ATTGTATTATATGATATTGT-TTATAATATAA-ATTATATCACATGAA
* * *
727664 ATTGTATGATATGATATTGGTTTATATGATATATTATCATATCACATGAA
1 ATTGTATTATATGATATT-GTTTATA--ATATA-AATTATATCACATGAA
727714 ATTGTATTATATGATATTGT
1 ATTGTATTATATGATATTGT
727734 AATATATTTT
Statistics
Matches: 95, Mismatches: 17, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
47 1 0.01
48 37 0.39
49 6 0.06
50 51 0.54
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (46 bp):
ATTGTATTATATGATATTGTTTATAATATAAATTATATCACATGAA
Found at i:727643 original size:18 final size:18
Alignment explanation
Indices: 727620--727654 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
727610 CATGAAATTG
*
727620 TATTATATGATATTGTAA
1 TATTATATAATATTGTAA
727638 TATTATATAATATTGTA
1 TATTATATAATATTGTA
727655 TCATACGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (18 bp):
TATTATATAATATTGTAA
Found at i:727659 original size:98 final size:97
Alignment explanation
Indices: 727532--727738 Score: 310
Period size: 98 Copynumber: 2.1 Consensus size: 97
727522 CTATGATACA
*
727532 ATATTGT-ATATTCTATAATATTGTATCATACAATATTGTATAATATGATATTGATTTCAGTA-A
1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGATTT-A-TAGA
*
727595 TATAGAATTATATCACATGAAATTGTATTATATG
64 TATAGAATCATATCACATGAAATTGTATTATATG
* * *
727629 ATATTGTAATATTATATAATATTGTATCATACGATATTGTATGATATGATATTGGTTTATATGAT
1 ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGATTTATA-GAT
**
727694 ATATTATCATATCACATGAAATTGTATTATATG
65 ATAGAATCATATCACATGAAATTGTATTATATG
727727 ATATTGTAATAT
1 ATATTGTAATAT
727739 ATTTTATTGT
Statistics
Matches: 100, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
96 2 0.02
97 8 0.08
98 90 0.90
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.45
Consensus pattern (97 bp):
ATATTGTAATATTATATAATATTGTATCATACAATATTGTATAATATGATATTGATTTATAGATA
TAGAATCATATCACATGAAATTGTATTATATG
Found at i:727732 original size:15 final size:15
Alignment explanation
Indices: 727611--727740 Score: 93
Period size: 15 Copynumber: 8.1 Consensus size: 15
727601 ATTATATCAC
*
727611 ATGAAATTGTATTAT
1 ATGATATTGTATTAT
727626 ATGATATTGTAATATTAT
1 ATGATATTG---TATTAT
* *
727644 ATAATATTGTATCAT
1 ATGATATTGTATTAT
* *
727659 ACGATATTGTATGAT
1 ATGATATTGTATTAT
727674 ATGATATTGGT-TTAT
1 ATGATATT-GTATTAT
727689 ATGATATAT-TATCATAT
1 ATGATAT-TGTAT--TAT
*
727706 CACATGAAATTGTATTAT
1 ---ATGATATTGTATTAT
*
727724 ATGATATTGTAATAT
1 ATGATATTGTATTAT
727739 AT
1 AT
727741 TTTATTGTGT
Statistics
Matches: 92, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 1 0.01
15 58 0.63
16 3 0.03
17 3 0.03
18 17 0.18
19 1 0.01
20 9 0.10
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (15 bp):
ATGATATTGTATTAT
Found at i:727754 original size:50 final size:50
Alignment explanation
Indices: 727604--727755 Score: 156
Period size: 50 Copynumber: 3.1 Consensus size: 50
727594 ATATAGAATT
*
727604 ATATCACATGAAATTGTATTATATGATATTGTAATATTATATAATATTGT-
1 ATATCACATGAAATTGTATTATATGATATTGTAATA-TATATTATATTGTC
* * * *
727654 ATCAT-AC--GATATTGTATGATATGATATTGGT-TTATATGA-TATATTATC
1 AT-ATCACATGAAATTGTATTATATGATATT-GTAATATAT-ATTATATTGTC
*
727702 ATATCACATGAAATTGTATTATATGATATTGTAATATATTTTAT-TGTGTC
1 ATATCACATGAAATTGTATTATATGATATTGTAATATATATTATAT-TGTC
727752 ATAT
1 ATAT
727756 GATGCAATAT
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
47 11 0.13
48 26 0.32
49 5 0.06
50 38 0.46
51 2 0.02
ACGTcount: A:0.36, C:0.05, G:0.12, T:0.47
Consensus pattern (50 bp):
ATATCACATGAAATTGTATTATATGATATTGTAATATATATTATATTGTC
Done.