Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold370
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: 1088289
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 123460 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:912154 original size:122 final size:122
Alignment explanation
Indices: 911918--912142 Score: 297
Period size: 122 Copynumber: 1.8 Consensus size: 122
911908 ACTATGGTAT
* * * * *
911918 ACAATCTATTGAAACAGACAGTTGTATTATGGTAGACAATCTATAGGAACAGACAGGTGTATTAC
1 ACAATCTATAGAAACAGACAGGTGTATTACGGTAGACAATCTACAGGAACAGACACGTGTATTAC
*
911983 GGTAGACAAACTATAGGAACAGACAGGTGTATTACGGTAGACAATCTATAGGAACAG
66 GGTAGACAAACTATAGGAAAAGACAGGTGTATTACGGTAGACAATCTATAGGAACAG
* * ** *
912040 ACAATCTATAGGAACAGACAGGTGTATTACGGTAGACAATCTCCAGGAACAGGTACGTGTGTTAC
1 ACAATCTATAGAAACAGACAGGTGTATTACGGTAGACAATCTACAGGAACAGACACGTGTATTAC
*** * **
912105 GGTATTTAATCTATAGGAAAAGGTAGGTGTATTACGGT
66 GGTAGACAAACTATAGGAAAAGACAGGTGTATTACGGT
912143 GTTCTGTCTA
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
122 86 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.25
Consensus pattern (122 bp):
ACAATCTATAGAAACAGACAGGTGTATTACGGTAGACAATCTACAGGAACAGACACGTGTATTAC
GGTAGACAAACTATAGGAAAAGACAGGTGTATTACGGTAGACAATCTATAGGAACAG
Found at i:912301 original size:75 final size:75
Alignment explanation
Indices: 912197--912436 Score: 229
Period size: 75 Copynumber: 3.1 Consensus size: 75
912187 AATATATCGG
* *
912197 ATAGGAACAGGTTAATGTAT-AACGGTGTACCGTCAATAAAAAAAGTACATACAGATGTATTATG
1 ATAGAAACAGGTTAATGTATCAA-GGTGTACCGTCAATAAAAAAAGTACATACAGATGTATTACG
912261 GTAGACAATCT
65 GTAGACAATCT
* **
912272 ATAGAAACAGG-TAGATGTATCAAGGTGTACCGTCGATAAAATACAATGTAGGTACAAGCAGGTG
1 ATAGAAACAGGTTA-ATGTATCAAGGTGTACCGTCAATAAAA-A-AA-GTACATAC-AG-A--TG
912336 TATTACGGTAGACAATCT
58 TATTACGGTAGACAATCT
* * * * * * * *
912354 ATAGGAACAGGTTAATGTA-CTACGGTGTTCTGTCTAT-AAAATAGTAACAGACAGGTGTATTAC
1 ATAGAAACAGGTTAATGTATC-AAGGTGTACCGTCAATAAAAAAAGT-ACATACAGATGTATTAC
912417 GGTAGA-AATCT
64 GGTAGACAATCT
912428 ATAGAAACA
1 ATAGAAACA
912437 AGTAGGCGTA
Statistics
Matches: 137, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
74 15 0.11
75 47 0.34
76 3 0.02
77 2 0.01
78 10 0.07
79 6 0.04
80 2 0.01
81 4 0.03
82 46 0.34
83 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (75 bp):
ATAGAAACAGGTTAATGTATCAAGGTGTACCGTCAATAAAAAAAGTACATACAGATGTATTACGG
TAGACAATCT
Found at i:912492 original size:44 final size:44
Alignment explanation
Indices: 912444--912573 Score: 113
Period size: 44 Copynumber: 3.2 Consensus size: 44
912434 ACAAGTAGGC
912444 GTATTACGGTGTACCGTGTATAAAATAGATATCTACAGACAGGT
1 GTATTACGGTGTACCGTGTATAAAATAGATATCTACAGACAGGT
** * **
912488 GTATTAC-G-G-ACAAT-T-T---ATAG-GA---ACAGGTAGGT
1 GTATTACGGTGTACCGTGTATAAAATAGATATCTACAGACAGGT
* *
912520 GTTTTATGGTGTACCGTGTATAAAATAGATATCTACAGACAGGT
1 GTATTACGGTGTACCGTGTATAAAATAGATATCTACAGACAGGT
912564 GTATTACGGT
1 GTATTACGGT
912574 AGACACAAGT
Statistics
Matches: 60, Mismatches: 14, Indels: 24
0.61 0.14 0.24
Matches are distributed among these distances:
32 13 0.22
33 1 0.02
34 1 0.02
35 4 0.07
36 5 0.08
37 1 0.02
39 1 0.02
40 5 0.08
41 4 0.07
42 1 0.02
43 1 0.02
44 23 0.38
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.32
Consensus pattern (44 bp):
GTATTACGGTGTACCGTGTATAAAATAGATATCTACAGACAGGT
Found at i:912535 original size:76 final size:78
Alignment explanation
Indices: 912242--912576 Score: 301
Period size: 76 Copynumber: 4.3 Consensus size: 78
912232 ATAAAAAAAG
* * * * ** * *
912242 TACATACAGATGTATTATGGTAGACAATCTATAGAAACAGGTAGATGTATCAAGGTGTACCGTCG
1 TACAGACAGGTGTATTACGGTAGA-AATCTATAGAAACAAGTAGGCGTATTACGGTGTACCGT-G
* **
912307 -ATAAAATACAATGTAGG
64 TATAAAATA-GA--TATC
* * ** * * *
912324 TACA-AGCAGGTGTATTACGGTAGACAATCTATAGGAACAGGTTA-ATGTACTACGGTGTTCTGT
1 TACAGA-CAGGTGTATTACGGTAGA-AATCTATAGAAACAAG-TAGGCGTATTACGGTGTACCGT
*
912387 CTATAAAATAG-TA--
63 GTATAAAATAGATATC
912400 -ACAGACAGGTGTATTACGGTAGAAATCTATAGAAACAAGTAGGCGTATTACGGTGTACCGTGTA
1 TACAGACAGGTGTATTACGGTAGAAATCTATAGAAACAAGTAGGCGTATTACGGTGTACCGTGTA
912464 TAAAATAGATATC
66 TAAAATAGATATC
* * * * * * *
912477 TACAGACAGGTGTATTACGG-A-CAATTTATAGGAACAGGTAGGTGTTTTATGGTGTACCGTGTA
1 TACAGACAGGTGTATTACGGTAGAAATCTATAGAAACAAGTAGGCGTATTACGGTGTACCGTGTA
912540 TAAAATAGATATC
66 TAAAATAGATATC
912553 TACAGACAGGTGTATTACGGTAGA
1 TACAGACAGGTGTATTACGGTAGA
912577 CACAAGTATT
Statistics
Matches: 216, Mismatches: 26, Indels: 26
0.81 0.10 0.10
Matches are distributed among these distances:
73 2 0.01
74 38 0.18
75 23 0.11
76 69 0.32
77 2 0.01
78 21 0.10
81 1 0.00
82 58 0.27
83 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (78 bp):
TACAGACAGGTGTATTACGGTAGAAATCTATAGAAACAAGTAGGCGTATTACGGTGTACCGTGTA
TAAAATAGATATC
Found at i:933206 original size:2 final size:2
Alignment explanation
Indices: 933199--933240 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
933189 TGTTAGCTCT
* *
933199 GA GA GA GA GA GA TA GA TA 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
933241 ACTATTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (2 bp):
GA
Found at i:936821 original size:11 final size:11
Alignment explanation
Indices: 936791--936831 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
936781 GTTTGATCTC
*
936791 AACGTATGTAA
1 AACGTATGTGA
936802 AAC--ATGTGA
1 AACGTATGTGA
936811 AACGTATGTGA
1 AACGTATGTGA
*
936822 AACATATGTG
1 AACGTATGTG
936832 TCAATTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 8 0.31
11 18 0.69
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (11 bp):
AACGTATGTGA
Found at i:939470 original size:40 final size:40
Alignment explanation
Indices: 939426--939642 Score: 133
Period size: 40 Copynumber: 5.4 Consensus size: 40
939416 AGGAACAGGT
*
939426 AGGTGTATTACGGTGTAGCGTCTATAAAATAGGTACAGAC
1 AGGTGTATTACGGTGTACCGTCTATAAAATAGGTACAGAC
* * *
939466 AGGTGTATAAC-GTGTACCGTTTATAAAATAGGTACA-AT
1 AGGTGTATTACGGTGTACCGTCTATAAAATAGGTACAGAC
** * * * * * *
939504 AGGTACAAT-CAGGTGTATTACG-GTAGACAATCTATAGGAACATG-T
1 AGGTGTATTAC-GGTGTA--CCGTCTATA-AA---ATAGGTACA-GAC
* * * *
939549 AGGTATAGTACGGTGTAGCGTCTATAAAATAGGTACAGGC
1 AGGTGTATTACGGTGTACCGTCTATAAAATAGGTACAGAC
* *
939589 AGGTGTATTACGGTGTACCATCTAT-AATTAAGGTACAGAC
1 AGGTGTATTACGGTGTACCGTCTATAAAAT-AGGTACAGAC
*
939629 ACGTGT-TTACGGTG
1 AGGTGTATTACGGTG
939643 GACAATTATA
Statistics
Matches: 137, Mismatches: 26, Indels: 29
0.71 0.14 0.15
Matches are distributed among these distances:
37 1 0.01
38 6 0.04
39 40 0.29
40 56 0.41
41 4 0.03
43 4 0.03
44 11 0.08
45 14 0.10
46 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (40 bp):
AGGTGTATTACGGTGTACCGTCTATAAAATAGGTACAGAC
Found at i:939492 original size:39 final size:40
Alignment explanation
Indices: 939426--939501 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
939416 AGGAACAGGT
* *
939426 AGGTGTATTACGGTGTAGCGTCTATAAAATAGGTACAGAC
1 AGGTGTATAACGGTGTACCGTCTATAAAATAGGTACAGAC
*
939466 AGGTGTATAAC-GTGTACCGTTTATAAAATAGGTACA
1 AGGTGTATAACGGTGTACCGTCTATAAAATAGGTACA
939502 ATAGGTACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 23 0.70
40 10 0.30
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (40 bp):
AGGTGTATAACGGTGTACCGTCTATAAAATAGGTACAGAC
Found at i:939520 original size:39 final size:39
Alignment explanation
Indices: 939437--939520 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 39
939427 GGTGTATTAC
* **
939437 GGTGTAGCGTCTATAAAATAGGTACAGACAGGTGTATAA
1 GGTGTACCGTCTATAAAATAGGTACAGACAGGTCAATAA
* * * *
939476 CGTGTACCGTTTATAAAATAGGTACA-ATAGGTACAATCA
1 GGTGTACCGTCTATAAAATAGGTACAGACAGGT-CAATAA
939515 GGTGTA
1 GGTGTA
939521 TTACGGTAGA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
38 5 0.14
39 31 0.86
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (39 bp):
GGTGTACCGTCTATAAAATAGGTACAGACAGGTCAATAA
Found at i:940457 original size:10 final size:10
Alignment explanation
Indices: 940442--940468 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
940432 AGTTGATGCT
940442 AACAAATGTA
1 AACAAATGTA
940452 AACAAATGTA
1 AACAAATGTA
940462 AACAAAT
1 AACAAAT
940469 ATCATATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.07, T:0.19
Consensus pattern (10 bp):
AACAAATGTA
Found at i:943907 original size:165 final size:165
Alignment explanation
Indices: 943635--943942 Score: 598
Period size: 165 Copynumber: 1.9 Consensus size: 165
943625 NNNNNNNNNN
* *
943635 TACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAA
1 TACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCCGGCTGATTAGTTTCTGAGAAGAA
943700 GATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
66 GATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
943765 TACCCCAGGGGTCATGATTTTCACAACTTGGAATC
131 TACCCCAGGGGTCATGATTTTCACAACTTGGAATC
943800 TACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCCGGCTGATTAGTTTCTGAGAAGAA
1 TACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCCGGCTGATTAGTTTCTGAGAAGAA
943865 GATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
66 GATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
943930 TACCCCAGGGGTC
131 TACCCCAGGGGTC
943943 NTACCAATTT
Statistics
Matches: 141, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 141 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.31
Consensus pattern (165 bp):
TACACTACCTGAGGATGCTTCCACACAAGTGTCAGCTTTCCCGGCTGATTAGTTTCTGAGAAGAA
GATTTTTAAAGATTTACTCTATATATTCCTATGTAAAACTTCGACCCCCCATTGTGGCCCCACCC
TACCCCAGGGGTCATGATTTTCACAACTTGGAATC
Found at i:945872 original size:2 final size:2
Alignment explanation
Indices: 945867--945927 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
945857 CTGCCCCCCC
945867 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
945909 CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT C
945928 ATTTTCCCTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:949650 original size:2 final size:2
Alignment explanation
Indices: 949643--949673 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
949633 AGGGTTATAA
949643 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 T
949674 GTGTGTGTGT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:952889 original size:2 final size:2
Alignment explanation
Indices: 952882--952915 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
952872 ATTTCCATCC
952882 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
952916 TGAGTGAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:963888 original size:2 final size:2
Alignment explanation
Indices: 963881--963956 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
963871 AAGCATCTCG
963881 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
963923 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
963957 AAAGTATGNT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:964842 original size:16 final size:16
Alignment explanation
Indices: 964821--964866 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
964811 GGGATAAGAG
964821 ATTGTCGATCCCGAAC
1 ATTGTCGATCCCGAAC
*
964837 ATTGTCTAT-CCGAAAC
1 ATTGTCGATCCCG-AAC
964853 ATTGTCGATCCCGA
1 ATTGTCGATCCCGA
964867 CTGCGTAGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (16 bp):
ATTGTCGATCCCGAAC
Found at i:967534 original size:180 final size:179
Alignment explanation
Indices: 967232--967580 Score: 689
Period size: 180 Copynumber: 1.9 Consensus size: 179
967222 GTTCGTTTTN
967232 CTATGTTTCTTATTATAAAGTAAGTCATATGCAAACAAAAATATCAACTATTCTACTAAATATTT
1 CTATGTTTCTTATTATAAAGTAAGTCATATGCAAACAAAAATATCAACTATTCTACTAAATATTT
967297 AAGAAATGCACTCAATGTTCACCCAAGTTATACGAGTATGACCTGGGTTGGAGCAATTTACGCTT
66 AAGAAATGCACTCAATGTTCACCCAAGTTATACGAGTATGACCTGGGTTGGAGCAATTTACGCTT
967362 TATAATCCGCGAAGCGTAAATTGCTCCAACCCAGGTCATNGTTCCGACGC
131 TATAATCCGCGAAGCGTAAATTGCTCCAACCCAGGTCAT-GTTCCGACGC
967412 CTATGTTTCTTATTATAAAGTAAGTCATATGCAAACAAAAATATCAACTATTCTACTAAATATTT
1 CTATGTTTCTTATTATAAAGTAAGTCATATGCAAACAAAAATATCAACTATTCTACTAAATATTT
967477 AAGAAATGCACTCAATGTTCACCCAAGTTATACGAGTATGACCTGGGTTGGAGCAATTTACGCTT
66 AAGAAATGCACTCAATGTTCACCCAAGTTATACGAGTATGACCTGGGTTGGAGCAATTTACGCTT
967542 TATAATCCGCGAAGCGTAAATTGCTCCAACCCAGGTCAT
131 TATAATCCGCGAAGCGTAAATTGCTCCAACCCAGGTCAT
967581 ACAAGTATAA
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
180 169 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (179 bp):
CTATGTTTCTTATTATAAAGTAAGTCATATGCAAACAAAAATATCAACTATTCTACTAAATATTT
AAGAAATGCACTCAATGTTCACCCAAGTTATACGAGTATGACCTGGGTTGGAGCAATTTACGCTT
TATAATCCGCGAAGCGTAAATTGCTCCAACCCAGGTCATGTTCCGACGC
Found at i:968360 original size:5 final size:5
Alignment explanation
Indices: 968350--968377 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
968340 ACGGTTCTAT
968350 ATTCA ATTCA ATTCA ATTCA ATTCA ATT
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATT
968378 TCTTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (5 bp):
ATTCA
Found at i:978779 original size:15 final size:15
Alignment explanation
Indices: 978759--978789 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
978749 ATTATGATAA
*
978759 TTTTGATTTCATTTG
1 TTTTGATGTCATTTG
978774 TTTTGATGTCATTTG
1 TTTTGATGTCATTTG
978789 T
1 T
978790 CTTTTGCTTG
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:0.13, C:0.06, G:0.16, T:0.65
Consensus pattern (15 bp):
TTTTGATGTCATTTG
Found at i:982151 original size:50 final size:50
Alignment explanation
Indices: 982084--982235 Score: 288
Period size: 50 Copynumber: 3.0 Consensus size: 50
982074 ATTATGATTA
982084 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTTTCTTATGTTT
1 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTTTCTTATGTTT
982134 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTTTCTTATGTTT
1 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTTTCTTATGTTT
982184 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTG-TTTTCTTTATGTTT
1 TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTTTC-TTATGTTT
982234 TT
1 TT
982236 TATTATTCTT
Statistics
Matches: 101, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
49 5 0.05
50 96 0.95
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.51
Consensus pattern (50 bp):
TTAGGTCTTTCCACCTTTCAGGTGAAAGACCTTTTGTTTTTCTTATGTTT
Found at i:982757 original size:11 final size:11
Alignment explanation
Indices: 982738--982778 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
982728 TGGAAAATTT
*
982738 GGGTCTACTCG
1 GGGTTTACTCG
**
982749 GGGTTTACTTT
1 GGGTTTACTCG
982760 GGGTTTACTCG
1 GGGTTTACTCG
982771 GGGTTTAC
1 GGGTTTAC
982779 CTGAATATTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.10, C:0.17, G:0.34, T:0.39
Consensus pattern (11 bp):
GGGTTTACTCG
Found at i:982762 original size:22 final size:22
Alignment explanation
Indices: 982735--982778 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
982725 TTTTGGAAAA
982735 TTTGGGTCTACTCGGGGTTTAC
1 TTTGGGTCTACTCGGGGTTTAC
*
982757 TTTGGGTTTACTCGGGGTTTAC
1 TTTGGGTCTACTCGGGGTTTAC
982779 CTGAATATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.16, G:0.32, T:0.43
Consensus pattern (22 bp):
TTTGGGTCTACTCGGGGTTTAC
Found at i:982972 original size:33 final size:33
Alignment explanation
Indices: 982935--983004 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
982925 TGGGCTTACT
* *
982935 CTCTGTGTCCACTCTGGGTTTACTTTG-GATCCA
1 CTCTGGGTCCACTCTGGGTTTACTCTGCG-TCCA
** *
982968 CTCTGGGTTTACTTTGGGTTTACTCTGCGTCCA
1 CTCTGGGTCCACTCTGGGTTTACTCTGCGTCCA
983001 CTCT
1 CTCT
983005 AGTAAACCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 30 0.97
34 1 0.03
ACGTcount: A:0.10, C:0.27, G:0.21, T:0.41
Consensus pattern (33 bp):
CTCTGGGTCCACTCTGGGTTTACTCTGCGTCCA
Found at i:982987 original size:11 final size:11
Alignment explanation
Indices: 982949--982991 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
982939 GTGTCCACTC
982949 TGGGTTTACTT
1 TGGGTTTACTT
* ** *
982960 TGGATCCACTC
1 TGGGTTTACTT
982971 TGGGTTTACTT
1 TGGGTTTACTT
982982 TGGGTTTACT
1 TGGGTTTACT
982992 CTGCGTCCAC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (11 bp):
TGGGTTTACTT
Found at i:982994 original size:22 final size:22
Alignment explanation
Indices: 982942--982984 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
982932 ACTCTCTGTG
982942 TCCACTCTGGGTTTACTTTGGA
1 TCCACTCTGGGTTTACTTTGGA
982964 TCCACTCTGGGTTTACTTTGG
1 TCCACTCTGGGTTTACTTTGG
982985 GTTTACTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.42
Consensus pattern (22 bp):
TCCACTCTGGGTTTACTTTGGA
Found at i:986072 original size:164 final size:159
Alignment explanation
Indices: 985733--986194 Score: 454
Period size: 168 Copynumber: 2.8 Consensus size: 159
985723 CGTTTGCCGG
* * * * *
985733 GGCTATAACAAAGTCCTATTTAACAGGAAGTTGACGTCCGATTGGTA-ATAAAATATATACCAGG
1 GGCTAAAACAAAGTCATATTTAACAGGAAGTTGACGTCCTATTGGTACA-AAAATATATCCCA-A
* *
985797 ATATGACATGCGT-AA-AAAAATAGTGTGTTAAAATGTCAAGCATCTGCGATAAATAGTTGCTGA
64 ATATGGCATGCCTAAACAAAAATAGTGTGTTAAAATGTCAAGCATCTGCGATAAATAGTTGC-GA
*
985860 GAAATCTTTAACGAAAATGGTTTAATAATTCT
128 GAAATCTTTAACGAAAATGGTTTAAAAATTCT
* **
985892 GGCTAGAAATAAACAAAGTCATATTTAACAGGAAGTTGACATTTTATTGGTACAAAAATATATCC
1 GGCT----A-AAACAAAGTCATATTTAACAGGAAGTTGACGTCCTATTGGTACAAAAATATATCC
* *
985957 CACAATATGGCATGCCTAAACAAATAGACTAAGTGTTTTAAAATTTCAAGCATCTGCTG-TAAAT
61 CA-AATATGGCATGCCTAAACAAA-A-A-T-AGTGTGTTAAAATGTCAAGCATCTGC-GATAAAT
* *
986021 AGTTG-GAGAAATCTTTAACGAAAATTTGTTTAAAAATTTT
120 AGTTGCGAGAAATCTTTAACGAAAA-TGGTTTAAAAATTCT
* * * *
986061 GGCTAAAACAAAAAATCTGTCATTTAACAAGAAGTTGATGTCCTATTGGTACAAAAATATATCCC
1 GGCTAAAAC--AAAGTC-AT-ATTTAACAGGAAGTTGACGTCCTATTGGTACAAAAATATATCCC
* * * *
986126 AAGATATGGCATGCCTAAATC-AAAA-AGTTTGTTAGAACT-TCAAGCATATGCGATAAACAGTT
62 AA-ATATGGCATGCCTAAA-CAAAAATAGTGTGTTA-AAATGTCAAGCATCTGCGATAAATAGTT
986188 GCTGAGA
124 GC-GAGA
986195 TAAATGCGAC
Statistics
Matches: 251, Mismatches: 28, Indels: 42
0.78 0.09 0.13
Matches are distributed among these distances:
159 4 0.02
162 1 0.00
163 28 0.11
164 66 0.26
165 8 0.03
166 9 0.04
167 4 0.02
168 78 0.31
169 18 0.07
170 34 0.14
171 1 0.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (159 bp):
GGCTAAAACAAAGTCATATTTAACAGGAAGTTGACGTCCTATTGGTACAAAAATATATCCCAAAT
ATGGCATGCCTAAACAAAAATAGTGTGTTAAAATGTCAAGCATCTGCGATAAATAGTTGCGAGAA
ATCTTTAACGAAAATGGTTTAAAAATTCT
Found at i:986097 original size:168 final size:170
Alignment explanation
Indices: 985739--986149 Score: 474
Period size: 168 Copynumber: 2.5 Consensus size: 170
985729 CCGGGGCTAT
* * * * * * *
985739 AACAAAGTCCTATTTAACAGGAAGTTGACGTCCGATTGGTA-ATAAAATATATACCAGGATATGA
1 AACAAAGTCATATTTAACAAGAAGTTGACATCCTATTGGTACA-AAAATATATCCCAAGATATGG
*
985803 CATGCGT-AA--AAA-A-A-T-AGTGTGTTAAAATGTCAAGCATCTGCGATAAATAGTTGCTGAG
65 CATGCCTAAATCAAATAGACTAAGTGTGTTAAAATGTCAAGCATCTGCGATAAATAGTTGC-GAG
* *
985861 AAATCTTTAACGAAAATGGTTTAATAATTCTGGCTAGAAATA
129 AAATCTTTAACGAAAATGGTTTAAAAATTCTGGCTAGAAACA
* **
985903 AACAAAGTCATATTTAACAGGAAGTTGACATTTTATTGGTACAAAAATATATCCCACA-ATATGG
1 AACAAAGTCATATTTAACAAGAAGTTGACATCCTATTGGTACAAAAATATATCCCA-AGATATGG
* *
985967 CATGCCTAAA-CAAATAGACTAAGTGTTTTAAAATTTCAAGCATCTGCTG-TAAATAGTTG-GAG
65 CATGCCTAAATCAAATAGACTAAGTGTGTTAAAATGTCAAGCATCTGC-GATAAATAGTTGCGAG
* *
986029 AAATCTTTAACGAAAATTTGTTTAAAAATTTTGGCTA-AAACA
129 AAATCTTTAACGAAAA-TGGTTTAAAAATTCTGGCTAGAAACA
* **
986071 AA-AAA-TCTGTCATTTAACAAGAAGTTGATGTCCTATTGGTACAAAAATATATCCCAAGATATG
1 AACAAAGTC-AT-ATTTAACAAGAAGTTGACATCCTATTGGTACAAAAATATATCCCAAGATATG
986134 GCATGCCTAAATCAAA
64 GCATGCCTAAATCAAA
986150 AAGTTTGTTA
Statistics
Matches: 212, Mismatches: 21, Indels: 23
0.83 0.08 0.09
Matches are distributed among these distances:
164 59 0.28
165 3 0.01
166 5 0.02
167 6 0.03
168 82 0.39
169 22 0.10
170 34 0.16
171 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (170 bp):
AACAAAGTCATATTTAACAAGAAGTTGACATCCTATTGGTACAAAAATATATCCCAAGATATGGC
ATGCCTAAATCAAATAGACTAAGTGTGTTAAAATGTCAAGCATCTGCGATAAATAGTTGCGAGAA
ATCTTTAACGAAAATGGTTTAAAAATTCTGGCTAGAAACA
Found at i:987352 original size:10 final size:10
Alignment explanation
Indices: 987337--987406 Score: 113
Period size: 10 Copynumber: 6.8 Consensus size: 10
987327 TGCGTCTTTT
987337 AACCCCAAGG
1 AACCCCAAGG
987347 AACCCCAAGG
1 AACCCCAAGG
987357 AAACCCCAAGG
1 -AACCCCAAGG
987368 AACCCCAAGG
1 AACCCCAAGG
*
987378 AACCTCAAGG
1 AACCCCAAGG
987388 ATACCCCAAGG
1 A-ACCCCAAGG
987399 AACCCCAA
1 AACCCCAA
987407 TGACAAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
10 37 0.66
11 19 0.34
ACGTcount: A:0.41, C:0.39, G:0.17, T:0.03
Consensus pattern (10 bp):
AACCCCAAGG
Found at i:987363 original size:21 final size:20
Alignment explanation
Indices: 987337--987406 Score: 113
Period size: 21 Copynumber: 3.4 Consensus size: 20
987327 TGCGTCTTTT
987337 AACCCCAAGGAACCCCAAGG
1 AACCCCAAGGAACCCCAAGG
987357 AAACCCCAAGGAACCCCAAGG
1 -AACCCCAAGGAACCCCAAGG
*
987378 AACCTCAAGGATACCCCAAGG
1 AACCCCAAGGA-ACCCCAAGG
987399 AACCCCAA
1 AACCCCAA
987407 TGACAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.22
21 36 0.78
ACGTcount: A:0.41, C:0.39, G:0.17, T:0.03
Consensus pattern (20 bp):
AACCCCAAGGAACCCCAAGG
Found at i:987375 original size:31 final size:31
Alignment explanation
Indices: 987337--987406 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
987327 TGCGTCTTTT
987337 AACCCCAAGGAACCCCAAGGAAACCCCAAGG
1 AACCCCAAGGAACCCCAAGGAAACCCCAAGG
* *
987368 AACCCCAAGGAACCTCAAGGATACCCCAAGG
1 AACCCCAAGGAACCCCAAGGAAACCCCAAGG
987399 AACCCCAA
1 AACCCCAA
987407 TGACAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.41, C:0.39, G:0.17, T:0.03
Consensus pattern (31 bp):
AACCCCAAGGAACCCCAAGGAAACCCCAAGG
Found at i:987693 original size:10 final size:11
Alignment explanation
Indices: 987666--987700 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
987656 CACCTCGTAG
987666 TACCCCAAGGA
1 TACCCCAAGGA
987677 TACCCCAAGGA
1 TACCCCAAGGA
*
987688 -ACCCCAAGTA
1 TACCCCAAGGA
987698 TAC
1 TAC
987701 TCATTAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.37, C:0.37, G:0.14, T:0.11
Consensus pattern (11 bp):
TACCCCAAGGA
Found at i:989157 original size:10 final size:10
Alignment explanation
Indices: 989134--989225 Score: 148
Period size: 10 Copynumber: 8.8 Consensus size: 10
989124 ATTTCTGTCA
989134 TTGGGGTATCC
1 TTGGGGT-TCC
989145 TTGGGGTTCC
1 TTGGGGTTCC
989155 TTGGGGTTTCC
1 TTGGGG-TTCC
989166 TTGGGGTTTCC
1 TTGGGG-TTCC
989177 TTGGGGTTCC
1 TTGGGGTTCC
989187 TTGGGGTTTCC
1 TTGGGG-TTCC
989198 TTGGGGTTCC
1 TTGGGGTTCC
989208 TTGGGGTTCC
1 TTGGGGTTCC
989218 TTGGGGTT
1 TTGGGGTT
989226 AAAAGACGTG
Statistics
Matches: 79, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
10 41 0.52
11 38 0.48
ACGTcount: A:0.01, C:0.17, G:0.39, T:0.42
Consensus pattern (10 bp):
TTGGGGTTCC
Found at i:989160 original size:21 final size:21
Alignment explanation
Indices: 989134--989225 Score: 152
Period size: 21 Copynumber: 4.4 Consensus size: 21
989124 ATTTCTGTCA
989134 TTGGGGTATCCTTGGGG-TTCC
1 TTGGGGT-TCCTTGGGGTTTCC
989155 TTGGGGTTTCCTTGGGGTTTCC
1 TTGGGG-TTCCTTGGGGTTTCC
989177 TTGGGGTTCCTTGGGGTTTCC
1 TTGGGGTTCCTTGGGGTTTCC
989198 TTGGGGTTCCTTGGGG-TTCC
1 TTGGGGTTCCTTGGGGTTTCC
989218 TTGGGGTT
1 TTGGGGTT
989226 AAAAGACGTG
Statistics
Matches: 69, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
20 12 0.17
21 46 0.67
22 11 0.16
ACGTcount: A:0.01, C:0.17, G:0.39, T:0.42
Consensus pattern (21 bp):
TTGGGGTTCCTTGGGGTTTCC
Found at i:990110 original size:20 final size:20
Alignment explanation
Indices: 990079--990134 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
990069 AAAATCATAT
*
990079 TGTTACACTATCATATAACA
1 TGTTACAATATCATATAACA
* ***
990099 TTTTACAATATCATATCTTA
1 TGTTACAATATCATATAACA
990119 TGTTACAATATCATAT
1 TGTTACAATATCATAT
990135 CTGATAATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (20 bp):
TGTTACAATATCATATAACA
Found at i:990734 original size:5 final size:5
Alignment explanation
Indices: 990715--990762 Score: 62
Period size: 5 Copynumber: 9.4 Consensus size: 5
990705 AAAAAGATCN
*
990715 CGTTT CGTTT -GATTT CATTT CGTTT CGTTT CGTTT CGATTT CGTTT CG
1 CGTTT CGTTT CG-TTT CGTTT CGTTT CGTTT CGTTT CG-TTT CGTTT CG
990763 CACTTTACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 1 0.03
5 32 0.84
6 5 0.13
ACGTcount: A:0.06, C:0.19, G:0.19, T:0.56
Consensus pattern (5 bp):
CGTTT
Found at i:991521 original size:11 final size:11
Alignment explanation
Indices: 991501--991556 Score: 71
Period size: 11 Copynumber: 5.3 Consensus size: 11
991491 TAAGTTAATG
*
991501 ATCGTCCGTGT
1 ATCGTGCGTGT
991512 ATCGTGCGTG-
1 ATCGTGCGTGT
*
991522 ATCGTTCGTGT
1 ATCGTGCGTGT
991533 ATCGTGCGTG-
1 ATCGTGCGTGT
*
991543 ATCGTTCGTGT
1 ATCGTGCGTGT
991554 ATC
1 ATC
991557 AGAATCGTGC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 18 0.46
11 21 0.54
ACGTcount: A:0.11, C:0.21, G:0.30, T:0.38
Consensus pattern (11 bp):
ATCGTGCGTGT
Found at i:991525 original size:21 final size:21
Alignment explanation
Indices: 991499--991556 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
991489 AGTAAGTTAA
*
991499 TGATCGTCCGTGTATCGTGCG
1 TGATCGTTCGTGTATCGTGCG
991520 TGATCGTTCGTGTATCGTGCG
1 TGATCGTTCGTGTATCGTGCG
991541 TGATCGTTCGTGTATC
1 TGATCGTTCGTGTATC
991557 AGAATCGTGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.10, C:0.21, G:0.31, T:0.38
Consensus pattern (21 bp):
TGATCGTTCGTGTATCGTGCG
Found at i:991531 original size:10 final size:10
Alignment explanation
Indices: 991499--991552 Score: 63
Period size: 10 Copynumber: 5.2 Consensus size: 10
991489 AGTAAGTTAA
*
991499 TGATCGTCCG
1 TGATCGTGCG
991509 TGTATCGTGCG
1 TG-ATCGTGCG
*
991520 TGATCGTTCG
1 TGATCGTGCG
991530 TGTATCGTGCG
1 TG-ATCGTGCG
*
991541 TGATCGTTCG
1 TGATCGTGCG
991551 TG
1 TG
991553 TATCAGAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
10 20 0.53
11 18 0.47
ACGTcount: A:0.09, C:0.20, G:0.33, T:0.37
Consensus pattern (10 bp):
TGATCGTGCG
Found at i:993040 original size:21 final size:22
Alignment explanation
Indices: 993016--993077 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
993006 TGCATGTTAG
*
993016 CATAACTATCTTGCATGTCG-A
1 CATAATTATCTTGCATGTCGAA
** *
993037 CATAATTAAATTGCATGTTGAA
1 CATAATTATCTTGCATGTCGAA
*
993059 CATAATTTATCTAGCATGT
1 CATAA-TTATCTTGCATGT
993078 TAGGGGCAGA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
21 16 0.50
22 6 0.19
23 10 0.31
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (22 bp):
CATAATTATCTTGCATGTCGAA
Found at i:993913 original size:33 final size:33
Alignment explanation
Indices: 993874--993944 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
993864 TACAAGAGGG
* *
993874 TGTTTAATTCTAGTGCAATTACAAGAATTTATA
1 TGTTTAATTCTAGTCCAATTACAAGAATATATA
993907 TGTTTAATTCTAGTCCAATTACAAGAATATATA
1 TGTTTAATTCTAGTCCAATTACAAGAATATATA
993940 TGTTT
1 TGTTT
993945 GTTTTATCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (33 bp):
TGTTTAATTCTAGTCCAATTACAAGAATATATA
Found at i:994213 original size:2 final size:2
Alignment explanation
Indices: 994206--994247 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
994196 TGTTTCTAAA
994206 CT CT CT CT CT CT CT CT CT CT CT CT CNT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT C
994248 GTCCGCAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1000176 original size:2 final size:2
Alignment explanation
Indices: 1000169--1000214 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1000159 ATTTCTATTA
1000169 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
1000211 TC TC
1 TC TC
1000215 NNNNNNNNNN
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1000267 original size:2 final size:2
Alignment explanation
Indices: 1000260--1000298 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1000250 NNNNNNNNNN
1000260 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1000299 GGGAAGATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1000592 original size:2 final size:2
Alignment explanation
Indices: 1000585--1000645 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1000575 ACTTTTTAAT
1000585 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
1000627 AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
1000646 AATAATTCTC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1004420 original size:2 final size:2
Alignment explanation
Indices: 1004413--1004485 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
1004403 GTTTTATTTT
* *
1004413 TC TC TC TC TC CC CC 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
1004455 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 T
1004486 GGGATGTTTA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:1004865 original size:8 final size:8
Alignment explanation
Indices: 1004826--1004867 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1004816 GATCACATTT
1004826 TGTCCGTC
1 TGTCCGTC
*
1004834 -GTCCGCC
1 TGTCCGTC
1004841 TGTCCGTC
1 TGTCCGTC
*
1004849 CGTCCGTC
1 TGTCCGTC
1004857 TGTCCGTC
1 TGTCCGTC
1004865 TGT
1 TGT
1004868 AAACTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.00, C:0.40, G:0.26, T:0.33
Consensus pattern (8 bp):
TGTCCGTC
Found at i:1005477 original size:17 final size:17
Alignment explanation
Indices: 1005455--1005490 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1005445 TATTCCATAA
1005455 TTCTAAAACGAGGTTCT
1 TTCTAAAACGAGGTTCT
1005472 TTCTAAAACGAGGTTCT
1 TTCTAAAACGAGGTTCT
1005489 TT
1 TT
1005491 GTTTAAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (17 bp):
TTCTAAAACGAGGTTCT
Found at i:1009912 original size:123 final size:122
Alignment explanation
Indices: 1009671--1009914 Score: 346
Period size: 123 Copynumber: 2.0 Consensus size: 122
1009661 CAGCTGACTG
* *
1009671 TTTACTTGCGCAAAAAGGACGCACCAACGGGTACCGTACATTAACAACATACTAAAATACAATTC
1 TTTACTTGCGCAAAAAAGACGCACCAACGGGTACCATACATTAACAACATACTAAAATACAATTC
* * * * * * *
1009736 TGTATTGGCGATGCGGTATGATCTTTGCGTAATGGTCGATTAATGCGATGTGTTTTT
66 TATATTGCCGATACAGTATGATCTTTGCGTAATGGTCAATTAATGCAACGTGTTTTT
* *
1009793 TTTACTTGCGCAAAATAAGACGCATCAACGGGTACCATACATTAGA-AACGTACTAAAATACAAT
1 TTTACTTGCGCAAAA-AAGACGCACCAACGGGTACCATACATTA-ACAACATACTAAAATACAAT
* *
1009857 TCTATTTTGCCGATACAGTATGATCTTTGCTTAATGGTCAATTAATGCAACGTGTTTT
64 TCTATATTGCCGATACAGTATGATCTTTGCGTAATGGTCAATTAATGCAACGTGTTTT
1009915 GTTAATTGCT
Statistics
Matches: 107, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
122 15 0.14
123 91 0.85
124 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (122 bp):
TTTACTTGCGCAAAAAAGACGCACCAACGGGTACCATACATTAACAACATACTAAAATACAATTC
TATATTGCCGATACAGTATGATCTTTGCGTAATGGTCAATTAATGCAACGTGTTTTT
Found at i:1017206 original size:2 final size:2
Alignment explanation
Indices: 1017199--1017239 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1017189 TTGTCGATAT
1017199 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
1017240 NNNNNNNNNN
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:1026336 original size:38 final size:38
Alignment explanation
Indices: 1026282--1026762 Score: 671
Period size: 38 Copynumber: 12.7 Consensus size: 38
1026272 CCCCCCCCCN
* * * * *
1026282 AGTAATGTAGTAGTGATTTCCCTTGGCTATCAGCTGTT
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* *
1026320 AGTAATGGAAGG-GTGATTTCCATTGGCTCTCAGTTGTA
1 AGTAAT-GAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* * *
1026358 AGTTATAAAGGAGTGATTTCCCTTTGCTGTCAGTTGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* *
1026396 AATAATGAAAGAGTGATTTCCCTTGGCTGTCAG-TGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* * **
1026433 AGTAATGGAGGAGTGATTTCCCATGGCTGTCAGTTACA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* * *
1026471 AGTAATTAAAGAGTTATTT-CCTTGGCTGTCAGTTGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* *
1026508 AGTAATGAAAGAGTGATTTCCCTTGGCTCTCAGTTGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
*
1026546 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGATGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* * *
1026584 AGCAATGAAGGAGTGATTTCCTTTGGCTGTCAGCTGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
*
1026622 AGTAATGAAGGAGTGATTTTCCTTGGCTGTCAGTTGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
1026660 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
* *
1026698 AATAATGAAGGAGTGATTTCCCTTTGCTGTCAGTTGTA
1 AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
*
1026736 AGTAATGAAGGAGTGATGTCCCTTGGC
1 AGTAATGAAGGAGTGATTTCCCTTGGC
1026763 GGTTAGGAGT
Statistics
Matches: 391, Mismatches: 48, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
37 69 0.18
38 319 0.82
39 3 0.01
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.35
Consensus pattern (38 bp):
AGTAATGAAGGAGTGATTTCCCTTGGCTGTCAGTTGTA
Found at i:1028062 original size:50 final size:50
Alignment explanation
Indices: 1027983--1028229 Score: 377
Period size: 50 Copynumber: 4.9 Consensus size: 50
1027973 CAAGCAGGTT
* * *
1027983 TGTGCTCTATATCTTGCCAGTGCTGTAAAACTTGTATATACGTGGTGGTA
1 TGTGCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACATGGTGGAA
* * *
1028033 TGTTCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACGTGGTGGTA
1 TGTGCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACATGGTGGAA
* **
1028083 TGTTCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACACAGTGGAA
1 TGTGCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACATGGTGGAA
**
1028133 TGTGCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACACAGTGGAA
1 TGTGCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACATGGTGGAA
* *
1028183 TGTGCTCTATATCTGGCCAGTGCTGTAAAACTGGTATTTACATGGTG
1 TGTGCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACATGGTG
1028230 AATACAATAC
Statistics
Matches: 186, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 186 1.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (50 bp):
TGTGCTCTATATCTGGCCAGTGCTGTAAAACTTGTATATACATGGTGGAA
Found at i:1028671 original size:2 final size:2
Alignment explanation
Indices: 1028664--1028710 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1028654 CACAGGTAAA
1028664 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1028706 TG TG T
1 TG TG T
1028711 TAAGTTTGAG
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1028815 original size:68 final size:67
Alignment explanation
Indices: 1028726--1028867 Score: 189
Period size: 68 Copynumber: 2.1 Consensus size: 67
1028716 TTGAGTTCAG
* * *
1028726 GTAAATGTGTATGAAGTTTGAGGATCC-ACATAAGCAAATGTGTA-TGTTGTTTGGGGACCCATA
1 GTAAATGTGTATGAAGTTTGAGGA-CCTACATAAGCAAATGTGTAGTGATGTTTGAGGACCCACA
1028789 TAA
65 TAA
* *
1028792 GTAAATGTGTATATGACGTTTGAGGACCTACATAAGGAAATGTGTAGGTGATGTTTGAGGACCCA
1 GTAAATGTG--TATGAAGTTTGAGGACCTACATAAGCAAATGTGTA-GTGATGTTTGAGGACCCA
1028857 CATAA
63 CATAA
1028862 GTAAAT
1 GTAAAT
1028868 ATGTGTTTAG
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
66 9 0.14
67 2 0.03
68 30 0.45
70 25 0.38
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (67 bp):
GTAAATGTGTATGAAGTTTGAGGACCTACATAAGCAAATGTGTAGTGATGTTTGAGGACCCACAT
AA
Found at i:1028827 original size:35 final size:33
Alignment explanation
Indices: 1028726--1028867 Score: 167
Period size: 35 Copynumber: 4.2 Consensus size: 33
1028716 TTGAGTTCAG
* *
1028726 GTAAATGTGTATGAAGTTTGAGGATCCACATAA
1 GTAAATGTGTATGATGTTTGAGGACCCACATAA
* * * *
1028759 GCAAATGTGTATGTTGTTTGGGGACCCATATAA
1 GTAAATGTGTATGATGTTTGAGGACCCACATAA
* *
1028792 GTAAATGTGTATATGACGTTTGAGGACCTACATAA
1 GTAAATGTG--TATGATGTTTGAGGACCCACATAA
*
1028827 GGAAATGTGTAGGTGATGTTTGAGGACCCACATAA
1 GTAAATGTGTA--TGATGTTTGAGGACCCACATAA
1028862 GTAAAT
1 GTAAAT
1028868 ATGTGTTTAG
Statistics
Matches: 89, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
33 37 0.42
35 52 0.58
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (33 bp):
GTAAATGTGTATGATGTTTGAGGACCCACATAA
Found at i:1028883 original size:35 final size:33
Alignment explanation
Indices: 1028728--1028885 Score: 133
Period size: 35 Copynumber: 4.6 Consensus size: 33
1028718 GAGTTCAGGT
* *
1028728 AAATGTGTATGAAGTTTGAGGATCCACATAAG-C
1 AAATGTGTATG-AGTTTGAGGACCCACATAAGTA
* * *
1028761 AAATGTGTATGTTGTTTGGGGACCCATATAAGT-
1 AAATGTGTATG-AGTTTGAGGACCCACATAAGTA
* *
1028794 AAATGTGTATATGACGTTTGAGGACCTACATAAG-G
1 AAATGTG--TATGA-GTTTGAGGACCCACATAAGTA
1028829 AAATGTGTAGGTGATGTTTGAGGACCCACATAAGTA
1 AAATGTGTA--TGA-GTTTGAGGACCCACATAAGTA
*
1028865 AATATGTGTTTAGAGTTTGAG
1 AA-ATGTGTAT-GAGTTTGAG
1028886 TTCTGTACTT
Statistics
Matches: 102, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
33 36 0.35
35 56 0.55
36 4 0.04
37 6 0.06
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (33 bp):
AAATGTGTATGAGTTTGAGGACCCACATAAGTA
Found at i:1028883 original size:70 final size:67
Alignment explanation
Indices: 1028726--1028885 Score: 184
Period size: 68 Copynumber: 2.3 Consensus size: 67
1028716 TTGAGTTCAG
* * *
1028726 GTAAATGTG--TATGAAGTTTGAGGATCCACATAAGCAAATGTGTATGTTGTTTGGGGACCCATA
1 GTAAATGTGTATATG-AGTTTGAGGATCCACATAAGCAAATGTGTATGATGTTTGAGGACCCACA
1028789 TAA
65 TAA
*
1028792 GTAAATGTGTATATGACGTTTGAGGA-CCTACATAAGGAAATGTGTAGGTGATGTTTGAGGACCC
1 GTAAATGTGTATATGA-GTTTGAGGATCC-ACATAAGCAAATGTGTA--TGATGTTTGAGGACCC
1028856 ACATAA
62 ACATAA
*
1028862 GTAAATATGTGTTTA-GAGTTTGAG
1 GT-AA-ATGTGTATATGAGTTTGAG
1028886 TTCTGTACTT
Statistics
Matches: 81, Mismatches: 5, Indels: 12
0.83 0.05 0.12
Matches are distributed among these distances:
66 9 0.11
67 3 0.04
68 29 0.36
70 28 0.35
71 4 0.05
72 8 0.10
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (67 bp):
GTAAATGTGTATATGAGTTTGAGGATCCACATAAGCAAATGTGTATGATGTTTGAGGACCCACAT
AA
Found at i:1029008 original size:20 final size:20
Alignment explanation
Indices: 1028983--1029209 Score: 274
Period size: 20 Copynumber: 11.2 Consensus size: 20
1028973 AGACAGTTAT
*
1028983 TGTTCCACCCACAGGTTAAC
1 TGTTCCACCCACAGGTAAAC
1029003 TGTTCCACCCACAGGTAAAC
1 TGTTCCACCCACAGGTAAAC
* *
1029023 TGTTCCACTCACAGGTTAAC
1 TGTTCCACCCACAGGTAAAC
* * *
1029043 TGTTTCACTCACAGGTTAAC
1 TGTTCCACCCACAGGTAAAC
*
1029063 TGTTCCACTCACAGGTAAAC
1 TGTTCCACCCACAGGTAAAC
* *
1029083 TGTTCTACCCACAGGTTAAC
1 TGTTCCACCCACAGGTAAAC
**
1029103 TGCTCTATACCCACAGGTAAAC
1 TG-T-TCCACCCACAGGTAAAC
* * *
1029125 TGTTCAATCCGCAGGTAAAC
1 TGTTCCACCCACAGGTAAAC
* * *
1029145 TGTTCCACCTACAGGTGAAT
1 TGTTCCACCCACAGGTAAAC
*
1029165 TGTTCCACCCACAGGTTAAC
1 TGTTCCACCCACAGGTAAAC
1029185 TGTTCCACCCACAGGTAAAC
1 TGTTCCACCCACAGGTAAAC
1029205 TGTTC
1 TGTTC
1029210 AAAGGTTAGG
Statistics
Matches: 180, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 161 0.89
21 2 0.01
22 17 0.09
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (20 bp):
TGTTCCACCCACAGGTAAAC
Found at i:1029206 original size:122 final size:122
Alignment explanation
Indices: 1028989--1029209 Score: 345
Period size: 122 Copynumber: 1.8 Consensus size: 122
1028979 TTATTGTTCC
* * * * *
1028989 ACCCACAGGTTAACTGTTCCACCCACAGGTAAACTGTTCCACTCACAGGTTAACTGTTTCACTCA
1 ACCCACAGGTAAACTGTTCAACCCACAGGTAAACTGTTCCACTCACAGGTGAACTGTTCCACCCA
*
1029054 CAGGTTAACTGTTCCACTCACAGGTAAACTGTTCTACCCACAGGTTAACTGCTCTAT
66 CAGGTTAACTGTTCCACCCACAGGTAAACTGTTCTACCCACAGGTTAACTGCTCTAT
* * *
1029111 ACCCACAGGTAAACTGTTCAATCCGCAGGTAAACTGTTCCAC-CTACAGGTGAATTGTTCCACCC
1 ACCCACAGGTAAACTGTTCAACCCACAGGTAAACTGTTCCACTC-ACAGGTGAACTGTTCCACCC
1029175 ACAGGTTAACTGTTCCACCCACAGGTAAACTGTTC
65 ACAGGTTAACTGTTCCACCCACAGGTAAACTGTTC
1029210 AAAGGTTAGG
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
121 1 0.01
122 88 0.99
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (122 bp):
ACCCACAGGTAAACTGTTCAACCCACAGGTAAACTGTTCCACTCACAGGTGAACTGTTCCACCCA
CAGGTTAACTGTTCCACCCACAGGTAAACTGTTCTACCCACAGGTTAACTGCTCTAT
Found at i:1030033 original size:23 final size:22
Alignment explanation
Indices: 1030003--1030051 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
1029993 AACATGCGCC
*
1030003 GTGGTATGTGCAGAGGAG-TACA
1 GTGGTATGTACAGAGG-GTTACA
*
1030025 GTGGCTATGTACAGTGGGTTACA
1 GTGG-TATGTACAGAGGGTTACA
1030048 GTGG
1 GTGG
1030052 GATACAGTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.22, C:0.10, G:0.41, T:0.27
Consensus pattern (22 bp):
GTGGTATGTACAGAGGGTTACA
Found at i:1030049 original size:10 final size:10
Alignment explanation
Indices: 1030034--1030085 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
1030024 AGTGGCTATG
1030034 TACAGTGGGT
1 TACAGTGGGT
*
1030044 TACAGTGGGA
1 TACAGTGGGT
**
1030054 TACAGTAGCTCT
1 TACAGT-G-GGT
1030066 GTACAGTGGGT
1 -TACAGTGGGT
1030077 TACAGTGGG
1 TACAGTGGG
1030086 AAACAGTAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
10 24 0.73
11 2 0.06
12 1 0.03
13 6 0.18
ACGTcount: A:0.23, C:0.13, G:0.37, T:0.27
Consensus pattern (10 bp):
TACAGTGGGT
Found at i:1030069 original size:33 final size:33
Alignment explanation
Indices: 1030021--1030105 Score: 143
Period size: 33 Copynumber: 2.6 Consensus size: 33
1030011 TGCAGAGGAG
* *
1030021 TACAGTGGCTATGTACAGTGGGTTACAGTGGGA
1 TACAGTAGCTCTGTACAGTGGGTTACAGTGGGA
1030054 TACAGTAGCTCTGTACAGTGGGTTACAGTGGGA
1 TACAGTAGCTCTGTACAGTGGGTTACAGTGGGA
*
1030087 AACAGTAGCTCTGTACAGT
1 TACAGTAGCTCTGTACAGT
1030106 AGATGTAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.26, C:0.15, G:0.32, T:0.27
Consensus pattern (33 bp):
TACAGTAGCTCTGTACAGTGGGTTACAGTGGGA
Found at i:1040481 original size:2 final size:2
Alignment explanation
Indices: 1040474--1040512 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1040464 CCTTATTAGT
1040474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1040513 GGAGCCGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1040499 original size:490 final size:487
Alignment explanation
Indices: 1039537--1040512 Score: 1437
Period size: 490 Copynumber: 2.0 Consensus size: 487
1039527 AATGATAAAC
1039537 TCGTTTTACTAACAAAATCAAAAATCAACATCCATAAAAAAACATACACAATTAGATTCCATATG
1 TCGTTTTACTAACAAAATCAAAAATCAACATCCATAAAAAAACATACACAATTAGATTCCATATG
* * *
1039602 GTTTCCAAAGTTCTTACAATTTTCTAAAACATTAAAAAACATACAGGATATTCTCACGATCAAGA
66 GTTTCCAAAGTTCGTACAATTTTCTAAAACATTAAAAAACATACAGAATATTCTCACAATCAAGA
* * * * **
1039667 TTAGTCAATTTTACACAGCTATGTATGCACCTATTTGTCTCATTACTTTTTTTTTAATTCTTTAC
131 TAAGGCAATTTTACACAGCTATGTATGAACCAATTTGTCTCATTACTAGTTTTTT-ATTCTTTAC
* * *
1039732 TGGTTTTTGCGTAATTTGAAATAAGAAAATTAAAAGGGAAGGGAATTTAAATGCATAAAAGATTA
195 TGGTTTTTGCGTAATTTGAAATAACAAAATTAAAAGGGAAGAGAATTTAAATGCAAAAAAGATTA
* *
1039797 TTTATTCACCTGCTTGATAATTCATGTGAAAATAAGAAAAATACACATTTTTACGAAAAGTTAAG
260 TTTATTCACCTGCTTGATAATTCAGGTGAAAATAAGAAAAATACACATTTCTACGAAAAGTTAAG
* * * * * * *
1039862 TACGGAACATTTGCACCTAAATGTCAAAATAACCAATAAATTACCTAAATGTATCCTTGATGAAA
325 TACGAAAAATATGCACCTAAATGTCAAAACAAACAATAAATTACCCAAATGTATCCTTGAAGAAA
* *
1039927 TACAAAATGCGCATTAAATTTCATGAATTTTTCCCACTCGTTATCTGATCCTTATTAGTTGATAA
390 TACAAAATGCACATTAAATGTCATGAA-TTTTCCCACTCGTTATCTGATCCTTATTAGTTGATAA
1039992 TAAAAAGGACGATATATATATATATATATATATA
454 TAAAAAGGACGATATATATATATATATATATATA
* * * *
1040026 NTCGTTTTACTAACAAAATCAAAAATGAACATTCATAAAATAAAAACATACACAATTATATTCTA
1 -TCGTTTTACTAACAAAATCAAAAATCAACATCCAT--AA-AAAAACATACACAATTAGATTCCA
* *
1040091 TATGGTTTCCAAAGTTCGTACAATTTTCTAAGACATT-AGAAACATACAGAATATTCTCACAATC
62 TATGGTTTCCAAAGTTCGTACAATTTTCTAAAACATTAAAAAACATACAGAATATTCTCACAATC
* *
1040155 AAGATAAGGCAATTTTACACAGCTGTGTATGAACCAATTTGTCTCATTGCTAGTTTTTT-TT-TT
127 AAGATAAGGCAATTTTACACAGCTATGTATGAACCAATTTGTCTCATTACTAGTTTTTTATTCTT
*
1040218 TACTGGTTTTTGTGTAATTTGAAATAACAAAATTAAAAGGGAAGAGAATTTAAATGCAAAAAAGA
192 TACTGGTTTTTGCGTAATTTGAAATAACAAAATTAAAAGGGAAGAGAATTTAAATGCAAAAAAGA
*
1040283 TTTTTTATTTCACCTGCTTGATAATTCAGGTGAAAATAAGAAAAATACAC-TTGTCTACGAAAAG
257 TTATTTA-TTCACCTGCTTGATAATTCAGGTGAAAATAAGAAAAATACACATT-TCTACGAAAAG
* *
1040347 TTAAGTATGAAAAATATGTACCTAAATGTCAAAACAAACAATAAATTACCCAAATGTATCCTTGA
320 TTAAGTACGAAAAATATGCACCTAAATGTCAAAACAAACAATAAATTACCCAAATGTATCCTTGA
* * *
1040412 AGAAATACAAAATGCACGTTAAATGTCATGAA-TTTCCCAGTCGTTATCTTATCCTTATTAGTT-
385 AGAAATACAAAATGCACATTAAATGTCATGAATTTTCCCACTCGTTATCTGATCCTTATTAGTTG
* * * *
1040475 ATATATATATA-TA-TATATATATATATATATATATATA
450 ATA-ATAAAAAGGACGATATATATATATATATATATATA
1040512 T
1 T
1040513 GGAGCCGTTT
Statistics
Matches: 438, Mismatches: 42, Indels: 17
0.88 0.08 0.03
Matches are distributed among these distances:
485 1 0.00
486 23 0.05
487 4 0.01
488 34 0.08
489 71 0.16
490 171 0.39
492 77 0.18
493 57 0.13
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (487 bp):
TCGTTTTACTAACAAAATCAAAAATCAACATCCATAAAAAAACATACACAATTAGATTCCATATG
GTTTCCAAAGTTCGTACAATTTTCTAAAACATTAAAAAACATACAGAATATTCTCACAATCAAGA
TAAGGCAATTTTACACAGCTATGTATGAACCAATTTGTCTCATTACTAGTTTTTTATTCTTTACT
GGTTTTTGCGTAATTTGAAATAACAAAATTAAAAGGGAAGAGAATTTAAATGCAAAAAAGATTAT
TTATTCACCTGCTTGATAATTCAGGTGAAAATAAGAAAAATACACATTTCTACGAAAAGTTAAGT
ACGAAAAATATGCACCTAAATGTCAAAACAAACAATAAATTACCCAAATGTATCCTTGAAGAAAT
ACAAAATGCACATTAAATGTCATGAATTTTCCCACTCGTTATCTGATCCTTATTAGTTGATAATA
AAAAGGACGATATATATATATATATATATATA
Found at i:1041614 original size:2 final size:2
Alignment explanation
Indices: 1041607--1041669 Score: 117
Period size: 2 Copynumber: 31.5 Consensus size: 2
1041597 TACATACCAA
*
1041607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1041649 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
1041670 GAGAGAGAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1041736 original size:2 final size:2
Alignment explanation
Indices: 1041731--1041778 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1041721 ATATATATAT
*
1041731 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1041773 AG AG AG
1 AG AG AG
1041779 TTTTCTAGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1046786 original size:22 final size:22
Alignment explanation
Indices: 1046758--1046801 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1046748 TAATCTTATC
*
1046758 AAAAATT-TCTACATTTATTTAA
1 AAAAATTATC-ACATGTATTTAA
1046780 AAAAATTATCACATGTATTTAA
1 AAAAATTATCACATGTATTTAA
1046802 TCAAAATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAAATTATCACATGTATTTAA
Found at i:1050183 original size:13 final size:13
Alignment explanation
Indices: 1050165--1050189 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1050155 GGCTGAAGCT
1050165 AGCAGCCACTAAC
1 AGCAGCCACTAAC
1050178 AGCAGCCACTAA
1 AGCAGCCACTAA
1050190 GCCCGTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (13 bp):
AGCAGCCACTAAC
Found at i:1055743 original size:2 final size:2
Alignment explanation
Indices: 1055736--1055793 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1055726 AAATGAATGT
1055736 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
1055778 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
1055794 AACTTGAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1059392 original size:156 final size:156
Alignment explanation
Indices: 1059232--1059538 Score: 408
Period size: 156 Copynumber: 2.0 Consensus size: 156
1059222 AACTTAAAAA
*
1059232 TACACTTCCTGAGGATGGTTACACGCCAATTTGAGC-TTTCTTGGCCAAATAGTTTTT-AAAAGA
1 TACACTACCTGAGGATGGTTACACGCCAATTTGAGCTTTTC-TGGCCAAATAGTTTTTGAAAAGA
* *
1059295 A-TTTTTTAAAAAGATTTTCTCTATATATTCCTATATAAAA-ATTTATCCCACAATTGTGGCCCC
65 AGATTTTT--AAAGATTTTCTCTATATATTCCTATATAAAACA-TGATCCCACAATTGTGGCCCC
1059358 ACCCTAACCCC-GGGGACCATGATTTGAATC
127 ACCCT-ACCCCTGGGGACCATGATTTGAATC
* * **** * *
1059388 TACACTACCTGAGGATGTTTCCATTTTAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAGAA
1 TACACTACCTGAGGATGGTTACACGCCAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAAAAGAA
* * *
1059453 GATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACATGATCCCCCTATTGTGGCCCCACCC
66 GATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACATGATCCCACAATTGTGGCCCCACCC
1059518 TACCCCTGGGGACCATGATTT
131 TACCCCTGGGGACCATGATTT
1059539 TAACAAAACT
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
155 5 0.04
156 111 0.84
157 11 0.08
158 5 0.04
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (156 bp):
TACACTACCTGAGGATGGTTACACGCCAATTTGAGCTTTTCTGGCCAAATAGTTTTTGAAAAGAA
GATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACATGATCCCACAATTGTGGCCCCACCC
TACCCCTGGGGACCATGATTTGAATC
Found at i:1063925 original size:20 final size:20
Alignment explanation
Indices: 1063900--1063937 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1063890 CTCTTGTTTA
1063900 AAATTGTATTAAACTGAATG
1 AAATTGTATTAAACTGAATG
*
1063920 AAATTGTATTAACCTGAA
1 AAATTGTATTAAACTGAA
1063938 CTGTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (20 bp):
AAATTGTATTAAACTGAATG
Found at i:1068606 original size:71 final size:71
Alignment explanation
Indices: 1068369--1068618 Score: 335
Period size: 72 Copynumber: 3.5 Consensus size: 71
1068359 TACTTACATG
* * * * *
1068369 TACTAGATTTAACCTCTCAATCTTTATCAAAATGACCCACAGGAGTAAAATTCAAAATTCC-AAA
1 TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCCCACTGGAGTAAAATTCAAAATTCCAAAA
1068433 AACACT
66 AACACT
* * * * * *
1068439 TACTAGATCTAAACTCTCCATCTTTAACAAAATGGCCCACTAGAGTAAAACTTGAAAAATT-AAA
1 TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCCCACTGGAGTAAAA-TT-CAAAATTCCAA
*
1068503 AAAACATT
64 AAAACACT
1068511 TACTAGAT-TCAACCTCTCCATCTTCATCAAAATGGCCCACTGGAGTAAAATTCAAAATTCCAAA
1 TACTAGATCT-AACCTCTCCATCTTCATCAAAATGGCCCACTGGAGTAAAATTCAAAATTCCAAA
1068575 AAACACT
65 AAACACT
*
1068582 TACTGGATCTAACCTCTCCATCTTCATCAAAATGGCC
1 TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCC
1068619 TGCAGGTGTA
Statistics
Matches: 156, Mismatches: 18, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
70 49 0.31
71 48 0.31
72 59 0.38
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.27
Consensus pattern (71 bp):
TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCCCACTGGAGTAAAATTCAAAATTCCAAAA
AACACT
Found at i:1068630 original size:71 final size:71
Alignment explanation
Indices: 1068369--1068633 Score: 331
Period size: 71 Copynumber: 3.7 Consensus size: 71
1068359 TACTTACATG
* * * *
1068369 TACTAGATTTAACCTCTCAATCTTTATCAAAATGACCCACAGGAGTAAAATTCAAAATTCC-AAA
1 TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCCCACAGGAGTAAAATTCAAAATTCCAAAA
1068433 AACACT
66 AACACT
* * * * *
1068439 TACTAGATCTAAACTCTCCATCTTTAACAAAATGGCCCACTA-GAGTAAAACTTGAAAAATT-AA
1 TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCCCAC-AGGAGTAAAA-TT-CAAAATTCCA
*
1068502 AAAAACATT
63 AAAAACACT
*
1068511 TACTAGAT-TCAACCTCTCCATCTTCATCAAAATGGCCCACTGGAGTAAAATTCAAAATTCCAAA
1 TACTAGATCT-AACCTCTCCATCTTCATCAAAATGGCCCACAGGAGTAAAATTCAAAATTCCAAA
1068575 AAACACT
65 AAACACT
* ** *
1068582 TACTGGATCTAACCTCTCCATCTTCATCAAAATGGCCTGCAGGTGTAAAATT
1 TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCCCACAGGAGTAAAATT
1068634 GGGGTCCCTG
Statistics
Matches: 167, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
70 49 0.29
71 60 0.36
72 58 0.35
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.27
Consensus pattern (71 bp):
TACTAGATCTAACCTCTCCATCTTCATCAAAATGGCCCACAGGAGTAAAATTCAAAATTCCAAAA
AACACT
Found at i:1072364 original size:87 final size:82
Alignment explanation
Indices: 1072263--1072491 Score: 248
Period size: 82 Copynumber: 2.7 Consensus size: 82
1072253 AAGGCTCAGT
* *
1072263 CAGTTACAATGATGTCAAGATCAATTCAATGCCAGCATGAGTAACACAATTCAA-AATATAATTA
1 CAGTTACAATGATGTCAAGATCAATTCAATGCCAGCATGAGGAACAAAATT-AAGAATAT-ATTA
*
1072327 TTCAATTTTTTTTATAAGAATAC
64 ---AATTTGTTTTA-AAGAATAC
* *
1072350 CAGTTACAATGATGTTGAA-ATCAATTCAATGCCAGCATGAGGGACAAAATTAAGAATATATTAA
1 CAGTTACAATGATG-TCAAGATCAATTCAATGCCAGCATGAGGAACAAAATTAAGAATATATTAA
* *
1072414 ATTTGTTTTAAGGAGTAC
65 ATTTGTTTTAAAGAATAC
* * * * * *
1072432 CAGTTACAATGATGTCAGGATCAAATCAATGTCAACATAAGGGAA-AAAATTCAGAATATA
1 CAGTTACAATGATGTCAAGATCAATTCAATGCCAGCATGA-GGAACAAAATTAAGAATATA
1072492 GTCATTTTTT
Statistics
Matches: 123, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
81 2 0.02
82 51 0.41
83 13 0.11
86 6 0.05
87 48 0.39
88 3 0.02
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (82 bp):
CAGTTACAATGATGTCAAGATCAATTCAATGCCAGCATGAGGAACAAAATTAAGAATATATTAAA
TTTGTTTTAAAGAATAC
Found at i:1084613 original size:13 final size:13
Alignment explanation
Indices: 1084595--1084619 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1084585 ACATATAGTA
1084595 AGGCTTGGCCTTT
1 AGGCTTGGCCTTT
1084608 AGGCTTGGCCTT
1 AGGCTTGGCCTT
1084620 GACAAGATTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.24, G:0.32, T:0.36
Consensus pattern (13 bp):
AGGCTTGGCCTTT
Found at i:1084987 original size:2 final size:2
Alignment explanation
Indices: 1084937--1084971 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1084927 CAATATATGA
* *
1084937 AG AG AG AG AG AG CG AG AG CG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1084972 AGGGGGGCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1086521 original size:33 final size:33
Alignment explanation
Indices: 1086484--1086550 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1086474 AATATTAGAA
*
1086484 AATACCCAAATATTAAAGGTTAAATAATTATAC
1 AATACCCAAATATTAAAGGTAAAATAATTATAC
*
1086517 AATACCCAAATTTTAAAGGTAAAATAATTATAC
1 AATACCCAAATATTAAAGGTAAAATAATTATAC
1086550 A
1 A
1086551 GATTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (33 bp):
AATACCCAAATATTAAAGGTAAAATAATTATAC
Done.