Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 3 of 106
Found at i:1128513 original size:20 final size:20
Alignment explanation
Indices: 1128440--1128513 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 20
1128430 CATACCTACT
*
1128440 TTTTTTTAATTTTTTATTTA
1 TTTTTTAAATTTTTTATTTA
*
1128460 TTTTTTATATTTTATTTTATTTTA
1 TTTTTTA-A-ATT-TTTTA-TTTA
1128484 TTATAATTTAAATTTTTTATTTA
1 TT-T--TTTAAATTTTTTATTTA
1128507 TTTTTTA
1 TTTTTTA
1128514 GGTCTCTACA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
20 10 0.23
21 1 0.02
22 3 0.07
23 11 0.25
24 11 0.25
25 3 0.07
26 1 0.02
27 4 0.09
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTAAATTTTTTATTTA
Found at i:1132542 original size:150 final size:149
Alignment explanation
Indices: 1132300--1132584 Score: 561
Period size: 150 Copynumber: 1.9 Consensus size: 149
1132290 TTTAGATTTG
1132300 TTTTTTTTTTCTTTTCATGTCTTTTCACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTA
1 TTTTTTTTTTCTTTTCATGTCTTTTCACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTA
1132365 AAAAGTATGATATTTTTTTTAATTGAAAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTT
66 AAAAGTATGATATTTTTTTTAATTGAAAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTT
1132430 AAATANCGACCATTTTTTTT
131 AAATA-CGACCATTTTTTTT
1132450 TTTTTTTTTTCTTTTCATGTCTTTTCACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTA
1 TTTTTTTTTTCTTTTCATGTCTTTTCACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTA
1132515 AAAAGTATGATATTTTTTTTAATTGAAAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTT
66 AAAAGTATGATATTTTTTTTAATTGAAAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTT
1132580 AAATA
131 AAATA
1132585 TTTTATTAAA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 135 1.00
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (149 bp):
TTTTTTTTTTCTTTTCATGTCTTTTCACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTA
AAAAGTATGATATTTTTTTTAATTGAAAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTT
AAATACGACCATTTTTTTT
Found at i:1136307 original size:269 final size:268
Alignment explanation
Indices: 1135538--1136311 Score: 1179
Period size: 269 Copynumber: 2.9 Consensus size: 268
1135528 CCCATGCTAA
* *
1135538 AACATCCTGCATTAAAAGAATTCGATTATTTAGATGTTAGAGATTAAGCATTACAACTAAAATAA
1 AACATCCTGCATTAAAAGAATTTGATTATTTAGATGTTAGAGATTAGGCATTACAACTAAAATAA
* * *
1135603 AACTATTGGTTTGGATTCAAGTTTGACCATTAAACTCAATCCATCGTGATTGTAGCTATCTCTGT
66 AACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCAATCCATCGTGATTGTTG-TTTCTCTGT
* * *
1135668 TTGCTTGGTCTTGCTCTAATTCAAAATCATCACTAGTCGTTACTTCATTTTCTTGGCCGCCCAAA
130 TTGCTTGGTCTTGCTCAAATTCAAAATCATCACTAGTCGTCACTTCAATTTCTTGGCCGCCCAAA
* * *
1135733 TTTGCTTCAACATCATTACGATTCCATAAAATTCCATGTTCCAAATAATTTTCACTATCAGCATT
195 TTTGCTTCAACATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTTTCACTATCAGCATT
1135798 TGCTTCAAC
260 TGCTTCAAC
* * * *
1135807 AACATCCTGCATTGAAAGAAATTGATTATTTAGATGTTATAGATTAGGCATTACAACTACAATAA
1 AACATCCTGCATTAAAAGAATTTGATTATTTAGATGTTAGAGATTAGGCATTACAACTAAAATAA
* * *
1135872 AACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCGATCCATCATGATTGTTGCTTTCACTGT
66 AACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCAATCCATCGTGATTGTTG-TTTCTCTGT
*
1135937 TTGCTTGGGCTTGCTCAAATTCAAAATCATCACTAGTCGTCACTTCAATTTCTTGGCCGCCCAAA
130 TTGCTTGGTCTTGCTCAAATTCAAAATCATCACTAGTCGTCACTTCAATTTCTTGGCCGCCCAAA
* *
1136002 TTTGCTACAGCATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTTTCACTATCAGCATT
195 TTTGCTTCAACATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTTTCACTATCAGCATT
1136067 TGCTTCAAC
260 TGCTTCAAC
*
1136076 AACATCCTGCATTAAAAGAATTTGATTATTTAGACGTTAGAGATTAGGCATTACAACTAAAATAA
1 AACATCCTGCATTAAAAGAATTTGATTATTTAGATGTTAGAGATTAGGCATTACAACTAAAATAA
* *
1136141 AACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCAAGCCATCGTGATTGTTGTTGCCTCTGT
66 AACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCAATCCATCGTGATTGTTGTT-TCTCTGT
* * ** * * * * ** *
1136206 TTGCTTGATCTTGCTCAAATACATTATCATCACCATTCGCCACTTGAATTTCTTGGTTGCTCAAA
130 TTGCTTGGTCTTGCTCAAATTCAAAATCATCACTAGTCGTCACTTCAATTTCTTGGCCGCCCAAA
* * *
1136271 TCTGCTTCAACATCATTACGAGTCGATAGCATTTCATGTTC
195 TTTGCTTCAACATCATTACGAGTCCATAGAATTTCATGTTC
1136312 TGGATAAATT
Statistics
Matches: 456, Mismatches: 48, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
268 2 0.00
269 454 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.36
Consensus pattern (268 bp):
AACATCCTGCATTAAAAGAATTTGATTATTTAGATGTTAGAGATTAGGCATTACAACTAAAATAA
AACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCAATCCATCGTGATTGTTGTTTCTCTGTT
TGCTTGGTCTTGCTCAAATTCAAAATCATCACTAGTCGTCACTTCAATTTCTTGGCCGCCCAAAT
TTGCTTCAACATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTTTCACTATCAGCATTT
GCTTCAAC
Found at i:1136429 original size:269 final size:269
Alignment explanation
Indices: 1135538--1136463 Score: 815
Period size: 269 Copynumber: 3.4 Consensus size: 269
1135528 CCCATGCTAA
* * * * ** *
1135538 AACATCCTGCATTAAAAGAATTCGATTATTTAGATGTTAGAGATTA-AGCATTACAACTAAAATA
1 AACACCCTGCATGAAAAGAATTTGATTATTTAAACATTAGAGACTAGA-CATTACAACTAAAATA
* ** * * * * *
1135602 AAACTATTGGTTTGGATTCAAGTTTGACCATTAAACTCAATCCATCGTGATTGTAGCTAT-CTCT
65 AAACTGTTAATTTAGATTCAAGTTTGACCATTAAACTCAAGCCATCATGATTGTTGCT-TCCACT
* * * ** *
1135666 GTTTGCTTG-GTCTTGCTCTAATTCAAAATCATCACTAGTCGTTACTTCATTTTCTTGGCCGCCC
129 GTTTGCTTGAG-CTTGCTCAAATACAAAATCATCACCAGTCGCCACTTCAATTTCTTGGCCGCCC
* * * * * ** * *
1135730 AAATTTGCTTCAACATCATTACGATTCCATAAAATTCCATGTTCCAAATAATTTTCACTATCAGC
193 AAATCTGCTACAACATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTAGCACGATCAAC
* *
1135795 ATTTGCTTCAAC
258 ATGTGCTCCAAC
* * * ** * * * *
1135807 AACATCCTGCATTG-AAAGAAATTGATTATTTAGATGTTATAGATTAGGCATTACAACTACAATA
1 AACACCCTGCA-TGAAAAGAATTTGATTATTTAAACATTAGAGACTAGACATTACAACTAAAATA
** * * * *
1135871 AAACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCGATCCATCATGATTGTTGCTTTCACTG
65 AAACTGTTAATTTAGATTCAAGTTTGACCATTAAACTCAAGCCATCATGATTGTTGCTTCCACTG
* * * *
1135936 TTTGCTTGGGCTTGCTCAAATTCAAAATCATCACTAGTCGTCACTTCAATTTCTTGGCCGCCCAA
130 TTTGCTTGAGCTTGCTCAAATACAAAATCATCACCAGTCGCCACTTCAATTTCTTGGCCGCCCAA
* * ** * *
1136001 ATTTGCTACAGCATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTTTCACTATCAGCAT
195 ATCTGCTACAACATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTAGCACGATCAACAT
* *
1136066 TTGCTTCAAC
260 GTGCTCCAAC
* * * * * *
1136076 AACATCCTGCATTAAAAGAATTTGATTATTTAGACGTTAGAGATTAGGCATTACAACTAAAATAA
1 AACACCCTGCATGAAAAGAATTTGATTATTTAAACATTAGAGACTAGACATTACAACTAAAATAA
** * * *
1136141 AACTGTTGGTTTGGATTCAAGTTTGACCATTAAACTCAAGCCATCGTGATTGTTG-TTGCCTCTG
66 AACTGTTAATTTAGATTCAAGTTTGACCATTAAACTCAAGCCATCATGATTGTTGCTT-CCACTG
* ** * * ** *
1136205 TTTGCTTGATCTTGCTCAAATACATTATCATCACCATTCGCCACTTGAATTTCTTGGTTGCTCAA
130 TTTGCTTGAGCTTGCTCAAATACAAAATCATCACCAGTCGCCACTTCAATTTCTTGGCCGCCCAA
* * * ***
1136270 ATCTGCTTCAACATCATTACGAGTCGATAGCATTTCATGTTCTGGATAAATTGAGC-CGAT-AAC
195 ATCTGCTACAACATCATTACGAGTCCATAGAATTTCATGTTCCAAAT-AATT-AGCACGATCAAC
* *
1136333 -TGGTGGTCCATC
258 AT-GTGCTCCAAC
* * * * * * *
1136345 AATACCCTGTATGAAAATAATTTGATTTTTTAAATATTAGAGCCTAGACATTATAACTAAAATAA
1 AACACCCTGCATGAAAAGAATTTGATTATTTAAACATTAGAGACTAGACATTACAACTAAAATAA
** * * * * * *
1136410 TGCTGTTAATTTAGATTCAATTTTGAACTTTCAACTCAAGCCATCCTAATTGTT
66 AACTGTTAATTTAGATTCAAGTTTGACCATTAAACTCAAGCCATCATGATTGTT
1136464 ACTGTCTCTA
Statistics
Matches: 567, Mismatches: 81, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
268 5 0.01
269 552 0.97
270 9 0.02
271 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (269 bp):
AACACCCTGCATGAAAAGAATTTGATTATTTAAACATTAGAGACTAGACATTACAACTAAAATAA
AACTGTTAATTTAGATTCAAGTTTGACCATTAAACTCAAGCCATCATGATTGTTGCTTCCACTGT
TTGCTTGAGCTTGCTCAAATACAAAATCATCACCAGTCGCCACTTCAATTTCTTGGCCGCCCAAA
TCTGCTACAACATCATTACGAGTCCATAGAATTTCATGTTCCAAATAATTAGCACGATCAACATG
TGCTCCAAC
Found at i:1139830 original size:142 final size:141
Alignment explanation
Indices: 1139560--1139840 Score: 521
Period size: 142 Copynumber: 2.0 Consensus size: 141
1139550 ATGTCTTTTC
1139560 ACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTAAAAAGTATGATATTTTTTTTAATTGA
1 ACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTAAAAAGTATGATATTTTTTTTAATTGA
1139625 AAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTTAAATATTTTTATTAAAAATAAAAATA
66 AAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTTAAATATTTTTATTAAAAATAAAAATA
1139690 TTTTTTTATTT
131 TTTTTTTATTT
1139701 ANCTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTAAAAAGTATGATATTTTTTTTAATTG
1 A-CTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTAAAAAGTATGATATTTTTTTTAATTG
1139766 AAAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTTAAATA-TTTTATT-AAAATAATAAA
65 AAAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTTAAATATTTTTATTAAAAAT-A-AAA
1139829 ATATTTTTTTAT
128 ATATTTTTTTAT
1139841 ATTAAGGTGA
Statistics
Matches: 137, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
140 5 0.04
141 9 0.07
142 123 0.90
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (141 bp):
ACTGACACTCCTAACCCTTTTTTTATTAACTTGACTTTAAAAAGTATGATATTTTTTTTAATTGA
AAAGTAATTAATATTTTTGAAATTCTAAAAAACAATTTTAAATATTTTTATTAAAAATAAAAATA
TTTTTTTATTT
Found at i:1145810 original size:39 final size:39
Alignment explanation
Indices: 1145753--1145831 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1145743 CAAACATACC
*
1145753 TGTAAAGTTATATAAAAAAATAACAAACAAAGGTAATTA
1 TGTAAAGCTATATAAAAAAATAACAAACAAAGGTAATTA
*
1145792 TGTAAAGCTATATGAAAAAATAACAAACAAAGGTAATTA
1 TGTAAAGCTATATAAAAAAATAACAAACAAAGGTAATTA
1145831 T
1 T
1145832 AATAATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.57, C:0.06, G:0.11, T:0.25
Consensus pattern (39 bp):
TGTAAAGCTATATAAAAAAATAACAAACAAAGGTAATTA
Found at i:1145848 original size:25 final size:22
Alignment explanation
Indices: 1145820--1145868 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
1145810 AATAACAAAC
*
1145820 AAAGGTAATTATAATAATATAATAA
1 AAAGATAA-TATAA-AATATAA-AA
*
1145845 AAAGATAATGTAAAATATAAAA
1 AAAGATAATATAAAATATAAAA
1145867 AA
1 AA
1145869 GTTATAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 7 0.32
24 4 0.18
25 7 0.32
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.27
Consensus pattern (22 bp):
AAAGATAATATAAAATATAAAA
Found at i:1147081 original size:22 final size:22
Alignment explanation
Indices: 1147056--1147102 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
1147046 AAACAATTCA
1147056 TATAAAAATTATAT-AAATAAAT
1 TATAAAAATTAT-TCAAATAAAT
*
1147078 TATAAAAATTATTCAAATGAAT
1 TATAAAAATTATTCAAATAAAT
1147100 TAT
1 TAT
1147103 TTTTAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.04
22 22 0.96
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
TATAAAAATTATTCAAATAAAT
Found at i:1147599 original size:15 final size:15
Alignment explanation
Indices: 1147554--1147596 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
1147544 AGAAATTATT
1147554 AAATAAAAAAATTAA
1 AAATAAAAAAATTAA
*
1147569 AATTAAAAAAATTAA
1 AAATAAAAAAATTAA
1147584 AAATAAAATAAAT
1 AAATAAAA-AAAT
1147597 AAATAAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAAAAAAATTAA
Found at i:1147878 original size:27 final size:25
Alignment explanation
Indices: 1147841--1147891 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
1147831 TTATTCAGAT
1147841 AAAATTAT-AAAATTTTATAAAAATA
1 AAAATTATAAAAATTTT-TAAAAATA
1147866 AAAATATATTAAAAATTTTTAAAAAT
1 AAAAT-TA-TAAAAATTTTTAAAAAT
1147892 TTTGTACGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.22
26 2 0.09
27 8 0.35
28 8 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
AAAATTATAAAAATTTTTAAAAATA
Found at i:1152059 original size:29 final size:29
Alignment explanation
Indices: 1152013--1152069 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1152003 TCTAATTATT
* *
1152013 ATTTTTATATAAAATACTCATTTGATTTC
1 ATTTTTATAAAAAATACTCACTTGATTTC
1152042 ATTTTTA-AAAAAATTACTCACTTGATTT
1 ATTTTTATAAAAAA-TACTCACTTGATTT
1152070 GTTAAATAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.49
Consensus pattern (29 bp):
ATTTTTATAAAAAATACTCACTTGATTTC
Found at i:1154473 original size:468 final size:466
Alignment explanation
Indices: 1153577--1155992 Score: 2585
Period size: 468 Copynumber: 5.2 Consensus size: 466
1153567 CTAAATTAAA
* * *
1153577 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCGTAATTAAAATAAAACTGTTGGTATGGAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
* *
1153642 TCAATTTTGAATTTTAAACTCAATCCATCCTGAATGTTACTGTCTCTATTT-CTTTTATCAAACA
66 TCAATTTTGAACTTTAAACTTAATCCATCCTGAATGTTACTG-CTCTATTTGC-TTTATC-AACA
* *
1153706 TACAAATGAGTAAATTATACATCAATATTGTTTTCATTTATAATTATAATAAAAAATTATTATTT
128 TACAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAA-TATTATTT
* * * *
1153771 CTTGAAAAAAAGTAATTTGACTGAT-CAACGCAAGTGAAATATAATACCCGATA-AAGTTGTAGA
192 CTTGAAAAAAAGTAATTTGAATGATGGAA-GTAAGTGAAATATAATACCCGAGACAA-TTGTAGA
* ** * * * *
1153834 CGACATAAACCAGGTATCTGAAAAAATAACAAACAAAGATAATTAAAATATAATAAGAGGATAAT
255 AGATGTAAA-CA-GT-CCTGAAAAAATAACAAACAAAGATAATTATAATAT-A-AATATGATAAT
* * * * *
1153899 TTAAAA-GAAAAA-A-ATATAACTATAGAAAAGTAAGTTTAAAATGTAAAAGGATCCAAAATTGT
315 GTAAAATAAAAAATATATATAACTATAGGAAAGTAAATTTAAAACGTAAAAGGATCCAAAATTGT
* * * * * * *
1153961 CATGAATAAAAGAAGAGTCGGCAATCAGGAATAATTTGTCAAAACAGAACACTAATGAAGTTGGT
380 CATGAACAAAAGAAAAGTAGGCAATCAGGAACAATATATCAAAACTGAACACTAATGAAGTTGGT
* * *
1154026 CTTGCTCAAATATAGCATCATT
445 CTTGCTCAAATACAACATCATC
* *
1154048 AGAATATGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAATTGTTGGTTTGGAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
* * *
1154113 TCGATTTTGAACTTTAAACTTGGA-CCATCTTGAATGTTACTG-TCTATTTGCTTTATCGAACAT
66 TCAATTTTGAACTTTAAACTT-AATCCATCCTGAATGTTACTGCTCTATTTGCTTTATC-AACAT
* * * *
1154176 ATAAATAAGTAAATTATACAACAATATTGTTTCCATTTATAATTACAATAAAAAATATTGTTTCT
129 ACAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTATTTCT
* *
1154241 TGAAAAAAAGTAATTCGAATGATGGAAGTAAGTGACATATAATACCCGAGACAATTGTAGAAGAT
194 TGAAAAAAAGTAATTTGAATGATGGAAGTAAGTGAAATATAATACCCGAGACAATTGTAGAAGAT
* * *
1154306 GTAAAGAGTCCTGAAAAAATAACAAACAAATATAATTATAGTATAACGATATGATAATGTAAAAT
259 GTAAACAGTCCTGAAAAAATAACAAACAAAGATAATTATAATATAA--ATATGATAATGTAAAAT
* *
1154371 AAAAAATATATATAACTATAGGAAAGTAAATTCAAAATGTAAAAGGATCCAAAATTGTCATGAAC
322 AAAAAATATATATAACTATAGGAAAGTAAATTTAAAACGTAAAAGGATCCAAAATTGTCATGAAC
** *
1154436 AAAAGAAAAGTAGGCAATCAATAACAATACATCAAAACTGAACACTAATGAAGTTGGTCTTGCTC
387 AAAAGAAAAGTAGGCAATCAGGAACAATATATCAAAACTGAACACTAATGAAGTTGGTCTTGCTC
*
1154501 AAATACAACATTATC
452 AAATACAACATCATC
* * * * * *
1154516 AGATTTTGATTATTTAGATGCTACAGACTAGATATCATAACTAAAATGAAATTATTGGTTTGGAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
* * * *
1154581 TCAATTTTGAGCTTTAAACTCAATCCATCCTGAATGTTATTGTCTCTATTTGCGTTATCAACATA
66 TCAATTTTGAACTTTAAACTTAATCCATCCTGAATGTTACTG-CTCTATTTGCTTTATCAACATA
*
1154646 CAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTGTTTCTT
130 CAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTATTTCTT
* * * * * *
1154711 G--AAAAAGTAATGTGAATGATAGAAGTAAGTGAAATATAATACCCGACG-GAGTCGTAGACGAC
195 GAAAAAAAGTAATTTGAATGATGGAAGTAAGTGAAATATAATACCCGA-GACAATTGTAGAAGA-
** * * *
1154773 T-TATATTAGGTAACTGAAAAAAAAAACAAAGAAAGATAATTATGATATAATAAGAGGATATTGT
258 TGTA-AACA-GT-CCTG-AAAAAATAACAAACAAAGATAATTAT-A-AT-AT-A-A--ATA-TG-
* ** * * *
1154837 AAAATAAAATAATATATAAATATATATATAACTATA-GAATGTAAATTCAGAACGTAAAAGGATC
310 ATAATGTAA-AATA-A-AAA-ATATATATAACTATAGGAAAGTAAATTTAAAACGTAAAAGGATC
* * * *
1154901 GAAAATTGTCATGAACAAAAGAAAAGTAGGTAATCAGGAACAATACATCAAAACTTAACACTAAT
371 CAAAATTGTCATGAACAAAAGAAAAGTAGGCAATCAGGAACAATATATCAAAACTGAACACTAAT
*
1154966 GAAGTTGGTCTTGCTCGAATACAACATCA--
436 GAAGTTGGTCTTGCTCAAATACAACATCATC
* * *
1154995 A-AATTTGATTATTTAGATGTTAGAGACTAAATATTATAACTTAAATAAAACTGTTGGTTTGGAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
*
1155059 TCAA-TTTGAACTTTAAACTTAATCCATCCTGAATGTTACTGTCTCTATTTGTTTTATCAACATA
66 TCAATTTTGAACTTTAAACTTAATCCATCCTGAATGTTACTG-CTCTATTTGCTTTATCAACATA
* * * *
1155123 CAAATGAGTAAATTATACGTCAACATTGTTTTCA-TT-T-A-T--AATAAAAAATATTATTTCTG
130 CAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTATTTCTT
* * * * *
1155182 GAAAATAAA-TAATTTGAATGATTGG-AGT---T-AAATACAATACCTGAGTGC-CTTGT-GCAG
195 GAAAA-AAAGTAATTTGAATGA-TGGAAGTAAGTGAAATATAATACCCGAG-ACAATTGTAGAAG
* *
1155239 AATGTAACACAAT-CTGAAAAAATAAC-AACAAAGATAATTATAATAATATAATAAGAGAATAAT
257 -ATGTAA-ACAGTCCTGAAAAAATAACAAACAAAGATAATTATAAT-ATA-AAT-A-TG-ATAAT
* * * * *
1155302 GTAAAATATAAGAA-A-ATATAACTATAGGAAAGTAAATTTAATACGTAAAATGATCGAAAATCG
315 GTAAAATA-AAAAATATATATAACTATAGGAAAGTAAATTTAAAACGTAAAAGGATCCAAAATTG
* * * *
1155365 TCAAGAACAAAAGAAAAGTAGGCAATCAGGAACAATATACCAAAACTGACCACTGATGAAGTTGG
379 TCATGAACAAAAGAAAAGTAGGCAATCAGGAACAATATATCAAAACTGAACACTAATGAAGTTGG
*
1155430 TCTTGGTCAAATACAACATCATC
444 TCTTGCTCAAATACAACATCATC
* * * ** *
1155453 ATAATTTGATTATTTAGATGTTAGAGATTAGATATCATAACTAACATAAAACTGTTAATTTGAAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
* * * * * *
1155518 TGAATTTTGACCTTTAAACTCTAA-CCATCCTGATTGTTACTATCTCTGTTTGCTTTATCAACAG
66 TCAATTTTGAACTTTAAACT-TAATCCATCCTGAATGTTACT-GCTCTATTTGCTTTATCAACAT
* *
1155582 ACAAATGAGTAAATTATACATCAACATTTGTTTCCATTTATGATTACAATAAAAAATATTATTTC
129 ACAAATGAGTAAATTATACATCAATA-TTGTTTCCATTTATAATTACAATAAAAAATATTATTTC
* * * ** * * * * ** * *
1155647 TTCAAAAAAAGTAATTTAAATTATCAAAGTGATTGAAATATGATACCCGAGGGGCCCTTTTA-CA
193 TTGAAAAAAAGTAATTTGAATGATGGAAGTAAGTGAAATATAATACCCGA--GACAATTGTAGAA
* **
1155711 -ACGTAAACCTTCCTGAAAAAATAACAAACAAAGAT-A--AT--TAT-AATA--AT-A--TAAAA
256 GATGTAAACAGTCCTGAAAAAATAACAAACAAAGATAATTATAATATAAATATGATAATGTAAAA
* * *
1155764 TAAAAAATATATAT--CTATAGGAAAGTAAATTTTAAACGTAAAAGGCTCAAAAATTGTCATGAA
321 TAAAAAATATATATAACTATAGGAAAGTAAATTTAAAACGTAAAAGGATCCAAAATTGTCATGAA
* * * * * *
1155827 TAAAAGAAAAGTCGACAATCAGGAACAATATATTAAAAATGACCACTAATGAAGTTGGTCTTGCT
386 CAAAAGAAAAGTAGGCAATCAGGAACAATATATCAAAACTGAACACTAATGAAGTTGGTCTTGCT
*
1155892 CAAATACATCATCATC
451 CAAATACAACATCATC
* * * * * * *
1155908 ATAATTTGATTATTTAAATATTAGAGAGTAAATATCATAACTAAAACAAAGCTGTTGGTTTGGAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
1155973 TCAATTTTGAACTTTAAACT
66 TCAATTTTGAACTTTAAACT
1155993 CGAATNACAA
Statistics
Matches: 1666, Mismatches: 212, Indels: 150
0.82 0.10 0.07
Matches are distributed among these distances:
455 202 0.12
456 116 0.07
457 5 0.00
458 4 0.00
459 68 0.04
460 81 0.05
461 13 0.01
462 7 0.00
463 4 0.00
464 19 0.01
465 54 0.03
466 16 0.01
467 92 0.06
468 286 0.17
469 165 0.10
470 23 0.01
471 168 0.10
472 13 0.01
473 25 0.02
474 8 0.00
475 2 0.00
476 7 0.00
477 88 0.05
478 64 0.04
479 5 0.00
480 1 0.00
481 115 0.07
482 15 0.01
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (466 bp):
AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
TCAATTTTGAACTTTAAACTTAATCCATCCTGAATGTTACTGCTCTATTTGCTTTATCAACATAC
AAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTATTTCTTG
AAAAAAAGTAATTTGAATGATGGAAGTAAGTGAAATATAATACCCGAGACAATTGTAGAAGATGT
AAACAGTCCTGAAAAAATAACAAACAAAGATAATTATAATATAAATATGATAATGTAAAATAAAA
AATATATATAACTATAGGAAAGTAAATTTAAAACGTAAAAGGATCCAAAATTGTCATGAACAAAA
GAAAAGTAGGCAATCAGGAACAATATATCAAAACTGAACACTAATGAAGTTGGTCTTGCTCAAAT
ACAACATCATC
Found at i:1155432 original size:937 final size:930
Alignment explanation
Indices: 1153577--1155992 Score: 2688
Period size: 937 Copynumber: 2.6 Consensus size: 930
1153567 CTAAATTAAA
* * *
1153577 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCGTAATTAAAATAAAACTGTTGGTATGGAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
*
1153642 TCAATTTTGAATTTTAAACTCAATCCATCCTGAATGTTACTGTCTCTATTT-CTTTTATCAAACA
66 TCAATTTTGAACTTTAAACTCAATCCATCCTGAATGTTACTGTCTCTATTTGC-TTTATC-AACA
* *
1153706 TACAAATGAGTAAATTATACATCAATATTGTTTTCATTTATAATTATAATAAAAAATTATTATTT
129 TACAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAA-TATTATTT
* * * * *
1153771 CTTGAAAAAAAGTAATTTGACTGATCAACGCAAGTGAAATATAATACCCGATAAAGTTGTAGACG
193 CTTG--AAAAAGTAATGTGAATGATCAAAGCAAGTGAAATATAATACCCGACAAAGTCGTAGACG
* *
1153836 ACATAAACCAGGTATCTGAAAAAATAACAAACAAAGATAATTAAAATATAATAAGAGGATAATTT
256 ACATAAACCAGGTAACTGAAAAAAAAACAAACAAAGATAATTAAAATATAATAAGAGGATAATTT
* * *
1153901 AAAAGAAAAAAATATAACTATAGAAAAGTAAGTTTAAAATGTAAAAGGATCCAAAATTGTCATGA
321 AAAAGAAAAAAATATAAATATAGAAAAATAAGTTTAAAACGTAAAAGGATCCAAAATTGTCATGA
* * * * ***
1153966 ATAAAAGAAGAGTCGGCAATCAGGAATAATTTGTCAAAACAGAACACTAATGAAGTTGGTCTTGC
386 ACAAAAGAAAAGTAGGCAATCAGGAACAATACATCAAAACAGAACACTAATGAAGTTGGTCTTGC
* * *
1154031 TCAAATATAGCATCATTAGAATATGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATA
451 TCAAATACAACATCA-TAGAATATGATTATTTAGATGTTAGAGACTAAATATCATAACTAAAATA
* * * *
1154096 AAATTGTTGGTTTGGATTCGATTTTGAACTTTAAACTTGGACCATCTTGAATGTTACTGTCTATT
515 AAACTGTTGGTTTGGATTCGAATTTGAACTTTAAACTTGAACCATCCTGAATGTTACTGTCTATT
* *
1154161 TGCTTTATCGAACATATAAATAAGTAAATTATACAACAATATTGTTTCCATTTATAATTACAATA
580 TGCTTTATCGAACATACAAATAAGTAAATTATACAACAACATTGTTTCCATTTATAATTA-AATA
* * * *
1154226 AAAAATATTGTTTCTTGAAAAAAAGTAATTCGAATGATGGAAGTAAGTGACATATAATACCCGAG
644 AAAAATATTATTTCTGGAAAAAAAGTAATTCGAATGATGGAAGT-A-TGAAATACAATACCCGAG
* * * *
1154291 ACAATTGTAGAAGATGTAAAGAGTCCTGAAAAAATAACAAACAAATATAATTATAGTATAACGAT
707 ACAATTGTAGAAGATGTAAACAATCCTGAAAAAATAACAAACAAAGATAATTATAATATAAC-AT
* *
1154356 ATGATAATGTAAAATAAAAAATATATATAACTATAGGAAAGTAAATTCAAAATGTAAAAGGATCC
771 AAGATAATGTAAAATAAAAAATATATATAACTATAGGAAAGTAAATTCAAAACGTAAAAGGATCC
* * * *
1154421 AAAATTGTCATGAACAAAAGAAAAGTAGGCAATCAATAACAATACATCAAAACTGAACACTAATG
836 AAAATCGTCAAGAACAAAAGAAAAGTAGGCAATCAAGAACAATACACCAAAACTGAACACTAATG
*
1154486 AAGTTGGTCTTGCTCAAATACAACATTATC
901 AAGTTGGTCTTGCTCAAATACAACATCATC
* * * * * *
1154516 AGATTTTGATTATTTAGATGCTACAGACTAGATATCATAACTAAAATGAAATTATTGGTTTGGAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
* * *
1154581 TCAATTTTGAGCTTTAAACTCAATCCATCCTGAATGTTATTGTCTCTATTTGCGTTATCAACATA
66 TCAATTTTGAACTTTAAACTCAATCCATCCTGAATGTTACTGTCTCTATTTGCTTTATCAACATA
*
1154646 CAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTGTTTCTT
131 CAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTATTTCTT
* ** *
1154711 GAAAAAGTAATGTGAATGAT-AGAAGTAAGTGAAATATAATACCCGACGGAGTCGTAGACGACTT
196 GAAAAAGTAATGTGAATGATCA-AAGCAAGTGAAATATAATACCCGACAAAGTCGTAGACGACAT
* ** * **
1154775 ATATTAGGTAACTGAAAAAAAAAACAAAGAAAGATAATTATGATATAATAAGAGGAT-ATTGTAA
260 AAACCAGGTAACTG-AAAAAAAAACAAACAAAGATAATTAAAATATAATAAGAGGATAATT-TAA
* * * *
1154839 AATAAAATAATATATAAATATATATATAACTATAGAATGTAAATTCAGAACGTAAAAGGATCGAA
323 AAGAAAA-AA-ATATAAATATAGA-A-AA--AT--AA-GT---TT-AAAACGTAAAAGGATCCAA
* **
1154904 AATTGTCATGAACAAAAGAAAAGTAGGTAATCAGGAACAATACATCAAAACTTAACACTAATGAA
375 AATTGTCATGAACAAAAGAAAAGTAGGCAATCAGGAACAATACATCAAAACAGAACACTAATGAA
* * *
1154969 GTTGGTCTTGCTCGAATACAACATCA-A-AATTTGATTATTTAGATGTTAGAGACTAAATATTAT
440 GTTGGTCTTGCTCAAATACAACATCATAGAATATGATTATTTAGATGTTAGAGACTAAATATCAT
*
1155032 AACTTAAATAAAACTGTTGGTTTGGATTC-AATTTGAACTTTAAACTT-AATCCATCCTGAATGT
505 AACTAAAATAAAACTGTTGGTTTGGATTCGAATTTGAACTTTAAACTTGAA-CCATCCTGAATGT
* * ** *
1155095 TACTGTCTCTATTTGTTTTATC-AACATACAAATGAGTAAATTATACGTCAACATTGTTTTCA-T
569 TACTG--TCTATTTGCTTTATCGAACATACAAATAAGTAAATTATACAACAACATTGTTTCCATT
*
1155158 T-T-A-T-AATAAAAAATATTATTTCTGGAAAATAAA-TAATTTGAATGATTGG-AGT-T-AAAT
632 TATAATTAAATAAAAAATATTATTTCTGGAAAA-AAAGTAATTCGAATGA-TGGAAGTATGAAAT
* * * *
1155215 ACAATACCTGAGTGC-CTTGT-GCAGAATGTAACACAAT-CTGAAAAAATAAC-AACAAAGATAA
695 ACAATACCCGAG-ACAATTGTAGAAG-ATGTAA-ACAATCCTGAAAAAATAACAAACAAAGATAA
*
1155276 TTATAATAATATA-ATAAGAGAATAATGTAAAATATAAGAA-A-ATATAACTATAGGAAAGTAAA
757 TTATAAT-ATA-ACAT-A-AG-ATAATGTAAAATA-AAAAATATATATAACTATAGGAAAGTAAA
* * * * * *
1155338 TTTAATACGTAAAATGATCGAAAATCGTCAAGAACAAAAGAAAAGTAGGCAATCAGGAACAATAT
816 TTCAAAACGTAAAAGGATCCAAAATCGTCAAGAACAAAAGAAAAGTAGGCAATCAAGAACAATAC
* * *
1155403 ACCAAAACTGACCACTGATGAAGTTGGTCTTGGTCAAATACAACATCATC
881 ACCAAAACTGAACACTAATGAAGTTGGTCTTGCTCAAATACAACATCATC
* * * ** *
1155453 ATAATTTGATTATTTAGATGTTAGAGATTAGATATCATAACTAACATAAAACTGTTAATTTGAAT
1 AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
* * * * * *
1155518 TGAATTTTGACCTTTAAACTCTAA-CCATCCTGATTGTTACTATCTCTGTTTGCTTTATCAACAG
66 TCAATTTTGAACTTTAAACTC-AATCCATCCTGAATGTTACTGTCTCTATTTGCTTTATCAACAT
* *
1155582 ACAAATGAGTAAATTATACATCAACATTTGTTTCCATTTATGATTACAATAAAAAATATTATTTC
130 ACAAATGAGTAAATTATACATCAATA-TTGTTTCCATTTATAATTACAATAAAAAATATTATTTC
* * * * ** * * *** * * ** *
1155647 TTCAAAAAAAGTAATTTAAATTATCAAAGTGATTGAAATATGATACCCGA-GGGGCCCTTTTACA
194 TT--GAAAAAGTAATGTGAATGATCAAAGCAAGTGAAATATAATACCCGACAAAG-TCGTAGACG
* ** *
1155711 ACGTAAACC---TTCCTGAAAAAATAACAAACAAAGATAA-T----TATAAT---A--AT-A--T
256 ACATAAACCAGGTAACTGAAAAAAAAACAAACAAAGATAATTAAAATATAATAAGAGGATAATTT
* ** * * * * * *
1155760 AAAATAAAAAATATATATCTATAGGAAAGTAAATTTTAAACGTAAAAGGCTCAAAAATTGTCATG
321 AAAAGAAAAAA-ATATAAATATAGAAAAATAAGTTTAAAACGTAAAAGGATCCAAAATTGTCATG
* * * * * *
1155825 AATAAAAGAAAAGTCGACAATCAGGAACAATATATTAAAA-ATGACCACTAATGAAGTTGGTCTT
385 AACAAAAGAAAAGTAGGCAATCAGGAACAATACATCAAAACA-GAACACTAATGAAGTTGGTCTT
* * * * * *
1155889 GCTCAAATACATCATCATCATAATTTGATTATTTAAATATTAGAGAGTAAATATCATAACTAAAA
449 GCTCAAATACAACATCAT-AGAATATGATTATTTAGATGTTAGAGACTAAATATCATAACTAAAA
* *
1155954 CAAAGCTGTTGGTTTGGATTC-AATTTTGAACTTTAAACT
513 TAAAACTGTTGGTTTGGATTCGAA-TTTGAACTTTAAACT
1155993 CGAATNACAA
Statistics
Matches: 1265, Mismatches: 170, Indels: 108
0.82 0.11 0.07
Matches are distributed among these distances:
911 94 0.07
912 2 0.00
913 1 0.00
914 60 0.05
915 16 0.01
916 2 0.00
918 1 0.00
920 2 0.00
921 1 0.00
922 12 0.01
923 10 0.01
926 3 0.00
928 1 0.00
931 6 0.00
934 1 0.00
935 87 0.07
936 107 0.08
937 276 0.22
938 123 0.10
939 117 0.09
940 86 0.07
941 7 0.01
942 2 0.00
943 1 0.00
944 4 0.00
945 38 0.03
946 94 0.07
947 15 0.01
948 2 0.00
949 94 0.07
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (930 bp):
AGAATTTGATTATTTAGATGTTAGAGACTAGATATCATAACTAAAATAAAACTGTTGGTTTGGAT
TCAATTTTGAACTTTAAACTCAATCCATCCTGAATGTTACTGTCTCTATTTGCTTTATCAACATA
CAAATGAGTAAATTATACATCAATATTGTTTCCATTTATAATTACAATAAAAAATATTATTTCTT
GAAAAAGTAATGTGAATGATCAAAGCAAGTGAAATATAATACCCGACAAAGTCGTAGACGACATA
AACCAGGTAACTGAAAAAAAAACAAACAAAGATAATTAAAATATAATAAGAGGATAATTTAAAAG
AAAAAAATATAAATATAGAAAAATAAGTTTAAAACGTAAAAGGATCCAAAATTGTCATGAACAAA
AGAAAAGTAGGCAATCAGGAACAATACATCAAAACAGAACACTAATGAAGTTGGTCTTGCTCAAA
TACAACATCATAGAATATGATTATTTAGATGTTAGAGACTAAATATCATAACTAAAATAAAACTG
TTGGTTTGGATTCGAATTTGAACTTTAAACTTGAACCATCCTGAATGTTACTGTCTATTTGCTTT
ATCGAACATACAAATAAGTAAATTATACAACAACATTGTTTCCATTTATAATTAAATAAAAAATA
TTATTTCTGGAAAAAAAGTAATTCGAATGATGGAAGTATGAAATACAATACCCGAGACAATTGTA
GAAGATGTAAACAATCCTGAAAAAATAACAAACAAAGATAATTATAATATAACATAAGATAATGT
AAAATAAAAAATATATATAACTATAGGAAAGTAAATTCAAAACGTAAAAGGATCCAAAATCGTCA
AGAACAAAAGAAAAGTAGGCAATCAAGAACAATACACCAAAACTGAACACTAATGAAGTTGGTCT
TGCTCAAATACAACATCATC
Found at i:1156210 original size:257 final size:256
Alignment explanation
Indices: 1155754--1156249 Score: 886
Period size: 257 Copynumber: 1.9 Consensus size: 256
1155744 ATAATTATAA
1155754 TAATATAAAATAAAAAATATATATCTATAGGAAAGTAAATTTTAAACGTAAAAGGCTCAAAAATT
1 TAATATAAAATAAAAAATATATATCTATAGGAAAGTAAATTTTAAACGTAAAAGGCTCAAAAATT
1155819 GTCATGAATAAAAGAAAAGTCGACAATCAGGAACAATATATTAAAAATGACCACTAATGAAGTTG
66 GTCATGAATAAAAGAAAAGTCGACAATCAGGAACAATATATTAAAAATGACCACTAATGAAGTTG
*
1155884 GTCTTGCTCAAATACATCATCATCATAATTTGATTATTTAAATATTAGAGAGTAAATATCATAAC
131 GTCTTGCTCAAATACATCATCATCATAATTTGATTATTTAAATATTAGAGAATAAATATCATAAC
* *
1155949 TAAAACA-AAGCTGTTGGTTTGGATTCAATTTTGAACTTTAAACTCGAATNACAAAATATATT
196 TAAAACACAA-CTGTTGCTTTAGATTCAATTTTGAACTTTAAACTCGAAT-ACAAAATATATT
1156011 TAATATAAAATAAAAAATATATATCTATAGGAAAGTAAATTTTAAACGTAAAAGGCTCAAAAATT
1 TAATATAAAATAAAAAATATATATCTATAGGAAAGTAAATTTTAAACGTAAAAGGCTCAAAAATT
1156076 GTCATGAATAAAAGAAAAGTCGACAATCAGGAACAATATATTAAAAATGACCACTAATGAAGTTG
66 GTCATGAATAAAAGAAAAGTCGACAATCAGGAACAATATATTAAAAATGACCACTAATGAAGTTG
* * * *
1156141 GTCTTGCTCAAATACATCATCATCATAATTTGATTATTTAGATGTTAGAGAATAGATGTCATAAC
131 GTCTTGCTCAAATACATCATCATCATAATTTGATTATTTAAATATTAGAGAATAAATATCATAAC
* *
1156206 TAAAATACAACTGTTGCTTTAGATTTAATTTTGAACTTTAAACT
196 TAAAACACAACTGTTGCTTTAGATTCAATTTTGAACTTTAAACT
1156250 TTAGCCATCC
Statistics
Matches: 229, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
257 227 0.99
258 2 0.01
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (256 bp):
TAATATAAAATAAAAAATATATATCTATAGGAAAGTAAATTTTAAACGTAAAAGGCTCAAAAATT
GTCATGAATAAAAGAAAAGTCGACAATCAGGAACAATATATTAAAAATGACCACTAATGAAGTTG
GTCTTGCTCAAATACATCATCATCATAATTTGATTATTTAAATATTAGAGAATAAATATCATAAC
TAAAACACAACTGTTGCTTTAGATTCAATTTTGAACTTTAAACTCGAATACAAAATATATT
Found at i:1157866 original size:31 final size:32
Alignment explanation
Indices: 1157828--1157889 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
1157818 TTATTTTTTA
1157828 TTTAAAATTAAAATAATTT-ATTTTTTTAATT
1 TTTAAAATTAAAATAATTTAATTTTTTTAATT
***
1157859 TTTAAAATTACTTTAATTTAATTTTTTTAAT
1 TTTAAAATTAAAATAATTTAATTTTTTTAAT
1157890 AATATCTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTAAAATTAAAATAATTTAATTTTTTTAATT
Found at i:1158008 original size:31 final size:30
Alignment explanation
Indices: 1157973--1158032 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
1157963 TATATTGTAT
1157973 AGAGATTAAATTGAATAAAAT-TAAAATATTG
1 AGAGATTAAATTGAA-AAAATAT-AAATATTG
* *
1158004 AGAGATTATATTTAAAAAATATAAATATT
1 AGAGATTAAATTGAAAAAATATAAATATT
1158033 TAAGTAGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
AGAGATTAAATTGAAAAAATATAAATATTG
Found at i:1158399 original size:22 final size:22
Alignment explanation
Indices: 1158374--1158430 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
1158364 ACGCAATATA
* *
1158374 TAAAAACTAGTCATGTAATG-C
1 TAAAAACTAATCACGTAATGAC
* *
1158395 TTAAAACCAATCACGTAATGAC
1 TAAAAACTAATCACGTAATGAC
1158417 TAAAAACTAATCAC
1 TAAAAACTAATCAC
1158431 ACGATAATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (22 bp):
TAAAAACTAATCACGTAATGAC
Found at i:1164746 original size:31 final size:32
Alignment explanation
Indices: 1164688--1164783 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 32
1164678 TATTTCACAT
**
1164688 AATGTTTAAATAAATTTTT-TAAATTATTTA-AA
1 AATG-TTAAATAAATTTTTAT-TTTTATTTATAA
**
1164720 AATGTTAAATAAATTTTTATTTTTATTATATTT
1 AATGTTAAATAAATTTTTATTTTTATT-TATAA
1164753 AA--TTAAATAAATTTTATATTTTTATTT-TAA
1 AATGTTAAATAAATTTT-TATTTTTATTTATAA
1164783 A
1 A
1164784 TCAAATAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
30 2 0.04
31 33 0.61
32 17 0.31
33 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
AATGTTAAATAAATTTTTATTTTTATTTATAA
Found at i:1164790 original size:29 final size:31
Alignment explanation
Indices: 1164726--1164797 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 31
1164716 TAAAAATGTT
* *
1164726 AAATAAATTTTTATTTTTATTATATTTAATT
1 AAATAAATTTTTATTTTTATTATATTAAATC
1164757 AAATAAATTTTATATTTTTA-T-T-TTAAATC
1 AAATAAATTTT-TATTTTTATTATATTAAATC
1164786 AAATAAATTTTT
1 AAATAAATTTTT
1164798 TATAATTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
28 1 0.03
29 16 0.42
30 1 0.03
31 12 0.32
32 8 0.21
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (31 bp):
AAATAAATTTTTATTTTTATTATATTAAATC
Found at i:1165098 original size:30 final size:30
Alignment explanation
Indices: 1165062--1165122 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
1165052 GTTATAGTGG
1165062 TTTATTTGACTT-AAAATAAAAATATAAAAA
1 TTTATTTGA-TTCAAAATAAAAATATAAAAA
1165092 TTTATTTGATTCAAAATAAAAATATAAAAA
1 TTTATTTGATTCAAAATAAAAATATAAAAA
1165122 T
1 T
1165123 ATAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (30 bp):
TTTATTTGATTCAAAATAAAAATATAAAAA
Found at i:1172226 original size:63 final size:64
Alignment explanation
Indices: 1172159--1172367 Score: 163
Period size: 66 Copynumber: 3.2 Consensus size: 64
1172149 TATAAGTCTA
* * * * *
1172159 GGTGAGGAAACTTCAAGCATGGCTAC-CTTAGGTCATGAAACTCCTAGCATTCCCACAAGCTTG
1 GGTGAAGAAACTCCAAGCATGCCTACACTTAGGTCAAGAAACTCCTAGCATTCCCACAACCTTG
* * * * *
1172222 GGTGAAGAAACTCCTAGCATTCCTACAAGCTTGGGTGAAGAAACTCCTAGCATTCTCACAACCTT
1 GGTGAAGAAACTCCAAGCATGCCTAC-A-CTTAGGTCAAGAAACTCCTAGCATTCCCACAACCTT
1172287 G
64 G
* * * * * * * ** *
1172288 GATGAAGAAACGCCTAGCGT-TCTCCCAACCTT-GGCTGAAGAAACGACTAGCGTTCCCACAACC
1 GGTGAAGAAACTCCAAGCATGCCT-AC-A-CTTAGG-TCAAGAAACTCCTAGCATTCCCACAACC
1172351 TTG
62 TTG
1172354 GGTGAAGAAACTCC
1 GGTGAAGAAACTCC
1172368 TTTCTATCCA
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
63 21 0.18
65 4 0.03
66 94 0.79
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (64 bp):
GGTGAAGAAACTCCAAGCATGCCTACACTTAGGTCAAGAAACTCCTAGCATTCCCACAACCTTG
Found at i:1172232 original size:33 final size:33
Alignment explanation
Indices: 1172195--1172794 Score: 335
Period size: 33 Copynumber: 18.2 Consensus size: 33
1172185 CTTAGGTCAT
*
1172195 GAAACTCCTAGCATTCCCACAAGCTTGGGTGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* *
1172228 GAAACTCCTAGCATTCCTACAAGCTTGGGTGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* *
1172261 GAAACTCCTAGCATTCTCACAACCTTGGATGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * *
1172294 GAAACGCCTAGCGTTCTCC-CAACCTTGGCTGAA
1 GAAACTCCTAGCATTC-CCACAACCTTGGGTGAA
** *
1172327 GAAACGACTAGCGTTCCCACAACCTTGGGTGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
** ** **
1172360 GAAACTCCTTTC-TAT-CCAGTGACCTTGGCAGAA
1 GAAACTCCTAGCAT-TCCCA-CAACCTTGGGTGAA
* * * **
1172393 GAAACCCCTATCATTCCCATAACCTTGGGCCAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * * * *
1172426 GAAACTCCTAACCTACGCACAACATTGGGTGAA
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
1172459 GAAACTCC-AGTCATTCCTC-CAACCTTGGGTGAA
1 GAAACTCCTAG-CATTCC-CACAACCTTGGGTGAA
** * *
1172492 GAAACTCCT-GCCATTCCTC-CAACCTTTAGCGAC
1 GAAACTCCTAG-CATTCC-CACAACCTTGGGTGAA
* * * *** *
1172525 GAAACTTCAACCA-TCATTGCAACCCTGGGT-AA
1 GAAACTCCTAGCATTC-CCACAACCTTGGGTGAA
* * * * *
1172557 GGAAACTCCGACCATTCCTACAACCATGGGTGAG
1 -GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * * * ** * *
1172591 GAAACTACAACCGTTCCTGCAACCTTGGTTGAG
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
* * **
1172624 GAAACTAC-AACTATTCCCACAACCTTGCATGAA
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * * *
1172657 GAAACT-CTTGCTGTTCCCACAACCTTGGCTGAG
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * *
1172690 GAAACTCC-AACTATTCCCACAACCTTGGGCGAG
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * * * *
1172723 GAAACTGCGA-CTATTCCCACCACCTTGGGCGAG
1 GAAACTCCTAGC-ATTCCCACAACCTTGGGTGAA
* * ** * *
1172756 GAAACTGCAAATATTCCCAAAACCTTGGGTGAG
1 GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
1172789 GAAACT
1 GAAACT
1172795 TCAACTAATT
Statistics
Matches: 456, Mismatches: 91, Indels: 40
0.78 0.16 0.07
Matches are distributed among these distances:
32 13 0.03
33 432 0.95
34 11 0.02
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (33 bp):
GAAACTCCTAGCATTCCCACAACCTTGGGTGAA
Found at i:1172813 original size:33 final size:33
Alignment explanation
Indices: 1172544--1172915 Score: 295
Period size: 33 Copynumber: 11.3 Consensus size: 33
1172534 ACCATCATTG
* * * * * *
1172544 CAACCCTGGGTAAGGAAACTCCGACCATTCCTA
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
* * ** **
1172577 CAACCATGGGTGAGGAAACTACAACCGTTCCTG
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
* *
1172610 CAACCTTGGTTGAGGAAACTACAACTATTCCCA
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
** * ** *
1172643 CAACCTTGCATGAAGAAAC-TCTTGCTGTTCCCA
1 CAACCTTGGGTGAGGAAACTTC-AACTATTCCCA
* *
1172676 CAACCTTGGCTGAGGAAACTCCAACTATTCCCA
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
* * *
1172709 CAACCTTGGGCGAGGAAACTGCGACTATTCCCA
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
* * * *
1172742 CCACCTTGGGCGAGGAAACTGCAAATATTCCCA
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
* *
1172775 AAACCTTGGGTGAGGAAACTTCAACTAATT-CTA
1 CAACCTTGGGTGAGGAAACTTCAACT-ATTCCCA
* **
1172808 CAACCTTGGGAGAGGAAACTTTGACTATT--CA
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
* ** * *
1172839 CAACCTCGGCAGAGGAAA-TTCCAACTACTCCGA
1 CAACCTTGGGTGAGGAAACTT-CAACTATTCCCA
* ** *
1172872 CAACCGTGACTGAGGAAACTTCGACTATTCCCA
1 CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
1172905 CAACCTTGGGT
1 CAACCTTGGGT
1172916 TTGGAAGCTT
Statistics
Matches: 272, Mismatches: 60, Indels: 14
0.79 0.17 0.04
Matches are distributed among these distances:
30 2 0.01
31 22 0.08
32 4 0.01
33 238 0.88
34 6 0.02
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (33 bp):
CAACCTTGGGTGAGGAAACTTCAACTATTCCCA
Found at i:1172853 original size:31 final size:33
Alignment explanation
Indices: 1172786--1172865 Score: 94
Period size: 31 Copynumber: 2.5 Consensus size: 33
1172776 AACCTTGGGT
* *
1172786 GAGGAAACTTCAACTAATTCTACAACCTTGGGA
1 GAGGAAACTTCAACTAATTCTACAACCTCGGCA
**
1172819 GAGGAAACTTTGACT-ATTC-ACAACCTCGGCA
1 GAGGAAACTTCAACTAATTCTACAACCTCGGCA
1172850 GAGGAAA-TTCCAACTA
1 GAGGAAACTT-CAACTA
1172866 CTCCGACAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
30 2 0.05
31 20 0.51
32 4 0.10
33 13 0.33
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.23
Consensus pattern (33 bp):
GAGGAAACTTCAACTAATTCTACAACCTCGGCA
Found at i:1196754 original size:15 final size:14
Alignment explanation
Indices: 1196729--1196772 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
1196719 TTTATAATTT
1196729 TATAATAATTATAA
1 TATAATAATTATAA
*
1196743 TATAATTAATTATAT
1 TATAA-TAATTATAA
*
1196758 TAAAATAATATATAA
1 TATAATAAT-TATAA
1196773 AAGTAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAATAATTATAA
Found at i:1211751 original size:91 final size:94
Alignment explanation
Indices: 1211600--1211812 Score: 271
Period size: 91 Copynumber: 2.3 Consensus size: 94
1211590 TGTACACCGC
* *
1211600 TTTT-CATTAGTTACATTTAACAC-TAAAAAATAGAATAGATAGTAAATCAATCTCTTTCAAAAC
1 TTTTACATTAGTTATATTTAACACTTAAAAAATAGAATAGATAGTAAATCAATCTCTCTCAAAAC
1211663 CCTATCTTTAGTTAGCT-A-ATAT-GCCA
66 CCTATCTTTAGTTAGCTGATATATAGCCA
* * *
1211689 TTTTACATTAGTTATATTTAACACTTTAAAAATAGAATATG-T-GATAATTTAATCTCTCTCAAA
1 TTTTACATTAGTTATATTTAACACTTAAAAAATAGAATA-GATAG-TAAATCAATCTCTCTCAAA
* * *
1211752 ACCTTATTTTTAGTTAGCTGATATATATCCA
64 ACCCTATCTTTAGTTAGCTGATATATAGCCA
*
1211783 -TTTACATTAGTTATATTTAACACTGAAAAA
1 TTTTACATTAGTTATATTTAACACTTAAAAA
1211813 TGATATGAGA
Statistics
Matches: 107, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
89 4 0.04
90 19 0.18
91 47 0.44
92 2 0.02
93 32 0.30
94 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (94 bp):
TTTTACATTAGTTATATTTAACACTTAAAAAATAGAATAGATAGTAAATCAATCTCTCTCAAAAC
CCTATCTTTAGTTAGCTGATATATAGCCA
Found at i:1212765 original size:17 final size:18
Alignment explanation
Indices: 1212743--1212807 Score: 89
Period size: 17 Copynumber: 3.7 Consensus size: 18
1212733 GGCTCTTGGC
1212743 ATGTTAA-AATTTTGAAT
1 ATGTTAATAATTTTGAAT
* *
1212760 ATGTTAATAATTGTTTAAC
1 ATGTTAATAATT-TTGAAT
1212779 ATGTTAA-AATTTTGAAT
1 ATGTTAATAATTTTGAAT
1212796 ATGTTAATAATT
1 ATGTTAATAATT
1212808 GTAAAAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 18 0.44
18 12 0.29
19 11 0.27
ACGTcount: A:0.40, C:0.02, G:0.11, T:0.48
Consensus pattern (18 bp):
ATGTTAATAATTTTGAAT
Found at i:1214018 original size:40 final size:40
Alignment explanation
Indices: 1213969--1214171 Score: 228
Period size: 40 Copynumber: 5.0 Consensus size: 40
1213959 AAAAATCTTA
*
1213969 AACATAAACTTAAATAACTAAA-ACCAAATATCCATACAAT
1 AACATAAACTTAAATAACTAAACA-CAAATATCCAAACAAT
* * * * *
1214009 GACGTAAACTTAAATAATTATACACACATATCCAAACAAT
1 AACATAAACTTAAATAACTAAACACAAATATCCAAACAAT
*
1214049 AACATAAACTTAAATAACTAAACACAAAGATCCAAACAAAT
1 AACATAAACTTAAATAACTAAACACAAATATCCAAAC-AAT
** * * *
1214090 AACATAAGGTTAAATAACCAAACACATATATCCAAACAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAACAAT
* *
1214130 AACAAAATAAACTTAAATAACTAAAAATAAATATCCAAACAA
1 AAC---ATAAACTTAAATAACTAAACACAAATATCCAAACAA
1214172 CTAGTGTATA
Statistics
Matches: 134, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
40 68 0.51
41 36 0.27
43 30 0.22
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.20
Consensus pattern (40 bp):
AACATAAACTTAAATAACTAAACACAAATATCCAAACAAT
Found at i:1214082 original size:80 final size:81
Alignment explanation
Indices: 1213969--1214171 Score: 230
Period size: 81 Copynumber: 2.5 Consensus size: 81
1213959 AAAAATCTTA
* * * * ** *
1213969 AACATAAACTTAAATAACTAAAACCAAATATCCATAC-AATGACGTAAACTTAAATAATTATACA
1 AACATAAACTTAAATAACTAAAACCAAAGATCCAAACAAATAACATAAACTTAAATAACCAAACA
*
1214033 CACATATCCAAACAAT
66 CACATATCCAAACAAC
**
1214049 AACATAAACTTAAATAACT-AAACACAAAGATCCAAACAAATAACATAAGGTTAAATAACCAAAC
1 AACATAAACTTAAATAACTAAAAC-CAAAGATCCAAACAAATAACATAAACTTAAATAACCAAAC
*
1214113 ACATATATCCAAACAAC
65 ACACATATCCAAACAAC
** *
1214130 AACAAAATAAACTTAAATAACTAAAAATAAATATCCAAACAA
1 AAC---ATAAACTTAAATAACTAAAACCAAAGATCCAAACAA
1214172 CTAGTGTATA
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
79 4 0.04
80 30 0.29
81 37 0.36
84 29 0.28
85 3 0.03
ACGTcount: A:0.58, C:0.19, G:0.02, T:0.20
Consensus pattern (81 bp):
AACATAAACTTAAATAACTAAAACCAAAGATCCAAACAAATAACATAAACTTAAATAACCAAACA
CACATATCCAAACAAC
Found at i:1215023 original size:328 final size:319
Alignment explanation
Indices: 1214434--1215074 Score: 912
Period size: 328 Copynumber: 2.0 Consensus size: 319
1214424 AACTAAACTC
* * *
1214434 AATATATATAAAGTAAATACATTAAAAGACATTACAAGTTAATTAATAATTATTATTTCATTTAA
1 AATATATATAAAGTAAAGACATTAAAAGACATTACAAGTTAATTAATAATCATAATTTCATTTAA
* **
1214499 TTTATTTAATTAATTATATGAGTTTGTCCTTAACTACATAAAATTTTAAAAAATAGCTAAATTTC
66 TTAATTTAATTAATTATATGAGTTTGTCCTTAACTACATAAAATTAAAAAAAATAGCTAAATTTC
* *
1214564 AAAACTATTCAATCTCATAACTTTCTTTTAGATTTATATGCTATAAGTTTATATAAACAAAAGTA
131 AAAACTATTCAATCTCATAACTTTCTTTTAGATTTATATCCTATAAGTTTATATAAACAAAAGAA
*
1214629 TATATATTATTTAGTAATTAATTTATACAATAATAATTATATTCTTTATAAATGAACATAATTTA
196 TATATATTATTTAGTAATTAATTTATACAATAATAATTATATTCTTCATAAATGAACATAATTTA
*
1214694 TAATATAAAGTGTATGTGTTAAAACATATTACAAGTTATATACTATAAAGTGTGTGTGT
261 TAATATAAAGTGTATGTGTTAAAACACATTACAAGTTATATACTATAAAGTGTGTGTGT
* * *
1214753 NAATATATATAAAGTATAGATATTAAAAGACATTACAATTTAATTAATAATCATAATTTCA-TTA
1 -AATATATATAAAGTAAAGACATTAAAAGACATTACAAGTTAATTAATAATCATAATTTCATTTA
* * * *
1214817 ATTAATTTAATTAATTATGT-AGATTTGTCTTTAATTACATGAAA-TAAAAAAAATAGCTAAATT
65 ATTAATTTAATTAATTATATGAG-TTTGTCCTTAACTACATAAAATTAAAAAAAATAGCTAAATT
*
1214880 TCAAAACTATTCAATCTCATAAC-TTCTTTTTAGATAATTAAGTTTATTCCATTATAAATTTTAT
129 TCAAAACTATTCAATCTCATAACTTTC-TTTTAGAT--TT-A---TA-TCC--TAT-AAGTTTAT
* * * *
1214944 ATAAACAAAGGAATATATATTATTTAGTAATTAATTTATATAATAGTAATTATTTTCTTCATAAA
183 ATAAACAAAAGAATATATATTATTTAGTAATTAATTTATACAATAATAATTATATTCTTCATAAA
* * *
1215009 TGAACGTAATTTATAATATAAAGTGTATGTGTTAAAAGACATTATAAGTTATATACTATAAAGTG
248 TGAACATAATTTATAATATAAAGTGTATGTGTTAAAACACATTACAAGTTATATACTATAAAGTG
1215074 T
313 T
1215075 CTATATATAT
Statistics
Matches: 284, Mismatches: 25, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
317 3 0.01
318 50 0.18
319 39 0.14
320 56 0.20
321 1 0.00
324 2 0.01
325 2 0.01
327 3 0.01
328 128 0.45
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (319 bp):
AATATATATAAAGTAAAGACATTAAAAGACATTACAAGTTAATTAATAATCATAATTTCATTTAA
TTAATTTAATTAATTATATGAGTTTGTCCTTAACTACATAAAATTAAAAAAAATAGCTAAATTTC
AAAACTATTCAATCTCATAACTTTCTTTTAGATTTATATCCTATAAGTTTATATAAACAAAAGAA
TATATATTATTTAGTAATTAATTTATACAATAATAATTATATTCTTCATAAATGAACATAATTTA
TAATATAAAGTGTATGTGTTAAAACACATTACAAGTTATATACTATAAAGTGTGTGTGT
Found at i:1215178 original size:17 final size:17
Alignment explanation
Indices: 1215148--1215194 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
1215138 AAACAGACAG
* *
1215148 TAAA-TATATTTATATT
1 TAAAGTATATATATAAT
1215164 TAAAGTATATATATAAT
1 TAAAGTATATATATAAT
*
1215181 AAAAGTAT-TATATA
1 TAAAGTATATATATA
1215195 CATAATATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (17 bp):
TAAAGTATATATATAAT
Found at i:1215506 original size:21 final size:22
Alignment explanation
Indices: 1215467--1215508 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1215457 TAAAAATATA
1215467 TATAATAGTAATTATATATTTT
1 TATAATAGTAATTATATATTTT
1215489 TATAATA-TAA-TATGATATTT
1 TATAATAGTAATTAT-ATATTT
1215509 ATATTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 9 0.47
22 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TATAATAGTAATTATATATTTT
Found at i:1215535 original size:27 final size:27
Alignment explanation
Indices: 1215466--1215546 Score: 78
Period size: 27 Copynumber: 2.9 Consensus size: 27
1215456 TTAAAAATAT
*
1215466 ATATAA-TAGTAATTATATATTTTTATA
1 ATATAATTAATAATT-TATATTTTTATA
*
1215493 ATATAATATGAT-ATTTATATTATTTA-A
1 ATATAAT-TAATAATTTATATT-TTTATA
1215520 ATATAATTAATAATTTAATAATTTTTA
1 ATATAATTAATAATTT-AT-ATTTTTA
1215547 ATTTATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
26 3 0.07
27 24 0.53
28 13 0.29
29 5 0.11
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
ATATAATTAATAATTTATATTTTTATA
Found at i:1215542 original size:15 final size:16
Alignment explanation
Indices: 1215520--1215563 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
1215510 TATTATTTAA
1215520 ATATAATTAATAATTT
1 ATATAATTAATAATTT
**
1215536 A-ATAATTTTTAATTT
1 ATATAATTAATAATTT
1215551 ATATATATTAATA
1 ATATA-ATTAATA
1215564 TCATTACATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
15 13 0.59
16 4 0.18
17 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATAATTAATAATTT
Found at i:1228159 original size:33 final size:33
Alignment explanation
Indices: 1228116--1228220 Score: 123
Period size: 33 Copynumber: 3.3 Consensus size: 33
1228106 TACACCTCAT
*
1228116 AATGAACGCTTGGAGCCGACTTACGCCAAATAA
1 AATGCACGCTTGGAGCCGACTTACGCCAAATAA
1228149 AATGCACGCTTGGAGCCGACTTA---C--ATAA
1 AATGCACGCTTGGAGCCGACTTACGCCAAATAA
*
1228177 TACTG-ATCGCTTGGAGCCGACTTACGCCAAATAA
1 -AATGCA-CGCTTGGAGCCGACTTACGCCAAATAA
*
1228211 AATACACGCT
1 AATGCACGCT
1228221 AAGTACAGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
28 5 0.08
29 20 0.33
30 1 0.02
32 1 0.02
33 28 0.47
34 5 0.08
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (33 bp):
AATGCACGCTTGGAGCCGACTTACGCCAAATAA
Found at i:1235756 original size:27 final size:27
Alignment explanation
Indices: 1235690--1235767 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
1235680 TTAAAGATAA
* * *
1235690 CATCATCGTTGAAGTCAATTATAACAT
1 CATCATCGTTGACGTCAATAATGACAT
* * *
1235717 CATCAAT-GATGACGTTAATGATGACAT
1 CATC-ATCGTTGACGTCAATAATGACAT
*
1235744 GATCATCGTTGACGTCAATAATGA
1 CATCATCGTTGACGTCAATAATGA
1235768 TATTATCGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 2 0.05
27 36 0.90
28 2 0.05
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Consensus pattern (27 bp):
CATCATCGTTGACGTCAATAATGACAT
Found at i:1246113 original size:28 final size:27
Alignment explanation
Indices: 1246067--1246134 Score: 68
Period size: 30 Copynumber: 2.4 Consensus size: 27
1246057 CAGCATAGTC
1246067 CTTTTTTTTTTCTTCTTTT-CTTTTCT
1 CTTTTTTTTTTCTTCTTTTACTTTTCT
1246093 CTTTTGTTTTTTAC-TCTTTTTCACTTTTCT
1 CTTTT-TTTTTT-CTTC-TTTT-ACTTTTCT
*
1246123 TTTTCTTTTTTT
1 CTTT-TTTTTTT
1246135 TTTATAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 5 0.14
27 8 0.23
28 5 0.14
30 16 0.46
31 1 0.03
ACGTcount: A:0.03, C:0.18, G:0.01, T:0.78
Consensus pattern (27 bp):
CTTTTTTTTTTCTTCTTTTACTTTTCT
Found at i:1246484 original size:23 final size:24
Alignment explanation
Indices: 1246455--1246499 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1246445 AAGGAATGAG
*
1246455 CCCTTACAGCCCG-AAAAGGAGAA
1 CCCTTACAACCCGAAAAAGGAGAA
1246478 CCCTTACAACCCGAAAAAGGAG
1 CCCTTACAACCCGAAAAAGGAG
1246500 CGTCCCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.40, C:0.31, G:0.20, T:0.09
Consensus pattern (24 bp):
CCCTTACAACCCGAAAAAGGAGAA
Found at i:1246881 original size:23 final size:25
Alignment explanation
Indices: 1246836--1246881 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
1246826 GTTAAAAATA
*
1246836 TAAATTCGTAATTTATAAGCTTACT
1 TAAATTCGTAATTTATAAACTTACT
*
1246861 TAAATTC-T-ATTTTTAAACTTA
1 TAAATTCGTAATTTATAAACTTA
1246882 TGACCATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
24 1 0.05
25 7 0.37
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (25 bp):
TAAATTCGTAATTTATAAACTTACT
Found at i:1268203 original size:51 final size:51
Alignment explanation
Indices: 1268123--1268222 Score: 182
Period size: 51 Copynumber: 2.0 Consensus size: 51
1268113 CAGAAGAATC
*
1268123 TTAGAAGTGCAGGGATCTTTCCTAAAACGCGTTTTCTAGAATCAAAGTGTG
1 TTAGAAGTGCAGGGATATTTCCTAAAACGCGTTTTCTAGAATCAAAGTGTG
*
1268174 TTAGAAGTGCAGGGATATTTCCTACAACGCGTTTTCTAGAATCAAAGTG
1 TTAGAAGTGCAGGGATATTTCCTAAAACGCGTTTTCTAGAATCAAAGTG
1268223 GAATATTGCG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (51 bp):
TTAGAAGTGCAGGGATATTTCCTAAAACGCGTTTTCTAGAATCAAAGTGTG
Found at i:1269709 original size:21 final size:21
Alignment explanation
Indices: 1269670--1269709 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1269660 TTGAAGTGTC
*
1269670 TAAAATTTTTATTATTTATGT
1 TAAAATTTTTATTAATTATGT
1269691 TAAAATTTTGTA-TAATTAT
1 TAAAATTTT-TATTAATTAT
1269710 AATGATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TAAAATTTTTATTAATTATGT
Found at i:1269747 original size:16 final size:15
Alignment explanation
Indices: 1269726--1269760 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1269716 GTTAATGAAT
1269726 TTATTAATATTTTTAA
1 TTATTAATA-TTTTAA
*
1269742 TTATTATTATTTTAA
1 TTATTAATATTTTAA
1269757 TTAT
1 TTAT
1269761 GATACTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTAATATTTTAA
Found at i:1271446 original size:2 final size:2
Alignment explanation
Indices: 1271439--1271494 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1271429 ATACACATTG
1271439 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT 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
1271481 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1271495 TAGTTTTAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1285242 original size:16 final size:16
Alignment explanation
Indices: 1285221--1285251 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1285211 GATATATTTT
*
1285221 AATTATTTTATTTATA
1 AATTATATTATTTATA
1285237 AATTATATTATTTAT
1 AATTATATTATTTAT
1285252 TAAGTTTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTATATTATTTATA
Found at i:1301431 original size:19 final size:19
Alignment explanation
Indices: 1301407--1301473 Score: 66
Period size: 19 Copynumber: 3.4 Consensus size: 19
1301397 TGATTCCAAC
1301407 TTTT-AATAAAATATTAGTA
1 TTTTAAATAAAATATTA-TA
* *
1301426 TTTTAAAATATTAATATTAAA
1 TTTT-AAATA-AAATATTATA
1301447 TTTTAAATAAAATATTA-A
1 TTTTAAATAAAATATTATA
1301465 TATTTAAAT
1 T-TTTAAAT
1301474 TATCAATTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.05
19 18 0.44
20 5 0.12
21 9 0.22
22 7 0.17
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
TTTTAAATAAAATATTATA
Found at i:1301434 original size:16 final size:16
Alignment explanation
Indices: 1301413--1301443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1301403 CAACTTTTAA
*
1301413 TAAAATATTAGTATTT
1 TAAAATATTAATATTT
1301429 TAAAATATTAATATT
1 TAAAATATTAATATT
1301444 AAATTTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:1301443 original size:22 final size:22
Alignment explanation
Indices: 1301411--1301501 Score: 88
Period size: 22 Copynumber: 4.4 Consensus size: 22
1301401 TCCAACTTTT
*
1301411 AATA-AAATATTAGTATTTTAA
1 AATATAAATATTAATATTTTAA
*
1301432 AATATTAATATTAA-ATTTT-A
1 AATATAAATATTAATATTTTAA
1301452 AATA-AAATATTAATA-TTTAA
1 AATATAAATATTAATATTTTAA
* *
1301472 ATTATCAATTATTAATA-TTTAA
1 AATAT-AAATATTAATATTTTAA
1301494 AA-ATAAAT
1 AATATAAAT
1301502 TAAAATAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
19 11 0.19
20 13 0.22
21 11 0.19
22 23 0.40
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (22 bp):
AATATAAATATTAATATTTTAA
Found at i:1301463 original size:41 final size:42
Alignment explanation
Indices: 1301407--1301500 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 42
1301397 TGATTCCAAC
* *
1301407 TTTT-AATAAAATATTAGTATTTTAAAATATTAA-TATTAA-A
1 TTTTAAATAAAATATTAATA-TTTAAAATATCAATTATTAATA
*
1301447 TTTTAAATAAAATATTAATATTTAAATTATCAATTATTAATA
1 TTTTAAATAAAATATTAATATTTAAAATATCAATTATTAATA
*
1301489 TTTAAAAATAAA
1 TTT-TAAATAAA
1301501 TTAAAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 15 0.33
41 20 0.43
42 4 0.09
43 7 0.15
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (42 bp):
TTTTAAATAAAATATTAATATTTAAAATATCAATTATTAATA
Found at i:1301712 original size:33 final size:32
Alignment explanation
Indices: 1301652--1301713 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
1301642 ATATTAAAAA
1301652 AATAAAATAAAATAAAATAAAAAATTAATCAT
1 AATAAAATAAAATAAAATAAAAAATTAATCAT
* * *
1301684 AATAATATATAAATTAAATAAAATATTAAT
1 AATAAAATA-AAATAAAATAAAAAATTAAT
1301714 ATTTAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (32 bp):
AATAAAATAAAATAAAATAAAAAATTAATCAT
Found at i:1301876 original size:28 final size:28
Alignment explanation
Indices: 1301843--1301912 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
1301833 NNAAAATTAA
* *
1301843 ATTAATATTATATATTAAATTATTA-ATT
1 ATTAATATTATAAATTAAATT-CTAGATT
*
1301871 ATTAATATTTTAAATTAAATTCTAGATT
1 ATTAATATTATAAATTAAATTCTAGATT
*
1301899 ATTAATATTTTAAA
1 ATTAATATTATAAA
1301913 AAATCTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.05
28 36 0.95
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
ATTAATATTATAAATTAAATTCTAGATT
Found at i:1306943 original size:24 final size:25
Alignment explanation
Indices: 1306896--1306943 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1306886 TTTATACAAG
*
1306896 TTTTTTTTTCTTTTTGTGGTAAACC
1 TTTTTTTTTCTTTTTGTGCTAAACC
1306921 TTTTTTTTT-TTTTT-TGCTCAAAC
1 TTTTTTTTTCTTTTTGTGCT-AAAC
1306944 AAGTTCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 9 0.43
25 9 0.43
ACGTcount: A:0.12, C:0.12, G:0.08, T:0.67
Consensus pattern (25 bp):
TTTTTTTTTCTTTTTGTGCTAAACC
Found at i:1313310 original size:18 final size:18
Alignment explanation
Indices: 1313284--1313318 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1313274 TTAGGCATAA
*
1313284 ATTTTAAAAATTTAAATT
1 ATTTAAAAAATTTAAATT
*
1313302 ATTTAAAAATTTTAAAT
1 ATTTAAAAAATTTAAAT
1313319 AAATTTTTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTAAAAAATTTAAATT
Found at i:1317472 original size:18 final size:17
Alignment explanation
Indices: 1317447--1317481 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1317437 TACATTATGA
1317447 ATTACTTGCAAATTAAT
1 ATTACTTGCAAATTAAT
1317464 ATTATCTTGCAAATTAAT
1 ATTA-CTTGCAAATTAAT
1317482 CTTTACAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (17 bp):
ATTACTTGCAAATTAAT
Found at i:1321165 original size:627 final size:626
Alignment explanation
Indices: 1319972--1321224 Score: 2488
Period size: 627 Copynumber: 2.0 Consensus size: 626
1319962 TACAACCGAT
*
1319972 CAGGCTATTAACAAACTTAACGGCTACTAAATTAATTACATCCTTTAGTATCAACTAAAACGGTG
1 CAGGCTATTAACAAACTTAACGGCTACGAAATTAATTACATCCTTTAGTATCAACTAAAACGGTG
1320037 TAGTATTGAAATACTTATGGCCTTCTTCCTAATAAAAATGAAACGGTGCGTTTCTTCAGTCTTTG
66 TAGTATTGAAATACTTATGGCCTTCTTCCTAATAAAAATGAAACGGTGCGTTTCTTCAGTCTTTG
1320102 TTCTTCTTCTGCTATGTACAAGTAGCAGTTTCCTGGTAGCAGCCTTGCTGCCTTTACCCTTCGGC
131 TTCTTCTTCTGCTATGTACAAGTAGCAGTTTCCTGGTAGCAGCCTTGCTGCCTTTACCCTTCGGC
1320167 TACATTAAAGTATTCATGTTCAGTCTTCCTGATTAATAATGTCCAAGAAATTGTCTCTGAAACTT
196 TACATTAAAGTATTCATGTTCAGTCTTCCTGATTAATAATGTCCAAGAAATTGTCTCTGAAACTT
1320232 CCACCTCCTTTCAAGGAAGACTCCTATTCTGGATTTGTTGATATTTTTCTCCTATTTAAGTGAAG
261 CCACCTCCTTTCAAGGAAGACTCCTATTCTGGATTTGTTGATATTTTTCTCCTATTTAAGTGAAG
1320297 CTGAGGAAATGCGATTTGAAAACGTCAAAAAAAGAAATTAAAAAAAAAAAAAGATGGAGAGTCAT
326 CTGAGGAAATGCGATTTGAAAACGTCAAAAAAAGAAATTAAAAAAAAAAAAAGATGGAGAGTCAT
1320362 GTGAATGAGTATTCTGAAGTGAAGGAGGCGCTCTTGTTGGAGGTAAAAAGGGCCCATATAGAATG
391 GTGAATGAGTATTCTGAAGTGAAGGAGGCGCTCTTGTTGGAGGTAAAAAGGGCCCATATAGAATG
1320427 TTCACGTGAATTAACCTCTTTTGTCTTTTTAAGGCAACTTTTTTTTACCAACTCAAGAAATAATT
456 TTCACGTGAATTAACCTCTTTTGTCTTTTTAAGGCAACTTTTTTTTACCAACTCAAGAAATAATT
1320492 CTAAAATTTTAACCCCTTTTTTTTTAATCTAGTATGGATAAATAATGTATACAACTATTTTACAA
521 CTAAAATTTTAACCCCTTTTTTTTTAATCTAGTATGGATAAATAATGTATACAACTATTTTACAA
1320557 TAAGATTATTTCAACAGTTAGTGAATGCTAAAACCAAGGGC
586 TAAGATTATTTCAACAGTTAGTGAATGCTAAAACCAAGGGC
1320598 NCAGGCTATTAACAAACTTAACGGCTACGAAATTAATTACATCCTTTAGTATCAACTAAAACGGT
1 -CAGGCTATTAACAAACTTAACGGCTACGAAATTAATTACATCCTTTAGTATCAACTAAAACGGT
1320663 GTAGTATTGAAATACTTATGGCCTTCTTCCTAATAAAAATGAAACGGTGCGTTTCTTCAGTCTTT
65 GTAGTATTGAAATACTTATGGCCTTCTTCCTAATAAAAATGAAACGGTGCGTTTCTTCAGTCTTT
1320728 GTTCTTCTTCTGCTATGTACAAGTAGCAGTTTCCTGGTAGCAGCCTTGCTGCCTTTACCCTTCGG
130 GTTCTTCTTCTGCTATGTACAAGTAGCAGTTTCCTGGTAGCAGCCTTGCTGCCTTTACCCTTCGG
1320793 CTACATTAAAGTATTCATGTTCAGTCTTCCTGATTAATAATGTCCAAGAAATTGTCTCTGAAACT
195 CTACATTAAAGTATTCATGTTCAGTCTTCCTGATTAATAATGTCCAAGAAATTGTCTCTGAAACT
1320858 TCCACCTCCTTTCAAGGAAGACTCCTATTCTGGATTTGTTGATATTTTTCTCCTATTTAAGTGAA
260 TCCACCTCCTTTCAAGGAAGACTCCTATTCTGGATTTGTTGATATTTTTCTCCTATTTAAGTGAA
1320923 GCTGAGGAAATGCGATTTGAAAACGTCAAAAAAAGAAATTAAAAAAAAAAAAAGATGGAGAGTCA
325 GCTGAGGAAATGCGATTTGAAAACGTCAAAAAAAGAAATTAAAAAAAAAAAAAGATGGAGAGTCA
1320988 TGTGAATGAGTATTCTGAAGTGAAGGAGGCGCTCTTGTTGGAGGTAAAAAGGGCCCATATAGAAT
390 TGTGAATGAGTATTCTGAAGTGAAGGAGGCGCTCTTGTTGGAGGTAAAAAGGGCCCATATAGAAT
1321053 GTTCACGTGAATTAACCTCTTTTGTCTTTTTAAGGCAACTTTTTTTTACCAACTCAAGAAATAAT
455 GTTCACGTGAATTAACCTCTTTTGTCTTTTTAAGGCAACTTTTTTTTACCAACTCAAGAAATAAT
1321118 TCTAAAATTTTAACCCCTTTTTTTTTAATCTAGTATGGATAAATAATGTATACAACTATTTTACA
520 TCTAAAATTTTAACCCCTTTTTTTTTAATCTAGTATGGATAAATAATGTATACAACTATTTTACA
1321183 ATAAGATTATTTCAACAGTTAGTGAATGCTAAAACCAAGGGC
585 ATAAGATTATTTCAACAGTTAGTGAATGCTAAAACCAAGGGC
1321225 GGAGTTAGCC
Statistics
Matches: 625, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
627 625 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (626 bp):
CAGGCTATTAACAAACTTAACGGCTACGAAATTAATTACATCCTTTAGTATCAACTAAAACGGTG
TAGTATTGAAATACTTATGGCCTTCTTCCTAATAAAAATGAAACGGTGCGTTTCTTCAGTCTTTG
TTCTTCTTCTGCTATGTACAAGTAGCAGTTTCCTGGTAGCAGCCTTGCTGCCTTTACCCTTCGGC
TACATTAAAGTATTCATGTTCAGTCTTCCTGATTAATAATGTCCAAGAAATTGTCTCTGAAACTT
CCACCTCCTTTCAAGGAAGACTCCTATTCTGGATTTGTTGATATTTTTCTCCTATTTAAGTGAAG
CTGAGGAAATGCGATTTGAAAACGTCAAAAAAAGAAATTAAAAAAAAAAAAAGATGGAGAGTCAT
GTGAATGAGTATTCTGAAGTGAAGGAGGCGCTCTTGTTGGAGGTAAAAAGGGCCCATATAGAATG
TTCACGTGAATTAACCTCTTTTGTCTTTTTAAGGCAACTTTTTTTTACCAACTCAAGAAATAATT
CTAAAATTTTAACCCCTTTTTTTTTAATCTAGTATGGATAAATAATGTATACAACTATTTTACAA
TAAGATTATTTCAACAGTTAGTGAATGCTAAAACCAAGGGC
Found at i:1321814 original size:16 final size:16
Alignment explanation
Indices: 1321789--1321847 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
1321779 ACATTTGAAC
1321789 AAAT-AAAATAAAAATT
1 AAATAAAAATAAAAA-T
*
1321805 AAA-AAAAATAAATAT
1 AAATAAAAATAAAAAT
1321820 AAATAAAAATAATAATAT
1 AAATAAAAATAA-AA-AT
1321838 AAATTAAAAA
1 AAA-TAAAAA
1321848 AATTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
15 4 0.11
16 20 0.56
17 1 0.03
18 5 0.14
19 6 0.17
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:1324826 original size:28 final size:28
Alignment explanation
Indices: 1324780--1324842 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1324770 ATCTATGGGC
* **
1324780 AATTTTTCAGTTTTTGGGGTAAAAATGT
1 AATTTTTCACTTTACGGGGTAAAAATGT
*
1324808 AATTTTTCACTTTACGGGGTAAAAGTGT
1 AATTTTTCACTTTACGGGGTAAAAATGT
1324836 AATTTTT
1 AATTTTT
1324843 AAAAATTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.46
Consensus pattern (28 bp):
AATTTTTCACTTTACGGGGTAAAAATGT
Found at i:1335340 original size:29 final size:29
Alignment explanation
Indices: 1335273--1335332 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1335263 ACAACAGTAT
1335273 GCCAAAATATTGATGATTACAGCAGTAAA
1 GCCAAAATATTGATGATTACAGCAGTAAA
1335302 GCCAAAATATTGATGATTACAGCAGTAAA
1 GCCAAAATATTGATGATTACAGCAGTAAA
1335331 GC
1 GC
1335333 TCATATATCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.23
Consensus pattern (29 bp):
GCCAAAATATTGATGATTACAGCAGTAAA
Found at i:1341894 original size:21 final size:20
Alignment explanation
Indices: 1341864--1341918 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
1341854 AAAAGAAAAA
*
1341864 AAATTTAAAAATAGATATTAT
1 AAATTAAAAAATA-ATATTAT
*
1341885 AAATTAAAAAATTAATTTTAT
1 AAATTAAAAAA-TAATATTAT
*
1341906 ATA-TAAAAAATAA
1 AAATTAAAAAATAA
1341919 AACAGTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.10
20 7 0.23
21 18 0.60
22 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATTAAAAAATAATATTAT
Found at i:1346375 original size:75 final size:75
Alignment explanation
Indices: 1346241--1346436 Score: 286
Period size: 75 Copynumber: 2.6 Consensus size: 75
1346231 AGCCAACCGG
* * *
1346241 AACCACCCACAGCACTGATCAAGCCATGGCATACAACCAGACGGACGGGCCTCGCGACCAAACTG
1 AACCTCCCACAGCACTGATCAAGCCATGGCATACAACCAGACGGAAGGGCCTCGCGACCAAACCG
1346306 TTTCCACTGT
66 TTTCCACTGT
** * *
1346316 AACCTCCCACAGCACTGATCAAGCCATGGCATACAAGAAGACGGAAGGG-CTCCGTGACCAACCC
1 AACCTCCCACAGCACTGATCAAGCCATGGCATACAACCAGACGGAAGGGCCT-CGCGACCAAACC
*
1346380 GTTTCCGCTGT
65 GTTTCCACTGT
* *
1346391 AACCTTCCACAGCACTGATCAGGCCATGGCATACAACCAGACGGAA
1 AACCTCCCACAGCACTGATCAAGCCATGGCATACAACCAGACGGAA
1346437 AGACTCAATG
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
74 2 0.02
75 106 0.98
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (75 bp):
AACCTCCCACAGCACTGATCAAGCCATGGCATACAACCAGACGGAAGGGCCTCGCGACCAAACCG
TTTCCACTGT
Found at i:1355607 original size:10 final size:11
Alignment explanation
Indices: 1355576--1355608 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1355566 ATTTTATATT
1355576 TACTATTTTTC
1 TACTATTTTTC
*
1355587 TACTATGTTTC
1 TACTATTTTTC
1355598 -ACTATTTTTC
1 TACTATTTTTC
1355608 T
1 T
1355609 TTTTCTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.18, C:0.18, G:0.03, T:0.61
Consensus pattern (11 bp):
TACTATTTTTC
Found at i:1361156 original size:2 final size:2
Alignment explanation
Indices: 1361149--1361175 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1361139 AAATGACATC
1361149 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 C
1361176 ACTAAGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1361219 original size:2 final size:2
Alignment explanation
Indices: 1361212--1361238 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1361202 TTAGTACTNC
1361212 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 C
1361239 ACTAAGCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1361247 original size:63 final size:61
Alignment explanation
Indices: 1361147--1361267 Score: 224
Period size: 63 Copynumber: 2.0 Consensus size: 61
1361137 ACAAATGACA
1361147 TCCTCTCTCTCTCTCTCTCTCTCTCTCTCACTAAGCTTTATTATGAGTAATTAATTTAGTAC
1 TCCTCTCTCTCTCTCTCTCTCTCTCTCTCACTAAGCTTTATTATGAG-AATTAATTTAGTAC
1361209 TNCCTCTCTCTCTCTCTCTCTCTCTCTCTCACTAAGCTTTATTATGAGAATTAATTTAG
1 T-CCTCTCTCTCTCTCTCTCTCTCTCTCTCACTAAGCTTTATTATGAGAATTAATTTAG
1361268 CAAAACTTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 12 0.21
63 46 0.79
ACGTcount: A:0.19, C:0.29, G:0.07, T:0.45
Consensus pattern (61 bp):
TCCTCTCTCTCTCTCTCTCTCTCTCTCTCACTAAGCTTTATTATGAGAATTAATTTAGTAC
Found at i:1366945 original size:21 final size:23
Alignment explanation
Indices: 1366921--1366974 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
1366911 TTTTTAAATA
1366921 TATTTTTAATT-AA-ATATATTT
1 TATTTTTAATTAAAGATATATTT
*
1366942 TATTTTTTATTACAAGTATATATTT
1 TATTTTTAATTA-AAG-ATATATTT
1366967 TATTTTTA
1 TATTTTTA
1366975 TTTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.37
23 2 0.07
25 15 0.56
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (23 bp):
TATTTTTAATTAAAGATATATTT
Found at i:1367831 original size:23 final size:23
Alignment explanation
Indices: 1367805--1367940 Score: 159
Period size: 23 Copynumber: 6.0 Consensus size: 23
1367795 CATTATTTAC
* * *
1367805 TAACTAGTCATGCAATGCCTTAC
1 TAACAAGTCACGCAATGCCTTAA
* *
1367828 TAACAAGTCACACAATACCTTAA
1 TAACAAGTCACGCAATGCCTTAA
*
1367851 TAACAAGTCACGCAATGCTTTAA
1 TAACAAGTCACGCAATGCCTTAA
1367874 TAACAAGTCACGCAATGCCTTAA
1 TAACAAGTCACGCAATGCCTTAA
*
1367897 TAACAAGTCACACAATG-CTT-A
1 TAACAAGTCACGCAATGCCTTAA
* * *
1367918 TCAACATGTCAAGTAATGCCTTA
1 T-AACAAGTCACGCAATGCCTTA
1367941 TCAGAAACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
21 2 0.02
22 15 0.16
23 79 0.82
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (23 bp):
TAACAAGTCACGCAATGCCTTAA
Found at i:1367974 original size:26 final size:25
Alignment explanation
Indices: 1367937--1368084 Score: 137
Period size: 26 Copynumber: 6.0 Consensus size: 25
1367927 CAAGTAATGC
*
1367937 CTTATCAGAAACTAATCACGCAATA
1 CTTATCAAAAACTAATCACGCAATA
* *
1367962 CCTTATCAAAAACTAGTCGCGCAAT-
1 -CTTATCAAAAACTAATCACGCAATA
* *
1367987 -TT-TC--AAAGTAAGTCACGTAATGA
1 CTTATCAAAAACTAA-TCACGCAAT-A
* *
1368010 CTTATCAAAAACTAATCATGTAATA
1 CTTATCAAAAACTAATCACGCAATA
*
1368035 TCTTATCAAAAACTAGTCACGCAATGA
1 -CTTATCAAAAACTAATCACGCAAT-A
1368062 CTTATC-AAAACTAATCACGCAAT
1 CTTATCAAAAACTAATCACGCAAT
1368085 GTCTAAAGTT
Statistics
Matches: 100, Mismatches: 13, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
20 5 0.05
21 7 0.07
22 2 0.02
23 2 0.02
24 2 0.02
25 19 0.19
26 56 0.56
27 7 0.07
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (25 bp):
CTTATCAAAAACTAATCACGCAATA
Found at i:1368119 original size:98 final size:99
Alignment explanation
Indices: 1367937--1368119 Score: 255
Period size: 98 Copynumber: 1.9 Consensus size: 99
1367927 CAAGTAATGC
* * * *
1367937 CTTATCAGAAACTAATCACGCAATACCTTATCAAAAACTAGTCGCGCAATTTTCAAAGTAAGTCA
1 CTTATCAAAAACTAATCACGCAATACCTTATCAAAAACTAATCACGCAATTCTCAAAGTAAGTCA
*
1368002 CGTAATGACTTATCAAAAACTAATCATGTAATAT
66 CGCAATGACTTATCAAAAACTAATCATGTAATAT
* *
1368036 CTTATCAAAAACTAGTCACGCAATGA-CTTATC-AAAACTAATCACGCAATGTCT-AAAGTTAGT
1 CTTATCAAAAACTAATCACGCAAT-ACCTTATCAAAAACTAATCACGCAAT-TCTCAAAGTAAGT
*
1368098 CACGCAATGCCTTATCAAAAAC
64 CACGCAATGACTTATCAAAAAC
1368120 CATGCACAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
98 43 0.58
99 30 0.41
100 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (99 bp):
CTTATCAAAAACTAATCACGCAATACCTTATCAAAAACTAATCACGCAATTCTCAAAGTAAGTCA
CGCAATGACTTATCAAAAACTAATCATGTAATAT
Found at i:1373401 original size:24 final size:24
Alignment explanation
Indices: 1373356--1373403 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1373346 TTGATGTTGG
* *
1373356 AGGTGGTGGTGGTGGTGATGATGA
1 AGGTGGTGGTGGTAGAGATGATGA
1373380 AGGTGGTGGTGG-AGAGACTGATGA
1 AGGTGGTGGTGGTAGAGA-TGATGA
1373404 TGGGGTTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.21, C:0.02, G:0.52, T:0.25
Consensus pattern (24 bp):
AGGTGGTGGTGGTAGAGATGATGA
Found at i:1373405 original size:27 final size:24
Alignment explanation
Indices: 1373347--1373393 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1373337 GGACTGCTTT
* * *
1373347 TGATGTTGGAGGTGGTGGTGGTGG
1 TGATGATGAAGGTGGTGGTGGAGG
1373371 TGATGATGAAGGTGGTGGTGGAG
1 TGATGATGAAGGTGGTGGTGGAG
1373394 AGACTGATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (24 bp):
TGATGATGAAGGTGGTGGTGGAGG
Found at i:1373455 original size:15 final size:15
Alignment explanation
Indices: 1373428--1373469 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1373418 ATTGTTGCTA
*
1373428 CTGTTGTTGTTGTTG
1 CTGTTGCTGTTGTTG
1373443 CTGTTGCTGTTGTTG
1 CTGTTGCTGTTGTTG
1373458 CT-TTGCTTGTTG
1 CTGTTGC-TGTTG
1373470 CTTTGCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.00, C:0.12, G:0.31, T:0.57
Consensus pattern (15 bp):
CTGTTGCTGTTGTTG
Found at i:1373467 original size:12 final size:13
Alignment explanation
Indices: 1373436--1373475 Score: 55
Period size: 12 Copynumber: 3.0 Consensus size: 13
1373426 TACTGTTGTT
1373436 GTTGTTGCTGTTGC
1 GTTGTTGCT-TTGC
1373450 TGTTGTTGCTTTGC
1 -GTTGTTGCTTTGC
1373464 -TTGTTGCTTTGC
1 GTTGTTGCTTTGC
1373476 AAATCTGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.48
14 4 0.16
15 9 0.36
ACGTcount: A:0.00, C:0.15, G:0.30, T:0.55
Consensus pattern (13 bp):
GTTGTTGCTTTGC
Found at i:1377855 original size:23 final size:22
Alignment explanation
Indices: 1377812--1377856 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
1377802 CATCCACAAA
* *
1377812 AATGGAAAAATTGATTCTTATT
1 AATGGAAAAATTGAATATTATT
1377834 AATGGAAAATATTGAATATTATT
1 AATGGAAAA-ATTGAATATTATT
1377857 TGAAATATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.40
Consensus pattern (22 bp):
AATGGAAAAATTGAATATTATT
Found at i:1378740 original size:5 final size:5
Alignment explanation
Indices: 1378712--1378763 Score: 56
Period size: 5 Copynumber: 11.0 Consensus size: 5
1378702 TTCAAGTCGG
* **
1378712 GAAAA GGAAA GAAAA TTAAA -AAAA G-AAA -AAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
1378759 GAAAA
1 GAAAA
1378764 AGGTGTTTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
4 9 0.23
5 30 0.77
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (5 bp):
GAAAA
Found at i:1378745 original size:22 final size:23
Alignment explanation
Indices: 1378719--1378764 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1378709 CGGGAAAAGG
**
1378719 AAAGAAAATTAAA-AAAAGAAAA
1 AAAGAAAAGAAAAGAAAAGAAAA
1378741 AAAGAAAAGAAAAGAAAAGAAAA
1 AAAGAAAAGAAAAGAAAAGAAAA
1378764 A
1 A
1378765 GGTGTTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (23 bp):
AAAGAAAAGAAAAGAAAAGAAAA
Found at i:1381804 original size:22 final size:23
Alignment explanation
Indices: 1381768--1381810 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1381758 ATGGAAAAGA
*
1381768 AAAAAGGAAGAGAGGGAGAGGAG
1 AAAAAGAAAGAGAGGGAGAGGAG
1381791 AAAAAGAAAG-GAGGGAGAGG
1 AAAAAGAAAGAGAGGGAGAGG
1381811 GACCCCAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAGAGAGGGAGAGGAG
Found at i:1383968 original size:48 final size:47
Alignment explanation
Indices: 1383905--1383995 Score: 146
Period size: 48 Copynumber: 1.9 Consensus size: 47
1383895 ACTATTTTAC
1383905 TTTTTATTTTAAGTTAAATAATGATTAACTAATTTCTATTAATCGTAT
1 TTTTTATTTTAAGTTAAATAATGATTAACTAATTT-TATTAATCGTAT
* * *
1383953 TTTTTATTTTGAGTTAAATAATGATTAATTAATTTTTTTAATC
1 TTTTTATTTTAAGTTAAATAATGATTAACTAATTTTATTAATC
1383996 AAAATATCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 7 0.17
48 33 0.82
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (47 bp):
TTTTTATTTTAAGTTAAATAATGATTAACTAATTTTATTAATCGTAT
Found at i:1386531 original size:51 final size:51
Alignment explanation
Indices: 1386449--1386569 Score: 197
Period size: 51 Copynumber: 2.4 Consensus size: 51
1386439 GAATGTGTTT
* *
1386449 CATTGGTGGTTGTTGATGTGGTCTACTTTTTTGCTGATGACTATGGTTTTA
1 CATTGGTGGTTGTTGATGTGGTCTACCTTTTTGCTGATGACTATGATTTTA
*
1386500 CATTGGTGGTTGTTGATGTGGTCTTCCTTTTTGCTGATGACTATGATTTTA
1 CATTGGTGGTTGTTGATGTGGTCTACCTTTTTGCTGATGACTATGATTTTA
* *
1386551 CATTGGTGATTGTTAATGT
1 CATTGGTGGTTGTTGATGT
1386570 TGTATATTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 65 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (51 bp):
CATTGGTGGTTGTTGATGTGGTCTACCTTTTTGCTGATGACTATGATTTTA
Found at i:1389252 original size:3 final size:3
Alignment explanation
Indices: 1389244--1389285 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1389234 AAGTGAAAGT
1389244 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1389286 AGGTCAGGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1390234 original size:31 final size:31
Alignment explanation
Indices: 1390163--1390302 Score: 167
Period size: 31 Copynumber: 4.6 Consensus size: 31
1390153 AATACATATG
* * *
1390163 TAATAGAAATCGAC-AAACATAGCTCTATAT
1 TAATAGAAATCGACAAAAAATAACTCTAAAT
* * *
1390193 TAATATAAATCGACAAAAAACAACTTTAAAT
1 TAATAGAAATCGACAAAAAATAACTCTAAAT
* * *
1390224 TAATAGAAATCGAC-AAACATAGCTCTATAT
1 TAATAGAAATCGACAAAAAATAACTCTAAAT
* *
1390254 TAATATAAATCGACAAAAAATAACTTTAAAT
1 TAATAGAAATCGACAAAAAATAACTCTAAAT
1390285 TAATAGAAATCGACAAAA
1 TAATAGAAATCGACAAAA
1390303 TGAACTCCAT
Statistics
Matches: 90, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
30 37 0.41
31 53 0.59
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.26
Consensus pattern (31 bp):
TAATAGAAATCGACAAAAAATAACTCTAAAT
Found at i:1390258 original size:61 final size:61
Alignment explanation
Indices: 1390163--1390301 Score: 269
Period size: 61 Copynumber: 2.3 Consensus size: 61
1390153 AATACATATG
1390163 TAATAGAAATCGACAAACATAGCTCTATATTAATATAAATCGACAAAAAACAACTTTAAAT
1 TAATAGAAATCGACAAACATAGCTCTATATTAATATAAATCGACAAAAAACAACTTTAAAT
*
1390224 TAATAGAAATCGACAAACATAGCTCTATATTAATATAAATCGACAAAAAATAACTTTAAAT
1 TAATAGAAATCGACAAACATAGCTCTATATTAATATAAATCGACAAAAAACAACTTTAAAT
1390285 TAATAGAAATCGACAAA
1 TAATAGAAATCGACAAA
1390302 ATGAACTCCA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 77 1.00
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (61 bp):
TAATAGAAATCGACAAACATAGCTCTATATTAATATAAATCGACAAAAAACAACTTTAAAT
Found at i:1392603 original size:2 final size:2
Alignment explanation
Indices: 1392596--1392654 Score: 109
Period size: 2 Copynumber: 29.0 Consensus size: 2
1392586 GTGAGAAATC
1392596 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
1392638 AG AG AG AG AG AG TAG AG
1 AG AG AG AG AG AG -AG AG
1392655 GTAATACATA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 54 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
AG
Found at i:1392707 original size:2 final size:2
Alignment explanation
Indices: 1392700--1392745 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1392690 AGAGNGCGAG
1392700 GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A 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
1392741 GA GA G
1 GA GA G
1392746 GTGATAATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1402200 original size:23 final size:24
Alignment explanation
Indices: 1402164--1402211 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1402154 AGCCTATTTA
*
1402164 TTTTTATAATTTTAGTTAATAAAT
1 TTTTTATAATTTTAATTAATAAAT
* *
1402188 TTTTTATTA-TTTAATTCATAAAT
1 TTTTTATAATTTTAATTAATAAAT
1402211 T
1 T
1402212 AAAATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTATAATTTTAATTAATAAAT
Found at i:1422553 original size:31 final size:33
Alignment explanation
Indices: 1422518--1422588 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
1422508 ACTTGTAATG
*
1422518 TTTAAGTTG-TTTGA-ATATTTGTTTTTAATTA
1 TTTAAGTTGATTTGAGATATTTATTTTTAATTA
*
1422549 TTTAAGTTGATATTTGAGATATTTATTTTTGATTA
1 TTTAAGTTG--ATTTGAGATATTTATTTTTAATTA
1422584 TTTAA
1 TTTAA
1422589 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 9 0.26
34 5 0.15
35 20 0.59
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (33 bp):
TTTAAGTTGATTTGAGATATTTATTTTTAATTA
Found at i:1432304 original size:29 final size:29
Alignment explanation
Indices: 1432258--1432356 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 29
1432248 GTATCTCTTC
* *
1432258 ACTATTCATCCA-CTCCTTGGTGGGTTGAA
1 ACTATACATCCATC-CCTTGGTGGGTTAAA
* * *
1432287 ACTATATATCCATCCCTTGATGAGTTAAA
1 ACTATACATCCATCCCTTGGTGGGTTAAA
* *
1432316 ACTATCCATCCATCCTTTGGTGGGTTAAA
1 ACTATACATCCATCCCTTGGTGGGTTAAA
* *
1432345 ATTATTCATCCA
1 ACTATACATCCA
1432357 CTTCTGGTGG
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
29 56 0.98
30 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.35
Consensus pattern (29 bp):
ACTATACATCCATCCCTTGGTGGGTTAAA
Found at i:1432383 original size:28 final size:28
Alignment explanation
Indices: 1432311--1432434 Score: 103
Period size: 28 Copynumber: 4.4 Consensus size: 28
1432301 CCTTGATGAG
* * *
1432311 TTAAAACTATCCATCCATCCTT-TGGTGGG
1 TTAAAATTATTCATCCA--CTTCTGGTGGA
1432340 TTAAAATTATTCATCCACTTCTGGTGGA
1 TTAAAATTATTCATCCACTTCTGGTGGA
* * *
1432368 TTAGAAATT-TTTATCCACTTTTAGTGG-
1 TTA-AAATTATTCATCCACTTCTGGTGGA
* * *
1432395 GTAAAATTATGCATCCACTTCTAGTGGA
1 TTAAAATTATTCATCCACTTCTGGTGGA
1432423 -TAAAATGTATTC
1 TTAAAAT-TATTC
1432435 TTAGAATTAG
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.06
27 26 0.33
28 28 0.35
29 20 0.25
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (28 bp):
TTAAAATTATTCATCCACTTCTGGTGGA
Found at i:1433006 original size:19 final size:19
Alignment explanation
Indices: 1432972--1433008 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1432962 AAACAATTAT
**
1432972 AAAAGAAAGTGTTTAGAGA
1 AAAAGAAAGTACTTAGAGA
1432991 AAAAGAAAGTACTTAGAG
1 AAAAGAAAGTACTTAGAG
1433009 GGAGTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (19 bp):
AAAAGAAAGTACTTAGAGA
Found at i:1433912 original size:29 final size:29
Alignment explanation
Indices: 1433870--1433928 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1433860 TGACACAAAA
1433870 ATTTTGATTGCTGCTGATGTTAGGTGCGT
1 ATTTTGATTGCTGCTGATGTTAGGTGCGT
1433899 ATTTTGATTGCTGCTGATGTTAGGTGCGT
1 ATTTTGATTGCTGCTGATGTTAGGTGCGT
1433928 A
1 A
1433929 CATGGGGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.15, C:0.10, G:0.31, T:0.44
Consensus pattern (29 bp):
ATTTTGATTGCTGCTGATGTTAGGTGCGT
Found at i:1437443 original size:14 final size:14
Alignment explanation
Indices: 1437424--1437451 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1437414 CACAATGATC
1437424 TTTATCTTGTTGAA
1 TTTATCTTGTTGAA
1437438 TTTATCTTGTTGAA
1 TTTATCTTGTTGAA
1437452 ATATGCTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (14 bp):
TTTATCTTGTTGAA
Found at i:1445234 original size:2 final size:2
Alignment explanation
Indices: 1445227--1445333 Score: 73
Period size: 2 Copynumber: 55.0 Consensus size: 2
1445217 ACAATACTTT
*
1445227 TA TA TA TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * * *
1445267 -A AA TA -A GTA -A AA TA AA TA GTA AA AA AA CTN T- TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
1445306 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1445334 CATAAGAATA
Statistics
Matches: 87, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
1 6 0.07
2 78 0.90
3 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (2 bp):
TA
Found at i:1445661 original size:13 final size:13
Alignment explanation
Indices: 1445643--1445668 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1445633 CTTGCGATAA
1445643 ATTTATTATTATT
1 ATTTATTATTATT
1445656 ATTTATTATTATT
1 ATTTATTATTATT
1445669 TGTCTGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTATTATTATT
Found at i:1450400 original size:17 final size:17
Alignment explanation
Indices: 1450378--1450414 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1450368 CTAACCAAAC
*
1450378 ATTCAAATGTAAAGATT
1 ATTCAAATGTAAAAATT
*
1450395 ATTCAATTGTAAAAATT
1 ATTCAAATGTAAAAATT
1450412 ATT
1 ATT
1450415 TAGAAAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (17 bp):
ATTCAAATGTAAAAATT
Found at i:1458205 original size:14 final size:14
Alignment explanation
Indices: 1458184--1458228 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
1458174 AAAGAAAGTG
1458184 AAAA-AGGAAAAGA
1 AAAAGAGGAAAAGA
1458197 AAAAGAGGAAAAAAGA
1 AAAAGAGG--AAAAGA
1458213 AAGAAGAGGAAAAGA
1 AA-AAGAGGAAAAGA
1458228 A
1 A
1458229 GTGAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.14
14 3 0.11
15 7 0.25
16 8 0.29
17 6 0.21
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAAAGAGGAAAAGA
Found at i:1458212 original size:16 final size:17
Alignment explanation
Indices: 1458191--1458225 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1458181 GTGAAAAAGG
1458191 AAAAGAAA-AAGAGGAA
1 AAAAGAAAGAAGAGGAA
1458207 AAAAGAAAGAAGAGGAA
1 AAAAGAAAGAAGAGGAA
1458224 AA
1 AA
1458226 GAAGTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAGAAAGAAGAGGAA
Found at i:1464717 original size:15 final size:15
Alignment explanation
Indices: 1464680--1464722 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1464670 GTTAAAAAAG
1464680 AAAAAAAACTATATT
1 AAAAAAAACTATATT
*
1464695 ---AGAAACTATATT
1 AAAAAAAACTATATT
1464707 AAAAAAAACTATATT
1 AAAAAAAACTATATT
1464722 A
1 A
1464723 GAAGTAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
12 11 0.48
15 12 0.52
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (15 bp):
AAAAAAAACTATATT
Found at i:1468019 original size:22 final size:23
Alignment explanation
Indices: 1467994--1468038 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1467984 TGAACACATT
*
1467994 AATAA-AATGGTGACTTAACAAA
1 AATAATAATGATGACTTAACAAA
*
1468016 AATAATAATTATGACTTAACAAA
1 AATAATAATGATGACTTAACAAA
1468039 GATGTTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.27
Consensus pattern (23 bp):
AATAATAATGATGACTTAACAAA
Found at i:1469423 original size:127 final size:127
Alignment explanation
Indices: 1469195--1469439 Score: 384
Period size: 127 Copynumber: 1.9 Consensus size: 127
1469185 AGATTCTATT
* *
1469195 AATATAAAATAATTAATAATTTCTAATAGTACCTGTCTTTTATATATAAAATAAATGACTAAAAG
1 AATATAAAATAATTAATAATTTCTAATAGTACCTGCCTTTTATACATAAAATAAATGACTAAAAG
**
1469260 TTGTCAAATTCAATTGATTTGTTTATTCAATAATGACTGTGTGCTATGTATTTTTAGAAATC
66 TTGTCAAATTCAATTGATTTGTTTATTCAATAATGACTGCATGCTATGTATTTTTAGAAATC
* * * * *
1469322 AATATAAAATAGTTATTAATTTCTAATAGTATCTGCCTTTTATACATAAAATGAATGATTAAAAG
1 AATATAAAATAATTAATAATTTCTAATAGTACCTGCCTTTTATACATAAAATAAATGACTAAAAG
*
1469387 TTGTCAAATGT-AATTGATTTGTTTATTCAATGATGACTGCATGCTATGTATTT
66 TTGTCAAAT-TCAATTGATTTGTTTATTCAATAATGACTGCATGCTATGTATTT
1469440 AAGAAATGAG
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
127 106 0.99
128 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (127 bp):
AATATAAAATAATTAATAATTTCTAATAGTACCTGCCTTTTATACATAAAATAAATGACTAAAAG
TTGTCAAATTCAATTGATTTGTTTATTCAATAATGACTGCATGCTATGTATTTTTAGAAATC
Found at i:1474084 original size:17 final size:17
Alignment explanation
Indices: 1474062--1474098 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1474052 CTAACCAAAC
1474062 ATTCAAATGTAAAAATT
1 ATTCAAATGTAAAAATT
* *
1474079 ATTCAATTGTAAAGATT
1 ATTCAAATGTAAAAATT
1474096 ATT
1 ATT
1474099 TAGAAAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (17 bp):
ATTCAAATGTAAAAATT
Found at i:1479424 original size:29 final size:29
Alignment explanation
Indices: 1479392--1479480 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
1479382 TCTTTTGCAT
1479392 GAGCATGTGCGGTGTGCGGCTGCTCGCAC
1 GAGCATGTGCGGTGTGCGGCTGCTCGCAC
1479421 GAGCATGTGCGGTGTGCGGCTGCTCGCAC
1 GAGCATGTGCGGTGTGCGGCTGCTCGCAC
*
1479450 GAGCATATGCGGTGTGCGGCTGCTCGCAC
1 GAGCATGTGCGGTGTGCGGCTGCTCGCAC
1479479 GA
1 GA
1479481 TTGTTTCTCG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.12, C:0.27, G:0.40, T:0.20
Consensus pattern (29 bp):
GAGCATGTGCGGTGTGCGGCTGCTCGCAC
Found at i:1486508 original size:25 final size:25
Alignment explanation
Indices: 1486480--1486533 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
1486470 GTCTAAGAGC
*
1486480 CTCTTCTGATCACTTCGATTTTGTA
1 CTCTACTGATCACTTCGATTTTGTA
1486505 CTCTACTGATCACTTCGATTTTGTA
1 CTCTACTGATCACTTCGATTTTGTA
1486530 CTCT
1 CTCT
1486534 GCTGCTGCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.17, C:0.26, G:0.11, T:0.46
Consensus pattern (25 bp):
CTCTACTGATCACTTCGATTTTGTA
Found at i:1490931 original size:29 final size:27
Alignment explanation
Indices: 1490890--1490952 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
1490880 ATTAATTATA
* *
1490890 AAAATTTATTTGATAAAAAATATAAATAT
1 AAAATTTAATTGA-AAAAAATA-AAAAAT
* *
1490919 AAAATTTAATTGAATACAATAAAAAAT
1 AAAATTTAATTGAAAAAAATAAAAAAT
1490946 AAAATTT
1 AAAATTT
1490953 TATTTAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 12 0.40
28 6 0.20
29 12 0.40
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAATTTAATTGAAAAAAATAAAAAAT
Found at i:1491778 original size:30 final size:30
Alignment explanation
Indices: 1491720--1491775 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1491710 TTTAGTTGAT
1491720 TTAGGATTTATTTTCTTTATTTTATTTAAA
1 TTAGGATTTATTTTCTTTATTTTATTTAAA
*
1491750 TTAGGA-TTCTTTTC-TTATTTTTATTT
1 TTAGGATTTATTTTCTTTA-TTTTATTT
1491776 TAATACTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 3 0.12
29 15 0.62
30 6 0.25
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.66
Consensus pattern (30 bp):
TTAGGATTTATTTTCTTTATTTTATTTAAA
Found at i:1492138 original size:40 final size:40
Alignment explanation
Indices: 1492083--1492160 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 40
1492073 TTGGCTATTT
*
1492083 TTCACCTTAGTGGGGTTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
*
1492123 TTCACCTTAGTGGGGTTTTCAACCTCGCCACGATTGGT
1 TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGT
1492161 ATTTTTCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (40 bp):
TTCACCTTAGTGGGGTTTTCAACCTCGCCAAGATTGGTGA
Found at i:1493292 original size:17 final size:17
Alignment explanation
Indices: 1493270--1493307 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1493260 TCTAACCAAA
1493270 TATTCAAATGTAAAAAT
1 TATTCAAATGTAAAAAT
* *
1493287 TATTCAATTGTAAAGAT
1 TATTCAAATGTAAAAAT
1493304 TATT
1 TATT
1493308 TAGAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (17 bp):
TATTCAAATGTAAAAAT
Found at i:1498865 original size:181 final size:179
Alignment explanation
Indices: 1498614--1498970 Score: 696
Period size: 181 Copynumber: 2.0 Consensus size: 179
1498604 ATAAGGAGGG
1498614 CTGTATTTTTTTTTTTTTTTTGAAAAGCATAATTTGTATATTCAGTGAGCCAAGAGTTACAGCAC
1 CTGTATTTTTTTTTTTTTTTTGAAAAGCATAATTTGTATATTCAGTGAGCCAAGAGTTACAGCAC
1498679 TATTCCACCTAAATTGATAGAATTAAGATAAAAGTTTAAAGATTAAGATTTAGACTTCTTAAATT
66 TATTCCACCTAAATTGATAGAATTAAGATAAAAGTTTAAAGATTAAGATTTAGACTTCTTAAATT
1498744 AAAGATTCTAGATATAGAGTAATTATATTTCTATGAATGGATAGGANGTT
131 AAAGATTCTAGATATAGAGTAATTATATTTCTATGAATGGATAGGA-GTT
1498794 CTGTATTTTTTTTTTTTTTTTTGAAAAGCATAATTTGTATATTCAGTGAGCCAAGAGTTACAGCA
1 CTGTA-TTTTTTTTTTTTTTTTGAAAAGCATAATTTGTATATTCAGTGAGCCAAGAGTTACAGCA
1498859 CTATTCCACCTAAATTGATAGAATTAAGATAAAAGTTTAAAGATTAAGATTTAGACTTCTTAAAT
65 CTATTCCACCTAAATTGATAGAATTAAGATAAAAGTTTAAAGATTAAGATTTAGACTTCTTAAAT
1498924 TAAAGATTCTAGATATAGAGTAATTATATTTCTATGAATGGATAGGA
130 TAAAGATTCTAGATATAGAGTAATTATATTTCTATGAATGGATAGGA
1498971 TTCAAATTTT
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
180 5 0.03
181 171 0.97
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.39
Consensus pattern (179 bp):
CTGTATTTTTTTTTTTTTTTTGAAAAGCATAATTTGTATATTCAGTGAGCCAAGAGTTACAGCAC
TATTCCACCTAAATTGATAGAATTAAGATAAAAGTTTAAAGATTAAGATTTAGACTTCTTAAATT
AAAGATTCTAGATATAGAGTAATTATATTTCTATGAATGGATAGGAGTT
Found at i:1499170 original size:18 final size:19
Alignment explanation
Indices: 1499131--1499168 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1499121 ATAATAGTAC
1499131 ATAGAAATGACATGGAAAA
1 ATAGAAATGACATGGAAAA
1499150 ATAGAAATGACATGGAAAA
1 ATAGAAATGACATGGAAAA
1499169 TACAAACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.21, T:0.16
Consensus pattern (19 bp):
ATAGAAATGACATGGAAAA
Found at i:1500711 original size:3 final size:3
Alignment explanation
Indices: 1500691--1500736 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
1500681 TTCATATGTA
* *
1500691 TAT TAA TAT TAA TAT TAT TAT TAT TAT TA- TAT TAT TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
1500736 T
1 T
1500737 TACTAATACT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1501301 original size:2 final size:2
Alignment explanation
Indices: 1501296--1501339 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
1501286 AGATTCTCTC
1501296 TA TA TA TA TA -A TA TA TA TA TA GTA TA TA TA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
1501337 TA T
1 TA T
1501340 CTGGAGTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1501339 original size:11 final size:11
Alignment explanation
Indices: 1501296--1501339 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
1501286 AGATTCTCTC
*
1501296 TATATATATAA
1 TATATATATAT
*
1501307 TATATATATAG
1 TATATATATAT
1501318 TATATATATAT
1 TATATATATAT
1501329 TATATATATAT
1 TATATATATAT
1501340 CTGGAGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
TATATATATAT
Found at i:1509299 original size:17 final size:17
Alignment explanation
Indices: 1509277--1509313 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1509267 CTAACCAAAC
1509277 ATTCAAATGTAAAAATT
1 ATTCAAATGTAAAAATT
* *
1509294 ATTCAATTGTAAAGATT
1 ATTCAAATGTAAAAATT
1509311 ATT
1 ATT
1509314 TAGAAAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (17 bp):
ATTCAAATGTAAAAATT
Found at i:1510706 original size:17 final size:17
Alignment explanation
Indices: 1510684--1510721 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1510674 TGTAACCAAA
*
1510684 TATTCAAATGTAAAGAT
1 TATTCAAATGTAAAAAT
*
1510701 TATTCAATTGTAAAAAT
1 TATTCAAATGTAAAAAT
1510718 TATT
1 TATT
1510722 TAGAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (17 bp):
TATTCAAATGTAAAAAT
Found at i:1515635 original size:27 final size:27
Alignment explanation
Indices: 1515581--1515635 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
1515571 GAATTACTTG
* *
1515581 TATTTTTATTTGAATCAAATAAGTTTA
1 TATTTTTATTTGAAACAAATAAGATTA
1515608 TATTTTTATTTTGAAACAAATAA-ATTA
1 TATTTTTA-TTTGAAACAAATAAGATTA
1515635 T
1 T
1515636 TATGGTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (27 bp):
TATTTTTATTTGAAACAAATAAGATTA
Found at i:1520192 original size:22 final size:22
Alignment explanation
Indices: 1520142--1520221 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
1520132 TATGAGTCAA
**
1520142 ATAATAATAATTTTTATTTAATT
1 ATAATAA-AATTAATATTTAATT
**
1520165 -TAATAATTTTATATATTTAATT
1 ATAATAAAATTA-ATATTTAATT
1520187 AT-ATAAAATTAATAATTTAATT
1 ATAATAAAATTAAT-ATTTAATT
*
1520209 ACTAATAATATTA
1 A-TAATAAAATTA
1520222 CTTATTTTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
21 4 0.09
22 31 0.69
23 2 0.04
24 8 0.18
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATAAAATTAATATTTAATT
Found at i:1522503 original size:25 final size:25
Alignment explanation
Indices: 1522474--1522527 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1522464 GATTAATAAT
*
1522474 ATTAATCTTCAT-GCAATAAATTAAC
1 ATTAATCTTCATAG-AATAAATAAAC
*
1522499 ATTAATCTTTATAGAATAAATAAAC
1 ATTAATCTTCATAGAATAAATAAAC
1522524 ATTA
1 ATTA
1522528 GTTTAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (25 bp):
ATTAATCTTCATAGAATAAATAAAC
Found at i:1528014 original size:3 final size:3
Alignment explanation
Indices: 1528006--1528042 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1527996 ACATCTCGAT
1528006 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1528043 ATGGTCAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1528713 original size:9 final size:8
Alignment explanation
Indices: 1528688--1528726 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
1528678 AATTATTGAG
1528688 TTAAATAT
1 TTAAATAT
1528696 TTAAATAT
1 TTAAATAT
1528704 TTATAATAT
1 TTA-AATAT
1528713 TTAAA-AT
1 TTAAATAT
*
1528720 TAAAATA
1 TTAAATA
1528727 AGAGAAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 6 0.21
8 14 0.50
9 8 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
TTAAATAT
Found at i:1530838 original size:69 final size:69
Alignment explanation
Indices: 1530749--1530877 Score: 195
Period size: 69 Copynumber: 1.9 Consensus size: 69
1530739 AGGACAAGAA
* **
1530749 GATGATGAAGAAGAAGATTATGGCTATCAGGAAGAAGGAGAAGATAGTGTGCTGGAGATGGAGGA
1 GATGATGAAGAAGAAGATTATGGCTATCAGGAAGAAGGAGAAGACAGTGACCTGGAGATGGAGGA
1530814 TGAT
66 TGAT
* * * *
1530818 GATGATGATGATGATGATTATGGCTATCTGGAAGAAGGAGAAGACAGTGACCTGGAGATG
1 GATGATGAAGAAGAAGATTATGGCTATCAGGAAGAAGGAGAAGACAGTGACCTGGAGATG
1530878 AAGAGAGAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.22
Consensus pattern (69 bp):
GATGATGAAGAAGAAGATTATGGCTATCAGGAAGAAGGAGAAGACAGTGACCTGGAGATGGAGGA
TGAT
Found at i:1543275 original size:4 final size:4
Alignment explanation
Indices: 1543266--1543291 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1543256 ACTCGAGATG
1543266 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
1543292 GTTGGTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1561203 original size:22 final size:21
Alignment explanation
Indices: 1561174--1561215 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1561164 ATCGGCTGCT
* *
1561174 CTTAAAAATATACTAAAAAAG
1 CTTAAAAAAAAACTAAAAAAG
1561195 CTTATAAAAAAAACTAAAAAA
1 CTTA-AAAAAAAACTAAAAAA
1561216 TATCAAGAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (21 bp):
CTTAAAAAAAAACTAAAAAAG
Found at i:1573042 original size:5 final size:5
Alignment explanation
Indices: 1573032--1573073 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
1573022 ATTCATGGTG
1573032 TTCTT TTCTT TTCTT TTCTT TT-TT TTCTT CTT-TT TTCCTT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT -TTCTT TT-CTT TT
1573074 TAAGTTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
4 6 0.18
5 21 0.64
6 6 0.18
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Done.