Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3273
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: 33118
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:2384 original size:11 final size:11
Alignment explanation
Indices: 2370--2402 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2360 CTTTTTACAC
2370 GAATTTTTTTT
1 GAATTTTTTTT
2381 GAA-TTTTTTT
1 GAATTTTTTTT
*
2391 CAATTTTTTTT
1 GAATTTTTTTT
2402 G
1 G
2403 GTAAAATGCA
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:0.03, G:0.09, T:0.70
Consensus pattern (11 bp):
GAATTTTTTTT
Found at i:3822 original size:9 final size:10
Alignment explanation
Indices: 3807--3846 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
3797 ACTTAGTAAT
3807 TAATTTAAAC
1 TAATTTAAAC
3817 -AATTTAAAC
1 TAATTTAAAC
3826 TAATTT-AAC
1 TAATTTAAAC
3835 TAATTT-AAC
1 TAATTTAAAC
3844 TAA
1 TAA
3847 AAACAGATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 24 0.83
10 5 0.17
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
TAATTTAAAC
Found at i:3829 original size:19 final size:18
Alignment explanation
Indices: 3807--3846 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
3797 ACTTAGTAAT
3807 TAATTTAAAC-AATTTAAAC
1 TAATTT-AACTAATTT-AAC
3826 TAATTTAACTAATTTAAC
1 TAATTTAACTAATTTAAC
3844 TAA
1 TAA
3847 AAACAGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATTTAACTAATTTAAC
Found at i:7331 original size:561 final size:552
Alignment explanation
Indices: 5777--7334 Score: 1473
Period size: 580 Copynumber: 2.7 Consensus size: 552
5767 TGTGGGCCAG
* * * *
5777 CATTAATGGCATC-CAACATCTCGTGTGAACTATCTTAAACCTCTTAACACGAAAACTTGA-ATT
1 CATTAATGGC-TCTCAACATCTCGTGTGATCTGTCTTAAACCTCTTAACACCAAAACTT-ATATC
* * * * * * *
5840 GACAATTATTAACTTCGTTTTTACTTTGTTACATTTGGCTCAAAGCTTTATTTATTTTAAGGATT
64 AACAATTATTAACTTCATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATT
*
5905 TGTTAATTTTTATTAATTAAAAAT-ATTATATAAATTGTAAGAAAATGAATACAAAAATATCATT
129 TGTTAATTTTTATTAATTAAAAATAATTACAT-AATTGTAAGAAAATGAATA-AAAAATATCATT
*
5969 TTATATAATACTTAAATTTTTTATCTATTAAACAAAAAATATTTACATAAATATTATATTTAATA
192 TTATATAATACTT-AATTTTTTATCTATTAAACAAAAAATATTTATATAAATATTATATTTAATA
** * ** *
6034 ATTTTAAATTATTTAAAAATAAAAAATTTAAACAATTATTATATATGTATCTATATTATTATTCA
256 ATTTTAAATTATTT--TTA-AAAAAATTTAAACAATTGTTATATACATATCTATATTATTATTTA
* * * * *
6099 AGTCCTGAGTTAAAATCACAAGTTAATCGAAATGTCACAAGTTAATCGAACACCAATTCAGTTAA
318 AGTCC----CT--AA-C-TAAGTT-A--G---TGTCACGAGTCAATCGAACACCAAATCAGTT-A
* * *
6164 AAAAATTACGAAAATGTCATTCCGTAATTAAAATAAATTATATTATTTGAGAATATTTCAATCTT
368 AAAAATTACGAAAATATCATTCTGTAATTAAAATAAA-GATA-TATTT--GAATATTT-AA---T
* * *
6229 TACTTAAAAAACAATAGAAAATTTGATGTAGATACTATATATGCATCTCCAAGAAGAGCGAAGCA
425 TACTTAAAAAACAATAGAAAATTTGACGTAGATACTATATATGCATCTCCAAGAACAGCCAAGCA
* * * *
6294 ATCTAAGGATTACCAAAACTTTGTCAAAGTATCTTCGTACCTCTCCAAACATTCTCACACCAC
490 ATCTAAAGATTACCAAAACTTAGTCAAACTATCTTCATACCTCTCCAAACATTCTCACACCAC
** * * * * *
6357 GGTTAATGGCTCTCAGCGTCTCATGTGAAT-TGTCTTAAACCTTTTAACACCAAAACTTGTATCA
1 CATTAATGGCTCTCAACATCTCGTGTG-ATCTGTCTTAAACCTCTTAACACCAAAACTTATATCA
* * * *
6421 ACAATTATTAACCTTCATTTTTGC-TTGGTACGTTTGGCTCCAAGGTTTATTTAATTCAAGGAGT
65 ACAATTATTAA-CTTCATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATT
* * *
6485 TATTAATTTTTATTAATT-AAAA-AA-TACATAAGTTGTAAGAAAATGAATACAAAATATAATTT
129 TGTTAATTTTTATTAATTAAAAATAATTACATAA-TTGTAAGAAAATGAATAAAAAATATCATTT
* *
6547 TATATAATACTTAATTCTTTTTATCTATTAATCAAAAGAACATTTATATAAATATTATATTTAAT
193 TATATAATACTTAA-T-TTTTTATCTATTAAACAAAA-AATATTTATATAAATATTATATTTAAT
*
6612 AATTTT-AA--A---TT----AAA-TTAAACAATTGTTATATACATATCTATATTATTAATTAAG
255 AATTTTAAATTATTTTTAAAAAAATTTAAACAATTGTTATATACATATCTATATTATTATTTAAG
* * * * * * * * * * *
6666 TCCCTAATTAAATTAATTTCAGGAATCAATTGAATACCAACTCAATTAAAGAAATTACAAAAATA
320 TCCCTAACTAAGTTAGTGTCACGAGTCAATCGAACACCAAATCAGTTAAA-AAATTACGAAAATA
* * * *
6731 TCATT-TCATAATCAAAATAAATTATATTTTTTGAAGATATTTTAATATTTATACTTAAAAATA-
384 TCATTCT-GTAATTAAAATAAA-GATA-TATTTG-A-ATA-TTT-A-A--T-TACTTAAAAA-AC
*
6794 AA-A-AAAA-TTGACGT-GAATACTATATGTAAAACCCTTGCATCTCCAATAACAGCCAAGCAAT
437 AATAGAAAATTTGACGTAG-ATACTATA--T---A----TGCATCTCCAAGAACAGCCAAGCAAT
*
6855 CTAAAGATTACCAAAACTGTCAGTCAAACTATCTTCATACCTCTTCAAACA-TCTCACACCAC
492 CTAAAGATTACCAAAACT-T-AGTCAAACTATCTTCATACCTCTCCAAACATTCTCACACCAC
* * *
6917 CATTAATAGCTCTCAACATCGCGTATGATCTGTCTTAAACCTCTTAACACCAAAACTTATATCAA
1 CATTAATGGCTCTCAACATCTCGTGTGATCTGTCTTAAACCTCTTAACACCAAAACTTATATCAA
* * *
6982 CAATTGTTAACTTGCATTTTTGCTTTACTATGTTTGGCTCAAAGGTTTATTTATTTCAAGGATTT
66 CAATTATTAACTT-CATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATTT
* *
7047 GTTCATTTTTATTAATTAAAAAATAATTACATAGATTGTAAGAAAATGAATATGAAAA-ATCATT
130 GTTAATTTTTATTAATT-AAAAATAATTACATA-ATTGTAAGAAAATGAATA-AAAAATATCATT
* ** *
7111 TGATATAATACTTAATTATTTTATCTATTAGCCAACAAATATTTATATAAATATTATATTTAATA
192 TTATATAATACTTAATT-TTTTATCTATTAAACAAAAAATATTTATATAAATATTATATTTAATA
* *
7176 ATTTTAAATTATTTTTTAAAAATAATTTAAACAATTGTTATATACATATTTATACTATTATTTAA
256 ATTTTAAATTA-TTTTTAAAAA-AATTTAAACAATTGTTATATACATATCTATATTATTATTTAA
* * * * * * *
7241 GACCCTAACTGAGTTAGTGTCATGAGTCAACCGAGCACCAAATCGGTCACAAAAATTACGAAAAT
319 GTCCCTAACTAAGTTAGTGTCACGAGTCAATCGAACACCAAATCAGTTA-AAAAATTACGAAAAT
7306 ATTC-TTCTGTAATTAAAAT-AAGATATATT
383 A-TCATTCTGTAATTAAAATAAAGATATATT
7335 ATTTGAGGGT
Statistics
Matches: 807, Mismatches: 116, Indels: 117
0.78 0.11 0.11
Matches are distributed among these distances:
549 2 0.00
550 18 0.02
551 68 0.08
552 8 0.01
553 13 0.02
554 1 0.00
555 1 0.00
556 1 0.00
557 4 0.00
559 47 0.06
560 82 0.10
561 77 0.10
563 37 0.05
564 21 0.03
565 80 0.10
566 9 0.01
570 2 0.00
573 3 0.00
574 4 0.00
575 4 0.00
576 96 0.12
577 31 0.04
578 42 0.05
579 38 0.05
580 107 0.13
581 11 0.01
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (552 bp):
CATTAATGGCTCTCAACATCTCGTGTGATCTGTCTTAAACCTCTTAACACCAAAACTTATATCAA
CAATTATTAACTTCATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATTTG
TTAATTTTTATTAATTAAAAATAATTACATAATTGTAAGAAAATGAATAAAAAATATCATTTTAT
ATAATACTTAATTTTTTATCTATTAAACAAAAAATATTTATATAAATATTATATTTAATAATTTT
AAATTATTTTTAAAAAAATTTAAACAATTGTTATATACATATCTATATTATTATTTAAGTCCCTA
ACTAAGTTAGTGTCACGAGTCAATCGAACACCAAATCAGTTAAAAAATTACGAAAATATCATTCT
GTAATTAAAATAAAGATATATTTGAATATTTAATTACTTAAAAAACAATAGAAAATTTGACGTAG
ATACTATATATGCATCTCCAAGAACAGCCAAGCAATCTAAAGATTACCAAAACTTAGTCAAACTA
TCTTCATACCTCTCCAAACATTCTCACACCAC
Found at i:8551 original size:42 final size:42
Alignment explanation
Indices: 8488--8634 Score: 142
Period size: 42 Copynumber: 3.5 Consensus size: 42
8478 TATTTGACAC
*
8488 AATTATATAACATAAATAAAATATCAAAATCAATATAATAAA
1 AATTATATAACATAAAAAAAATATCAAAATCAATATAATAAA
*** * *
8530 AATTA-ATAACATACAAAAAAATAT-TTGA-CAATAT-TTGACAC
1 AATTATATAACATA-AAAAAAATATCAAAATCAATATAAT-A-AA
* *
8571 AATTATATAACATAAATAAATATATCAGAATCAATATAATAAA
1 AATTATATAACATAAA-AAAAATATCAAAATCAATATAATAAA
8614 AATTA-ATAACATACAAAAAAA
1 AATTATATAACATA-AAAAAAA
8635 CATATTTTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
39 1 0.01
40 7 0.08
41 17 0.20
42 41 0.49
43 9 0.11
44 7 0.08
45 1 0.01
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (42 bp):
AATTATATAACATAAAAAAAATATCAAAATCAATATAATAAA
Found at i:8557 original size:83 final size:84
Alignment explanation
Indices: 8467--8634 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
8457 AATAAATTGT
8467 ATATTTGACAATATTTGACACAATTATATAACATAAATAAA-ATATCAAAATCAATATAATAAAA
1 ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAAAATCAATATAATAAAA
8531 ATTAATAACATACAAAAAA
66 ATTAATAACATACAAAAAA
*
8550 ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAGAATCAATATAATAAAA
1 ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAAAATCAATATAATAAAA
8615 ATTAATAACATACAAAAAA
66 ATTAATAACATACAAAAAA
8634 A
1 A
8635 CATATTTTTA
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 41 0.49
84 42 0.51
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (84 bp):
ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAAAATCAATATAATAAAA
ATTAATAACATACAAAAAA
Found at i:10107 original size:13 final size:14
Alignment explanation
Indices: 10083--10112 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
10073 ATTTTATTAC
10083 TTAATATTAATTTT
1 TTAATATTAATTTT
10097 TTAAT-TTAATTTT
1 TTAATATTAATTTT
10110 TTA
1 TTA
10113 TAATTACAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAATATTAATTTT
Found at i:10470 original size:15 final size:15
Alignment explanation
Indices: 10450--10479 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10440 ATCCTTTCCC
10450 TAAAATTATAAATTT
1 TAAAATTATAAATTT
*
10465 TAAAATTTTAAATTT
1 TAAAATTATAAATTT
10480 AAATTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAATTATAAATTT
Found at i:10543 original size:10 final size:10
Alignment explanation
Indices: 10528--10566 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
10518 ATTACTAATT
*
10528 TTTAATATTA
1 TTTAATTTTA
10538 TTTAATTTTTA
1 TTTAA-TTTTA
10549 TCTTAATTTTA
1 T-TTAATTTTA
10560 TTTAATT
1 TTTAATT
10567 AATCAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 11 0.42
11 11 0.42
12 4 0.15
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:10626 original size:23 final size:23
Alignment explanation
Indices: 10598--10646 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
10588 AAATATTATT
*
10598 AAAGAGAATTGATTTTGTGTTAG
1 AAAGAGAATTGATTTTCTGTTAG
10621 AAAGAGAATTGATTTTCTGTTAG
1 AAAGAGAATTGATTTTCTGTTAG
10644 AAA
1 AAA
10647 ATGTATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (23 bp):
AAAGAGAATTGATTTTCTGTTAG
Found at i:13406 original size:20 final size:19
Alignment explanation
Indices: 13375--13429 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 19
13365 ACAAATATAT
*
13375 AAAAATACATAAATATTTTCA
1 AAAAATA-ATAAAAATTTT-A
13396 AAAAATAATAATAAATTTTA
1 AAAAATAATAA-AAATTTTA
13416 AAAAAT-ATAAAAAT
1 AAAAATAATAAAAAT
13430 ATAAAATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 11 0.34
21 13 0.41
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATAATAAAAATTTTA
Found at i:13453 original size:51 final size:51
Alignment explanation
Indices: 13371--13482 Score: 140
Period size: 49 Copynumber: 2.2 Consensus size: 51
13361 TCTAACAAAT
13371 ATATAAAAATACATAAATATTTTCAAAAAATAATA-AT-AAATTTTAAAAA
1 ATATAAAAATACATAAATATTTTCAAAAAATAATATATAAAATTTTAAAAA
* * *
13420 ATATAAAAATATA-AAATATTGTTGATAAGAAATAATATATAAAATTTTAAAAT
1 ATATAAAAATACATAAATATT-TTCA-AA-AAATAATATATAAAATTTTAAAAA
13473 ATATTAAAAA
1 ATA-TAAAAA
13483 ATTCAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
48 7 0.13
49 15 0.28
50 2 0.04
51 8 0.15
52 2 0.04
53 14 0.26
54 6 0.11
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.34
Consensus pattern (51 bp):
ATATAAAAATACATAAATATTTTCAAAAAATAATATATAAAATTTTAAAAA
Found at i:13476 original size:19 final size:19
Alignment explanation
Indices: 13449--13509 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
13439 TGTTGATAAG
13449 AAATAATATATAAAATTTTA
1 AAAT-ATATATAAAATTTTA
* **
13469 AAATATATTAAAAAATTCAA
1 AAATATA-TATAAAATTTTA
*
13489 AAATATA-ATAATAAATTTA
1 AAATATATATAA-AATTTTA
13508 AA
1 AA
13510 TTTTATACCA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.09
19 9 0.28
20 20 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATATATATAAAATTTTA
Found at i:13483 original size:20 final size:20
Alignment explanation
Indices: 13460--13509 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
13450 AATAATATAT
* *
13460 AAAATTTTAAAATATATTAA
1 AAAATTTAAAAATATAATAA
*
13480 AAAATTCAAAAATATAATAA
1 AAAATTTAAAAATATAATAA
*
13500 TAAATTTAAA
1 AAAATTTAAA
13510 TTTTATACCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTTAAAAATATAATAA
Found at i:13638 original size:51 final size:51
Alignment explanation
Indices: 13561--13664 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 51
13551 AATCCCTCAC
*
13561 CCCTTTCCCCTTCCCCCACCAAACCTCCCCCACCACCATCATTTTCTCTCT
1 CCCTTTCCCCTTCCCCCACCAAACCTCCCCCACCACCATCATTCTCTCTCT
* * **
13612 CCCTTTCCCC-TCCCTCCACCAGACCTCCCTCACCACTGTCATTCTCTCTCT
1 CCCTTTCCCCTTCCC-CCACCAAACCTCCCCCACCACCATCATTCTCTCTCT
13663 CC
1 CC
13665 TTATTTGCTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 4 0.09
51 43 0.91
ACGTcount: A:0.13, C:0.57, G:0.02, T:0.28
Consensus pattern (51 bp):
CCCTTTCCCCTTCCCCCACCAAACCTCCCCCACCACCATCATTCTCTCTCT
Found at i:18674 original size:11 final size:11
Alignment explanation
Indices: 18660--18692 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
18650 CTTTTTACAC
18660 GAATTTTTTTT
1 GAATTTTTTTT
18671 GAA-TTTTTTT
1 GAATTTTTTTT
*
18681 CAATTTTTTTT
1 GAATTTTTTTT
18692 G
1 G
18693 GTAAAATGCA
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:0.03, G:0.09, T:0.70
Consensus pattern (11 bp):
GAATTTTTTTT
Found at i:20112 original size:9 final size:10
Alignment explanation
Indices: 20097--20136 Score: 59
Period size: 9 Copynumber: 4.3 Consensus size: 10
20087 ACTTAGTAAT
20097 TAATTTAAAC
1 TAATTTAAAC
20107 -AATTTAAAC
1 TAATTTAAAC
20116 TAATTT-AAC
1 TAATTTAAAC
20125 TAATTT-AAC
1 TAATTTAAAC
20134 TAA
1 TAA
20137 AAACAGATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
9 24 0.83
10 5 0.17
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (10 bp):
TAATTTAAAC
Found at i:20119 original size:19 final size:18
Alignment explanation
Indices: 20097--20136 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
20087 ACTTAGTAAT
20097 TAATTTAAAC-AATTTAAAC
1 TAATTT-AACTAATTT-AAC
20116 TAATTTAACTAATTTAAC
1 TAATTTAACTAATTTAAC
20134 TAA
1 TAA
20137 AAACAGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATTTAACTAATTTAAC
Found at i:23621 original size:561 final size:552
Alignment explanation
Indices: 22067--23624 Score: 1473
Period size: 580 Copynumber: 2.7 Consensus size: 552
22057 TGTGGGCCAG
* * * *
22067 CATTAATGGCATC-CAACATCTCGTGTGAACTATCTTAAACCTCTTAACACGAAAACTTGA-ATT
1 CATTAATGGC-TCTCAACATCTCGTGTGATCTGTCTTAAACCTCTTAACACCAAAACTT-ATATC
* * * * * * *
22130 GACAATTATTAACTTCGTTTTTACTTTGTTACATTTGGCTCAAAGCTTTATTTATTTTAAGGATT
64 AACAATTATTAACTTCATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATT
*
22195 TGTTAATTTTTATTAATTAAAAAT-ATTATATAAATTGTAAGAAAATGAATACAAAAATATCATT
129 TGTTAATTTTTATTAATTAAAAATAATTACAT-AATTGTAAGAAAATGAATA-AAAAATATCATT
*
22259 TTATATAATACTTAAATTTTTTATCTATTAAACAAAAAATATTTACATAAATATTATATTTAATA
192 TTATATAATACTT-AATTTTTTATCTATTAAACAAAAAATATTTATATAAATATTATATTTAATA
** * ** *
22324 ATTTTAAATTATTTAAAAATAAAAAATTTAAACAATTATTATATATGTATCTATATTATTATTCA
256 ATTTTAAATTATTT--TTA-AAAAAATTTAAACAATTGTTATATACATATCTATATTATTATTTA
* * * * *
22389 AGTCCTGAGTTAAAATCACAAGTTAATCGAAATGTCACAAGTTAATCGAACACCAATTCAGTTAA
318 AGTCC----CT--AA-C-TAAGTT-A--G---TGTCACGAGTCAATCGAACACCAAATCAGTT-A
* * *
22454 AAAAATTACGAAAATGTCATTCCGTAATTAAAATAAATTATATTATTTGAGAATATTTCAATCTT
368 AAAAATTACGAAAATATCATTCTGTAATTAAAATAAA-GATA-TATTT--GAATATTT-AA---T
* * *
22519 TACTTAAAAAACAATAGAAAATTTGATGTAGATACTATATATGCATCTCCAAGAAGAGCGAAGCA
425 TACTTAAAAAACAATAGAAAATTTGACGTAGATACTATATATGCATCTCCAAGAACAGCCAAGCA
* * * *
22584 ATCTAAGGATTACCAAAACTTTGTCAAAGTATCTTCGTACCTCTCCAAACATTCTCACACCAC
490 ATCTAAAGATTACCAAAACTTAGTCAAACTATCTTCATACCTCTCCAAACATTCTCACACCAC
** * * * * *
22647 GGTTAATGGCTCTCAGCGTCTCATGTGAAT-TGTCTTAAACCTTTTAACACCAAAACTTGTATCA
1 CATTAATGGCTCTCAACATCTCGTGTG-ATCTGTCTTAAACCTCTTAACACCAAAACTTATATCA
* * * *
22711 ACAATTATTAACCTTCATTTTTGC-TTGGTACGTTTGGCTCCAAGGTTTATTTAATTCAAGGAGT
65 ACAATTATTAA-CTTCATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATT
* * *
22775 TATTAATTTTTATTAATT-AAAA-AA-TACATAAGTTGTAAGAAAATGAATACAAAATATAATTT
129 TGTTAATTTTTATTAATTAAAAATAATTACATAA-TTGTAAGAAAATGAATAAAAAATATCATTT
* *
22837 TATATAATACTTAATTCTTTTTATCTATTAATCAAAAGAACATTTATATAAATATTATATTTAAT
193 TATATAATACTTAA-T-TTTTTATCTATTAAACAAAA-AATATTTATATAAATATTATATTTAAT
*
22902 AATTTT-AA--A---TT----AAA-TTAAACAATTGTTATATACATATCTATATTATTAATTAAG
255 AATTTTAAATTATTTTTAAAAAAATTTAAACAATTGTTATATACATATCTATATTATTATTTAAG
* * * * * * * * * * *
22956 TCCCTAATTAAATTAATTTCAGGAATCAATTGAATACCAACTCAATTAAAGAAATTACAAAAATA
320 TCCCTAACTAAGTTAGTGTCACGAGTCAATCGAACACCAAATCAGTTAAA-AAATTACGAAAATA
* * * *
23021 TCATT-TCATAATCAAAATAAATTATATTTTTTGAAGATATTTTAATATTTATACTTAAAAATA-
384 TCATTCT-GTAATTAAAATAAA-GATA-TATTTG-A-ATA-TTT-A-A--T-TACTTAAAAA-AC
*
23084 AA-A-AAAA-TTGACGT-GAATACTATATGTAAAACCCTTGCATCTCCAATAACAGCCAAGCAAT
437 AATAGAAAATTTGACGTAG-ATACTATA--T---A----TGCATCTCCAAGAACAGCCAAGCAAT
*
23145 CTAAAGATTACCAAAACTGTCAGTCAAACTATCTTCATACCTCTTCAAACA-TCTCACACCAC
492 CTAAAGATTACCAAAACT-T-AGTCAAACTATCTTCATACCTCTCCAAACATTCTCACACCAC
* * *
23207 CATTAATAGCTCTCAACATCGCGTATGATCTGTCTTAAACCTCTTAACACCAAAACTTATATCAA
1 CATTAATGGCTCTCAACATCTCGTGTGATCTGTCTTAAACCTCTTAACACCAAAACTTATATCAA
* * *
23272 CAATTGTTAACTTGCATTTTTGCTTTACTATGTTTGGCTCAAAGGTTTATTTATTTCAAGGATTT
66 CAATTATTAACTT-CATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATTT
* *
23337 GTTCATTTTTATTAATTAAAAAATAATTACATAGATTGTAAGAAAATGAATATGAAAA-ATCATT
130 GTTAATTTTTATTAATT-AAAAATAATTACATA-ATTGTAAGAAAATGAATA-AAAAATATCATT
* ** *
23401 TGATATAATACTTAATTATTTTATCTATTAGCCAACAAATATTTATATAAATATTATATTTAATA
192 TTATATAATACTTAATT-TTTTATCTATTAAACAAAAAATATTTATATAAATATTATATTTAATA
* *
23466 ATTTTAAATTATTTTTTAAAAATAATTTAAACAATTGTTATATACATATTTATACTATTATTTAA
256 ATTTTAAATTA-TTTTTAAAAA-AATTTAAACAATTGTTATATACATATCTATATTATTATTTAA
* * * * * * *
23531 GACCCTAACTGAGTTAGTGTCATGAGTCAACCGAGCACCAAATCGGTCACAAAAATTACGAAAAT
319 GTCCCTAACTAAGTTAGTGTCACGAGTCAATCGAACACCAAATCAGTTA-AAAAATTACGAAAAT
23596 ATTC-TTCTGTAATTAAAAT-AAGATATATT
383 A-TCATTCTGTAATTAAAATAAAGATATATT
23625 ATTTGAGGGT
Statistics
Matches: 807, Mismatches: 116, Indels: 117
0.78 0.11 0.11
Matches are distributed among these distances:
549 2 0.00
550 18 0.02
551 68 0.08
552 8 0.01
553 13 0.02
554 1 0.00
555 1 0.00
556 1 0.00
557 4 0.00
559 47 0.06
560 82 0.10
561 77 0.10
563 37 0.05
564 21 0.03
565 80 0.10
566 9 0.01
570 2 0.00
573 3 0.00
574 4 0.00
575 4 0.00
576 96 0.12
577 31 0.04
578 42 0.05
579 38 0.05
580 107 0.13
581 11 0.01
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (552 bp):
CATTAATGGCTCTCAACATCTCGTGTGATCTGTCTTAAACCTCTTAACACCAAAACTTATATCAA
CAATTATTAACTTCATTTTTGCTTTGCTACGTTTGGCTCAAAGGTTTATTTATTTCAAGGATTTG
TTAATTTTTATTAATTAAAAATAATTACATAATTGTAAGAAAATGAATAAAAAATATCATTTTAT
ATAATACTTAATTTTTTATCTATTAAACAAAAAATATTTATATAAATATTATATTTAATAATTTT
AAATTATTTTTAAAAAAATTTAAACAATTGTTATATACATATCTATATTATTATTTAAGTCCCTA
ACTAAGTTAGTGTCACGAGTCAATCGAACACCAAATCAGTTAAAAAATTACGAAAATATCATTCT
GTAATTAAAATAAAGATATATTTGAATATTTAATTACTTAAAAAACAATAGAAAATTTGACGTAG
ATACTATATATGCATCTCCAAGAACAGCCAAGCAATCTAAAGATTACCAAAACTTAGTCAAACTA
TCTTCATACCTCTCCAAACATTCTCACACCAC
Found at i:24842 original size:42 final size:42
Alignment explanation
Indices: 24779--24925 Score: 142
Period size: 42 Copynumber: 3.5 Consensus size: 42
24769 TATTTGACAC
*
24779 AATTATATAACATAAATAAAATATCAAAATCAATATAATAAA
1 AATTATATAACATAAAAAAAATATCAAAATCAATATAATAAA
*** * *
24821 AATTA-ATAACATACAAAAAAATAT-TTGA-CAATAT-TTGACAC
1 AATTATATAACATA-AAAAAAATATCAAAATCAATATAAT-A-AA
* *
24862 AATTATATAACATAAATAAATATATCAGAATCAATATAATAAA
1 AATTATATAACATAAA-AAAAATATCAAAATCAATATAATAAA
24905 AATTA-ATAACATACAAAAAAA
1 AATTATATAACATA-AAAAAAA
24926 CATATTTTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
39 1 0.01
40 7 0.08
41 17 0.20
42 41 0.49
43 9 0.11
44 7 0.08
45 1 0.01
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (42 bp):
AATTATATAACATAAAAAAAATATCAAAATCAATATAATAAA
Found at i:24848 original size:83 final size:84
Alignment explanation
Indices: 24758--24925 Score: 320
Period size: 84 Copynumber: 2.0 Consensus size: 84
24748 AATAAATTGT
24758 ATATTTGACAATATTTGACACAATTATATAACATAAATAAA-ATATCAAAATCAATATAATAAAA
1 ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAAAATCAATATAATAAAA
24822 ATTAATAACATACAAAAAA
66 ATTAATAACATACAAAAAA
*
24841 ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAGAATCAATATAATAAAA
1 ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAAAATCAATATAATAAAA
24906 ATTAATAACATACAAAAAA
66 ATTAATAACATACAAAAAA
24925 A
1 A
24926 CATATTTTTA
Statistics
Matches: 83, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
83 41 0.49
84 42 0.51
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (84 bp):
ATATTTGACAATATTTGACACAATTATATAACATAAATAAATATATCAAAATCAATATAATAAAA
ATTAATAACATACAAAAAA
Found at i:26398 original size:13 final size:14
Alignment explanation
Indices: 26374--26403 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
26364 ATTTTATTAC
26374 TTAATATTAATTTT
1 TTAATATTAATTTT
26388 TTAAT-TTAATTTT
1 TTAATATTAATTTT
26401 TTA
1 TTA
26404 TAATTACAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAATATTAATTTT
Found at i:26762 original size:15 final size:15
Alignment explanation
Indices: 26742--26771 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26732 ATCCTTTCCC
26742 TAAAATTATAAATTT
1 TAAAATTATAAATTT
*
26757 TAAAATTTTAAATTT
1 TAAAATTATAAATTT
26772 AAATTTAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAAAATTATAAATTT
Found at i:26835 original size:10 final size:10
Alignment explanation
Indices: 26820--26858 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
26810 ATTACTAATT
*
26820 TTTAATATTA
1 TTTAATTTTA
26830 TTTAATTTTTA
1 TTTAA-TTTTA
26841 TCTTAATTTTA
1 T-TTAATTTTA
26852 TTTAATT
1 TTTAATT
26859 AATCAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 11 0.42
11 11 0.42
12 4 0.15
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:26918 original size:23 final size:23
Alignment explanation
Indices: 26890--26938 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
26880 AAATATTATT
*
26890 AAAGAGAATTGATTTTGTGTTAG
1 AAAGAGAATTGATTTTCTGTTAG
26913 AAAGAGAATTGATTTTCTGTTAG
1 AAAGAGAATTGATTTTCTGTTAG
26936 AAA
1 AAA
26939 ATGTATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (23 bp):
AAAGAGAATTGATTTTCTGTTAG
Found at i:29700 original size:22 final size:21
Alignment explanation
Indices: 29667--29725 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
29657 ACAAATATAT
*
29667 AAAAATA-CATAAATATTTTCA
1 AAAAATATAATAAATATTTT-A
*
29688 AAAAATATAATAATAAATTTTA
1 AAAAATATAATAA-ATATTTTA
29710 AAAAATATAA-AAATAT
1 AAAAATATAATAAATAT
29726 AAAATATTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 3 0.09
21 9 0.27
22 15 0.45
23 6 0.18
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAATATAATAAATATTTTA
Found at i:29713 original size:23 final size:22
Alignment explanation
Indices: 29681--29724 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29671 ATACATAAAT
*
29681 ATTTTCAAAAAATATAATAATAA
1 ATTTT-AAAAAATATAAAAATAA
29704 ATTTTAAAAAATATAAAAATA
1 ATTTTAAAAAATATAAAAATA
29725 TAAAATATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
ATTTTAAAAAATATAAAAATAA
Found at i:29720 original size:51 final size:53
Alignment explanation
Indices: 29663--29776 Score: 137
Period size: 51 Copynumber: 2.2 Consensus size: 53
29653 TCTAACAAAT
29663 ATATAAAAATACATAAATATT-TTCA-AAAAATATAATA-AT-AAATTTTAAAAA
1 ATATAAAAATACA-AAATATTGTTCATAAAAA-ATAATATATAAAATTTTAAAAA
* * * *
29714 ATATAAAAATATAAAATATTGTTGATAAGAAATAATATATAAAATTTTAAAAT
1 ATATAAAAATACAAAATATTGTTCATAAAAAATAATATATAAAATTTTAAAAA
29767 ATATTAAAAA
1 ATA-TAAAAA
29777 ATTCAAAAAT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
50 7 0.13
51 21 0.39
52 6 0.11
53 14 0.26
54 6 0.11
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (53 bp):
ATATAAAAATACAAAATATTGTTCATAAAAAATAATATATAAAATTTTAAAAA
Found at i:29747 original size:53 final size:51
Alignment explanation
Indices: 29663--29776 Score: 126
Period size: 53 Copynumber: 2.2 Consensus size: 51
29653 TCTAACAAAT
29663 ATATAAAAATACATAAATATTTTCAAAAAAT-ATA-ATAATAAATTTTAAAAA
1 ATATAAAAATACATAAATATTTTCAAAAAATAATATAT-A-AAATTTTAAAAA
* * *
29714 ATATAAAAATATA-AAATATTGTTGATAAGAAATAATATATAAAATTTTAAAAT
1 ATATAAAAATACATAAATATT-TTCA-AA-AAATAATATATAAAATTTTAAAAA
29767 ATATTAAAAA
1 ATA-TAAAAA
29777 ATTCAAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
50 7 0.13
51 15 0.28
52 2 0.04
53 18 0.33
54 10 0.19
55 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (51 bp):
ATATAAAAATACATAAATATTTTCAAAAAATAATATATAAAATTTTAAAAA
Found at i:29770 original size:19 final size:19
Alignment explanation
Indices: 29743--29803 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
29733 TGTTGATAAG
29743 AAATAATATATAAAATTTTA
1 AAAT-ATATATAAAATTTTA
* **
29763 AAATATATTAAAAAATTCAA
1 AAATATA-TATAAAATTTTA
*
29783 AAATATA-ATAATAAATTTA
1 AAATATATATAA-AATTTTA
29802 AA
1 AA
29804 TTTTATACCA
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.09
19 9 0.28
20 20 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATATATATAAAATTTTA
Found at i:29777 original size:20 final size:20
Alignment explanation
Indices: 29754--29803 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
29744 AATAATATAT
* *
29754 AAAATTTTAAAATATATTAA
1 AAAATTTAAAAATATAATAA
*
29774 AAAATTCAAAAATATAATAA
1 AAAATTTAAAAATATAATAA
*
29794 TAAATTTAAA
1 AAAATTTAAA
29804 TTTTATACCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATTTAAAAATATAATAA
Found at i:29931 original size:50 final size:51
Alignment explanation
Indices: 29855--29957 Score: 147
Period size: 50 Copynumber: 2.0 Consensus size: 51
29845 AATCCCTCAC
*
29855 CCCTTTCCCCTTCCCCCACCAAACCTCCC-CACCACCATCATTTTCTCTCT
1 CCCTTTCCCCTTCCCCCACCAAACCTCCCTCACCACCATCATTCTCTCTCT
* **
29905 CCCTTTCCCC-TCCCTCCACCAGACCTCCCTCACCACTGTCATTCTCTCTCT
1 CCCTTTCCCCTTCCC-CCACCAAACCTCCCTCACCACCATCATTCTCTCTCT
29956 CC
1 CC
29958 TTATTTGCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
49 4 0.09
50 23 0.49
51 20 0.43
ACGTcount: A:0.14, C:0.56, G:0.02, T:0.28
Consensus pattern (51 bp):
CCCTTTCCCCTTCCCCCACCAAACCTCCCTCACCACCATCATTCTCTCTCT
Done.