Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2068
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: 71886
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:13720 original size:16 final size:16
Alignment explanation
Indices: 13699--13730 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
13689 CTCGAAACTG
13699 ATCCGAACCCGAAAGA
1 ATCCGAACCCGAAAGA
13715 ATCCGAACCCGAAAGA
1 ATCCGAACCCGAAAGA
13731 GTCCAAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.31, G:0.19, T:0.06
Consensus pattern (16 bp):
ATCCGAACCCGAAAGA
Found at i:22293 original size:20 final size:19
Alignment explanation
Indices: 22267--22338 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
22257 AAGACATAAC
22267 GTATCGATACATTGAAGAAT
1 GTATCGATACATTGAA-AAT
* * *
22287 ATATCGATACATTCATACAT
1 GTATCGATACATTGA-AAAT
*
22307 GTATCGATATATTGAAAAAT
1 GTATCGATACATTG-AAAAT
22327 GTATCGATACAT
1 GTATCGATACAT
22339 CTGGGTAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 40 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (19 bp):
GTATCGATACATTGAAAAT
Found at i:25459 original size:3 final size:3
Alignment explanation
Indices: 25451--25491 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
25441 TTTATGTAAG
25451 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
25492 GACAATGATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:26064 original size:21 final size:21
Alignment explanation
Indices: 26018--26068 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
26008 ATTTTTATTT
* *
26018 TATTTAATTTTTTTAAAAAAA
1 TATTTAAATTATTTAAAAAAA
* *
26039 T-TTTAAATTATTTAAATATA
1 TATTTAAATTATTTAAAAAAA
26059 TATTTAAATT
1 TATTTAAATT
26069 TTATTTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATTTAAATTATTTAAAAAAA
Found at i:26348 original size:20 final size:18
Alignment explanation
Indices: 26325--26385 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
26315 AATCATGAAA
*
26325 AATATTCTTAATATTAAAAT
1 AATATTATT-ATATT-AAAT
*
26345 AATAATAATTATATTAAAT
1 AAT-ATTATTATATTAAAT
26364 AATATTTATTAT-TTAAAT
1 AATA-TTATTATATTAAAT
26382 AATA
1 AATA
26386 AAAGATTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 11 0.31
19 13 0.36
20 8 0.22
21 4 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTATTATATTAAAT
Found at i:26571 original size:6 final size:5
Alignment explanation
Indices: 26553--26593 Score: 64
Period size: 5 Copynumber: 7.8 Consensus size: 5
26543 TATCGTGTCG
26553 AATTA AATTA AATTTA AATTTA AATTA AATTA AATTA AATT
1 AATTA AATTA AA-TTA AA-TTA AATTA AATTA AATTA AATT
26594 TACAAGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 24 0.69
6 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
AATTA
Found at i:26580 original size:22 final size:21
Alignment explanation
Indices: 26553--26595 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
26543 TATCGTGTCG
26553 AATTAAATTAAATTTAAATTTA
1 AATTAAATTAAA-TTAAATTTA
26575 AATTAAATTAAATTAAATTTA
1 AATTAAATTAAATTAAATTTA
26596 CAAGTTTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTAAATTAAATTAAATTTA
Found at i:28501 original size:28 final size:29
Alignment explanation
Indices: 28448--28502 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
28438 GATATTAAAT
*
28448 TTTTAATAAAATATTTTAACTCTTTTTAA
1 TTTTAATAAAATATTTTAACTATTTTTAA
* *
28477 TTTTAA-AATATATTTTAATTATTTTT
1 TTTTAATAAAATATTTTAACTATTTTT
28503 GAAAGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAATAAAATATTTTAACTATTTTTAA
Found at i:29211 original size:15 final size:16
Alignment explanation
Indices: 29170--29219 Score: 84
Period size: 15 Copynumber: 3.1 Consensus size: 16
29160 CATTATTATA
29170 TTAAACGAGTTCAAAT
1 TTAAACGAGTTCAAAT
29186 TTAATACGAGTTCAAAT
1 TTAA-ACGAGTTCAAAT
29203 TT-AACGAGTTCAAAT
1 TTAAACGAGTTCAAAT
29218 TT
1 TT
29220 CAACAGTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
15 14 0.42
16 5 0.15
17 14 0.42
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
TTAAACGAGTTCAAAT
Found at i:29453 original size:284 final size:283
Alignment explanation
Indices: 28918--29457 Score: 1053
Period size: 284 Copynumber: 1.9 Consensus size: 283
28908 GAATGTAAAT
28918 ATTTAACGAGTTCAAATTTCAACAGTTAATATTATTTAATTCATATTCAAAAAATAATATTCGAA
1 ATTTAACGAGTTCAAATTTCAACAGTTAATATTATTTAATTCATATTCAAAAAATAATATTCGAA
28983 TTTAATACGAATTATAAATTCAAATTTTAAAATAATTATTACGAATTCAAATCTTTAAAAAAAAT
66 TTTAATACGAATTATAAATTCAAATTTTAAAATAATTATTACGAATTCAAATCTTTAAAAAAAAT
*
29048 CCAAATCACTATCATTCTTAAAGCCAACCTGATCATGAACATATGAAATGTCTGAAGCTTATAAT
131 CCAAATCACTATCATCCTTAAAGCCAACCTGATCATGAACATATGAAATGTCTGAAGCTTATAAT
29113 GATATATATATATATATAATGAAAAATCTAAACATATTAGTATAAAACATTATTATATTAAACGA
196 GATATATATATATATATAATGAAAAATCTAAACATATTAGTATAAAACATTATTATATTAAACGA
29178 GTTCAAATTTAATACGAGTTCAA
261 GTTCAAATTTAATACGAGTTCAA
29201 ATTTAACGAGTTCAAATTTCAACAGTTAATATTATTTAATTCATATTCAAAAAATAATATTCGAA
1 ATTTAACGAGTTCAAATTTCAACAGTTAATATTATTTAATTCATATTCAAAAAATAATATTCGAA
29266 TTTAATACGAATTATAAATTCAAATTTTAAAATAATTATTACGAATTCAAATCTTTAAAAAAAAA
66 TTTAATACGAATTATAAATTCAAATTTTAAAATAATTATTACGAATTCAAATCTTT-AAAAAAAA
29331 TCCAAATCACTATCATCCTTAAAGCCAACCTGATCATGAACATATGAAATGTCTGAAGCTTATAA
130 TCCAAATCACTATCATCCTTAAAGCCAACCTGATCATGAACATATGAAATGTCTGAAGCTTATAA
*
29396 TGATATATATATATATATAATGAAAAATCTAAACATATTAGTATAAAATATTATTATATTAA
195 TGATATATATATATATATAATGAAAAATCTAAACATATTAGTATAAAACATTATTATATTAA
29458 GGAATTAATC
Statistics
Matches: 254, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
283 121 0.48
284 133 0.52
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.36
Consensus pattern (283 bp):
ATTTAACGAGTTCAAATTTCAACAGTTAATATTATTTAATTCATATTCAAAAAATAATATTCGAA
TTTAATACGAATTATAAATTCAAATTTTAAAATAATTATTACGAATTCAAATCTTTAAAAAAAAT
CCAAATCACTATCATCCTTAAAGCCAACCTGATCATGAACATATGAAATGTCTGAAGCTTATAAT
GATATATATATATATATAATGAAAAATCTAAACATATTAGTATAAAACATTATTATATTAAACGA
GTTCAAATTTAATACGAGTTCAA
Found at i:30822 original size:2 final size:2
Alignment explanation
Indices: 30815--30854 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
30805 CTTGTTGAAC
* *
30815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30855 TTGTATTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:30855 original size:12 final size:12
Alignment explanation
Indices: 30815--30870 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
30805 CTTGTTGAAC
*
30815 ATATATATATAT
1 ATATTTATATAT
*
30827 ATATATATATAT
1 ATATTTATATAT
*
30839 ATATTTATATGT
1 ATATTTATATAT
* *
30851 ATATTTGTATTT
1 ATATTTATATAT
30863 GATATTTA
1 -ATATTTA
30871 CCTTAAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
12 32 0.84
13 6 0.16
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (12 bp):
ATATTTATATAT
Found at i:31440 original size:16 final size:16
Alignment explanation
Indices: 31416--31447 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31406 TTGAAATTGG
*
31416 TTTTCATTTATATTAT
1 TTTTAATTTATATTAT
31432 TTTTAATTTATATTAT
1 TTTTAATTTATATTAT
31448 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTAATTTATATTAT
Found at i:31575 original size:24 final size:23
Alignment explanation
Indices: 31534--31599 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
31524 AATAAATATC
* *
31534 TAAAAATATTCTAATAAATTACACT
1 TAAAAATATACT-TTAAATTACA-T
*
31559 TAAAAATAATA-TTTAAAATTATAT
1 TAAAAAT-ATACTTT-AAATTACAT
31583 TAAAAATATACTTTAAA
1 TAAAAATATACTTTAAA
31600 AAATAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
23 6 0.17
24 12 0.34
25 15 0.43
26 2 0.06
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAATATACTTTAAATTACAT
Found at i:31582 original size:12 final size:12
Alignment explanation
Indices: 31561--31634 Score: 62
Period size: 12 Copynumber: 6.0 Consensus size: 12
31551 ATTACACTTA
31561 AAAATAATATTT
1 AAAATAATATTT
* *
31573 AAAATTATATTA
1 AAAATAATATTT
31585 AAAAT-ATACTTT
1 AAAATAATA-TTT
31597 AAAA-AATAATTT
1 AAAATAAT-ATTT
31609 ACAAAATAATATTT
1 --AAAATAATATTT
* *
31623 ATAATTATATTT
1 AAAATAATATTT
31635 TATACATCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
11 3 0.06
12 36 0.71
13 1 0.02
14 8 0.16
15 3 0.06
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (12 bp):
AAAATAATATTT
Found at i:31600 original size:24 final size:25
Alignment explanation
Indices: 31549--31629 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 25
31539 ATATTCTAAT
31549 AAATTACACTTAAAAATAATATTTA
1 AAATTACACTTAAAAATAATATTTA
*
31574 AAATTATA-TTAAAAAT-ATACTTTAA
1 AAATTACACTTAAAAATAATA-TTT-A
* *
31599 AAAATA-ATTTACAAAATAATATTTA
1 AAATTACACTTA-AAAATAATATTTA
*
31624 TAATTA
1 AAATTA
31630 TATTTTATAC
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.06
24 12 0.26
25 21 0.45
26 8 0.17
27 3 0.06
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATTACACTTAAAAATAATATTTA
Found at i:31668 original size:20 final size:21
Alignment explanation
Indices: 31643--31683 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31633 TTTATACATC
*
31643 ATATTTA-ATATTAAATAATA
1 ATATTTATATATAAAATAATA
31663 ATATTTATATATAAAATAATA
1 ATATTTATATATAAAATAATA
31684 GTTATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTTATATATAAAATAATA
Found at i:31712 original size:21 final size:21
Alignment explanation
Indices: 31687--31727 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31677 AATAATAGTT
* *
31687 ATATATTGAATTATATTTTAA
1 ATATATTAAAATATATTTTAA
31708 ATATATTAAAATATATTTTA
1 ATATATTAAAATATATTTTA
31728 TTTTTCTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATATATTAAAATATATTTTAA
Found at i:31815 original size:99 final size:102
Alignment explanation
Indices: 31638--31828 Score: 216
Period size: 99 Copynumber: 1.9 Consensus size: 102
31628 TATATTTTAT
* *
31638 ACATCATATTTAATATTAAATAATAATATTTATATATAAAATAATAGTTATATATTGAATTATAT
1 ACATCATACTTAATATTAAATAATAATATTTAAATATAAAATAATAGTTATATATTGAATTATAT
*
31703 TTTAAATATATT-A-AAATATATTTTATTTTTCTATAG
66 TTTAAATAAATTAATAAATA-ATTTTATTTTTCTATAG
* * * *
31739 ACATCATACTTAATA-T-AA-AATAATTTTTAAATATAAAAATTATATTTATATAGTT-TATTAT
1 ACATCATACTTAATATTAAATAATAATATTTAAATAT-AAAATAATAGTTATATA-TTGAATTAT
**
31800 ATTTT-TTTGAAATTAATAAATAATTTTAT
64 ATTTTAAAT-AAATTAATAAATAATTTTAT
31829 ATTAAAATAT
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
98 15 0.20
99 31 0.41
100 11 0.14
101 19 0.25
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (102 bp):
ACATCATACTTAATATTAAATAATAATATTTAAATATAAAATAATAGTTATATATTGAATTATAT
TTTAAATAAATTAATAAATAATTTTATTTTTCTATAG
Found at i:32534 original size:30 final size:32
Alignment explanation
Indices: 32498--32566 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
32488 TCTCAAAACT
*
32498 CACAAGTCAGTGACATC-CTTT-TAAAGCCCA
1 CACAAGTCAGTGACAACTCTTTCTAAAGCCCA
* * *
32528 CACAAGTCGGTGGCAACTTTTTCTAAAGCCCA
1 CACAAGTCAGTGACAACTCTTTCTAAAGCCCA
32560 CACAAGT
1 CACAAGT
32567 TGGTGGCAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 14 0.42
31 3 0.09
32 16 0.48
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (32 bp):
CACAAGTCAGTGACAACTCTTTCTAAAGCCCA
Found at i:34169 original size:16 final size:15
Alignment explanation
Indices: 34143--34183 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
34133 ATAAAAAAGA
34143 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
34158 ATTTTGTTATTATTTTTT
1 ATTTT-TTATTA--TTTT
34176 ATTTTTTA
1 ATTTTTTA
34184 ATTCTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 3 0.13
18 9 0.39
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:35162 original size:20 final size:20
Alignment explanation
Indices: 35137--35177 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
35127 CCCATCATTT
35137 CATGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
35157 CATGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
35177 C
1 C
35178 GTGATAGCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (20 bp):
CATGTTTTCTACAAGCTTCA
Found at i:36025 original size:42 final size:42
Alignment explanation
Indices: 35929--37263 Score: 1043
Period size: 42 Copynumber: 31.8 Consensus size: 42
35919 ATTCTCCCAC
* * * * *
35929 GTCAAAGCCAACGGGCAGACTTAGGGAAAG-AAAGT-TTCATG
1 GTCAAAGCCGACAGGCAGAC-TAAGGAAAGAAAAGTCTCCAGG
35970 GTCAAAGCCGACAGGCAGACTAAGGATAAGAAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTAAGGA-AAGAAAAGTCTCCAGG
* * * *** *
36013 GTC-AAGTCGACAGGTAGACTGAGGGTTGAAAAGTCTCCGGG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* * * *** *
36054 GTCAAAGCCGACAGGAAGATTGAGGGTTGAAAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* * * * ***
36096 GTTAAAGCTGCCAAGCAGACTAAGGGTTGAAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* *
36138 GTCAAAGCTGACAGGCAGACTAAGGGAAA-AAAGGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTAA-GGAAAGAAAAGTCTCCAGG
* *
36180 GAT-GAAGCCGACAGGCAGACTGAAAG-AAGAAAAGTCTCCAGG
1 G-TCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* * * *
36222 GAT-GAAGCCGATAGGCAAACTGAAAG-AAGAAAAGTCTCCAGG
1 G-TCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* * * * *
36264 GACGAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* * ** *
36306 GTCAAAACCGACAAGCAGACT-AGGGGAGGAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* * *** *
36347 GTCAAAG-CTACCAAGCAGACTAAGGGTTGAAAAGTCTCAAGG
1 GTCAAAGCCGA-CAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* *
36389 ATCAAAGCCGACAGGCAGACTAAGGGAAA-AAAAGTCTCAAGG
1 GTCAAAGCCGACAGGCAGACTAA-GGAAAGAAAAGTCTCCAGG
* *** ** *
36431 GAT-GAAGATAACAGGCAGACTGCGGGAAAG-AAAGTCTCTAGG
1 G-TCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* * * *
36473 GACGAAGCCAACAGGCAGACTGAAAG-AAGAAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* * * * * *
36515 GACGAAGCCGATAGGCAGACTGAAAG-AAGAAAAGTCTCTAAG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* * * *
36557 GACGAAGCCGACAGGCAAACTGAAAG-AAGAAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* * *
36599 GACAAAGCCGACAGGCAGACTAAGGGAAGAAAAGTCTCCAAG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* * *
36641 GTCAAAGTCGACAGGCAGACT-AGGAGAGGAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* * * ***
36682 GTCAAAG-CTACCAAGCAGACTGAGGGTTGAAAAGTCTCCAGG
1 GTCAAAGCCGA-CAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
*
36724 GTCAAAGCCGACAGGCAGACTAAGGGAAA-AAAAGTCTACAGG
1 GTCAAAGCCGACAGGCAGACTAA-GGAAAGAAAAGTCTCCAGG
* * ** * *
36766 GACGAAGATGACAGGCAGACTACGGGAAAG-AAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTA-AGGAAAGAAAAGTCTCCAGG
* * * * *
36808 GACGAAGCCGACAGGCAGATTGAAAGAAAGAAAA-TCTCCAAG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* ** * *
36850 GTCAAAGCCGACAAGCAGACT-AGGGGAGGAAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
* * *
36891 GTCAAAGCCGACAGGTAGAGTAGAGG-AAGGAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTA-AGGAAAGAAAAGTCTCCAGG
*
36933 GTCAAAGCCGATAGGCAGACTGAAGGAAAG-AAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* * **
36975 GTCAAAGCCGACAGGCAGACTTTA-G-ACGAGGCAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGAC-TAAGGAAAGA-AAAGTCTCCAGG
* ** * *
37017 GCCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGTCTCTAGG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
*
37060 GTCAAAGCCGACAGGCAGACTGAAGG-AAGGAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
* ** ***
37102 GTCAAAGCCGACAGGCAGACTTTA-GATGGGGCAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGAC-TAAGGAAAGAAAAGTCTCCAGG
* * * *
37144 GCCGAAGCTGACAGGCAGACTAAGGGAAGAAAAGTCTCCAGG
1 GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
** * **
37186 GTCAAAGCCGACAGGCAGACTAAAGGGTAGGAAAGTCTGTAGG
1 GTCAAAGCCGACAGGCAGACT-AAGGAAAGAAAAGTCTCCAGG
37229 GTCAAAGCCGACAGGCAGACTAAGTGAAAGCAAAA
1 GTCAAAGCCGACAGGCAGACTAAG-GAAAG-AAAA
37264 TGATGAAGAG
Statistics
Matches: 1068, Mismatches: 181, Indels: 87
0.80 0.14 0.07
Matches are distributed among these distances:
40 18 0.02
41 143 0.13
42 793 0.74
43 110 0.10
44 4 0.00
ACGTcount: A:0.37, C:0.19, G:0.31, T:0.12
Consensus pattern (42 bp):
GTCAAAGCCGACAGGCAGACTAAGGAAAGAAAAGTCTCCAGG
Found at i:36552 original size:335 final size:335
Alignment explanation
Indices: 35931--37245 Score: 1360
Period size: 335 Copynumber: 3.9 Consensus size: 335
35921 TCTCCCACGT
* * * * *
35931 CAAAGCCAACGGGCAGACTTAGGGAAAGAAAGT-TTCATGGTCAAAGCCGACAGGCAGACTAAGG
1 CAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACT-AGG
* * * * * * *
35995 ATAAGAAAAGTCTCCAGGGTC-AAGTCGACAGGTAGACTGAGGGTTGAAAAGTCTCCGGGGTCAA
65 A-GAGGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTAAGGGTTGAAAAGTCTCCAGGGTCAA
* * * *** * * * * * * * *
36059 AGCCGACAGGAAGATTGAGGGTTGAAAAGTCTCTAGGGTTAAAGCTGCCAAGCAGACTAAGGG-T
129 AGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCAAGGGATGAAGATGACAGGCAGACTACGGGAA
* * * * * * *
36123 TGAAAAGTCTCCAGGGTCAAAGCTGACAGGCAGACT-AAGGGAA-AAAAGGTCTCCAGGGATGAA
194 AG-AAAGTCTCTAGGGACGAAGCCGACAGGCAGACTGAA-AGAAGAAAA-GTCTCCAGGGACGAA
* *
36186 GCCGACAGGCAGACTGAAAGAAGAAAAGTCTCCAGGGATGAAGCCGATAGGCAAACTGAAAGAAG
256 GCCGACAGGCAGACTGAAAGAAGAAAAGTCTCTAGGGATGAAGCCGACAGGCAAACTGAAAGAAG
36251 AAAAGTCTCCAGGGA
321 AAAAGTCTCCAGGGA
* * * * *
36266 CGAAGCCGACAGGCAGACTAAGGGAAGGAAAGTCTCCAAGGTCAAAACCGACAAGCAGACTAGGG
1 CAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAGGA
* * *
36331 GAGGAAAGTCTCCAGGGTCAAAG-CTACCAAGCAGACTAAGGGTTGAAAAGTCTCAAGGATCAAA
66 GAGGAAAGTCTCCAGGGTCAAAGCCGA-CAAGCAGACTAAGGGTTGAAAAGTCTCCAGGGTCAAA
* *
36395 GCCGACAGGCAGACTAAGGGAAAAAAAGTCTCAAGGGATGAAGATAACAGGCAGACTGCGGGAAA
130 GCCGACAGGCAGACTAAGGGAAAAAAAGTCTCAAGGGATGAAGATGACAGGCAGACTACGGGAAA
*
36460 GAAAGTCTCTAGGGACGAAGCCAACAGGCAGACTGAAAGAAGAAAAGTCTCCAGGGACGAAGCCG
195 GAAAGTCTCTAGGGACGAAGCCGACAGGCAGACTGAAAGAAGAAAAGTCTCCAGGGACGAAGCCG
* * *
36525 ATAGGCAGACTGAAAGAAGAAAAGTCTCTAAGGACGAAGCCGACAGGCAAACTGAAAGAAGAAAA
260 ACAGGCAGACTGAAAGAAGAAAAGTCTCTAGGGATGAAGCCGACAGGCAAACTGAAAGAAGAAAA
36590 GTCTCCAGGGA
325 GTCTCCAGGGA
*
36601 CAAAGCCGACAGGCAGACTAAGGG-AAGAAAAGTCTCCAAGGTCAAAGTCGACAGGCAGACTAGG
1 CAAAGCCGACAGGCAGACTAAGGGAAAG-AAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAGG
* *
36665 AGAGGAAAGTCTCCAGGGTCAAAG-CTACCAAGCAGACTGAGGGTTGAAAAGTCTCCAGGGTCAA
65 AGAGGAAAGTCTCCAGGGTCAAAGCCGA-CAAGCAGACTAAGGGTTGAAAAGTCTCCAGGGTCAA
*
36729 AGCCGACAGGCAGACTAAGGGAAAAAAAGTCT-ACAGGGACGAAGATGACAGGCAGACTACGGGA
129 AGCCGACAGGCAGACTAAGGGAAAAAAAGTCTCA-AGGGATGAAGATGACAGGCAGACTACGGGA
* * * *
36793 AAGAAAGTCTCTAGGGACGAAGCCGACAGGCAGATTGAAAGAAAGAAAA-TCTCCAAGGTCAAAG
193 AAGAAAGTCTCTAGGGACGAAGCCGACAGGCAGACTGAAAG-AAGAAAAGTCTCCAGGGACGAAG
* ** * * * * * * *
36857 CCGACAAGCAGACT-AGGGGAGGAAAGTCTCTAGGG-TCAAAGCCGACAGGTAGAGT-AGAGGAA
257 CCGACAGGCAGACTGAAAGAAGAAAAGTCTCTAGGGAT-GAAGCCGACAGGCAAACTGA-AAGAA
* *
36919 GGAAAGTCTCCAGGGT
320 GAAAAGTCTCCAGGGA
* *
36935 CAAAGCCGATAGGCAGACTGAA-GGAAAGAAAGTCTCCAGGGTCAAAGCCGACAGGCAGACTTTA
1 CAAAGCCGACAGGCAGACT-AAGGGAAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGAC--TA
* * * * * *
36999 -GACGAGG-CAGTCTCCAGGGCCAAAGCCGACAGGCAGACTGAAGGGTAGGAAAGTCTCTAGGGT
63 GGA-GAGGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACT-AAGGGTTGAAAAGTCTCCAGGGT
** * * ** *
37062 CAAAGCCGACAGGCAGACTGAA-GGAAGGAAAGTCTCCAGGG-TCAAAGCCGACAGGCAGACT-T
126 CAAAGCCGACAGGCAGACT-AAGGGAAAAAAAGTCTCAAGGGAT-GAAGATGACAGGCAGACTAC
** ** ** * * * * *
37124 TAGATGGGGCAGTCTCCAGGGCCGAAGCTGACAGGCAGACT-AAGGGAAGAAAAGTCTCCAGGGT
189 GGGA-AAGAAAGTCTCTAGGGACGAAGCCGACAGGCAGACTGAA-AGAAGAAAAGTCTCCAGGGA
* * * * *
37188 CAAAGCCGACAGGCAGACT-AAAGGGTAGGAAAGTCTGTAGGG-TCAAAGCCGACAGGCA
252 CGAAGCCGACAGGCAGACTGAAA--GAAGAAAAGTCTCTAGGGAT-GAAGCCGACAGGCA
37246 GACTAAGTGA
Statistics
Matches: 837, Mismatches: 117, Indels: 49
0.83 0.12 0.05
Matches are distributed among these distances:
333 1 0.00
334 120 0.14
335 513 0.61
336 170 0.20
337 2 0.00
338 31 0.04
ACGTcount: A:0.37, C:0.20, G:0.31, T:0.12
Consensus pattern (335 bp):
CAAAGCCGACAGGCAGACTAAGGGAAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAGACTAGGA
GAGGAAAGTCTCCAGGGTCAAAGCCGACAAGCAGACTAAGGGTTGAAAAGTCTCCAGGGTCAAAG
CCGACAGGCAGACTAAGGGAAAAAAAGTCTCAAGGGATGAAGATGACAGGCAGACTACGGGAAAG
AAAGTCTCTAGGGACGAAGCCGACAGGCAGACTGAAAGAAGAAAAGTCTCCAGGGACGAAGCCGA
CAGGCAGACTGAAAGAAGAAAAGTCTCTAGGGATGAAGCCGACAGGCAAACTGAAAGAAGAAAAG
TCTCCAGGGA
Found at i:49958 original size:16 final size:15
Alignment explanation
Indices: 49932--49972 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 15
49922 ATAAAAAAGA
49932 ATTTTTTATTATTTT
1 ATTTTTTATTATTTT
49947 ATTTTGTTATTATTTTTT
1 ATTTT-TTATTA--TTTT
49965 ATTTTTTA
1 ATTTTTTA
49973 ATTCTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.22
16 6 0.26
17 3 0.13
18 9 0.39
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (15 bp):
ATTTTTTATTATTTT
Found at i:50942 original size:20 final size:20
Alignment explanation
Indices: 50917--50980 Score: 119
Period size: 20 Copynumber: 3.2 Consensus size: 20
50907 CCCATCATTT
50917 CATGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
*
50937 CATGTTTTCTACATGCTTCA
1 CATGTTTTCTACAAGCTTCA
50957 CATGTTTTCTACAAGCTTCA
1 CATGTTTTCTACAAGCTTCA
50977 CATG
1 CATG
50981 ATGGCAACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (20 bp):
CATGTTTTCTACAAGCTTCA
Found at i:52210 original size:41 final size:40
Alignment explanation
Indices: 52153--52289 Score: 181
Period size: 41 Copynumber: 3.4 Consensus size: 40
52143 TTTTACCCAG
*
52153 ATGTATCGATACATTACCTAGATGTATCAATACATCTTCCA
1 ATGTATCGATACATTACCTAGATGTATCGATACATCTT-CA
* *
52194 ATGTATCGATATATTACCCAGATGTATCGATACATCTTTCA
1 ATGTATCGATACATTACCTAGATGTATCGATACATC-TTCA
52235 ATGTATCGATACATGTA--T-GAATGTATCGATACATTCTTCA
1 ATGTATCGATACAT-TACCTAG-ATGTATCGATACA-TCTTCA
52275 ATGTATCGATACATT
1 ATGTATCGATACATT
52290 CTGTCTTTTT
Statistics
Matches: 87, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
39 2 0.02
40 31 0.36
41 50 0.57
42 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.36
Consensus pattern (40 bp):
ATGTATCGATACATTACCTAGATGTATCGATACATCTTCA
Found at i:52289 original size:20 final size:20
Alignment explanation
Indices: 52153--52291 Score: 126
Period size: 20 Copynumber: 6.8 Consensus size: 20
52143 TTTTACCCAG
*
52153 ATGTATCGATACATTACCT-A
1 ATGTATCGATACATT-CTTCA
*
52173 GATGTATCAATACA-TCTTCCA
1 -ATGTATCGATACATTCTT-CA
* *
52194 ATGTATCGATATATTAC-CCA
1 ATGTATCGATACATT-CTTCA
52214 GATGTATCGATACA-TCTTTCA
1 -ATGTATCGATACATTC-TTCA
* *
52235 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
52255 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
52275 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
52292 GTCTTTTTAC
Statistics
Matches: 97, Mismatches: 11, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.04
20 63 0.65
21 28 0.29
22 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:55137 original size:17 final size:16
Alignment explanation
Indices: 55115--55150 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
55105 GATCATATTG
55115 AACCAATATCAAGTCGA
1 AACCAATATCAAGTC-A
*
55132 AACCAATGTCAAGTCA
1 AACCAATATCAAGTCA
55148 AAC
1 AAC
55151 ATAGCTAGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.47, C:0.25, G:0.11, T:0.17
Consensus pattern (16 bp):
AACCAATATCAAGTCA
Found at i:56235 original size:26 final size:25
Alignment explanation
Indices: 56206--56270 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
56196 TAATAAATTA
56206 ATAATTTATATTATATACGT-TTTGAT
1 ATAATTTATATTATAT-CGTATTT-AT
*
56232 ATAATTATATATTCTATCGTATTTAT
1 ATAATT-TATATTATATCGTATTTAT
*
56258 ATTATTTTATATT
1 A-TAATTTATATT
56271 TTAATATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (25 bp):
ATAATTTATATTATATCGTATTTAT
Found at i:56292 original size:21 final size:20
Alignment explanation
Indices: 56255--56294 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
56245 CTATCGTATT
56255 TATATTATTTTATATTTTAA
1 TATATTATTTTATATTTTAA
*
56275 TATATTTTTTTCATATTTTA
1 TATATTATTTT-ATATTTTA
56295 GCCATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (20 bp):
TATATTATTTTATATTTTAA
Found at i:57461 original size:15 final size:16
Alignment explanation
Indices: 57428--57466 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
57418 AAATATAATT
*
57428 TTTTTTATTTTAATCAA
1 TTTTTTATTTT-ATAAA
57445 TTTTTTATTTT-TAAA
1 TTTTTTATTTTATAAA
57460 TTTTTTA
1 TTTTTTA
57467 AAATAATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
17 11 0.52
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTATTTTATAAA
Done.