Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1909
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: 46261
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:988 original size:1 final size:1
Alignment explanation
Indices: 982--1024 Score: 86
Period size: 1 Copynumber: 43.0 Consensus size: 1
972 GCTTAAATAC
982 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1025 CCCCAATAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:8842 original size:54 final size:54
Alignment explanation
Indices: 8740--8847 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
8730 TGGATTTATA
* * * *
8740 CACTTAATAATTTTAAATCAAATTTTATTTAAAAAAGGTATTTTAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
* *
8794 CACTTAATAATCTTAAATCGAATTTGA-TTAGAAACAGGGATTTCAATCTTAAAT
1 CACTTAATAATCTTAAATCAAATTTGATTTA-AAAAAGGGATTTCAATCTTAAAT
8848 TAGTGACGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 3 0.06
54 44 0.94
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (54 bp):
CACTTAATAATCTTAAATCAAATTTGATTTAAAAAAGGGATTTCAATCTTAAAT
Found at i:10644 original size:17 final size:17
Alignment explanation
Indices: 10623--10656 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10613 TTATTATTAA
10623 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
10640 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
10657 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17941 original size:120 final size:120
Alignment explanation
Indices: 17703--18049 Score: 644
Period size: 120 Copynumber: 2.9 Consensus size: 120
17693 ACTAGCATCA
*
17703 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAACATTAATTATTAAGAA-TTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
17767 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
17822 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
17887 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
66 AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
* *
17942 ACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTA
1 ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
18007 AATTATATA-TTGTAATTAAAATATATTTAATAATAATTATGTT
66 AATTATATAGTT-TAATTAAAATATATTTAATAATAATTATGTT
18050 TAAATATGAT
Statistics
Matches: 223, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
119 58 0.26
120 165 0.74
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (120 bp):
ACAGTATCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTTTTA
AATTATATAGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTT
Found at i:18246 original size:44 final size:45
Alignment explanation
Indices: 18197--18287 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
18187 ACCTCTATTC
* * *
18197 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
18241 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
18286 CA
1 CA
18288 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:18289 original size:16 final size:16
Alignment explanation
Indices: 18268--18336 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
18258 GATTAGCTAT
18268 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
18284 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
18301 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
18317 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
18333 TACA
1 TACA
18337 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:18310 original size:33 final size:32
Alignment explanation
Indices: 18268--18336 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
18258 GATTAGCTAT
18268 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
18301 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
18333 TACA
1 TACA
18337 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:23555 original size:24 final size:22
Alignment explanation
Indices: 23528--23571 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
23518 AAAATTCAAA
23528 ATTTTTCTTTCCATTTATTAAAAG
1 ATTTTTC--TCCATTTATTAAAAG
*
23552 ATTTTTCTGCATTTATTAAA
1 ATTTTTCTCCATTTATTAAA
23572 TCTATATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.55
Consensus pattern (22 bp):
ATTTTTCTCCATTTATTAAAAG
Found at i:26102 original size:34 final size:32
Alignment explanation
Indices: 26062--26143 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 32
26052 GATCCAAAGT
*
26062 TTTATGTAAGTTATGATATGATATAT-ATTTATGTA
1 TTTATGTAAGTTATGATAAG-T-TATGA--TATGTA
26097 -TTATGTAAGTTATG-TAAGTTATGATATGTA
1 TTTATGTAAGTTATGATAAGTTATGATATGTA
26127 TTTATGTAAGTTATGAT
1 TTTATGTAAGTTATGAT
26144 CCAAAGTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
30 6 0.14
31 17 0.40
32 3 0.07
33 3 0.07
34 14 0.33
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (32 bp):
TTTATGTAAGTTATGATAAGTTATGATATGTA
Found at i:30929 original size:22 final size:22
Alignment explanation
Indices: 30904--30946 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
30894 ACACCAAAAC
*
30904 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
*
30926 AGGCCTTTAGCGGTGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
30947 AGCGCCGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.28, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:31140 original size:42 final size:43
Alignment explanation
Indices: 31086--31182 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 43
31076 CTAGCACAAA
* * * *
31086 CGCCGCTGAAGACTAAGACCTTTAGCGGCGCTTTAGTG-GAAG
1 CGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAGGGAGAAG
** * * *
31128 CGCCGCTAAAGACCCTGATCTTTAGCGACGTTTTTGGGAGAAG
1 CGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAGGGAGAAG
31171 CGCCGCTAAAGA
1 CGCCGCTAAAGA
31183 TCAGGGTCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
42 29 0.64
43 16 0.36
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.22
Consensus pattern (43 bp):
CGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAGGGAGAAG
Found at i:31462 original size:86 final size:86
Alignment explanation
Indices: 31210--31462 Score: 267
Period size: 86 Copynumber: 2.9 Consensus size: 86
31200 ATTTTTTTCT
* * * * * * *
31210 CAAACGCCGCAATAGACCCTGATCTATACCGGCGCTTTGACCATAAGCGCCA-TGAAAGAACCTA
1 CAAACACCGCAATAGACCATGATCTATAGCGGCGCTTCGACCACAAACACCACT-AAAGAACCTA
* *
31274 ATCTTTAGCGACGCTTTCCCCT
65 ATCTTTAGCGGCGCTTTCCCCA
* *
31296 CAAACACTGCAATAGACCCTGATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTAA
1 CAAACACCGCAATAGACCATGATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTAA
*
31361 TCTTTAGCGGTGCTTTCCCCA
66 TCTTTAGCGGCGCTTTCCCCA
* * * * *** * * * *
31382 CAAACGCCGCTAA-AGACCATGATCTTTAGTGGCGTTTTTTCCACAAACGCCGCTAAAGACCCTT
1 CAAACACCGC-AATAGACCATGATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTA
31446 ATCTTTAGCGGCGCTTT
65 ATCTTTAGCGGCGCTTT
31463 GACAAAAAAC
Statistics
Matches: 141, Mismatches: 24, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
86 138 0.98
87 3 0.02
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (86 bp):
CAAACACCGCAATAGACCATGATCTATAGCGGCGCTTCGACCACAAACACCACTAAAGAACCTAA
TCTTTAGCGGCGCTTTCCCCA
Found at i:31481 original size:43 final size:43
Alignment explanation
Indices: 31223--31481 Score: 198
Period size: 43 Copynumber: 6.0 Consensus size: 43
31213 ACGCCGCAAT
* * * * *
31223 AGACCCTGATCTATACCGGCGCTTTGACCATAAGCGCCA-TGAA
1 AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACACCACT-AA
* * * ** * **
31266 AGAACCTAATCTTTAGCGACGCTTTCCCCTCAAACACTGC-AA
1 AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACACCACTAA
* *
31308 TAGACCCTGATCTATAGCGGCGCTTCGACCACAAACACCACTAA
1 -AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACACCACTAA
* * * ** * *
31352 AGAACCTAATCTTTAGCGGTGCTTTCCCCACAAACGCCGCTAA
1 AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACACCACTAA
* * * ** * *
31395 AGACCATGATCTTTAGTGGCGTTTTTTCCACAAACGCCGCTAA
1 AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACACCACTAA
* * *
31438 AGACCCTTATCTTTAGCGGCGCTTTGACAAAAAACACCACTAA
1 AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACACCACTAA
31481 A
1 A
31482 TATGGCAGAT
Statistics
Matches: 163, Mismatches: 50, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
42 2 0.01
43 159 0.98
44 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (43 bp):
AGACCCTGATCTTTAGCGGCGCTTTGACCACAAACACCACTAA
Found at i:31823 original size:21 final size:21
Alignment explanation
Indices: 31789--31848 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 21
31779 TTTGACGCTG
* *
31789 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCTCTCGCTGCAGC
* * *
31810 CTGTACTTCTCTCGTTGCCGC
1 CTCTACTTCTCTCGCTGCAGC
* *
31831 CTCTGCTTCTCTTGCTGC
1 CTCTACTTCTCTCGCTGC
31849 TGCATCTGCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.03, C:0.42, G:0.18, T:0.37
Consensus pattern (21 bp):
CTCTACTTCTCTCGCTGCAGC
Found at i:31907 original size:66 final size:66
Alignment explanation
Indices: 31830--31995 Score: 210
Period size: 66 Copynumber: 2.5 Consensus size: 66
31820 CTCGTTGCCG
* * *
31830 CCTCTGCTTCTCTTGCTGCTGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTG-TAGCTAGAGTTCTTCATATCTTT-GTT
31893 GAA
64 GAA
* * *
31896 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTAGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGA
31961 A
66 A
* * * *
31962 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAG
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG
31996 TTGTGTAATT
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 82 0.94
67 4 0.05
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGA
A
Found at i:37417 original size:9 final size:9
Alignment explanation
Indices: 37381--37742 Score: 161
Period size: 9 Copynumber: 43.0 Consensus size: 9
37371 AATTGCACGG
37381 GTAAGTTAT
1 GTAAGTTAT
*
37390 GT-A-TTGT
1 GTAAGTTAT
*
37397 GTAAGCTAT
1 GTAAGTTAT
*
37406 GTAAGTTGT
1 GTAAGTTAT
37415 GT-A-TTAT
1 GTAAGTTAT
37422 GTAAGTTAT
1 GTAAGTTAT
37431 -T-A-TTAT
1 GTAAGTTAT
37437 GCTTTAAGTTAT
1 G---TAAGTTAT
*
37449 GTAAGTAAT
1 GTAAGTTAT
37458 GT-A-TTAT
1 GTAAGTTAT
*
37465 GTAAGTTGT
1 GTAAGTTAT
*
37474 GT-A-TAAT
1 GTAAGTTAT
*
37481 GTTAGTTAT
1 GTAAGTTAT
**
37490 CAAAGTTAT
1 GTAAGTTAT
37499 GT-A-TTAT
1 GTAAGTTAT
37506 GTAAGTTAT
1 GTAAGTTAT
*
37515 TTAAGTTAT
1 GTAAGTTAT
*
37524 GTAA--CAT
1 GTAAGTTAT
*
37531 GTAAATTAT
1 GTAAGTTAT
*
37540 GTAAGTTGT
1 GTAAGTTAT
*
37549 GT-A-TAAT
1 GTAAGTTAT
*
37556 GTTAGTTAT
1 GTAAGTTAT
**
37565 CAAAGTTAT
1 GTAAGTTAT
37574 GT-A-TTAT
1 GTAAGTTAT
*
37581 GCAAGTTAT
1 GTAAGTTAT
*
37590 TTAAGTTAT
1 GTAAGTTAT
*
37599 GTAA--CAT
1 GTAAGTTAT
*
37606 GTAAATTAT
1 GTAAGTTAT
37615 GTAAGTTAT
1 GTAAGTTAT
* *
37624 GTAGGCTAT
1 GTAAGTTAT
* *
37633 GTATGTTAA
1 GTAAGTTAT
*
37642 GTAAGTAAT
1 GTAAGTTAT
37651 GT-A-TTAT
1 GTAAGTTAT
*
37658 GTAAGTTGT
1 GTAAGTTAT
*
37667 GT-A-TAAT
1 GTAAGTTAT
*
37674 GTTAGTTAT
1 GTAAGTTAT
**
37683 CAAAGTTAT
1 GTAAGTTAT
37692 GT-A-TTAT
1 GTAAGTTAT
***
37699 GTGTTTCTAT
1 GTAAGT-TAT
*
37709 TTAAGTTAT
1 GTAAGTTAT
*
37718 GTAAGTTGT
1 GTAAGTTAT
37727 GT-A-TTAT
1 GTAAGTTAT
37734 GTAAGTTAT
1 GTAAGTTAT
37743 TAAAAATTGA
Statistics
Matches: 256, Mismatches: 64, Indels: 66
0.66 0.17 0.17
Matches are distributed among these distances:
6 4 0.02
7 67 0.26
8 22 0.09
9 151 0.59
10 6 0.02
11 1 0.00
12 5 0.02
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:37422 original size:16 final size:16
Alignment explanation
Indices: 37403--37682 Score: 90
Period size: 16 Copynumber: 17.8 Consensus size: 16
37393 TTGTGTAAGC
*
37403 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
37419 TATGTAAGTTAT-TAT
1 TATGTAAGTTATGTAT
*
37434 TATGCT---TTAAG--T
1 TATG-TAAGTTATGTAT
*
37446 TATGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
37462 TATGTAAGTTGTGTA-
1 TATGTAAGTTATGTAT
*
37477 TA---ATGTTA-G--T
1 TATGTAAGTTATGTAT
**
37487 TATCAAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
37503 TATGTAAGTTATTTAAGT
1 TATGTAAGTTATGT-A-T
*
37521 TATGTAA--CATGTAAAT
1 TATGTAAGTTATGT--AT
*
37537 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * **
37553 AATGTTAGTTATCAAAGT
1 TATGTAAGTTAT-GTA-T
*
37571 TATGT-A-TTATGCAAGT
1 TATGTAAGTTATG-TA-T
* *
37587 TATTTAAGTTATGTAA
1 TATGTAAGTTATGTAT
* *
37603 CATGTAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
37621 TATGTAGGCTATGTATGT
1 TATGTAAGTTATGTA--T
* *
37639 TAAGTAAGTAATGTAT
1 TATGTAAGTTATGTAT
*
37655 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* *
37671 AATGTTAGTTAT
1 TATGTAAGTTAT
37683 CAAAGTTATG
Statistics
Matches: 193, Mismatches: 44, Indels: 54
0.66 0.15 0.19
Matches are distributed among these distances:
10 2 0.01
11 2 0.01
12 9 0.05
13 8 0.04
14 4 0.02
15 9 0.05
16 106 0.55
17 9 0.05
18 44 0.23
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:37489 original size:25 final size:25
Alignment explanation
Indices: 37441--37669 Score: 180
Period size: 25 Copynumber: 9.1 Consensus size: 25
37431 TATTATGCTT
37441 TAAGTTATGTAAGTAATGT-A-TTATG
1 TAAGTTATGT-A-TAATGTAAGTTATG
* * *
37466 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATAATGTAAGTTATG
* * *
37491 AAAGTTATGTATTATGTAAGTTATT
1 TAAGTTATGTATAATGTAAGTTATG
*
37516 TAAGTTATGTA-ACATGTAAATTATG
1 TAAGTTATGTATA-ATGTAAGTTATG
* * *
37541 TAAGTTGTGTATAATGTTAGTTATC
1 TAAGTTATGTATAATGTAAGTTATG
* * * *
37566 AAAGTTATGTATTATGCAAGTTATT
1 TAAGTTATGTATAATGTAAGTTATG
*
37591 TAAGTTATGTA-ACATGTAAATTATG
1 TAAGTTATGTATA-ATGTAAGTTATG
* *
37616 TAAGTTATGTAGGCT-ATGTATGTTAAG
1 TAAGTTATGTA---TAATGTAAGTTATG
* * *
37643 TAAGTAATGTATTATGTAAGTTGTG
1 TAAGTTATGTATAATGTAAGTTATG
37668 TA
1 TA
37670 TAATGTTAGT
Statistics
Matches: 161, Mismatches: 33, Indels: 20
0.75 0.15 0.09
Matches are distributed among these distances:
23 6 0.04
24 3 0.02
25 132 0.82
26 1 0.01
27 19 0.12
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (25 bp):
TAAGTTATGTATAATGTAAGTTATG
Found at i:37520 original size:50 final size:50
Alignment explanation
Indices: 37461--37700 Score: 162
Period size: 50 Copynumber: 4.9 Consensus size: 50
37451 AAGTAATGTA
*
37461 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
1 TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
* * * ** * * *
37511 TTATTTAAGTTATGTA-ACATGTAAATTATGTAAGTTGTGTATAATGTTAG
1 TTATGTAAGTTATGTATA-ATGTTAGTTATCAAAGTTATGTATTATGTAAG
** * ** ** ** *
37561 TTATCAAAGTTATGTATTATGCAAGTTATTTAAGTTATGTAACATGTAAA
1 TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
*
37611 TTATGTAAGTTATGTAGGCT-ATG-TA-TGT-T--AAG-TAAGTA--ATGT-A-
1 TTATGTAAGTTATGTA---TAATGTTAGT-TATCAAAGTTATGTATTATGTAAG
*
37654 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGT
1 TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGT
37701 GTTTCTATTT
Statistics
Matches: 149, Mismatches: 26, Indels: 32
0.72 0.13 0.15
Matches are distributed among these distances:
40 1 0.01
41 3 0.02
42 3 0.02
43 17 0.11
44 1 0.01
45 7 0.05
46 5 0.03
47 5 0.03
48 7 0.05
49 1 0.01
50 93 0.62
51 2 0.01
52 3 0.02
53 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.45
Consensus pattern (50 bp):
TTATGTAAGTTATGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAG
Found at i:37520 original size:75 final size:74
Alignment explanation
Indices: 37439--37626 Score: 297
Period size: 75 Copynumber: 2.5 Consensus size: 74
37429 ATTATTATGC
37439 TTTAAGTTATGTAAGTAATGT-ATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTAT
1 TTTAAGTTATGTAA--AATGTAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTAT
*
37503 TATGTAAGTTA
64 TATGCAAGTTA
*
37514 TTTAAGTTATGTAACATGTAAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATT
1 TTTAAGTTATGTAAAATGT-AATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATT
37579 ATGCAAGTTA
65 ATGCAAGTTA
* *
37589 TTTAAGTTATGTAACATGTAAATTATGTAAGTTATGTA
1 TTTAAGTTATGTAAAATGT-AATTATGTAAGTTGTGTA
37627 GGCTATGTAT
Statistics
Matches: 108, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
73 4 0.04
75 104 0.96
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.45
Consensus pattern (74 bp):
TTTAAGTTATGTAAAATGTAATTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTA
TGCAAGTTA
Found at i:37727 original size:26 final size:25
Alignment explanation
Indices: 37498--37742 Score: 76
Period size: 25 Copynumber: 9.7 Consensus size: 25
37488 ATCAAAGTTA
* *
37498 TGTATTATGTAAGTTATTTAAGT-TA
1 TGTATTATGTAAGTTATGT-AGTATG
** *
37523 TGTAACATGTAAATTATGTAAGT-TG
1 TGTATTATGTAAGTTATGT-AGTATG
* * ** *
37548 TGTATAATGTTAGTTATCAAAGT-TA
1 TGTATTATGTAAGTTAT-GTAGTATG
* * *
37573 TGTATTATGCAAGTTATTTAAGT-TA
1 TGTATTATGTAAGTTATGT-AGTATG
** *
37598 TGTAACATGTAAATTATGTAAGTTATG
1 TGTATTATGTAAGTTATGT-AG-TATG
** * * *
37625 TAG-GCTATGTATGTTAAGTAAGTA-A
1 T-GTATTATGTAAGTTATGT-AGTATG
*
37650 TGTATTATGTAAGTTGTGTA-TAATG
1 TGTATTATGTAAGTTATGTAGT-ATG
** *
37675 T-TAGTTATCAAAGTTATGTATTATG
1 TGTA-TTATGTAAGTTATGTAGTATG
* *
37700 TGTTTCTATTTAAGTTATGTAAGT-TG
1 TGTAT-TATGTAAGTTATGT-AGTATG
37726 TGTATTATGTAAGTTAT
1 TGTATTATGTAAGTTAT
37743 TAAAAATTGA
Statistics
Matches: 162, Mismatches: 45, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
23 1 0.01
24 5 0.03
25 115 0.71
26 23 0.14
27 17 0.10
28 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.19, T:0.46
Consensus pattern (25 bp):
TGTATTATGTAAGTTATGTAGTATG
Found at i:37829 original size:27 final size:27
Alignment explanation
Indices: 37799--37854 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
37789 TTTATTAAAA
*
37799 ATATAGGTTTTAATATTTTAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
37826 ATATAGGTTTTAATATTTAAAAATAAC
1 ATATAGGTTTTAATATTTAAAAATAAC
37853 AT
1 AT
37855 TTACAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (27 bp):
ATATAGGTTTTAATATTTAAAAATAAC
Found at i:38679 original size:8 final size:8
Alignment explanation
Indices: 38668--38701 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
38658 TTTTTATTTC
38668 ATTTTTAT
1 ATTTTTAT
38676 ATTTTTAT
1 ATTTTTAT
38684 ATTTTTAT
1 ATTTTTAT
38692 ATTTTT-T
1 ATTTTTAT
38699 ATT
1 ATT
38702 CCAAATTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.15
8 22 0.85
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTAT
Found at i:39326 original size:14 final size:14
Alignment explanation
Indices: 39306--39406 Score: 94
Period size: 14 Copynumber: 6.9 Consensus size: 14
39296 CACCCTAAAT
39306 TCCTAACCCCTAAC
1 TCCTAACCCCTAAC
*
39320 TCTTAACCCCTAAATC
1 TCCTAACCCCT-AA-C
* * *
39336 TCTTAGCCCCTAAAT
1 TCCTAACCCCT-AAC
39351 TCCTAACCCCTAAC
1 TCCTAACCCCTAAC
*
39365 TCCTAACTCCTAAC
1 TCCTAACCCCTAAC
* *
39379 CCCTAAATCCCTAAC
1 TCCT-AACCCCTAAC
*
39394 CCCTAACCCCTAA
1 TCCTAACCCCTAA
39407 ACCTTATATC
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
14 36 0.49
15 23 0.32
16 14 0.19
ACGTcount: A:0.30, C:0.45, G:0.01, T:0.25
Consensus pattern (14 bp):
TCCTAACCCCTAAC
Found at i:39364 original size:7 final size:7
Alignment explanation
Indices: 39352--39406 Score: 74
Period size: 7 Copynumber: 7.7 Consensus size: 7
39342 CCCCTAAATT
39352 CCTAACC
1 CCTAACC
*
39359 CCTAACT
1 CCTAACC
*
39366 CCTAACT
1 CCTAACC
39373 CCTAACC
1 CCTAACC
*
39380 CCTAAATC
1 CCT-AACC
39388 CCTAACC
1 CCTAACC
39395 CCTAACC
1 CCTAACC
39402 CCTAA
1 CCTAA
39407 ACCTTATATC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
7 37 0.86
8 6 0.14
ACGTcount: A:0.31, C:0.49, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAACC
Found at i:39407 original size:22 final size:21
Alignment explanation
Indices: 39352--39407 Score: 85
Period size: 22 Copynumber: 2.6 Consensus size: 21
39342 CCCCTAAATT
* *
39352 CCTAACCCCTAACTCCTAACT
1 CCTAACCCCTAAATCCTAACC
39373 CCTAACCCCTAAATCCCTAACC
1 CCTAACCCCTAAAT-CCTAACC
39395 CCTAACCCCTAAA
1 CCTAACCCCTAAA
39408 CCTTATATCC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 13 0.41
22 19 0.59
ACGTcount: A:0.32, C:0.48, G:0.00, T:0.20
Consensus pattern (21 bp):
CCTAACCCCTAAATCCTAACC
Found at i:39417 original size:29 final size:29
Alignment explanation
Indices: 39358--39424 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
39348 AATTCCTAAC
* * *
39358 CCCTAACTCCTAACTCCTAACCCCTAAAT
1 CCCTAACCCCTAACCCCTAAACCCTAAAT
* *
39387 CCCTAACCCCTAACCCCTAAACCTTATAT
1 CCCTAACCCCTAACCCCTAAACCCTAAAT
*
39416 CCCAAACCC
1 CCCTAACCC
39425 TAATAATCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.48, G:0.00, T:0.21
Consensus pattern (29 bp):
CCCTAACCCCTAACCCCTAAACCCTAAAT
Found at i:39423 original size:22 final size:22
Alignment explanation
Indices: 39355--39424 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
39345 CTAAATTCCT
* * *
39355 AACCCCTAACT-CCTAACTCCT
1 AACCCCTAAATCCCTAACCCCA
*
39376 AACCCCTAAATCCCTAACCCCT
1 AACCCCTAAATCCCTAACCCCA
* *
39398 AACCCCTAAA-CCTTATATCCCA
1 AACCCCTAAATCCCTA-ACCCCA
39420 AACCC
1 AACCC
39425 TAATAATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 14 0.33
22 28 0.67
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (22 bp):
AACCCCTAAATCCCTAACCCCA
Found at i:40123 original size:19 final size:19
Alignment explanation
Indices: 40099--40141 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
40089 AAAATTATAT
*
40099 TTTTTATTTTTTTATTTCA
1 TTTTTATTTTTGTATTTCA
*
40118 TTTTTATTTTTGTATTTTA
1 TTTTTATTTTTGTATTTCA
40137 TTTTT
1 TTTTT
40142 TCTTATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTTGTATTTCA
Found at i:41512 original size:41 final size:41
Alignment explanation
Indices: 41452--41731 Score: 375
Period size: 41 Copynumber: 6.8 Consensus size: 41
41442 TTATTATTAC
* * * *
41452 TAGCGGCGCTTTTTTAAAAACGCCGCTAAAGGCCACAGCAA
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* * ** *
41493 TACCGGCGCTTCTTTAAAAACGCCGCTAAAGATCTGAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
41534 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAAGACAGAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
41575 TAGCGGCGCATT-TTCAAAAACGCCGCTAAAAGACAGAGCAT
1 TAGCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
*
41616 TAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
*
41657 TAGCGGCACTTAC-TCAAAAACGCCGCTAAAGGCCAGAGCAT
1 TAGCGGCGCTT-CTTCAAAAACGCCGCTAAAGGCCAGAGCAT
* *
41698 TAGCGGCGTTTATTCAAAAACGCCGCTAAAGGCC
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
41732 CCAAAAACTC
Statistics
Matches: 215, Mismatches: 20, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
40 2 0.01
41 211 0.98
42 2 0.01
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (41 bp):
TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCAT
Found at i:41892 original size:40 final size:40
Alignment explanation
Indices: 41786--41904 Score: 134
Period size: 40 Copynumber: 3.0 Consensus size: 40
41776 GCTTTTTTCA
* * *
41786 GAAAA-CGCCGCTAATGCT-TATTTTTAGCGGAATTTTTG
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
* * **
41824 GATAAGCGCAGCTAATGCTCTACCTTTAGTGGCATTTTTT
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
* * *
41864 TAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCGTTTTTT
1 GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
41904 G
1 G
41905 TCCAAACGCC
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
38 4 0.06
39 12 0.19
40 48 0.75
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.38
Consensus pattern (40 bp):
GAAAAGCGCCGCTAATGCTCTATTTTTAGTGGCATTTTTT
Found at i:43685 original size:75 final size:73
Alignment explanation
Indices: 43593--43765 Score: 184
Period size: 75 Copynumber: 2.3 Consensus size: 73
43583 TTTTTCGGTT
*
43593 TATCCGACTAGCGCTGGGCGCAATCACCGTTAGTTTATCCAACTAGAGCTAGGCTCACAATTATT
1 TATCCGACTAGCGCTGGGCGCAAT-ACCGTTAGTCTATCCAACTAGAGCTAGGCTCACAATTATT
43658 ATCATCGGCA
65 ATCATCGG-A
* *** *** * *
43668 TATCCGACTAGCACTGGGTAAAAATATTTTTGGTCTATCCAACTAGAGCTGGGCTCACAATTATT
1 TATCCGACTAGCGCTGGG-CGCAATACCGTTAGTCTATCCAACTAGAGCTAGGCTCACAATTATT
** *
43733 ATTGTCGGT
65 ATCATCGGA
*
43742 TAATCCAACTAGCGCTGGGCGCAA
1 T-ATCCGACTAGCGCTGGGCGCAA
43766 CCTTTTCTGT
Statistics
Matches: 78, Mismatches: 18, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
74 3 0.04
75 72 0.92
76 3 0.04
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (73 bp):
TATCCGACTAGCGCTGGGCGCAATACCGTTAGTCTATCCAACTAGAGCTAGGCTCACAATTATTA
TCATCGGA
Found at i:43759 original size:40 final size:39
Alignment explanation
Indices: 43629--43761 Score: 109
Period size: 40 Copynumber: 3.5 Consensus size: 39
43619 CCGTTAGTTT
* * *
43629 ATCCAACTAGAGCTAGGCTCACAATTATTATCATCGG-CA
1 ATCCAACTAGAGCTGGGCTCACAATTATTAT-TTCGGTTA
* * *
43668 TATCCGACTAGCA-CTGGG-T-AAAAATATT-TTT-GGTCT-
1 -ATCCAACTAG-AGCTGGGCTCACAATTATTATTTCGGT-TA
43704 ATCCAACTAGAGCTGGGCTCACAATTATTATTGTCGGTTA
1 ATCCAACTAGAGCTGGGCTCACAATTATTATT-TCGGTTA
*
43744 ATCCAACTAGCGCTGGGC
1 ATCCAACTAGAGCTGGGC
43762 GCAACCTTTT
Statistics
Matches: 73, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
34 1 0.01
35 16 0.22
36 2 0.03
37 8 0.11
38 9 0.12
39 3 0.04
40 33 0.45
41 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (39 bp):
ATCCAACTAGAGCTGGGCTCACAATTATTATTTCGGTTA
Done.