Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1707
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: 51646
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Found at i:3167 original size:17 final size:17
Alignment explanation
Indices: 3129--3169 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3119 TATTATAGTA
* * *
3129 ATTTAATGATTAAATTG
1 ATTTTATGACTAAAGTG
3146 ATTTTATGACTAAAGTG
1 ATTTTATGACTAAAGTG
3163 ATTTTAT
1 ATTTTAT
3170 CCTTGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (17 bp):
ATTTTATGACTAAAGTG
Found at i:5031 original size:27 final size:28
Alignment explanation
Indices: 4993--5063 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
4983 GCCACCTATT
4993 TGTTTGTCAAAAATGGTGGTTAT-TTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
* *
5020 TGTTTGTTAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATGGTGGTTATCTTTG
* *
5048 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
5064 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.23, C:0.04, G:0.24, T:0.49
Consensus pattern (28 bp):
TGTTTGTCAAAAATGGTGGTTATCTTTG
Found at i:5164 original size:20 final size:20
Alignment explanation
Indices: 5139--5184 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
5129 AAATAGAGGC
*
5139 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
5159 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
5179 TCCCTC
1 TCCCTC
5185 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:7665 original size:21 final size:22
Alignment explanation
Indices: 7636--7681 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
7626 TATTCAGACA
** *
7636 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
7658 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
7679 AGT
1 AGT
7682 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:9620 original size:28 final size:27
Alignment explanation
Indices: 9565--9635 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
9555 GCCATCCATT
9565 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
9592 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
9620 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
9636 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:10257 original size:97 final size:97
Alignment explanation
Indices: 10085--10262 Score: 239
Period size: 97 Copynumber: 1.8 Consensus size: 97
10075 ATTTTCTACG
* *
10085 AAGGATGCTCTATCTCAAATTCAAGGAATTATTATAAAATTTCCTTACAAAGGAAAATTACATCT
1 AAGGATGCTCCATCTCAAATTCAAGGAATTATTACAAAATTTCCTTACAAAGGAAAATTACATCT
10150 GAATTCCACTTGAATGCTGGGGGATTTAGATT
66 GAATTCCACTTGAATGCTGGGGGATTTAGATT
* * * ** * * * * *
10182 AAGGGTGCTCCATCTCAAATTCAAGGGATTGTTACGGAATTTCTTTGCAAGGGAGAATTACTTCT
1 AAGGATGCTCCATCTCAAATTCAAGGAATTATTACAAAATTTCCTTACAAAGGAAAATTACATCT
*
10247 GAATTTCACTTGAATG
66 GAATTCCACTTGAATG
10263 GTTGGGAATA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
97 68 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (97 bp):
AAGGATGCTCCATCTCAAATTCAAGGAATTATTACAAAATTTCCTTACAAAGGAAAATTACATCT
GAATTCCACTTGAATGCTGGGGGATTTAGATT
Found at i:10552 original size:186 final size:186
Alignment explanation
Indices: 10238--10623 Score: 567
Period size: 186 Copynumber: 2.1 Consensus size: 186
10228 GCAAGGGAGA
* * * * * * *
10238 ATTACTTCTGAATTTCACTTGAATGGTTGGGAATATAGATGAAGTCTTCGACGTTAAAAACTTTT
1 ATTACTTCTTAATTCCACTTAAATGGTTAGAAATATAGATGAAGTCTTCAACGTCAAAAACTTTT
*
10303 AAATAAAAAGACATTACGAGAAATATAATAATATTTCTAATAAAATGTATTAAGTAAATTATTTT
66 AAATAAAAAGACATTACGAGAAATATAATAATATTTCTAATAAAATGCATTAAGTAAATTATTTT
* * *
10368 AAGTATTAAAATTAAAATTATTTTTTCAAAATAAAGATAACATGAAATTAATATGT
131 AAGTATTAAAATTAAAATCATTTTCTCAAAATAAAGATAAAATGAAATTAATATGT
* * * *
10424 ATTACTTCTTAATTCCACTTAAATGTTTAGAAATTTAGATGAAGTCTTCAATGTCAAAAATTTTT
1 ATTACTTCTTAATTCCACTTAAATGGTTAGAAATATAGATGAAGTCTTCAACGTCAAAAACTTTT
* * * *
10489 AAATAAAAAGACATTACGAGAAATATAATAATGTTTTTAGTAAAATGCATTAAGTGAATTATTTT
66 AAATAAAAAGACATTACGAGAAATATAATAATATTTCTAATAAAATGCATTAAGTAAATTATTTT
*
10554 AAGTATTAAAATTAAAATCATTTTCTCAAAATGAAGATAAAATGAAATTAATATGT
131 AAGTATTAAAATTAAAATCATTTTCTCAAAATAAAGATAAAATGAAATTAATATGT
*
10610 ACTATCTT-TTAATT
1 ATTA-CTTCTTAATT
10624 GATATTATAA
Statistics
Matches: 178, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
186 175 0.98
187 3 0.02
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (186 bp):
ATTACTTCTTAATTCCACTTAAATGGTTAGAAATATAGATGAAGTCTTCAACGTCAAAAACTTTT
AAATAAAAAGACATTACGAGAAATATAATAATATTTCTAATAAAATGCATTAAGTAAATTATTTT
AAGTATTAAAATTAAAATCATTTTCTCAAAATAAAGATAAAATGAAATTAATATGT
Found at i:15359 original size:2 final size:2
Alignment explanation
Indices: 15354--15382 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15344 GGATATTCAA
15354 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
15383 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:15387 original size:2 final size:2
Alignment explanation
Indices: 15382--15414 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15372 TCTCTCTCTC
15382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15415 GTTAGAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21536 original size:32 final size:29
Alignment explanation
Indices: 21500--21567 Score: 75
Period size: 32 Copynumber: 2.3 Consensus size: 29
21490 AGCAAGAAAC
*
21500 ATTTAATAGATATGAAAAATATAATAAATATG
1 ATTTAATAGAT-TGAAAAAT-T-ATAAAAATG
* *
21532 ATTTAATATATTTAAAAATTATAAAAATG
1 ATTTAATAGATTGAAAAATTATAAAAATG
21561 A-TTAATA
1 ATTTAATA
21568 TAACATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 6 0.18
29 9 0.27
30 1 0.03
31 7 0.21
32 10 0.30
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (29 bp):
ATTTAATAGATTGAAAAATTATAAAAATG
Found at i:21613 original size:17 final size:19
Alignment explanation
Indices: 21566--21634 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 19
21556 AAATGATTAA
*
21566 TATAACATATTTAATACATAT
1 TATAATATATTTAATA-AT-T
*
21587 TAT-TTATATTTAA-AATT
1 TATAATATATTTAATAATT
21604 T-TAATATATTTAATAATT
1 TATAATATATTTAATAATT
*
21622 TATATTATATTTA
1 TATAATATATTTA
21635 TATTTACATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.02
17 11 0.27
18 7 0.17
19 11 0.27
20 8 0.20
21 3 0.07
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TATAATATATTTAATAATT
Found at i:22762 original size:14 final size:15
Alignment explanation
Indices: 22730--22762 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22720 AGTTATTTTC
*
22730 AATTTTAAATTGTTT
1 AATTTTAAATTGATT
22745 AATTTTAAATT-ATT
1 AATTTTAAATTGATT
22759 AATT
1 AATT
22763 ATTTTCATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
AATTTTAAATTGATT
Found at i:22767 original size:32 final size:33
Alignment explanation
Indices: 22693--22767 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 33
22683 TTATTTTGAG
* *
22693 TTAATT-TTTTAAATCTTTTTAAGTTTAAGTTA
1 TTAATTATTTTAAATCTGTTTAAGTTTAAATTA
*
22725 TT--TTCAATTTTAAAT-TGTTTAATTTTAAATTA
1 TTAATT--ATTTTAAATCTGTTTAAGTTTAAATTA
22757 TTAATTATTTT
1 TTAATTATTTT
22768 CATCCAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
30 2 0.06
32 23 0.66
33 8 0.23
34 2 0.06
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (33 bp):
TTAATTATTTTAAATCTGTTTAAGTTTAAATTA
Found at i:26502 original size:20 final size:21
Alignment explanation
Indices: 26458--26502 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
26448 TTCAAAATAA
26458 ATTAATTTAAATATTAATTTT
1 ATTAATTTAAATATTAATTTT
26479 -TTAATTTAAA-A-TAATTATT
1 ATTAATTTAAATATTAATT-TT
26498 ATTAA
1 ATTAA
26503 ACAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.23
19 3 0.14
20 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAATTTAAATATTAATTTT
Found at i:27267 original size:15 final size:15
Alignment explanation
Indices: 27247--27278 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27237 ATCTATTTTT
27247 TAAAATTACAAATTA
1 TAAAATTACAAATTA
*
27262 TAAAATTATAAATTA
1 TAAAATTACAAATTA
27277 TA
1 TA
27279 TGTATTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATTACAAATTA
Found at i:27519 original size:19 final size:19
Alignment explanation
Indices: 27495--27535 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
27485 ATAAATATAC
* *
27495 ATTTTTATTTTATATTTTA
1 ATTTTTATATAATATTTTA
*
27514 ATTTTTATATAATTTTTTA
1 ATTTTTATATAATATTTTA
27533 ATT
1 ATT
27536 AAGTTAATGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTATATAATATTTTA
Found at i:28324 original size:2 final size:2
Alignment explanation
Indices: 28317--28369 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
28307 TCATGATCAG
28317 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
28359 TA TA TA TA TA T
1 TA TA TA TA TA T
28370 CAAACAAGCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30058 original size:8 final size:9
Alignment explanation
Indices: 30045--30123 Score: 56
Period size: 9 Copynumber: 8.9 Consensus size: 9
30035 ATTTAAAATA
30045 TTATAT-TT
1 TTATATATT
30053 TTATATATT
1 TTATATATT
* *
30062 TTTTATATA
1 TTATATATT
30071 TTA-ATATT
1 TTATATATT
*
30079 TTATTTTATT
1 TTA-TATATT
30089 TTATAATATT
1 TTAT-ATATT
* *
30099 TT-TATGTA
1 TTATATATT
* *
30107 TAATTTATT
1 TTATATATT
30116 TTATATAT
1 TTATATAT
30124 GAGAGGAAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
8 17 0.33
9 22 0.42
10 13 0.25
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (9 bp):
TTATATATT
Found at i:30077 original size:32 final size:31
Alignment explanation
Indices: 30020--30085 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
30010 TTTGTTTATA
*
30020 TTTATAATTTTTTGTATTTAAAATATTATATT
1 TTTATAATTTTTTATATTT-AAATATTATATT
*
30052 TTTATATATTTTTTATATATT-AATATTTTATT
1 TTTATA-ATTTTTTATAT-TTAAATATTATATT
30084 TT
1 TT
30086 ATTTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 18 0.60
33 10 0.33
34 2 0.07
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (31 bp):
TTTATAATTTTTTATATTTAAATATTATATT
Found at i:30080 original size:26 final size:26
Alignment explanation
Indices: 30036--30098 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 26
30026 ATTTTTTGTA
*
30036 TTTAAAATATTATATTTTTATATATT-T
1 TTTATAATATTATATTTTTAT-T-TTAT
30063 TTTAT-ATATTA-ATATTTTATTTTAT
1 TTTATAATATTATAT-TTTTATTTTAT
30088 TTTATAATATT
1 TTTATAATATT
30099 TTTATGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 2 0.06
25 9 0.28
26 17 0.53
27 4 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTATAATATTATATTTTTATTTTAT
Found at i:30087 original size:20 final size:20
Alignment explanation
Indices: 30062--30100 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30052 TTTATATATT
30062 TTTTA-TATATTAATATTTTA
1 TTTTATTATA-TAATATTTTA
*
30082 TTTTATTTTATAATATTTT
1 TTTTATTATATAATATTTT
30101 TATGTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATTATATAATATTTTA
Found at i:30221 original size:4 final size:4
Alignment explanation
Indices: 30212--30276 Score: 73
Period size: 4 Copynumber: 16.8 Consensus size: 4
30202 GTTTTGCTGA
*
30212 AAAG AAAG AAAG AAAG AAAA AAAG AAAG AAAG AAAG -AAG AAA- AATAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA-AG
* *
30259 AAA- AAAA AAAG AAGG AAA
1 AAAG AAAG AAAG AAAG AAA
30277 ATAATTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
3 8 0.15
4 42 0.81
5 2 0.04
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:30229 original size:12 final size:12
Alignment explanation
Indices: 30212--30277 Score: 82
Period size: 12 Copynumber: 5.7 Consensus size: 12
30202 GTTTTGCTGA
*
30212 AAAGAAAGAAAG
1 AAAGAAAAAAAG
30224 AAAGAAAAAAAG
1 AAAGAAAAAAAG
*
30236 AAAGAAAGAAAG
1 AAAGAAAAAAAG
*
30248 -AAGAAAAATAG
1 AAAGAAAAAAAG
30259 AAA-AAAAAAAG
1 AAAGAAAAAAAG
*
30270 AAGGAAAA
1 AAAGAAAA
30278 TAATTTTATG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
11 18 0.39
12 28 0.61
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:30236 original size:20 final size:21
Alignment explanation
Indices: 30211--30277 Score: 84
Period size: 20 Copynumber: 3.2 Consensus size: 21
30201 CGTTTTGCTG
30211 AAAAGAAAGAAAGAAAGAA-A
1 AAAAGAAAGAAAGAAAGAAGA
30231 AAAAGAAAGAAAGAAAGAAGAA
1 AAAAGAAAGAAAGAAAGAAG-A
* *
30253 AAATAGAAA-AAAAAAAGAAGG
1 AAA-AGAAAGAAAGAAAGAAGA
30274 AAAA
1 AAAA
30278 TAATTTTATG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 20 0.48
21 3 0.07
22 14 0.33
23 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (21 bp):
AAAAGAAAGAAAGAAAGAAGA
Found at i:31692 original size:31 final size:30
Alignment explanation
Indices: 31624--31692 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 30
31614 TATATGTTTG
*
31624 TATTTATATTTTTTTATATTTAAAATATTA
1 TATTTATATTTTTTTACATTTAAAATATTA
31654 TATTTTATATATTTTTTACATATTAATAAT-TTA
1 TA-TTTATAT-TTTTTTACAT-TTAA-AATATTA
31687 -ATTTAT
1 TATTTAT
31693 TTTATGTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
30 2 0.06
31 12 0.35
32 10 0.29
33 7 0.21
34 3 0.09
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTTATATTTTTTTACATTTAAAATATTA
Found at i:32419 original size:8 final size:8
Alignment explanation
Indices: 32406--32432 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
32396 TTATATATAT
32406 AATTTTAA
1 AATTTTAA
32414 AATTTTAA
1 AATTTTAA
32422 AATTTTAA
1 AATTTTAA
32430 AAT
1 AAT
32433 CAAGTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:33378 original size:27 final size:28
Alignment explanation
Indices: 33343--33396 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
33333 ACATCATGTC
* *
33343 ATTTGTTAAAAATAATATTATTGTATTT
1 ATTTGTTAAAAAAAAAATTATTGTATTT
*
33371 ATTT-TTAAAAAAAAAATTATTTTATT
1 ATTTGTTAAAAAAAAAATTATTGTATT
33397 AATTAACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (28 bp):
ATTTGTTAAAAAAAAAATTATTGTATTT
Found at i:33571 original size:7 final size:7
Alignment explanation
Indices: 33559--33583 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
33549 TTTTTTTATT
33559 ATTTTAA
1 ATTTTAA
33566 ATTTTAA
1 ATTTTAA
33573 ATTTTAA
1 ATTTTAA
33580 ATTT
1 ATTT
33584 ATATATTACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTTAA
Found at i:35796 original size:29 final size:28
Alignment explanation
Indices: 35771--35866 Score: 90
Period size: 32 Copynumber: 3.3 Consensus size: 28
35761 CACAATATTA
35771 AAAAATATA-T-AAATTTAATATAAATAT
1 AAAAATATATTAAAATTT-ATATAAATAT
35798 AAAAATATATTAAAATTTATAT-AATAT
1 AAAAATATATTAAAATTTATATAAATAT
* *
35825 AAATTATCAACATATTAAAATTTATATAAAAAT
1 -AA--A--AATATATTAAAATTTATATAAATAT
35858 ATAAAATAT
1 A-AAAATAT
35867 TTTCAATATA
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
27 14 0.25
28 7 0.12
29 10 0.18
30 1 0.02
31 1 0.02
32 19 0.33
33 5 0.09
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAAATATATTAAAATTTATATAAATAT
Found at i:35823 original size:27 final size:27
Alignment explanation
Indices: 35771--35827 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
35761 CACAATATTA
35771 AAAAATATATAAATTTAATATAAATAT
1 AAAAATATATAAATTTAATATAAATAT
35798 AAAAATATATTAAAATTT-ATAT-AATAT
1 AAAAATATA-T-AAATTTAATATAAATAT
35825 AAA
1 AAA
35828 TTATCAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 17 0.61
28 5 0.18
29 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAAATATATAAATTTAATATAAATAT
Found at i:35845 original size:32 final size:33
Alignment explanation
Indices: 35786--35853 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
35776 TATATAAATT
*
35786 TAATATAAATATAAAAATATATTAAAATTTATA
1 TAATATAAATATAAAAACATATTAAAATTTATA
**
35819 TAATATAAAT-TATCAACATATTAAAATTTATA
1 TAATATAAATATAAAAACATATTAAAATTTATA
35851 TAA
1 TAA
35854 AAATATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (33 bp):
TAATATAAATATAAAAACATATTAAAATTTATA
Found at i:35909 original size:24 final size:23
Alignment explanation
Indices: 35872--35917 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
35862 AATATTTTCA
* *
35872 ATATAATTATAATATAATAAAAT
1 ATATAATTAAAATAAAATAAAAT
35895 ATATAAATTAAAATAAAATAAAA
1 ATAT-AATTAAAATAAAATAAAA
35918 ACACAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAATTAAAATAAAATAAAAT
Found at i:37067 original size:22 final size:22
Alignment explanation
Indices: 37035--37076 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
37025 TTAATAAGTT
37035 GAAAAAAAAAAGAAAGAAAGGA
1 GAAAAAAAAAAGAAAGAAAGGA
*
37057 GAAAAACAAAAGAAAGAAAG
1 GAAAAAAAAAAGAAAGAAAG
37077 AAATTATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAAGAAAGAAAGGA
Found at i:37124 original size:20 final size:20
Alignment explanation
Indices: 37095--37141 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
37085 ATCATATTTG
*
37095 TATTAT-TTTTTACATAAAA
1 TATTATATTTTTACAAAAAA
*
37114 TATTATATTTTTATAAAAAA
1 TATTATATTTTTACAAAAAA
*
37134 TTTTATAT
1 TATTATAT
37142 ATTAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTATATTTTTACAAAAAA
Found at i:37149 original size:20 final size:20
Alignment explanation
Indices: 37110--37149 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
37100 TTTTTTACAT
* *
37110 AAAATATTATATTTTTATAA
1 AAAATATTATATATTAATAA
*
37130 AAAATTTTATATATTAATAA
1 AAAATATTATATATTAATAA
37150 TTTATTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATATTATATATTAATAA
Found at i:37156 original size:20 final size:19
Alignment explanation
Indices: 37133--37187 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
37123 TTTATAAAAA
*
37133 ATTTTATATATTAATAATTT
1 ATTTTATAT-TTAATAATAT
37153 ATTTTAT-TTT-AT-ATAT
1 ATTTTATATTTAATAATAT
37169 ATTTTTATATGTTAATAAT
1 A-TTTTATAT-TTAATAAT
37188 GTTAATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
16 4 0.14
17 8 0.28
18 3 0.10
19 3 0.10
20 9 0.31
21 2 0.07
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
ATTTTATATTTAATAATAT
Found at i:37493 original size:21 final size:20
Alignment explanation
Indices: 37454--37520 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
37444 AGATTATACC
*
37454 ATATAAAAAATTATAATATA
1 ATATAAAAAATAATAATATA
*
37474 ATATAAAATATAATTAATATA
1 ATATAAAAAATAA-TAATATA
* *
37495 ATACGAACAAATAAT-ATA-A
1 ATA-TAAAAAATAATAATATA
37514 ATATAAA
1 ATATAAA
37521 TATATATAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 2 0.05
19 4 0.11
20 14 0.37
21 11 0.29
22 7 0.18
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (20 bp):
ATATAAAAAATAATAATATA
Found at i:37553 original size:18 final size:18
Alignment explanation
Indices: 37508--37558 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
37498 CGAACAAATA
37508 ATATAAATA-TAAA-TAT
1 ATATAAATATTAAATTAT
*
37524 ATATAAACATATTAAATTTT
1 ATAT-AA-ATATTAAATTAT
*
37544 ATATAAATATAAAAT
1 ATATAAATATTAAAT
37559 ACTTTACGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 11 0.38
19 6 0.21
20 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATATTAAATTAT
Found at i:37890 original size:20 final size:21
Alignment explanation
Indices: 37848--37891 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
37838 ATTATGATAA
**
37848 ATAAATTAATAAATTAATTTT
1 ATAAATTAATAAATTAAAATT
*
37869 ATAAA-TAATAATTTAAAATT
1 ATAAATTAATAAATTAAAATT
37889 ATA
1 ATA
37892 TAAAAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAAATTAATAAATTAAAATT
Found at i:38491 original size:25 final size:25
Alignment explanation
Indices: 38456--38505 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
38446 TATATTTAAT
* *
38456 AAATAATTATTT-TATTAAAATTTTA
1 AAATAAATATTTAAATT-AAATTTTA
38481 AAATAAATATTTAAATTAAATTTTA
1 AAATAAATATTTAAATTAAATTTTA
38506 TTATAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAATAAATATTTAAATTAAATTTTA
Found at i:38493 original size:13 final size:12
Alignment explanation
Indices: 38473--38515 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
38463 TATTTTATTA
38473 AAATTTTAAAAT
1 AAATTTTAAAAT
*
38485 AAATATTTAAATT
1 AAAT-TTTAAAAT
**
38498 AAATTTTATTAT
1 AAATTTTAAAAT
38510 AAATTT
1 AAATTT
38516 ATATTCTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTTTAAAAT
Found at i:40833 original size:10 final size:10
Alignment explanation
Indices: 40820--40853 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
40810 ATGAGTTTTT
*
40820 TAATTTTTTA
1 TAATTTTTAA
40830 TAATTTTTAA
1 TAATTTTTAA
40840 TTAATTTTTAA
1 -TAATTTTTAA
40851 TAA
1 TAA
40854 AAATTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:40844 original size:11 final size:11
Alignment explanation
Indices: 40819--40851 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
40809 TATGAGTTTT
*
40819 TTAATTTTTTA
1 TTAATTTTTAA
40830 -TAATTTTTAA
1 TTAATTTTTAA
40840 TTAATTTTTAA
1 TTAATTTTTAA
40851 T
1 T
40852 AAAAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTAATTTTTAA
Found at i:43255 original size:27 final size:25
Alignment explanation
Indices: 43200--43292 Score: 82
Period size: 26 Copynumber: 3.6 Consensus size: 25
43190 AAGCCACCCA
*
43200 TTTGTTTGTCAAAAATAGTGGTTAT
1 TTTGTTTGTCAAAAATGGTGGTTAT
43225 TTTGTGTTGTCAAAAATGGTGGTT-T
1 TTTGT-TTGTCAAAAATGGTGGTTAT
* *
43250 CCTTTGTATTTGTCAAATATGGAGGCTTA-
1 --TTTG--TTTGTCAAAAATGGTGG-TTAT
*
43279 TTTATTTGTCAAAA
1 TTTGTTTGTCAAAA
43293 TTTGTGGCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
25 15 0.27
26 17 0.30
27 7 0.12
28 14 0.25
29 3 0.05
ACGTcount: A:0.26, C:0.08, G:0.20, T:0.46
Consensus pattern (25 bp):
TTTGTTTGTCAAAAATGGTGGTTAT
Found at i:45876 original size:21 final size:22
Alignment explanation
Indices: 45847--45892 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
45837 TGTTCAGACA
** *
45847 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
45869 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
45890 AGT
1 AGT
45893 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:47831 original size:28 final size:29
Alignment explanation
Indices: 47771--47846 Score: 97
Period size: 27 Copynumber: 2.8 Consensus size: 29
47761 CAAAAGCCAC
*
47771 CCTTT-TGTTTGTCAAAAATGGTGGTTAT
1 CCTTTGTGTTTGTCAAAAATGGTGATTAT
47799 --TTTGTGTTTGTCAAAAATGGTGATT-T
1 CCTTTGTGTTTGTCAAAAATGGTGATTAT
* *
47825 CCTTTGTATTTGTCAAATATGG
1 CCTTTGTGTTTGTCAAAAATGG
47847 AGGCTTGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.10
27 20 0.48
28 18 0.43
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.47
Consensus pattern (29 bp):
CCTTTGTGTTTGTCAAAAATGGTGATTAT
Found at i:50508 original size:20 final size:21
Alignment explanation
Indices: 50475--50523 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
50465 AAAATAGTTG
50475 TTATATTAATATTTATAT-TT
1 TTATATTAATATTTATATATT
50495 TTATAATTAA-ATTTATATATT
1 TTAT-ATTAATATTTATATATT
*
50516 TTTTATTA
1 TTATATTA
50524 TTAATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATTAATATTTATATATT
Found at i:50529 original size:22 final size:20
Alignment explanation
Indices: 50478--50529 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
50468 ATAGTTGTTA
50478 TATTAATATTTATATTTTTAT
1 TATTAAT-TTTATATTTTTAT
*
50499 AATTAAATTTATATATTTTTTAT
1 TATT-AATTT-TATA-TTTTTAT
50522 TATTAATT
1 TATTAATT
50530 AATAATTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 11 0.42
23 10 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTAATTTTATATTTTTAT
Found at i:51322 original size:97 final size:97
Alignment explanation
Indices: 51151--51345 Score: 275
Period size: 97 Copynumber: 2.0 Consensus size: 97
51141 TTTCTACGAG
* * * * *
51151 GGATGCTCCATCTGAAATTCAAGGGATTATTACGGAATTTTTTTACAAAGGAGAATTGCTTCTGA
1 GGATGCTCCATCTCAAATTCAAGGGACTATTACGGAATTTCTTTACAAAGGAAAATTACTTCTGA
51216 ATTTCACTTGAATGATGGGGAATTGAGATGAA
66 ATTTCACTTGAATGATGGGGAATTGAGATGAA
** *
51248 GGATGCTCCATCTCAAATTCAAGGGACTATTACTTACTTTCTTTACAAAGGAAAATTACTTCTGA
1 GGATGCTCCATCTCAAATTCAAGGGACTATTACGGAATTTCTTTACAAAGGAAAATTACTTCTGA
* **
51313 A-TTCTACTTGAATGCTGGGGAATTTTGATGAA
66 ATTTC-ACTTGAATGATGGGGAATTGAGATGAA
51345 G
1 G
51346 TCTTCTACGT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
96 3 0.03
97 83 0.97
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (97 bp):
GGATGCTCCATCTCAAATTCAAGGGACTATTACGGAATTTCTTTACAAAGGAAAATTACTTCTGA
ATTTCACTTGAATGATGGGGAATTGAGATGAA
Done.