Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold245
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: 333457
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 3 of 3
Found at i:297303 original size:21 final size:19
Alignment explanation
Indices: 297260--297316 Score: 51
Period size: 21 Copynumber: 2.8 Consensus size: 19
297250 TTTTATTCTC
*
297260 AATTTATAATTTTTTTATAAA
1 AATTTA-AA-TTTTATATAAA
297281 AATTTAAATATTTATATAAAA
1 AATTTAAAT-TTTATAT-AAA
* *
297302 AAATCAAATTTTATA
1 AATTTAAATTTTATA
297317 AATGATAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.03
20 14 0.45
21 16 0.52
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTAAATTTTATATAAA
Found at i:297952 original size:3 final size:3
Alignment explanation
Indices: 297944--297982 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
297934 GTTGGCTCTC
297944 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
297983 ATGTTGGGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:301007 original size:19 final size:18
Alignment explanation
Indices: 300959--301000 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
300949 AAATTTATTA
300959 AATATAATT-TATAAATAT
1 AATA-AATTATATAAATAT
*
300977 ATTAAATTATATATAATAT
1 AATAAATTATATA-AATAT
300996 AATAA
1 AATAA
301001 TTAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 7 0.35
19 9 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATTATATAAATAT
Found at i:301274 original size:6 final size:6
Alignment explanation
Indices: 301263--301299 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
301253 TTATTAATTT
* *
301263 TTTATA TTTATA TTTATA TTTATA TTTTTA TTAATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
301300 AAATTTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:301968 original size:20 final size:20
Alignment explanation
Indices: 301927--301979 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
301917 AATATATATT
301927 AAAATAA-AAAATATTTTAA
1 AAAATAAGAAAATATTTTAA
*
301946 AAAATAAGATAATAATTTTAA
1 AAAATAAGAAAAT-ATTTTAA
*
301967 AAAGTAAGCAAAA
1 AAAATAAG-AAAA
301980 CAAATAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.25
20 4 0.14
21 14 0.50
22 3 0.11
ACGTcount: A:0.66, C:0.02, G:0.06, T:0.26
Consensus pattern (20 bp):
AAAATAAGAAAATATTTTAA
Found at i:302540 original size:17 final size:18
Alignment explanation
Indices: 302520--302561 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
302510 TTTTAAAAAA
302520 TAATATTTAATAA-AT-TT
1 TAAT-TTTAATAATATATT
*
302537 TAATTTTTATAATATATT
1 TAATTTTAATAATATATT
302555 TAATTTT
1 TAATTTT
302562 TACTTTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATTTTAATAATATATT
Found at i:302555 original size:19 final size:18
Alignment explanation
Indices: 302527--302563 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
302517 AAATAATATT
302527 TAATAAATTTTAATTTTTA
1 TAATAAA-TTTAATTTTTA
*
302546 TAATATATTTAATTTTTA
1 TAATAAATTTAATTTTTA
302564 CTTTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TAATAAATTTAATTTTTA
Found at i:303041 original size:32 final size:32
Alignment explanation
Indices: 302979--303047 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
302969 AAAAATTTAT
*
302979 ATAAAATTAATATATTTGTGTCTTCTTTTAAA
1 ATAAAATTAATATATTTATGTCTTCTTTTAAA
*
303011 ATAAAATTAAT-TATTTCAT-TTTTCTATTTAAA
1 ATAAAATTAATATATTT-ATGTCTTCT-TTTAAA
303043 A-AAAA
1 ATAAAA
303048 CTATCTACCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
31 14 0.42
32 19 0.58
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (32 bp):
ATAAAATTAATATATTTATGTCTTCTTTTAAA
Found at i:304404 original size:14 final size:14
Alignment explanation
Indices: 304385--304412 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
304375 TTAATTATAA
304385 AATATAAAAATATT
1 AATATAAAAATATT
304399 AATATAAAAATATT
1 AATATAAAAATATT
304413 TTATATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATATAAAAATATT
Found at i:306698 original size:52 final size:52
Alignment explanation
Indices: 306641--306740 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
306631 TTATTATAAA
306641 GGTAAATGCCAAATGTTGTTACAATT-ACTTGTCTTTACCATGAATAACTAGG
1 GGTAAATGCCAAATGTTGTTACAATTAAC-TGTCTTTACCATGAATAACTAGG
* ** **
306693 GGTAAATGCTAAATGTTGTTGTAATTAACTGTCTTTATTATGAATAAC
1 GGTAAATGCCAAATGTTGTTACAATTAACTGTCTTTACCATGAATAAC
306741 ATAAATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 40 0.95
53 2 0.05
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (52 bp):
GGTAAATGCCAAATGTTGTTACAATTAACTGTCTTTACCATGAATAACTAGG
Found at i:307113 original size:19 final size:21
Alignment explanation
Indices: 307077--307135 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
307067 ACAAATTATA
* *
307077 TTATATGACAATGTAATAA-T
1 TTATATAACAAGGTAATAACT
307097 TTATATAA-AAGGTAATAACT
1 TTATATAACAAGGTAATAACT
*
307117 TTTTATAACAAGGATAATA
1 TTATATAACAAGG-TAATA
307136 CAAATCGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 9 0.27
20 15 0.45
21 4 0.12
22 5 0.15
ACGTcount: A:0.47, C:0.05, G:0.10, T:0.37
Consensus pattern (21 bp):
TTATATAACAAGGTAATAACT
Found at i:308436 original size:25 final size:24
Alignment explanation
Indices: 308349--308443 Score: 82
Period size: 25 Copynumber: 3.8 Consensus size: 24
308339 ATTTAATTAT
** *
308349 AAAAATTAAAAATGATTAAGATAA
1 AAAAATTAAAAATTTTTAAAATAA
*
308373 AAAATTATAAATTAATTTTTAAAATAA
1 AAAAAT-TAAA--AATTTTTAAAATAA
* *
308400 AATAAGTGAAAAATTTTTAAAAATAA
1 AA-AAATTAAAAATTTTT-AAAATAA
*
308426 AAAAATTAAAACTTTTTA
1 AAAAATTAAAAATTTTTA
308444 CCAATCAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
24 6 0.11
25 23 0.40
26 9 0.16
27 16 0.28
28 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (24 bp):
AAAAATTAAAAATTTTTAAAATAA
Found at i:309033 original size:16 final size:15
Alignment explanation
Indices: 309012--309043 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
309002 CAGACATTGC
*
309012 TTTTTTTTCCTGTTT
1 TTTTTTTTTCTGTTT
309027 TTTTTTTTTCTGTTT
1 TTTTTTTTTCTGTTT
309042 TT
1 TT
309044 CTTTCTTGTC
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:0.00, C:0.09, G:0.06, T:0.84
Consensus pattern (15 bp):
TTTTTTTTTCTGTTT
Found at i:309991 original size:18 final size:19
Alignment explanation
Indices: 309968--310012 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
309958 AATTATCTAC
*
309968 TTTAGAATC-TCATTTTAA
1 TTTAGAATCTTCATTTAAA
309986 TTTAGAATCTTTCATTTAAA
1 TTTAGAATC-TTCATTTAAA
310006 TTTAGAA
1 TTTAGAA
310013 CATTGCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
20 15 0.62
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTAGAATCTTCATTTAAA
Found at i:310021 original size:20 final size:20
Alignment explanation
Indices: 309968--310022 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
309958 AATTATCTAC
*
309968 TTTAGAATC-T-CATTTTAA
1 TTTAGAATCTTGCATTTAAA
*
309986 TTTAGAATCTTTCATTTAAA
1 TTTAGAATCTTGCATTTAAA
310006 TTTAGAA-CATTGCATTT
1 TTTAGAATC-TTGCATTT
310023 TATGAAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 9 0.28
19 2 0.06
20 21 0.66
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTAGAATCTTGCATTTAAA
Found at i:313517 original size:2 final size:2
Alignment explanation
Indices: 313510--313544 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
313500 AGTAAAAATG
*
313510 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
313545 AAGGATTTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:313831 original size:2 final size:2
Alignment explanation
Indices: 313826--313859 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
313816 TTCTCTTAAT
313826 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
313860 AAGAAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:314278 original size:2 final size:2
Alignment explanation
Indices: 314266--314299 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
314256 GAAACAGATC
*
314266 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
314300 AATACATCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314863 original size:24 final size:23
Alignment explanation
Indices: 314832--314877 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
314822 TCTTATTTTT
314832 TCTTTTTTTTCTGGGTTTTTCTA
1 TCTTTTTTTTCTGGGTTTTTCTA
314855 TCTTATTTTTTCTGGGTTTTTCT
1 TCTT-TTTTTTCTGGGTTTTTCT
314878 TTGTTTTCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (23 bp):
TCTTTTTTTTCTGGGTTTTTCTA
Found at i:314885 original size:33 final size:33
Alignment explanation
Indices: 314814--314877 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
314804 GCAGGTATTT
* **
314814 TTTTTATATCTTATTTTTTCTTTTTTTTCTGGG
1 TTTTTCTATCTTATTTTTTCTGGTTTTTCTGGG
314847 TTTTTCTATCTTATTTTTTCTGGGTTTTTCT
1 TTTTTCTATCTTATTTTTTCT-GGTTTTTCT
314878 TTGTTTTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 20 0.74
34 7 0.26
ACGTcount: A:0.08, C:0.11, G:0.09, T:0.72
Consensus pattern (33 bp):
TTTTTCTATCTTATTTTTTCTGGTTTTTCTGGG
Found at i:319194 original size:21 final size:21
Alignment explanation
Indices: 319145--319185 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
319135 AAGTTTTATT
* *
319145 TAAATTTTATTATAAAATAAA
1 TAAATATTACTATAAAATAAA
319166 TAAATATTACTATAAAATAA
1 TAAATATTACTATAAAATAA
319186 TTTTATATTT
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:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAATATTACTATAAAATAAA
Found at i:323303 original size:78 final size:78
Alignment explanation
Indices: 323171--323589 Score: 380
Period size: 78 Copynumber: 5.4 Consensus size: 78
323161 ATTTTATTCG
* * * * *
323171 AGTCTCTAGGGTCATGTGAGAACTTTCACGTCGATACATGTCTATTA-AAGTTATTTAAGTAATA
1 AGTCTCTAAGGTCATGTGAGAACTTTCATGTCGATACATGTCTATTAGGA-TTACTTAGGTAATA
* * *
323235 TCACATTAACACCA
65 TTACATTAATATCA
* * * ** * * * *
323249 AGTCTCTAAGGTCATGTGGGAACTTTTATGTTGATATTTGTCCATTAGGATTATTTTGGTAACAT
1 AGTCTCTAAGGTCATGTGAGAACTTTCATGTCGATACATGTCTATTAGGATTACTTAGGTAATAT
*
323314 TACATTAATATCG
66 TACATTAATATCA
* * * * * * *
323327 AGTCT-TTAGAGTCATGTAAAAACTTTTATGTCGAGACATGTCTATTAAGGCTTA-TTAGGTGAT
1 AGTCTCTAAG-GTCATGTGAGAACTTTCATGTCGATACATGTCTATT-AGGATTACTTAGGTAAT
* *
323390 ATTATATTAATACCA
64 ATTACATTAATATCA
* * * * * *
323405 AGTCTCTAAAGTCATGTGGGAACTTTCATGTCGATATATGTTTATTAGGGTTACTTAGGTTATAT
1 AGTCTCTAAGGTCATGTGAGAACTTTCATGTCGATACATGTCTATTAGGATTACTTAGGTAATAT
*
323470 TACATTAAAATCA
66 TACATTAATATCA
* * * * * * *
323483 AGTCTCT-AGGATCGTGTGTGAACTTTCGTGTTGATACATATCTATTAGGGTTACTTAGGTGATA
1 AGTCTCTAAGG-TCATGTGAGAACTTTCATGTCGATACATGTCTATTAGGATTACTTAGGTAATA
323547 TTACATTAATATCA
65 TTACATTAATATCA
*
323561 AGTCTCCAAGGTCATGT-ATGAACTTTCAT
1 AGTCTCTAAGGTCATGTGA-GAACTTTCAT
323590 TTAGATTATA
Statistics
Matches: 273, Mismatches: 60, Indels: 16
0.78 0.17 0.05
Matches are distributed among these distances:
77 11 0.04
78 250 0.92
79 12 0.04
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (78 bp):
AGTCTCTAAGGTCATGTGAGAACTTTCATGTCGATACATGTCTATTAGGATTACTTAGGTAATAT
TACATTAATATCA
Found at i:323452 original size:156 final size:155
Alignment explanation
Indices: 323168--323589 Score: 477
Period size: 156 Copynumber: 2.7 Consensus size: 155
323158 GTTATTTTAT
* * * * *
323168 TCGAGTCTCTAGGGTCATGTGAGAACTTTCACGTCGATACATGTCTATTAAAGTTATTTAAGTAA
1 TCGAGTCTCTA-GGTCATGTGAGAACTTTCATGTCGATACATGTCTATTAAGGTTACTTAGGTGA
* * * * *
323233 TATCACATTAACACCAAGTCTCTAAGGTCATGTGGGAACTTTTATGTTGATATTTGTCCATTAGG
65 TATTACATTAATACCAAGTCTCTAAGGTCATGTGGGAACTTTCATGTCGATATATGTCCATTAGG
* * *
323298 ATTATTTTGGTAACATTACATTAATA
130 ATTACTTAGGTAACATTACATTAAAA
* * * * *
323324 TCGAGTCTTTAGAGTCATGTAAAAACTTTTATGTCGAGACATGTCTATTAAGGCTTA-TTAGGTG
1 TCGAGTCTCTAG-GTCATGTGAGAACTTTCATGTCGATACATGTCTATTAAGG-TTACTTAGGTG
* * **
323388 ATATTATATTAATACCAAGTCTCTAAAGTCATGTGGGAACTTTCATGTCGATATATGTTTATTAG
64 ATATTACATTAATACCAAGTCTCTAAGGTCATGTGGGAACTTTCATGTCGATATATGTCCATTAG
* * *
323453 GGTTACTTAGGTTATATTACATTAAAA
129 GATTACTTAGGTAACATTACATTAAAA
* * * * * * *
323480 TCAAGTCTCTAGGATCGTGTGTGAACTTTCGTGTTGATACATATCTATTAGGGTTACTTAGGTGA
1 TCGAGTCTCTAGG-TCATGTGAGAACTTTCATGTCGATACATGTCTATTAAGGTTACTTAGGTGA
* * **
323545 TATTACATTAATATCAAGTCTCCAAGGTCATGTATGAACTTTCAT
65 TATTACATTAATACCAAGTCTCTAAGGTCATGTGGGAACTTTCAT
323590 TTAGATTATA
Statistics
Matches: 220, Mismatches: 42, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
155 5 0.02
156 212 0.96
157 3 0.01
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (155 bp):
TCGAGTCTCTAGGTCATGTGAGAACTTTCATGTCGATACATGTCTATTAAGGTTACTTAGGTGAT
ATTACATTAATACCAAGTCTCTAAGGTCATGTGGGAACTTTCATGTCGATATATGTCCATTAGGA
TTACTTAGGTAACATTACATTAAAA
Found at i:328273 original size:17 final size:18
Alignment explanation
Indices: 328253--328289 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
328243 GAACTGACCG
328253 ATTAAAATCGA-CCCCTA
1 ATTAAAATCGACCCCCTA
328270 ATTAAAATCGACCCCCTA
1 ATTAAAATCGACCCCCTA
328288 AT
1 AT
328290 CCTAAAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.41, C:0.30, G:0.05, T:0.24
Consensus pattern (18 bp):
ATTAAAATCGACCCCCTA
Found at i:328905 original size:38 final size:38
Alignment explanation
Indices: 328863--328998 Score: 211
Period size: 38 Copynumber: 3.6 Consensus size: 38
328853 GACTAATTCT
* *
328863 AAATTGAATTCTCTAGTCGTCAGCCGCCGGTCAATTTC
1 AAATTGAATTCTCTAATCGTCAGCCGCCAGTCAATTTC
* *
328901 AAATTGAATTCTCTAACCGTCAGCTGCCAG-CTAATTTC
1 AAATTGAATTCTCTAATCGTCAGCCGCCAGTC-AATTTC
*
328939 AAATTGAATTCTCTAATCGTCAGCCGCCAATCAATTTC
1 AAATTGAATTCTCTAATCGTCAGCCGCCAGTCAATTTC
328977 AAATTGAATTCTCTAATCGTCA
1 AAATTGAATTCTCTAATCGTCA
328999 ACTAATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
37 1 0.01
38 87 0.98
39 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.32
Consensus pattern (38 bp):
AAATTGAATTCTCTAATCGTCAGCCGCCAGTCAATTTC
Found at i:328943 original size:76 final size:76
Alignment explanation
Indices: 328855--328998 Score: 236
Period size: 76 Copynumber: 1.9 Consensus size: 76
328845 CAGTCACCGA
* **
328855 CTAATTCTAAATTGAATTCTCTAGTCGTCAGCCGCCGGTCAATTTCAAATTGAATTCTCTAACCG
1 CTAATTCTAAATTGAATTCTCTAATCGTCAGCCGCCAATCAATTTCAAATTGAATTCTCTAACCG
328920 TCAGCTGCCAG
66 TCAGCTGCCAG
*
328931 CTAATT-TCAAATTGAATTCTCTAATCGTCAGCCGCCAATCAATTTCAAATTGAATTCTCTAATC
1 CTAATTCT-AAATTGAATTCTCTAATCGTCAGCCGCCAATCAATTTCAAATTGAATTCTCTAACC
328995 GTCA
65 GTCA
328999 ACTAATTCAA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 1 0.02
76 62 0.98
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (76 bp):
CTAATTCTAAATTGAATTCTCTAATCGTCAGCCGCCAATCAATTTCAAATTGAATTCTCTAACCG
TCAGCTGCCAG
Found at i:332026 original size:12 final size:12
Alignment explanation
Indices: 332009--332054 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
331999 ACGTTCGATT
*
332009 ATATGTTTATGA
1 ATATATTTATGA
* **
332021 ATATGTTTATTT
1 ATATATTTATGA
332033 ATATATTTATGA
1 ATATATTTATGA
332045 ATATATTTAT
1 ATATATTTAT
332055 TTAATTCTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.57
Consensus pattern (12 bp):
ATATATTTATGA
Found at i:332034 original size:24 final size:24
Alignment explanation
Indices: 332007--332057 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
331997 ACACGTTCGA
* *
332007 TTATATGTTTATGAATATGTTTAT
1 TTATATATTTATGAATATATTTAT
332031 TTATATATTTATGAATATATTTAT
1 TTATATATTTATGAATATATTTAT
332055 TTA
1 TTA
332058 ATTCTAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (24 bp):
TTATATATTTATGAATATATTTAT
Found at i:332621 original size:16 final size:14
Alignment explanation
Indices: 332598--332635 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
332588 TAGGTTGAAA
332598 AAAAAAAAGAAAATG
1 AAAAAAAAGAAAA-G
332613 AAAAGAAAAGAAAAG
1 AAAA-AAAAGAAAAG
332628 AAAAAAAA
1 AAAAAAAA
332636 AATTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 9 0.41
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:332636 original size:10 final size:10
Alignment explanation
Indices: 332597--332636 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
332587 GTAGGTTGAA
332597 AAAAAAAAAG
1 AAAAAAAAAG
*
332607 AAAATGAAAAG
1 AAAA-AAAAAG
*
332618 AAAAGAAAAG
1 AAAAAAAAAG
332628 AAAAAAAAA
1 AAAAAAAAA
332637 ATTATATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:332637 original size:16 final size:17
Alignment explanation
Indices: 332596--332637 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
332586 GGTAGGTTGA
332596 AAAAAAAAAAGAAAATG
1 AAAAAAAAAAGAAAATG
*
332613 -AAAAGAAAAGAAAA-G
1 AAAAAAAAAAGAAAATG
332628 AAAAAAAAAA
1 AAAAAAAAAA
332638 TTATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.86, C:0.00, G:0.12, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAGAAAATG
Found at i:332696 original size:20 final size:22
Alignment explanation
Indices: 332673--332716 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
332663 TTATATAAAA
*
332673 TTTTATAT-TTTATAA-TTATT
1 TTTTATATATTAATAATTTATT
332693 TTTTATATATTAATAATTTATT
1 TTTTATATATTAATAATTTATT
332715 TT
1 TT
332717 ATTTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 7 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTATATATTAATAATTTATT
Found at i:332717 original size:20 final size:20
Alignment explanation
Indices: 332672--332722 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
332662 TTTATATAAA
*
332672 ATTTTATATTTTATAATTAT
1 ATTTTATATTTAATAATTAT
*
332692 TTTTTATATATTAATAATT-T
1 ATTTTATAT-TTAATAATTAT
332712 ATTTTAT-TTTA
1 ATTTTATATTTA
332723 TGTATATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.11
19 1 0.04
20 15 0.56
21 8 0.30
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTATATTTAATAATTAT
Done.