Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1021
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: 44370
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:3677 original size:39 final size:39
Alignment explanation
Indices: 3628--3723 Score: 124
Period size: 40 Copynumber: 2.4 Consensus size: 39
3618 TAACTAAACG
**
3628 GGTTAAGTCCCGAAGCATTCGTGTGCAG-TATTTAAATCC
1 GGTTAAGTCCCGAAGCATTCG-CCGCAGTTATTTAAATCC
*
3667 GGTTAGGTCCCGAAGGCATTCGCCGCAGTTATTTAAATCC
1 GGTTAAGTCCCGAA-GCATTCGCCGCAGTTATTTAAATCC
3707 -GTTACAGTCCCGAAGCA
1 GGTTA-AGTCCCGAAGCA
3724 GTCTAGCGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
39 24 0.48
40 26 0.52
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (39 bp):
GGTTAAGTCCCGAAGCATTCGCCGCAGTTATTTAAATCC
Found at i:3700 original size:40 final size:38
Alignment explanation
Indices: 3628--3762 Score: 116
Period size: 39 Copynumber: 3.5 Consensus size: 38
3618 TAACTAAACG
**
3628 GGTTAAGTCCCGAAGCATTCGTGTGCAGTATTTAAATCC
1 GGTTAAGTCCCGAAGCATTCG-CAGCAGTATTTAAATCC
* *
3667 GGTTAGGTCCCGAAGGCATTCGCCGCAGTTATTTAAATCC
1 GGTTAAGTCCCGAA-GCATTCGCAGCAG-TATTTAAATCC
* * *
3707 -GTTACAGTCCCGAAGCAGTC-TAGC-GATGTTTAAATCC
1 GGTTA-AGTCCCGAAGCATTCGCAGCAG-TATTTAAATCC
*
3744 GGTT-TGTCCCGAAGGCATT
1 GGTTAAGTCCCGAA-GCATT
3763 GTGCAGTACT
Statistics
Matches: 80, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
36 8 0.10
37 15 0.19
38 5 0.06
39 26 0.32
40 26 0.32
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (38 bp):
GGTTAAGTCCCGAAGCATTCGCAGCAGTATTTAAATCC
Found at i:14226 original size:39 final size:39
Alignment explanation
Indices: 14172--14330 Score: 230
Period size: 39 Copynumber: 4.1 Consensus size: 39
14162 CCAGGTACGA
*
14172 TTCCAGCACGTAGCCTGCGG-CCTTCAAGTCCGGATATAT
1 TTCCAGCACATAGCCTGCGGACC-TCAAGTCCGGATATAT
* *
14211 TTCCATCACATAGCCTGCGGACTTCAAGTCCGGATATAT
1 TTCCAGCACATAGCCTGCGGACCTCAAGTCCGGATATAT
* *
14250 TTCTAGCACATAGCCTGCGGACCTCATGTCCGGATATAT
1 TTCCAGCACATAGCCTGCGGACCTCAAGTCCGGATATAT
* * *
14289 TCCCAGCATATAGCCTGCGGACCTCATGTCCGGATATAT
1 TTCCAGCACATAGCCTGCGGACCTCAAGTCCGGATATAT
14328 TTC
1 TTC
14331 AAATATCATG
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
39 107 0.99
40 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCTCAAGTCCGGATATAT
Found at i:24958 original size:145 final size:143
Alignment explanation
Indices: 24650--25345 Score: 1157
Period size: 145 Copynumber: 4.9 Consensus size: 143
24640 CCCTTCGGGA
* * * * * * *
24650 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACAC
*
24715 TTTCACATTCATCACATCGGCCATTAGGCCTCATCAC--ATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
24778 TCGGCTATTAGGC
131 TCGGCCATTAGGC
*
24791 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCAC--ATATATAC
24856 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
* *
24921 CATTGGCCATTCGGC
129 CATCGGCCATTAGGC
* *
24936 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGACCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACAC
25001 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
25066 TCGGCCATTAGGC
131 TCGGCCATTAGGC
25079 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
*
25144 ACTTTCACATTCATCACATCGGCCACTAGGCCTTATCACATATATATACACTTTCACATTCATCA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCA
25209 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
*
25224 CTTATCACATATATATATACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
*
25289 ACTTTCACATTCATCACACCGGCCATTAGGCCTTATCACATATATATACA--TTCACAT
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACAT
25346 CACAATTATC
Statistics
Matches: 528, Mismatches: 21, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
141 47 0.09
143 147 0.28
145 334 0.63
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:24988 original size:192 final size:190
Alignment explanation
Indices: 24650--25345 Score: 1153
Period size: 192 Copynumber: 3.6 Consensus size: 190
24640 CCCTTCGGGA
* * * * * * *
24650 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
24713 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
*
24778 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24838 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
* *
24903 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
24968 CATCGGCCATTAGACCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 CATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25030 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
*
25095 ACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
*
25160 CATCGGCCACTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 CATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
25224 CTTATCACATATATATATACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* * *
25289 ACTTTCACATTCATCACACCGGCCATTAGGCCTTATCACATATATATACATTCACAT
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
25346 CACAATTATC
Statistics
Matches: 481, Mismatches: 21, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
188 10 0.02
189 1 0.00
190 37 0.08
192 339 0.70
194 94 0.20
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (190 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:25306 original size:47 final size:47
Alignment explanation
Indices: 24650--25345 Score: 1104
Period size: 47 Copynumber: 14.6 Consensus size: 47
24640 CCCTTCGGGA
* * * * * *
24650 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
24697 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
24744 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24791 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24838 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
24887 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
24936 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24983 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25030 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
25079 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
25128 CTTATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
25175 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
25224 CTTATCACATATATATATACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
25273 CTTATCACATATATACACTTTCACATTCATCACACCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
25320 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
25346 CACAATTATC
Statistics
Matches: 612, Mismatches: 31, Indels: 12
0.93 0.05 0.02
Matches are distributed among these distances:
47 330 0.54
49 282 0.46
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28302 original size:28 final size:28
Alignment explanation
Indices: 28271--28335 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
28261 ATTTACTAGA
* *
28271 ATACCCTTATGTATGCAAAATTACCAT-T
1 ATACCCCTATGTATGCAAAATAACC-TCT
28299 ATACCCCTATGTATGCAAAATAACCTCT
1 ATACCCCTATGTATGCAAAATAACCTCT
28327 ATACCCCTA
1 ATACCCCTA
28336 GGGTTAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATAACCTCT
Found at i:28499 original size:27 final size:27
Alignment explanation
Indices: 28441--28530 Score: 112
Period size: 28 Copynumber: 3.2 Consensus size: 27
28431 AGGAAGCGTC
28441 CTGGTGG-CTATGCCACAAATTATCTGTT
1 CTGGTGGCCT-TGCCACAAA-TATCTGTT
*
28469 CTGGTGGCCTTGCCACATATATCTGTT
1 CTGGTGGCCTTGCCACAAATATCTGTT
28496 CTGGTGGCAC-TGCCACAAAATATCTGTAT
1 CTGGTGGC-CTTGCCAC-AAATATCTGT-T
28525 CTGGTG
1 CTGGTG
28531 ACTCTGTCAC
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
27 22 0.39
28 25 0.45
29 9 0.16
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCCTTGCCACAAATATCTGTT
Found at i:28549 original size:55 final size:56
Alignment explanation
Indices: 28441--28555 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 56
28431 AGGAAGCGTC
* *
28441 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCTTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCTTGCCACATATATCTGTAT
* *
28496 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGA-CTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCT-TGCCACATATATCTGTAT
28552 CTGG
1 CTGG
28556 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
54 1 0.02
55 32 0.62
56 19 0.37
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCTTGCCACATATATCTGTAT
Found at i:29574 original size:17 final size:18
Alignment explanation
Indices: 29540--29585 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
29530 AAGATTTCCA
29540 AAAAAAAATCGGTTTTTTT
1 AAAAAAAATCGG-TTTTTT
*
29559 AAAAAAAATTGG-TTTTT
1 AAAAAAAATCGGTTTTTT
29576 AAAAAAAATC
1 AAAAAAAATC
29586 TGGACTCCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.56
19 11 0.44
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (18 bp):
AAAAAAAATCGGTTTTTT
Found at i:30395 original size:15 final size:15
Alignment explanation
Indices: 30375--30406 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30365 ATGTGGACGC
*
30375 CCGTAGGAAAGAATT
1 CCGTAGGAAAAAATT
30390 CCGTAGGAAAAAATT
1 CCGTAGGAAAAAATT
30405 CC
1 CC
30407 TGAATCTGGT
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:0.41, C:0.19, G:0.22, T:0.19
Consensus pattern (15 bp):
CCGTAGGAAAAAATT
Found at i:33291 original size:56 final size:56
Alignment explanation
Indices: 33226--33345 Score: 222
Period size: 56 Copynumber: 2.1 Consensus size: 56
33216 ACAAGGGATG
33226 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGA
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGA
* *
33282 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGA
33338 ATGGGCAA
1 ATGGGCAA
33346 TAAACTAATA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGA
Found at i:34654 original size:40 final size:39
Alignment explanation
Indices: 34472--34655 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
34462 CGAATGATGT
* * * *
34472 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
* * *
34512 CCGGACTAAGAT-CCGAAGGCAGTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
*
34552 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* *
34590 TCCGGGTTAAGTCCCGGAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
34631 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
34656 AACAAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 34 0.28
40 79 0.65
41 9 0.07
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:34677 original size:79 final size:79
Alignment explanation
Indices: 34472--34688 Score: 214
Period size: 79 Copynumber: 2.7 Consensus size: 79
34462 CGAATGATGT
* *
34472 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACCATATCCGGACTAAGATCCGAAGGCAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-AAGTAG-CTATATCCGG-TTAAGATCCGAAGGCAGT
*
34535 TGTGCGAGTTACTAATT
63 TGTGCGAGTTACTAATA
* * * * *
34552 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTA-CTAAATCCGGGTTAAG-TCCCGGAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TAGCTATATCC-GGTTAAGAT-CCGAAGGCAGT
34614 TGTGCGAGTTACT-ATAA
63 TGTGCGAGTTACTAAT-A
* **
34631 CCGGGCTATGTCCCGAAGGCATTTGAACAAGTAGCTATATCCGGTTAA-ATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGTTAAGA-TCCGAAGG
34689 TACGTGATTT
Statistics
Matches: 112, Mismatches: 15, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
78 3 0.03
79 66 0.59
80 43 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTAGCTATATCCGGTTAAGATCCGAAGGCAGTTGT
GCGAGTTACTAATA
Found at i:41877 original size:38 final size:38
Alignment explanation
Indices: 41835--41972 Score: 115
Period size: 38 Copynumber: 3.6 Consensus size: 38
41825 GCTACTTGTT
*
41835 CAAATGCCTTGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
41873 CAAATGCCTCCGGACTTAACCCGGATT-TAGTAACT-TCA
1 CAAATGCCT-TGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
41911 CCAATGCCTTCGGGCTTAG-CCGG-AATTAGTAACTCGCA
1 CAAATGCCTT-GGACTTAGCCCGGTTA-TAGTAACTCGCA
*
41949 C-AATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTT-GGA-CTTAGCCCGG
41973 ATATGGTCAC
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
37 23 0.28
38 33 0.41
39 23 0.28
40 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (38 bp):
CAAATGCCTTGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:41940 original size:37 final size:38
Alignment explanation
Indices: 41861--41966 Score: 108
Period size: 37 Copynumber: 2.8 Consensus size: 38
41851 AGCCCGGTTA
* * * *
41861 TAGTAACTCGCACAAATGCCTCCGGACTTAACCCGGATT
1 TAGTAACT-TCACCAATGCCTTCGGACTTAACCCGGAAT
* *
41900 TAGTAACTTCACCAATGCCTTCGGGCTT-AGCCGGAAT
1 TAGTAACTTCACCAATGCCTTCGGACTTAACCCGGAAT
*
41937 TAGTAAC-TCGCACAATGCCTTCGGATCTTA
1 TAGTAACTTCAC-CAATGCCTTCGGA-CTTA
41967 GTCCGGATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
36 3 0.05
37 26 0.46
38 19 0.34
39 8 0.14
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (38 bp):
TAGTAACTTCACCAATGCCTTCGGACTTAACCCGGAAT
Found at i:43213 original size:57 final size:55
Alignment explanation
Indices: 43138--43257 Score: 197
Period size: 57 Copynumber: 2.1 Consensus size: 55
43128 TATTAGTTTA
43138 TTGCCCATGCTTTCTATTTTATTCTTCCATTAAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTTCTATTTTATTCTTCCATT-AACACAACATG-TTCATGACATGTT
*
43195 TTGCCCATGC-TTCTTATTTTATTTTTCCATTAACACAACATGTTCATGACATGTT
1 TTGCCCATGCTTTC-TATTTTATTCTTCCATTAACACAACATGTTCATGACATGTT
43250 TTGCCCAT
1 TTGCCCAT
43258 CATCCCTGTC
Statistics
Matches: 61, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
55 21 0.34
56 14 0.23
57 26 0.43
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (55 bp):
TTGCCCATGCTTTCTATTTTATTCTTCCATTAACACAACATGTTCATGACATGTT
Done.