Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2079
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: 31592
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Found at i:1204 original size:40 final size:40
Alignment explanation
Indices: 1159--1345 Score: 226
Period size: 40 Copynumber: 4.8 Consensus size: 40
1149 ATAACCACAA
* * *
1159 GCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
1199 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
1239 GCACAAATGCCTTCGGGTCTTAGCCCGGATA-A--AA-TC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* * *
1275 ACTAGCAAATGCCTTCGGGACTTAGCCCGGATA-A--AACTA
1 GC-A-CAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* *
1314 GCATAAATGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1346 CATTCAAATG
Statistics
Matches: 134, Mismatches: 9, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
36 3 0.02
37 30 0.22
38 31 0.23
39 3 0.02
40 67 0.50
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:9351 original size:40 final size:40
Alignment explanation
Indices: 9300--9624 Score: 366
Period size: 40 Copynumber: 8.3 Consensus size: 40
9290 TCTTCGGAAT
* * *
9300 TTAG-CCGG-TATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* * *
9338 TTAACCCGGGTATAGCAACTCA-CACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACT-AGCACAAATGCCTTCGGGTC
* *
9378 TTAGCCCGGATATATCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
9418 TTAGCCCGGATAAAATC-ACTAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
* * * *
9458 TTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
9498 TTAGCCCGGATATATCAACTCGCACAAATGCCTTC-GGTC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
* *
9537 TTAGCCCGGATAAAATC-ACTAGCAC-AATTCCTTCGGGTC
1 TTAGCCCGGATATAA-CAACTAGCACAAATGCCTTCGGGTC
* *
9576 TTA-CCCGG--ATAGCAACT-GCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
9612 TTAGCCCGGATAT
1 TTAGCCCGGATAT
9625 CATTCAAATG
Statistics
Matches: 244, Mismatches: 30, Indels: 25
0.82 0.10 0.08
Matches are distributed among these distances:
35 5 0.02
36 20 0.08
37 5 0.02
38 16 0.07
39 38 0.16
40 158 0.65
41 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAACAACTAGCACAAATGCCTTCGGGTC
Found at i:9531 original size:120 final size:119
Alignment explanation
Indices: 9318--9624 Score: 552
Period size: 120 Copynumber: 2.6 Consensus size: 119
9308 TATAACCACA
*
9318 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCACACAAATGCCTTCGGGTCTTAGC
1 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
9383 CCGGATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATCACT
66 CCGGATATATCAACTCGCACAAATGCCTTC-GGTCTTAGCCCGGATAAAATCACT
9438 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
9503 CCGGATATATCAACTCGCACAAATGCCTTCGGTCTTAGCCCGGATAAAATCACT
66 CCGGATATATCAACTCGCACAAATGCCTTCGGTCTTAGCCCGGATAAAATCACT
*
9557 AGCACAATT-CCTTCGGGTCTT-ACCC-GG-ATAGCAACT-GCACAAATGCCTTCGGGACTTAGC
1 AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
9617 CCGGATAT
66 CCGGATAT
9625 CATTCAAATG
Statistics
Matches: 185, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
114 31 0.17
115 9 0.05
116 2 0.01
117 4 0.02
118 12 0.06
119 33 0.18
120 94 0.51
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (119 bp):
AGCACAATTGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
CCGGATATATCAACTCGCACAAATGCCTTCGGTCTTAGCCCGGATAAAATCACT
Found at i:15984 original size:52 final size:52
Alignment explanation
Indices: 15903--16030 Score: 215
Period size: 52 Copynumber: 2.5 Consensus size: 52
15893 AAATGATGAT
* *
15903 GAAAAAAAAAGAAA-GAAAAGAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
1 GAAAGAAAAAGAAAGGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
15954 GAAAGAAAAAGAAAGGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
1 GAAAGAAAAAGAAAGGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
*
16006 GAAAGAAAAAG-AAGGAAAAAGAGCT
1 GAAAGAAAAAGAAAGGAAAAAAAGCT
16031 TTGAGGAAAT
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
51 26 0.36
52 47 0.64
ACGTcount: A:0.50, C:0.10, G:0.23, T:0.16
Consensus pattern (52 bp):
GAAAGAAAAAGAAAGGAAAAAAAGCTCTCATGTTGTTCTTGGCCGAATAGAA
Found at i:17265 original size:40 final size:40
Alignment explanation
Indices: 17160--17366 Score: 287
Period size: 40 Copynumber: 5.2 Consensus size: 40
17150 GGATTGATAA
* *
17160 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
* * *
17200 TCGGGCTAA-TCCCGAAGGCAATTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
17239 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
17279 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
17319 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
17359 CC-GGCTAA
1 CCGGGCTAA
17367 ACTCCGAAGG
Statistics
Matches: 150, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 40 0.27
40 110 0.73
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:17357 original size:80 final size:79
Alignment explanation
Indices: 17156--17376 Score: 306
Period size: 79 Copynumber: 2.8 Consensus size: 79
17146 ATTCGGATTG
17156 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTA-ATTTCGGGCTAATCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTAG-CTATA-TTCGGGCTAATCCCGAAGGC
*
17219 AATTGTGTGAGTTACT
64 AATTGTGCGAGTTACT
* *
17235 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATTCGGGCTAAGTCCCGAAGGC
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TAGCTATATTCGGGCTAA-TCCCGAAGGC
*
17299 ATTTGTGCGAGTTACT
64 AATTGTGCGAGTTACT
* * *
17315 ATAACCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTAGCTATA-TCCGGCTAAACTCCGAAGG
1 ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTAGCTATATTCGGGCTAATC-CCGAAGG
17377 TACTTGGTTT
Statistics
Matches: 127, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
78 1 0.01
79 63 0.50
80 63 0.50
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (79 bp):
ATAACCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTAGCTATATTCGGGCTAATCCCGAAGGCAA
TTGTGCGAGTTACT
Found at i:17642 original size:22 final size:21
Alignment explanation
Indices: 17601--17644 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
17591 GAATGTGCAT
17601 ATATGAAGTTATCCATTTAGCC
1 ATATGAAGTTATCCA-TTAGCC
17623 ATATGAATGTTATACC-TTAGCC
1 ATATGAA-GTTAT-CCATTAGCC
17645 GAAACTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.65
23 5 0.25
24 2 0.10
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (21 bp):
ATATGAAGTTATCCATTAGCC
Found at i:22138 original size:37 final size:37
Alignment explanation
Indices: 22080--22184 Score: 174
Period size: 37 Copynumber: 2.8 Consensus size: 37
22070 GCTCAGACGA
* * *
22080 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
22117 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
22154 AATCTCCACACGTAGTCATCGGGTATTACCC
1 AATCTCCACACGTAGTCATCGGGTCTTACCC
22185 AGAATATATT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:22458 original size:47 final size:47
Alignment explanation
Indices: 22396--22935 Score: 630
Period size: 47 Copynumber: 11.1 Consensus size: 47
22386 ACACGTTTCG
* * *
22396 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
*
22443 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * *
22490 CATTGGCCATCCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
22537 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ATATATGCATGTTCACATTCATCA
* *
22590 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
22637 CATTGGCCATTCGGCCTTATCATGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ATATATGCATGTTCACATTCATCA
* *
22690 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* **
22737 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATATGCATGTTCACATTCATCA
* * * *
22788 CATTTGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * **
22835 CAGTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CAC--ATATATGCATGTTCACATTCATCA
* * * *
22886 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
22933 CAT
1 CAT
22936 AAAATCCTAA
Statistics
Matches: 420, Mismatches: 53, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
47 246 0.59
49 14 0.03
51 76 0.18
53 84 0.20
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:22659 original size:25 final size:25
Alignment explanation
Indices: 22584--22659 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
22574 AGGTTCACAT
22584 TCATCACATTGGCCATTCGGCCTTA
1 TCATCACATTGGCCATTCGGCCTTA
** * *
22609 TCA-CACATACG-CATGTTC--ACAT-
1 TCATCACATTGGCCA--TTCGGCCTTA
22631 TCATCACATTGGCCATTCGGCCTTA
1 TCATCACATTGGCCATTCGGCCTTA
22656 TCAT
1 TCAT
22660 GCATATATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.32
Consensus pattern (25 bp):
TCATCACATTGGCCATTCGGCCTTA
Found at i:22834 original size:98 final size:98
Alignment explanation
Indices: 22396--22935 Score: 854
Period size: 100 Copynumber: 5.5 Consensus size: 98
22386 ACACGTTTCG
* * * **
22396 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
22461 AT--CTC--ATATATGCATGTTCACATTCATCA
66 ATCACACATATATATACAGGTTCACATTCATCA
*
22490 CATTGGCCATCCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
22555 ATCACGCATATATATATACAGGTTCACATTCATCA
66 ATCA--CACATATATATACAGGTTCACATTCATCA
22590 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
22655 ATCATGCATATATATATACAGGTTCACATTCATCA
66 ATCA--CACATATATATACAGGTTCACATTCATCA
22690 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
22755 ATCACACATATATATACGGGTTCACATTCATCA
66 ATCACACATATATATACAGGTTCACATTCATCA
* * *
22788 CATTTGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCACAGTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
22853 ATCACACATATATATACGGGTTCACATTCATCA
66 ATCACACATATATATACAGGTTCACATTCATCA
* *
22886 CATTGGCCATTCAGCCTTATCACACATACGCATGTTCACATCCATCACAT
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
22936 AAAATCCTAA
Statistics
Matches: 420, Mismatches: 20, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
94 61 0.15
98 170 0.40
100 189 0.45
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (98 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATATATATACAGGTTCACATTCATCA
Found at i:25251 original size:85 final size:85
Alignment explanation
Indices: 25122--25300 Score: 340
Period size: 85 Copynumber: 2.1 Consensus size: 85
25112 TATTTTATTG
*
25122 CCCATGCCCTTTATTTTATTAACCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAACCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
25187 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
*
25207 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAACCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
25272 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
25292 CCCATGCTC
1 CCCATGCTC
25301 ATGGCCGGCC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 92 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAACCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:26822 original size:57 final size:58
Alignment explanation
Indices: 26750--26858 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 58
26740 GCCCACTGAT
* *
26750 CGATCTCGCACACATAGTGCTTGGTT-GAAGAACTCGCACACACAGTGCCTCAATTAC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
* * *
26807 CGATTTCGCACACATAGTGCTCGGTTAAAAGAATTTGCACACACAGTGCCTC
1 CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTC
26859 TAATCATTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 24 0.52
58 22 0.48
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (58 bp):
CGATCTCGCACACATAGTGCTCGGTTAAAAGAACTCGCACACACAGTGCCTCAATTAC
Found at i:27101 original size:40 final size:40
Alignment explanation
Indices: 27069--27420 Score: 551
Period size: 40 Copynumber: 8.8 Consensus size: 40
27059 CCAGCATGAT
* * * *
27069 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* ** *
27109 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* ** *
27149 TGCTCTTCGAAACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
* *
27189 TGCTCCTCGAGACTTAGCCCAGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
27229 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
27269 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
27309 TGCTCCTCGGGACTTAGCCCGGATATACCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
27349 TGCTCCTCGGGACTTAGCCCGGATACATCACTAGCACGAA
1 TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
*
27389 TGCTCTTCGGGACTTAGCCCGGATATATCACT
1 TGCTCCTCGGGACTTAGCCCGGATATATCACT
27421 CTCAATTCTC
Statistics
Matches: 289, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 289 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
TGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAA
Found at i:28778 original size:36 final size:37
Alignment explanation
Indices: 28673--28816 Score: 245
Period size: 37 Copynumber: 3.9 Consensus size: 37
28663 GCTCAGACGA
* * * *
28673 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
28710 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
28747 AATCTCCACACGTAGTCATC-GGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
28783 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
28817 ATATATTTCC
Statistics
Matches: 102, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
36 36 0.35
37 66 0.65
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:28793 original size:73 final size:74
Alignment explanation
Indices: 28673--28816 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 74
28663 GCTCAGACGA
* *
28673 AATCTCCACATGAAGTTATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTTA
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTTA
28738 CCCGGACAT
66 CCCGGACAT
* *
28747 AATCTCCACACGTAGTCATC-GGTCTTACCCGGACATAATCTCCACACGTAGTCATCGGGTCTTA
1 AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTTA
28811 CCCGGA
66 CCCGGA
28817 ATATATTTCC
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
73 49 0.74
74 17 0.26
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (74 bp):
AATCTCCACACGAAGTCATCGGGTCTTACCCGGACAAAATCTCCACACGTAGTCATCGGGTCTTA
CCCGGACAT
Found at i:29083 original size:93 final size:93
Alignment explanation
Indices: 29027--29507 Score: 651
Period size: 93 Copynumber: 5.0 Consensus size: 93
29017 ACACGTTTCG
*
29027 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
29092 ATCTCATATATGCATGTTCACATTCATCA
66 ATCACACATACGCATGTTCACATT-ATCA
* * **
29121 CATTGGCCA-TCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
29185 ATCACACATACGCATGTTCACATTCATCA
66 ATCACACATACGCATGTTCACATT-ATCA
* *
29214 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCACATT-GCCATTC
1 CATTGGCCATTCGGCC-T-T-AC-CACATATAT-T-CATGTTCACATTCATCACATTGGCCATTC
29278 GGCCTTATCACACATACGCATGTTCACATTCATCA
60 GGCCTTATCACACATACGCATGTTCACATT-ATCA
**
29313 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGG
1 CATTGGCCATTCGGCCTTA-C-CACATATAT-T-CATGTTCACATTCATCACATTGGCCATTCGG
*
29378 CCTTATCACACATACGCATGTTCACATCCATCA
62 CCTTATCACACATACGCATGTTCACAT-TATCA
* * **
29411 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
29476 ATCACACATACGCATGTTCACATCCATCA
66 ATCACACATACGCATGTTCACAT-TATCA
29505 CAT
1 CAT
29508 AAAATCCTAA
Statistics
Matches: 353, Mismatches: 24, Indels: 20
0.89 0.06 0.05
Matches are distributed among these distances:
93 86 0.24
94 79 0.22
95 1 0.00
96 9 0.03
97 34 0.10
98 66 0.19
99 58 0.16
100 20 0.06
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (93 bp):
CATTGGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATACGCATGTTCACATTATCA
Found at i:29089 original size:47 final size:47
Alignment explanation
Indices: 29027--29507 Score: 705
Period size: 47 Copynumber: 10.1 Consensus size: 47
29017 ACACGTTTCG
* * * **
29027 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
29074 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
29121 CATTGGCCA-TCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
29167 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* ** *
29214 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ACATACGCATGTTCACATTCATCA
29267 CATT-GCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
29313 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
29364 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
29411 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
29458 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
29505 CAT
1 CAT
29508 AAAATCCTAA
Statistics
Matches: 398, Mismatches: 24, Indels: 24
0.89 0.05 0.05
Matches are distributed among these distances:
46 67 0.17
47 244 0.61
49 1 0.00
50 1 0.00
51 44 0.11
52 17 0.04
53 24 0.06
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:29168 original size:23 final size:23
Alignment explanation
Indices: 29142--29216 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
29132 GGCCTTATCA
29142 CACATACGCATGTTCACATTCAT
1 CACATACGCATGTTCACATTCAT
** * *
29165 CACATTGGCCA--TTCGGCCTT-AT
1 CACATACG-CATGTTC-ACATTCAT
29187 CACACATACGCATGTTCACATTCAT
1 --CACATACGCATGTTCACATTCAT
29212 CACAT
1 CACAT
29217 TGGCCATTCG
Statistics
Matches: 37, Mismatches: 8, Indels: 14
0.63 0.14 0.24
Matches are distributed among these distances:
22 5 0.14
23 16 0.43
24 11 0.30
25 5 0.14
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.29
Consensus pattern (23 bp):
CACATACGCATGTTCACATTCAT
Found at i:29393 original size:197 final size:187
Alignment explanation
Indices: 29027--29507 Score: 721
Period size: 192 Copynumber: 2.5 Consensus size: 187
29017 ACACGTTTCG
* * *
29027 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * * *
29092 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATCGGCCTTATCACACATACGCATGTTC
66 ATCACACATACGCATGTTCACATTCATCACATTGGCCATCGGCCTTATCACACATACACATGTTC
*
29157 ACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
131 ACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
*
29214 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCACATT-GCCATTC
1 CATTGGCCATTCGGCCTTATCA--C----ATATATACATGTTCACATTCATCACATTGGCCATTC
*
29278 GGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATA
60 GGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCA-TCGGCCTTATCACACATACA
*
29343 TATACGGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCA
124 CAT----GTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCA
29408 TCA
185 TCA
* **
29411 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
29476 ATCACACATACGCATGTTCACATCCATCACAT
66 ATCACACATACGCATGTTCACATTCATCACAT
29508 AAAATCCTAA
Statistics
Matches: 266, Mismatches: 16, Indels: 19
0.88 0.05 0.06
Matches are distributed among these distances:
187 20 0.08
189 1 0.00
191 24 0.09
192 92 0.35
193 46 0.17
195 1 0.00
197 82 0.31
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (187 bp):
CATTGGCCATTCGGCCTTATCACATATATACATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACACATACGCATGTTCACATTCATCACATTGGCCATCGGCCTTATCACACATACACATGTTC
ACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
Found at i:29456 original size:244 final size:240
Alignment explanation
Indices: 29027--29485 Score: 776
Period size: 244 Copynumber: 1.9 Consensus size: 240
29017 ACACGTTTCG
* **
29027 CATTAGCCATTCGGCCTTACCACATATATTCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
* * *
29092 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATCGGCCTTATCACACATACGCATGTTC
66 ATCACATATATACAGGTTCACATTCATCACATTGGCCATCGGCCTTATCACACATACGCATGTTC
*
29157 ACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCC
131 ACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCC
*
29222 ATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
196 ATTCGGCCTTATCACACATATATATATACAGGTTCACATTCATCA
*
29267 CATT-GCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
1 CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
*
29331 ATCACACATATATATACGGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCA
66 AT--CAC--ATATATACAGGTTCACATTCATCACATTGGCCA-TCGGCCTTATCACACATACGCA
29396 TGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
126 TGTTCACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACAT
29461 TGGCCATTCGGCCTTATCACACATA
191 TGGCCATTCGGCCTTATCACACATA
29486 CGCATGTTCA
Statistics
Matches: 204, Mismatches: 10, Indels: 6
0.93 0.05 0.03
Matches are distributed among these distances:
239 58 0.28
240 4 0.02
241 2 0.01
243 30 0.15
244 110 0.54
ACGTcount: A:0.26, C:0.31, G:0.12, T:0.31
Consensus pattern (240 bp):
CATTAGCCATTCGGCCTTACCACACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTT
ATCACATATATACAGGTTCACATTCATCACATTGGCCATCGGCCTTATCACACATACGCATGTTC
ACATCCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCACATTGGCC
ATTCGGCCTTATCACACATATATATATACAGGTTCACATTCATCA
Done.