Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1248
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: 46819
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:719 original size:45 final size:45
Alignment explanation
Indices: 652--740 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
642 TATATATACA
* * *
652 CATCTCATACATATCTCACATTAGCCATTTGGCTTACCACATATC
1 CATCTCATACACATCTCACATTAACCATTCGGCTTACCACATATC
* * * *
697 CATCTCATACGCATTTCGCATTAACCATTCGGCTTCCCACATAT
1 CATCTCATACACATCTCACATTAACCATTCGGCTTACCACATAT
741 ATACACATCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.33
Consensus pattern (45 bp):
CATCTCATACACATCTCACATTAACCATTCGGCTTACCACATATC
Found at i:1044 original size:186 final size:187
Alignment explanation
Indices: 750--1153 Score: 605
Period size: 186 Copynumber: 2.2 Consensus size: 187
740 TATACACATC
* * * *
750 CACATTCATCACATTGGCCATTCTGCCTTATCACATGTATGCATGTTCACATTTATCACATTGGT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
* * * *
815 CATTCGGCCTTATCACATATATGCATGTTCATATTCTTCACATTGGCCATTCGGCCTTATCACAC
66 CATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* * * *
880 ATATGCATGTTCACATTCATCACA-TTGGCATTCGGCCTTATCACAGATAA-CATGTT
131 AAATGCATGTTCACATTCATCACATTTGCCATTCGGCCTTAGCACACA-AAGCATGTT
* * *
936 CATATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCATATTCATCACGTTGGC
1 CACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
*
1001 CATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGTCTTATCACAC
66 CATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
* *
1066 AAATGCATGTTCACATTCATCACATTTTCCATTTGGCCTTAGCACACAAATGCATGTT
131 AAATGCATGTTCACATTCATCACATTTGCCATTCGGCCTTAGCACACAAA-GCATGTT
*
1124 CACATTCATCACATTTGCCATTCGGCCTTA
1 CACATTCATCACATTGGCCATTCGGCCTTA
1154 GCTCATGTAT
Statistics
Matches: 195, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
186 143 0.73
187 18 0.09
188 34 0.17
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (187 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCACATTGGC
CATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACAC
AAATGCATGTTCACATTCATCACATTTGCCATTCGGCCTTAGCACACAAAGCATGTT
Found at i:1155 original size:47 final size:47
Alignment explanation
Indices: 750--1153 Score: 587
Period size: 47 Copynumber: 8.6 Consensus size: 47
740 TATACACATC
* **
750 CACATTCATCACATTGGCCATTCTGCCTTATCACATGTATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* * *
797 CACATTTATCACATTGGTCATTCGGCCTTATCACATATATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* *
844 CATATTCTTCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* *
891 CACATTCATCACATTGG-CATTCGGCCTTATCACAGATA-ACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* *
936 CATATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* * *
983 CATATTCATCACGTTGGCCATTCGGCCTTATCACACATATACATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
* *
1030 CACATTCATCACATTGGCCATTCGGTCTTATCACACAAATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
** * * *
1077 CACATTCATCACATTTTCCATTTGGCCTTAGCACACAAATGCATGTT
1 CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
*
1124 CACATTCATCACATTTGCCATTCGGCCTTA
1 CACATTCATCACATTGGCCATTCGGCCTTA
1154 GCTCATGTAT
Statistics
Matches: 324, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
45 22 0.07
46 40 0.12
47 262 0.81
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (47 bp):
CACATTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTT
Found at i:2255 original size:42 final size:44
Alignment explanation
Indices: 2196--2278 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
2186 GCTAAATAAG
2196 TATAGATAGAGATGTTT-A-ATTCTGATCAATAGTGTTTACATA
1 TATAGATAGAGATGTTTAATATTCTGATCAATAGTGTTTACATA
2238 TATAGATAGAGATGTTTAATATTCTGATCAATAGTGTTTAC
1 TATAGATAGAGATGTTTAATATTCTGATCAATAGTGTTTAC
2279 TTATTATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 17 0.44
43 1 0.03
44 21 0.54
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.41
Consensus pattern (44 bp):
TATAGATAGAGATGTTTAATATTCTGATCAATAGTGTTTACATA
Found at i:2275 original size:22 final size:23
Alignment explanation
Indices: 2214--2283 Score: 67
Period size: 22 Copynumber: 3.1 Consensus size: 23
2204 GAGATGTTTA
2214 ATTCTGATCAATAGTGTTTACAT
1 ATTCTGATCAATAGTGTTTACAT
* *
2237 ATAT-AGAT--AGAGATGTTTA-AT
1 AT-TCTGATCAATAG-TGTTTACAT
*
2258 ATTCTGATCAATAGTGTTTACTT
1 ATTCTGATCAATAGTGTTTACAT
2281 ATT
1 ATT
2284 ATTAACATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 12
0.68 0.09 0.23
Matches are distributed among these distances:
20 1 0.03
21 10 0.28
22 12 0.33
23 12 0.33
24 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (23 bp):
ATTCTGATCAATAGTGTTTACAT
Found at i:5525 original size:40 final size:40
Alignment explanation
Indices: 4810--5529 Score: 963
Period size: 40 Copynumber: 18.0 Consensus size: 40
4800 ACACATCACC
* * * *
4810 AGCATGAATGCTCTTCGGGACTTAGCCCTGATATAACTCC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * * *
4850 AGCACGTATGCTCTTCGGGACTTAGCCCTGATATAACTCC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * *
4890 AGCACGAATGCTCTTCGAGACTAAGCCCGGATATAACTCT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * * *
4930 AGCACGAATGCTCTTTGAGACTTAGCCCAGATATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * * *
4970 AGCACGTATGCTCTTCGGGACTTAGCCCTGATATAACTCC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* *
5010 AGCACGAATGCTCTTCGAGACTTAGCCCGGATATAACTCT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* *
5050 AGCACGAATGCTCTTCGAGACTTAGCCCGGATATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * * *
5090 AGCACGTATGCTCTTCGGGACTTAGCCCTGATATAACTCC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* *
5130 AGCACGAATGCTCTTCGAGACTTAGCCCGGATATAACTCT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * *
5170 AGCACGAATGCTCTTTGAGACTTAGCCCGGATATAACTCT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
*
5210 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACC
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * * *
5250 AGCACGTATGCTCTTCGGGACTTAACCCGGATATATCATT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* *
5290 AGCGCGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* *
5330 AGCACGAATGCTCTTCGGGACTTAGCCCTGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * * *
5370 AGCATGAATGCTCCTCGGGACTTAGCTCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * *
5410 AGCACGAATGCTCCTCAGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* * *
5450 AGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCAGT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
* *
5490 AGTACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
5530 CTCAATTCTC
Statistics
Matches: 621, Mismatches: 59, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 621 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AGCACGAATGCTCTTCGGGACTTAGCCCGGATATAACACT
Found at i:7069 original size:46 final size:46
Alignment explanation
Indices: 7016--7106 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
7006 TATATATACA
* * *
7016 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
* * * *
7062 CATCTCATACGCATTTCGCATTAACCATTCGGCTTTCCCACATAT
1 CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATAT
7107 ATACACATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.26, C:0.32, G:0.08, T:0.34
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAACCATTCGGCTTTACCACATATC
Found at i:7523 original size:47 final size:47
Alignment explanation
Indices: 7120--7521 Score: 561
Period size: 47 Copynumber: 8.6 Consensus size: 47
7110 CACATCTACG
* **
7120 TTCATCACATTGGCCATTCTGCCTTATCACATGTATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
* * * * *
7167 TTTATAACATTGGTCATTCGGCCTTATCACATATATGCATGTTCATA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
*
7214 TTCTTCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
* * *
7261 TTCATCACATTGGCCATTCGGCCTTATCACAGATATACATGTTCATA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
** * * *
7308 TTCATCACATTGGCCATTCGATCTTATCACATATATACATGTTCATA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
* *
7355 TTCATCACGTTGGCCATTCGGCCTTATCACACATATACATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
* *
7402 TTCATCACATTGGCCATTCGGTCTTATCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
** * * *
7449 TTCATCACATTTTCCATTTGGCCTTAGCACACAAATGCATGTTCACA
1 TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
*
7496 TTCATCACATTTGCCATTCGGCCTTA
1 TTCATCACATTGGCCATTCGGCCTTA
7522 GCTCATGTAT
Statistics
Matches: 320, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 320 1.00
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATCACATTGGCCATTCGGCCTTATCACACATATGCATGTTCACA
Found at i:7541 original size:141 final size:141
Alignment explanation
Indices: 7086--7552 Score: 560
Period size: 141 Copynumber: 3.3 Consensus size: 141
7076 TTCGCATTAA
* ** * * *
7086 CCATTCGGCTTTCCCACATATATACACA-TCTACGTTCATCACATTGGCCATTCTGCCTTATCAC
1 CCATTCGGCCTTATCACACATATACACATTC-ACATTCATCACATTGGCCATTCGGCCTTATCAC
** * *
7150 ATGTATGCATGTTCACATTTATAACATTGGT-CATTCGGCCTTATCACATATATGCATGTTCATA
65 ACATATGCATGTTCACATTCATCACATT-GTCCATTCGGCCTTATCACATATATGCATGTTCATA
*
7214 TTCTTCACATTGG
129 TTCATCACATTGG
* **
7227 CCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACA
1 CCATTCGGCCTTATCACACATATACACATTCACATTCATCACATTGGCCATTCGGCCTTATCACA
* * * * ** *
7292 GATATACATGTTCATATTCATCACATTGGCCATTCGATCTTATCACATATATACATGTTCATATT
66 CATATGCATGTTCACATTCATCACATTGTCCATTCGGCCTTATCACATATATGCATGTTCATATT
*
7357 CATCACGTTGG
131 CATCACATTGG
** *
7368 CCATTCGGCCTTATCACACATATACATGTTCACATTCATCACATTGGCCATTCGGTCTTATCACA
1 CCATTCGGCCTTATCACACATATACACATTCACATTCATCACATTGGCCATTCGGCCTTATCACA
* * * * * * *
7433 CAAATGCATGTTCACATTCATCACATTTTCCATTTGGCCTTAGCACACAAATGCATGTTCACATT
66 CATATGCATGTTCACATTCATCACATTGTCCATTCGGCCTTATCACATATATGCATGTTCATATT
*
7498 CATCACATTTG
131 CATCACATTGG
* * ** *
7509 CCATTCGGCCTTAGCTCATGTATACACATTCACATCCATCACAT
1 CCATTCGGCCTTATCACACATATACACATTCACATTCATCACAT
7553 AAAATCCTAA
Statistics
Matches: 278, Mismatches: 46, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
140 1 0.00
141 275 0.99
142 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.34
Consensus pattern (141 bp):
CCATTCGGCCTTATCACACATATACACATTCACATTCATCACATTGGCCATTCGGCCTTATCACA
CATATGCATGTTCACATTCATCACATTGTCCATTCGGCCTTATCACATATATGCATGTTCATATT
CATCACATTGG
Found at i:11731 original size:28 final size:29
Alignment explanation
Indices: 11670--11733 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
11660 GGGGTTTTTC
* * *
11670 TGGGCCTCGATGGGCCATATGAATGTGAT
1 TGGGCCTCGACGGGCCATATGAACGAGAT
* *
11699 CGGGCCT-GACGGGCCATGTGAACGAGAT
1 TGGGCCTCGACGGGCCATATGAACGAGAT
11727 TGGGCCT
1 TGGGCCT
11734 AAAGAGGCCA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.19, C:0.22, G:0.38, T:0.22
Consensus pattern (29 bp):
TGGGCCTCGACGGGCCATATGAACGAGAT
Found at i:12331 original size:160 final size:160
Alignment explanation
Indices: 12063--12497 Score: 542
Period size: 160 Copynumber: 2.7 Consensus size: 160
12053 TTACTAAAAT
* ** * *
12063 ACCCTCGATTTGTAAAATTATTGAAATACCCTTAATTGTGAAATTACTGATATACCCTCGATTTG
1 ACCCTCGATTTGTAAAATTATCGAAATACCCTCGATT-TGAAATTAATGAAATACCCTCGA-TTG
* * * *
12128 TAAAATTACCAAAATACCCTC-AATTGTGAAATTACCTAAATACCCT-TGATTTGTGAAATTATC
64 TAAAATTACCAAAATACCCTCTATTTGTAAAATTACCGAAATACCCTCTGATTTGTGAAATTACC
*
12191 GAAATACCCCTAATTTGTAAAATTATCGAAAC
129 GAAACACCCCTAATTTGTAAAATTATCGAAAC
12223 ACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTCTGAAATTAATGAAATACCCTCGATTGT
1 ACCCTCGATTTGTAAAATTATCGAAATACCCTCGATT-TGAAATTAATGAAATACCCTCGATTGT
*
12288 AAAATTACTAAAATACCCTCTATTTGTAAAATTACCGAAATA-CCTCTGATTTGTGAAATTACCG
65 AAAATTACCAAAATACCCTCTATTTGTAAAATTACCGAAATACCCTCTGATTTGTGAAATTACCG
* *
12352 AAACACCCTTGATTTGTAAAATTATCGAAAC
130 AAACACCCCTAATTTGTAAAATTATCGAAAC
* * * *
12383 ACCCTCGATTCGTAAAATTACCGAAACACCC-CTGATTTGGAAAATT-ATCGAAATACCCTTGTA
1 ACCCTCGATTTGTAAAATTATCGAAATACCCTC-GATTT-G-AAATTAAT-GAAATACCCTCG-A
* * * * *
12446 GTGTAAAATTACCGAAATACCCT-TATAGTGTAAAATGACCGACATA-CCTCTG
61 TTGTAAAATTACCAAAATACCCTCTAT-TTGTAAAATTACCGAAATACCCTCTG
12498 TAGGGTAAAA
Statistics
Matches: 243, Mismatches: 24, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
159 28 0.12
160 153 0.63
161 19 0.08
162 43 0.18
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.31
Consensus pattern (160 bp):
ACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTTGAAATTAATGAAATACCCTCGATTGTA
AAATTACCAAAATACCCTCTATTTGTAAAATTACCGAAATACCCTCTGATTTGTGAAATTACCGA
AACACCCCTAATTTGTAAAATTATCGAAAC
Found at i:12469 original size:27 final size:27
Alignment explanation
Indices: 12050--12493 Score: 393
Period size: 27 Copynumber: 16.6 Consensus size: 27
12040 TAATAAAGAG
** *
12050 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTTGATTTGTA
** * *
12077 AAATTATTGAAATACCCTT-AATTGTG
1 AAATTACCGAAATACCCTTGATTTGTA
* * *
12103 AAATTACTGATATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTTGATTTGTA
* * * *
12130 AAATTACCAAAATACCC-TCAATTGTG
1 AAATTACCGAAATACCCTTGATTTGTA
* *
12156 AAATTACCTAAATACCCTTGATTTGTG
1 AAATTACCGAAATACCCTTGATTTGTA
* * *
12183 AAATTATCGAAATACCCCTAATTTGTA
1 AAATTACCGAAATACCCTTGATTTGTA
* * *
12210 AAATTATCGAAACACCCTCGATTTGTA
1 AAATTACCGAAATACCCTTGATTTGTA
* *
12237 AAATTATCGAAATACCCTCGATTCTG--
1 AAATTACCGAAATACCCTTGATT-TGTA
** *
12263 AAATTAATGAAATACCCTCGA-TTGTA
1 AAATTACCGAAATACCCTTGATTTGTA
**
12289 AAATTACTAAAATACCCTCT-ATTTGTA
1 AAATTACCGAAATACCCT-TGATTTGTA
*
12316 AAATTACCGAAATA-CCTCTGATTTGTG
1 AAATTACCGAAATACCCT-TGATTTGTA
*
12343 AAATTACCGAAACACCCTTGATTTGTA
1 AAATTACCGAAATACCCTTGATTTGTA
* * * *
12370 AAATTATCGAAACACCCTCGATTCGTA
1 AAATTACCGAAATACCCTTGATTTGTA
* * *
12397 AAATTACCGAAACACCCCTGATTTGGA
1 AAATTACCGAAATACCCTTGATTTGTA
* *
12424 AAATTATCGAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCTTGAT-TTGTA
*
12451 AAATTACCGAAATACCCTT-ATAGTGTA
1 AAATTACCGAAATACCCTTGAT-TTGTA
* *
12478 AAATGACCGACATACC
1 AAATTACCGAAATACC
12494 TCTGTAGGGT
Statistics
Matches: 350, Mismatches: 56, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
24 2 0.01
25 1 0.00
26 84 0.24
27 258 0.74
28 5 0.01
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (27 bp):
AAATTACCGAAATACCCTTGATTTGTA
Found at i:12487 original size:81 final size:81
Alignment explanation
Indices: 12050--12468 Score: 451
Period size: 80 Copynumber: 5.2 Consensus size: 81
12040 TAATAAAGAG
** ** * *
12050 AAATTACTAAAATACCCTCGATTTGTAAAATTATTGAAATA-CCCTTAATTGTGAAATTA-CTGA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCTGATTTGTGAAATTATC-GA
* *
12113 TATACCCTCGATTTGTA
65 AATACCCTTGATTTGTA
* * * * *
12130 AAATTACCAAAATACCCTC-AATTGTGAAATTACCTAAATACCCTTGATTTGTGAAATTATCGAA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCTGATTTGTGAAATTATCGAA
* *
12194 ATACCCCTAATTTGTA
66 ATACCCTTGATTTGTA
* * * *
12210 AAATTATCGAAACACCCTCGATTTGTAAAATTATCGAAATA-CCCTCGA-TTCTGAAATTAAT-G
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCT-GATTTGTGAAATT-ATCG
*
12272 AAATACCCTCGA-TTGTA
64 AAATACCCTTGATTTGTA
** * * *
12289 AAATTACTAAAATACCCTCTATTTGTAAAATTACCGAAATACCTCTGATTTGTGAAATTACCGAA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCTGATTTGTGAAATTATCGAA
*
12354 ACACCCTTGATTTGTA
66 ATACCCTTGATTTGTA
* * * *
12370 AAATTATCGAAACACCCTCGATTCGTAAAATTACCGAAACACCCCTGATTTG-GAAAATTATCGA
1 AAATTACCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCTGATTTGTG-AAATTATCGA
*
12434 AATACCCTTG-TAGTGTA
65 AATACCCTTGAT-TTGTA
12451 AAATTACCGAAATACCCT
1 AAATTACCGAAATACCCT
12469 TATAGTGTAA
Statistics
Matches: 279, Mismatches: 49, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
79 59 0.21
80 111 0.40
81 109 0.39
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (81 bp):
AAATTACCGAAATACCCTCGATTTGTAAAATTACCGAAATACCCCTGATTTGTGAAATTATCGAA
ATACCCTTGATTTGTA
Found at i:12505 original size:27 final size:27
Alignment explanation
Indices: 12431--12511 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
12421 GGAAAATTAT
*
12431 CGAAATACCCTTGTAGTGTAAAATTAC
1 CGAAATACCCTTGTAGTGTAAAATGAC
*
12458 CGAAATACCCTTATAGTGTAAAATGAC
1 CGAAATACCCTTGTAGTGTAAAATGAC
* *
12485 CGACATA-CCTCTGTAGGGTAAAATGAC
1 CGAAATACCCT-TGTAGTGTAAAATGAC
12512 TATTTTGCCC
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 3 0.06
27 45 0.94
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (27 bp):
CGAAATACCCTTGTAGTGTAAAATGAC
Found at i:15741 original size:27 final size:27
Alignment explanation
Indices: 15711--16101 Score: 349
Period size: 27 Copynumber: 14.7 Consensus size: 27
15701 TAATAAAGAG
*
15711 AAATTACTAAAATACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
15738 AAATTA-TCAAAATACCCTCGA-TTGTG
1 AAATTACT-GAAATACCCTCGATTTGTA
*
15764 AAATTACTGAAATACCCTCGATTT-AA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
15790 AAATTACTGAGATACCCTC-AATTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
** * *
15816 AAATTACCAAAATACCCCCGATTTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* *
15843 TAATTACCGAAATAACCCT-GATTTGTA
1 AAATTACTGAAAT-ACCCTCGATTTGTA
* *
15870 AAATTA-TCAAAATAACCTCGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
*
15897 AAATTA-TCGAAATACCCTCGA-TTGTG
1 AAATTACT-GAAATACCCTCGATTTGTA
* *
15923 AAATTACTAAAATACCCTC-AATTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* * *
15949 AAATTACTAAAAGACCCTCGATTTGTG
1 AAATTACTGAAATACCCTCGATTTGTA
* *
15976 AAATTACCGAAACACCCTCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
16003 AAATTA-TCGAAACACCCTTGATTTGTA
1 AAATTACT-GAAATACCCTCGATTTGTA
* * *
16030 AAATTACCGAAACACCCCCGATTTGTA
1 AAATTACTGAAATACCCTCGATTTGTA
* *
16057 AAATTA-TCGAAATACCCTTG-TAGTGTA
1 AAATTACT-GAAATACCCTCGAT-TTGTA
16084 AAATTA-TCGAAATACCCT
1 AAATTACT-GAAATACCCT
16102 TGTAGTGTAA
Statistics
Matches: 306, Mismatches: 43, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.01
26 103 0.34
27 195 0.64
28 4 0.01
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGATTTGTA
Found at i:15953 original size:133 final size:132
Alignment explanation
Indices: 15710--16062 Score: 469
Period size: 133 Copynumber: 2.7 Consensus size: 132
15700 ATAATAAAGA
** *
15710 GAAATTACTAAAATACCCTCGATTTGTAAAATTATCAAAATACCCTCGA-TTGTGAAATTACTGA
1 GAAATTACCGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTAC-GA
* * * *
15774 AATACCCTCGATT-TAAAAATTACTGAGATACCCTCAATTGTGAAATTACCAAAATACCCCCGAT
65 AATACCCTCGATTGT-AAAATTACTAAAATACCCTCAATTGTAAAATTACCAAAAGACCCCCGAT
15838 TTGT
129 TTGT
* *
15842 GTAATTACCGAAATAACCCT-GATTTGTAAAATTATCAAAATAACCTCGATTTGTAAAATTATCG
1 GAAATTACCGAAAT-ACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTA-CG
* * *
15906 AAATACCCTCGATTGTGAAATTACTAAAATACCCTCAATTGTAAAATTACTAAAAGACCCTCGAT
64 AAATACCCTCGATTGTAAAATTACTAAAATACCCTCAATTGTAAAATTACCAAAAGACCCCCGAT
15971 TTGT
129 TTGT
* * * *
15975 GAAATTACCGAAACACCCTCGATTTGTAAAATTATCGAAACACCCTTGATTTGTAAAATTACCGA
1 GAAATTACCGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTA-CGA
* *
16040 AACACCCCCGATTTGTAAAATTA
65 AATACCCTCGA-TTGTAAAATTA
16063 TCGAAATACC
Statistics
Matches: 193, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
132 44 0.23
133 137 0.71
134 12 0.06
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (132 bp):
GAAATTACCGAAATACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTTGTAAAATTACGAA
ATACCCTCGATTGTAAAATTACTAAAATACCCTCAATTGTAAAATTACCAAAAGACCCCCGATTT
GT
Found at i:16084 original size:81 final size:79
Alignment explanation
Indices: 15711--16101 Score: 376
Period size: 79 Copynumber: 4.9 Consensus size: 79
15701 TAATAAAGAG
* * * *
15711 AAATTACTAAAATACCCTCGATTTGTAAAATTATCAAAATACCCTCGATTGTGAAATTA-CTGAA
1 AAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTGTAAAATTATC-GAA
*
15775 ATACCCTCGATTT-AA
65 ATACCCT-GATTTGTA
** * * * * * * * ** *
15790 AAATTACTGAGATACCCTC-AATTGTGAAATTACCAAAATACCCCCGATTTGTGTAATTACCGAA
1 AAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTCGA-TTGTAAAATTATCGAA
15854 ATAACCCTGATTTGTA
65 AT-ACCCTGATTTGTA
* * * * *
15870 AAATTATCAAAATAACCTCGATTTGTAAAATTATCGAAATACCCTCGATTGTGAAATTA-CTAAA
1 AAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTGTAAAATTATC-GAA
* *
15934 ATACCCTCAATTGTA
65 ATACCCTGATTTGTA
* * * * *
15949 AAATTACTAAAAGACCCTCGATTTGTGAAATTACCGAAACACCCTCGATTTGTAAAATTATCGAA
1 AAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTCGA-TTGTAAAATTATCGAA
*
16014 ACACCCTTGATTTGTA
65 ATACCC-TGATTTGTA
* * * *
16030 AAATTACCGAAACACCCCCGATTTGTAAAATTATCGAAATACCCTTGTAGTGTAAAATTATCGAA
1 AAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTCG-ATTGTAAAATTATCGAA
16095 ATACCCT
65 ATACCCT
16102 TGTAGTGTAA
Statistics
Matches: 258, Mismatches: 44, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
78 24 0.09
79 90 0.35
80 53 0.21
81 90 0.35
82 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (79 bp):
AAATTACCAAAACACCCTCGATTTGTAAAATTATCGAAATACCCTCGATTGTAAAATTATCGAAA
TACCCTGATTTGTA
Found at i:16102 original size:27 final size:27
Alignment explanation
Indices: 15999--16141 Score: 146
Period size: 27 Copynumber: 5.3 Consensus size: 27
15989 ACCCTCGATT
* *
15999 TGTAAAATTATCGAAACACCCTTG-ATT
1 TGTAAAATTATCGAAATACCCTTGTA-G
* * ** *
16026 TGTAAAATTACCGAAACACCCCCG-ATT
1 TGTAAAATTATCGAAATACCCTTGTA-G
16053 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
16080 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
* * * *
16107 TGTAAAATGACCGATATATCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
*
16134 GGTAAAAT
1 TGTAAAAT
16142 AACTATTTTG
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 101 0.99
28 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (27 bp):
TGTAAAATTATCGAAATACCCTTGTAG
Found at i:22370 original size:21 final size:22
Alignment explanation
Indices: 22329--22370 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
22319 GCAGAAAATT
*
22329 CTGCTAGTAAAAATGTAGATAG
1 CTGCCAGTAAAAATGTAGATAG
22351 CTGCCAGTAAAAATGT-GATA
1 CTGCCAGTAAAAATGTAGATA
22371 AATTGCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (22 bp):
CTGCCAGTAAAAATGTAGATAG
Found at i:25449 original size:28 final size:29
Alignment explanation
Indices: 25339--25453 Score: 137
Period size: 29 Copynumber: 4.0 Consensus size: 29
25329 GTGAGCATGA
* *
25339 ATATGAATGTGA-CTGGGCCTAACGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
* *
25367 ATATAAATGTGATTTAGGCCTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
*
25396 ATA-GACAGGTGATTTGGGCCTAATGGGCC
1 ATATGA-ATGTGATTTGGGCCTAATGGGCC
* *
25425 ATATGAATATGA-TTGGGCTTAATGGGCC
1 ATATGAATGTGATTTGGGCCTAATGGGCC
25453 A
1 A
25454 GATACAGGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
28 28 0.38
29 44 0.59
30 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.27
Consensus pattern (29 bp):
ATATGAATGTGATTTGGGCCTAATGGGCC
Found at i:31417 original size:40 final size:40
Alignment explanation
Indices: 31371--31557 Score: 197
Period size: 39 Copynumber: 4.7 Consensus size: 40
31361 ACTACTTGCT
31371 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAG-CCCGGTTATAGTAACTAGCA
* *
31411 CAAATGCCTTCGGGACTTAGCCCAGTTCA-A-TAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTT-ATAGTAACTAGCA
* * *
31450 CCAATGCCTTCGGGACTTAGCCCGGATATAATAACTCA-CA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACT-AGCA
* * ** * *
31490 CAATTGCCTTCGGG-TTTAGCAAGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTAGCA
31529 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
31558 CATCCGAATA
Statistics
Matches: 119, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
38 3 0.03
39 61 0.51
40 52 0.44
41 3 0.03
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
Found at i:31474 original size:79 final size:78
Alignment explanation
Indices: 31371--31557 Score: 211
Period size: 79 Copynumber: 2.4 Consensus size: 78
31361 ACTACTTGCT
* *
31371 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACT-AGCACAAATGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGACTTAG-CCCGGTTATAATAACTCA-CACAAATGCCTTCGGG-CTTAG-CA
*
31434 A-G-TTCAATAACTCGCA
62 AGGATT-AATAACTAGCA
* * * *
31450 CCAATGCCTTCGGGACTTAGCCCGGATATAATAACTCACACAATTGCCTTCGGGTTTAGCAAGGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAATAACTCACACAAATGCCTTCGGGCTTAGCAAGG-
* *
31515 ATTAGTCACTAGCA
65 ATTAATAACTAGCA
31529 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
31558 CATCCGAATA
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
77 2 0.02
78 5 0.05
79 81 0.88
80 4 0.04
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAATAACTCACACAAATGCCTTCGGGCTTAGCAAGGA
TTAATAACTAGCA
Found at i:39465 original size:40 final size:40
Alignment explanation
Indices: 39420--39599 Score: 208
Period size: 39 Copynumber: 4.5 Consensus size: 40
39410 ACTACTTGCT
39420 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTAGCA
1 CAAATGCCTTCGGGACTTAG-CCCGGTTATAGTAACTAGCA
*
39460 CAAATGCCTTCGGGACTTAGCCCGGTTCA-A-TAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTT-ATAGTAACTAGCA
* * * *
39499 CCAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
* * * * *
39539 CAATTGCCTTCAGG-TTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTAGCA
39578 CAAATGCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
39600 GTTATCATCC
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 64 0.53
40 52 0.43
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTAGCA
Found at i:39584 original size:79 final size:79
Alignment explanation
Indices: 39420--39599 Score: 222
Period size: 79 Copynumber: 2.3 Consensus size: 79
39410 ACTACTTGCT
* * *
39420 CAAATGCCTTCGGGACTT-GACCCGGTTATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAG-CCCGGATATAATAACTAGCACAAATGCCTTCAGGACTTAGCCCG
*
39484 GTTCAATAACTCGCA
65 GTTCAATAACTAGCA
* * * *
39499 CCAATGCCTTCGGGACTTAGCCCGGATATAATAACTCGCACAATTGCCTTCAGG-TTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACAAATGCCTTCAGGACTTAGCCCGG
* *
39563 AATT-AGTCACTAGCA
66 --TTCAATAACTAGCA
39578 CAAATGCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
39600 GTTATCATCC
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
78 9 0.10
79 75 0.86
80 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACAAATGCCTTCAGGACTTAGCCCGG
TTCAATAACTAGCA
Found at i:41425 original size:20 final size:20
Alignment explanation
Indices: 41400--41446 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
41390 ATTCTGATAT
41400 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
41420 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
41440 AGATGAT
1 ACATGAT
41447 GTATTCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.36, C:0.09, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:41529 original size:26 final size:25
Alignment explanation
Indices: 41493--41577 Score: 100
Period size: 26 Copynumber: 3.4 Consensus size: 25
41483 AGGAAGTGCA
41493 AAAAGGGCTTTTGCCCCAGTTTACC
1 AAAAGGGCTTTTGCCCCAGTTTACC
*
41518 GAAAAGGGCTTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTTGCCCCAGTTTACC
* * * *
41544 AAAAAGGTTTTTTCCCCAG-TTACT
1 AAAAGGGCTTTTGCCCCAGTTTACC
41568 AAAAGAGGCT
1 AAAAG-GGCT
41578 AGGCCTCCAG
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
24 7 0.14
25 19 0.38
26 24 0.48
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
AAAAGGGCTTTTGCCCCAGTTTACC
Found at i:41555 original size:25 final size:25
Alignment explanation
Indices: 41491--41577 Score: 95
Period size: 25 Copynumber: 3.4 Consensus size: 25
41481 GGAGGAAGTG
41491 CAAAAAGGGCTTTTGCCCCAGTTTAC
1 CAAAAA-GGCTTTTGCCCCAGTTTAC
* *
41517 CGAAAAGGGCTTTTGCCCCAGTTTAT
1 C-AAAAAGGCTTTTGCCCCAGTTTAC
* *
41543 CAAAAAGGTTTTTTCCCCAG-TTAC
1 CAAAAAGGCTTTTGCCCCAGTTTAC
*
41567 TAAAAGAGGCT
1 CAAAA-AGGCT
41578 AGGCCTCCAG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
24 7 0.14
25 20 0.39
26 20 0.39
27 4 0.08
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.29
Consensus pattern (25 bp):
CAAAAAGGCTTTTGCCCCAGTTTAC
Done.