Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold676
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: 59038
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Found at i:949 original size:40 final size:40
Alignment explanation
Indices: 866--1128 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
856 TTGAATGCTG
* * * * * *
866 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
906 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
946 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
986 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
1026 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1066 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
1105 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
1129 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:1148 original size:79 final size:80
Alignment explanation
Indices: 905--1163 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
895 AAGTGAATAT
* * * * * * *
905 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
969 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
985 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
1050 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
1065 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
1129 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
1144 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
1164 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:8255 original size:40 final size:40
Alignment explanation
Indices: 8172--8434 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
8162 TTGAATGCTG
* * * * * *
8172 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
8212 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
8252 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
8292 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
8332 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
8372 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
8411 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
8435 TGAACAAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:8454 original size:79 final size:80
Alignment explanation
Indices: 8211--8469 Score: 220
Period size: 80 Copynumber: 3.3 Consensus size: 80
8201 AAGTGAATAT
* * * * * * *
8211 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * * *
8275 TCGTGCGAGTTA-TTAA
65 TCGAACAAG-GAGCTAA
* * *
8291 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** * ** *
8356 CGTGCGAGTTGTTAA
66 CGAACAAGGAGCTAA
* * * *
8371 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
8435 TGAACAAGGAGCTAT
66 CGAACAAGGAGCTAA
*
8450 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
8470 TACGTGATTT
Statistics
Matches: 153, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 46 0.30
80 93 0.61
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACAAGGAGCTAA
Found at i:19563 original size:40 final size:40
Alignment explanation
Indices: 19499--19635 Score: 141
Period size: 40 Copynumber: 3.4 Consensus size: 40
19489 CACATCAATT
* *
19499 TGTGGATAAGCCACCAACAATGCAGATAAAATGCCAGAAA
1 TGTGGACAAGCCACCAATAATGCAGATAAAATGCCAGAAA
* * * ** ** *
19539 TGTGGACAAGCCACTAGTATTGCAGACGAGCTGCCAGTAA
1 TGTGGACAAGCCACCAATAATGCAGATAAAATGCCAGAAA
* * *
19579 TGTGGACAAGCTACCAATAATGCAGATAAATTGCCA-ATAT
1 TGTGGACAAGCCACCAATAATGCAGATAAAATGCCAGA-AA
19619 TGTGGACAAGCCACCAA
1 TGTGGACAAGCCACCAA
19636 AATTGCAAAC
Statistics
Matches: 75, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (40 bp):
TGTGGACAAGCCACCAATAATGCAGATAAAATGCCAGAAA
Found at i:19590 original size:20 final size:20
Alignment explanation
Indices: 19532--19600 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 20
19522 AGATAAAATG
* *
19532 CCAGAAATGTGGACAAGCCA
1 CCAGTAATGTGGACAAGCTA
* * ** * *
19552 CTAGTATTGCAGACGAGCTG
1 CCAGTAATGTGGACAAGCTA
19572 CCAGTAATGTGGACAAGCTA
1 CCAGTAATGTGGACAAGCTA
*
19592 CCAATAATG
1 CCAGTAATG
19601 CAGATAAATT
Statistics
Matches: 34, Mismatches: 15, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (20 bp):
CCAGTAATGTGGACAAGCTA
Found at i:19632 original size:80 final size:80
Alignment explanation
Indices: 19499--19657 Score: 212
Period size: 80 Copynumber: 2.0 Consensus size: 80
19489 CACATCAATT
* * ** *
19499 TGTGGATAAGCCACCAACAATGCAGATAAAATGCCAGAAATGTGGACAAGCCACTAGTATTGCAG
1 TGTGGACAAGCCACCAACAATGCAGATAAAATGCCAGAAATGTGGACAAGCCACCAAAATTGCAA
*
19564 ACGAGCTGCCAGTAA
66 ACAAGCTGCCAGTAA
* * * *
19579 TGTGGACAAGCTACCAATAATGCAGATAAATTGCCA-ATATTGTGGACAAGCCACCAAAATTGCA
1 TGTGGACAAGCCACCAACAATGCAGATAAAATGCCAGA-AATGTGGACAAGCCACCAAAATTGCA
19643 AACAAGCTGCCAGTA
65 AACAAGCTGCCAGTA
19658 CTTCTTCCTT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.01
80 67 0.99
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (80 bp):
TGTGGACAAGCCACCAACAATGCAGATAAAATGCCAGAAATGTGGACAAGCCACCAAAATTGCAA
ACAAGCTGCCAGTAA
Found at i:19654 original size:40 final size:40
Alignment explanation
Indices: 19499--19654 Score: 129
Period size: 40 Copynumber: 3.9 Consensus size: 40
19489 CACATCAATT
* * **
19499 TGTGGATAAGCCACCAACAA-TGCAGATAAAATGCCAGA-AA
1 TGTGGACAAGCCACCAA-AATTGCAGACAAGCTGCCA-ATAA
* ** * *
19539 TGTGGACAAGCCACTAGTATTGCAGACGAGCTGCCAGTAA
1 TGTGGACAAGCCACCAAAATTGCAGACAAGCTGCCAATAA
* * ** *
19579 TGTGGACAAGCTACCAATAA-TGCAGATAAATTGCCAATAT
1 TGTGGACAAGCCACCAA-AATTGCAGACAAGCTGCCAATAA
*
19619 TGTGGACAAGCCACCAAAATTGCAAACAAGCTGCCA
1 TGTGGACAAGCCACCAAAATTGCAGACAAGCTGCCA
19655 GTACTTCTTC
Statistics
Matches: 88, Mismatches: 24, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
39 3 0.03
40 84 0.95
41 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (40 bp):
TGTGGACAAGCCACCAAAATTGCAGACAAGCTGCCAATAA
Found at i:21393 original size:104 final size:104
Alignment explanation
Indices: 21213--21436 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
21203 TGTATATAAA
** * *
21213 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
21278 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
21317 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
21381 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
21421 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
21437 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:21488 original size:71 final size:72
Alignment explanation
Indices: 21355--21506 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
21345 TCATTGGTGG
* *
21355 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
21420 GAGGGGT
66 GAGGGGT
***
21427 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
21491 GAGGGGT
66 GAGGGGT
21498 TGCTAAGTG
1 TGCTAAGTG
21507 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:24383 original size:25 final size:25
Alignment explanation
Indices: 24348--24405 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
24338 GATTTATATT
*
24348 GATTTATAGC-TCATGAGAGCATACC
1 GATTTACAGCTTCA-GAGAGCATACC
*
24373 GATTTACAGCTTCAGTGAGCATACC
1 GATTTACAGCTTCAGAGAGCATACC
*
24398 AATTTACA
1 GATTTACA
24406 ACTCGTATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 26 0.90
26 3 0.10
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (25 bp):
GATTTACAGCTTCAGAGAGCATACC
Found at i:26584 original size:27 final size:27
Alignment explanation
Indices: 26554--26846 Score: 335
Period size: 27 Copynumber: 10.8 Consensus size: 27
26544 TCATCTACTA
* *
26554 GGGGTATATCAGTCATTTTACCATATG
1 GGGGTATTTCAGTCATTTTACCCTATG
*
26581 GGGGTATTTCGGTCATTTTACCCTAT-
1 GGGGTATTTCAGTCATTTTACCCTATG
** * *
26607 AAGGTATTTCGGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
26634 GGGGTATTTCAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
** * *
26661 GGATTATTTC-GATCATTATTACCTTACG
1 GGGGTATTTCAG-TCATT-TTACCCTATG
26689 GGGGTATTTCTA-TCATTTTTACCCTATG
1 GGGGTATTTC-AGTCA-TTTTACCCTATG
26717 GGGGTATTTCAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
26744 AGGGTATTTCGGTCATTTTATCCTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
26771 GGGGTATTTCGGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
26798 GGGGTATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
26825 AGGGTATTTC-GATCATTTTACC
1 GGGGTATTTCAG-TCATTTTACC
26847 TATTTTGGGG
Statistics
Matches: 230, Mismatches: 28, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
26 25 0.11
27 163 0.71
28 40 0.17
29 2 0.01
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:26814 original size:137 final size:135
Alignment explanation
Indices: 26569--26843 Score: 406
Period size: 137 Copynumber: 2.0 Consensus size: 135
26559 ATATCAGTCA
* * *
26569 TTTTACCATATGGGGGTATTTCGGTCATTTTACCCTATAAGGTATTTCGGTTATTTTACCCTATG
1 TTTTACCATATGGGGGTATTTCAGTCATTTTACCCTATAAGGTATTTCGGTCATTTTACCCTATA
* * *
26634 GGGGTATTTCAGTCATTTTACCCTATGGGATTATTTCGATCATTATTACCTTACGGGGGTATTTC
66 GGGGTATTTCAGTCATTTTACCCTATGGGAGTATTTCGATCATT-TTACCCTACGAGGGTATTTC
*
26699 TATCAT
130 GATCAT
* * *
26705 TTTTACCCTATGGGGGTATTTCAGTCATTTTACCCTATGAGGGTATTTCGGTCATTTTATCCTAT
1 TTTTACCATATGGGGGTATTTCAGTCATTTTACCCTAT-AAGGTATTTCGGTCATTTTACCCTAT
* * * *
26770 AGGGGTATTTCGGTCATTTTACCTTATGGGGGTATTTCGATCATTTTACCCTATGAGGGTATTTC
65 AGGGGTATTTCAGTCATTTTACCCTATGGGAGTATTTCGATCATTTTACCCTACGAGGGTATTTC
26835 GATCAT
130 GATCAT
26841 TTT
1 TTT
26844 ACCTATTTTG
Statistics
Matches: 124, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
136 61 0.49
137 63 0.51
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (135 bp):
TTTTACCATATGGGGGTATTTCAGTCATTTTACCCTATAAGGTATTTCGGTCATTTTACCCTATA
GGGGTATTTCAGTCATTTTACCCTATGGGAGTATTTCGATCATTTTACCCTACGAGGGTATTTCG
ATCAT
Found at i:29411 original size:29 final size:29
Alignment explanation
Indices: 29364--29423 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
29354 AACACACAAC
29364 CAACCACCAGACCAACAGGCCCATTCGGA
1 CAACCACCAGACCAACAGGCCCATTCGGA
* * *
29393 CAACCACCAGACTAGCAGGCCCATTCTGA
1 CAACCACCAGACCAACAGGCCCATTCGGA
29422 CA
1 CA
29424 CTAGAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.40, G:0.17, T:0.10
Consensus pattern (29 bp):
CAACCACCAGACCAACAGGCCCATTCGGA
Found at i:31708 original size:11 final size:11
Alignment explanation
Indices: 31692--31728 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
31682 AAGAGAGAAT
*
31692 GATGCTTGATG
1 GATGCTTGAGG
31703 GATGCTTGAGG
1 GATGCTTGAGG
*
31714 GATGATTGAGG
1 GATGCTTGAGG
31725 GATG
1 GATG
31729 ATGAATGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.05, G:0.43, T:0.30
Consensus pattern (11 bp):
GATGCTTGAGG
Found at i:37566 original size:22 final size:21
Alignment explanation
Indices: 37532--37572 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
37522 ACACCTATGT
*
37532 GGAGGGGTACATGCCCGTGCA
1 GGAGGGGCACATGCCCGTGCA
37553 GGAGGAGGCACATGCCCGTG
1 GGAGG-GGCACATGCCCGTG
37573 TGACCTAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.20, C:0.24, G:0.44, T:0.12
Consensus pattern (21 bp):
GGAGGGGCACATGCCCGTGCA
Found at i:39363 original size:21 final size:21
Alignment explanation
Indices: 39324--39365 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39314 ATTGGAAAAG
**
39324 GAGAGAAAAAAGATGAGAGAA
1 GAGAGAAAAAAGAAAAGAGAA
*
39345 GAGAGTAAAAAGAAAAGAGAA
1 GAGAGAAAAAAGAAAAGAGAA
39366 ACAAAACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.31, T:0.05
Consensus pattern (21 bp):
GAGAGAAAAAAGAAAAGAGAA
Found at i:40384 original size:28 final size:28
Alignment explanation
Indices: 40348--40413 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
40338 CCTTGAGATT
* *
40348 TTAGGTGTTAAATGAT-TAATTTGAAATA
1 TTAGTTGTTAAATGATAAAATTT-AAATA
*
40376 TTATTTGTTAAATGATAAAATTTAAATA
1 TTAGTTGTTAAATGATAAAATTTAAATA
40404 TTAGTTGTTA
1 TTAGTTGTTA
40414 TTTAAAAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (28 bp):
TTAGTTGTTAAATGATAAAATTTAAATA
Found at i:40685 original size:29 final size:29
Alignment explanation
Indices: 40650--40891 Score: 199
Period size: 29 Copynumber: 8.4 Consensus size: 29
40640 TCATCGACCA
40650 ATGAAAAGGGATAGCTTCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGACTATCGATT
* * * * * *
40679 ATGAAAAGGGATAGTTTTGGCCATTGAAT
1 ATGAAAAGGGATAGCTTCGACTATCGATT
* *
40708 ATG-AAAGGGATAGCTTCGGCTATCGAAT
1 ATGAAAAGGGATAGCTTCGACTATCGATT
*
40736 ATGAATAGGGATAGCTTCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGACTATCGATT
* * * * *
40765 ATGAAAAGGGAT-GGTGACGACCATCAACT
1 ATGAAAAGGGATAGCT-TCGACTATCGATT
* * * *
40794 ATG-AAAGGGAT-GGTGACGACCATCGAAT
1 ATGAAAAGGGATAGCT-TCGACTATCGATT
*
40822 ATGAAAAGGGATAGCTTC-AGCTGTCGATT
1 ATGAAAAGGGATAGCTTCGA-CTATCGATT
* * *
40851 ATGAAAATGGACAGC-TCTAGCTATCGATT
1 ATGAAAAGGGATAGCTTCGA-CTATCGATT
*
40880 ATAAAAAGGGAT
1 ATGAAAAGGGAT
40892 GGTGGCGACC
Statistics
Matches: 175, Mismatches: 32, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
28 55 0.31
29 118 0.67
30 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.25
Consensus pattern (29 bp):
ATGAAAAGGGATAGCTTCGACTATCGATT
Found at i:40768 original size:57 final size:58
Alignment explanation
Indices: 40650--40866 Score: 194
Period size: 57 Copynumber: 3.8 Consensus size: 58
40640 TCATCGACCA
* * * * *
40650 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATAGTTTTGGCCATTGAAT
1 ATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTCGACCATCGAAT
* * * *
40708 ATG-AAAGGGATAGCTTCGGCTATCGAATATGAATAGGGATAGCTTCGACTATCGATT
1 ATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTCGACCATCGAAT
* * * * *
40765 ATGAAAAGGGAT-GGTGACGACCATC-AACTATG-AAAGGGAT-GGTGACGACCATCGAAT
1 ATGAAAAGGGATAGCT-TCGACTATCGAA-TATGAAAAGGGATAGCT-TCGACCATCGAAT
* * * *
40822 ATGAAAAGGGATAGCTTC-AGCTGTCGATTATGAAAATGGACAGCT
1 ATGAAAAGGGATAGCTTCGA-CTATCGAATATGAAAAGGGATAGCT
40867 CTAGCTATCG
Statistics
Matches: 124, Mismatches: 26, Indels: 17
0.74 0.16 0.10
Matches are distributed among these distances:
56 3 0.02
57 89 0.72
58 30 0.24
59 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (58 bp):
ATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTCGACCATCGAAT
Found at i:40797 original size:86 final size:86
Alignment explanation
Indices: 40650--40857 Score: 260
Period size: 86 Copynumber: 2.4 Consensus size: 86
40640 TCATCGACCA
*** * *
40650 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATAGTTTTGGCCATTGAATATGAAAG
1 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATAGTGACGACCATTCAATATGAAAG
* * *
40715 GGATAGCT-TCGGCTATCGAAT
66 GGAT-GCTGACGACCATCGAAT
* *
40736 ATGAATAGGGATAGCTTCGACTATCGATTATGAAAAGGGATGGTGACGACCA-TCAACTATGAAA
1 ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATAGTGACGACCATTCAA-TATGAAA
*
40800 GGGATGGTGACGACCATCGAAT
65 GGGATGCTGACGACCATCGAAT
*
40822 ATGAAAAGGGATAGCTTC-AGCTGTCGATTATGAAAA
1 ATGAAAAGGGATAGCTTCGA-CTATCGATTATGAAAA
40858 TGGACAGCTC
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
85 6 0.06
86 100 0.94
ACGTcount: A:0.35, C:0.13, G:0.27, T:0.25
Consensus pattern (86 bp):
ATGAAAAGGGATAGCTTCGACTATCGATTATGAAAAGGGATAGTGACGACCATTCAATATGAAAG
GGATGCTGACGACCATCGAAT
Found at i:40830 original size:115 final size:116
Alignment explanation
Indices: 40699--40977 Score: 357
Period size: 115 Copynumber: 2.4 Consensus size: 116
40689 ATAGTTTTGG
* * * *
40699 CCATTGAATATG-AAAGGGATAGCTTCGGCTATCGAATATGAATAGGGATAGCTTCGA-CTATCG
1 CCATCGAATATGAAAAGGGATAGCTTCAGCTATCGAATATGAAAAGGGACAGC-TCGAGCTATCG
* *
40762 ATTATGAAAAGGGATGGTGACGACCATCAACTATG-AAAGGGATGGTGACGA
65 ATTATAAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACAA
* * * *
40813 CCATCGAATATGAAAAGGGATAGCTTCAGCTGTCGATTATGAAAATGGACAGCTCTAGCTATCGA
1 CCATCGAATATGAAAAGGGATAGCTTCAGCTATCGAATATGAAAAGGGACAGCTCGAGCTATCGA
* *
40878 TTATAAAAAGGGATGGTGGCGACCATCAACTATGAAAAGGGTTGGTGACAA
66 TTATAAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACAA
* * * * * *
40929 CCATCGATTAATTAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGG
1 CCATCGAAT-ATGAAAAGGGATAGCTTCAGCTATCGAATATGAAAAGGG
40978 TCGGTTACAA
Statistics
Matches: 140, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
114 14 0.10
115 73 0.52
116 22 0.16
117 31 0.22
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (116 bp):
CCATCGAATATGAAAAGGGATAGCTTCAGCTATCGAATATGAAAAGGGACAGCTCGAGCTATCGA
TTATAAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACAA
Found at i:40948 original size:30 final size:29
Alignment explanation
Indices: 40758--40977 Score: 151
Period size: 29 Copynumber: 7.6 Consensus size: 29
40748 AGCTTCGACT
*
40758 ATCGATTATGAAAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACAACC
* * *
40787 ATCAACTATG-AAAGGGATGGTGACGACC
1 ATCGATTATGAAAAGGGATGGTGACAACC
* * * * *
40815 ATCGAATATGAAAAGGGATAGCT-TCAGCT
1 ATCGATTATGAAAAGGGAT-GGTGACAACC
* * * * * *
40844 GTCGATTATGAAAATGGACAGCT--CTAGCT
1 ATCGATTATGAAAAGGGA-TGGTGAC-AACC
* * *
40873 ATCGATTATAAAAAGGGATGGTGGCGACC
1 ATCGATTATGAAAAGGGATGGTGACAACC
* * *
40902 ATCAACTATGAAAAGGGTTGGTGACAACC
1 ATCGATTATGAAAAGGGATGGTGACAACC
* **
40931 ATCGATTAATTAAAAGGGATGGTTTCAACC
1 ATCGATT-ATGAAAAGGGATGGTGACAACC
*
40961 ATCGAATATGAAAAGGG
1 ATCGATTATGAAAAGGG
40978 TCGGTTACAA
Statistics
Matches: 149, Mismatches: 35, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
28 29 0.19
29 93 0.62
30 27 0.18
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (29 bp):
ATCGATTATGAAAAGGGATGGTGACAACC
Found at i:40962 original size:59 final size:58
Alignment explanation
Indices: 40873--40993 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 58
40863 AGCTCTAGCT
* *
40873 ATCGATTATAAAAAGGGATGGTGGCGACCATC-AACTATGAAAAGGGTTGGTGACAACC
1 ATCGATTATAAAAAGGGATGGTGGCAACCATCGAA-TATGAAAAGGGTCGGTGACAACC
* ** * *
40931 ATCGATTAATTAAAAGGGATGGTTTCAACCATCGAATATGAAAAGGGTCGGTTACAACT
1 ATCGATT-ATAAAAAGGGATGGTGGCAACCATCGAATATGAAAAGGGTCGGTGACAACC
40990 ATCG
1 ATCG
40994 TTTAGCACAC
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 7 0.13
59 45 0.83
60 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (58 bp):
ATCGATTATAAAAAGGGATGGTGGCAACCATCGAATATGAAAAGGGTCGGTGACAACC
Found at i:40983 original size:29 final size:28
Alignment explanation
Indices: 40899--40993 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 28
40889 GATGGTGGCG
*
40899 ACCATC-AACTATGAAAAGGGTTGGTGACA
1 ACCATCGAA-TATGAAAAGGG-TGGTTACA
* * *
40928 ACCATCGATTAATTAAAAGGGATGGTTTCA
1 ACCATCGAAT-ATGAAAAGGG-TGGTTACA
40958 ACCATCGAATATGAAAAGGGTCGGTTACA
1 ACCATCGAATATGAAAAGGGT-GGTTACA
*
40987 ACTATCG
1 ACCATCG
40994 TTTAGCACAC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.52
30 25 0.46
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (28 bp):
ACCATCGAATATGAAAAGGGTGGTTACA
Found at i:42051 original size:20 final size:20
Alignment explanation
Indices: 42026--42064 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
42016 AACATTAAAA
42026 ATACCATAATCACAA-CCAAG
1 ATACCATAA-CACAAGCCAAG
42046 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
42065 ACCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.05, T:0.13
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAG
Found at i:43219 original size:27 final size:27
Alignment explanation
Indices: 43180--43233 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
43170 TACAAGCTAT
43180 AAATCGGTATGC-TCACACGAGATGTGA
1 AAATCGGTATGCTTC-CACGAGATGTGA
* * *
43207 AAATGGGTCTGCTTCCACGAGCTGTGA
1 AAATCGGTATGCTTCCACGAGATGTGA
43234 GTCAGAACGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (27 bp):
AAATCGGTATGCTTCCACGAGATGTGA
Found at i:48827 original size:40 final size:40
Alignment explanation
Indices: 48744--49006 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
48734 TTGAATGCTG
* * * * * *
48744 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
48784 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
48824 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
48864 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
48904 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
48944 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
48983 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
49007 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:49026 original size:79 final size:80
Alignment explanation
Indices: 48783--49041 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
48773 AAGTGAATAT
* * * * * * *
48783 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
48847 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
48863 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
48928 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
48943 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
49007 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
49022 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
49042 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:56761 original size:40 final size:40
Alignment explanation
Indices: 56678--56940 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
56668 TTGAATGCTG
* * * * * *
56678 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
56718 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
56758 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
56798 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
56838 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
56878 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
56917 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
56941 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:56960 original size:79 final size:80
Alignment explanation
Indices: 56717--56975 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
56707 AAGTGAATAT
* * * * * * *
56717 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
56781 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
56797 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
56862 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
56877 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
56941 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
56956 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
56976 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Done.