Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2116
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: 76946
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:5045 original size:40 final size:40
Alignment explanation
Indices: 4820--5045 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
4810 GCTACTCGTT
*
4820 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
4860 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
4900 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
4940 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * *
4980 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
5021 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5046 CATCATTCAA
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 154 0.91
41 12 0.07
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:8146 original size:30 final size:30
Alignment explanation
Indices: 8112--8172 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
8102 TCCTTAACTC
*
8112 AAACTTTTGTAAAATTACAATTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
* * *
8142 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGCAAAATTACAATTTTGCCCCT
8172 A
1 A
8173 GACTCGGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.41
Consensus pattern (30 bp):
AAACTTTTGCAAAATTACAATTTTGCCCCT
Found at i:12024 original size:43 final size:41
Alignment explanation
Indices: 11892--12046 Score: 175
Period size: 42 Copynumber: 3.7 Consensus size: 41
11882 TTTAGGCTAT
* *
11892 GTGTAAGACCATATCTAGGATATGGCATCAATATGAGACTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
** * *
11934 GTGTAAGACCATATCTGGGATATGAAATCGATGTGAGATTTT
1 GTGTAAGACCATATCTGGGATATGGCATCGATATGAGA-TTC
* * *
11976 GTGTAAGACCATAGCTGGGCTATTGGCATCGATACGAGATTAC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGATATGAGATT-C
* *
12019 ATGTAAGACCATATCTAGGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
12047 TGGTATGGTA
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
42 63 0.68
43 30 0.32
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (41 bp):
GTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTC
Found at i:14152 original size:29 final size:29
Alignment explanation
Indices: 14118--14425 Score: 152
Period size: 29 Copynumber: 10.6 Consensus size: 29
14108 TCAAAGTCTC
14118 GCCACATAA-GCATCCTTTTAACAAAGATA
1 GCCACA-AAGGCATCCTTTTAACAAAGATA
* * *
14147 GCCACAAGGGCATCCATTTAACTAAGATA
1 GCCACAAAGGCATCCTTTTAACAAAGATA
* * ***
14176 GCCAAAAAGGTATCCTTTTAATTGAGATA
1 GCCACAAAGGCATCCTTTTAACAAAGATA
* * * * * *
14205 GCCATAAATGAATCCTTTTAACAGAGGTT
1 GCCACAAAGGCATCCTTTTAACAAAGATA
* * * * * * *
14234 TCCACGAAGGAATTCATTTAATAGAGATA
1 GCCACAAAGGCATCCTTTTAACAAAGATA
* * * *
14263 GCCATAAAGGCATCATTTTTAACAGAGATC
1 GCCACAAAGGCATC-CTTTTAACAAAGATA
* * * * *
14293 GCCACAAGGGCATTCATTGAATAAAGA-A
1 GCCACAAAGGCATCCTTTTAACAAAGATA
* * *
14321 GCCAGAAAGGCATCCTTTTTAACAGAGATT
1 GCCACAAAGGCATCC-TTTTAACAAAGATA
* * * * * * *
14351 TCCATAAAGGCTTCCTTATAATAGAGATC
1 GCCACAAAGGCATCCTTTTAACAAAGATA
* * * * *
14380 GCCATAAAGGCTTCCTTATAATAGAGATA
1 GCCACAAAGGCATCCTTTTAACAAAGATA
* *
14409 GCTACAAAGGCTTCCTT
1 GCCACAAAGGCATCCTT
14426 ATAATAGAAA
Statistics
Matches: 214, Mismatches: 61, Indels: 8
0.76 0.22 0.03
Matches are distributed among these distances:
28 13 0.06
29 167 0.78
30 34 0.16
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (29 bp):
GCCACAAAGGCATCCTTTTAACAAAGATA
Found at i:14426 original size:29 final size:29
Alignment explanation
Indices: 14142--14461 Score: 148
Period size: 29 Copynumber: 11.0 Consensus size: 29
14132 CTTTTAACAA
* *
14142 AGATAGCCACAAGGGCATCCATT-TAACTA-
1 AGATAGCCACAAAGGCTTCC-TTATAA-TAG
* * *
14171 AGATAGCCAAAAAGG-TATCCTTTTAATTG
1 AGATAGCCACAAAGGCT-TCCTTATAATAG
* * ** * *
14200 AGATAGCCATAAATGAATCCTTTTAACAG
1 AGATAGCCACAAAGGCTTCCTTATAATAG
* ** * * *
14229 AGGTTTCCACGAAGGAATTCATT-TAATAG
1 AGATAGCCACAAAGG-CTTCCTTATAATAG
* * * * *
14258 AGATAGCCATAAAGGCATCATTTTTAACAG
1 AGATAGCCACAAAGGCTTC-CTTATAATAG
* * * * *
14288 AGATCGCCACAAGGGCATTCATT-GAATAA
1 AGATAGCCACAAAGGC-TTCCTTATAATAG
* * * *
14317 AGA-AGCCAGAAAGGCATCCTTTTTAACAG
1 AGATAGCCACAAAGGCTTCC-TTATAATAG
** *
14346 AGATTTCCATAAAGGCTTCCTTATAATAG
1 AGATAGCCACAAAGGCTTCCTTATAATAG
* *
14375 AGATCGCCATAAAGGCTTCCTTATAATAG
1 AGATAGCCACAAAGGCTTCCTTATAATAG
*
14404 AGATAGCTACAAAGGCTTCCTTATAATAG
1 AGATAGCCACAAAGGCTTCCTTATAATAG
* * * * * *
14433 AAATTGCCATAAGGGGTTCTTTATAATAG
1 AGATAGCCACAAAGGCTTCCTTATAATAG
14462 GGAGTACATT
Statistics
Matches: 219, Mismatches: 61, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
27 2 0.01
28 16 0.07
29 162 0.74
30 37 0.17
31 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (29 bp):
AGATAGCCACAAAGGCTTCCTTATAATAG
Found at i:24645 original size:16 final size:17
Alignment explanation
Indices: 24612--24646 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
24602 TTTAAATGTC
24612 ATTATTAGATTGGTTTT
1 ATTATTAGATTGGTTTT
24629 ATTATTAGATT-GTTTT
1 ATTATTAGATTGGTTTT
24645 AT
1 AT
24647 AATAGTTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (17 bp):
ATTATTAGATTGGTTTT
Found at i:25065 original size:19 final size:19
Alignment explanation
Indices: 25041--25078 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
25031 ATATTAACTC
25041 GTTTTAGTGGTCGTAATTA
1 GTTTTAGTGGTCGTAATTA
25060 GTTTTAGTGGTCGTAATTA
1 GTTTTAGTGGTCGTAATTA
25079 ACTTCAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.47
Consensus pattern (19 bp):
GTTTTAGTGGTCGTAATTA
Found at i:27496 original size:39 final size:39
Alignment explanation
Indices: 27441--27657 Score: 294
Period size: 39 Copynumber: 5.6 Consensus size: 39
27431 TTCCAACCCA
* * *
27441 AATGCCTTCGGAACTTAGCCTGGATATAACATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
*
27480 AATGCCTTTGGGACTTAGCCCGGATATAATATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* *
27519 AATGTCTTCGGGACTTAGCCCGGATATAATACCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
* * *
27558 AACGCCTTCGAGACTTAACCCGGATATAATATCAGCACG
1 AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
*
27597 AATGCCTTCGGGACTTAGCCCGGATATAAATCTCA-CAC-
1 AATGCCTTCGGGACTTAGCCCGGATAT-AATATCAGCACG
* * *
27635 AAGGCCTGCGGGTCTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
27658 TTAAAATCCT
Statistics
Matches: 158, Mismatches: 19, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
38 20 0.13
39 132 0.84
40 6 0.04
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATATCAGCACG
Found at i:30514 original size:23 final size:22
Alignment explanation
Indices: 30462--30514 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
30452 TCCACGTCTT
*
30462 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
30484 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
30507 TTTCTTTT
1 TTTCTTTT
30515 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:32878 original size:6 final size:6
Alignment explanation
Indices: 32867--32897 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
32857 GTAAATAAAT
32867 AAATAA AAATAA AAATAA AAAT-A AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AA
32898 CTTTACAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:32882 original size:12 final size:11
Alignment explanation
Indices: 32863--32897 Score: 54
Period size: 12 Copynumber: 3.2 Consensus size: 11
32853 CTAAGTAAAT
32863 AAAT-AAATAA
1 AAATAAAATAA
32873 AAATAAAAATAA
1 AAAT-AAAATAA
32885 AAATAAAATAA
1 AAATAAAATAA
32896 AA
1 AA
32898 CTTTACAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.17
11 9 0.39
12 10 0.43
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:40100 original size:39 final size:39
Alignment explanation
Indices: 40055--40142 Score: 140
Period size: 39 Copynumber: 2.3 Consensus size: 39
40045 ATTTCCAACC
* *
40055 CAAATGCCTTTGGAACTTAGCCCGGATATAACATTAGCA
1 CAAATGCCTTCGGAACTTAGCCCGGATATAACATCAGCA
*
40094 CAAATGCCTTCGGAACTTAGCCCGGATATAATATCAGCA
1 CAAATGCCTTCGGAACTTAGCCCGGATATAACATCAGCA
*
40133 CGAATGCCTT
1 CAAATGCCTT
40143 ATAATACCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGAACTTAGCCCGGATATAACATCAGCA
Found at i:40148 original size:22 final size:22
Alignment explanation
Indices: 40120--40164 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
40110 TTAGCCCGGA
*
40120 TATAATATCAGCACGAATGCCT
1 TATAATACCAGCACGAATGCCT
40142 TATAATACCAGCACGAATGCCT
1 TATAATACCAGCACGAATGCCT
40164 T
1 T
40165 CGGGACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (22 bp):
TATAATACCAGCACGAATGCCT
Found at i:40222 original size:39 final size:39
Alignment explanation
Indices: 40142--40224 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
40132 ACGAATGCCT
*
40142 TATAATACCAGCACGAATGCCTTCGGGACTTAACCCGGA
1 TATAATACCAGCACGAATGCCTTCGGGACTTAACCCAGA
* * *
40181 TATAATATCAGCACGAATGCCTTCGGGACTTAGCTCAGA
1 TATAATACCAGCACGAATGCCTTCGGGACTTAACCCAGA
40220 TATAA
1 TATAA
40225 ATCTCACACA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (39 bp):
TATAATACCAGCACGAATGCCTTCGGGACTTAACCCAGA
Found at i:43682 original size:26 final size:26
Alignment explanation
Indices: 43611--43687 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 26
43601 CCAATTTCCA
*
43611 TAAAAGGACACCTTTATTGCTATCTC
1 TAAAAGGACACCTTTATGGCTATCTC
* ** * *
43637 TGAAAGGATGCCTTTGTGGCCATCTC
1 TAAAAGGACACCTTTATGGCTATCTC
*
43663 TAAAAGGACACATTTATGGCTATCT
1 TAAAAGGACACCTTTATGGCTATCT
43688 TAGTTAAAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (26 bp):
TAAAAGGACACCTTTATGGCTATCTC
Found at i:43833 original size:29 final size:29
Alignment explanation
Indices: 43679--43927 Score: 225
Period size: 29 Copynumber: 8.6 Consensus size: 29
43669 GACACATTTA
** *
43679 TGGCTATCT-TAGTTAAAAGTGAGCCTTTA
1 TGGCTATCTCT-GTTAAAAGAAAGCCTTTG
* **
43708 TGGCTATCTCAGTTAAAAGTGAGCCTTTG
1 TGGCTATCTCTGTTAAAAGAAAGCCTTTG
** *
43737 TGGCTATCT-TAGTTAAAAGTGAGCCTTTT
1 TGGCTATCTCT-GTTAAAAGAAAGCCTTTG
* * **
43766 TGGTTATCTCAGTTAAAAGTGAGCCTTTG
1 TGGCTATCTCTGTTAAAAGAAAGCCTTTG
* *
43795 TGGCGATCTCTGTTATAAGAAAGCCTTTG
1 TGGCTATCTCTGTTAAAAGAAAGCCTTTG
*
43824 TGGCTATCTCTGTTATAAGAAAGCCTTTG
1 TGGCTATCTCTGTTAAAAGAAAGCCTTTG
* *
43853 TAG-TGATCTCTGTTATAAGAAAGCCTTTG
1 TGGCT-ATCTCTGTTAAAAGAAAGCCTTTG
* * * * * *
43882 TGGCGATCCCTGCTAAAAGGATGCCTTTT
1 TGGCTATCTCTGTTAAAAGAAAGCCTTTG
*
43911 TGTCTATCTCTGTTAAA
1 TGGCTATCTCTGTTAAA
43928 GGAATGTCTG
Statistics
Matches: 188, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
28 1 0.01
29 187 0.99
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.37
Consensus pattern (29 bp):
TGGCTATCTCTGTTAAAAGAAAGCCTTTG
Found at i:43849 original size:87 final size:87
Alignment explanation
Indices: 43683--43927 Score: 267
Period size: 87 Copynumber: 2.8 Consensus size: 87
43673 CATTTATGGC
* * * * **
43683 TATCTTAGTTAAAAGTGAGCCTTTATGGCTATCTCAGTTAAAAGTGAGCCTTTGTGGCTATCT-T
1 TATCTCAGTTAAAAGTGAGCCTTTGTGGCGATCTCTGTTAAAAGAAAGCCTTTGTGGCTATCTCT
** * *
43747 AGTTAAAAGTGAGCCTTTTTGGT
66 -GTTAAAAGAAAGCCTTTGTAGT
*
43770 TATCTCAGTTAAAAGTGAGCCTTTGTGGCGATCTCTGTTATAAGAAAGCCTTTGTGGCTATCTCT
1 TATCTCAGTTAAAAGTGAGCCTTTGTGGCGATCTCTGTTAAAAGAAAGCCTTTGTGGCTATCTCT
*
43835 GTTATAAGAAAGCCTTTGTAGT
66 GTTAAAAGAAAGCCTTTGTAGT
* * * ** * * * * * *
43857 GATCTCTGTTATAAGAAAGCCTTTGTGGCGATCCCTGCTAAAAGGATGCCTTTTTGTCTATCTCT
1 TATCTCAGTTAAAAGTGAGCCTTTGTGGCGATCTCTGTTAAAAGAAAGCCTTTGTGGCTATCTCT
43922 GTTAAA
66 GTTAAA
43928 GGAATGTCTG
Statistics
Matches: 132, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
87 131 0.99
88 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (87 bp):
TATCTCAGTTAAAAGTGAGCCTTTGTGGCGATCTCTGTTAAAAGAAAGCCTTTGTGGCTATCTCT
GTTAAAAGAAAGCCTTTGTAGT
Found at i:44123 original size:22 final size:21
Alignment explanation
Indices: 44097--44142 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
44087 AAGCAAGGAT
44097 AAAAGT-TAAGATTAAGAATAGA
1 AAAAGTATAA-ATTAAGAA-AGA
44119 AAAAGTACTAAATTAAGAAAGA
1 AAAAGTA-TAAATTAAGAAAGA
44141 AA
1 AA
44143 TGGAAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 11 0.50
23 8 0.36
24 3 0.14
ACGTcount: A:0.63, C:0.02, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAGTATAAATTAAGAAAGA
Found at i:44673 original size:53 final size:50
Alignment explanation
Indices: 44556--44675 Score: 141
Period size: 50 Copynumber: 2.3 Consensus size: 50
44546 TTAATAAAGC
* * * *
44556 CACGTATTATGTAACTCTCATGTTAGTTAAGTTTGCATAATAAATTATGA
1 CACGCATTATGTAACTCCCATGTTAGTTAAGTTTGCATAATAAATCAAGA
* * *
44606 CATGCATTATGTAACTCCCATGTTAGTTTAAAGTTTGCATCATTAAATCAAGT
1 CACGCATTATGTAACTCCCATGTTAG-TT-AAGTTTGCAT-AATAAATCAAGA
*
44659 CACGCATTAAGTAACTC
1 CACGCATTATGTAACTC
44676 ATTTGTTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 23 0.40
51 2 0.03
52 10 0.17
53 23 0.40
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (50 bp):
CACGCATTATGTAACTCCCATGTTAGTTAAGTTTGCATAATAAATCAAGA
Found at i:51725 original size:38 final size:38
Alignment explanation
Indices: 51682--51884 Score: 302
Period size: 38 Copynumber: 5.4 Consensus size: 38
51672 GTAGGCTATA
*
51682 TGCTGG-AATTATATCCGGGTTAAATCCTGCAGGCTTCG
1 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
* *
51720 TGCTGGTAATATATCTGGGTTAAATCCCGTAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
51758 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* *
51796 TACT-GTAATATATCCGGGTTAAATCCCACAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
51833 TGTTGGTAATATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
*
51871 TGCTGGTATTATAT
1 TGCTGGTAATATAT
51885 TCGAGCCTTC
Statistics
Matches: 149, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
37 34 0.23
38 113 0.76
39 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (38 bp):
TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:51840 original size:75 final size:76
Alignment explanation
Indices: 51682--51884 Score: 293
Period size: 75 Copynumber: 2.7 Consensus size: 76
51672 GTAGGCTATA
* * *
51682 TGCTGG-AATTATATCCGGGTTAAATCCTGCAGGCTTCGTGCTGGTAATATATCTGGGTTAAATC
1 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGTAATATATCCGGGTTAAATC
**
51746 CCGTAGGCTTCG
65 CCACAGGCTTCG
51758 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTACT-GTAATATATCCGGGTTAAATCC
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGTAATATATCCGGGTTAAATCC
51822 CACAGGCTTCG
66 CACAGGCTTCG
* * * * *
51833 TGTTGGTAATATATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTATAT
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGTAATATAT
51885 TCGAGCCTTC
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 68 0.59
76 45 0.39
77 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (76 bp):
TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCGTACTGGTAATATATCCGGGTTAAATCC
CACAGGCTTCG
Found at i:51939 original size:43 final size:43
Alignment explanation
Indices: 51861--52035 Score: 246
Period size: 43 Copynumber: 4.1 Consensus size: 43
51851 GTTAAATCCC
* * * *
51861 GCAGGCCTAGTGCTGGT-AT-TATATTCGAGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
51902 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCCA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
51945 GCAGGCTTTGTGATGATGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
**
51988 GCAGGCTTCGTGCCAGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
52031 GCAGG
1 GCAGG
52036 TGTAATGCCG
Statistics
Matches: 118, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
41 15 0.13
42 2 0.02
43 101 0.86
ACGTcount: A:0.13, C:0.23, G:0.33, T:0.31
Consensus pattern (43 bp):
GCAGGCTTCGTGCTGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:54095 original size:27 final size:27
Alignment explanation
Indices: 54061--54115 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
54051 TTTTCCAAGC
54061 CTTTGGTCACCCTCTATCAACCAATCA
1 CTTTGGTCACCCTCTATCAACCAATCA
54088 CTTTGGTCACCCTCTATCAACCAATCA
1 CTTTGGTCACCCTCTATCAACCAATCA
54115 C
1 C
54116 ACTTATAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.38, G:0.07, T:0.29
Consensus pattern (27 bp):
CTTTGGTCACCCTCTATCAACCAATCA
Found at i:59173 original size:10 final size:10
Alignment explanation
Indices: 59158--59216 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
59148 ACACGCCAAC
59158 AAGAGCTCAA
1 AAGAGCTCAA
*
59168 AAGAGCTTAA
1 AAGAGCTCAA
* *
59178 CAGAAGCTGAA
1 AAG-AGCTCAA
*
59189 AAGAGCTGAA
1 AAGAGCTCAA
*
59199 TAGAAGCTCAA
1 AAG-AGCTCAA
59210 AAGAGCT
1 AAGAGCT
59217 AATCCACCCG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 24 0.60
11 16 0.40
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.14
Consensus pattern (10 bp):
AAGAGCTCAA
Found at i:59185 original size:21 final size:21
Alignment explanation
Indices: 59161--59216 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
59151 CGCCAACAAG
*
59161 AGCTCAAAAGAGCTTAACAGA
1 AGCTCAAAAGAGCTGAACAGA
* *
59182 AGCTGAAAAGAGCTGAATAGA
1 AGCTCAAAAGAGCTGAACAGA
59203 AGCTCAAAAGAGCT
1 AGCTCAAAAGAGCT
59217 AATCCACCCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.14
Consensus pattern (21 bp):
AGCTCAAAAGAGCTGAACAGA
Found at i:64482 original size:46 final size:46
Alignment explanation
Indices: 64432--64607 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
64422 TGGTTGAGCA
64432 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
64478 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
64523 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
64571 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
64608 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:64588 original size:93 final size:93
Alignment explanation
Indices: 64429--64600 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
64419 GGATGGTTGA
* *
64429 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
64494 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
64522 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
64587 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
64601 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:72089 original size:46 final size:46
Alignment explanation
Indices: 71988--72114 Score: 211
Period size: 46 Copynumber: 2.8 Consensus size: 46
71978 GGTTGAGCAT
* *
71988 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
72033 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
72079 CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
72115 CGGGTTACAT
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 34 0.44
46 43 0.56
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Done.