Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold490
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: 30570
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Found at i:1618 original size:39 final size:39
Alignment explanation
Indices: 1566--1736 Score: 202
Period size: 39 Copynumber: 4.3 Consensus size: 39
1556 GGACTAAGAT
*
1566 CCGAAGGCATTTGTGCGAGATACAAGTTCCGGGTTAAG-C
1 CCGAAGGCATTTGTGCGAGATACAA-ATCCGGGTTAAGTC
*
1605 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
* * *
1645 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
1685 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATAC-AAATCCGGGTTAAGTC
1724 CCGAAGGCATTTG
1 CCGAAGGCATTTG
1737 AACGAGGAGC
Statistics
Matches: 115, Mismatches: 12, Indels: 9
0.85 0.09 0.07
Matches are distributed among these distances:
39 65 0.57
40 50 0.43
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (39 bp):
CCGAAGGCATTTGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:1649 original size:79 final size:79
Alignment explanation
Indices: 1513--1736 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 79
1503 TTGAATGCTG
* * * * * * *
1513 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAAACCGGGCTAAG-TCCCGAAGGCAT
*
1576 TTGTGCGAGATA-CAAGT
63 TTGTGCGAGATATCAA-A
* * * *
1593 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTT
* *
1657 GTGCGAGTTATTAAA
65 GTGCGAGATATCAAA
* * *
1672 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
1737 AACGAGGAGC
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
78 1 0.01
79 90 0.74
80 30 0.25
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATATCAAA
Found at i:1754 original size:79 final size:80
Alignment explanation
Indices: 1593--1769 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
1583 AGATACAAGT
* * *
1593 TCCGGGTTAAG-CCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
1657 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
1672 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
1736 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
1751 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
1770 TACGTGATTT
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
78 16 0.19
79 59 0.71
80 8 0.10
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:9636 original size:39 final size:39
Alignment explanation
Indices: 9432--9654 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
9422 TTGAATGCTG
* * * * * *
9432 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
9472 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
9512 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
9552 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
9592 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
9631 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
9655 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:9674 original size:79 final size:80
Alignment explanation
Indices: 9512--9689 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
9502 AGATACAAGT
* * * *
9512 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
9577 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
9592 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
9656 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
9671 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
9690 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:11348 original size:50 final size:52
Alignment explanation
Indices: 11237--11351 Score: 171
Period size: 50 Copynumber: 2.2 Consensus size: 52
11227 AATGAACAAA
*
11237 TGAGTTACTTAATGCATGAATTAATTTAATGATGCAAACTTTAACTAACATG
1 TGAGTTACATAATGCATGAATTAATTTAATGATGCAAACTTTAACTAACATG
* ** *
11289 GGAGTTACATAATGCATGTCTTAATTT-ATGATGCAAAC-TTAACTTACATG
1 TGAGTTACATAATGCATGAATTAATTTAATGATGCAAACTTTAACTAACATG
11339 TGAGTTACATAAT
1 TGAGTTACATAAT
11352 TAAAGACTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
50 23 0.40
51 11 0.19
52 23 0.40
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (52 bp):
TGAGTTACATAATGCATGAATTAATTTAATGATGCAAACTTTAACTAACATG
Found at i:11371 original size:51 final size:51
Alignment explanation
Indices: 11263--11372 Score: 123
Period size: 50 Copynumber: 2.2 Consensus size: 51
11253 TGAATTAATT
* * * * *
11263 TAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGTCTTAAT
1 TAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGAAAGACTCAAC
* * * *
11314 TTATGATGCAAAC-TTAACTTACATGTGAGTTACATAATTAAAGACTCACAC
1 TAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGAAAGACTCA-AC
11365 TAATGATG
1 TAATGATG
11373 TTCAAACTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 28 0.58
51 20 0.42
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (51 bp):
TAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGAAAGACTCAAC
Found at i:12222 original size:6 final size:6
Alignment explanation
Indices: 12211--12403 Score: 164
Period size: 6 Copynumber: 31.8 Consensus size: 6
12201 AACCAAAATG
* *
12211 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGTATT AGTAA-C
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AG-AATC
* * * *
12259 AGAATC AAAATC AAAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC
1 AGAATC AGAATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC
* * * *
12308 AGAATC AGAGTT AGTAA-C AGAATC AGAATC AGAATC AGTATT AGTAAT-
1 AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGAATC AG-AATC
* *
12356 AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC AGAAT
12404 GTGAATGCAA
Statistics
Matches: 152, Mismatches: 21, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
5 11 0.07
6 129 0.85
7 10 0.07
8 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (6 bp):
AGAATC
Found at i:12360 original size:67 final size:60
Alignment explanation
Indices: 12211--12403 Score: 212
Period size: 67 Copynumber: 3.1 Consensus size: 60
12201 AACCAAAATG
* *
12211 AGAATCAGAATCAGAATCAGTA-ACAGAATCAGAATCAGTATTAGTAACAGAATCAAAATC
1 AGAATCAGAATCAGAATCAGAATACAGAATCAGAATCAG-ATTAGTAACAGAATCAGAATC
*
12271 AAAATCAGAATCAGAATCAGAATTAGGTGACAGAATCAGAATCAGAGTTAGTAACAGAATCAGAA
1 AGAATCAGAATCAGAATCAG-A--A--T-ACAGAATCAGAATCAGA-TTAGTAACAGAATCAGAA
12336 TC
59 TC
* * *
12338 AGAATCAGTATTAGTAAT-AGAAT-CAGAATCAGAATCAGAATTAGGTGACAGAATCAGAATC
1 AGAATCAGAATCAG-AATCAGAATACAGAATCAGAATCAG-ATTA-GTAACAGAATCAGAATC
12399 AGAAT
1 AGAAT
12404 GTGAATGCAA
Statistics
Matches: 115, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
60 37 0.32
61 22 0.19
62 1 0.01
63 1 0.01
64 1 0.01
66 2 0.02
67 48 0.42
68 3 0.03
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (60 bp):
AGAATCAGAATCAGAATCAGAATACAGAATCAGAATCAGATTAGTAACAGAATCAGAATC
Found at i:12364 original size:85 final size:88
Alignment explanation
Indices: 12211--12403 Score: 275
Period size: 85 Copynumber: 2.2 Consensus size: 88
12201 AACCAAAATG
* *
12211 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGTATTAGTAACAGAATCAAAATCAAAAT
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTAACAG-AT--AAATCAAAAT
12276 CAGAATCAGAATCAGAATTAGGTGAC
63 CAGAATCAGAATCAGAATTAGGTGAC
* * ** *
12302 AGAATCAGAATCAGAGTTAGTAACAGAATCAGAATCAGAATCAGTATTAG-T-AAT-AGAATCAG
1 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTAACAGATAAATCAAAATCAG
12364 AATCAGAATCAGAATTAGGTGAC
66 AATCAGAATCAGAATTAGGTGAC
12387 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
12404 GTGAATGCAA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
85 46 0.49
86 3 0.03
89 1 0.01
91 44 0.47
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (88 bp):
AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAGTAACAGATAAATCAAAATCAG
AATCAGAATCAGAATTAGGTGAC
Found at i:12591 original size:27 final size:27
Alignment explanation
Indices: 12521--12594 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
12511 AGCATGGCTG
* *
12521 CCAGAA-CAGAT-ATCGTGACAGAGTCA
1 CCAGAATCAGATAAT-GTGGCAGAGCCA
*
12547 CCAGATAT-AGATATTGTGGCAGAGCCA
1 CCAGA-ATCAGATAATGTGGCAGAGCCA
12574 CCAGAATCAGATAATGTGGCA
1 CCAGAATCAGATAATGTGGCA
12595 AACCCACCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 7 0.17
27 32 0.80
28 1 0.03
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (27 bp):
CCAGAATCAGATAATGTGGCAGAGCCA
Found at i:12601 original size:27 final size:27
Alignment explanation
Indices: 12545--12602 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
12535 GTGACAGAGT
* * *
12545 CACCAGATATAGATATTGTGGCAGAGC
1 CACCAGATATAGATAATGTGGCAAACC
12572 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATAT-AGATAATGTGGCAAACC
12599 CACC
1 CACC
12603 TAACAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (27 bp):
CACCAGATATAGATAATGTGGCAAACC
Found at i:12807 original size:22 final size:22
Alignment explanation
Indices: 12759--12817 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
12749 GTAAATACGT
*
12759 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
12781 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
12803 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
12818 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:12984 original size:27 final size:26
Alignment explanation
Indices: 12905--12987 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
12895 TCGATCGGTC
* * *
12905 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
*
12931 ATACAGATATTGTAGCAGAGCCACCAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
12958 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
12985 AAC
1 AAC
12988 GCTTCCTCCG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
26 8 0.16
27 41 0.84
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:13216 original size:27 final size:27
Alignment explanation
Indices: 13186--13381 Score: 203
Period size: 27 Copynumber: 7.3 Consensus size: 27
13176 GGGGCAAAAT
* * *
13186 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
13213 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
13240 GGTATTTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
13267 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
13294 GGTAATTCTATCCTATAAGGCTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
13321 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * *
13348 GAAAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
13375 AGTAATT
1 GGTAATT
13382 TCACAATCAA
Statistics
Matches: 139, Mismatches: 30, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 139 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:13330 original size:81 final size:81
Alignment explanation
Indices: 13188--13381 Score: 244
Period size: 81 Copynumber: 2.4 Consensus size: 81
13178 GGCAAAATGG
* * * * * * * *
13188 TAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGGTATTTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGCTATTTCAGTAATTCTACCC
*
13253 TACAAGGGTATTTTGA
66 TACAAGGGTATTTCGA
* *
13269 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGCTATTTCAGTAATTCTACCC
1 TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGCTATTTCAGTAATTCTACCC
* *
13334 TATAGGGGTATTTCGA
66 TACAAGGGTATTTCGA
* * *
13350 AAATTCTACCTTACAGGGGTATTTCAGTAATT
1 TAATTCTACCCTACAGGGGTATTTCGGTAATT
13382 TCACAATCAA
Statistics
Matches: 96, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 96 1.00
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (81 bp):
TAATTCTACCCTACAGGGGTATTTCGGTAATTCTACCCTATAAGGCTATTTCAGTAATTCTACCC
TACAAGGGTATTTCGA
Found at i:13416 original size:27 final size:27
Alignment explanation
Indices: 13386--13687 Score: 354
Period size: 27 Copynumber: 11.2 Consensus size: 27
13376 GTAATTTCAC
* * *
13386 AATCAAGGGTAAAATGGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
13413 AATCGAGGGTAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
13440 AA-CTGAGGGTAAACCAGTAATTCTGTA
1 AATC-GAGGGTAAAACGGTAATTCTGTA
* * **
13467 AATCAAGGGTAAAACGGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
13494 AATCAAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * **
13521 AATCGAGGGTAAAACAGTAATTTTACA
1 AATCGAGGGTAAAACGGTAATTCTGTA
*
13548 AATCGAGGGTAAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
13575 AATCGAGGGTAACACAGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* * **
13602 AATCAAGGGTAAAACGGTAATTTTAAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
* *
13629 AATCAAGGGTAAAACGGTAATTCTGAA
1 AATCGAGGGTAAAACGGTAATTCTGTA
13656 AATCGAGGGTAAAACGGTAATTCTGTA
1 AATCGAGGGTAAAACGGTAATTCTGTA
13683 AATCG
1 AATCG
13688 GTAGTACTTT
Statistics
Matches: 238, Mismatches: 35, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
26 1 0.00
27 236 0.99
28 1 0.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTCTGTA
Found at i:13716 original size:54 final size:53
Alignment explanation
Indices: 13376--13718 Score: 253
Period size: 54 Copynumber: 6.4 Consensus size: 53
13366 GGGTATTTCA
* * * * * * *
13376 GTAATTTCAC-AATCAAGGGTAAAATGGTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGAGT-ACACG
* ** * * * * * *
13429 ATAATTTTGTAAA-CTGAGGGTAAACCAGTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTTTACAAATC-GAGGGTAAAACGGTAATTCTATAAATCGAGAGT-ACACG
* * * *
13483 GTAATTTTACAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAACA
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGAGT-ACACG
* *
13537 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTAACACA
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGAGT-ACACG
* ** * * * * * *
13591 GTAATTCTGTAAATCAAGGGTAAAACGGTAATTTTAAAAATCAAGGGTAAAACG
1 GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGAGT-ACACG
* * **
13645 GTAATTCTGA-AAATCGAGGGTAAAACGGTAATTCTGTAAATCG-GTAGTACTTTG
1 GTAATT-TTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAG-AGTAC-ACG
*
13699 GTAATTTTACAAGTCGAGGG
1 GTAATTTTACAAATCGAGGG
13719 CATTTCAGTA
Statistics
Matches: 239, Mismatches: 44, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
53 11 0.05
54 227 0.95
55 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (53 bp):
GTAATTTTACAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGAGTACACG
Found at i:16952 original size:37 final size:37
Alignment explanation
Indices: 16902--16980 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
16892 TTATTACGAA
* *
16902 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
16939 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
16976 GTCTT
1 GTCTT
16981 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:17218 original size:47 final size:47
Alignment explanation
Indices: 17094--17579 Score: 906
Period size: 47 Copynumber: 10.3 Consensus size: 47
17084 AAATGCCCTG
17094 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17141 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
*
17190 TCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17237 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17284 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17331 TCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17380 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17427 TCACATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17473 TCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17518 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
17565 TCACATATATACACT
1 TCACATATATACACT
17580 GTCCTGGCTG
Statistics
Matches: 430, Mismatches: 2, Indels: 14
0.96 0.00 0.03
Matches are distributed among these distances:
44 28 0.07
45 16 0.04
46 16 0.04
47 276 0.64
49 94 0.22
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
Found at i:17352 original size:143 final size:140
Alignment explanation
Indices: 17094--17579 Score: 904
Period size: 143 Copynumber: 3.4 Consensus size: 140
17084 AAATGCCCTG
17094 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTT
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTT
17159 TCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGG
64 TCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATACACTTTCACATTCATCACATCGG
17224 CCATTAGGCCTTA
128 CCATTAGGCCTTA
17237 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
17302 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGG
66 ACATTCATCACATCGGCCATTAGGCCTTATCAC--A-ATATACACTTTCACATTCATCACATCGG
17367 CCATTAGGCCTTA
128 CCATTAGGCCTTA
17380 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
17445 ACATTCATCACATCGG-CATTAGGCCTTATCAC-ATATACACTTTCACATTCATCACATCGGCCA
66 ACATTCATCACATCGGCCATTAGGCCTTATCACAATATACACTTTCACATTCATCACATCGGCCA
17508 TTAGGCCTTA
131 TTAGGCCTTA
17518 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
17580 GTCCTGGCTG
Statistics
Matches: 340, Mismatches: 1, Indels: 9
0.97 0.00 0.03
Matches are distributed among these distances:
138 103 0.30
141 47 0.14
142 16 0.05
143 174 0.51
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (140 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTATCACAATATACACTTTCACATTCATCACATCGGCCA
TTAGGCCTTA
Found at i:17417 original size:190 final size:189
Alignment explanation
Indices: 17094--17579 Score: 926
Period size: 190 Copynumber: 2.6 Consensus size: 189
17084 AAATGCCCTG
17094 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTT
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTT
*
17159 TCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGG
66 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
17224 CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
131 CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG-CATTAGGCCTTA
17284 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTT
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTT
17349 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
66 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
17414 CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTA
131 CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTA
17473 TCAC--ATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTT
1 TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTT
17534 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
66 TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACT
17580 GTCCTGGCTG
Statistics
Matches: 295, Mismatches: 1, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
185 58 0.20
187 45 0.15
189 16 0.05
190 176 0.60
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (189 bp):
TCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTT
TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGG
CCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCATTAGGCCTTA
Found at i:21267 original size:80 final size:79
Alignment explanation
Indices: 21100--21293 Score: 214
Period size: 80 Copynumber: 2.4 Consensus size: 79
21090 GCCCGAATAC
* * * * *
21100 ACGTCACCAGCATGATTGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAATGCTCTTCG
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGC-CGGATATATAACTAGCACCAATGCTCTTCG
21165 GAACTTAGCCCGGAT
65 GAACTTAGCCCGGAT
* * *
21180 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCGGATTTAGTAACTCGCACCAATGC-CTTCG
1 ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCGGATATA-TAACTAGCACCAATGCTCTTCG
* *
21244 GATCTTAGTCCGGAT
65 GAACTTAGCCCGGAT
* * *
21259 ATGGTCACTTAGCA-CAAAGC-CTTCGGGACTTAGCC
1 A-CGTCAC-TAGCATGAATGCTCTTCGGGACTTAGCC
21294 CGGACATCAT
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
79 41 0.42
80 51 0.53
81 5 0.05
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (79 bp):
ACGTCACTAGCATGAATGCTCTTCGGGACTTAGCCGGATATATAACTAGCACCAATGCTCTTCGG
AACTTAGCCCGGAT
Found at i:21283 original size:79 final size:79
Alignment explanation
Indices: 21117--21293 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 79
21107 CAGCATGATT
* * *
21117 GCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATAC
1 GCTCTTCGGGACTTAGC-CGGATATATAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATAC
* *
21182 ATCACTAGCATGAAT
65 ATCACTAGCATCAAA
* * * *
21197 GCTCTTCGGGACTTAGCCGGATTTAGTAACTCGCACCAATGC-CTTCGGATCTTAGTCCGGATAT
1 GCTCTTCGGGACTTAGCCGGATATA-TAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATA-
**
21261 GGTCACTTAGCA-CAAA
64 CATCAC-TAGCATCAAA
21277 GC-CTTCGGGACTTAGCC
1 GCTCTTCGGGACTTAGCC
21294 CGGACATCAT
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
79 41 0.49
80 37 0.45
81 5 0.06
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.27
Consensus pattern (79 bp):
GCTCTTCGGGACTTAGCCGGATATATAACTAGCACCAATGCTCTTCGGAACTTAGCCCGGATACA
TCACTAGCATCAAA
Found at i:21297 original size:40 final size:40
Alignment explanation
Indices: 21116--21297 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
21106 CCAGCATGAT
* * *
21116 TGCTCTTCGGGATTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
* * **
21156 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
* * *
21196 TGCTCTTCGGGACTTAG-CCGGATTTAGTAACTCGCACCAA
1 TGCTCTTCGGGACTTAGCCCGGATATA-TCACTAGCACCAA
* *
21236 TGC-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAA
1 TGCTCTTCGGGA-CTTAGCCCGGATAT-ATCAC-TAGCACCAA
*
21276 AGC-CTTCGGGACTTAGCCCGGA
1 TGCTCTTCGGGACTTAGCCCGGA
21298 CATCATTCGA
Statistics
Matches: 118, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 3 0.03
39 16 0.14
40 92 0.78
41 7 0.06
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATATATCACTAGCACCAA
Found at i:21643 original size:29 final size:29
Alignment explanation
Indices: 21604--21682 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
21594 CTTAATAATC
*
21604 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
21634 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
21663 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
21683 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:21725 original size:43 final size:43
Alignment explanation
Indices: 21664--21766 Score: 206
Period size: 43 Copynumber: 2.4 Consensus size: 43
21654 TGCATTTCAA
21664 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
21707 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
21750 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
21767 TGAAAACCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:23696 original size:36 final size:37
Alignment explanation
Indices: 23624--23701 Score: 106
Period size: 36 Copynumber: 2.1 Consensus size: 37
23614 TTATTACGAA
* *
23624 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
*
23661 GTCTTACCCGGA-AAAAT-TCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCT-CCACACGAAGTCATCGG
23697 GTCTT
1 GTCTT
23702 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 1 0.03
36 24 0.65
37 12 0.32
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCTCCACACGAAGTCATCGG
Found at i:23898 original size:47 final size:47
Alignment explanation
Indices: 23820--24216 Score: 686
Period size: 47 Copynumber: 8.4 Consensus size: 47
23810 CCCTTCGGGA
* * * * * * *
23820 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
23867 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
23914 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
23961 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24008 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24055 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24104 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24151 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24198 CTTATCACATATATACACT
1 CTTATCACATATATACACT
24217 GTCTTGGCTG
Statistics
Matches: 335, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
47 288 0.86
49 47 0.14
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:24133 original size:143 final size:143
Alignment explanation
Indices: 23820--24212 Score: 682
Period size: 143 Copynumber: 2.8 Consensus size: 143
23810 CCCTTCGGGA
* * * * * * * * *
23820 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
23885 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
*
23948 TCGGCTATTAGGC
131 TCGGCCATTAGGC
23961 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
24026 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
24091 TCGGCCATTAGGC
131 TCGGCCATTAGGC
24104 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
24169 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
24213 CACTGTCTTG
Statistics
Matches: 240, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
141 93 0.39
143 147 0.61
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:24141 original size:190 final size:188
Alignment explanation
Indices: 23820--24216 Score: 686
Period size: 190 Copynumber: 2.1 Consensus size: 188
23810 CCCTTCGGGA
* * * * * *
23820 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
23885 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
*
23950 GGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
24008 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCAC--ATATATAC
24073 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
64 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
24138 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
24198 CTTATCACATATATACACT
1 CTTATCACATATATACACT
24217 GTCTTGGCTG
Statistics
Matches: 197, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 46 0.23
190 151 0.77
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (188 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:26835 original size:6 final size:6
Alignment explanation
Indices: 26805--27020 Score: 178
Period size: 6 Copynumber: 36.3 Consensus size: 6
26795 AAGAAACATT
* * * *
26805 ATCAGA ATTAGA ACCAAA ATGAGA ATCAGA ATCAGA ATCAGTA A-CAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A ATCAGA
* * *
26853 ATCAGA ATCAGA ATCAGT ATTAG- -TAAGA ATCA-A ATCAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * *
26898 ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA ATTAGA GTCAGTA A-CAGA
1 ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA ATCAG-A ATCAGA
* * *
26947 ATCAGA ATCAGA ATCAGT ATTAGA A-CAGA GTCAGA ATCAGA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* *
26994 ATTAG- GTGACAGA ATCAGA ATCAGA AT
1 ATCAGA AT--CAGA ATCAGA ATCAGA AT
27021 GTGAATGCAA
Statistics
Matches: 166, Mismatches: 30, Indels: 28
0.74 0.13 0.12
Matches are distributed among these distances:
4 3 0.02
5 14 0.08
6 140 0.84
7 7 0.04
8 2 0.01
ACGTcount: A:0.48, C:0.13, G:0.19, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:27184 original size:27 final size:26
Alignment explanation
Indices: 27136--27208 Score: 85
Period size: 27 Copynumber: 2.8 Consensus size: 26
27126 AGCATGGCTG
* * *
27136 CCAGAACAGA-ATCGTGACAGAGTCA
1 CCAGAACAGATATTGTGGCAGAGCCA
27161 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAGAGCCA
*
27188 CCAGAATCAGATAATGTGGCA
1 CCAGAA-CAGATATTGTGGCA
27209 AACCCACCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.12
26 6 0.15
27 30 0.73
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAGAGCCA
Found at i:27215 original size:27 final size:27
Alignment explanation
Indices: 27159--27216 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
27149 GTGACAGAGT
* * *
27159 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
27186 CACCAGA-ATCAGATAATGTGGCAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
27213 CACC
1 CACC
27217 TAACGAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.16
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:27587 original size:25 final size:26
Alignment explanation
Indices: 27514--27594 Score: 101
Period size: 27 Copynumber: 3.1 Consensus size: 26
27504 TCGATCGGTC
* * *
27514 AACAGATATTGTGACAGAGTCACCAA
1 AACAGATATTGTGGCAGAGCCACCAG
*
27540 ATACAGATATTGTGGCAGAGCCACTAG
1 A-ACAGATATTGTGGCAGAGCCACCAG
*
27567 AACAGATATTG-GGCATAGCCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
27592 AAC
1 AAC
27595 GCTTCCTCCG
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
25 15 0.31
26 11 0.23
27 22 0.46
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:27833 original size:26 final size:26
Alignment explanation
Indices: 27785--27974 Score: 163
Period size: 26 Copynumber: 7.3 Consensus size: 26
27775 GGGGCAAAAT
* * * * *
27785 GGTAATTTTACCCACAAGCGTATCTC
1 GGTAATTCTACCTACAGGGGTATTTC
27811 GGTAATTCT-CCTACAGGGGGTATTTC
1 GGTAATTCTACCTACA-GGGGTATTTC
* *
27837 GGTATTTCTACCCTACA-AGGTATTTC
1 GGTAATTCTA-CCTACAGGGGTATTTC
* *
27863 GATAATTCTACCTACAGGGGTATTTT
1 GGTAATTCTACCTACAGGGGTATTTC
* *
27889 GGTAATTCTATCCTATA-AGGTATTTC
1 GGTAATTCTA-CCTACAGGGGTATTTC
* *
27915 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTA-CCTACAGGGGTATTTC
* *
27942 GGAAATTCTACCTTATA-GGGTATTTC
1 GGTAATTCTACC-TACAGGGGTATTTC
*
27968 AGTAATT
1 GGTAATT
27975 TCACAATCAA
Statistics
Matches: 135, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
25 11 0.08
26 93 0.69
27 25 0.19
28 6 0.04
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (26 bp):
GGTAATTCTACCTACAGGGGTATTTC
Found at i:27968 original size:53 final size:51
Alignment explanation
Indices: 27785--27974 Score: 204
Period size: 52 Copynumber: 3.6 Consensus size: 51
27775 GGGGCAAAAT
* * * * *
27785 GGTAATTTTACCCACAAGCGTATCTCGGTAATTCT-CCTACAGGGGGTATTTC
1 GGTAATTCTACCTATAAG-GTATTTCAGTAATTCTACCTACA-GGGGTATTTC
* * *
27837 GGTATTTCTACCCTACAAGGTATTTC-GATAATTCTACCTACAGGGGTATTTT
1 GGTAATTCTA-CCTATAAGGTATTTCAG-TAATTCTACCTACAGGGGTATTTC
*
27889 GGTAATTCTATCCTATAAGGTATTTCAGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTA-CCTATAAGGTATTTCAGTAATTCTA-CCTACAGGGGTATTTC
* *
27942 GGAAATTCTACCTTATAGGGTATTTCAGTAATT
1 GGTAATTCTACC-TATAAGGTATTTCAGTAATT
27975 TCACAATCAA
Statistics
Matches: 120, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
51 1 0.01
52 63 0.52
53 56 0.47
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (51 bp):
GGTAATTCTACCTATAAGGTATTTCAGTAATTCTACCTACAGGGGTATTTC
Found at i:28022 original size:23 final size:23
Alignment explanation
Indices: 27979--28023 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
27969 GTAATTTCAC
* *
27979 AATCAAGGGTAAAATGGTAATTA
1 AATCAAGGGTAAAACGATAATTA
*
28002 AATCGAGGGTAAAACGATAATT
1 AATCAAGGGTAAAACGATAATT
28024 TTGTAAACTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.24
Consensus pattern (23 bp):
AATCAAGGGTAAAACGATAATTA
Found at i:28170 original size:53 final size:54
Alignment explanation
Indices: 28000--28269 Score: 333
Period size: 54 Copynumber: 5.1 Consensus size: 54
27990 AAATGGTAAT
* * *
28000 TAAATCGAGGGTAAAACGATAATTTTGTAAACTGA-GGT-AAACAGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTG
** * ** *
28052 TAAATTAAGGGTAAAACGGTAATTTTACAAATTGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTG
* * *
28106 TAAATCGAGGGTAAAACAGCAATTCTGTAAACTAAGGGTAAAAC-GTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTG
*
28159 TAAATCGAGGGTAAAATGGTAATTCTGTAAACTGA-GGTAAAACGGTAA--CTG
1 TAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTG
*
28210 T-AATCGAGGGTAAAACGGTAATT-T-TAAAAATCGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTGT-AAACT-GAGGGTAAAACGGTAATTCTG
28263 TAAATCG
1 TAAATCG
28270 GGAGTACTTT
Statistics
Matches: 187, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
48 1 0.01
49 5 0.03
50 23 0.12
51 17 0.09
52 37 0.20
53 51 0.27
54 53 0.28
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (54 bp):
TAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGGTAATTCTG
Found at i:28268 original size:27 final size:27
Alignment explanation
Indices: 28000--28269 Score: 299
Period size: 27 Copynumber: 10.3 Consensus size: 27
27990 AAATGGTAAT
* *
28000 TAAATCGAGGGTAAAACGATAATTTTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
*
28027 TAAA-CTGA-GGT-AAACAGTAATTCTG
1 TAAATC-GAGGGTAAAACGGTAATTCTG
** * *
28052 TAAATTAAGGGTAAAACGGTAATTTTA
1 TAAATCGAGGGTAAAACGGTAATTCTG
* *
28079 CAAATTGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
* *
28106 TAAATCGAGGGTAAAACAGCAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
*
28133 TAAA-CTAAGGGTAAAAC-GTAATTCTG
1 TAAATC-GAGGGTAAAACGGTAATTCTG
*
28159 TAAATCGAGGGTAAAATGGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
28186 TAAA-CTGA-GGTAAAACGGTAA--CTG
1 TAAATC-GAGGGTAAAACGGTAATTCTG
* *
28210 T-AATCGAGGGTAAAACGGTAATTTTA
1 TAAATCGAGGGTAAAACGGTAATTCTG
*
28236 AAAATCGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACGGTAATTCTG
28263 TAAATCG
1 TAAATCG
28270 GGAGTACTTT
Statistics
Matches: 203, Mismatches: 27, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
23 4 0.02
24 18 0.09
25 16 0.08
26 43 0.21
27 122 0.60
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACGGTAATTCTG
Done.