Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1074
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: 55219
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1307 original size:9 final size:9
Alignment explanation
Indices: 1295--1319 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1285 TAATTAAATA
1295 ATAAATATT
1 ATAAATATT
1304 ATAAATATT
1 ATAAATATT
1313 ATAAATA
1 ATAAATA
1320 ATATTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
ATAAATATT
Found at i:4701 original size:52 final size:52
Alignment explanation
Indices: 4553--4681 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
4543 CGAAATATGA
4553 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
4605 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
4657 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
4682 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:4708 original size:13 final size:13
Alignment explanation
Indices: 4690--4714 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4680 CAAAGATCAG
4690 TGTATCGATACAA
1 TGTATCGATACAA
4703 TGTATCGATACA
1 TGTATCGATACA
4715 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4781 original size:19 final size:18
Alignment explanation
Indices: 4757--4886 Score: 110
Period size: 19 Copynumber: 7.8 Consensus size: 18
4747 TAGCTTATAT
4757 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
4776 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
4789 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
4808 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
4821 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
4840 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
4853 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
4873 TGTATCGATACAAA
1 TGTATCGATACAAA
4887 TCATATCATT
Statistics
Matches: 92, Mismatches: 0, Indels: 38
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.36
14 3 0.03
16 6 0.07
18 2 0.02
19 35 0.38
20 13 0.14
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:4794 original size:13 final size:13
Alignment explanation
Indices: 4776--4864 Score: 70
Period size: 13 Copynumber: 5.9 Consensus size: 13
4766 ACAAAACTTA
4776 TGTATCGATACAT
1 TGTATCGATACAT
4789 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
4807 ATGTATCGATACAT
1 -TGTATCGATACAT
4821 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
4839 ATGTATCGATACAT
1 -TGTATCGATACAT
4853 TGTATCGATACA
1 TGTATCGATACA
4865 ACACTTTATG
Statistics
Matches: 64, Mismatches: 0, Indels: 24
0.73 0.00 0.27
Matches are distributed among these distances:
13 30 0.47
14 2 0.03
16 12 0.19
18 2 0.03
19 18 0.28
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4796 original size:32 final size:32
Alignment explanation
Indices: 4755--4884 Score: 242
Period size: 32 Copynumber: 4.0 Consensus size: 32
4745 AGTAGCTTAT
*
4755 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
4787 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
4819 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
4851 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
4884 A
1 A
4885 AATCATATCA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 81 0.84
33 15 0.16
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:9583 original size:20 final size:20
Alignment explanation
Indices: 9558--9633 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
9548 GTAAAAAGAC
9558 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
9578 AGAATGTATCGATACATT-A
1 AGAATGTATCGATACATTGA
*
9597 TA-AATGTATCGATATATTGA
1 -AGAATGTATCGATACATTGA
*
9617 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
9634 CTAGGTAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
19 17 0.33
20 34 0.67
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:17021 original size:112 final size:114
Alignment explanation
Indices: 16888--17115 Score: 343
Period size: 114 Copynumber: 2.0 Consensus size: 114
16878 AAAAACTTAA
** *
16888 AAGCTCAGGTAAACATAGAAAATAAAAAGAAATACATAAAAAA-CAAAAA-AAAAGTTAATGAAA
1 AAGCTCAAATAAACATAGAAAATAAAAAGAAATAAATAAAAAATCAAAAAGAAAAGTTAATGAAA
* ** * *
16951 ATCCCAAATTAGCAAAGCTTAAGAAAACATACAACTGAAAAGCCTAAAG
66 ATCCCAAACTAGCAAAGCACAAAAAAACATACAACGGAAAAGCCTAAAG
*
17000 AAGCTCAAATAAACATAGAAAATAAAGAGAAATAAATAAAAAATCAAAAAGAAAAGTTAATGAAA
1 AAGCTCAAATAAACATAGAAAATAAAAAGAAATAAATAAAAAATCAAAAAGAAAAGTTAATGAAA
* *
17065 ATCCTAAACTAGCAAAGCACAAAAAAACATATAACGGAAAAGCCTAAAG
66 ATCCCAAACTAGCAAAGCACAAAAAAACATACAACGGAAAAGCCTAAAG
17114 AA
1 AA
17116 AAATAGGTGA
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 39 0.38
113 6 0.06
114 58 0.56
ACGTcount: A:0.61, C:0.13, G:0.11, T:0.14
Consensus pattern (114 bp):
AAGCTCAAATAAACATAGAAAATAAAAAGAAATAAATAAAAAATCAAAAAGAAAAGTTAATGAAA
ATCCCAAACTAGCAAAGCACAAAAAAACATACAACGGAAAAGCCTAAAG
Found at i:19537 original size:54 final size:53
Alignment explanation
Indices: 19469--19591 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 53
19459 TGACTAAAAT
**
19469 CTAAATCTAAAATGATTTGAACTCGATTTAACTCGAATGTTAAACCCAATTGAC
1 CTAAATCTAAAATGACATGAACTCGA-TTAACTCGAATGTTAAACCCAATTGAC
* * *
19523 CTAAATCTAGAATGACATGAACTCGATTAATTCGAGTGTTAAACCCAATTGAC
1 CTAAATCTAAAATGACATGAACTCGATTAACTCGAATGTTAAACCCAATTGAC
* *
19576 CAAAATCTGAAATGAC
1 CTAAATCTAAAATGAC
19592 CTAAACTCAA
Statistics
Matches: 61, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
53 38 0.62
54 23 0.38
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (53 bp):
CTAAATCTAAAATGACATGAACTCGATTAACTCGAATGTTAAACCCAATTGAC
Found at i:19988 original size:8 final size:8
Alignment explanation
Indices: 19925--20003 Score: 58
Period size: 7 Copynumber: 10.0 Consensus size: 8
19915 AATGTATTAT
19925 AAAATATA
1 AAAATATA
*
19933 AAAA-ATT
1 AAAATATA
19940 AAAATAT-
1 AAAATATA
*
19947 CAAATA-A
1 AAAATATA
* *
19954 AATATATTT
1 AAAATA-TA
19963 AAAATAATA
1 AAAAT-ATA
19972 AAAAT-TA
1 AAAATATA
19979 AAAATATA
1 AAAATATA
19987 AAAATAATA
1 AAAAT-ATA
*
19996 AAATTATA
1 AAAATATA
20004 TCATATAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
7 22 0.39
8 16 0.29
9 17 0.30
10 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (8 bp):
AAAATATA
Found at i:19996 original size:9 final size:9
Alignment explanation
Indices: 19949--19998 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
19939 TAAAATATCA
19949 AATAAAATAT
1 AATAAAA-AT
* *
19959 ATTTAAAAT
1 AATAAAAAT
19968 AATAAAAAT
1 AATAAAAAT
19977 --TAAAAAT
1 AATAAAAAT
19984 -ATAAAAAT
1 AATAAAAAT
19992 AATAAAA
1 AATAAAA
19999 TTATATCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
7 7 0.21
8 7 0.21
9 15 0.44
10 5 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AATAAAAAT
Found at i:24263 original size:2 final size:2
Alignment explanation
Indices: 24256--24296 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
24246 TACCTAGTTT
24256 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24297 GTTTAACATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24729 original size:6 final size:6
Alignment explanation
Indices: 24718--24761 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
24708 TTTTATACTT
* *
24718 TTAAAA TTAAAA TAAAAA ATAAAA TTAATAA TTAAAA -TAAAA TT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAA-AA TTAAAA TTAAAA TT
24762 TATCATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
TTAAAA
Found at i:24742 original size:18 final size:18
Alignment explanation
Indices: 24719--24772 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
24709 TTTATACTTT
24719 TAAAATTAA-AATAAAAAA
1 TAAAATTAATAAT-AAAAA
*
24737 TAAAATTAATAATTAAAA
1 TAAAATTAATAATAAAAA
* *
24755 TAAAATTTATCATAAAAA
1 TAAAATTAATAATAAAAA
24773 AAACTGATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAATTAATAATAAAAA
Found at i:26174 original size:16 final size:16
Alignment explanation
Indices: 26153--26186 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
26143 TTTGAATTTG
26153 AATTAATTATATTAAT
1 AATTAATTATATTAAT
26169 AATTAATTATATTAAT
1 AATTAATTATATTAAT
26185 AA
1 AA
26187 ATATTAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATTATATTAAT
Found at i:26223 original size:23 final size:23
Alignment explanation
Indices: 26165--26213 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
26155 TTAATTATAT
*
26165 TAATAATTAATTATATTAATAAA
1 TAATAAGTAATTATATTAATAAA
*
26188 TATTAAGTAATTATATTAATAAA
1 TAATAAGTAATTATATTAATAAA
26211 TAA
1 TAA
26214 ATATTGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATAAGTAATTATATTAATAAA
Found at i:30226 original size:28 final size:28
Alignment explanation
Indices: 30184--30258 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 28
30174 AAAATAAAAT
* * *
30184 CAGGGTTTGAGTATCCTCTCAAAAATAA
1 CAGGGTTGGAGTATCCCCGCAAAAATAA
* * *
30212 CGGGGTTGGACTATCCCCGCGAAAATAA
1 CAGGGTTGGAGTATCCCCGCAAAAATAA
30240 CAGGGTTGGAGTATCCCCG
1 CAGGGTTGGAGTATCCCCG
30259 ATTGTGAGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (28 bp):
CAGGGTTGGAGTATCCCCGCAAAAATAA
Found at i:30333 original size:106 final size:107
Alignment explanation
Indices: 30105--30336 Score: 281
Period size: 107 Copynumber: 2.2 Consensus size: 107
30095 GAAATAAAAT
** * * * *** *
30105 CGGGGTTGGAGTATCCCCTTGGAAATAACAGGGTTGGAGTATTCCTAATTATAGAAAATTGGTGT
1 CGGGGTTGGAGTATCCCCGCGAAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAATAT
*
30170 TTTGAAAATAAAATCAGGGTTTGAGTATCCTCTCAAAAATAA
66 TTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAA
* * *
30212 CGGGGTTGGACTATCCCCGCGAAAATAACAGGGTTGGAGTATCCCCGATTGT-GAGAAATCAATA
1 CGGGGTTGGAGTATCCCCGCGAAAATAACAGGGTTGGAGTATCCCCAATTATAGA-AAATCAATA
* *
30276 TTTT-AGGAATAAAA-CTGGGTTGGAGTATCCTCTCAAAAATAA
65 TTTTGA-AAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAA
*
30318 TGGGGTTGGAGTATCCCCG
1 CGGGGTTGGAGTATCCCCG
30337 ATTGTGAGAA
Statistics
Matches: 106, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
106 46 0.43
107 60 0.57
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCGCGAAAATAACAGGGTTGGAGTATCCCCAATTATAGAAAATCAATAT
TTTGAAAATAAAATCAGGGTTGGAGTATCCTCTCAAAAATAA
Found at i:30423 original size:79 final size:79
Alignment explanation
Indices: 30212--30733 Score: 814
Period size: 79 Copynumber: 6.6 Consensus size: 79
30202 TCAAAAATAA
* * *
30212 CGGGGTTGGACTATCCCCGC-GAAAATAACAGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA
1 CGGGGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATA
*
30276 TTTTAGGAATAAA-A
65 TTTTAGGAATAAAGC
* * * *
30290 CTGGGTTGGAGTATCCTCTCAAAAATAATGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
30355 TTTAGGAATAAAGC
66 TTTAGGAATAAAGC
*
30369 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTAACCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
* *
30434 TTTAGAAATAAAAC
66 TTTAGGAATAAAGC
* *
30448 CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGCTGGAGTATCCCCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
30513 TTTAGGAATAAAGC
66 TTTAGGAATAAAGC
* * * * *
30527 CGAGGTTGGAGTATCCCCTCGGAAATAACGGGGTTAGAGTATCCCTGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
*
30592 TTTAGGAATAAAGT
66 TTTAGGAATAAAGC
*
30606 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
30671 TTTAGGAATAAAGC
66 TTTAGGAATAAAGC
** *
30685 TAGGGTTGGAGTATCCCCTCAGAAATAATGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGAT
30734 GATTAACGGG
Statistics
Matches: 406, Mismatches: 36, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
78 69 0.17
79 337 0.83
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAGAAATCAATAT
TTTAGGAATAAAGC
Found at i:30752 original size:27 final size:28
Alignment explanation
Indices: 30687--30756 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
30677 AATAAAGCTA
*
30687 GGGTTGGAGTATCCCCTCAGAAATAATG
1 GGGTTGGAGTATCCCCTCAGAAATAACG
* *
30715 GGGTTGGAGTATCCCC-GATG-ATTAACG
1 GGGTTGGAGTATCCCCTCA-GAAATAACG
30742 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
30757 TGATTATGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.23, C:0.19, G:0.33, T:0.26
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTCAGAAATAACG
Found at i:33198 original size:13 final size:13
Alignment explanation
Indices: 33180--33205 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33170 ACAAAGATCG
33180 ATGTATCGATACA
1 ATGTATCGATACA
33193 ATGTATCGATACA
1 ATGTATCGATACA
33206 TTCTACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:36408 original size:52 final size:52
Alignment explanation
Indices: 36328--36456 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
36318 CGAAATATGA
36328 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
36380 AAATTTGCTTGTATGTATCGATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
* *
36432 AAATTGGCCTGCATGTATCGATACA
1 AAATTTGCTTGCATGTATCGATACA
36457 AAGATTAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:36466 original size:52 final size:52
Alignment explanation
Indices: 36328--36476 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 52
36318 CGAAATATGA
* * **
36328 AAATTTGCTTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTGGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
* * * * **
36380 AAATTTGCTTGTATGTATCGATATATTTCATAGTGTATCGATACATCTGGGC
1 AAATTGGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
*
36432 AAATTGGCCTGCATGTATCGATACA-AAGATTAGTGTATCGATACA
1 AAATTGGCCTGCATGTATCGATACATAACA-TAGTGTATCGATACA
36477 ATATATCGAT
Statistics
Matches: 87, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
51 1 0.01
52 86 0.99
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTGGCCTGCATGTATCGATACATAACATAGTGTATCGATACATCTGGGC
Found at i:36579 original size:13 final size:13
Alignment explanation
Indices: 36561--36585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36551 ACAAAACTTA
36561 TGTATCGATACAT
1 TGTATCGATACAT
36574 TGTATCGATACA
1 TGTATCGATACA
36586 AATCGTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:36910 original size:19 final size:21
Alignment explanation
Indices: 36886--36937 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
36876 AGCGATACAC
*
36886 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
36905 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
36926 TGTATCGATACA
1 TGTATCGATACA
36938 AATTATTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 5 0.17
21 13 0.43
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:49934 original size:52 final size:51
Alignment explanation
Indices: 49856--49971 Score: 205
Period size: 52 Copynumber: 2.3 Consensus size: 51
49846 AGTTGCTTGT
*
49856 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA-TTGCCTGC
*
49908 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTGC
49959 ATGTATCGATACA
1 ATGTATCGATACA
49972 AAGATCAGTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 21 0.34
52 41 0.66
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTGCCTGC
Found at i:49984 original size:51 final size:52
Alignment explanation
Indices: 49856--49991 Score: 188
Period size: 52 Copynumber: 2.6 Consensus size: 52
49846 AGTTGCTTGT
*
49856 ATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
*** *
49908 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-TTGCCTGC
1 ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
49959 ATGTATCGATACA-AAGATCAGTGTATCGATACA
1 ATGTATCGATACATAAGAT-AGTGTATCGATACA
49992 ATGTATCGAT
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
50 2 0.03
51 36 0.47
52 38 0.50
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:49998 original size:13 final size:13
Alignment explanation
Indices: 49980--50004 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49970 CAAAGATCAG
49980 TGTATCGATACAA
1 TGTATCGATACAA
49993 TGTATCGATACA
1 TGTATCGATACA
50005 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:50082 original size:33 final size:33
Alignment explanation
Indices: 50045--50111 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
50035 AGTAGCTTAA
50045 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* * ***
50078 ATTGTATCGATGCAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
50111 A
1 A
50112 CATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:51152 original size:49 final size:49
Alignment explanation
Indices: 50992--51220 Score: 308
Period size: 49 Copynumber: 4.7 Consensus size: 49
50982 AAAAGGATGT
* * *
50992 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGC
*
51044 CAATATGCTGATTCAAGGCCAGCTTTATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
51087 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
51136 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
51185 CAATATGGTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
51221 GAAGGGTTGC
Statistics
Matches: 159, Mismatches: 12, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
43 40 0.25
48 1 0.01
49 87 0.55
52 31 0.19
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
Found at i:51247 original size:30 final size:30
Alignment explanation
Indices: 51213--51301 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
51203 CCAGCTATAT
*
51213 TGGGCTTAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
*
51243 TGGGCTTTGGAAAAGGG-TGCCACTGA-TT-TG
1 TGGGC-TT--AGAAGGGTTGCCACTGACTTGTG
*
51273 TGGGCTTTGAA-GGTTGCCACTGACTTGTG
1 TGGGCTTAGAAGGGTTGCCACTGACTTGTG
51302 GGCTTTCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 2 0.04
27 11 0.22
28 2 0.04
29 4 0.08
30 12 0.24
31 4 0.08
32 8 0.16
33 6 0.12
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.30
Consensus pattern (30 bp):
TGGGCTTAGAAGGGTTGCCACTGACTTGTG
Found at i:51328 original size:30 final size:29
Alignment explanation
Indices: 51241--51691 Score: 353
Period size: 30 Copynumber: 15.3 Consensus size: 29
51231 CACCGACTTG
* * *
51241 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
* *
51271 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* *
51298 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
*
51328 TGTGGGCTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * * *
51357 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* * *
51387 TGTGGGCTTT-TAAAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
51415 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* * *
51445 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGC-TTTGAAAAAGATGCCACTGACT
* *
51475 TGTGGG--TTG-AAAAGAGTGCTA-TAGAGT
1 TGTGGGCTTTGAAAAAGA-TGCCACT-GACT
* * * * *
51502 TATGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT-----TGAAAAAGA-TGCCACTGACT
* * *
51537 TGTGGACTTTGGAAAAGATGCCACCGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* * * *
51566 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTT-TGAAAAAGATGCCACTGACT
* *
51596 TGTGGGCTTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
* *
51623 TGTGGGCTTTCGAAAAAAATGCCATTGACT
1 TGTGGGCTTT-GAAAAAGATGCCACTGACT
*
51653 TGTGGGCTTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTGAAAAAGATGCCACTGACT
*
51682 TGTGGACTTT
1 TGTGGGCTTT
51692 TGAAGGGTGA
Statistics
Matches: 342, Mismatches: 58, Indels: 43
0.77 0.13 0.10
Matches are distributed among these distances:
26 5 0.01
27 61 0.18
28 23 0.07
29 77 0.23
30 154 0.45
34 1 0.00
35 21 0.06
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAAGATGCCACTGACT
Found at i:51448 original size:88 final size:88
Alignment explanation
Indices: 51225--51480 Score: 331
Period size: 88 Copynumber: 2.9 Consensus size: 88
51215 GGCTTAGAAG
* *** * *
51225 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACCGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
51288 GCCACTGACTTGTGGGCTTTCGAAAA
64 GCCACTAACTTGTGGGCTTTC-AAAA
***
51314 AAATGCCACCGACTTGTGGGC-TTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
*
51378 CCACTAACTTGTGGGCTTT-TAAA
65 CCACTAACTTGTGGGCTTTCAAAA
*
51401 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTG
1 GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
51466 CCACTAACTTGTGGG
65 CCACTAACTTGTGGG
51481 TTGAAAAGAG
Statistics
Matches: 147, Mismatches: 15, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
86 24 0.16
87 31 0.21
88 57 0.39
89 35 0.24
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.30
Consensus pattern (88 bp):
GGTTGCCACCGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTCAAAA
Found at i:51602 original size:209 final size:206
Alignment explanation
Indices: 51309--51686 Score: 549
Period size: 209 Copynumber: 1.8 Consensus size: 206
51299 GTGGGCTTTC
* * * ** *
51309 GAAAAAAATGCCACCGACTTGTGGGCTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAG
1 GAAAAAAATGCCACCGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAG
* *
51374 GGTGCCACTAACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCA
66 GGTGCCACTAACTTGTGGGC-TTTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCA
***
51439 CTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGTTGAAAAGAGTGCTATAGAGTTA
130 CTGACTTGTGGGC-TTTGAAAAAAATGCCACTAACTTGTGGGTTGAAAAGAGTGCTATAGAGTTA
51504 TGAGCTTACAAAA
194 TGAGCTTACAAAA
* * * *
51517 GAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAA
1 GAAAAA-AATGCCACCGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAA
* * *
51582 GGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCA
65 GGGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCA
* *
51647 TTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
130 CTGACTTGTGGGCTTTGAAAAAAATGCCACTAACTTGTGG
51687 ACTTTTGAAG
Statistics
Matches: 149, Mismatches: 20, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
207 23 0.15
208 59 0.40
209 67 0.45
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (206 bp):
GAAAAAAATGCCACCGACTTGTGGACTTTGAAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAG
GGTGCCACTAACTTGTGGGCTTTAAAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCAC
TGACTTGTGGGCTTTGAAAAAAATGCCACTAACTTGTGGGTTGAAAAGAGTGCTATAGAGTTATG
AGCTTACAAAA
Found at i:51625 original size:57 final size:57
Alignment explanation
Indices: 51222--51691 Score: 324
Period size: 59 Copynumber: 7.9 Consensus size: 57
51212 TTGGGCTTAG
* * *
51222 AAGGGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGCTTTG--
1 AAGGG-TGCCACTGAC-T-TGTGGGCTTT-G-AAAGGATGCCACTGACTTGTGGGCTTTGAA
* ** *
51282 AAGGTTGCCACTGACTTGTGGGCTTTCGAAAAAAATGCCACCGACTTGTGGGCTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTT-G-AAAGGATGCCACTGACTTGTGGGCTTTGAA
*** * * *
51341 AAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTT-TA
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA-AGGATGCCACTGACTTGTGGGCTTTGAA
* **
51399 AAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGC-TTTG-AAAGGATGCCACTGACTTGTGGGC-TTTGAA
* * * * * * *
51459 AAGGGTGCCACTAACTTGTGGG--TTGAAAAGAGTGCTA-TAGAGTTATGAGCTTACAAAAGAAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCACT-GACTTGTGGGCTT-----TG-AA
* * * * * * *
51521 AAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAA
1 AAGGGTGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCTT-TGAA
* *
51580 AAGGGTGCCACTGATTTGTGGGCTTTG-AAGGTTGCCACTGACTTGTGGGCTTTCGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAA
*** * ** *
51637 AAAAATGCCATTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGACTTT
1 AAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTT
51692 TGAAGGGTGA
Statistics
Matches: 326, Mismatches: 62, Indels: 45
0.75 0.14 0.10
Matches are distributed among these distances:
56 8 0.02
57 97 0.30
58 48 0.15
59 101 0.31
60 29 0.09
61 1 0.00
62 19 0.06
64 16 0.05
65 7 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (57 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAA
Found at i:53120 original size:1 final size:1
Alignment explanation
Indices: 53116--53238 Score: 102
Period size: 1 Copynumber: 123.0 Consensus size: 1
53106 CCGGACCCCC
* * * * * * * *
53116 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTTGTTTTTTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * ** **
53181 TTTTTTGTTTTTGTTTCTTTTTTTTTTTGTTTTTTTCATTTTTTTTCGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53239 AGAGGACGCC
Statistics
Matches: 92, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:53146 original size:21 final size:21
Alignment explanation
Indices: 53116--53214 Score: 119
Period size: 21 Copynumber: 4.6 Consensus size: 21
53106 CCGGACCCCC
53116 TTTTTTGTTTTTGTTTGTTTT
1 TTTTTTGTTTTTGTTTGTTTT
*
53137 TTTATTGTTTTTGTTT-TTTT
1 TTTTTTGTTTTTGTTTGTTTT
* *
53157 TTTTGTTTTTTTTTTTTGTTTTTT
1 TTTT-TTGTTTTTGTTTG--TTTT
*
53181 TTTTTTGTTTTTGTTTCTTTTT
1 TTTTTTGTTTTTGTTT-GTTTT
53203 TTTTTTGTTTTT
1 TTTTTTGTTTTT
53215 TTCATTTTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
20 7 0.11
21 25 0.38
22 16 0.24
23 10 0.15
24 8 0.12
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (21 bp):
TTTTTTGTTTTTGTTTGTTTT
Found at i:53189 original size:44 final size:44
Alignment explanation
Indices: 53116--53226 Score: 152
Period size: 43 Copynumber: 2.5 Consensus size: 44
53106 CCGGACCCCC
* *
53116 TTTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTGTTT-TTTTTTTATTGTTTTTGTTTCTTTTTTT
53161 GTTTTTTTTTTTTGTTTTTTTTTT-TTGTTTTTGTTTCTTTTTTT
1 -TTTTTTTTTTTTGTTTTTTTTTTATTGTTTTTGTTTCTTTTTTT
* **
53205 TTTTGTTTTTTTCATTTTTTTT
1 TTTTTTTTTTTTGTTTTTTTTT
53227 CGTTTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
43 19 0.32
44 19 0.32
45 7 0.12
46 15 0.25
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (44 bp):
TTTTTTTTTTTTGTTTTTTTTTTATTGTTTTTGTTTCTTTTTTT
Found at i:53222 original size:21 final size:19
Alignment explanation
Indices: 53116--53238 Score: 131
Period size: 19 Copynumber: 6.2 Consensus size: 19
53106 CCGGACCCCC
*
53116 TTTTTTGTTTTTGTTTGTTT
1 TTTTTTTTTTTTGTTT-TTT
*
53136 TTTTATTGTTTTTGTTTTTT
1 TTTT-TTTTTTTTGTTTTTT
*
53156 TTTTTGTTTTTTT-TTTTTG
1 TTTTT-TTTTTTTGTTTTTT
53175 TTTTTTTTTTTTGTTTTTGTT
1 TTTTTTTTTTTTG-TTTT-TT
53196 TCTTTTTTTTTTTGTTTTTT
1 T-TTTTTTTTTTTGTTTTTT
** *
53216 TCATTTTTTTTCGTTTTTT
1 TTTTTTTTTTTTGTTTTTT
53235 TTTT
1 TTTT
53239 AGAGGACGCC
Statistics
Matches: 89, Mismatches: 8, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
18 7 0.08
19 28 0.31
20 24 0.27
21 18 0.20
22 12 0.13
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (19 bp):
TTTTTTTTTTTTGTTTTTT
Found at i:53238 original size:12 final size:12
Alignment explanation
Indices: 53116--53216 Score: 116
Period size: 12 Copynumber: 8.2 Consensus size: 12
53106 CCGGACCCCC
53116 TTTTTTGTTTTT
1 TTTTTTGTTTTT
53128 GTTTGTTT-TTTTAT
1 -TTT-TTTGTTTT-T
53142 TGTTTTTGTTTTT
1 T-TTTTTGTTTTT
53155 TTTTTTGTTTTTT
1 TTTTTTG-TTTTT
53168 TTTTTTGTTTTT
1 TTTTTTGTTTTT
*
53180 TTTTTT-TGTTT
1 TTTTTTGTTTTT
* *
53191 TTGTTTCTTTTT
1 TTTTTTGTTTTT
53203 TTTTTTGTTTTT
1 TTTTTTGTTTTT
53215 TT
1 TT
53217 CATTTTTTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
11 9 0.12
12 33 0.43
13 25 0.32
14 10 0.13
ACGTcount: A:0.01, C:0.01, G:0.10, T:0.88
Consensus pattern (12 bp):
TTTTTTGTTTTT
Done.