Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, whole genome shotgun sequence
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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 6 of 195
Found at i:1079857 original size:1 final size:1
Alignment explanation
Indices: 1079851--1079915 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
1079841 AAAGTCAAAT
*** *** **
1079851 AAAAAAAAAAATTCAAAAAAAAAAAAAAATTCAAAAAAAAAATCAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1079916 CAAACCTGGA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.88, C:0.05, G:0.00, T:0.08
Consensus pattern (1 bp):
A
Found at i:1079870 original size:13 final size:12
Alignment explanation
Indices: 1079870--1079919 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
1079860 AATTCAAAAA
1079870 AAAAAAAAAATTC
1 AAAAAAAAAA-TC
1079883 AAAAAAAAAATC
1 AAAAAAAAAATC
1079895 AAAAAAAAAA--
1 AAAAAAAAAATC
*
1079905 AAAAAAAAAAAC
1 AAAAAAAAAATC
1079917 AAA
1 AAA
1079920 CCTGGAGCGG
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.29
12 15 0.43
13 10 0.29
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:1079910 original size:31 final size:31
Alignment explanation
Indices: 1079852--1079909 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
1079842 AAGTCAAATA
1079852 AAAAAAAAAATTCAAAAAAAAAAAAAAATTC
1 AAAAAAAAAATTCAAAAAAAAAAAAAAATTC
1079883 AAAAAAAAAA-TCAAAAAAAAAAAAAAA
1 AAAAAAAAAATTCAAAAAAAAAAAAAAA
1079910 AAAAAACAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.09
Consensus pattern (31 bp):
AAAAAAAAAATTCAAAAAAAAAAAAAAATTC
Found at i:1080462 original size:14 final size:14
Alignment explanation
Indices: 1080424--1080461 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1080414 AAATTTCCAG
1080424 AAAAAATTTTTCGC
1 AAAAAATTTTTCGC
* *
1080438 AAAAAAATTTTC-T
1 AAAAAATTTTTCGC
1080451 AAAAAATTTTT
1 AAAAAATTTTT
1080462 TTCAGATCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (14 bp):
AAAAAATTTTTCGC
Found at i:1080908 original size:3 final size:3
Alignment explanation
Indices: 1080900--1080928 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1080890 ATCTTACAAA
1080900 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1080929 ATATATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1081044 original size:15 final size:16
Alignment explanation
Indices: 1081021--1081055 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1081011 ATAAAAATAC
*
1081021 AAAAGAAAA-GAAAAA
1 AAAAAAAAAGGAAAAA
1081036 AAAAAAAAAGGAAAAA
1 AAAAAAAAAGGAAAAA
1081052 AAAA
1 AAAA
1081056 TAATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAGGAAAAA
Found at i:1081116 original size:20 final size:20
Alignment explanation
Indices: 1081098--1081176 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
1081088 CCATTTGGGC
* *
1081098 CAGGCCCAAATGATCTGGGT
1 CAGGCCCAATTGATCCGGGT
1081118 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
1081138 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
1081158 CAGGCCCAATTGATCCGGG
1 CAGGCCCAATTGATCCGGG
1081177 CCCAGACCTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.22, C:0.29, G:0.30, T:0.19
Consensus pattern (20 bp):
CAGGCCCAATTGATCCGGGT
Found at i:1081289 original size:7 final size:7
Alignment explanation
Indices: 1081279--1081368 Score: 71
Period size: 7 Copynumber: 12.7 Consensus size: 7
1081269 CAACTCAACA
1081279 TTTTTAT
1 TTTTTAT
*
1081286 TTTTGAT
1 TTTTTAT
1081293 TTTTT-T
1 TTTTTAT
*
1081299 TTTTTGT
1 TTTTTAT
1081306 TTTTATATT
1 TTTT-TA-T
1081315 TTTTTAT
1 TTTTTAT
1081322 TTTTT-T
1 TTTTTAT
1081328 TTATTT-T
1 TT-TTTAT
1081335 TTTTTGAT
1 TTTTT-AT
1081343 TTTTT-T
1 TTTTTAT
*
1081349 GTTTTTGT
1 -TTTTTAT
*
1081357 TTTTTGT
1 TTTTTAT
1081364 TTTTT
1 TTTTT
1081369 TGTTTTTTTG
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
6 13 0.18
7 44 0.61
8 10 0.14
9 5 0.07
ACGTcount: A:0.08, C:0.00, G:0.07, T:0.86
Consensus pattern (7 bp):
TTTTTAT
Found at i:1081296 original size:1 final size:1
Alignment explanation
Indices: 1081292--1081396 Score: 93
Period size: 1 Copynumber: 105.0 Consensus size: 1
1081282 TTATTTTTGA
* * * * * ** * *
1081292 TTTTTTTTTTTTGTTTTTATATTTTTTTATTTTTTTTTATTTTTTTTTGATTTTTTTGTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
1081357 TTTTTGTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1081397 GGCCGAAGCT
Statistics
Matches: 79, Mismatches: 25, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.88
Consensus pattern (1 bp):
T
Found at i:1081323 original size:29 final size:27
Alignment explanation
Indices: 1081279--1081396 Score: 130
Period size: 29 Copynumber: 4.2 Consensus size: 27
1081269 CAACTCAACA
*
1081279 TTTTTA-TTTTTGATTTTTTTTTTTTGT
1 TTTTTATTTTTTTATTTTTTTTTTTT-T
1081306 TTTTATATTTTTTTATTTTTTTTTATTTT
1 TTTT-TATTTTTTTATTTTTTTTT-TTTT
*
1081335 TTTTTGATTTTTTTGTTTTTGTTTTTTGTT
1 TTTTT-ATTTTTTTATTTTT-TTTTTT-TT
* * *
1081365 TTTTTGTTTTTTTGTTTTTTTGTTTTT
1 TTTTTATTTTTTTATTTTTTTTTTTTT
1081392 TTTTT
1 TTTTT
1081397 GGCCGAAGCT
Statistics
Matches: 81, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
27 11 0.14
28 8 0.10
29 48 0.59
30 14 0.17
ACGTcount: A:0.06, C:0.00, G:0.08, T:0.86
Consensus pattern (27 bp):
TTTTTATTTTTTTATTTTTTTTTTTTT
Found at i:1081449 original size:41 final size:40
Alignment explanation
Indices: 1081404--1082056 Score: 889
Period size: 41 Copynumber: 16.0 Consensus size: 40
1081394 TTTGGCCGAA
*
1081404 GCTCCTCTAAACAGAGACTCAACG-ACTTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAG--GCAACGAAC-TTTGAAAAGTAAATT
* *
1081445 GCTCCTCTAAACAGAGGCAACGGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
*
1081485 GCTCCTCTAAACAGAGGCAAC-ACGACTTTGGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACGA--ACTTT-GAAAAGTAAATT
*
1081527 GCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAAC-GAACTTTGAAAAGTAAATT
1081568 GCTCCTCTAAACAGAGGCACCACG-ACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGAAC-TTTGAAAAGTAAATT
*
1081610 GCTCCTCTAAACAGAGGCAACGAAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAACG-AACTTTGAAAAGTAAATT
1081651 GCTCCTCTAAACAGAGGCACCACG-ACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGAAC-TTTGAAAAGTAAATT
*
1081693 GCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAAC-GAACTTTGAAAAGTAAATT
1081734 GCTCCTCTAAACAGAGGCACCACG-ACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGAAC-TTTGAAAAGTAAATT
*
1081776 GCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAAC-GAACTTTGAAAAGTAAATT
1081817 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
*
1081857 GCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAAC-GAACTTTGAAAAGTAAATT
1081898 GCTCCTCTAAACAGAGGCACCACG-ACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGAAC-TTTGAAAAGTAAATT
*
1081940 GCTCCTCTAAACAGAGGCAACGGAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCAAC-GAACTTTGAAAAGTAAATT
1081981 GCTCCTCT-AACAGAGGCAACGAACTTTGAAAAGT--ATT
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
*
1082018 GCTCCTCT-AACAGAGGCACCACG-ACTTTGGAAAGTAAAT
1 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAAT
1082057 ACTCCTAGAC
Statistics
Matches: 564, Mismatches: 16, Indels: 65
0.87 0.02 0.10
Matches are distributed among these distances:
37 21 0.04
38 11 0.02
39 25 0.04
40 95 0.17
41 223 0.40
42 179 0.32
43 9 0.02
44 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATT
Found at i:1081585 original size:83 final size:83
Alignment explanation
Indices: 1081404--1082035 Score: 1081
Period size: 83 Copynumber: 7.7 Consensus size: 83
1081394 TTTGGCCGAA
* * *
1081404 GCTCCTCTAAACAGAGACTCAACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
* *
1081468 -ACTTTGGAAAGTAAATT
66 AACTTTGAAAAATAAATT
* * *
1081485 GCTCCTCTAAACAGAGGCAACACGACTTTGGAAAAATAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1081550 AACTTTGAAAAATAAATT
66 AACTTTGAAAAATAAATT
*
1081568 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1081633 AACTTTGAAAAATAAATT
66 AACTTTGAAAAATAAATT
1081651 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1081716 AACTTTGAAAAATAAATT
66 AACTTTGAAAAATAAATT
1081734 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1081799 AACTTTGAAAAATAAATT
66 AACTTTGAAAAATAAATT
1081817 GCTCCTCTAAACAGAGGCA--ACGAAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
1081879 GAACTTTGAAAAATAAATT
65 GAACTTTGAAAAATAAATT
1081898 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
1081963 AACTTTGAAAAATAAATT
66 AACTTTGAAAAATAAATT
1081981 GCTCCTCT-AACAGAGGCA--ACGAAC-TTTGAAAAGT--ATTGCTCCTCT-AACAGAGGCA
1 GCTCCTCTAAACAGAGGCACCACG-ACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA
1082036 CCACGACTTT
Statistics
Matches: 531, Mismatches: 13, Indels: 18
0.94 0.02 0.03
Matches are distributed among these distances:
77 10 0.02
78 11 0.02
80 13 0.02
81 106 0.20
82 46 0.09
83 345 0.65
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGG
AACTTTGAAAAATAAATT
Found at i:1083090 original size:18 final size:18
Alignment explanation
Indices: 1083075--1083174 Score: 62
Period size: 18 Copynumber: 5.4 Consensus size: 18
1083065 TCACTTTTTC
*
1083075 TTTTTTTCCATTTTTTCCA
1 TTTTTTT-CTTTTTTTCCA
1083094 TTTTTTT-TTCATTTTT-CA
1 TTTTTTTCTT--TTTTTCCA
* *
1083112 TCATTTTTCATTTTTTCCA
1 T-TTTTTTCTTTTTTTCCA
**
1083131 -TTTTTTCATTTTTTTTTA
1 TTTTTTTC-TTTTTTTCCA
* **
1083149 TTTTTTTATTTTTTTGTA
1 TTTTTTTCTTTTTTTCCA
1083167 TTTTTTTC
1 TTTTTTTC
1083175 AAGCATAGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
17 7 0.11
18 31 0.48
19 25 0.39
20 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.01, T:0.76
Consensus pattern (18 bp):
TTTTTTTCTTTTTTTCCA
Found at i:1083108 original size:7 final size:8
Alignment explanation
Indices: 1083064--1083144 Score: 65
Period size: 8 Copynumber: 9.2 Consensus size: 8
1083054 TCCTTTTTCA
*
1083064 TTCACTTT
1 TTCATTTT
*
1083072 TTCTTTTT
1 TTCATTTT
1083080 TTCCATTTT
1 TT-CATTTT
1083089 TTCCATTTTTTT
1 TT-CA---TTTT
1083101 TTCA-TTT
1 TTCATTTT
1083108 TTCATCATTT
1 TTCAT--TTT
1083118 TTCATTTT
1 TTCATTTT
1083126 TTCCATTTT
1 TT-CATTTT
1083135 TTCATTTT
1 TTCATTTT
1083143 TT
1 TT
1083145 TTTATTTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
7 7 0.11
8 21 0.34
9 18 0.29
10 8 0.13
11 2 0.03
12 6 0.10
ACGTcount: A:0.11, C:0.17, G:0.00, T:0.72
Consensus pattern (8 bp):
TTCATTTT
Found at i:1083119 original size:11 final size:10
Alignment explanation
Indices: 1083076--1083162 Score: 52
Period size: 9 Copynumber: 9.6 Consensus size: 10
1083066 CACTTTTTCT
1083076 TTTTTTC-CA
1 TTTTTTCTCA
1083085 TTTTTTC-CA
1 TTTTTTCTCA
*
1083094 TTTTTTTTTCA
1 -TTTTTTCTCA
1083105 -TTTTTCATCA
1 TTTTTTC-TCA
1083115 --TTTT-TCA
1 TTTTTTCTCA
1083122 TTTTTTC-CA
1 TTTTTTCTCA
1083131 -TTTTT-TCA
1 TTTTTTCTCA
* *
1083139 TTTTTTTTTA
1 TTTTTTCTCA
1083149 TTTTTT-T-A
1 TTTTTTCTCA
1083157 TTTTTT
1 TTTTTT
1083163 TGTATTTTTT
Statistics
Matches: 66, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
7 3 0.05
8 14 0.21
9 30 0.45
10 17 0.26
11 2 0.03
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTCTCA
Found at i:1083145 original size:9 final size:9
Alignment explanation
Indices: 1083069--1083175 Score: 80
Period size: 10 Copynumber: 11.8 Consensus size: 9
1083059 TTTCATTCAC
1083069 TTTTTC-TT
1 TTTTTCATT
1083077 TTTTTCCATT
1 TTTTT-CATT
*
1083087 TTTTCCATT
1 TTTTTCATT
1083096 TTTTT--TT
1 TTTTTCATT
*
1083103 CATTTTTCATCA
1 --TTTTTCAT-T
1083115 TTTTTCATT
1 TTTTTCATT
*
1083124 TTTTCCA-T
1 TTTTTCATT
1083132 TTTTTCATTT
1 TTTTTCA-TT
*
1083142 TTTTTTATT
1 TTTTTCATT
1083151 TTTTT-ATT
1 TTTTTCATT
*
1083159 TTTTTGTATT
1 TTTTT-CATT
1083169 TTTTTCA
1 TTTTTCA
1083176 AGCATAGTAT
Statistics
Matches: 80, Mismatches: 8, Indels: 21
0.73 0.07 0.19
Matches are distributed among these distances:
7 2 0.03
8 20 0.25
9 28 0.35
10 29 0.36
11 1 0.01
ACGTcount: A:0.11, C:0.12, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTTTCATT
Found at i:1083155 original size:46 final size:48
Alignment explanation
Indices: 1083057--1083153 Score: 157
Period size: 46 Copynumber: 2.1 Consensus size: 48
1083047 TGAGTCCTCC
*
1083057 TTTTTCATTCACTTTTTCTTTTTTTCCATTTTTTCCATTTTTTTTTCA
1 TTTTTCATTCACTTTTTCATTTTTTCCATTTTTTCCATTTTTTTTTCA
1083105 TTTTTCA-TCA-TTTTTCATTTTTTCCATTTTTT-CATTTTTTTTT-A
1 TTTTTCATTCACTTTTTCATTTTTTCCATTTTTTCCATTTTTTTTTCA
1083149 TTTTT
1 TTTTT
1083154 TTATTTTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
44 6 0.12
45 11 0.23
46 21 0.44
47 3 0.06
48 7 0.15
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.73
Consensus pattern (48 bp):
TTTTTCATTCACTTTTTCATTTTTTCCATTTTTTCCATTTTTTTTTCA
Found at i:1088085 original size:15 final size:14
Alignment explanation
Indices: 1088061--1088090 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1088051 TCTTTCTCCT
1088061 TCTTTAGCCTTCTC
1 TCTTTAGCCTTCTC
1088075 TCTTCTAGCCTTCTC
1 TCTT-TAGCCTTCTC
1088090 T
1 T
1088091 AGCATTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.07, C:0.37, G:0.07, T:0.50
Consensus pattern (14 bp):
TCTTTAGCCTTCTC
Found at i:1093782 original size:156 final size:156
Alignment explanation
Indices: 1093376--1094282 Score: 1565
Period size: 156 Copynumber: 5.8 Consensus size: 156
1093366 TAGTTGTTGA
1093376 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
*
1093441 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAGAAAAATCA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAATCA
*
1093506 AGATCAACCAATTAATTAA-TATCGA
131 AGATCAACCAATTAATTAATTATCGG
* * *
1093531 AAATTA-TCTCAATTGACTCTAATACTTTTAGCAGAAACTTGAGAAAATTTCCTCACCTCAGGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
1093595 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAATCA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAATCA
1093660 AGATCAACCAATTAATTAATTATCGG
131 AGATCAACCAATTAATTAATTATCGG
1093686 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
*
1093751 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAGAAAAATCA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAATCA
1093816 AGATCAACCAATTAATTAATTATCGG
131 AGATCAACCAATTAATTAATTATCGG
*
1093842 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCTCTCACCTCAAGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
*
1093907 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTATTTAAAGAAAAATCA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAATCA
*
1093972 AGATCAACC----AATTAATTATCGA
131 AGATCAACCAATTAATTAATTATCGG
*
1093994 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
1094059 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAAAAA
66 TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAG-----AAA
* * * *
1094124 AATCAAAATCAGCCAAGTAATTAATTATCAG
126 AATCAAGATCAACCAATTAATTAATTATCGG
*
1094155 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAGGAG
1 AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
* *
1094220 TATGCAAGAAAAACTACTGTTTTTACTTGTAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
66 TATGCAAGAAAAACTACTG-TTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAA
1094283 AAAAAAAAAA
Statistics
Matches: 720, Mismatches: 20, Indels: 22
0.94 0.03 0.03
Matches are distributed among these distances:
152 131 0.18
154 138 0.19
155 17 0.02
156 283 0.39
157 20 0.03
161 95 0.13
162 36 0.05
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (156 bp):
AAATTATTCTCAATTGACTCTAATACTTTTAGCAGAAAATTGAGAAAATTCCCTCACCTCAAGAG
TATGCAAGAAAAACTACTGTTTCACTTGCAGAGGCTCCGTCGTCGGATTAATTAAAGAAAAATCA
AGATCAACCAATTAATTAATTATCGG
Found at i:1094335 original size:13 final size:12
Alignment explanation
Indices: 1094334--1094368 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
1094324 AAATTCAAAA
1094334 AAAAAAAAAATTC
1 AAAAAAAAAA-TC
1094347 AAAAAAAAAATC
1 AAAAAAAAAATC
1094359 AAAAAAAAAA
1 AAAAAAAAAA
1094369 AAAAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.86, C:0.06, G:0.00, T:0.09
Consensus pattern (12 bp):
AAAAAAAAAATC
Found at i:1094367 original size:17 final size:17
Alignment explanation
Indices: 1094278--1094375 Score: 83
Period size: 17 Copynumber: 5.7 Consensus size: 17
1094268 TTAATTAAAG
1094278 AAAAAAAAAAAAAAATC
1 AAAAAAAAAAAAAAATC
** ** *
1094295 AAGATCAAAATCAAAGTC
1 AA-AAAAAAAAAAAAATC
* *
1094313 AAATAAAAAAAAAATTC
1 AAAAAAAAAAAAAAATC
*
1094330 AAAAAAAAAAAAAATTC
1 AAAAAAAAAAAAAAATC
1094347 AAAAAAAAAATCAAAAA--
1 AAAAAAAAAA--AAAAATC
1094364 AAAAAAAAAAAA
1 AAAAAAAAAAAA
1094376 CAAACCTGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
15 2 0.03
17 49 0.73
18 12 0.18
19 4 0.06
ACGTcount: A:0.81, C:0.07, G:0.02, T:0.10
Consensus pattern (17 bp):
AAAAAAAAAAAAAAATC
Found at i:1094369 original size:13 final size:14
Alignment explanation
Indices: 1094317--1094369 Score: 65
Period size: 13 Copynumber: 3.7 Consensus size: 14
1094307 AAAGTCAAAT
1094317 AAAAAAAAAATTCAAAA
1 AAAAAAAAAATTC---A
1094334 AAAAAAAAAATTC-
1 AAAAAAAAAATTCA
1094347 AAAAAAAAAA-TCA
1 AAAAAAAAAATTCA
1094360 AAAAAAAAAA
1 AAAAAAAAAA
1094370 AAAAAACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.06
13 20 0.57
17 13 0.37
ACGTcount: A:0.85, C:0.06, G:0.00, T:0.09
Consensus pattern (14 bp):
AAAAAAAAAATTCA
Found at i:1094373 original size:30 final size:30
Alignment explanation
Indices: 1094317--1094372 Score: 105
Period size: 29 Copynumber: 1.9 Consensus size: 30
1094307 AAAGTCAAAT
1094317 AAAAAAAAAATTCAAAAAAAAAAAAAATTC
1 AAAAAAAAAATTCAAAAAAAAAAAAAATTC
1094347 AAAAAAAAAA-TCAAAAAAAAAAAAAA
1 AAAAAAAAAATTCAAAAAAAAAAAAAA
1094373 AAACAAACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.86, C:0.05, G:0.00, T:0.09
Consensus pattern (30 bp):
AAAAAAAAAATTCAAAAAAAAAAAAAATTC
Found at i:1094732 original size:19 final size:19
Alignment explanation
Indices: 1094690--1094736 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
1094680 AGAACACCGG
*
1094690 TGCCGGATTCTGGAAATGT
1 TGCCGGAATCTGGAAATGT
* * *
1094709 CGCCGGAATCTGGAATTTT
1 TGCCGGAATCTGGAAATGT
1094728 TGCCGGAAT
1 TGCCGGAAT
1094737 ATGGCCGGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (19 bp):
TGCCGGAATCTGGAAATGT
Found at i:1095368 original size:3 final size:3
Alignment explanation
Indices: 1095360--1095388 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1095350 ATCTTACAAA
1095360 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1095389 ATATATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1095505 original size:16 final size:17
Alignment explanation
Indices: 1095481--1095516 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1095471 ATAAAAATAC
*
1095481 AAAAGAAAA-GAAAAAA
1 AAAAAAAAAGGAAAAAA
1095497 AAAAAAAAAGGAAAAAA
1 AAAAAAAAAGGAAAAAA
1095514 AAA
1 AAA
1095517 TAATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGGAAAAAA
Found at i:1095577 original size:20 final size:20
Alignment explanation
Indices: 1095559--1095637 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
1095549 CCATTTGGGC
* *
1095559 CAGGCCCAAATGATCTGGGT
1 CAGGCCCAATTGATCCGGGT
1095579 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
1095599 CAGGCCCAATTGATCCGGGT
1 CAGGCCCAATTGATCCGGGT
1095619 CAGGCCCAATTGATCCGGG
1 CAGGCCCAATTGATCCGGG
1095638 CCCAGACCTG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.22, C:0.29, G:0.30, T:0.19
Consensus pattern (20 bp):
CAGGCCCAATTGATCCGGGT
Found at i:1095710 original size:23 final size:23
Alignment explanation
Indices: 1095680--1095724 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1095670 TATTCCATAT
1095680 GAAAAAAAATG-TTTTTCTTTTTA
1 GAAAAAAAA-GATTTTTCTTTTTA
*
1095703 GAAAAAAAAGATTTTTTTTTTT
1 GAAAAAAAAGATTTTTCTTTTT
1095725 TTTAAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (23 bp):
GAAAAAAAAGATTTTTCTTTTTA
Found at i:1102485 original size:22 final size:22
Alignment explanation
Indices: 1102415--1102499 Score: 66
Period size: 22 Copynumber: 3.9 Consensus size: 22
1102405 TTGAGATTTG
** *
1102415 TAAGACCTCCAGGCATAATCTC
1 TAAGACCTTTAGGCATAATCTT
* * * *
1102437 TAATACTTTTAAGCACAA-CTT
1 TAAGACCTTTAGGCATAATCTT
1102458 TCAAGACCTTTAGGCATAATCTT
1 T-AAGACCTTTAGGCATAATCTT
*
1102481 TAAGA-CTTTCGAGCATAAT
1 TAAGACCTTTAG-GCATAAT
1102500 TTTGATTCGC
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
21 8 0.17
22 36 0.75
23 4 0.08
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (22 bp):
TAAGACCTTTAGGCATAATCTT
Found at i:1102646 original size:131 final size:132
Alignment explanation
Indices: 1102472--1103100 Score: 551
Period size: 131 Copynumber: 4.8 Consensus size: 132
1102462 GACCTTTAGG
*** *
1102472 CATAATCTTTAAGACTTTCGAGCATAATTTTGATTCGCGATGTTATC-CTAATTAATTTTTAATT
1 CATAATCTTTAAGACCACCGAGCATAATTTTGATTCGCGATGTTATCTC-GATTAATTTTTAATT
* * * *
1102536 TTTTGACTTGCGGTGTTATC-CTAATCGATTTTGTAAGACCTTCGAACAAAATTTTTAAAACCTC
65 TTTTGACTTGCGGTGTTATCTC-AATCAATTCTGTAAGACCTCCGAACAAAATTTTTAAGACCTC
1102600 TGGA
129 TGGA
**
1102604 CATAATCTTTAAGACCACCG-GCATAATTTTGATTCGCGATGTTATCTCGATTAATTTTTTGTTT
1 CATAATCTTTAAGACCACCGAGCATAATTTTGATTCGCGATGTTATCTCGATTAATTTTTAATTT
* * * ** * *
1102668 TTTGACTTGCGATATTATCACGGTCAATTCTGTAAGACCTCCGAACATAATTTTTAAGATCT-TC
66 TTTGACTTGCGGTGTTATCTCAATCAATTCTGTAAGACCTCCGAACAAAATTTTTAAGACCTCT-
*
1102732 GGG
130 GGA
* * * *
1102735 CATAATCTTTAATG--CATCCGGGTATAATTTTGATTCGCGATATTATCTCGATCAATTTTTAAT
1 CATAATCTTTAA-GACCA-CCGAGCATAATTTTGATTCGCGATGTTATCTCGATTAATTTTTAAT
* * * * * * * * * *
1102798 TTTTTGACTTGTGGTGTTATCTCGATCGATTTTATAAAACCTCCGGA-TATATTTCTAAGACCTC
64 TTTTTGACTTGCGGTGTTATCTCAATCAATTCTGTAAGACCTCCGAACAAAATTTTTAAGACCT-
*
1102862 CAGGA
128 CTGGA
* *** *
1102867 -ATAATCTTTAAGGCTTTCGAGCATAATTTTGATTCGCGATGTTATC-CTGATCGAA-TTTTAAT
1 CATAATCTTTAAGACCACCGAGCATAATTTTGATTCGCGATGTTATCTC-GAT-TAATTTTTAAT
* * * * **
1102929 TTTCTAACTTGCAGTGTTATCTCAATCAATTCTGTAAGATCTCCGAACATGATTTTTAAGACCTC
64 TTTTTGACTTGCGGTGTTATCTCAATCAATTCTGTAAGACCTCCGAACAAAATTTTTAAGACCTC
1102994 TGGA
129 TGGA
* * * * ** * ** * *
1102998 TATAATCTCTAAAATCTTCAAGCATAATTTTGATTTACGGTGTTATCTCGATCAATTTTTAATTT
1 CATAATCTTTAAGACCACCGAGCATAATTTTGATTCGCGATGTTATCTCGATTAATTTTTAATTT
* * * * * *
1103063 TTTAATTTACGGTATTATC-CTGATCAATTCTATAAGAC
66 TTTGACTTGCGGTGTTATCTC-AATCAATTCTGTAAGAC
1103101 ATTCGGGCAT
Statistics
Matches: 400, Mismatches: 80, Indels: 34
0.78 0.16 0.07
Matches are distributed among these distances:
130 5 0.01
131 207 0.52
132 187 0.47
133 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (132 bp):
CATAATCTTTAAGACCACCGAGCATAATTTTGATTCGCGATGTTATCTCGATTAATTTTTAATTT
TTTGACTTGCGGTGTTATCTCAATCAATTCTGTAAGACCTCCGAACAAAATTTTTAAGACCTCTG
GA
Found at i:1103005 original size:263 final size:263
Alignment explanation
Indices: 1102492--1103097 Score: 629
Period size: 263 Copynumber: 2.3 Consensus size: 263
1102482 AAGACTTTCG
* *
1102492 AGCATAATTTTGATTCGCGATGTTATC-CTAATTAATTTTTAATTTTTTGACTTGCGGTGTTATC
1 AGCATAATTTTGATTCGCGATGTTATCTC-GATCAATTTTTAATTTTTTGACTTGCGGTGTTATC
* * * * *
1102556 CTAATCGATTTTGTAAGACCTTCGAACAAAATTTTTAAAACCTCTGGACATAATCTTTAAGACCA
65 CTAATCGATTTTATAAAACCTCCGAACAAAATTTCTAAAACCTCAGGACATAATCTTTAAGACCA
* ** * *
1102621 CCGGCATAATTTTGATTCGCGATGTTATCTCGATTAATTTTTTGTTTTTTGACTTGCGATATTAT
130 CCGGCATAATTTTGATTCGCGATGTTATCTCGATGAATTTTTAATTTTCTAACTTGCGATATTAT
** * * *
1102686 CACGGTCAATTCTGTAAGACCTCCGAACATAATTTTTAAGATCTTCGGGCATAATCT-T-TAATG
195 CACAATCAATTCTGTAAGACCTCCGAACATAATTTTTAAGACCTTCGGACATAATCTCTAAAAT-
*
1102749 CATCCG
259 C-TCCA
* * * *
1102755 GGTATAATTTTGATTCGCGATATTATCTCGATCAATTTTTAATTTTTTGACTTGTGGTGTTAT-C
1 AGCATAATTTTGATTCGCGATGTTATCTCGATCAATTTTTAATTTTTTGACTTGCGGTGTTATCC
* * * * * * *
1102819 TCGATCGATTTTATAAAACCTCCGGA-TATATTTCTAAGACCTCCAGGA-ATAATCTTTAAGGCT
66 T-AATCGATTTTATAAAACCTCCGAACAAAATTTCTAAAACCT-CAGGACATAATCTTTAAGACC
**
1102882 TTCGAGCATAATTTTGATTCGCGATGTTATC-CTGATCGAA-TTTTAATTTTCTAACTTGC-AGT
129 ACCG-GCATAATTTTGATTCGCGATGTTATCTC-GAT-GAATTTTTAATTTTCTAACTTGCGA-T
* * * * *
1102944 GTTATCTCAATCAATTCTGTAAGATCTCCGAACATGATTTTTAAGACC-TCTGGATATAATCTCT
190 ATTATCACAATCAATTCTGTAAGACCTCCGAACATAATTTTTAAGACCTTC-GGACATAATCTCT
*
1103008 AAAATCTTCA
254 AAAATCTCCA
** * * * * *
1103018 AGCATAATTTTGATTTACGGTGTTATCTCGATCAATTTTTAATTTTTTAATTTACGGTATTATCC
1 AGCATAATTTTGATTCGCGATGTTATCTCGATCAATTTTTAATTTTTTGACTTGCGGTGTTATCC
* * *
1103083 TGATCAATTCTATAA
66 TAATCGATTTTATAA
1103098 GACATTCGGG
Statistics
Matches: 282, Mismatches: 50, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
262 33 0.12
263 239 0.85
264 7 0.02
265 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (263 bp):
AGCATAATTTTGATTCGCGATGTTATCTCGATCAATTTTTAATTTTTTGACTTGCGGTGTTATCC
TAATCGATTTTATAAAACCTCCGAACAAAATTTCTAAAACCTCAGGACATAATCTTTAAGACCAC
CGGCATAATTTTGATTCGCGATGTTATCTCGATGAATTTTTAATTTTCTAACTTGCGATATTATC
ACAATCAATTCTGTAAGACCTCCGAACATAATTTTTAAGACCTTCGGACATAATCTCTAAAATCT
CCA
Found at i:1103334 original size:110 final size:109
Alignment explanation
Indices: 1103007--1103335 Score: 301
Period size: 110 Copynumber: 3.0 Consensus size: 109
1102997 ATATAATCTC
* * * * * * *
1103007 TAAAATCTTCAAGCATAATTTTGATTTACGGTGTT-ATCTCGATCAATTTTTAATTTTTTAATTT
1 TAAAACCTTCAGGCATAATTTTGATTTGCGATGTTGA-CTCAATCGATTTTTAATTTTTTAACTT
* * * * * * * *
1103071 ACGGTATTATCCTGATCAATTCTATAAGACATTCGGGCATAATCTT
65 GCGGTGTTATCCCGATCAATTCTGTAAGAC-CTCCGGCATGATTTT
* * * *
1103117 TAAGACCTTCAGACATAATTTTGATTCGCAGTAT-TATG-CT-AATCGATTTTTAATTTTTTGAC
1 TAAAACCTTCAGGCATAATTTTGATTTGC-G-ATGT-TGACTCAATCGATTTTTAATTTTTTAAC
* * *
1103179 TTGCGGTGTTATCTC-AGTCAATTCTGTAAGATCTCCGGACGTGATTTT
63 TTGCGGTGTTATCCCGA-TCAATTCTGTAAGACCTCCGG-CATGATTTT
* *
1103227 TAAAACCTTCAGGCATAATTTCGATTTGCGATGTTGACTCAATCGATTCTTT-ATTTTTTTACTT
1 TAAAACCTTCAGGCATAATTTTGATTTGCGATGTTGACTCAATCGATT-TTTAATTTTTTAACTT
* *
1103291 GCGGTGTTATCCCGATCGATTCTGTAAGACCTCCAAGCATGATTT
65 GCGGTGTTATCCCGATCAATTCTGTAAGACCTCC-GGCATGATTT
1103336 ATAAGATTTT
Statistics
Matches: 175, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
108 4 0.02
109 9 0.05
110 151 0.86
111 9 0.05
112 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (109 bp):
TAAAACCTTCAGGCATAATTTTGATTTGCGATGTTGACTCAATCGATTTTTAATTTTTTAACTTG
CGGTGTTATCCCGATCAATTCTGTAAGACCTCCGGCATGATTTT
Found at i:1103351 original size:22 final size:21
Alignment explanation
Indices: 1103326--1103380 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
1103316 AAGACCTCCA
* *
1103326 AGCATGATTTATAAGATTTTCG
1 AGCATAATTT-TAAGACTTTCG
1103348 AGCATAATCTTTAAGACTTTCG
1 AGCATAAT-TTTAAGACTTTCG
*
1103370 GGCATAATTTT
1 AGCATAATTTT
1103381 GATTTGCGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.10
22 24 0.83
23 2 0.07
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (21 bp):
AGCATAATTTTAAGACTTTCG
Found at i:1103582 original size:22 final size:22
Alignment explanation
Indices: 1103535--1103600 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
1103525 GTTGATTTTG
*
1103535 TAAGACCTCCGGACATGATTTC
1 TAAGACCTCCGGACATAATTTC
1103557 TAAGACCTCC-GAGCATAATCTT-
1 TAAGACCTCCGGA-CATAAT-TTC
** *
1103579 TAAGATTTCTGGACATAATTTC
1 TAAGACCTCCGGACATAATTTC
1103601 GATTTGCAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
21 4 0.11
22 28 0.78
23 4 0.11
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (22 bp):
TAAGACCTCCGGACATAATTTC
Found at i:1103628 original size:220 final size:219
Alignment explanation
Indices: 1103239--1103670 Score: 523
Period size: 220 Copynumber: 2.0 Consensus size: 219
1103229 AAACCTTCAG
* * * * ** *
1103239 GCATAATTTCGATTTGCGATGTTGACTCAATCGATTCTTTATTTTTTTACTTGCGGTGTTATCCC
1 GCATAATTTCGATTCGCAATGTTGACCCAATCGATTCTTTATTTTTTGACTCACGGTGTTATCCA
** *
1103304 GATCGATTCTGTAAGACCTCCAAGCATGATTTATAAGATTTTCGAGCATAATCTTTAAGACTTTC
66 GATCGATTCTGTAAGACCTCCAAGCATGATTTATAAGACCTCCGAGCATAATCTTTAAGACTTTC
* * * * * * * *
1103369 GGGCATAATTTTGATTTGCGGTTTTGTTTCGATCGATTTTTTATTTTTTGACTTGCGATGTTAT-
131 GGACATAATTTCGATTTGCAGTGTTATCTCGAACGATTTTTTA-TTTTTAACTTGCGATGTTATC
*
1103433 TCCGATCAATTTTGTAAGATCTCCGA
195 T-CGATCAATTTTATAAGATCTCCGA
* * * *
1103459 GCATAATTTTGATTCGCAATGTTGTCCCAATCGATTTTTTATTTTTTGACTCACGGTGTTGTCTC
1 GCATAATTTCGATTCGCAATGTTGACCCAATCGATTCTTTATTTTTTGACTCACGGTGTTATC-C
* * * *
1103524 AG-TTGATTTTGTAAGACCTCC-GGACATGATTTCTAAGACCTCCGAGCATAATCTTTAAGA-TT
65 AGATCGATTCTGTAAGACCTCCAAG-CATGATTTATAAGACCTCCGAGCATAATCTTTAAGACTT
1103586 TCTGGACATAATTTCGATTTGCAGTGTTATC-CTGAACGATTTTTTATTTTTAACTTGCGATGTT
129 TC-GGACATAATTTCGATTTGCAGTGTTATCTC-GAACGATTTTTTATTTTTAACTTGCGATGTT
*
1103650 ATCTCGATCGATTTTATAAGA
192 ATCTCGATCAATTTTATAAGA
1103671 CTTTTGAGCA
Statistics
Matches: 179, Mismatches: 28, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
219 40 0.22
220 137 0.77
221 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (219 bp):
GCATAATTTCGATTCGCAATGTTGACCCAATCGATTCTTTATTTTTTGACTCACGGTGTTATCCA
GATCGATTCTGTAAGACCTCCAAGCATGATTTATAAGACCTCCGAGCATAATCTTTAAGACTTTC
GGACATAATTTCGATTTGCAGTGTTATCTCGAACGATTTTTTATTTTTAACTTGCGATGTTATCT
CGATCAATTTTATAAGATCTCCGA
Found at i:1103795 original size:37 final size:37
Alignment explanation
Indices: 1103717--1103795 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
1103707 TTTGATTCGC
* * * * *
1103717 GGTGTTATCATGATCGATTTTTTATTTCTTGACTTAT
1 GGTGTTATCATGATCGATTCTTTACTTCTTAACTCAG
1103754 GGTGTTATTC-TGATCGATTCTTTACTTCTTAACTCAG
1 GGTGTTA-TCATGATCGATTCTTTACTTCTTAACTCAG
1103791 GGTGT
1 GGTGT
1103796 CATCCCGGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (37 bp):
GGTGTTATCATGATCGATTCTTTACTTCTTAACTCAG
Found at i:1104080 original size:13 final size:13
Alignment explanation
Indices: 1104051--1104091 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1104041 AAAAAACAAC
*
1104051 AAAA-AAGAAACA
1 AAAAGAAGAAAGA
1104063 AAAAG-AGAAAAGA
1 AAAAGAAG-AAAGA
1104076 AAAAGAAGAAAGA
1 AAAAGAAGAAAGA
1104089 AAA
1 AAA
1104092 TCGGGATGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 6 0.24
13 17 0.68
14 2 0.08
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAAAGA
Found at i:1104941 original size:10 final size:10
Alignment explanation
Indices: 1104926--1104954 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1104916 CATCCAGTGA
1104926 ACTGGTTTGG
1 ACTGGTTTGG
1104936 ACTGGTTTGG
1 ACTGGTTTGG
1104946 ACTGGTTTG
1 ACTGGTTTG
1104955 AATCGCCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.10, G:0.38, T:0.41
Consensus pattern (10 bp):
ACTGGTTTGG
Found at i:1105244 original size:10 final size:9
Alignment explanation
Indices: 1105227--1105251 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1105217 AATATTTTAA
1105227 TATTTTTTT
1 TATTTTTTT
1105236 TATTTTTTT
1 TATTTTTTT
1105245 TATTTTT
1 TATTTTT
1105252 CCTACCTAGA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TATTTTTTT
Found at i:1105335 original size:14 final size:15
Alignment explanation
Indices: 1105316--1105345 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1105306 GATGTTAGAG
1105316 AATTATT-ATAAAAA
1 AATTATTAATAAAAA
1105330 AATTATTAATAAAAA
1 AATTATTAATAAAAA
1105345 A
1 A
1105346 GGGTATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTATTAATAAAAA
Found at i:1105356 original size:3 final size:3
Alignment explanation
Indices: 1105350--1105389 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1105340 AAAAAAGGGT
1105350 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1105390 AAATTTTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1105549 original size:15 final size:14
Alignment explanation
Indices: 1105515--1105636 Score: 65
Period size: 15 Copynumber: 8.7 Consensus size: 14
1105505 CGTTTTCTTT
1105515 AAACCCTAAAATTC
1 AAACCCTAAAATTC
*
1105529 AAACCCTAAATTTC
1 AAACCCTAAAATTC
*
1105543 AAAACCC-AAAAATC
1 -AAACCCTAAAATTC
*
1105557 AAAACTCC-GAAATT-
1 -AAAC-CCTAAAATTC
* * * *
1105571 AAGCCCCAAACCTCC
1 AAACCCTAAA-ATTC
*
1105586 AAACCTTAAAATT-
1 AAACCCTAAAATTC
* * *
1105599 GAACCCCAAACTTCC
1 AAACCCTAAAATT-C
1105614 AAACCCTAAAATT-
1 AAACCCTAAAATTC
1105627 AAACCCTAAA
1 AAACCCTAAA
1105637 CCCTCTAAAC
Statistics
Matches: 80, Mismatches: 21, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
12 2 0.03
13 24 0.30
14 25 0.31
15 29 0.36
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.18
Consensus pattern (14 bp):
AAACCCTAAAATTC
Found at i:1105597 original size:28 final size:27
Alignment explanation
Indices: 1105566--1105653 Score: 104
Period size: 28 Copynumber: 3.1 Consensus size: 27
1105556 CAAAACTCCG
*
1105566 AAATTAAGCCCCAAACCTCCAAACCTTA
1 AAATTAA-CCCCAAACCTCCAAACCCTA
*
1105594 AAATTGAACCCCAAACTTCCAAACCCTA
1 AAATT-AACCCCAAACCTCCAAACCCTA
* *
1105622 AAATTAAACCCTAAACCCTCTAAACCCTA
1 AAATT-AACCCCAAA-CCTCCAAACCCTA
1105651 AAA
1 AAA
1105654 ATGAAACCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
28 36 0.69
29 16 0.31
ACGTcount: A:0.45, C:0.34, G:0.02, T:0.18
Consensus pattern (27 bp):
AAATTAACCCCAAACCTCCAAACCCTA
Found at i:1105734 original size:30 final size:29
Alignment explanation
Indices: 1105581--1105743 Score: 139
Period size: 30 Copynumber: 5.6 Consensus size: 29
1105571 AAGCCCCAAA
* ** *
1105581 CCTCCAAACCTTAAAATTGAACCCCAAA-
1 CCTCCAAACCCTAAAATCAAACCCTAAAC
* *
1105609 CTTCCAAACCCTAAAATTAAACCCTAAAC
1 CCTCCAAACCCTAAAATCAAACCCTAAAC
* * *
1105638 CCTCTAAACCCTAAAAATGAAACCTTAAAC
1 CCTCCAAACCCT-AAAATCAAACCCTAAAC
*** * *
1105668 CCTATGAACCCTAAAAACGAAACCTTAAAC
1 CCTCCAAACCCTAAAATC-AAACCCTAAAC
*
1105698 CCTCCAAACCCTAAAATCAAATCCCTAAAA
1 CCTCCAAACCCTAAAATCAAA-CCCTAAAC
* *
1105728 CATCCAAACCTTAAAA
1 CCTCCAAACCCTAAAA
1105744 CTAAAACCTC
Statistics
Matches: 111, Mismatches: 20, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
28 24 0.22
29 17 0.15
30 70 0.63
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.18
Consensus pattern (29 bp):
CCTCCAAACCCTAAAATCAAACCCTAAAC
Found at i:1105744 original size:16 final size:16
Alignment explanation
Indices: 1105674--1105744 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 16
1105664 AAACCCTATG
*
1105674 AACCCTAAAA-A-CGA
1 AACCCTAAAACATCCA
* * *
1105688 AACCTTAAACCCTCCA
1 AACCCTAAAACATCCA
1105704 AACCCT-AAA-AT-CA
1 AACCCTAAAACATCCA
1105717 AATCCCTAAAACATCCA
1 AA-CCCTAAAACATCCA
*
1105734 AACCTTAAAAC
1 AACCCTAAAAC
1105745 TAAAACCTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
13 4 0.09
14 13 0.30
15 5 0.12
16 17 0.40
17 4 0.09
ACGTcount: A:0.49, C:0.34, G:0.01, T:0.15
Consensus pattern (16 bp):
AACCCTAAAACATCCA
Found at i:1105764 original size:21 final size:22
Alignment explanation
Indices: 1105722--1105764 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
1105712 AATCAAATCC
**
1105722 CTAAAACATCCAAACCTTAAAA
1 CTAAAACATCCAAACCCCAAAA
*
1105744 CTAAAACCT-CAAACCCCAAAA
1 CTAAAACATCCAAACCCCAAAA
1105765 TTGAAACCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.14
Consensus pattern (22 bp):
CTAAAACATCCAAACCCCAAAA
Found at i:1105800 original size:22 final size:21
Alignment explanation
Indices: 1105759--1105853 Score: 84
Period size: 22 Copynumber: 4.3 Consensus size: 21
1105749 ACCTCAAACC
*
1105759 CCAAAAT-TGAAACCCTAAAAT
1 CCAAAATCTCAAA-CCTAAAAT
*
1105780 CCAAAATCCCAAACCTAAAAAT
1 CCAAAATCTCAAACCT-AAAAT
* *
1105802 CCAAATTTCTAAAACCCCTAAAAT
1 CCAAA-ATCTCAAA--CCTAAAAT
*
1105826 TCAAAATCTCAAACCTTAAAAT
1 CCAAAATCTCAAACC-TAAAAT
1105848 CCAAAA
1 CCAAAA
1105854 CCTTAAAATC
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
21 12 0.20
22 24 0.41
23 11 0.19
24 9 0.15
25 3 0.05
ACGTcount: A:0.52, C:0.27, G:0.01, T:0.20
Consensus pattern (21 bp):
CCAAAATCTCAAACCTAAAAT
Found at i:1105861 original size:46 final size:46
Alignment explanation
Indices: 1105771--1105861 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
1105761 AAAATTGAAA
**
1105771 CCCTAAAATCCAAAATCCCAAACCTAAAAATCCAAATTTCTAAAAC
1 CCCTAAAATCCAAAATCCCAAACCTAAAAATCCAAACCTCTAAAAC
* * *
1105817 CCCTAAAATTCAAAATCTCAAACCTTAAAATCCAAAACCT-TAAAA
1 CCCTAAAATCCAAAATCCCAAACCTAAAAATCC-AAACCTCTAAAA
1105862 TCTAAAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 35 0.90
47 4 0.10
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.21
Consensus pattern (46 bp):
CCCTAAAATCCAAAATCCCAAACCTAAAAATCCAAACCTCTAAAAC
Found at i:1105876 original size:15 final size:15
Alignment explanation
Indices: 1105828--1105868 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
1105818 CCTAAAATTC
*
1105828 AAAATCTCAAACCTT
1 AAAATCTAAAACCTT
*
1105843 AAAATCCAAAACCTT
1 AAAATCTAAAACCTT
1105858 AAAATCTAAAA
1 AAAATCTAAAA
1105869 TTCTAAAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (15 bp):
AAAATCTAAAACCTT
Found at i:1108563 original size:21 final size:22
Alignment explanation
Indices: 1108539--1108580 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1108529 TATAAAATAT
*
1108539 ATATTTTTAA-TTTTATTAAAC
1 ATATTTATAATTTTTATTAAAC
1108560 ATATTTATAATTTTTATTAAA
1 ATATTTATAATTTTTATTAAA
1108581 ATTTTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATTTATAATTTTTATTAAAC
Found at i:1112483 original size:24 final size:23
Alignment explanation
Indices: 1112419--1112494 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 23
1112409 ATTCATATGA
*
1112419 ATAATTTTCTTAAATGATACATAAG
1 ATAATTTT-TTAAAT-ATAAATAAG
*
1112444 --AATTTTTTTAA-A-AAATAAG
1 ATAATTTTTTAAATATAAATAAG
*
1112463 ATAATTTTTTAAATTATAAATTAG
1 ATAATTTTTTAAA-TATAAATAAG
1112487 ATAATTTT
1 ATAATTTT
1112495 AAATTTATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 6 0.14
20 1 0.02
21 10 0.24
22 4 0.10
23 7 0.17
24 14 0.33
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (23 bp):
ATAATTTTTTAAATATAAATAAG
Found at i:1119469 original size:22 final size:23
Alignment explanation
Indices: 1119444--1119493 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
1119434 AATTGAGATC
*
1119444 TTAA-ATATCTATTTTCATCCAA
1 TTAACATATATATTTTCATCCAA
* *
1119466 TTAAACATTTATATTTTCATTCAA
1 TT-AACATATATATTTTCATCCAA
1119490 TTAA
1 TTAA
1119494 GCCATCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 2 0.09
23 4 0.17
24 17 0.74
ACGTcount: A:0.38, C:0.14, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAACATATATATTTTCATCCAA
Found at i:1126116 original size:7 final size:6
Alignment explanation
Indices: 1126052--1126112 Score: 59
Period size: 6 Copynumber: 9.3 Consensus size: 6
1126042 GTGTAGATTG
* *
1126052 AATTTA AATTAATA TAATATTA AATTTA AATTTA AATTTG ATTTTA AATTTA
1 AATTTA AATT--TA -AAT-TTA AATTTA AATTTA AATTTA AATTTA AATTTA
1126104 ACATTTA AA
1 A-ATTTA AA
1126113 ATTTGATTTG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
6 29 0.63
7 9 0.20
8 4 0.09
9 3 0.07
10 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
AATTTA
Found at i:1129648 original size:18 final size:19
Alignment explanation
Indices: 1129613--1129650 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1129603 ATTAAAATAA
1129613 TTTTATATCATTTCATATT
1 TTTTATATCATTTCATATT
1129632 TTTTATA-CAGTTT-ATATT
1 TTTTATATCA-TTTCATATT
1129650 T
1 T
1129651 ATTAATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTTATATCATTTCATATT
Found at i:1149256 original size:2 final size:2
Alignment explanation
Indices: 1149243--1149294 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
1149233 TATTCAAATG
* * *
1149243 TA TA TA TG TA TA TA TA T- TA TA TA TA TA TA CA TA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1149284 TA TA TA TA TA T
1 TA TA TA TA TA T
1149295 TACATATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1155886 original size:72 final size:72
Alignment explanation
Indices: 1155769--1155905 Score: 265
Period size: 72 Copynumber: 1.9 Consensus size: 72
1155759 AAAGTATGAT
*
1155769 TTGAAATTGCAATGAAATATTAACAAATACATAAGTACATAAATTCATATTTCCTGTCAATTTTT
1 TTGAAATTGCAATGAAATATTAACAAATACATAAGTACATAAATTCATATTTCCTGTAAATTTTT
1155834 TATCGAG
66 TATCGAG
1155841 TTGAAATTGCAATGAAATATTAACAAATACATAAGTACATAAATTCATATTTCCTGTAAATTTTT
1 TTGAAATTGCAATGAAATATTAACAAATACATAAGTACATAAATTCATATTTCCTGTAAATTTTT
1155906 ATCAACACAA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 64 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (72 bp):
TTGAAATTGCAATGAAATATTAACAAATACATAAGTACATAAATTCATATTTCCTGTAAATTTTT
TATCGAG
Found at i:1161250 original size:3 final size:3
Alignment explanation
Indices: 1161242--1161285 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1161232 TGGGAAGCAA
1161242 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1161286 AAGCAAAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1161832 original size:16 final size:17
Alignment explanation
Indices: 1161811--1161853 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
1161801 TGCAATGAGG
1161811 AAAAAAAATAG-AAACA
1 AAAAAAAATAGAAAACA
*
1161827 AAAAAAAA-AGCAAAATA
1 AAAAAAAATAG-AAAACA
1161844 AAAAAAAATA
1 AAAAAAAATA
1161854 TAAGGAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 8 0.35
17 12 0.52
18 1 0.04
ACGTcount: A:0.84, C:0.05, G:0.05, T:0.07
Consensus pattern (17 bp):
AAAAAAAATAGAAAACA
Found at i:1163104 original size:16 final size:17
Alignment explanation
Indices: 1163077--1163111 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1163067 TATATCGGTA
1163077 TATATTTATAATTTTTT
1 TATATTTATAATTTTTT
1163094 TATATTT-TAATTTTTT
1 TATATTTATAATTTTTT
1163110 TA
1 TA
1163112 AAAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATTTATAATTTTTT
Found at i:1163447 original size:14 final size:13
Alignment explanation
Indices: 1163428--1163510 Score: 61
Period size: 14 Copynumber: 6.5 Consensus size: 13
1163418 TTAAAATTAC
*
1163428 ATTATAATTAATCA
1 ATTATAATTAA-AA
1163442 ATTATAATTAAAA
1 ATTATAATTAAAA
1163455 ATTAT-ATT--AA
1 ATTATAATTAAAA
1163465 ATT-T-ATTAAAA
1 ATTATAATTAAAA
* *
1163476 TTTTATATATT-TAA
1 -ATTATA-ATTAAAA
1163490 ATTATAATTAAATA
1 ATTATAATTAAA-A
1163504 ATTATAA
1 ATTATAA
1163511 AATTATACTA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
9 4 0.07
10 5 0.09
11 2 0.04
12 8 0.14
13 13 0.23
14 21 0.38
15 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (13 bp):
ATTATAATTAAAA
Found at i:1163516 original size:22 final size:23
Alignment explanation
Indices: 1163488--1163534 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1163478 TTATATATTT
*
1163488 AAATTATAAT-TAAATAATTATA
1 AAATTATAATAAAAATAATTATA
*
1163510 AAATTATACTAAAAATAATTATA
1 AAATTATAATAAAAATAATTATA
1163533 AA
1 AA
1163535 TGAAATGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAATTATAATAAAAATAATTATA
Found at i:1164024 original size:25 final size:25
Alignment explanation
Indices: 1163996--1164106 Score: 75
Period size: 25 Copynumber: 4.4 Consensus size: 25
1163986 ATATAATACG
1163996 AAAATAATATAAAAATATATAATTT
1 AAAATAATATAAAAATATATAATTT
** * *
1164021 AAAATTTTAAAAAAATTATAAATATTT
1 AAAATAATATAAAAA-TATATA-ATTT
*
1164048 AATAA-AA-ATAAAAATATATATTTT
1 AA-AATAATATAAAAATATATAATTT
* **
1164072 AAATATAACATATCAATATA-AATTAT
1 AAA-ATAATATAAAAATATATAATT-T
*
1164098 AACATAATA
1 AAAATAATA
1164107 AATTTAATAT
Statistics
Matches: 65, Mismatches: 14, Indels: 14
0.70 0.15 0.15
Matches are distributed among these distances:
23 1 0.02
24 6 0.09
25 27 0.42
26 23 0.35
27 6 0.09
28 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (25 bp):
AAAATAATATAAAAATATATAATTT
Found at i:1164062 original size:19 final size:19
Alignment explanation
Indices: 1164016--1164064 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1164006 AAAAATATAT
*
1164016 AATTTAAAAT-TTTAAAAA
1 AATTAAAAATATTTAAAAA
*
1164034 AATTATAAATATTTAATAAA
1 AATTAAAAATATTTAA-AAA
1164054 AA-TAAAAATAT
1 AATTAAAAATAT
1164065 ATATTTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 13 0.50
20 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATTAAAAATATTTAAAAA
Found at i:1164920 original size:22 final size:21
Alignment explanation
Indices: 1164877--1164923 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
1164867 TAAATTGTAT
** *
1164877 AAATTGATTAAAATTCATTTA
1 AAATTGATTAAAATAAAATTA
1164898 AAATTGATTGAAAATAAAATTA
1 AAATTGATT-AAAATAAAATTA
1164920 AAAT
1 AAAT
1164924 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (21 bp):
AAATTGATTAAAATAAAATTA
Found at i:1165493 original size:22 final size:22
Alignment explanation
Indices: 1165465--1165516 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1165455 TCTTTTAAAA
*
1165465 TTTTTTTTTCCTTT-TTAGTTC
1 TTTTTTTTTCCTTTCTTAGTAC
* *
1165486 TTTTTTTTTCTTTTCTTTGTAC
1 TTTTTTTTTCCTTTCTTAGTAC
1165508 TTTTTTTTT
1 TTTTTTTTT
1165517 TTTTTAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.04, C:0.12, G:0.04, T:0.81
Consensus pattern (22 bp):
TTTTTTTTTCCTTTCTTAGTAC
Found at i:1165503 original size:25 final size:24
Alignment explanation
Indices: 1165465--1165521 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
1165455 TCTTTTAAAA
* *
1165465 TTTTTTTTTCCTTTTTAGTTCTTT
1 TTTTTTTTTCCTTTGTACTTCTTT
*
1165489 TTTTTTCTTTTCTTTGTACTT-TTT
1 TTTTTT-TTTCCTTTGTACTTCTTT
1165513 TTTTTTTTT
1 TTTTTTTTT
1165522 AATTTTCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.10
24 15 0.52
25 11 0.38
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.82
Consensus pattern (24 bp):
TTTTTTTTTCCTTTGTACTTCTTT
Found at i:1166807 original size:13 final size:13
Alignment explanation
Indices: 1166778--1166810 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1166768 TTGGATAATG
*
1166778 CTTTTACTTTTTT
1 CTTTTAATTTTTT
1166791 -TTTTAATTTTTT
1 CTTTTAATTTTTT
1166803 CTTTTAAT
1 CTTTTAAT
1166811 AGAAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (13 bp):
CTTTTAATTTTTT
Found at i:1175159 original size:29 final size:29
Alignment explanation
Indices: 1175124--1175187 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
1175114 TTAATTAATT
* *
1175124 TAAAAATCAACAAAATTAAAAGTACAGCAA
1 TAAAATTCAACAAAATTAAAA-TACAACAA
* *
1175154 TAAAATTCAATAAAATTAAAATACAACGA
1 TAAAATTCAACAAAATTAAAATACAACAA
1175183 TAAAA
1 TAAAA
1175188 CATTCACCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.64, C:0.11, G:0.05, T:0.20
Consensus pattern (29 bp):
TAAAATTCAACAAAATTAAAATACAACAA
Found at i:1181643 original size:11 final size:11
Alignment explanation
Indices: 1181627--1181652 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1181617 TATGACAAAC
1181627 TTTTTTTCTTT
1 TTTTTTTCTTT
1181638 TTTTTTTCTTT
1 TTTTTTTCTTT
1181649 TTTT
1 TTTT
1181653 AATAGTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:1181820 original size:116 final size:118
Alignment explanation
Indices: 1181679--1181914 Score: 370
Period size: 116 Copynumber: 2.0 Consensus size: 118
1181669 GTCACCCTAC
* * *
1181679 AATCTATTTTCAGGAGTAAATCTATAACAAACCCTAATTTGAGTATGAGATCATAAATTCAATAT
1 AATCTATTCTCAAGAGTAAATCTATAACAAACCCTAATTAGAGTATGAGATCATAAATTCAATAT
1181744 TAAAATGGAATGCCTC-AT-TTTT-TGAATTTTAGCTAGACCAACCCTATACT
66 TAAAATGGAATGCCTCAATGTTTTGTGAATTTTAGCTAGACCAACCCTATACT
**
1181794 AATCTATTCTCAAGAGTGAAATCTATAGTAAACCCTAATTAGAGTATGAGATCATAAATTCAATA
1 AATCTATTCTCAAGAGT-AAATCTATAACAAACCCTAATTAGAGTATGAGATCATAAATTCAATA
* * *
1181859 TTAAAATGGTATGCCTCAATGTTTTGTGAATTTTAGTTGGACCAACCCTATACT
65 TTAAAATGGAATGCCTCAATGTTTTGTGAATTTTAGCTAGACCAACCCTATACT
1181913 AA
1 AA
1181915 CTTACCATTA
Statistics
Matches: 109, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
115 15 0.14
116 60 0.55
117 2 0.02
118 4 0.04
119 28 0.26
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (118 bp):
AATCTATTCTCAAGAGTAAATCTATAACAAACCCTAATTAGAGTATGAGATCATAAATTCAATAT
TAAAATGGAATGCCTCAATGTTTTGTGAATTTTAGCTAGACCAACCCTATACT
Found at i:1183446 original size:2 final size:2
Alignment explanation
Indices: 1183441--1183471 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1183431 ACAATTCTCA
1183441 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1183472 AAAGAAGAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1194820 original size:12 final size:11
Alignment explanation
Indices: 1194790--1194846 Score: 55
Period size: 10 Copynumber: 5.1 Consensus size: 11
1194780 TAAAATTTTA
*
1194790 ATTTTTTATAT
1 ATTTTTAATAT
1194801 ATTATTTTAATAT
1 A-T-TTTTAATAT
1194814 GATTTTTAATAT
1 -ATTTTTAATAT
*
1194826 A-TTTAAATAT
1 ATTTTTAATAT
1194836 ATTTTT-ATAT
1 ATTTTTAATAT
1194846 A
1 A
1194847 AAATAATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
10 14 0.36
11 5 0.13
12 10 0.26
13 9 0.23
14 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:1194823 original size:32 final size:32
Alignment explanation
Indices: 1194785--1194845 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1194775 ATTTTTAAAA
* *
1194785 TTTTAAT-TTTTTATATATTATTTTAATATGAT
1 TTTTAATATATTTAAATA-TATTTTAATATGAT
*
1194817 TTTTAATATATTTAAATATATTTTTATAT
1 TTTTAATATATTTAAATATATTTTAATAT
1194846 AAAATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 17 0.68
33 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (32 bp):
TTTTAATATATTTAAATATATTTTAATATGAT
Found at i:1194885 original size:17 final size:18
Alignment explanation
Indices: 1194865--1194912 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1194855 ATTTTTATTT
*
1194865 TATAAAATTTTA-AAAAA
1 TATAAAATTTAATAAAAA
*
1194882 TATAAAAATTAATAAAAA
1 TATAAAATTTAATAAAAA
*
1194900 TATATAATTTAAT
1 TATAAAATTTAAT
1194913 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
17 10 0.38
18 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TATAAAATTTAATAAAAA
Found at i:1205250 original size:23 final size:23
Alignment explanation
Indices: 1205224--1205274 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1205214 AAGGAGGAGT
* *
1205224 ATTATTCAATGATGTAAGAGTTG
1 ATTATTCAATAATGTAAGAATTG
* *
1205247 ATTATTTAATAATGTAATAATTG
1 ATTATTCAATAATGTAAGAATTG
1205270 ATTAT
1 ATTAT
1205275 ATGAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (23 bp):
ATTATTCAATAATGTAAGAATTG
Found at i:1211187 original size:2 final size:2
Alignment explanation
Indices: 1211180--1211231 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1211170 TCATCTTGTA
1211180 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1211222 CT CT CT CT CT
1 CT CT CT CT CT
1211232 ATAAAAGCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1217024 original size:22 final size:22
Alignment explanation
Indices: 1216966--1217032 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
1216956 ACTTACCTTT
1216966 GAAAAAGG-AAAAA--ATAAAA
1 GAAAAAGGAAAAAATTATAAAA
* * *
1216985 TAAAATGAGATAAAATTATAAAA
1 GAAAAAG-GAAAAAATTATAAAA
1217008 GAAAAAGGAAAAAATTATAACAA
1 GAAAAAGGAAAAAATTATAA-AA
1217031 GA
1 GA
1217033 GGAAACAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.14
20 1 0.03
21 4 0.11
22 12 0.32
23 15 0.41
ACGTcount: A:0.70, C:0.01, G:0.13, T:0.15
Consensus pattern (22 bp):
GAAAAAGGAAAAAATTATAAAA
Found at i:1235858 original size:30 final size:30
Alignment explanation
Indices: 1235802--1235858 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1235792 TTTATTATTT
* *
1235802 TCAAATAAGCCTTTAACCTATGATTTACAC
1 TCAAATAAGCCTTTAACATATAATTTACAC
* *
1235832 TCAAATAAGCCTTTATCATTTAATTTA
1 TCAAATAAGCCTTTAACATATAATTTA
1235859 TATATAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (30 bp):
TCAAATAAGCCTTTAACATATAATTTACAC
Found at i:1237604 original size:14 final size:14
Alignment explanation
Indices: 1237566--1237604 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1237556 AATCAAATAG
1237566 TCAATACAATAAAT
1 TCAATACAATAAAT
*
1237580 T-AATAATAATAAAT
1 TCAAT-ACAATAAAT
1237594 TCAATACAATA
1 TCAATACAATA
1237605 TACAATCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 3 0.14
14 15 0.71
15 3 0.14
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (14 bp):
TCAATACAATAAAT
Found at i:1238811 original size:25 final size:25
Alignment explanation
Indices: 1238787--1238841 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1238777 GAAATTAATA
1238787 AAATATTTTT-TAAAAATATAAAAT
1 AAATATTTTTATAAAAATATAAAAT
* *
1238811 -ATTATTTTTAATATAAATATAAAATT
1 AAATATTTTT-ATAAAAATATAAAA-T
1238837 AAATA
1 AAATA
1238842 AAATATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
23 8 0.33
25 12 0.50
26 1 0.04
27 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAATATTTTTATAAAAATATAAAAT
Found at i:1238831 original size:6 final size:6
Alignment explanation
Indices: 1238820--1238860 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
1238810 TATTATTTTT
*
1238820 AATATA AATATA AA-ATTA AATA-A AATATA AATATA TATATA
1 AATATA AATATA AATA-TA AATATA AATATA AATATA AATATA
1238861 TAATTAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
5 6 0.19
6 24 0.77
7 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:1238892 original size:33 final size:31
Alignment explanation
Indices: 1238821--1238892 Score: 90
Period size: 33 Copynumber: 2.3 Consensus size: 31
1238811 ATTATTTTTA
* *
1238821 ATATAAATATAAAATTAAATAAAATATAAAT
1 ATATATATATAAAATTAAATAAAAAATAAAT
* *
1238852 ATATATATATAATTAATTAATTAAAAAATAATT
1 ATATATATATAA--AATTAAATAAAAAATAAAT
1238885 ATATATAT
1 ATATATAT
1238893 GAAGTCGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 11 0.31
33 24 0.69
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
ATATATATATAAAATTAAATAAAAAATAAAT
Found at i:1241042 original size:10 final size:10
Alignment explanation
Indices: 1241027--1241064 Score: 76
Period size: 10 Copynumber: 3.8 Consensus size: 10
1241017 AACCGAGGAA
1241027 CGTTGTGTTG
1 CGTTGTGTTG
1241037 CGTTGTGTTG
1 CGTTGTGTTG
1241047 CGTTGTGTTG
1 CGTTGTGTTG
1241057 CGTTGTGT
1 CGTTGTGT
1241065 GGTGTGGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.00, C:0.11, G:0.39, T:0.50
Consensus pattern (10 bp):
CGTTGTGTTG
Found at i:1241074 original size:20 final size:20
Alignment explanation
Indices: 1241031--1241074 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1241021 GAGGAACGTT
* *
1241031 GTGTTGCGTTGTGTTGCGTT
1 GTGTTGCGTTGTGTGGCGTG
*
1241051 GTGTTGCGTTGTGTGGTGTG
1 GTGTTGCGTTGTGTGGCGTG
1241071 GTGT
1 GTGT
1241075 GAAGTTGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.00, C:0.07, G:0.45, T:0.48
Consensus pattern (20 bp):
GTGTTGCGTTGTGTGGCGTG
Found at i:1245469 original size:2 final size:2
Alignment explanation
Indices: 1245464--1245488 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1245454 TGAAGGGTTC
1245464 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 T
1245489 CAAAGGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1251288 original size:1 final size:1
Alignment explanation
Indices: 1251282--1251306 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1251272 AGATTTGCAG
1251282 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
1251307 CCCAGCTACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1252434 original size:2 final size:2
Alignment explanation
Indices: 1252427--1252458 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1252417 GTTAAGGATG
1252427 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1252459 TTGAAGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1260000 original size:3 final size:3
Alignment explanation
Indices: 1259992--1260029 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1259982 CCCATGTTAA
*
1259992 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1260030 ATTTAAGCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1264687 original size:22 final size:22
Alignment explanation
Indices: 1264662--1264707 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1264652 TAATAATTAT
1264662 TATTATA-ATTATAATAAAAAAA
1 TATTATATA-TATAATAAAAAAA
*
1264684 TATTATATATATAATTAAAAAA
1 TATTATATATATAATAAAAAAA
1264706 TA
1 TA
1264708 ATAATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TATTATATATATAATAAAAAAA
Found at i:1264720 original size:21 final size:22
Alignment explanation
Indices: 1264671--1264722 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
1264661 TTATTATAAT
* *
1264671 TATAATAAAAAAATATTATATA
1 TATAATTAAAAAATATAATATA
1264693 TATAATTAAAAAATAATAATA-A
1 TATAATTAAAAAAT-ATAATATA
1264715 TA-AATTAA
1 TATAATTAA
1264723 TATTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 6 0.22
22 16 0.59
23 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TATAATTAAAAAATATAATATA
Found at i:1264764 original size:23 final size:24
Alignment explanation
Indices: 1264716--1264768 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1264706 TAATAATAAT
*
1264716 AAATTAATATTAAATAAATTTTATTA
1 AAATTAATATT--ATAAATTTAATTA
1264742 AAATTAATATT-TAAATTTAATTA
1 AAATTAATATTATAAATTTAATTA
1264765 AAAT
1 AAAT
1264769 ATGATAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 15 0.58
26 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATTAATATTATAAATTTAATTA
Found at i:1264880 original size:5 final size:5
Alignment explanation
Indices: 1264870--1264910 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
1264860 AATAATTTAA
*
1264870 AATAT AATAT AATAT AATAT -A-AT AATAT AAATAT ATTAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AA
1264911 AATATAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 22 0.71
6 5 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:1264901 original size:29 final size:29
Alignment explanation
Indices: 1264860--1264926 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
1264850 TGATAGATTG
* *
1264860 AATAATTTAAAATATA-ATATAATATAATA
1 AATAATATAAAATATATATAAAATATAA-A
1264889 TAATAATAT-AAATATATTATAAAATATAAA
1 -AATAATATAAAATATA-TATAAAATATAAA
1264919 AATAATAT
1 AATAATAT
1264927 GATTTAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 15 0.45
30 8 0.24
31 10 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAATATAAAATATATATAAAATATAAA
Found at i:1264918 original size:18 final size:19
Alignment explanation
Indices: 1264873--1264926 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
1264863 AATTTAAAAT
1264873 ATAATAT-AATATAATATA
1 ATAATATAAATATAATATA
*
1264891 ATAATATAAATATATTATA
1 ATAATATAAATATAATATA
*
1264910 A-AATATAAAAATAATAT
1 ATAATATAAATATAATAT
1264927 GATTTAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 21 0.66
19 11 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATAATATAAATATAATATA
Found at i:1264967 original size:56 final size:64
Alignment explanation
Indices: 1264906--1265037 Score: 158
Period size: 56 Copynumber: 2.2 Consensus size: 64
1264896 ATAAATATAT
1264906 TATAAAATATAAAAATAATAT-GA-TTTAAAATTTTA-A-T-A-AT-AATTAT-ATATAATTTTA
1 TATAAAATATAAAAA-AATATAGATTTTAAAATTTTATATTGACATAAATTATGATATAATTTTA
* * *
1264963 -ATAAAAT-TAAAAAAATATATATTTTATATTTTTATATTGACATAAATTATGATATAATTTTA
1 TATAAAATATAAAAAAATATAGATTTTAAAATTTTATATTGACATAAATTATGATATAATTTTA
1265025 TATAAAATATAAA
1 TATAAAATATAAA
1265038 TATTTTAATA
Statistics
Matches: 62, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
54 5 0.08
55 7 0.11
56 17 0.27
57 1 0.02
58 1 0.02
59 1 0.02
60 2 0.03
61 6 0.10
62 11 0.18
63 7 0.11
64 4 0.06
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (64 bp):
TATAAAATATAAAAAAATATAGATTTTAAAATTTTATATTGACATAAATTATGATATAATTTTA
Found at i:1272874 original size:20 final size:21
Alignment explanation
Indices: 1272846--1272884 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1272836 AAATGTCTGG
*
1272846 TTTTCTATT-TTTTTTTTCTT
1 TTTTCTATTATATTTTTTCTT
*
1272866 TTTTGTATTATATTTTTTC
1 TTTTCTATTATATTTTTTC
1272885 CTAGTTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTTCTATTATATTTTTTCTT
Found at i:1278277 original size:15 final size:15
Alignment explanation
Indices: 1278257--1278286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1278247 GTTGAGACTC
1278257 AACTTCCAGGATTGT
1 AACTTCCAGGATTGT
*
1278272 AACTTCTAGGATTGT
1 AACTTCCAGGATTGT
1278287 GCAGTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (15 bp):
AACTTCCAGGATTGT
Found at i:1294831 original size:17 final size:17
Alignment explanation
Indices: 1294809--1294843 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1294799 TCTTGACATG
1294809 ATTTAACTACA-AATAAA
1 ATTTAACT-CATAATAAA
1294826 ATTTAACTCATAATAAA
1 ATTTAACTCATAATAAA
1294843 A
1 A
1294844 GTAGTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (17 bp):
ATTTAACTCATAATAAA
Found at i:1298875 original size:18 final size:18
Alignment explanation
Indices: 1298849--1298883 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1298839 TGTATAACAT
*
1298849 AGAGAGAGATAGAGATAG
1 AGAGAGAGAAAGAGATAG
*
1298867 AGAGTGAGAAAGAGATA
1 AGAGAGAGAAAGAGATA
1298884 AAAAAACTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.37, T:0.11
Consensus pattern (18 bp):
AGAGAGAGAAAGAGATAG
Found at i:1307534 original size:20 final size:20
Alignment explanation
Indices: 1307509--1307547 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1307499 AATGGAAAGA
1307509 TATCTATAACTACATATATG
1 TATCTATAACTACATATATG
* *
1307529 TATCTATATCTATATATAT
1 TATCTATAACTACATATAT
1307548 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
TATCTATAACTACATATATG
Found at i:1312314 original size:42 final size:42
Alignment explanation
Indices: 1312267--1312350 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1312257 TGATTTAATC
* *
1312267 CGTCCATATATGAATGTTTATCAAAGAAGGATATCCAGGTCA
1 CGTCCATATATGAATGTTGATCAAAGAAGCATATCCAGGTCA
*
1312309 CGTCCATATTTGAATGTTGATCAAAGAAGCATATCCAGGTCA
1 CGTCCATATATGAATGTTGATCAAAGAAGCATATCCAGGTCA
1312351 TGCAAAACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (42 bp):
CGTCCATATATGAATGTTGATCAAAGAAGCATATCCAGGTCA
Found at i:1315044 original size:10 final size:10
Alignment explanation
Indices: 1315001--1315037 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1314991 TTTTGAATTT
1315001 ATAAA-TTTA
1 ATAAATTTTA
1315010 A-AAATTTTA
1 ATAAATTTTA
1315019 ATAAATTTTA
1 ATAAATTTTA
1315029 ATAAATTTT
1 ATAAATTTT
1315038 CAAAAATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 3 0.12
9 6 0.23
10 17 0.65
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
ATAAATTTTA
Found at i:1316225 original size:22 final size:24
Alignment explanation
Indices: 1316199--1316251 Score: 83
Period size: 22 Copynumber: 2.3 Consensus size: 24
1316189 TCTGAAATTA
1316199 ATAAAATATTATTTTT-TAT-AAT
1 ATAAAATATTATTTTTATATAAAT
*
1316221 ATAAAATATTATTTTTATGTAAAT
1 ATAAAATATTATTTTTATATAAAT
1316245 ATAAAAT
1 ATAAAAT
1316252 TAAATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 16 0.57
23 2 0.07
24 10 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
ATAAAATATTATTTTTATATAAAT
Found at i:1316257 original size:12 final size:12
Alignment explanation
Indices: 1316240--1316281 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1316230 TATTTTTATG
1316240 TAAATATAAAAT
1 TAAATATAAAAT
*
1316252 TAAATA-AATAT
1 TAAATATAAAAT
1316263 ATAAATATAAAAT
1 -TAAATATAAAAT
1316276 TAAATA
1 TAAATA
1316282 AATAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 18 0.69
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:1316267 original size:24 final size:24
Alignment explanation
Indices: 1316240--1316285 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1316230 TATTTTTATG
1316240 TAAATATAAAATTAAATAAATATA
1 TAAATATAAAATTAAATAAATATA
1316264 TAAATATAAAATTAAATAAATA
1 TAAATATAAAATTAAATAAATA
1316286 ATTTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
TAAATATAAAATTAAATAAATATA
Found at i:1316288 original size:12 final size:12
Alignment explanation
Indices: 1316240--1316300 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
1316230 TATTTTTATG
1316240 TAAATATAA-AAT
1 TAAATA-AATAAT
1316252 TAAATAAAT-AT
1 TAAATAAATAAT
1316263 ATAAATATAA-AAT
1 -TAAATA-AATAAT
1316276 TAAATAAATAAT
1 TAAATAAATAAT
*
1316288 TTAA-AAATAAT
1 TAAATAAATAAT
1316299 TA
1 TA
1316301 TATATATTGA
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
11 14 0.33
12 24 0.57
13 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATAAATAAT
Found at i:1317014 original size:11 final size:11
Alignment explanation
Indices: 1316970--1317032 Score: 62
Period size: 11 Copynumber: 6.1 Consensus size: 11
1316960 AAGGTTATGG
1316970 AAATATAATAT
1 AAATATAATAT
* *
1316981 AAAAAGAATA-
1 AAATATAATAT
* *
1316991 AAATA-ATTTT
1 AAATATAATAT
1317001 AAATATAATAT
1 AAATATAATAT
1317012 AAATATAATAT
1 AAATATAATAT
1317023 -AATA-AATAT
1 AAATATAATAT
1317032 A
1 A
1317033 TAAAATTATA
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
9 7 0.17
10 13 0.31
11 22 0.52
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1317599 original size:18 final size:18
Alignment explanation
Indices: 1317566--1317600 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1317556 TATTTAAATT
1317566 ATAAATTTATTAATTAAC
1 ATAAATTTATTAATTAAC
1317584 ATAATATTTATT-ATTAA
1 ATAA-ATTTATTAATTAA
1317601 TATGATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAATTTATTAATTAAC
Found at i:1318048 original size:15 final size:16
Alignment explanation
Indices: 1318028--1318060 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1318018 GCAACTGATG
*
1318028 ATATAAAA-ATTTATA
1 ATATAAAATAATTATA
1318043 ATATAAAATAATTATA
1 ATATAAAATAATTATA
1318059 AT
1 AT
1318061 TTTGAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATAAAATAATTATA
Found at i:1318127 original size:28 final size:26
Alignment explanation
Indices: 1318067--1318127 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 26
1318057 TAATTTTGAG
* *
1318067 ATAAAAA-AATTTTAATTTATATATT
1 ATAAAAATAATATTAATTTATAAATT
1318092 A-AATAAATAATATTAATTATTATAAATT
1 ATAA-AAATAATATTAA-T-TTATAAATT
1318120 ATAAAAAT
1 ATAAAAAT
1318128 TATAATTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
24 2 0.07
25 4 0.14
26 7 0.24
27 1 0.03
28 13 0.45
29 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAAAATAATATTAATTTATAAATT
Found at i:1318421 original size:14 final size:14
Alignment explanation
Indices: 1318404--1318448 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1318394 ATTTATTAAG
1318404 ATTATTTTAAATAT
1 ATTATTTTAAATAT
*
1318418 ATTATTTATAATTAT
1 ATTATTT-TAAATAT
1318433 -TTATTTTAAAT-T
1 ATTATTTTAAATAT
1318445 ATTA
1 ATTA
1318449 AATATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 1 0.04
13 7 0.26
14 13 0.48
15 6 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
ATTATTTTAAATAT
Found at i:1318421 original size:27 final size:27
Alignment explanation
Indices: 1318391--1318448 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
1318381 TTTATCGATG
1318391 ATTATTTATTAA-GA-TTATTTTAAATAT
1 ATTATTTA-TAATGATTTATTTTAAAT-T
*
1318418 ATTATTTATAATTATTTATTTTAAATT
1 ATTATTTATAATGATTTATTTTAAATT
1318445 ATTA
1 ATTA
1318449 AATATAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 3 0.11
27 14 0.50
28 11 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (27 bp):
ATTATTTATAATGATTTATTTTAAATT
Found at i:1318472 original size:28 final size:27
Alignment explanation
Indices: 1318405--1318470 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 27
1318395 TTTATTAAGA
**
1318405 TTATTTTAAATATATTATTTATAATTAT
1 TTATTTTAAAT-TATTAAATATAATTAT
1318433 TTATTTTAAATTATTAAATATAATATATT
1 TTATTTTAAATTATTAAATATAAT-TA-T
1318462 TTATTTTAA
1 TTATTTTAA
1318471 TTTAAAAGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 11 0.32
28 13 0.38
29 10 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATTTTAAATTATTAAATATAATTAT
Found at i:1322006 original size:18 final size:18
Alignment explanation
Indices: 1321983--1322017 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1321973 ATTTAAGCAG
*
1321983 TTAAATTAAATTATAAAT
1 TTAAATTAAAGTATAAAT
*
1322001 TTAAATTTAAGTATAAA
1 TTAAATTAAAGTATAAA
1322018 AAATAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
TTAAATTAAAGTATAAAT
Found at i:1326302 original size:2 final size:2
Alignment explanation
Indices: 1326295--1326319 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1326285 TTAGTTTTTG
1326295 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 T
1326320 TAATTGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1334996 original size:2 final size:2
Alignment explanation
Indices: 1334985--1335014 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1334975 AAAATTTATC
1334985 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1335015 CACACATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1337294 original size:24 final size:21
Alignment explanation
Indices: 1337254--1337298 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 21
1337244 AATATATTTT
1337254 TTATTTTATTAAATTTAAATA
1 TTATTTTATTAAATTTAAATA
1337275 TTATTATTATTAAAATTTTAAATA
1 TTATT-TTATT-AAA-TTTAAATA
1337299 ATATCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 5 0.24
23 3 0.14
24 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTTTATTAAATTTAAATA
Found at i:1342267 original size:19 final size:19
Alignment explanation
Indices: 1342243--1342280 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1342233 GCATGCATTA
* *
1342243 ATCCCTATTTGATAAGACT
1 ATCCCTATCTAATAAGACT
1342262 ATCCCTATCTAATAAGACT
1 ATCCCTATCTAATAAGACT
1342281 GTTCTCTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (19 bp):
ATCCCTATCTAATAAGACT
Found at i:1353727 original size:10 final size:10
Alignment explanation
Indices: 1353712--1353752 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1353702 CAAATATATA
1353712 TTTAATAATT
1 TTTAATAATT
1353722 TTTAAT-A-T
1 TTTAATAATT
1353730 TTTAATATATT
1 TTTAATA-ATT
*
1353741 TTTAAAAATT
1 TTTAATAATT
1353751 TT
1 TT
1353753 GAGCTCTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.26
9 1 0.04
10 12 0.44
11 7 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTAATAATT
Found at i:1353741 original size:19 final size:19
Alignment explanation
Indices: 1353707--1353745 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
1353697 TGATTCAAAT
1353707 ATATATTTAATAATTTTTA
1 ATATATTTAATAATTTTTA
1353726 ATAT-TTTAATATATTTTTA
1 ATATATTTAATA-ATTTTTA
1353745 A
1 A
1353746 AAATTTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATATATTTAATAATTTTTA
Done.