Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 125 of 170
Found at i:38155784 original size:25 final size:24
Alignment explanation
Indices: 38155727--38155784 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 24
38155717 ATCCCTTCAC
* *
38155727 TTCCTCTTCTCTTCCTCTTTACAT
1 TTCCTCTTCTCTCCCACTTTACAT
38155751 TT-CTGCTTCTACTCCCACTTCT-CAT
1 TTCCT-CTTCT-CTCCCACTT-TACAT
38155776 TTCCTCTTC
1 TTCCTCTTC
38155785 CCCTGTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 2 0.07
24 7 0.25
25 16 0.57
26 3 0.11
ACGTcount: A:0.09, C:0.40, G:0.02, T:0.50
Consensus pattern (24 bp):
TTCCTCTTCTCTCCCACTTTACAT
Found at i:38157796 original size:6 final size:7
Alignment explanation
Indices: 38157779--38157805 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38157769 TGGGATCCAA
38157779 TTTTTTC
1 TTTTTTC
38157786 TTTTTTC
1 TTTTTTC
38157793 TTTTTTC
1 TTTTTTC
38157800 TTTTTT
1 TTTTTT
38157806 TACATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:38157798 original size:16 final size:16
Alignment explanation
Indices: 38157780--38157816 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38157770 GGGATCCAAT
*
38157780 TTTTTC-TTTTTT-CT
1 TTTTTCTTTTTTTACA
38157794 TTTTTCTTTTTTTACA
1 TTTTTCTTTTTTTACA
38157810 TTTTTCT
1 TTTTTCT
38157817 CTTAACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 6 0.30
15 6 0.30
16 8 0.40
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTTTTTACA
Found at i:38158268 original size:17 final size:17
Alignment explanation
Indices: 38158246--38158278 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38158236 TTTACTCTCA
38158246 TTTTTTCTCCATTTTAC
1 TTTTTTCTCCATTTTAC
*
38158263 TTTTTTCTTCATTTTA
1 TTTTTTCTCCATTTTA
38158279 TCTTCTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTTCTCCATTTTAC
Found at i:38158460 original size:23 final size:23
Alignment explanation
Indices: 38158415--38158460 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
38158405 TTTAGATTAT
*
38158415 TTATTTTAATTTTTAAAATTTAA
1 TTATTTTAATTTTAAAAATTTAA
*
38158438 TTATTTTGA-TTTAAAAATGTTAA
1 TTATTTTAATTTTAAAAAT-TTAA
38158461 AAATTCCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TTATTTTAATTTTAAAAATTTAA
Found at i:38158732 original size:21 final size:21
Alignment explanation
Indices: 38158682--38158733 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
38158672 ACCGTTATTT
* *
38158682 TAATCTCACCACTACAGTATC
1 TAATATCACCACTACAGTAAC
* *
38158703 CAATATCACCACTACATTAAC
1 TAATATCACCACTACAGTAAC
*
38158724 TAATTTCACC
1 TAATATCACC
38158734 GCCACCATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.33, G:0.02, T:0.29
Consensus pattern (21 bp):
TAATATCACCACTACAGTAAC
Found at i:38160878 original size:18 final size:18
Alignment explanation
Indices: 38160831--38160871 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
38160821 TTTTAAAATC
* *
38160831 ATAAAAAATTTAA-AAAA
1 ATAAAAAAATAAACAAAA
38160848 ATAAAAAAATAAACAAAA
1 ATAAAAAAATAAACAAAA
38160866 ATAAAA
1 ATAAAA
38160872 TTATAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (18 bp):
ATAAAAAAATAAACAAAA
Found at i:38166875 original size:21 final size:22
Alignment explanation
Indices: 38166849--38166889 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38166839 ATAGTGATAT
*
38166849 AATGAGA-TTAATTATTATAAC
1 AATGAGATTTAAGTATTATAAC
38166870 AATGAGATTTAAGTATTATA
1 AATGAGATTTAAGTATTATA
38166890 TCGGTGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (22 bp):
AATGAGATTTAAGTATTATAAC
Found at i:38167154 original size:19 final size:19
Alignment explanation
Indices: 38167117--38167155 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
38167107 AAAATGGAAT
38167117 TATTAAAAATATTTATATTA
1 TATTAAAAATA-TTATATTA
38167137 TATTAAATAATA-TATATTA
1 TATTAAA-AATATTATATTA
38167156 AAATTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 7 0.39
21 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTAAAAATATTATATTA
Found at i:38173486 original size:45 final size:45
Alignment explanation
Indices: 38173422--38173508 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
38173412 CAGATACTCG
* *
38173422 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
*
38173467 GTGGAATCAGCACATAGCAACCACCTTACTAATTAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
38173509 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:38173577 original size:51 final size:50
Alignment explanation
Indices: 38173510--38173701 Score: 208
Period size: 51 Copynumber: 3.8 Consensus size: 50
38173500 TAATGATGTT
* *
38173510 CGGTTCACATAGTAGCCTGCACATAGTACTATCAC-TGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTA-CACATGTGACCA-TACCATC
* * * * *
38173561 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * * * * *
38173612 CGGTACGCATAGTAGCCTGTACATAGCACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
*
38173662 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA
38173702 TCGTCACTTT
Statistics
Matches: 114, Mismatches: 24, Indels: 7
0.79 0.17 0.05
Matches are distributed among these distances:
49 2 0.02
50 40 0.35
51 70 0.61
52 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:38173682 original size:101 final size:101
Alignment explanation
Indices: 38173517--38173704 Score: 290
Period size: 101 Copynumber: 1.9 Consensus size: 101
38173507 GTTCGGTTCA
* *
38173517 CATAGTAGCCTGCACATAGTACTATCACTGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGCACTATCACTGCGACCA-TACCATCCGATACACGTAGTAGCCTGCA
38173582 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCGAAACTATCCGGTACG
* * *
38173619 CATAGTAGCCTGTACATAGCACTA-CACATGCGACC-TATCATTCCGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTGCACATAGCACTATCAC-TGCGACCATACCA-TCCGATACACGTAGTAGCCTGC
38173682 ACATAGTACTACACACGTGATCG
64 ACATAGTACTACACACGTGATCG
38173705 TCACTTTCAC
Statistics
Matches: 79, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
100 4 0.05
101 47 0.59
102 28 0.35
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGCACTATCACTGCGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCGAAACTATCCGGTACG
Found at i:38175952 original size:17 final size:18
Alignment explanation
Indices: 38175914--38175952 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
38175904 TTGATTTTAT
*
38175914 TTATTGATAAAAATTGAA
1 TTATTGATAAAAATAGAA
38175932 -TATT-ATAAAAATAGAA
1 TTATTGATAAAAATAGAA
38175948 TTATT
1 TTATT
38175953 TCTTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (18 bp):
TTATTGATAAAAATAGAA
Found at i:38179442 original size:30 final size:30
Alignment explanation
Indices: 38179408--38179467 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
38179398 TATTTTATTA
38179408 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
*
38179438 TTAATTTTGTTATTATTTTAGAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGCATTTG
38179468 CTTGTTAAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGCATTTG
Found at i:38183832 original size:27 final size:25
Alignment explanation
Indices: 38183802--38183858 Score: 60
Period size: 27 Copynumber: 2.2 Consensus size: 25
38183792 AAATTAACTT
*
38183802 AAATCAAGTTTAATATTATTATATTAA
1 AAATAAAGTTTAATATTATT-T-TTAA
* * *
38183829 AAATAAATTTTATTTTTATTTTTAA
1 AAATAAAGTTTAATATTATTTTTAA
38183854 AAATA
1 AAATA
38183859 TTTAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 9 0.35
26 1 0.04
27 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
AAATAAAGTTTAATATTATTTTTAA
Found at i:38183993 original size:16 final size:19
Alignment explanation
Indices: 38183945--38184000 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 19
38183935 TTTAGTCCTA
38183945 TAATAAATTATTAATATAAT
1 TAATAAATTATTAATAT-AT
38183965 TAATATAATTTATT-AT-T-T
1 TAATA-AA-TTATTAATATAT
38183983 TAATAAATTATTTAATAT
1 TAATAAATTA-TTAATAT
38184001 TTCAATTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 8 0.26
19 1 0.03
20 6 0.19
21 4 0.13
22 5 0.16
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATAAATTATTAATATAT
Found at i:38184035 original size:15 final size:13
Alignment explanation
Indices: 38184010--38184049 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
38184000 TTTCAATTTT
38184010 ATTTT-AATAATA
1 ATTTTAAATAATA
38184022 GATTTTAAAATAATA
1 -ATTTT-AAATAATA
38184037 ATTTTAAATAATA
1 ATTTTAAATAATA
38184050 TTCCTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 5 0.20
15 7 0.28
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (13 bp):
ATTTTAAATAATA
Found at i:38185024 original size:20 final size:21
Alignment explanation
Indices: 38184999--38185039 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
38184989 AATTAACATT
38184999 AATAATAATT-TTAA-ATTTTA
1 AATAAT-ATTCTTAATATTTTA
38185019 AATAATATTCTTAATATTTTA
1 AATAATATTCTTAATATTTTA
38185040 TTGAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 10 0.53
21 6 0.32
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATAATATTCTTAATATTTTA
Found at i:38188256 original size:17 final size:17
Alignment explanation
Indices: 38188234--38188267 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
38188224 TCTCTTAAAT
38188234 AGATATAACTATTCAAG
1 AGATATAACTATTCAAG
38188251 AGATATAACTATTCAAG
1 AGATATAACTATTCAAG
38188268 TATTACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
AGATATAACTATTCAAG
Found at i:38189664 original size:19 final size:19
Alignment explanation
Indices: 38189616--38189665 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
38189606 TTTTTATCAA
**
38189616 TATTTTGAAATTTAAAAAT
1 TATTTTGATTTTTAAAAAT
* *
38189635 TATTTTAATTTTTGAAAAT
1 TATTTTGATTTTTAAAAAT
38189654 TATTTTGATTTT
1 TATTTTGATTTT
38189666 CTTTTTGTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TATTTTGATTTTTAAAAAT
Found at i:38190629 original size:13 final size:13
Alignment explanation
Indices: 38190611--38190641 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
38190601 AGTGTATTAC
38190611 CCTTATGTGATAT
1 CCTTATGTGATAT
38190624 CCTTATGTGATAT
1 CCTTATGTGATAT
38190637 CCTTA
1 CCTTA
38190642 ATCTCTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (13 bp):
CCTTATGTGATAT
Found at i:38191409 original size:6 final size:6
Alignment explanation
Indices: 38191398--38191441 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
38191388 AACCCATCAC
38191398 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
38191442 CATCGTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:38206267 original size:60 final size:60
Alignment explanation
Indices: 38206174--38206296 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 60
38206164 CTATTGAGTC
* * *
38206174 TTCCATTATACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCTAGGCA
1 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGACA
38206234 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGACA
1 TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGACA
38206294 TTC
1 TTC
38206297 TTTCCACTCT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.33
Consensus pattern (60 bp):
TTCCATTAAACAAGAATCTATTATCAAGAGTTCCATACCATTGCCTTTGGTAGCAAGACA
Found at i:38208338 original size:38 final size:38
Alignment explanation
Indices: 38208287--38208364 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
38208277 AGGATACAAT
*
38208287 TGGCATGTCAATAGGTTATATCGCGCTTTGTATGAGTC
1 TGGCATGTCAATAGGTTATATCGCGCTTTGTACGAGTC
38208325 TGGCATGTCAATAGGTTATATCGCGCTTTGTACGAGTC
1 TGGCATGTCAATAGGTTATATCGCGCTTTGTACGAGTC
38208363 TG
1 TG
38208365 ACTTGAGATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.36
Consensus pattern (38 bp):
TGGCATGTCAATAGGTTATATCGCGCTTTGTACGAGTC
Found at i:38209248 original size:29 final size:29
Alignment explanation
Indices: 38209192--38209248 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
38209182 TTAAAATTAT
* * *
38209192 TAAAATTTTAAAAAATATATAATTATTTA
1 TAAAATTATAAAAAATATAAAATGATTTA
38209221 TAAAATTAT-AAAAATATAAAAATGATTT
1 TAAAATTATAAAAAATAT-AAAATGATTT
38209249 TTTAAAAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAAATTATAAAAAATATAAAATGATTTA
Found at i:38211194 original size:14 final size:15
Alignment explanation
Indices: 38211172--38211248 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38211162 CAATCAAACA
38211172 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
38211186 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
38211201 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
38211221 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
38211235 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
38211249 ACTGGTAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:38211213 original size:20 final size:20
Alignment explanation
Indices: 38211188--38211227 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38211178 AATATTTTCC
*
38211188 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
38211208 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
38211228 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:38211233 original size:34 final size:35
Alignment explanation
Indices: 38211176--38211242 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38211166 CAAACACCAG
*
38211176 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
38211211 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38211243 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38212173 original size:17 final size:17
Alignment explanation
Indices: 38212140--38212171 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
38212130 AAATTTCAAG
38212140 AAAAATAATGTATTTTA
1 AAAAATAATGTATTTTA
38212157 AAAAAT-ATGTATTTT
1 AAAAATAATGTATTTT
38212172 TATATTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
AAAAATAATGTATTTTA
Found at i:38215464 original size:134 final size:134
Alignment explanation
Indices: 38215102--38215513 Score: 480
Period size: 133 Copynumber: 3.1 Consensus size: 134
38215092 GCGCTTCCCC
** * * *
38215102 AAAAACGCCGCAAAAAATTGGAATATAGCGGCGTTTTCTGAGAAACGCCGATAACGATAA-CGAA
1 AAAAACGCCGC-AAAAATTGGAATATAGCGGCGTTTTAGGAGAAACGCCGGTAAAGA-AATCTAA
* *
38215166 TTTGAGGAAAAAATCTGAGCAAAACAGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGC
64 TTTGAGGAAAAAATTTGAGCAAAACGGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGC
*
38215231 ATTTTA
129 ATTGTA
* * * *
38215237 AAAAACGCCAG-AAAAGAAT-GCAT-TAGCGGCGTTTTTAGG-GAAACACCGGTAAAGATATCTA
1 AAAAACGCC-GCAAAA-ATTGGAATATAGCGGCG-TTTTAGGAGAAACGCCGGTAAAGAAATCTA
* * * *
38215298 ATTTGAGGAAAAAATTT-AGACAAAACGCTACCGTTTTATTGCTTCATTTTATTTCCTTAGTGGC
63 ATTTGAGGAAAAAATTTGAG-CAAAACGGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGC
38215362 GCATTGTA
127 GCATTGTA
* * *
38215370 AAAAACGCCGCAAATATTGGGATATAGTGGCGTTATT-GGAGAAACGCCGGTAAAGAAATCTAAT
1 AAAAACGCCGCAAAAATTGGAATATAGCGGCGTT-TTAGGAGAAACGCCGGTAAAGAAATCTAAT
* * * *
38215434 TTGAGGAAAAATTTTGAGCAAAACGGTACCGTTTTGTTGTTTCCTTTTA-TGCTTTAGTGGCGAA
65 TTGAGGAAAAAATTTGAGCAAAACGGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCA
*
38215498 ATGTTA
130 TTG-TA
38215504 AAAAACGCCG
1 AAAAACGCCG
38215514 GAAACGGTTC
Statistics
Matches: 234, Mismatches: 31, Indels: 25
0.81 0.11 0.09
Matches are distributed among these distances:
132 6 0.03
133 118 0.50
134 96 0.41
135 13 0.06
136 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (134 bp):
AAAAACGCCGCAAAAATTGGAATATAGCGGCGTTTTAGGAGAAACGCCGGTAAAGAAATCTAATT
TGAGGAAAAAATTTGAGCAAAACGGTACCGTTTTGTTGTTTCATTTTATTTCTTTAGTGGCGCAT
TGTA
Found at i:38215901 original size:21 final size:20
Alignment explanation
Indices: 38215862--38215914 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
38215852 TTTGTGATAT
*
38215862 GGGCTTAGAGTTTAGGTTTA
1 GGGCTTAGAGTTGAGGTTTA
*
38215882 GGGCTTGGAGATTGAGGTTTA
1 GGGCTTAGAG-TTGAGGTTTA
* *
38215903 AGGTTTAGAGTT
1 GGGCTTAGAGTT
38215915 TGTATTTCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.21, C:0.04, G:0.38, T:0.38
Consensus pattern (20 bp):
GGGCTTAGAGTTGAGGTTTA
Found at i:38217788 original size:17 final size:18
Alignment explanation
Indices: 38217752--38217792 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
38217742 ATAATTTCGT
*
38217752 AATAATGCATCAATTTAA
1 AATAATGCATCAATTCAA
*
38217770 AATAATGTAT-AATTCAA
1 AATAATGCATCAATTCAA
38217787 AATAAT
1 AATAAT
38217793 AAAATACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.54, C:0.07, G:0.05, T:0.34
Consensus pattern (18 bp):
AATAATGCATCAATTCAA
Found at i:38220318 original size:17 final size:17
Alignment explanation
Indices: 38220298--38220330 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38220288 TTAATATCTA
*
38220298 TATAAGTTTTCTAAATT
1 TATAAGTTTTATAAATT
38220315 TATAAGTTTTATAAAT
1 TATAAGTTTTATAAAT
38220331 AAGTTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (17 bp):
TATAAGTTTTATAAATT
Found at i:38220369 original size:16 final size:16
Alignment explanation
Indices: 38220339--38220377 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
38220329 ATAAGTTTTC
*
38220339 TAAAA-TTATTTGTAT
1 TAAAATTTATTAGTAT
38220354 TAAAATTTATTAGTAT
1 TAAAATTTATTAGTAT
38220370 T-AAATTTA
1 TAAAATTTA
38220378 CTTCGTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
TAAAATTTATTAGTAT
Found at i:38220622 original size:21 final size:21
Alignment explanation
Indices: 38220596--38220674 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
38220586 TGTTATAATA
*
38220596 CATAACTTGTATATAAGCTTG
1 CATAACTTATATATAAGCTTG
*
38220617 CATAACTTATATTTAAGCTTG
1 CATAACTTATATATAAGCTTG
* * *
38220638 CATAACTTACATAATAA-TTTA
1 CATAACTTATAT-ATAAGCTTG
38220659 CATAACTTATATATAA
1 CATAACTTATATATAA
38220675 TAGCATAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 4 0.08
21 43 0.86
22 3 0.06
ACGTcount: A:0.41, C:0.14, G:0.06, T:0.39
Consensus pattern (21 bp):
CATAACTTATATATAAGCTTG
Found at i:38220628 original size:116 final size:116
Alignment explanation
Indices: 38220501--38220741 Score: 448
Period size: 116 Copynumber: 2.1 Consensus size: 116
38220491 TTATATAATA
38220501 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACA-A
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
38220565 CATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
66 -ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
* *
38220617 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACATAACTTATATATAATAGCATA
1 CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
38220682 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
66 ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
38220733 CATAACTTA
1 CATAACTTA
38220742 CATAAATTAA
Statistics
Matches: 122, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
116 121 0.99
117 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (116 bp):
CATAACTTATATTTAAGCTTGCATAACTTACATAATAATTTACAGAACTTATATATAATAACATA
ATAAATTACATAATACTTTATGTTATAATACATAACTTGTATATAAGCTTG
Found at i:38220755 original size:9 final size:9
Alignment explanation
Indices: 38220710--38220982 Score: 260
Period size: 9 Copynumber: 29.8 Consensus size: 9
38220700 TATGTTATAA
38220710 TACATAACTT
1 TACATAAC-T
*
38220720 GTATATAAGCT
1 -TACATAA-CT
*
38220731 TGCATAACT
1 TACATAACT
*
38220740 TACATAAAT
1 TACATAACT
*
38220749 TAAATAACT
1 TACATAACT
38220758 TACATAACT
1 TACATAACT
38220767 TACATAAGC-
1 TACATAA-CT
*
38220776 TACATAAAT
1 TACATAACT
*
38220785 TAAATAACT
1 TACATAACT
*
38220794 TACATACCT
1 TACATAACT
*
38220803 TACATAAAT
1 TACATAACT
*
38220812 TAAATAACT
1 TACATAACT
38220821 TACATAACT
1 TACATAACT
38220830 TACATAAACT
1 TACAT-AACT
* *
38220840 TGCATAAAT
1 TACATAACT
*
38220849 TAAATAACT
1 TACATAACT
*
38220858 TACATTACT
1 TACATAACT
*
38220867 TACATAACC
1 TACATAACT
*
38220876 TACATAAAT
1 TACATAACT
*
38220885 TAAATAACT
1 TACATAACT
38220894 TACATAACT
1 TACATAACT
*
38220903 TACATAAAT
1 TACATAACT
*
38220912 TAAATAACT
1 TACATAACT
38220921 TACATAACT
1 TACATAACT
*
38220930 TACATAAAT
1 TACATAACT
* *
38220939 TCCATGGACT
1 TACAT-AACT
* *
38220949 GACATAACC
1 TACATAACT
*
38220958 TACATAAAT
1 TACATAACT
*
38220967 TAAATAACT
1 TACATAACT
38220976 TACATAA
1 TACATAA
38220983 ATTAAATATT
Statistics
Matches: 207, Mismatches: 50, Indels: 12
0.77 0.19 0.04
Matches are distributed among these distances:
9 180 0.87
10 19 0.09
11 7 0.03
12 1 0.00
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (9 bp):
TACATAACT
Found at i:38220848 original size:100 final size:99
Alignment explanation
Indices: 38220736--38220990 Score: 368
Period size: 100 Copynumber: 2.5 Consensus size: 99
38220726 AAGCTTGCAT
*
38220736 AACTTACATAAATTAAATAACTTACATAACTTACATAAGCTACATAAATTAAATAACTTACATAC
1 AACTTACATAAATTAAATAACTTACATAACTTACATAA-CTACATAAATTAAATAACTTACATAA
38220801 CTTACATAAATTAAATAACTTACATAACTTACATA
65 CTTACATAAATTAAATAACTTACATAACTTACATA
* *
38220836 AACTTGCATAAATTAAATAACTTACATTACTTACATAACCTACATAAATTAAATAACTTACATAA
1 AACTTACATAAATTAAATAACTTACATAACTTACATAA-CTACATAAATTAAATAACTTACATAA
38220901 CTTACATAAATTAAATAACTTACATAACTTACATA
65 CTTACATAAATTAAATAACTTACATAACTTACATA
* * * * * * * *
38220936 AA-TTCCATGGACTGACATAACCTACATAAATTAAATAACTTACATAAATTAAATA
1 AACTTACAT-AAATTAAATAACTTACATAACTTACATAAC-TACATAAATTAAATA
38220991 TTTATTAACA
Statistics
Matches: 140, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
99 6 0.04
100 134 0.96
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (99 bp):
AACTTACATAAATTAAATAACTTACATAACTTACATAACTACATAAATTAAATAACTTACATAAC
TTACATAAATTAAATAACTTACATAACTTACATA
Found at i:38237946 original size:12 final size:12
Alignment explanation
Indices: 38237928--38237960 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38237918 GGGGCCACAC
38237928 GCCCGTGTCCTTA
1 GCCCGTGTCC-TA
38237941 -CCCGTGTCCTA
1 GCCCGTGTCCTA
38237952 GCCCGTGTC
1 GCCCGTGTC
38237961 TAAACTAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 17 0.89
ACGTcount: A:0.06, C:0.42, G:0.24, T:0.27
Consensus pattern (12 bp):
GCCCGTGTCCTA
Found at i:38240691 original size:15 final size:15
Alignment explanation
Indices: 38240671--38240703 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
38240661 TAACATGTCT
38240671 TTATTAAGAAAAAAA
1 TTATTAAGAAAAAAA
38240686 TTATTAAGAAAAAAA
1 TTATTAAGAAAAAAA
38240701 TTA
1 TTA
38240704 GTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (15 bp):
TTATTAAGAAAAAAA
Found at i:38243956 original size:50 final size:50
Alignment explanation
Indices: 38243806--38244083 Score: 205
Period size: 50 Copynumber: 5.7 Consensus size: 50
38243796 TTGAGGAAAC
* * * *
38243806 AAGATTCGTCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * **
38243856 AAGATCCGTCGTTGT-GCTTCAATC--TT----TGCAATGTCAGGGAAACC
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGG-AAGT
*
38243900 AA-ATCCGCCGTCATAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* * * * * ** * * * **
38243949 AAGATCCGCCATTGTGGCTTCAATTTTTTTAATTGCAATGTC-GGAGAAAC
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGG-GAAGT
* * * * *
38243999 CAGATCTGCCGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGT
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
* *
38244049 AAGATCCGCCGTCGTGGCTTCAATCTTTTCCACTG
1 AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTG
38244084 TAATACTAAA
Statistics
Matches: 168, Mismatches: 49, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
43 18 0.11
44 13 0.08
46 2 0.01
47 2 0.01
49 15 0.09
50 116 0.69
51 2 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
AAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGT
Found at i:38244025 original size:100 final size:97
Alignment explanation
Indices: 38243815--38244077 Score: 356
Period size: 100 Copynumber: 2.7 Consensus size: 97
38243805 CAAGATTCGT
*
38243815 CGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGTCGTTGT-GCTTCAA-
1 CGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAAT
*
38243878 --TCTTTGCAATGTCAGGGAAACCAAATCCGC
66 TTTTTTTGCAATGTCAGGGAAACCAAATCCGC
* * * *
38243908 CGTCATAGCTTCAATCTGTTCCACTGCACTGCCAGGGAAGTAAGATCCGCCATTGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAA-
* *
38243973 TTTTTTAATTGCAATGTC-GGAGAAACCAGATCTGC
65 TTTTTT--TTGCAATGTCAGG-GAAACCAAATCCGC
* *
38244008 CGTTGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTCGTGGCTTCAAT
1 CGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAAT
*
38244073 CTTTT
66 TTTTT
38244078 CCACTGTAAT
Statistics
Matches: 147, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
93 51 0.35
94 7 0.05
98 2 0.01
99 7 0.05
100 80 0.54
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.29
Consensus pattern (97 bp):
CGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAAT
TTTTTTTGCAATGTCAGGGAAACCAAATCCGC
Found at i:38258610 original size:13 final size:13
Alignment explanation
Indices: 38258592--38258621 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38258582 TTTTACCTTT
*
38258592 TTAATTTTCTTAG
1 TTAATTTACTTAG
38258605 TTAATTTACTTAG
1 TTAATTTACTTAG
38258618 TTAA
1 TTAA
38258622 AATCTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:38261538 original size:26 final size:25
Alignment explanation
Indices: 38261457--38261544 Score: 95
Period size: 26 Copynumber: 3.4 Consensus size: 25
38261447 TATTTTATTT
38261457 TTATTAAATTATATTTAATAATGATA
1 TTATTAAATTATATTTAATAAT-ATA
* * * * *
38261483 ATATTAAAATATGATTAAATTATGTA
1 TTATTAAATTAT-ATTTAATAATATA
*
38261509 TTATTAAATTATATTTAATAATAATC
1 TTATTAAATTATATTTAATAAT-ATA
38261535 TTATTAAATT
1 TTATTAAATT
38261545 TTAATAGCAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
25 8 0.16
26 33 0.67
27 8 0.16
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (25 bp):
TTATTAAATTATATTTAATAATATA
Found at i:38262194 original size:9 final size:9
Alignment explanation
Indices: 38262164--38262215 Score: 52
Period size: 10 Copynumber: 5.7 Consensus size: 9
38262154 ATTAATTTTT
38262164 AAAATT-TA
1 AAAATTATA
38262172 AAAATTCATA
1 AAAATT-ATA
*
38262182 AAAATTATT
1 AAAATTATA
*
38262191 AAAATTATTT
1 AAAATTA-TA
*
38262201 AAAAGTATA
1 AAAATTATA
38262210 AAAATT
1 AAAATT
38262216 TATTTTAGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.16
9 15 0.41
10 16 0.43
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
AAAATTATA
Found at i:38262218 original size:20 final size:19
Alignment explanation
Indices: 38262161--38262220 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
38262151 TTTATTAATT
* *
38262161 TTTAAAATTTAAAAATTCA
1 TTTAAAATATAAAAATTTA
* *
38262180 -TAAAAATTATTAAAA-TTA
1 TTTAAAA-TATAAAAATTTA
38262198 TTTAAAAGTATAAAAATTTA
1 TTTAAAA-TATAAAAATTTA
38262218 TTT
1 TTT
38262221 TAGCATTCCA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
18 7 0.23
19 18 0.58
20 6 0.19
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTAAAATATAAAAATTTA
Found at i:38263785 original size:16 final size:16
Alignment explanation
Indices: 38263757--38263798 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
38263747 ATTTAATTTT
38263757 TTTTTAATTTTTA-TGAA
1 TTTTTAA-TTTTAGT-AA
38263774 TTTTTAATTTTAGTAA
1 TTTTTAATTTTAGTAA
*
38263790 TTTTAAATT
1 TTTTTAATT
38263799 ATTTTTATAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (16 bp):
TTTTTAATTTTAGTAA
Found at i:38264732 original size:10 final size:10
Alignment explanation
Indices: 38264717--38264742 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
38264707 AAAAAATTTA
38264717 TTTTTTTATT
1 TTTTTTTATT
38264727 TTTTTTTATT
1 TTTTTTTATT
38264737 TTTTTT
1 TTTTTT
38264743 ATGATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:38266538 original size:17 final size:17
Alignment explanation
Indices: 38266502--38266536 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38266492 TTTGTTCTCA
*
38266502 TATTTCTTTTTTATTTT
1 TATTTCTTTGTTATTTT
38266519 TATTTACTTTGTTATTTT
1 TATTT-CTTTGTTATTTT
38266537 ATGAGTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.14, C:0.06, G:0.03, T:0.77
Consensus pattern (17 bp):
TATTTCTTTGTTATTTT
Found at i:38272303 original size:29 final size:29
Alignment explanation
Indices: 38272270--38272385 Score: 112
Period size: 29 Copynumber: 4.0 Consensus size: 29
38272260 ATGCAGAGTT
*
38272270 GCACCAAAGTGCAATAACAGAACAAAGTG
1 GCACCGAAGTGCAATAACAGAACAAAGTG
* *
38272299 GCACCGAAGTGCAATATCCA-AACAGAA-TA
1 GCACCGAAGTGCAATA-ACAGAACA-AAGTG
** * * *
38272328 GCACCGAAGTGCTCTATCAGAATAGAGTG
1 GCACCGAAGTGCAATAACAGAACAAAGTG
38272357 GCACCGAAGTGC-ATAACAGAACAAGAGTG
1 GCACCGAAGTGCAATAACAGAACAA-AGTG
38272386 CGCTGAATGT
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
28 11 0.16
29 54 0.78
30 4 0.06
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (29 bp):
GCACCGAAGTGCAATAACAGAACAAAGTG
Found at i:38274142 original size:28 final size:29
Alignment explanation
Indices: 38274106--38274166 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
38274096 CCTCCAACTT
*
38274106 TTTTAAATA-T-ACACTTTAACCCCTCAAC
1 TTTTAAATATTCACACTTTAACCCATC-AC
* *
38274134 TTTTGAATATTCACACTTTGACCCATCAC
1 TTTTAAATATTCACACTTTAACCCATCAC
38274163 TTTT
1 TTTT
38274167 CATTTTTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.29
29 7 0.25
30 13 0.46
ACGTcount: A:0.30, C:0.26, G:0.03, T:0.41
Consensus pattern (29 bp):
TTTTAAATATTCACACTTTAACCCATCAC
Found at i:38274641 original size:26 final size:24
Alignment explanation
Indices: 38274605--38274654 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
38274595 TTAGAAAATT
* *
38274605 TTAAAAAATTAATATTTTTTAAAA
1 TTAAAAAATTAAAATTATTTAAAA
38274629 TTAAAAATTATTAAAATTATTTAAAA
1 TTAAAAA--ATTAAAATTATTTAAAA
38274655 AGAATGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
26 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTAAAAAATTAAAATTATTTAAAA
Found at i:38274642 original size:16 final size:16
Alignment explanation
Indices: 38274609--38274647 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
38274599 AAAATTTTAA
* * *
38274609 AAAATTAATATTTTTT
1 AAAATTAAAAATTATT
38274625 AAAATTAAAAATTATT
1 AAAATTAAAAATTATT
38274641 AAAATTA
1 AAAATTA
38274648 TTTAAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAAATTAAAAATTATT
Found at i:38282613 original size:14 final size:14
Alignment explanation
Indices: 38282588--38282622 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
38282578 AATTATCCAC
38282588 TTAAAT-AAAATTA
1 TTAAATAAAAATTA
38282601 TTAAATAAAAATTA
1 TTAAATAAAAATTA
38282615 TTAAATAA
1 TTAAATAA
38282623 TAATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TTAAATAAAAATTA
Found at i:38292935 original size:25 final size:25
Alignment explanation
Indices: 38292901--38292952 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
38292891 AACCCGATGT
*
38292901 GAATGATTCCACTTACTATCAGTGG
1 GAATGATTCCACTTACTATCAATGG
38292926 GAATGATTCCACTTACTATCAATGG
1 GAATGATTCCACTTACTATCAATGG
38292951 GA
1 GA
38292953 CTTTGATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (25 bp):
GAATGATTCCACTTACTATCAATGG
Found at i:38297220 original size:23 final size:23
Alignment explanation
Indices: 38297190--38297262 Score: 85
Period size: 25 Copynumber: 3.0 Consensus size: 23
38297180 ATCTACCTTG
*
38297190 TTTGGACAGCTCTTATACATC-AA
1 TTTGGACAGCT-TTATACACCAAA
38297213 TTTGGACAGCATTTATACACCAAAA
1 TTTGGACAGC-TTTATACACC-AAA
*
38297238 TTTGGACAGCTTATATACAACAAA
1 TTTGGACAGCTT-TATACACCAAA
38297262 T
1 T
38297263 GGGCAGCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 18 0.41
24 7 0.16
25 19 0.43
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (23 bp):
TTTGGACAGCTTTATACACCAAA
Found at i:38297337 original size:69 final size:69
Alignment explanation
Indices: 38297218--38297623 Score: 554
Period size: 69 Copynumber: 5.9 Consensus size: 69
38297208 ATCAATTTGG
* * * *
38297218 ACAGCATTTATACACCAAAATTTGGACAGCTTATATACAACAAATGGGCAGCATATACATACCAA
1 ACAGCATTTTTACACCAAAATTT-AACAGCATATATACAACAAATAGGCAGCATATACATACC-A
38297283 AATT-A
64 AATTGA
* *
38297288 ACAGCACTTTTACACCAAAATTTAACAGCATATATACAGCAAATAGGCAGCATATACATACCAAA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
*
38297353 TTTA
66 TTGA
** * *
38297357 ACAGCACATTTACACAAAAATTTAACAGCTTATATACAACAAA-AGGGGCAGCATATACATACCA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATA--GGCAGCATATACATACCA
38297421 AATTGA
64 AATTGA
** * *
38297427 GTAGCATTTTTACACCAAAATTTAACAACATATATACAACAAATAGGCAACATATACATACCAAA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
38297492 TTGA
66 TTGA
* * *
38297496 GCAGCATTTTTATACCAAAATTTAATAGC----ATACAACAAATAGGCAGCATATACATACCAAA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
38297557 TTGA
66 TTGA
* *
38297561 GCAGCATTTTTATACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCA
1 ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCA
38297624 CATCATATAC
Statistics
Matches: 303, Mismatches: 25, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
65 63 0.21
68 6 0.02
69 153 0.50
70 80 0.26
71 1 0.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.25
Consensus pattern (69 bp):
ACAGCATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAA
TTGA
Found at i:38297470 original size:139 final size:138
Alignment explanation
Indices: 38297228--38297623 Score: 570
Period size: 139 Copynumber: 2.9 Consensus size: 138
38297218 ACAGCATTTA
* * *
38297228 TACACCAAAATTTGGACAGCTTATATACAACAAATGGGCAGCATATACATACCAAAATT-AACAG
1 TACACCAAAATTT-AACAGCTTATATACAACAAAAGGGCAGCATATACATACC-AAATTGAGCAG
* * *
38297292 CACTTTTACACCAAAATTTAACAGCATATATACAGCAAATAGGCAGCATATACATACCAAATTTA
64 CATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAATTGA
38297357 ACAGCACATT
129 ACAGCACATT
* *
38297367 TACACAAAAATTTAACAGCTTATATACAACAAAAGGGGCAGCATATACATACCAAATTGAGTAGC
1 TACACCAAAATTTAACAGCTTATATACAACAAAA-GGGCAGCATATACATACCAAATTGAGCAGC
* * *
38297432 ATTTTTACACCAAAATTTAACAACATATATACAACAAATAGGCAACATATACATACCAAATTGAG
65 ATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAATTGAA
**
38297497 CAGCATTTT
130 CAGCACATT
* *
38297506 TATACCAAAATTTAATAGC----ATACAACAAATA-GGCAGCATATACATACCAAATTGAGCAGC
1 TACACCAAAATTTAACAGCTTATATACAACAAA-AGGGCAGCATATACATACCAAATTGAGCAGC
*
38297566 ATTTTTATACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCA
65 ATTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCA
38297624 CATCATATAC
Statistics
Matches: 234, Mismatches: 20, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
134 83 0.35
135 10 0.04
136 1 0.00
138 24 0.10
139 116 0.50
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (138 bp):
TACACCAAAATTTAACAGCTTATATACAACAAAAGGGCAGCATATACATACCAAATTGAGCAGCA
TTTTTACACCAAAATTTAACAGCATATATACAACAAATAGGCAGCATATACATACCAAATTGAAC
AGCACATT
Found at i:38297511 original size:23 final size:23
Alignment explanation
Indices: 38297484--38297579 Score: 67
Period size: 23 Copynumber: 4.3 Consensus size: 23
38297474 CAACATATAC
38297484 ATACCAAATTGAGCAGCATTTTT
1 ATACCAAATTGAGCAGCATTTTT
* **
38297507 ATACCAAAATTTAATAGCA----T
1 ATACC-AAATTGAGCAGCATTTTT
* * * * **
38297527 ACAACAAATAG-GCAGCATATAC
1 ATACCAAATTGAGCAGCATTTTT
38297549 ATACCAAATTGAGCAGCATTTTT
1 ATACCAAATTGAGCAGCATTTTT
38297572 ATACCAAA
1 ATACCAAA
38297580 ATTTAACAGC
Statistics
Matches: 51, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
18 4 0.08
19 4 0.08
20 4 0.08
22 8 0.16
23 21 0.41
24 10 0.20
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (23 bp):
ATACCAAATTGAGCAGCATTTTT
Found at i:38297551 original size:24 final size:24
Alignment explanation
Indices: 38297524--38297621 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 24
38297514 AATTTAATAG
38297524 CATACAACAAATAGGCAGCATATA
1 CATACAACAAATAGGCAGCATATA
* * *
38297548 CATAC--CAAATTGAGCAGCATTTT
1 CATACAACAAATAG-GCAGCATATA
* * *
38297571 TATACCAA-AATTTA-ACAGCATAT-
1 CATA-CAACAA-ATAGGCAGCATATA
38297594 -ATACAACAAATAGGCAGCATATA
1 CATACAACAAATAGGCAGCATATA
38297617 CATAC
1 CATAC
38297622 CACATCATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
21 5 0.09
22 19 0.35
23 11 0.20
24 17 0.31
25 2 0.04
26 1 0.02
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.23
Consensus pattern (24 bp):
CATACAACAAATAGGCAGCATATA
Found at i:38298547 original size:41 final size:41
Alignment explanation
Indices: 38298431--38298580 Score: 212
Period size: 41 Copynumber: 3.7 Consensus size: 41
38298421 ATAAAACACT
* * * * *
38298431 GGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
*
38298472 GGCACAAAGCCTGCTA-GAATAAAGCCTGATATAATTCACC
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
*
38298512 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACT
1 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
38298553 GGCATAAAACCTGCTAGGCATAAAGCCT
1 GGCACAAAGCCTGCTAGGCATAAAGCCT
38298581 AAACTTACAG
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 35 0.36
41 63 0.64
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (41 bp):
GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
Found at i:38298551 original size:81 final size:82
Alignment explanation
Indices: 38298431--38298580 Score: 212
Period size: 81 Copynumber: 1.8 Consensus size: 82
38298421 ATAAAACACT
* * *
38298431 GGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTTCACCGGCACAAAGCCTGCTA-GAATAAA
1 GGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATTCACCGGCACAAAACCTGCTAGGAATAAA
38298495 GCCTGATATAATTCACC
66 GCCTGATATAATTCACC
* * * * * *
38298512 GGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACTGGCATAAAACCTGCTAGGCATAAA
1 GGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATTCACCGGCACAAAACCTGCTAGGAATAAA
38298577 GCCT
66 GCCT
38298581 AAACTTACAG
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 49 0.83
82 10 0.17
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (82 bp):
GGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATTCACCGGCACAAAACCTGCTAGGAATAAA
GCCTGATATAATTCACC
Found at i:38299453 original size:28 final size:26
Alignment explanation
Indices: 38299422--38299474 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
38299412 TTTTTAATGT
*
38299422 TTATTATAATATAATAATATATTATACC
1 TTATTATAACAT-AT-ATATATTATACC
38299450 TTATTATAACATATATATATTATAC
1 TTATTATAACATATATATATTATAC
38299475 TAATAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.46
27 2 0.08
28 11 0.46
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (26 bp):
TTATTATAACATATATATATTATACC
Found at i:38306290 original size:29 final size:29
Alignment explanation
Indices: 38306248--38306330 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 29
38306238 TCCACCATGA
38306248 CACGAACTCTCAATGAATAAGTTCTTTAC
1 CACGAACTCTCAATGAATAAGTTCTTTAC
* *
38306277 CACGAATTCTCAATGAATAAGCTCTTTAC
1 CACGAACTCTCAATGAATAAGTTCTTTAC
* *
38306306 CACGAACTCTCAACGAACAAGTTCT
1 CACGAACTCTCAATGAATAAGTTCT
38306331 CCACCTCTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.28
Consensus pattern (29 bp):
CACGAACTCTCAATGAATAAGTTCTTTAC
Found at i:38317355 original size:70 final size:70
Alignment explanation
Indices: 38317277--38317412 Score: 245
Period size: 70 Copynumber: 1.9 Consensus size: 70
38317267 CAACAAGCCA
* *
38317277 ATGCAAGAAATGAAATAAATATTTTGAACTCAAAATGAAATAAGTAAAAACAACAAGAAAGACAA
1 ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGAAAAAACAACAAGAAAGACAA
38317342 CATTG
66 CATTG
*
38317347 ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGAAAAAACAAGAAGAAAGACAA
1 ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGAAAAAACAACAAGAAAGACAA
38317412 C
66 C
38317413 GTTGGGCAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.18
Consensus pattern (70 bp):
ATGCAAGAAATGAAATAAATAATTTGAACTCAAAATGAAATAAGAAAAAACAACAAGAAAGACAA
CATTG
Found at i:38321344 original size:2 final size:2
Alignment explanation
Indices: 38321337--38321362 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38321327 AACGTTTTGT
38321337 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
38321363 GTAAAACAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38323133 original size:19 final size:19
Alignment explanation
Indices: 38323099--38323148 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
38323089 TTGTAATAAG
*
38323099 TTGTGTAATTAAGTAAT-T
1 TTGTGTAATTGAGTAATGT
*
38323117 CTTGTGTAATTGGGTAATGT
1 -TTGTGTAATTGAGTAATGT
38323137 TATGTGTAATTG
1 T-TGTGTAATTG
38323149 TATAATTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (19 bp):
TTGTGTAATTGAGTAATGT
Found at i:38327530 original size:402 final size:402
Alignment explanation
Indices: 38326794--38327590 Score: 1350
Period size: 402 Copynumber: 2.0 Consensus size: 402
38326784 CAAAAAGAAA
38326794 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
38326859 TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
66 TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
*
38326924 TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGGCTGGCATCAAGCAACT
131 TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
*
38326989 AATCAGAATCGACAATAAGAATGTTAACAGCATGATTTTATCAAAATGCCTTCAGCATGTAATAC
196 AATC--AA-C-ACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATAC
* *
38327054 TTTCCAACTTATAACCAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGA
257 TTTCCAACTTAAAAACAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGA
* * *
38327119 TGGAAAGGATGTAAGATAATTTGACTGGATAAGGTAAGAAGAGTAAGGTAAAGGTAAGGAAAATT
322 TGGAAAGGATGTAAGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATG
38327184 ATGCTACAAAACTGTC
387 ATGCTACAAAACTGTC
38327200 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCCA-GAATTGGAGAAAGAG
1 TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGA-CCAGGAATTGGAGAAAGAG
*
38327264 TTCGAAAACAATTCAGCAGTTAAGAGTAGGTAGCAACACATATGCTGCTTGGATGCAAATAAAGA
65 TTCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACAC--ATGCTGCTTGGATGCAAATAAAGA
* *
38327329 CCTTTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGGTTGACACGCCTGGCGTCAAGCA
128 CCTTTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCA
38327394 ACTAATC-A-ACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACT
193 ACTAATCAACACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACT
* * *
38327457 TTCCAACTTAAAAACAGTATTCATCATACATAGAA-AGATATACAGGAAATGTACTTTAAAGGGA
258 TTCCAACTTAAAAACAGAATTCATCATACA-AAAAGAGAAATACAGGAAATGTACTTTAAAGGGA
* * *
38327521 TGGAAAGGATGTACGTTAATTTGATTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATG
322 TGGAAAGGATGTAAGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATG
38327586 ATGCT
387 ATGCT
38327591 TTATTGTCTG
Statistics
Matches: 371, Mismatches: 16, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
402 173 0.47
403 3 0.01
405 1 0.00
406 98 0.26
407 3 0.01
408 93 0.25
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (402 bp):
TGCTTGCAAATAATTCCATCCAACCTGGCATGCTACAAAACTTGACCAGGAATTGGAGAAAGAGT
TCGAAAACAATTCAGCAGTTAAGAGTAGGTAACAACACATGCTGCTTGGATGCAAATAAAGACCT
TTGCATTTATTAGAAACACATTATATTTAAGAGATAAAGCTTGACACGCCTGGCATCAAGCAACT
AATCAACACAATAAGAATGTTAACAGCATGATTTCATCAAAATGCCTTCAGCATGTAATACTTTC
CAACTTAAAAACAGAATTCATCATACAAAAAGAGAAATACAGGAAATGTACTTTAAAGGGATGGA
AAGGATGTAAGATAATTTGACTGGACAAGGTAAGAAGAGTAAGGTAAAGGGAAGGAAAATGATGC
TACAAAACTGTC
Found at i:38328043 original size:15 final size:16
Alignment explanation
Indices: 38328016--38328045 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38328006 CTTTGATCCC
38328016 CTTTCCATCCACTTTT
1 CTTTCCATCCACTTTT
38328032 CTTTCC-TCCACTTT
1 CTTTCCATCCACTTT
38328046 GGGAAACAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.10, C:0.40, G:0.00, T:0.50
Consensus pattern (16 bp):
CTTTCCATCCACTTTT
Found at i:38337110 original size:35 final size:35
Alignment explanation
Indices: 38337064--38337148 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 35
38337054 GTATTTTATT
* *
38337064 AATAAAAAATCAAGGTCTGTCAAAAAATAAAATAA
1 AATAAAAAATCAAGCTCTATCAAAAAATAAAATAA
*
38337099 AATAAAAAATCAAGCTCTATCAACAAATAAAATAA
1 AATAAAAAATCAAGCTCTATCAAAAAATAAAATAA
*
38337134 AATAAAAAGTCAAGC
1 AATAAAAAATCAAGC
38337149 AAATTACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.19
Consensus pattern (35 bp):
AATAAAAAATCAAGCTCTATCAAAAAATAAAATAA
Found at i:38337764 original size:20 final size:20
Alignment explanation
Indices: 38337739--38337788 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
38337729 TGGCTTAAAA
38337739 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
38337759 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
38337776 GTGGTAGTGGATT
1 TTGGTAGTGGATT
38337789 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:38342394 original size:20 final size:20
Alignment explanation
Indices: 38342369--38342418 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
38342359 TGGCTTAAAA
38342369 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
38342389 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
38342406 GTGGTAGTGGATT
1 TTGGTAGTGGATT
38342419 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:38353715 original size:34 final size:34
Alignment explanation
Indices: 38353650--38353732 Score: 82
Period size: 34 Copynumber: 2.5 Consensus size: 34
38353640 ATGTTAAGTT
* *
38353650 TACATATATATATATATGGGTAGTATTGAATACG
1 TACAAATATATATATATAGGTAGTATTGAATACG
* * *
38353684 TACAAATATATATGTATAGTTAGT-TTCGAATAGG
1 TACAAATATATATATATAGGTAGTATT-GAATACG
*
38353718 T--GAATATATATATAT
1 TACAAATATATATATAT
38353733 GTAAAATTCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
32 12 0.29
33 2 0.05
34 27 0.66
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (34 bp):
TACAAATATATATATATAGGTAGTATTGAATACG
Found at i:38354029 original size:41 final size:41
Alignment explanation
Indices: 38353984--38354087 Score: 165
Period size: 41 Copynumber: 2.5 Consensus size: 41
38353974 GACTTTAAGT
* *
38353984 CTAGCAGGCTAAGTGCCGGTGATCT-GAATTAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGAT-TGGAATCAGGCTATAAAC
*
38354025 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
38354066 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
38354088 ATATGTTAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.02
41 58 0.98
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATTGGAATCAGGCTATAAAC
Found at i:38363955 original size:20 final size:20
Alignment explanation
Indices: 38363930--38364005 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
38363920 AAGTTTATGC
*
38363930 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
38363950 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
38363970 TGAGTAAATGAAATAGAAAG
1 TAAGTAAATGAAATGGAAAG
*
38363990 TAAGTAAATGGAATGG
1 TAAGTAAATGAAATGG
38364006 TTAGAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:38364018 original size:40 final size:40
Alignment explanation
Indices: 38363934--38364021 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
38363924 TTATGCTAAG
* * ** *
38363934 TAAATGGAATGGAAAGTAAGTAAATGAAATGGAAAGTGAG
1 TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
* **
38363974 TAAATGAAATAGAAAGTAAGTAAATGGAATGGTTAGAAAA
1 TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
38364014 TAAATGAA
1 TAAATGAA
38364022 GTGGTTCATA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (40 bp):
TAAATGAAATAGAAAGTAAGTAAATGAAATGGAAAGAAAA
Found at i:38366939 original size:16 final size:16
Alignment explanation
Indices: 38366920--38366954 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
38366910 AATAATGAGT
38366920 AAAT-AAAATAACAATG
1 AAATAAAAATAA-AATG
38366936 AAATAAAAATAAAATG
1 AAATAAAAATAAAATG
38366952 AAA
1 AAA
38366955 ACAAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAAATG
Found at i:38368387 original size:142 final size:142
Alignment explanation
Indices: 38368131--38368413 Score: 485
Period size: 142 Copynumber: 2.0 Consensus size: 142
38368121 TTCTGAACTC
* *
38368131 AGGTATCGATATTTTTACATCTAGTATCGATACCTAATCTTATGAAAGTTTTAAAACAAATAAAA
1 AGGTATCGATATTTTTACATCTAGTATCGATACCTAACCTTATGAAAGTTTTAAAACAAACAAAA
* * *
38368196 TGCCAAAATGGCACCGATTTTTATTTAAGTACTGAAACTTTTTCATAAAGTATTGATACCATAAA
66 GGCCAAAATGGCACCGATTTTTATTTAAGTACCGAAACTTTTTCATAAAGTATCGATACCATAAA
38368261 ATAAATATCGAT
131 ATAAATATCGAT
* *
38368273 AGGTATCGATTTTTTTACATCTAGTATCGATACCTGACCTTATGAAAGTTTTAAAACAAACAAAA
1 AGGTATCGATATTTTTACATCTAGTATCGATACCTAACCTTATGAAAGTTTTAAAACAAACAAAA
* *
38368338 GGCCAAAATGGTACCGATTTTTATTTAAGTACCGATACTTTTTCATAAAGTATCGATACCATAAA
66 GGCCAAAATGGCACCGATTTTTATTTAAGTACCGAAACTTTTTCATAAAGTATCGATACCATAAA
38368403 ATAAATATCGA
131 ATAAATATCGA
38368414 CGCCATTGAT
Statistics
Matches: 132, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
142 132 1.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.34
Consensus pattern (142 bp):
AGGTATCGATATTTTTACATCTAGTATCGATACCTAACCTTATGAAAGTTTTAAAACAAACAAAA
GGCCAAAATGGCACCGATTTTTATTTAAGTACCGAAACTTTTTCATAAAGTATCGATACCATAAA
ATAAATATCGAT
Found at i:38369854 original size:7 final size:7
Alignment explanation
Indices: 38369829--38369884 Score: 71
Period size: 7 Copynumber: 8.0 Consensus size: 7
38369819 GTTTTCCCAA
38369829 TTTCAAT
1 TTTCAAT
38369836 TTT-ATAT
1 TTTCA-AT
38369843 TTTCAAT
1 TTTCAAT
*
38369850 ATTCAAAT
1 TTTC-AAT
38369858 TTT-AAT
1 TTTCAAT
38369864 TTTCAAT
1 TTTCAAT
38369871 TTTCAAT
1 TTTCAAT
38369878 TTTCAAT
1 TTTCAAT
38369885 CCTCATTCCT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 7 0.16
7 30 0.70
8 6 0.14
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (7 bp):
TTTCAAT
Found at i:38369864 original size:28 final size:28
Alignment explanation
Indices: 38369827--38369883 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
38369817 ACGTTTTCCC
38369827 AATTTCAATTTT-ATATTTTCAATATTCA
1 AATTTCAATTTTCA-ATTTTCAATATTCA
* *
38369855 AATTTTAATTTTCAATTTTCAATTTTCA
1 AATTTCAATTTTCAATTTTCAATATTCA
38369883 A
1 A
38369884 TCCTCATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.35, C:0.11, G:0.00, T:0.54
Consensus pattern (28 bp):
AATTTCAATTTTCAATTTTCAATATTCA
Found at i:38372259 original size:51 final size:52
Alignment explanation
Indices: 38372195--38372300 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 52
38372185 TATGGAGTGT
*
38372195 GCCTCGCATTTCAGATAAAACAGAGCCAATACTGAGATGAGGAAGAGTTGAC
1 GCCTCGCATTTCAGATAAAACAGAGCCAATACTGAGATGAGGAAAAGTTGAC
38372247 GCCT-GCATTTCAGATAAAACAGAGCCAATACTGAGATGAGGAAAAGTTGAC
1 GCCTCGCATTTCAGATAAAACAGAGCCAATACTGAGATGAGGAAAAGTTGAC
38372298 GCC
1 GCC
38372301 CCGACGAGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 49 0.92
52 4 0.08
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.19
Consensus pattern (52 bp):
GCCTCGCATTTCAGATAAAACAGAGCCAATACTGAGATGAGGAAAAGTTGAC
Found at i:38378410 original size:40 final size:40
Alignment explanation
Indices: 38378350--38378426 Score: 136
Period size: 40 Copynumber: 1.9 Consensus size: 40
38378340 AATAGGAATG
* *
38378350 AAATGAAAGATGTCGCACAGTTGTTAGTACCCTGTAGCAA
1 AAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAGCAA
38378390 AAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAG
1 AAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAG
38378427 TAGAATGGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (40 bp):
AAATAAAAGATATCGCACAGTTGTTAGTACCCTGTAGCAA
Found at i:38390578 original size:16 final size:17
Alignment explanation
Indices: 38390519--38390577 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
38390509 TAAAAGAAAT
38390519 AAAGAAAGACAAAAGCA-
1 AAAGAAAGACAAAAG-AG
*
38390536 AAACAAA-ACAAAA-AG
1 AAAGAAAGACAAAAGAG
38390551 AAAGAAAAAGA-AAAAGAG
1 AAAG--AAAGACAAAAGAG
38390569 AAAGAAAGA
1 AAAGAAAGA
38390578 AGAACCTACG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 11 0.31
17 13 0.37
18 7 0.20
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAGACAAAAGAG
Found at i:38395547 original size:23 final size:21
Alignment explanation
Indices: 38395506--38395554 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
38395496 TAATAGGATG
*
38395506 TTTTTTTT-GTCACCTAATTAT
1 TTTTTTTTGGTCACCAAATT-T
*
38395527 TTATTTTTTGGTGACCAAATTT
1 TT-TTTTTTGGTCACCAAATTT
38395549 TTTTTT
1 TTTTTT
38395555 ATTTGCAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 6 0.25
22 9 0.38
23 9 0.38
ACGTcount: A:0.18, C:0.10, G:0.08, T:0.63
Consensus pattern (21 bp):
TTTTTTTTGGTCACCAAATTT
Found at i:38396926 original size:17 final size:15
Alignment explanation
Indices: 38396889--38396939 Score: 52
Period size: 17 Copynumber: 3.3 Consensus size: 15
38396879 GATTTTCTCT
38396889 ATTTTTTAA-A-ATA
1 ATTTTTTAATATATA
*
38396902 ATTTTTTTATTATTATGA
1 A-TTTTTTAATA-TAT-A
38396920 ATTTTTTAATATATA
1 ATTTTTTAATATATA
38396935 ATTTT
1 ATTTT
38396940 GATCAAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 1 0.03
14 7 0.23
15 7 0.23
16 3 0.10
17 11 0.35
18 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTTTTTAATATATA
Found at i:38398583 original size:30 final size:30
Alignment explanation
Indices: 38398514--38398586 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
38398504 TGGTAAGTAT
* *
38398514 TGTTCTGGAAGAAATAAATTTGACAAGATG
1 TGTTCTGAAAAAAATAAATTTGACAAGATG
* * * **
38398544 AGATATGAAAAAAATAAATTTGACGTGATG
1 TGTTCTGAAAAAAATAAATTTGACAAGATG
38398574 TGTTCTGAAAAAA
1 TGTTCTGAAAAAA
38398587 TTATTTTGAT
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (30 bp):
TGTTCTGAAAAAAATAAATTTGACAAGATG
Found at i:38398979 original size:156 final size:155
Alignment explanation
Indices: 38398640--38398979 Score: 448
Period size: 156 Copynumber: 2.2 Consensus size: 155
38398630 TAATTGTATA
* *
38398640 GAAAAAGCTT-CCAGCTGGATGTTTTTTTTGTACTATTGATTCTGAAAAATAATTTTGAGAAGCG
1 GAAAAAG-TTCCCAGCTGGATGCTTTTTTTGTACTATTGATTCTGAAAAATAATTTTGAGAAGAG
* ** * * **
38398704 GGTTTTGAAAATTTATCCCGAGATTCTTGGGAAATCTAATAGTTGGGGTTGAAAAGTGCTTCAAG
65 GGTTTTCAAAAAATATCCCGAGATTCATGGGAAATCTAATAGTTGGGGATGAAAAACGCTTCAAG
* *
38398769 TAGGATGCACTGTTAGCAAAAATACT
130 CAGGATGCACTGTCAGCAAAAATACT
* * * * * *
38398795 AAAAAAGCTCCCAGCTAGATACTTTTTTTGTACTATTGGTTCTGAAAAAATAATTTTGAGAAGAT
1 GAAAAAGTTCCCAGCTGGATGCTTTTTTTGTACTATTGATTCTG-AAAAATAATTTTGAGAAGAG
* * *
38398860 GGTTTTCAAAAAATATCCTGGGATTCATGGGAAATCTGATAGTTGGGGATGAAAAACGCTTCAAG
65 GGTTTTCAAAAAATATCCCGAGATTCATGGGAAATCTAATAGTTGGGGATGAAAAACGCTTCAAG
*
38398925 CAGGATGCACTGTCAGCAAAAGTACT
130 CAGGATGCACTGTCAGCAAAAATACT
* *
38398951 GAAAAAGTTCCCAGTTGGATGCTCTTTTT
1 GAAAAAGTTCCCAGCTGGATGCTTTTTTT
38398980 AGTAATGCTG
Statistics
Matches: 156, Mismatches: 27, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
154 1 0.01
155 36 0.23
156 119 0.76
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (155 bp):
GAAAAAGTTCCCAGCTGGATGCTTTTTTTGTACTATTGATTCTGAAAAATAATTTTGAGAAGAGG
GTTTTCAAAAAATATCCCGAGATTCATGGGAAATCTAATAGTTGGGGATGAAAAACGCTTCAAGC
AGGATGCACTGTCAGCAAAAATACT
Found at i:38402045 original size:59 final size:59
Alignment explanation
Indices: 38401975--38402200 Score: 346
Period size: 59 Copynumber: 3.8 Consensus size: 59
38401965 TAATTCCATA
* *
38401975 TTTATTAAATGAAACAATGA-AAAAATAATTTGTACAAACATATTCTAAAGAACTTCTAT
1 TTTATTAAATGAAACAAT-ATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
* * *
38402034 TTTATTGAATGAAACAATATAAAAATATTTTGTACAAAAATATTCAAAAGAACTTCTGT
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
* * *
38402093 TTTATTAAAAGAAATAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTCCTAT
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
* *
38402152 TTTATTAAATAAAACAATATAAAAATAATTTGTACAAATATATTCAAAA
1 TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAA
38402201 ATAAATCAAT
Statistics
Matches: 151, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
58 1 0.01
59 150 0.99
ACGTcount: A:0.52, C:0.08, G:0.06, T:0.34
Consensus pattern (59 bp):
TTTATTAAATGAAACAATATAAAAATAATTTGTACAAAAATATTCAAAAGAACTTCTAT
Found at i:38404602 original size:40 final size:40
Alignment explanation
Indices: 38404497--38404602 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
38404487 TTGGTGGAAA
* * *
38404497 ACACGGGGTAAAGCGCGTCGAT-GTCAGCGCGTTTTTGTTG
1 ACACGGGGTAAAGCGCGTC-CTCGTCAGCGCGCTTTTGCTG
* ** * * *
38404537 ACACAGGGTAAAGTACGCCCACGTCAGTGCGCTTTTGCTG
1 ACACGGGGTAAAGCGCGTCCTCGTCAGCGCGCTTTTGCTG
38404577 ACACGGGGTAAAGCGCGTCCTCGTCA
1 ACACGGGGTAAAGCGCGTCCTCGTCA
38404603 ACATGCTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (40 bp):
ACACGGGGTAAAGCGCGTCCTCGTCAGCGCGCTTTTGCTG
Found at i:38406833 original size:34 final size:34
Alignment explanation
Indices: 38406757--38406833 Score: 84
Period size: 34 Copynumber: 2.3 Consensus size: 34
38406747 GGAAATTGTT
* * * *
38406757 GCATTTGTTTTGATATTGTTCTTGAATTGTTCTG
1 GCATTTGTTTTGATAGTCTGCTGGAATTGTTCTG
* *
38406791 GCAGTTGTTTTGATAGTCTGCTGGAAATTGTTCTT
1 GCATTTGTTTTGATAGTCTGCTGG-AATTGTTCTG
38406826 G-ATTTGTT
1 GCATTTGTT
38406834 AGTCAGTAGA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
34 25 0.71
35 10 0.29
ACGTcount: A:0.16, C:0.09, G:0.23, T:0.52
Consensus pattern (34 bp):
GCATTTGTTTTGATAGTCTGCTGGAATTGTTCTG
Found at i:38406862 original size:107 final size:107
Alignment explanation
Indices: 38406676--38406961 Score: 464
Period size: 107 Copynumber: 2.7 Consensus size: 107
38406666 TTTTATTGGT
* * * * *
38406676 TTGTTCTGGAAATTGTTTTGATAGTCTGCAGAAAAATGTTATTGATTTGTTAGTGAGTAGAAGAT
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
*
38406741 GAAACTGGAAATTGTTGCATTTGTTTTGATATTGTTCTTGAA
66 GAAACTGAAAATTGTTGCATTTGTTTTGATATTGTTCTTGAA
* *
38406783 TTGTTCTGGCAGTTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
*
38406848 GAAACTGAAAATTGTTGCATTTGTTTTGATATTGTTCTTGAT
66 GAAACTGAAAATTGTTGCATTTGTTTTGATATTGTTCTTGAA
* * *
38406890 TTGTTCTGGAAATTGTTTTGATTGTCTACTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAATAT
1 TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
38406955 GAAACTG
66 GAAACTG
38406962 GAACTTGATT
Statistics
Matches: 165, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 165 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.44
Consensus pattern (107 bp):
TTGTTCTGGAAATTGTTTTGATAGTCTGCTGGAAATTGTTCTTGATTTGTTAGTCAGTAGAAGAT
GAAACTGAAAATTGTTGCATTTGTTTTGATATTGTTCTTGAA
Found at i:38406921 original size:23 final size:22
Alignment explanation
Indices: 38406878--38406936 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
38406868 TTGTTTTGAT
38406878 ATTGTTCTTGATTTGTTCTGGAA
1 ATTGTTCTTGA-TTGTTCTGGAA
38406901 ATTGTT-TTGATTGTCTACTGGAA
1 ATTGTTCTTGATTGT-T-CTGGAA
38406924 ATTGTTCTTGATT
1 ATTGTTCTTGATT
38406937 TGTTAGTCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 18 0.55
24 6 0.18
ACGTcount: A:0.19, C:0.08, G:0.20, T:0.53
Consensus pattern (22 bp):
ATTGTTCTTGATTGTTCTGGAA
Found at i:38408154 original size:37 final size:37
Alignment explanation
Indices: 38408111--38408199 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
38408101 ATCATAAATA
*
38408111 AATAAACTAATCAATGTTCAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
38408148 ATTAAACTAATCAATGTTAAAACTTTGAACATGCTTT
1 AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
*
38408185 AATGAACTAATCAAT
1 AATAAACTAATCAAT
38408200 ATATTTATAC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.35
Consensus pattern (37 bp):
AATAAACTAATCAATGTTAAAACTTTGAACATGCTTT
Found at i:38408451 original size:33 final size:33
Alignment explanation
Indices: 38408414--38408479 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
38408404 AATCTAAAAA
38408414 ATACCAACAATTAATTTTAGGTCAATTACACAT
1 ATACCAACAATTAATTTTAGGTCAATTACACAT
*
38408447 ATACCAACAATTAATTTTAGGTCAATTATACAT
1 ATACCAACAATTAATTTTAGGTCAATTACACAT
38408480 GCTTTATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (33 bp):
ATACCAACAATTAATTTTAGGTCAATTACACAT
Found at i:38409463 original size:24 final size:24
Alignment explanation
Indices: 38409431--38409509 Score: 149
Period size: 24 Copynumber: 3.3 Consensus size: 24
38409421 GGGAAGGTTC
38409431 AGTTGCCGATGGACGGGTTCTTCG
1 AGTTGCCGATGGACGGGTTCTTCG
38409455 AGTTGCCGATGGACGGGTTCTTCG
1 AGTTGCCGATGGACGGGTTCTTCG
38409479 AGTTGCCGATGGACGGGTTCTTCG
1 AGTTGCCGATGGACGGGTTCTTCG
*
38409503 AGATGCC
1 AGTTGCC
38409510 ATTAGTAGAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.14, C:0.22, G:0.37, T:0.28
Consensus pattern (24 bp):
AGTTGCCGATGGACGGGTTCTTCG
Found at i:38410069 original size:11 final size:11
Alignment explanation
Indices: 38410053--38410079 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
38410043 TAGAAATTAG
38410053 TTTGTGAAACT
1 TTTGTGAAACT
38410064 TTTGTGAAACT
1 TTTGTGAAACT
38410075 TTTGT
1 TTTGT
38410080 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:38411531 original size:17 final size:15
Alignment explanation
Indices: 38411504--38411542 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
38411494 ATATAAGAAC
*
38411504 ATTTTATTATTAAATT
1 ATTTTAATATT-AATT
38411520 ATATTTAATATTAATT
1 AT-TTTAATATTAATT
38411536 ATTTTAA
1 ATTTTAA
38411543 ATTGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTAATATTAATT
Found at i:38411756 original size:59 final size:58
Alignment explanation
Indices: 38411691--38411879 Score: 166
Period size: 59 Copynumber: 3.2 Consensus size: 58
38411681 ATTTTATTAA
*
38411691 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTATTT-AAATTATATTTTATAGT
* * ** * * * * * * * * *
38411750 ATCATATATTATGATTTTAGTAAATTCATGTAAAAATT-TTGATTATTAAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTA-AATT-A-TATTTTA-TAGT
*
38411811 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTAAATTATATTTTATAGT
38411870 ATCATATATT
1 ATCATATATT
38411880 ATGATTTGAG
Statistics
Matches: 93, Mismatches: 29, Indels: 16
0.67 0.21 0.12
Matches are distributed among these distances:
58 3 0.03
59 41 0.44
60 15 0.16
61 30 0.32
62 4 0.04
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (58 bp):
ATCATATATTTTAATTAAAATATATTTAATAATAATTATTTAAATTATATTTTATAGT
Found at i:38411810 original size:120 final size:120
Alignment explanation
Indices: 38411680--38411977 Score: 490
Period size: 120 Copynumber: 2.5 Consensus size: 120
38411670 AATTATTTTA
* *
38411680 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
* * *
38411744 TATAGTATCATATATTATGATTTTAGTAAATTCATGTAAAAATTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTGATTATTAAG
38411800 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
38411865 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTGATTATTAAG
* * *
38411920 AATTTTATTAAATTACATATTTTAATTATAATATATTTAATAATATTTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
38411978 ATGATTAAAT
Statistics
Matches: 167, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
120 159 0.95
121 8 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAAAATATTGATTATTAAG
Found at i:38411829 original size:18 final size:17
Alignment explanation
Indices: 38411801--38411835 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38411791 ATTATTAAGA
*
38411801 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
38411818 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
38411836 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:38416465 original size:60 final size:60
Alignment explanation
Indices: 38416332--38416468 Score: 211
Period size: 60 Copynumber: 2.3 Consensus size: 60
38416322 GCCAGTTTCT
* *
38416332 TGGGCAGAATAATAGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTGGGCTTGTTAG
1 TGGGCAGAATAATGGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTAGGCTTGTTAG
* ** * *
38416392 TGGGCAGAATAATGGGCAGCATTTTGGGCCGAATGTAGGTCAGTCTCTTAGGTTTGTTAG
1 TGGGCAGAATAATGGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTAGGCTTGTTAG
38416452 TGGGCAGAATAATGGGC
1 TGGGCAGAATAATGGGC
38416469 CGAATAGTGG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 70 1.00
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (60 bp):
TGGGCAGAATAATGGGCAACATTTTGGGCCGAATACAGGCCAGTCTCTTAGGCTTGTTAG
Found at i:38425045 original size:29 final size:29
Alignment explanation
Indices: 38424995--38425051 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
38424985 AACCCTGTGA
* *
38424995 CAAGTGGTATCAGAGCTGTTGGTTTGAAC
1 CAAGTGATATCAGAGCTATTGGTTTGAAC
* *
38425024 CAAGTGATATCCGAGTTATTGGTTTGAA
1 CAAGTGATATCAGAGCTATTGGTTTGAA
38425052 GGCACGTTGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (29 bp):
CAAGTGATATCAGAGCTATTGGTTTGAAC
Found at i:38432510 original size:18 final size:17
Alignment explanation
Indices: 38432468--38432527 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 17
38432458 AAAACAATAA
*
38432468 ATTTTATAATTTTTTAGT
1 ATTTTATAA-TTTTTAAT
*
38432486 ATGTTATAATTTTTAAT
1 ATTTTATAATTTTTAAT
* *
38432503 ATTTTTATAATCATTTACT
1 A-TTTTATAAT-TTTTAAT
38432522 ATTTTA
1 ATTTTA
38432528 AATAATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 8 0.23
18 21 0.60
19 6 0.17
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTTATAATTTTTAAT
Found at i:38432950 original size:9 final size:8
Alignment explanation
Indices: 38432925--38432954 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
38432915 AAAATATTTT
38432925 AAAAAT-A
1 AAAAATAA
38432932 AAAAATAA
1 AAAAATAA
38432940 AAAAATAA
1 AAAAATAA
38432948 AAAAATA
1 AAAAATA
38432955 TTTTTAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:38432982 original size:8 final size:7
Alignment explanation
Indices: 38432968--38433004 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
38432958 TTAAAGTATT
*
38432968 TAAAAAT
1 TAAAAAA
38432975 TAAAAAA
1 TAAAAAA
38432982 TAAAAAA
1 TAAAAAA
38432989 T-AAAAA
1 TAAAAAA
38432995 T-AAAAA
1 TAAAAAA
38433001 TAAA
1 TAAA
38433005 TATTTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAAAAA
Found at i:38432987 original size:14 final size:13
Alignment explanation
Indices: 38432968--38433001 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38432958 TTAAAGTATT
38432968 TAAAAATTAAAAAA
1 TAAAAATT-AAAAA
*
38432982 TAAAAAATAAAAA
1 TAAAAATTAAAAA
38432995 TAAAAAT
1 TAAAAAT
38433002 AAATATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
TAAAAATTAAAAA
Found at i:38433549 original size:19 final size:20
Alignment explanation
Indices: 38433514--38433551 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38433504 TTTTTAAAAA
*
38433514 TTTTAAAATATATTTTTTAT
1 TTTTAAAATATAATTTTTAT
38433534 TTTTAAAATA-AATTTTTA
1 TTTTAAAATATAATTTTTA
38433552 GTGTTCATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAAAATATAATTTTTAT
Found at i:38438490 original size:17 final size:16
Alignment explanation
Indices: 38438473--38438502 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38438463 ATTTTTGAAT
38438473 TATTTTTATTTTATAA
1 TATTTTTATTTTATAA
38438489 T-TTTTTATTTTATA
1 TATTTTTATTTTATA
38438503 TAATTGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 13 0.93
16 1 0.07
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTATTTTATAA
Found at i:38438640 original size:39 final size:42
Alignment explanation
Indices: 38438596--38438682 Score: 110
Period size: 41 Copynumber: 2.1 Consensus size: 42
38438586 TTCATGTGTT
* *
38438596 TATAATTTTTTG-TT-CTATATATTAT-AATTTTTTTAATTTA
1 TATAATTTTTTGATTGATATATATT-TGAATTTTTATAATTTA
*
38438636 -ATAATTTTTTGATTGATATATATTTGAATTTTTATATTTTA
1 TATAATTTTTTGATTGATATATATTTGAATTTTTATAATTTA
38438677 TATAAT
1 TATAAT
38438683 GTATATATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 11 0.28
40 3 0.08
41 21 0.52
42 5 0.12
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.62
Consensus pattern (42 bp):
TATAATTTTTTGATTGATATATATTTGAATTTTTATAATTTA
Found at i:38441914 original size:20 final size:20
Alignment explanation
Indices: 38441889--38441928 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38441879 GCCTGTTACC
38441889 CAAAAGCTATTCCCGTTTCT
1 CAAAAGCTATTCCCGTTTCT
38441909 CAAAAGCTATTCCCGTTTCT
1 CAAAAGCTATTCCCGTTTCT
38441929 TTCTTTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.10, T:0.35
Consensus pattern (20 bp):
CAAAAGCTATTCCCGTTTCT
Found at i:38448436 original size:2 final size:2
Alignment explanation
Indices: 38448429--38448509 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
38448419 TGATGTCAAA
38448429 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
38448471 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
38448510 AAATAGGATC
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:38450200 original size:21 final size:21
Alignment explanation
Indices: 38450145--38450200 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
38450135 TTCTCACATC
*
38450145 AATTTAATATTAAAGAATAAT
1 AATTTAATATAAAAGAATAAT
**
38450166 -ATTTTCTATCAAAAGAATAAT
1 AATTTAATAT-AAAAGAATAAT
38450187 AATTTAATATAAAA
1 AATTTAATATAAAA
38450201 TATTATTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 7 0.25
21 14 0.50
22 7 0.25
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (21 bp):
AATTTAATATAAAAGAATAAT
Found at i:38450228 original size:23 final size:22
Alignment explanation
Indices: 38450202--38450257 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
38450192 AATATAAAAT
*
38450202 ATTATTTTAATATTTTATATTAA
1 ATTATATTAA-ATTTTATATTAA
*
38450225 ATTATATTAAATTTTTTATT--
1 ATTATATTAAATTTTATATTAA
*
38450245 TTTATATTAAATT
1 ATTATATTAAATT
38450258 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.40
22 9 0.30
23 9 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATATTAAATTTTATATTAA
Found at i:38450231 original size:10 final size:10
Alignment explanation
Indices: 38450216--38450274 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 10
38450206 TTTTAATATT
38450216 TTATATTAAA
1 TTATATTAAA
38450226 TTATATTAAA
1 TTATATTAAA
* **
38450236 TT-TTTTATTT
1 TTATATTA-AA
38450246 TTATATTAAA
1 TTATATTAAA
*
38450256 TTATTTTAAA
1 TTATATTAAA
*
38450266 ATAT-TTAAA
1 TTATATTAAA
38450275 ATATTTTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
9 9 0.23
10 26 0.67
11 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATATTAAA
Found at i:38450282 original size:40 final size:40
Alignment explanation
Indices: 38450216--38450292 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
38450206 TTTTAATATT
* *
38450216 TTATATTAAATTATATTAAATTTTTTATTTTTATATTAAA
1 TTATATTAAAATATATTAAATATTTTATTTTTATATTAAA
*
38450256 TTATTTTAAAATAT-TTAAAATATTTTATTTTTATATT
1 TTATATTAAAATATATT-AAATATTTTATTTTTATATT
38450293 TTCTGAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (40 bp):
TTATATTAAAATATATTAAATATTTTATTTTTATATTAAA
Found at i:38450898 original size:69 final size:68
Alignment explanation
Indices: 38450786--38450960 Score: 201
Period size: 69 Copynumber: 2.5 Consensus size: 68
38450776 ATCATCCTGA
* * *
38450786 AATTACATACAAAAAGTTATAATACTCCACCACCACACCCATTTAAACATTCAAAAAGT-AGCAA
1 AATTACATACAAAAAGTTATATTA-TCCACCACCACACACATTTAAACATACAAAAAGTGA-CAA
38450850 -CCTAC
64 CCCT-C
* * * * *
38450855 AATTACATACAAAAAGTTATATTAGTTCACCACCACATACATTTACACATAGACAAAGTGACAAC
1 AATTACATACAAAAAGTTATATTA-TCCACCACCACACACATTTAAACATACAAAAAGTGACAAC
38450920 CCTC
65 CCTC
* *
38450924 TATGACATACAAAAAGTTATATTCATCCACCACCACA
1 AATTACATACAAAAAGTTATATT-ATCCACCACCACA
38450961 ATCACATCTT
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
69 86 0.95
70 5 0.05
ACGTcount: A:0.45, C:0.26, G:0.06, T:0.23
Consensus pattern (68 bp):
AATTACATACAAAAAGTTATATTATCCACCACCACACACATTTAAACATACAAAAAGTGACAACC
CTC
Found at i:38456515 original size:25 final size:25
Alignment explanation
Indices: 38456443--38456544 Score: 88
Period size: 25 Copynumber: 4.2 Consensus size: 25
38456433 AAGTTCAAGC
**
38456443 GAGCCA-T-ATCGGGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCCAAA
**
38456466 GAG-CATTAATCAAGAAGCTCACAAA
1 GAGCCATTAATCGGGAAGCTC-CAAA
*
38456491 GAGCCTTTAATCGGGAAGCTCCAAA
1 GAGCCATTAATCGGGAAGCTCCAAA
*
38456516 GAGCCA-TATATCGAGAAGCT-CATAA
1 GAGCCATTA-ATCGGGAAGCTCCA-AA
38456541 GAGC
1 GAGC
38456545 TGCGGTGTGT
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
22 2 0.03
23 4 0.06
24 14 0.22
25 30 0.47
26 14 0.22
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCCAAA
Found at i:38459141 original size:24 final size:23
Alignment explanation
Indices: 38459062--38459148 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
38459052 TTAGTGTTCA
**
38459062 TGAACATGTTCATTTAAC-TTAAT
1 TGAACATGTTCA-CGAACATTAAT
*
38459085 TGAACATGTTCACGAACATTAAA
1 TGAACATGTTCACGAACATTAAT
* * *
38459108 TGAACTTGTTCATGGACATATAAT
1 TGAACATGTTCACGAACAT-TAAT
38459132 TGAACATGTTCACGAAC
1 TGAACATGTTCACGAAC
38459149 CTTGTTAATA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.62
24 17 0.33
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCACGAACATTAAT
Found at i:38465209 original size:25 final size:25
Alignment explanation
Indices: 38465172--38465222 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
38465162 ACAGTAAACA
* * *
38465172 CGAATTATGTAGAAAGCCTTTGTGG
1 CGAATTATCTAGAAAACCCTTGTGG
*
38465197 CGAATTCTCTAGAAAACCCTTGTGG
1 CGAATTATCTAGAAAACCCTTGTGG
38465222 C
1 C
38465223 ACACTCGCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (25 bp):
CGAATTATCTAGAAAACCCTTGTGG
Found at i:38466480 original size:41 final size:41
Alignment explanation
Indices: 38466423--38466501 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
38466413 TATAGACATT
** * * *
38466423 ACCTTTAGCGGTGCTTTCCCCACAAATGTTGCTAAAGAACA
1 ACCTTTAGCGACGCTTTCCCCAAAAACGCTGCTAAAGAACA
38466464 ACCTTTAGCGACGCTTTCCCCAAAAACGCTGCTAAAGA
1 ACCTTTAGCGACGCTTTCCCCAAAAACGCTGCTAAAGA
38466502 CCATATCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (41 bp):
ACCTTTAGCGACGCTTTCCCCAAAAACGCTGCTAAAGAACA
Done.