Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001711.1 Hibiscus syriacus cultivar Beakdansim tig00003454_pilon, 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: 4148933
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:2844583 original size:28 final size:28
Alignment explanation
Indices: 2844543--2844627 Score: 152
Period size: 28 Copynumber: 3.0 Consensus size: 28
2844533 GGCTCATCGC
2844543 AAGCTAATGTTTGTTCTATAACAAAAGT
1 AAGCTAATGTTTGTTCTATAACAAAAGT
*
2844571 AAGCTAATGTTTGTTCTATAACAAAATT
1 AAGCTAATGTTTGTTCTATAACAAAAGT
*
2844599 AAGCTAATGTTTGTTCTATAACATAAGT
1 AAGCTAATGTTTGTTCTATAACAAAAGT
2844627 A
1 A
2844628 TAAATTAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.38
Consensus pattern (28 bp):
AAGCTAATGTTTGTTCTATAACAAAAGT
Found at i:2845220 original size:19 final size:20
Alignment explanation
Indices: 2845196--2845234 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2845186 CAAAATGATC
*
2845196 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
2845215 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
2845235 TCATTTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:2852361 original size:12 final size:12
Alignment explanation
Indices: 2852344--2852368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2852334 CCTTGAGAAG
2852344 AAAGTAGAAATC
1 AAAGTAGAAATC
2852356 AAAGTAGAAATC
1 AAAGTAGAAATC
2852368 A
1 A
2852369 TGATTCTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAGTAGAAATC
Found at i:2857179 original size:22 final size:21
Alignment explanation
Indices: 2857127--2857179 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
2857117 TTTTCCAGAA
* *
2857127 TGCTACAGGGGTATCGATACCC
1 TGCTACA-GTGTACCGATACCC
*
2857149 TGCTTCAGTGTACCGATACCC
1 TGCTACAGTGTACCGATACCC
2857170 TTGCTACAGT
1 -TGCTACAGT
2857180 AATTTCGGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (21 bp):
TGCTACAGTGTACCGATACCC
Found at i:2857994 original size:32 final size:32
Alignment explanation
Indices: 2857883--2858075 Score: 290
Period size: 32 Copynumber: 6.1 Consensus size: 32
2857873 GCTCTTATAA
2857883 TAAT-CTGTCCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
2857914 TAA-ACTGTCCATATGTCCCG-AAGAACATAGG
1 TAATACTGTCCATATGTCCCGAAAG-ACATAGG
*
2857945 TAA-ACTGTCCATCTGTCCCGAATA-ACATAGG
1 TAATACTGTCCATATGTCCCGAA-AGACATAGG
*
2857976 TAATACTGTTCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
2858008 TAATACTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
*
2858040 TAATATTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCGAAAGACATAGG
2858072 TAAT
1 TAAT
2858076 CCTCGACTCT
Statistics
Matches: 152, Mismatches: 5, Indels: 9
0.92 0.03 0.05
Matches are distributed among these distances:
31 60 0.39
32 91 0.60
33 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCGAAAGACATAGG
Found at i:2861121 original size:12 final size:12
Alignment explanation
Indices: 2861104--2861130 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2861094 ATTTCAATCC
2861104 CAACTAGCACTA
1 CAACTAGCACTA
2861116 CAACTAGCACTA
1 CAACTAGCACTA
2861128 CAA
1 CAA
2861131 TTCATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.33, G:0.07, T:0.15
Consensus pattern (12 bp):
CAACTAGCACTA
Found at i:2861909 original size:10 final size:11
Alignment explanation
Indices: 2861881--2861913 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
2861871 GTTTGATACT
2861881 TTCTCT-TTGA
1 TTCTCTCTTGA
2861891 TTCTCTCTTGA
1 TTCTCTCTTGA
2861902 TTCT-TCTTGA
1 TTCTCTCTTGA
2861912 TT
1 TT
2861914 GATGTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.09, C:0.21, G:0.09, T:0.61
Consensus pattern (11 bp):
TTCTCTCTTGA
Found at i:2862259 original size:45 final size:46
Alignment explanation
Indices: 2862179--2862269 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
2862169 TGAAAAGCTA
* * *
2862179 GAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCATT
1 GAGTGCATCGAAGCATGGTCATGTGCATCGATGCATAAAATGCATT
*
2862225 GAGTGCATTGAAGCATGGT-ATGTGCATCGATGCATAAAATGCATT
1 GAGTGCATCGAAGCATGGTCATGTGCATCGATGCATAAAATGCATT
2862270 CGATGTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 24 0.59
46 17 0.41
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.30
Consensus pattern (46 bp):
GAGTGCATCGAAGCATGGTCATGTGCATCGATGCATAAAATGCATT
Found at i:2862312 original size:20 final size:20
Alignment explanation
Indices: 2862287--2862324 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2862277 TGAAAAATTA
2862287 ATTGGTGCATCGCTGCATGG
1 ATTGGTGCATCGCTGCATGG
*
2862307 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGCTGCAT
2862325 CACTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.18, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGCTGCATGG
Found at i:2863454 original size:21 final size:21
Alignment explanation
Indices: 2863430--2863473 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2863420 GAGCCGGAGG
* *
2863430 AGGAGGAGCACGAGAGGAGCT
1 AGGAGCAGCACGAGAGGAACT
* *
2863451 AGGAGCAGCTCGTGAGGAACT
1 AGGAGCAGCACGAGAGGAACT
2863472 AG
1 AG
2863474 CTCCCGGAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.43, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAGGAACT
Found at i:2869827 original size:20 final size:20
Alignment explanation
Indices: 2869802--2869853 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
2869792 CGTTAAACAG
2869802 TGGGGGGAATCGATACACCC
1 TGGGGGGAATCGATACACCC
*
2869822 TGGGGGGAATCGATACCCCC
1 TGGGGGGAATCGATACACCC
*
2869842 TGGTGGGAATCG
1 TGGGGGGAATCG
2869854 GTTCCCTCCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.17
Consensus pattern (20 bp):
TGGGGGGAATCGATACACCC
Found at i:2871556 original size:21 final size:22
Alignment explanation
Indices: 2871526--2871568 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2871516 TTAGGATCAA
*
2871526 TGGGATTAAAAATAGGATTTGG
1 TGGGATTAAAAAGAGGATTTGG
*
2871548 TGGGA-TAAAAGGAGGATTTGG
1 TGGGATTAAAAAGAGGATTTGG
2871569 AGGAGGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (22 bp):
TGGGATTAAAAAGAGGATTTGG
Found at i:2872324 original size:22 final size:22
Alignment explanation
Indices: 2872250--2872330 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
2872240 AGAACCCTTG
*
2872250 GGGGGTATCGATTCCCC-T-AA
1 GGGGGAATCGATTCCCCTTCAA
*
2872270 GGGGGAATC-AGTTCCCATTCAAA
1 GGGGGAATCGA-TTCCCCTTC-AA
* *
2872293 GGGGGAATCGGTTCCCCTTCAT
1 GGGGGAATCGATTCCCCTTCAA
*
2872315 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
2872331 TCTGCCCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 13 0.27
21 1 0.02
22 15 0.31
23 19 0.39
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:2884694 original size:21 final size:21
Alignment explanation
Indices: 2884668--2884726 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
2884658 GTTGGGAGCG
2884668 TAAGTGCATCGATGCATACCC
1 TAAGTGCATCGATGCATACCC
2884689 TAAGTGCATCGATGCATACCC
1 TAAGTGCATCGATGCATACCC
* *
2884710 TAGGTGCATCGGTGCAT
1 TAAGTGCATCGATGCAT
2884727 CAGTGTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (21 bp):
TAAGTGCATCGATGCATACCC
Found at i:2885523 original size:48 final size:45
Alignment explanation
Indices: 2885447--2885573 Score: 148
Period size: 48 Copynumber: 2.8 Consensus size: 45
2885437 TATAAAATTT
2885447 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTT-CCAAAATA
* * *
2885493 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATCCCATAAGCTCATAAGCTTATTTTTCCAAAATA
* * * * *
2885540 CTTTCCA-ATATTCCGTAAGCTCATAAGATTATTT
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTT
2885574 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
44 22 0.31
46 11 0.15
47 13 0.18
48 25 0.35
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTTCCAAAATA
Found at i:2885572 original size:44 final size:46
Alignment explanation
Indices: 2885460--2885573 Score: 142
Period size: 44 Copynumber: 2.5 Consensus size: 46
2885450 ACCATTTATC
2885460 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATTTAAATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCA--TAAATT
* * * *
2885508 CCATAAGCTCGTAAGCTTATTTTT-CCAATATACTTTCCA-ATATT
1 CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATAAATT
* *
2885552 CCGTAAGCTCATAAGATTATTT
1 CCATAAGCTCATAAGCTTATTT
2885574 GCATGGTTAC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 23 0.39
47 13 0.22
48 23 0.39
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (46 bp):
CCATAAGCTCATAAGCTTATTTTTACCAAAATACTTACCATAAATT
Found at i:2889464 original size:6 final size:6
Alignment explanation
Indices: 2889448--2889539 Score: 53
Period size: 6 Copynumber: 14.3 Consensus size: 6
2889438 ATCTCTCATT
* * * *
2889448 TTTTCTC TTTTTC -TTTTC TTTCTC ATTTTCATT TTTTTC TTCTTC GTTTTC
1 TTTT-TC TTTTTC TTTTTC TTTTTC -TTTT--TC TTTTTC TTTTTC TTTTTC
*
2889499 TTTTTC TTTTTC TATTATTT TTTTTC TTCTATT- TTTTTC TT
1 TTTTTC TTTTTC T-TT-TTC TTTTTC TT-T-TTC TTTTTC TT
2889540 CTTATAATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
5 7 0.11
6 35 0.53
7 14 0.21
8 9 0.14
9 1 0.02
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:2889483 original size:33 final size:33
Alignment explanation
Indices: 2889443--2889527 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
2889433 TTTTCATCTC
*
2889443 TCATTTTTTCTCTTTTTC-TTTTCTTTCTCATTT
1 TCATTTTTT-TCTTCTTCGTTTTCTTTCTCATTT
* *
2889476 TCATTTTTTTCTTCTTCGTTTTCTTTTTCTTTT
1 TCATTTTTTTCTTCTTCGTTTTCTTTCTCATTT
*
2889509 TCTATTATTTTTTTTCTTC
1 TC-ATT-TTTTTCTTCTTC
2889528 TATTTTTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 7 0.16
33 24 0.53
34 3 0.07
35 11 0.24
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (33 bp):
TCATTTTTTTCTTCTTCGTTTTCTTTCTCATTT
Found at i:2889501 original size:38 final size:38
Alignment explanation
Indices: 2889456--2889528 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
2889446 TTTTTTCTCT
*
2889456 TTTTC-TTTTCTTTCTC-ATTTTCATTTTTTTCTTCTTCG
1 TTTTCTTTTTCTTTCTCTATTAT--TTTTTTTCTTCTTCG
*
2889494 TTTTCTTTTTCTTTTTCTATTATTTTTTTTCTTCT
1 TTTTCTTTTTCTTTCTCTATTATTTTTTTTCTTCT
2889529 ATTTTTTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 17 0.55
39 10 0.32
40 4 0.13
ACGTcount: A:0.05, C:0.18, G:0.01, T:0.75
Consensus pattern (38 bp):
TTTTCTTTTTCTTTCTCTATTATTTTTTTTCTTCTTCG
Found at i:2889511 original size:21 final size:22
Alignment explanation
Indices: 2889453--2889511 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
2889443 TCATTTTTTC
*
2889453 TCTTTTTCTTTTCTTTCTCATTT
1 TCTTTTTCTTTT-TCTCTCATTT
* *
2889476 TCATTTTT-TTCTTCT-TCGTTT
1 TC-TTTTTCTTTTTCTCTCATTT
2889497 TCTTTTTCTTTTTCT
1 TCTTTTTCTTTTTCT
2889512 ATTATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.17
21 13 0.43
22 2 0.07
23 5 0.17
24 5 0.17
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (22 bp):
TCTTTTTCTTTTTCTCTCATTT
Found at i:2889519 original size:17 final size:16
Alignment explanation
Indices: 2889445--2889539 Score: 79
Period size: 17 Copynumber: 5.7 Consensus size: 16
2889435 TTCATCTCTC
2889445 ATTTTTTCTCTTTTTCT
1 ATTTTTT-TCTTTTTCT
*
2889462 -TTTCTTTCTCATTTTC-
1 ATTT-TTT-TCTTTTTCT
*
2889478 ATTTTTTTCTTCTTCGT
1 ATTTTTTTCTTTTTC-T
*
2889495 TTTCTTTTTCTTTTTCT
1 ATT-TTTTTCTTTTTCT
2889512 ATTATTTTT-TTTCTTCT
1 ATT-TTTTTCTTT-TTCT
2889529 ATTTTTTTCTT
1 ATTTTTTTCTT
2889540 CTTATAATAT
Statistics
Matches: 64, Mismatches: 7, Indels: 14
0.75 0.08 0.16
Matches are distributed among these distances:
15 6 0.09
16 14 0.22
17 33 0.52
18 11 0.17
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (16 bp):
ATTTTTTTCTTTTTCT
Found at i:2889531 original size:14 final size:13
Alignment explanation
Indices: 2889478--2889541 Score: 55
Period size: 13 Copynumber: 5.0 Consensus size: 13
2889468 TCTCATTTTC
2889478 ATTTTTTTCTTCT
1 ATTTTTTTCTTCT
**
2889491 -TCGTTTTCTT-T
1 ATTTTTTTCTTCT
2889502 -TTCTTTTTCTAT-T
1 ATT-TTTTTCT-TCT
2889515 ATTTTTTTTCTTCT
1 A-TTTTTTTCTTCT
2889529 ATTTTTTTCTTCT
1 ATTTTTTTCTTCT
2889542 TATAATATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 2 0.05
12 14 0.33
13 15 0.36
14 9 0.21
15 2 0.05
ACGTcount: A:0.06, C:0.16, G:0.02, T:0.77
Consensus pattern (13 bp):
ATTTTTTTCTTCT
Found at i:2892341 original size:48 final size:45
Alignment explanation
Indices: 2892265--2892393 Score: 154
Period size: 48 Copynumber: 2.8 Consensus size: 45
2892255 TATAAAATTT
2892265 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTTACCAAAATA
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTT-CCAAAATA
* * *
2892311 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATCCCATAAGCTCATAAGCTTATTTTTCCAAAATA
* * * *
2892358 CTTGCCA-TTATTCCGTAAGCTCATAAGATT-TTTTTC
1 CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTTC
2892394 ATGGTTACCA
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
43 6 0.08
44 18 0.24
46 12 0.16
47 13 0.18
48 25 0.34
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCATAAGCTTATTTTTCCAAAATA
Found at i:2892542 original size:40 final size:40
Alignment explanation
Indices: 2892496--2892577 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
2892486 ACCGTAGTGC
2892496 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2892536 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
2892576 TA
1 TA
2892578 TAAACCTGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:2894732 original size:19 final size:20
Alignment explanation
Indices: 2894689--2894741 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
2894679 AAAAGCCAAA
2894689 GTGCATCGATGCATGGTATT
1 GTGCATCGATGCATGGTATT
*
2894709 GTGCAACGATGCATGGTA-T
1 GTGCATCGATGCATGGTATT
2894728 GTGCATCGATGCAT
1 GTGCATCGATGCAT
2894742 AAAATGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATGGTATT
Found at i:2894794 original size:20 final size:20
Alignment explanation
Indices: 2894769--2894806 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2894759 TGAAAAATTA
2894769 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
* *
2894789 ATTGGTTCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2894807 CACTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2897577 original size:26 final size:26
Alignment explanation
Indices: 2897548--2897600 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2897538 ACGGTCTGAC
* *
2897548 GTGGTAGTTTCTAGAAGGTCCAGTCA
1 GTGGCAGTTTCTAGAAGATCCAGTCA
*
2897574 GTGGCAGTTTCTAGAAGATCTAGTCA
1 GTGGCAGTTTCTAGAAGATCCAGTCA
2897600 G
1 G
2897601 CGCGCCTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (26 bp):
GTGGCAGTTTCTAGAAGATCCAGTCA
Found at i:2905455 original size:17 final size:17
Alignment explanation
Indices: 2905429--2905462 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2905419 TATGAACTTG
2905429 ACTTTGAATTTTACGCC
1 ACTTTGAATTTTACGCC
* *
2905446 ACTTTTAATTTTTCGCC
1 ACTTTGAATTTTACGCC
2905463 GAATCGTCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.47
Consensus pattern (17 bp):
ACTTTGAATTTTACGCC
Found at i:2907818 original size:26 final size:26
Alignment explanation
Indices: 2907760--2907810 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2907750 GGTTTGACAT
* * *
2907760 GACAATTTCTAGAAGGTCTAGTCAGC
1 GACAGTTTCTAGAAGATCCAGTCAGC
2907786 GACAGTTTCTAGAAGATCCAGTCAG
1 GACAGTTTCTAGAAGATCCAGTCAG
2907811 ACATAGTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (26 bp):
GACAGTTTCTAGAAGATCCAGTCAGC
Found at i:2908057 original size:26 final size:27
Alignment explanation
Indices: 2908002--2908058 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
2907992 AAATTCTCTC
*
2908002 TTTTATTTTATTTTTCAAGTTTTCGGT
1 TTTTATTTTATTTTTCAAGCTTTCGGT
* *
2908029 TTTTCTTTTATTTTT-AAGCTTT-GTT
1 TTTTATTTTATTTTTCAAGCTTTCGGT
2908054 TTTTA
1 TTTTA
2908059 ATATGCTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 6 0.23
26 6 0.23
27 14 0.54
ACGTcount: A:0.14, C:0.07, G:0.09, T:0.70
Consensus pattern (27 bp):
TTTTATTTTATTTTTCAAGCTTTCGGT
Found at i:2912247 original size:138 final size:139
Alignment explanation
Indices: 2912017--2912487 Score: 411
Period size: 138 Copynumber: 3.4 Consensus size: 139
2912007 TAAATATTCC
* * * * * * * * * *
2912017 CCTATATTAAGAACTAAAATGAAATTAAACCGAAAATTAAGACTTTAATATT-AATCTTAACCAA
1 CCTAAATTAAGGACTAAAGTGAAATTAAACCTAAAATAAAGGCTCTAATATTAAAACCTAACCAT
* * * * * * *
2912081 CTTTAACAGTTTACTGGGTCGAATAACTAAAATGGAACCTCAAGTAAAAATGCT-AAGACCAAAT
66 TTTTAACAATTTATTGGATCAAATAACTAAAATAGAACCTCAAGCAAAAATG-TGAAGACCAAAT
*
2912145 AAGATATTAT
130 AAGAAATTAT
* *
2912155 CCTAATTTAAGGACTAAAGTGAAATT-AATCTAAAATAAAGGCTCTAATATTAAAACCTAACCAT
1 CCTAAATTAAGGACTAAAGTGAAATTAAACCTAAAATAAAGGCTCTAATATTAAAACCTAACCAT
* * * *
2912219 TTTTAACAATTTATTGGATCAAATAACTAAAATAGAACCTCAAGCATAATTGTGAGGACCAAATC
66 TTTTAACAATTTATTGGATCAAATAACTAAAATAGAACCTCAAGCAAAAATGTGAAGACCAAATA
*
2912284 AGAAATTCT
131 AGAAATTAT
* **
2912293 CCTAAATTAAGAGACT-AAGATGAAGTTAAACCTAAAATGGAGGCTCTAATATTAAAACCTAACC
1 CCTAAATTAAG-GACTAAAG-TGAAATTAAACCTAAAATAAAGGCTCTAATATTAAAACCTAACC
* * * * ** * * * * *
2912357 ATTTTTAACCATTTATTGAAAT-GAATAATTAATTTGGAACTTCCAGC-AAAA-GCGACGACCCA
64 ATTTTTAACAATTTATTG-GATCAAATAACTAAAATAGAACCTCAAGCAAAAATGTGAAGA-CCA
* *
2912419 ATTAA-AAATT-C
127 AATAAGAAATTAT
* * **
2912430 CTCTAAATTAAGGGACTAAGGTGAAATTAAATCTAAAATGGAGGCTCTAATATTAAAA
1 C-CTAAATTAA-GGACTAAAGTGAAATTAAACCTAAAATAAAGGCTCTAATATTAAAA
2912488 AACTATTTAT
Statistics
Matches: 274, Mismatches: 49, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
137 22 0.08
138 161 0.59
139 21 0.08
140 68 0.25
141 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (139 bp):
CCTAAATTAAGGACTAAAGTGAAATTAAACCTAAAATAAAGGCTCTAATATTAAAACCTAACCAT
TTTTAACAATTTATTGGATCAAATAACTAAAATAGAACCTCAAGCAAAAATGTGAAGACCAAATA
AGAAATTAT
Found at i:2913050 original size:2 final size:2
Alignment explanation
Indices: 2913043--2913085 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2913033 ATTAAATGTA
2913043 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2913084 AT
1 AT
2913086 TGAAATACGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2918861 original size:13 final size:13
Alignment explanation
Indices: 2918843--2918867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2918833 AAAAATGAGA
2918843 TGGACATTTTATT
1 TGGACATTTTATT
2918856 TGGACATTTTAT
1 TGGACATTTTAT
2918868 ACAATTTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (13 bp):
TGGACATTTTATT
Found at i:2919079 original size:52 final size:51
Alignment explanation
Indices: 2919007--2919147 Score: 140
Period size: 53 Copynumber: 2.7 Consensus size: 51
2918997 CGTCATGTTG
* * * ** * *
2919007 AGGTGACAAATTTTTATAAAAAAATATTTTTTTATTATAATTTTTTATCTCG
1 AGGTGA-AGATTTTAATAAAAAAATATTTTTTTATTAGAATTAGTCATCTCA
*
2919059 ATGTGATAGATTTTAATAAAAAAA-ATTATATTTTATTAGAATTAGTCATCTCA
1 AGGTGA-AGATTTTAATAAAAAAATATT-T-TTTTATTAGAATTAGTCATCTCA
* *
2919112 AGGTGACGAGTTTGAATAAAAAAATATTTTTTTATT
1 AGGTGAAGA-TTTTAATAAAAAAATATTTTTTTATT
2919148 CAAACTCATC
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
51 3 0.04
52 30 0.41
53 37 0.51
54 3 0.04
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.45
Consensus pattern (51 bp):
AGGTGAAGATTTTAATAAAAAAATATTTTTTTATTAGAATTAGTCATCTCA
Found at i:2919784 original size:8 final size:7
Alignment explanation
Indices: 2919754--2919783 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2919744 ATTTTATCAC
2919754 TATTTATT
1 TATTT-TT
2919762 TATTTTT
1 TATTTTT
2919769 TATTTTT
1 TATTTTT
2919776 TATTTTT
1 TATTTTT
2919783 T
1 T
2919784 TCCTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TATTTTT
Found at i:2919820 original size:12 final size:13
Alignment explanation
Indices: 2919791--2919820 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2919781 TTTTCCTTTT
2919791 TTTCCCTTTTCTA
1 TTTCCCTTTTCTA
2919804 TTTCCCTTTTC-A
1 TTTCCCTTTTCTA
2919816 TTTCC
1 TTTCC
2919821 TCTCTACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTCCCTTTTCTA
Found at i:2924954 original size:32 final size:32
Alignment explanation
Indices: 2924869--2924945 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
2924859 TAAGGTGACC
2924869 CTTGGGTAGGCTCCGAAGCCCCGAGAAACTTT
1 CTTGGGTAGGCTCCGAAGCCCCGAGAAACTTT
*
2924901 CTTGAGTAGGCTCCGAAGCCCCGAGAAACTTT
1 CTTGGGTAGGCTCCGAAGCCCCGAGAAACTTT
2924933 CTTGGGTAGGCTC
1 CTTGGGTAGGCTC
2924946 TTAGGCCCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23
Consensus pattern (32 bp):
CTTGGGTAGGCTCCGAAGCCCCGAGAAACTTT
Found at i:2926413 original size:2 final size:2
Alignment explanation
Indices: 2926406--2926432 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2926396 TTTTATAAAT
2926406 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2926433 TTAATATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2936149 original size:90 final size:90
Alignment explanation
Indices: 2936033--2936210 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
2936023 TAATCCTGAA
* * * *
2936033 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
2936098 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
2936123 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTTAAATAATAAAAACCCTAATATGAC
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
2936188 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
2936211 GTGTGTTAGG
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:2942993 original size:90 final size:90
Alignment explanation
Indices: 2942872--2943049 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
2942862 TAATCCCGAA
* * * * *
2942872 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
2942937 TAGGGTAGCTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
2942962 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
*
2943027 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
2943050 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 81 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAC
TAGGGTAACTTGGATATAAAAGGAT
Found at i:2947472 original size:20 final size:19
Alignment explanation
Indices: 2947401--2947475 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 19
2947391 AGTTGTGAAA
2947401 AAATATAAAAAGA-AAATAAT
1 AAATATAAAAA-ATAAA-AAT
* *
2947421 AAATGATGATAAATAAAAAT
1 AAAT-ATAAAAAATAAAAAT
*
2947441 AAATACTGAAAAATAAAAAT
1 AAATA-TAAAAAATAAAAAT
2947461 AAAATATAAAAAATA
1 -AAATATAAAAAATA
2947476 TGTATATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 33 0.70
21 13 0.28
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.21
Consensus pattern (19 bp):
AAATATAAAAAATAAAAAT
Found at i:2947858 original size:5 final size:5
Alignment explanation
Indices: 2947850--2947888 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
2947840 CGAAACGAAA
*
2947850 AAAAT AAAAT AAATAT AAAAAT AAAAT AAAAT GAAAT AA
1 AAAAT AAAAT AAA-AT -AAAAT AAAAT AAAAT AAAAT AA
2947889 TGTCGGTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 23 0.77
6 4 0.13
7 3 0.10
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:2951476 original size:20 final size:18
Alignment explanation
Indices: 2951435--2951477 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
2951425 ATCAGTACTT
2951435 TGTGTGCTTTAGGCACTA
1 TGTGTGCTTTAGGCACTA
2951453 TGTGTGCTTTAGGCACTA
1 TGTGTGCTTTAGGCACTA
2951471 TGTGTGC
1 TGTGTGC
2951478 ATCCATGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.16, G:0.30, T:0.40
Consensus pattern (18 bp):
TGTGTGCTTTAGGCACTA
Found at i:2959069 original size:27 final size:28
Alignment explanation
Indices: 2959039--2959099 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
2959029 TTATTAAATA
2959039 AATATTAAAATAATAAATTATA-TTTTT
1 AATATTAAAATAATAAATTATATTTTTT
* * * * *
2959066 AATATTTAAATTATCACTTTTATTTTTT
1 AATATTAAAATAATAAATTATATTTTTT
2959094 AATATT
1 AATATT
2959100 TGAATTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (28 bp):
AATATTAAAATAATAAATTATATTTTTT
Found at i:2959094 original size:21 final size:20
Alignment explanation
Indices: 2959052--2959117 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
2959042 ATTAAAATAA
* * *
2959052 TAAATTATATTTTTAATATT
1 TAAATTATAATTTTATTTTT
*
2959072 TAAATTATCACTTTTATTTTT
1 TAAATTAT-AATTTTATTTTT
2959093 TAATATT-TGAATTTTATTTTT
1 TAA-ATTAT-AATTTTATTTTT
2959114 TAAA
1 TAAA
2959118 ATCATACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 9 0.23
21 27 0.69
22 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (20 bp):
TAAATTATAATTTTATTTTT
Found at i:2959755 original size:21 final size:21
Alignment explanation
Indices: 2959730--2959771 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
2959720 AGCATATAGA
2959730 GCTACCATGACATAAGTGAAT
1 GCTACCATGACATAAGTGAAT
2959751 GCTACCATGACATAAGTGAAT
1 GCTACCATGACATAAGTGAAT
2959772 TTCTCCTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
GCTACCATGACATAAGTGAAT
Found at i:2960037 original size:21 final size:21
Alignment explanation
Indices: 2960013--2960064 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
2960003 TTGAAATGCT
2960013 ATGCTTGAATTA-AATATTAGA
1 ATGCTTGAATTATAATATT-GA
* *
2960034 ATGCTTG-ATTATATTATTGG
1 ATGCTTGAATTATAATATTGA
2960054 ATGCTTGAATT
1 ATGCTTGAATT
2960065 TGAAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (21 bp):
ATGCTTGAATTATAATATTGA
Found at i:2960964 original size:48 final size:48
Alignment explanation
Indices: 2960873--2960965 Score: 134
Period size: 48 Copynumber: 1.9 Consensus size: 48
2960863 CCATCGATCA
* * *
2960873 TGTATCAGTGCATTTGTGCACTCTCGTATTATTATATTCGTGTACGCC
1 TGTATCAGTGCATTTGTGCACTCCCGTATTAGTATAGTCGTGTACGCC
*
2960921 TGTATGAGTGCATTTGTGCACTCCCGTATTAGTATTAGT-GTGTAC
1 TGTATCAGTGCATTTGTGCACTCCCGTATTAGTA-TAGTCGTGTAC
2960966 TTCTTGTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 37 0.93
49 3 0.08
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (48 bp):
TGTATCAGTGCATTTGTGCACTCCCGTATTAGTATAGTCGTGTACGCC
Found at i:2962374 original size:21 final size:21
Alignment explanation
Indices: 2962348--2962387 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2962338 CAAAGAATTC
2962348 TTCATCATTAAGTTCTTCAAG
1 TTCATCATTAAGTTCTTCAAG
2962369 TTCATCATTAAGTTCTTCA
1 TTCATCATTAAGTTCTTCA
2962388 TAAGGGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (21 bp):
TTCATCATTAAGTTCTTCAAG
Found at i:2977863 original size:362 final size:362
Alignment explanation
Indices: 2977198--2977921 Score: 1376
Period size: 362 Copynumber: 2.0 Consensus size: 362
2977188 CTCACCACCT
*
2977198 TCCTAGAAGAAACAATCAAAGGTCTTGAAGACTTTTTTAGGATCGGTTGGAATGATGATGTTGGT
1 TCCTAGAAGAAACAATCAAAGGTCTTGAAGACTTTTTTAGGATCAGTTGGAATGATGATGTTGGT
2977263 TGTCACCTTTGGCACCTCTTTGCATTTTTCTTTCTTTGTTTCCTTTCTTTAGTTTTTCTTCACTT
66 TGTCACCTTTGGCACCTCTTTGCATTTTTCTTTCTTTGTTTCCTTTCTTTAGTTTTTCTTCACTT
*
2977328 GGAATCCCTTGTTGATGTTGGGACTAACTTGCTGATTTTTTTGCACTTCTCTTTTTGATTTCTTT
131 GGAATCCCATGTTGATGTTGGGACTAACTTGCTGATTTTTTTGCACTTCTCTTTTTGATTTCTTT
*
2977393 TTATTGAATGGTAGGATGTTGCTTTTGCTTCTTCTTGTTGCAATCCACCTTAGCTCTGATACCGT
196 TTATTGAATGGTAGGATGTTGCTTTTGCTTCTTCTTGTTGCAATCCACCTTAGCTCTGATACCAT
*
2977458 ATGATACAGTTCAACCTAGCCTCACTTGGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTT
261 ATGATACAATTCAACCTAGCCTCACTTGGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTT
*
2977523 TCGATCTAGGAAAGCAGCAAGTATCCTGCACAAATAA
326 TCGATCTAGGAAAGCAACAAGTATCCTGCACAAATAA
2977560 TCCTAGAAGAAACAATCAAAGGTCTTGAAGACTTTTTTAGGATCAGTTGGAATGATGATGTTGGT
1 TCCTAGAAGAAACAATCAAAGGTCTTGAAGACTTTTTTAGGATCAGTTGGAATGATGATGTTGGT
2977625 TGTCACCTTTGGCACCTCTTTGCATTTTTCTTTCTTTGTTTCCTTTCTTTAGTTTTTCTTCACTT
66 TGTCACCTTTGGCACCTCTTTGCATTTTTCTTTCTTTGTTTCCTTTCTTTAGTTTTTCTTCACTT
2977690 GGAATCCCATGTTGATGTTGGGACTAACTTGCTGATTTTTTTGCACTTCTCTTTTTGATTTCTTT
131 GGAATCCCATGTTGATGTTGGGACTAACTTGCTGATTTTTTTGCACTTCTCTTTTTGATTTCTTT
*
2977755 TTATTGAATGGTAGGATGTTGCTTTTGCTTGTTCTTGTTGCAATCCACCTTAGCTCTGATACCAT
196 TTATTGAATGGTAGGATGTTGCTTTTGCTTCTTCTTGTTGCAATCCACCTTAGCTCTGATACCAT
*
2977820 ATGATACAATTCAACCTAGCCTCACTTGGATGGATGGTGAAGTCAAGGTTGTACCTTTGATTGTT
261 ATGATACAATTCAACCTAGCCTCACTTGGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTT
*
2977885 TCGATCTAGGAAAGCAACAAGTATCCTGCACGAATAA
326 TCGATCTAGGAAAGCAACAAGTATCCTGCACAAATAA
2977922 GGAAGCTAAA
Statistics
Matches: 354, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
362 354 1.00
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (362 bp):
TCCTAGAAGAAACAATCAAAGGTCTTGAAGACTTTTTTAGGATCAGTTGGAATGATGATGTTGGT
TGTCACCTTTGGCACCTCTTTGCATTTTTCTTTCTTTGTTTCCTTTCTTTAGTTTTTCTTCACTT
GGAATCCCATGTTGATGTTGGGACTAACTTGCTGATTTTTTTGCACTTCTCTTTTTGATTTCTTT
TTATTGAATGGTAGGATGTTGCTTTTGCTTCTTCTTGTTGCAATCCACCTTAGCTCTGATACCAT
ATGATACAATTCAACCTAGCCTCACTTGGATGGATGGTGAAGTCAAGGTTATACCTTTGATTGTT
TCGATCTAGGAAAGCAACAAGTATCCTGCACAAATAA
Found at i:2991695 original size:162 final size:162
Alignment explanation
Indices: 2991423--2991746 Score: 591
Period size: 162 Copynumber: 2.0 Consensus size: 162
2991413 TGCTTATAAC
2991423 ACATATAAAGCATAAATGATAATAAATAATAAAATATGTAAGAACTCCCTTAGAATCATCTTGGA
1 ACATATAAAGCATAAATGATAATAAATAATAAAATATGTAAGAACTCCCTTAGAATCATCTTGGA
2991488 AGAACTTCAAGTTGTGAGCATGTTTTGTTGAACTTGGTGGGTCGGTAGGATCACATCATTCCCCC
66 AGAACTTCAAGTTGTGAGCATGTTTTGTTGAACTTGGTGGGTCGGTAGGATCACATCATTCCCCC
2991553 CTTCTTTAAGACGATTTGTCCCCAAATCGATA
131 CTTCTTTAAGACGATTTGTCCCCAAATCGATA
*
2991585 ACATATAAAGCATAAATG--AGTAAATAAATAAAATATGTAAGAACTCCCTTAGAATCATCTTGG
1 ACATATAAAGCATAAATGATAATAAAT-AATAAAATATGTAAGAACTCCCTTAGAATCATCTTGG
2991648 AAGAACTTCAAAGTTGTGAGCATGTTTTGTTTGAACTTGGT-GGTCGGTAGGATCACATCATTCC
65 AAGAACTTC-AAGTTGTGAGCATGTTTTG-TTGAACTTGGTGGGTCGGTAGGATCACATCATTCC
2991712 CCCCTTCTTTAAGACGATTTGTCCCCAAATCGATA
128 CCCCTTCTTTAAGACGATTTGTCCCCAAATCGATA
2991747 CTTAGTACAT
Statistics
Matches: 158, Mismatches: 1, Indels: 6
0.96 0.01 0.04
Matches are distributed among these distances:
160 6 0.04
161 46 0.29
162 95 0.60
163 11 0.07
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (162 bp):
ACATATAAAGCATAAATGATAATAAATAATAAAATATGTAAGAACTCCCTTAGAATCATCTTGGA
AGAACTTCAAGTTGTGAGCATGTTTTGTTGAACTTGGTGGGTCGGTAGGATCACATCATTCCCCC
CTTCTTTAAGACGATTTGTCCCCAAATCGATA
Found at i:2994469 original size:27 final size:27
Alignment explanation
Indices: 2994427--2994484 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
2994417 TCATTTTAAT
*
2994427 ATTATTTTCTCGTCCATGCATGTCTTC
1 ATTATTTTCTCATCCATGCATGTCTTC
2994454 ATTATTTTCTCATCCATGCATGTCTTC
1 ATTATTTTCTCATCCATGCATGTCTTC
2994481 ATTA
1 ATTA
2994485 ATTCAAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.09, T:0.48
Consensus pattern (27 bp):
ATTATTTTCTCATCCATGCATGTCTTC
Found at i:2994774 original size:18 final size:18
Alignment explanation
Indices: 2994733--2994776 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2994723 ATCTAAAGAG
* *
2994733 CTAGTTT-AATTAATGAA
1 CTAGTTTAAATGAATCAA
*
2994750 CTGGTTTAAATGAATCAA
1 CTAGTTTAAATGAATCAA
2994768 CTAGTTTAA
1 CTAGTTTAA
2994777 TTAGTGTAGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (18 bp):
CTAGTTTAAATGAATCAA
Found at i:2995940 original size:36 final size:38
Alignment explanation
Indices: 2995900--2995974 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 38
2995890 TTTTCAACCA
2995900 CACTCTCAAT-CTTTTT-AACTC-CGATTTCTTTTTCTT
1 CACTCTCAATCCTTTTTCAACTCTC-ATTTCTTTTTCTT
2995936 CACTCTCAATGCCTTTTTCAACTCTCATTTCTTTTTCTT
1 CACTCTCAAT-CCTTTTTCAACTCTCATTTCTTTTTCTT
2995975 TTTTGCAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
36 10 0.29
38 6 0.17
39 18 0.51
40 1 0.03
ACGTcount: A:0.16, C:0.29, G:0.03, T:0.52
Consensus pattern (38 bp):
CACTCTCAATCCTTTTTCAACTCTCATTTCTTTTTCTT
Found at i:2995969 original size:18 final size:19
Alignment explanation
Indices: 2995901--2995972 Score: 55
Period size: 21 Copynumber: 3.9 Consensus size: 19
2995891 TTTCAACCAC
2995901 ACTCTCAA--TCTTTTT-A
1 ACTCTCAATTTCTTTTTCA
* *
2995917 ACTC-CGATTTCTTTTTCTTC
1 ACTCTCAATTTCTTTTTC--A
**
2995937 ACTCTCAATGCCTTTTTCA
1 ACTCTCAATTTCTTTTTCA
2995956 ACTCTC-ATTTCTTTTTC
1 ACTCTCAATTTCTTTTTC
2995973 TTTTTTGCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
15 2 0.05
16 4 0.10
17 7 0.17
18 9 0.21
19 6 0.14
20 4 0.10
21 10 0.24
ACGTcount: A:0.17, C:0.29, G:0.03, T:0.51
Consensus pattern (19 bp):
ACTCTCAATTTCTTTTTCA
Found at i:2998017 original size:24 final size:24
Alignment explanation
Indices: 2997966--2998011 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
2997956 CTTGGTTTGA
* *
2997966 ATGATTAAATCAACCTTGAATTAG
1 ATGATTAAATCAACATTGAATGAG
2997990 ATGATTAAATCAACATTGAATG
1 ATGATTAAATCAACATTGAATG
2998012 CTATGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (24 bp):
ATGATTAAATCAACATTGAATGAG
Found at i:2998451 original size:18 final size:18
Alignment explanation
Indices: 2998428--2998462 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2998418 TAGTTTAATT
*
2998428 AATGAACCATTTTAAATG
1 AATGAACCAATTTAAATG
*
2998446 AATGAACTAATTTAAAT
1 AATGAACCAATTTAAAT
2998463 AGTTAATAGC
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:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (18 bp):
AATGAACCAATTTAAATG
Found at i:3002816 original size:54 final size:54
Alignment explanation
Indices: 3002747--3003178 Score: 614
Period size: 54 Copynumber: 8.0 Consensus size: 54
3002737 CACTGTGTAC
* *
3002747 GCAACCTAAGAAATTCAGAATGAGTTTATGAATTTCCGTATTGGCACTATGTGT
1 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
* * * *
3002801 GCAACCAAAGAAATTCA-AATGAGTTTATGAATTTCTGTATTGGCACTAAGTGT
1 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
* *
3002854 GCAACCAAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATATGT
1 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
** * **
3002908 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGTACTACCTGT
1 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
*
3002962 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTATGTGT
1 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
* *
3003016 GCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCTTATTGGCACTATGTGT
1 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
* * *
3003070 TCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTATGT
1 GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
* * * ** * *
3003124 GCAACCCCATGTAATTCATAATAAGTTTATGAATGACCTTATTGGCACTACGTGT
1 GCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
3003179 TCAAACTATA
Statistics
Matches: 341, Mismatches: 35, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
53 51 0.15
54 249 0.73
55 41 0.12
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (54 bp):
GCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTATGTGT
Found at i:3003394 original size:82 final size:82
Alignment explanation
Indices: 3003257--3003445 Score: 317
Period size: 82 Copynumber: 2.3 Consensus size: 82
3003247 TTTTTCTAAA
* *
3003257 ATGAAAGACTAAATGCCTAACTGTGCATTTGGAAGAAATGTGCCAATAATACAAGTTAGATTAAA
1 ATGAAAGACTAAATGCCTAACTGTGCATTTGGAAGAAATGTGCCAAAAATACAAGTTAGATGAAA
3003322 GGTTAAATGCCTTTGGG
66 GGTTAAATGCCTTTGGG
* *
3003339 ATGAAAGACTAAATGCCTAACTGTGCATTTGGAAGAAA-GATGTCAAAAATGCAAGTTAGATGAA
1 ATGAAAGACTAAATGCCTAACTGTGCATTTGGAAGAAATG-TGCCAAAAATACAAGTTAGATGAA
3003403 AGGTTAAATGCCTTTGGG
65 AGGTTAAATGCCTTTGGG
*
3003421 ATGAAAGACTAAATACCTAACTGTG
1 ATGAAAGACTAAATGCCTAACTGTG
3003446 TTTTTTGGCA
Statistics
Matches: 101, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
81 1 0.01
82 100 0.99
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (82 bp):
ATGAAAGACTAAATGCCTAACTGTGCATTTGGAAGAAATGTGCCAAAAATACAAGTTAGATGAAA
GGTTAAATGCCTTTGGG
Found at i:3003596 original size:46 final size:46
Alignment explanation
Indices: 3003543--3003667 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
3003533 AAAAACAATA
3003543 CATAATTGGCATGAAAGGATGCCACAAATGAAAATGTATATCAGTG
1 CATAATTGGCATGAAAGGATGCCACAAATGAAAATGTATATCAGTG
* * * *
3003589 CATAATTGGCATGAAAGGATGCCACAATTAAAAATGTGTATTAGTG
1 CATAATTGGCATGAAAGGATGCCACAAATGAAAATGTATATCAGTG
* *
3003635 CATAGTTGACATGAAAGGATGCCACAAATGAAA
1 CATAATTGGCATGAAAGGATGCCACAAATGAAA
3003668 TTACATAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 71 1.00
ACGTcount: A:0.42, C:0.13, G:0.22, T:0.24
Consensus pattern (46 bp):
CATAATTGGCATGAAAGGATGCCACAAATGAAAATGTATATCAGTG
Found at i:3023110 original size:2 final size:2
Alignment explanation
Indices: 3023103--3023152 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
3023093 TAAAAATGAA
3023103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3023145 AT AT AT AT
1 AT AT AT AT
3023153 GTGTATGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3024947 original size:2 final size:2
Alignment explanation
Indices: 3024940--3024964 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3024930 AAAGAATGGG
3024940 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
3024965 CAGAAATCTC
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:3028988 original size:139 final size:141
Alignment explanation
Indices: 3028738--3029018 Score: 548
Period size: 139 Copynumber: 2.0 Consensus size: 141
3028728 AGAAGAATTA
3028738 AAAGAAAAGAATCTTTGAATGAACAATATAATCAGCTCTTGAAAATGAACTCTTGTTGTATTGTA
1 AAAGAAAAGAATCTTTGAATGAACAATATAATCAGCTCTTGAAAATGAACTCTTGTTGTATTGTA
3028803 TATAAGAAAAGAATTTGTGCTTACAATGATGGGAGGAGCCTCC-TT-TATAGGTTTTGAGGAGTC
66 TATAAGAAAAGAATTTGTGCTTACAATGATGGGAGGAGCCTCCTTTATATAGGTTTTGAGGAGTC
3028866 CTTTTCGTATT
131 CTTTTCGTATT
3028877 AAAGAAAAGAATCTTTGAATGAACAATATAATCAGCTCTTGAAAATGAACTCTTGTTGTATTGTA
1 AAAGAAAAGAATCTTTGAATGAACAATATAATCAGCTCTTGAAAATGAACTCTTGTTGTATTGTA
3028942 TATAAGAAAAGAATTTGTGCTTACAATGATGGGAGGAGCCTCCTTTATATAGGTTTTGAGGAGTC
66 TATAAGAAAAGAATTTGTGCTTACAATGATGGGAGGAGCCTCCTTTATATAGGTTTTGAGGAGTC
3029007 CTTTTCGTATT
131 CTTTTCGTATT
3029018 A
1 A
3029019 TAACTATGGA
Statistics
Matches: 140, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
139 108 0.77
140 2 0.01
141 30 0.21
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (141 bp):
AAAGAAAAGAATCTTTGAATGAACAATATAATCAGCTCTTGAAAATGAACTCTTGTTGTATTGTA
TATAAGAAAAGAATTTGTGCTTACAATGATGGGAGGAGCCTCCTTTATATAGGTTTTGAGGAGTC
CTTTTCGTATT
Found at i:3035737 original size:11 final size:11
Alignment explanation
Indices: 3035723--3035747 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3035713 ACAACCCATT
3035723 TTACTAATTCA
1 TTACTAATTCA
3035734 TTACTAATTCA
1 TTACTAATTCA
3035745 TTA
1 TTA
3035748 ATCTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
TTACTAATTCA
Found at i:3041430 original size:23 final size:23
Alignment explanation
Indices: 3041404--3041479 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
3041394 CCCAAATGAT
*
3041404 CACATAGGTTTGTCCCGAAGGAC
1 CACATAGGTTTATCCCGAAGGAC
* *
3041427 CACATAGGTTTATCCCAAATGAC
1 CACATAGGTTTATCCCGAAGGAC
* ** * **
3041450 CATATATATTTTTCTTGAAGGAC
1 CACATAGGTTTATCCCGAAGGAC
3041473 CACATAG
1 CACATAG
3041480 AACCCTCGAC
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (23 bp):
CACATAGGTTTATCCCGAAGGAC
Found at i:3046686 original size:54 final size:54
Alignment explanation
Indices: 3046543--3046660 Score: 173
Period size: 54 Copynumber: 2.2 Consensus size: 54
3046533 TATGTGTACA
* * * * * *
3046543 ATCGGCACTAAGTGTGAAACCCTCGAAATTCATAATAAGTTTATGAACGATCGT
1 ATCGGCACTAAGTGAGCAACCCACAAAATTCATAATAAGTTTATGAACGACCAT
3046597 ATCGGCACTAAGTGAGCAACCCACAAAATTCATAATAAGTTTATGAACGACCAT
1 ATCGGCACTAAGTGAGCAACCCACAAAATTCATAATAAGTTTATGAACGACCAT
*
3046651 ATCGGTACTA
1 ATCGGCACTA
3046661 CGTGTGCACA
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (54 bp):
ATCGGCACTAAGTGAGCAACCCACAAAATTCATAATAAGTTTATGAACGACCAT
Found at i:3048634 original size:88 final size:88
Alignment explanation
Indices: 3048485--3048652 Score: 300
Period size: 88 Copynumber: 1.9 Consensus size: 88
3048475 AAGACTAATG
* *
3048485 AATCCATATTTTTTATTAACATGTATTTGTTTTGAATGACCCTGGTTCTACACACTCTTATATTT
1 AATCCATATTTTTCATTAACATGTATTTGTTTTGAATGACACTGGTTCTACACACTCTTATATTT
3048550 GTACAAAGTTGATTAACATGTAC
66 GTACAAAGTTGATTAACATGTAC
* *
3048573 AATCCATCTTTTTCGTTAACATGTATTTGTTTTGAATGACACTGGTTCTACACACTCTTATATTT
1 AATCCATATTTTTCATTAACATGTATTTGTTTTGAATGACACTGGTTCTACACACTCTTATATTT
3048638 GTACAAAGTTGATTA
66 GTACAAAGTTGATTA
3048653 GAGCTAGAGT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 76 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (88 bp):
AATCCATATTTTTCATTAACATGTATTTGTTTTGAATGACACTGGTTCTACACACTCTTATATTT
GTACAAAGTTGATTAACATGTAC
Found at i:3053237 original size:54 final size:54
Alignment explanation
Indices: 3053178--3053512 Score: 474
Period size: 54 Copynumber: 6.2 Consensus size: 54
3053168 CAATGTGTAC
* ** *
3053178 TATCGGCACTAAATGTATAACCCATGGAATTCATAATAAGTTTATGAACGACTG
1 TATCGGCACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCG
* * * *
3053232 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGATCGACTG
1 TATCGGCACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCG
* * *
3053286 TATCGGCACTAAGTTTGCAACCCA-CGAATTTCATAATAAGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCATGGAA-TTCATAATAAGTTTATGAACGACCG
* * *
3053340 TATCGACACTAAGTGTGCAACCCATGAAATTCATTATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCG
* *
3053394 TATCGACACTAAGTGTGCAACCCATAGAATTCATAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCG
* * * *
3053448 TATCGGCCCTAAGTGTACAACCCATAGAATTCATAATAAGTTTATGAACGACCA
1 TATCGGCACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCG
3053502 TATCGGCACTA
1 TATCGGCACTA
3053513 CGTATGCACC
Statistics
Matches: 253, Mismatches: 26, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
53 2 0.01
54 249 0.98
55 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCATGGAATTCATAATAAGTTTATGAACGACCG
Found at i:3058397 original size:27 final size:29
Alignment explanation
Indices: 3058367--3058423 Score: 91
Period size: 27 Copynumber: 2.0 Consensus size: 29
3058357 TTTACATGTT
3058367 CTTAAATCATTTC-CT-TCTTTTCATTTC
1 CTTAAATCATTTCTCTATCTTTTCATTTC
3058394 CTTAAATCATTTCTTCTATCTTTTCATTTC
1 CTTAAATCATTTC-TCTATCTTTTCATTTC
3058424 ATCTTTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 13 0.48
29 2 0.07
30 12 0.44
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (29 bp):
CTTAAATCATTTCTCTATCTTTTCATTTC
Found at i:3063261 original size:38 final size:38
Alignment explanation
Indices: 3063213--3063325 Score: 115
Period size: 37 Copynumber: 3.0 Consensus size: 38
3063203 ATAAATTTGT
* * *
3063213 AATATTATATTCGTATTTTAATTCAATATAGATTCATA
1 AATAATATATTCTTATTTTAATTCAATATAAATTCATA
* *
3063251 AATAATATATT-TTCA-TTTAA-TCAAATATACATTTATA
1 AATAATATATTCTT-ATTTTAATTC-AATATAAATTCATA
* * *
3063288 AATAATATATTCTTGTTTTAATTGAATGTAAATTCATA
1 AATAATATATTCTTATTTTAATTCAATATAAATTCATA
3063326 TTTTAATTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
36 2 0.03
37 29 0.48
38 29 0.48
39 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (38 bp):
AATAATATATTCTTATTTTAATTCAATATAAATTCATA
Found at i:3069486 original size:38 final size:38
Alignment explanation
Indices: 3069404--3069536 Score: 148
Period size: 37 Copynumber: 3.5 Consensus size: 38
3069394 TTGTTTTAAG
*
3069404 ATTTATATTCAATTAAAATATGAATATATTA-TTATAA
1 ATTTATATTCAATTAAAATAGGAATATATTATTTATAA
* *
3069441 ATTTATATTCGATTGAAATAGGAATATATTATTTATAA
1 ATTTATATTCAATTAAAATAGGAATATATTATTTATAA
* * * *
3069479 ATTTATATTTGAA-T-AAAT-GCAAATATATTTATTTTTGA
1 ATTTATA-TTCAATTAAAATAG-GAATATA-TTATTTATAA
3069517 ATTTATATTCAATTAAAATA
1 ATTTATATTCAATTAAAATA
3069537 CAAATAAATC
Statistics
Matches: 80, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
36 1 0.01
37 42 0.52
38 30 0.38
39 7 0.09
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (38 bp):
ATTTATATTCAATTAAAATAGGAATATATTATTTATAA
Found at i:3069508 original size:34 final size:36
Alignment explanation
Indices: 3069426--3069510 Score: 93
Period size: 38 Copynumber: 2.3 Consensus size: 36
3069416 TTAAAATATG
* *
3069426 AATATATTATTATAAATTTATATTCGATTGAAATAGGA
1 AATATA-T-TTATAAATTTATATTCGAATGAAATAGCA
*
3069464 ATATATTATTTATAAATTTATATTTGAAT-AAAT-GCA
1 A-ATA-TATTTATAAATTTATATTCGAATGAAATAGCA
3069500 AATATATTTAT
1 AATATATTTAT
3069511 TTTTGAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
34 7 0.17
35 3 0.07
36 3 0.07
37 4 0.10
38 19 0.45
39 4 0.10
40 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (36 bp):
AATATATTTATAAATTTATATTCGAATGAAATAGCA
Found at i:3076455 original size:12 final size:12
Alignment explanation
Indices: 3076438--3076466 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3076428 TCAAATTAGG
3076438 ATTTATTTTTAT
1 ATTTATTTTTAT
3076450 ATTTATTTTTAT
1 ATTTATTTTTAT
3076462 -TTTAT
1 ATTTAT
3076467 GAATTATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTATTTTTAT
Found at i:3076473 original size:18 final size:19
Alignment explanation
Indices: 3076439--3076499 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 19
3076429 CAAATTAGGA
*
3076439 TTTATTTTTATATTTAT-T
1 TTTATTTTTATAATTATCT
3076457 TTTA-TTTTATGAATTATCTT
1 TTTATTTTTAT-AATTATC-T
*
3076477 TTTAATTTTA-AATGTATCT
1 TTTATTTTTATAAT-TATCT
3076496 TTTA
1 TTTA
3076500 AGGTTTTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 6 0.16
18 9 0.24
19 8 0.22
20 9 0.24
21 5 0.14
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.67
Consensus pattern (19 bp):
TTTATTTTTATAATTATCT
Found at i:3076484 original size:21 final size:19
Alignment explanation
Indices: 3076455--3076498 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
3076445 TTTATATTTA
3076455 TTTTTATTTTATGAAT-TATC
1 TTTTTATTTTA--AATGTATC
3076475 TTTTTAATTTTAAATGTATC
1 TTTTT-ATTTTAAATGTATC
3076495 TTTT
1 TTTT
3076499 AAGGTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 13 0.59
21 6 0.27
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.66
Consensus pattern (19 bp):
TTTTTATTTTAAATGTATC
Found at i:3077867 original size:560 final size:560
Alignment explanation
Indices: 3076800--3077924 Score: 2036
Period size: 560 Copynumber: 2.0 Consensus size: 560
3076790 CTAGATTGGC
3076800 GATCGGTCTTTCTTAATCAAAAATATATTTTGGCTAGGATGTTGTTATGGTTTAAAGTTGGGATT
1 GATCGGTCTTTCTTAATCAAAAATATATTTTGGCTAGGATGTTGTTATGGTTTAAAGTTGGGATT
* * *
3076865 ATAGAATCAATTTATTCGAATTTCCTTGAACACAATTAGCGATGGCACGCTAAGGGAAATTAGGA
66 ATAGAATCAATTGATTCGAATTCCCTTGAACACAATTAGCGATGGCACACTAAGGGAAATTAGGA
* *
3076930 TCGAGTTTGACTTTCATAGAGAAAGCATAATTCGAGTAAGGTTTTTCCAAGCGCTTTTAAATTGT
131 TCGAGTTTGACTTTCATAGAGAAAACATAATTCAAGTAAGGTTTTTCCAAGCGCTTTTAAATTGT
3076995 TTTGAATTAACAGCGATAGTCGAAGTTGATTTGAACAAGGATTGCGATTCCTAAAATAGATTTGT
196 TTTGAATTAACAGCGATAGTCGAAGTTGATTTGAACAAGGATTGCGATTCCTAAAATAGATTTGT
*
3077060 GAAAATCAATCACAAAGAGAAAAAATGAGCTACAAGGATTGAACCTTGCGGACTCAAACTGACAT
261 GAAAATCAATCACAAAGAGAAAAAATGAGCTACAAGGATTAAACCTTGCGGACTCAAACTGACAT
* *
3077125 TTAAATGTAGGAAAAATCCTATTCAATGATCGATTCGAATTTGAAACACGCGAAAGCCTAAGGCT
326 TTAAATGTAGGAAAAATCCTATTCAATGATCGATTCGAATTTGAAACACACAAAAGCCTAAGGCT
*
3077190 AATTTCATCATAATGGTTTTTAATTTTACTTTCTTCAATTCTTTATCTTCCTTTGAATCATTATT
391 AATTTCATCATAATGGTTTTTAATTTTACTTTCTTCAATTCTTTATCTTCCTTTGAAACATTATT
* * *
3077255 TGCTTATTCAATTTCTCAACAAACCCCCTTTTTACTTTACTTACATTTTTTTGCCTAGATCTAAG
456 TGCGTATTCAATTTCTCAACAAACCCCCTTTTTACTTTACTTACATTTTTTTGCATAGATCAAAG
3077320 ATCAAGAACAATCATTTCAGCATCGTCCTTAGTCCTTGTG
521 ATCAAGAACAATCATTTCAGCATCGTCCTTAGTCCTTGTG
*
3077360 GATCGGTCTTTCTTAATCAAAAATATATTTTGGCTTGGATGTTGTTATGGTTTAAAGTTGGGATT
1 GATCGGTCTTTCTTAATCAAAAATATATTTTGGCTAGGATGTTGTTATGGTTTAAAGTTGGGATT
* *
3077425 ATAGAATCAATTGATTCGAATTCCCTTGAACACAATTAGCGATGGCTCACTAAGGGAAATTGGGA
66 ATAGAATCAATTGATTCGAATTCCCTTGAACACAATTAGCGATGGCACACTAAGGGAAATTAGGA
*
3077490 TGGAGTTTGACTTTCATAGAGAAAACATAATTCAAGTAAGGTTTTTCCAAGCGCTTTTAAATTGT
131 TCGAGTTTGACTTTCATAGAGAAAACATAATTCAAGTAAGGTTTTTCCAAGCGCTTTTAAATTGT
*
3077555 TTTGAATTAACAGCGATAGTCGAAGTTGATTTGAACAAGGATTGTGATTCCTAAAATAGATTTGT
196 TTTGAATTAACAGCGATAGTCGAAGTTGATTTGAACAAGGATTGCGATTCCTAAAATAGATTTGT
*
3077620 GAAAATCAATCACAAAGAGAAAAAATGAGCTACAAGGATTAAACCTTGTGGACTCAAACTGACAT
261 GAAAATCAATCACAAAGAGAAAAAATGAGCTACAAGGATTAAACCTTGCGGACTCAAACTGACAT
3077685 TTAAATGTAGGAAAAATCCTATTCAATGATCGATTCGAATTTGAAACACACAAAAGCCTAAGGCT
326 TTAAATGTAGGAAAAATCCTATTCAATGATCGATTCGAATTTGAAACACACAAAAGCCTAAGGCT
* *
3077750 AATTTCATCATAATGGTTTTTTATTTTACTTTCTTCAATTCTTTATCTTCCTTTGAAACTTTATT
391 AATTTCATCATAATGGTTTTTAATTTTACTTTCTTCAATTCTTTATCTTCCTTTGAAACATTATT
* *
3077815 TTCGTATTCAATTTCTCAACAAACCCCCTTTTTTACTTTACTTGCA-TTTTTTGCATAGATCAAA
456 TGCGTATTCAATTTCTCAACAAACCCCC-TTTTTACTTTACTTACATTTTTTTGCATAGATCAAA
3077879 GATCAAGAACAATCATTTCAGCATCGTCCTTAGTCCTTGTG
520 GATCAAGAACAATCATTTCAGCATCGTCCTTAGTCCTTGTG
3077920 GATCG
1 GATCG
3077925 ACTCTAGTCC
Statistics
Matches: 542, Mismatches: 22, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
560 526 0.97
561 16 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (560 bp):
GATCGGTCTTTCTTAATCAAAAATATATTTTGGCTAGGATGTTGTTATGGTTTAAAGTTGGGATT
ATAGAATCAATTGATTCGAATTCCCTTGAACACAATTAGCGATGGCACACTAAGGGAAATTAGGA
TCGAGTTTGACTTTCATAGAGAAAACATAATTCAAGTAAGGTTTTTCCAAGCGCTTTTAAATTGT
TTTGAATTAACAGCGATAGTCGAAGTTGATTTGAACAAGGATTGCGATTCCTAAAATAGATTTGT
GAAAATCAATCACAAAGAGAAAAAATGAGCTACAAGGATTAAACCTTGCGGACTCAAACTGACAT
TTAAATGTAGGAAAAATCCTATTCAATGATCGATTCGAATTTGAAACACACAAAAGCCTAAGGCT
AATTTCATCATAATGGTTTTTAATTTTACTTTCTTCAATTCTTTATCTTCCTTTGAAACATTATT
TGCGTATTCAATTTCTCAACAAACCCCCTTTTTACTTTACTTACATTTTTTTGCATAGATCAAAG
ATCAAGAACAATCATTTCAGCATCGTCCTTAGTCCTTGTG
Found at i:3077932 original size:20 final size:20
Alignment explanation
Indices: 3077909--3077946 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3077899 GCATCGTCCT
*
3077909 TAGTCCTTGTGGATCGACTC
1 TAGTCCCTGTGGATCGACTC
3077929 TAGTCCCTGTGGATCGAC
1 TAGTCCCTGTGGATCGAC
3077947 CCTTGCTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.32
Consensus pattern (20 bp):
TAGTCCCTGTGGATCGACTC
Found at i:3078747 original size:15 final size:15
Alignment explanation
Indices: 3078722--3078764 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
3078712 CAATACTGTG
*
3078722 CAGTATCGATACTGC
1 CAGTATTGATACTGC
*
3078737 TAGTATTGATACTGC
1 CAGTATTGATACTGC
3078752 CAGTATTGATACT
1 CAGTATTGATACT
3078765 TCTCTTGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (15 bp):
CAGTATTGATACTGC
Found at i:3078839 original size:20 final size:21
Alignment explanation
Indices: 3078814--3078852 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3078804 TTTTCCCTAA
3078814 TTCAT-CCACTATCGATACAG
1 TTCATCCCACTATCGATACAG
*
3078834 TTCATCCCAGTATCGATAC
1 TTCATCCCACTATCGATAC
3078853 TCGTACCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (21 bp):
TTCATCCCACTATCGATACAG
Found at i:3082243 original size:20 final size:20
Alignment explanation
Indices: 3082218--3082292 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
3082208 TATCGTTTGA
*
3082218 ATTTATGTTCGTTTACATCT
1 ATTTATGTTCGTTTACATTT
**
3082238 ATTTATGTTCGTTTGTATTT
1 ATTTATGTTCGTTTACATTT
*
3082258 GA-TTGTGTTCGTTTACATTT
1 -ATTTATGTTCGTTTACATTT
*
3082278 GTTTATGTTCGTTTA
1 ATTTATGTTCGTTTA
3082293 TCATATTAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 44 0.98
21 1 0.02
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.59
Consensus pattern (20 bp):
ATTTATGTTCGTTTACATTT
Found at i:3086850 original size:19 final size:18
Alignment explanation
Indices: 3086817--3086856 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
3086807 GAAATTGTTC
*
3086817 TCTTCTTCAAGCTCTCTT
1 TCTTCTTCAAGCTCTATT
*
3086835 TCTTCTCTCAATCTCTATT
1 TCTTCT-TCAAGCTCTATT
3086854 TCT
1 TCT
3086857 ATTTCTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.12, C:0.33, G:0.03, T:0.53
Consensus pattern (18 bp):
TCTTCTTCAAGCTCTATT
Found at i:3091105 original size:11 final size:11
Alignment explanation
Indices: 3091089--3091113 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3091079 ACTTCTCTTT
3091089 TTAAATTTAAG
1 TTAAATTTAAG
3091100 TTAAATTTAAG
1 TTAAATTTAAG
3091111 TTA
1 TTA
3091114 CTAGAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
TTAAATTTAAG
Found at i:3091304 original size:8 final size:8
Alignment explanation
Indices: 3091273--3091302 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3091263 TTTTTTATAA
3091273 TTTAATCT
1 TTTAATCT
3091281 TTTAATCT
1 TTTAATCT
*
3091289 TTTAATTT
1 TTTAATCT
3091297 TTTAAT
1 TTTAAT
3091303 TTAATTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTAATCT
Found at i:3091476 original size:16 final size:16
Alignment explanation
Indices: 3091467--3091505 Score: 69
Period size: 17 Copynumber: 2.4 Consensus size: 16
3091457 ATATTTATTT
3091467 TTTTTAATATTTTTAA
1 TTTTTAATATTTTTAA
3091483 TTTTTAATATTTTTTAA
1 TTTTTAATA-TTTTTAA
3091500 TTTTTA
1 TTTTTA
3091506 TAGTGTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAATATTTTTAA
Found at i:3091496 original size:17 final size:17
Alignment explanation
Indices: 3091455--3091505 Score: 72
Period size: 16 Copynumber: 3.1 Consensus size: 17
3091445 GCAAGACATA
3091455 TAATATTTATTT--TTTT
1 TAATATTT-TTTAATTTT
3091471 TAATA-TTTTTAATTTT
1 TAATATTTTTTAATTTT
3091487 TAATATTTTTTAATTTT
1 TAATATTTTTTAATTTT
3091504 TA
1 TA
3091506 TAGTGTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.09
15 2 0.06
16 14 0.44
17 13 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TAATATTTTTTAATTTT
Found at i:3091514 original size:17 final size:17
Alignment explanation
Indices: 3091467--3091514 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
3091457 ATATTTATTT
3091467 TTTTTAATAT-TTTTAA
1 TTTTTAATATGTTTTAA
*
3091483 TTTTTAATATTTTTTAA
1 TTTTTAATATGTTTTAA
3091500 TTTTT-ATAGTGTTTT
1 TTTTTAATA-TGTTTT
3091515 TAGTACTTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (17 bp):
TTTTTAATATGTTTTAA
Found at i:3092082 original size:14 final size:13
Alignment explanation
Indices: 3092061--3092090 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
3092051 CATTTCACGA
3092061 TTTTATAAATAAT
1 TTTTATAAATAAT
3092074 TTTTCATAAATAAT
1 TTTT-ATAAATAAT
3092088 TTT
1 TTT
3092091 AAAGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTATAAATAAT
Found at i:3092940 original size:15 final size:15
Alignment explanation
Indices: 3092920--3092950 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3092910 TATTTATTTA
3092920 ATGTCATTAAAATGG
1 ATGTCATTAAAATGG
3092935 ATGTCATTAAAATGG
1 ATGTCATTAAAATGG
3092950 A
1 A
3092951 AATAAAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (15 bp):
ATGTCATTAAAATGG
Found at i:3095911 original size:19 final size:20
Alignment explanation
Indices: 3095875--3095922 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3095865 TCTAAATCCT
* *
3095875 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
3095895 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
3095914 CTTTCAAAA
1 TTTTCAAAA
3095923 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:3097883 original size:18 final size:18
Alignment explanation
Indices: 3097860--3097894 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3097850 TATACATAGT
*
3097860 GGTATCGATACCCTTTTG
1 GGTATCGATACCATTTTG
3097878 GGTATCGATACCATTTT
1 GGTATCGATACCATTTT
3097895 TGCATTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (18 bp):
GGTATCGATACCATTTTG
Found at i:3098039 original size:20 final size:19
Alignment explanation
Indices: 3097983--3098039 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
3097973 GGCACCATAT
*
3097983 GAACAGTATCGGTACTTGTT
1 GAACAGTATCGGTAC-TGTG
* * *
3098003 TAACTAGTACCGATACTGTAG
1 GAAC-AGTATCGGTACTGT-G
3098024 GAACAGTATCGGTACT
1 GAACAGTATCGGTACT
3098040 ACTTGTTCAG
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (19 bp):
GAACAGTATCGGTACTGTG
Found at i:3099222 original size:25 final size:25
Alignment explanation
Indices: 3099178--3099232 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
3099168 GGAACCTATG
*
3099178 GTGCAATTCTACGAGGCACTTTCAA
1 GTGCAATTCTACGAGACACTTTCAA
* * *
3099203 GTGCAATTTTATGAGACACTTTTAA
1 GTGCAATTCTACGAGACACTTTCAA
3099228 GTGCA
1 GTGCA
3099233 TATAGCACGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (25 bp):
GTGCAATTCTACGAGACACTTTCAA
Found at i:3120888 original size:18 final size:18
Alignment explanation
Indices: 3120867--3120901 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3120857 GTCCTTCGGG
*
3120867 ACATAGTTGTCATTCGAC
1 ACATAGTGGTCATTCGAC
*
3120885 ACATAGTGGTCCTTCGA
1 ACATAGTGGTCATTCGA
3120902 GACAAATTCT
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:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (18 bp):
ACATAGTGGTCATTCGAC
Found at i:3121671 original size:8 final size:8
Alignment explanation
Indices: 3121658--3121684 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3121648 ATGCTTGTAT
3121658 TCATGGAA
1 TCATGGAA
3121666 TCATGGAA
1 TCATGGAA
3121674 TCATGGAA
1 TCATGGAA
3121682 TCA
1 TCA
3121685 AAACATTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (8 bp):
TCATGGAA
Found at i:3122089 original size:35 final size:32
Alignment explanation
Indices: 3122043--3122106 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
3122033 GCTCTAAAAA
*
3122043 TGGTACCGATACTTAAACATTGGTATCGATACCCC
1 TGGTACCGATAC-T--ACATCGGTATCGATACCCC
*
3122078 TGGTACTGATACTACATCGGTATCGATAC
1 TGGTACCGATACTACATCGGTATCGATAC
3122107 TCTTTGAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 15 0.56
34 1 0.04
35 11 0.41
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (32 bp):
TGGTACCGATACTACATCGGTATCGATACCCC
Found at i:3129139 original size:3 final size:3
Alignment explanation
Indices: 3129131--3129207 Score: 64
Period size: 3 Copynumber: 25.3 Consensus size: 3
3129121 ATTTTTTATT
* * * *
3129131 TAA TAA TAA TAA TTA TTA TAA TAA TAA TAA TAA TAC TAA TATT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
* * ** *
3129177 TAT TAA TAA TAG TAA TCT TAA AAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3129208 TTACGTGAAA
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
3 55 0.96
4 2 0.04
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:3129152 original size:18 final size:17
Alignment explanation
Indices: 3129126--3129161 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
3129116 TATTTATTTT
3129126 TTATTTAATAATAATAA
1 TTATTTAATAATAATAA
3129143 TTATTATAATAATAATAA
1 TTATT-TAATAATAATAA
3129161 T
1 T
3129162 AATACTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTATTTAATAATAATAA
Found at i:3133239 original size:79 final size:79
Alignment explanation
Indices: 3133126--3133284 Score: 257
Period size: 79 Copynumber: 2.0 Consensus size: 79
3133116 ATACTTAATG
* *
3133126 AGGCATAATTAATAATACAAAATGAAACACACTAAAAATGATACAAAACATATCATATGCA-AGT
1 AGGCATAATTAATAATACAAAATAAAACACACTAAAAATAATACAAAACATATCATATG-AGAGT
3133190 ATATGAACATATAAA
65 ATATGAACATATAAA
* *
3133205 AGGCATAATTAATAATACAAAATAAAACATACTAATAATAATACAAAACATATCATATGAGAGTA
1 AGGCATAATTAATAATACAAAATAAAACACACTAAAAATAATACAAAACATATCATATGAGAGTA
*
3133270 TATGAACCTATAAA
66 TATGAACATATAAA
3133284 A
1 A
3133285 CAAACTTATA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
78 1 0.01
79 73 0.99
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (79 bp):
AGGCATAATTAATAATACAAAATAAAACACACTAAAAATAATACAAAACATATCATATGAGAGTA
TATGAACATATAAA
Found at i:3134620 original size:47 final size:48
Alignment explanation
Indices: 3134497--3134626 Score: 142
Period size: 47 Copynumber: 2.8 Consensus size: 48
3134487 ATATAAATTT
* *
3134497 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA-TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* ** *
3134543 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTGTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTT-TTACCAAAATA
* *
3134593 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
3134627 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
46 6 0.08
47 26 0.37
48 20 0.28
49 5 0.07
50 14 0.20
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.42
Consensus pattern (48 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
Found at i:3139946 original size:6 final size:6
Alignment explanation
Indices: 3139929--3139959 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3139919 ACCCTTGTGT
*
3139929 CATGAC CGTGAC CATGAC CATGAC CATGAC C
1 CATGAC CATGAC CATGAC CATGAC CATGAC C
3139960 TATGGGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.19, T:0.16
Consensus pattern (6 bp):
CATGAC
Found at i:3141747 original size:47 final size:48
Alignment explanation
Indices: 3141624--3141753 Score: 142
Period size: 47 Copynumber: 2.8 Consensus size: 48
3141614 ATATAAATTT
* *
3141624 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA-TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
* ** *
3141670 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTGTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTT-TTACCAAAATA
* *
3141720 CTTTCCA-TT-ATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTT
3141754 GCATGGTTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
46 6 0.08
47 26 0.37
48 20 0.28
49 5 0.07
50 14 0.20
ACGTcount: A:0.29, C:0.22, G:0.07, T:0.42
Consensus pattern (48 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTACCAAAATA
Found at i:3150469 original size:23 final size:21
Alignment explanation
Indices: 3150413--3150493 Score: 110
Period size: 21 Copynumber: 3.8 Consensus size: 21
3150403 CAAAGTGTCA
3150413 AAGTACACAAAGTACTACTAC
1 AAGTACACAAAGTACTACTAC
3150434 AAGTACACAAAGTACT-CGTACC
1 AAGTACACAAAGTACTAC-TA-C
* *
3150456 ATAGTTCACAAAGTACTACTTC
1 A-AGTACACAAAGTACTACTAC
3150478 AAGTACACAAAGTACT
1 AAGTACACAAAGTACT
3150494 CTTACGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.02
21 32 0.60
22 4 0.08
23 15 0.28
24 1 0.02
ACGTcount: A:0.43, C:0.23, G:0.11, T:0.22
Consensus pattern (21 bp):
AAGTACACAAAGTACTACTAC
Found at i:3152218 original size:17 final size:17
Alignment explanation
Indices: 3152196--3152237 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
3152186 TGAACAAATT
3152196 ATTTTACCCTTTTCCCA
1 ATTTTACCCTTTTCCCA
3152213 ATTTTACCCTTTTCCCA
1 ATTTTACCCTTTTCCCA
3152230 ATTTTACC
1 ATTTTACC
3152238 AAGCATATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTTACCCTTTTCCCA
Found at i:3155983 original size:12 final size:12
Alignment explanation
Indices: 3155951--3155990 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
3155941 TACGGAAAAA
3155951 TTAAAATC-A-T
1 TTAAAATCTATT
3155961 TT-AAATCTATT
1 TTAAAATCTATT
*
3155972 TTAAAATTTATT
1 TTAAAATCTATT
3155984 TTAAAAT
1 TTAAAAT
3155991 ATAGATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 3 0.12
12 15 0.58
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (12 bp):
TTAAAATCTATT
Found at i:3156002 original size:22 final size:22
Alignment explanation
Indices: 3155977--3156209 Score: 315
Period size: 22 Copynumber: 10.6 Consensus size: 22
3155967 CTATTTTAAA
* *
3155977 ATTTATTTTAAAATATAGATTC
1 ATTTATTTTAAAATATGGATTG
*
3155999 ATTTATTTTAGAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
3156021 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
3156043 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
***
3156065 ATTTATTTTAAAATATGGAAAA
1 ATTTATTTTAAAATATGGATTG
*
3156087 ATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAAATATGGATTG
3156109 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
***
3156131 ATTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
3156152 ATTTTATTTTAAAATATGGATTG
1 A-TTTATTTTAAAATATGGATTG
*
3156175 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
3156197 ATTTATTTTAAAA
1 ATTTATTTTAAAA
3156210 AATTTATTAT
Statistics
Matches: 182, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
21 3 0.02
22 176 0.97
23 3 0.02
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:3156290 original size:31 final size:31
Alignment explanation
Indices: 3156233--3156291 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3156223 AGTTGTATGG
*
3156233 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
3156264 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
3156292 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:3168866 original size:16 final size:17
Alignment explanation
Indices: 3168847--3168883 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3168837 TAAAATATTA
3168847 TTTTA-AATAATTAC-AT
1 TTTTACAATAA-TACTAT
3168863 TTTTACAATAATACTAT
1 TTTTACAATAATACTAT
3168880 TTTT
1 TTTT
3168884 GTCATCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTTACAATAATACTAT
Found at i:3170759 original size:22 final size:22
Alignment explanation
Indices: 3170733--3170777 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
3170723 TTTTCATATT
3170733 AACATCATATTTCTCTATGTTA
1 AACATCATATTTCTCTATGTTA
*
3170755 AACATCATATTTCTTTATGTTA
1 AACATCATATTTCTCTATGTTA
3170777 A
1 A
3170778 CATTACATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.33, C:0.16, G:0.04, T:0.47
Consensus pattern (22 bp):
AACATCATATTTCTCTATGTTA
Found at i:3170790 original size:21 final size:22
Alignment explanation
Indices: 3170733--3170790 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 22
3170723 TTTTCATATT
* * *
3170733 AACATCATATTTCTCTATGTTA
1 AACATCACATATCTTTATGTTA
* *
3170755 AACATCATATTTCTTTATGTT-
1 AACATCACATATCTTTATGTTA
*
3170776 AACATTACATATCTT
1 AACATCACATATCTT
3170791 CATATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (22 bp):
AACATCACATATCTTTATGTTA
Found at i:3171025 original size:21 final size:21
Alignment explanation
Indices: 3170987--3171028 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3170977 TATAGAAGAG
*
3170987 AATATCTTTCCGTATTAATAT
1 AATATCTTTCCATATTAATAT
* *
3171008 AATATCTTTTCATGTTAATAT
1 AATATCTTTCCATATTAATAT
3171029 TATGTATCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (21 bp):
AATATCTTTCCATATTAATAT
Found at i:3175519 original size:21 final size:20
Alignment explanation
Indices: 3175469--3175521 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3175459 CCCTTCAAGG
3175469 AGTATCGATACTTAGGGTCC
1 AGTATCGATACTTAGGGTCC
* *
3175489 AGTATTGATACTTAGAGGGT-T
1 AGTATCGATACTT--AGGGTCC
3175510 AGTATCGATACT
1 AGTATCGATACT
3175522 GAGGCATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 12 0.43
21 11 0.39
22 5 0.18
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTTAGGGTCC
Found at i:3175576 original size:18 final size:20
Alignment explanation
Indices: 3175555--3175604 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
3175545 GCCAAATTTG
3175555 GTATCGATACTCAGGG-G-A
1 GTATCGATACTCAGGGTGAA
* *
3175573 GTATCTATACCCAGGGTGAA
1 GTATCGATACTCAGGGTGAA
*
3175593 GCATCGATACTC
1 GTATCGATACTC
3175605 CCCATATGAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 14 0.56
19 1 0.04
20 10 0.40
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (20 bp):
GTATCGATACTCAGGGTGAA
Found at i:3182631 original size:21 final size:22
Alignment explanation
Indices: 3182607--3182665 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 22
3182597 GGGATTGACA
3182607 ATTGA-TATTTTAAGTTTAGTG
1 ATTGACTATTTTAAGTTTAGTG
3182628 ATTGCACTATTTATTTAAGTTTAGTG
1 ATTG-ACTA--T-TTTAAGTTTAGTG
3182654 ATT-ACTATTTTA
1 ATTGACTATTTTA
3182666 TTTTTCTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
21 8 0.24
22 2 0.06
23 2 0.06
24 4 0.12
25 1 0.03
26 16 0.48
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (22 bp):
ATTGACTATTTTAAGTTTAGTG
Found at i:3182645 original size:26 final size:25
Alignment explanation
Indices: 3182615--3182668 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 25
3182605 CAATTGATAT
3182615 TTTAAGTTTAGTGATTGCACTA-TTTA
1 TTTAAGTTTAGTGATT--ACTATTTTA
3182641 TTTAAGTTTAGTGATTACTATTTTA
1 TTTAAGTTTAGTGATTACTATTTTA
3182666 TTT
1 TTT
3182669 TTCTTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 4 0.15
25 7 0.26
26 16 0.59
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.56
Consensus pattern (25 bp):
TTTAAGTTTAGTGATTACTATTTTA
Found at i:3186585 original size:16 final size:16
Alignment explanation
Indices: 3186564--3186596 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3186554 GATTGATAGT
3186564 TTTTATTATAA-GAAAA
1 TTTTATTA-AAGGAAAA
3186580 TTTTATTAAAGGAAAA
1 TTTTATTAAAGGAAAA
3186596 T
1 T
3186597 AATTTTCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (16 bp):
TTTTATTAAAGGAAAA
Found at i:3190572 original size:19 final size:20
Alignment explanation
Indices: 3190548--3190598 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
3190538 CAGAAATGGC
*
3190548 ATCGATACTGTTATAG-AGT
1 ATCGATACTATTATAGAAGT
3190567 ATCGATACCATATTATAGAAGT
1 ATCGATA-C-TATTATAGAAGT
*
3190589 ATCGGTACTA
1 ATCGATACTA
3190599 AGAAAAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.26
20 3 0.11
21 8 0.30
22 9 0.33
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (20 bp):
ATCGATACTATTATAGAAGT
Found at i:3190643 original size:33 final size:33
Alignment explanation
Indices: 3190606--3190715 Score: 202
Period size: 33 Copynumber: 3.3 Consensus size: 33
3190596 CTAAGAAAAA
*
3190606 GGTATCGATACCAAGGATCCATAATGTAGAAAT
1 GGTATCGATACCAAGGATCCAGAATGTAGAAAT
3190639 GGTATCGATACCAAGGATCCAGAATGTAGAAAT
1 GGTATCGATACCAAGGATCCAGAATGTAGAAAT
*
3190672 GGTATCAATACCAAGGATCCAGAATGTAGAAAT
1 GGTATCGATACCAAGGATCCAGAATGTAGAAAT
3190705 GGTATCGATAC
1 GGTATCGATAC
3190716 TGAAAGGGAG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.23
Consensus pattern (33 bp):
GGTATCGATACCAAGGATCCAGAATGTAGAAAT
Found at i:3191596 original size:54 final size:54
Alignment explanation
Indices: 3191098--3191584 Score: 706
Period size: 54 Copynumber: 9.0 Consensus size: 54
3191088 TACAGAATGA
* ** *
3191098 CACTATATGTGCAACTTAAGAAATTCATAACAAGTTTATGAATTTCCGTATTGA
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
* **
3191152 CACTATGTGTGAAACTTAAGAAATTCATAATGAGTTTATGAATTTTTGTATTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
* *
3191206 CACTATGTGTGCAACTTAAGATATTCATAATGAGTTTATGAATTTCTGTATTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
* *
3191260 CACTATATGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTACTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
* *
3191314 CACTATGTGTGCAACATAAGAAATTCATAATGAGTTTATGAATTTTCGTATTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
* * * *
3191368 CACTATGTGTGCAACTTAAGAAATTCATAACGAATTTATGAATTTTCGTATTGA
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
* *
3191422 CACTTTGTGTGCAACTTAAGAAATTCATAATGCGTTTATG-ATTTCCGTATTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
* *
3191475 CACTATATGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCTGTATTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
*** ** * **
3191529 TTGTATGTGTGCAACTTAAGATTTTCATAATAAGTTTATGAATTTTTGTATTGG
1 CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
3191583 CA
1 CA
3191585 ATGGGTGTGC
Statistics
Matches: 390, Mismatches: 42, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
53 48 0.12
54 342 0.88
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (54 bp):
CACTATGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGG
Found at i:3196014 original size:29 final size:29
Alignment explanation
Indices: 3195974--3196041 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
3195964 GCCCAAAACA
3195974 AAAAATCTTTTTCCAAGGTGATACTTTAAG
1 AAAAA-CTTTTTCCAAGGTGATACTTTAAG
3196004 AAAAACTTTTTCCAAGGTGATACTTTAAG
1 AAAAACTTTTTCCAAGGTGATACTTTAAG
3196033 AAAAACTTT
1 AAAAACTTT
3196042 ATCACATTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 33 0.87
30 5 0.13
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (29 bp):
AAAAACTTTTTCCAAGGTGATACTTTAAG
Found at i:3202020 original size:12 final size:12
Alignment explanation
Indices: 3201998--3202031 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3201988 TTCGTTTGTT
3201998 GTGCTTGCTCCTC
1 GTGC-TGCTCCTC
3202011 GTGCTGCTCCTC
1 GTGCTGCTCCTC
3202023 GTGCTGCTC
1 GTGCTGCTC
3202032 AAGCTCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.35
Consensus pattern (12 bp):
GTGCTGCTCCTC
Done.