Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2888089 original size:37 final size:36
Alignment explanation
Indices: 2887914--2888251 Score: 274
Period size: 37 Copynumber: 9.4 Consensus size: 36
2887904 TACATATATA
* * *
2887914 TATATATTATATAG-TTTGCAAACGGTTTTTGAAATACT
1 TATATAATATATAGTTTTGAAAAC-ATTTTTGAAA-A-T
*
2887952 TATATAATATATAGTTTT-AAAACATTTTTGAAAAC
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* *
2887987 TATATAATATAT--TTTTTAAAACATTTTAGAAAAT
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAAT
* ** * * *
2888021 ATTTATGCTATGTATTTTTTAAAATCA-TTTTGAAAACT
1 -TATATAATATATAGTTTTGAAAA-CATTTTTGAAAA-T
2888059 TATATAATATATAGTTTTGAAAACATTTTTGAAAATT
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAA-T
2888096 TATATAATATATAGTTTTGAAAACA--TTT----A-
1 TATATAATATATAGTTTTGAAAACATTTTTGAAAAT
*
2888125 TATAT--TATATAGTTTTTGAAAAACATTTTAG-AAAT
1 TATATAATATATAG-TTTTG-AAAACATTTTTGAAAAT
* *
2888160 ATATATAATATATAGTTTTTTAAAACATTTTTGAATAT
1 -TATATAATATATAG-TTTTGAAAACATTTTTGAAAAT
* * *
2888198 ATATATATTATATAGATTTTTAAAACGTTTTTGGAAAAT
1 -TATATAATATATAG-TTTTGAAAACATTTTT-GAAAAT
2888237 ATATATAATATATAG
1 -TATATAATATATAG
2888252 CCTTTAAAAA
Statistics
Matches: 252, Mismatches: 27, Indels: 41
0.79 0.08 0.13
Matches are distributed among these distances:
27 7 0.03
28 5 0.02
29 11 0.04
31 3 0.01
33 4 0.02
34 16 0.06
35 23 0.09
36 8 0.03
37 89 0.35
38 64 0.25
39 22 0.09
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
TATATAATATATAGTTTTGAAAACATTTTTGAAAAT
Found at i:2888133 original size:27 final size:28
Alignment explanation
Indices: 2888084--2888152 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 28
2888074 TTTGAAAACA
2888084 TTTTTG-AAA-ATTTATATAATATATAG
1 TTTTTGAAAACATTTATATAATATATAG
*
2888110 -TTTTGAAAACATTTATATATTATATAG
1 TTTTTGAAAACATTTATATAATATATAG
2888137 TTTTTGAAAAACATTT
1 TTTTTG-AAAACATTT
2888153 TAGAAATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 5 0.13
26 3 0.08
27 16 0.42
28 5 0.13
29 9 0.24
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (28 bp):
TTTTTGAAAACATTTATATAATATATAG
Found at i:2888162 original size:29 final size:27
Alignment explanation
Indices: 2888085--2888164 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
2888075 TTGAAAACAT
*
2888085 TTTTG-AAA-ATTTATATAATATATAG
1 TTTTGAAAACATTTATAAAATATATAG
* *
2888110 TTTTGAAAACATTTATATATTATATAG
1 TTTTGAAAACATTTATAAAATATATAG
2888137 TTTTTGAAAAACATTT-TAGAAATATATA
1 -TTTTG-AAAACATTTATA-AAATATATA
2888165 TAATATATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 5 0.11
26 3 0.06
27 16 0.34
28 7 0.15
29 16 0.34
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (27 bp):
TTTTGAAAACATTTATAAAATATATAG
Found at i:2888171 original size:65 final size:65
Alignment explanation
Indices: 2888048--2888189 Score: 202
Period size: 66 Copynumber: 2.2 Consensus size: 65
2888038 TTTAAAATCA
* *
2888048 TTTTGAAAAC--TTATATAATATATAGTTTTGAAAACATTTTTGAAAATTTATATAATATATAG-
1 TTTTGAAAACATTTATATAATATATAGTTTTGAAAACATTTTAGAAAATATATATAATATATAGT
*
2888110 TTTTGAAAACATTTATATATTATATAGTTTTTGAAAAACATTTTAG-AAATATATATAATATATA
1 TTTTGAAAACATTTATATAATATATAG-TTTTG-AAAACATTTTAGAAAATATATATAATATATA
2888174 GT
64 GT
*
2888176 TTTTTAAAACATTT
1 TTTTGAAAACATTT
2888190 TTGAATATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
62 10 0.14
64 14 0.20
65 23 0.32
66 24 0.34
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (65 bp):
TTTTGAAAACATTTATATAATATATAGTTTTGAAAACATTTTAGAAAATATATATAATATATAGT
Found at i:2888218 original size:39 final size:37
Alignment explanation
Indices: 2888123--2888293 Score: 168
Period size: 38 Copynumber: 4.5 Consensus size: 37
2888113 TGAAAACATT
* * *
2888123 TATATATTATATAGTTTTTGAAAAACATTTTAGAAATA
1 TATATAATATATAGTTTTT-TAAAACATTTTTGAAATA
2888161 TATATAATATATAGTTTTTTAAAACATTTTTGAATATA
1 TATATAATATATAGTTTTTTAAAACATTTTTGAA-ATA
* * *
2888199 TATATATTATATAGATTTTTAAAACGTTTTTGGAAAATA
1 TATATAATATATAGTTTTTTAAAACATTTTT-G-AAATA
** *
2888238 TATATAATATATAG-CCTTTAAAAAATATTTTAGAAAT-
1 TATATAATATATAGTTTTTTAAAACAT-TTTT-GAAATA
*
2888275 TAATATATTATAT-GTTTTT
1 T-ATATAATATATAGTTTTT
2888294 GAATTTTTTT
Statistics
Matches: 112, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
37 15 0.13
38 73 0.65
39 22 0.20
40 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (37 bp):
TATATAATATATAGTTTTTTAAAACATTTTTGAAATA
Found at i:2888281 original size:77 final size:75
Alignment explanation
Indices: 2888123--2888293 Score: 199
Period size: 77 Copynumber: 2.3 Consensus size: 75
2888113 TGAAAACATT
** *
2888123 TATATATTATATAGTTTTTGAAAAACATTTTAGAAATATATATAATATATAGTTTTTTAAAACAT
1 TATATATTATATAGTTTTT-AAAAACATTTTAGAAATATATATAATATATAGTCCTTTAAAAAAT
2888188 TTTTGAATATA
65 TTTTGAATATA
* *
2888199 TATATATTATATAGATTTTT-AAAACGTTTTTGGAAAATATATATAATATATAG-CCTTTAAAAA
1 TATATATTATATAG-TTTTTAAAAAC-ATTTTAG-AAATATATATAATATATAGTCCTTTAAAAA
2888262 ATATTTTAGAA-AT-
63 AT-TTTT-GAATATA
2888275 TAATATATTATAT-GTTTTT
1 T-ATATATTATATAGTTTTT
2888294 GAATTTTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
75 10 0.12
76 30 0.36
77 41 0.49
78 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (75 bp):
TATATATTATATAGTTTTTAAAAACATTTTAGAAATATATATAATATATAGTCCTTTAAAAAATT
TTTGAATATA
Found at i:2888331 original size:16 final size:16
Alignment explanation
Indices: 2888299--2888345 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2888289 TTTTTGAATT
*
2888299 TTTTTATTTAATT-TTA
1 TTTTT-TTTATTTCTTA
2888315 TTTTTTTTATTTCTTA
1 TTTTTTTTATTTCTTA
* *
2888331 TTTATTTAATTTCTT
1 TTTTTTTTATTTCTT
2888346 TTTATTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTTATTTCTTA
Found at i:2888331 original size:26 final size:26
Alignment explanation
Indices: 2888302--2888353 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
2888292 TTGAATTTTT
*
2888302 TTATTTAATTTTATTT-TTTTTATTTC
1 TTATTT-ATTTAATTTCTTTTTATTTC
2888328 TTATTTATTTAATTTCTTTTTATTTC
1 TTATTTATTTAATTTCTTTTTATTTC
2888354 ATGGTCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (26 bp):
TTATTTATTTAATTTCTTTTTATTTC
Found at i:2888856 original size:12 final size:12
Alignment explanation
Indices: 2888841--2888871 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2888831 CCAGTAGAAA
2888841 AACCAAACAAAT
1 AACCAAACAAAT
*
2888853 AACCAAACACAT
1 AACCAAACAAAT
2888865 AACCAAA
1 AACCAAA
2888872 AACCGAAGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.65, C:0.29, G:0.00, T:0.06
Consensus pattern (12 bp):
AACCAAACAAAT
Found at i:2889461 original size:19 final size:19
Alignment explanation
Indices: 2889425--2889473 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
2889415 TTTCATTTTA
2889425 TTTTTATTTTACGTGATATT
1 TTTTTATTTTACG-GATATT
2889445 TTTTTATTTATAC-GATATT
1 TTTTTATTT-TACGGATATT
* *
2889464 ATATTATTTT
1 TTTTTATTTT
2889474 TATTTTTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 9 0.35
21 3 0.12
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.65
Consensus pattern (19 bp):
TTTTTATTTTACGGATATT
Found at i:2889489 original size:26 final size:25
Alignment explanation
Indices: 2889420--2889496 Score: 68
Period size: 26 Copynumber: 3.0 Consensus size: 25
2889410 CTTTTTTTCA
*
2889420 TTTTATTTTTAT-TTTACGTGATATTT
1 TTTTATTTTTATCTTTA--TTATATTT
* **
2889446 TTTTATTTATA-CGATATTATATTAT
1 TTTTATTTTTATCTTTATTATATT-T
*
2889471 TTTTATTTTTATCTTTATTTTATTT
1 TTTTATTTTTATCTTTATTATATTT
2889496 T
1 T
2889497 AATCCTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
24 6 0.15
25 13 0.32
26 21 0.52
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.70
Consensus pattern (25 bp):
TTTTATTTTTATCTTTATTATATTT
Found at i:2889490 original size:18 final size:18
Alignment explanation
Indices: 2889467--2889554 Score: 55
Period size: 17 Copynumber: 5.1 Consensus size: 18
2889457 CGATATTATA
2889467 TTATTTTTATTTTTATCT
1 TTATTTTTATTTTTATCT
*
2889485 TTA-TTTTATTTTAATCCT
1 TTATTTTTATTTTTAT-CT
*
2889503 TTA--ATTATTTTTA---
1 TTATTTTTATTTTTATCT
2889516 TTATTTTTCATTTGTTTAT-T
1 TTATTTTT-A-TT-TTTATCT
* *
2889536 ATATTTTTATTTTTTTCT
1 TTATTTTTATTTTTATCT
2889554 T
1 T
2889555 CTACATTATT
Statistics
Matches: 54, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
13 3 0.06
15 2 0.04
16 1 0.02
17 25 0.46
18 15 0.28
19 1 0.02
20 7 0.13
ACGTcount: A:0.19, C:0.06, G:0.01, T:0.74
Consensus pattern (18 bp):
TTATTTTTATTTTTATCT
Found at i:2889491 original size:17 final size:18
Alignment explanation
Indices: 2889471--2889516 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
2889461 ATTATATTAT
2889471 TTTTATTTTTAT-CTTTA
1 TTTTATTTTTATCCTTTA
*
2889488 TTTTATTTTAATCCTTTA
1 TTTTATTTTTATCCTTTA
*
2889506 -ATTATTTTTAT
1 TTTTATTTTTAT
2889517 TATTTTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATTTTTATCCTTTA
Found at i:2889584 original size:2 final size:2
Alignment explanation
Indices: 2889577--2889651 Score: 120
Period size: 2 Copynumber: 39.0 Consensus size: 2
2889567 TACGTATTTC
2889577 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
*
2889619 AT AT AT AT AT -T AT AT -T AT -T AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2889652 TATTTCTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
1 3 0.04
2 65 0.96
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2889735 original size:19 final size:18
Alignment explanation
Indices: 2889698--2889740 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
2889688 ACTTTTTTAA
* *
2889698 TTTTTTATTTTATTTTAT
1 TTTTTTATTTTAATGTAT
2889716 TTTTTTATCTTTAATGTAT
1 TTTTTTAT-TTTAATGTAT
2889735 TTTTTT
1 TTTTTT
2889741 CCTTTCTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (18 bp):
TTTTTTATTTTAATGTAT
Found at i:2889836 original size:23 final size:24
Alignment explanation
Indices: 2889794--2889868 Score: 66
Period size: 23 Copynumber: 3.1 Consensus size: 24
2889784 TTTTGTTCCC
*
2889794 TTATTTCTTCTTACTATATATTTT
1 TTATTTCTTATTACTATATATTTT
*
2889818 TTATTT-TTATTATTATATATTATAT
1 TTATTTCTTATTACTATATATT-T-T
*
2889843 TTA--TCCTATTTATCTATATATTTT
1 TTATTTCTTA-TTA-CTATATATTTT
2889867 TT
1 TT
2889869 TTCATTGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
23 14 0.33
24 12 0.29
25 8 0.19
26 8 0.19
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (24 bp):
TTATTTCTTATTACTATATATTTT
Found at i:2889895 original size:15 final size:15
Alignment explanation
Indices: 2889859--2889910 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
2889849 TATTTATCTA
2889859 TATATTTTTTTTCAT
1 TATATTTTTTTTCAT
** *
2889874 TGCATTTTTTTTCTT
1 TATATTTTTTTTCAT
2889889 TATATTTTTTATT-AT
1 TATATTTTTT-TTCAT
2889904 TAT-TTTT
1 TATATTTT
2889911 ATCCTTTTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 4 0.13
15 24 0.80
16 2 0.07
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (15 bp):
TATATTTTTTTTCAT
Found at i:2889917 original size:28 final size:28
Alignment explanation
Indices: 2889851--2889913 Score: 67
Period size: 30 Copynumber: 2.2 Consensus size: 28
2889841 ATTTATCCTA
*
2889851 TTTATCTATATATTTTTTTTCATTGCATTT
1 TTTATCTTTATATTTTTTTTCATT-CA-TT
*
2889881 TTTTTCTTTATATTTTTTATT-ATT-ATT
1 TTTATCTTTATATTTTTT-TTCATTCATT
2889908 TTTATC
1 TTTATC
2889914 CTTTTTGTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
27 7 0.24
28 1 0.03
30 19 0.66
31 2 0.07
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (28 bp):
TTTATCTTTATATTTTTTTTCATTCATT
Found at i:2891999 original size:30 final size:30
Alignment explanation
Indices: 2891965--2892023 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2891955 TTTCATCCCT
* *
2891965 AAACTTT-TCAAAGTGTATACTTTGGTCACC
1 AAACTTTACCAAA-TGTATAATTTGGTCACC
*
2891995 AAACTTTACCAAATTTATAATTTGGTCAC
1 AAACTTTACCAAATGTATAATTTGGTCAC
2892024 TAAATAAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (30 bp):
AAACTTTACCAAATGTATAATTTGGTCACC
Found at i:2903124 original size:15 final size:14
Alignment explanation
Indices: 2903099--2903139 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
2903089 AAGTTTGGAG
2903099 TTTTTTT-AAATAT
1 TTTTTTTAAAATAT
2903112 TTTATTTTAAAATAT
1 TTT-TTTTAAAATAT
2903127 TTTTTTTACAAAT
1 TTTTTTTA-AAAT
2903140 TATATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 3 0.12
14 9 0.36
15 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTTAAAATAT
Found at i:2906836 original size:14 final size:15
Alignment explanation
Indices: 2906819--2906861 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
2906809 TTTGACCGGT
2906819 CTGACCCGACCCGA-
1 CTGACCCGACCCGAC
*
2906833 CTGACCCGATCCGAC
1 CTGACCCGACCCGAC
2906848 CGTTGACCCGACCC
1 C--TGACCCGACCC
2906862 AACCGTTGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 13 0.54
15 1 0.04
17 10 0.42
ACGTcount: A:0.19, C:0.49, G:0.21, T:0.12
Consensus pattern (15 bp):
CTGACCCGACCCGAC
Found at i:2906856 original size:17 final size:17
Alignment explanation
Indices: 2906834--2906872 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2906824 CCGACCCGAC
* *
2906834 TGACCCGATCCGACCGT
1 TGACCCGACCCAACCGT
2906851 TGACCCGACCCAACCGT
1 TGACCCGACCCAACCGT
2906868 TGACC
1 TGACC
2906873 GTTGACTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.15
Consensus pattern (17 bp):
TGACCCGACCCAACCGT
Found at i:2913342 original size:20 final size:21
Alignment explanation
Indices: 2913317--2913355 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2913307 GAGGGCTGGA
2913317 AACCGGTT-TGACCGGTTTTC
1 AACCGGTTCTGACCGGTTTTC
*
2913337 AACCGGTTCTGATCGGTTT
1 AACCGGTTCTGACCGGTTT
2913356 CGATCGGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (21 bp):
AACCGGTTCTGACCGGTTTTC
Found at i:2913363 original size:20 final size:20
Alignment explanation
Indices: 2913340--2913386 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
2913330 GGTTTTCAAC
*
2913340 CGGTTCTGA-TCGGTTTCGAT
1 CGGTTCTGAGCCGGTTT-GAT
2913360 CGGTTC-GAGCCGGTTTGAT
1 CGGTTCTGAGCCGGTTTGAT
2913379 CGG-TCTGA
1 CGGTTCTGA
2913387 CCCGACCCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.08
19 10 0.42
20 12 0.50
ACGTcount: A:0.11, C:0.21, G:0.34, T:0.34
Consensus pattern (20 bp):
CGGTTCTGAGCCGGTTTGAT
Found at i:2913445 original size:14 final size:14
Alignment explanation
Indices: 2913412--2913445 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2913402 TTGACCCGAC
* *
2913412 TTGACCGTTGACCG
1 TTGACTGTTGACCA
2913426 TTGACTGTTGACCA
1 TTGACTGTTGACCA
2913440 TTGACT
1 TTGACT
2913446 TCCTTTGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (14 bp):
TTGACTGTTGACCA
Found at i:2915185 original size:60 final size:60
Alignment explanation
Indices: 2915111--2915268 Score: 262
Period size: 60 Copynumber: 2.6 Consensus size: 60
2915101 AATAGTTTGG
*
2915111 GACTCAACAAAACACCACCCTATAATCAAATGATCATTTTGTAAGTTTTAATAGTCAAAT
1 GACTCAACAAAACACCACCCTATAATCAAATGATCATTTTGTAAGTTTTAACAGTCAAAT
2915171 GACTCAACAAAACACCACCCTATAATCAAATGATCATTTTGTAAGTTTTAACAGTCAAAT
1 GACTCAACAAAACACCACCCTATAATCAAATGATCATTTTGTAAGTTTTAACAGTCAAAT
*** **
2915231 GACTCAACAAAACAATTCCCTATAATCAAGGGATCATT
1 GACTCAACAAAACACCACCCTATAATCAAATGATCATT
2915269 CGTATACTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.28
Consensus pattern (60 bp):
GACTCAACAAAACACCACCCTATAATCAAATGATCATTTTGTAAGTTTTAACAGTCAAAT
Found at i:2918619 original size:2 final size:2
Alignment explanation
Indices: 2918612--2918652 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2918602 CAGTTAATTT
2918612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2918653 TATTTTATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2919627 original size:2 final size:2
Alignment explanation
Indices: 2919620--2919646 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2919610 GGAGAAACAT
2919620 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
2919647 GGAGTTTGTT
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2926182 original size:18 final size:18
Alignment explanation
Indices: 2926161--2926203 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2926151 GTTGTTTTTA
*
2926161 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
2926179 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
2926197 AAATAAA
1 AAATAAA
2926204 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:2927009 original size:76 final size:74
Alignment explanation
Indices: 2926796--2927021 Score: 264
Period size: 76 Copynumber: 3.1 Consensus size: 74
2926786 TAAAACATCT
* * *
2926796 TAAATCTTAATTAAAACACTTAAAA-CTATTTAAACTAAAATAC---CTAAAAAATAATATTTAA
1 TAAATCTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAA
*
2926857 AATAATATTC
65 AATAATATCC
* * * *
2926867 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATA-TA
1 TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAATAAA-ATATAATATTT
2926931 AAAATAATATCC
63 AAAATAATATCC
* * *
2926943 TAAAACTTAATTAAAATACTAAAACCTATTTAAATTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-ATAAAATATAATATTTAA
*
2927008 AATATTATCC
65 AATAATATCC
2927018 TAAA
1 TAAA
2927022 CTTGAGTTTA
Statistics
Matches: 130, Mismatches: 16, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
70 5 0.04
71 34 0.26
72 1 0.01
74 9 0.07
75 21 0.16
76 54 0.42
77 6 0.05
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.31
Consensus pattern (74 bp):
TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
ATAATATCC
Found at i:2928689 original size:11 final size:11
Alignment explanation
Indices: 2928670--2928722 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
2928660 AGTTTGCTAA
2928670 AAAAT-AAAAG
1 AAAATAAAAAG
*
2928680 AAAAAGAAAAAG
1 -AAAATAAAAAG
*
2928692 AAAATAAAACG
1 AAAATAAAAAG
2928703 AAAATAAAAATG
1 AAAATAAAAA-G
2928715 -AAATAAAA
1 AAAATAAAA
2928723 TAAAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 30 0.83
12 6 0.17
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAATAAAAAG
Found at i:2928689 original size:17 final size:17
Alignment explanation
Indices: 2928669--2928711 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2928659 AAGTTTGCTA
2928669 AAAAATAAAAGAAAAAG
1 AAAAATAAAAGAAAAAG
* * *
2928686 AAAAAGAAAATAAAACG
1 AAAAATAAAAGAAAAAG
2928703 -AAAATAAAA
1 AAAAATAAAA
2928712 ATGAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.81, C:0.02, G:0.09, T:0.07
Consensus pattern (17 bp):
AAAAATAAAAGAAAAAG
Found at i:2928695 original size:22 final size:21
Alignment explanation
Indices: 2928670--2928730 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
2928660 AGTTTGCTAA
2928670 AAAATAAAAGAAAAAGAAAAAG
1 AAAATAAAAGAAAAA-AAAAAG
*
2928692 AAAATAAAACGAAAATAAAAATG
1 AAAATAAAA-GAAAA-AAAAAAG
*
2928715 -AAATAAAATAAAAAAA
1 AAAATAAAAGAAAAAAA
2928731 TAGAACAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 3 0.09
21 4 0.11
22 17 0.49
23 10 0.29
24 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.08, T:0.10
Consensus pattern (21 bp):
AAAATAAAAGAAAAAAAAAAG
Found at i:2934357 original size:18 final size:18
Alignment explanation
Indices: 2934336--2934378 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2934326 GTTGTTTTTA
*
2934336 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
2934354 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
2934372 AAATAAA
1 AAATAAA
2934379 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:2935130 original size:19 final size:19
Alignment explanation
Indices: 2935106--2935143 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2935096 AAATAATATC
*
2935106 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
2935125 CTAAAACCTATTTAAAATA
1 CTAAAACCTAATTAAAATA
2935144 AAATACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:2935173 original size:76 final size:74
Alignment explanation
Indices: 2934967--2935188 Score: 240
Period size: 76 Copynumber: 3.0 Consensus size: 74
2934957 TCTTAAATCC
* * * *
2934967 TAATTAAAACACTTAAATCTATTTAAACTAAAATAC---CTAAAAAATAATATTTAAAATAATAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAAAATAATATTTAAAATAATAT
* *
2935029 TCT-AAATT
66 CCTAAAACT
* * *
2935037 CTAATTAAAATACTAAAACCTATTTAAACTAAAATACATAAA-ACAAAGATAAAATATAAAAATA
1 -TAATTAAAATACTAAAACCTATTTAAACTAAAATACA-AAATA-AAAAATAATAT-TTAAAATA
2935101 ATATCCTAAAACT
62 ATATCCTAAAACT
* * * *
2935114 TAATTAAAATACTAAAACCTATTTAAAATAAAATACAAAGATAAAATATAATGTTTAAAATATTA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-ATAAAAAATAATATTTAAAATAATA
2935179 TCC-AAAACT
65 TCCTAAAACT
2935188 T
1 T
2935189 GAGTTTAATT
Statistics
Matches: 127, Mismatches: 15, Indels: 15
0.81 0.10 0.10
Matches are distributed among these distances:
71 33 0.26
74 8 0.06
75 23 0.18
76 58 0.46
77 5 0.04
ACGTcount: A:0.57, C:0.11, G:0.01, T:0.31
Consensus pattern (74 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAAAATAATATTTAAAATAATAT
CCTAAAACT
Found at i:2943388 original size:14 final size:15
Alignment explanation
Indices: 2943364--2943392 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2943354 GTCTCAAAAT
2943364 AAATATCAATATTTC
1 AAATATCAATATTTC
2943379 AAAT-TCAATATTTC
1 AAATATCAATATTTC
2943393 TATAATAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATATCAATATTTC
Found at i:2944371 original size:57 final size:57
Alignment explanation
Indices: 2944302--2944426 Score: 223
Period size: 57 Copynumber: 2.2 Consensus size: 57
2944292 GAATGGCCAA
*
2944302 AGAGACCCTTTCCAGAAAATGTACTTGGTTGGCACGTACTCATATCTTACATTTAAC
1 AGAGACCCTTTCCAGAAAATATACTTGGTTGGCACGTACTCATATCTTACATTTAAC
* *
2944359 AGAGACCCTTTCCAGAAAATATACTTGGTTGGCACGTACTCGTATCTTACATTTAAT
1 AGAGACCCTTTCCAGAAAATATACTTGGTTGGCACGTACTCATATCTTACATTTAAC
2944416 AGAGACCCTTT
1 AGAGACCCTTT
2944427 TACATTTAAC
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (57 bp):
AGAGACCCTTTCCAGAAAATATACTTGGTTGGCACGTACTCATATCTTACATTTAAC
Found at i:2944431 original size:21 final size:21
Alignment explanation
Indices: 2944405--2944447 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2944395 TACTCGTATC
*
2944405 TTACATTTAATAGAGACCCTT
1 TTACATTTAACAGAGACCCTT
*
2944426 TTACATTTAACATAGACCCTT
1 TTACATTTAACAGAGACCCTT
2944447 T
1 T
2944448 CAGAAAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.40
Consensus pattern (21 bp):
TTACATTTAACAGAGACCCTT
Found at i:2946190 original size:38 final size:39
Alignment explanation
Indices: 2946082--2946178 Score: 142
Period size: 39 Copynumber: 2.5 Consensus size: 39
2946072 TAGGGGGGGG
* *
2946082 ATTTAAGAGTCTCTTGGGAGTTAAAGTGTTTTATTGTGA
1 ATTTAAGAGTCTCTTGGAAGTTAGAGTGTTTTATTGTGA
* * *
2946121 AATAAAGAGTCTCTTGAAAGTTAGAGTGTTTTATTGTGA
1 ATTTAAGAGTCTCTTGGAAGTTAGAGTGTTTTATTGTGA
2946160 ATTTAAGAGT-TCTTGGAAG
1 ATTTAAGAGTCTCTTGGAAG
2946179 ATGGAGAGTT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
38 8 0.16
39 42 0.84
ACGTcount: A:0.30, C:0.05, G:0.25, T:0.40
Consensus pattern (39 bp):
ATTTAAGAGTCTCTTGGAAGTTAGAGTGTTTTATTGTGA
Found at i:2975575 original size:20 final size:20
Alignment explanation
Indices: 2975550--2975590 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
2975540 AAGAAATTTT
*
2975550 GAGATTTGCAAGT-CTCCATC
1 GAGATTTACAA-TCCTCCATC
2975570 GAGATTTACAATCCTCCATC
1 GAGATTTACAATCCTCCATC
2975590 G
1 G
2975591 TATAAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (20 bp):
GAGATTTACAATCCTCCATC
Found at i:2977151 original size:3 final size:3
Alignment explanation
Indices: 2977143--2977295 Score: 74
Period size: 3 Copynumber: 47.7 Consensus size: 3
2977133 TAGTATTTTA
* * * * * * *
2977143 AAT AAT AAT AAT AAT AAT AAT AAT AAGC ATT ACT AACC ATT GAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT
* * * *
2977190 AAA AAGT AAT AAT AAT AATT AAT AAT AAT AAAT ACT GAT AACA AAT AAT
1 AAT AA-T AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AA-T AAT AAT
* * *
2977239 AAT AATT AAT ATTT ATT AAT AA- GAT CAAT AAT AAAT AAT AAT AAT AACT
1 AAT AA-T AAT A-AT AAT AAT AAT AAT -AAT AAT -AAT AAT AAT AAT AA-T
2977288 AAT AAT AA
1 AAT AAT AA
2977296 CCAATAAGAA
Statistics
Matches: 114, Mismatches: 24, Indels: 24
0.70 0.15 0.15
Matches are distributed among these distances:
2 1 0.01
3 88 0.77
4 25 0.22
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2977212 original size:13 final size:13
Alignment explanation
Indices: 2977196--2977295 Score: 71
Period size: 13 Copynumber: 7.7 Consensus size: 13
2977186 TAACAAAAAG
2977196 TAATAATAATAAT
1 TAATAATAATAAT
2977209 TAATAATAAT-A-
1 TAATAATAATAAT
* * *
2977220 -AATACTGATAAC
1 TAATAATAATAAT
*
2977232 AAATAATAATAAT
1 TAATAATAATAAT
* *
2977245 TAATATTTATTAAT
1 TAATA-ATAATAAT
* *
2977259 AAGATCAATAATAAA
1 TA-AT-AATAATAAT
*
2977274 TAATAATAATAAC
1 TAATAATAATAAT
2977287 TAATAATAA
1 TAATAATAA
2977296 CCAATAAGAA
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
10 7 0.10
11 1 0.01
12 1 0.01
13 40 0.60
14 9 0.13
15 8 0.12
16 1 0.01
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:2977296 original size:10 final size:9
Alignment explanation
Indices: 2977143--2977295 Score: 74
Period size: 10 Copynumber: 15.9 Consensus size: 9
2977133 TAGTATTTTA
2977143 AATAATAAT
1 AATAATAAT
2977152 AATAATAAT
1 AATAATAAT
*
2977161 AATAATAAGC
1 AATAATAA-T
* * *
2977171 ATTACTAACC
1 AATAATAA-T
* * *
2977181 ATTGATAAC
1 AATAATAAT
*
2977190 AAAAAGTAAT
1 AATAA-TAAT
2977200 AATAATAATT
1 AATAATAA-T
2977210 AATAATAAT
1 AATAATAAT
* *
2977219 AAATACTGAT
1 -AATAATAAT
*
2977229 AACAAATAAT
1 AA-TAATAAT
2977239 AATAATTAAT
1 AATAA-TAAT
* *
2977249 ATTTATTAAT
1 A-ATAATAAT
*
2977259 AA-GATCAAT
1 AATAAT-AAT
2977268 AATAAATAAT
1 AAT-AATAAT
2977278 AATAATAACT
1 AATAATAA-T
2977288 AATAATAA
1 AATAATAA
2977296 CCAATAAGAA
Statistics
Matches: 110, Mismatches: 23, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
8 1 0.01
9 38 0.35
10 67 0.61
11 4 0.04
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (9 bp):
AATAATAAT
Found at i:2977868 original size:60 final size:60
Alignment explanation
Indices: 2977793--2977922 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 60
2977783 GTCGAATGAT
* * ** * *
2977793 CATTTTGTAACTTTTAATAGTTG-GGAGACTCAACAAAATAATACCCTATAGTTGAAGGAC
1 CATTTTATAAATTTTAATAACTGAGG-GACTCAACAAAATAACACCCTATAATTGAAGGAC
* * *
2977853 CATTTTATAAATTTTAATAACTGAGGGACTCAACAAAGTACCACCCTATAATTGAGGGAC
1 CATTTTATAAATTTTAATAACTGAGGGACTCAACAAAATAACACCCTATAATTGAAGGAC
2977913 CATTTGTATA
1 CATTT-TATA
2977923 CTTTACCAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 53 0.90
61 6 0.10
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (60 bp):
CATTTTATAAATTTTAATAACTGAGGGACTCAACAAAATAACACCCTATAATTGAAGGAC
Found at i:2978901 original size:20 final size:21
Alignment explanation
Indices: 2978876--2978916 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
2978866 CTCCCAAAAT
2978876 AACTCTCCCCA-ACCTCTCAA
1 AACTCTCCCCACACCTCTCAA
* *
2978896 AACTCTCTCCACACTTCTCAA
1 AACTCTCCCCACACCTCTCAA
2978917 CTTGCATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.29, C:0.46, G:0.00, T:0.24
Consensus pattern (21 bp):
AACTCTCCCCACACCTCTCAA
Found at i:2979854 original size:14 final size:14
Alignment explanation
Indices: 2979837--2979878 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
2979827 AAAAAAAAAG
2979837 AATAAATAAAAATA
1 AATAAATAAAAATA
2979851 AATAAATAAAACA-A
1 AATAAATAAAA-ATA
2979865 AATAAAATAAAAAT
1 AAT-AAATAAAAAT
2979879 TGAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 16 0.64
15 9 0.36
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:2979858 original size:18 final size:18
Alignment explanation
Indices: 2979837--2979888 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
2979827 AAAAAAAAAG
2979837 AATAAATAAAAATAAATA
1 AATAAATAAAAATAAATA
2979855 AATAAA-ACAAAATAAAATA
1 AATAAATA-AAAAT-AAATA
* *
2979874 AA-AATTGAAAATAAA
1 AATAAATAAAAATAAA
2979889 ATACTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 4 0.14
18 18 0.62
19 7 0.24
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (18 bp):
AATAAATAAAAATAAATA
Found at i:2979946 original size:17 final size:17
Alignment explanation
Indices: 2979924--2979988 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
2979914 CTTTCGAAAA
2979924 ATATGTTTTCAAAAACT
1 ATATGTTTTCAAAAACT
* *
2979941 ATATGTTTCCAAAAAACC
1 ATATGTTTTC-AAAAACT
*
2979959 AT-T-TTTT-ATAAACT
1 ATATGTTTTCAAAAACT
*
2979973 ATATATTTTCAAAAAC
1 ATATGTTTTCAAAAAC
2979989 AATTTTGAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
14 7 0.18
15 1 0.03
16 7 0.18
17 15 0.39
18 8 0.21
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (17 bp):
ATATGTTTTCAAAAACT
Found at i:2980054 original size:35 final size:35
Alignment explanation
Indices: 2979972--2980102 Score: 117
Period size: 35 Copynumber: 3.6 Consensus size: 35
2979962 TTTTATAAAC
* * *
2979972 TATATAT-TTTCAAAAACAATTTTGAAAACTATATA
1 TATATATGTTTCAAAAA-TATTTTCAAAAATATATA
*
2980007 CTATATA-ATTTCAAAAATATTTT-AAAAATATATA
1 -TATATATGTTTCAAAAATATTTTCAAAAATATATA
2980041 TATTATATGTTTCAAAAATGCATTTTCAAAAACTATAT-
1 TA-TATATGTTTCAAAAAT--ATTTTCAAAAA-TATATA
*
2980079 TATATATTGTTTTTAAAAATATTT
1 TATATA-TG-TTTCAAAAATATTT
2980103 AAATTATATT
Statistics
Matches: 82, Mismatches: 4, Indels: 17
0.80 0.04 0.17
Matches are distributed among these distances:
33 2 0.02
34 14 0.17
35 15 0.18
36 15 0.18
37 13 0.16
38 9 0.11
39 14 0.17
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (35 bp):
TATATATGTTTCAAAAATATTTTCAAAAATATATA
Found at i:2980078 original size:37 final size:35
Alignment explanation
Indices: 2979972--2980249 Score: 161
Period size: 36 Copynumber: 7.9 Consensus size: 35
2979962 TTTTATAAAC
* * * *
2979972 TATATATTTTCAAAAACAATTTTGAAAACTATATAC
1 TATATGTTTTCAAAAA-TATTTTCAAAACTATATAT
** * *
2980008 TATATAATTTCAAAAATATTTTAAAAATATATATAT
1 TATATGTTTTCAAAAATATTTTCAAAA-CTATATAT
2980044 TATATG-TTTCAAAAATGCATTTTCAAAAACTATAT-T
1 TATATGTTTTCAAAAAT--ATTTTC-AAAACTATATAT
*
2980080 ATATATTGTTTTTAAAAATA-TTT---AA--AT-TA-
1 -TATA-TGTTTTCAAAAATATTTTCAAAACTATATAT
* * *
2980109 TAT-T-CTTTCAAAAATGTGTTTTCAAAACTACATAT
1 TATATGTTTTCAAAAA--TATTTTCAAAACTATATAT
* * *
2980144 TTTATGTTTTCAAAAACATGTTTTCAAAAC--CATAT
1 TATATGTTTTC-AAAA-ATATTTTCAAAACTATATAT
* * *
2980179 TATATGTTTTCCAAAACTGATTTTTGAAAACTATATTT
1 TATATGTTTT-CAAAAAT-A-TTTTCAAAACTATATAT
2980217 TATATGTTTTCAAAAATATTTTCAAAAACTATA
1 TATATGTTTTCAAAAATATTTTC-AAAACTATA
2980250 CTATATTATT
Statistics
Matches: 191, Mismatches: 23, Indels: 56
0.71 0.09 0.21
Matches are distributed among these distances:
25 8 0.04
26 1 0.01
27 1 0.01
28 6 0.03
29 1 0.01
30 2 0.01
31 2 0.01
32 2 0.01
33 1 0.01
34 3 0.02
35 43 0.23
36 51 0.27
37 37 0.19
38 23 0.12
39 10 0.05
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (35 bp):
TATATGTTTTCAAAAATATTTTCAAAACTATATAT
Found at i:2980167 original size:21 final size:22
Alignment explanation
Indices: 2980125--2980167 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
2980115 TTCAAAAATG
2980125 TGTTTTCAAAACTACATATTTTA
1 TGTTTTCAAAAC-ACATATTTTA
*
2980148 TGTTTTCAAAA-ACATGTTTT
1 TGTTTTCAAAACACATATTTT
2980168 CAAAACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (22 bp):
TGTTTTCAAAACACATATTTTA
Found at i:2980238 original size:36 final size:37
Alignment explanation
Indices: 2980106--2980249 Score: 140
Period size: 37 Copynumber: 3.9 Consensus size: 37
2980096 AATATTTAAA
* *
2980106 TTATAT-TCTTTCAAAAATGTGTTTTCAAAACTACATAT
1 TTATATGT-TTTCAAAAATATGTTTTCAAAACTATAT-T
* *
2980144 TT-TATGTTTTCAAAAACATGTTTTCAAAACCATA--
1 TTATATGTTTTCAAAAATATGTTTTCAAAACTATATT
* *
2980178 TTATATGTTTTCCAAAACTGAT-TTTTGAAAACTATATT
1 TTATATGTTTT-CAAAAAT-ATGTTTTCAAAACTATATT
2980216 TTATATGTTTTCAAAAATA--TTTTCAAAAACTATA
1 TTATATGTTTTCAAAAATATGTTTTC-AAAACTATA
2980250 CTATATTATT
Statistics
Matches: 89, Mismatches: 10, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
34 2 0.02
35 12 0.13
36 27 0.30
37 34 0.38
38 14 0.16
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (37 bp):
TTATATGTTTTCAAAAATATGTTTTCAAAACTATATT
Found at i:2981902 original size:42 final size:43
Alignment explanation
Indices: 2981856--2981936 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 43
2981846 AGACCTCTCT
* ** *
2981856 TTTTTTTCAACTTAGAATGCCCTTTC-GGTTTTCACCCTGACC
1 TTTTTTTCAAATTAGAACACCCTCTCAGGTTTTCACCCTGACC
*
2981898 TTTTTTTCAAATTAGAGCACCCTCTCAGGTTTTCACCCT
1 TTTTTTTCAAATTAGAACACCCTCTCAGGTTTTCACCCT
2981937 AAGGGAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 21 0.64
43 12 0.36
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (43 bp):
TTTTTTTCAAATTAGAACACCCTCTCAGGTTTTCACCCTGACC
Found at i:2987927 original size:13 final size:13
Alignment explanation
Indices: 2987909--2987933 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2987899 ATGGTGTGGA
2987909 AAAAGTATCATCC
1 AAAAGTATCATCC
2987922 AAAAGTATCATC
1 AAAAGTATCATC
2987934 ATAAGTACAC
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:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAGTATCATCC
Found at i:2990321 original size:24 final size:24
Alignment explanation
Indices: 2990256--2990314 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
2990246 TGATGAAGCT
*
2990256 TGTGCTTTTGTAGTAGATAAAGTG
1 TGTGCTTTTGCAGTAGATAAAGTG
2990280 TGTGCTTTTGCAGTAGATAAAGTG
1 TGTGCTTTTGCAGTAGATAAAGTG
2990304 TGTGCCTTTTG
1 TGTG-CTTTTG
2990315 AGCAGATGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.20, C:0.08, G:0.29, T:0.42
Consensus pattern (24 bp):
TGTGCTTTTGCAGTAGATAAAGTG
Found at i:2995561 original size:37 final size:36
Alignment explanation
Indices: 2995380--2995666 Score: 255
Period size: 36 Copynumber: 8.0 Consensus size: 36
2995370 TTTTTTTTAA
* ** * *
2995380 ATTATATGTTTTCATAAACCATTTTAAAAACAATAA
1 ATTATATGTTTTCAAAAATTATTTTAAAAACTATAT
*
2995416 ATTATATGTTTTCAAAAA-TATTTAAAAAACTAT-T
1 ATTATATGTTTTCAAAAATTATTTTAAAAACTATAT
*
2995450 -TTATATGTTTTCAAAAATACATTTTCAAAAACTATATT
1 ATTATATGTTTTCAAAAAT-TATTTT-AAAAACTATA-T
2995488 ATATATATGTTTTCAAAAA-TA-TTTAAAAACTATAT
1 AT-TATATGTTTTCAAAAATTATTTTAAAAACTATAT
* * *
2995523 ATTATACGTTTTCAAAAATGTGTTTTCAAAACTATAT
1 ATTATATGTTTTCAAAAAT-TATTTTAAAAACTATAT
** * * * *
2995560 ATTATACATTTTAAAAAAATTGTTTTCAAAAC--CAT
1 ATTATATGTTTT-CAAAAATTATTTTAAAAACTATAT
***
2995595 ATTATATGTTTTCCAAAACCGATTTTAAAAACTATAT
1 ATTATATGTTTT-CAAAAATTATTTTAAAAACTATAT
* * * *
2995632 TTTATATATTTTAAAAAAATATTTTAAAAACTATA
1 ATTATATGTTTTCAAAAATTATTTTAAAAACTATA
2995667 CTATATCATT
Statistics
Matches: 208, Mismatches: 30, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
33 17 0.08
34 15 0.07
35 44 0.21
36 56 0.27
37 51 0.25
38 8 0.04
39 1 0.00
40 16 0.08
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (36 bp):
ATTATATGTTTTCAAAAATTATTTTAAAAACTATAT
Found at i:2995655 original size:13 final size:13
Alignment explanation
Indices: 2995637--2995661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2995627 TATATTTTAT
2995637 ATATTTTAAAAAA
1 ATATTTTAAAAAA
2995650 ATATTTTAAAAA
1 ATATTTTAAAAA
2995662 CTATACTATA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATTTTAAAAAA
Found at i:2998506 original size:12 final size:12
Alignment explanation
Indices: 2998489--2998514 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2998479 TTGAAAGCTC
2998489 TGATCATGAATT
1 TGATCATGAATT
2998501 TGATCATGAATT
1 TGATCATGAATT
2998513 TG
1 TG
2998515 TATTTATCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (12 bp):
TGATCATGAATT
Found at i:3001433 original size:6 final size:6
Alignment explanation
Indices: 3001422--3001457 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3001412 GCATCAAACT
* *
3001422 TGTTTC TGTTTC TGTTTC TATTTC TGTTTC TATTTC
1 TGTTTC TGTTTC TGTTTC TGTTTC TGTTTC TGTTTC
3001458 AGTCTGTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.06, C:0.17, G:0.11, T:0.67
Consensus pattern (6 bp):
TGTTTC
Found at i:3001437 original size:12 final size:12
Alignment explanation
Indices: 3001422--3001457 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
3001412 GCATCAAACT
*
3001422 TGTTTCTGTTTC
1 TGTTTCTATTTC
3001434 TGTTTCTATTTC
1 TGTTTCTATTTC
3001446 TGTTTCTATTTC
1 TGTTTCTATTTC
3001458 AGTCTGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.06, C:0.17, G:0.11, T:0.67
Consensus pattern (12 bp):
TGTTTCTATTTC
Found at i:3005099 original size:60 final size:60
Alignment explanation
Indices: 3005005--3005138 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
3004995 CTTTTTTGGT
* * * * **
3005005 AAAG-TATACAAATGGTCCATCAATTATAGAGTGTTACTTTGTTTAGTC-CATTGGTTATCA
1 AAAGTTATA-AAATGGTCCATCAACTATAGAGTGTTAATTTGTTGAGTCTC-CTGACTATCA
* * *
3005065 AAAGTTATAAAATGGTCCTTCAACTATAGGGTGTTAATTTGTTGAGTCTCCTGACTATTA
1 AAAGTTATAAAATGGTCCATCAACTATAGAGTGTTAATTTGTTGAGTCTCCTGACTATCA
3005125 AAAGTTATAAAATG
1 AAAGTTATAAAATG
3005139 ATCATTAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 58 0.92
61 5 0.08
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (60 bp):
AAAGTTATAAAATGGTCCATCAACTATAGAGTGTTAATTTGTTGAGTCTCCTGACTATCA
Found at i:3007424 original size:19 final size:17
Alignment explanation
Indices: 3007400--3007444 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
3007390 ATTTCCAAGC
3007400 AAATAATATAAACATACAT
1 AAATAATATAAACA-A-AT
*
3007419 AAATAATACAAACAAAT
1 AAATAATATAAACAAAT
*
3007436 ATATAATAT
1 AAATAATAT
3007445 CCATACATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
19 13 0.57
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAATATAAACAAAT
Found at i:3008131 original size:135 final size:129
Alignment explanation
Indices: 3007877--3008269 Score: 426
Period size: 135 Copynumber: 3.0 Consensus size: 129
3007867 AAGTTAGCAA
* * * *
3007877 TTAGCAGAGTTCGAACCATAATAATGCGGG-TTATACCCCGGATCGGGTCACCACAAAGTCGAAT
1 TTAGCAAAGTTCGAACCATAATAATG-GGGATCATACCCCAGATCGGGTCACCACAAGGTCGAAT
** * * * * * * *
3007941 TGAATAATT-CAAACAA-ATATATACAAATAAAA---TAAAAATAAAAT-AAATAAAAGTTA-GA
65 CAAAT-ATTAGAAACAATAAATAAATAAATAAAATGGTTAAAGTGAAATAAAATAAAAGTTATGA
3007999 GG
129 -G
* * *
3008001 TTTGCAAAGTTTGAACCATAATAATGTGGATCATACCCCAGATCGGGTCACCACAAGGTCGAATC
1 TTAGCAAAGTTCGAACCATAATAATGGGGATCATACCCCAGATCGGGTCACCACAAGGTCGAATC
* *
3008066 GAATATTAGAAACAATAAATAAACAGATAAATAAAAAATGGTTAGAGTGAAATAAAATAAAAGTT
66 AAATATTAGAAACAATAAAT--A-A-ATAAAT--AAAATGGTTAAAGTGAAATAAAATAAAAGTT
*
3008131 ATTAG
125 ATGAG
* *
3008136 TTAGCAGAGTTCGTACCATAATAATGGGGATCATACCCCAGATCGGGTCACCACAAGGTCGAATC
1 TTAGCAAAGTTCGAACCATAATAATGGGGATCATACCCCAGATCGGGTCACCACAAGGTCGAATC
* *
3008201 AAATATTAGAAACAATAAATAAATAAATACAATGGTTAAAGTGCAATAAAATAAAAGTTACT-AG
66 AAATATTAGAAACAATAAATAAATAAATAAAATGGTTAAAGTGAAATAAAATAAAAGTTA-TGAG
3008265 TTAGC
1 TTAGC
3008270 TTGAAATAAA
Statistics
Matches: 228, Mismatches: 26, Indels: 25
0.82 0.09 0.09
Matches are distributed among these distances:
123 5 0.02
124 64 0.28
125 3 0.01
127 1 0.00
129 41 0.18
130 1 0.00
131 10 0.04
132 1 0.00
133 1 0.00
134 8 0.04
135 92 0.40
136 1 0.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (129 bp):
TTAGCAAAGTTCGAACCATAATAATGGGGATCATACCCCAGATCGGGTCACCACAAGGTCGAATC
AAATATTAGAAACAATAAATAAATAAATAAAATGGTTAAAGTGAAATAAAATAAAAGTTATGAG
Found at i:3009453 original size:139 final size:139
Alignment explanation
Indices: 3009206--3009708 Score: 621
Period size: 139 Copynumber: 3.6 Consensus size: 139
3009196 ATTTTTGGAT
* * * * *
3009206 ATAATTTGGAGACAATATGGTTCCTACGTGATGAGGAAGTATGGTTATCTGAGGATGACGCTGCT
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGCT
* * * *
3009271 CCTACATGTTGAGGAGATCTAGTCGGTGGATGACATTTTTCCTATGTGATGAGGACATCTAGCCG
66 CCTACACGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACGTCTAGCCG
*
3009336 TCTTTAGAT
131 TCTTTAGAG
* * * *
3009345 ATAATTTGGAAACAACACGGTTCCTACATGATGATGTAGTCTGATTATCTGAGGATGACACTGCT
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGCT
** * *
3009410 CCTACACGTTGAGGAGATCTGGTCGGTATATGACATTATTCCTACGCGATGAGGACGTCTAGCCG
66 CCTACACGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACGTCTAGCCG
*
3009475 TCTTTAGGG
131 TCTTTAGAG
* ** *
3009484 ATAATTTGGAGACAACACTGTTCCTACGTGATGAGGAAGTCTGATT-TCCTGAGGATGACGTTGT
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTAT-CTGAGGATGACACTGC
** * * * * *
3009548 TCCTATGCGTTGGGGAGATCTTGTAGGTGGATGACATTGTTCCTATGTGATGAGGACGTCTAGTC
65 TCCTACACGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACGTCTAGCC
* * *
3009613 ATTTTTAGGG
130 GTCTTTAGAG
** * * * *
3009623 ATAATTTGGAGACAACATAGTTCCTACGTGATGAGGAAGTCTGGTTATATAAGGATGACACTACT
1 ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGCT
**
3009688 CCTATGCGTTGAGGAGATCTG
66 CCTACACGTTGAGGAGATCTG
3009709 TTTGGTTGCC
Statistics
Matches: 311, Mismatches: 51, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
138 1 0.00
139 309 0.99
140 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (139 bp):
ATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTCTGATTATCTGAGGATGACACTGCT
CCTACACGTTGAGGAGATCTGGTCGGTGGATGACATTATTCCTATGTGATGAGGACGTCTAGCCG
TCTTTAGAG
Found at i:3009703 original size:278 final size:278
Alignment explanation
Indices: 3009206--3009708 Score: 704
Period size: 278 Copynumber: 1.8 Consensus size: 278
3009196 ATTTTTGGAT
* *
3009206 ATAATTTGGAGACAATATGGTTCCTACGTGATGAGGAAGTATGGTTATCTGAGGATGACGCTGCT
1 ATAATTTGGAGACAACATGGTTCCTACGTGATGAGGAAGTATGATTATCTGAGGATGACGCTGCT
* * * *
3009271 CCTACATGTTGAGGAGATCTAGTCGGTGGATGACATTTTTCCTATGTGATGAGGACATCTAGCCG
66 CCTACACGTTGAGGAGATCTAGTAGGTGGATGACATTGTTCCTATGTGATGAGGACATCTAGCCA
* * * * * *
3009336 TCTTTAGATATAATTTGGAAACAACACGGTTCCTACATGATGATGTAGTCTGATTATCTGAGGAT
131 TCTTTAGAGATAATTTGGAAACAACACAGTTCCTACATGATGAGGAAGTCTGATTATATAAGGAT
*
3009401 GACACTGCTCCTACACGTTGAGGAGATCTGGTCGGTATATGACATTATTCCTACGCGATGAGGAC
196 GACACTACTCCTACACGTTGAGGAGATCTGGTCGGTATATGACATTATTCCTACGCGATGAGGAC
3009466 GTCTAGCCGTCTTTAGGG
261 GTCTAGCCGTCTTTAGGG
* *
3009484 ATAATTTGGAGACAACACT-GTTCCTACGTGATGAGGAAGTCTGATT-TCCTGAGGATGACGTTG
1 ATAATTTGGAGACAACA-TGGTTCCTACGTGATGAGGAAGTATGATTAT-CTGAGGATGACGCTG
* ** * * * *
3009547 TTCCTATGCGTTGGGGAGATCTTGTAGGTGGATGACATTGTTCCTATGTGATGAGGACGTCTAGT
64 CTCCTACACGTTGAGGAGATCTAGTAGGTGGATGACATTGTTCCTATGTGATGAGGACATCTAGC
* * * * * *
3009612 CATTTTTAGGGATAATTTGGAGACAACATAGTTCCTACGTGATGAGGAAGTCTGGTTATATAAGG
129 CATCTTTAGAGATAATTTGGAAACAACACAGTTCCTACATGATGAGGAAGTCTGATTATATAAGG
**
3009677 ATGACACTACTCCTATGCGTTGAGGAGATCTG
194 ATGACACTACTCCTACACGTTGAGGAGATCTG
3009709 TTTGGTTGCC
Statistics
Matches: 193, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
277 1 0.01
278 191 0.99
279 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.31
Consensus pattern (278 bp):
ATAATTTGGAGACAACATGGTTCCTACGTGATGAGGAAGTATGATTATCTGAGGATGACGCTGCT
CCTACACGTTGAGGAGATCTAGTAGGTGGATGACATTGTTCCTATGTGATGAGGACATCTAGCCA
TCTTTAGAGATAATTTGGAAACAACACAGTTCCTACATGATGAGGAAGTCTGATTATATAAGGAT
GACACTACTCCTACACGTTGAGGAGATCTGGTCGGTATATGACATTATTCCTACGCGATGAGGAC
GTCTAGCCGTCTTTAGGG
Found at i:3009944 original size:30 final size:30
Alignment explanation
Indices: 3009910--3010088 Score: 117
Period size: 30 Copynumber: 5.5 Consensus size: 30
3009900 CTTTGTTTTG
*
3009910 AGAGAAATAATCTCAATGGTTTATGTTTCA
1 AGAGAAACAATCTCAATGGTTTATGTTTCA
* * *
3009940 AGAGAAACTATCTCAAGTGAGACAAAACTT-TGTTTCG
1 AGAGAAACAATCTCAA-TG-G------TTTATGTTTCA
*
3009977 AGAGAAACAATCTCAAAGGTTTATGTTTCA
1 AGAGAAACAATCTCAATGGTTTATGTTTCA
** *** *
3010007 AGAGAAACTGTCTCAAGTGAGGAAAAACTTATTTCA
1 AGAGAAACAATCTCAA-T--GG-TTTA--TGTTTCA
*
3010043 AGAGAAACAATCTCAAAGGTTTATGTTTCA
1 AGAGAAACAATCTCAATGGTTTATGTTTCA
3010073 AGAGAAACAATCTCAA
1 AGAGAAACAATCTCAA
3010089 ACGAAACAAA
Statistics
Matches: 112, Mismatches: 22, Indels: 30
0.68 0.13 0.18
Matches are distributed among these distances:
29 2 0.02
30 56 0.50
31 2 0.02
32 2 0.02
33 4 0.04
34 1 0.01
35 1 0.01
36 21 0.19
37 21 0.19
38 2 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (30 bp):
AGAGAAACAATCTCAATGGTTTATGTTTCA
Found at i:3010087 original size:66 final size:67
Alignment explanation
Indices: 3009865--3010304 Score: 544
Period size: 67 Copynumber: 6.6 Consensus size: 67
3009855 TCAAAATTTG
* * *** ** * *
3009865 TGTTTCAAGGGAAAATTGTCTCAAGCGAGGTGAAACTTTGTTTTGAGAGAAATAATCTCAATGGT
1 TGTTTCAAGAG-AAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGT
3009930 TTA
65 TTA
* * *
3009933 TGTTTCAAGAGAAACTATCTCAAGTGAGACAAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
3009998 TA
66 TA
* *
3010000 TGTTTCAAGAGAAACTGTCTCAAGTGAGGA-AAAAC-TTATTTCAAGAGAAACAATCTCAAAGGT
1 TGTTTCAAGAGAAACTGTCTCAAGCGA-GACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGT
3010063 TTA
65 TTA
** * * *
3010066 TGTTTCAAGAGAAACAATCTCAAACGAAACAAAA-TTTGTTTCAAGAGAAACAATCTTAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGG-T
3010130 TTA
65 TTA
* * **
3010133 TGTTTCAAGATAAATTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAATGATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
3010198 TA
66 TA
* ** * *
3010200 TGCTTCAAGAGAAAAGGTCTCAAGCGATACAAAACTTTGTTTCAAGAGAAACGATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
3010265 TA
66 TA
* * * *
3010267 TGTTTCCATAAAAACTGTCTCAAGCGAGACAACACTTT
1 TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTT
3010305 TTTTAGGAAG
Statistics
Matches: 324, Mismatches: 43, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
65 1 0.00
66 81 0.25
67 205 0.63
68 37 0.11
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (67 bp):
TGTTTCAAGAGAAACTGTCTCAAGCGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGGTT
TA
Found at i:3010089 original size:30 final size:30
Alignment explanation
Indices: 3009970--3010142 Score: 123
Period size: 30 Copynumber: 5.3 Consensus size: 30
3009960 GACAAAACTT
*
3009970 TGTTTCGAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
** ***
3010000 TGTTTCAAGAGAAACTGTCTCAAGTGAGGAAAAA
1 TGTTTCAAGAGAAACAATCTCAA---AGG-TTTA
*
3010034 CTTATTTCAAGAGAAACAATCTCAAAGGTTTA
1 --TGTTTCAAGAGAAACAATCTCAAAGGTTTA
**
3010066 TGTTTCAAGAGAAACAATCTCAAACGAAACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAAA-G------GTTTA
*
3010102 TGTTTCAAGAGAAACAATCTTAAAGGTTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGG-TTTA
3010133 TGTTTCAAGA
1 TGTTTCAAGA
3010143 TAAATTGTCT
Statistics
Matches: 110, Mismatches: 18, Indels: 29
0.70 0.11 0.18
Matches are distributed among these distances:
30 45 0.41
31 11 0.10
32 1 0.01
33 6 0.05
34 1 0.01
35 1 0.01
36 43 0.39
37 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:3010164 original size:200 final size:200
Alignment explanation
Indices: 3009901--3010272 Score: 541
Period size: 200 Copynumber: 1.9 Consensus size: 200
3009891 GAGGTGAAAC
** * * *
3009901 TTTGTTTTGAGAGAAATAATCTCAATGGTTTATGTTTCAAGAGAAACTATCTCAAGTGAGACAAA
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAAA
* * ** *
3009966 ACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAAGTGAGGA-
66 ACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGCTTCAAGAGAAAAGGTCTCAAGCGA-GAC
3010030 AAAAC-TTATTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAACGAA
130 AAAACTTTATTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAACGAA
3010094 ACAAAA
195 ACAAAA
* * * *
3010100 TTTGTTTCAAGAGAAACAATCTTAAAGGTTTTATGTTTCAAGATAAATTGTCTCAAGCGAGACAA
1 TTTGTTTCAAGAGAAACAATCTCAAAGG-TTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAA
** *
3010165 AACTTTGTTTCAAGAGAAATGATCTCAAAGGTTTATGCTTCAAGAGAAAAGGTCTCAAGCGATAC
65 AACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGCTTCAAGAGAAAAGGTCTCAAGCGAGAC
* *
3010230 AAAACTTTGTTTCAAGAGAAACGATCTCAAAGGTTTATGTTTC
130 AAAACTTTATTTCAAGAGAAACAATCTCAAAGGTTTATGTTTC
3010273 CATAAAAACT
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
199 24 0.16
200 92 0.61
201 35 0.23
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (200 bp):
TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAAA
ACTTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGCTTCAAGAGAAAAGGTCTCAAGCGAGACA
AAACTTTATTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAACGAAA
CAAAA
Found at i:3010191 original size:37 final size:37
Alignment explanation
Indices: 3010133--3010259 Score: 101
Period size: 37 Copynumber: 3.6 Consensus size: 37
3010123 AAAGGTTTTA
*
3010133 TGTTTCAAGATAAATTG-TCTCAAGCGAGACAAAACTT
1 TGTTTCAAGAGAAA-TGATCTCAAGCGAGACAAAACTT
**
3010170 TGTTTCAAGAGAAATGATCTCAA---AG-----GTTT
1 TGTTTCAAGAGAAATGATCTCAAGCGAGACAAAACTT
* * * *
3010199 ATGCTTCAAGAGAAAAGGTCTCAAGCGATACAAAACTT
1 -TGTTTCAAGAGAAATGATCTCAAGCGAGACAAAACTT
*
3010237 TGTTTCAAGAGAAACGATCTCAA
1 TGTTTCAAGAGAAATGATCTCAA
3010260 AGGTTTATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
29 2 0.03
30 20 0.29
33 1 0.01
34 2 0.03
36 2 0.03
37 39 0.57
38 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAATGATCTCAAGCGAGACAAAACTT
Found at i:3012465 original size:43 final size:44
Alignment explanation
Indices: 3012393--3012481 Score: 135
Period size: 43 Copynumber: 2.0 Consensus size: 44
3012383 TCTCGTCTTC
* * *
3012393 CTGGATGATACGGGCCTTCAAAAATGCCCCAACATTTATCATTT
1 CTGGAAGATACGGGCCTTAAAAAATGCCCCAACACTTATCATTT
*
3012437 CTGGAAGATATGGGCC-TAAAAAATGCCCCAACACTTATCATTT
1 CTGGAAGATACGGGCCTTAAAAAATGCCCCAACACTTATCATTT
3012480 CT
1 CT
3012482 TGCTCCAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 27 0.66
44 14 0.34
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (44 bp):
CTGGAAGATACGGGCCTTAAAAAATGCCCCAACACTTATCATTT
Found at i:3012638 original size:25 final size:24
Alignment explanation
Indices: 3012599--3012661 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
3012589 TTTTATTTTC
3012599 AAAATTTT-AACAAAT-ATCAATTAA
1 AAAATTTTGAA-AAATGATCAA-TAA
* *
3012623 AAGAATTTTGAAAAATGTTTAATAA
1 AA-AATTTTGAAAAATGATCAATAA
3012648 AAAATTTTGAAAAA
1 AAAATTTTGAAAAA
3012662 AAATATTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 14 0.41
25 15 0.44
26 5 0.15
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.33
Consensus pattern (24 bp):
AAAATTTTGAAAAATGATCAATAA
Found at i:3013578 original size:15 final size:15
Alignment explanation
Indices: 3013560--3013599 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
3013550 CTTTTTTTAA
3013560 CTTTGTTTTTTTCCT
1 CTTTGTTTTTTTCCT
3013575 CTTTGCTTTTTTTCCT
1 CTTTG-TTTTTTTCCT
*
3013591 -TTTCTTTTT
1 CTTTGTTTTT
3013600 GTTTTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 8 0.35
16 10 0.43
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (15 bp):
CTTTGTTTTTTTCCT
Found at i:3013592 original size:14 final size:15
Alignment explanation
Indices: 3013546--3013599 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 15
3013536 CTTTTTATTT
*
3013546 CTTT-CTTTTTTTAA
1 CTTTGCTTTTTTTAC
*
3013560 CTTTG-TTTTTTTCC
1 CTTTGCTTTTTTTAC
3013574 TCTTTGCTTTTTTT-C
1 -CTTTGCTTTTTTTAC
*
3013589 CTTTTCTTTTT
1 CTTTGCTTTTT
3013600 GTTTTTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 21 0.62
15 6 0.18
16 7 0.21
ACGTcount: A:0.04, C:0.19, G:0.04, T:0.74
Consensus pattern (15 bp):
CTTTGCTTTTTTTAC
Found at i:3013604 original size:18 final size:17
Alignment explanation
Indices: 3013581--3013640 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
3013571 TCCTCTTTGC
*
3013581 TTTTTTTCCT-TTTCTT
1 TTTTTTTTCTGTTTCTT
*
3013597 TTTGTTTTTTTGTTTCTT
1 TTT-TTTTTCTGTTTCTT
*
3013615 TTTTTTTT-GGTTT-TT
1 TTTTTTTTCTGTTTCTT
3013630 TTTTATTTTCT
1 TTTT-TTTTCT
3013641 TTGATTTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 10 0.28
18 9 0.25
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (17 bp):
TTTTTTTTCTGTTTCTT
Found at i:3013607 original size:23 final size:22
Alignment explanation
Indices: 3013581--3013642 Score: 79
Period size: 23 Copynumber: 2.8 Consensus size: 22
3013571 TCCTCTTTGC
* *
3013581 TTTTTTTCCTTTTCTTTTTGTT
1 TTTTTTTTCTTTTCTTTTTGGT
*
3013603 TTTTTGTTTCTTTTTTTTTTGGT
1 TTTTT-TTTCTTTTCTTTTTGGT
*
3013626 TTTTTTTTATTTTCTTT
1 TTTTTTTTCTTTTCTTT
3013643 GATTTGATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.84
Consensus pattern (22 bp):
TTTTTTTTCTTTTCTTTTTGGT
Found at i:3013621 original size:15 final size:15
Alignment explanation
Indices: 3013595--3013638 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
3013585 TTTCCTTTTC
*
3013595 TTTTTGTTTTTTT-G
1 TTTTTTTTTTTTTGG
3013609 TTTCTTTTTTTTTTGG
1 TTT-TTTTTTTTTTGG
3013625 TTTTTTTTTATTTT
1 TTTTTTTTT-TTTT
3013639 CTTTGATTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 15 0.58
16 8 0.31
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTTTTGG
Found at i:3014489 original size:24 final size:24
Alignment explanation
Indices: 3014456--3014510 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
3014446 TGCTCAATTA
*
3014456 TTCAACCTTAGAAGGTAGCACAAC
1 TTCAATCTTAGAAGGTAGCACAAC
3014480 TTCAATCTTAGAAGGTAGCACAAC
1 TTCAATCTTAGAAGGTAGCACAAC
3014504 TTCAATC
1 TTCAATC
3014511 ATTAAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (24 bp):
TTCAATCTTAGAAGGTAGCACAAC
Found at i:3016520 original size:21 final size:23
Alignment explanation
Indices: 3016495--3016541 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
3016485 ATAACAATTT
3016495 TTTTTAAAAA-AATTA-AATATA
1 TTTTTAAAAACAATTATAATATA
*
3016516 TTTTTAAAAACAATTATAATTTA
1 TTTTTAAAAACAATTATAATATA
3016539 TTT
1 TTT
3016542 GAAAAATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.43
22 5 0.22
23 8 0.35
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTTTAAAAACAATTATAATATA
Found at i:3016546 original size:22 final size:20
Alignment explanation
Indices: 3016490--3016547 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 20
3016480 CTTTCATAAC
*
3016490 AATTTTTTTTAAAAAAATTA
1 AATTTATTTTAAAAAAATTA
*
3016510 AATATATTTTTAAAAACAATTA
1 AATTTA-TTTTAAAAA-AATTA
*
3016532 TAATTTATTTGAAAAA
1 -AATTTATTTTAAAAA
3016548 TTGGTGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 9 0.29
22 13 0.42
23 5 0.16
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
AATTTATTTTAAAAAAATTA
Found at i:3017430 original size:16 final size:15
Alignment explanation
Indices: 3017406--3017439 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
3017396 AAAGATAATA
*
3017406 AAAAGGCATAAATTT
1 AAAAGGCATAAAGTT
3017421 AAAAGTGCATAAAGTT
1 AAAAG-GCATAAAGTT
3017437 AAA
1 AAA
3017440 TAATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.56, C:0.06, G:0.15, T:0.24
Consensus pattern (15 bp):
AAAAGGCATAAAGTT
Found at i:3017465 original size:16 final size:16
Alignment explanation
Indices: 3017441--3017471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3017431 AAAGTTAAAT
*
3017441 AATATAAATAAAATGC
1 AATACAAATAAAATGC
3017457 AATACAAATAAAATG
1 AATACAAATAAAATG
3017472 TTAGTATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (16 bp):
AATACAAATAAAATGC
Found at i:3017874 original size:13 final size:13
Alignment explanation
Indices: 3017856--3017880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3017846 AACACACACC
3017856 AACACCCTAAACT
1 AACACCCTAAACT
3017869 AACACCCTAAAC
1 AACACCCTAAAC
3017881 CAAGAAAAAA
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:0.48, C:0.40, G:0.00, T:0.12
Consensus pattern (13 bp):
AACACCCTAAACT
Found at i:3022369 original size:2 final size:2
Alignment explanation
Indices: 3022362--3022414 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
3022352 ATGGATCCTA
3022362 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
*
3022404 TT AT AT AT AT A
1 AT AT AT AT AT A
3022415 CACTTCAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3022600 original size:25 final size:25
Alignment explanation
Indices: 3022566--3022632 Score: 134
Period size: 25 Copynumber: 2.7 Consensus size: 25
3022556 AATAACAATA
3022566 CTAGTCAACAATTTAATTCTTAATC
1 CTAGTCAACAATTTAATTCTTAATC
3022591 CTAGTCAACAATTTAATTCTTAATC
1 CTAGTCAACAATTTAATTCTTAATC
3022616 CTAGTCAACAATTTAAT
1 CTAGTCAACAATTTAAT
3022633 AAAACAATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.39
Consensus pattern (25 bp):
CTAGTCAACAATTTAATTCTTAATC
Found at i:3037181 original size:14 final size:14
Alignment explanation
Indices: 3037162--3037192 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3037152 ATAGATGGGA
3037162 TATACAAGTGTGAC
1 TATACAAGTGTGAC
*
3037176 TATACAAGTGTGCC
1 TATACAAGTGTGAC
3037190 TAT
1 TAT
3037193 TCTATATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (14 bp):
TATACAAGTGTGAC
Found at i:3038106 original size:31 final size:29
Alignment explanation
Indices: 3038071--3038149 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 29
3038061 ATTTATAAGG
3038071 AGTGATCAGTTTGTTACAAATTA-ATAATGTT
1 AGTGA-CA-TTTGTTACAAA-TAGATAATGTT
3038102 AGTGACTATTGTGTTACAAATAGATAATGTT
1 AGTGAC-ATT-TGTTACAAATAGATAATGTT
3038133 AGTGACCAATTTGTTAC
1 AGTGA-C-ATTTGTTAC
3038150 TCTAGAAACT
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
30 5 0.12
31 34 0.79
32 4 0.09
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (29 bp):
AGTGACATTTGTTACAAATAGATAATGTT
Found at i:3039250 original size:55 final size:55
Alignment explanation
Indices: 3039189--3039302 Score: 228
Period size: 55 Copynumber: 2.1 Consensus size: 55
3039179 ATGTATACCT
3039189 AAAATAATTTACATAAAGATAAAAAAGAGTTTGTTATAACAATAAGCACATGACA
1 AAAATAATTTACATAAAGATAAAAAAGAGTTTGTTATAACAATAAGCACATGACA
3039244 AAAATAATTTACATAAAGATAAAAAAGAGTTTGTTATAACAATAAGCACATGACA
1 AAAATAATTTACATAAAGATAAAAAAGAGTTTGTTATAACAATAAGCACATGACA
3039299 AAAA
1 AAAA
3039303 CATAAAGGCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.25
Consensus pattern (55 bp):
AAAATAATTTACATAAAGATAAAAAAGAGTTTGTTATAACAATAAGCACATGACA
Found at i:3039327 original size:49 final size:48
Alignment explanation
Indices: 3039199--3039392 Score: 203
Period size: 55 Copynumber: 3.9 Consensus size: 48
3039189 AAAATAATTT
* *
3039199 ACATAAAGATAAAAAAGAGTTTGTTATAACAATAAGCACATGACAAAAATAA
1 ACATAAAGACAAAAAAGA-TTTGTTACAACAATAAGCACATGAC--AAAT-A
* *
3039251 TTTACATAAAGATAAAAAAGAGTTTGTTATAACAATAAGCACATGACAAA-A
1 ---ACATAAAGACAAAAAAGA-TTTGTTACAACAATAAGCACATGACAAATA
* * *
3039302 ACATAAAGGCAAAAAAAGAATTTGTTGCAACAATAAGAACATGACAAATA
1 ACATAAAGAC-AAAAAAG-ATTTGTTACAACAATAAGCACATGACAAATA
* *
3039352 ACATAAAGACAAAAAAG-TTAGTTACAACAATAAGCAAATGA
1 ACATAAAGACAAAAAAGATTTGTTACAACAATAAGCACATGA
3039393 AGAATAAATA
Statistics
Matches: 126, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
47 20 0.16
48 8 0.06
49 39 0.31
50 11 0.09
51 1 0.01
53 3 0.02
55 44 0.35
ACGTcount: A:0.56, C:0.11, G:0.12, T:0.21
Consensus pattern (48 bp):
ACATAAAGACAAAAAAGATTTGTTACAACAATAAGCACATGACAAATA
Found at i:3044494 original size:18 final size:17
Alignment explanation
Indices: 3044471--3044514 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
3044461 ATTGGTATTA
3044471 TTTATTTTTTATCATATC
1 TTTATTTTTT-TCATATC
* *
3044489 TTTATTTTTTTTATTTC
1 TTTATTTTTTTCATATC
3044506 TTTATTTTT
1 TTTATTTTT
3044515 CTGTTGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTTTTCATATC
Found at i:3044500 original size:20 final size:17
Alignment explanation
Indices: 3044471--3044533 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 17
3044461 ATTGGTATTA
* *
3044471 TTTATTTTTTATCATATC
1 TTTATTTTTT-TTATTTC
3044489 TTTATTTTTTTTATTTC
1 TTTATTTTTTTTATTTC
*
3044506 TTTATTTTTCTGTTGTTTC
1 TTTATTTTT-T-TTATTTC
3044525 TTTATTTTT
1 TTTATTTTT
3044534 CAGTAATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
17 14 0.35
18 11 0.28
19 15 0.38
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.76
Consensus pattern (17 bp):
TTTATTTTTTTTATTTC
Found at i:3045536 original size:24 final size:24
Alignment explanation
Indices: 3045505--3045561 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
3045495 ATTCAGAAAT
* *
3045505 AAACAAATTTCAGACTCATATGTA
1 AAACAAATTTCAAACTCATATATA
*
3045529 AAATAAATTTCAAACTCATATATA
1 AAACAAATTTCAAACTCATATATA
3045553 AAACAAATT
1 AAACAAATT
3045562 ACAACCTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.30
Consensus pattern (24 bp):
AAACAAATTTCAAACTCATATATA
Found at i:3047975 original size:18 final size:18
Alignment explanation
Indices: 3047954--3047988 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3047944 AATAGGTGTG
3047954 TTTTTGAAAAAGTTAACT
1 TTTTTGAAAAAGTTAACT
**
3047972 TTTTTGTCAAAGTTAAC
1 TTTTTGAAAAAGTTAAC
3047989 GGGTTGACTC
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:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (18 bp):
TTTTTGAAAAAGTTAACT
Found at i:3053418 original size:23 final size:24
Alignment explanation
Indices: 3053373--3053418 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
3053363 TATCAAAATC
3053373 ATGATCCATTAGTCTATTGAAAAA
1 ATGATCCATTAGTCTATTGAAAAA
*
3053397 ATGAT-CATATAGT-TATTTAAAA
1 ATGATCCAT-TAGTCTATTGAAAA
3053419 CACATGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (24 bp):
ATGATCCATTAGTCTATTGAAAAA
Found at i:3055733 original size:19 final size:19
Alignment explanation
Indices: 3055713--3055777 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
3055703 ACGGTTAATG
* **
3055713 GGTCAGGTGAAAGTCAATG
1 GGTCAGGTCAAAGTCAACA
*
3055732 GGTTAGGTCAAAGTCAACA
1 GGTCAGGTCAAAGTCAACA
*
3055751 GGTCGGGTCAAAGTCAACA
1 GGTCAGGTCAAAGTCAACA
3055770 GGTCAGGT
1 GGTCAGGT
3055778 TAACTCAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.31, C:0.15, G:0.34, T:0.20
Consensus pattern (19 bp):
GGTCAGGTCAAAGTCAACA
Found at i:3060219 original size:28 final size:28
Alignment explanation
Indices: 3060179--3060264 Score: 118
Period size: 28 Copynumber: 3.1 Consensus size: 28
3060169 AAATTCATTG
*
3060179 ATGTATTTACCAACTAGCAATGTGTACC
1 ATGTATTTACCAACTATCAATGTGTACC
*
3060207 ATGTGTTTACCAACTATCAATGTGTACC
1 ATGTATTTACCAACTATCAATGTGTACC
*** *
3060235 ACACATTTACCAACTATCAATATGTACC
1 ATGTATTTACCAACTATCAATGTGTACC
3060263 AT
1 AT
3060265 AATGCATACA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.33
Consensus pattern (28 bp):
ATGTATTTACCAACTATCAATGTGTACC
Found at i:3070185 original size:24 final size:24
Alignment explanation
Indices: 3070125--3070192 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
3070115 TCTGACTTGA
* * *
3070125 ATTCTGATATAATACATGACCTGG
1 ATTCTGATATGATACTTGACCTAG
*
3070149 ATTCTGATCTGATACTTGACCTAG
1 ATTCTGATATGATACTTGACCTAG
* *
3070173 ATTCTGATTTGATGCTTGAC
1 ATTCTGATATGATACTTGAC
3070193 TTGAATTATG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACCTAG
Found at i:3070328 original size:35 final size:35
Alignment explanation
Indices: 3070279--3070345 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
3070269 GTATACCTGG
* *
3070279 AGGCTCCTCTGCTTTGTGCTCAGGGCCTTACTTAC
1 AGGCTCCTCGGCTTTGTGCTCAAGGCCTTACTTAC
* * *
3070314 AGGCTGCTCGGCTTTGTTCTCAATGCCTTACT
1 AGGCTCCTCGGCTTTGTGCTCAAGGCCTTACT
3070346 GGACTTGACG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.12, C:0.30, G:0.22, T:0.36
Consensus pattern (35 bp):
AGGCTCCTCGGCTTTGTGCTCAAGGCCTTACTTAC
Found at i:3070477 original size:14 final size:14
Alignment explanation
Indices: 3070458--3070488 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
3070448 TACTAAAATA
3070458 TTTTATCTGTATCT
1 TTTTATCTGTATCT
3070472 TTTTATCTGTATCT
1 TTTTATCTGTATCT
3070486 TTT
1 TTT
3070489 CACTGGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.06, T:0.68
Consensus pattern (14 bp):
TTTTATCTGTATCT
Found at i:3074179 original size:16 final size:15
Alignment explanation
Indices: 3074148--3074194 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
3074138 GATTTATTGG
*
3074148 TTTAATAATAATTATA
1 TTTAAAAATAA-TATA
3074164 TTTAAAATATAATATA
1 TTTAAAA-ATAATATA
*
3074180 -TTAATAATAATATA
1 TTTAAAAATAATATA
3074194 T
1 T
3074195 GTAGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 8 0.30
15 5 0.19
16 10 0.37
17 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTTAAAAATAATATA
Found at i:3075241 original size:2 final size:2
Alignment explanation
Indices: 3075236--3075469 Score: 107
Period size: 2 Copynumber: 116.5 Consensus size: 2
3075226 AATTGAAACA
*
3075236 AT AT AT AT AT AT AT AT AT -T AC AT AT GA- ACT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT
* * *
3075277 GT AT AA AT -T AT AGT TT AT AT AT GA- AGT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT -AT A-T AT AT AT AT AT AT AT
* * *
3075317 AT AT AA ACT AT AT AGT TT AT AT TT AT AT -T AT -T AT AT ACT AT
1 AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
3075358 AT AT AA AT -T AT AT AT AA ACT AT AT AGT GT AT AT AT AA AGT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T AT
* * * * *
3075400 AT AA ACT AT AT AT AT AA ACT AT AA AT -T AT AT AT AT AT AA AG A-
1 AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
3075442 AT A- AGT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A
3075470 AAGTATAATT
Statistics
Matches: 175, Mismatches: 30, Indels: 54
0.68 0.12 0.21
Matches are distributed among these distances:
1 13 0.07
2 147 0.84
3 15 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3075319 original size:11 final size:11
Alignment explanation
Indices: 3075236--3075469 Score: 84
Period size: 11 Copynumber: 21.5 Consensus size: 11
3075226 AATTGAAACA
3075236 ATATATA-TAT
1 ATATATATTAT
*
3075246 ATATATATTAC
1 ATATATATTAT
*
3075257 ATATGA-ACTAT
1 ATAT-ATATTAT
3075268 ATATATTATGTAT
1 ATATA-TAT-TAT
*
3075281 AAATTATAGTT-T
1 ATA-TATA-TTAT
3075293 ATATATGA--AGT
1 ATATAT-ATTA-T
3075304 ATATATATTAT
1 ATATATATTAT
*
3075315 ATATATA-AACT
1 ATATATATTA-T
3075326 ATATAGT-TTAT
1 ATATA-TATTAT
*
3075337 ATTTATATTAT
1 ATATATATTAT
*
3075348 -TATATACTAT
1 ATATATATTAT
*
3075358 ATATAAATTAT
1 ATATATATTAT
* *
3075369 ATATAAACTAT
1 ATATATATTAT
*
3075380 ATAGTGTA-TAT
1 ATA-TATATTAT
*
3075391 ATA-A-AGTAT
1 ATATATATTAT
*
3075400 ATAAACTA-TAT
1 ATATA-TATTAT
* *
3075411 ATATAAACTAT
1 ATATATATTAT
*
3075422 AAAT-TATATAT
1 ATATATAT-TAT
* **
3075433 ATATAAAGAAT
1 ATATATATTAT
3075444 A-AGTATATTAT
1 ATA-TATATTAT
3075455 ATATATA-TAT
1 ATATATATTAT
3075465 ATATA
1 ATATA
3075470 AAGTATAATT
Statistics
Matches: 168, Mismatches: 29, Indels: 54
0.67 0.12 0.22
Matches are distributed among these distances:
8 1 0.01
9 6 0.04
10 31 0.18
11 105 0.62
12 14 0.08
13 8 0.05
14 3 0.02
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (11 bp):
ATATATATTAT
Found at i:3075422 original size:29 final size:29
Alignment explanation
Indices: 3075368--3075431 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
3075358 ATATAAATTA
* *
3075368 TATATAAACTATATAGTGTATATATAAAG
1 TATATAAACTATATAGTATAAATATAAAG
*
3075397 TATATAAACTATATA-TATAAACTATAAAT
1 TATATAAACTATATAGTATAAA-TATAAAG
3075426 TATATA
1 TATATA
3075432 TATATAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (29 bp):
TATATAAACTATATAGTATAAATATAAAG
Found at i:3075511 original size:54 final size:54
Alignment explanation
Indices: 3075406--3075544 Score: 124
Period size: 54 Copynumber: 2.5 Consensus size: 54
3075396 GTATATAAAC
* ** *
3075406 TATATATATAAACTATAAATTATATATATATAAAGAATAAGTATATTATATATA
1 TATATATATAAACTATAAATTATATATAGATAAAGAATAACCATATAATATATA
* *
3075460 TATATATATAAAGTAT-AATTATA-A-AGACTAAAGTATATAACCATATAATATAAA
1 TATATATATAAACTATAAATTATATATAGA-TAAAG-A-ATAACCATATAATATATA
*
3075514 GTATATGAGTATATAACT-TAAAGTATATATA
1 -TATAT-A-TATA-AACTATAAATTATATATA
3075545 CATATAAAGT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
51 2 0.03
52 6 0.09
53 8 0.12
54 29 0.43
55 5 0.07
56 1 0.01
57 5 0.07
58 9 0.13
59 1 0.01
60 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (54 bp):
TATATATATAAACTATAAATTATATATAGATAAAGAATAACCATATAATATATA
Found at i:3075513 original size:22 final size:21
Alignment explanation
Indices: 3075488--3075551 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
3075478 TTATAAAGAC
3075488 TAAAGTATATAACCATATAA-T
1 TAAAGTATATAA-CATATAACT
**
3075509 ATAAAGTATATGAGTATATAACT
1 -TAAAGTATAT-AACATATAACT
3075532 TAAAGTATATATACATATAA
1 TAAAGTATATA-ACATATAA
3075552 AGTATAAGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 1 0.03
22 32 0.91
23 2 0.06
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (21 bp):
TAAAGTATATAACATATAACT
Found at i:3075538 original size:44 final size:42
Alignment explanation
Indices: 3075452--3075551 Score: 116
Period size: 44 Copynumber: 2.4 Consensus size: 42
3075442 ATAAGTATAT
* *
3075452 TATATATATATAT-ATATAAAGTATAATTATAAAGACTAAAG
1 TATATATACATATAATATAAAGTATAAGTATAAAGACTAAAG
*
3075493 TATATA-ACCATATAATATAAAGTATATGAGTATATA-ACTTAAAG
1 TATATATA-CATATAATATAAAGTATA--AGTATAAAGAC-TAAAG
3075537 TATATATACATATAA
1 TATATATACATATAA
3075552 AGTATAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
40 1 0.02
41 10 0.20
42 12 0.24
43 2 0.04
44 24 0.48
45 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (42 bp):
TATATATACATATAATATAAAGTATAAGTATAAAGACTAAAG
Found at i:3078103 original size:47 final size:43
Alignment explanation
Indices: 3077940--3078087 Score: 233
Period size: 43 Copynumber: 3.3 Consensus size: 43
3077930 GTAAGTATGC
*
3077940 AAATAAGCTTACGAGCTTATGAATAATAGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGAATAATGGCAAGTATATTGATA
3077983 AAATAAGCTTACGAGCTTATGAATAATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGAATAATGGCAAGTATATTGATA
* *
3078026 AAATAAGCTTACGAGCTTATGGAATTTAAATGGCAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTAT-GAA--T-AATGGCAAGTATATTGATA
3078073 AAATAAGCTTACGAG
1 AAATAAGCTTACGAG
3078088 AGGTTATGGG
Statistics
Matches: 98, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
43 62 0.63
44 3 0.03
46 1 0.01
47 32 0.33
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.30
Consensus pattern (43 bp):
AAATAAGCTTACGAGCTTATGAATAATGGCAAGTATATTGATA
Found at i:3078947 original size:2 final size:2
Alignment explanation
Indices: 3078847--3078928 Score: 84
Period size: 2 Copynumber: 42.5 Consensus size: 2
3078837 TGTTACAATG
* * *
3078847 TA TA TA TA TA TA TA TA TA TA TA AA CTA TA TA GTT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
3078891 T- TA T- TA T- TA T- TA T- 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 TA TA TA TA TA TA TA TA
3078928 T
1 T
3078929 TATGTAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
1 5 0.07
2 60 0.90
3 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (2 bp):
TA
Found at i:3079016 original size:20 final size:20
Alignment explanation
Indices: 3078899--3079025 Score: 73
Period size: 20 Copynumber: 6.4 Consensus size: 20
3078889 TATTATTATT
*
3078899 ATTAT-TATA-TATATATAT
1 ATTATATATACTATATATAA
* * *
3078917 ATATATATATATTATGTAAAA
1 AT-TATATATACTATATATAA
* * *
3078938 ACTATATATACCATGTATAA
1 ATTATATATACTATATATAA
* * ** *
3078958 AATATAGATTTTTATATATGA
1 ATTATATA-TACTATATATAA
*
3078979 ACTAT-TGA-ACTATATATAA
1 ATTATAT-ATACTATATATAA
*
3078998 ATTATATATACTATGTATAA
1 ATTATATATACTATATATAA
3079018 ATTATATA
1 ATTATATA
3079026 GTTTAATATA
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
18 2 0.02
19 16 0.20
20 44 0.54
21 19 0.23
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTATATATACTATATATAA
Found at i:3079049 original size:8 final size:9
Alignment explanation
Indices: 3079031--3079059 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3079021 ATATAGTTTA
3079031 ATATAAAGT
1 ATATAAAGT
3079040 ATAT-AAGT
1 ATATAAAGT
3079048 ATATAAAGT
1 ATATAAAGT
3079057 ATA
1 ATA
3079060 ATTATAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (9 bp):
ATATAAAGT
Found at i:3079059 original size:15 final size:15
Alignment explanation
Indices: 3079031--3079080 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
3079021 ATATAGTTTA
3079031 ATATAAAGTATATAAGT
1 ATATAAAG-ATATAA-T
3079048 ATATAAAG-TATAAT
1 ATATAAAGATATAAT
*
3079062 -TATAAAGACTAAAAT
1 ATATAAAGA-TATAAT
3079077 ATAT
1 ATAT
3079081 TTGCATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
13 7 0.24
14 1 0.03
15 10 0.34
16 3 0.10
17 8 0.28
ACGTcount: A:0.56, C:0.02, G:0.08, T:0.34
Consensus pattern (15 bp):
ATATAAAGATATAAT
Found at i:3079146 original size:20 final size:19
Alignment explanation
Indices: 3079048--3079193 Score: 67
Period size: 22 Copynumber: 6.9 Consensus size: 19
3079038 GTATATAAGT
*
3079048 ATATAAAGTATAATTATAA
1 ATATAAAGTATAAATATAA
* * **
3079067 AGACTAAAATATATTTGCATATA
1 ATA-TAAAGTATAAAT--ATA-A
*
3079090 ATACAAAGTATATAAGTATATA
1 ATATAAAGTATA-AA-TATA-A
* *
3079112 ATAGAAAACGTATAAGTATTAA
1 ATA-TAAA-GTATAAATA-TAA
*
3079134 ATATAAAGTATAATTATAA
1 ATATAAAGTATAAATATAA
*
3079153 AGACTAAAGTATATAATATAA
1 ATA-TAAAGTATA-AATATAA
*
3079174 AGTATATAAGTATATATATA
1 A-TATA-AAGTATAAATATA
3079194 CTTATATACT
Statistics
Matches: 98, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
19 7 0.07
20 27 0.28
21 17 0.17
22 32 0.33
23 9 0.09
24 6 0.06
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (19 bp):
ATATAAAGTATAAATATAA
Found at i:3079174 original size:14 final size:15
Alignment explanation
Indices: 3079095--3079187 Score: 65
Period size: 14 Copynumber: 6.5 Consensus size: 15
3079085 ATATAATACA
3079095 AAGTATATAAGTATAT
1 AAGTATA-AAGTATAT
* ***
3079111 AA-TAGAAAACGTAT
1 AAGTATAAAGTATAT
3079125 AAGTATTAAA-TATA-
1 AAGTA-TAAAGTATAT
*
3079139 AAGTAT-AATTATA-
1 AAGTATAAAGTATAT
3079152 AAG-ACTAAAGTATAT
1 AAGTA-TAAAGTATAT
3079167 AA-TATAAAGTATAT
1 AAGTATAAAGTATAT
3079181 AAGTATA
1 AAGTATA
3079188 TATATACTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
12 3 0.05
13 9 0.15
14 30 0.49
15 14 0.23
16 5 0.08
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (15 bp):
AAGTATAAAGTATAT
Found at i:3079355 original size:10 final size:9
Alignment explanation
Indices: 3079315--3079381 Score: 56
Period size: 8 Copynumber: 8.0 Consensus size: 9
3079305 TATACTTCAT
3079315 ATTATATA-
1 ATTATATAC
*
3079323 TTTATATAC
1 ATTATATAC
* *
3079332 TTTATAT-T
1 ATTATATAC
3079340 ATTATATAC
1 ATTATATAC
3079349 ATATATATAC
1 AT-TATATAC
3079359 ATTATAT--
1 ATTATATAC
3079366 -TTATATAC
1 ATTATATAC
3079374 -TTATATAC
1 ATTATATAC
3079382 TTTAGTCTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
6 6 0.12
8 21 0.42
9 14 0.28
10 9 0.18
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTATATAC
Found at i:3079369 original size:33 final size:33
Alignment explanation
Indices: 3079280--3079381 Score: 93
Period size: 35 Copynumber: 2.9 Consensus size: 33
3079270 ATATTTAATA
*
3079280 ATTATATACTTATATTTA-ATTCTTATATACTTCAT
1 ATTATATACTTATATTTATATTATTATATA---CAT
*
3079315 ATTATATATTTATATACTTTATATTATTATATACAT
1 ATTATATA-CT-TATA-TTTATATTATTATATACAT
3079351 A-TATATACATTATATTTATA-TACTTATATAC
1 ATTATATAC-TTATATTTATATTA-TTATATAC
3079382 TTTAGTCTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
32 2 0.03
33 14 0.24
34 4 0.07
35 15 0.26
36 5 0.09
37 4 0.07
38 4 0.07
39 10 0.17
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (33 bp):
ATTATATACTTATATTTATATTATTATATACAT
Found at i:3079370 original size:50 final size:47
Alignment explanation
Indices: 3079252--3079787 Score: 160
Period size: 43 Copynumber: 11.3 Consensus size: 47
3079242 TGTATGTATG
*
3079252 TATACATATGTATACTTTATATTTA-ATAATTATATAC-TTATATTTA
1 TATACATATATATAC-TTATATTTATATAATTATATACTTTATATTTA
* *
3079298 -ATTC-T-TATATACTTCATA-TTATATATTTATATACTTTATATTATTA
1 TATACATATATATACTT-ATATTTATATAATTATATACTTTATA-T-TTA
* *
3079344 TATACATATATATACATTATATTTATATACTTATATACTTTAGTCTTTA
1 TATACATATATATAC-TTATATTTATATAATTATATACTTTA-TATTTA
* * * * * * * *
3079393 TA-A-TTATACTTTTCATATATATAATATACTTATGCTTATACTTTATACTAA
1 TATACATATA-TATACTTATAT-TTATATAATTA----TATACTTTATATTTA
* ** * * * *
3079444 AACTTTACATATATGCTTATACTTTATAGT--TTATATA-TATATATATA
1 TA-TACATATATATACTTATA-TTTATA-TAATTATATACTTTATATTTA
* ** *
3079491 TATATATATATATACTTACTTTATATTATATGCTTATATACTTTAGTCTTTA
1 TATACATATATATACTTA---TAT-TTATATAATTATATACTTTA-TATTTA
* * * *
3079543 TA-A-TTATACTTTA-TATATATATAATATACATACATATACTTTATATTTA
1 TATACATATA-TATACT-TATAT-TTATATA-AT-TATATACTTTATATTTA
*
3079592 -ATAC-T-TATATACTTTATATTTA-ATACTTATATAC-TTATATTTA
1 TATACATATATATAC-TTATATTTATATAATTATATACTTTATATTTA
* * * * *
3079635 -ATGC-T-TATATACTTCATA-TTATATACTAAAATACTTTAGTCTTTA
1 TATACATATATATACTT-ATATTTATATAATTATATACTTTA-TATTTA
* * *
3079680 TA-A-TTATACAT-TTTATATATATAATATACATATACTTATACTTTATATTTA
1 TATACATATATATACTTATAT-T-T-ATATA-AT-TA--TATACTTTATATTTA
* * *
3079731 -ATAC-T-TATATACCTATACTTA-ATACTTATATACTTTATATTATTA
1 TATACATATATATACTTATATTTATATAATTATATACTTTATA-T-TTA
*
3079776 TATACCTATATA
1 TATACATATATA
3079788 CAGTTTATAC
Statistics
Matches: 369, Mismatches: 60, Indels: 120
0.67 0.11 0.22
Matches are distributed among these distances:
42 10 0.03
43 64 0.17
44 19 0.05
45 18 0.05
46 30 0.08
47 29 0.08
48 48 0.13
49 33 0.09
50 51 0.14
51 25 0.07
52 26 0.07
53 11 0.03
54 5 0.01
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.51
Consensus pattern (47 bp):
TATACATATATATACTTATATTTATATAATTATATACTTTATATTTA
Found at i:3079482 original size:2 final size:2
Alignment explanation
Indices: 3079475--3079504 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3079465 CTTTATAGTT
3079475 TA TA 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 TA TA
3079505 CTTACTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3079486 original size:22 final size:21
Alignment explanation
Indices: 3079461--3079661 Score: 96
Period size: 22 Copynumber: 9.3 Consensus size: 21
3079451 CATATATGCT
3079461 TATACTTTATAGTTTATATATA
1 TATACTTTATA-TTTATATATA
* *
3079483 TATA-TATATATATATATATA
1 TATACTTTATATTTATATATA
*
3079503 TACTTACTTTATA-TTATATGCTTA
1 TA--TACTTTATATTTATAT--ATA
*
3079527 TATACTTTAGTCTTTATA-AT-
1 TATACTTTA-TATTTATATATA
*
3079547 TATACTTTATATATATATA-A
1 TATACTTTATATTTATATATA
* *
3079567 TATACATACATATACTTTATATTTA
1 TATAC-T--TTATA-TTTATATATA
*
3079592 -ATACTTATATACTTTATATTTA
1 TATACTT-TATA-TTTATATATA
* *
3079614 -ATACTTATATACTTATATTTA
1 TATACTT-TATATTTATATATA
* *
3079635 -ATGCTTATATACTTCATAT-TA
1 TATACTT-TATA-TTTATATATA
3079656 TATACT
1 TATACT
3079662 AAAATACTTT
Statistics
Matches: 144, Mismatches: 18, Indels: 34
0.73 0.09 0.17
Matches are distributed among these distances:
19 6 0.04
20 26 0.18
21 28 0.19
22 53 0.37
23 11 0.08
24 19 0.13
25 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.02, T:0.52
Consensus pattern (21 bp):
TATACTTTATATTTATATATA
Found at i:3079488 original size:32 final size:31
Alignment explanation
Indices: 3079396--3079528 Score: 78
Period size: 32 Copynumber: 4.2 Consensus size: 31
3079386 GTCTTTATAA
*
3079396 TTATACTTT-T-CATATATATAATATACTTATGC
1 TTATACTTTATACTTATATAT-ATATA--TATGC
* * * *
3079428 TTATACTTTATACTAAAACTTTACATATATGC
1 TTATACTTTATACTTATA-TATATATATATGC
* *
3079460 TTATACTTTATAGTTTATATATATATATAT-A
1 TTATACTTTATA-CTTATATATATATATATGC
*
3079491 TATATA-TATATATACTTACTTTATAT-TATATGC
1 T-TATACT-T-TATACTTA-TATATATATATATGC
3079524 TTATA
1 TTATA
3079529 TACTTTAGTC
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
31 2 0.03
32 52 0.67
33 15 0.19
34 7 0.09
35 2 0.03
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (31 bp):
TTATACTTTATACTTATATATATATATATGC
Done.