Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006863.1 Hibiscus syriacus cultivar Beakdansim tig00017459_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: 149789
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:18198 original size:248 final size:248
Alignment explanation
Indices: 17754--18248 Score: 918
Period size: 248 Copynumber: 2.0 Consensus size: 248
17744 AGTACACCCG
17754 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
1 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
*
17819 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAGTCATGAACAT
66 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
*
17884 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTGAGAGCAATTT
131 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTCAGAGCAATTT
17949 TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTGC
196 TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTGC
* *
18002 TGACAGAACTAAAAATTATCCAACAATCTCACCACTGTTCCATGTATGAAAATTTGAATTCAATA
1 TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
* *
18067 ACAAGGGATTCGTGATATACCTTAGTTTATTAGAATAACAGCAAATCAGCAGCAATCATGAACAT
66 ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
18132 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTCAGAGCAATTT
131 TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTCAGAGCAATTT
* *
18197 TCTTTTCTCAAAATGGTTTTGAGAAATATTGTCAAGAGGATTTAAACGGCTG
196 TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTG
18249 TTAGGGCATC
Statistics
Matches: 239, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
248 239 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (248 bp):
TGACACAACTAAAAATTATCCAACAATCTCACCACTGATCCATGTATGAAAATTTGAATTCAATA
ACAAGGGATTCGTGATATACCTTAGGTTATTAGAATAACAACAAATCAGCAGCAATCATGAACAT
TTCAATTCCTAAACTCCACGTAATTGTTTCAGTCTCAACTAAGTTCGCCCAATTCAGAGCAATTT
TCTTTTCTCAAAACGGTTTTGAGAAATATTATCAAGAGGATTTAAACGGCTGC
Found at i:18416 original size:2 final size:2
Alignment explanation
Indices: 18357--18401 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
18347 AAATTAAAAT
*
18357 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA AA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
18400 TA
1 TA
18402 AACTTTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 39 0.98
3 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25734 original size:56 final size:57
Alignment explanation
Indices: 25641--25748 Score: 132
Period size: 56 Copynumber: 1.9 Consensus size: 57
25631 ATATTCTCTC
*
25641 CCCATTACGATACTTTCATACTAATTTTATATA-TTTT-TTCACGTTATCTCACTAAT
1 CCCATTACGATACTTTCATACTAATTTTACATATTTTTCTTCACG-TATCTCACTAAT
* * * *
25697 CCCATTACGGTATTTTCAT-GTCAATTTTACATGTTTTTCTTCACGTATCTCA
1 CCCATTACGATACTTTCATACT-AATTTTACATATTTTTCTTCACGTATCTCA
25749 TAGTTCTTGC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
55 1 0.02
56 26 0.59
57 11 0.25
58 6 0.14
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.46
Consensus pattern (57 bp):
CCCATTACGATACTTTCATACTAATTTTACATATTTTTCTTCACGTATCTCACTAAT
Found at i:26513 original size:14 final size:14
Alignment explanation
Indices: 26496--26522 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26486 ATATTAAATA
26496 ATAAATATAATTAT
1 ATAAATATAATTAT
26510 ATAAATATAATTA
1 ATAAATATAATTA
26523 AAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:28608 original size:37 final size:37
Alignment explanation
Indices: 28244--28623 Score: 469
Period size: 37 Copynumber: 10.4 Consensus size: 37
28234 TTAAATCGGT
28244 TTTTGAAATATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAA-ATATATATAATATATAGTTTTTGAAAACA
* *
28282 TTTTG--AA-A-ACAT-ATATATAGTTTTTAAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
28314 TTTTGAAAA-ATTATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATA-TATATAATATATAGTTTTTGAAAACA
28351 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
28388 TTTT-AAATATGTATATAATATATAGTTTTTGAAAACA
1 TTTTGAAA-ATATATATAATATATAGTTTTTGAAAACA
*
28425 TTTTGAAAATTTATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
28462 TTTTGAAAACT-TATATAATATATAG-TTTTGAAAATA
1 TTTTGAAAA-TATATATAATATATAGTTTTTGAAAACA
** *
28498 TTTTTGAAAGCATATATAATATAT-TTTTTTGAAAACA
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * *
28535 TTTTTGAAAACATATATAATATATAG-TTTTAAAAATA
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
* * * *
28572 TTTTTGAAAAAATATATATTATATAGTTTTGGAAATA-T
1 -TTTTGAAAATATATATAATATATAGTTTTTGAAA-ACA
28610 TTTTGAAAATATAT
1 TTTTGAAAATATAT
28624 TATTATTATT
Statistics
Matches: 306, Mismatches: 21, Indels: 31
0.85 0.06 0.09
Matches are distributed among these distances:
32 24 0.08
33 3 0.01
34 4 0.01
35 1 0.00
36 17 0.06
37 240 0.78
38 16 0.05
39 1 0.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (37 bp):
TTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:28629 original size:3 final size:3
Alignment explanation
Indices: 28621--28663 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
28611 TTTGAAAATA
* *
28621 TAT TAT TAT TAT TAT TAT TAT TAT CTCT TCT T-T TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT T
28664 TTTTATTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:28672 original size:18 final size:18
Alignment explanation
Indices: 28629--28672 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
28619 TATATTATTA
28629 TTATTATTATTATTATCTC
1 TTATT-TTATTATTATCTC
* * *
28648 TTCTTTTATTATTATTTT
1 TTATTTTATTATTATCTC
28666 TTATTTT
1 TTATTTT
28673 TTCTTCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTTTATTATTATCTC
Found at i:28690 original size:30 final size:30
Alignment explanation
Indices: 28623--28682 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 30
28613 TGAAAATATA
28623 TTATTATTATTATTATTATTATCTCTTCTT
1 TTATTATTATTATTATTATTATCTCTTCTT
* *
28653 TTATTATTATT-TT-TTATTTTTTCTTCTT
1 TTATTATTATTATTATTATTATCTCTTCTT
28681 TT
1 TT
28683 TATTTATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 15 0.54
29 2 0.07
30 11 0.39
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.73
Consensus pattern (30 bp):
TTATTATTATTATTATTATTATCTCTTCTT
Found at i:29760 original size:24 final size:23
Alignment explanation
Indices: 29733--29810 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 23
29723 GTTTCCCCCC
29733 TTTTTTAGCATTTTTTATTTTATT
1 TTTTTTA-CATTTTTTATTTTATT
** * * *
29757 TTTTAAATCATTATTTGTTTTATA
1 TTTTTTA-CATTTTTTATTTTATT
*
29781 TTTTTTACTTATTTTTATTTT-TT
1 TTTTTTACAT-TTTTTATTTTATT
*
29804 TATTTTA
1 TTTTTTA
29811 TTACTCTTAA
Statistics
Matches: 40, Mismatches: 13, Indels: 3
0.71 0.23 0.05
Matches are distributed among these distances:
23 9 0.22
24 31 0.77
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.73
Consensus pattern (23 bp):
TTTTTTACATTTTTTATTTTATT
Found at i:29802 original size:7 final size:8
Alignment explanation
Indices: 29767--29809 Score: 50
Period size: 9 Copynumber: 4.9 Consensus size: 8
29757 TTTTAAATCA
29767 TTATTTGTT
1 TTATTT-TT
29776 TTATATTTT
1 TTAT-TTTT
29785 TTACTTATTT
1 TTA-TT-TTT
29795 TTATTTTT
1 TTATTTTT
29803 TTATTTT
1 TTATTTT
29810 ATTACTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 10 0.32
9 12 0.39
10 9 0.29
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.79
Consensus pattern (8 bp):
TTATTTTT
Found at i:29840 original size:5 final size:5
Alignment explanation
Indices: 29830--29891 Score: 51
Period size: 5 Copynumber: 13.2 Consensus size: 5
29820 AAATTTAAAA
** * * *
29830 TATTT TATTT T-TTT TATTT TA-TT CCTTT GA-TT TATTT AATAT T-TTT
1 TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT TATTT
29876 TATTT TATTT TATTT T
1 TATTT TATTT TATTT T
29892 TTCCTTTGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
4 12 0.27
5 32 0.73
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:29847 original size:14 final size:14
Alignment explanation
Indices: 29830--29891 Score: 61
Period size: 14 Copynumber: 4.1 Consensus size: 14
29820 AAATTTAAAA
29830 TATTTTATTTTTTT
1 TATTTTATTTTTTT
29844 TATTTTATTCCTTTGATT
1 TATTTTATT--TTT--TT
* *
29862 TATTTAATATTTTT
1 TATTTTATTTTTTT
29876 TATTTTATTTTATTT
1 TATTTTATTTT-TTT
29891 T
1 T
29892 TTCCTTTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.51
15 4 0.10
16 6 0.15
18 9 0.23
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (14 bp):
TATTTTATTTTTTT
Found at i:29891 original size:17 final size:17
Alignment explanation
Indices: 29837--29931 Score: 63
Period size: 17 Copynumber: 5.5 Consensus size: 17
29827 AAATATTTTA
29837 TTTT-TTTTATTTTATT
1 TTTTATTTTATTTTATT
*
29853 CCTTTGA-TTTATTTAATATT
1 --TTTTATTTTATTT--TATT
29873 TTTTATTTTATTTTATT
1 TTTTATTTTATTTTATT
* *
29890 TTTTCCTTTGATTTT-TT
1 TTTT-ATTTTATTTTATT
*
29907 TATTATTTTGA-TTTATT
1 TTTTATTTT-ATTTTATT
*
29924 TATTATTT
1 TTTTATTT
29932 CTTATCTAAC
Statistics
Matches: 63, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
16 6 0.10
17 24 0.38
18 22 0.35
19 7 0.11
20 4 0.06
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTATTTTATTTTATT
Found at i:29914 original size:41 final size:41
Alignment explanation
Indices: 29792--29915 Score: 139
Period size: 41 Copynumber: 3.1 Consensus size: 41
29782 TTTTTACTTA
* ** *
29792 TTTTTA-TTTTTTTATTTTATTACTCTT-A-AAATTTAAAAT
1 TTTTTATTTTTTTTATTTTATTCCT-TTGATTTATTTAATAT
*
29831 ATTTTATTTTTTTTATTTTATTCCTTTGATTTATTTAATAT
1 TTTTTATTTTTTTTATTTTATTCCTTTGATTTATTTAATAT
* *
29872 TTTTTATTTTATTTTATTTT-TTCCTTTGATTTTTTTATTAT
1 TTTTTATTTT-TTTTATTTTATTCCTTTGATTTATTTAATAT
29913 TTT
1 TTT
29916 GATTTATTTA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
39 7 0.10
40 18 0.25
41 39 0.53
42 9 0.12
ACGTcount: A:0.22, C:0.05, G:0.02, T:0.72
Consensus pattern (41 bp):
TTTTTATTTTTTTTATTTTATTCCTTTGATTTATTTAATAT
Found at i:29930 original size:41 final size:39
Alignment explanation
Indices: 29828--29931 Score: 129
Period size: 41 Copynumber: 2.5 Consensus size: 39
29818 TAAAATTTAA
29828 AATATTTTATTTTTTTTATTTTATTCCTTTGATTTATTT
1 AATATTTTATTTTTTTTATTTTATTCCTTTGATTTATTT
*
29867 AATATTTTTTATTTTATTTTATTTT-TTCCTTTGATTTTTTT
1 AATA--TTTTATTTT-TTTTATTTTATTCCTTTGATTTATTT
*
29908 ATTATTTTGATTTATTTATTATTT
1 AATATTTT-ATTT-TTT-TTATTT
29932 CTTATCTAAC
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
39 8 0.14
40 6 0.11
41 34 0.60
42 9 0.16
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.73
Consensus pattern (39 bp):
AATATTTTATTTTTTTTATTTTATTCCTTTGATTTATTT
Found at i:31226 original size:23 final size:23
Alignment explanation
Indices: 31200--31259 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
31190 TTAATTTTTA
*
31200 AAATCATATTATTTATTTATTTG
1 AAATAATATTATTTATTTATTTG
*
31223 AAATAATATTAATTATTTATTTG
1 AAATAATATTATTTATTTATTTG
31246 AAATAATATTATTT
1 AAATAATATTATTT
31260 TTAAATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (23 bp):
AAATAATATTATTTATTTATTTG
Found at i:31256 original size:19 final size:19
Alignment explanation
Indices: 31212--31292 Score: 64
Period size: 23 Copynumber: 4.2 Consensus size: 19
31202 ATCATATTAT
31212 TTATTTATTTGAAATAATATTAA
1 TTATTTATTTGAAAT-A-A-T-A
31235 TTATTTATTTGAAATAATA
1 TTATTTATTTGAAATAATA
31254 TTA-TT-TTT-AAAT--TA
1 TTATTTATTTGAAATAATA
*
31268 TCTATTTAATTTTAAATAATA
1 T-TATTT-ATTTGAAATAATA
31289 TTAT
1 TTAT
31293 ACAGAACCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 17
0.75 0.00 0.25
Matches are distributed among these distances:
14 3 0.06
15 2 0.04
16 6 0.12
17 3 0.06
18 5 0.10
19 8 0.16
20 4 0.08
21 4 0.08
22 1 0.02
23 15 0.29
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (19 bp):
TTATTTATTTGAAATAATA
Found at i:31399 original size:23 final size:22
Alignment explanation
Indices: 31373--31448 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 22
31363 TAGATAATTT
31373 ATAAATAATATTATTTCAAATAA
1 ATAAATAATATTATTTCAAAT-A
* *
31396 ATAATTAATATTATTTTAAATA
1 ATAAATAATATTATTTCAAATA
* *
31418 TTAAATAAATATT-TTTACAATATT
1 ATAAAT-AATATTATTT-CAA-ATA
31442 ATAAATA
1 ATAAATA
31449 TACTTTTTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
22 8 0.19
23 28 0.65
24 7 0.16
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATAATATTATTTCAAATA
Found at i:31455 original size:22 final size:20
Alignment explanation
Indices: 31409--31449 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
31399 ATTAATATTA
31409 TTTTAAATATTAAATAAATAT
1 TTTTAAATATT-AATAAATAT
31430 TTTTACAATATT-ATAAATAT
1 TTTTA-AATATTAATAAATAT
31450 ACTTTTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAATATTAATAAATAT
Found at i:31465 original size:24 final size:22
Alignment explanation
Indices: 31409--31500 Score: 68
Period size: 22 Copynumber: 4.2 Consensus size: 22
31399 ATTAATATTA
*
31409 TTTTA-AATATTA-AATAAATAT
1 TTTTATAATATTATAA-ATATAT
*
31430 TTTTACAATATTATAAATATACT
1 TTTTATAATATTATAAATATA-T
*
31453 TTTTATAATTATT-T-CATATAT
1 TTTTATAA-TATTATAAATATAT
*
31474 TTTTATAAAAATATATAAAT-TAT
1 TTTTAT-AATAT-TATAAATATAT
31497 TTTT
1 TTTT
31501 TATTTTTATT
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
21 14 0.24
22 19 0.33
23 19 0.33
24 6 0.10
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTATAATATTATAAATATAT
Found at i:32497 original size:21 final size:20
Alignment explanation
Indices: 32468--32510 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
32458 TATATTTTTA
*
32468 TTATACATTTTTGTCTATCT
1 TTATACATTTTTATCTATCT
*
32488 TTATGACATTTTTATTTATCT
1 TTAT-ACATTTTTATCTATCT
32509 TT
1 TT
32511 TGGCATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.21, C:0.12, G:0.05, T:0.63
Consensus pattern (20 bp):
TTATACATTTTTATCTATCT
Found at i:33381 original size:19 final size:21
Alignment explanation
Indices: 33359--33400 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
33349 TAAAATTAAT
*
33359 TATATTAAT-TTA-AACAAAA
1 TATATTAATAATATAACAAAA
33378 TATATTAATAATATAACAAAA
1 TATATTAATAATATAACAAAA
33399 TA
1 TA
33401 AAATTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
TATATTAATAATATAACAAAA
Found at i:33762 original size:15 final size:15
Alignment explanation
Indices: 33739--33769 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33729 AAATCAACTA
33739 ACTTCAACAATTAAG
1 ACTTCAACAATTAAG
*
33754 ACTTTAACAATTAAG
1 ACTTCAACAATTAAG
33769 A
1 A
33770 TTAAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.29
Consensus pattern (15 bp):
ACTTCAACAATTAAG
Found at i:40569 original size:110 final size:110
Alignment explanation
Indices: 40376--40585 Score: 420
Period size: 110 Copynumber: 1.9 Consensus size: 110
40366 TTTATCAAAT
40376 AAAAATTCTTTGGAAGCCACACTCCAAGATTTCATGGCTACTACAAAGGCTATGATCAATTTACA
1 AAAAATTCTTTGGAAGCCACACTCCAAGATTTCATGGCTACTACAAAGGCTATGATCAATTTACA
40441 CAAACTAGTCATGCCATGCTATCATGTATCCTAAAGATTTCATAA
66 CAAACTAGTCATGCCATGCTATCATGTATCCTAAAGATTTCATAA
40486 AAAAATTCTTTGGAAGCCACACTCCAAGATTTCATGGCTACTACAAAGGCTATGATCAATTTACA
1 AAAAATTCTTTGGAAGCCACACTCCAAGATTTCATGGCTACTACAAAGGCTATGATCAATTTACA
40551 CAAACTAGTCATGCCATGCTATCATGTATCCTAAA
66 CAAACTAGTCATGCCATGCTATCATGTATCCTAAA
40586 TTCAAAAAGA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 100 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (110 bp):
AAAAATTCTTTGGAAGCCACACTCCAAGATTTCATGGCTACTACAAAGGCTATGATCAATTTACA
CAAACTAGTCATGCCATGCTATCATGTATCCTAAAGATTTCATAA
Found at i:52314 original size:16 final size:16
Alignment explanation
Indices: 52293--52333 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
52283 TTTACTTTTA
52293 TCCGATTATTCGTTTC
1 TCCGATTATTCGTTTC
* *
52309 TCCGATTACTCTTTTC
1 TCCGATTATTCGTTTC
52325 TCCG-TTATT
1 TCCGATTATT
52334 TTCGATTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.12, C:0.27, G:0.10, T:0.51
Consensus pattern (16 bp):
TCCGATTATTCGTTTC
Found at i:73216 original size:24 final size:24
Alignment explanation
Indices: 73189--73236 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
73179 TTGGGTTATT
73189 GGAAGGGCATTATGATCTTTTCAA
1 GGAAGGGCATTATGATCTTTTCAA
* *
73213 GGAAGGGTATTATGGTCTTTTCAA
1 GGAAGGGCATTATGATCTTTTCAA
73237 AAAAGGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.10, G:0.27, T:0.35
Consensus pattern (24 bp):
GGAAGGGCATTATGATCTTTTCAA
Found at i:73242 original size:24 final size:24
Alignment explanation
Indices: 73191--73242 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
73181 GGGTTATTGG
**
73191 AAGGGCATTATGATCTTTTCAAGG
1 AAGGGCATTATGATCTTTTCAAAA
* *
73215 AAGGGTATTATGGTCTTTTCAAAA
1 AAGGGCATTATGATCTTTTCAAAA
73239 AAGG
1 AAGG
73243 ATTTTTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (24 bp):
AAGGGCATTATGATCTTTTCAAAA
Found at i:75432 original size:30 final size:30
Alignment explanation
Indices: 75396--75457 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
75386 TCTTAAATTT
* *
75396 TTTAGGGATTAAATTGAAATT-TTAGTTAAA
1 TTTAGGGACTAAAAT-AAATTCTTAGTTAAA
*
75426 TTTAGGGACTAAAATAAATTCTTATTTAAA
1 TTTAGGGACTAAAATAAATTCTTAGTTAAA
75456 TT
1 TT
75458 CAGATCCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (30 bp):
TTTAGGGACTAAAATAAATTCTTAGTTAAA
Found at i:81009 original size:31 final size:32
Alignment explanation
Indices: 80950--81009 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
80940 ATTAAATATT
* * **
80950 TTGATTTCATGATATTTGTTTTTTCGTATGCA
1 TTGATTTCATGATATCTGATTTACCGTATGCA
80982 TTGATTTC-TGATATCTGATTTACCGTAT
1 TTGATTTCATGATATCTGATTTACCGTAT
81010 ACTTTTAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 16 0.67
32 8 0.33
ACGTcount: A:0.20, C:0.12, G:0.15, T:0.53
Consensus pattern (32 bp):
TTGATTTCATGATATCTGATTTACCGTATGCA
Found at i:86737 original size:56 final size:56
Alignment explanation
Indices: 86671--86778 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
86661 ACTTAGGCTT
*
86671 ATTTTAATGTTTCTGCTACAAAACTGATGCTATGACATTGTTAATGTTGTAGTCTG
1 ATTTTAATGTTTCTACTACAAAACTGATGCTATGACATTGTTAATGTTGTAGTCTG
* * *
86727 ATTTTAATGTTTCTACTACAAAACTGATGTTGTGACTTTGTTAATGTTGTAG
1 ATTTTAATGTTTCTACTACAAAACTGATGCTATGACATTGTTAATGTTGTAG
86779 CCGTTGCTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.44
Consensus pattern (56 bp):
ATTTTAATGTTTCTACTACAAAACTGATGCTATGACATTGTTAATGTTGTAGTCTG
Found at i:103090 original size:20 final size:20
Alignment explanation
Indices: 103065--103102 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
103055 ACAAGTATCG
103065 ATACTACAAGAACAATATTA
1 ATACTACAAGAACAATATTA
*
103085 ATACTATAAGAACAATAT
1 ATACTACAAGAACAATAT
103103 CATTAATAAA
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:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (20 bp):
ATACTACAAGAACAATATTA
Found at i:118471 original size:21 final size:20
Alignment explanation
Indices: 118425--118462 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
118415 ATGAAAGGAG
118425 TAAGAATAAACAAAAAAAAA
1 TAAGAATAAACAAAAAAAAA
*
118445 TAAGAATCAACAAAAAAA
1 TAAGAATAAACAAAAAAA
118463 TGAATAGAAA
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:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (20 bp):
TAAGAATAAACAAAAAAAAA
Found at i:129168 original size:44 final size:45
Alignment explanation
Indices: 129083--129169 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 45
129073 TCATACTTAT
* *
129083 AATGCCCCATTATGCATTTTCATTTATGGCATTATTTCATGCCAA
1 AATGCCCCATTATGCATTTTCATTGATGGCATCATTTCATGCCAA
*
129128 AATGCACCCA-TATGCATTTT-ATTGATGGCATCCTTTCATGCC
1 AATGC-CCCATTATGCATTTTCATTGATGGCATCATTTCATGCC
129170 TTTTTTACAC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 19 0.50
45 15 0.39
46 4 0.11
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (45 bp):
AATGCCCCATTATGCATTTTCATTGATGGCATCATTTCATGCCAA
Found at i:129191 original size:45 final size:45
Alignment explanation
Indices: 129142--129256 Score: 158
Period size: 45 Copynumber: 2.6 Consensus size: 45
129132 CACCCATATG
* * * * *
129142 CATTTTATTGATGGCATCCTTTCATGCCTTTTTTACACCGTTATA
1 CATTTCATTTATGGAATCCTTTCATGCCTTTTATACACCATTATA
* * *
129187 CATTTCCTTTATGGAATCCATTCATGCCTTTTATACACTATTATA
1 CATTTCATTTATGGAATCCTTTCATGCCTTTTATACACCATTATA
129232 CATTTCATTTATGGAATCCTTTCAT
1 CATTTCATTTATGGAATCCTTTCAT
129257 ACCCATTATG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (45 bp):
CATTTCATTTATGGAATCCTTTCATGCCTTTTATACACCATTATA
Found at i:129397 original size:49 final size:46
Alignment explanation
Indices: 129234--129409 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 46
129224 CTATTATACA
* * * * *
129234 TTTCATTTATGGA-ATCCTTTCATACCCATTATGTATTGTTTATGTT
1 TTTCCTTTAT-GACATCCATTCATACCAATTATGCATTGTTTACGTT
* * *
129280 TTTCCTTTAAGACATCCATTCATACCGATTATGTATTGTTTACGTT
1 TTTCCTTTATGACATCCATTCATACCAATTATGCATTGTTTACGTT
*
129326 TTTCCTTTATGACATCCATTCATACCAATTATGCATTGTTGTACATT
1 TTTCCTTTATGACATCCATTCATACCAATTATGCATTGTT-TACGTT
* * * *
129373 TTATATCTATATGACATCCTTTCATACCACTTATGCA
1 TT-T-CCTTTATGACATCCATTCATACCAATTATGCA
129410 CCGTTTATAT
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
45 2 0.02
46 75 0.66
47 7 0.06
48 1 0.01
49 28 0.25
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (46 bp):
TTTCCTTTATGACATCCATTCATACCAATTATGCATTGTTTACGTT
Found at i:129546 original size:81 final size:81
Alignment explanation
Indices: 129439--130003 Score: 681
Period size: 81 Copynumber: 7.0 Consensus size: 81
129429 TTATAATTCC
* * * * *
129439 TTTAGTCTTTTACCCAAAGG-CATTTAACCTTTCATCTAACTTGCATGATTGACACTTTTCTGCC
1 TTTA-TCTTTTACTCAACGGTC-TTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGCC
* *
129503 AAATGCATAGTTAGGCCA
64 AAATGCACAGCTAGGCCA
* * * * *
129521 TTTATCTTTTACTCAACGGTCTTTAACTGTTCATCTATCTGGCATAATTGATACATTTCTACCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGCCAA
* *
129586 ATACACAGCTAGGTCA
66 ATGCACAGCTAGGCCA
* * * * *
129602 TTTATCATTTACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTGCCAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGCCAA
129667 ATGCACAGCTAGGCCA
66 ATGCACAGCTAGGCCA
* * * * * *
129683 TTTATCTTTAAATCAACGGTCTTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCAAA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGCCAA
* * **
129748 ATACACAACTACTCCA
66 ATGCACAGCTAGGCCA
* *
129764 TTTATCTTTTACTCAACAGTCTTTAACTGTTCATCTAACTAT-CATAATTGACACATTTCTGCCA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACT-TGCATAATTGACACATTTCTGCCA
* *
129828 AATGCACAACAAGGCCA
65 AATGCACAGCTAGGCCA
* * *
129845 TTTATCTTTCACTCAATGGTCTTTAACCGTTCATCTAA-TTGGCATAATTGACACATTTCTACCA
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTT-GCATAATTGACACATTTCTGCCA
* *
129909 AAAGCACAACTAGGCCA
65 AATGCACAGCTAGGCCA
* *
129926 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAAC-TGCATAATTGACACTTTTCTGTC-A
1 TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGCCAA
* *
129989 ATACACAGTTAGGCC
66 ATGCACAGCTAGGCC
130004 TCAAAGGCAC
Statistics
Matches: 415, Mismatches: 63, Indels: 13
0.85 0.13 0.03
Matches are distributed among these distances:
79 13 0.03
80 20 0.05
81 377 0.91
82 5 0.01
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (81 bp):
TTTATCTTTTACTCAACGGTCTTTAACCGTTCATCTAACTTGCATAATTGACACATTTCTGCCAA
ATGCACAGCTAGGCCA
Found at i:129849 original size:243 final size:242
Alignment explanation
Indices: 129461--129985 Score: 755
Period size: 243 Copynumber: 2.2 Consensus size: 242
129451 CCCAAAGGCA
* * * * * ** *
129461 TTTAACCTTTCATCTAACTTGCATGATTGACACTTTTCTGCCAAATGCATAGTTAGGCCATTTAT
1 TTTAACCGTTCATCTAAC-TGCATAATTGACACTTTTCTGCAAAATACACAACTACGCCATTTAT
* * * *
129526 CTTTTACTCAACGGTCTTTAACTGTTCATCTATCTGGCATAATTGATACATTTCTACCAAATACA
65 CTTTTACTCAACAGTCTTTAACTGTTCATCTAACTAGCATAATTGACACATTTCTACCAAATACA
* * *
129591 CAGCTAGGTCATTTATCATTT-ACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACA
130 CAACAAGGCCATTTATC-TTTCACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACA
* * * *
129655 CCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTAAATCAACGGTC
194 CATTTCTACCAAAAGCACAACTAGGCCATTTATCTTTAAATCAACGGTC
* * *
129704 TTTAATCGTTCATCTAACTGGCATAATTGACACCTTTCTGCAAAATACACAACTACTCCATTTAT
1 TTTAACCGTTCATCTAACT-GCATAATTGACACTTTTCTGCAAAATACACAACTACGCCATTTAT
* * *
129769 CTTTTACTCAACAGTCTTTAACTGTTCATCTAACTATCATAATTGACACATTTCTGCCAAATGCA
65 CTTTTACTCAACAGTCTTTAACTGTTCATCTAACTAGCATAATTGACACATTTCTACCAAATACA
* *
129834 CAACAAGGCCATTTATCTTTCACTCAATGGTCTTTAACCGTTCATCTAATTGGCATAATTGACAC
130 CAACAAGGCCATTTATCTTTCACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACAC
* *
129899 ATTTCTACCAAAAGCACAACTAGGCCATTTATCTTTTACTCAACGGTC
195 ATTTCTACCAAAAGCACAACTAGGCCATTTATCTTTAAATCAACGGTC
129947 TTTAACCGTTCATCTAACTGCATAATTGACACTTTTCTG
1 TTTAACCGTTCATCTAACTGCATAATTGACACTTTTCTG
129986 TCAATACACA
Statistics
Matches: 249, Mismatches: 31, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
242 23 0.09
243 226 0.91
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (242 bp):
TTTAACCGTTCATCTAACTGCATAATTGACACTTTTCTGCAAAATACACAACTACGCCATTTATC
TTTTACTCAACAGTCTTTAACTGTTCATCTAACTAGCATAATTGACACATTTCTACCAAATACAC
AACAAGGCCATTTATCTTTCACTCAATGGTCTTTAACCATTCATCTAACTGGCATAATTGACACA
TTTCTACCAAAAGCACAACTAGGCCATTTATCTTTAAATCAACGGTC
Found at i:130207 original size:67 final size:67
Alignment explanation
Indices: 129955--130205 Score: 396
Period size: 67 Copynumber: 3.8 Consensus size: 67
129945 TCTTTAACCG
*
129955 TTCATCTAACT-GCATAATTGACACTTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
130019 CT
66 CT
* * *
130021 TTCATCTAACTGGCATAATTGACACCTTTCAGTCAATAAACAGTTAGGTCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
130086 CT
66 CT
* * * *
130088 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTGAGGCCTTAAAGGCATTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
130153 CT
66 CT
* * *
130155 TTCATTTAACTGGTATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATACACAGTTAGGCCT
130206 TATAAACTTT
Statistics
Matches: 170, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
66 11 0.06
67 159 0.94
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATACACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:130910 original size:19 final size:20
Alignment explanation
Indices: 130841--130911 Score: 74
Period size: 19 Copynumber: 3.5 Consensus size: 20
130831 TGGCTCCTCA
* * *
130841 GTATCGATATTCGTACCATG
1 GTATCGATACTCATACTATG
130861 GTATCGATACTACTATACTATG
1 GTATCGATACT-C-ATACTATG
130883 GTA-CTGATACTC-TACTATG
1 GTATC-GATACTCATACTATG
130902 GTATCGATAC
1 GTATCGATAC
130912 CATTTTTGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
19 15 0.34
20 11 0.25
21 3 0.07
22 15 0.34
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
GTATCGATACTCATACTATG
Found at i:133062 original size:2 final size:2
Alignment explanation
Indices: 133055--133091 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
133045 CATTAACCAT
133055 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 T
133092 CTAACATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:134839 original size:30 final size:32
Alignment explanation
Indices: 134803--134862 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
134793 TTCATGCCTT
*
134803 TTTTACA-AC-ATTATACATTTCCTTTATGCC
1 TTTTACACACTATTATACATTTCATTTATGCC
134833 TTTTACACACTATTATACATTTCATTTATG
1 TTTTACACACTATTATACATTTCATTTATG
134863 GCATTCTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.26
31 2 0.07
32 18 0.67
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.48
Consensus pattern (32 bp):
TTTTACACACTATTATACATTTCATTTATGCC
Found at i:135128 original size:81 final size:81
Alignment explanation
Indices: 135057--135492 Score: 542
Period size: 81 Copynumber: 5.4 Consensus size: 81
135047 AGCTTGCGGG
* * *
135057 ATTGACACTTTTCTGCCAAATGCACAGTTAGGCCATTTATCTTTTACTCAACGGTCTTTAATCGT
1 ATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCGT
135122 TCATCTAA-TTGGCATA
66 TCATCTAACTT-GCATA
* * * * * **
135138 ATTAACACCTTTCTGTCAAATGCACATCTAGGCCATTTATATTTTACTCAACAATCTTTAACCGT
1 ATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCGT
* *
135203 GCATCTAACTGGCATA
66 TCATCTAACTTGCATA
* **
135219 A-TGTACACATTTCTACCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACTA
1 ATTG-ACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
* * *
135283 TTCATTTGACTGGCATA
65 TTCATCTAACTTGCATA
* * * *
135300 ATTGACACATTTCTGCTAAATACACAGCTAGGCCATTTATCGTTTACTCAATGGTCTTTAACCGT
1 ATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCGT
135365 TCATCTAAC-TGACATA
66 TCATCTAACTTG-CATA
* * *
135381 ATTGCCACATTTCTGCCAAATGCACACCTAGGCCATTTATCCTTTACTCAACGGTCTTTAACCGT
1 ATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCGT
135446 TCATCTAACTAT--ATA
66 TCATCTAACT-TGCATA
* * *
135461 ATTGACACTTTTCTGTC-AATGCACAGTTAGGC
1 ATTGACACATTTCTGCCAAATGCACAGCTAGGC
135493 ATCAAAGGCA
Statistics
Matches: 304, Mismatches: 45, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
79 13 0.04
80 19 0.06
81 268 0.88
82 3 0.01
83 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.35
Consensus pattern (81 bp):
ATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCGT
TCATCTAACTTGCATA
Found at i:135697 original size:67 final size:67
Alignment explanation
Indices: 135445--135695 Score: 353
Period size: 67 Copynumber: 3.8 Consensus size: 67
135435 TCTTTAACCG
** * *
135445 TTCATCTAACT-ATATAATTGACACTTTTCTGTCAATGCACAGTTAGGCATCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
135509 CT
66 CT
* * *
135511 TTCATCTAACTGGCATAATTGATACCTTTCTGTCAATGCAAAGTTAGGCCTCAACGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
135576 CT
66 CT
* * *
135578 TTCCTCTAACTGGCATAATTGACACCTTTCT-TCCAATGCACAGTTAGGCCTTAAAGGCACTTGG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGT-CAATGCACAGTTAGGCCTCAAAGGCACTTAG
135642 CCT
65 CCT
* * * *
135645 GTCATCTAACTGGCATAATTGACACATTTCTTTCAATGCACAGTTATGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCT
135696 TATAATATTT
Statistics
Matches: 165, Mismatches: 17, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
66 12 0.07
67 152 0.92
68 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (67 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
CT
Found at i:136324 original size:22 final size:20
Alignment explanation
Indices: 136299--136357 Score: 84
Period size: 22 Copynumber: 2.9 Consensus size: 20
136289 TTCTACAACA
*
136299 ATACCATGGTATCGATACTAC
1 ATACTATGGTATCGATACT-C
136320 TATACTATGGTATCGATACTC
1 -ATACTATGGTATCGATACTC
136341 -TACTATGGTATCGATAC
1 ATACTATGGTATCGATAC
136358 CATTTTTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 17 0.47
21 1 0.03
22 18 0.50
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (20 bp):
ATACTATGGTATCGATACTC
Found at i:142490 original size:22 final size:21
Alignment explanation
Indices: 142439--142504 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
142429 GTTTCGTTAT
* *
142439 TCTACTTTCTAAAAAATAATCA
1 TCTACTTT-AAAAAAAAAATCA
* **
142461 ACTACTTTTAAAATGAAAATCA
1 TCTAC-TTTAAAAAAAAAATCA
*
142483 TCTTCTTTAAAAAAAAAATCA
1 TCTACTTTAAAAAAAAAATCA
142504 T
1 T
142505 GACCTTGATA
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
21 15 0.44
22 16 0.47
23 3 0.09
ACGTcount: A:0.48, C:0.15, G:0.02, T:0.35
Consensus pattern (21 bp):
TCTACTTTAAAAAAAAAATCA
Found at i:142949 original size:38 final size:36
Alignment explanation
Indices: 142898--142974 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 36
142888 TATTTAAGAT
**
142898 AATATTAGTACAATGGTTAATGAAAGATGTTCAAAATA
1 AATATTAGTACAATAATTAATGAAAGATGTT-AAAA-A
142936 AATATTAGTACAATAATTAATGAAAGATGTTAAAAA
1 AATATTAGTACAATAATTAATGAAAGATGTTAAAAA
142972 AAT
1 AAT
142975 TTGATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 4 0.11
37 4 0.11
38 29 0.78
ACGTcount: A:0.52, C:0.04, G:0.13, T:0.31
Consensus pattern (36 bp):
AATATTAGTACAATAATTAATGAAAGATGTTAAAAA
Found at i:143789 original size:18 final size:18
Alignment explanation
Indices: 143757--143802 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
143747 TTAAAATATA
*
143757 ATTTAATA-TAGAAATATT
1 ATTTAATACTATAAAT-TT
*
143775 -TTTTATACTATAAATTT
1 ATTTAATACTATAAATTT
143792 ATTTAATACTA
1 ATTTAATACTA
143803 ACTATAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTAATACTATAAATTT
Found at i:144424 original size:59 final size:59
Alignment explanation
Indices: 144264--144440 Score: 200
Period size: 59 Copynumber: 3.0 Consensus size: 59
144254 TGTTAACCCG
* * * * *
144264 GACACATAAGGT-TGTGCCCACTATCTGCGCTAGTTATACTTTAGTACAGT-CTCGAATAT
1 GACACATAAGGTCTG-G-CCACCATATGCACTAGTTATACTTTAGTGCAATCCTCGAATAT
* * *
144323 GACACATAAGGTCTTGCCCCCATATGTACTAGTTATACTTTAGTGCAATCCT-GAATAT
1 GACACATAAGGTCTGGCCACCATATGCACTAGTTATACTTTAGTGCAATCCTCGAATAT
* * *
144381 GACACATAAGGTCATGGCCATCATATGCACTAGTTATACTTTAGTGTAATCC-CCAATAT
1 GACACATAAGGTC-TGGCCACCATATGCACTAGTTATACTTTAGTGCAATCCTCGAATAT
144440 G
1 G
144441 TAGCTTGCTT
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
58 45 0.45
59 54 0.54
60 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (59 bp):
GACACATAAGGTCTGGCCACCATATGCACTAGTTATACTTTAGTGCAATCCTCGAATAT
Found at i:147937 original size:29 final size:29
Alignment explanation
Indices: 147895--147953 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
147885 TCATCATTCC
147895 TTAAGGAATTCAATCCATTTCCTTTATTT
1 TTAAGGAATTCAATCCATTTCCTTTATTT
147924 TTAAGGAATTCAATCCATTTCCTTTATTT
1 TTAAGGAATTCAATCCATTTCCTTTATTT
147953 T
1 T
147954 CACTCCTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.49
Consensus pattern (29 bp):
TTAAGGAATTCAATCCATTTCCTTTATTT
Done.