Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008461.1 Hibiscus syriacus cultivar Beakdansim tig00111274_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: 100279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3040 original size:35 final size:36
Alignment explanation
Indices: 2999--3073 Score: 143
Period size: 35 Copynumber: 2.1 Consensus size: 36
2989 CTCTCATGTC
2999 TTTTGCACTCGCATAAATGTTTTGAGACACTCTTT-
1 TTTTGCACTCGCATAAATGTTTTGAGACACTCTTTA
3034 TTTTGCACTCGCATAAATGTTTTGAGACACTCTTTA
1 TTTTGCACTCGCATAAATGTTTTGAGACACTCTTTA
3070 TTTT
1 TTTT
3074 CACATTGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
35 35 0.90
36 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (36 bp):
TTTTGCACTCGCATAAATGTTTTGAGACACTCTTTA
Found at i:5664 original size:11 final size:11
Alignment explanation
Indices: 5616--5662 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
5606 TTTTTTGAAA
*
5616 TTTTGGCTTTT
1 TTTTGCCTTTT
5627 TTTGTGCCTTTT
1 TTT-TGCCTTTT
5639 TTTTGCCTTTT
1 TTTTGCCTTTT
5650 TTTTG--TTTT
1 TTTTGCCTTTT
5659 TTTT
1 TTTT
5663 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
9 8 0.24
11 16 0.47
12 10 0.29
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.77
Consensus pattern (11 bp):
TTTTGCCTTTT
Found at i:14967 original size:35 final size:35
Alignment explanation
Indices: 14901--15018 Score: 103
Period size: 35 Copynumber: 3.4 Consensus size: 35
14891 AGTTTGCATC
* * * * *
14901 GATTCAAGTTGAATGGAATGAAGCATCGCACTTTT
1 GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
* *
14936 GATTCTAGTAGAAAGGAAGGAAACATTGCACTTCT
1 GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
* * * **
14971 GATTCAAGTCGAACGGAAGTAGGCATCGCACTT-T
1 GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
*
15005 CGATTCAACTAGAA
1 -GATTCAAGTAGAA
15019 CAGATGGTTT
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
34 1 0.02
35 65 0.98
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (35 bp):
GATTCAAGTAGAAAGGAAGGAAACATCGCACTTCT
Found at i:16210 original size:24 final size:26
Alignment explanation
Indices: 16172--16262 Score: 96
Period size: 24 Copynumber: 3.4 Consensus size: 26
16162 TATATTATAG
* *
16172 ATATTAATTTTAATATTAATTTTTTA
1 ATATAAATTATAATATTAATTTTTTA
16198 A-ATAAATTA-AATATTAATTTTTTA
1 ATATAAATTATAATATTAATTTTTTA
* *
16222 ATATATATTATAGATATTTAATTTTATATC
1 ATATAAATTATA-ATA-TTAATTTT-T-TA
16252 ATATAAATTAT
1 ATATAAATTAT
16263 TTATATATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
24 16 0.30
25 13 0.24
26 2 0.04
27 3 0.06
28 8 0.15
29 1 0.02
30 11 0.20
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
ATATAAATTATAATATTAATTTTTTA
Found at i:16287 original size:16 final size:16
Alignment explanation
Indices: 16241--16290 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
16231 ATAGATATTT
*
16241 AATTTTATATCATATAA
1 AATTTTATATTAT-TAA
16258 ATTATTTATATATTATTAA
1 A--ATTT-TATATTATTAA
16277 AATTTTATATTATT
1 AATTTTATATTATT
16291 TTAATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 9 0.31
17 5 0.17
19 8 0.28
20 7 0.24
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTATATTATTAA
Found at i:16945 original size:31 final size:31
Alignment explanation
Indices: 16910--16969 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
16900 TAGCTCTATG
* *
16910 AATTATTTAAATTTTAGTATT-CTAAAACTAA
1 AATTATTTAAATCTCAGTATTGC-AAAACTAA
16941 AATTATTTAAATCTCAGTATTGCAAAACT
1 AATTATTTAAATCTCAGTATTGCAAAACT
16970 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGCAAAACTAA
Found at i:17887 original size:23 final size:25
Alignment explanation
Indices: 17861--17912 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
17851 AAATCGGTGT
*
17861 AAATCACAC-AATAA-CACACACGA
1 AAATCACACGAAAAATCACACACGA
* *
17884 AAATCATACGAAAAATCACAGACGA
1 AAATCACACGAAAAATCACACACGA
17909 AAAT
1 AAAT
17913 AGGCAAGCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 8 0.33
24 4 0.17
25 12 0.50
ACGTcount: A:0.58, C:0.23, G:0.08, T:0.12
Consensus pattern (25 bp):
AAATCACACGAAAAATCACACACGA
Found at i:18444 original size:16 final size:15
Alignment explanation
Indices: 18425--18458 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
18415 TTTTTCTTTA
18425 TTTTTATTTGTTTTGT
1 TTTTTATTTGTTTT-T
*
18441 TTTTTCTTTGTTTTT
1 TTTTTATTTGTTTTT
18456 TTT
1 TTT
18459 AATTTTCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.85
Consensus pattern (15 bp):
TTTTTATTTGTTTTT
Found at i:18464 original size:26 final size:26
Alignment explanation
Indices: 18405--18464 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
18395 TTTGTTGCAA
18405 TTAATTTCTTTTTTTCTTTATTTTTAT
1 TTAATTT-TTTTTTTCTTTATTTTTAT
* *
18432 TT-GTTTTGTTTTTTCTTTGTTTTT-T
1 TTAATTTT-TTTTTTCTTTATTTTTAT
18457 TTAATTTT
1 TTAATTTT
18465 CTTTACATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 4 0.14
26 22 0.79
27 2 0.07
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (26 bp):
TTAATTTTTTTTTTCTTTATTTTTAT
Found at i:18491 original size:6 final size:6
Alignment explanation
Indices: 18480--18541 Score: 60
Period size: 6 Copynumber: 10.8 Consensus size: 6
18470 CATAACGTTC
* * *
18480 TATTTT TATTTTT TATTTT T-TATT T-TTTG TAGTTT TATTTT TATTTT
1 TATTTT TA-TTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
18527 TA-TTT TA-TTT TATTT
1 TATTTT TATTTT TATTT
18542 CTTTTGTGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 17 0.36
6 24 0.51
7 6 0.13
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:18494 original size:7 final size:7
Alignment explanation
Indices: 18482--18532 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
18472 TAACGTTCTA
18482 TTTTTAT
1 TTTTTAT
18489 TTTTTAT
1 TTTTTAT
18496 TTTTTAT
1 TTTTTAT
*
18503 TTTTTGT
1 TTTTTAT
*
18510 AGTTTTA-
1 -TTTTTAT
18517 TTTTTA-
1 TTTTTAT
18523 TTTTTAT
1 TTTTTAT
18530 TTT
1 TTT
18533 ATTTTATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
6 11 0.29
7 23 0.61
8 4 0.11
ACGTcount: A:0.14, C:0.00, G:0.04, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:18507 original size:22 final size:22
Alignment explanation
Indices: 18482--18541 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 22
18472 TAACGTTCTA
18482 TTTTTATTTTTTATTTTTTATT
1 TTTTTATTTTTTATTTTTTATT
*
18504 TTTTGTA-GTTTTA-TTTTTATT
1 TTTT-TATTTTTTATTTTTTATT
18525 TTTATT-TTATTTTATTT
1 TTT-TTATT-TTTTATTT
18542 CTTTTGTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
21 12 0.39
22 15 0.48
23 4 0.13
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (22 bp):
TTTTTATTTTTTATTTTTTATT
Found at i:18556 original size:109 final size:113
Alignment explanation
Indices: 18421--18695 Score: 300
Period size: 114 Copynumber: 2.5 Consensus size: 113
18411 TCTTTTTTTC
* *
18421 TTTATTTTTATTTGTTTTGT-TTTTTCTTTGTTT-TTTTTAATTTTC-TTTACA-TAAC-GTTCT
1 TTTA-TTTTATTTCTTTTGTGTTTTTCTTTGTTTCTCTTT-A-TTTCGTTTA-ATTAACTGTTCT
* *
18481 ATTTTTA-TTT-TTTA-TTTTTTA-TTTTTTGTAGTTTTATTTTTATTTTTAT
62 ATTTTTATTTTATTTAGTTATTTATTTTTTTGTAGTTTTA-TTTTATATTTAT
* ** * * *
18530 TTTATTTTATTTCTTTTGTGCTTTTCTTTGTTTCTCTTTATTTCGGTTTAATTTTCTTTTTTCTT
1 TTTATTTTATTTCTTTTGTGTTTTTCTTTGTTTCTCTTTATTTC-GTTTAATTAACTGTTCTATT
18595 TTTATTTTATTTAGTTATTTATTTTTTTGTAGTTTTATTTTATATTTAT
65 TTTATTTTATTTAGTTATTTATTTTTTTGTAGTTTTATTTTATATTTAT
* *
18644 TTTATTTT-TTTCTTTTGTGTTTTTCTTTGTTTCTGTTTCTTTTCGGTTTAAT
1 TTTATTTTATTTCTTTTGTGTTTTTCTTTGTTTCTCTTT-ATTTC-GTTTAAT
18696 CTTCTTTTTA
Statistics
Matches: 142, Mismatches: 13, Indels: 17
0.83 0.08 0.10
Matches are distributed among these distances:
108 18 0.13
109 18 0.13
110 10 0.07
111 9 0.06
112 3 0.02
113 32 0.23
114 37 0.26
115 15 0.11
ACGTcount: A:0.12, C:0.07, G:0.07, T:0.74
Consensus pattern (113 bp):
TTTATTTTATTTCTTTTGTGTTTTTCTTTGTTTCTCTTTATTTCGTTTAATTAACTGTTCTATTT
TTATTTTATTTAGTTATTTATTTTTTTGTAGTTTTATTTTATATTTAT
Found at i:18602 original size:5 final size:5
Alignment explanation
Indices: 18594--18651 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
18584 TCTTTTTTCT
*
18594 TTTTA TTTTA -TTTA -GTTA -TTTA TTTT- TTTGTA GTTTTA TTTTA TATTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA -TTTTA TTTTA T-TTTA
18643 TTTTA TTTT
1 TTTTA TTTT
18652 TTTCTTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
4 13 0.28
5 23 0.50
6 7 0.15
7 3 0.07
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:18718 original size:6 final size:5
Alignment explanation
Indices: 18701--18753 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
18691 TTAATCTTCT
* * *
18701 TTTTA TTTTA TTTCTA TTTTC TTTTA CTTTG TTTTA -TTTA TTTTA -TTTA
1 TTTTA TTTTA TTT-TA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
18750 TTTT
1 TTTT
18754 TTGTGTTTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 8 0.21
5 26 0.67
6 5 0.13
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:18746 original size:9 final size:10
Alignment explanation
Indices: 18701--18753 Score: 56
Period size: 9 Copynumber: 5.4 Consensus size: 10
18691 TTAATCTTCT
18701 TTTTATTTTA
1 TTTTATTTTA
*
18711 TTTCTATTTTC
1 TTT-TATTTTA
* *
18722 TTTTACTTTG
1 TTTTATTTTA
18732 TTTTA-TTTA
1 TTTTATTTTA
18741 TTTTA-TTTA
1 TTTTATTTTA
18750 TTTT
1 TTTT
18754 TTGTGTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
9 16 0.42
10 13 0.34
11 9 0.24
ACGTcount: A:0.15, C:0.06, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTATTTTA
Found at i:18780 original size:33 final size:31
Alignment explanation
Indices: 18728--18794 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
18718 TTTCTTTTAC
* * *
18728 TTTGTTTTATTTATTTTATTTATTTTTTGTGT
1 TTTGCTTTATTTATGTTATTTAATTTTTGT-T
18760 TTTGCTTTATTTCATGTTATTTAATTTTTGTT
1 TTTGCTTTATTT-ATGTTATTTAATTTTTGTT
18792 TTT
1 TTT
18795 AGGGTTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
32 15 0.48
33 16 0.52
ACGTcount: A:0.13, C:0.03, G:0.09, T:0.75
Consensus pattern (31 bp):
TTTGCTTTATTTATGTTATTTAATTTTTGTT
Found at i:18803 original size:33 final size:32
Alignment explanation
Indices: 18734--18804 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
18724 TTACTTTGTT
* * *
18734 TTATTTATTTTATTTATTTTTTGTGTTTTGCT
1 TTATTTATGTTATTTAATTTTTGTGTTTTGCG
*
18766 TTATTTCATGTTATTTAATTTTTGT-TTTTAGGG
1 TTATTT-ATGTTATTTAATTTTTGTGTTTT-GCG
18799 TTATTT
1 TTATTT
18805 GTTTTTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
32 10 0.30
33 23 0.70
ACGTcount: A:0.15, C:0.03, G:0.11, T:0.70
Consensus pattern (32 bp):
TTATTTATGTTATTTAATTTTTGTGTTTTGCG
Found at i:18898 original size:4 final size:4
Alignment explanation
Indices: 18889--18929 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
18879 CACTCAATCT
* *
18889 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA GTTA TTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA
18930 GGGTTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 28 0.88
5 4 0.12
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:19726 original size:2 final size:2
Alignment explanation
Indices: 19719--19759 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
19709 TCAAAGAATA
19719 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19760 ATTCTCACAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20527 original size:18 final size:19
Alignment explanation
Indices: 20501--20540 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
20491 TTAAACTAAA
20501 TTATGACTATAAAAATATT
1 TTATGACTATAAAAATATT
* *
20520 TTAT-ACTATCATAATATT
1 TTATGACTATAAAAATATT
20538 TTA
1 TTA
20541 AATAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.42, C:0.07, G:0.03, T:0.47
Consensus pattern (19 bp):
TTATGACTATAAAAATATT
Found at i:21342 original size:2 final size:2
Alignment explanation
Indices: 21335--21366 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21325 AGTGTGACAA
21335 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21367 ATATATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21371 original size:2 final size:2
Alignment explanation
Indices: 21366--21390 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21356 TCTCTCTCTC
21366 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
21391 GCTACTGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22948 original size:2 final size:2
Alignment explanation
Indices: 22941--22969 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22931 ACTCTTAGAT
22941 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 T
22970 TCAGCATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23862 original size:20 final size:20
Alignment explanation
Indices: 23837--23874 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
23827 AAAACTTGCA
23837 TAGGGGTATCGGTACCCTAT
1 TAGGGGTATCGGTACCCTAT
23857 TAGGGGTATCGGTACCCT
1 TAGGGGTATCGGTACCCT
23875 CTGGGCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.32, T:0.29
Consensus pattern (20 bp):
TAGGGGTATCGGTACCCTAT
Found at i:33356 original size:77 final size:78
Alignment explanation
Indices: 33253--33409 Score: 289
Period size: 77 Copynumber: 2.0 Consensus size: 78
33243 TCGTTTAATA
33253 AAACTTATCTCAAATTCCATGAATCTAACACTAAATAATTTA-TTTTTTTATTCTCTAATATCCT
1 AAACTTATCTCAAATTCCATGAATCTAACACTAAATAATTTATTTTTTTTATTCTCTAATATCCT
33317 TTGTTTGATGTTG
66 TTGTTTGATGTTG
* *
33330 AAACTTGTCTCAAATTCTATGAATCTAACACTAAATAATTTATTTTTTTTATTCTCTAATATCCT
1 AAACTTATCTCAAATTCCATGAATCTAACACTAAATAATTTATTTTTTTTATTCTCTAATATCCT
33395 TTGTTTGATGTTG
66 TTGTTTGATGTTG
33408 AA
1 AA
33410 CGGAGTTTGA
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
77 40 0.52
78 37 0.48
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (78 bp):
AAACTTATCTCAAATTCCATGAATCTAACACTAAATAATTTATTTTTTTTATTCTCTAATATCCT
TTGTTTGATGTTG
Found at i:34255 original size:2 final size:2
Alignment explanation
Indices: 34248--34280 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34238 AGATTAATCA
34248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34281 AAAACATGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34478 original size:2 final size:2
Alignment explanation
Indices: 34471--34504 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
34461 AACTAACTCG
34471 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
34505 TATGGATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44099 original size:36 final size:37
Alignment explanation
Indices: 44058--44138 Score: 101
Period size: 36 Copynumber: 2.2 Consensus size: 37
44048 TTCACCCTAA
* * *
44058 ACCCGACCCGATCTAAATATCACAC-TAAAAAAACCG
1 ACCCGAACCGACCCAAATATCACACTTAAAAAAACCG
* * *
44094 ACCCGAATCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGAACCGACCCAAATATCACACTTAAAAAAACCG
44131 ACCCGAAC
1 ACCCGAAC
44139 AAAATAAAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 20 0.54
37 17 0.46
ACGTcount: A:0.42, C:0.36, G:0.10, T:0.12
Consensus pattern (37 bp):
ACCCGAACCGACCCAAATATCACACTTAAAAAAACCG
Found at i:44253 original size:2 final size:2
Alignment explanation
Indices: 44246--44274 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44236 TTTAATTGAA
44246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44275 AAGGGGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44430 original size:5 final size:5
Alignment explanation
Indices: 44422--44447 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
44412 ATAAAATTTC
44422 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
44448 ATATATGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:47709 original size:29 final size:29
Alignment explanation
Indices: 47663--47747 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
47653 CGTCGTCGAT
** *
47663 GGTTACTATTCCCTGCTACATTAATTCTC
1 GGTTACTATTCCAGGCTACAGTAATTCTC
* * *
47692 GGTTACTATTCTAGGCTAGAGTAATTCTT
1 GGTTACTATTCCAGGCTACAGTAATTCTC
**
47721 TTTTACTATTCCAGGCTACAGTAATTC
1 GGTTACTATTCCAGGCTACAGTAATTC
47748 AGTTATGAGC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (29 bp):
GGTTACTATTCCAGGCTACAGTAATTCTC
Found at i:50985 original size:17 final size:17
Alignment explanation
Indices: 50951--50997 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
50941 TGATCATATT
50951 TTTTTA-ATATTTTAAA
1 TTTTTATATATTTTAAA
50967 TTTTTATATAATTTT-AA
1 TTTTTATAT-ATTTTAAA
*
50984 TTTTTGTATATTTT
1 TTTTTATATATTTT
50998 CTATTAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 11 0.39
17 12 0.43
18 5 0.18
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTTATATATTTTAAA
Found at i:58494 original size:39 final size:39
Alignment explanation
Indices: 58435--58514 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
58425 GGAGATTCTA
* *
58435 TGGTACATCAGCTCAACTTAATAAAAGGTTAATGAAAGG
1 TGGTACAGCAGCTCAACTTAATAAAAGGTCAATGAAAGG
* * *
58474 TGGTACAGCAGCTTAGCTTAATACAAGGTCAATGAAAGG
1 TGGTACAGCAGCTCAACTTAATAAAAGGTCAATGAAAGG
58513 TG
1 TG
58515 TGATCTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (39 bp):
TGGTACAGCAGCTCAACTTAATAAAAGGTCAATGAAAGG
Found at i:70719 original size:2 final size:2
Alignment explanation
Indices: 70712--70741 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
70702 CACGTTTTTA
70712 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
70742 TTCAAAATAG
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):
AT
Found at i:81480 original size:19 final size:20
Alignment explanation
Indices: 81440--81488 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
81430 AAATTTTTAT
*
81440 GTTCGAGTTACAAAATAGAA
1 GTTCGAGTTACAAAATAAAA
81460 GTTCGAGTTAC-AAATAAAA
1 GTTCGAGTTACAAAATAAAA
*
81479 GTTCGCGTTA
1 GTTCGAGTTA
81489 TGAATTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (20 bp):
GTTCGAGTTACAAAATAAAA
Found at i:82787 original size:14 final size:13
Alignment explanation
Indices: 82765--82806 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
82755 AATTAAGTAG
82765 TTTTAAAATATAT
1 TTTTAAAATATAT
*
82778 TTTATAAAATTTAAT
1 TTT-TAAAATAT-AT
82793 TTTTAAAA-ATAT
1 TTTTAAAATATAT
82805 TT
1 TT
82807 AAAATAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 4 0.16
13 4 0.16
14 12 0.48
15 5 0.20
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TTTTAAAATATAT
Found at i:83318 original size:15 final size:14
Alignment explanation
Indices: 83293--83326 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
83283 GTTTTAAATA
83293 TTTAATAATAATTT
1 TTTAATAATAATTT
83307 TTTAATTAATAATTT
1 TTTAA-TAATAATTT
83322 TTTAA
1 TTTAA
83327 AAAGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAATAATAATTT
Found at i:83532 original size:4 final size:4
Alignment explanation
Indices: 83523--83549 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
83513 CAATGCATAT
83523 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
83550 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:92735 original size:24 final size:24
Alignment explanation
Indices: 92694--92740 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
92684 CTCAGATAAT
** * *
92694 TTTAAAATTTTCATTTTTTTAAAA
1 TTTAAAATTTAAAATTTTATAAAA
92718 TTTAAAATTTAAAATTTTATAAA
1 TTTAAAATTTAAAATTTTATAAA
92741 GGTCACACGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTAAAATTTAAAATTTTATAAAA
Found at i:92869 original size:29 final size:29
Alignment explanation
Indices: 92817--92872 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
92807 ATTGAAAACG
* ***
92817 TTAGACACCTAAATTAGTCGAAATATAAT
1 TTAGACACCTAAATAAGAAAAAATATAAT
92846 TTAGACACCTAAATAAGAAAAAATATA
1 TTAGACACCTAAATAAGAAAAAATATA
92873 CAATTTAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (29 bp):
TTAGACACCTAAATAAGAAAAAATATAAT
Found at i:94570 original size:19 final size:19
Alignment explanation
Indices: 94546--94582 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
94536 ATGACTAACA
*
94546 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
94565 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
94583 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:94664 original size:12 final size:12
Alignment explanation
Indices: 94647--94673 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
94637 GATTTTAGAA
94647 AATCGCAATGCG
1 AATCGCAATGCG
94659 AATCGCAATGCG
1 AATCGCAATGCG
94671 AAT
1 AAT
94674 ATGTAAATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (12 bp):
AATCGCAATGCG
Found at i:94767 original size:21 final size:21
Alignment explanation
Indices: 94700--94836 Score: 140
Period size: 21 Copynumber: 6.6 Consensus size: 21
94690 GATTCTGACT
*
94700 ATCGCAACGTGATAATACATA
1 ATCGCAACGCGATAATACATA
**
94721 AT-GACAACGCGATTCTGAC-T-
1 ATCG-CAACGCGATAAT-ACATA
94741 ATCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACATA
*
94762 ATCGCAACACGATAATACATA
1 ATCGCAACGCGATAATACATA
**
94783 ATCGCAACGCGATTCTGAC-T-
1 ATCGCAACGCGATAAT-ACATA
*
94803 ATCGCAATGCGATAATACATA
1 ATCGCAACGCGATAATACATA
*
94824 ATCGCAACTCGAT
1 ATCGCAACGCGAT
94837 TTTGACTATC
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
19 4 0.04
20 28 0.30
21 58 0.62
22 4 0.04
ACGTcount: A:0.38, C:0.24, G:0.15, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATAATACATA
Found at i:94776 original size:62 final size:62
Alignment explanation
Indices: 94700--94871 Score: 233
Period size: 62 Copynumber: 2.8 Consensus size: 62
94690 GATTCTGACT
**
94700 ATCGCAACGTGATAATACATAAT-GACAACGCGATTCTGACTATCGCAACGCGATAATACATA
1 ATCGCAACACGATAATACATAATCG-CAACGCGATTCTGACTATCGCAACGCGATAATACATA
*
94762 ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACTATCGCAATGCGATAATACATA
1 ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
* ** * *
94824 ATCGCAACTCGATTTTGAC-T-ATCGCAACGCGATTCTGATTGTCGCAAC
1 ATCGCAACACGATAAT-ACATAATCGCAACGCGATTCTGACTATCGCAAC
94872 AGGTTTTAGT
Statistics
Matches: 99, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
61 25 0.25
62 71 0.72
63 3 0.03
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.24
Consensus pattern (62 bp):
ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACATA
Found at i:94817 original size:41 final size:41
Alignment explanation
Indices: 94762--94856 Score: 154
Period size: 41 Copynumber: 2.3 Consensus size: 41
94752 ATAATACATA
*
94762 ATCGCAACACGATAATACATAATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
* * *
94803 ATCGCAATGCGATAATACATAATCGCAACTCGATTTTGACT
1 ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
94844 ATCGCAACGCGAT
1 ATCGCAACGCGAT
94857 TCTGATTGTC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (41 bp):
ATCGCAACGCGATAATACATAATCGCAACGCGATTCTGACT
Found at i:94868 original size:20 final size:20
Alignment explanation
Indices: 94680--94871 Score: 124
Period size: 20 Copynumber: 9.4 Consensus size: 20
94670 GAATATGTAA
*
94680 ATCGCAAAGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
94700 ATCGCAACGTGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
94720 AAT-GACAACGCGATTCTGACT
1 -ATCG-CAACGCGATTCTGACT
**
94741 ATCGCAACGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* **
94761 AATCGCAACACGATAAT-ACAT
1 -ATCGCAACGCGATTCTGAC-T
94782 AATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
* **
94803 ATCGCAATGCGATAAT-ACAT
1 ATCGCAACGCGATTCTGAC-T
* *
94823 AATCGCAACTCGATTTTGACT
1 -ATCGCAACGCGATTCTGACT
*
94844 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
*
94864 GTCGCAAC
1 ATCGCAAC
94872 AGGTTTTAGT
Statistics
Matches: 137, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
19 6 0.04
20 65 0.47
21 60 0.44
22 6 0.04
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Done.