Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006396.1 Hibiscus syriacus cultivar Beakdansim tig00015408_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: 128237
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:572 original size:22 final size:18
Alignment explanation
Indices: 529--571 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 18
519 TGGTAATTTT
529 AAAATTTATTTTTTATAA
1 AAAATTTATTTTTTATAA
547 AAAATATTATTATGTTTATAA
1 AAAAT-TTATT-T-TTTATAA
568 AAAA
1 AAAA
572 ACCTAACATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.23
19 5 0.23
20 1 0.05
21 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
AAAATTTATTTTTTATAA
Found at i:6251 original size:14 final size:14
Alignment explanation
Indices: 6232--6261 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6222 AAACGATAGT
*
6232 TTGAAATACATTTG
1 TTGAAAGACATTTG
6246 TTGAAAGACATTTG
1 TTGAAAGACATTTG
6260 TT
1 TT
6262 TCGTTTTTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (14 bp):
TTGAAAGACATTTG
Found at i:6796 original size:2 final size:2
Alignment explanation
Indices: 6791--6823 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
6781 ACACACACAC
6791 AT AT AT AT AT AT AT AT AT AT AT AT A- AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6824 ATCAACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6941 original size:2 final size:2
Alignment explanation
Indices: 6934--6972 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6924 ATAAACAATT
6934 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 T
6973 TATTTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7838 original size:2 final size:2
Alignment explanation
Indices: 7831--7855 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
7821 CTCAGGGTAA
7831 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
7856 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9334 original size:15 final size:15
Alignment explanation
Indices: 9316--9344 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9306 TAATGATTTG
9316 ATGATTAGGGTTTAT
1 ATGATTAGGGTTTAT
9331 ATGATTAGGGTTTA
1 ATGATTAGGGTTTA
9345 GGGTTTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.28, T:0.45
Consensus pattern (15 bp):
ATGATTAGGGTTTAT
Found at i:11451 original size:2 final size:2
Alignment explanation
Indices: 11446--11477 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
11436 AAGGTACAAG
11446 TA 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 TA
11478 AAAGTAAAGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25844 original size:20 final size:21
Alignment explanation
Indices: 25807--25849 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
25797 TTATTTTTAG
25807 TTTAATCCATAAACTTAT-TT
1 TTTAATCCATAAACTTATCTT
* *
25827 TTTAATCCATATATTTATCTT
1 TTTAATCCATAAACTTATCTT
25848 TT
1 TT
25850 CAATAATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTAATCCATAAACTTATCTT
Found at i:29953 original size:121 final size:121
Alignment explanation
Indices: 29704--29945 Score: 360
Period size: 121 Copynumber: 2.0 Consensus size: 121
29694 TTTCTGTGTT
*
29704 CTGCTCTCTTGCTGTTTCTTACATTCTATATTTGTACAAAGCTCTGGATTTTTAGGCAAATCGAT
1 CTGCTCTCTTGCTGTTTCTTACATTCTATATTTGTACAAAGCTCTGGATTTTTAGGCAAATCGAC
* * ** * ***
29769 GTGATTCCTTATCAGTTTAACAAATGCTGGTCGCCGTGTAAACTTTTTTCTGTGTT
66 GTGATTCCTTATAAGTTTAACAAATGCTGGTCGCCATGTAAACTAATATCTGTCAA
29825 CTGCTCTCTTGCTGTTTCTTACATTCTATATTTGTACAAAGCTCTGGATTTTTAGGCAAATCGAC
1 CTGCTCTCTTGCTGTTTCTTACATTCTATATTTGTACAAAGCTCTGGATTTTTAGGCAAATCGAC
** * *
29890 GTGATTCCTTA-AAGTTTAATGAATGCTGGTCGTCATGTAAACTAATATCTTTCAA
66 GTGATTCCTTATAAGTTTAACAAATGCTGGTCGCCATGTAAACTAATATCTGTCAA
29945 C
1 C
29946 AATCTCTCCC
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
120 33 0.31
121 75 0.69
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (121 bp):
CTGCTCTCTTGCTGTTTCTTACATTCTATATTTGTACAAAGCTCTGGATTTTTAGGCAAATCGAC
GTGATTCCTTATAAGTTTAACAAATGCTGGTCGCCATGTAAACTAATATCTGTCAA
Found at i:33155 original size:20 final size:20
Alignment explanation
Indices: 33132--33208 Score: 91
Period size: 20 Copynumber: 3.8 Consensus size: 20
33122 ATTCGCATTG
33132 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
33152 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
33173 AAAATCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATTTTC
33193 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
33209 AGTCTACAGT
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:33248 original size:19 final size:19
Alignment explanation
Indices: 33224--33268 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
33214 ACAGTTGTCG
*
33224 TTGCGATTTTCTAAATTCA
1 TTGCGATTTTCCAAATTCA
*
33243 TTGCGATTTTCCAAATTCG
1 TTGCGATTTTCCAAATTCA
33262 TTGCGAT
1 TTGCGAT
33269 AGTCGTTGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCCAAATTCA
Found at i:33276 original size:12 final size:12
Alignment explanation
Indices: 33259--33284 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
33249 TTTTCCAAAT
33259 TCGTTGCGATAG
1 TCGTTGCGATAG
33271 TCGTTGCGATAG
1 TCGTTGCGATAG
33283 TC
1 TC
33285 TACAGTTGTT
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:0.15, C:0.19, G:0.31, T:0.35
Consensus pattern (12 bp):
TCGTTGCGATAG
Found at i:33298 original size:22 final size:22
Alignment explanation
Indices: 33270--33324 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
33260 CGTTGCGATA
33270 GTCGTTGCGATAGTCTACAGTT
1 GTCGTTGCGATAGTCTACAGTT
*
33292 GTTGTTGCGATAGTCTACAGTT
1 GTCGTTGCGATAGTCTACAGTT
33314 GTCGTTGCGAT
1 GTCGTTGCGAT
33325 TTTTCAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.29, T:0.38
Consensus pattern (22 bp):
GTCGTTGCGATAGTCTACAGTT
Found at i:33452 original size:6 final size:6
Alignment explanation
Indices: 33443--33467 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33433 TTACCATTAT
33443 CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC C
33468 CGAGACGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:33478 original size:5 final size:5
Alignment explanation
Indices: 33468--33504 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
33458 GACCACGACC
33468 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
1 CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CGAGA CG
33505 GCGGCGGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.38, C:0.22, G:0.41, T:0.00
Consensus pattern (5 bp):
CGAGA
Found at i:34106 original size:22 final size:22
Alignment explanation
Indices: 34041--34113 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
34031 TGTTTGGAAA
*
34041 ATCGCAACGACAACTGTAAACT
1 ATCGCAACAACAACTGTAAACT
34063 AT---AACAACGAACTTGTAAACT
1 ATCGCAACAAC-AAC-TGTAAACT
*
34084 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAAACT
34106 ATCGCAAC
1 ATCGCAAC
34114 GAATTTGGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
19 5 0.11
20 3 0.07
21 10 0.23
22 17 0.39
23 3 0.07
24 6 0.14
ACGTcount: A:0.42, C:0.26, G:0.12, T:0.19
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAAACT
Found at i:34131 original size:19 final size:19
Alignment explanation
Indices: 34106--34153 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
34096 ACTGTAGACT
34106 ATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
*
34125 ATTGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAAA
34144 ATCGCAACGA
1 ATCGCAACGA
34154 CAACTGTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
ATCGCAACGAATTTGGAAA
Found at i:34194 original size:20 final size:20
Alignment explanation
Indices: 34166--34234 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
34156 ACTGTAGACT
*
34166 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
34186 ATCGAAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGGAAA
34206 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
34226 ATCACAACG
1 ATCGCAACG
34235 TGATTTTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:34539 original size:10 final size:10
Alignment explanation
Indices: 34524--34553 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
34514 TCTTAGCTTA
34524 ATAAAAAAAT
1 ATAAAAAAAT
34534 ATAAAAAAAT
1 ATAAAAAAAT
34544 A-AAAAAAAT
1 ATAAAAAAAT
34553 A
1 A
34554 ATCTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (10 bp):
ATAAAAAAAT
Found at i:35682 original size:2 final size:2
Alignment explanation
Indices: 35675--35747 Score: 93
Period size: 2 Copynumber: 39.0 Consensus size: 2
35665 TTGTTTGTAT
* *
35675 TA TA TA TA -A T- TA -A TA TA -A AA TA TA AA TA T- 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
35712 TA TA TA 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 TA TA TA
35748 ATCGGGGCGG
Statistics
Matches: 63, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
1 5 0.08
2 58 0.92
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:37869 original size:15 final size:15
Alignment explanation
Indices: 37816--37872 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
37806 CCCGCCCCGT
* **
37816 ATCCGCCCACCCCCC
1 ATCCGCCCGCCCTAC
*
37831 ATCTGCCCGCCCTAC
1 ATCCGCCCGCCCTAC
*
37846 ATCTGCCCGCCCTAC
1 ATCCGCCCGCCCTAC
37861 ATCCGCCCGCCC
1 ATCCGCCCGCCC
37873 AACTAAATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.12, C:0.61, G:0.12, T:0.14
Consensus pattern (15 bp):
ATCCGCCCGCCCTAC
Found at i:39454 original size:15 final size:15
Alignment explanation
Indices: 39434--39490 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
39424 AACCGGATAT
39434 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
**
39449 CGGGTACCCGTAAAATC
1 CGGGTACCCG-ATTA-C
*
39466 TGGGTACCCGATTAC
1 CGGGTACCCGATTAC
39481 CGGGTACCCG
1 CGGGTACCCG
39491 TAACATCCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.21, C:0.32, G:0.28, T:0.19
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:39476 original size:32 final size:32
Alignment explanation
Indices: 39434--39502 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
39424 AACCGGATAT
39434 CGGGTACCCGATTACCGGGTACCCGTAAAATC
1 CGGGTACCCGATTACCGGGTACCCGTAAAATC
* *
39466 TGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCCGATTACCGGGTACCCGTAAAATC
39498 CGGGT
1 CGGGT
39503 CGAGACACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (32 bp):
CGGGTACCCGATTACCGGGTACCCGTAAAATC
Found at i:39502 original size:17 final size:17
Alignment explanation
Indices: 39448--39502 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
39438 TACCCGATTA
39448 CCGGGTACCCGTAAAAT
1 CCGGGTACCCGTAAAAT
* **
39465 CTGGGTACCCG-ATTA-
1 CCGGGTACCCGTAAAAT
*
39480 CCGGGTACCCGTAACAT
1 CCGGGTACCCGTAAAAT
39497 CCGGGT
1 CCGGGT
39503 CGAGACACGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 10 0.33
16 4 0.13
17 16 0.53
ACGTcount: A:0.22, C:0.31, G:0.27, T:0.20
Consensus pattern (17 bp):
CCGGGTACCCGTAAAAT
Found at i:54489 original size:2 final size:2
Alignment explanation
Indices: 54482--54511 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
54472 CGGCTACCCA
*
54482 AT AT AT AT AT GT 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
54512 GATGATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59137 original size:2 final size:2
Alignment explanation
Indices: 59130--59174 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
59120 CAAGGATAAT
59130 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
59172 AG A
1 AG A
59175 AGGAAAGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:63435 original size:29 final size:29
Alignment explanation
Indices: 63403--63488 Score: 163
Period size: 29 Copynumber: 3.0 Consensus size: 29
63393 GCATCTATAC
*
63403 TTGATTTGAGCTTGAAACTGATTATCTAT
1 TTGATTTGAGCTTCAAACTGATTATCTAT
63432 TTGATTTGAGCTTCAAACTGATTATCTAT
1 TTGATTTGAGCTTCAAACTGATTATCTAT
63461 TTGATTTGAGCTTCAAACTGATTATCTA
1 TTGATTTGAGCTTCAAACTGATTATCTA
63489 GGTTTACTGG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (29 bp):
TTGATTTGAGCTTCAAACTGATTATCTAT
Found at i:65399 original size:6 final size:6
Alignment explanation
Indices: 65388--65427 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
65378 GATCTGATTC
65388 AGATGG AGATGG AGATGG AGATGG AGATGG AGATGG AGAT
1 AGATGG AGATGG AGATGG AGATGG AGATGG AGATGG AGAT
65428 AAGTGATAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.17
Consensus pattern (6 bp):
AGATGG
Found at i:67348 original size:13 final size:13
Alignment explanation
Indices: 67330--67355 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67320 GAAACGAACT
67330 TATAAAATTTTAA
1 TATAAAATTTTAA
67343 TATAAAATTTTAA
1 TATAAAATTTTAA
67356 GAGAATATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATAAAATTTTAA
Found at i:68329 original size:69 final size:69
Alignment explanation
Indices: 68218--68355 Score: 267
Period size: 69 Copynumber: 2.0 Consensus size: 69
68208 GAAAATCATC
*
68218 CCTAAACATATATTTATAAATATTGTGTATCTTTTAGATTGGGACATTTCATCTCCTCCATGAGA
1 CCTAAACATATATTTATAAATATTGTGTATCTTTTAGATTGGGACATTTCATCTCCTCCACGAGA
68283 TCAA
66 TCAA
68287 CCTAAACATATATTTATAAATATTGTGTATCTTTTAGATTGGGACATTTCATCTCCTCCACGAGA
1 CCTAAACATATATTTATAAATATTGTGTATCTTTTAGATTGGGACATTTCATCTCCTCCACGAGA
68352 TCAA
66 TCAA
68356 TTGGGTTTTC
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (69 bp):
CCTAAACATATATTTATAAATATTGTGTATCTTTTAGATTGGGACATTTCATCTCCTCCACGAGA
TCAA
Found at i:68384 original size:2 final size:2
Alignment explanation
Indices: 68377--68424 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
68367 TTTGGAGACG
68377 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
68419 AT AT AT
1 AT AT AT
68425 TTCTAAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71663 original size:60 final size:59
Alignment explanation
Indices: 71585--71698 Score: 131
Period size: 60 Copynumber: 1.9 Consensus size: 59
71575 GGTCCCAAAT
* * *
71585 TTTTTGAATATTCCAATTTCATCACC-AAACTATGGCTCTCATTCTAAATTAGTCCTTACA
1 TTTTGGAACATTCCAATTT-ATCACCTAAACTATGAC-CTCATTCTAAATTAGTCCTTACA
* * * * *
71645 TTTTGGAACATTCTAATTTTTTACCTAAACTATGACCTCTTTCTAAATTGGTCC
1 TTTTGGAACATTCCAATTTATCACCTAAACTATGACCTCATTCTAAATTAGTCC
71699 CAGACTTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
59 20 0.44
60 25 0.56
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (59 bp):
TTTTGGAACATTCCAATTTATCACCTAAACTATGACCTCATTCTAAATTAGTCCTTACA
Found at i:73412 original size:17 final size:17
Alignment explanation
Indices: 73390--73422 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
73380 CAATATCACA
73390 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
73407 ATATTATATTTTATAT
1 ATATTATATTTTATAT
73423 AAATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:88048 original size:16 final size:16
Alignment explanation
Indices: 88024--88074 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
88014 CAAATGTATC
88024 AAATCAATAGGTATGA
1 AAATCAATAGGTATGA
* ** *
88040 AAATTAATATATAT-C
1 AAATCAATAGGTATGA
88055 AAATCAATAGGTATGA
1 AAATCAATAGGTATGA
88071 AAAT
1 AAAT
88075 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 11 0.42
16 15 0.58
ACGTcount: A:0.53, C:0.06, G:0.12, T:0.29
Consensus pattern (16 bp):
AAATCAATAGGTATGA
Found at i:97464 original size:12 final size:12
Alignment explanation
Indices: 97447--97471 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
97437 ATAAAATCAG
97447 TAAAAAATTATT
1 TAAAAAATTATT
97459 TAAAAAATTATT
1 TAAAAAATTATT
97471 T
1 T
97472 TTTTACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAAAAATTATT
Found at i:98998 original size:29 final size:27
Alignment explanation
Indices: 98946--99005 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
98936 TTACGGAATG
98946 AAACGTTAGACACCAAACAAAAACTAAA
1 AAACGTTAGACACCAAACAAAAAC-AAA
* * **
98974 TAAACGTTAGGCACTAAACTGAAACAAA
1 -AAACGTTAGACACCAAACAAAAACAAA
99002 AAAC
1 AAAC
99006 ATACGTTGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.15
28 3 0.11
29 20 0.74
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.13
Consensus pattern (27 bp):
AAACGTTAGACACCAAACAAAAACAAA
Found at i:99842 original size:31 final size:31
Alignment explanation
Indices: 99779--99842 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
99769 TAGTGATCAC
* * *
99779 ATCTTAGTTAAATGAAAACAAAATTTATCAT
1 ATCTTAATTAAATGAAAACAAAATGTACCAT
*
99810 ATCTTAATTAAATGAAAACGAAA-GTACCCAT
1 ATCTTAATTAAATGAAAACAAAATGTA-CCAT
99841 AT
1 AT
99843 ATCATAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.48, C:0.12, G:0.08, T:0.31
Consensus pattern (31 bp):
ATCTTAATTAAATGAAAACAAAATGTACCAT
Found at i:101619 original size:2 final size:2
Alignment explanation
Indices: 101577--101606 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
101567 AATATATATA
101577 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
101607 CGCGCGCGTG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:105869 original size:15 final size:14
Alignment explanation
Indices: 105822--105873 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
105812 ATAGTTATTT
105822 AAATATTAAAAATA
1 AAATATTAAAAATA
* *
105836 GAATATTCTAGAAAT-
1 AAATA-T-TAAAAATA
105851 AAATATTAAAATATA
1 AAATATTAAAA-ATA
105866 AAATATTA
1 AAATATTA
105874 GAGAGCCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 13 0.43
16 6 0.20
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (14 bp):
AAATATTAAAAATA
Found at i:106906 original size:18 final size:19
Alignment explanation
Indices: 106883--106919 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
106873 CCAGTAATCC
106883 TATTCC-CTGATAATCTTT
1 TATTCCACTGATAATCTTT
106901 TATTCCTACTGATAATCTT
1 TATTCC-ACTGATAATCTT
106920 ACATTCCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTCCACTGATAATCTTT
Found at i:106925 original size:20 final size:20
Alignment explanation
Indices: 106889--106926 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
106879 ATCCTATTCC
**
106889 CTGATAATCTTTTATTCCTA
1 CTGATAATCTTACATTCCTA
106909 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
106927 CTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.24, G:0.05, T:0.45
Consensus pattern (20 bp):
CTGATAATCTTACATTCCTA
Found at i:108138 original size:15 final size:15
Alignment explanation
Indices: 108101--108157 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
108091 TCGCACTATA
108101 AAATTTTTA-ATTTTT
1 AAATTTTTATA-TTTT
*
108116 AATTTTTTTATATTTT
1 AA-ATTTTTATATTTT
*
108132 ATA-TTTTAT-TTTT
1 AAATTTTTATATTTT
108145 AAATTTTT-TATTT
1 AAATTTTTATATTT
108158 ATTATCTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
13 7 0.21
14 13 0.38
15 2 0.06
16 11 0.32
17 1 0.03
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
AAATTTTTATATTTT
Found at i:108145 original size:20 final size:20
Alignment explanation
Indices: 108120--108157 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
108110 ATTTTTAATT
*
108120 TTTTTATATTTTATATTTTA
1 TTTTTAAATTTTATATTTTA
*
108140 TTTTTAAATTTTTTATTT
1 TTTTTAAATTTTATATTT
108158 ATTATCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTAAATTTTATATTTTA
Found at i:109864 original size:23 final size:21
Alignment explanation
Indices: 109828--109883 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
109818 ATATTTCAAA
* *
109828 AAAAT-AATAATTAATGAAACTT
1 AAAATCAATATTTAAT--AACTC
*
109850 AAAATCTATATTTAATAACTC
1 AAAATCAATATTTAATAACTC
109871 AAAATCAATATTT
1 AAAATCAATATTT
109884 CTAATCATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 16 0.55
22 5 0.17
23 8 0.28
ACGTcount: A:0.54, C:0.09, G:0.02, T:0.36
Consensus pattern (21 bp):
AAAATCAATATTTAATAACTC
Found at i:117260 original size:21 final size:20
Alignment explanation
Indices: 117234--117272 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
117224 AATATATTCA
117234 TTATTTTTATTATAATTTTTT
1 TTATTTTTATTA-AATTTTTT
117255 TTATTTTTATTAAATTTT
1 TTATTTTTATTAAATTTT
117273 ACAATATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTTATTAAATTTTTT
Found at i:119535 original size:2 final size:2
Alignment explanation
Indices: 119528--119558 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
119518 CCAGAATCTC
119528 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
119559 ATAGTCAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:119864 original size:2 final size:2
Alignment explanation
Indices: 119857--119903 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
119847 ACTTTGAGCA
119857 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
119899 AT AT A
1 AT AT A
119904 AAGCATGAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:123255 original size:59 final size:60
Alignment explanation
Indices: 123132--123260 Score: 170
Period size: 59 Copynumber: 2.2 Consensus size: 60
123122 AATTAGTCTT
* * * * * * * *
123132 TAAACTTTTAAACATTTTGATTTCATCCCAAAACTATGACTTTCATTCTAAATCAGTCCT
1 TAAACTTTTGAACATTCTAATTTCATACCAAAACTATGAATATCATTCTAAATCAATCCC
*
123192 TAAACTTTTGAACATTCTAATTTCATACC-AAACTATGAATATCATTCTAAATTAATCCC
1 TAAACTTTTGAACATTCTAATTTCATACCAAAACTATGAATATCATTCTAAATCAATCCC
123251 TAAACTTTTG
1 TAAACTTTTG
123261 CATATCCAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 35 0.58
60 25 0.42
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAACTTTTGAACATTCTAATTTCATACCAAAACTATGAATATCATTCTAAATCAATCCC
Found at i:123282 original size:59 final size:59
Alignment explanation
Indices: 123151--123282 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 59
123141 AAACATTTTG
* * * * * *
123151 ATTTCATCCCAAAACTATGACTTTCATTCTAAATCAGTCCTTAAACTTTTGAACATTCTA
1 ATTTCATCCCCAAACTATGAATATCATTCTAAATCAATCCCTAAACTTTTG-ACATTCCA
* *
123211 ATTTCAT-ACCAAACTATGAATATCATTCTAAATTAATCCCTAAACTTTTG-CATATCCA
1 ATTTCATCCCCAAACTATGAATATCATTCTAAATCAATCCCTAAACTTTTGACAT-TCCA
*
123269 ATTTTATCCCCAAA
1 ATTTCATCCCCAAA
123283 TTCATCCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
57 3 0.05
58 9 0.15
59 41 0.68
60 7 0.12
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (59 bp):
ATTTCATCCCCAAACTATGAATATCATTCTAAATCAATCCCTAAACTTTTGACATTCCA
Found at i:126307 original size:23 final size:23
Alignment explanation
Indices: 126281--126328 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
126271 TTTTAGTAAT
126281 TTTGTCTTCATGACACGATTT-TC
1 TTTG-CTTCATGACACGATTTCTC
* *
126304 TTTGCTTTATGTCACGATTTCTC
1 TTTGCTTCATGACACGATTTCTC
126327 TT
1 TT
126329 ACCTTTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.15, C:0.21, G:0.12, T:0.52
Consensus pattern (23 bp):
TTTGCTTCATGACACGATTTCTC
Done.