Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009496.1 Hibiscus syriacus cultivar Beakdansim tig00114708_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: 61526
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:1090 original size:35 final size:35
Alignment explanation
Indices: 1044--1115 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
1034 CGTCACTAAC
*
1044 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1079 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1114 AG
1 AG
1116 AAATCTTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.31, T:0.08
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:1224 original size:23 final size:23
Alignment explanation
Indices: 1198--1283 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
1188 ATTCAAGTCA
* *
1198 AGTATCATATCAGAATCCATATC
1 AGTATCAGATCAGAATCCATGTC
*
1221 AGTATCAGATTAGAATCCATGTC
1 AGTATCAGATCAGAATCCATGTC
* *
1244 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCATGTC
* *
1267 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
1284 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 41 0.77
24 12 0.23
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATGTC
Found at i:2433 original size:18 final size:18
Alignment explanation
Indices: 2412--2447 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2402 CTTCCATCCG
*
2412 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
2430 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
2448 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:3653 original size:15 final size:15
Alignment explanation
Indices: 3633--3672 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
3623 TGGTCAACGT
3633 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
3648 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
3663 GGGTCAACGG
1 GGGTCAACGG
3673 GTCAGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:3654 original size:8 final size:8
Alignment explanation
Indices: 3614--3688 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
3604 TCAAAGTTTT
3614 GGTCAACAG
1 GGTCAAC-G
3623 TGGTCAACGTG
1 -GGTCAAC--G
3634 GGTCAAC-
1 GGTCAACG
3641 GGTCAACG
1 GGTCAACG
3649 GGTCAAC-
1 GGTCAACG
3656 GGTCAACG
1 GGTCAACG
3664 GGTCAACG
1 GGTCAACG
3672 GGTC-A--
1 GGTCAACG
3677 GGTCAACG
1 GGTCAACG
3685 GGTC
1 GGTC
3689 GGGTCAGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 4 0.07
6 1 0.02
7 15 0.26
8 23 0.40
10 14 0.24
11 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:3693 original size:18 final size:18
Alignment explanation
Indices: 3656--3710 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
3646 ACGGGTCAAC
3656 GGTCAACGGGTCAACGGGTCA
1 GGTCAACGGGT---CGGGTCA
3677 GGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
*
3695 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
3711 AAACGGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:3706 original size:13 final size:13
Alignment explanation
Indices: 3664--3694 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3654 ACGGTCAACG
3664 GGTCAACGGGTCA
1 GGTCAACGGGTCA
*
3677 GGTCAACGGGTCG
1 GGTCAACGGGTCA
3690 GGTCA
1 GGTCA
3695 GGTCAACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:5741 original size:35 final size:35
Alignment explanation
Indices: 5695--5766 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
5685 CGTCACTAAC
*
5695 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
5730 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
5765 AG
1 AG
5767 AAATCTTCCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.31, T:0.08
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:5879 original size:24 final size:23
Alignment explanation
Indices: 5851--5937 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
5841 ATTCAAGTCA
* *
5851 AGTATCATATCAGAATCCATATC
1 AGTATCAGATCAGAATCCATGTC
*
5874 ATGTATCAGATTAGAATCCATGTC
1 A-GTATCAGATCAGAATCCATGTC
* *
5898 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCATGTC
* *
5921 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
5938 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
23 21 0.40
24 32 0.60
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATGTC
Found at i:5937 original size:47 final size:48
Alignment explanation
Indices: 5847--5937 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 48
5837 CATAATTCAA
* * * **
5847 GTCAAGTATCATATCAGAATCCATATCATGTATCAGATTAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
* *
5895 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAAT
5938 TCAAATTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 31 0.86
48 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
Found at i:7087 original size:18 final size:18
Alignment explanation
Indices: 7066--7101 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7056 CTTCCATCCG
*
7066 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
7084 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
7102 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:8313 original size:15 final size:15
Alignment explanation
Indices: 8293--8332 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
8283 TGGTCAACGT
8293 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
8308 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
8323 GGGTCAACGG
1 GGGTCAACGG
8333 GTCAGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:8314 original size:8 final size:8
Alignment explanation
Indices: 8274--8348 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
8264 TCAAAGTTTT
8274 GGTCAACAG
1 GGTCAAC-G
8283 TGGTCAACGTG
1 -GGTCAAC--G
8294 GGTCAAC-
1 GGTCAACG
8301 GGTCAACG
1 GGTCAACG
8309 GGTCAAC-
1 GGTCAACG
8316 GGTCAACG
1 GGTCAACG
8324 GGTCAACG
1 GGTCAACG
8332 GGTC-A--
1 GGTCAACG
8337 GGTCAACG
1 GGTCAACG
8345 GGTC
1 GGTC
8349 GGGTCAGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 4 0.07
6 1 0.02
7 15 0.26
8 23 0.40
10 14 0.24
11 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:8353 original size:18 final size:18
Alignment explanation
Indices: 8316--8370 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
8306 ACGGGTCAAC
8316 GGTCAACGGGTCAACGGGTCA
1 GGTCAACGGGT---CGGGTCA
8337 GGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
*
8355 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
8371 AAACGGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 22 0.67
21 11 0.33
ACGTcount: A:0.18, C:0.22, G:0.42, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:8366 original size:13 final size:13
Alignment explanation
Indices: 8324--8354 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8314 ACGGTCAACG
8324 GGTCAACGGGTCA
1 GGTCAACGGGTCA
*
8337 GGTCAACGGGTCG
1 GGTCAACGGGTCA
8350 GGTCA
1 GGTCA
8355 GGTCAACTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCA
Found at i:20336 original size:19 final size:18
Alignment explanation
Indices: 20312--20374 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 18
20302 GCTGCTGGAA
20312 ACCGGTTCAACCGGTTCTG
1 ACCGGTTCAACCGGTT-TG
** *
20331 ACCGGTTTGACTGGTTTCG
1 ACCGGTTCAACCGGTTT-G
20350 ACCGGTTCGAACCGGTTTG
1 ACCGGTTC-AACCGGTTTG
20369 ACCGGT
1 ACCGGT
20375 CTGACCCGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 1 0.03
19 28 0.78
20 7 0.19
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (18 bp):
ACCGGTTCAACCGGTTTG
Found at i:20372 original size:9 final size:9
Alignment explanation
Indices: 20321--20380 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 9
20311 AACCGGTTCA
20321 ACCGGTTCTG
1 ACCGGTT-TG
20331 ACCGGTTTG
1 ACCGGTTTG
*
20340 ACTGGTTTCG
1 ACCGGTTT-G
*
20350 ACCGGTTCG
1 ACCGGTTTG
20359 AACCGGTTTG
1 -ACCGGTTTG
*
20369 ACCGGTCTG
1 ACCGGTTTG
20378 ACC
1 ACC
20381 CGACCAACCG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
9 21 0.49
10 22 0.51
ACGTcount: A:0.13, C:0.28, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:20411 original size:12 final size:12
Alignment explanation
Indices: 20394--20431 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
20384 CCAACCGACC
20394 TGACCCGACCGT
1 TGACCCGACCGT
20406 TGACCCGACC--
1 TGACCCGACCGT
*
20416 CGACCCGACCGT
1 TGACCCGACCGT
20428 TGAC
1 TGAC
20432 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:20413 original size:22 final size:22
Alignment explanation
Indices: 20388--20431 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
20378 ACCCGACCAA
*
20388 CCGACCTGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
20410 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
20432 TTTCTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:24365 original size:455 final size:455
Alignment explanation
Indices: 23514--24427 Score: 1828
Period size: 455 Copynumber: 2.0 Consensus size: 455
23504 ATTCTACCCC
23514 ATACTTTGCATTATTGGACAATGGCTCCACTCACTCCTATGTATCGAGCTCAGTATCTCAAAACC
1 ATACTTTGCATTATTGGACAATGGCTCCACTCACTCCTATGTATCGAGCTCAGTATCTCAAAACC
23579 TTCAGATTTCGATCGAGAACACTGAAAATACTGTTACAGTTACAAGTCCAGTAGGACAAGCGGTA
66 TTCAGATTTCGATCGAGAACACTGAAAATACTGTTACAGTTACAAGTCCAGTAGGACAAGCGGTA
23644 TTAGTGAATAAAGTATTTCGGCGTTCTCCTCTCGAGGTTCTGATATGATCCAAACTAGCTCCAAT
131 TTAGTGAATAAAGTATTTCGGCGTTCTCCTCTCGAGGTTCTGATATGATCCAAACTAGCTCCAAT
23709 TTTCTCCATGACTTGATCGGTCTATGGACGTTTTTAACTACTGCTTCTAATGGAGTTCTTCCTTA
196 TTTCTCCATGACTTGATCGGTCTATGGACGTTTTTAACTACTGCTTCTAATGGAGTTCTTCCTTA
23774 CCCTATCTTATATTATATCATTTATACATTATATTCTATCATAACCATGCATTCACATGTTAGTA
261 CCCTATCTTATATTATATCATTTATACATTATATTCTATCATAACCATGCATTCACATGTTAGTA
23839 TAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGATCATGTCTCTCATATTATTCAAATA
326 TAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGATCATGTCTCTCATATTATTCAAATA
23904 TATGTTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGA
391 TATGTTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGA
23969 ATACTTTGCATTATTGGACAATGGCTCCACTCACTCCTATGTATCGAGCTCAGTATCTCAAAACC
1 ATACTTTGCATTATTGGACAATGGCTCCACTCACTCCTATGTATCGAGCTCAGTATCTCAAAACC
24034 TTCAGATTTCGATCGAGAACACTGAAAATACTGTTACAGTTACAAGTCCAGTAGGACAAGCGGTA
66 TTCAGATTTCGATCGAGAACACTGAAAATACTGTTACAGTTACAAGTCCAGTAGGACAAGCGGTA
24099 TTAGTGAATAAAGTATTTCGGCGTTCTCCTCTCGAGGTTCTGATATGATCCAAACTAGCTCCAAT
131 TTAGTGAATAAAGTATTTCGGCGTTCTCCTCTCGAGGTTCTGATATGATCCAAACTAGCTCCAAT
24164 TTTCTCCATGACTTGATCGGTCTATGGACGTTTTTAACTACTGCTTCTAATGGAGTTCTTCCTTA
196 TTTCTCCATGACTTGATCGGTCTATGGACGTTTTTAACTACTGCTTCTAATGGAGTTCTTCCTTA
24229 CCCTATCTTATATTATATCATTTATACATTATATTCTATCATAACCATGCATTCACATGTTAGTA
261 CCCTATCTTATATTATATCATTTATACATTATATTCTATCATAACCATGCATTCACATGTTAGTA
24294 TAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGATCATGTCTCTCATATTATTCAAATA
326 TAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGATCATGTCTCTCATATTATTCAAATA
24359 TATGTTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGA
391 TATGTTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGA
24424 ATAC
1 ATAC
24428 CATATTATAT
Statistics
Matches: 459, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
455 459 1.00
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.39
Consensus pattern (455 bp):
ATACTTTGCATTATTGGACAATGGCTCCACTCACTCCTATGTATCGAGCTCAGTATCTCAAAACC
TTCAGATTTCGATCGAGAACACTGAAAATACTGTTACAGTTACAAGTCCAGTAGGACAAGCGGTA
TTAGTGAATAAAGTATTTCGGCGTTCTCCTCTCGAGGTTCTGATATGATCCAAACTAGCTCCAAT
TTTCTCCATGACTTGATCGGTCTATGGACGTTTTTAACTACTGCTTCTAATGGAGTTCTTCCTTA
CCCTATCTTATATTATATCATTTATACATTATATTCTATCATAACCATGCATTCACATGTTAGTA
TAAATTATTATCTTATTATTTCTATCCTATGCTTATTTGATCATGTCTCTCATATTATTCAAATA
TATGTTATGATTACATATCATTTCTTAGGATATTATTATTACATGTTTCCATTTATCATTTATGA
Found at i:33725 original size:19 final size:18
Alignment explanation
Indices: 33706--33768 Score: 90
Period size: 19 Copynumber: 3.4 Consensus size: 18
33696 TTCAACAGGT
33706 TCTGACCGGTTTGACCGG
1 TCTGACCGGTTTGACCGG
*
33724 TTTCGACCGGTTTGACCGG
1 TCT-GACCGGTTTGACCGG
*
33743 TCTGAACCGATTTGACCGG
1 TCTG-ACCGGTTTGACCGG
33762 TCTGACC
1 TCTGACC
33769 CGACCGACCG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.15
19 34 0.85
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (18 bp):
TCTGACCGGTTTGACCGG
Found at i:33731 original size:10 final size:9
Alignment explanation
Indices: 33703--33768 Score: 78
Period size: 9 Copynumber: 7.0 Consensus size: 9
33693 CGGTTCAACA
33703 GGTTCTGACC
1 GGTT-TGACC
33713 GGTTTGACC
1 GGTTTGACC
33722 GGTTTCGACC
1 GGTTT-GACC
33732 GGTTTGACC
1 GGTTTGACC
*
33741 GGTCTGAACC
1 GGTTTG-ACC
*
33751 GATTTGACC
1 GGTTTGACC
*
33760 GGTCTGACC
1 GGTTTGACC
33769 CGACCGACCG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
9 29 0.59
10 20 0.41
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (9 bp):
GGTTTGACC
Found at i:33739 original size:28 final size:28
Alignment explanation
Indices: 33703--33768 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
33693 CGGTTCAACA
* *
33703 GGTTCTGACCGGTTTG-ACCGGTTTCGACC
1 GGTT-TGACCGGTCTGAACCGATTT-GACC
33732 GGTTTGACCGGTCTGAACCGATTTGACC
1 GGTTTGACCGGTCTGAACCGATTTGACC
*
33760 GGTCTGACC
1 GGTTTGACC
33769 CGACCGACCG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 22 0.67
29 11 0.33
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (28 bp):
GGTTTGACCGGTCTGAACCGATTTGACC
Found at i:33784 original size:5 final size:5
Alignment explanation
Indices: 33765--33813 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
33755 TGACCGGTCT
*
33765 GACCC GA-CC GA-CC GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC
33814 GTTGACCGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
7 4 0.10
ACGTcount: A:0.20, C:0.53, G:0.22, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:33801 original size:22 final size:22
Alignment explanation
Indices: 33776--33820 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
33766 ACCCGACCGA
33776 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
33798 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
33820 C
1 C
33821 GTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.51, G:0.22, T:0.09
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:36027 original size:19 final size:18
Alignment explanation
Indices: 36005--36053 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
35995 GGTCGGGTAT
36005 GACCGGTCAAACC-AGTTC
1 GACCGGTCAAACCGA-TTC
*
36023 AGACCGGTTAAACCGATTC
1 -GACCGGTCAAACCGATTC
36042 GAACCGGTCAAA
1 G-ACCGGTCAAA
36054 ACCGGTCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 24 0.92
20 1 0.04
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (18 bp):
GACCGGTCAAACCGATTC
Found at i:36056 original size:10 final size:9
Alignment explanation
Indices: 36006--36068 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 9
35996 GTCGGGTATG
36006 ACCGGTCAA
1 ACCGGTCAA
* *
36015 ACCAGTTCAG
1 ACC-GGTCAA
*
36025 ACCGGTTAA
1 ACCGGTCAA
* *
36034 ACCGATTCGA
1 ACCG-GTCAA
36044 ACCGGTCAAA
1 ACCGGTC-AA
36054 ACCGGTCAA
1 ACCGGTCAA
36063 ACCGGT
1 ACCGGT
36069 TTTCCAGCAG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
9 20 0.49
10 21 0.51
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:43134 original size:9 final size:9
Alignment explanation
Indices: 43116--43184 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
43106 GGTTGGGTCG
*
43116 GGTCAGACC
1 GGTCAAACC
43125 GGTCAAACC
1 GGTCAAACC
*
43134 GGTTCATACC
1 GG-TCAAACC
43144 GGTCAAACC
1 GGTCAAACC
*
43153 GGTTCATACC
1 GG-TCAAACC
* *
43163 GGTCGGAATC
1 GGTC-AAACC
43173 GGTCAAACC
1 GGTCAAACC
43182 GGT
1 GGT
43185 TTTCCAACAG
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 26 0.54
10 22 0.46
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:43146 original size:10 final size:10
Alignment explanation
Indices: 43122--43165 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
43112 GTCGGGTCAG
43122 ACCGG-TCAA
1 ACCGGTTCAA
*
43131 ACCGGTTCAT
1 ACCGGTTCAA
43141 ACCGG-TCAA
1 ACCGGTTCAA
*
43150 ACCGGTTCAT
1 ACCGGTTCAA
43160 ACCGGT
1 ACCGGT
43166 CGGAATCGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
9 13 0.43
10 17 0.57
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:43146 original size:19 final size:19
Alignment explanation
Indices: 43122--43166 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
43112 GTCGGGTCAG
43122 ACCGGTCAAACCGGTTCAT
1 ACCGGTCAAACCGGTTCAT
43141 ACCGGTCAAACCGGTTCAT
1 ACCGGTCAAACCGGTTCAT
43160 ACCGGTC
1 ACCGGTC
43167 GGAATCGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.33, G:0.22, T:0.20
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAT
Found at i:50312 original size:17 final size:17
Alignment explanation
Indices: 50290--50326 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
50280 GTCAAAGGAA
*
50290 GTCAACGGACGGGTCGG
1 GTCAACGGACAGGTCGG
*
50307 GTCAACGGTCAGGTCGG
1 GTCAACGGACAGGTCGG
50324 GTC
1 GTC
50327 GGGTCGGGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.16
Consensus pattern (17 bp):
GTCAACGGACAGGTCGG
Found at i:50370 original size:9 final size:9
Alignment explanation
Indices: 50352--50445 Score: 98
Period size: 9 Copynumber: 10.0 Consensus size: 9
50342 AGTCGGGTCG
*
50352 GGTCAGACC
1 GGTCAAACC
50361 GGTCAAACC
1 GGTCAAACC
50370 GGTCAAACC
1 GGTCAAACC
*
50379 GGTTCGAACC
1 GG-TCAAACC
*
50389 GGTCGGAACC
1 GGTC-AAACC
50399 GGTCAAACC
1 GGTCAAACC
*
50408 GGTCAAACT
1 GGTCAAACC
*
50417 GGTTCGAACC
1 GG-TCAAACC
*
50427 GGTCGGAACC
1 GGTC-AAACC
50437 GGTCAAACC
1 GGTCAAACC
50446 AGTTTTCCAG
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
9 41 0.55
10 33 0.45
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:50390 original size:19 final size:18
Alignment explanation
Indices: 50352--50445 Score: 98
Period size: 19 Copynumber: 5.0 Consensus size: 18
50342 AGTCGGGTCG
*
50352 GGTCAGACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
*
50370 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGG-TCAAACC
*
50389 GGTCGGAACCGGTCAAACC
1 GGTC-AAACCGGTCAAACC
* *
50408 GGTCAAACTGGTTCGAACC
1 GGTCAAACCGG-TCAAACC
*
50427 GGTCGGAACCGGTCAAACC
1 GGTC-AAACCGGTCAAACC
50446 AGTTTTCCAG
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
18 15 0.24
19 36 0.58
20 11 0.18
ACGTcount: A:0.27, C:0.31, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:50401 original size:38 final size:38
Alignment explanation
Indices: 50358--50445 Score: 167
Period size: 38 Copynumber: 2.3 Consensus size: 38
50348 GTCGGGTCAG
50358 ACCGGTCAAACCGGTCAAACCGGTTCGAACCGGTCGGA
1 ACCGGTCAAACCGGTCAAACCGGTTCGAACCGGTCGGA
*
50396 ACCGGTCAAACCGGTCAAACTGGTTCGAACCGGTCGGA
1 ACCGGTCAAACCGGTCAAACCGGTTCGAACCGGTCGGA
50434 ACCGGTCAAACC
1 ACCGGTCAAACC
50446 AGTTTTCCAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.27, C:0.32, G:0.27, T:0.14
Consensus pattern (38 bp):
ACCGGTCAAACCGGTCAAACCGGTTCGAACCGGTCGGA
Found at i:56442 original size:9 final size:9
Alignment explanation
Indices: 56428--56496 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
56418 CTGCTGGAAA
56428 ACCGGTTTG
1 ACCGGTTTG
*
56437 ACCGGTTCG
1 ACCGGTTTG
56446 AACCGGTTTG
1 -ACCGGTTTG
*
56456 ACCGGTCTG
1 ACCGGTTTG
56465 AACCGGTTTG
1 -ACCGGTTTG
*
56475 ACCGGTCTG
1 ACCGGTTTG
*
56484 AACCGGGTTG
1 -ACCGGTTTG
56494 ACC
1 ACC
56497 CGACCCGACT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
9 27 0.54
10 23 0.46
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.25
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:56451 original size:19 final size:19
Alignment explanation
Indices: 56427--56496 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
56417 GCTGCTGGAA
56427 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
56446 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
56465 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
56484 AACCGGGTTGACC
1 AACCGGTTTGACC
56497 CGACCCGACT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 48 0.98
20 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.24
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:56512 original size:17 final size:17
Alignment explanation
Indices: 56490--56530 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
56480 TCTGAACCGG
*
56490 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
56507 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
56524 GTTGACC
1 GTTGACC
56531 GTGACCGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:56537 original size:6 final size:7
Alignment explanation
Indices: 56520--56549 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
56510 GACCCGACCC
56520 GACCGTT
1 GACCGTT
56527 GACCG-T
1 GACCGTT
56533 GACCGTT
1 GACCGTT
56540 GACCGTT
1 GACCGTT
56547 GAC
1 GAC
56550 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:56538 original size:13 final size:13
Alignment explanation
Indices: 56520--56545 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56510 GACCCGACCC
56520 GACCGTTGACCGT
1 GACCGTTGACCGT
56533 GACCGTTGACCGT
1 GACCGTTGACCGT
56546 TGACTTTCTT
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:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:57477 original size:63 final size:63
Alignment explanation
Indices: 57409--57532 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
57399 CTAATGTGAC
* ** * *
57409 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
57472 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
57533 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Done.