Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008688.1 Hibiscus syriacus cultivar Beakdansim tig00111712_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: 67242
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2339 original size:23 final size:23
Alignment explanation
Indices: 2313--2361 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
2303 ATAAAGAACC
*
2313 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
2336 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
2359 AAA
1 AAA
2362 CTAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:5670 original size:20 final size:20
Alignment explanation
Indices: 5645--5689 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
5635 GAGAAAAAGT
*
5645 AAAAGTGAAAAATGAAATAG
1 AAAAGTGAAAAATGAAAGAG
* **
5665 AAAAGTTAAGGATGAAAGAG
1 AAAAGTGAAAAATGAAAGAG
5685 AAAAG
1 AAAAG
5690 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.13
Consensus pattern (20 bp):
AAAAGTGAAAAATGAAAGAG
Found at i:11998 original size:16 final size:16
Alignment explanation
Indices: 11979--12018 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
11969 TGAAAAGTGG
11979 TAAAAAAGAAAATAAA
1 TAAAAAAGAAAATAAA
*
11995 TAAAAAATAAAATAAA
1 TAAAAAAGAAAATAAA
12011 -AAAAAAGA
1 TAAAAAAGA
12019 TAATCCTCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.12
Consensus pattern (16 bp):
TAAAAAAGAAAATAAA
Found at i:12523 original size:23 final size:23
Alignment explanation
Indices: 12497--12545 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
12487 ATAAAGAACC
*
12497 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
12520 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
12543 AAA
1 AAA
12546 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:22567 original size:29 final size:30
Alignment explanation
Indices: 22498--22556 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
22488 AATTTAAGGC
22498 AAAATGGTTTTTGGACTTGAATTGAATTTAA
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAA
22529 AAAATGTTTTTGGACTT-AATTGAATTTA
1 AAAATGTTTTTGGACTTGAATTGAATTTA
22557 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.39
30 12 0.43
31 5 0.18
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAA
Found at i:22693 original size:17 final size:16
Alignment explanation
Indices: 22671--22735 Score: 78
Period size: 17 Copynumber: 4.0 Consensus size: 16
22661 TATTGCTCGG
*
22671 ATGGTATCTATACCCCC
1 ATGGTATCGATA-CCCC
22688 ATGGTATCGATA-CCC
1 ATGGTATCGATACCCC
22703 ATGGTATCGATACCCC
1 ATGGTATCGATACCCC
* *
22719 AAGTGTATCTATACCCC
1 ATG-GTATCGATACCCC
22736 CTGGCTGCAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
15 15 0.35
16 5 0.12
17 23 0.53
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (16 bp):
ATGGTATCGATACCCC
Found at i:22705 original size:15 final size:15
Alignment explanation
Indices: 22671--22717 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
22661 TATTGCTCGG
*
22671 ATGGTATCTATACCCCC
1 ATGGTATCGATA--CCC
22688 ATGGTATCGATACCC
1 ATGGTATCGATACCC
22703 ATGGTATCGATACCC
1 ATGGTATCGATACCC
22718 CAAGTGTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 18 0.62
17 11 0.38
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (15 bp):
ATGGTATCGATACCC
Found at i:22727 original size:32 final size:32
Alignment explanation
Indices: 22671--22734 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
22661 TATTGCTCGG
* *
22671 ATGGTATCTATACCCCCATGGTATCGATACCC
1 ATGGTATCGATACCCCAATGGTATCGATACCC
*
22703 ATGGTATCGATACCCCAA-GTGTATCTATACCC
1 ATGGTATCGATACCCCAATG-GTATCGATACCC
22735 CCTGGCTGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.28
Consensus pattern (32 bp):
ATGGTATCGATACCCCAATGGTATCGATACCC
Found at i:22793 original size:21 final size:21
Alignment explanation
Indices: 22767--22808 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
22757 ATTTGAATTT
22767 TATGAAG-GAGTACCGATACCC
1 TATGAAGAG-GTACCGATACCC
22788 TATGAAGAGGTACCGATACCC
1 TATGAAGAGGTACCGATACCC
22809 CCTGTACGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (21 bp):
TATGAAGAGGTACCGATACCC
Found at i:22875 original size:20 final size:22
Alignment explanation
Indices: 22837--22876 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
22827 TTTTAGCAGA
22837 AAAATCATCCCCAAACGGATCC
1 AAAATCATCCCCAAACGGATCC
22859 AAAA-CATCCCC-AACGGAT
1 AAAATCATCCCCAAACGGAT
22877 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.42, C:0.35, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGATCC
Found at i:23133 original size:34 final size:32
Alignment explanation
Indices: 23090--23159 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
23080 TTTTGTAAAG
* *
23090 GGGAAAGGTTCTAGCTTATCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
23124 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
23156 GGGA
1 GGGA
23160 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:25326 original size:34 final size:30
Alignment explanation
Indices: 25288--25356 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
25278 TTGATATAAC
25288 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
25322 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
25351 AATTTA
1 AATTTA
25357 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:25367 original size:29 final size:30
Alignment explanation
Indices: 25297--25356 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
25287 CAATTTAAGG
25297 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
25328 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
25357 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:25485 original size:22 final size:21
Alignment explanation
Indices: 25436--25487 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
25426 TATGGTACCG
25436 ATACCCCCTGCAGGGGTATCC
1 ATACCCCCTGCAGGGGTATCC
25457 ATACCCCCTGCAGGGGTATCC
1 ATACCCCCTGCAGGGGTATCC
25478 ATACCCCCTG
1 ATACCCCCTG
25488 AAGGCTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.19, C:0.40, G:0.21, T:0.19
Consensus pattern (21 bp):
ATACCCCCTGCAGGGGTATCC
Found at i:25515 original size:16 final size:16
Alignment explanation
Indices: 25491--25530 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
25481 CCCCCTGAAG
* *
25491 GCTCAAATTTCATATT
1 GCTCGAATTCCATATT
25507 GCTCGAATTCCATATT
1 GCTCGAATTCCATATT
25523 GCTCGAAT
1 GCTCGAAT
25531 GGTACCCATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (16 bp):
GCTCGAATTCCATATT
Found at i:26737 original size:27 final size:27
Alignment explanation
Indices: 26707--26762 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
26697 CACTTAGAGG
*
26707 TTCAACTTCACTATCCTCGTTTATGGA
1 TTCAACTTCACTATCCTCGTTCATGGA
* * *
26734 TTCACCTTCATTGTCCTCGTTCATGGA
1 TTCAACTTCACTATCCTCGTTCATGGA
26761 TT
1 TT
26763 TATTTCTACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.27, G:0.12, T:0.43
Consensus pattern (27 bp):
TTCAACTTCACTATCCTCGTTCATGGA
Found at i:29541 original size:8 final size:8
Alignment explanation
Indices: 29528--29580 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
29518 CAACCCGACA
29528 TGACCCGT
1 TGACCCGT
*
29536 TGACCCGACC
1 TGACCCG--T
*
29546 CGACCCGT
1 TGACCCGT
29554 TGA-CCGT
1 TGACCCGT
29561 TGACCCGT
1 TGACCCGT
29569 TGA-CCGT
1 TGACCCGT
29576 TGACC
1 TGACC
29581 GGAGTTGACC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 14 0.38
8 17 0.46
10 6 0.16
ACGTcount: A:0.15, C:0.40, G:0.25, T:0.21
Consensus pattern (8 bp):
TGACCCGT
Found at i:29543 original size:18 final size:18
Alignment explanation
Indices: 29520--29558 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29510 ACCGGTCACA
*
29520 ACCCGACATGACCCGTTG
1 ACCCGACACGACCCGTTG
*
29538 ACCCGACCCGACCCGTTG
1 ACCCGACACGACCCGTTG
29556 ACC
1 ACC
29559 GTTGACCCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.46, G:0.21, T:0.13
Consensus pattern (18 bp):
ACCCGACACGACCCGTTG
Found at i:29562 original size:7 final size:7
Alignment explanation
Indices: 29550--29581 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
29540 CCGACCCGAC
29550 CCGTTGA
1 CCGTTGA
29557 CCGTTGA
1 CCGTTGA
29564 CCCGTTGA
1 -CCGTTGA
29572 CCGTTGA
1 CCGTTGA
29579 CCG
1 CCG
29582 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:29567 original size:15 final size:15
Alignment explanation
Indices: 29547--29580 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
29537 GACCCGACCC
29547 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
29562 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
29577 GACC
1 GACC
29581 GGAGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.35, G:0.26, T:0.24
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:32139 original size:24 final size:24
Alignment explanation
Indices: 32043--32151 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
32033 GAATATTTTA
* *
32043 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
32067 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
32091 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
32115 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
32139 TTTGATTTCTGAT
1 TCTGATATCTGAT
32152 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:34319 original size:12 final size:13
Alignment explanation
Indices: 34299--34334 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
34289 CCGTTGAACC
34299 GACCCGACCCGTT
1 GACCCGACCCGTT
*
34312 TA-CCGACCCGTT
1 GACCCGACCCGTT
34324 GACCCGACCCG
1 GACCCGACCCG
34335 ACCCGTTGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:34322 original size:30 final size:30
Alignment explanation
Indices: 34281--34346 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
34271 GTCACAACCC
34281 GACCTGACCCGTTGAACCGACCCGACCCGTT
1 GACC-GACCCGTTGAACCGACCCGACCCGTT
* *
34312 TACCGACCCGTTGACCCGACCCGACCCGTT
1 GACCGACCCGTTGAACCGACCCGACCCGTT
34342 GACCG
1 GACCG
34347 TTGACCCGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.18, C:0.44, G:0.23, T:0.15
Consensus pattern (30 bp):
GACCGACCCGTTGAACCGACCCGACCCGTT
Found at i:34337 original size:18 final size:18
Alignment explanation
Indices: 34277--34345 Score: 69
Period size: 18 Copynumber: 4.2 Consensus size: 18
34267 ACCGGTCACA
*
34277 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
34295 AACCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
34312 ----TA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
34325 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
34343 ACC
1 ACC
34346 GTTGACCCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 10 0.24
13 1 0.02
17 1 0.02
18 29 0.71
ACGTcount: A:0.19, C:0.46, G:0.20, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:34347 original size:25 final size:28
Alignment explanation
Indices: 34286--34354 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
34276 AACCCGACCT
*
34286 GACCCGTTGAACCGACCCGACCCGTTTACC
1 GACCCGTTGACCCGACCCGACCCGTTT--C
34316 GACCCGTTGACCCGACCCGACCCG-TT-
1 GACCCGTTGACCCGACCCGACCCGTTTC
34342 GA-CCGTTGACCCG
1 GACCCGTTGACCCG
34355 TTGACCGCTG
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 11 0.29
26 2 0.05
29 2 0.05
30 23 0.61
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.16
Consensus pattern (28 bp):
GACCCGTTGACCCGACCCGACCCGTTTC
Found at i:34354 original size:15 final size:15
Alignment explanation
Indices: 34334--34367 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
34324 GACCCGACCC
*
34334 GACCCGTTGACCGTT
1 GACCCGTTGACCGCT
34349 GACCCGTTGACCGCT
1 GACCCGTTGACCGCT
34364 GACC
1 GACC
34368 GGAGTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.38, G:0.26, T:0.21
Consensus pattern (15 bp):
GACCCGTTGACCGCT
Found at i:36925 original size:24 final size:24
Alignment explanation
Indices: 36829--36937 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
36819 GAATATTTTA
* *
36829 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
36853 TTTGACATCTGATCTGAAATCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
36877 TCTGAT-TCCTAACCTGGATTCTGT
1 TCTGATAT-CTGATCTGAATTCTGT
*
36901 TCTGATATCTGATCTGAATTATGT
1 TCTGATATCTGATCTGAATTCTGT
* *
36925 TTTGATTTCTGAT
1 TCTGATATCTGAT
36938 ATCTCCGTTT
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
23 1 0.02
24 64 0.97
25 1 0.02
ACGTcount: A:0.20, C:0.16, G:0.17, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:39573 original size:2 final size:2
Alignment explanation
Indices: 39566--39597 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39556 GCAAAAGAAT
39566 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
39598 GAGAGAGAGA
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:44594 original size:33 final size:33
Alignment explanation
Indices: 44555--44617 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
44545 TTGTGTTGTT
* *
44555 CGTTTATGTTCATTTGTTGTGTTCGTTTATGTC
1 CGTTTATGTTCATTTATTATGTTCGTTTATGTC
*
44588 CGTTTATGTTTATTTATTATGTTCGTTTAT
1 CGTTTATGTTCATTTATTATGTTCGTTTAT
44618 TTTCTTTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.13, C:0.10, G:0.17, T:0.60
Consensus pattern (33 bp):
CGTTTATGTTCATTTATTATGTTCGTTTATGTC
Found at i:46675 original size:22 final size:21
Alignment explanation
Indices: 46644--46691 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
46634 TTACTCCAAC
* * *
46644 TTCTTCTATTGTTGTTTTTGA
1 TTCTTATATTCTTGTTTTAGA
46665 GTTCTTATATTCTTGTTTTAGA
1 -TTCTTATATTCTTGTTTTAGA
46687 TTCTT
1 TTCTT
46692 GATTTGGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.65
Consensus pattern (21 bp):
TTCTTATATTCTTGTTTTAGA
Found at i:48246 original size:42 final size:44
Alignment explanation
Indices: 48187--48296 Score: 131
Period size: 42 Copynumber: 2.6 Consensus size: 44
48177 CACTTGGAGA
*
48187 CACTAAAGACAAGATAATTAGTA-GG-ATTTGTGGC-CAAAAGGC
1 CACTAAAGACAAGATAATTAG-ACGGCATTTGTGGCTAAAAAGGC
* *
48229 CACTAAAGACAAGATAATTA-ACGGCGTTTGTGGCTAAAAATGC
1 CACTAAAGACAAGATAATTAGACGGCATTTGTGGCTAAAAAGGC
* *
48272 CACTACAGACAAGAGAATTAG-CGGC
1 CACTAAAGACAAGATAATTAGACGGC
48297 GTTTATAGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 1 0.02
41 2 0.03
42 28 0.47
43 28 0.47
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.20
Consensus pattern (44 bp):
CACTAAAGACAAGATAATTAGACGGCATTTGTGGCTAAAAAGGC
Found at i:48291 original size:43 final size:42
Alignment explanation
Indices: 48187--48321 Score: 130
Period size: 43 Copynumber: 3.2 Consensus size: 42
48177 CACTTGGAGA
* * * *
48187 CACTAAAGACAAGATAATTAGTA-GG-ATTTGTGGCCAAAAGGC
1 CACTAAAGACAAGAGAATTA--ACGGCGTTTGTGGCAAAAATGC
*
48229 CACTAAAGACAAGATAATTAACGGCGTTTGTGGCTAAAAATGC
1 CACTAAAGACAAGAGAATTAACGGCGTTTGTGGC-AAAAATGC
* * * * *
48272 CACTACAGACAAGAGAATTAGCGGCGTTTATAGCCAGAAATGC
1 CACTAAAGACAAGAGAATTAACGGCGTTTGT-GGCAAAAATGC
48315 CACTAAA
1 CACTAAA
48322 TATATTATAA
Statistics
Matches: 79, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
40 1 0.01
41 2 0.03
42 28 0.35
43 46 0.58
44 2 0.03
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.21
Consensus pattern (42 bp):
CACTAAAGACAAGAGAATTAACGGCGTTTGTGGCAAAAATGC
Found at i:49839 original size:9 final size:9
Alignment explanation
Indices: 49825--49862 Score: 60
Period size: 9 Copynumber: 4.2 Consensus size: 9
49815 TGTTGTTAAA
49825 GAGATGGAG
1 GAGATGGAG
49834 GAGATGGA-
1 GAGATGGAG
49842 GAGAATGGAG
1 GAG-ATGGAG
49852 GAGATGGAG
1 GAGATGGAG
49861 GA
1 GA
49863 TAACGAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 3 0.11
9 21 0.78
10 3 0.11
ACGTcount: A:0.37, C:0.00, G:0.53, T:0.11
Consensus pattern (9 bp):
GAGATGGAG
Found at i:59589 original size:89 final size:91
Alignment explanation
Indices: 59426--59622 Score: 319
Period size: 89 Copynumber: 2.2 Consensus size: 91
59416 CTAGAACTGC
* *
59426 GTCCGTAGGGCTTACCCTAAGCACACAACAAAAGGGAGACAACCTAAGGATATTCCTTGGGGCCT
1 GTCCGTAAGGCTTACCCTAAGCACACAACAAAAGGGAGACAACCTAAGGATATGCCTTGGGGCCT
59491 ATGGGCCTACCCAAGGATATCCTTAG
66 ATGGGCCTACCCAAGGATATCCTTAG
*
59517 GTCCGTAAGG-TTACCCTAAGCACACAAC-AAAGGTA-ACCAACCTAAGGATATGCCTTGGGGCC
1 GTCCGTAAGGCTTACCCTAAGCACACAACAAAAGGGAGA-CAACCTAAGGATATGCCTTGGGGCC
*
59579 TATGGGCCTACCCAAGGGTATCCTTAG
65 TATGGGCCTACCCAAGGATATCCTTAG
59606 GTCCGTAAGGACTTACC
1 GTCCGTAAGG-CTTACC
59623 AGCTGGATCA
Statistics
Matches: 99, Mismatches: 4, Indels: 6
0.91 0.04 0.06
Matches are distributed among these distances:
88 1 0.01
89 66 0.67
90 18 0.18
91 14 0.14
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (91 bp):
GTCCGTAAGGCTTACCCTAAGCACACAACAAAAGGGAGACAACCTAAGGATATGCCTTGGGGCCT
ATGGGCCTACCCAAGGATATCCTTAG
Done.