Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005085.1 Hibiscus syriacus cultivar Beakdansim tig00011424_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: 106123
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:696 original size:19 final size:19
Alignment explanation
Indices: 661--699 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
651 GTAGTATTTG
**
661 TTTTTTATATTGTTAAATA
1 TTTTTTATATTCATAAATA
680 TTTTTTATATTCATAAATA
1 TTTTTTATATTCATAAATA
699 T
1 T
700 ATAATAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTTTATATTCATAAATA
Found at i:8475 original size:12 final size:12
Alignment explanation
Indices: 8458--8482 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8448 GCAATCATTC
8458 TTTACATTTTTT
1 TTTACATTTTTT
8470 TTTACATTTTTT
1 TTTACATTTTTT
8482 T
1 T
8483 ACATTTATTT
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:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTACATTTTTT
Found at i:12035 original size:11 final size:10
Alignment explanation
Indices: 12015--12070 Score: 67
Period size: 11 Copynumber: 5.2 Consensus size: 10
12005 ATGCTTGAAG
12015 AAAAAGAAAA
1 AAAAAGAAAA
12025 AAAAGAGAAAA
1 AAAA-AGAAAA
*
12036 GAAAAAAAAAA
1 -AAAAAGAAAA
12047 GAAAAAGAAAAA
1 -AAAAAG-AAAA
12059 AAAAAGAAAA
1 AAAAAGAAAA
12069 AA
1 AA
12071 GGGGGGTCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 10 0.24
11 23 0.56
12 8 0.20
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:12044 original size:18 final size:17
Alignment explanation
Indices: 12012--12069 Score: 100
Period size: 17 Copynumber: 3.5 Consensus size: 17
12002 ATTATGCTTG
12012 AAGAAAAAGAAAAAAAA
1 AAGAAAAAGAAAAAAAA
*
12029 GAG-AAAAGAAAAAAAA
1 AAGAAAAAGAAAAAAAA
12045 AAGAAAAAGAAAAAAAA
1 AAGAAAAAGAAAAAAAA
12062 AAGAAAAA
1 AAGAAAAA
12070 AGGGGGGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.39
17 23 0.61
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAAA
Found at i:12437 original size:19 final size:20
Alignment explanation
Indices: 12404--12445 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
12394 TTCAAGTTCA
*
12404 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
12424 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
12443 ATT
1 ATT
12446 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:13328 original size:84 final size:84
Alignment explanation
Indices: 13210--13469 Score: 443
Period size: 84 Copynumber: 3.1 Consensus size: 84
13200 CAATTAAATG
* * *
13210 GAAGATGATTGTGCT-AATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACA
1 GAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
13274 GAACCAATCATTGAATTTA
66 GAACCAATCATTGAATTTA
13293 GAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
1 GAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
13358 GAACCAATCATTGAATTTA
66 GAACCAATCATTGAATTTA
*
13377 GAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACA
1 GAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
*
13442 GAACCAATCGTTGGAA-TTA
66 GAACCAATCATT-GAATTTA
*
13461 AAAGATGAA
1 GAAGATGAA
13470 CTGCATGATC
Statistics
Matches: 169, Mismatches: 6, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
83 14 0.08
84 152 0.90
85 3 0.02
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (84 bp):
GAAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
GAACCAATCATTGAATTTA
Found at i:14356 original size:113 final size:113
Alignment explanation
Indices: 14158--14829 Score: 1121
Period size: 113 Copynumber: 6.0 Consensus size: 113
14148 CAAAGATTCA
* *
14158 AATCCATCATCTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
14223 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
* *
14271 AATCCATCATTTGGTGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAATAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
14336 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
* *
14384 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
14449 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTAAATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
* *
14497 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
14562 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTATATG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
* *
14610 AATCCATCATTTAATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
14675 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
* * * * *
14723 AATTCATCAATTGATGGATTATCTTTTCCGGAGA-AGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATCCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
14787 AGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAAACTTTT
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
14830 TGCATAATTC
Statistics
Matches: 533, Mismatches: 26, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
112 69 0.13
113 464 0.87
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
AATCCATCATTTGATGGATCAGCTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACATG
Found at i:15161 original size:3 final size:3
Alignment explanation
Indices: 15153--15264 Score: 197
Period size: 3 Copynumber: 37.3 Consensus size: 3
15143 TACCCATATC
15153 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
15201 ATT ATT ATT ATC ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
15249 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
15265 AATATATTAA
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:16676 original size:18 final size:18
Alignment explanation
Indices: 16641--16679 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
16631 GTAGTATTTG
**
16641 TATTTTTATATTGTTAAA
1 TATTTTTATATTCATAAA
16659 TATTTTTATATTCATAAA
1 TATTTTTATATTCATAAA
16677 TAT
1 TAT
16680 ATATAATAAA
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:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (18 bp):
TATTTTTATATTCATAAA
Found at i:18357 original size:33 final size:33
Alignment explanation
Indices: 18320--18389 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
18310 GCGACCTACC
*
18320 CTCGCTCGACTT-CCCTCGGATTCCCTCGCATAG
1 CTCGCTCG-CTTGCCCTCGGATGCCCTCGCATAG
*
18353 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGCTTGCCCTCGGATGCCCTCGCATAG
18386 CTCG
1 CTCG
18390 TTCGGATGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.10, C:0.41, G:0.23, T:0.26
Consensus pattern (33 bp):
CTCGCTCGCTTGCCCTCGGATGCCCTCGCATAG
Found at i:18403 original size:33 final size:33
Alignment explanation
Indices: 18332--18404 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
18322 CGCTCGACTT
* *
18332 CCCTCGGATTCCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
*
18365 CCCTCGGATGCCCTCGCATAGCTCGTTCGGATG
1 CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
*
18398 GCCTCGG
1 CCCTCGG
18405 TCGGATGGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.10, C:0.38, G:0.27, T:0.25
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCGCTCGGATG
Found at i:18408 original size:14 final size:14
Alignment explanation
Indices: 18386--18432 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
18376 CCTCGCATAG
*
18386 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
18400 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
18414 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
18428 CTCGG
1 CTCGG
18433 ATGCCCAGCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.06, C:0.30, G:0.40, T:0.23
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:23849 original size:2 final size:2
Alignment explanation
Indices: 23842--23876 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23832 CCTTCGCATG
23842 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 A
23877 ACCGCATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25705 original size:146 final size:143
Alignment explanation
Indices: 25372--25777 Score: 572
Period size: 145 Copynumber: 2.8 Consensus size: 143
25362 CAATACATAT
* * * *
25372 TCAT-TGATGAAAA-TTC-GATCCTTATTAGTTGATTGTAAGAATCAGCAGCTCGTCTGATTCTC
1 TCATCTGATGAAAATTTCAG-TCCTTATTAGTTGATTGAAAGAATTAGCAGCTC-ACTGATTCTT
*
25434 TACATACCCAAAAATAGAAAAATCATATTAATTAATTATTATTTTTATGATTTA-TTTAATATCA
64 TACATACCCAAAAATAGAAAAATCATATTAATTAATTA--CTTTTTATGATTTATTTTAATATCA
25498 AAATAACAATTAACAAC
127 AAATAACAATTAACAAC
* *
25515 TCATCTGAT-AAAATTTTCAATCCTTATTAGTTGATTGAAAGAATTAGCAGCCCACCTGATTCTT
1 TCATCTGATGAAAA-TTTCAGTCCTTATTAGTTGATTGAAAGAATTAGCAGCTCA-CTGATTCTT
* * *
25579 TACATGCCCGAAAATAGAAAAATCATATTAATTAATTACTGTTTTCATGATTTATTTTTATATCA
64 TACATACCCAAAAATAGAAAAATCATATTAATTAATTACT-TTTT-ATGATTTATTTTAATATCA
* *
25644 AAATAACTATTAACAGC
127 AAATAACAATTAACAAC
**
25661 TCATCTGATGAAAATTTCAGTCCTTATTAGTTTTTTGAAAGAATTAGCAGCTCA-TGATTCTTTA
1 TCATCTGATGAAAATTTCAGTCCTTATTAGTTGATTGAAAGAATTAGCAGCTCACTGATTCTTTA
25725 CATACCCAAAAATAGAAAAATCATATTAATTAATTACTTTTTATGATTTATTT
66 CATACCCAAAAATAGAAAAATCATATTAATTAATTACTTTTTATGATTTATTT
25778 AAAATAAAAA
Statistics
Matches: 236, Mismatches: 18, Indels: 19
0.86 0.07 0.07
Matches are distributed among these distances:
142 11 0.05
143 13 0.06
144 54 0.23
145 85 0.36
146 69 0.29
147 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (143 bp):
TCATCTGATGAAAATTTCAGTCCTTATTAGTTGATTGAAAGAATTAGCAGCTCACTGATTCTTTA
CATACCCAAAAATAGAAAAATCATATTAATTAATTACTTTTTATGATTTATTTTAATATCAAAAT
AACAATTAACAAC
Found at i:31939 original size:28 final size:28
Alignment explanation
Indices: 31873--31942 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
31863 CCAACCCACT
*
31873 ATCATATTTTCTTTATCTATTAATCAAA
1 ATCATATTTTCATTATCTATTAATCAAA
*
31901 ATGATATTTTCATTATCTATTAATTC-AA
1 ATCATATTTTCATTATCTATTAA-TCAAA
* *
31929 TTCATAATTTCATT
1 ATCATATTTTCATT
31943 TTCTTTTAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
28 34 0.94
29 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.01, T:0.51
Consensus pattern (28 bp):
ATCATATTTTCATTATCTATTAATCAAA
Found at i:32635 original size:19 final size:19
Alignment explanation
Indices: 32607--32643 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
32597 ATTTCAGTAA
*
32607 CCAAATTTAATAAGATGAC
1 CCAAAATTAATAAGATGAC
*
32626 CCAAAATTAATAATATGA
1 CCAAAATTAATAAGATGA
32644 ACCACTTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (19 bp):
CCAAAATTAATAAGATGAC
Found at i:33922 original size:21 final size:21
Alignment explanation
Indices: 33885--33924 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
33875 TTTTCTACTA
*
33885 TATATTATATAATAATTACCG
1 TATATTATATAAAAATTACCG
33906 TATATTAT-TAAAAAATTAC
1 TATATTATAT-AAAAATTAC
33925 AGAGAGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (21 bp):
TATATTATATAAAAATTACCG
Found at i:34977 original size:21 final size:22
Alignment explanation
Indices: 34943--34986 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
34933 GCTTTACATC
34943 TTTTTAATGAAAAATAGTGTTT
1 TTTTTAATGAAAAATAGTGTTT
34965 TTTTTAATG-AAAATAGTGTTT
1 TTTTTAATGAAAAATAGTGTTT
34986 T
1 T
34987 ACATTGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (22 bp):
TTTTTAATGAAAAATAGTGTTT
Found at i:35318 original size:29 final size:31
Alignment explanation
Indices: 35284--35367 Score: 112
Period size: 25 Copynumber: 3.0 Consensus size: 31
35274 TACATTGTAC
35284 AAAAATTATTAAATATGCAT-TT-TTTTTTG
1 AAAAATTATTAAATATGCATATTATTTTTTG
35313 AAAAATTATTAAATATGCATATTATTTTTT-
1 AAAAATTATTAAATATGCATATTATTTTTTG
35343 -----TTATTAAATATGCATATTATTTTTT
1 AAAAATTATTAAATATGCATATTATTTTTT
35368 TATGAAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
25 25 0.47
29 20 0.38
30 2 0.04
31 6 0.11
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.54
Consensus pattern (31 bp):
AAAAATTATTAAATATGCATATTATTTTTTG
Found at i:39414 original size:15 final size:15
Alignment explanation
Indices: 39394--39430 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
39384 TGAGACATTA
*
39394 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
39409 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
39424 CCCGCCC
1 CCCGCCC
39431 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:42105 original size:15 final size:15
Alignment explanation
Indices: 42085--42121 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
42075 TGAGACATTA
*
42085 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
42100 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
42115 CCCGCCC
1 CCCGCCC
42122 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:43573 original size:16 final size:16
Alignment explanation
Indices: 43548--43589 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43538 GAATTTTAGT
43548 TAAACCGAAAATAACC
1 TAAACCGAAAATAACC
*
43564 TAAACTGAAAATAACC
1 TAAACCGAAAATAACC
**
43580 CGAACCGAAA
1 TAAACCGAAA
43590 GCAACATGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.55, C:0.24, G:0.10, T:0.12
Consensus pattern (16 bp):
TAAACCGAAAATAACC
Found at i:44042 original size:55 final size:55
Alignment explanation
Indices: 43977--44086 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
43967 AAACATCTAA
*
43977 CATCTAATTAAAAAATTTAGTTGAGAATAAAATTTATAATTCAAAATTTAATTCT
1 CATCTAATTAAAAAATTTAATTGAGAATAAAATTTATAATTCAAAATTTAATTCT
* *
44032 CATCTAATTAAAAACTTTAATTGAGAATAATATTTATAATTCAAAATTTAATTCT
1 CATCTAATTAAAAAATTTAATTGAGAATAAAATTTATAATTCAAAATTTAATTCT
44087 TCACCAAATA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (55 bp):
CATCTAATTAAAAAATTTAATTGAGAATAAAATTTATAATTCAAAATTTAATTCT
Found at i:44421 original size:32 final size:31
Alignment explanation
Indices: 44384--44456 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
44374 TATTCAATCC
* *
44384 GATATTGACCTGACCCGAAAATCAATCGATCT
1 GATATTGACC-GACCCAAAAATCAACCGATCT
*
44416 GATATTGATCCGACCCAAAAATCAACCGGTCT
1 GATATTGA-CCGACCCAAAAATCAACCGATCT
44448 GATATTGAC
1 GATATTGAC
44457 GAGATTCGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.92
33 2 0.05
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (31 bp):
GATATTGACCGACCCAAAAATCAACCGATCT
Found at i:45107 original size:26 final size:26
Alignment explanation
Indices: 45078--45128 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
45068 AATTTTGCAT
45078 TTGTCCCTGTCCATATGGCTCATTGC
1 TTGTCCCTGTCCATATGGCTCATTGC
45104 TTGTCCCTGTCCATATGGCTCATTG
1 TTGTCCCTGTCCATATGGCTCATTG
45129 TTTGAAACCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.12, C:0.29, G:0.20, T:0.39
Consensus pattern (26 bp):
TTGTCCCTGTCCATATGGCTCATTGC
Found at i:48705 original size:30 final size:30
Alignment explanation
Indices: 48671--48732 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
48661 TAATATAAAC
48671 TTTTAAATTTTAGACGTTCTTTTTAAATTG
1 TTTTAAATTTTAGACGTTCTTTTTAAATTG
*
48701 TTTTAAATTTTAGATGTTCTTTTTAAATTG
1 TTTTAAATTTTAGACGTTCTTTTTAAATTG
48731 TT
1 TT
48733 GGATAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTTAAATTTTAGACGTTCTTTTTAAATTG
Found at i:53738 original size:2 final size:2
Alignment explanation
Indices: 53731--53756 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
53721 ATCTTACTTC
53731 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
53757 TCCATTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57229 original size:2 final size:2
Alignment explanation
Indices: 57222--57246 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57212 GATAAACTTT
57222 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
57247 GAATGAGAAG
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:60476 original size:9 final size:8
Alignment explanation
Indices: 60464--60545 Score: 53
Period size: 9 Copynumber: 9.9 Consensus size: 8
60454 AATATTTTAT
60464 ATATAATTA
1 ATATAA-TA
*
60473 ATATAAAAA
1 ATAT-AATA
60482 ATATAA-A
1 ATATAATA
*
60489 ATATTATA
1 ATATAATA
60497 TATATAATTA
1 -ATATAA-TA
*
60507 ATATAAAA
1 ATATAATA
60515 ATATAA-A
1 ATATAATA
*
60522 ATATTAT-
1 ATATAATA
60529 ATATATATA
1 ATATA-ATA
60538 TATATAAT
1 -ATATAAT
60546 CGGGGTGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
7 16 0.27
8 12 0.20
9 22 0.37
10 9 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATATAATA
Found at i:60492 original size:25 final size:26
Alignment explanation
Indices: 60464--60525 Score: 65
Period size: 25 Copynumber: 2.4 Consensus size: 26
60454 AATATTTTAT
60464 ATATAAT-TAATATAAAAAATAT-AAA
1 ATATAATAT-ATATAAAAAATATAAAA
* **
60489 ATATTATATATATAATTAATATAAAA
1 ATATAATATATATAAAAAATATAAAA
*
60515 ATATAAAATAT
1 ATATAATATAT
60526 TATATATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
ATATAATATATATAAAAAATATAAAA
Found at i:60520 original size:33 final size:34
Alignment explanation
Indices: 60452--60535 Score: 152
Period size: 33 Copynumber: 2.5 Consensus size: 34
60442 CCCAAACCCG
*
60452 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
60486 AAAATATTATATATATAATTAATAT-AAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
60519 AAAATATTATATATATA
1 AAAATATTATATATATA
60536 TATATATAAT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 25 0.51
34 24 0.49
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:66398 original size:22 final size:22
Alignment explanation
Indices: 66366--66407 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
66356 GTTTACTGGC
*
66366 TTATATACTAGCTCATGGTGGT
1 TTATATACTAGCTCAAGGTGGT
*
66388 TTATATGCTAGCTCAAGGTG
1 TTATATACTAGCTCAAGGTG
66408 ATTGAGGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (22 bp):
TTATATACTAGCTCAAGGTGGT
Found at i:68331 original size:21 final size:22
Alignment explanation
Indices: 68307--68353 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
68297 CAGATTTCAA
68307 ACAGGGAACCGATT-CCCTGCT
1 ACAGGGAACCGATTCCCCTGCT
**
68328 ACAGGGTGCCGATTCCCCTGCT
1 ACAGGGAACCGATTCCCCTGCT
68350 ACAG
1 ACAG
68354 TATTGCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.21, C:0.34, G:0.26, T:0.19
Consensus pattern (22 bp):
ACAGGGAACCGATTCCCCTGCT
Found at i:69245 original size:32 final size:32
Alignment explanation
Indices: 69096--69285 Score: 190
Period size: 32 Copynumber: 6.0 Consensus size: 32
69086 TCTCAGCAAT
* * * *
69096 TGTCCATAGGTCCCGTAGAACCTAGGTAA-AC
1 TGTCCATATGTTCCGTAGAACATAGGTAATTC
* *
69127 TGTCCATATGTTCCTTAGAACATAGGT-ATAC
1 TGTCCATATGTTCCGTAGAACATAGGTAATTC
*** * *
69158 TGTCCATATGTCTCAAAAGAA-ATATGTAATTA
1 TGTCCATATGT-TCCGTAGAACATAGGTAATTC
* * * *
69190 TGCCCATATGTCCCG-AAAGACATAAGTAATTC
1 TGTCCATATGTTCCGTAGA-ACATAGGTAATTC
69222 TGTCCATATGTTCCGTAGAACATAGGTAATTC
1 TGTCCATATGTTCCGTAGAACATAGGTAATTC
*
69254 TGTCTATATGTTCCGTAGAACATAGGTAATTC
1 TGTCCATATGTTCCGTAGAACATAGGTAATTC
69286 CTCGACTCTT
Statistics
Matches: 131, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
30 3 0.02
31 43 0.33
32 83 0.63
33 2 0.02
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (32 bp):
TGTCCATATGTTCCGTAGAACATAGGTAATTC
Found at i:72502 original size:21 final size:22
Alignment explanation
Indices: 72478--72524 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
72468 CAGATTTCAA
72478 ACAGGGAACTGATT-CCCTGCT
1 ACAGGGAACTGATTCCCCTGCT
*
72499 ACAGGGTACTGATTCCCCTGCT
1 ACAGGGAACTGATTCCCCTGCT
72521 ACAG
1 ACAG
72525 TACTGCTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.23
Consensus pattern (22 bp):
ACAGGGAACTGATTCCCCTGCT
Found at i:72529 original size:20 final size:20
Alignment explanation
Indices: 72485--72529 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
72475 CAAACAGGGA
72485 ACTGATTCCCTGCTACAGGGT
1 ACTGATTCCCTGCTACA-GGT
72506 ACTGATTCCCCTGCTACA-GT
1 ACTGATT-CCCTGCTACAGGT
72526 ACTG
1 ACTG
72530 CTACAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.26
21 7 0.30
22 10 0.43
ACGTcount: A:0.20, C:0.31, G:0.20, T:0.29
Consensus pattern (20 bp):
ACTGATTCCCTGCTACAGGT
Found at i:73461 original size:32 final size:32
Alignment explanation
Indices: 73272--73481 Score: 223
Period size: 32 Copynumber: 6.6 Consensus size: 32
73262 TCCATAGATC
* * *
73272 CCGTAGAACCTAGGTAA-ACAATCCATATGTT
1 CCGTAGAACATAGGTAATTCTATCCATATGTT
* * *
73303 CCTTAGAACATAGGT-ATACTGTCCATATG-T
1 CCGTAGAACATAGGTAATTCTATCCATATGTT
* * * * * * *
73333 CTC-AAAATACATAGTTAATTTTGTCTATATGTC
1 C-CGTAGA-ACATAGGTAATTCTATCCATATGTT
* *
73366 CCG-AAAGACATAGGTAATTCTGTCCATATGTT
1 CCGTAGA-ACATAGGTAATTCTATCCATATGTT
73398 CCGTAGAACATAGGTAATTCTATCCATATGTT
1 CCGTAGAACATAGGTAATTCTATCCATATGTT
73430 CCGTAGAACATAGGTAATTCTATCCATATGTT
1 CCGTAGAACATAGGTAATTCTATCCATATGTT
73462 CCGTAGAACATAGGTAATTC
1 CCGTAGAACATAGGTAATTC
73482 CTCGACTCTT
Statistics
Matches: 154, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
30 5 0.03
31 31 0.20
32 115 0.75
33 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (32 bp):
CCGTAGAACATAGGTAATTCTATCCATATGTT
Found at i:73985 original size:12 final size:12
Alignment explanation
Indices: 73970--74081 Score: 183
Period size: 12 Copynumber: 9.3 Consensus size: 12
73960 ATCATTTCTC
73970 ATATTCATATAT
1 ATATTCATATAT
73982 ATATTC--ATAT
1 ATATTCATATAT
73992 ATATTCATATAT
1 ATATTCATATAT
74004 ATATTCATATAT
1 ATATTCATATAT
74016 ATATTCACATATAT
1 ATATT--CATATAT
74030 ATATTCATATAT
1 ATATTCATATAT
74042 ATATTCATATAT
1 ATATTCATATAT
74054 ATATTCATATAT
1 ATATTCATATAT
*
74066 ATATTCACATAT
1 ATATTCATATAT
74078 ATAT
1 ATAT
74082 ATATGGTTCA
Statistics
Matches: 95, Mismatches: 1, Indels: 8
0.91 0.01 0.08
Matches are distributed among these distances:
10 10 0.11
12 73 0.77
14 12 0.13
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATTCATATAT
Found at i:75798 original size:12 final size:12
Alignment explanation
Indices: 75781--75805 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75771 GTTTAATTTA
75781 AAAAATTATATT
1 AAAAATTATATT
75793 AAAAATTATATT
1 AAAAATTATATT
75805 A
1 A
75806 TATAATTTTC
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATTATATT
Found at i:76206 original size:19 final size:19
Alignment explanation
Indices: 76179--76228 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
76169 TAAAAAAATA
*
76179 TATATATATATTATTGTTT
1 TATAAATATATTATTGTTT
*
76198 TATAAATATATTTATTTTTT
1 TATAAATATA-TTATTGTTT
*
76218 TA-AAAAATATT
1 TATAAATATATT
76229 TCTATTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 15 0.56
20 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATAAATATATTATTGTTT
Found at i:76206 original size:21 final size:20
Alignment explanation
Indices: 76177--76229 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
76167 TTTAAAAAAA
*
76177 TATATATATATATTATTGTTT
1 TATAAATATAT-TTATTGTTT
*
76198 TATAAATATATTTATTTTTT
1 TATAAATATATTTATTGTTT
*
76218 TA-AAAAATATTT
1 TATAAATATATTT
76230 CTATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 9 0.31
20 10 0.34
21 10 0.34
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATAAATATATTTATTGTTT
Found at i:76236 original size:19 final size:19
Alignment explanation
Indices: 76195--76247 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
76185 TATATTATTG
* *
76195 TTTTATAAATATATTTATTT
1 TTTTA-AAAAATATTTATAT
*
76215 TTTTAAAAAATATTTCTAT
1 TTTTAAAAAATATTTATAT
*
76234 TTTAAAAAGAATAT
1 TTTTAAAA-AATAT
76248 AAACACGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 18 0.64
20 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTAAAAAATATTTATAT
Found at i:76236 original size:20 final size:21
Alignment explanation
Indices: 76190--76236 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
76180 ATATATATAT
*
76190 TATTGTTTTATAAATATATTTA
1 TATT-TTTTATAAAAATATTTA
*
76212 T-TTTTTTA-AAAAATATTTC
1 TATTTTTTATAAAAATATTTA
76231 TATTTT
1 TATTTT
76237 AAAAAGAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.45
20 9 0.41
21 2 0.09
22 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TATTTTTTATAAAAATATTTA
Found at i:78076 original size:18 final size:18
Alignment explanation
Indices: 78048--78083 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
78038 GATATTAATA
78048 AAATATTAAAATACTTATT
1 AAATATTAAAATA-TTATT
78067 AAAT-TTAAAATATTATT
1 AAATATTAAAATATTATT
78084 TATCATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATATTAAAATATTATT
Found at i:79538 original size:14 final size:14
Alignment explanation
Indices: 79515--79561 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
79505 CGCTGGGCAT
*
79515 CCGAGACCATCCGA
1 CCGAGGCCATCCGA
79529 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
79543 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
79557 ACGAG
1 CCGAG
79562 CTATGCGAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.26, C:0.40, G:0.28, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:79595 original size:33 final size:33
Alignment explanation
Indices: 79543--79693 Score: 239
Period size: 33 Copynumber: 4.6 Consensus size: 33
79533 GGCCATCCGA
* * * *
79543 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
* *
79576 CCGAGTGCAACCGAGCGAGCTATACGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
*
79609 CCGAGTGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
79642 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
79675 CCGAGGGCAACCGAGCGAG
1 CCGAGGGCAACCGAGCGAG
79694 GGTAGGTTGC
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 110 1.00
ACGTcount: A:0.27, C:0.26, G:0.36, T:0.10
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:79648 original size:10 final size:11
Alignment explanation
Indices: 79567--79689 Score: 64
Period size: 10 Copynumber: 11.4 Consensus size: 11
79557 ACGAGCTATG
79567 CGAGGGC-ATC
1 CGAGGGCAATC
*
79577 CGAGTGCAA-C
1 CGAGGGCAATC
* *
79587 CGAGCGAGCTATA
1 CGAG-G-GCAATC
79600 CGAGGG-AATC
1 CGAGGGCAATC
*
79610 CGAGTGCAA-C
1 CGAGGGCAATC
* *
79620 CGAGCGAGCTATG
1 CGAG-G-GCAATC
79633 CGAGGG-AATC
1 CGAGGGCAATC
79643 CGAGGGCAA-C
1 CGAGGGCAATC
* *
79653 CGAGCGAGCTATG
1 CGAG-G-GCAATC
79666 CGAGGG-AATC
1 CGAGGGCAATC
79676 CGAGGGCAA-C
1 CGAGGGCAATC
79686 CGAG
1 CGAG
79690 CGAGGGTAGG
Statistics
Matches: 84, Mismatches: 16, Indels: 26
0.67 0.13 0.21
Matches are distributed among these distances:
10 49 0.58
11 11 0.13
12 12 0.14
13 12 0.14
ACGTcount: A:0.28, C:0.25, G:0.37, T:0.10
Consensus pattern (11 bp):
CGAGGGCAATC
Found at i:79768 original size:10 final size:10
Alignment explanation
Indices: 79738--79836 Score: 63
Period size: 10 Copynumber: 9.5 Consensus size: 10
79728 CGCTCGGTTG
*
79738 CTCGGATTCC
1 CTCGGATGCC
*
79748 GCTCGGTTGCC
1 -CTCGGATGCC
79759 CTCGGATGCC
1 CTCGGATGCC
*
79769 CTCGCATAGCTC
1 CTCGGAT-GC-C
* *
79781 GTTCGGATGTC
1 -CTCGGATGCC
* *
79792 ATCGGATGCT
1 CTCGGATGCC
*
79802 CTCGGATGGC
1 CTCGGATGCC
*
79812 CTCGGATGCT
1 CTCGGATGCC
* *
79822 TTCGGATGGC
1 CTCGGATGCC
79832 CTCGG
1 CTCGG
79837 TCGAATGGCC
Statistics
Matches: 66, Mismatches: 19, Indels: 7
0.72 0.21 0.08
Matches are distributed among these distances:
10 48 0.73
11 11 0.17
12 2 0.03
13 5 0.08
ACGTcount: A:0.10, C:0.31, G:0.31, T:0.27
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:79808 original size:20 final size:20
Alignment explanation
Indices: 79783--79836 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
79773 CATAGCTCGT
*
79783 TCGGATGTCATCGGATGCTC
1 TCGGATGGCATCGGATGCTC
* *
79803 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCATCGGATGCTC
*
79823 TCGGATGGCCTCGG
1 TCGGATGGCATCGG
79837 TCGAATGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.26, G:0.35, T:0.28
Consensus pattern (20 bp):
TCGGATGGCATCGGATGCTC
Found at i:86407 original size:15 final size:15
Alignment explanation
Indices: 86387--86432 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
86377 AGTTTTTTTT
86387 TATAAAATATAAACA
1 TATAAAATATAAACA
*
86402 TATAAAATAGAACACA
1 TATAAAATATAA-ACA
* *
86418 TATATAATTTAAACA
1 TATAAAATATAAACA
86433 CGCATGTAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
15 14 0.54
16 12 0.46
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (15 bp):
TATAAAATATAAACA
Found at i:86690 original size:6 final size:6
Alignment explanation
Indices: 86679--86705 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
86669 AAATTATCGG
86679 AAAAGA AAAAGA AAAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAA
86706 TGAAGAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:89744 original size:2 final size:2
Alignment explanation
Indices: 89739--89763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89729 TAATCATTTA
89739 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 A
89764 ATTATTGTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:93559 original size:22 final size:22
Alignment explanation
Indices: 93531--93572 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
93521 CTAATATATT
*
93531 TATATATTATAATATAAATTTG
1 TATATATTAAAATATAAATTTG
*
93553 TATATATTAAAATTTAAATT
1 TATATATTAAAATATAAATT
93573 AATTATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TATATATTAAAATATAAATTTG
Found at i:98103 original size:17 final size:17
Alignment explanation
Indices: 98081--98115 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
98071 TGTGTATTCA
98081 TGGAGGGATAGAGTATT
1 TGGAGGGATAGAGTATT
98098 TGGAGGGATAGAGTATT
1 TGGAGGGATAGAGTATT
98115 T
1 T
98116 TTTTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.31
Consensus pattern (17 bp):
TGGAGGGATAGAGTATT
Found at i:102781 original size:13 final size:14
Alignment explanation
Indices: 102763--102791 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
102753 ACCTCTCTTT
102763 CTCTCTTCTT-TCC
1 CTCTCTTCTTCTCC
102776 CTCTCTTCTTCTCC
1 CTCTCTTCTTCTCC
102790 CT
1 CT
102792 GATTTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (14 bp):
CTCTCTTCTTCTCC
Found at i:105750 original size:29 final size:29
Alignment explanation
Indices: 105708--105771 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
105698 TTTTCCTATC
105708 ATGTAAGAATTTTTAATGAATGTTTTGAT
1 ATGTAAGAATTTTTAATGAATGTTTTGAT
105737 ATGTAAGAATTTTTAATGAATGTTTTGAT
1 ATGTAAGAATTTTTAATGAATGTTTTGAT
105766 ATGTAA
1 ATGTAA
105772 TAACCCACTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (29 bp):
ATGTAAGAATTTTTAATGAATGTTTTGAT
Done.