Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016083.1 Corchorus olitorius cultivar O-4 contig16116, 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: 94669
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2216 original size:31 final size:31
Alignment explanation
Indices: 2178--2242 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
2168 AAGGGACTGA
2178 TTTGTCCCAAAAGAAAAACATAAGAAACTTT
1 TTTGTCCCAAAAGAAAAACATAAGAAACTTT
* *
2209 TTTGTCCCAAAAGAAAAACATAAGAGATTTT
1 TTTGTCCCAAAAGAAAAACATAAGAAACTTT
2240 TTT
1 TTT
2243 AGTATTTAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (31 bp):
TTTGTCCCAAAAGAAAAACATAAGAAACTTT
Found at i:2995 original size:125 final size:127
Alignment explanation
Indices: 2862--3101 Score: 353
Period size: 127 Copynumber: 1.9 Consensus size: 127
2852 CTTATTTTTC
* **
2862 AAATATATTTCTTAAATGTCATT-TTTAAACTTTTACAATTTTA-CTCAATTAAAAA-CTCTATT
1 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATCTC-ACCAAAAATCTCTATT
*
2924 TTTATTTAATCAAA-TCTAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
65 TTTATTTAATCAAATTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * * *
2987 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAGTTTTATTTCACCAAAAATTTTTATTT
1 AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATCTCACCAAAAATCTCTATTT
*
3052 TTATTTAATCAAATTCAATATTTTTATAACTATTTTATCTTTACCATTTT
66 TTATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
3102 TTTAGGCAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
125 22 0.22
126 25 0.25
127 53 0.52
128 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.01, T:0.52
Consensus pattern (127 bp):
AAATATATTTCTTAAATGACATTATTTAAACTTTTACAATTTTATCTCACCAAAAATCTCTATTT
TTATTTAATCAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:3202 original size:7 final size:7
Alignment explanation
Indices: 3190--3235 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
3180 GGAGGAGAAG
3190 GAAAAAA
1 GAAAAAA
3197 GAAAAAA
1 GAAAAAA
3204 GAAAAAA
1 GAAAAAA
*
3211 GAAAAAT
1 GAAAAAA
*
3218 GAAAAAT
1 GAAAAAA
3225 GAAAAAA
1 GAAAAAA
3232 -AAAA
1 GAAAA
3236 TCAATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
6 4 0.11
7 33 0.89
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (7 bp):
GAAAAAA
Found at i:3316 original size:32 final size:32
Alignment explanation
Indices: 3277--3371 Score: 158
Period size: 32 Copynumber: 3.0 Consensus size: 32
3267 ACTAAATACT
3277 AAAAAATCCCTAATGTTTTTCTTTTGGGACAA
1 AAAAAATCCCTAATGTTTTTCTTTTGGGACAA
*
3309 AAAAAATCCCTCATGTTTTTCTTTTGGGAC-A
1 AAAAAATCCCTAATGTTTTTCTTTTGGGACAA
*
3340 AAAAAATCCCTTATGTTTTT-TTTTGGGACAA
1 AAAAAATCCCTAATGTTTTTCTTTTGGGACAA
3371 A
1 A
3372 TTAGTCCCTT
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
30 9 0.15
31 22 0.37
32 29 0.48
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (32 bp):
AAAAAATCCCTAATGTTTTTCTTTTGGGACAA
Found at i:12365 original size:66 final size:66
Alignment explanation
Indices: 12213--12396 Score: 246
Period size: 66 Copynumber: 2.8 Consensus size: 66
12203 TCGTGGTTTT
* *
12213 TGTCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGCGATTT-CCGATGTTTATCAGCGGCTC
1 TGTCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAGGCTC
12277 C
66 C
* * * *
12278 TATCCATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATTTTTATCAGAGGTTC
1 TGTCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAGGCTC
12343 C
66 C
** * * *
12344 TGTCAATTTTCAATGCTGACACTC-GCCTGAAGTCTCCGTGATTTCCCAATGTT
1 TGTCAATTTTCTCTGCAGACACTCTG-CTGAAATCTCCGTGATTTCCCGATGTT
12397 CCTTGAAAGA
Statistics
Matches: 103, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
65 42 0.41
66 61 0.59
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.36
Consensus pattern (66 bp):
TGTCAATTTTCTCTGCAGACACTCTGCTGAAATCTCCGTGATTTCCCGATGTTTATCAGAGGCTC
C
Found at i:12399 original size:55 final size:55
Alignment explanation
Indices: 12352--12458 Score: 187
Period size: 55 Copynumber: 1.9 Consensus size: 55
12342 CCTGTCAATT
*
12352 TTCAATGCTGACACTCGCCTGAAGTCTCCGTGATTTCCCAATGTTCCTTGAAAGA
1 TTCAATGCTGACACTCGCCTGAAATCTCCGTGATTTCCCAATGTTCCTTGAAAGA
* *
12407 TTCAATGCTGACACTCGCCTGAAATCTCCGTGATTTCTCAGTGTTCCTTGAA
1 TTCAATGCTGACACTCGCCTGAAATCTCCGTGATTTCCCAATGTTCCTTGAA
12459 GACAGATATC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (55 bp):
TTCAATGCTGACACTCGCCTGAAATCTCCGTGATTTCCCAATGTTCCTTGAAAGA
Found at i:16698 original size:21 final size:21
Alignment explanation
Indices: 16672--16712 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16662 TTTAAACCCT
16672 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
16693 ATTGGATCTAAGTGGTACTA
1 ATTGGAACTAAGTGGTACTA
16713 GGGTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:25490 original size:19 final size:18
Alignment explanation
Indices: 25453--25498 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
25443 TGAAATTTAT
25453 TAATTATTTATTAAATAA
1 TAATTATTTATTAAATAA
25471 TAATTATTT-TTCAGAATAA
1 TAATTATTTATT-A-AATAA
*
25490 TTATTATTT
1 TAATTATTT
25499 CCTTCTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 2 0.08
18 10 0.40
19 13 0.52
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TAATTATTTATTAAATAA
Found at i:26919 original size:55 final size:55
Alignment explanation
Indices: 26832--26938 Score: 178
Period size: 55 Copynumber: 1.9 Consensus size: 55
26822 CCTGTCAATT
* * * *
26832 TTCAATGCTGACACTCGCCTGAAGTCTTCGTGATTTCCCAGTGTTCCTTGAAAGA
1 TTCAATGCGGACACTCGCATGAAATCTCCGTGATTTCCCAGTGTTCCTTGAAAGA
26887 TTCAATGCGGACACTCGCATGAAATCTCCGTGATTTCCCAGTGTTCCTTGAA
1 TTCAATGCGGACACTCGCATGAAATCTCCGTGATTTCCCAGTGTTCCTTGAA
26939 GACATATATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (55 bp):
TTCAATGCGGACACTCGCATGAAATCTCCGTGATTTCCCAGTGTTCCTTGAAAGA
Found at i:42074 original size:15 final size:15
Alignment explanation
Indices: 42054--42091 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
42044 GTTAAACTTC
*
42054 ATTATATGAATAATT
1 ATTATATGAATAATA
42069 ATTATATGAATAATA
1 ATTATATGAATAATA
42084 ATT-TATGA
1 ATTATATGA
42092 TAAAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.23
15 17 0.77
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (15 bp):
ATTATATGAATAATA
Found at i:43279 original size:132 final size:130
Alignment explanation
Indices: 43098--43355 Score: 367
Period size: 132 Copynumber: 2.0 Consensus size: 130
43088 ATTTAAGAAA
* * *
43098 TATATTTTAAAAATTCTAATATATCTAAGTTTTTAATTAAATTAGTAAAATGATAAAAATAAAAT
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAAAATGATAAAAATAAAAT
* *
43163 AGGTATAAGAATATTATACTTAAAT-AA-AAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
66 AGGTATAAGAATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
* *
43226 TATATTTAAAAAAATTCTAATATATATAAGATTTTTTTAATTAAAATAGTAAAATGGTAAAAATT
1 TATATTT-AAAAAATTCTAATATATATAAG---TTTTTAATTAAAATAGTAAAATGATAAAAATA
** * *
43291 AAATATTTATAAGGATATTAGAATTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
62 AAATAGGTATAAGAATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATA
43356 CAAATTTAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
128 7 0.06
129 20 0.18
132 52 0.46
133 2 0.02
134 32 0.28
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.38
Consensus pattern (130 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTAATTAAAATAGTAAAATGATAAAAATAAAAT
AGGTATAAGAATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTATAAAAG
Found at i:45014 original size:93 final size:93
Alignment explanation
Indices: 44914--45082 Score: 295
Period size: 93 Copynumber: 1.8 Consensus size: 93
44904 AGTAATATCA
* * *
44914 TAAAAATAAAATAGGTT-TAAGGATATTAGATTTAATTAAATAAAAATAGGGTTTTTAGTTGAGT
1 TAAAAATAAAATA-GTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACT
44978 AAAACTATAAAAGTAGAATAGTAAAATGG
65 AAAACTATAAAAGTAGAATAGTAAAATGG
45007 TAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
1 TAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
45072 AAACTATAAAA
66 AAACTATAAAA
45083 AATTAAAAAA
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 3 0.04
93 69 0.96
ACGTcount: A:0.51, C:0.02, G:0.14, T:0.33
Consensus pattern (93 bp):
TAAAAATAAAATAGTTATAAGAATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGACTA
AAACTATAAAAGTAGAATAGTAAAATGG
Found at i:46692 original size:78 final size:78
Alignment explanation
Indices: 46563--46719 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
46553 ATGTGTTGGA
46563 ACTGGTTCATGTAATAATTTCTGCACAATTGGAGTGAAATGCTTATATCTATCTATCTTTATATA
1 ACTGGTTCATGTAATAATTTCTGCACAATTGGAGTGAAATGCTTATATCTATCTATCTTTATATA
46628 TATATATATATAT
66 TATATATATATAT
46641 ACTGGTTCATGTAATAATTTCTGCACAATTGGAGTGAAATGCTTATATCTATCTATCTTTATATA
1 ACTGGTTCATGTAATAATTTCTGCACAATTGGAGTGAAATGCTTATATCTATCTATCTTTATATA
46706 TATATATATATAT
66 TATATATATATAT
46719 A
1 A
46720 TATATATATA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (78 bp):
ACTGGTTCATGTAATAATTTCTGCACAATTGGAGTGAAATGCTTATATCTATCTATCTTTATATA
TATATATATATAT
Found at i:46707 original size:2 final size:2
Alignment explanation
Indices: 46700--46731 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46690 TATCTATCTT
46700 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
46732 CACTAGTTTT
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:48491 original size:31 final size:31
Alignment explanation
Indices: 48399--48500 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 31
48389 AGAACCTAAA
* * * * *
48399 TAGTCCCTGTACTATCGAAAAAAGATCATTT
1 TAGTCCCTCTACTATTGGAAAATGATCAATT
* * *
48430 TAGTCCCTCCATTA-T-GAAATCTG-TCAATT
1 TAGTCCCTCTACTATTGGAAA-ATGATCAATT
48459 TAGTCCCTCTACTATTGGAAAATGATCAATT
1 TAGTCCCTCTACTATTGGAAAATGATCAATT
48490 TAGTCCCTCTA
1 TAGTCCCTCTA
48501 TTTAATTGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
29 20 0.36
30 4 0.07
31 32 0.57
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (31 bp):
TAGTCCCTCTACTATTGGAAAATGATCAATT
Found at i:48632 original size:22 final size:21
Alignment explanation
Indices: 48601--48658 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
48591 TGTAAATTAA
*
48601 TTTTTATTTTAAAAATCTGAAT
1 TTTTTTTTTTAAAAATCTG-AT
**
48623 TTTTTTTTTTCGGAAATCTGAT
1 TTTTTTTTTT-AAAAATCTGAT
48645 TTTTTAATTTTTAA
1 TTTTT--TTTTTAA
48659 TTTTTTTAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
22 16 0.57
23 7 0.25
24 5 0.18
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (21 bp):
TTTTTTTTTTAAAAATCTGAT
Found at i:49774 original size:31 final size:30
Alignment explanation
Indices: 49739--49837 Score: 103
Period size: 31 Copynumber: 3.3 Consensus size: 30
49729 AATTAAACGG
49739 AGGGACTAAATTGATCGTTTTCCAATAGTAA
1 AGGGACTAAATTGATCGTTTT-CAATAGTAA
* * *
49770 AGGGACTAAATTGA-CAGATTTC-ATAATAG
1 AGGGACTAAATTGATC-GTTTTCAATAGTAA
* * *
49799 AGGGACTAAAATGATCTTTTTTCAATAGTAC
1 AGGGACTAAATTGATC-GTTTTCAATAGTAA
49830 AGGGACTA
1 AGGGACTA
49838 TTTAGGTTCT
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
29 18 0.32
30 7 0.12
31 31 0.55
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (30 bp):
AGGGACTAAATTGATCGTTTTCAATAGTAA
Found at i:51421 original size:7 final size:7
Alignment explanation
Indices: 51409--51452 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
51399 GAAGATGAGT
51409 GATCCAA
1 GATCCAA
51416 GATCCAA
1 GATCCAA
51423 GATCCAA
1 GATCCAA
51430 GATCCAA
1 GATCCAA
51437 GATCCAA
1 GATCCAA
51444 GATCCAA
1 GATCCAA
51451 GA
1 GA
51453 GGGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.43, C:0.27, G:0.16, T:0.14
Consensus pattern (7 bp):
GATCCAA
Found at i:53112 original size:2 final size:2
Alignment explanation
Indices: 53105--53129 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53095 TAAAACTCCT
53105 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
53130 TTTGTAAAAT
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:53674 original size:22 final size:22
Alignment explanation
Indices: 53639--53694 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
53629 TAATTACACT
* *
53639 AATTTTTATGACC-TCCTTATAA
1 AATTTTAATAACCTTCC-TATAA
* *
53661 AATTTTGATAACCTTCCTATGA
1 AATTTTAATAACCTTCCTATAA
53683 AATTTTAATAAC
1 AATTTTAATAAC
53695 GATACAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (22 bp):
AATTTTAATAACCTTCCTATAA
Found at i:54025 original size:21 final size:21
Alignment explanation
Indices: 53977--54025 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
53967 TGAAAATGCT
* *
53977 AATTATAAAGAAAAGCAATCA
1 AATTAAAAAGAAAAGCAAACA
*
53998 AACTAAAAAGAAAA-CAAACTA
1 AATTAAAAAGAAAAGCAAAC-A
54019 AATTAAA
1 AATTAAA
54026 TCTGAACTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.67, C:0.10, G:0.06, T:0.16
Consensus pattern (21 bp):
AATTAAAAAGAAAAGCAAACA
Found at i:55067 original size:29 final size:29
Alignment explanation
Indices: 55022--55109 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
55012 TCTTTCTGAT
*
55022 TTTGTTTAAGTGCGGGTTGTGCACTTGTG
1 TTTGTTTAAGTGTGGGTTGTGCACTTGTG
* * *
55051 TTTGTTCAAGTGTGGGTTGTACACTTGGG
1 TTTGTTTAAGTGTGGGTTGTGCACTTGTG
* * *
55080 ATTGTTTTGAGTGTGGGTT-TGCACTCGTG
1 TTTG-TTTAAGTGTGGGTTGTGCACTTGTG
55109 T
1 T
55110 CAAAGCTTTG
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
29 35 0.74
30 12 0.26
ACGTcount: A:0.11, C:0.10, G:0.34, T:0.44
Consensus pattern (29 bp):
TTTGTTTAAGTGTGGGTTGTGCACTTGTG
Found at i:56614 original size:30 final size:30
Alignment explanation
Indices: 56557--56618 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
56547 CAATTCTTGC
**
56557 TTCTTGAAATAATTCTTCAATGGTCTTCAA
1 TTCTTGAAATAATTCTTCAATAATCTTCAA
*
56587 TTCTTGAAATTA-TCTTCAATAAATCTTCAA
1 TTCTTGAAATAATTCTTCAAT-AATCTTCAA
56617 TT
1 TT
56619 ACGAACTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.45
Consensus pattern (30 bp):
TTCTTGAAATAATTCTTCAATAATCTTCAA
Found at i:57008 original size:23 final size:23
Alignment explanation
Indices: 56941--57187 Score: 111
Period size: 22 Copynumber: 11.5 Consensus size: 23
56931 AATCACACCT
* *
56941 TGAAATTTTGA-AAATCACACTA
1 TGAAATTTTGATAAACCTCACTA
* * *
56963 TGAAATTGTGA-CAACCTCGCTA
1 TGAAATTTTGATAAACCTCACTA
56985 TGAAATTTTGATAAACCATC-CTA
1 TGAAATTTTGATAAACC-TCACTA
*
57008 TAAAATTTTGAT-AACCTC-CTTA
1 TGAAATTTTGATAAACCTCAC-TA
*
57030 TGAAATCTTGAT-AA-CT-AC--
1 TGAAATTTTGATAAACCTCACTA
*
57048 --AAATTTTGAT-AACCTCCCTA
1 TGAAATTTTGATAAACCTCACTA
** * * *
57068 TGATTTTTTTAT-AA-CTCATTG
1 TGAAATTTTGATAAACCTCACTA
* * *
57089 TGAAATTTTG-TTAATCTCCCTA
1 TGAAATTTTGATAAACCTCACTA
* * ** *
57111 TAAAATTCTGATCTACAT-ACTA
1 TGAAATTTTGATAAACCTCACTA
* *
57133 TGAAATTTTGATAACCCTC-TTA
1 TGAAATTTTGATAAACCTCACTA
*
57155 TGAAATTTTGA-AAA-CTAAACTA
1 TGAAATTTTGATAAACCT-CACTA
57177 TGAAATTTTGA
1 TGAAATTTTGA
57188 AATCCTCCCT
Statistics
Matches: 168, Mismatches: 41, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
16 11 0.07
17 2 0.01
18 1 0.01
20 3 0.02
21 21 0.12
22 107 0.64
23 21 0.12
24 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
TGAAATTTTGATAAACCTCACTA
Found at i:57014 original size:45 final size:45
Alignment explanation
Indices: 56941--57043 Score: 122
Period size: 45 Copynumber: 2.3 Consensus size: 45
56931 AATCACACCT
* *
56941 TGAAATTTTGA-AAATCACACTATGAAATTGTGACAACCTCGC-TA
1 TGAAATTTTGATAAACCACACTATAAAATTGTGACAACCTC-CTTA
* *
56985 TGAAATTTTGATAAACCATC-CTATAAAATTTTGATAACCTCCTTA
1 TGAAATTTTGATAAACCA-CACTATAAAATTGTGACAACCTCCTTA
*
57030 TGAAATCTTGATAA
1 TGAAATTTTGATAA
57044 CTACAAATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 12 0.24
45 38 0.75
46 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (45 bp):
TGAAATTTTGATAAACCACACTATAAAATTGTGACAACCTCCTTA
Found at i:57431 original size:22 final size:22
Alignment explanation
Indices: 57291--57727 Score: 120
Period size: 22 Copynumber: 19.7 Consensus size: 22
57281 GAAATACCAC
* *
57291 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAACCTCAT
* * * *
57313 TTTGAAAATTTGATAAAACTCTT
1 TATGAAATTTTGAT-AACCTCAT
* *
57336 TATCAAATTTTGATAACCTCAC
1 TATGAAATTTTGATAACCTCAT
* * *
57358 TAT-AAATTTTGTTGACC-CCT
1 TATGAAATTTTGATAACCTCAT
* *
57378 CTATGAAATTTTGATAATCACAT
1 -TATGAAATTTTGATAACCTCAT
* * *
57401 CATGTAATTTTGATAACCTCGT
1 TATGAAATTTTGATAACCTCAT
* ** *
57423 TTTGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCAT
* * *
57445 TATGCAATTTTGATAATTCTTC-C
1 TATGAAATTTTGATAA--CCTCAT
57468 TAT-AAATTTTGATAATCCGATC-T
1 TATGAAATTTTGATAA-CC--TCAT
*
57491 CTATGAAATTTCGATAA--TCACT
1 -TATGAAATTTTGATAACCTCA-T
*
57513 CTATGAGA-TTTGATAACCT--T
1 -TATGAAATTTTGATAACCTCAT
* * *
57533 CTATTAAATTTTGGTACTCCTCAT
1 -TATGAAATTTTGATA-ACCTCAT
* *
57557 GAAATTGAGACTTTT-ATAACCTTCA-
1 --TA-TGA-AATTTTGATAACC-TCAT
* *
57582 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAACCTCAT
** *
57604 TAAAAAAGTTTGATAA-C-CA-
1 TATGAAATTTTGATAACCTCAT
* * *
57623 AACCGAAATTTTGATAACCTCCCCT
1 TA-TGAAATTTTGATAACCT--CAT
* *
57648 TA--AAATATT-AGTAACCTCCT
1 TATGAAATTTTGA-TAACCTCAT
* * *
57668 TATGAAATTTTGTTAACCACAC
1 TATGAAATTTTGATAACCTCAT
* **
57690 TATGATATTCTT-ATAACCTCGC
1 TATGAAATT-TTGATAACCTCAT
*
57712 TATGATATTTTGATAA
1 TATGAAATTTTGATAA
57728 TCTCTTTGAT
Statistics
Matches: 306, Mismatches: 73, Indels: 72
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.00
20 28 0.09
21 42 0.14
22 173 0.57
23 28 0.09
24 7 0.02
25 15 0.05
26 7 0.02
27 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAT
Found at i:57454 original size:88 final size:88
Alignment explanation
Indices: 57290--57456 Score: 221
Period size: 88 Copynumber: 1.9 Consensus size: 88
57280 AGAAATACCA
** **
57290 CTATGAAATTTTGATAATCACATTTTGAAAATTTGATAAAACTCTTTATCAAATTTTGATAACCT
1 CTATGAAATTTTGATAATCACATCATGAAAATTTGATAAAACTCTTTATCAAATTTTGATAACAA
57355 CACTATAAATTTTGTTGACCCCT
66 CACTATAAATTTTGTTGACCCCT
* * * *
57378 CTATGAAATTTTGATAATCACATCATGTAATTTTGAT-AACCTCGTTT-TGAAATTTTGATAACA
1 CTATGAAATTTTGATAATCACATCATGAAAATTTGATAAAACTC-TTTATCAAATTTTGATAACA
*
57441 ACACTATGCAATTTTG
65 ACACTAT-AAATTTTG
57457 ATAATTCTTC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
87 25 0.37
88 43 0.63
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.41
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATCATGAAAATTTGATAAAACTCTTTATCAAATTTTGATAACAA
CACTATAAATTTTGTTGACCCCT
Found at i:57475 original size:88 final size:88
Alignment explanation
Indices: 57290--57484 Score: 216
Period size: 88 Copynumber: 2.2 Consensus size: 88
57280 AGAAATACCA
** **
57290 CTATGAAATTTTGATAATCACATTTTGAAAATTTGATAAAACTCTTTATCAAATTTTGATAACCT
1 CTATGAAATTTTGATAATCACATCATGAAAATTTGATAAAACTCTTTATCAAATTTTGATAACAA
* *
57355 CACTATAAATTTTGTTGACCCCT
66 CACTATAAATTTTGATAACCCCT
* * * *
57378 CTATGAAATTTTGATAATCACATCATGTAATTTTGAT-AACCTCGTTT-TGAAATTTTGATAACA
1 CTATGAAATTTTGATAATCACATCATGAAAATTTGATAAAACTC-TTTATCAAATTTTGATAACA
* ** *
57441 ACACTATGCAATTTTGATAATTCTT
65 ACACTAT-AAATTTTGATAACCCCT
57466 CCTAT-AAATTTTGATAATC
1 -CTATGAAATTTTGATAATC
57485 CGATCTCTAT
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
87 25 0.28
88 61 0.68
89 4 0.04
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.42
Consensus pattern (88 bp):
CTATGAAATTTTGATAATCACATCATGAAAATTTGATAAAACTCTTTATCAAATTTTGATAACAA
CACTATAAATTTTGATAACCCCT
Found at i:57783 original size:22 final size:22
Alignment explanation
Indices: 57749--57807 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 22
57739 ACCTTTATAT
* *
57749 AAAATTGTGATAACCGCACT-AT
1 AAAATT-TAATAACCGCACTAAG
**
57771 AAAATTTCAATAACCTTACTAAG
1 AAAATTT-AATAACCGCACTAAG
57794 AAAATTTAATAACC
1 AAAATTTAATAACC
57808 CGATCCTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 22 0.71
23 8 0.26
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (22 bp):
AAAATTTAATAACCGCACTAAG
Found at i:57842 original size:22 final size:22
Alignment explanation
Indices: 57814--57966 Score: 114
Period size: 22 Copynumber: 7.0 Consensus size: 22
57804 AACCCGATCC
*
57814 TATGAAATTTTGGTAACCACAT
1 TATGAAATTTTGATAACCACAT
* *
57836 TATGAAATTTTGATAACCTTC-C
1 TATGAAATTTTGATAACC-ACAT
* ** *
57858 CATGAAATTTTGATAACTTCCT
1 TATGAAATTTTGATAACCACAT
* *
57880 GATGAAATTTTTG-TAACCACAC
1 TATGAAA-TTTTGATAACCACAT
* * *
57902 TATGGAATTTTGATAACCTCCT
1 TATGAAATTTTGATAACCACAT
* * * *
57924 CACGAAATTATAATAACCATC-T
1 TATGAAATTTTGATAACCA-CAT
57946 TATGAAATTTTGATAACCACA
1 TATGAAATTTTGATAACCACA
57967 CAGAGACACG
Statistics
Matches: 99, Mismatches: 26, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
21 8 0.08
22 84 0.85
23 7 0.07
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAT
Found at i:57885 original size:44 final size:43
Alignment explanation
Indices: 57811--57963 Score: 146
Period size: 44 Copynumber: 3.5 Consensus size: 43
57801 AATAACCCGA
* * * *
57811 TCCTATGAAATTTTGGTAACCACATTATGAAATTTTGATAACC
1 TCCTATGAAATTTTGATAACCTCCTCATGAAATTTTGATAACC
* * *
57854 TTCCCATGAAATTTTGATAACTTCCTGATGAAATTTTTG-TAACC
1 -TCCTATGAAATTTTGATAACCTCCTCATGAAA-TTTTGATAACC
* * * * *
57898 ACACTATGGAATTTTGATAACCTCCTCACGAAATTATAATAACC
1 TC-CTATGAAATTTTGATAACCTCCTCATGAAATTTTGATAACC
*
57942 ATCTTATGAAATTTTGATAACC
1 -TCCTATGAAATTTTGATAACC
57964 ACACAGAGAC
Statistics
Matches: 88, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
43 4 0.05
44 78 0.89
45 6 0.07
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (43 bp):
TCCTATGAAATTTTGATAACCTCCTCATGAAATTTTGATAACC
Found at i:57931 original size:66 final size:66
Alignment explanation
Indices: 57759--57967 Score: 201
Period size: 66 Copynumber: 3.1 Consensus size: 66
57749 AAAATTGTGA
* * ** * * *
57759 TAACCGCACTATAAAATTTCAATAACCTTACTAAGAAAATT-TAATAACCCGATCCTATGAAATT
1 TAACCACACTATGAAATTTTGATAACCTTCCCACG-AAATTATAATAA-CC-ATCCTATGAAATT
*
57823 TTGG
63 TTTG
* * * * *
57827 TAACCACATTATGAAATTTTGATAACCTTCCCATGAAATTTTGATAA-CTTCCTGATGAAATTTT
1 TAACCACACTATGAAATTTTGATAACCTTCCCACGAAATTATAATAACCATCCT-ATGAAATTTT
57891 TG
65 TG
* *
57893 TAACCACACTATGGAATTTTGATAACC-TCCTCACGAAATTATAATAACCATCTTATGAAA-TTT
1 TAACCACACTATGAAATTTTGATAACCTTCC-CACGAAATTATAATAACCATCCTATGAAATTTT
57956 TG
65 TG
57958 ATAACCACAC
1 -TAACCACAC
57968 AGAGACACGA
Statistics
Matches: 118, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
65 12 0.10
66 65 0.55
67 9 0.08
68 32 0.27
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (66 bp):
TAACCACACTATGAAATTTTGATAACCTTCCCACGAAATTATAATAACCATCCTATGAAATTTTT
G
Found at i:58155 original size:20 final size:20
Alignment explanation
Indices: 58130--58168 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
58120 TATTGACACT
*
58130 TAAAATTTTGAAATT-AAAAG
1 TAAAATATT-AAATTCAAAAG
58150 TAAAATATTAAATTCAAAA
1 TAAAATATTAAATTCAAAA
58169 AAATTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (20 bp):
TAAAATATTAAATTCAAAAG
Found at i:61071 original size:19 final size:19
Alignment explanation
Indices: 61047--61083 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61037 TTTTTCACTT
61047 ACTTTGTCATTGATTTTTA
1 ACTTTGTCATTGATTTTTA
*
61066 ACTTTGTTATTGATTTTT
1 ACTTTGTCATTGATTTTT
61084 TTTAACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.08, G:0.11, T:0.62
Consensus pattern (19 bp):
ACTTTGTCATTGATTTTTA
Found at i:65144 original size:3 final size:3
Alignment explanation
Indices: 65138--65257 Score: 195
Period size: 3 Copynumber: 39.7 Consensus size: 3
65128 AGATTATTAT
* *
65138 TAA TAA TAA TAA TCA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TCA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
65186 TAA TAA TCA TAA TAA TAA TCA TAA TAA TCAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
65232 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
65258 TATACCCTAT
Statistics
Matches: 108, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
3 105 0.97
4 3 0.03
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:74083 original size:92 final size:92
Alignment explanation
Indices: 73926--74110 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
73916 GTAGAACAAA
73926 TATTCTAAGCCATCAACCGTTTCTGAAAAGAAAACTCTCTAACATTTTGCTAGCACAACACAAAA
1 TATTCTAAGCCATCAACCGTTTCTGAAAAGAAAACTCTCTAACATTTTGCTAGCACAACACAAAA
73991 GAGACTCAAGCTTCAATCTTGATTGCT
66 GAGACTCAAGCTTCAATCTTGATTGCT
*
74018 TATTCTAAGCCATCAACCGTTTCTGAAAAGAAAACTCTCTAACGTTTTGCTAGCACAACACAAAA
1 TATTCTAAGCCATCAACCGTTTCTGAAAAGAAAACTCTCTAACATTTTGCTAGCACAACACAAAA
74083 GAGACTCAAGCTTCAATCTTGATTGCT
66 GAGACTCAAGCTTCAATCTTGATTGCT
74110 T
1 T
74111 GTTGATCGTG
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (92 bp):
TATTCTAAGCCATCAACCGTTTCTGAAAAGAAAACTCTCTAACATTTTGCTAGCACAACACAAAA
GAGACTCAAGCTTCAATCTTGATTGCT
Found at i:81761 original size:22 final size:22
Alignment explanation
Indices: 81736--81780 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
81726 AGGAAAAAAA
*
81736 AGAAGATCATTAATGTAAAATC
1 AGAAGATCATTAATGGAAAATC
*
81758 AGAAGATCGTTAATGGAAAATC
1 AGAAGATCATTAATGGAAAATC
81780 A
1 A
81781 CCAAATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24
Consensus pattern (22 bp):
AGAAGATCATTAATGGAAAATC
Found at i:89250 original size:19 final size:21
Alignment explanation
Indices: 89215--89260 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
89205 TTTTTTAGAT
89215 TAACTA-TATATATATTG-AA
1 TAACTATTATATATATTGTAA
*
89234 TAACTATTATTTA-ATTGTAA
1 TAACTATTATATATATTGTAA
*
89254 TATCTAT
1 TAACTAT
89261 ACCTCTATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (21 bp):
TAACTATTATATATATTGTAA
Found at i:91345 original size:5 final size:5
Alignment explanation
Indices: 91331--91360 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
91321 AAAAAAAAAG
91331 AAGAA GAAGAA AAGAA AAGAA AAGAA AAGA
1 AAGAA -AAGAA AAGAA AAGAA AAGAA AAGA
91361 TGAAGAGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:91355 original size:15 final size:16
Alignment explanation
Indices: 91320--91366 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 16
91310 CCGAATCGAG
*
91320 GAAAAAAAAAGAAGAA
1 GAAAAGAAAAGAAGAA
91336 G--AAGAAAAGAA-AA
1 GAAAAGAAAAGAAGAA
*
91349 GAAAAGAAAAGATGAA
1 GAAAAGAAAAGAAGAA
91365 GA
1 GA
91367 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 9 0.35
15 9 0.35
16 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (16 bp):
GAAAAGAAAAGAAGAA
Found at i:91998 original size:14 final size:14
Alignment explanation
Indices: 91961--92003 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
91951 CTTATTACTG
91961 TTTTATT-AAT-AT
1 TTTTATTAAATGAT
91973 GTTTTA-TAAATGAT
1 -TTTTATTAAATGAT
91987 TTTTATTAAATGAT
1 TTTTATTAAATGAT
92001 TTT
1 TTT
92004 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.04
13 13 0.48
14 13 0.48
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (14 bp):
TTTTATTAAATGAT
Found at i:94519 original size:30 final size:30
Alignment explanation
Indices: 94463--94519 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
94453 AGGGTTTGTT
*
94463 ACAGACCCAAGAGCTCTATGCTCCATAAAA
1 ACAGACCCAAGAGCTCTATGCCCCATAAAA
* * *
94493 ACAGACCCAGGAGCTTTGTGCCCCATA
1 ACAGACCCAAGAGCTCTATGCCCCATA
94520 TCTCTGAAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.18
Consensus pattern (30 bp):
ACAGACCCAAGAGCTCTATGCCCCATAAAA
Found at i:94625 original size:2 final size:2
Alignment explanation
Indices: 94618--94665 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
94608 TCAAGGAGTT
94618 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
94660 GA GA GA
1 GA GA GA
94666 CGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Done.