Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014353.1 Corchorus capsularis cultivar CVL-1 contig14374, 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: 90485
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5262 original size:43 final size:43
Alignment explanation
Indices: 5201--5283 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
5191 GAGATCTCGG
5201 CCCTAAGTTTTGTAAGTTTTCTTATGCCTCTCATGGATTTGGA
1 CCCTAAGTTTTGTAAGTTTTCTTATGCCTCTCATGGATTTGGA
*
5244 CCCTAAGTTTTGTAAGTTTTGTTATGCCTCTCATGGATTT
1 CCCTAAGTTTTGTAAGTTTTCTTATGCCTCTCATGGATTT
5284 CGAAAAATCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (43 bp):
CCCTAAGTTTTGTAAGTTTTCTTATGCCTCTCATGGATTTGGA
Found at i:5898 original size:31 final size:32
Alignment explanation
Indices: 5850--5922 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
5840 ATAGTTTCAC
* *
5850 CGGGTCATT-CGGCTTTCGGGTCATCTGGGT-T
1 CGGGTCATTCCAG-TTTCGGGTCATCCGGGTCT
* *
5881 CGGGTTATTCCAGTTTCGGGTTATCCGGGTCT
1 CGGGTCATTCCAGTTTCGGGTCATCCGGGTCT
5913 CGGGTCATTC
1 CGGGTCATTC
5923 GGGTCTCGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.08, C:0.23, G:0.33, T:0.36
Consensus pattern (32 bp):
CGGGTCATTCCAGTTTCGGGTCATCCGGGTCT
Found at i:5915 original size:16 final size:16
Alignment explanation
Indices: 5865--5934 Score: 63
Period size: 16 Copynumber: 4.4 Consensus size: 16
5855 CATTCGGCTT
* *
5865 TCGGGTCATCTGGGT-
1 TCGGGTTATCCGGGTC
* *
5880 TCGGGTTATTCC-AGTT
1 TCGGGTTA-TCCGGGTC
5896 TCGGGTTATCCGGGTC
1 TCGGGTTATCCGGGTC
* *
5912 TCGGGTCATTCGGGTC
1 TCGGGTTATCCGGGTC
5928 TCGGGTT
1 TCGGGTT
5935 GGGCGGGTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
15 12 0.27
16 32 0.73
ACGTcount: A:0.07, C:0.21, G:0.36, T:0.36
Consensus pattern (16 bp):
TCGGGTTATCCGGGTC
Found at i:6218 original size:42 final size:42
Alignment explanation
Indices: 6159--6240 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
6149 TAGATATTAA
*
6159 TTTTGAATATTAAATACATAATTGATTATCAGGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
6201 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
6241 TGTGTCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.37, C:0.05, G:0.20, T:0.39
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:6785 original size:32 final size:32
Alignment explanation
Indices: 6768--6859 Score: 148
Period size: 32 Copynumber: 2.9 Consensus size: 32
6758 CATGTCACTC
*
6768 GGGTTACGGGTCATTCGGGTTTCGGGTCATCT
1 GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
*
6800 GGGTTACAGGTCATTCGGGTCTCGGGTCATCT
1 GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
* *
6832 GGGTTGCGGGTCATCCGGGTCTCGGGTC
1 GGGTTACGGGTCATTCGGGTCTCGGGTC
6860 GGGCGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.09, C:0.22, G:0.39, T:0.30
Consensus pattern (32 bp):
GGGTTACGGGTCATTCGGGTCTCGGGTCATCT
Found at i:6826 original size:48 final size:48
Alignment explanation
Indices: 6751--6852 Score: 127
Period size: 48 Copynumber: 2.1 Consensus size: 48
6741 ATTCGGGTTT
* *
6751 CGGGTCACATGTCACTCGGGTTACGGGTCAT-TCGGGTTTCGGGTCATC
1 CGGGTCACAGGTCACTCGGGTTACGGGTCATCT-GGGTTGCGGGTCATC
* * *
6799 TGGGTTACAGGTCATTCGGGTCT-CGGGTCATCTGGGTTGCGGGTCATC
1 CGGGTCACAGGTCACTCGGGT-TACGGGTCATCTGGGTTGCGGGTCATC
6847 CGGGTC
1 CGGGTC
6853 TCGGGTCGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
48 43 0.96
49 2 0.04
ACGTcount: A:0.11, C:0.24, G:0.36, T:0.29
Consensus pattern (48 bp):
CGGGTCACAGGTCACTCGGGTTACGGGTCATCTGGGTTGCGGGTCATC
Found at i:6857 original size:16 final size:15
Alignment explanation
Indices: 6767--6859 Score: 87
Period size: 16 Copynumber: 5.8 Consensus size: 15
6757 ACATGTCACT
*
6767 CGGGTTACGGGTCATT
1 CGGGTT-CGGGTCATC
6783 CGGGTTTCGGGTCATC
1 CGGG-TTCGGGTCATC
* * *
6799 TGGGTTACAGGTCATT
1 CGGGTT-CGGGTCATC
6815 CGGGTCTCGGGTCATC
1 CGGGT-TCGGGTCATC
*
6831 TGGGTTGCGGGTCATC
1 CGGGTT-CGGGTCATC
6847 CGGGTCTCGGGTC
1 CGGGT-TCGGGTC
6860 GGGCGGTTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
15 3 0.05
16 56 0.89
17 4 0.06
ACGTcount: A:0.09, C:0.23, G:0.39, T:0.30
Consensus pattern (15 bp):
CGGGTTCGGGTCATC
Found at i:12779 original size:22 final size:22
Alignment explanation
Indices: 12749--12796 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
12739 TGTGGCTGGT
12749 TGTGCATGG-GCAAGGCCGGGTCA
1 TGTGCATGGTG-AAGGCCGGG-CA
*
12772 TGTG-ATGGTGATGGCCGGGCA
1 TGTGCATGGTGAAGGCCGGGCA
12793 TGTG
1 TGTG
12797 GCCGGTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.15, C:0.17, G:0.46, T:0.23
Consensus pattern (22 bp):
TGTGCATGGTGAAGGCCGGGCA
Found at i:14318 original size:11 final size:11
Alignment explanation
Indices: 14302--14326 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14292 CTCCTTGATA
14302 AACTCATATTG
1 AACTCATATTG
14313 AACTCATATTG
1 AACTCATATTG
14324 AAC
1 AAC
14327 ATAACGCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (11 bp):
AACTCATATTG
Found at i:14691 original size:33 final size:33
Alignment explanation
Indices: 14631--14702 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
14621 TTCTTTTCAC
* * * *
14631 CCAATACAAAATTATTTTCAATGCTATGATCAT
1 CCAAAACAAAATTATTTGCAATACTATGATCAA
*
14664 CCAAAACAGAATTATTTGCAATACTATGATCAA
1 CCAAAACAAAATTATTTGCAATACTATGATCAA
14697 CCAAAA
1 CCAAAA
14703 TAAATTTGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.29
Consensus pattern (33 bp):
CCAAAACAAAATTATTTGCAATACTATGATCAA
Found at i:17224 original size:22 final size:22
Alignment explanation
Indices: 17194--17241 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
17184 TGTGGCTAGT
17194 TGTGCATGG-GCAAGGCCGGGTCA
1 TGTGCATGGTG-AAGGCCGGG-CA
*
17217 TGTG-ATGGTGATGGCCGGGCA
1 TGTGCATGGTGAAGGCCGGGCA
17238 TGTG
1 TGTG
17242 GCCGGTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.15, C:0.17, G:0.46, T:0.23
Consensus pattern (22 bp):
TGTGCATGGTGAAGGCCGGGCA
Found at i:21547 original size:2 final size:2
Alignment explanation
Indices: 21540--21586 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
21530 CTAGTGTATA
21540 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
21582 TG TG T
1 TG TG T
21587 CTATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:22125 original size:11 final size:11
Alignment explanation
Indices: 22109--22151 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
22099 TATACTATAT
22109 CTAATTAATAG
1 CTAATTAATAG
* *
22120 CTAATTACTAT
1 CTAATTAATAG
*
22131 CTAATTAATGG
1 CTAATTAATAG
*
22142 TTAATTAATA
1 CTAATTAATA
22152 ATAATGAACA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:22133 original size:22 final size:22
Alignment explanation
Indices: 22106--22148 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
22096 CATTATACTA
22106 TATCTAATTAATAGCTAATTAC
1 TATCTAATTAATAGCTAATTAC
* *
22128 TATCTAATTAATGGTTAATTA
1 TATCTAATTAATAGCTAATTA
22149 ATAATAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (22 bp):
TATCTAATTAATAGCTAATTAC
Found at i:23528 original size:19 final size:19
Alignment explanation
Indices: 23504--23588 Score: 75
Period size: 19 Copynumber: 4.4 Consensus size: 19
23494 TCATATTACA
23504 TTTAATGAATTTAATGTGT
1 TTTAATGAATTTAATGTGT
*** *
23523 TTTAATTTGTTGAAATTGTGT
1 TTTAATGAATT-TAA-TGTGT
23544 ATTT--TGAATTTAATCGTGT
1 -TTTAATGAATTTAAT-GTGT
*
23563 TTTAATGGATTTAATGTGT
1 TTTAATGAATTTAATGTGT
23582 TTTAATG
1 TTTAATG
23589 TGTTTAATGA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
18 4 0.08
19 25 0.49
20 14 0.27
21 5 0.10
22 3 0.06
ACGTcount: A:0.27, C:0.01, G:0.18, T:0.54
Consensus pattern (19 bp):
TTTAATGAATTTAATGTGT
Found at i:23587 original size:10 final size:10
Alignment explanation
Indices: 23552--23597 Score: 60
Period size: 9 Copynumber: 4.7 Consensus size: 10
23542 GTATTTTGAA
23552 TTTAATCGTGT
1 TTTAAT-GTGT
*
23563 TTTAATG-GA
1 TTTAATGTGT
23572 TTTAATGTGT
1 TTTAATGTGT
23582 TTTAATGTG-
1 TTTAATGTGT
23591 TTTAATG
1 TTTAATG
23598 AATTGTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 15 0.47
10 11 0.34
11 6 0.19
ACGTcount: A:0.24, C:0.02, G:0.20, T:0.54
Consensus pattern (10 bp):
TTTAATGTGT
Found at i:23594 original size:19 final size:19
Alignment explanation
Indices: 23513--23597 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
23503 ATTTAATGAA
*
23513 TTTAATGTGTTTTAATTTG
1 TTTAATGTGTTTTAATGTG
* **
23532 TTGAAATTGTGTATTT--TGAA
1 TT-TAA-TGTGT-TTTAATGTG
23552 TTTAATCGTGTTTTAATG-G
1 TTTAAT-GTGTTTTAATGTG
23571 ATTTAATGTGTTTTAATGTG
1 -TTTAATGTGTTTTAATGTG
23591 TTTAATG
1 TTTAATG
23598 AATTGTGTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
18 4 0.08
19 26 0.50
20 14 0.27
21 5 0.10
22 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.19, T:0.55
Consensus pattern (19 bp):
TTTAATGTGTTTTAATGTG
Found at i:24565 original size:2 final size:2
Alignment explanation
Indices: 24503--24545 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
24493 AAAATCGGAT
*
24503 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
24545 T
1 T
24546 TATTTTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:24652 original size:29 final size:28
Alignment explanation
Indices: 24611--24668 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
24601 TATAATGTAT
*
24611 AAAACATTTACTAATT-TATCCAACAAAA
1 AAAACATCTACTAATTGTATCCAA-AAAA
*
24639 AAAACCATCTACTAATTGTTTCCAAAAAA
1 AAAA-CATCTACTAATTGTATCCAAAAAA
24668 A
1 A
24669 CCCTACTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 4 0.15
29 16 0.62
30 6 0.23
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.28
Consensus pattern (28 bp):
AAAACATCTACTAATTGTATCCAAAAAA
Found at i:31195 original size:22 final size:21
Alignment explanation
Indices: 31170--31212 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
31160 AACAAACACG
31170 TAACCCAAATGACCCAAGAAAT
1 TAACCCAAATGACCCAA-AAAT
**
31192 TAACCCGGATGACCCAAAAAT
1 TAACCCAAATGACCCAAAAAT
31213 ATTATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.47, C:0.28, G:0.12, T:0.14
Consensus pattern (21 bp):
TAACCCAAATGACCCAAAAAT
Found at i:32851 original size:131 final size:130
Alignment explanation
Indices: 32710--32967 Score: 365
Period size: 132 Copynumber: 2.0 Consensus size: 130
32700 AGAAATATAT
* *
32710 TTTAAAAATTCTAATATATCTAAG-TTTTTAATTAAATTAGCAAAATGATAAAAATAAAATAGGT
1 TTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGCAAAATGATAAAAATAAAATAGGT
32774 ATAAGGATATTAGATTTAAGTAAATAAAAAATAGAATTTGTAGTTGAGTAAAACTATAAAAGTAT
66 ATAAGGATATTAGATTTAAGTAAAT-AAAAATAGAATTTGTAGTTGAGTAAAACTATAAAAGTAT
32839 C
130 C
* *** * * *
32840 TTTAAATAATTCTAATATGTATAAGTTTTTTAATTAAAATAGTGCAATGGTAAAAATTAAATAGT
1 TTTAAA-AATTCTAATATATATAAGTTTTTTAATTAAAATAGCAAAATGATAAAAATAAAATAGG
* * * * *
32905 TATAAGGATATTAGATTTAATTGAATAAAAATAGAGTTTTTAGTTTAGTAAAACTATAAAAGT
65 TATAAGGATATTAGATTTAAGTAAATAAAAATAGAATTTGTAGTTGAGTAAAACTATAAAAGT
32968 TTAAACAATG
Statistics
Matches: 112, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
130 6 0.05
131 50 0.45
132 56 0.50
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.37
Consensus pattern (130 bp):
TTTAAAAATTCTAATATATATAAGTTTTTTAATTAAAATAGCAAAATGATAAAAATAAAATAGGT
ATAAGGATATTAGATTTAAGTAAATAAAAATAGAATTTGTAGTTGAGTAAAACTATAAAAGTATC
Found at i:33904 original size:25 final size:27
Alignment explanation
Indices: 33852--33904 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
33842 TTACTCAACT
* **
33852 AAAAACTCTATTTTTATTTTTCTGTAA
1 AAAAACTCTATTTTCATTTTAATGTAA
33879 AAAAACTCTATTTTCA-TTTAAT-TAA
1 AAAAACTCTATTTTCATTTTAATGTAA
33904 A
1 A
33905 TCTAATATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 4 0.17
26 4 0.17
27 15 0.65
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (27 bp):
AAAAACTCTATTTTCATTTTAATGTAA
Found at i:35602 original size:2 final size:2
Alignment explanation
Indices: 35595--35621 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35585 ACTATTTTAG
35595 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
35622 TCGAAGTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37978 original size:23 final size:22
Alignment explanation
Indices: 37946--37991 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
37936 ACTTCACATT
37946 ATAATTAGT-ATAGATTATTATA
1 ATAATTAGTAATA-ATTATTATA
37968 ATAATATAGTAATAATTATTATA
1 ATAAT-TAGTAATAATTATTATA
37991 A
1 A
37992 CATCTAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.23
23 14 0.64
24 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (22 bp):
ATAATTAGTAATAATTATTATA
Found at i:39631 original size:21 final size:21
Alignment explanation
Indices: 39607--39660 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
39597 CATCGGACCT
39607 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
39628 AATGGCATCTTCAATGGATCA
1 AATGGCATCTTCAATGGATCA
39649 AATGGCATCTTC
1 AATGGCATCTTC
39661 TTGGTGCTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (21 bp):
AATGGCATCTTCAATGGATCA
Found at i:39802 original size:30 final size:30
Alignment explanation
Indices: 39768--39830 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
39758 CATATTCAAG
* * * *
39768 TCCATGATAAGTCTTTGGCGCATCATTTCC
1 TCCATGATAAGCCTTGGGCACATCATTCCC
39798 TCCATGATAAGCCTTGGGCACATCATTCCC
1 TCCATGATAAGCCTTGGGCACATCATTCCC
39828 TCC
1 TCC
39831 CCCTTGAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGCCTTGGGCACATCATTCCC
Found at i:41835 original size:16 final size:17
Alignment explanation
Indices: 41805--41895 Score: 93
Period size: 16 Copynumber: 5.6 Consensus size: 17
41795 GTCATTTTCA
41805 GGTTCGGGCTTGAA-TCG
1 GGTTCGGG-TTGAATTCG
*
41822 GGTTCGGGTTGAATTTG
1 GGTTCGGGTTGAATTCG
**
41839 GG-TCAAGTT-AATTCG
1 GGTTCGGGTTGAATTCG
*
41854 GGTTCGGGTTGAATTTG
1 GGTTCGGGTTGAATTCG
*
41871 GG-TCAGGTT-AATTCG
1 GGTTCGGGTTGAATTCG
41886 GGTTCGGGTT
1 GGTTCGGGTT
41896 CAGTCTGGGT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
15 14 0.23
16 27 0.45
17 19 0.32
ACGTcount: A:0.14, C:0.11, G:0.38, T:0.36
Consensus pattern (17 bp):
GGTTCGGGTTGAATTCG
Found at i:41856 original size:15 final size:15
Alignment explanation
Indices: 41828--41888 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
41818 ATCGGGTTCG
*
41828 GGTTGAATTTGGGTCA
1 GGTT-AATTCGGGTCA
* *
41844 AGTTAATTCGGGTTCG
1 GGTTAATTCGGG-TCA
*
41860 GGTTGAATTTGGGTCA
1 GGTT-AATTCGGGTCA
41876 GGTTAATTCGGGT
1 GGTTAATTCGGGT
41889 TCGGGTTCAG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 15 0.42
16 14 0.39
17 7 0.19
ACGTcount: A:0.18, C:0.08, G:0.36, T:0.38
Consensus pattern (15 bp):
GGTTAATTCGGGTCA
Found at i:41905 original size:32 final size:32
Alignment explanation
Indices: 41819--41895 Score: 145
Period size: 32 Copynumber: 2.4 Consensus size: 32
41809 CGGGCTTGAA
41819 TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
*
41851 TCGGGTTCGGGTTGAATTTGGGTCAGGTTAAT
1 TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
41883 TCGGGTTCGGGTT
1 TCGGGTTCGGGTT
41896 CAGTCTGGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (32 bp):
TCGGGTTCGGGTTGAATTTGGGTCAAGTTAAT
Found at i:42064 original size:16 final size:16
Alignment explanation
Indices: 42043--42138 Score: 68
Period size: 16 Copynumber: 6.0 Consensus size: 16
42033 TTTTCATAAA
*
42043 TTTTCGAATTCGGGTT
1 TTTTCGAGTTCGGGTT
* *
42059 TTTTCGAGTTTGAGCTT
1 TTTTCGAGTTCG-GGTT
*
42076 TTTT-GGGTTCGGGTT
1 TTTTCGAGTTCGGGTT
* * * *
42091 TTTTCGGGTTTGAGCT
1 TTTTCGAGTTCGGGTT
* *
42107 TTTTCGGGTTCAGGTT
1 TTTTCGAGTTCGGGTT
* *
42123 TTTTCGGGTTCAGGTT
1 TTTTCGAGTTCGGGTT
42139 CAGGCGGGTT
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
15 7 0.11
16 51 0.78
17 7 0.11
ACGTcount: A:0.07, C:0.11, G:0.30, T:0.51
Consensus pattern (16 bp):
TTTTCGAGTTCGGGTT
Found at i:42129 original size:32 final size:32
Alignment explanation
Indices: 42055--42132 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
42045 TTCGAATTCG
* * *
42055 GGTTTTTTCGAGTTTGAGCTTTTTTGGGTTCG
1 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCA
42087 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCA
1 GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCA
42119 GGTTTTTTCGGGTT
1 GGTTTTTTCGGGTT
42133 CAGGTTCAGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.05, C:0.10, G:0.32, T:0.53
Consensus pattern (32 bp):
GGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCA
Found at i:42211 original size:15 final size:16
Alignment explanation
Indices: 42191--42220 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42181 CGGGTTCGAG
42191 TTTTCGGG-CGGGTTT
1 TTTTCGGGTCGGGTTT
42206 TTTTCGGGTCGGGTT
1 TTTTCGGGTCGGGTT
42221 CACTTTGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.00, C:0.13, G:0.40, T:0.47
Consensus pattern (16 bp):
TTTTCGGGTCGGGTTT
Found at i:42693 original size:25 final size:25
Alignment explanation
Indices: 42659--42719 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
42649 GAATCCACTA
42659 TGATTTTTCAAAGTTTCTGATTTTT
1 TGATTTTTCAAAGTTTCTGATTTTT
42684 TGATTTTTCAAAGTTTCTGATTTTT
1 TGATTTTTCAAAGTTTCTGATTTTT
42709 TGATTTTTCAA
1 TGATTTTTCAA
42720 CTAGATGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.59
Consensus pattern (25 bp):
TGATTTTTCAAAGTTTCTGATTTTT
Found at i:43505 original size:56 final size:57
Alignment explanation
Indices: 43344--43505 Score: 164
Period size: 56 Copynumber: 2.9 Consensus size: 57
43334 TTAATTACGT
43344 TTAATTGCATTGTTCTTTGTAATTTTTTTATAAGTGGTACATTAACTTGATTTAATTTTA
1 TTAATTGCATTGTTCTTTGTAATTTTTTTATAAGTGGTACATTAACTTGA-TT--TTTTA
* * **
43404 TTAATTG-ATT-TT-TTTCT-TTTTTTTTGGATAA-T--T-TTTTAA-TTGATTTTTT-
1 TTAATTGCATTGTTCTTTGTAATTTTTTT--ATAAGTGGTACATTAACTTGATTTTTTA
*
43453 TTCATTGCATTGTTCTTTGTAATTTTTTTATAAGTGGTACATTAACTTGATTT
1 TTAATTGCATTGTTCTTTGTAATTTTTTTATAAGTGGTACATTAACTTGATTT
43506 AATTAATTGA
Statistics
Matches: 82, Mismatches: 9, Indels: 26
0.70 0.08 0.22
Matches are distributed among these distances:
49 6 0.07
50 7 0.09
51 6 0.07
52 7 0.09
53 11 0.13
54 5 0.06
55 5 0.06
56 14 0.17
57 5 0.06
58 6 0.07
59 3 0.04
60 7 0.09
ACGTcount: A:0.23, C:0.06, G:0.11, T:0.60
Consensus pattern (57 bp):
TTAATTGCATTGTTCTTTGTAATTTTTTTATAAGTGGTACATTAACTTGATTTTTTA
Found at i:45351 original size:30 final size:29
Alignment explanation
Indices: 45307--45373 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
45297 ACAAAAGGGA
* * *
45307 TTATCTGA-CAAAATTGGTAATCTAGGGGC
1 TTATTTGACCAAAATT-GAAATCCAGGGGC
*
45336 TTATTTGACCAAAATTGAAATCCATGGGC
1 TTATTTGACCAAAATTGAAATCCAGGGGC
45365 TTATTTGAC
1 TTATTTGAC
45374 TATTGATGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 26 0.79
30 7 0.21
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.34
Consensus pattern (29 bp):
TTATTTGACCAAAATTGAAATCCAGGGGC
Found at i:45436 original size:74 final size:74
Alignment explanation
Indices: 45315--45464 Score: 282
Period size: 74 Copynumber: 2.0 Consensus size: 74
45305 GATTATCTGA
45315 CAAAATTGGTAATCTAGGGGCTTATTTGACCAAAATTGAAATCCATGGGCTTATTTGACTATTGA
1 CAAAATTGGTAATCTAGGGGCTTATTTGACCAAAATTGAAATCCATGGGCTTATTTGACTATTGA
*
45380 TGGAAGATT
66 CGGAAGATT
*
45389 CAAAATTGGTAATTTAGGGGCTTATTTGACCAAAATTGAAATCCATGGGCTTATTTGACTATTGA
1 CAAAATTGGTAATCTAGGGGCTTATTTGACCAAAATTGAAATCCATGGGCTTATTTGACTATTGA
45454 CGGAAGATT
66 CGGAAGATT
45463 CA
1 CA
45465 GGGCCTTTTT
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (74 bp):
CAAAATTGGTAATCTAGGGGCTTATTTGACCAAAATTGAAATCCATGGGCTTATTTGACTATTGA
CGGAAGATT
Found at i:55273 original size:14 final size:14
Alignment explanation
Indices: 55254--55285 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
55244 TCGAGTCTGA
55254 AAAATCTGAACCCG
1 AAAATCTGAACCCG
*
55268 AAAATCTGAACCTG
1 AAAATCTGAACCCG
55282 AAAA
1 AAAA
55286 ACCCGAACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.22, G:0.12, T:0.16
Consensus pattern (14 bp):
AAAATCTGAACCCG
Found at i:55734 original size:11 final size:11
Alignment explanation
Indices: 55720--55757 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
55710 ATTCATAACA
55720 AATTTATAATT
1 AATTTATAATT
55731 AATTTATAATT
1 AATTTATAATT
55742 -ATTTGATAATT
1 AATTT-ATAATT
*
55753 TATTT
1 AATTT
55758 TATCTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:55942 original size:70 final size:70
Alignment explanation
Indices: 55859--56013 Score: 231
Period size: 70 Copynumber: 2.2 Consensus size: 70
55849 TTGTTTAGGT
* * * *
55859 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACT
*
55923 ATTTTA
65 ATTATA
*
55929 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
55994 TTATA
66 TTATA
*
55999 TTTTACCATTTTACT
1 TTTTACTATTTTACT
56014 ATTTTAATTA
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
70 75 0.97
71 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATA
Found at i:56142 original size:23 final size:23
Alignment explanation
Indices: 56113--56156 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
56103 AAACTTTTGC
*
56113 AATTGAAAACACTATTTTTATTT
1 AATTGAAAACAATATTTTTATTT
**
56136 AATTGAATTCAATATTTTTAT
1 AATTGAAAACAATATTTTTAT
56157 AATATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.50
Consensus pattern (23 bp):
AATTGAAAACAATATTTTTATTT
Found at i:63136 original size:19 final size:21
Alignment explanation
Indices: 63112--63155 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
63102 GAAAATAATT
63112 ATTATTATTT-TTAA-AAATA
1 ATTATTATTTATTAATAAATA
*
63131 ATTATTATTTATTAATTAATA
1 ATTATTATTTATTAATAAATA
63152 ATTA
1 ATTA
63156 ATTTCGGCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 4 0.18
21 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTATTTATTAATAAATA
Found at i:73141 original size:15 final size:16
Alignment explanation
Indices: 73123--73160 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
73113 ATAAATTGAG
73123 TTCGGGTTAATTC-AA
1 TTCGGGTTAATTCGAA
*
73138 TTCGGGTTAATTCGGA
1 TTCGGGTTAATTCGAA
73154 TTCGGGT
1 TTCGGGT
73161 CACTTACACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.18, C:0.13, G:0.29, T:0.39
Consensus pattern (16 bp):
TTCGGGTTAATTCGAA
Found at i:73421 original size:29 final size:29
Alignment explanation
Indices: 73388--73445 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
73378 CCTATAATAG
*
73388 CTACCATAAATTTGTTGGAAGTTTATCTA
1 CTACCATAAATTTGTTGGAAGTTGATCTA
* *
73417 CTACCGTACATTTGTTGGAAGTTGATCTA
1 CTACCATAAATTTGTTGGAAGTTGATCTA
73446 TATTTGAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (29 bp):
CTACCATAAATTTGTTGGAAGTTGATCTA
Found at i:76182 original size:11 final size:10
Alignment explanation
Indices: 76164--76197 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
76154 AATTGTCTTC
76164 AAATCTTCAA
1 AAATCTTCAA
76174 AATATCTTCAA
1 AA-ATCTTCAA
76185 GAAATCTTCAA
1 -AAATCTTCAA
76196 AA
1 AA
76198 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:78820 original size:11 final size:11
Alignment explanation
Indices: 78804--78846 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
78794 TATAATATAT
78804 CTAATTAATAG
1 CTAATTAATAG
*
78815 CTAATTAATAT
1 CTAATTAATAG
78826 CTAATTAATAG
1 CTAATTAATAG
*
78837 TTAATTAATA
1 CTAATTAATA
78847 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:78827 original size:22 final size:22
Alignment explanation
Indices: 78800--78846 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
78790 CCATTATAAT
78800 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
78822 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
78844 ATA
1 ATA
78847 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:79828 original size:12 final size:12
Alignment explanation
Indices: 79811--79843 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
79801 AGTGCTAGTA
*
79811 ACTAGTTTATAT
1 ACTAGTATATAT
79823 ACTAGTATATAT
1 ACTAGTATATAT
79835 ACTA-TATAT
1 ACTAGTATAT
79844 TATTTTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (12 bp):
ACTAGTATATAT
Found at i:80016 original size:74 final size:72
Alignment explanation
Indices: 79938--80080 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 72
79928 CACTTTCGAG
79938 TGACTAAAAAGCCCCTCTATGAGTTTCCCATATTCCTTTTCCTTCTACCCTTTTTCGTAATTACA
1 TGACTAAAAAGCCCCTCTATGAGTTTCCC--ATTCCTTTTCCTTCTACCCTTTTTCGTAATTACA
*
80003 CTTTTCGGA
64 CATTTCGGA
80012 TGACTAAAAAGCCCCTCTATGAGTTTCCCATTCCTTTTCCTTCTACCCTTTTTCGTAATTACACA
1 TGACTAAAAAGCCCCTCTATGAGTTTCCCATTCCTTTTCCTTCTACCCTTTTTCGTAATTACACA
80077 TTTC
66 TTTC
80081 CCTTCCTTAA
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
72 39 0.57
74 29 0.43
ACGTcount: A:0.22, C:0.29, G:0.08, T:0.41
Consensus pattern (72 bp):
TGACTAAAAAGCCCCTCTATGAGTTTCCCATTCCTTTTCCTTCTACCCTTTTTCGTAATTACACA
TTTCGGA
Found at i:83382 original size:5 final size:5
Alignment explanation
Indices: 83372--83402 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
83362 TTTAAATATC
83372 ATTAT ATTAT ATTAT ATTAT ATTATT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTA-T ATTAT
83403 TATTCACTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTAT
Found at i:83600 original size:3 final size:3
Alignment explanation
Indices: 83582--83622 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
83572 ATGCTCATAA
*
83582 ATT ATT CTT A-T 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
83623 TTGAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:88539 original size:20 final size:20
Alignment explanation
Indices: 88500--88539 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
88490 TGTTTTTATA
* *
88500 GCTATTTTTCTATACTTTTT
1 GCTATTTTTATATACATTTT
*
88520 GCTATTTTTATATGCATTTT
1 GCTATTTTTATATACATTTT
88540 ACCCCTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.17, C:0.12, G:0.07, T:0.62
Consensus pattern (20 bp):
GCTATTTTTATATACATTTT
Done.