Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012222.1 Corchorus capsularis cultivar CVL-1 contig12243, 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: 115156
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:1568 original size:19 final size:19
Alignment explanation
Indices: 1544--1582 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1534 CCACCAGACC
1544 ACCATTTCGTACGGTACGT
1 ACCATTTCGTACGGTACGT
1563 ACCATTTCGTACGGTACGT
1 ACCATTTCGTACGGTACGT
1582 A
1 A
1583 TGGTAATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (19 bp):
ACCATTTCGTACGGTACGT
Found at i:2787 original size:26 final size:26
Alignment explanation
Indices: 2734--2788 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2724 TGGATCTTCT
**
2734 TTCAATAATTCCCCAATAACTGGGTC
1 TTCAATAATTCCCCAATAACTGAATC
* * *
2760 TTCAGTAATTCTCCAATAATTGAATC
1 TTCAATAATTCCCCAATAACTGAATC
2786 TTC
1 TTC
2789 TTTGAAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (26 bp):
TTCAATAATTCCCCAATAACTGAATC
Found at i:5369 original size:31 final size:32
Alignment explanation
Indices: 5309--5374 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
5299 TCGGGTTGGG
*
5309 AAAGAAGGAGAAGAGGAAAAAAAGAAAAAGAA
1 AAAGAAGGAAAAGAGGAAAAAAAGAAAAAGAA
* *
5341 AAAGAA-GAAAAGAGGGAAAATAAGAAAAGGAA
1 AAAGAAGGAAAAGA-GGAAAAAAAGAAAAAGAA
5373 AA
1 AA
5375 TGAAAAAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (32 bp):
AAAGAAGGAAAAGAGGAAAAAAAGAAAAAGAA
Found at i:8971 original size:303 final size:303
Alignment explanation
Indices: 8420--9026 Score: 980
Period size: 303 Copynumber: 2.0 Consensus size: 303
8410 TACTTCTCAA
* * *
8420 GCAGAAGAAGATGGTGAAATACCGATGACTGAGGCACAGGTGTTCCACGTTTTTATACTTTTTTT
1 GCAGAAGAAGATGGTGAAATACCGATGACTGAGGCACAGGTATTCCACGTTTTTATACTCTTCTT
* * *
8485 CGCAATTGTTAACTCACTTAAGTTTTTATATATAGGATCTTCAAGAGTCTTCTTAACAAATGTAT
66 CACAATTGCTAACTCACTTAAGTTTTTATATATAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* * * *
8550 CGTGACAAACTTTACCCAATACCATGAGTTCACCGCAACACTTCTTAGTGACAGTTCCGGTTTTG
131 CATGACAAACTTTACCCAATACCACGAGTTCACCGCAACACTTCTAAGTGACAGCTCCGGTTTTG
*
8615 AATATACTTGTGAAAACTTCCCTCACACAGGGTAGGCCCATTTTTGTCTTGCAATTATTTTCCTT
196 AATATACTTGTGAAAACTTCCCTCACACAGGGTAGGCCCATTTTTGGCTTGCAATTATTTTCCTT
*
8680 AATAATCAAGTCTGGGTTTTCTGCAGCGGAAACGACTCCACTT
261 AATAATCAAGTCTGGATTTTCTGCAGCGGAAACGACTCCACTT
* ** * *
8723 GCAGAAGAAGATGGTGATATGTCGATGACTGAGGCACATGTATTCCATGTTTTTATACTCTTCTT
1 GCAGAAGAAGATGGTGAAATACCGATGACTGAGGCACAGGTATTCCACGTTTTTATACTCTTCTT
* * *
8788 CACAATTGCTGACTCACTTAGGTTTTTATATATAGGATCTTCAAGAGTCTTCTTCACAAATGCAT
66 CACAATTGCTAACTCACTTAAGTTTTTATATATAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
* *
8853 CATGACAAACTTTTCCCAATACGACGAGTTCACCGCAACACTTCTAAGTGACAGCTCCGGTTTTG
131 CATGACAAACTTTACCCAATACCACGAGTTCACCGCAACACTTCTAAGTGACAGCTCCGGTTTTG
* *
8918 AATATACTTGTGAAAACTTCCCTCACACATGGTAGGCCCATTTTTGGCTTGCAATTATTTTTCTT
196 AATATACTTGTGAAAACTTCCCTCACACAGGGTAGGCCCATTTTTGGCTTGCAATTATTTTCCTT
* *
8983 AATAATCAAGTCTGGATTTTCTGCAGCTGAAACGACTCCGCTT
261 AATAATCAAGTCTGGATTTTCTGCAGCGGAAACGACTCCACTT
9026 G
1 G
9027 TTAAAACAAT
Statistics
Matches: 278, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
303 278 1.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (303 bp):
GCAGAAGAAGATGGTGAAATACCGATGACTGAGGCACAGGTATTCCACGTTTTTATACTCTTCTT
CACAATTGCTAACTCACTTAAGTTTTTATATATAGGATCTTCAAGAGTCTTCTTAACAAATGCAT
CATGACAAACTTTACCCAATACCACGAGTTCACCGCAACACTTCTAAGTGACAGCTCCGGTTTTG
AATATACTTGTGAAAACTTCCCTCACACAGGGTAGGCCCATTTTTGGCTTGCAATTATTTTCCTT
AATAATCAAGTCTGGATTTTCTGCAGCGGAAACGACTCCACTT
Found at i:12398 original size:31 final size:30
Alignment explanation
Indices: 12362--12446 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
12352 AAATTTAATC
* *
12362 ATTTTGTCCCCTAACCTTTTAAAATCTTGAA
1 ATTTTG-CACCTAAACTTTTAAAATCTTGAA
*
12393 GTTTTGCACCTAAACTTTTAAAATCTTGAA
1 ATTTTGCACCTAAACTTTTAAAATCTTGAA
* * *
12423 ATTTTACTCTCAAAACTTTTAAAA
1 ATTTTGCAC-CTAAACTTTTAAAA
12447 GTTTGTTGAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
30 28 0.61
31 18 0.39
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (30 bp):
ATTTTGCACCTAAACTTTTAAAATCTTGAA
Found at i:26667 original size:2 final size:2
Alignment explanation
Indices: 26660--26684 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
26650 ACCCATGTTC
26660 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
26685 AATTTTTATC
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:36232 original size:19 final size:19
Alignment explanation
Indices: 36208--36244 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
36198 TGTTTAGTAC
36208 ACCGTTTCACCACCGTTTA
1 ACCGTTTCACCACCGTTTA
*
36227 ACCGTTTCATCACCGTTT
1 ACCGTTTCACCACCGTTT
36245 TGGGTCCAAG
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:0.35, G:0.11, T:0.35
Consensus pattern (19 bp):
ACCGTTTCACCACCGTTTA
Found at i:36732 original size:2 final size:2
Alignment explanation
Indices: 36725--36780 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
36715 TAGTTTAATA
* *
36725 AT AT AT AT AA AT -T AT AT AT AT AT AT AT AT AA AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
36764 AA AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
36781 TTTAATTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
1 4 0.09
2 40 0.91
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:40631 original size:3 final size:3
Alignment explanation
Indices: 40623--40664 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
40613 TAAACAGTTA
40623 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40665 ATAATATCAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:41106 original size:40 final size:41
Alignment explanation
Indices: 41027--41109 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 41
41017 AAATAAAATA
*
41027 AAATCAATTAGAGTACATATAGACAAGTTTAGTGGGGTACAT
1 AAATCAATTAGAGTACATATAGA-AAGTTAAGTGGGGTACAT
41069 AAATCAATTAGAGTACATATAG-AAGTTAAGTGGGGTACAT
1 AAATCAATTAGAGTACATATAGAAAGTTAAGTGGGGTACAT
41109 A
1 A
41110 TTTATATTAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 18 0.45
42 22 0.55
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (41 bp):
AAATCAATTAGAGTACATATAGAAAGTTAAGTGGGGTACAT
Found at i:56745 original size:25 final size:25
Alignment explanation
Indices: 56717--56767 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
56707 GGGGAAACTC
*
56717 ATAGAGGAGCTTTTTAGTCATCCGA
1 ATAGAGAAGCTTTTTAGTCATCCGA
56742 ATAGAGAAGCTTTTTAGTCATCCGA
1 ATAGAGAAGCTTTTTAGTCATCCGA
56767 A
1 A
56768 AATTGAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (25 bp):
ATAGAGAAGCTTTTTAGTCATCCGA
Found at i:57351 original size:13 final size:13
Alignment explanation
Indices: 57329--57359 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
57319 ATATTTTTAT
*
57329 ATATACTAATATA
1 ATATAATAATATA
57342 ATATAATAATATA
1 ATATAATAATATA
57355 ATATA
1 ATATA
57360 CATTGAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:57409 original size:2 final size:2
Alignment explanation
Indices: 57402--57435 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
57392 TTGAACTTAG
57402 TA TA TA TA TA TA TA -A TA T- 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 TA TA
57436 CATCCTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58069 original size:84 final size:84
Alignment explanation
Indices: 57928--58097 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 84
57918 GCCAACAAAT
*
57928 AAACCCAATGAAATCTCATTACAATTCAAATAAATCTCTATGCCCATAAATAAACTACCTACCTA
1 AAACCCAATGAAATCTCATTACAATTCAAATAAATCTCTATGCCCATAAATAAACTACATACCTA
57993 CCAAATACATAAATAAACA
66 CCAAATACATAAATAAACA
58012 AAACCCAATGAAATCTCATTACAATTCAAATAAATCTCTATGCCCATAAATAAACTACATACCTA
1 AAACCCAATGAAATCTCATTACAATTCAAATAAATCTCTATGCCCATAAATAAACTACATACCTA
58077 CCAAATACATAAATAAACA
66 CCAAATACATAAATAAACA
58096 AA
1 AA
58098 TTACAAATAA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (84 bp):
AAACCCAATGAAATCTCATTACAATTCAAATAAATCTCTATGCCCATAAATAAACTACATACCTA
CCAAATACATAAATAAACA
Found at i:58831 original size:12 final size:12
Alignment explanation
Indices: 58813--58856 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 12
58803 GTATGGTGAT
58813 AATAATATAATA
1 AATAATATAATA
*
58825 TATAATATAATA
1 AATAATATAATA
58837 AATATATAAATAATA
1 AATA-AT--ATAATA
58852 AATAA
1 AATAA
58857 GTAGTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 14 0.52
13 2 0.07
14 1 0.04
15 10 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
AATAATATAATA
Found at i:58852 original size:7 final size:7
Alignment explanation
Indices: 58813--58856 Score: 52
Period size: 8 Copynumber: 5.7 Consensus size: 7
58803 GTATGGTGAT
58813 AATAATA
1 AATAATA
58820 TAATATATA
1 -AATA-ATA
58829 ATATAATA
1 A-ATAATA
58837 AATATATA
1 AATA-ATA
58845 AATAATA
1 AATAATA
58852 AATAA
1 AATAA
58857 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 11 0.33
8 16 0.48
9 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
AATAATA
Found at i:58864 original size:20 final size:20
Alignment explanation
Indices: 58811--58866 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
58801 TGGTATGGTG
*
58811 ATAAT-AATATAATATATAAT
1 ATAATAAATAT-ATAAATAAT
58831 ATAATAAATATATAAATAAT
1 ATAATAAATATATAAATAAT
*
58851 A-AATAAGTAGTATAAA
1 ATAATAAATA-TATAAA
58867 AAGGAGGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.22
20 20 0.62
21 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
ATAATAAATATATAAATAAT
Found at i:61054 original size:11 final size:11
Alignment explanation
Indices: 61032--61061 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
61022 CTATTGACCG
61032 AAGAAGAAAAAA
1 AAGAA-AAAAAA
61044 AAGAAAAAAAA
1 AAGAAAAAAAA
61055 AAGAAAA
1 AAGAAAA
61062 TATATCAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:61725 original size:24 final size:25
Alignment explanation
Indices: 61680--61745 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
61670 AGATGAAGAG
*
61680 AAAAACGAATAAAGAATAATAA-AA
1 AAAAAAGAATAAAGAATAATAACAA
** *
61704 AAAAAAGAATAAAGCTTTATAACGCAA
1 AAAAAAGAATAAAGAATAATAA--CAA
61731 AAAAAAGGAATAAAG
1 AAAAAA-GAATAAAG
61746 TTTTTATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 18 0.53
27 8 0.24
28 8 0.24
ACGTcount: A:0.68, C:0.06, G:0.12, T:0.14
Consensus pattern (25 bp):
AAAAAAGAATAAAGAATAATAACAA
Found at i:62710 original size:22 final size:25
Alignment explanation
Indices: 62685--62739 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
62675 CCATTATCTC
62685 TTATTTATTT-C-AT-AAAAATCAA
1 TTATTTATTTGCAATAAAAAATCAA
62707 TTATTT-TTTGGCAATAAAAAATCAA
1 TTATTTATTT-GCAATAAAAAATCAA
62732 TTAATTTA
1 TT-ATTTA
62740 AGTATGTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 3 0.11
22 6 0.22
23 1 0.04
24 2 0.07
25 11 0.41
26 4 0.15
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (25 bp):
TTATTTATTTGCAATAAAAAATCAA
Found at i:65984 original size:14 final size:14
Alignment explanation
Indices: 65965--65994 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
65955 ATAGCATGTA
65965 AGGAATTTTAAATG
1 AGGAATTTTAAATG
65979 AGGAATTTTAAATG
1 AGGAATTTTAAATG
65993 AG
1 AG
65995 CCAAAAAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (14 bp):
AGGAATTTTAAATG
Found at i:72565 original size:31 final size:29
Alignment explanation
Indices: 72524--72592 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
72514 CAAATTTAGA
* *
72524 CTCAAATTGGTGCATTTTGATAAGGTTTAAG
1 CTCAAATTGGTACAGTTT-A-AAGGTTTAAG
*
72555 CTCAATTTGGTACAGTTTAAAGGTTT-AG
1 CTCAAATTGGTACAGTTTAAAGGTTTAAG
72583 ACTCAAATTG
1 -CTCAAATTG
72593 AGCAAGTTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 15 0.45
30 1 0.03
31 15 0.45
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (29 bp):
CTCAAATTGGTACAGTTTAAAGGTTTAAG
Found at i:75644 original size:22 final size:22
Alignment explanation
Indices: 75613--75656 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
75603 GATGAGAAAG
*
75613 TCTTGACCGAAGCCAAGCCTAA
1 TCTTGACCGAAACCAAGCCTAA
*
75635 TCTTGGCCGAAACCAAGCCTAA
1 TCTTGACCGAAACCAAGCCTAA
75657 AGAAGGGGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (22 bp):
TCTTGACCGAAACCAAGCCTAA
Found at i:83560 original size:18 final size:18
Alignment explanation
Indices: 83533--83574 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
83523 ATCTACTCCC
* *
83533 AAAAAGAAAAGAAAAG-A
1 AAAAAAAAAAAAAAAGTA
*
83550 AAAAAAAAAAACAAAGTA
1 AAAAAAAAAAAAAAAGTA
83568 AAAAAAA
1 AAAAAAA
83575 GTCAGATAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAAAAAAGTA
Found at i:83576 original size:10 final size:9
Alignment explanation
Indices: 83533--83575 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
83523 ATCTACTCCC
83533 AAAAAGAAA
1 AAAAAGAAA
83542 AGAAAAGAAA
1 A-AAAAGAAA
83552 AAAAA-AAA
1 AAAAAGAAA
*
83560 ACAAAGTAAA
1 AAAAAG-AAA
83570 AAAAAG
1 AAAAAG
83576 TCAGATAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 7 0.24
9 5 0.17
10 17 0.59
ACGTcount: A:0.84, C:0.02, G:0.12, T:0.02
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:84908 original size:94 final size:94
Alignment explanation
Indices: 84788--84979 Score: 375
Period size: 94 Copynumber: 2.0 Consensus size: 94
84778 TCTTTCTTAA
*
84788 TGAATAGATTTCTTATTCAATATTTTCATCAACTCCAGATAACAAAAGAGCAAGTAGACTGACGA
1 TGAATAGATCTCTTATTCAATATTTTCATCAACTCCAGATAACAAAAGAGCAAGTAGACTGACGA
84853 ACCAAGAATACAAACATTGCAACACCCAG
66 ACCAAGAATACAAACATTGCAACACCCAG
84882 TGAATAGATCTCTTATTCAATATTTTCATCAACTCCAGATAACAAAAGAGCAAGTAGACTGACGA
1 TGAATAGATCTCTTATTCAATATTTTCATCAACTCCAGATAACAAAAGAGCAAGTAGACTGACGA
84947 ACCAAGAATACAAACATTGCAACACCCAG
66 ACCAAGAATACAAACATTGCAACACCCAG
84976 TGAA
1 TGAA
84980 GCTGAAAGAT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (94 bp):
TGAATAGATCTCTTATTCAATATTTTCATCAACTCCAGATAACAAAAGAGCAAGTAGACTGACGA
ACCAAGAATACAAACATTGCAACACCCAG
Found at i:85808 original size:33 final size:33
Alignment explanation
Indices: 85766--85832 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
85756 CCAAAAGAAA
85766 AAAGTTATGAGTATCAACTCAAACTATGACTGG
1 AAAGTTATGAGTATCAACTCAAACTATGACTGG
85799 AAAGTTATGAGTATCAACTCAAACTATGACTGG
1 AAAGTTATGAGTATCAACTCAAACTATGACTGG
85832 A
1 A
85833 TTTAATTTGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (33 bp):
AAAGTTATGAGTATCAACTCAAACTATGACTGG
Found at i:94740 original size:109 final size:105
Alignment explanation
Indices: 94547--94789 Score: 364
Period size: 109 Copynumber: 2.3 Consensus size: 105
94537 ATTTAGTTTT
*
94547 AATTTTAATTTGGACTAAACTTAGTG-AA-TTAGTTATATATTTTATTTCTAAAACTCTATAACA
1 AATTTTAATTTGGACTAAACTTAGTGAAATTTAGTTATATATTTTATTTCTAAAACCCTATAACA
*
94610 ATATTATTAATTATGAAATTTACCCTTAAGATAAAAATAA
66 ATATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* *
94650 AATTTTAATTTGGAACTAAACTTAGTGAAATTATAGTTTTGTATTTTATTTCTAAAACCCTATAA
1 AATTTTAATTTGG-ACTAAACTTAGTGAAATT-TAGTTATATATTTTATTTCTAAAACCCTATAA
*
94715 CAATAAATTATTAATTTTGAAATTTACCCTTAAAATAAAAATAA
64 CAAT--ATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
* *
94759 AATTTTAATTTGGGGCTAAAGTTAGTGAAAT
1 AATTTTAATTT-GGACTAAACTTAGTGAAAT
94790 AAGACTAAAC
Statistics
Matches: 126, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
103 13 0.10
104 13 0.10
105 2 0.02
106 1 0.01
107 33 0.26
109 62 0.49
110 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (105 bp):
AATTTTAATTTGGACTAAACTTAGTGAAATTTAGTTATATATTTTATTTCTAAAACCCTATAACA
ATATTATTAATTATGAAATTTACCCTTAAAATAAAAATAA
Found at i:99057 original size:27 final size:27
Alignment explanation
Indices: 99019--99123 Score: 120
Period size: 27 Copynumber: 3.9 Consensus size: 27
99009 CCAAGTAAGA
*
99019 TGCCGCATCAACCCAAAATTGCAAAAT
1 TGCCGCAACAACCCAAAATTGCAAAAT
* *
99046 TGCCGCAGCAACCCAAAATTGCAAAGT
1 TGCCGCAACAACCCAAAATTGCAAAAT
* * * *
99073 TGCCGCAACTAGCCAAAATTACAAAAA
1 TGCCGCAACAACCCAAAATTGCAAAAT
* * *
99100 TCCCGCAACTAGCCAAAATTGCAA
1 TGCCGCAACAACCCAAAATTGCAA
99124 GAACCCTGCA
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.41, C:0.30, G:0.13, T:0.16
Consensus pattern (27 bp):
TGCCGCAACAACCCAAAATTGCAAAAT
Found at i:99134 original size:27 final size:27
Alignment explanation
Indices: 99075--99145 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
99065 TGCAAAGTTG
99075 CCGCAACTAGCCAAAATTACAAAAATC
1 CCGCAACTAGCCAAAATTACAAAAATC
* *
99102 CCGCAACTAGCCAAAATTGCAAGAA-C
1 CCGCAACTAGCCAAAATTACAAAAATC
* *
99128 CCTGCAACAAGACAAAAT
1 CC-GCAACTAGCCAAAAT
99146 CACCAAGGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
26 3 0.08
27 36 0.92
ACGTcount: A:0.46, C:0.30, G:0.11, T:0.13
Consensus pattern (27 bp):
CCGCAACTAGCCAAAATTACAAAAATC
Found at i:103745 original size:33 final size:34
Alignment explanation
Indices: 103685--103753 Score: 113
Period size: 33 Copynumber: 2.0 Consensus size: 34
103675 CAGTTTTAGG
*
103685 GGTCAAGAAGGTTTTTTTTATAAAAGTCACATGTA
1 GGTCAAGAAGG-TTTTTGTATAAAAGTCACATGTA
103720 GGTCAAGAAGG-TTTTGTATAAAAGTCACATGTA
1 GGTCAAGAAGGTTTTTGTATAAAAGTCACATGTA
103753 G
1 G
103754 ATGGAACCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
33 22 0.67
35 11 0.33
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.33
Consensus pattern (34 bp):
GGTCAAGAAGGTTTTTGTATAAAAGTCACATGTA
Found at i:109873 original size:18 final size:18
Alignment explanation
Indices: 109850--109885 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
109840 TGAAGATATG
109850 GAACCAACTAAAACAACA
1 GAACCAACTAAAACAACA
109868 GAACCAACTAAAACAACA
1 GAACCAACTAAAACAACA
109886 TCAGTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.28, G:0.06, T:0.06
Consensus pattern (18 bp):
GAACCAACTAAAACAACA
Found at i:114960 original size:14 final size:14
Alignment explanation
Indices: 114941--114968 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
114931 TTACCTATTA
114941 TAATTATATTATAT
1 TAATTATATTATAT
114955 TAATTATATTATAT
1 TAATTATATTATAT
114969 AGTAATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTATATTATAT
Found at i:114962 original size:9 final size:10
Alignment explanation
Indices: 114899--114968 Score: 56
Period size: 10 Copynumber: 6.6 Consensus size: 10
114889 ATACAAGTAC
114899 TTATAATTATA
1 TTAT-ATTATA
114910 -TATA-TATA
1 TTATATTATA
114918 TATATATATATA
1 T-TATAT-TATA
114930 CTTACCTATTATAA
1 -TTA--TATTAT-A
114944 TTATATTATA
1 TTATATTATA
114954 TTA-ATTATA
1 TTATATTATA
114963 TTATAT
1 TTATAT
114969 AGTAATATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
8 4 0.08
9 10 0.20
10 13 0.26
11 6 0.12
12 6 0.12
13 7 0.14
14 4 0.08
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (10 bp):
TTATATTATA
Done.