Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013119.1 Corchorus capsularis cultivar CVL-1 contig13140, 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: 92337
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1848 original size:14 final size:15
Alignment explanation
Indices: 1813--1850 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1803 GAATTTTCTT
*
1813 AACCCGAAACTGACCC
1 AACCC-AAACTGACCA
1829 AACCCAAACT-ACCA
1 AACCCAAACTGACCA
1843 AACCCAAA
1 AACCCAAA
1851 TCCAACCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
15 5 0.24
16 5 0.24
ACGTcount: A:0.47, C:0.42, G:0.05, T:0.05
Consensus pattern (15 bp):
AACCCAAACTGACCA
Found at i:6363 original size:54 final size:54
Alignment explanation
Indices: 6300--6408 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
6290 CAAGGGGACA
6300 GTCAAGTGGTTAAGAGCTTGGCCCTCTAAAAGGAGATTTGAGGTTCAAATCCTG
1 GTCAAGTGGTTAAGAGCTTGGCCCTCTAAAAGGAGATTTGAGGTTCAAATCCTG
6354 GTCAAGTGGTTAAGAGCTTGGCCCTCTAAAAGGAGATTTGAGGTTCAAATCCTG
1 GTCAAGTGGTTAAGAGCTTGGCCCTCTAAAAGGAGATTTGAGGTTCAAATCCTG
6408 G
1 G
6409 ACAGACGGGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (54 bp):
GTCAAGTGGTTAAGAGCTTGGCCCTCTAAAAGGAGATTTGAGGTTCAAATCCTG
Found at i:6976 original size:22 final size:22
Alignment explanation
Indices: 6945--7002 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
6935 GACGAACAAA
6945 GCCTGGTCGCGACCTGCACCATG
1 GCCT-GTCGCGACCTGCACCATG
6968 GCCTGTCGCGACCTGCACCATG
1 GCCTGTCGCGACCTGCACCATG
6990 GCCTGTCGCGACC
1 GCCTGTCGCGACC
7003 CGAGCCAGGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 31 0.89
23 4 0.11
ACGTcount: A:0.12, C:0.41, G:0.29, T:0.17
Consensus pattern (22 bp):
GCCTGTCGCGACCTGCACCATG
Found at i:7077 original size:14 final size:14
Alignment explanation
Indices: 7045--7078 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
7035 ACTTCTTCTT
*
7045 CTTTAAAGATTTTT
1 CTTTAAAGATTTTC
*
7059 TTTTAAAGATTTTC
1 CTTTAAAGATTTTC
7073 CTTTAA
1 CTTTAA
7079 TTTCCTTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (14 bp):
CTTTAAAGATTTTC
Found at i:16192 original size:5 final size:5
Alignment explanation
Indices: 16182--16208 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
16172 AAGTTAAACC
16182 TTTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TT
16209 CTCAATACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTTAA
Found at i:27663 original size:24 final size:25
Alignment explanation
Indices: 27631--27679 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
27621 TTGAATGATT
*
27631 GAGATTTG-AAAGTTTGAAGGTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
*
27655 GAGAATTGAAAAGTTTGAAGTTTGA
1 GAGAATTGAAAAGTTTGAAGGTTGA
27680 AGTTTGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.37, C:0.00, G:0.31, T:0.33
Consensus pattern (25 bp):
GAGAATTGAAAAGTTTGAAGGTTGA
Found at i:27755 original size:20 final size:21
Alignment explanation
Indices: 27715--27757 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
27705 AAAATAGTCC
*
27715 AAAAGGGGGGCGGTGTCTAGT
1 AAAAGGGGGGCGGTATCTAGT
*
27736 AAAA-GGGGGCGGTATTTAGT
1 AAAAGGGGGGCGGTATCTAGT
27756 AA
1 AA
27758 TACCCTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.30, C:0.07, G:0.42, T:0.21
Consensus pattern (21 bp):
AAAAGGGGGGCGGTATCTAGT
Found at i:28929 original size:2 final size:2
Alignment explanation
Indices: 28913--28959 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
28903 GTTAAAAATA
* *
28913 AT AT AT A- AT AA AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
28954 AA AT AT
1 AT AT AT
28960 TTAAAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28959 original size:14 final size:14
Alignment explanation
Indices: 28908--28950 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28898 TAGTAGTTAA
28908 AAATA-ATATATAAT
1 AAATATATATAT-AT
28922 AAATATATATATAT
1 AAATATATATATAT
**
28936 ATTTATATATATAT
1 AAATATATATATAT
28950 A
1 A
28951 TATAAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATATATATATAT
Found at i:29016 original size:42 final size:42
Alignment explanation
Indices: 28969--29052 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
28959 TTTAAAATTA
28969 TAAAGGTGCAACATATTTAAAATTATAATACTTTCGAACTTT
1 TAAAGGTGCAACATATTTAAAATTATAATACTTTCGAACTTT
*
29011 TAAAGGTGCAATATATTTAAAATTATAATACTTTCGAACTTT
1 TAAAGGTGCAACATATTTAAAATTATAATACTTTCGAACTTT
29053 CCTACGCATC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (42 bp):
TAAAGGTGCAACATATTTAAAATTATAATACTTTCGAACTTT
Found at i:30868 original size:2 final size:2
Alignment explanation
Indices: 30863--30928 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
30853 AAATCACAAA
30863 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30905 AG AG A- AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
30929 ATGGCAAGAA
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31561 original size:11 final size:11
Alignment explanation
Indices: 31535--31568 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31525 TAGTATGTGT
*
31535 TTATTTATAT-
1 TTATTTATTTA
31545 TTATTTATTTA
1 TTATTTATTTA
31556 TTATTTATTTA
1 TTATTTATTTA
31567 TT
1 TT
31569 GGTCTGCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:31562 original size:15 final size:14
Alignment explanation
Indices: 31534--31568 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
31524 ATAGTATGTG
31534 TTTATTTATATTTA
1 TTTATTTATATTTA
31548 TTTATTTATTATTTA
1 TTTATTTA-TATTTA
31563 TTTATT
1 TTTATT
31569 GGTCTGCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTATTTATATTTA
Found at i:42223 original size:16 final size:15
Alignment explanation
Indices: 42194--42236 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
42184 AAGTCTTATT
* * *
42194 TTTTCATTTATTAAT
1 TTTTAATTTTTTAAC
42209 TTTTAATTCTTTTAAC
1 TTTTAATT-TTTTAAC
42225 TTTTAATTTTTT
1 TTTTAATTTTTT
42237 CTTTTGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATTTTTTAAC
Found at i:44249 original size:42 final size:43
Alignment explanation
Indices: 44184--44266 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
44174 CGTGTTTGGC
*
44184 TTATCGTGTCTCGTGTTTGAATCGTGTC-AGACACGATTAAGA
1 TTATCGTGTCTCGTGTGTGAATCGTGTCAAGACACGATTAAGA
*
44226 TTATCGTGTTTCGTGTCGT-AATCGTGTCAAGACACGATTAA
1 TTATCGTGTCTCGTGT-GTGAATCGTGTCAAGACACGATTAA
44267 CACGATTAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 24 0.65
43 13 0.35
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (43 bp):
TTATCGTGTCTCGTGTGTGAATCGTGTCAAGACACGATTAAGA
Found at i:44449 original size:2 final size:2
Alignment explanation
Indices: 44442--44473 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
44432 TATCTTTAAT
44442 TA TA TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44474 GTTTAGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45850 original size:28 final size:28
Alignment explanation
Indices: 45817--45910 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 28
45807 CCGCTGTAAT
45817 CATGCTTCAATTATGATCCTGCGGTAGA
1 CATGCTTCAATTATGATCCTGCGGTAGA
* * * *
45845 CCTGCTT-GATTGATTTGAATCCCGCTGTA-A
1 CATGCTTCAATT-A--TG-ATCCTGCGGTAGA
*
45875 TCATGCTTCAATCATGATCCTGCGGTAGA
1 -CATGCTTCAATTATGATCCTGCGGTAGA
45904 CATGCTT
1 CATGCTT
45911 GATTGATTTC
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
27 3 0.06
28 23 0.46
29 3 0.06
30 3 0.06
31 16 0.32
32 2 0.04
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (28 bp):
CATGCTTCAATTATGATCCTGCGGTAGA
Found at i:45896 original size:59 final size:59
Alignment explanation
Indices: 45804--45919 Score: 214
Period size: 59 Copynumber: 2.0 Consensus size: 59
45794 TCAATCTTGG
* *
45804 ATCCCGCTGTAATCATGCTTCAATTATGATCCTGCGGTAGACCTGCTTGATTGATTTGA
1 ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATGCTTGATTGATTTGA
45863 ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATGCTTGATTGATTT
1 ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATGCTTGATTGATTT
45920 CATCACTCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (59 bp):
ATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACATGCTTGATTGATTTGA
Found at i:54859 original size:15 final size:15
Alignment explanation
Indices: 54839--54880 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
54829 ATCCAAGTTT
54839 CTCATCTTCTTGTGG
1 CTCATCTTCTTGTGG
*
54854 CTCATCTTCTGGTGG
1 CTCATCTTCTTGTGG
54869 CTCATCTTCTTG
1 CTCATCTTCTTG
54881 CTTAGCAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.29, G:0.19, T:0.45
Consensus pattern (15 bp):
CTCATCTTCTTGTGG
Found at i:67792 original size:6 final size:6
Alignment explanation
Indices: 67783--67814 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
67773 TATATTCTGC
67783 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
67815 GCTTTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:71691 original size:21 final size:21
Alignment explanation
Indices: 71643--71691 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
71633 TAAAAAGATT
* * **
71643 AATTATAAAGAAAGCAAATTA
1 AATTAAAAACAAAGCAAAGCA
*
71664 AACTAAAAACAAAGCAAAGCA
1 AATTAAAAACAAAGCAAAGCA
71685 AATTAAA
1 AATTAAA
71692 TCTAAATCTA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.65, C:0.10, G:0.08, T:0.16
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGCA
Found at i:79190 original size:12 final size:12
Alignment explanation
Indices: 79173--79207 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
79163 AACCAAAACT
79173 AGCTAAAGCATG
1 AGCTAAAGCATG
79185 AGCTAAAGCATG
1 AGCTAAAGCATG
79197 AGCTAAAGCAT
1 AGCTAAAGCAT
79208 TCCCATCTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (12 bp):
AGCTAAAGCATG
Found at i:86615 original size:32 final size:31
Alignment explanation
Indices: 86526--86622 Score: 108
Period size: 32 Copynumber: 3.0 Consensus size: 31
86516 TGCTGCGCAA
86526 TAGCGGCGTCTAATGAAATAAACGCCACTATT
1 TAGCGGCGTCTAATGAAAT-AACGCCACTATT
86558 TAGCGGCG-CTTAATG-AATCCAACGCCACTATT
1 TAGCGGCGTC-TAATGAAAT--AACGCCACTATT
* * *
86590 TAGCGGCGTCAAACGAAATAGACGCCGCTATT
1 TAGCGGCGTCTAATGAAATA-ACGCCACTATT
86622 T
1 T
86623 GGTGGAGTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 5 0.09
32 47 0.84
33 4 0.07
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (31 bp):
TAGCGGCGTCTAATGAAATAACGCCACTATT
Found at i:87354 original size:188 final size:188
Alignment explanation
Indices: 87048--87414 Score: 626
Period size: 188 Copynumber: 2.0 Consensus size: 188
87038 TAAACTAAGT
* *
87048 AGACGCCGCTATTTGGGTGGAGTCCATCTGGGCTCCCAGTTACCACCCAATTGGGAGCCCGGTTG
1 AGACGCCGCTATTTGGGTGGAGTCCATCTGGGATCACAGTTACCACCCAATTGGGAGCCCGGTTG
* * * * *
87113 GACCCTTCAATTTGGGGCGAAGTCATTGTCCTGACTGGGAGCCGACTTCGCCCCCAGCCGGGCCC
66 GACCCTTCAATTTGAGGCGAAGTCACTGTCCTGACTGGGAGCCAACATCGCCCCCAACCGGGCCC
* *
87178 CCAGGTCTCATTTCTTGTCTAATTTATTTCCTCGTAAATGGTGGCGTCTTAGGTAACA
131 CCAGGTCTCATTTCTTGTCTAATTTATTTCCTCATAAATGGCGGCGTCTTAGGTAACA
87236 AGACGCCGCTATTTGGGTGGAGTCCATCTGGGATCACAGTTACCACCCAATTGGGAGCCCGGTTG
1 AGACGCCGCTATTTGGGTGGAGTCCATCTGGGATCACAGTTACCACCCAATTGGGAGCCCGGTTG
*
87301 GACCCTTCAATTTGAGGCGAAGTCACTGTCCTGACTGGGAGCCAACATCGCCCCGAACCGGGCCC
66 GACCCTTCAATTTGAGGCGAAGTCACTGTCCTGACTGGGAGCCAACATCGCCCCCAACCGGGCCC
* *
87366 CCAGGTCTCCTTTCTTGTCTAATTTATTTCCTCATAGATGGCGGCGTCT
131 CCAGGTCTCATTTCTTGTCTAATTTATTTCCTCATAAATGGCGGCGTCT
87415 GAGTTGTTAA
Statistics
Matches: 167, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
188 167 1.00
ACGTcount: A:0.18, C:0.29, G:0.26, T:0.26
Consensus pattern (188 bp):
AGACGCCGCTATTTGGGTGGAGTCCATCTGGGATCACAGTTACCACCCAATTGGGAGCCCGGTTG
GACCCTTCAATTTGAGGCGAAGTCACTGTCCTGACTGGGAGCCAACATCGCCCCCAACCGGGCCC
CCAGGTCTCATTTCTTGTCTAATTTATTTCCTCATAAATGGCGGCGTCTTAGGTAACA
Found at i:87719 original size:6 final size:6
Alignment explanation
Indices: 87708--87743 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
87698 TCATCATTTG
*
87708 TTTCCT TTTCCT TTTCC- TTTCCT TCTCCT TTTCCT T
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT T
87744 CCGTCAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TTTCCT
Found at i:87730 original size:17 final size:17
Alignment explanation
Indices: 87708--87743 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
87698 TCATCATTTG
*
87708 TTTCCTTTTCCTTTTCC
1 TTTCCTTCTCCTTTTCC
87725 TTTCCTTCTCCTTTTCC
1 TTTCCTTCTCCTTTTCC
87742 TT
1 TT
87744 CCGTCAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTCCTTCTCCTTTTCC
Found at i:87781 original size:23 final size:23
Alignment explanation
Indices: 87755--87839 Score: 66
Period size: 25 Copynumber: 3.5 Consensus size: 23
87745 CGTCAGTTCT
87755 CCCTTCTCCTCTCATTCGATTCG
1 CCCTTCTCCTCTCATTCGATTCG
*
87778 CCCTTC-CTCTCCATCAATTCGCA-GCG
1 CCCTTCTC-CT-C-TC-ATTCG-ATTCG
* *
87804 GCCTTCTCCTCTCCTTCGATTCATG
1 CCCTTCTCCTCTCATTCGATTC--G
87829 CCCTTCTCCTC
1 CCCTTCTCCTC
87840 AAGAGTAAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
22 2 0.04
23 13 0.27
24 3 0.06
25 14 0.29
26 14 0.29
27 2 0.04
ACGTcount: A:0.09, C:0.46, G:0.09, T:0.35
Consensus pattern (23 bp):
CCCTTCTCCTCTCATTCGATTCG
Found at i:87870 original size:6 final size:6
Alignment explanation
Indices: 87859--87894 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
87849 TCATCATTTG
*
87859 TTTCCT TTTCCT TTTCC- TTTCCT TCTCCT TTTCCT T
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT T
87895 CCGTCAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
TTTCCT
Found at i:87871 original size:151 final size:151
Alignment explanation
Indices: 87597--87905 Score: 582
Period size: 151 Copynumber: 2.0 Consensus size: 151
87587 TTTTTCTCCA
* * *
87597 CAGTTCTCCCTTCTCCTCTCCTTCGATTCGCCCTTCCTCTCCATCGATTCGCAGTGGCCTTCTCC
1 CAGTTCTCCCTTCTCCTCTCATTCGATTCGCCCTTCCTCTCCATCAATTCGCAGCGGCCTTCTCC
87662 TCTCCTTCGATTCACGCCCTTCTCCTCAAGAGTAAGTCATCATTTGTTTCCTTTTCCTTTTCCTT
66 TCTCCTTCGATTCACGCCCTTCTCCTCAAGAGTAAGTCATCATTTGTTTCCTTTTCCTTTTCCTT
87727 TCCTTCTCCTTTTCCTTCCGT
131 TCCTTCTCCTTTTCCTTCCGT
87748 CAGTTCTCCCTTCTCCTCTCATTCGATTCGCCCTTCCTCTCCATCAATTCGCAGCGGCCTTCTCC
1 CAGTTCTCCCTTCTCCTCTCATTCGATTCGCCCTTCCTCTCCATCAATTCGCAGCGGCCTTCTCC
*
87813 TCTCCTTCGATTCATGCCCTTCTCCTCAAGAGTAAGTCATCATTTGTTTCCTTTTCCTTTTCCTT
66 TCTCCTTCGATTCACGCCCTTCTCCTCAAGAGTAAGTCATCATTTGTTTCCTTTTCCTTTTCCTT
87878 TCCTTCTCCTTTTCCTTCCGT
131 TCCTTCTCCTTTTCCTTCCGT
87899 CAGTTCT
1 CAGTTCT
87906 GCTTTCGTTT
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 154 1.00
ACGTcount: A:0.10, C:0.39, G:0.10, T:0.42
Consensus pattern (151 bp):
CAGTTCTCCCTTCTCCTCTCATTCGATTCGCCCTTCCTCTCCATCAATTCGCAGCGGCCTTCTCC
TCTCCTTCGATTCACGCCCTTCTCCTCAAGAGTAAGTCATCATTTGTTTCCTTTTCCTTTTCCTT
TCCTTCTCCTTTTCCTTCCGT
Found at i:87881 original size:17 final size:17
Alignment explanation
Indices: 87859--87894 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
87849 TCATCATTTG
*
87859 TTTCCTTTTCCTTTTCC
1 TTTCCTTCTCCTTTTCC
87876 TTTCCTTCTCCTTTTCC
1 TTTCCTTCTCCTTTTCC
87893 TT
1 TT
87895 CCGTCAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTCCTTCTCCTTTTCC
Found at i:89600 original size:24 final size:24
Alignment explanation
Indices: 89568--89622 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
89558 GGATTTAGCA
89568 GCAAATGACGACCCAATTGAGGCT
1 GCAAATGACGACCCAATTGAGGCT
*
89592 GCAAATGACGACCCCATTGAGGCT
1 GCAAATGACGACCCAATTGAGGCT
89616 GCAAATG
1 GCAAATG
89623 GAGAGGATGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.16
Consensus pattern (24 bp):
GCAAATGACGACCCAATTGAGGCT
Found at i:89686 original size:27 final size:27
Alignment explanation
Indices: 89649--89738 Score: 101
Period size: 27 Copynumber: 3.3 Consensus size: 27
89639 TCCGGCCCTC
89649 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* ** * *
89676 CCCACTGCGACCGAAGCAGTGGTTCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* *
89703 CCCACTTCGACCCCA-ACTGTGGATCAT
1 CCCACTTCGACCCCAGA-AGTGGATCCT
89730 CCCACTTCG
1 CCCACTTCG
89739 CCTCGGGTCG
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (27 bp):
CCCACTTCGACCCCAGAAGTGGATCCT
Found at i:92289 original size:24 final size:24
Alignment explanation
Indices: 92250--92337 Score: 113
Period size: 24 Copynumber: 3.7 Consensus size: 24
92240 AATGCATATA
* * **
92250 GCGGCGTCCAGGCGCCCCCAAATG
1 GCGGCGTCCAGACGCCCCTATTTG
* *
92274 GTGGCGTCTAGACGCCCCTATTTG
1 GCGGCGTCCAGACGCCCCTATTTG
92298 GCGGCGTCCAGACGCCCCTATTTG
1 GCGGCGTCCAGACGCCCCTATTTG
*
92322 GCGGCGTCTAGACGCC
1 GCGGCGTCCAGACGCC
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.14, C:0.36, G:0.32, T:0.18
Consensus pattern (24 bp):
GCGGCGTCCAGACGCCCCTATTTG
Done.