Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014020.1 Corchorus capsularis cultivar CVL-1 contig14041, 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: 96911
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3576 original size:13 final size:13
Alignment explanation
Indices: 3554--3594 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
3544 TCCATGGTAA
3554 TGATTCTTGAATT
1 TGATTCTTGAATT
*
3567 TGATTTTTGAATT
1 TGATTCTTGAATT
3580 TGATTCTTGAATT
1 TGATTCTTGAATT
3593 TG
1 TG
3595 CACTTTGTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.56
Consensus pattern (13 bp):
TGATTCTTGAATT
Found at i:9095 original size:17 final size:16
Alignment explanation
Indices: 9060--9112 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
9050 TATGATATCC
9060 TTTCCCTTCCTTCCTA
1 TTTCCCTTCCTTCCTA
*
9076 TTTCCCTTCTCTTGCTA
1 TTTCCCTTC-CTTCCTA
* *
9093 TTTCCTTTCCTTTCTA
1 TTTCCCTTCCTTCCTA
9109 TTTC
1 TTTC
9113 TTTCCTCCCT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.06, C:0.36, G:0.02, T:0.57
Consensus pattern (16 bp):
TTTCCCTTCCTTCCTA
Found at i:9176 original size:64 final size:64
Alignment explanation
Indices: 9075--9200 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 64
9065 CTTCCTTCCT
* *
9075 ATTTCCCTTCTCTTGCTATTTCCTTTCCTTTCTATTTCTTTCCTCCCTACCAAACAGACTCTAA
1 ATTTCCCTTCTCTTGCTATTTCCTTTCCTTTCTATTTCTTTCCTCCCAACCAAACAAACTCTAA
**
9139 ATTTCCCTTCTCTTGCTATTTCCTTTCCTTTCTATTTCTTTCCTTTCAACCAAACAAACTCT
1 ATTTCCCTTCTCTTGCTATTTCCTTTCCTTTCTATTTCTTTCCTCCCAACCAAACAAACTCT
9201 TAGAGTCTGT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.17, C:0.33, G:0.02, T:0.47
Consensus pattern (64 bp):
ATTTCCCTTCTCTTGCTATTTCCTTTCCTTTCTATTTCTTTCCTCCCAACCAAACAAACTCTAA
Found at i:9181 original size:15 final size:16
Alignment explanation
Indices: 9139--9185 Score: 60
Period size: 15 Copynumber: 2.9 Consensus size: 16
9129 CAGACTCTAA
* *
9139 ATTTCCCTTCTCTTGCT
1 ATTTCCTTTC-CTTTCT
9156 ATTTCCTTTCCTTTCT
1 ATTTCCTTTCCTTTCT
9172 ATTT-CTTTCCTTTC
1 ATTTCCTTTCCTTTC
9186 AACCAAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 10 0.36
16 9 0.32
17 9 0.32
ACGTcount: A:0.06, C:0.32, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTCCTTTCCTTTCT
Found at i:9743 original size:23 final size:24
Alignment explanation
Indices: 9710--9780 Score: 92
Period size: 26 Copynumber: 3.0 Consensus size: 24
9700 TTTCACACAT
*
9710 AAAAAAA-TAGCAGCCCATTT-CA
1 AAAAAAAGTAGCAGCCCATTTAAA
*
9732 AAAAAAAGTAGCAGGCCATTTGAAA
1 AAAAAAAGTAGCAGCCCATTT-AAA
9757 AAAAAATAGTAGCAGCCCATTTAA
1 AAAAAA-AGTAGCAGCCCATTTAA
9781 CCAAAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 7 0.17
23 12 0.29
25 9 0.21
26 14 0.33
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.18
Consensus pattern (24 bp):
AAAAAAAGTAGCAGCCCATTTAAA
Found at i:10074 original size:15 final size:15
Alignment explanation
Indices: 10051--10103 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
10041 AAAGAACTAT
*
10051 TTTCCTTCCTTCCCA
1 TTTCTTTCCTTCCCA
* *
10066 TTTCTTTCCAT-CCG
1 TTTCTTTCCTTCCCA
10080 TCTTCTTTCCTTCCCA
1 T-TTCTTTCCTTCCCA
10096 TTTCTTTC
1 TTTCTTTC
10104 GGACCAAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
14 3 0.10
15 25 0.81
16 3 0.10
ACGTcount: A:0.06, C:0.40, G:0.02, T:0.53
Consensus pattern (15 bp):
TTTCTTTCCTTCCCA
Found at i:16957 original size:3 final size:3
Alignment explanation
Indices: 16949--16998 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
16939 GACCTTCTTT
16949 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16997 TT
1 TT
16999 GTATATGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:17362 original size:2 final size:2
Alignment explanation
Indices: 17355--17383 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
17345 CATTTTGTAT
17355 TA 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 TA T
17384 TGAGTTACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20853 original size:209 final size:209
Alignment explanation
Indices: 20526--20943 Score: 730
Period size: 209 Copynumber: 2.0 Consensus size: 209
20516 CATAGATTTT
* *
20526 TTTGCTCATTATTTTTAGAGTTTAATTTCCTGGGATTCTGCAGGTAACTTGCGTACATAGCATGT
1 TTTGCTCATTATTTTTAGAGTTTAATTTCCTGAGATTCTGCAGGTAACTTACGTACATAGCATGT
**
20591 CTGCATCAAGACTTGGTTGCTGCCTTTGTTAGTTGGTTGTTCTGAAGAAGAGAAGGTTATTCTAA
66 CTGCATCAAGACTTGGTTGCTGCCTTTGTTAGTTGGTTGTTCTGAAGAAGAGAAGGCCATTCTAA
* * *
20656 CTTTTGTTTATCATTTTTTTAAATCATTTAATATTTTCACTGACATG-AAATTTCATTCTATATG
131 CTTTTCTTTATCATTTTTTT-AATCATTTAAGATTTTCACTGACATGAAAATTTAATTCTATATG
20720 ATTTTCAGTTTTAGA
195 ATTTTCAGTTTTAGA
20735 TTTGCTCATTATTTTTAGAGTTTAATTTCCTGAGATTCTGCAGGTAACTTACGTACATAGCATGT
1 TTTGCTCATTATTTTTAGAGTTTAATTTCCTGAGATTCTGCAGGTAACTTACGTACATAGCATGT
*
20800 CTGCATCAAGACTTGGTTTCTGCCTTTGTTAGTTGGTTGTTCTGAAGAAGAGAAGGCCATTCTAA
66 CTGCATCAAGACTTGGTTGCTGCCTTTGTTAGTTGGTTGTTCTGAAGAAGAGAAGGCCATTCTAA
* *
20865 CTTTTCTTTGTCATTTTTTTTATCATTTAAGATTTTCACTGACATGAAAATTTAATTCTATATGA
131 CTTTTCTTTATCATTTTTTTAATCATTTAAGATTTTCACTGACATGAAAATTTAATTCTATATGA
20930 TTTTCAGTTTTAGA
196 TTTTCAGTTTTAGA
20944 GATCATTTGG
Statistics
Matches: 198, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
208 24 0.12
209 174 0.88
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (209 bp):
TTTGCTCATTATTTTTAGAGTTTAATTTCCTGAGATTCTGCAGGTAACTTACGTACATAGCATGT
CTGCATCAAGACTTGGTTGCTGCCTTTGTTAGTTGGTTGTTCTGAAGAAGAGAAGGCCATTCTAA
CTTTTCTTTATCATTTTTTTAATCATTTAAGATTTTCACTGACATGAAAATTTAATTCTATATGA
TTTTCAGTTTTAGA
Found at i:24509 original size:22 final size:22
Alignment explanation
Indices: 24481--24531 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
24471 AATTCATTCC
*
24481 TTTGTTTCTT-TTTGCCCTATAT
1 TTTGTTTCTTATTTGCCCAAT-T
*
24503 TTTGTTT-TTATTTGGCCAATT
1 TTTGTTTCTTATTTGCCCAATT
24524 TTTGTTTC
1 TTTGTTTC
24532 AGTTGACAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.10, C:0.14, G:0.12, T:0.65
Consensus pattern (22 bp):
TTTGTTTCTTATTTGCCCAATT
Found at i:25494 original size:58 final size:58
Alignment explanation
Indices: 25383--25494 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 58
25373 CTATTTAATT
* *
25383 TAACTACAAATCACATTGTAAATTGTATGATTTTTTACCTTATTTCAATAATTTTTTC
1 TAACTACAAATCACATCGTAAATTGTATGATTTTTTACCTTATTTCAAGAATTTTTTC
* *
25441 TAACTACAAATCCCATCGTAGATTGTATGATTTCTTTTACCTTA-TT-AAGAATTT
1 TAACTACAAATCACATCGTAAATTGTATGA-TT-TTTTACCTTATTTCAAGAATTT
25495 CACATTCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 34 0.71
59 4 0.08
60 10 0.21
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (58 bp):
TAACTACAAATCACATCGTAAATTGTATGATTTTTTACCTTATTTCAAGAATTTTTTC
Found at i:27646 original size:33 final size:33
Alignment explanation
Indices: 27603--27687 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
27593 CATATTTGAT
* *
27603 TAAAACCCATACCTAATAAACGTATCTAATTAC
1 TAAAACCCATACTTAATAAACATATCTAATTAC
* * *
27636 TAGAACCCATACTTAATAAACATGTCTGATTAC
1 TAAAACCCATACTTAATAAACATATCTAATTAC
27669 TAAAACCCATACTTAATAA
1 TAAAACCCATACTTAATAA
27688 CTATGTCCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.45, C:0.22, G:0.05, T:0.28
Consensus pattern (33 bp):
TAAAACCCATACTTAATAAACATATCTAATTAC
Found at i:27694 original size:33 final size:34
Alignment explanation
Indices: 27603--27699 Score: 121
Period size: 33 Copynumber: 2.9 Consensus size: 34
27593 CATATTTGAT
* *
27603 TAAAACCCATACCTAATAAACGTA--TCTAATTAC
1 TAAAACCCATACTTAATAAAC-TATGTCTGATTAC
*
27636 TAGAACCCATACTTAATAAAC-ATGTCTGATTAC
1 TAAAACCCATACTTAATAAACTATGTCTGATTAC
*
27669 TAAAACCCATACTTAAT-AACTATGTCCGATT
1 TAAAACCCATACTTAATAAACTATGTCTGATT
27700 CCTTGTCCAA
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
31 1 0.02
32 3 0.05
33 52 0.93
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (34 bp):
TAAAACCCATACTTAATAAACTATGTCTGATTAC
Found at i:28745 original size:2 final size:2
Alignment explanation
Indices: 28738--28770 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28728 ACCACTATTC
28738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28771 ATGAAAACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30892 original size:2 final size:2
Alignment explanation
Indices: 30885--30930 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
30875 TTTAAAAATA
*
30885 AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30927 AT AT
1 AT AT
30931 CGAAGAGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31614 original size:22 final size:22
Alignment explanation
Indices: 31574--31615 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
31564 CTCTTTTGTT
* **
31574 GGTACCGTAATTTTTTTTTTTA
1 GGTACCGTAAATTCATTTTTTA
31596 GGTACCGTAAATTCATTTTT
1 GGTACCGTAAATTCATTTTT
31616 GAGCATAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.52
Consensus pattern (22 bp):
GGTACCGTAAATTCATTTTTTA
Found at i:34354 original size:3 final size:3
Alignment explanation
Indices: 34348--34379 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
34338 ATACCTTTTT
34348 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
34380 TGCTGCAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:42057 original size:16 final size:16
Alignment explanation
Indices: 42038--42085 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
42028 TGTACTACCT
*
42038 TTTTTTCTTTGGGAGA
1 TTTTTTCTTTCGGAGA
* ** *
42054 TTTTTTTTTTTTGAGT
1 TTTTTTCTTTCGGAGA
42070 TTTTTTCTTTCGGAGA
1 TTTTTTCTTTCGGAGA
42086 ATTAAATTTA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.06, G:0.19, T:0.65
Consensus pattern (16 bp):
TTTTTTCTTTCGGAGA
Found at i:46165 original size:14 final size:14
Alignment explanation
Indices: 46140--46178 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
46130 ATGTCATGAG
46140 CCTTTT-TTTTTTT
1 CCTTTTCTTTTTTT
46153 CCTTTTCTTTTTTT
1 CCTTTTCTTTTTTT
46167 CCTTTTCTTTTT
1 CCTTTTCTTTTT
46179 GTTAGATTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
CCTTTTCTTTTTTT
Found at i:47877 original size:29 final size:29
Alignment explanation
Indices: 47844--47899 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
47834 TTTCTCGGAA
47844 TTTAAAATGATTTTTTCACCAAAAAAAAT
1 TTTAAAATGATTTTTTCACCAAAAAAAAT
47873 TTTAAAATGATTTTTTCACCAAAAAAA
1 TTTAAAATGATTTTTTCACCAAAAAAA
47900 TTTATCCGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTAAAATGATTTTTTCACCAAAAAAAAT
Found at i:48390 original size:45 final size:45
Alignment explanation
Indices: 48326--48459 Score: 226
Period size: 45 Copynumber: 3.1 Consensus size: 45
48316 TTAGTCTTTT
48326 TAATTGAGATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG
1 TAATTGAGATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG
48371 TAATTGAGATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG
1 TAATTGAGATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG
48416 ----T-A-ATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG
1 TAATTGAGATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG
48455 TAATT
1 TAATT
48460 TTCCCTTTAC
Statistics
Matches: 85, Mismatches: 0, Indels: 10
0.89 0.00 0.11
Matches are distributed among these distances:
39 37 0.44
40 1 0.01
41 1 0.01
43 1 0.01
45 45 0.53
ACGTcount: A:0.22, C:0.13, G:0.12, T:0.52
Consensus pattern (45 bp):
TAATTGAGATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG
Found at i:48433 original size:39 final size:39
Alignment explanation
Indices: 48334--48461 Score: 202
Period size: 39 Copynumber: 3.1 Consensus size: 39
48324 TTTAATTGAG
48334 ATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTGTAATTGA
1 ATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTG----T-A
48378 GATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTGTA
1 -ATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTGTA
48418 ATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTGTA
1 ATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTGTA
48457 ATTTT
1 ATTTT
48462 CCCTTTACTT
Statistics
Matches: 83, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
39 44 0.53
40 1 0.01
41 1 0.01
45 37 0.45
ACGTcount: A:0.21, C:0.14, G:0.11, T:0.54
Consensus pattern (39 bp):
ATTTTTATGCATAATTTCCCATTTGTCCTTTATTGTGTA
Found at i:51545 original size:2 final size:2
Alignment explanation
Indices: 51538--51567 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
51528 ATTTTAGTAC
51538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51568 TAGCCACATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55809 original size:17 final size:17
Alignment explanation
Indices: 55771--55803 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
55761 CTCATAGTAC
55771 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
55788 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
55804 GATAGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:58719 original size:2 final size:2
Alignment explanation
Indices: 58714--58764 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
58704 TGTGTGAGTC
58714 TA TA TA TA TA 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 TA TA TA TA TA
58756 TA TA TA TA T
1 TA TA TA TA T
58765 GCCTCAGAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64984 original size:2 final size:2
Alignment explanation
Indices: 64979--65017 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
64969 TATGATAGGC
64979 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
65018 GAGAGTACTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65746 original size:18 final size:20
Alignment explanation
Indices: 65708--65752 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
65698 TGTCAAAAAA
65708 AAATAGACAGACTATCAGAT
1 AAATAGACAGACTATCAGAT
65728 AAATAGACAGAC-A-CAGAT
1 AAATAGACAGACTATCAGAT
*
65746 AGATAGA
1 AAATAGA
65753 TGAATAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.46
19 1 0.04
20 12 0.50
ACGTcount: A:0.53, C:0.13, G:0.18, T:0.16
Consensus pattern (20 bp):
AAATAGACAGACTATCAGAT
Found at i:73668 original size:10 final size:10
Alignment explanation
Indices: 73655--73680 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
73645 ATATCTCGAT
73655 ATATCCGTAA
1 ATATCCGTAA
73665 ATATCCGTAA
1 ATATCCGTAA
73675 ATATCC
1 ATATCC
73681 ATATTAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (10 bp):
ATATCCGTAA
Found at i:79571 original size:14 final size:14
Alignment explanation
Indices: 79552--79583 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
79542 TAACAATTGC
79552 GACTGTAACAAAAA
1 GACTGTAACAAAAA
*
79566 GACTGTAACGAAAA
1 GACTGTAACAAAAA
79580 GACT
1 GACT
79584 ATATAAACTT
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:0.16, G:0.19, T:0.16
Consensus pattern (14 bp):
GACTGTAACAAAAA
Found at i:80419 original size:60 final size:60
Alignment explanation
Indices: 80355--80494 Score: 221
Period size: 60 Copynumber: 2.3 Consensus size: 60
80345 AATGTTTGCC
* *
80355 AAAATGCTAAAATAAGGGTCC-AATCTTTTAATTTGGCCAAATAAGGGCCT-AACGTTATTG
1 AAAATGCTCAAATAAGGG-CCAAATCTTTTAATTTGGCCAAATAAGGGCCTAAAC-TTATCG
*
80415 AAAATGCTCAAATAAGGGCCAAATCTTTTAATTTTGCCAAATAAGGGCCTAAACTTATCG
1 AAAATGCTCAAATAAGGGCCAAATCTTTTAATTTGGCCAAATAAGGGCCTAAACTTATCG
80475 AAAATGCTCAAATAAGGGCC
1 AAAATGCTCAAATAAGGGCC
80495 TGGCGTCAGT
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
59 2 0.03
60 70 0.93
61 3 0.04
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCAAATCTTTTAATTTGGCCAAATAAGGGCCTAAACTTATCG
Found at i:80430 original size:31 final size:30
Alignment explanation
Indices: 80392--80495 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 30
80382 TTAATTTGGC
80392 CAAATAAGGGCCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAAC-TTATTGAAAATGCT
* **
80423 CAAATAAGGGCCAAATCTT-TT-AATTTTGC-
1 CAAATAAGGGCCTAA-CTTATTGAA-AATGCT
*
80452 CAAATAAGGGCCTAAACTTATCGAAAATGCT
1 CAAATAAGGGCCT-AACTTATTGAAAATGCT
80483 CAAATAAGGGCCT
1 CAAATAAGGGCCT
80496 GGCGTCAGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
29 17 0.28
30 11 0.18
31 31 0.52
32 1 0.02
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (30 bp):
CAAATAAGGGCCTAACTTATTGAAAATGCT
Found at i:80463 original size:29 final size:28
Alignment explanation
Indices: 80364--80463 Score: 96
Period size: 29 Copynumber: 3.4 Consensus size: 28
80354 CAAAATGCTA
*
80364 AAATAAGGGTCCAATCTTTTAATTTGGCC
1 AAATAAGGG-CCAATCTTTTAATTTTGCC
**
80393 AAATAAGGGCCTAA-CGTTATTGAA-AATGCTC
1 AAATAAGGGCC-AATC-TT-TT-AATTTTGC-C
80424 AAATAAGGGCCAAATCTTTTAATTTTGCC
1 AAATAAGGGCC-AATCTTTTAATTTTGCC
80453 AAATAAGGGCC
1 AAATAAGGGCC
80464 TAAACTTATC
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
28 3 0.05
29 27 0.47
30 9 0.16
31 18 0.31
32 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (28 bp):
AAATAAGGGCCAATCTTTTAATTTTGCC
Found at i:80633 original size:60 final size:59
Alignment explanation
Indices: 80538--80694 Score: 203
Period size: 60 Copynumber: 2.7 Consensus size: 59
80528 AATGTCAAAC
* * *
80538 CCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAAATAAAAGATCGAGT
1 CCTTATTTGAACATTTTGGCAAACATTAGGACCTTATTTGGCCAAAATAAAAGATC-AGG
** *
80598 CCTTATTTGAACATTTTGGCAAATGTTAGGACCTTATTTGGCCAAATTAAAAGATCAGG
1 CCTTATTTGAACATTTTGGCAAACATTAGGACCTTATTTGGCCAAAATAAAAGATCAGG
* *
80657 CCGTTATTTG---ATTTTAGCAAACATTAGGCCCTTATTTG
1 CC-TTATTTGAACATTTTGGCAAACATTAGGACCTTATTTG
80695 AGCAATTAAC
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 24 0.28
59 4 0.05
60 58 0.67
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (59 bp):
CCTTATTTGAACATTTTGGCAAACATTAGGACCTTATTTGGCCAAAATAAAAGATCAGG
Found at i:81756 original size:45 final size:45
Alignment explanation
Indices: 81680--81766 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 45
81670 TTCCTCAGAG
* *
81680 GGTGTGTAAGAATTTTGAGAAAAATCTACCTTAATCGAATCAATA
1 GGTGTGTAAGAATTTTGAGAAAAATCCACCTTAATCCAATCAATA
81725 GGTGTGTAAGAA-TTTGCA-AAAGAATCCACCTTAATCCAATCA
1 GGTGTGTAAGAATTTTG-AGAAA-AATCCACCTTAATCCAATCA
81767 GAACTGTCTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
44 7 0.18
45 31 0.82
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (45 bp):
GGTGTGTAAGAATTTTGAGAAAAATCCACCTTAATCCAATCAATA
Found at i:88208 original size:27 final size:28
Alignment explanation
Indices: 88177--88235 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
88167 AACTTTTTCC
*
88177 TTTATTGCCGGCAGAG-TTTTTTGCACT
1 TTTATTGCCGACAGAGTTTTTTTGCACT
*
88204 TTTA-TGCCGATAGAGTTTTTTTGCACT
1 TTTATTGCCGACAGAGTTTTTTTGCACT
88231 TTTAT
1 TTTAT
88236 CTTCATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.49
Consensus pattern (28 bp):
TTTATTGCCGACAGAGTTTTTTTGCACT
Found at i:89613 original size:35 final size:35
Alignment explanation
Indices: 89572--89667 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
89562 AAAAGAGCAA
* *
89572 ACTATTAGATTTATGTATTGCAAGTAGTATCAAAC
1 ACTATTAGATATATGAATTGCAAGTAGTATCAAAC
* *
89607 ACTATTACATATATGAATTGCAAGTAGTATCAAAT
1 ACTATTAGATATATGAATTGCAAGTAGTATCAAAC
89642 ACTATTAGATATATGAATTGCAAGTA
1 ACTATTAGATATATGAATTGCAAGTA
89668 TTCCAAACAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (35 bp):
ACTATTAGATATATGAATTGCAAGTAGTATCAAAC
Done.