Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010923.1 Corchorus capsularis cultivar CVL-1 contig10944, 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: 63184
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--26 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1 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
27 TACATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2026 original size:17 final size:17
Alignment explanation
Indices: 2006--2040 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1996 TAAATATTAA
2006 GAGATCTTTATGCAATC
1 GAGATCTTTATGCAATC
2023 GAGATCTTTATGCAATC
1 GAGATCTTTATGCAATC
2040 G
1 G
2041 TTGTCCGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (17 bp):
GAGATCTTTATGCAATC
Found at i:5643 original size:21 final size:20
Alignment explanation
Indices: 5607--5648 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
5597 TTCTCACGAT
*
5607 TTATTTCTGTAGTCATTTAA
1 TTATTTCTGTAGTCATGTAA
5627 TTATTATCTGT-GATCATGTAA
1 TTATT-TCTGTAG-TCATGTAA
5648 T
1 T
5649 CTTCATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (20 bp):
TTATTTCTGTAGTCATGTAA
Found at i:16354 original size:156 final size:156
Alignment explanation
Indices: 15967--16354 Score: 414
Period size: 156 Copynumber: 2.5 Consensus size: 156
15957 CAGACTTCGT
* * * *
15967 ATGAAAAACTTATGCTAGTTTTTCAATTAAGGACAATTTGGGGTGTCAAACCTACTTCTCTATGC
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAATTCACTATG-
* * * * *
16032 TAGAGAGG-TCAGTTTTACTTAGAATATTTCTCATAGCTTCATGGGGATAATCTAAGTCTACTGG
65 AAGGGAGGCTCGGTTTTACTTAGAATATTTCTCATAGCTTCATGGAGAGAATCTAAGTCTACTGG
* * * *
16096 TAGAAAATCAGTTTCATTGGACTTAGG
130 TAGAAAATCAGTCTCATTAGAATTAGA
** * * * *
16123 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAACCTGGGGAGAGAAACCTAATTCACCATCA
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAATTCACTATGA
* * *
16188 A-GGAGAGCTCGGTTTTACTTGGAATTCTTTC-CATAG-TCTCATGGAGAGAATCTAAGTC-CCT
66 AGGGAG-GCTCGGTTTTACTTAGAA-TATTTCTCATAGCT-TCATGGAGAGAATCTAAGTCTAC-
*
16249 TGG-A-AAAGTTTCAG-CTCATTCAGAATTAGA
127 TGGTAGAAA--ATCAGTCTCATT-AGAATTAGA
* * *
16279 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAAACCTAGTTCACTATGA
1 ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAATTCACTATGA
16344 AGGGAGGCTCG
66 AGGGAGGCTCG
16355 AATCAAGCCA
Statistics
Matches: 191, Mismatches: 32, Indels: 18
0.79 0.13 0.07
Matches are distributed among these distances:
154 6 0.03
155 10 0.05
156 166 0.87
157 9 0.05
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (156 bp):
ATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAATTTGGGGTGTGAAACCTAATTCACTATGA
AGGGAGGCTCGGTTTTACTTAGAATATTTCTCATAGCTTCATGGAGAGAATCTAAGTCTACTGGT
AGAAAATCAGTCTCATTAGAATTAGA
Found at i:17141 original size:30 final size:30
Alignment explanation
Indices: 17107--17171 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
17097 AGAAGATGGG
17107 ATCGCACCAAAGACAT-CCA-TGGATGGAGGA
1 ATCGCACCAAAG--ATGCCATTGGATGGAGGA
17137 ATCGCACCAAAGATGCCATTGGATGGAGGA
1 ATCGCACCAAAGATGCCATTGGATGGAGGA
17167 ATCGC
1 ATCGC
17172 GGTAAAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 2 0.06
29 3 0.09
30 28 0.85
ACGTcount: A:0.34, C:0.23, G:0.28, T:0.15
Consensus pattern (30 bp):
ATCGCACCAAAGATGCCATTGGATGGAGGA
Found at i:21156 original size:17 final size:17
Alignment explanation
Indices: 21134--21172 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
21124 TCATGGTACC
21134 AGGTAACATGAGGCACT
1 AGGTAACATGAGGCACT
*
21151 AGGTAACATGAGGTACT
1 AGGTAACATGAGGCACT
21168 AGGTA
1 AGGTA
21173 GCATCTGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.21
Consensus pattern (17 bp):
AGGTAACATGAGGCACT
Found at i:21697 original size:155 final size:155
Alignment explanation
Indices: 21489--21901 Score: 528
Period size: 155 Copynumber: 2.7 Consensus size: 155
21479 GGTTTGAGCC
* *
21489 CTCCTTCATGGTGAACTAGGTTTCACACCTCAAATTGTCCTTAAATGAAAAACTAGCATAAGTTT
1 CTCCTTCATGGTGAACT-GGTTTCTCACCTCAAATTGTCCTTAAATGAAAAACTTGCATAAGTTT
* * * * *
21554 TTTATTCTAAGTCTGGTTGAGATTAAACTTTGCCACGGGACTTAGATTATATCCATAAAAC-TAT
65 TTCATTCTAAGTCTGGTTGAGATGAAACTTGGCCAAGAGACTTAGATTATATCCA-AAAACTTAT
*
21618 GGAAAAAATTCTAAGTAAAA-CTAAGCT
129 GGAAAAAATTCTAAGTAAAACCGAA-CT
* ** *
21645 CTCCTTGATGGTGAACTGACTTCTCACCTCAAATTGTCCTTAACTGAAAAACTTGCATAAGTTTT
1 CTCCTTCATGGTGAACTGGTTTCTCACCTCAAATTGTCCTTAAATGAAAAACTTGCATAAGTTTT
* ** * *
21710 TCATTCTAAGTTTTTTTGAGATGAAACTTGGCCAAGAGACTTAGATTATCTCCACAAACTTATGG
66 TCATTCTAAGTCTGGTTGAGATGAAACTTGGCCAAGAGACTTAGATTATATCCAAAAACTTATGG
21775 AAAAAATTCTAAGTAAAACCGAACT
131 AAAAAATTCTAAGTAAAACCGAACT
* * * *
21800 C-CCTATCATGGTGAAGTGGTTTCTCACCCCAAACTGTCCTTAATTGAAAAACTTGCATAAGTTT
1 CTCCT-TCATGGTGAACTGGTTTCTCACCTCAAATTGTCCTTAAATGAAAAACTTGCATAAGTTT
*** *
21864 TTCA-TCTTAAGTCCATTTGAGATGAAACTTAGCCAAGA
65 TTCATTC-TAAGTCTGGTTGAGATGAAACTTGGCCAAGA
21902 TGGTCCACAT
Statistics
Matches: 225, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
154 9 0.04
155 197 0.88
156 19 0.08
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (155 bp):
CTCCTTCATGGTGAACTGGTTTCTCACCTCAAATTGTCCTTAAATGAAAAACTTGCATAAGTTTT
TCATTCTAAGTCTGGTTGAGATGAAACTTGGCCAAGAGACTTAGATTATATCCAAAAACTTATGG
AAAAAATTCTAAGTAAAACCGAACT
Found at i:30677 original size:34 final size:34
Alignment explanation
Indices: 30628--30697 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 34
30618 TTCTTCCTTT
30628 TATTTATTTTTAAAAAAATTATAAACAATTATAA
1 TATTTATTTTTAAAAAAATTATAAACAATTATAA
30662 TATTT-TTTTTAAAAAAAATTATAAACAATTATAA
1 TATTTATTTTT-AAAAAAATTATAAACAATTATAA
30696 TA
1 TA
30698 ATATAATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 5 0.14
34 30 0.86
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (34 bp):
TATTTATTTTTAAAAAAATTATAAACAATTATAA
Found at i:45917 original size:25 final size:20
Alignment explanation
Indices: 45868--45931 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 20
45858 TTAACGCAAT
45868 AGCTAAAATCAAGGAGACAGC
1 AGCT-AAATCAAGGAGACAGC
45889 AGCTGAAATCAAGGAAGTAACAGTC
1 AGCT-AAATCAAGG-AG--ACAG-C
45914 AGCTAGAATCAAGG-GACA
1 AGCTA-AATCAAGGAGACA
45932 CTACACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
21 16 0.43
22 2 0.05
23 1 0.03
24 5 0.14
25 13 0.35
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.12
Consensus pattern (20 bp):
AGCTAAATCAAGGAGACAGC
Found at i:46774 original size:20 final size:20
Alignment explanation
Indices: 46751--46954 Score: 216
Period size: 20 Copynumber: 10.2 Consensus size: 20
46741 TTCAGTAATC
*
46751 TTTTCCTGTTCAATTACTGT
1 TTTTCCTGTTTAATTACTGT
* *
46771 TTTTCTTGTTTAATTACTGA
1 TTTTCCTGTTTAATTACTGT
**
46791 TTTT-CTGCGTAATTACTGTT
1 TTTTCCTGTTTAATTACTG-T
** *
46811 TTTTTTTGTTTACTTACTGT
1 TTTTCCTGTTTAATTACTGT
* *
46831 TTTTCCTGTTCAATTATTGT
1 TTTTCCTGTTTAATTACTGT
*
46851 TTTTCCTGTTTAATTACTGA
1 TTTTCCTGTTTAATTACTGT
**
46871 TTTT-CTGCGTAATTACT-T
1 TTTTCCTGTTTAATTACTGT
* *
46889 TTCTTTCTGTTTACTTACTGT
1 TT-TTCCTGTTTAATTACTGT
*
46910 TTTTCCTGTTCAATTACTGT
1 TTTTCCTGTTTAATTACTGT
*
46930 TTTTGCTGTTTAATTACTGT
1 TTTTCCTGTTTAATTACTGT
46950 TTTTC
1 TTTTC
46955 ACGCTTGTCG
Statistics
Matches: 148, Mismatches: 31, Indels: 10
0.78 0.16 0.05
Matches are distributed among these distances:
18 2 0.01
19 24 0.16
20 109 0.74
21 13 0.09
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.59
Consensus pattern (20 bp):
TTTTCCTGTTTAATTACTGT
Found at i:46838 original size:80 final size:78
Alignment explanation
Indices: 46751--46954 Score: 336
Period size: 79 Copynumber: 2.6 Consensus size: 78
46741 TTCAGTAATC
*
46751 TTTTCCTGTTCAATTACTGTTTTTCTTGTTTAATTACTGATTTTCTGCGTAATTACTGTTTTTTT
1 TTTTCCTGTTCAATTACTGTTTTTC-TGTTTAATTACTGATTTTCTGCGTAATTACT-TTTCTTT
*
46816 TTGTTTACTTACTGT
64 CTGTTTACTTACTGT
*
46831 TTTTCCTGTTCAATTATTGTTTTTCCTGTTTAATTACTGATTTTCTGCGTAATTACTTTTCTTTC
1 TTTTCCTGTTCAATTACTGTTTTT-CTGTTTAATTACTGATTTTCTGCGTAATTACTTTTCTTTC
46896 TGTTTACTTACTGT
65 TGTTTACTTACTGT
*
46910 TTTTCCTGTTCAATTACTGTTTTTGCTGTTTAATTACTGTTTTTC
1 TTTTCCTGTTCAATTACTGTTTTT-CTGTTTAATTACTGATTTTC
46955 ACGCTTGTCG
Statistics
Matches: 117, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
79 62 0.53
80 54 0.46
81 1 0.01
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.59
Consensus pattern (78 bp):
TTTTCCTGTTCAATTACTGTTTTTCTGTTTAATTACTGATTTTCTGCGTAATTACTTTTCTTTCT
GTTTACTTACTGT
Found at i:48275 original size:8 final size:8
Alignment explanation
Indices: 48256--48380 Score: 65
Period size: 8 Copynumber: 15.8 Consensus size: 8
48246 AGCATAACTT
*
48256 TGAAGTTC
1 TGAAGTTA
*
48264 TGAAATTA
1 TGAAGTTA
48272 TGAAGTTA
1 TGAAGTTA
*
48280 TGAAGTTC
1 TGAAGTTA
*
48288 TGAAATTA
1 TGAAGTTA
* **
48296 TCAAGTCC
1 TGAAGTTA
*
48304 TGAAATTA
1 TGAAGTTA
48312 TGAAGTTA
1 TGAAGTTA
* *
48320 TTAAGTTC
1 TGAAGTTA
48328 TGGAA-TTA
1 T-GAAGTTA
* **
48336 TTAAGTCC
1 TGAAGTTA
* *
48344 TGAAATCA
1 TGAAGTTA
48352 TGAAGTTA
1 TGAAGTTA
* *
48360 TTAAGTTC
1 TGAAGTTA
*
48368 TGAAATTA
1 TGAAGTTA
48376 T-AAGT
1 TGAAGT
48381 CATCAAATCA
Statistics
Matches: 82, Mismatches: 33, Indels: 5
0.68 0.28 0.04
Matches are distributed among these distances:
7 5 0.06
8 75 0.91
9 2 0.02
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (8 bp):
TGAAGTTA
Found at i:48288 original size:24 final size:24
Alignment explanation
Indices: 48256--48301 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
48246 AGCATAACTT
*
48256 TGAAGTTCTGAAATTATGAAGTTA
1 TGAAGTTCTGAAATTATCAAGTTA
48280 TGAAGTTCTGAAATTATCAAGT
1 TGAAGTTCTGAAATTATCAAGT
48302 CCTGAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (24 bp):
TGAAGTTCTGAAATTATCAAGTTA
Found at i:48307 original size:24 final size:24
Alignment explanation
Indices: 48256--48325 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
48246 AGCATAACTT
* *
48256 TGAAGTTCTGAAATTATGAAGTTA
1 TGAAGTTCTGAAATTATCAAGTCA
*
48280 TGAAGTTCTGAAATTATCAAGTCC
1 TGAAGTTCTGAAATTATCAAGTCA
* * * *
48304 TGAAATTATGAAGTTATTAAGT
1 TGAAGTTCTGAAATTATCAAGT
48326 TCTGGAATTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (24 bp):
TGAAGTTCTGAAATTATCAAGTCA
Found at i:48318 original size:40 final size:39
Alignment explanation
Indices: 48258--48397 Score: 199
Period size: 40 Copynumber: 3.5 Consensus size: 39
48248 CATAACTTTG
* * *
48258 AAGTTCTGAAATTATGAAGTTATGAAGTTCTGAAATTAT
1 AAGTCCTGAAATCATGAAGTTATTAAGTTCTGAAATTAT
* *
48297 CAAGTCCTGAAATTATGAAGTTATTAAGTTCTGGAATTATT
1 -AAGTCCTGAAATCATGAAGTTATTAAGTTCTGAAATTA-T
48338 AAGTCCTGAAATCATGAAGTTATTAAGTTCTGAAATTAT
1 AAGTCCTGAAATCATGAAGTTATTAAGTTCTGAAATTAT
* *
48377 AAGTCATCAAATCATGAAGTT
1 AAGTCCTGAAATCATGAAGTT
48398 CTAAAATCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
39 20 0.22
40 71 0.77
41 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (39 bp):
AAGTCCTGAAATCATGAAGTTATTAAGTTCTGAAATTAT
Found at i:49573 original size:69 final size:69
Alignment explanation
Indices: 49462--49600 Score: 260
Period size: 69 Copynumber: 2.0 Consensus size: 69
49452 TGATCCCAAA
49462 CATGTATGGTGGCATTAATTTATCAGAATTCAGTTCATGCTACTTTCCTGGTCTGTTTACATTCA
1 CATGTATGGTGGCATTAATTTATCAGAATTCAGTTCATGCTACTTTCCTGGTCTGTTTACATTCA
49527 ATTT
66 ATTT
* *
49531 CATGTGTGGTGGCATTAGTTTATCAGAATTCAGTTCATGCTACTTTCCTGGTCTGTTTACATTCA
1 CATGTATGGTGGCATTAATTTATCAGAATTCAGTTCATGCTACTTTCCTGGTCTGTTTACATTCA
49596 ATTT
66 ATTT
49600 C
1 C
49601 TCAGCTGGTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (69 bp):
CATGTATGGTGGCATTAATTTATCAGAATTCAGTTCATGCTACTTTCCTGGTCTGTTTACATTCA
ATTT
Found at i:54746 original size:2 final size:2
Alignment explanation
Indices: 54739--54766 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
54729 AGAATGAAAC
54739 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
54767 AACCTAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58092 original size:2 final size:2
Alignment explanation
Indices: 58085--58113 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
58075 CCCTCATTTC
58085 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
58114 TAACAAATTA
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:61577 original size:2 final size:2
Alignment explanation
Indices: 61570--61602 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
61560 ATCAATTAGT
61570 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61603 GAGCAAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:61760 original size:60 final size:60
Alignment explanation
Indices: 61665--61821 Score: 199
Period size: 60 Copynumber: 2.6 Consensus size: 60
61655 TAATTGCTCG
* * * * * * *
61665 AATAAGGACCTAACGTTTGTC-AAAATGTTCGAATAAGGATCTGATCTTTTAATCTGGCCA
1 AATAAGGGCCTAACG-TTATCGAAAATGCTCAAATAAGGACCCGATCTTTTAATCTGACCA
* * * *
61725 AATAAGGGTCTAACGTTATTGAAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGACCA
1 AATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCCGATCTTTTAATCTGACCA
61785 AATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAG
1 AATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAG
61822 AGCCTAATGT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 3 0.04
60 80 0.96
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (60 bp):
AATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGACCCGATCTTTTAATCTGACCA
Found at i:61761 original size:31 final size:31
Alignment explanation
Indices: 61723--61854 Score: 137
Period size: 31 Copynumber: 4.3 Consensus size: 31
61713 TTAATCTGGC
* *
61723 CAAATAAGGGTCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* * * **
61754 CAAATAAGGGCCCGATC-TT-T-TAATTTGAC-
1 CAAATAAGGG-CCTAACGTTATCGAAAATG-CT
61783 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
* *
61814 CAAATAAGAGCCTAATGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATCGAAAATGCT
61845 CAAATAAGGG
1 CAAATAAGGG
61855 TCTGATGTCA
Statistics
Matches: 81, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
28 4 0.05
29 16 0.20
30 4 0.05
31 54 0.67
32 3 0.04
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCT
Found at i:61958 original size:60 final size:61
Alignment explanation
Indices: 61885--62048 Score: 262
Period size: 59 Copynumber: 2.7 Consensus size: 61
61875 CGCGTGAGAC
* *
61885 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGAT-G
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCG
*
61945 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTA-TTGACTAAATTAAAAGATCG
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCG
* *
62005 -GACCCTTATTTGAGCATTTTGACAAATGTTAGGCCCTTATTTGA
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGA
62049 GCAATTAGCC
Statistics
Matches: 97, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
59 52 0.54
60 45 0.46
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (61 bp):
AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGACCAAATTAAAAGATCG
Found at i:63137 original size:1 final size:1
Alignment explanation
Indices: 63131--63184 Score: 108
Period size: 1 Copynumber: 54.0 Consensus size: 1
63121 GAGAGAGAAG
63131 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.