Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017496.1 Corchorus olitorius cultivar O-4 contig17529, 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: 135813
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:1438 original size:19 final size:19
Alignment explanation
Indices: 1402--1440 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1392 TTAGGCCTAA
* *
1402 ATACTATATAGATGAAATT
1 ATACTATACAGATCAAATT
*
1421 ATACTATACCGATCAAATT
1 ATACTATACAGATCAAATT
1440 A
1 A
1441 GATATTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (19 bp):
ATACTATACAGATCAAATT
Found at i:2739 original size:7 final size:7
Alignment explanation
Indices: 2727--2752 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2717 AACACAACAC
2727 CTCTCAG
1 CTCTCAG
2734 CTCTCAG
1 CTCTCAG
2741 CTCTCAG
1 CTCTCAG
2748 CTCTC
1 CTCTC
2753 TCCCCACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.46, G:0.12, T:0.31
Consensus pattern (7 bp):
CTCTCAG
Found at i:13472 original size:13 final size:13
Alignment explanation
Indices: 13454--13480 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13444 AAACGGAAAA
13454 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
13467 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
13480 T
1 T
13481 TTAGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:29740 original size:2 final size:2
Alignment explanation
Indices: 29733--29757 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29723 TTAGCCAAAC
29733 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 T
29758 TATTCTTCTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31146 original size:45 final size:45
Alignment explanation
Indices: 31047--31181 Score: 173
Period size: 45 Copynumber: 3.0 Consensus size: 45
31037 AGATCTTTTC
* * *
31047 TTTGTTTGTAAAGGAAAAGATTCTGATTTTGTTCTTGATGAAGGA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
*
31092 TTTGTTTGTGAAGGAGAAGATTTTGATTTTGTTCTTGATGAAGAA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
* * * * *
31137 TTTGTTTGTGAGGGAGAGGAGTCTGAGTTTG-TCATTGATGGAGAA
1 TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTC-TTGATGAAGAA
31182 AGATTGGAGA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
44 2 0.03
45 77 0.97
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.41
Consensus pattern (45 bp):
TTTGTTTGTGAAGGAGAAGATTCTGATTTTGTTCTTGATGAAGAA
Found at i:35873 original size:14 final size:14
Alignment explanation
Indices: 35856--35896 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
35846 TTCCTTTTAC
35856 CTTTCATGTTT-TTT
1 CTTTC-TGTTTGTTT
*
35870 CTTTTTGTTTGTTT
1 CTTTCTGTTTGTTT
35884 CTTTCTGTTTGTT
1 CTTTCTGTTTGTT
35897 AATTTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.02, C:0.12, G:0.12, T:0.73
Consensus pattern (14 bp):
CTTTCTGTTTGTTT
Found at i:35894 original size:18 final size:17
Alignment explanation
Indices: 35862--35896 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35852 TTACCTTTCA
*
35862 TGTTTTTTCTTTTTGTT
1 TGTTTTTTCTGTTTGTT
35879 TGTTTCTTTCTGTTTGTT
1 TGTTT-TTTCTGTTTGTT
35897 AATTTAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (17 bp):
TGTTTTTTCTGTTTGTT
Found at i:42536 original size:27 final size:27
Alignment explanation
Indices: 42505--42559 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
42495 TCTAGAATTT
42505 TTTGAAAATATACAAATCTAAACTCCA
1 TTTGAAAATATACAAATCTAAACTCCA
*
42532 TTTGAAAATATACAAATCTGAACTCCA
1 TTTGAAAATATACAAATCTAAACTCCA
42559 T
1 T
42560 GTTATGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.31
Consensus pattern (27 bp):
TTTGAAAATATACAAATCTAAACTCCA
Found at i:42794 original size:20 final size:20
Alignment explanation
Indices: 42769--42808 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42759 TATTTTGGCA
42769 TGTCGTTTTTCCCCTGGTTC
1 TGTCGTTTTTCCCCTGGTTC
42789 TGTCGTTTTTCCCCTGGTTC
1 TGTCGTTTTTCCCCTGGTTC
42809 GTTGAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.00, C:0.30, G:0.20, T:0.50
Consensus pattern (20 bp):
TGTCGTTTTTCCCCTGGTTC
Found at i:44971 original size:11 final size:11
Alignment explanation
Indices: 44951--44985 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
44941 TTGACAGCGC
44951 AACAAAAACAA
1 AACAAAAACAA
*
44962 AACGAAAACAA
1 AACAAAAACAA
44973 AACAAAAACAA
1 AACAAAAACAA
44984 AA
1 AA
44986 ATCAGAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:47305 original size:143 final size:141
Alignment explanation
Indices: 47125--47399 Score: 410
Period size: 143 Copynumber: 1.9 Consensus size: 141
47115 ATGAGGCTCT
*
47125 ATTTGAACTTTTTTTGTCCTCTTTTTATCTTTTCTCACTTGGCAAATTACTAAAAAAGCCCTGAG
1 ATTTGAACTTTTTTTGTCATCTTTTTATCTTTTCTCACTTGGCAAATTACTAAAAAAGCCCTGAG
* *
47190 TTAGTTAATCCGGCCTAAAATAGGCCCATTTAACGATTTTAG-CACGCTGGCCCAGTTAGTGAAG
66 TTAGTTAATCCGGCCTAAAATAGGCCCATCTAACGATTTTAGTC-CACTGGCCCAGTTAGTGAAG
47254 AAGTTAGGTTCC
130 AAGTTAGGTTCC
* * *
47266 ATTTGAACTTTTTTTTGTCAT-TTTCTGTTTTTTTTCTCACTTGTCAAATTACTAAAAAAGCCCT
1 ATTTGAAC-TTTTTTTGTCATCTTT-T-TATCTTTTCTCACTTGGCAAATTACTAAAAAAGCCCT
* * * *
47330 GAGTTAGTTAATTCGGCCTAAAATAGGCCCATCTAAGGATTTTAGTCCATTGGCCCAGTTTGTGA
63 GAGTTAGTTAATCCGGCCTAAAATAGGCCCATCTAACGATTTTAGTCCACTGGCCCAGTTAGTGA
47395 AGAAG
128 AGAAG
47400 CTTAAAGAAT
Statistics
Matches: 120, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
141 11 0.09
142 12 0.10
143 96 0.80
144 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (141 bp):
ATTTGAACTTTTTTTGTCATCTTTTTATCTTTTCTCACTTGGCAAATTACTAAAAAAGCCCTGAG
TTAGTTAATCCGGCCTAAAATAGGCCCATCTAACGATTTTAGTCCACTGGCCCAGTTAGTGAAGA
AGTTAGGTTCC
Found at i:50226 original size:18 final size:18
Alignment explanation
Indices: 50184--50227 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
50174 AGGGAAAATT
*
50184 AATAATAATTATTCTGAA
1 AATAATTATTATTCTGAA
50202 AATAATTATTATT-TGATA
1 AATAATTATTATTCTGA-A
50220 AATAATTA
1 AATAATTA
50228 ATAATTTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (18 bp):
AATAATTATTATTCTGAA
Found at i:65517 original size:67 final size:64
Alignment explanation
Indices: 65393--65517 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 64
65383 AGGAGAACTC
* * *
65393 AATTTTACTTTCAATTTTTCACAAGAGTTGAATCGCAATCAATTACTATAAAGAAAGAATTCAA
1 AATTTTACTTTAAATTTCTCACAAGAGTTGAATCGAAATCAATTACTATAAAGAAAGAATTCAA
*
65457 AATTTTACTTTTAAAATTTCTCACAAGAGTTGAATCTAATATCAATTACTATAAAGAAAGA
1 AATTTTAC-TTT-AAATTTCTCACAAGAGTTGAATCGAA-ATCAATTACTATAAAGAAAGA
65518 TGATCCCTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
64 8 0.15
65 3 0.06
66 22 0.41
67 21 0.39
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (64 bp):
AATTTTACTTTAAATTTCTCACAAGAGTTGAATCGAAATCAATTACTATAAAGAAAGAATTCAA
Found at i:77914 original size:123 final size:123
Alignment explanation
Indices: 77695--77940 Score: 492
Period size: 123 Copynumber: 2.0 Consensus size: 123
77685 CTAATTGCTT
77695 CTTATTACCTTTTTCCTTATTCCTTTAGTGCTTTTGGTTGGGCTAAAAGCCAAAACTCAACTGGT
1 CTTATTACCTTTTTCCTTATTCCTTTAGTGCTTTTGGTTGGGCTAAAAGCCAAAACTCAACTGGT
77760 ACAAGTTTAAATAACACGACTTGTAAAACAATAAAATATAATAAATCCTAAAGATTAC
66 ACAAGTTTAAATAACACGACTTGTAAAACAATAAAATATAATAAATCCTAAAGATTAC
77818 CTTATTACCTTTTTCCTTATTCCTTTAGTGCTTTTGGTTGGGCTAAAAGCCAAAACTCAACTGGT
1 CTTATTACCTTTTTCCTTATTCCTTTAGTGCTTTTGGTTGGGCTAAAAGCCAAAACTCAACTGGT
77883 ACAAGTTTAAATAACACGACTTGTAAAACAATAAAATATAATAAATCCTAAAGATTAC
66 ACAAGTTTAAATAACACGACTTGTAAAACAATAAAATATAATAAATCCTAAAGATTAC
77941 AAGTTTAGTT
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 123 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (123 bp):
CTTATTACCTTTTTCCTTATTCCTTTAGTGCTTTTGGTTGGGCTAAAAGCCAAAACTCAACTGGT
ACAAGTTTAAATAACACGACTTGTAAAACAATAAAATATAATAAATCCTAAAGATTAC
Found at i:94086 original size:21 final size:19
Alignment explanation
Indices: 94062--94103 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
94052 TTGTAGAAAT
*
94062 GGGAAGGGATTTTGGCCTTTG
1 GGGAAGGG-TTTT-GACTTTG
94083 GGGAAGGGTTTTGACTTTG
1 GGGAAGGGTTTTGACTTTG
94102 GG
1 GG
94104 AATTTCACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.14, C:0.07, G:0.45, T:0.33
Consensus pattern (19 bp):
GGGAAGGGTTTTGACTTTG
Found at i:108986 original size:21 final size:21
Alignment explanation
Indices: 108961--109000 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
108951 ACGCCTCTTG
* *
108961 GGAGGTAGGAGGCATCTCCTA
1 GGAGGAAGGAAGCATCTCCTA
108982 GGAGGAAGGAAGCATCTCC
1 GGAGGAAGGAAGCATCTCC
109001 CTCTTTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.20, G:0.38, T:0.15
Consensus pattern (21 bp):
GGAGGAAGGAAGCATCTCCTA
Found at i:116276 original size:32 final size:32
Alignment explanation
Indices: 116235--116300 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
116225 GATGGCAAAT
116235 AAGATAAATAGAATAGAAAAAATACAAGAAAA
1 AAGATAAATAGAATAGAAAAAATACAAGAAAA
116267 AAGATAAATAGAATAGAAAAAATACAAGAAAA
1 AAGATAAATAGAATAGAAAAAATACAAGAAAA
116299 AA
1 AA
116301 ATGATTGATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.12
Consensus pattern (32 bp):
AAGATAAATAGAATAGAAAAAATACAAGAAAA
Found at i:116286 original size:18 final size:18
Alignment explanation
Indices: 116235--116286 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
116225 GATGGCAAAT
116235 AAGATAAATAGAATAGAA
1 AAGATAAATAGAATAGAA
* *
116253 AAAATACA-AG-A-A-AA
1 AAGATAAATAGAATAGAA
116267 AAGATAAATAGAATAGAA
1 AAGATAAATAGAATAGAA
116285 AA
1 AA
116287 AATACAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 8 0.31
15 3 0.12
16 2 0.08
17 3 0.12
18 10 0.38
ACGTcount: A:0.71, C:0.02, G:0.13, T:0.13
Consensus pattern (18 bp):
AAGATAAATAGAATAGAA
Found at i:117264 original size:24 final size:24
Alignment explanation
Indices: 117237--117283 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
117227 ATGTCAAAAT
*
117237 TAAATAAGATGTCTGTTATATATA
1 TAAATAAGATGTCTGTTAAATATA
117261 TAAATAAGATGTCTGTTAAATAT
1 TAAATAAGATGTCTGTTAAATAT
117284 CAAAAGGGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.40
Consensus pattern (24 bp):
TAAATAAGATGTCTGTTAAATATA
Found at i:117481 original size:24 final size:25
Alignment explanation
Indices: 117439--117489 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
117429 TCTCCTGTAT
117439 AGCCGATTAAAAAAAAAATTGCAGC
1 AGCCGATTAAAAAAAAAATTGCAGC
*
117464 AGCCGATT-AAAAAGAAATTGCAGC
1 AGCCGATTAAAAAAAAAATTGCAGC
117488 AG
1 AG
117490 GGGATTACCG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 17 0.68
25 8 0.32
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.16
Consensus pattern (25 bp):
AGCCGATTAAAAAAAAAATTGCAGC
Found at i:120266 original size:118 final size:118
Alignment explanation
Indices: 120113--120345 Score: 412
Period size: 118 Copynumber: 2.0 Consensus size: 118
120103 TGGAAGAACA
*
120113 TCCACCACAACCATGAATATTGTCTTCAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTCTTCAAGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
* * *
120178 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAGTTCTTAGATCCCAAATGC
66 CTATTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAAATCCCAAATGC
* *
120231 TCCACCACAACCATGAATATTGTTTTGAAGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTCTTCAAGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
120296 CTATTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAAATCCCAAA
66 CTATTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAAATCCCAAA
120346 CCCGTTAACA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (118 bp):
TCCACCACAACCATGAATATTGTCTTCAAGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
CTATTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAAATCCCAAATGC
Found at i:121609 original size:22 final size:22
Alignment explanation
Indices: 121576--121852 Score: 142
Period size: 22 Copynumber: 12.4 Consensus size: 22
121566 TCAATCAAAC
*
121576 CAAAATTACATAGGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* *
121598 CAAATTTTCATAGTG-TGGTTA-
1 CAAAATTTCATAG-GAAGGTTAT
121619 CTAAAATTTCATATGG-AGGTTAT
1 C-AAAATTTCATA-GGAAGGTTAT
** *
121642 CAAAACGTCATAGTGTA-GTTAT
1 CAAAATTTCATAG-GAAGGTTAT
* * * *
121664 CAAAATTCCATA-CAGACGTTAC
1 CAAAATTTCATAGGA-AGGTTAT
* **
121686 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
* * *
121708 CAAAATTTCTTA-GAGTGTCGTTAA
1 CAAAATTTCATAGGA-AG--GTTAT
* *
121732 CAAAATTTTATACGAAGGTTAT
1 CAAAATTTCATAGGAAGGTTAT
*
121754 CAAAATTT-ATAGTG-TGGTTAT
1 CAAAATTTCATAG-GAAGGTTAT
121775 CAAAATTTCATAGGGAGGGAGGTTAT
1 CAAAATTTCATA-GGA---AGGTTAT
* * * *
121801 CAAAGTATCCTAGGGAGGTTAAT
1 CAAAATTTCATAGGAAGGTT-AT
121824 -AAAATTTCATAGGAAGGTTA-
1 CAAAATTTCATAGGAAGGTTAT
121844 CAACAATTT
1 CAA-AATTT
121853 TATGGAGATT
Statistics
Matches: 194, Mismatches: 38, Indels: 46
0.70 0.14 0.17
Matches are distributed among these distances:
21 24 0.12
22 128 0.66
23 8 0.04
24 15 0.08
25 4 0.02
26 15 0.08
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGGAAGGTTAT
Found at i:121764 original size:21 final size:21
Alignment explanation
Indices: 121727--121787 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
121717 TTAGAGTGTC
*
121727 GTTAACAAAATTTTATACG-AAG
1 GTTATCAAAA-TTTATA-GTAAG
**
121749 GTTATCAAAATTTATAGTGTG
1 GTTATCAAAATTTATAGTAAG
121770 GTTATCAAAATTTCATAG
1 GTTATCAAAATTT-ATAG
121788 GGAGGGAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.03
21 20 0.59
22 13 0.38
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (21 bp):
GTTATCAAAATTTATAGTAAG
Found at i:121814 original size:26 final size:26
Alignment explanation
Indices: 121769--121818 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
121759 TTTATAGTGT
*
121769 GGTTATCAAAATTTCATAGGGAGGGA
1 GGTTATCAAAATATCATAGGGAGGGA
* *
121795 GGTTATCAAAGTATCCTAGGGAGG
1 GGTTATCAAAATATCATAGGGAGG
121819 TTAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.26
Consensus pattern (26 bp):
GGTTATCAAAATATCATAGGGAGGGA
Found at i:121936 original size:22 final size:22
Alignment explanation
Indices: 121911--122096 Score: 131
Period size: 22 Copynumber: 8.7 Consensus size: 22
121901 CTCATAGGAG
* *
121911 GGTTATCTAAACTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
121933 GGTTATCAAAA-TT-ATATGAAGA
1 GGTTATCAAAATTTCATA-G-TGT
* *
121955 GGTTATCAAAATTTTCATAATGC
1 GGTTATCAAAA-TTTCATAGTGT
* * * *
121978 GGTTA-C--AATTTAACACTGA
1 GGTTATCAAAATTTCATAGTGT
121997 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
122019 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* *
122041 GTTTATCAAATTTTCATA----
1 GGTTATCAAAATTTCATAGTGT
* *
122059 GGTTATCTAAATTTCATAATGAT
1 GGTTATCAAAATTTCATAGTG-T
*
122082 -GTTATCAAATTTTCA
1 GGTTATCAAAATTTCA
122097 CACCATTATG
Statistics
Matches: 130, Mismatches: 21, Indels: 26
0.73 0.12 0.15
Matches are distributed among these distances:
18 15 0.12
19 12 0.09
20 6 0.05
21 3 0.02
22 83 0.64
23 6 0.05
24 2 0.02
25 3 0.02
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:122074 original size:40 final size:40
Alignment explanation
Indices: 122019--122096 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
122009 TTCATAGTGT
*
122019 GGTTATCAAAATTTCATAGTG-TGTTTATCAAATTTTCATA
1 GGTTATCAAAATTTCATAATGATG-TTATCAAATTTTCATA
*
122059 GGTTATCTAAATTTCATAATGATGTTATCAAATTTTCA
1 GGTTATCAAAATTTCATAATGATGTTATCAAATTTTCA
122097 CACCATTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (40 bp):
GGTTATCAAAATTTCATAATGATGTTATCAAATTTTCATA
Found at i:122552 original size:70 final size:70
Alignment explanation
Indices: 122475--122619 Score: 281
Period size: 70 Copynumber: 2.1 Consensus size: 70
122465 TGCATGTTTG
122475 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
1 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
122540 TATGT
66 TATGT
*
122545 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATGAATGCTCA
1 TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
122610 TATGT
66 TATGT
122615 TGTGT
1 TGTGT
122620 TTCGGAGTTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 74 1.00
ACGTcount: A:0.25, C:0.06, G:0.24, T:0.45
Consensus pattern (70 bp):
TGTGTAGAACGTTGTTTTGGAGAAAATGTTTATTTCGAATGTGTTATTTGTGTAATCAATGCTCA
TATGT
Found at i:123146 original size:38 final size:38
Alignment explanation
Indices: 123092--123170 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
123082 GATACATATA
*
123092 TAACTTTTTTTTATAACCGCTATAGCTTTTTGAGTAAT
1 TAACTTTTTTTCATAACCGCTATAGCTTTTTGAGTAAT
*
123130 TAACTTTTTTTCATAACCGTTATAGCTTTTTGAGTAAT
1 TAACTTTTTTTCATAACCGCTATAGCTTTTTGAGTAAT
123168 TAA
1 TAA
123171 GTATTGTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (38 bp):
TAACTTTTTTTCATAACCGCTATAGCTTTTTGAGTAAT
Found at i:123395 original size:17 final size:18
Alignment explanation
Indices: 123370--123403 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
123360 GTTGGTTCAC
*
123370 ATATCATTTTT-AATAAT
1 ATATAATTTTTCAATAAT
123387 ATATAATTTTTCAATAA
1 ATATAATTTTTCAATAA
123404 CTACTGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATAATTTTTCAATAAT
Found at i:130223 original size:23 final size:23
Alignment explanation
Indices: 130193--130240 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
130183 ATACATTATA
130193 TGACGTGCATTTGCCTTTGGACC
1 TGACGTGCATTTGCCTTTGGACC
*
130216 TGACGTGCATTTGTCTTTGGACC
1 TGACGTGCATTTGCCTTTGGACC
130239 TG
1 TG
130241 TAGTTTGCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.23, G:0.27, T:0.38
Consensus pattern (23 bp):
TGACGTGCATTTGCCTTTGGACC
Done.