Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022395.1 Corchorus olitorius cultivar O-4 contig22428, 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: 114232
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:15309 original size:19 final size:19
Alignment explanation
Indices: 15285--15333 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
15275 AATACAGCAC
15285 AGAGAGGAGAGAAAG-AGAA
1 AGAGAGGA-AGAAAGAAGAA
15304 AGAGA-GAAGAAAGAAAGAA
1 AGAGAGGAAGAAAG-AAGAA
15323 AGAGAGAGAAG
1 AGAGAG-GAAG
15334 CTCTTCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.23
18 2 0.08
19 14 0.54
21 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (19 bp):
AGAGAGGAAGAAAGAAGAA
Found at i:15318 original size:21 final size:21
Alignment explanation
Indices: 15285--15333 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
15275 AATACAGCAC
* *
15285 AGAGAGGAGAGAAAGAGAA-AG
1 AGAGAAGAAAGAAAGA-AAGAG
15306 AGAGAAGAAAGAAAGAAAGAG
1 AGAGAAGAAAGAAAGAAAGAG
15327 AGAGAAG
1 AGAGAAG
15334 CTCTTCTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (21 bp):
AGAGAAGAAAGAAAGAAAGAG
Found at i:23264 original size:1 final size:1
Alignment explanation
Indices: 23253--23284 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
23243 CATTGATTAC
*
23253 AAAAAACAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23285 GAACAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:29516 original size:21 final size:19
Alignment explanation
Indices: 29491--29548 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
29481 GTTGTTCTAA
29491 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
29512 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
29531 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
29549 TGTTAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:32462 original size:21 final size:21
Alignment explanation
Indices: 32436--32478 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
32426 CGCTGCTCTA
* *
32436 ATAATCTCATATGTATAGTAT
1 ATAATCTAATATGTACAGTAT
*
32457 ATAATCTAATCTGTACAGTAT
1 ATAATCTAATATGTACAGTAT
32478 A
1 A
32479 ATCCCATCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (21 bp):
ATAATCTAATATGTACAGTAT
Found at i:32480 original size:19 final size:19
Alignment explanation
Indices: 32456--32494 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
32446 ATGTATAGTA
*
32456 TATAATCTAATCTGTACAG
1 TATAATCCAATCTGTACAG
*
32475 TATAATCCCATCTGTACAG
1 TATAATCCAATCTGTACAG
32494 T
1 T
32495 TGCCAAACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (19 bp):
TATAATCCAATCTGTACAG
Found at i:33107 original size:12 final size:12
Alignment explanation
Indices: 33033--33098 Score: 89
Period size: 12 Copynumber: 5.5 Consensus size: 12
33023 TTGTCATTTA
33033 TTTCTTTTCGTC
1 TTTCTTTTCGTC
33045 TTTCTTTTCGTC
1 TTTCTTTTCGTC
* *
33057 CTTCTTTTCATC
1 TTTCTTTTCGTC
33069 TTTCTTTTCGTC
1 TTTCTTTTCGTC
*
33081 TTT-TTTCTCTTC
1 TTTCTTT-TCGTC
33093 TTTCTT
1 TTTCTT
33099 CTCTTCTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
11 3 0.06
12 42 0.89
13 2 0.04
ACGTcount: A:0.02, C:0.26, G:0.05, T:0.68
Consensus pattern (12 bp):
TTTCTTTTCGTC
Found at i:33107 original size:36 final size:36
Alignment explanation
Indices: 33033--33107 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
33023 TTGTCATTTA
*
33033 TTTCTTTTCGTCTTTCTTTTCGTCCTTCTTTTCATC
1 TTTCTTTTCGTCTTTCTTTTCGTCCTTCTTCTCATC
* * *
33069 TTTCTTTTCGTCTTT-TTTCTCTTCTTTCTTCTCTTC
1 TTTCTTTTCGTCTTTCTTT-TCGTCCTTCTTCTCATC
33105 TTT
1 TTT
33108 AGCTGGTCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 3 0.09
36 31 0.91
ACGTcount: A:0.01, C:0.27, G:0.04, T:0.68
Consensus pattern (36 bp):
TTTCTTTTCGTCTTTCTTTTCGTCCTTCTTCTCATC
Found at i:40546 original size:2 final size:2
Alignment explanation
Indices: 40541--40576 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40531 TATTAATTTA
40541 AT AT AT 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
40577 TTGAAAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41984 original size:14 final size:14
Alignment explanation
Indices: 41965--41992 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41955 TTTGATTAAG
41965 GCAAATTATACAAT
1 GCAAATTATACAAT
41979 GCAAATTATACAAT
1 GCAAATTATACAAT
41993 ACACCGTCAG
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:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
GCAAATTATACAAT
Found at i:72026 original size:12 final size:15
Alignment explanation
Indices: 71989--72017 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
71979 GCAATGGTCC
71989 AATATATAATAATAT
1 AATATATAATAATAT
72004 AATATATAATAATA
1 AATATATAATAATA
72018 AAAATAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATATAATAATAT
Found at i:75747 original size:17 final size:17
Alignment explanation
Indices: 75727--75760 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
75717 GCTTACAAAG
75727 TACAAAATTTGTTCCAA
1 TACAAAATTTGTTCCAA
75744 TACAAAATTTGTTCCAA
1 TACAAAATTTGTTCCAA
75761 GAACAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
TACAAAATTTGTTCCAA
Found at i:75769 original size:17 final size:17
Alignment explanation
Indices: 75728--75767 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
75718 CTTACAAAGT
*
75728 ACAAAATTTGTTCCAAT
1 ACAAAATTTGTTCCAAA
75745 ACAAAATTTGTTCCAAGA
1 ACAAAATTTGTTCCAA-A
75763 ACAAA
1 ACAAA
75768 TTGACAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.28
Consensus pattern (17 bp):
ACAAAATTTGTTCCAAA
Found at i:78198 original size:15 final size:15
Alignment explanation
Indices: 78157--78202 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
78147 CATCTTCATC
*
78157 TTCATCTTTGTCT-T
1 TTCATTTTTGTCTGT
78171 TTC-TTTTCT-TCTGT
1 TTCATTTT-TGTCTGT
78185 TTCATTTTTGTCTGT
1 TTCATTTTTGTCTGT
78200 TTC
1 TTC
78203 CTTCTTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 6 0.22
14 9 0.33
15 12 0.44
ACGTcount: A:0.04, C:0.20, G:0.09, T:0.67
Consensus pattern (15 bp):
TTCATTTTTGTCTGT
Found at i:88833 original size:30 final size:29
Alignment explanation
Indices: 88794--88910 Score: 117
Period size: 30 Copynumber: 3.7 Consensus size: 29
88784 TTCCCTTAAT
88794 AAAAATACTTATACTATATTAATGCCAAA
1 AAAAATACTTATACTATATTAATGCCAAA
* *
88823 AAAAAGTACTTATACTATATAGTACGAATTTCCCTTAAT
1 AAAAA-TACTTATACTATAT--T---AA--TGCC--AAA
88862 AAAAATACTTATACTATATTAATGCCAAA
1 AAAAATACTTATACTATATTAATGCCAAA
88891 AAAAAGTACTTATACTATAT
1 AAAAA-TACTTATACTATAT
88911 AGTACGTAGT
Statistics
Matches: 73, Mismatches: 4, Indels: 21
0.74 0.04 0.21
Matches are distributed among these distances:
29 12 0.16
30 28 0.38
31 3 0.04
32 1 0.01
33 2 0.03
35 2 0.03
36 1 0.01
37 3 0.04
38 14 0.19
39 7 0.10
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAAATACTTATACTATATTAATGCCAAA
Found at i:88889 original size:68 final size:68
Alignment explanation
Indices: 88780--88916 Score: 274
Period size: 68 Copynumber: 2.0 Consensus size: 68
88770 GGGCTACATG
88780 GAATTTCCCTTAATAAAAATACTTATACTATATTAATGCCAAAAAAAAGTACTTATACTATATAG
1 GAATTTCCCTTAATAAAAATACTTATACTATATTAATGCCAAAAAAAAGTACTTATACTATATAG
88845 TAC
66 TAC
88848 GAATTTCCCTTAATAAAAATACTTATACTATATTAATGCCAAAAAAAAGTACTTATACTATATAG
1 GAATTTCCCTTAATAAAAATACTTATACTATATTAATGCCAAAAAAAAGTACTTATACTATATAG
88913 TAC
66 TAC
88916 G
1 G
88917 TAGTTTGATA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.34
Consensus pattern (68 bp):
GAATTTCCCTTAATAAAAATACTTATACTATATTAATGCCAAAAAAAAGTACTTATACTATATAG
TAC
Found at i:90766 original size:41 final size:40
Alignment explanation
Indices: 90721--90802 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 40
90711 CGGCTGTTTT
* * *
90721 ATTTTATGAGTTCTTTTAAGAAAATTCAGTTAATAAATAGA
1 ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAA-AGA
*
90762 ATTTTATAAGTGCTTTTAAGAAAATTTAGTTAAGAAAAGA
1 ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAGA
90802 A
1 A
90803 AGTCATTAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 4 0.11
41 33 0.89
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.39
Consensus pattern (40 bp):
ATTTTATAAGTGCTTTTAAGAAAATTCAGTTAAGAAAAGA
Found at i:92876 original size:11 final size:11
Alignment explanation
Indices: 92852--92886 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
92842 TTGACAGCAC
92852 AACAAAAACAA
1 AACAAAAACAA
* *
92863 AACGAAAACGA
1 AACAAAAACAA
92874 AACAAAAACAA
1 AACAAAAACAA
92885 AA
1 AA
92887 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:100220 original size:2 final size:2
Alignment explanation
Indices: 100215--100246 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
100205 ACACTGATTG
100215 AT 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
100247 TCTAAAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101595 original size:42 final size:42
Alignment explanation
Indices: 101543--101627 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
101533 ATTAATGTTA
101543 GTTTCATGATTTCCGGAGGGAAAATTGGACTGTTAGGTTATG
1 GTTTCATGATTTCCGGAGGGAAAATTGGACTGTTAGGTTATG
* *
101585 GTTTTATGATTTCCGGAGGGAAAATTGGATTGTTAGGTTATG
1 GTTTCATGATTTCCGGAGGGAAAATTGGACTGTTAGGTTATG
101627 G
1 G
101628 GGTAAAGCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.07, G:0.32, T:0.38
Consensus pattern (42 bp):
GTTTCATGATTTCCGGAGGGAAAATTGGACTGTTAGGTTATG
Found at i:102423 original size:328 final size:328
Alignment explanation
Indices: 101720--102648 Score: 1101
Period size: 328 Copynumber: 2.8 Consensus size: 328
101710 GACCGTTAGT
* * * * *
101720 AGATTGAAGGGC-TTTCTACACTTCTAATATCGTTTTTCTTATTTTTT-CGAATTATTTTTTAAT
1 AGATTGAAAGGCTTTTC-ACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTATAAT
** * *
101783 TAAATCGAAACATAATTTTGATGCTCGTAAAAACAAATCCTAAAATCCAATGCGGTTGAGATTTG
65 TAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGCGCTTGAGATTTG
* ** *
101848 GTTTA-ATGAATATAGATATTTCAATGAGACATGGCGTAAAAAATTATGC-AAACCGACCGAGTC
130 G-TTAGATGAATATAGATATTTCAATGAGACTTGGCGTAAAAAATTATGCAAAACAAACCGGGTC
* * * **
101911 CCG-GAACTCGTTTTTAG-CAAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGCA
194 CAGAG-ACACGTTTTTAGTC-AAAAA-CGTGATGATTAGTACACGTTTTAAGCTAAAA-TTTGCA
* * **
101974 AAAATT-AACTCGAAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAGATTTATAATTC
255 AAAATTGATC-CAAAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAGAAATATAATTC
102038 AACGCCAAAA
319 AACGCCAAAA
* * * *
102048 ACATTAAAAGGCTTTTTACGCTTATAATATCGTTTTTCCTA-TTTTTCCGAATTAATTTATAATT
1 AGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTATAATT
* * * * * *
102112 AAATCGCAACATTATTCAGATGCTTGTAAAAACAAATCCTTAAATCCAATGCGCCTAAGATTTTG
66 AAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGCGCTTGAGATTTGG
102177 TTAGATGAATATAGATATTTCAATGAGACTTGGCG-ACAAAAATTATGCAAAACAAAGCCGGGTC
131 TTAGATGAATATAGATATTTCAATGAGACTTGGCGTA-AAAAATTATGCAAAACAAA-CCGGGTC
* *
102241 CAGAGACACG-TTTTAGTCAAAAATGCGATGATTAGTACACGTTTTAAGCTAAAATTGTGCAAAA
194 CAGAGACACGTTTTTAGTCAAAAACGTGATGATTAGTACACGTTTTAAGCTAAAATT-TGCAAAA
* * * * *
102305 ATTGATCCAAAAGAGTTTTCCTCAATTTTTGGCCATGATACTGATAAAA-AAATATATTTTAACG
258 ATTGATCCAAAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAGAAATATAATTCAACG
*
102369 CCTAAA
323 CCAAAA
* *
102375 AGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCTAATC
1 AGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTATAATT
* * ** * * *
102440 AAATTGAAACATGATTCAGATTATCGTAAAAACAATTCTTTAAATCCAATGTGCTTGAGATTTGG
66 AAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGCGCTTGAGATTTGG
* * *
102505 TTAGATGAATATAGATATTTCATTGAGACTTGGCGTAAAAAATCATGCAAAACAGAACCGGGGCC
131 TTAGATGAATATAGATATTTCAATGAGACTTGGCGTAAAAAATTATGCAAAACA-AACCGGGTCC
* * * *
102570 TTA-AAACACGTTTTTAGTCCAAAACCGTGATGATTAGTATACGGTTTCAA-CTAAAAATTTGCA
195 --AGAGACACGTTTTTAGT-CAAAAACGTGATGATTAGTACAC-GTTTTAAGCT-AAAATTTGCA
*
102633 AAAATTGTTCCGAAAA
255 AAAATTGATCC-AAAA
102649 CTATAAAATT
Statistics
Matches: 513, Mismatches: 68, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
327 64 0.12
328 346 0.67
329 30 0.06
330 21 0.04
331 36 0.07
332 16 0.03
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (328 bp):
AGATTGAAAGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTATAATT
AAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGCGCTTGAGATTTGG
TTAGATGAATATAGATATTTCAATGAGACTTGGCGTAAAAAATTATGCAAAACAAACCGGGTCCA
GAGACACGTTTTTAGTCAAAAACGTGATGATTAGTACACGTTTTAAGCTAAAATTTGCAAAAATT
GATCCAAAAGAATTTTCCTCAATTTTTGGCCACGATACTCATAAAAGAAATATAATTCAACGCCA
AAA
Found at i:109444 original size:45 final size:45
Alignment explanation
Indices: 109380--109478 Score: 180
Period size: 45 Copynumber: 2.2 Consensus size: 45
109370 TTGTGCACTC
109380 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
1 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
*
109425 GGCAATCATGGGGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
1 GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
*
109470 GGCAGTCAT
1 GGCAATCAT
109479 AGATTCTAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (45 bp):
GGCAATCATGGAGCCAAAGCTCTCTTTGATCTCCTTAAAGCATTT
Found at i:110379 original size:34 final size:34
Alignment explanation
Indices: 110341--110464 Score: 212
Period size: 34 Copynumber: 3.6 Consensus size: 34
110331 AGCACCACTG
*
110341 TGTCTTCTCGTTTACCTTCGTGTCTGTCTTCCTC
1 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
*
110375 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTG
1 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
* *
110409 TGTCTTCTCGTGTACCTTCGTGCCTGTCTCCCTC
1 TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
110443 TGTCTTCTCGTGTACCTTCGTG
1 TGTCTTCTCGTGTACCTTCGTG
110465 CCTGCTGGCC
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 85 1.00
ACGTcount: A:0.03, C:0.32, G:0.19, T:0.46
Consensus pattern (34 bp):
TGTCTTCTCGTGTACCTTCGTGTCTGTCTTCCTC
Found at i:110536 original size:62 final size:62
Alignment explanation
Indices: 110439--110663 Score: 351
Period size: 62 Copynumber: 3.5 Consensus size: 62
110429 TGCCTGTCTC
110439 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
1 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
110501 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTTCCT
1 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGG----------CCT
110566 CTTCCTT
56 CTTCCTT
*
110573 CCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
1 CCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
110635 CCTCTGTCTTCTCGTGTACCTTCGTGCCT
1 CCTCTGTCTTCTCGTGTACCTTCGTGCCT
110664 CGTGTCTGTC
Statistics
Matches: 151, Mismatches: 2, Indels: 20
0.87 0.01 0.12
Matches are distributed among these distances:
62 90 0.60
72 61 0.40
ACGTcount: A:0.03, C:0.40, G:0.21, T:0.35
Consensus pattern (62 bp):
CCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCTCTTCCTT
Found at i:110567 original size:72 final size:72
Alignment explanation
Indices: 110491--110639 Score: 289
Period size: 72 Copynumber: 2.1 Consensus size: 72
110481 CCTGCGGAGG
*
110491 CCTCTTCCTTCCTCTGTCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
110556 CTTCCTT
66 CTTCCTT
110563 CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
1 CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
110628 CTTCCTT
66 CTTCCTT
110635 CCTCT
1 CCTCT
110640 GTCTTCTCGT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 76 1.00
ACGTcount: A:0.03, C:0.42, G:0.19, T:0.36
Consensus pattern (72 bp):
CCTCTTCCTTCCTCTGGCTTCTCGTGTACCTTCGTGCCTGCTGGCCTCGCCTCCTGCGGAGGCCT
CTTCCTT
Found at i:110568 original size:10 final size:10
Alignment explanation
Indices: 110553--110577 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
110543 CCTGCGGAGG
110553 CCTCTTCCTT
1 CCTCTTCCTT
110563 CCTCTTCCTT
1 CCTCTTCCTT
110573 CCTCT
1 CCTCT
110578 GGCTTCTCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (10 bp):
CCTCTTCCTT
Found at i:111398 original size:20 final size:20
Alignment explanation
Indices: 111373--111432 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
111363 ATGAGACTCC
111373 TTTTCTACA-TATCACATGAT
1 TTTTCTACATTA-CACATGAT
* *
111393 TTTTCTGCATTACATATGAT
1 TTTTCTACATTACACATGAT
* *
111413 TTTTCTGCATTACATATGAT
1 TTTTCTACATTACACATGAT
111433 ATAGCTCAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 35 0.95
21 2 0.05
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (20 bp):
TTTTCTACATTACACATGAT
Found at i:111406 original size:25 final size:22
Alignment explanation
Indices: 111388--111429 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
111378 TACATATCAC
111388 ATGATTTTTCTGCATTAC--AT
1 ATGATTTTTCTGCATTACATAT
111408 ATGATTTTTCTGCATTACATAT
1 ATGATTTTTCTGCATTACATAT
111430 GATATAGCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.90
22 2 0.10
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (22 bp):
ATGATTTTTCTGCATTACATAT
Done.