Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019337.1 Corchorus olitorius cultivar O-4 contig19370, 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: 67723
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9283 original size:18 final size:19
Alignment explanation
Indices: 9260--9304 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
9250 TGAAATTTAT
9260 TAATTATTTATT-AG-ATAA
1 TAATTATTT-TTCAGAATAA
9278 TAATTATTTTTCAGAATAA
1 TAATTATTTTTCAGAATAA
*
9297 TTATTATT
1 TAATTATT
9305 AATATTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 2 0.08
18 11 0.46
19 11 0.46
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
TAATTATTTTTCAGAATAA
Found at i:12126 original size:5 final size:5
Alignment explanation
Indices: 12116--12148 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
12106 CTTCCCTCCT
12116 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTT
1 CTTTC CTTTC CTTTC CTTTC CTTTC CTTTC CTT
12149 AAATTACTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
CTTTC
Found at i:12513 original size:34 final size:34
Alignment explanation
Indices: 12474--12542 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
12464 GGCTATTTTA
* *
12474 GCTATTTTAGGAAGCCAAAATCAAGTTGGCTTTG
1 GCTATTTTAGGAAGCCAAAACCAAGTCGGCTTTG
12508 GCTATTTTAGGAAGCCAAAACCAAGTCGGCTTTG
1 GCTATTTTAGGAAGCCAAAACCAAGTCGGCTTTG
12542 G
1 G
12543 GCTTTGGCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (34 bp):
GCTATTTTAGGAAGCCAAAACCAAGTCGGCTTTG
Found at i:20469 original size:105 final size:106
Alignment explanation
Indices: 20285--20485 Score: 288
Period size: 105 Copynumber: 1.9 Consensus size: 106
20275 CAAACAAAAC
* *
20285 CTTAGTGAATTAGTTATATATTTTATTTCTAAAATCCTACATTAATAAGTTATTAATTATGAAAT
1 CTTAGTGAATTAGTTATATATTTTATTTCTAAAATCCTACATCAATAAATTATTAATTATGAAAT
20350 TTACCCTTAAAATAAAAATAAAATTTTAATTTTGGGTTAAA
66 TTACCCTTAAAATAAAAATAAAATTTTAATTTTGGGTTAAA
*
20391 CTTAGTGAAATTAGTT-TCGTATTTTATTTCTAAAA-CTCTA-A-CAATAAATTATTAATT-TCG
1 CTTAGTG-AATTAGTTAT-ATATTTTATTTCTAAAATC-CTACATCAATAAATTATTAATTAT-G
20451 AAATTTACCC-TAATAATAAAAATAAAATTTTAATT
62 AAATTTACCCTTAA-AATAAAAATAAAATTTTAATT
20486 GGGTATTACT
Statistics
Matches: 87, Mismatches: 3, Indels: 11
0.86 0.03 0.11
Matches are distributed among these distances:
104 4 0.05
105 46 0.53
106 10 0.11
107 27 0.31
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (106 bp):
CTTAGTGAATTAGTTATATATTTTATTTCTAAAATCCTACATCAATAAATTATTAATTATGAAAT
TTACCCTTAAAATAAAAATAAAATTTTAATTTTGGGTTAAA
Found at i:20975 original size:21 final size:22
Alignment explanation
Indices: 20946--20991 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
20936 TTTTTAAAAA
* *
20946 TTAATAATTAGGTATTCTT-TT
1 TTAAAAATTAGGTATTATTATT
*
20967 TTAAAAATTAGTTATTATTATT
1 TTAAAAATTAGGTATTATTATT
20989 TTA
1 TTA
20992 TATGATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (22 bp):
TTAAAAATTAGGTATTATTATT
Found at i:21871 original size:108 final size:105
Alignment explanation
Indices: 21609--21871 Score: 379
Period size: 105 Copynumber: 2.5 Consensus size: 105
21599 ATTTTTCTAA
* ** *
21609 ACCCTTAAAATAAAATTTTAATTTTAATTT-TGGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* * *
21672 TTTCTAAAACTCTATAACAATATTATTAATTATGGAATTT
66 TTTCTAAAACCCTATAACAATATTATAAATTATGAAATTT
* *
21712 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
21777 TTTCTAAAACCCTATAACAATAAATTA-AAATTTTGAAATTT
66 TTTCTAAAACCCTATAACAAT--ATTATAAATTATGAAATTT
21818 ACCCTTAAAATAAAAATAAAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAAT--AAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
21872 AGGCTAAACT
Statistics
Matches: 144, Mismatches: 10, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
103 27 0.19
104 14 0.10
105 36 0.25
106 28 0.19
107 4 0.03
108 35 0.24
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
TTTCTAAAACCCTATAACAATATTATAAATTATGAAATTT
Found at i:21914 original size:2 final size:2
Alignment explanation
Indices: 21907--21933 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21897 AAATAGAAAA
21907 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
21934 AGACACGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27133 original size:99 final size:102
Alignment explanation
Indices: 26883--27175 Score: 362
Period size: 99 Copynumber: 2.8 Consensus size: 102
26873 TTTTTTTATT
* ** *
26883 ATTATTATTATAGAATTTTTGAAATAAAATATAAAACTAATTTCACTAAGTTTAGCCCCAAATTA
1 ATTATTGTTATAGGGTTTTAGAAATAAAATAT-AAACTAATTTCACTAAGTTTAGCCCCAAATT-
* *
26948 AAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATTAATA
64 -AA-TTTATTTTTATTTTAAGGATAAATTCCAAAATTAATA
*
26989 ATTTATTGTTATAGGGTTTTAGAAATAAAATACAAACTAATTTCACTAAGTTTAGCCCCAAATTA
1 A-TTATTGTTATAGGGTTTTAGAAATAAAATATAAACTAATTTCACTAAGTTTAGCCCCAAATTA
*
27054 A-TT-TTTTTATTTTAAGGATAAATTCCATAATTAATA
65 ATTTATTTTTATTTTAAGGATAAATTCCAAAATTAATA
* *
27090 A-TATTGTTATAGGGTTTTAGAAATAAAATATATAACTAA-TTCACCAAGTTTAG-TCCAAATTA
1 ATTATTGTTATAGGGTTTTAGAAATAAAATATA-AACTAATTTCACTAAGTTTAGCCCCAAATT-
* *
27152 AAATTAAAATTTTATTTTAAGGAT
64 -AATT-TATTTTTATTTTAAGGAT
27176 TAGAAAAATT
Statistics
Matches: 167, Mismatches: 13, Indels: 17
0.85 0.07 0.09
Matches are distributed among these distances:
98 7 0.04
99 43 0.26
100 8 0.05
101 32 0.19
102 2 0.01
103 15 0.09
104 2 0.01
106 32 0.19
107 26 0.16
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.41
Consensus pattern (102 bp):
ATTATTGTTATAGGGTTTTAGAAATAAAATATAAACTAATTTCACTAAGTTTAGCCCCAAATTAA
TTTATTTTTATTTTAAGGATAAATTCCAAAATTAATA
Found at i:29156 original size:22 final size:22
Alignment explanation
Indices: 29132--29174 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29122 GGGTTTTCTT
29132 TTTTAA-TCTTTTTAGATTTTA
1 TTTTAATTCTTTTTAGATTTTA
* *
29153 TTTTAATTTTTTTTATATTTTA
1 TTTTAATTCTTTTTAGATTTTA
29175 ATAAGTAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTAATTCTTTTTAGATTTTA
Found at i:30646 original size:10 final size:10
Alignment explanation
Indices: 30631--30661 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
30621 GTAGCTCACT
30631 ACTCGGCTCG
1 ACTCGGCTCG
30641 ACTCGGCTCG
1 ACTCGGCTCG
*
30651 ACTCGACTCG
1 ACTCGGCTCG
30661 A
1 A
30662 TTACACCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.16, C:0.39, G:0.26, T:0.19
Consensus pattern (10 bp):
ACTCGGCTCG
Found at i:31011 original size:45 final size:44
Alignment explanation
Indices: 30952--31065 Score: 115
Period size: 45 Copynumber: 2.6 Consensus size: 44
30942 AAGACCTCAC
* * *
30952 TATGAAATTTTGATAA-CTCCCTAATAAAATTTTGATAACCAACAT
1 TATGAAATGTTGATAACCTCCAT-ATAAAATATTGATAACC-ACAT
* * *
30997 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACAT
1 TATGAAATGTTGATAACCTCCATATAAAATATTGATAACCACAT
* *
31041 TATGAAAAT-TTAAAAACCTCCATAT
1 TATG-AAATGTTGATAACCTCCATAT
31066 GAATTGTTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 22 0.38
45 31 0.53
46 5 0.09
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (44 bp):
TATGAAATGTTGATAACCTCCATATAAAATATTGATAACCACAT
Found at i:31160 original size:23 final size:23
Alignment explanation
Indices: 31132--31186 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
31122 CGTCACAATG
*
31132 AAATTTTGATAAACCTTCCTATA
1 AAATTTTGATAAACCTCCCTATA
31155 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCCTATA
31178 AAATTTTGA
1 AAATTTTGA
31187 GAACCTAACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.38
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCCTATA
Found at i:31271 original size:22 final size:22
Alignment explanation
Indices: 30908--31404 Score: 237
Period size: 22 Copynumber: 22.6 Consensus size: 22
30898 TTAATCTTCT
* *
30908 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
30930 AAAGGAAA-TTTGA-AGACCTCAC
1 -TATGAAATTTTGATA-ACCTCAC
*
30952 TATGAAATTTTGATAA-CTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
30973 TAATAAAATTTTGATAACCAACAT
1 T-ATGAAATTTTGATAACC-TCAC
* *
30997 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * * *
31018 ATATGATATATTGATAACCACAT
1 -TATGAAATTTTGATAACCTCAC
* * *
31041 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* *
31062 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTCAC
* * *
31085 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* *
31107 TATG-AATTGTGATAACGTCAC
1 TATGAAATTTTGATAACCTCAC
*
31128 AATGAAATTTTGATAAACCTTC-C
1 TATGAAATTTTGAT-AACC-TCAC
* *
31151 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
*
31174 TATAAAATTTTGAGAACCTAACCTC-C
1 TATGAAATTTT--G-A--TAACCTCAC
*
31200 TTATGAAATCTTGATAA-CT-AC
1 -TATGAAATTTTGATAACCTCAC
*
31221 ----AAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
31239 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
* * *
31261 TATGAAATTTTGTTAATCTCTC
1 TATGAAATTTTGATAACCTCAC
* *
31283 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
*
31305 TATGAAATTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
31327 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
** *
31349 GGTGAAATTTTGGTAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
31371 TATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCAC
*
31392 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
31405 TACTCCATAA
Statistics
Matches: 358, Mismatches: 77, Indels: 81
0.69 0.15 0.16
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
18 1 0.00
20 14 0.04
21 39 0.11
22 199 0.56
23 66 0.18
24 6 0.02
25 2 0.01
26 2 0.01
27 15 0.04
28 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:31272 original size:44 final size:44
Alignment explanation
Indices: 30908--32091 Score: 368
Period size: 44 Copynumber: 27.4 Consensus size: 44
30898 TTAATCTTCT
* * *
30908 TATGAAATTTTGTTAACCTCCCAAAGGAAA-TTTGA-AGACCTCAC
1 TATGAAATTTTGATAACCTCCC-TATGAAATTTTGATA-ACCTCAC
* * *
30952 TATGAAATTTTGATAA-CTCCCTAATAAAATTTTGATAACCAACAT
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACC-TCAC
* * * * * * *
30997 TATGAGATGTTGATAACCTCCATATGATATATTGATAACCACAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * * *
31041 TATGAAAATTTAAAAACCTCCATATG-AATTGTT-AGTAATCACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATT-TTGA-TAACCTCAC
* * * * * *
31085 TCTGAAATTTTGATAATCACACTATG-AATTGTGATAACGTCAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * *
31128 AATGAAATTTTGATAAACCTTCCTATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCCTATGAAATTTTGAT-AACCTCAC
* * *
31174 TATAAAATTTTGAGAACCTAACCTCCTTATGAAATCTTGATAA-CT-AC
1 TATGAAATTTT--G-A--TAACCTCCCTATGAAATTTTGATAACCTCAC
** *
31221 ----AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * *
31261 TATGAAATTTTGTTAATCTCTCTATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGAT-AACCTCAC
* * *
31305 TATGAAATTTTGATAACC-CTCTTATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCTC-CCTATGAAATTTTGATAACCT-CAC
** * * * *
31349 GGTGAAATTTTGGTAACCTTCATATGAAATTTTGATATCCTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * * *
31392 -CTGAAATTTTGATTA-CTCCATAATAAAAGTTTAATAACCT---
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACCTCAC
** * * *
31432 T-TCTAATTTTG-TAACCAT-ACTATGAAATTTTGATAACATCTC
1 TATGAAATTTTGATAACC-TCCCTATGAAATTTTGATAACCTCAC
* * * * * *
31474 CA-G-AA-----AT-A-C-CACTATGAAATTTTGGTAATCACAT
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * ** ** * *
31508 TTTGAAAATTTGATAAGTTCTTTATGGAATTTTGATAACCTCTC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * * * *
31552 TATAAAATTTTGTTGACC-CCTCTATGAAATTTGGATAATCACAT
1 TATGAAATTTTGATAACCTCC-CTATGAAATTTTGATAACCTCAC
* * * **
31596 TATGTAATTTTGATAACCTCGCTTTGAAATTTTGATAACAACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * * *
31640 TATAAAATTTTGATAATCCGATCTCTATGAAATTTCGATAATCACTC
1 TATGAAATTTTGATAA-CC--TCCCTATGAAATTTTGATAACCTCAC
* * * *
31687 TATGAGA-TTTGATAACCT-TCTATCAAATTTTGGT-A-CTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * *
31726 TTATGAAATTGAGACTTTTATAACCTTCGTATGAAATTTTG---ACC-C-C
1 -TATGAAA-T-----TTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * * *
31772 -ATGAAATATT-AGTAACCTCCTTATAAAATTTTGTTAACCACAC
1 TATGAAATTTTGA-TAACCTCCCTATGAAATTTTGATAACCTCAC
* ** *
31815 TATAAAATTCTT-ATAATTACCTTGCTATGACATTTTGATAA--TC-C
1 TATGAAATT-TTGAT-A--ACCTCCCTATGAAATTTTGATAACCTCAC
* ** * * *
31859 -------CTTTGATAACCTTTCTATAAAATATTGATAACCAT-GC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCAC
* ** * * * *
31896 TATAAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATCC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCA--C
* * *
31942 TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTC-C
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACC-TCAC
* * * * * *
31986 CATGAAATTTTGATAACTTCCATGTGAAATTTTGGTAACCACAC
1 TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
* * * *
32030 TATGGAATTTTGATAACCT-CCTCATGAAATTATAATAACCAT-AT
1 TATGAAATTTTGATAACCTCCCT-ATGAAATTTTGATAACC-TCAC
32074 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
32092 ACACAGAGAC
Statistics
Matches: 832, Mismatches: 215, Indels: 186
0.67 0.17 0.15
Matches are distributed among these distances:
34 37 0.04
35 2 0.00
36 6 0.01
37 7 0.01
38 41 0.05
39 19 0.02
40 20 0.02
41 15 0.02
42 43 0.05
43 48 0.06
44 385 0.46
45 55 0.07
46 63 0.08
47 55 0.07
48 14 0.02
49 3 0.00
50 18 0.02
51 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTGATAACCTCCCTATGAAATTTTGATAACCTCAC
Found at i:31560 original size:22 final size:22
Alignment explanation
Indices: 31510--31718 Score: 145
Period size: 22 Copynumber: 9.5 Consensus size: 22
31500 AATCACATTT
* ** *
31510 TGAAAATTTGATAAGTTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
31532 TGGAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
31554 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * *
31576 TGAAATTTGGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* * *
31598 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTCTCTA
** *
31620 TGAAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTCTA
*
31642 TAAAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTCTA
* * *
31667 TGAAATTTCGATAATCACTCTA
1 TGAAATTTTGATAACCTCTCTA
*
31689 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTCTA
*
31709 TCAAATTTTG
1 TGAAATTTTG
31719 GTACTCCTTA
Statistics
Matches: 140, Mismatches: 41, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
20 7 0.05
21 12 0.09
22 102 0.73
23 2 0.01
24 1 0.01
25 16 0.11
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:31911 original size:22 final size:21
Alignment explanation
Indices: 31864--31951 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 21
31854 AATCCCTTTG
* *
31864 ATAACCTTTCTATAAAATATTG
1 ATAACCTTCCTATAAAAT-TTA
* *
31886 ATAACCATGCTATAAAATTTCA
1 ATAACCTTCCTATAAAATTT-A
31908 ATAACCTTCCTA-AGAAATTTTA
1 ATAACCTTCCTATA-AAA-TTTA
*
31930 ATAACCTGATCCTATGAAATTT
1 ATAACCT--TCCTATAAAATTT
31952 TGGTAACCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
21 3 0.06
22 37 0.69
23 6 0.11
24 8 0.15
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (21 bp):
ATAACCTTCCTATAAAATTTA
Found at i:31969 original size:22 final size:22
Alignment explanation
Indices: 31941--32095 Score: 147
Period size: 22 Copynumber: 7.0 Consensus size: 22
31931 TAACCTGATC
*
31941 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
31963 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
31985 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
* *
32008 -TGTGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
32029 CTATGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* * *
32050 CTCATGAAATTATAATAACCATA
1 CT-ATGAAATTTTGATAACCACA
*
32073 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
32095 C
1 C
32096 AGAGACAAAA
Statistics
Matches: 105, Mismatches: 20, Indels: 16
0.74 0.14 0.11
Matches are distributed among these distances:
20 1 0.01
21 4 0.04
22 97 0.92
23 2 0.02
24 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:32039 original size:66 final size:67
Alignment explanation
Indices: 31864--32095 Score: 242
Period size: 66 Copynumber: 3.5 Consensus size: 67
31854 AATCCCTTTG
* * * * ** * ** * *
31864 ATAACCT-TTCTATAAAATATTGATAACCATGCTATAAAATTTCAATAACCTTCCTAAGAAATTT
1 ATAACCTATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTT
31928 TA
66 TA
31930 ATAACCTGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT-ATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
*
31995 TTG
65 TTA
* *
31998 ATAA-CT-TCCATGTGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-TCCTCATGAAAT
1 ATAACCTATCC-TATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCC-CATGAAAT
*
32060 TATA
64 TTTA
*
32064 ATAACCATAT--TATGAAATTTTGATAACCACAC
1 ATAACC-TATCCTATGAAATTTTGGTAACCACAC
32096 AGAGACAAAA
Statistics
Matches: 141, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
65 6 0.04
66 79 0.56
67 3 0.02
68 52 0.37
69 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (67 bp):
ATAACCTATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTT
TA
Found at i:34378 original size:2 final size:2
Alignment explanation
Indices: 34371--34400 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
34361 GGTGGATCTG
34371 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
34401 TAATGAAACT
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:36476 original size:22 final size:22
Alignment explanation
Indices: 36408--36571 Score: 95
Period size: 22 Copynumber: 7.5 Consensus size: 22
36398 TCATAGTGCT
* *
36408 GGTTATCAAAATTTCGTAGTGAA
1 GGTTATCAAAATTTCATA-AGAA
* * * *
36431 -GTCT-TCAAAATTCCTTAGGGA
1 GGT-TATCAAAATTTCATAAGAA
*
36452 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
* ** *
36474 GGTAAAAAAAAATTT-ATAAAAA
1 GGT-TATCAAAATTTCATAAGAA
* * *
36496 GGTTCTCGAAATTTCAT-AGTAT
1 GGTTATCAAAATTTCATAAG-AA
* *
36518 CGTTATTAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
*
36540 GGTTATC-AAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGAA
*
36561 GGTCATCAAAA
1 GGTTATCAAAA
36572 ATAGTGTAAT
Statistics
Matches: 105, Mismatches: 28, Indels: 17
0.70 0.19 0.11
Matches are distributed among these distances:
21 29 0.28
22 64 0.61
23 12 0.11
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:40839 original size:17 final size:17
Alignment explanation
Indices: 40817--40850 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40807 GGCATGTCAC
*
40817 TTTGCTTAACTTGCTAG
1 TTTGCTTAACCTGCTAG
*
40834 TTTGCTTCACCTGCTAG
1 TTTGCTTAACCTGCTAG
40851 CTAATTGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (17 bp):
TTTGCTTAACCTGCTAG
Found at i:50185 original size:270 final size:266
Alignment explanation
Indices: 49660--50153 Score: 648
Period size: 270 Copynumber: 1.8 Consensus size: 266
49650 CTAAAGTTTT
* ** *
49660 GCCACAATAATGTTACTTAAAACTTAAAACTGTGTATGGTTATTACGAAAAGTAAAATTATCACA
1 GCCACAATAATGTTACTTAAAACCTAAAACTGTGTATGGTTATTAAAAAAAGTAAAATAATCACA
** * *
49725 TCCACTATCAGTGTAGTTTACTATTAGATTGTACAAATGGGGTTAAAAGTTTGACATGTGTCTTT
66 TCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACAGGGTTAAAAGATTGACATGAGTCTTT
* * * * *
49790 TTAGTGTATATTTTTTAAGGAAAAATATTTTATGCATCGTTAGTGAAGTTTAGCTGACTGCACAT
131 TTAGTGTATATTTTTTAAGGAAAAATATCTTATCCACCATTAGTGAAGTTTAGCAGACTGCACAT
* * * *** *
49855 GCAGGGTTACAGTTAAAGGGTTGACATGTTTTAGGGAGTAGTTTTGATTTTTGAACATTAATTAA
196 GCAAGGTTACAGTTAAAGGGTCGACATGTTTTACGGAG-AGGAATGAGTTTTGAACATTAATTAA
49920 GTAAAAA
260 GTAAAAA
* * *
49927 GCCATAATAATGTTACTTAAATTAAACCTAAAAGTGTTTATGGTTATTAAAAAAAGTAAAATAAT
1 GCCACAATAATGTTACTT--A--AAACCTAAAACTGTGTATGGTTATTAAAAAAAGTAAAATAAT
* * * *
49992 CACATCCACTATTAGTGTAGTTTACTATTAGATTG-CCAAACAGGGTTAAAGGATTGGCATGAGT
62 CACATCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACAGGGTTAAAAGATTGACATGAGT
* * *
50056 CTTTTTCGTGTATATTTTTTTAGGAAAATTATCTTATCCACCATTAGTGAAGTTTAGCAGACTGC
127 CTTTTTAGTGTATATTTTTTAAGGAAAAATATCTTATCCACCATTAGTGAAGTTTAGCAGACTGC
**
50121 ACATGCAAGGTTAGGGTTAAAGGGTCGACATGT
192 ACATGCAAGGTTACAGTTAAAGGGTCGACATGT
50154 GTGTCTCCTT
Statistics
Matches: 196, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
267 17 0.09
269 1 0.01
270 108 0.55
271 70 0.36
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.36
Consensus pattern (266 bp):
GCCACAATAATGTTACTTAAAACCTAAAACTGTGTATGGTTATTAAAAAAAGTAAAATAATCACA
TCCACTATCAGTGTAGTTTACTATTAGATTGTACAAACAGGGTTAAAAGATTGACATGAGTCTTT
TTAGTGTATATTTTTTAAGGAAAAATATCTTATCCACCATTAGTGAAGTTTAGCAGACTGCACAT
GCAAGGTTACAGTTAAAGGGTCGACATGTTTTACGGAGAGGAATGAGTTTTGAACATTAATTAAG
TAAAAA
Found at i:52329 original size:2 final size:2
Alignment explanation
Indices: 52322--52402 Score: 112
Period size: 2 Copynumber: 41.5 Consensus size: 2
52312 AAAATCAGAC
* *
52322 TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
52364 TA TA TA TA TA TA TA TA -A TA GA TT TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52403 TCAAACATAG
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
1 2 0.03
2 67 0.97
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:53125 original size:2 final size:2
Alignment explanation
Indices: 53113--53143 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
53103 ATCGGTACAA
53113 AT AT A- 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
53144 TTAGGCCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53609 original size:12 final size:12
Alignment explanation
Indices: 53581--53612 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
53571 AAATGATTTC
53581 AAATTAAA-ATT
1 AAATTAAACATT
53592 -AATTAAACATT
1 AAATTAAACATT
53603 AAATTAAACA
1 AAATTAAACA
53613 AATTATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 7 0.37
11 3 0.16
12 9 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATTAAACATT
Found at i:54587 original size:149 final size:149
Alignment explanation
Indices: 54315--54598 Score: 523
Period size: 149 Copynumber: 1.9 Consensus size: 149
54305 GTTGATCGGG
*
54315 TTCGGATCATTTCAGGTTCGAGTAGCCAAAATTTCGGAACATTTTTGGGTTGGGTTAGTTTCGGT
1 TTCGGATCATTTCAGGTTCGAGTAGCCAAAATTTCGGAACATTTTTGGGTTGGGTCAGTTTCGGT
54380 ATCAAGTTGGGCGGATTCAGGTTGTTGACTTTTTTTGGTCAAATCGGGTTTGGCTTCGGGCGGTC
66 ATCAAGTTGGGCGGATTCAGGTTGTTGACTTTTTTTGGTCAAATCGGGTTTGGCTTCGGGCGGTC
54445 GGGTCAAATTTTGTCAGCT
131 GGGTCAAATTTTGTCAGCT
*
54464 TTCGGATCATTTCGGGTTCGAGTAGCCAAAATTTCGGAACATTTTTGGGTTGGGTCAGTTTCGGT
1 TTCGGATCATTTCAGGTTCGAGTAGCCAAAATTTCGGAACATTTTTGGGTTGGGTCAGTTTCGGT
* * *
54529 ATCGAGTTGGGCGGATTCAGTTTGTTGACTTTTTTTGGTCAAATCGGGTTTGGTTTCGGGCGGTC
66 ATCAAGTTGGGCGGATTCAGGTTGTTGACTTTTTTTGGTCAAATCGGGTTTGGCTTCGGGCGGTC
54594 GGGTC
131 GGGTC
54599 GAGTACCCGT
Statistics
Matches: 130, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 130 1.00
ACGTcount: A:0.16, C:0.15, G:0.31, T:0.38
Consensus pattern (149 bp):
TTCGGATCATTTCAGGTTCGAGTAGCCAAAATTTCGGAACATTTTTGGGTTGGGTCAGTTTCGGT
ATCAAGTTGGGCGGATTCAGGTTGTTGACTTTTTTTGGTCAAATCGGGTTTGGCTTCGGGCGGTC
GGGTCAAATTTTGTCAGCT
Found at i:56715 original size:25 final size:25
Alignment explanation
Indices: 56681--56729 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
56671 GATTGGTTTG
*
56681 TAGAGATCGAGCGAGAGTGCTCAAA
1 TAGACATCGAGCGAGAGTGCTCAAA
56706 TAGACATCGAGCGAGAGTGCTCAA
1 TAGACATCGAGCGAGAGTGCTCAA
56730 GATTGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.18, G:0.31, T:0.16
Consensus pattern (25 bp):
TAGACATCGAGCGAGAGTGCTCAAA
Found at i:57635 original size:25 final size:25
Alignment explanation
Indices: 57595--57643 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
57585 AATTGGTTTG
57595 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
* *
57620 TAGAGACTGAGTGAGAGTGCTCAA
1 TAGAGACCGAGCGAGAGTGCTCAA
57644 GATTGTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:66061 original size:17 final size:17
Alignment explanation
Indices: 66039--66073 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
66029 TAATCCTTAA
66039 TCGGGCCGGGCTCGGGC
1 TCGGGCCGGGCTCGGGC
*
66056 TCGGGCCGGGCTTGGGC
1 TCGGGCCGGGCTCGGGC
66073 T
1 T
66074 TTCGTTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.31, G:0.51, T:0.17
Consensus pattern (17 bp):
TCGGGCCGGGCTCGGGC
Found at i:67279 original size:14 final size:14
Alignment explanation
Indices: 67256--67302 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 14
67246 TAATGCACCC
67256 AAAACAATTTATTT
1 AAAACAATTTATTT
*
67270 AAAACCATTTA-TT
1 AAAACAATTTATTT
*
67283 -AAACAATTTA-AT
1 AAAACAATTTATTT
67295 AAAACAAT
1 AAAACAAT
67303 AATAAAATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 10 0.34
13 9 0.31
14 10 0.34
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAACAATTTATTT
Done.