Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013690.1 Corchorus olitorius cultivar O-4 contig13723, 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: 56578
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1369 original size:29 final size:29
Alignment explanation
Indices: 1327--1382 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
1317 TTAGGATTAG
1327 TTATTTATGCTTTAA-TTTCAA-TTTCCT
1 TTATTTATGCTTTAATTTTCAAGTTTCCT
1354 TTATCTTATGTCTTTAATTTTCAAGTTTC
1 TTAT-TTATG-CTTTAATTTTCAAGTTTC
1383 ATTAATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 4 0.16
28 5 0.20
29 6 0.24
30 6 0.24
31 4 0.16
ACGTcount: A:0.21, C:0.14, G:0.05, T:0.59
Consensus pattern (29 bp):
TTATTTATGCTTTAATTTTCAAGTTTCCT
Found at i:14236 original size:38 final size:37
Alignment explanation
Indices: 14179--14325 Score: 172
Period size: 38 Copynumber: 3.9 Consensus size: 37
14169 GGCTGTGCAT
* **
14179 AGTGGACCCGTACCTCA-GGGGTTAAACTAATGGTAAAG
1 AGTGGACCCATA-CTCAGGGGGTTAAACTGTTGGT-AAG
14217 AGTGGACCCATACTACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCATACT-CAGGGGGTTAAACTGTTGGTAAG
** *
14255 AGTGGACCTGTGCCTCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCAT-ACTCAGGGGGTTAAACTGTTGGTAAG
*
14293 AGTGGACCCATGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCAT-ACTCAGGGGGTTAAACTGTTGG
14326 CTAGACTCGA
Statistics
Matches: 98, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
37 11 0.11
38 70 0.71
39 17 0.17
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (37 bp):
AGTGGACCCATACTCAGGGGGTTAAACTGTTGGTAAG
Found at i:14312 original size:76 final size:75
Alignment explanation
Indices: 14179--14325 Score: 208
Period size: 76 Copynumber: 1.9 Consensus size: 75
14169 GGCTGTGCAT
14179 AGTGGACCCGTACCTCAGGGGTTAAACTAATGGTAAAGAGTGGACCCATACTACAGGGGGTTAAA
1 AGTGGACCCGTACCTCAGGGGTTAAACTAATGGTAAAGAGTGGACCCATACTACAGGGGGTT-AA
14244 CTGTTGGTAAG
65 CTGTTGGTAAG
* * ** *
14255 AGTGGACCTGTGCCTCAGGGGGTTAAACTGTTGGT-AAGAGTGGACCCATGCCT-CAGGGGGTTA
1 AGTGGACCCGTACCTCA-GGGGTTAAACTAATGGTAAAGAGTGGACCCAT-ACTACAGGGGGTTA
14318 ACTGTTGG
64 ACTGTTGG
14326 CTAGACTCGA
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
75 9 0.14
76 38 0.59
77 17 0.27
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (75 bp):
AGTGGACCCGTACCTCAGGGGTTAAACTAATGGTAAAGAGTGGACCCATACTACAGGGGGTTAAC
TGTTGGTAAG
Found at i:14365 original size:6 final size:6
Alignment explanation
Indices: 14354--14395 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
14344 CCGTTAACGG
* * *
14354 ATGATT ATGATT ATGATT GTGATT GTGATT GTGATT ATGATT
1 ATGATT ATGATT ATGATT ATGATT ATGATT ATGATT ATGATT
14396 GTGGTGCAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (6 bp):
ATGATT
Found at i:14371 original size:12 final size:12
Alignment explanation
Indices: 14354--14398 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
14344 CCGTTAACGG
*
14354 ATGATTATGATT
1 ATGATTGTGATT
14366 ATGATTGTGATT
1 ATGATTGTGATT
*
14378 GTGATTGTGATT
1 ATGATTGTGATT
14390 ATGATTGTG
1 ATGATTGTG
14399 GTGCAGCCTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (12 bp):
ATGATTGTGATT
Found at i:14382 original size:18 final size:18
Alignment explanation
Indices: 14354--14398 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
14344 CCGTTAACGG
*
14354 ATGATTATGATTATGATT
1 ATGATTGTGATTATGATT
* *
14372 GTGATTGTGATTGTGATT
1 ATGATTGTGATTATGATT
14390 ATGATTGTG
1 ATGATTGTG
14399 GTGCAGCCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (18 bp):
ATGATTGTGATTATGATT
Found at i:14536 original size:20 final size:22
Alignment explanation
Indices: 14499--14538 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
14489 GTTATATGAA
14499 AAGTATGATTTCTTATTATAGT
1 AAGTATGATTTCTTATTATAGT
14521 AAGTATGA-TT-TTATTATA
1 AAGTATGATTTCTTATTATA
14539 CTTGATCCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (22 bp):
AAGTATGATTTCTTATTATAGT
Found at i:15769 original size:52 final size:52
Alignment explanation
Indices: 15708--15878 Score: 288
Period size: 52 Copynumber: 3.3 Consensus size: 52
15698 AAACTAAAAC
*
15708 CTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAAATTGAATACTTTGAAGA
1 CTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAGATTGAATACTTTGAAGA
* *
15760 CTGATGGGAACTTTCCCAAATTGAAAAAGAGCTAGATTGAATACTTTGAAGA
1 CTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAGATTGAATACTTTGAAGA
* * *
15812 TTGATGGGAACTTTCCCGACTTGAAAAAGAGGTAGATTGAATACTTTGAAGG
1 CTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAGATTGAATACTTTGAAGA
15864 CTGATGGGAACTTTC
1 CTGATGGGAACTTTC
15879 TGTAGACACC
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 110 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (52 bp):
CTGATGGGAACTTTCCCGACTTGAAAAAGAGCTAGATTGAATACTTTGAAGA
Found at i:15945 original size:10 final size:10
Alignment explanation
Indices: 15916--15967 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
15906 ATTCTCATGA
*
15916 TTTTTTTTTC
1 TTTTCTTTTC
*
15926 TTTCTTTTTTC
1 TTT-TCTTTTC
15937 TTTTCTTTTC
1 TTTTCTTTTC
15947 TTTTC-TTTC
1 TTTTCTTTTC
15956 -TTTCTTCTTC
1 TTTTCTT-TTC
15966 TT
1 TT
15968 CTTTCCTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 4 0.11
9 5 0.14
10 17 0.46
11 11 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTTTC
Found at i:15950 original size:26 final size:27
Alignment explanation
Indices: 15916--15971 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
15906 ATTCTCATGA
* *
15916 TTTTTTTTTCTTTCTTTTTTCTT-TTC
1 TTTTCTTTTCTTTCTTTCTTCTTCTTC
15942 TTTTCTTTTCTTTCTTTCTTCTTCTTC
1 TTTTCTTTTCTTTCTTTCTTCTTCTTC
15969 TTT
1 TTT
15972 CCTCATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (27 bp):
TTTTCTTTTCTTTCTTTCTTCTTCTTC
Found at i:15986 original size:2 final size:2
Alignment explanation
Indices: 15979--16009 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15969 TTTCCTCATT
15979 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 T
16010 CTAATTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34046 original size:107 final size:104
Alignment explanation
Indices: 33819--34106 Score: 425
Period size: 107 Copynumber: 2.7 Consensus size: 104
33809 TTTCTAACCC
* ** * *
33819 TTAAAATAAAATTTTAATTTTAATTTGGGCTAAACTTAGTG-AATTAGTTATATAGTTTATTTCT
1 TTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCT
* **
33883 AAAACCCTATAACAATATTATTAATTATGGAATTTACCC
66 AAAACCCTATAACAATATTATTAATTATGAAATTTACAA
*
33922 TTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTTTGTATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTTGGG-CTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
*
33987 TAAAACCCTATAACAATAAATTATTAATTTTGAAATTTACAA
65 TAAAACCCTATAACAAT--ATTATTAATTATGAAATTTACAA
*
34029 TTAAAATAGAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
1 TTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTC
*
34094 TAAAACTCTATAA
65 TAAAACCCTATAA
34107 TAAAAAACCT
Statistics
Matches: 167, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
103 26 0.16
104 12 0.07
105 36 0.22
107 90 0.54
108 3 0.02
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
TTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTTTATATTTTATTTCT
AAAACCCTATAACAATATTATTAATTATGAAATTTACAA
Found at i:35265 original size:52 final size:52
Alignment explanation
Indices: 35209--35557 Score: 509
Period size: 52 Copynumber: 6.7 Consensus size: 52
35199 TGTTTGAATG
* *
35209 CTTTGAAAACCTGATGGGAACTTTCTCACTTTGAAAAGACCTAAATTGAACA
1 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACA
* ** *
35261 CTTTGAAAACCTGATGGGAACTTTCCCACTTTGAAAAGACCTGGATCGAACA
1 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACA
* * *
35313 CTTTGAAAACTTGATGGGGACTTTCCCCCTTTGAAAAGAGCTAAATTGAACA
1 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACA
* *
35365 TTTTGAAAACTTGATGGGAACTTTCCCACTTTGGAAAGACCTAAATTGAACA
1 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACA
* * * *
35417 CTTTGAAAACTTTAAGGGAACTTTCCCACTTTGAAAAGAGCTAAATTGAACG
1 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACA
* * *
35469 CTTTGAAAAGTTGATGGGAACTTTCCCACTTTGAAAAGACTTATATTGAACA
1 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACA
* * *
35521 CTTTGAAAACCTGATGGAAACTCTCCCACTTTGAAAA
1 CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAA
35558 CTTTGGAGGA
Statistics
Matches: 264, Mismatches: 33, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 264 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
CTTTGAAAACTTGATGGGAACTTTCCCACTTTGAAAAGACCTAAATTGAACA
Found at i:36717 original size:326 final size:326
Alignment explanation
Indices: 36124--36778 Score: 1247
Period size: 326 Copynumber: 2.0 Consensus size: 326
36114 TCCAACTTTA
36124 CTCCATTTATTGAAATTAAGAACTTAATTATTACCAAATTAATTATGAAAATCAACTTTAAATTA
1 CTCCATTTATTGAAATTAAGAACTTAATTATTACCAAATTAATTATGAAAATCAACTTTAAATTA
36189 TCTTTAATCTAAAGCTCCAGGGACTCGACTGCACTGAAATCTAACTAAAAGGACTCAATTACACT
66 TCTTTAATCTAAAGCTCCAGGGACTCGACTGCACTGAAATCTAACTAAAAGGACTCAATTACACT
36254 AGATTAGACACTTAAATGAACACTCTGACAACTTATTAGACTCGATTGAATTAAATAACCACCTA
131 AGATTAGACACTTAAATGAACACTCTGACAACTTATTAGACTCGATTGAATTAAATAACCACCTA
*
36319 ATAAGGGACCTAAATGCATAAAATATGGTTTAAATTGAAATAAAGTTGAGGAATTTGTCTGAGGC
196 ATAAGGGACCTAAATGCATAAAATATGGTTTAAATTGAAATAAAATTGAGGAATTTGTCTGAGGC
*
36384 GAGTTGGCCCACGGATCTGTTGGTCAAACGGGTTGGGTTCAATGGGTTGTATAAATACCTTCGTT
261 GAGTTGGCCCACGGATCTGTTGGTCAAACGGGTCGGGTTCAATGGGTTGTATAAATACCTTCGTT
36449 T
326 T
36450 CTCCATTTATTGAAATTAAGAACTTAATTATTACCAAATTAATTATGAAAATCAACTTTAAATTA
1 CTCCATTTATTGAAATTAAGAACTTAATTATTACCAAATTAATTATGAAAATCAACTTTAAATTA
**
36515 TCTTTAATCTAAAGCTGTAGGGACTCGACTGCACTGAAATCTAACTAAAAGGACTCAATTACACT
66 TCTTTAATCTAAAGCTCCAGGGACTCGACTGCACTGAAATCTAACTAAAAGGACTCAATTACACT
*
36580 AGATTAGGCACTTAAATGAACACTCTGACAACTTATTAGACTCGATTGAATTAAATAACCACCTA
131 AGATTAGACACTTAAATGAACACTCTGACAACTTATTAGACTCGATTGAATTAAATAACCACCTA
*
36645 ATAAGGGACCTAAATGCATCAAATATGGTTTAAATTGAAATAAAATTGAGGAATTTGTCTGAGGC
196 ATAAGGGACCTAAATGCATAAAATATGGTTTAAATTGAAATAAAATTGAGGAATTTGTCTGAGGC
*
36710 GAGTTGGCCCATGGATCTGTTGGTCAAACGGGTCGGGTTCAATGGGTTGTATAAATACCTTCGTT
261 GAGTTGGCCCACGGATCTGTTGGTCAAACGGGTCGGGTTCAATGGGTTGTATAAATACCTTCGTT
36775 T
326 T
36776 CTC
1 CTC
36779 TTTAGGTTTT
Statistics
Matches: 322, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
326 322 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (326 bp):
CTCCATTTATTGAAATTAAGAACTTAATTATTACCAAATTAATTATGAAAATCAACTTTAAATTA
TCTTTAATCTAAAGCTCCAGGGACTCGACTGCACTGAAATCTAACTAAAAGGACTCAATTACACT
AGATTAGACACTTAAATGAACACTCTGACAACTTATTAGACTCGATTGAATTAAATAACCACCTA
ATAAGGGACCTAAATGCATAAAATATGGTTTAAATTGAAATAAAATTGAGGAATTTGTCTGAGGC
GAGTTGGCCCACGGATCTGTTGGTCAAACGGGTCGGGTTCAATGGGTTGTATAAATACCTTCGTT
T
Found at i:39619 original size:2 final size:2
Alignment explanation
Indices: 39612--39643 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
39602 CATTCGTTCT
39612 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
39644 GATTTAGATT
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):
TA
Found at i:40110 original size:2 final size:2
Alignment explanation
Indices: 40103--40159 Score: 53
Period size: 2 Copynumber: 29.0 Consensus size: 2
40093 GAGCCTTCAG
* * * *
40103 TC TC TC TC TC TC TC TC TC TC TC TC -C TC CC CC TC CC TC CC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
* *
40144 CC TC CC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC
40160 GGATGGTTTC
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (2 bp):
TC
Found at i:40625 original size:31 final size:29
Alignment explanation
Indices: 40567--40626 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
40557 TCCTAACGGA
** *
40567 TTATTTGCACATTTTTTCACTTGAGGGAC
1 TTATTTGCACATTTCATCACTTCAGGGAC
40596 TTATTTGCACATTCTCCATCACTTCAGGGAC
1 TTATTTGCACATT-T-CATCACTTCAGGGAC
40627 CAATTCTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 13 0.50
30 1 0.04
31 12 0.46
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (29 bp):
TTATTTGCACATTTCATCACTTCAGGGAC
Found at i:50895 original size:11 final size:11
Alignment explanation
Indices: 50881--50997 Score: 55
Period size: 11 Copynumber: 10.5 Consensus size: 11
50871 GACCAAAAAG
* *
50881 ATTTTTTTATT
1 ATTTATTTACT
50892 ATTTATTTACT
1 ATTTATTTACT
**
50903 ATTTATCTTTTT
1 ATTTAT-TTACT
50915 ATTTA-TT-CT
1 ATTTATTTACT
*
50924 -TTAACTATTATCT
1 ATTTA-T-TTA-CT
*
50937 ATCTATTTACT
1 ATTTATTTACT
**
50948 ATTTATCTTTTT
1 ATTTAT-TTACT
*
50960 ATTTATTT-TT
1 ATTTATTTACT
*
50970 AATTA-TTATCT
1 ATTTATTTA-CT
50981 ATTTATTTACT
1 ATTTATTTACT
50992 ATTTAT
1 ATTTAT
50998 CCTTTTGTTT
Statistics
Matches: 81, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
8 3 0.04
9 3 0.04
10 8 0.10
11 39 0.48
12 23 0.28
13 3 0.04
14 2 0.02
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTATTTACT
Found at i:50898 original size:7 final size:7
Alignment explanation
Indices: 50894--51089 Score: 54
Period size: 7 Copynumber: 27.7 Consensus size: 7
50884 TTTTTATTAT
50894 TTATTTA
1 TTATTTA
*
50901 CTATTTA
1 TTATTTA
*
50908 -TCTTT-
1 TTATTTA
50913 TTATTTA
1 TTATTTA
*
50920 TTCTTTA
1 TTATTTA
*
50927 --ACT-A
1 TTATTTA
*
50931 TTATCTA
1 TTATTTA
50938 TCTATTTA
1 T-TATTTA
*
50946 CTATTTA
1 TTATTTA
*
50953 TCTTTTTA
1 T-TATTTA
50961 TTTATTT-
1 -TTATTTA
*
50968 TTAATTA
1 TTATTTA
*
50975 TTATCTA
1 TTATTTA
50982 TTTATTTA
1 -TTATTTA
*
50990 CTATTTA
1 TTATTTA
*
50997 TCCT-TTTGT
1 T--TATTT-A
*
51006 TTATTAA
1 TTATTTA
*
51013 TTTAATTA
1 -TTATTTA
*
51021 TTATCTA
1 TTATTTA
51028 TTTATTTA
1 -TTATTTA
*
51036 CTATTTA
1 TTATTTA
*
51043 -TCTTT-
1 TTATTTA
51048 TTATTTA
1 TTATTTA
51055 TTAATTTA
1 TT-ATTTA
51063 GTTA-TTA
1 -TTATTTA
51070 TCTATTTA
1 T-TATTTA
51078 TGTA-TTA
1 T-TATTTA
51085 TTATT
1 TTATT
51090 ATCTTTTTTT
Statistics
Matches: 135, Mismatches: 31, Indels: 46
0.64 0.15 0.22
Matches are distributed among these distances:
4 1 0.01
5 1 0.01
6 25 0.19
7 55 0.41
8 48 0.36
9 5 0.04
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.65
Consensus pattern (7 bp):
TTATTTA
Found at i:50899 original size:4 final size:4
Alignment explanation
Indices: 50881--51083 Score: 69
Period size: 4 Copynumber: 53.8 Consensus size: 4
50871 GACCAAAAAG
* * *
50881 ATTT TTTT A-TT ATTT ATTT A-CT ATTT ATCTT -TTT ATTT A-TT CTTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT
** * * *
50926 AACT A-TT ATCT ATCT ATTT A-CT ATTT ATCTT -TTT ATTT A-TT -TTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT
* * * * * *
50970 AATT A-TT ATCT ATTT ATTT A-CT ATTT ATCCT -TTT GTTT ATTA ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT
* * * *
51016 AATT A-TT ATCT ATTT ATTT A-CT ATTT ATCTT -TTT ATTT ATTA ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT-TT ATTT ATTT ATTT ATTT
* * *
51062 AGTT A-TT ATCT ATTT ATGT ATT
1 ATTT ATTT ATTT ATTT ATTT ATT
51084 ATTATTATCT
Statistics
Matches: 144, Mismatches: 35, Indels: 40
0.66 0.16 0.18
Matches are distributed among these distances:
3 35 0.24
4 102 0.71
5 7 0.05
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.66
Consensus pattern (4 bp):
ATTT
Found at i:50917 original size:19 final size:19
Alignment explanation
Indices: 50893--51054 Score: 72
Period size: 19 Copynumber: 7.4 Consensus size: 19
50883 TTTTTTATTA
50893 TTTATTTACTATTTATCTT
1 TTTATTTACTATTTATCTT
*
50912 TTTATTTATTCTTTAACTATTATCTA
1 TTTATTTA--C--T-A-T-TTATCTT
*
50938 TCTATTTACTATTTATCTT
1 TTTATTTACTATTTATCTT
* *
50957 TTTATTTATTTTTAATTATTATCTA
1 TTTATTTA---CT-A-T-TTATCTT
50982 TTTATTTACTATTTATCCTTTT
1 TTTATTTACTATTTAT-C--TT
* * *
51004 GTTTATTAATTTAATTATTATCTA
1 -TTTATTTA-CT-A-T-TTATCTT
51028 TTTATTTACTATTTATCTT
1 TTTATTTACTATTTATCTT
51047 TTTATTTA
1 TTTATTTA
51055 TTAATTTAGT
Statistics
Matches: 108, Mismatches: 14, Indels: 42
0.66 0.09 0.26
Matches are distributed among these distances:
19 39 0.36
20 4 0.04
21 4 0.04
22 5 0.05
23 16 0.15
24 5 0.05
25 16 0.15
26 15 0.14
27 4 0.04
ACGTcount: A:0.25, C:0.09, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTATTTACTATTTATCTT
Found at i:51032 original size:8 final size:8
Alignment explanation
Indices: 51030--51155 Score: 50
Period size: 8 Copynumber: 16.1 Consensus size: 8
51020 ATTATCTATT
51030 TATTTA-C
1 TATTTATC
51037 TATTTATC
1 TATTTATC
* *
51045 TTTTTATT
1 TATTTATC
* *
51053 TATTAATT
1 TATTTATC
51061 TAGTTATTATC
1 TA--T-TTATC
*
51072 TATTTATG
1 TATTTATC
51080 TA-TTAT-
1 TATTTATC
51086 TA-TTATC
1 TATTTATC
*
51093 T-TTT-TT
1 TATTTATC
** *
51099 TAGCTACC
1 TATTTATC
51107 TATTTATC
1 TATTTATC
51115 TA-TTATTC
1 TATTTA-TC
* *
51123 TCTGTATC
1 TATTTATC
51131 TATTTATC
1 TATTTATC
* *
51139 TCTATATC
1 TATTTATC
51147 TATTTATC
1 TATTTATC
51155 T
1 T
51156 TTTTTTTATT
Statistics
Matches: 86, Mismatches: 23, Indels: 19
0.67 0.18 0.15
Matches are distributed among these distances:
6 8 0.09
7 17 0.20
8 52 0.60
9 3 0.03
10 1 0.01
11 5 0.06
ACGTcount: A:0.24, C:0.12, G:0.03, T:0.61
Consensus pattern (8 bp):
TATTTATC
Found at i:51033 original size:46 final size:45
Alignment explanation
Indices: 50887--51097 Score: 300
Period size: 46 Copynumber: 4.6 Consensus size: 45
50877 AAAGATTTTT
* *
50887 TTAT-TATTTATTTACTATTTATCTTTTTATTTATTCTTTAACTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTATTTAATTA
*
50931 TTATCTATCTATTTACTATTTATCTTTTTATTTATT-TTTAATTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATTATTTAATTA
* *
50975 TTATCTATTTATTTACTATTTATCCTTTTGTTTATTAATTTAATTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATT-ATTTAATTA
*
51021 TTATCTATTTATTTACTATTTATCTTTTTATTTATTAATTTAGTTA
1 TTATCTATTTATTTACTATTTATCTTTTTATTTATT-ATTTAATTA
* *
51067 TTATCTATTTATGTATTATTATTATCTTTTT
1 TTATCTATTTATTTACTA-T-TTATCTTTTT
51098 TTAGCTACCT
Statistics
Matches: 152, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
44 44 0.29
45 30 0.20
46 67 0.44
47 1 0.01
48 10 0.07
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.65
Consensus pattern (45 bp):
TTATCTATTTATTTACTATTTATCTTTTTATTTATTATTTAATTA
Found at i:51035 original size:27 final size:27
Alignment explanation
Indices: 51005--51084 Score: 68
Period size: 27 Copynumber: 3.3 Consensus size: 27
50995 TATCCTTTTG
51005 TTTATTAATTTAATTATTATCTATTTA
1 TTTATTAATTTAATTATTATCTATTTA
* *
51032 --T-TT-A-CT-A-T-TTATCTTTTTA
1 TTTATTAATTTAATTATTATCTATTTA
*
51051 TTTATTAATTTAGTTATTATCTATTTA
1 TTTATTAATTTAATTATTATCTATTTA
*
51078 TGTATTA
1 TTTATTA
51085 TTATTATCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 16
0.64 0.10 0.26
Matches are distributed among these distances:
19 10 0.26
20 1 0.03
21 2 0.05
22 3 0.08
23 2 0.05
24 3 0.08
25 1 0.03
26 1 0.03
27 16 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTATTAATTTAATTATTATCTATTTA
Found at i:51076 original size:15 final size:14
Alignment explanation
Indices: 50887--51089 Score: 85
Period size: 15 Copynumber: 13.6 Consensus size: 14
50877 AAAGATTTTT
50887 TTATTATTTATTTA
1 TTATTATTTATTTA
*
50901 CTATTTATCTT-TTTA
1 TTA-TTAT-TTATTTA
* **
50916 TTTATTCTTTAACTA
1 -TTATTATTTATTTA
*
50931 TTATCTATCTATTTA
1 TTAT-TATTTATTTA
*
50946 CTATTTATCTT-TTTA
1 TTA-TTAT-TTATTTA
*
50961 TTTATT-TTTAATTA
1 -TTATTATTTATTTA
50975 TTATCTATTTATTTA
1 TTAT-TATTTATTTA
*
50990 CTATTTATCCTT-TTGT-
1 TTA-TTAT--TTATT-TA
*
51006 TTATTAATTTAATTA
1 TTATT-ATTTATTTA
51021 TTATCTATTTATTTA
1 TTAT-TATTTATTTA
*
51036 CTATTTATCTT-TTTA
1 TTA-TTAT-TTATTTA
*
51051 TTTATTAATTTAGTTA
1 -TTATT-ATTTATTTA
*
51067 TTATCTATTTATGTA
1 TTAT-TATTTATTTA
51082 TTATTATT
1 TTATTATT
51090 ATCTTTTTTT
Statistics
Matches: 141, Mismatches: 23, Indels: 50
0.66 0.11 0.23
Matches are distributed among these distances:
13 6 0.04
14 20 0.14
15 85 0.60
16 27 0.19
17 3 0.02
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.65
Consensus pattern (14 bp):
TTATTATTTATTTA
Found at i:51132 original size:16 final size:16
Alignment explanation
Indices: 51111--51155 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
51101 GCTACCTATT
*
51111 TATCTA-TTATTCTCTG
1 TATCTATTTA-TCTCTA
51127 TATCTATTTATCTCTA
1 TATCTATTTATCTCTA
51143 TATCTATTTATCT
1 TATCTATTTATCT
51156 TTTTTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 24 0.89
17 3 0.11
ACGTcount: A:0.22, C:0.18, G:0.02, T:0.58
Consensus pattern (16 bp):
TATCTATTTATCTCTA
Found at i:55303 original size:21 final size:21
Alignment explanation
Indices: 55279--55335 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
55269 ATCCAACATC
55279 TGAGGCAGGCACAAGAAGAAA
1 TGAGGCAGGCACAAGAAGAAA
* ** * *
55300 TGAGACATTCCCAAGAAGAGA
1 TGAGGCAGGCACAAGAAGAAA
*
55321 TGAGGCAGGAACAAG
1 TGAGGCAGGCACAAG
55336 GTGTTATAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.32, T:0.09
Consensus pattern (21 bp):
TGAGGCAGGCACAAGAAGAAA
Done.