Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008173.1 Corchorus capsularis cultivar CVL-1 contig08194, 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: 113001
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Found at i:310 original size:56 final size:58
Alignment explanation
Indices: 223--337 Score: 180
Period size: 56 Copynumber: 2.0 Consensus size: 58
213 AGATTTCAGG
223 TTGGGTCTCTTGCATTATGCATCTCATTTTTTACCCTGCTTCTTATTGTGCACCTTTTGC
1 TTGGGTCTCTTGC--TATGCATCTCATTTTTTACCCTGCTTCTTATTGTGCACCTTTTGC
**
283 TTGGGTCTCTTGC-A-GCATCTCATTTTTTTGCCTGCTTCTTATTGTGCACCTTTTG
1 TTGGGTCTCTTGCTATGCATCTCATTTTTTACCCTGCTTCTTATTGTGCACCTTTTG
338 GAGGTTTGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
56 39 0.74
57 1 0.02
60 13 0.25
ACGTcount: A:0.10, C:0.24, G:0.17, T:0.49
Consensus pattern (58 bp):
TTGGGTCTCTTGCTATGCATCTCATTTTTTACCCTGCTTCTTATTGTGCACCTTTTGC
Found at i:845 original size:13 final size:13
Alignment explanation
Indices: 827--853 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
817 CGATTGTGCT
827 ATACCTGTTTGCA
1 ATACCTGTTTGCA
840 ATACCTGTTTGCA
1 ATACCTGTTTGCA
853 A
1 A
854 AACTTTTATT
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:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (13 bp):
ATACCTGTTTGCA
Found at i:1298 original size:194 final size:193
Alignment explanation
Indices: 936--1298 Score: 566
Period size: 194 Copynumber: 1.9 Consensus size: 193
926 ATTTTCTGCT
* *
936 TTATTTTCTTCTTAGCTCATGTATTAACGATTTTTTTGGCCAAACATCTATTAACGTTAAGTGAC
1 TTATTTTCTGCTTAGCTCATATATTAACG--TTTTTTGGCCAAACATCTATTAACGTTAAGTGAC
* * * *
1001 TAGGATTTCACAAGTTAGTATGTATTAGGTGATATCAAGTCATGAGTTTACCTTGCCTTAAATAA
64 TAGGATTTCACAACTTAGTATGTATTAGGTGATATAAAGTCATGACTTTACCTTACCTTAAATAA
1066 ATCATAAAATGTGTCAGTACACAGGTTAATCTTTAACATATTTGATCTTAAAATCTTTAACATAG
129 ATCATAAAATGTGTCAGTACACAGGTTAATCTTTAACATATTTGATCTTAAAATCTTTAACATAG
*
1131 TTATTTTCTGCTTAGCTCATATATTAACG-TTTTTGGCCAAATATCTATTAACGTTAAGTGACTA
1 TTATTTTCTGCTTAGCTCATATATTAACGTTTTTTGGCCAAACATCTATTAACGTTAAGTGACTA
* * *
1195 GGATTTGACAACTTAGTATGTATTAGGTCATATATAAAGTCATGACTTTACCTTACCTTAAATCA
66 GGATTTCACAACTTAGTATGTATTAGGT--GATATAAAGTCATGACTTTACCTTACCTTAAATAA
** *
1260 ATCATAAAATGTGTGGGTACACGGGTTAATCTTTAACAT
129 ATCATAAAATGTGTCAGTACACAGGTTAATCTTTAACAT
1299 GTTCAAAAAA
Statistics
Matches: 153, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
192 60 0.39
194 66 0.43
195 27 0.18
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (193 bp):
TTATTTTCTGCTTAGCTCATATATTAACGTTTTTTGGCCAAACATCTATTAACGTTAAGTGACTA
GGATTTCACAACTTAGTATGTATTAGGTGATATAAAGTCATGACTTTACCTTACCTTAAATAAAT
CATAAAATGTGTCAGTACACAGGTTAATCTTTAACATATTTGATCTTAAAATCTTTAACATAG
Found at i:2168 original size:40 final size:40
Alignment explanation
Indices: 2124--2203 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
2114 TTCTTGCTTG
2124 TCATTGCTTTAATTCTGAGGTTTTATGTTCAATGGTTTGA
1 TCATTGCTTTAATTCTGAGGTTTTATGTTCAATGGTTTGA
*
2164 TCATTGCTTTAATTCTGAGGTTTTCTGTTCAATGGTTTGA
1 TCATTGCTTTAATTCTGAGGTTTTATGTTCAATGGTTTGA
2204 CTAAGTATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.19, C:0.11, G:0.20, T:0.50
Consensus pattern (40 bp):
TCATTGCTTTAATTCTGAGGTTTTATGTTCAATGGTTTGA
Found at i:25150 original size:29 final size:29
Alignment explanation
Indices: 25108--25182 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
25098 CTCATATTGC
25108 AAGTTTAGAGGGTAAAAAATAACAAATTA
1 AAGTTTAGAGGGTAAAAAATAACAAATTA
25137 AAGTTTAGAGGGTAAAAAATAACAAATTA
1 AAGTTTAGAGGGTAAAAAATAACAAATTA
*
25166 AAGTTTAGAGGGCAAAA
1 AAGTTTAGAGGGTAAAA
25183 TGTCAATTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.23
Consensus pattern (29 bp):
AAGTTTAGAGGGTAAAAAATAACAAATTA
Found at i:29087 original size:26 final size:26
Alignment explanation
Indices: 29038--29087 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
29028 CCGTTCCTAA
* * *
29038 TTTGGAACGGGTTTAGGTATGAGAAT
1 TTTGGAACGGGATTAGGAACGAGAAT
*
29064 TTTGGAATGGGATTAGGAACGAGA
1 TTTGGAACGGGATTAGGAACGAGA
29088 TGCCACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (26 bp):
TTTGGAACGGGATTAGGAACGAGAAT
Found at i:29743 original size:2 final size:2
Alignment explanation
Indices: 29736--29804 Score: 69
Period size: 2 Copynumber: 37.5 Consensus size: 2
29726 GTTTAATAAT
*
29736 TA TA TA TA TA TA TA TC TA -A TA T- TA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
29775 TA -A TA AA TA TT TA -A T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29805 TACTAAACGG
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
1 6 0.11
2 49 0.89
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29764 original size:23 final size:22
Alignment explanation
Indices: 29729--29806 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
29719 TTGAACCGTT
*
29729 TAATAATTATATATATATATATC
1 TAAT-ATTATATATATATATATA
29752 TAATATTATTATATATATATATA
1 TAATATTA-TATATATATATATA
* *
29775 TAATA-AATATTTAATTATATATA
1 TAATATTATATAT-A-TATATATA
29798 TATATATTA
1 TA-ATATTA
29807 CTAAACGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.09
22 6 0.13
23 32 0.70
24 3 0.07
25 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATTATATATATATATATA
Found at i:29774 original size:27 final size:29
Alignment explanation
Indices: 29732--29804 Score: 109
Period size: 25 Copynumber: 2.7 Consensus size: 29
29722 AACCGTTTAA
*
29732 TAATTATATATATATATAT-CT-AATA-T
1 TAATTATATATATATATATAATAAATATT
29758 T-ATTATATATATATATATAATAAATATT
1 TAATTATATATATATATATAATAAATATT
29786 TAATTATATATATATATAT
1 TAATTATATATATATATAT
29805 TACTAAACGG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 17 0.40
26 2 0.05
27 4 0.10
28 2 0.05
29 17 0.40
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
TAATTATATATATATATATAATAAATATT
Found at i:32256 original size:6 final size:6
Alignment explanation
Indices: 32245--32276 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
32235 TCTATTCTGT
32245 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
32277 GCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:33702 original size:151 final size:151
Alignment explanation
Indices: 33428--33726 Score: 562
Period size: 151 Copynumber: 2.0 Consensus size: 151
33418 TTTGTAGCTT
33428 AGAATTAGGCTTCAAATGCATTATGGTCCTCTTTTGGTAGCCCGCATATTTTCTCGAAATTGGGT
1 AGAATTAGGCTTCAAATGCATTATGGTCCTCTTTTGGTAGCCCGCATATTTTCTCGAAATTGGGT
* *
33493 CATAAAGGAATTTCACTAGGATGGGGACTAGAGTTGAATTCAGTAGTTTGCCAATGAGGGCGACA
66 CATAAAGGAATTTCACTAGGATGGGGACTAGAGTTAAATTCAGTAGTTTGCCAATGAGGACGACA
33558 CAAAAGCTTGGATTTTGACTC
131 CAAAAGCTTGGATTTTGACTC
* *
33579 AGAATTAGGCTTCAAATGCATTATGGTCCTCTTTTGGTAGCCTGTATATTTTCTCGAAATTGGGT
1 AGAATTAGGCTTCAAATGCATTATGGTCCTCTTTTGGTAGCCCGCATATTTTCTCGAAATTGGGT
33644 CATAAAGGAATTTCACTAGGATGGGGACTAGAGTTAAATTCAGTAGTTTGCCAATGAGGACGACA
66 CATAAAGGAATTTCACTAGGATGGGGACTAGAGTTAAATTCAGTAGTTTGCCAATGAGGACGACA
33709 CAAAAGCTTGGATTTTGA
131 CAAAAGCTTGGATTTTGA
33727 ATAATATGCA
Statistics
Matches: 144, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
151 144 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (151 bp):
AGAATTAGGCTTCAAATGCATTATGGTCCTCTTTTGGTAGCCCGCATATTTTCTCGAAATTGGGT
CATAAAGGAATTTCACTAGGATGGGGACTAGAGTTAAATTCAGTAGTTTGCCAATGAGGACGACA
CAAAAGCTTGGATTTTGACTC
Found at i:35057 original size:33 final size:33
Alignment explanation
Indices: 35010--35096 Score: 156
Period size: 33 Copynumber: 2.6 Consensus size: 33
35000 TGCCACATCA
35010 ATGGTTTGGTCTGACGTGGCAATGCCACGTGTGT
1 ATGG-TTGGTCTGACGTGGCAATGCCACGTGTGT
*
35044 ATGGTTGGTCTGACGTGGTAATGCCACGTGTGT
1 ATGGTTGGTCTGACGTGGCAATGCCACGTGTGT
35077 ATGGTTGGTCTGACGTGGCA
1 ATGGTTGGTCTGACGTGGCA
35097 TTTCGTGCCA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 47 0.92
34 4 0.08
ACGTcount: A:0.15, C:0.16, G:0.37, T:0.32
Consensus pattern (33 bp):
ATGGTTGGTCTGACGTGGCAATGCCACGTGTGT
Found at i:36367 original size:19 final size:18
Alignment explanation
Indices: 36343--36379 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
36333 ATTATTTATA
36343 CCCATTATTCTCTACAAAG
1 CCCATTATTCTCTA-AAAG
*
36362 CCCATTTTTCTCTAAAAG
1 CCCATTATTCTCTAAAAG
36380 GGCACTATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.30, C:0.30, G:0.05, T:0.35
Consensus pattern (18 bp):
CCCATTATTCTCTAAAAG
Found at i:49232 original size:33 final size:33
Alignment explanation
Indices: 49190--49539 Score: 378
Period size: 33 Copynumber: 10.6 Consensus size: 33
49180 CCCGGAAACC
49190 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
49223 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
* * *
49256 CCTTTGCCGCCGCCAGCAACGCCTCAAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
* * * *
49289 CCATTGCTGCCGCCAACAACACCTAAAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
* *
49322 CCTTTACCGCCCCCAGCAACTCCTAAAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
* * * * * * *
49355 CCATTGCTGCCGCCAACAACTCCTCAAACCCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
* * * * *
49388 CCGTTGCTGCCCCCAACAACTCCTAAAACCCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
*
49421 CCGTTGCCGCCCCCAGCAACACCTAAAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
* * * * ** **
49454 CCGTTGCCACCGCCAACAATGCCTCGAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
* * * *
49487 CCGTTGCTGCCGCCAACAACACCTAAAACTCCA
1 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
49520 -CTGTTGCCGCCCCCAGCAAC
1 CCT-TTGCCGCCCCCAGCAAC
49540 GCCTCGAACC
Statistics
Matches: 271, Mismatches: 45, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
32 1 0.00
33 270 1.00
ACGTcount: A:0.27, C:0.47, G:0.11, T:0.15
Consensus pattern (33 bp):
CCTTTGCCGCCCCCAGCAACACCTAAAACTCCA
Found at i:49309 original size:66 final size:66
Alignment explanation
Indices: 49190--49591 Score: 439
Period size: 66 Copynumber: 6.1 Consensus size: 66
49180 CCCGGAAACC
* * * * *
49190 CCTTTGCCGCCCCCAGCAACACCTAAAACTCCACCTTTGCCGCCCCCAGCAACACCTAAAACTCC
1 CCTTTGCCGCCCCCAGCAACGCCTAAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTCC
49255 A
66 A
* *
49256 CCTTTGCCGCCGCCAGCAACGCCTCAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTCC
1 CCTTTGCCGCCCCCAGCAACGCCTAAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTCC
49321 A
66 A
* * * * *
49322 CCTTTACCGCCCCCAGCAACTCCTAAAACTCCACCATTGCTGCCGCCAACAACTCCTCAAACCCC
1 CCTTTGCCGCCCCCAGCAACGCCTAAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTCC
49387 A
66 A
* * * * * * * * *
49388 CCGTTGCTGCCCCCAACAACTCCTAAAACCCCACCGTTGCCGCCCCCAGCAACACCTAAAACTCC
1 CCTTTGCCGCCCCCAGCAACGCCTAAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTCC
49453 A
66 A
* * * * * ** *
49454 CCGTTGCCACCGCCAACAATGCCTCGAACTCCACCGTTGCTGCCGCCAACAACACCTAAAACTCC
1 CCTTTGCCGCCCCCAGCAACGCCTAAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTCC
49519 A
66 A
** * * ** * *
49520 -CTGTTGCCGCCCCCAGCAACGCCTCGAACCCCACCACTGCTGCC-CCTGCAACGCCTCAAACTC
1 CCT-TTGCCGCCCCCAGCAACGCCTAAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTC
49583 CA
65 CA
*
49585 CCATTGC
1 CCTTTGC
49592 TGCCGCCAAT
Statistics
Matches: 284, Mismatches: 50, Indels: 5
0.84 0.15 0.01
Matches are distributed among these distances:
65 22 0.08
66 262 0.92
ACGTcount: A:0.26, C:0.48, G:0.11, T:0.15
Consensus pattern (66 bp):
CCTTTGCCGCCCCCAGCAACGCCTAAAACTCCACCATTGCTGCCGCCAACAACACCTAAAACTCC
A
Found at i:49368 original size:99 final size:99
Alignment explanation
Indices: 49206--49600 Score: 542
Period size: 99 Copynumber: 4.0 Consensus size: 99
49196 CCGCCCCCAG
*
49206 CAACACCTAAAACTCCACCTTTGCCGCCCCCAGCAACACCTAAAACTCCACCTTTGCCGCCGCCA
1 CAACACCTAAAACTCCACCTTTGCCGCCCCCAGCAACACCTAAAACTCCACCATTGCCGCCGCCA
*
49271 GCAACGCCTCAAACTCCACCATTGCTGCCGCCAA
66 ACAACGCCTCAAACTCCACCATTGCTGCCGCCAA
* * *
49305 CAACACCTAAAACTCCACCTTTACCGCCCCCAGCAACTCCTAAAACTCCACCATTGCTGCCGCCA
1 CAACACCTAAAACTCCACCTTTGCCGCCCCCAGCAACACCTAAAACTCCACCATTGCCGCCGCCA
* * * *
49370 ACAACTCCTCAAACCCCACCGTTGCTGCCCCCAA
66 ACAACGCCTCAAACTCCACCATTGCTGCCGCCAA
* * * * *
49404 CAACTCCTAAAACCCCACCGTTGCCGCCCCCAGCAACACCTAAAACTCCACCGTTGCCACCGCCA
1 CAACACCTAAAACTCCACCTTTGCCGCCCCCAGCAACACCTAAAACTCCACCATTGCCGCCGCCA
* * *
49469 ACAATGCCTCGAACTCCACCGTTGCTGCCGCCAA
66 ACAACGCCTCAAACTCCACCATTGCTGCCGCCAA
* ** * * *
49503 CAACACCTAAAACTCCA-CTGTTGCCGCCCCCAGCAACGCCTCGAACCCCACCACTGCTGCC-CC
1 CAACACCTAAAACTCCACCT-TTGCCGCCCCCAGCAACACCTAAAACTCCACCATTGCCGCCGCC
**
49566 TGCAACGCCTCAAACTCCACCATTGCTGCCGCCAA
65 AACAACGCCTCAAACTCCACCATTGCTGCCGCCAA
49601 TAATCCCATC
Statistics
Matches: 257, Mismatches: 38, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
98 33 0.13
99 224 0.87
ACGTcount: A:0.27, C:0.47, G:0.11, T:0.15
Consensus pattern (99 bp):
CAACACCTAAAACTCCACCTTTGCCGCCCCCAGCAACACCTAAAACTCCACCATTGCCGCCGCCA
ACAACGCCTCAAACTCCACCATTGCTGCCGCCAA
Found at i:49572 original size:32 final size:32
Alignment explanation
Indices: 49200--49595 Score: 153
Period size: 33 Copynumber: 12.1 Consensus size: 32
49190 CCTTTGCCGC
* * * ** *
49200 CCCCAGCAACACCTAAAACTCCACCTTTGCCG
1 CCCCAGCAACGCCTCAAACCCCACCACTGCTG
* * * ** *
49232 CCCCCAGCAACACCTAAAACTCCACCTTTGCCG
1 -CCCCAGCAACGCCTCAAACCCCACCACTGCTG
* *
49265 CCGCCAGCAACGCCTCAAACTCCACCATTGCTG
1 CC-CCAGCAACGCCTCAAACCCCACCACTGCTG
* * * * ** * *
49298 CCGCCAACAACACCTAAAACTCCACCTTTACCG
1 CC-CCAGCAACGCCTCAAACCCCACCACTGCTG
* * * *
49331 CCCCCAGCAACTCCTAAAACTCCACCATTGCTG
1 -CCCCAGCAACGCCTCAAACCCCACCACTGCTG
* * **
49364 CCGCCAACAACTCCTCAAACCCCACCGTTGCTG
1 CC-CCAGCAACGCCTCAAACCCCACCACTGCTG
* * * ** *
49397 CCCCCAACAACTCCTAAAACCCCACCGTTGCCG
1 -CCCCAGCAACGCCTCAAACCCCACCACTGCTG
* * * ** **
49430 CCCCCAGCAACACCTAAAACTCCACCGTTGCCA
1 -CCCCAGCAACGCCTCAAACCCCACCACTGCTG
* * * * **
49463 CCGCCAACAATGCCTCGAACTCCACCGTTGCTG
1 CC-CCAGCAACGCCTCAAACCCCACCACTGCTG
* * * * *** *
49496 CCGCCAACAACACCTAAAACTCCACTGTTGCCG
1 CC-CCAGCAACGCCTCAAACCCCACCACTGCTG
*
49529 CCCCCAGCAACGCCTCGAACCCCACCACTGCTG
1 -CCCCAGCAACGCCTCAAACCCCACCACTGCTG
* * *
49562 CCCCTGCAACGCCTCAAACTCCACCATTGCTG
1 CCCCAGCAACGCCTCAAACCCCACCACTGCTG
49594 CC
1 CC
49596 GCCAATAATC
Statistics
Matches: 306, Mismatches: 51, Indels: 13
0.83 0.14 0.04
Matches are distributed among these distances:
32 36 0.12
33 264 0.86
34 6 0.02
ACGTcount: A:0.26, C:0.47, G:0.11, T:0.15
Consensus pattern (32 bp):
CCCCAGCAACGCCTCAAACCCCACCACTGCTG
Found at i:54743 original size:134 final size:134
Alignment explanation
Indices: 54503--54760 Score: 299
Period size: 134 Copynumber: 1.9 Consensus size: 134
54493 GTCGCCTCCG
* * ** * *
54503 CCTGAACCTTAACCACCGTGCCGGAATCCTCCAACAATCATCAAGGTGCTTCGTTTTCTCTTCTA
1 CCTGAACCTTAACCACCGTGCCGGAATCCTCCAACAACCACCAAGGTGCTTCGTTCCCCCTCCTA
* * **
54568 AACTCTTTTAGTCTTGAAATTTCTTGATTCAACCTTCAAAT-CTCTGGAATCCGAGTTACAAGAA
66 AACTCTTTTAGCCTTGAAATTTCTTGATTAAACCACCAAATCCT-TGGAATCCGAGTTACAAGAA
54632 ACCCA
130 ACCCA
* * * *
54637 CCTGAACCTTAGCCACCGTGCCGGAGTCCTCCGAA-AGCCACCAAGGT-TTTCGTTCCCCCTCCT
1 CCTGAACCTTAACCACCGTGCCGGAATCCTCC-AACAACCACCAAGGTGCTTCGTTCCCCCTCCT
* * *
54700 AAGCTCTTATTTAGCCTTG-ATTTTCTTGATTAAACCACCAAATCCTTGGAATCTGAGTTAC
65 AAACTC-T-TTTAGCCTTGAAATTTCTTGATTAAACCACCAAATCCTTGGAATCCGAGTTAC
54761 CAGACACCAA
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
133 16 0.16
134 74 0.72
135 13 0.13
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.31
Consensus pattern (134 bp):
CCTGAACCTTAACCACCGTGCCGGAATCCTCCAACAACCACCAAGGTGCTTCGTTCCCCCTCCTA
AACTCTTTTAGCCTTGAAATTTCTTGATTAAACCACCAAATCCTTGGAATCCGAGTTACAAGAAA
CCCA
Found at i:56987 original size:12 final size:12
Alignment explanation
Indices: 56970--57052 Score: 61
Period size: 12 Copynumber: 7.3 Consensus size: 12
56960 CCGTTTAATA
*
56970 ATTATATTTATT
1 ATTATATATATT
**
56982 ATTATATATAAA
1 ATTATATATATT
56994 ATTATATATATT
1 ATTATATATATT
*
57006 -TAATAT-TATT
1 ATTATATATATT
* *
57016 A-TAAATATA-A
1 ATTATATATATT
57026 ATTATATAT-TT
1 ATTATATATATT
57037 AATTATATATA-T
1 -ATTATATATATT
57049 ATTA
1 ATTA
57053 ATAAACGGTC
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
10 8 0.15
11 17 0.31
12 29 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTATATATATT
Found at i:57398 original size:13 final size:13
Alignment explanation
Indices: 57380--57407 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
57370 CAAGAACAAC
57380 ATATATTATGTAG
1 ATATATTATGTAG
57393 ATATATTATGTAG
1 ATATATTATGTAG
57406 AT
1 AT
57408 GTGGATGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (13 bp):
ATATATTATGTAG
Found at i:58625 original size:25 final size:25
Alignment explanation
Indices: 58591--58641 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
58581 AGAAAATACA
*
58591 AAAGTTTTTAGATTAATCTTGAAAG
1 AAAGTTTTTAGATTAATCTCGAAAG
58616 AAAGTTTTTAGATTAATCTCGAAAG
1 AAAGTTTTTAGATTAATCTCGAAAG
58641 A
1 A
58642 GCTCTGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (25 bp):
AAAGTTTTTAGATTAATCTCGAAAG
Found at i:62386 original size:15 final size:16
Alignment explanation
Indices: 62366--62395 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62356 ATTGAAGTTG
62366 TAGTTT-GAAAAAGTA
1 TAGTTTAGAAAAAGTA
62381 TAGTTTAGAAAAAGT
1 TAGTTTAGAAAAAGT
62396 GCTTTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (16 bp):
TAGTTTAGAAAAAGTA
Found at i:65139 original size:2 final size:2
Alignment explanation
Indices: 65132--65173 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
65122 AAATCCAAAA
65132 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
65174 GTTTATCTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:69002 original size:30 final size:31
Alignment explanation
Indices: 68968--69031 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
68958 TTTTTGGATT
* * *
68968 TTTTTTTTTATC-ATTGAAGTGTCTTTGGTG
1 TTTTTTTTTAGCAATGGAAGTGTCTATGGTG
*
68998 TTTTTTTTTGGCAATGGAAGTGTCTATGGTG
1 TTTTTTTTTAGCAATGGAAGTGTCTATGGTG
69029 TTT
1 TTT
69032 ACTAATACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.14, C:0.06, G:0.23, T:0.56
Consensus pattern (31 bp):
TTTTTTTTTAGCAATGGAAGTGTCTATGGTG
Found at i:81567 original size:11 final size:11
Alignment explanation
Indices: 81553--81590 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
81543 ATTCATAACA
81553 AATTTATAATT
1 AATTTATAATT
81564 AATTTATAATT
1 AATTTATAATT
81575 -ATTTGATAATT
1 AATTT-ATAATT
*
81586 TATTT
1 AATTT
81591 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:82258 original size:25 final size:24
Alignment explanation
Indices: 82229--82280 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
82219 TTCAAACCCT
* *
82229 AAACTTCATTTCTCACAACTTCTTC
1 AAACTTCATTTCTAACAA-ATCTTC
82254 AAACTTCATTTCTAACAAATCTTC
1 AAACTTCATTTCTAACAAATCTTC
82278 AAA
1 AAA
82281 TTAATTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.37
Consensus pattern (24 bp):
AAACTTCATTTCTAACAAATCTTC
Found at i:82327 original size:15 final size:15
Alignment explanation
Indices: 82297--82364 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
82287 TTTCTTCATT
82297 TTAATCATAAACTAA
1 TTAATCATAAACTAA
82312 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
82323 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
82338 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
82349 TTAAACATAAACTAA
1 TTAATCATAAACTAA
82364 T
1 T
82365 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:82327 original size:26 final size:26
Alignment explanation
Indices: 82297--82364 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
82287 TTTCTTCATT
82297 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
82323 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
82349 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
82365 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:82651 original size:19 final size:21
Alignment explanation
Indices: 82626--82669 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
82616 AAAAATTATA
* *
82626 AAAAAGGGG-CGGTGTTTAGC
1 AAAAGGGGGACGGTGTTTAAC
82646 AAAAGGGGGACGGTGTTTAAC
1 AAAAGGGGGACGGTGTTTAAC
82667 AAA
1 AAA
82670 CCCCTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGACGGTGTTTAAC
Found at i:83079 original size:21 final size:21
Alignment explanation
Indices: 83045--83108 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
83035 TCAGTTGGAG
*
83045 TAAAATTGGTTACTGTACATG-
1 TAAAATTTGTTACTGTACA-GA
* *
83066 TTAGATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
83087 TAAAATTTGTTACTGTACAGA
1 TAAAATTTGTTACTGTACAGA
83108 T
1 T
83109 GAGAATATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 36 0.97
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (21 bp):
TAAAATTTGTTACTGTACAGA
Found at i:88098 original size:2 final size:2
Alignment explanation
Indices: 88091--88120 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
88081 CGAATTAATA
88091 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
88121 CTATGTAAAA
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:92638 original size:15 final size:15
Alignment explanation
Indices: 92618--92648 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
92608 TATTATATGC
92618 TAAAGAAATGAAACA
1 TAAAGAAATGAAACA
92633 TAAAGAAATGAAACA
1 TAAAGAAATGAAACA
92648 T
1 T
92649 GGCAGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.65, C:0.06, G:0.13, T:0.16
Consensus pattern (15 bp):
TAAAGAAATGAAACA
Found at i:97875 original size:32 final size:32
Alignment explanation
Indices: 97834--97905 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
97824 CTCCTGAGGT
97834 AAAATGTCTTGGAATTAGGAAGTTCAGCGGGC
1 AAAATGTCTTGGAATTAGGAAGTTCAGCGGGC
* * *
97866 AAAATGTCTTGGATTTGGGAAGTTCAGGGGGC
1 AAAATGTCTTGGAATTAGGAAGTTCAGCGGGC
97898 AAAATGTC
1 AAAATGTC
97906 ATGATTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.31, C:0.11, G:0.32, T:0.26
Consensus pattern (32 bp):
AAAATGTCTTGGAATTAGGAAGTTCAGCGGGC
Found at i:99063 original size:29 final size:30
Alignment explanation
Indices: 99015--99072 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
99005 TTTCGAGTCA
*
99015 AGGACGTTTTGCCCCATGAACTT-CAAATC
1 AGGACATTTTGCCCCATGAACTTCCAAATC
*
99044 AGGACATTTTGCCCTC-TGAATTTCCAAAT
1 AGGACATTTTGCCC-CATGAACTTCCAAAT
99073 TCAGAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (30 bp):
AGGACATTTTGCCCCATGAACTTCCAAATC
Found at i:102346 original size:29 final size:29
Alignment explanation
Indices: 102291--102347 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
102281 TATTGCGTCA
* * *
102291 AGGACATTTTGTCCTATGAATTTCAAATC
1 AGGACATTTTGACCCATAAATTTCAAATC
102320 AGGACATTTT-ACCCATAAATTTCCAAAT
1 AGGACATTTTGACCCATAAATTT-CAAAT
102348 TCCTAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (29 bp):
AGGACATTTTGACCCATAAATTTCAAATC
Found at i:104943 original size:19 final size:19
Alignment explanation
Indices: 104913--104969 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
104903 GGTAAGATAA
104913 ACAAAT-TGCAGAAAATGC
1 ACAAATCTGCAGAAAATGC
* *
104931 ACAAATCTGCAGAAACTTGA
1 ACAAATCTGCAGAAA-ATGC
*
104951 AC-AAGCTGCAGAAAATGC
1 ACAAATCTGCAGAAAATGC
104969 A
1 A
104970 GAAACATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 9 0.28
19 19 0.59
20 4 0.12
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (19 bp):
ACAAATCTGCAGAAAATGC
Found at i:104970 original size:28 final size:30
Alignment explanation
Indices: 104937--105003 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 30
104927 ATGCACAAAT
104937 CTGCAGAAAC-TTGAAC-AAGCTGCAG-AAAA
1 CTGCAGAAACATT-AACAAAG-TGCAGTAAAA
104966 -TGCAGAAACATTAACAAAGTGCAGTAAAA
1 CTGCAGAAACATTAACAAAGTGCAGTAAAA
104995 CTGCAGAAA
1 CTGCAGAAA
105004 ACATACACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
28 17 0.50
29 9 0.26
30 8 0.24
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (30 bp):
CTGCAGAAACATTAACAAAGTGCAGTAAAA
Found at i:110355 original size:28 final size:30
Alignment explanation
Indices: 110319--110377 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
110309 ATGTTATGCC
* *
110319 CCCTAAACTT-CAGA-TCAAGATATTTTGT
1 CCCTAAACTTCCAAATTCAAGACATTTTGT
*
110347 CCCTTAACTTCCAAATTCAAGACATTTTGT
1 CCCTAAACTTCCAAATTCAAGACATTTTGT
110377 C
1 C
110378 AACTCCGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 9 0.35
29 3 0.12
30 14 0.54
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (30 bp):
CCCTAAACTTCCAAATTCAAGACATTTTGT
Found at i:110427 original size:32 final size:31
Alignment explanation
Indices: 110386--110504 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 31
110376 TCAACTCCGT
110386 TGGATTTGGGAAGTTCAACGGGCAAAATATCC
1 TGGATTTGGGAAGTTCAA-GGGCAAAATATCC
* *
110418 TGGATTTGGGAAGTTCAGGGGGGTAAAATATCC
1 TGGATTTGGGAAGTTCA--AGGGCAAAATATCC
* * *
110451 TGAATTT-AGAAGTTC-AGGGACAAAATATCA
1 TGGATTTGGGAAGTTCAAGGG-CAAAATATCC
*
110481 T-GATTT--GAAATTCAAGGGACAAAA
1 TGGATTTGGGAAGTTCAAGGG-CAAAA
110505 CGTCTTTGAC
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
28 6 0.08
29 17 0.23
30 9 0.12
32 24 0.32
33 18 0.24
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (31 bp):
TGGATTTGGGAAGTTCAAGGGCAAAATATCC
Found at i:110451 original size:33 final size:33
Alignment explanation
Indices: 110386--110469 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 33
110376 TCAACTCCGT
**
110386 TGGATTTGGGAAGTTCA-ACGGGCAAAATATCC
1 TGGATTTGGGAAGTTCAGGGGGGCAAAATATCC
*
110418 TGGATTTGGGAAGTTCAGGGGGGTAAAATATCC
1 TGGATTTGGGAAGTTCAGGGGGGCAAAATATCC
* *
110451 TGAATTT-AGAAGTTCAGGG
1 TGGATTTGGGAAGTTCAGGG
110470 ACAAAATATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 28 0.61
33 18 0.39
ACGTcount: A:0.30, C:0.11, G:0.32, T:0.27
Consensus pattern (33 bp):
TGGATTTGGGAAGTTCAGGGGGGCAAAATATCC
Found at i:110499 original size:29 final size:30
Alignment explanation
Indices: 110442--110504 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
110432 TCAGGGGGGT
* *
110442 AAAATATCCTGAATTTAGAAGTTCAGGGAC
1 AAAATATCATGAATTTAGAAATTCAGGGAC
110472 AAAATATCATG-ATTT-GAAATTCAAGGGAC
1 AAAATATCATGAATTTAGAAATTC-AGGGAC
110501 AAAA
1 AAAA
110505 CGTCTTTGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 14 0.47
30 10 0.33
ACGTcount: A:0.46, C:0.11, G:0.17, T:0.25
Consensus pattern (30 bp):
AAAATATCATGAATTTAGAAATTCAGGGAC
Done.