Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010645.1 Corchorus capsularis cultivar CVL-1 contig10666, 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: 17902
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2832 original size:6 final size:6
Alignment explanation
Indices: 2823--2848 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2813 TTTTCCTTCA
2823 TTCATT TTCATT TTCATT TTCATT TT
1 TTCATT TTCATT TTCATT TTCATT TT
2849 TTCATTTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCATT
Found at i:3304 original size:69 final size:69
Alignment explanation
Indices: 3109--3376 Score: 362
Period size: 69 Copynumber: 3.9 Consensus size: 69
3099 TGGAAAACCC
* * * ** * *
3109 CTGCTTGGATGGAACCAAGG-GTAAACTAACTCACATGGAAACGAGTTTGGCTAGTGGAAAAGCC
1 CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCC
*
3173 CTTG
66 CCTG
* * * *
3177 CTGCTTGGATGGAACCAAGGC-T-AAATAGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAAAAC
1 CTGCTTGGATGGAACCAAGGCTTGAACT-GACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGC
*
3240 CCCTA
65 CCCTG
3245 CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCC
1 CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCC
*
3310 GCTG
66 CCTG
* *
3314 CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTAACTTATGGAAAAG
1 CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAG
3377 TCGAAGCATT
Statistics
Matches: 179, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
67 3 0.02
68 75 0.42
69 98 0.55
70 3 0.02
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (69 bp):
CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCC
CCTG
Found at i:3316 original size:137 final size:137
Alignment explanation
Indices: 3109--3362 Score: 379
Period size: 137 Copynumber: 1.9 Consensus size: 137
3099 TGGAAAACCC
*
3109 CTGCTTGGATGGAACCAAGGGTAAACTAACTCACATGGAAACGAGTTTGGCTAGTGGAAAAGCCC
1 CTGCTTGGATGGAACCAAGGGTAAACTAACTCACATGGAAACGAGTTTAGCTAGTGGAAAAGCCC
*
3174 TTGCTGCTTGGATGGAACCAAGGC-T-AAATAGACTCGTGTGGAAACGAGTTTGGCTTGTGGAAA
66 TTGCTGCTTGGATGGAACCAAGGCTTGAAAT-GACTCGTATGGAAACGAGTTTGGCTTGTGGAAA
3237 AACCCCTA
130 AACCCCTA
* * * ** *
3245 CTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTTAGCTTGTGGAAAAGCC
1 CTGCTTGGATGGAACCAAGG-GTAAACTAACTCACATGGAAACGAGTTTAGCTAGTGGAAAAGCC
*
3310 GC-TGCTGCTTGGATGGAACCAAGGCTTGAACTGACTCGTATGGAAACGAGTTT
65 -CTTGCTGCTTGGATGGAACCAAGGCTTGAAATGACTCGTATGGAAACGAGTTT
3363 AACTTATGGA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
136 20 0.19
137 60 0.57
138 22 0.21
139 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (137 bp):
CTGCTTGGATGGAACCAAGGGTAAACTAACTCACATGGAAACGAGTTTAGCTAGTGGAAAAGCCC
TTGCTGCTTGGATGGAACCAAGGCTTGAAATGACTCGTATGGAAACGAGTTTGGCTTGTGGAAAA
ACCCCTA
Found at i:3923 original size:50 final size:50
Alignment explanation
Indices: 3859--3957 Score: 153
Period size: 50 Copynumber: 2.0 Consensus size: 50
3849 AAAATGTCCT
*
3859 TTGAAAAGCAAATTTTGATCTTGGACTCACAAATGGAACGCAATCTTATC
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAACGCAATCTTATC
* * * *
3909 TTGAAAATCGAATTTTGATATTGGACTTACAAATGGAATGCAATCTTAT
1 TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAACGCAATCTTAT
3958 TATAAAACTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (50 bp):
TTGAAAAGCAAATTTTGATATTGGACTCACAAATGGAACGCAATCTTATC
Found at i:4260 original size:11 final size:11
Alignment explanation
Indices: 4241--4299 Score: 70
Period size: 11 Copynumber: 5.5 Consensus size: 11
4231 TTTTCTTCAT
4241 TTTCATTTTTT-
1 TTTC-TTTTTTC
4252 TTTC-TTTTTC
1 TTTCTTTTTTC
4262 TTTCATTTTTTC
1 TTTC-TTTTTTC
*
4274 TCTCTTTTTTC
1 TTTCTTTTTTC
4285 TTTCTTTTTT-
1 TTTCTTTTTTC
4295 TTTCT
1 TTTCT
4300 CTTTCATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
9 5 0.12
10 9 0.21
11 20 0.47
12 9 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:4281 original size:27 final size:25
Alignment explanation
Indices: 4249--4301 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
4239 ATTTTCATTT
4249 TTTTTTCTTTTTCTTTCATTTTTTCTCTC
1 TTTTTTC--TTTCTTT--TTTTTTCTCTC
4278 TTTTTTCTTTCTTTTTTTTTCTCT
1 TTTTTTCTTTCTTTTTTTTTCTCT
4302 TTCATTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.42
27 7 0.29
29 7 0.29
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (25 bp):
TTTTTTCTTTCTTTTTTTTTCTCTC
Found at i:4282 original size:23 final size:22
Alignment explanation
Indices: 4241--4303 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 22
4231 TTTTCTTCAT
*
4241 TTTCATTTTTTTTTC-TTTTTC
1 TTTCATTTTTTTCTCTTTTTTC
4262 TTTCATTTTTTCTCTCTTTTTTC
1 TTTCATTTTTT-TCTCTTTTTTC
*
4285 TTTCTTTTTTTTTCTCTTT
1 TTTC-ATTTTTTTCTCTTT
4304 CATTTTTTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.30
22 3 0.08
23 17 0.46
24 6 0.16
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCATTTTTTTCTCTTTTTTC
Found at i:5563 original size:15 final size:14
Alignment explanation
Indices: 5538--5576 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
5528 TCATTCATTT
5538 TTTCATTTTCATCA
1 TTTCATTTTCATCA
5552 TTTCATTTTTCATCA
1 TTTCA-TTTTCATCA
5567 --TCATTTTCAT
1 TTTCATTTTCAT
5577 TCATCATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 7 0.29
13 3 0.12
14 5 0.21
15 9 0.38
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTCATTTTCATCA
Found at i:5572 original size:13 final size:13
Alignment explanation
Indices: 5543--5587 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 13
5533 CATTTTTTCA
5543 TTTTCATCATTTCAT
1 TTTTCATCA--TCAT
5558 TTTTCATCATCA-
1 TTTTCATCATCAT
5570 TTTTCATTCATCAT
1 TTTTCA-TCATCAT
5584 TTTT
1 TTTT
5588 TTCTCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 4 0.14
15 9 0.32
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTCATCATCAT
Found at i:6083 original size:75 final size:76
Alignment explanation
Indices: 5979--6129 Score: 205
Period size: 75 Copynumber: 2.0 Consensus size: 76
5969 TGGATTCAAT
* * *
5979 CACCTCGAAATCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACTC-ATCAT
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACCCAATCAC
6043 TCTTTTACTCA
66 TCTTTTACTCA
* * * * * *
6054 CACCTTGAAACCATTGGTTTGATTGAAACTGATTTTGAAAGATGTTTTGATTAAAACCCAATCAC
1 CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACCCAATCAC
*
6119 TCTTTTGCTCA
66 TCTTTTACTCA
6130 TAGTCTAGAT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
75 51 0.78
76 14 0.22
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (76 bp):
CACCTCGAAACCATTGCTTTGACTAAAACTGATTTTGAAACATCTTTTGATTAAAACCCAATCAC
TCTTTTACTCA
Found at i:8091 original size:6 final size:6
Alignment explanation
Indices: 8075--8105 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
8065 CTAAGCAAAG
8075 TAAAT- TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TA
8106 TGGCAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:9483 original size:11 final size:11
Alignment explanation
Indices: 9467--9496 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
9457 GGTCTTCAAT
*
9467 TCTTCAAATTA
1 TCTTCAAATAA
9478 TCTTCAAATAA
1 TCTTCAAATAA
9489 TCTTCAAA
1 TCTTCAAA
9497 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:10899 original size:21 final size:21
Alignment explanation
Indices: 10874--10914 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10864 CAATCAAGCA
10874 AATCA-AGCAATTCAAAGCATC
1 AATCATAGC-ATTCAAAGCATC
*
10895 AATCATAGCATTCATAGCAT
1 AATCATAGCATTCAAAGCAT
10915 ATGAGTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (21 bp):
AATCATAGCATTCAAAGCATC
Found at i:12927 original size:22 final size:21
Alignment explanation
Indices: 12897--12955 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
12887 AATTCTTGCT
* *
12897 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
12919 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
12938 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
12956 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:12942 original size:11 final size:11
Alignment explanation
Indices: 12925--12956 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
12915 ATTGTCTTCA
12925 AATCTTCAAAT
1 AATCTTCAAAT
*
12936 TATCTTCAAAT
1 AATCTTCAAAT
12947 AATCTTCAAA
1 AATCTTCAAA
12957 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:12956 original size:22 final size:22
Alignment explanation
Indices: 12897--12956 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
12887 AATTCTTGCT
* *
12897 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
12919 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
12938 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
12957 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:14433 original size:11 final size:11
Alignment explanation
Indices: 14417--14446 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
14407 GGTCTTCAAT
*
14417 TCTTCAAATTA
1 TCTTCAAATAA
14428 TCTTCAAATAA
1 TCTTCAAATAA
14439 TCTTCAAA
1 TCTTCAAA
14447 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:16617 original size:24 final size:24
Alignment explanation
Indices: 16570--16627 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
16560 AAGCATAAAT
16570 ATAGGCAAGCATAAACAATGATAA
1 ATAGGCAAGCATAAACAATGATAA
* *
16594 ATAGGCATGGATAAACAA-GAATAA
1 ATAGGCAAGCATAAACAATG-ATAA
*
16618 A-ATGCAAGCA
1 ATAGGCAAGCA
16628 GACAACCAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 7 0.25
24 21 0.75
ACGTcount: A:0.53, C:0.12, G:0.19, T:0.16
Consensus pattern (24 bp):
ATAGGCAAGCATAAACAATGATAA
Found at i:17207 original size:19 final size:19
Alignment explanation
Indices: 17180--17221 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
17170 ATATTTTGCT
* * *
17180 TTTTTTTACTGATTACCCC
1 TTTTCTTACTGAATACCAC
17199 TTTTCTTACTGAATACCAC
1 TTTTCTTACTGAATACCAC
17218 TTTT
1 TTTT
17222 TACTCTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTTCTTACTGAATACCAC
Found at i:17249 original size:27 final size:28
Alignment explanation
Indices: 17198--17422 Score: 131
Period size: 27 Copynumber: 8.4 Consensus size: 28
17188 CTGATTACCC
* *
17198 CTTTTCTTACTGAA-TACCACTTTTTACT
1 CTTTT-TTACTTAATTACCATTTTTTACT
17226 C-TTTTTACTTAATTACCATTTTTTACTCT
1 CTTTTTTACTTAATTACCATTTTTTA--CT
*
17255 CCCTTTTTTACTCAA-TACCA-TTTTTAC-
1 --CTTTTTTACTTAATTACCATTTTTTACT
*
17282 CTTTTTT--TT--TTACCA-TTTTTACC
1 CTTTTTTACTTAATTACCATTTTTTACT
* * * *
17305 CCTTTTTACTGAA-TACCACTTTTTCCT
1 CTTTTTTACTTAATTACCATTTTTTACT
* *
17332 CTTTTTTA-TTGATTACCATTTCTTACT
1 CTTTTTTACTTAATTACCATTTTTTACT
* * *
17359 CTTTATTAC-CAATTACTC-TATTTTAC-
1 CTTTTTTACTTAATTAC-CATTTTTTACT
* *
17385 CTTTTTTAC-TGATCACCATTTTTTACT
1 CTTTTTTACTTAATTACCATTTTTTACT
*
17412 CATTTCTTACT
1 C-TTTTTTACT
17423 CTTTTTACTG
Statistics
Matches: 152, Mismatches: 25, Indels: 39
0.70 0.12 0.18
Matches are distributed among these distances:
22 12 0.08
23 7 0.05
25 9 0.06
26 33 0.22
27 57 0.38
28 10 0.07
29 2 0.01
30 6 0.04
31 6 0.04
32 10 0.07
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (28 bp):
CTTTTTTACTTAATTACCATTTTTTACT
Found at i:17310 original size:22 final size:22
Alignment explanation
Indices: 17270--17311 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17260 TTTTACTCAA
**
17270 TACCATTTTTACCTTTTTTTTT
1 TACCATTTTTACCCCTTTTTTT
17292 TACCATTTTTACCCCTTTTT
1 TACCATTTTTACCCCTTTTT
17312 ACTGAATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.24, G:0.00, T:0.62
Consensus pattern (22 bp):
TACCATTTTTACCCCTTTTTTT
Found at i:17403 original size:106 final size:106
Alignment explanation
Indices: 17192--17407 Score: 248
Period size: 106 Copynumber: 2.0 Consensus size: 106
17182 TTTTTACTGA
*
17192 TTACCCCTTTTCTTACTGAATACCACTTTTTACTCTTTTTACTTAATTACCATTTTTTACTCTCC
1 TTACCCCTTTTCTTACTGAATACCACTTTTTACTCTTTTTACTTAATTACCATTTCTTAC-CT-C
* * *
17257 CTTTTTTACTCAATACCATTTTTACCTTTTTTTTTTACCATTT
64 CTTTATTACTCAATACCATTTTTACCTTTTTTTATCACCATTT
* *
17300 TTACCCC-TTT-TTACTGAATACCACTTTTTCCTCTTTTTTA-TTGATTACCATTTCTTA-CT-C
1 TTACCCCTTTTCTTACTGAATACCACTTTTTACTC-TTTTTACTTAATTACCATTTCTTACCTCC
17360 TTTATTAC-CAATTACTC-TATTTTACCTTTTTTACTGATCACCATTT
65 TTTATTACTCAA-TAC-CAT-TTTTACCTTTTTT--T-ATCACCATTT
17406 TT
1 TT
17408 TACTCATTTC
Statistics
Matches: 95, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
101 3 0.03
102 12 0.13
103 14 0.15
104 2 0.02
105 1 0.01
106 47 0.49
107 9 0.09
108 7 0.07
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.54
Consensus pattern (106 bp):
TTACCCCTTTTCTTACTGAATACCACTTTTTACTCTTTTTACTTAATTACCATTTCTTACCTCCT
TTATTACTCAATACCATTTTTACCTTTTTTTATCACCATTT
Found at i:17416 original size:64 final size:64
Alignment explanation
Indices: 17344--17476 Score: 182
Period size: 64 Copynumber: 2.1 Consensus size: 64
17334 TTTTTATTGA
*
17344 TTAC-CATTTCTTACTCTTTATTACCAATTACTCTATT-TTAC-CTTTTTTACTGATCACCATTT
1 TTACTCATTTCTTACTCTTT-TTACCAATTACTCTATTCTTACTCTTTTTTACTGATCACCA-CT
17406 T
64 T
** * *
17407 TTACTCATTTCTTACTCTTTTTACTGATTACTCTTTTCTTACTCTTTTTTACTGATTACCACTT
1 TTACTCATTTCTTACTCTTTTTACCAATTACTCTATTCTTACTCTTTTTTACTGATCACCACTT
17471 TTACTC
1 TTACTC
17477 TTCTTCTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
63 18 0.29
64 27 0.44
65 17 0.27
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (64 bp):
TTACTCATTTCTTACTCTTTTTACCAATTACTCTATTCTTACTCTTTTTTACTGATCACCACTT
Found at i:17430 original size:37 final size:37
Alignment explanation
Indices: 17371--17459 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 37
17361 TTATTACCAA
17371 TTACTCTATT-TTAC-CTTTTTTACTGATCAC-CATTTT-
1 TTACTCT-TTCTTACTC-TTTTTACTGATCACTC-TTTTC
*
17407 TTACTCATTTCTTACTCTTTTTACTGATTACTCTTTTC
1 TTACTC-TTTCTTACTCTTTTTACTGATCACTCTTTTC
*
17445 TTACTCTTTTTTACT
1 TTACTCTTTCTTACT
17460 GATTACCACT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
36 8 0.17
37 30 0.65
38 8 0.17
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.58
Consensus pattern (37 bp):
TTACTCTTTCTTACTCTTTTTACTGATCACTCTTTTC
Found at i:17464 original size:28 final size:27
Alignment explanation
Indices: 17407--17478 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
17397 TCACCATTTT
17407 TTACTCATTTCTTACTCTTTTTACTGA
1 TTACTCATTTCTTACTCTTTTTACTGA
*
17434 TTACTCTTTTCTTACTCTTTTTTACTGA
1 TTACTCATTTCTTACTC-TTTTTACTGA
*
17462 TTAC-CACTT-TTACTCTT
1 TTACTCATTTCTTACTCTT
17479 CTTCTTTTTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 2 0.05
26 6 0.15
27 19 0.46
28 14 0.34
ACGTcount: A:0.17, C:0.24, G:0.03, T:0.57
Consensus pattern (27 bp):
TTACTCATTTCTTACTCTTTTTACTGA
Found at i:17481 original size:29 final size:27
Alignment explanation
Indices: 17414--17472 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 27
17404 TTTTTACTCA
*
17414 TTTCTTA-CTCTTTTTACTGATTACTCT
1 TTTCTTATCT-TTTTTACTGATTACACT
17441 TTTCTTACTCTTTTTTACTGATTACCACT
1 TTTCTTA-TCTTTTTTACTGATTA-CACT
17470 TTT
1 TTT
17473 ACTCTTCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 7 0.25
28 13 0.46
29 8 0.29
ACGTcount: A:0.15, C:0.22, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTCTTATCTTTTTTACTGATTACACT
Found at i:17484 original size:38 final size:36
Alignment explanation
Indices: 17434--17516 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 36
17424 TTTTTACTGA
* * *
17434 TTACTCTTTTCTTACTCTTTTTTACTGATTACCACTT
1 TTACTCTTTTCTTACTCTCTTTTACTAACTACCA-TT
**
17471 TTACTCTTCTTCTTTTTCTCTTTTACTAACTACCATT
1 TTACTCTT-TTCTTACTCTCTTTTACTAACTACCATT
17508 TTACTCTTT
1 TTACTCTTT
17517 GAATTTAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
36 1 0.03
37 18 0.45
38 21 0.52
ACGTcount: A:0.16, C:0.25, G:0.01, T:0.58
Consensus pattern (36 bp):
TTACTCTTTTCTTACTCTCTTTTACTAACTACCATT
Found at i:17673 original size:22 final size:22
Alignment explanation
Indices: 17537--17790 Score: 111
Period size: 22 Copynumber: 11.4 Consensus size: 22
17527 ACTAACTATC
* *
17537 ATTTTACTCTTTACTAATTATT
1 ATTTTACTCTTTACTGATTACT
* * *
17559 TTTTTACTTTTTTATTGATTACT
1 ATTTTAC-TCTTTACTGATTACT
*
17582 ATTTTACTC-TTACTGATTACC
1 ATTTTACTCTTTACTGATTACT
* *
17603 A--TTACTTTTTGAACTTAATTACT
1 ATTTTACTCTTT--AC-TGATTACT
*
17626 GATTACCCTT-TTACTTTTACTGATTACT
1 -ATT----TTACT-C-TTTACTGATTACT
* *
17654 ATTTTACTCTTTACTAATTACC
1 ATTTTACTCTTTACTGATTACT
* * *
17676 ATTTTACCCTTTAC-AAATACCT
1 ATTTTACTCTTTACTGATTA-CT
*
17698 -CTTTACT-TTCTACTGATTACCT
1 ATTTTACTCTT-TACTGATTA-CT
* *
17720 -TTTTACTCTTTACTAATTACC
1 ATTTTACTCTTTACTGATTACT
17741 ATTTTAC-CTTTTACTGATTA-T
1 ATTTTACTC-TTTACTGATTACT
17762 CATTATT--T-TTTACTGATTACT
1 -ATT-TTACTCTTTACTGATTACT
17783 ATTTTACT
1 ATTTTACT
17791 ATTTGAATTT
Statistics
Matches: 175, Mismatches: 30, Indels: 55
0.67 0.12 0.21
Matches are distributed among these distances:
19 7 0.04
20 18 0.10
21 27 0.15
22 73 0.42
23 30 0.17
24 2 0.01
27 3 0.02
28 7 0.04
29 3 0.02
30 2 0.01
31 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.03, T:0.54
Consensus pattern (22 bp):
ATTTTACTCTTTACTGATTACT
Found at i:17717 original size:65 final size:63
Alignment explanation
Indices: 17635--17790 Score: 208
Period size: 65 Copynumber: 2.4 Consensus size: 63
17625 TGATTACCCT
17635 TTTACTTTTACTGATTACTATTTTACTCTTTACTAATTACCATTTTACCCTTTAC-AAATACCTC
1 TTTACTTTTACTGATTACTATTTTACTCTTTACTAATTACCATTTTACCCTTTACTAAATA--TC
* * *
17699 TTTACTTTCTACTGATTACCT-TTTTACTCTTTACTAATTACCATTTTACCTTTTACTGATTATC
1 TTTACTTT-TACTGATTA-CTATTTTACTCTTTACTAATTACCATTTTACCCTTTACTAAATATC
* *
17763 ATTATTTTTTACTGATTACTATTTTACT
1 TTTA-CTTTTACTGATTACTATTTTACT
17791 ATTTGAATTT
Statistics
Matches: 82, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
63 2 0.02
64 29 0.35
65 46 0.56
66 5 0.06
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.53
Consensus pattern (63 bp):
TTTACTTTTACTGATTACTATTTTACTCTTTACTAATTACCATTTTACCCTTTACTAAATATC
Found at i:17863 original size:30 final size:30
Alignment explanation
Indices: 17829--17902 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 30
17819 TTTACTCTTT
*
17829 ACTGATTGCTTTTTCTTATTTAACTTAATC
1 ACTGATTGCTTTTTCTTATTGAACTTAATC
* *
17859 ACTGATTACTTTTTCTTATTGAACTTAATT
1 ACTGATTGCTTTTTCTTATTGAACTTAATC
*
17889 ACTGATTGCCTTTT
1 ACTGATTGCTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.23, C:0.16, G:0.08, T:0.53
Consensus pattern (30 bp):
ACTGATTGCTTTTTCTTATTGAACTTAATC
Done.