Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013070.1 Corchorus capsularis cultivar CVL-1 contig13091, 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: 51790
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4301 original size:34 final size:35
Alignment explanation
Indices: 4263--4336 Score: 96
Period size: 34 Copynumber: 2.1 Consensus size: 35
4253 GTATATATAG
* *
4263 ATCACAATCATATGTACGTAGCATTTGGAACCAT-
1 ATCACAATCACATGTACGAAGCATTTGGAACCATA
** *
4297 ATCACTGTCACATGTATGAAGCATTTGGAACCATA
1 ATCACAATCACATGTACGAAGCATTTGGAACCATA
4332 ATCAC
1 ATCAC
4337 TTAGTAAAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 29 0.85
35 5 0.15
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (35 bp):
ATCACAATCACATGTACGAAGCATTTGGAACCATA
Found at i:5145 original size:2 final size:2
Alignment explanation
Indices: 5138--5167 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5128 GAATTCTTTC
5138 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
5168 GCATTTCAAA
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:5418 original size:29 final size:31
Alignment explanation
Indices: 5382--5441 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5372 CGTTTAACTT
*
5382 TTTTTCTTTTTA-A-CTCCTTAAAATTATTC
1 TTTTTCTTTTTATAGCTCCTTAAAATAATTC
*
5411 TTTTTCTTTTTATAGCTTCTTAAAATAATTC
1 TTTTTCTTTTTATAGCTCCTTAAAATAATTC
5442 ATCTTTCCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 12 0.44
30 1 0.04
31 14 0.52
ACGTcount: A:0.25, C:0.15, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTTTCTTTTTATAGCTCCTTAAAATAATTC
Found at i:7617 original size:132 final size:132
Alignment explanation
Indices: 7380--7642 Score: 508
Period size: 132 Copynumber: 2.0 Consensus size: 132
7370 GGTAAATTGC
7380 TCTTCAAAATCACACCATATCACTGAAAATCTTCGAAATTAACATCAAGTTTGTTTATCGATCCA
1 TCTTCAAAATCACACCATATCACTGAAAATCTTCGAAATTAACATCAAGTTTGTTTATCGATCCA
*
7445 CCTACAAAACCTGCATTTGTTTTTGGATTGGGATGCATTCAAAAAGTTATTTCTCCAGGTGAAAA
66 CCTACAAAACCTGCATTTGTTTTTGGATTGGGATGCATTCAAAAAGTTATTTCTCCAAGTGAAAA
7510 AA
131 AA
*
7512 TCTTCGAAATCACACCATATCACTGAAAATCTTCGAAATTAACATCAAGTTTGTTTATCGATCCA
1 TCTTCAAAATCACACCATATCACTGAAAATCTTCGAAATTAACATCAAGTTTGTTTATCGATCCA
7577 CCTACAAAACCTGCATTTGTTTTTGGATTGGGATGCATTCAAAAAGTTATTTCTCCAAGTGAAAA
66 CCTACAAAACCTGCATTTGTTTTTGGATTGGGATGCATTCAAAAAGTTATTTCTCCAAGTGAAAA
7642 A
131 A
7643 TTTTTCTACA
Statistics
Matches: 129, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 129 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (132 bp):
TCTTCAAAATCACACCATATCACTGAAAATCTTCGAAATTAACATCAAGTTTGTTTATCGATCCA
CCTACAAAACCTGCATTTGTTTTTGGATTGGGATGCATTCAAAAAGTTATTTCTCCAAGTGAAAA
AA
Found at i:8130 original size:3 final size:3
Alignment explanation
Indices: 8122--8149 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
8112 ACACAAAGGG
8122 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA G
8150 TTTTCTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:8259 original size:81 final size:84
Alignment explanation
Indices: 8096--8263 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 84
8086 TCCCCCCTTC
8096 CTCCTCCTTAGTTGACACACAAAGGGGGAGGAGGAGGAGGAGGAGGAGGAGGAGTTTTCTTTTAA
1 CTCCTCCTTAGTTGACACACAAA---GGAGGAGGAGGAGGAGGAGGAGGAGGAGTTTTCTTTTAA
8161 TTTATTTATTTGCTTTAATAAA
63 TTTATTTATTTGCTTTAATAAA
*
8183 CTCCTCTTTAGTTGACACACAAA-G-GG-GGAGGAGGAGGAGGAGGAGGAGTTTTCTTTTAATTT
1 CTCCTCCTTAGTTGACACACAAAGGAGGAGGAGGAGGAGGAGGAGGAGGAGTTTTCTTTTAATTT
*
8245 ATTTATTTGTTTTAATAAA
66 ATTTATTTGCTTTAATAAA
8264 ATAGTTAGAT
Statistics
Matches: 79, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
81 54 0.68
82 2 0.03
83 1 0.01
87 22 0.28
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (84 bp):
CTCCTCCTTAGTTGACACACAAAGGAGGAGGAGGAGGAGGAGGAGGAGGAGTTTTCTTTTAATTT
ATTTATTTGCTTTAATAAA
Found at i:8320 original size:18 final size:19
Alignment explanation
Indices: 8299--8338 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
8289 AGTAAGTTTA
8299 TCAG-TTTGTCCTGTTGAG
1 TCAGTTTTGTCCTGTTGAG
*
8317 TCAGTTTTGTGCTGTTGAG
1 TCAGTTTTGTCCTGTTGAG
8336 TCA
1 TCA
8339 ATTATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.12, C:0.15, G:0.28, T:0.45
Consensus pattern (19 bp):
TCAGTTTTGTCCTGTTGAG
Found at i:9447 original size:2 final size:2
Alignment explanation
Indices: 9440--9466 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9430 AATTTAAGAA
9440 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
9467 AACTAATGAC
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16200 original size:15 final size:16
Alignment explanation
Indices: 16180--16209 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16170 TTAATTGAAA
16180 ACAAAATA-AAAAAAT
1 ACAAAATAGAAAAAAT
16195 ACAAAATAGAAAAAA
1 ACAAAATAGAAAAAA
16210 AAGTAAACCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (16 bp):
ACAAAATAGAAAAAAT
Found at i:16754 original size:172 final size:173
Alignment explanation
Indices: 16467--16811 Score: 593
Period size: 172 Copynumber: 2.0 Consensus size: 173
16457 AAGATCATCA
* * **
16467 TTGCTAACCCCTTACAATTTAACACAAACCCTAGTCCCCAAATTGATAGATTAACAAACCCCAAA
1 TTGCTAAACCCTTACAATTTAACACAAACCCTAATCCCCAAATTGATAGAAGAACAAACCCCAAA
* *
16532 TTTCTAGAATCCATCGCAAACCCATAAACCATTCCTACAAATAATTTCAGAAACCCAATACCCAA
66 TTTCTAAAATCCATCACAAACCCATAAACCATTCCTACAAATAATTTCAGAAACCCAATACCCAA
16597 AATCAACATAACAAAACGAATCAAAAACAGAAAACCCAACCAT
131 AATCAACATAACAAAACGAATCAAAAACAGAAAACCCAACCAT
* * *
16640 TTGCTAAACCCTTACAATTTAACACAAACCC-AATCCCCATATTGATCGAAGAACAAACCCTAAA
1 TTGCTAAACCCTTACAATTTAACACAAACCCTAATCCCCAAATTGATAGAAGAACAAACCCCAAA
16704 TTTCTAAAATCCATCACAAACCCATAAACCATTCCTACAAATAATTTCAGAAACCCAATACCCAA
66 TTTCTAAAATCCATCACAAACCCATAAACCATTCCTACAAATAATTTCAGAAACCCAATACCCAA
*
16769 AATCAACATAACAAAATGAATCAAAAACAGAAAACCCAACCAT
131 AATCAACATAACAAAACGAATCAAAAACAGAAAACCCAACCAT
16812 AAATCCTACA
Statistics
Matches: 162, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
172 132 0.81
173 30 0.19
ACGTcount: A:0.47, C:0.29, G:0.05, T:0.20
Consensus pattern (173 bp):
TTGCTAAACCCTTACAATTTAACACAAACCCTAATCCCCAAATTGATAGAAGAACAAACCCCAAA
TTTCTAAAATCCATCACAAACCCATAAACCATTCCTACAAATAATTTCAGAAACCCAATACCCAA
AATCAACATAACAAAACGAATCAAAAACAGAAAACCCAACCAT
Found at i:17192 original size:18 final size:21
Alignment explanation
Indices: 17171--17218 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
17161 TTATTAGTAA
17171 ATTAGTAAAT-A-T-TTATTT
1 ATTAGTAAATAATTATTATTT
*
17189 ATTAGTATATAATTATTATTT
1 ATTAGTAAATAATTATTATTT
17210 ATTAGTAAA
1 ATTAGTAAA
17219 ACATATCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 1 0.04
21 14 0.56
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
ATTAGTAAATAATTATTATTT
Found at i:34544 original size:12 final size:12
Alignment explanation
Indices: 34527--34573 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
34517 TCTTGATCGA
34527 AATTATATAAAT
1 AATTATATAAAT
34539 AATTATATAAAT
1 AATTATATAAAT
*
34551 AATTACCAT-AA-
1 AATTA-TATAAAT
34562 AATTATATAAAT
1 AATTATATAAAT
34574 GCATGCAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 2 0.07
11 7 0.23
12 19 0.63
13 2 0.07
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (12 bp):
AATTATATAAAT
Found at i:35043 original size:14 final size:14
Alignment explanation
Indices: 35023--35057 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
35013 GAAAAAGAAG
35023 AAGAAAACGGAAAA
1 AAGAAAACGGAAAA
* *
35037 TAGAAAATGGAAAA
1 AAGAAAACGGAAAA
35051 AAGAAAA
1 AAGAAAA
35058 AAACTAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.20, T:0.06
Consensus pattern (14 bp):
AAGAAAACGGAAAA
Found at i:35382 original size:53 final size:54
Alignment explanation
Indices: 35271--35385 Score: 169
Period size: 57 Copynumber: 2.1 Consensus size: 54
35261 CTTGATTCCA
* *
35271 ACCATATTTGCTACAAACAAACTGCTATACATACTAGATCTAGTTAAAGAACCAAAC
1 ACCATATTTGCTACAAACAAACTGCTATACATACTAAATC---TCAAAGAACCAAAC
*
35328 ACCATATTTGCTACAAACAAACTGCTATACATACTAAATC-CAAAGAACCCAAC
1 ACCATATTTGCTACAAACAAACTGCTATACATACTAAATCTCAAAGAACCAAAC
35381 ACCAT
1 ACCAT
35386 GTATGTCTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
53 16 0.29
57 39 0.71
ACGTcount: A:0.44, C:0.26, G:0.07, T:0.23
Consensus pattern (54 bp):
ACCATATTTGCTACAAACAAACTGCTATACATACTAAATCTCAAAGAACCAAAC
Found at i:40017 original size:16 final size:16
Alignment explanation
Indices: 39968--40085 Score: 114
Period size: 16 Copynumber: 7.4 Consensus size: 16
39958 GACAGTTTTC
*
39968 TCGGATCATTCGGGTT
1 TCGGGTCATTCGGGTT
* *
39984 TTGGGTCA-TCTAGG-T
1 TCGGGTCATTC-GGGTT
* *
39999 TCGGGTTATTTGGGTT
1 TCGGGTCATTCGGGTT
* *
40015 TCGGGTCATTCGGATA
1 TCGGGTCATTCGGGTT
* *
40031 TCGAGTCATACGGGTT
1 TCGGGTCATTCGGGTT
*
40047 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
*
40063 TCGGGTCATTCGGGTC
1 TCGGGTCATTCGGGTT
40079 TCGGGTC
1 TCGGGTC
40086 TACCGGGTCT
Statistics
Matches: 81, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
15 11 0.14
16 70 0.86
ACGTcount: A:0.11, C:0.19, G:0.35, T:0.36
Consensus pattern (16 bp):
TCGGGTCATTCGGGTT
Found at i:40026 original size:9 final size:9
Alignment explanation
Indices: 40014--40078 Score: 61
Period size: 9 Copynumber: 7.9 Consensus size: 9
40004 TTATTTGGGT
40014 TTCGGGTCA
1 TTCGGGTCA
*
40023 TTCGGAT-A
1 TTCGGGTCA
*
40031 -TCGAGTCA
1 TTCGGGTCA
*
40039 TACGGGT--
1 TTCGGGTCA
40046 TTCGGGTCA
1 TTCGGGTCA
40055 TTCGGGTC-
1 TTCGGGTCA
40063 -TCGGGTCA
1 TTCGGGTCA
40071 TTCGGGTC
1 TTCGGGTC
40079 TCGGGTCTAC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
7 17 0.39
8 2 0.05
9 25 0.57
ACGTcount: A:0.12, C:0.22, G:0.34, T:0.32
Consensus pattern (9 bp):
TTCGGGTCA
Found at i:40066 original size:7 final size:7
Alignment explanation
Indices: 40041--40100 Score: 57
Period size: 7 Copynumber: 7.7 Consensus size: 7
40031 TCGAGTCATA
*
40041 CGGGTTT
1 CGGGTCT
40048 CGGGTCATT
1 CGGGTC--T
40057 CGGGTCT
1 CGGGTCT
40064 CGGGTCATT
1 CGGGTC--T
40073 CGGGTCT
1 CGGGTCT
40080 CGGGTCT
1 CGGGTCT
40087 ACCGGGTCT
1 --CGGGTCT
40096 CGGGT
1 CGGGT
40101 TGGGTGGGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
7 25 0.54
9 21 0.46
ACGTcount: A:0.05, C:0.25, G:0.40, T:0.30
Consensus pattern (7 bp):
CGGGTCT
Found at i:40092 original size:16 final size:16
Alignment explanation
Indices: 40010--40100 Score: 85
Period size: 16 Copynumber: 5.7 Consensus size: 16
40000 CGGGTTATTT
* *
40010 GGGTTTCGGGTCATTC
1 GGGTCTCGGGTCATCC
* * * *
40026 GGATATCGAGTCATAC
1 GGGTCTCGGGTCATCC
* *
40042 GGGTTTCGGGTCATTC
1 GGGTCTCGGGTCATCC
*
40058 GGGTCTCGGGTCATTC
1 GGGTCTCGGGTCATCC
40074 GGGTCTCGGGTC-TACC
1 GGGTCTCGGGTCAT-CC
40090 GGGTCTCGGGT
1 GGGTCTCGGGT
40101 TGGGTGGGTT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
15 1 0.02
16 63 0.98
ACGTcount: A:0.10, C:0.22, G:0.37, T:0.31
Consensus pattern (16 bp):
GGGTCTCGGGTCATCC
Found at i:40093 original size:32 final size:32
Alignment explanation
Indices: 39966--40100 Score: 94
Period size: 32 Copynumber: 4.2 Consensus size: 32
39956 CAGACAGTTT
* * * * **
39966 TCTCGGATCATTCGGGTTTTGGGTCATCTAGG
1 TCTCGGGTCATACGGGTCTCGGGTCATCCGGG
* ** * * *
39998 T-TCGGGTTATTTGGGTTTCGGGTCATTCGGA
1 TCTCGGGTCATACGGGTCTCGGGTCATCCGGG
* * * *
40029 TATCGAGTCATACGGGTTTCGGGTCATTCGGG
1 TCTCGGGTCATACGGGTCTCGGGTCATCCGGG
*
40061 TCTCGGGTCATTCGGGTCTCGGGTC-TACCGGG
1 TCTCGGGTCATACGGGTCTCGGGTCAT-CCGGG
40093 TCTCGGGT
1 TCTCGGGT
40101 TGGGTGGGTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
31 24 0.29
32 59 0.71
ACGTcount: A:0.10, C:0.20, G:0.35, T:0.35
Consensus pattern (32 bp):
TCTCGGGTCATACGGGTCTCGGGTCATCCGGG
Found at i:40099 original size:48 final size:48
Alignment explanation
Indices: 39999--40100 Score: 125
Period size: 48 Copynumber: 2.1 Consensus size: 48
39989 TCATCTAGGT
* * * *
39999 TCGGGTTATTTGGGTTTCGGGTCATTCGGATATCGAGTCATACGGGTT
1 TCGGGTCATTCGGGTCTCGGGTCATTCGGATATCGAGTCATACGGGTC
* * *
40047 TCGGGTCATTCGGGTCTCGGGTCATTCGGGTCTCGGGTC-TACCGGGTC
1 TCGGGTCATTCGGGTCTCGGGTCATTCGGATATCGAGTCATA-CGGGTC
40095 TCGGGT
1 TCGGGT
40101 TGGGTGGGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
47 2 0.04
48 44 0.96
ACGTcount: A:0.10, C:0.21, G:0.36, T:0.33
Consensus pattern (48 bp):
TCGGGTCATTCGGGTCTCGGGTCATTCGGATATCGAGTCATACGGGTC
Found at i:40367 original size:63 final size:63
Alignment explanation
Indices: 40288--40413 Score: 252
Period size: 63 Copynumber: 2.0 Consensus size: 63
40278 AAAGGATAAA
40288 ATACTTGATAGTGTCTCCTTAGATATTAATTTTGAATATTAAATACATAAGTGATTATCAGGT
1 ATACTTGATAGTGTCTCCTTAGATATTAATTTTGAATATTAAATACATAAGTGATTATCAGGT
40351 ATACTTGATAGTGTCTCCTTAGATATTAATTTTGAATATTAAATACATAAGTGATTATCAGGT
1 ATACTTGATAGTGTCTCCTTAGATATTAATTTTGAATATTAAATACATAAGTGATTATCAGGT
40414 GAGGTAGGTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (63 bp):
ATACTTGATAGTGTCTCCTTAGATATTAATTTTGAATATTAAATACATAAGTGATTATCAGGT
Found at i:41017 original size:16 final size:15
Alignment explanation
Indices: 40991--41087 Score: 81
Period size: 16 Copynumber: 6.1 Consensus size: 15
40981 GGTTAACTTC
*
40991 TCGGGTTTCGGGTCA
1 TCGGGTCTCGGGTCA
41006 TACGGGTCTCGGGTCA
1 T-CGGGTCTCGGGTCA
* *
41022 CTTGGGTTTCGGGTCA
1 -TCGGGTCTCGGGTCA
41038 TCTGGGT-TACGGGTCA
1 TC-GGGTCT-CGGGTCA
*
41054 TTCGTGTCTCGGGTCA
1 -TCGGGTCTCGGGTCA
41070 TCTGGGT-TGCGGGTCA
1 TC-GGGTCT-CGGGTCA
41086 TC
1 TC
41088 AGAGTCTCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
15 6 0.09
16 58 0.85
17 4 0.06
ACGTcount: A:0.08, C:0.22, G:0.37, T:0.33
Consensus pattern (15 bp):
TCGGGTCTCGGGTCA
Found at i:41051 original size:32 final size:31
Alignment explanation
Indices: 40991--41086 Score: 115
Period size: 32 Copynumber: 3.0 Consensus size: 31
40981 GGTTAACTTC
40991 TCGGGTTTCGGGTCATAC-GGGTCTCGGGTCACT
1 TCGGGTTTCGGGTCAT-CTGGGT-TCGGGTCA-T
41024 T-GGGTTTCGGGTCATCTGGGTTACGGGTCAT
1 TCGGGTTTCGGGTCATCTGGGTT-CGGGTCAT
* *
41055 TCGTGTCTCGGGTCATCTGGGTTGCGGGTCAT
1 TCGGGTTTCGGGTCATCTGGGTT-CGGGTCAT
41087 CAGAGTCTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
31 4 0.07
32 52 0.91
33 1 0.02
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.33
Consensus pattern (31 bp):
TCGGGTTTCGGGTCATCTGGGTTCGGGTCAT
Found at i:41052 original size:48 final size:48
Alignment explanation
Indices: 40993--41087 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
40983 TTAACTTCTC
* *
40993 GGGTTTCGGGTCATACGGGTCTCGGGTCA-CTTGGGTTTCGGGTCATCT
1 GGGTTACGGGTCATACGGGTCTCGGGTCATC-TGGGTTGCGGGTCATCT
* *
41041 GGGTTACGGGTCATTCGTGTCTCGGGTCATCTGGGTTGCGGGTCATC
1 GGGTTACGGGTCATACGGGTCTCGGGTCATCTGGGTTGCGGGTCATC
41088 AGAGTCTCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 41 0.98
49 1 0.02
ACGTcount: A:0.08, C:0.21, G:0.38, T:0.33
Consensus pattern (48 bp):
GGGTTACGGGTCATACGGGTCTCGGGTCATCTGGGTTGCGGGTCATCT
Found at i:41095 original size:32 final size:32
Alignment explanation
Indices: 41030--41096 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
41020 CACTTGGGTT
*
41030 TCGGGTCATCTGGGTTACGGGTCATTCGTGTC
1 TCGGGTCATCTGGGTTACGGGTCATTCGAGTC
*
41062 TCGGGTCATCTGGGTTGCGGGTCA-TCAGAGTC
1 TCGGGTCATCTGGGTTACGGGTCATTC-GAGTC
41094 TCG
1 TCG
41097 AGTCGGACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.10, C:0.22, G:0.36, T:0.31
Consensus pattern (32 bp):
TCGGGTCATCTGGGTTACGGGTCATTCGAGTC
Found at i:42375 original size:19 final size:20
Alignment explanation
Indices: 42329--42376 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
42319 TGTGGCACGC
*
42329 CACATGTACCAAAAAGTCGTGC
1 CACATGTACCAAAAA--CGTGA
42351 CACATGTACCAAAAA-GTGA
1 CACATGTACCAAAAACGTGA
42370 CACATGT
1 CACATGT
42377 CAGGCCACGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 10 0.40
22 15 0.60
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CACATGTACCAAAAACGTGA
Found at i:42384 original size:53 final size:53
Alignment explanation
Indices: 42296--42398 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
42286 GACATGGCAC
**
42296 GCCACATGTACCAAAAAGTGACATGTGGCACGCCACATGTACCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
* * *
42349 GCCACATGTACCAAAAAGTGACACATGTCAGGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGT
42399 GACACGTGGC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATGTACCAAAAAGTCGT
Found at i:42390 original size:31 final size:31
Alignment explanation
Indices: 42348--42446 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
42338 CAAAAAGTCG
*
42348 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
* * *
42379 GGCCACGTGTACCAAAAAGTGACACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
** * *
42410 TGCCACATGTTTCAAAAAATGGCACATGGCA
1 TGCCACATGTACCAAAAAGTGACACATGGCA
42441 TGCCAC
1 TGCCAC
42447 GTGCACAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACATGGCA
Found at i:43466 original size:17 final size:18
Alignment explanation
Indices: 43438--43471 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
43428 TGCCGATGAT
*
43438 GATGATGATGATGATAAA
1 GATGATGATGATAATAAA
43456 GATGA-GATGATAATAA
1 GATGATGATGATAATAA
43472 TCATGGAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (18 bp):
GATGATGATGATAATAAA
Found at i:44606 original size:30 final size:30
Alignment explanation
Indices: 44570--44645 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 30
44560 AATTAAATTA
44570 TAACTTGTTATGAATTCAAAAAAATTATAG
1 TAACTTGTTATGAATTCAAAAAAATTATAG
44600 TAACTTGTTATTAGCTGAATTCAAAAAAATTATAG
1 TAACTTG---TTA--TGAATTCAAAAAAATTATAG
44635 TAACTTGTTAT
1 TAACTTGTTAT
44646 TAGCTTATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
30 8 0.20
32 3 0.07
33 3 0.07
35 27 0.66
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (30 bp):
TAACTTGTTATGAATTCAAAAAAATTATAG
Found at i:44656 original size:34 final size:35
Alignment explanation
Indices: 44580--44650 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
44570 TAACTTGTTA
44580 TGAATTCAAAAAAATTATAGTAACTTGTTATTAGC
1 TGAATTCAAAAAAATTATAGTAACTTGTTATTAGC
44615 TGAATTCAAAAAAATTATAGTAACTTGTTATTAGC
1 TGAATTCAAAAAAATTATAGTAACTTGTTATTAGC
44650 T
1 T
44651 TATTCATAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.38
Consensus pattern (35 bp):
TGAATTCAAAAAAATTATAGTAACTTGTTATTAGC
Found at i:48788 original size:7 final size:7
Alignment explanation
Indices: 48776--48816 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
48766 GCCCCTCCTC
48776 AGGGCTA
1 AGGGCTA
48783 AGGGCTA
1 AGGGCTA
48790 AGGGCTA
1 AGGGCTA
48797 AGGGCTA
1 AGGGCTA
48804 AGGGCTA
1 AGGGCTA
48811 AGGGCT
1 AGGGCT
48817 CAGGCCTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.44, T:0.15
Consensus pattern (7 bp):
AGGGCTA
Found at i:50993 original size:183 final size:176
Alignment explanation
Indices: 50641--51001 Score: 596
Period size: 183 Copynumber: 2.0 Consensus size: 176
50631 TCCATAAACA
* *
50641 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATAGTTTTATAATTTATGCTATTTAAT
1 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
* *
50706 CCTTACAATTATATGTTGGACGATTGAATGTTTCAGCTTTAATTGTTTTTTTTTCTATTTGACCG
66 CCTTACAATTATAGGTTGGACGATTGAATGTTTCAGCTTTAATTATTTTTTTTTCTATTTGACCG
*
50771 ATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTCCATGGTCTAC
131 ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
50817 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
1 AATCA-TTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
* *
50882 TCACTTACAATTATGGGTTGGACGATTGAATGTTTCGGCTTTAATTCTTTTATTTTTTTTTCTAT
65 TC-CTTACAATTATAGGTTGGACGATTGAATGTTTCAGCTTTAA-----TTATTTTTTTTTCTAT
50947 TTGACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
124 TTGACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
51000 AA
1 AA
51002 CTTTCATGAA
Statistics
Matches: 171, Mismatches: 7, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
176 5 0.03
177 59 0.35
178 38 0.22
183 69 0.40
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (176 bp):
AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
CCTTACAATTATAGGTTGGACGATTGAATGTTTCAGCTTTAATTATTTTTTTTTCTATTTGACCG
ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
Done.