Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011645.1 Corchorus capsularis cultivar CVL-1 contig11666, 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: 119390
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5429 original size:31 final size:31
Alignment explanation
Indices: 5383--5490 Score: 112
Period size: 31 Copynumber: 3.5 Consensus size: 31
5373 GGCAGTTTTA
* *
5383 TCGGGTCATAAGGGTTTCGGGTCATTTGGAT
1 TCGGGTCATACGGGTTTCGGGTCATTCGGAT
* * * ** *
5414 TCGGGTTATTCGGGTTTCGGATCAGCCGGTT
1 TCGGGTCATACGGGTTTCGGGTCATTCGGAT
*
5445 TCGGGTCATACGGGTTTCGGGTCATTCGGTT
1 TCGGGTCATACGGGTTTCGGGTCATTCGGAT
5476 TCCGGGTC-T-CGGGTT
1 T-CGGGTCATACGGGTT
5491 GGGCGTGTTC
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 6 0.10
31 51 0.81
32 6 0.10
ACGTcount: A:0.10, C:0.19, G:0.36, T:0.35
Consensus pattern (31 bp):
TCGGGTCATACGGGTTTCGGGTCATTCGGAT
Found at i:5477 original size:15 final size:15
Alignment explanation
Indices: 5395--5483 Score: 88
Period size: 16 Copynumber: 5.7 Consensus size: 15
5385 GGGTCATAAG
*
5395 GGTTTCGGGTCATTT
1 GGTTTCGGGTCATTC
* *
5410 GGATTCGGGTTATTC
1 GGTTTCGGGTCATTC
* **
5425 GGGTTTCGGATCAGCC
1 -GGTTTCGGGTCATTC
*
5441 GGTTTCGGGTCATAC
1 GGTTTCGGGTCATTC
5456 GGGTTTCGGGTCATTC
1 -GGTTTCGGGTCATTC
5472 GGTTTCCGGGTC
1 GGTTT-CGGGTC
5484 TCGGGTTGGG
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
15 29 0.49
16 30 0.51
ACGTcount: A:0.09, C:0.19, G:0.36, T:0.36
Consensus pattern (15 bp):
GGTTTCGGGTCATTC
Found at i:5490 original size:15 final size:15
Alignment explanation
Indices: 5383--5490 Score: 85
Period size: 16 Copynumber: 7.0 Consensus size: 15
5373 GGCAGTTTTA
*
5383 TCGGGTCATAAGGGTT
1 TCGGGTCAT-CGGGTT
** *
5399 TCGGGTCATTTGGAT
1 TCGGGTCATCGGGTT
*
5414 TCGGGTTATTCGGGTT
1 TCGGGTCA-TCGGGTT
* * *
5430 TCGGATCAGCCGGTT
1 TCGGGTCATCGGGTT
5445 TCGGGTCATACGGGTT
1 TCGGGTCAT-CGGGTT
5461 TCGGGTCATTC-GGTT
1 TCGGGTCA-TCGGGTT
5476 TCCGGGTC-TCGGGTT
1 T-CGGGTCATCGGGTT
5491 GGGCGTGTTC
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
14 2 0.03
15 31 0.42
16 39 0.53
17 1 0.01
ACGTcount: A:0.10, C:0.19, G:0.36, T:0.35
Consensus pattern (15 bp):
TCGGGTCATCGGGTT
Found at i:6353 original size:32 final size:32
Alignment explanation
Indices: 6316--6388 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
6306 CGGGTTAACT
* *
6316 TCTCGGGTTATTCGGGTT-TCGAGTCATACGGG
1 TCTCGGGTCACTCGGGTTATCGA-TCATACGGG
* * *
6348 TCTCGGATCACTCGGGTTATGGATCATTCGGG
1 TCTCGGGTCACTCGGGTTATCGATCATACGGG
6380 TCTCGGGTC
1 TCTCGGGTC
6389 GTTTACTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 31 0.91
33 3 0.09
ACGTcount: A:0.12, C:0.22, G:0.33, T:0.33
Consensus pattern (32 bp):
TCTCGGGTCACTCGGGTTATCGATCATACGGG
Found at i:6363 original size:16 final size:16
Alignment explanation
Indices: 6344--6385 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
6334 TCGAGTCATA
6344 CGGGTCTCGGATCACT
1 CGGGTCTCGGATCACT
* *
6360 CGGGT-TATGGATCATT
1 CGGGTCT-CGGATCACT
6376 CGGGTCTCGG
1 CGGGTCTCGG
6386 GTCGTTTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
15 1 0.05
16 19 0.90
17 1 0.05
ACGTcount: A:0.12, C:0.24, G:0.36, T:0.29
Consensus pattern (16 bp):
CGGGTCTCGGATCACT
Found at i:6452 original size:25 final size:26
Alignment explanation
Indices: 6416--6466 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
6406 TGGTCAAATC
6416 GGGTTGGACGGGTTC-GGGTTCGGGA
1 GGGTTGGACGGGTTCAGGGTTCGGGA
*
6441 GGGTTGGGCGGGTTCTAGGGTTCGGG
1 GGGTTGGACGGGTTC-AGGGTTCGGG
6467 TCAGCTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.61
27 9 0.39
ACGTcount: A:0.06, C:0.12, G:0.57, T:0.25
Consensus pattern (26 bp):
GGGTTGGACGGGTTCAGGGTTCGGGA
Found at i:7853 original size:2 final size:2
Alignment explanation
Indices: 7842--7875 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
7832 GACATACCTT
7842 TA TA -A 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 TA TA T
7876 GTGCTATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12131 original size:13 final size:14
Alignment explanation
Indices: 12107--12135 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
12097 AACTCCCTCC
12107 GTCCCGTTTTACAT
1 GTCCCGTTTTACAT
12121 GTCCC-TTTTACAT
1 GTCCCGTTTTACAT
12134 GT
1 GT
12136 TTTACGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.14, C:0.28, G:0.14, T:0.45
Consensus pattern (14 bp):
GTCCCGTTTTACAT
Found at i:15516 original size:21 final size:21
Alignment explanation
Indices: 15492--15651 Score: 150
Period size: 21 Copynumber: 7.8 Consensus size: 21
15482 TCTAACTCTA
*
15492 ACATGGAAGAGGCTGATTTCG
1 ACATGGAAGAGGCTGATTTTG
*
15513 ACATGGAAGATGCTGATTTTG
1 ACATGGAAGAGGCTGATTTTG
* *
15534 ACGCT-GAAGAGGCTTATTTTG
1 AC-ATGGAAGAGGCTGATTTTG
* *
15555 ACAT-G--GAGGCTTATTTGG
1 ACATGGAAGAGGCTGATTTTG
* * ** *
15573 ACTTTGTTGAGGCTGGTTTTG
1 ACATGGAAGAGGCTGATTTTG
* *
15594 ACATGGAA-ATGGCTTATCTTG
1 ACATGGAAGA-GGCTGATTTTG
15615 ACATGGAAGAGGCTGATTTTG
1 ACATGGAAGAGGCTGATTTTG
15636 ACATGGAAGAGGCTGA
1 ACATGGAAGAGGCTGA
15652 AGTTCAAGGA
Statistics
Matches: 113, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
18 15 0.13
19 1 0.01
20 3 0.03
21 92 0.81
22 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (21 bp):
ACATGGAAGAGGCTGATTTTG
Found at i:19304 original size:23 final size:24
Alignment explanation
Indices: 19278--19325 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
19268 TTACTCCAAT
*
19278 AATATTTCAATTTCAC-CAGACAA
1 AATATTTCAATTTCACTCAAACAA
19301 AATATTTCAATTTCACTCAAACAA
1 AATATTTCAATTTCACTCAAACAA
19325 A
1 A
19326 GAACGTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (24 bp):
AATATTTCAATTTCACTCAAACAA
Found at i:24239 original size:11 final size:11
Alignment explanation
Indices: 24216--24249 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
24206 CCTAAGATCA
*
24216 CTATCCAAACC
1 CTATCCGAACC
*
24227 CTTTCCGAACC
1 CTATCCGAACC
24238 CTATCCGAACC
1 CTATCCGAACC
24249 C
1 C
24250 ATTACGGGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.47, G:0.06, T:0.21
Consensus pattern (11 bp):
CTATCCGAACC
Found at i:26592 original size:42 final size:42
Alignment explanation
Indices: 26540--26637 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
26530 ATTTAATGTT
* *
26540 CGTCAGTATAGATGCAGCATATTCCGACCACATAGTATATTC
1 CGTCAGTATAGATGCAGCATATTCCGACCACATAGCACATTC
*
26582 CGTCAGTATAGATGCAGCCTATTCCGACCACATAGCACATTC
1 CGTCAGTATAGATGCAGCATATTCCGACCACATAGCACATTC
*
26624 CGTTAGTATAGATG
1 CGTCAGTATAGATG
26638 AATGGTATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
CGTCAGTATAGATGCAGCATATTCCGACCACATAGCACATTC
Found at i:35232 original size:4 final size:4
Alignment explanation
Indices: 35223--35247 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
35213 AAGTATGGTC
35223 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
35248 ATAGCTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:50769 original size:17 final size:17
Alignment explanation
Indices: 50744--50803 Score: 72
Period size: 16 Copynumber: 3.7 Consensus size: 17
50734 GGGTTTGGGC
50744 TTAAA-TTGGGTTCGGA
1 TTAAATTTGGGTTCGGA
50760 TTAAATTTGGG-TCGGA
1 TTAAATTTGGGTTCGGA
* * *
50776 TT-GATTCGGGTTCGGG
1 TTAAATTTGGGTTCGGA
50792 TTAAATTTGGGT
1 TTAAATTTGGGT
50804 CATGTTGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 6 0.17
16 18 0.50
17 12 0.33
ACGTcount: A:0.20, C:0.07, G:0.33, T:0.40
Consensus pattern (17 bp):
TTAAATTTGGGTTCGGA
Found at i:50788 original size:32 final size:32
Alignment explanation
Indices: 50751--50855 Score: 149
Period size: 32 Copynumber: 3.3 Consensus size: 32
50741 GGCTTAAATT
50751 GGGTTCGGATTAAATTTGGGTC-GGATTGATTC
1 GGGTTCGGATTAAATTTGGGTCAGG-TTGATTC
* *
50783 GGGTTCGGGTTAAATTTGGGTCATGTTGATTC
1 GGGTTCGGATTAAATTTGGGTCAGGTTGATTC
* * *
50815 GGGTTCGGGTTAATTTTGGGTCAGGTTAATTC
1 GGGTTCGGATTAAATTTGGGTCAGGTTGATTC
50847 GGGTTCGGA
1 GGGTTCGGA
50856 CTCGGATTGG
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
32 65 0.98
33 1 0.02
ACGTcount: A:0.16, C:0.10, G:0.36, T:0.38
Consensus pattern (32 bp):
GGGTTCGGATTAAATTTGGGTCAGGTTGATTC
Found at i:50843 original size:16 final size:16
Alignment explanation
Indices: 50790--50845 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
50780 TTCGGGTTCG
*
50790 GGTTAAATTTGGGTCA
1 GGTTAATTTTGGGTCA
* * * *
50806 TGTTGA-TTCGGGTTCG
1 GGTTAATTTTGGG-TCA
50822 GGTTAATTTTGGGTCA
1 GGTTAATTTTGGGTCA
50838 GGTTAATT
1 GGTTAATT
50846 CGGGTTCGGA
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.18, C:0.07, G:0.32, T:0.43
Consensus pattern (16 bp):
GGTTAATTTTGGGTCA
Found at i:51030 original size:20 final size:20
Alignment explanation
Indices: 50997--51035 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
50987 CATAGATGAA
*
50997 ATTTTCAGAAATTATTATTT
1 ATTTTCAGAAATTAGTATTT
51017 ATTTTCA-AATATTAGTATT
1 ATTTTCAGAA-ATTAGTATT
51036 GAATTCAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCAGAAATTAGTATTT
Found at i:51085 original size:16 final size:16
Alignment explanation
Indices: 51066--51107 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
51056 TCGGATTCGG
51066 GTTTTTTCGGG-TTCA
1 GTTTTTTCGGGTTTCA
51081 TGTTTTTTCGGGTTTCA
1 -GTTTTTTCGGGTTTCA
*
51098 GATTTTTCGG
1 GTTTTTTCGG
51108 CATCTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.07, C:0.12, G:0.26, T:0.55
Consensus pattern (16 bp):
GTTTTTTCGGGTTTCA
Found at i:57417 original size:95 final size:96
Alignment explanation
Indices: 57279--57468 Score: 364
Period size: 95 Copynumber: 2.0 Consensus size: 96
57269 TCCATTTCGG
57279 TAATCAATATATTTGGTCATGTTAACTCATTAGAAGAGGAAAAACATATA-TTTCAATATAAAAC
1 TAATCAATATATTTGGTCATGTTAACTCATTAGAAGAGGAAAAACATATATTTTCAATATAAAAC
57343 ACCAGGATACATTAGTTTATATACAACCAGT
66 ACCAGGATACATTAGTTTATATACAACCAGT
*
57374 TAATCAATATATTTGGTCATGTTAACTCATTAGAAGAGGAAAAACATATATTTTCAATATGAAAC
1 TAATCAATATATTTGGTCATGTTAACTCATTAGAAGAGGAAAAACATATATTTTCAATATAAAAC
57439 ACCAGGATACATTAGTTTATATACAACCAG
66 ACCAGGATACATTAGTTTATATACAACCAG
57469 AGAAAATCTA
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
95 50 0.54
96 43 0.46
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.32
Consensus pattern (96 bp):
TAATCAATATATTTGGTCATGTTAACTCATTAGAAGAGGAAAAACATATATTTTCAATATAAAAC
ACCAGGATACATTAGTTTATATACAACCAGT
Found at i:57561 original size:18 final size:20
Alignment explanation
Indices: 57538--57575 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
57528 AGCATTTAGG
57538 CTGTC-AATCCCT-CTAATT
1 CTGTCAAATCCCTACTAATT
57556 CTGTCAAATCCCTACTAATT
1 CTGTCAAATCCCTACTAATT
57576 AGTCTGTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.26, C:0.32, G:0.05, T:0.37
Consensus pattern (20 bp):
CTGTCAAATCCCTACTAATT
Found at i:79688 original size:13 final size:15
Alignment explanation
Indices: 79665--79703 Score: 57
Period size: 13 Copynumber: 2.8 Consensus size: 15
79655 ATCCGGTGGG
79665 GAGAA-AAGAGAA-A
1 GAGAATAAGAGAATA
79678 GA-AATAAGAGAATA
1 GAGAATAAGAGAATA
79692 GAGAATAAGAGA
1 GAGAATAAGAGA
79704 TGAGCAGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 3 0.13
15 9 0.39
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (15 bp):
GAGAATAAGAGAATA
Found at i:84215 original size:15 final size:16
Alignment explanation
Indices: 84147--84209 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
84137 TAAGAGTAAA
84147 AGTAAAAGGAGTAATC
1 AGTAAAAGGAGTAATC
*
84163 AGTAAAATG-GTAAT-
1 AGTAAAAGGAGTAATC
*
84177 --T--AA-GAGTAA-A
1 AGTAAAAGGAGTAATC
84187 AGTAAAAGGAGTAATC
1 AGTAAAAGGAGTAATC
84203 AGTAAAA
1 AGTAAAA
84210 TGGTAATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
9 1 0.03
10 6 0.16
12 2 0.05
14 2 0.05
15 11 0.30
16 15 0.41
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.21
Consensus pattern (16 bp):
AGTAAAAGGAGTAATC
Found at i:84255 original size:40 final size:40
Alignment explanation
Indices: 84134--84248 Score: 214
Period size: 40 Copynumber: 2.9 Consensus size: 40
84124 TGATTAGTAG
84134 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
1 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
84174 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
1 AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
84214 AATTAAGAGTAAAAGTAAAA-GAGGTAATCAGTAAA
1 AATTAAGAGTAAAAGTAAAAGGA-GTAATCAGTAAA
84249 TCGGTAAAGA
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
39 2 0.03
40 72 0.97
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (40 bp):
AATTAAGAGTAAAAGTAAAAGGAGTAATCAGTAAAATGGT
Found at i:84352 original size:32 final size:33
Alignment explanation
Indices: 84292--84374 Score: 125
Period size: 32 Copynumber: 2.5 Consensus size: 33
84282 AGTAATCGGT
84292 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
1 AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
*
84325 AAAGAGTAAAAT-G-ACAAATGGTGATTAAATTC
1 AAAGAGTAAAATAGTA-AAATGGTAATTAAATTC
84357 AAAGAGTGAAAATAGTAA
1 AAAGAGT-AAAATAGTAA
84375 TTAAATTCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
33 17 0.38
34 2 0.04
35 1 0.02
ACGTcount: A:0.54, C:0.04, G:0.18, T:0.24
Consensus pattern (33 bp):
AAAGAGTAAAATAGTAAAATGGTAATTAAATTC
Found at i:84377 original size:26 final size:26
Alignment explanation
Indices: 84307--84401 Score: 93
Period size: 26 Copynumber: 3.4 Consensus size: 26
84297 GTAAAATAGT
*
84307 AAAATGGTAATTAAATTCAAAGAGTAAAATG
1 AAAATAGTAATTAAATTCAAAGAG-----TG
* *
84338 ACAAATGGTGATTAAATTCAAAGAGTG
1 A-AAATAGTAATTAAATTCAAAGAGTG
84365 AAAATAGTAATTAAATTCAAGAGAGT-
1 AAAATAGTAATTAAATTCAA-AGAGTG
84391 AAAATAGTAAT
1 AAAATAGTAAT
84402 CAGTAAAGAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
26 28 0.47
27 8 0.14
31 1 0.02
32 22 0.37
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.26
Consensus pattern (26 bp):
AAAATAGTAATTAAATTCAAAGAGTG
Found at i:84433 original size:28 final size:28
Alignment explanation
Indices: 84396--84467 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
84386 AGAGTAAAAT
84396 AGTAATCAGTAAAGAGGAAAAA-GTAAA
1 AGTAATCAGTAAAGAGGAAAAAGGTAAA
*
84423 GAGTAATCAGTAAA-AGTAAAAATGGTAAA
1 -AGTAATCAGTAAAGAGGAAAAA-GGTAAA
84452 AGTAATCAGTAAAGAG
1 AGTAATCAGTAAAGAG
84468 TAATCAGCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
27 7 0.17
28 26 0.65
29 7 0.17
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (28 bp):
AGTAATCAGTAAAGAGGAAAAAGGTAAA
Found at i:84434 original size:14 final size:14
Alignment explanation
Indices: 84396--84546 Score: 86
Period size: 14 Copynumber: 11.0 Consensus size: 14
84386 AGAGTAAAAT
84396 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* **
84410 AGGAAAAAGTAAAG
1 AGTAATCAGTAAAG
84424 AGTAATCAGTAAA-
1 AGTAATCAGTAAAG
**
84437 AGTAAAAATGGTAAA-
1 AGTAATCA--GTAAAG
84452 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
84466 AGTAATCAGCGAAA-
1 AGTAATCAG-TAAAG
* *
84480 AGTAAAAT-GGCAAAG
1 AGT--AATCAGTAAAG
*
84495 AGTAGT-A--AAAG
1 AGTAATCAGTAAAG
* *
84506 -GTATTCAGGCAAA-
1 AGTAATCA-GTAAAG
84519 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
84533 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
84547 GAAGAATGAT
Statistics
Matches: 106, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
10 4 0.04
11 5 0.05
13 17 0.16
14 59 0.56
15 18 0.17
16 3 0.03
ACGTcount: A:0.52, C:0.07, G:0.23, T:0.19
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:84480 original size:28 final size:27
Alignment explanation
Indices: 84396--84484 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 27
84386 AGAGTAAAAT
* *
84396 AGTAATCAGTAAAGAGGAAAAAGTAAA
1 AGTAATCAGTAAAGAGTAAAAAGGAAA
84423 GAGTAATCAGTAAA-AGTAAAAATGGTAAA
1 -AGTAATCAGTAAAGAGTAAAAA-GG-AAA
**
84452 AGTAATCAGTAAAGAGTAATCAGCGAAA
1 AGTAATCAGTAAAGAGTAAAAAG-GAAA
84480 AGTAA
1 AGTAA
84485 AATGGCAAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
27 7 0.13
28 36 0.68
29 10 0.19
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (27 bp):
AGTAATCAGTAAAGAGTAAAAAGGAAA
Found at i:84487 original size:42 final size:43
Alignment explanation
Indices: 84417--84546 Score: 123
Period size: 42 Copynumber: 3.2 Consensus size: 43
84407 AAGAGGAAAA
* *
84417 AGTAAAGAGTAATCAGTAAAAGTAAAAATGGTAAA-AGTAATC
1 AGTAAAGAGTAATCAGGAAAAGTAAAAATGGCAAAGAGTAATC
*
84459 AGTAAAGAGTAATCAGCGAAAAGT-AAAATGGCAAAGAGTAGT-
1 AGTAAAGAGTAATCAG-GAAAAGTAAAAATGGCAAAGAGTAATC
* ** *
84501 A--AAAG-GTATTCAGGCAAAAGTAATCA--GTAAAGAGTAATC
1 AGTAAAGAGTAATCAGG-AAAAGTAAAAATGGCAAAGAGTAATC
84540 AGTAAAG
1 AGTAAAG
84547 GAAGAATGAT
Statistics
Matches: 73, Mismatches: 8, Indels: 15
0.76 0.08 0.16
Matches are distributed among these distances:
38 11 0.15
39 14 0.19
40 6 0.08
41 4 0.05
42 27 0.37
43 11 0.15
ACGTcount: A:0.52, C:0.07, G:0.22, T:0.19
Consensus pattern (43 bp):
AGTAAAGAGTAATCAGGAAAAGTAAAAATGGCAAAGAGTAATC
Found at i:84613 original size:22 final size:22
Alignment explanation
Indices: 84588--84693 Score: 72
Period size: 22 Copynumber: 4.8 Consensus size: 22
84578 GAGCAAGACG
*
84588 GTAATCAGTAAAGAGTAAAATA
1 GTAATCAGTAAAAAGTAAAATA
* *
84610 GTAATCAGCAAAAAGTAAGAA-G
1 GTAATCAGTAAAAAGTAA-AATA
* * *
84632 GCAATCAGTAAAGAGTGAAATA
1 GTAATCAGTAAAAAGTAAAATA
* * *
84654 TTAA-GAGTAAAAAGGTAAAATG
1 GTAATCAGTAAAAA-GTAAAATA
** *
84676 GTAAAAAGTAAAAGGTAA
1 GTAATCAGTAAAAAGTAA
84694 TCAGTAAAGG
Statistics
Matches: 63, Mismatches: 17, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
21 9 0.14
22 45 0.71
23 9 0.14
ACGTcount: A:0.55, C:0.05, G:0.22, T:0.19
Consensus pattern (22 bp):
GTAATCAGTAAAAAGTAAAATA
Found at i:84699 original size:14 final size:14
Alignment explanation
Indices: 84660--84709 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
84650 AATATTAAGA
84660 GTAAAAAGGTAAAATG
1 GTAAAAA-GTAAAA-G
84676 GTAAAAAGTAAAAG
1 GTAAAAAGTAAAAG
** *
84690 GTAATCAGTAAAGG
1 GTAAAAAGTAAAAG
84704 GTAAAA
1 GTAAAA
84710 TGGTAATTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
14 16 0.55
15 6 0.21
16 7 0.24
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18
Consensus pattern (14 bp):
GTAAAAAGTAAAAG
Found at i:84729 original size:22 final size:22
Alignment explanation
Indices: 84676--84740 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
84666 AGGTAAAATG
84676 GTAAAAAGTAAAA-GGTAATCA
1 GTAAAAAGTAAAATGGTAATCA
** *
84697 GTAAAGGGTAAAATGGTAATTA
1 GTAAAAAGTAAAATGGTAATCA
* *
84719 GTAAAAAGTAAGATGGCAATCA
1 GTAAAAAGTAAAATGGTAATCA
84741 ATAAGAAGAG
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
21 11 0.31
22 24 0.69
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.22
Consensus pattern (22 bp):
GTAAAAAGTAAAATGGTAATCA
Found at i:85602 original size:38 final size:38
Alignment explanation
Indices: 85551--85623 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
85541 CTTGCATCAC
*
85551 TGATAGAATCACACTTCTTT-GAAGGTATTGGTTGCCAA
1 TGATAAAATCACACTT-TTTCGAAGGTATTGGTTGCCAA
85589 TGATAAAATCACACTTTTTCGAAGGTATTGGTTGC
1 TGATAAAATCACACTTTTTCGAAGGTATTGGTTGC
85624 AAGCAAATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
37 3 0.09
38 30 0.91
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (38 bp):
TGATAAAATCACACTTTTTCGAAGGTATTGGTTGCCAA
Found at i:89354 original size:18 final size:18
Alignment explanation
Indices: 89319--89360 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
89309 CTTCCCCCTG
*
89319 AAAAAAAATAAAATAGAA
1 AAAAAAAATAAAAGAGAA
89337 TAAAAAAAAT-AAAGAGAA
1 -AAAAAAAATAAAAGAGAA
89355 AAAAAA
1 AAAAAA
89361 CAGTATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 7 0.32
19 9 0.41
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (18 bp):
AAAAAAAATAAAAGAGAA
Found at i:89360 original size:19 final size:19
Alignment explanation
Indices: 89319--89360 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
89309 CTTCCCCCTG
* *
89319 AAAAAAAATAAAATAGAAT
1 AAAAAAAATAAAAGAGAAA
89338 AAAAAAAAT-AAAGAGAAA
1 AAAAAAAATAAAAGAGAAA
89356 AAAAA
1 AAAAA
89361 CAGTATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAAAATAAAAGAGAAA
Done.