Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009469.1 Corchorus capsularis cultivar CVL-1 contig09490, 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: 30685
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Found at i:5176 original size:27 final size:27
Alignment explanation
Indices: 5173--5274 Score: 96
Period size: 27 Copynumber: 3.5 Consensus size: 27
5163 GGGTAATTAA
* *
5173 GTAATTCAGTAATTAACTTAATTCAGG
1 GTAATTAAGTAATCAACTTAATTCAGG
5200 GTAATTAAGTAATTCAGTAATCAACTTAATTCAGG
1 GTAATTAAG----T-A---ATCAACTTAATTCAGG
*
5235 GTAATTAAGTAATTAACTTAATTCAGG
1 GTAATTAAGTAATCAACTTAATTCAGG
*
5262 GTAATTACGTAAT
1 GTAATTAAGTAAT
5275 TTGGTAATAA
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
27 35 0.56
30 1 0.02
31 2 0.03
32 1 0.02
35 24 0.38
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (27 bp):
GTAATTAAGTAATCAACTTAATTCAGG
Found at i:5178 original size:8 final size:8
Alignment explanation
Indices: 5165--5250 Score: 55
Period size: 8 Copynumber: 10.0 Consensus size: 8
5155 TTATTTCAGG
5165 GTAATTAA
1 GTAATTAA
*
5173 GTAATTCA
1 GTAATTAA
5181 GTAATTAA
1 GTAATTAA
* *
5189 CTTAATTCAGG
1 -GTAATT-A-A
5200 GTAATTAA
1 GTAATTAA
*
5208 GTAATTCA
1 GTAATTAA
*
5216 GTAATCAA
1 GTAATTAA
* *
5224 CTTAATTCAGG
1 -GTAATT-A-A
5235 GTAATTAA
1 GTAATTAA
5243 GTAATTAA
1 GTAATTAA
5251 CTTAATTCAG
Statistics
Matches: 58, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
8 35 0.60
9 11 0.19
10 12 0.21
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (8 bp):
GTAATTAA
Found at i:5179 original size:35 final size:35
Alignment explanation
Indices: 5133--6119 Score: 1452
Period size: 35 Copynumber: 28.3 Consensus size: 35
5123 AGGAAATAAG
*
5133 ATTAAGTAATTCAGTAATCAACTTATTTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5168 ATTAAGTAATTCAGTAATTAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
5203 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
5238 ATTAAGT-A---A-T--T-AACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
* * *
5265 ATTACGTAATTTGGTAATAATCAACTTAATTCAGGGTA
1 ATTAAGTAA-TT--CAGTAATCAACTTAATTCAGGGTA
* *
5303 ATTAACTATTTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5338 ATTAAGTATTTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5373 ATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5408 ATTAAGTATTTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5443 ATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
***
5478 ATTAAGTGGGTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
* *
5513 ATTAAGTAAGTCAGTAATCAACTTAGTTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5548 ATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5583 ATTAAGTAATTC-GCTAATTAACTTAATTCAGGGTA
1 ATTAAGTAATTCAG-TAATCAACTTAATTCAGGGTA
* *
5618 ATTAAGTGAGTCAGTAATAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAG---TAATCAACTTAATTCAGGGTA
* *
5656 ATTAACTATTTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
* *
5691 ATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5726 ATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5761 ATTAAGTATTTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
* *
5796 ATTAAGTGAGTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
5831 ATTAAGTAATTCAATAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
***
5866 ATTAAGTGGGTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
* *
5901 ATTAAGTAAGTCAGTAATCAACTTAGTTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
* *
5936 ATTAAGTAATTCAATAATCAACTTAATTCGGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*** *
5971 ATTAAGTGGGTCAGTAATCAACTTAATACAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
6006 ATTAAGTAAGTCAGTAATCAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
* *
6041 ATTAAGTAAGTCAGTAATGAACTTAATTCAGGGTA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
*
6076 ATTAAGTAATTCAGTAATCAACTTAATTCAGGATA
1 ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
6111 ATTAAGTAA
1 ATTAAGTAA
6120 GTAAAAAGCA
Statistics
Matches: 862, Mismatches: 75, Indels: 30
0.89 0.08 0.03
Matches are distributed among these distances:
27 22 0.03
28 2 0.00
30 1 0.00
31 1 0.00
34 2 0.00
35 778 0.90
36 1 0.00
37 3 0.00
38 52 0.06
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (35 bp):
ATTAAGTAATTCAGTAATCAACTTAATTCAGGGTA
Found at i:5275 original size:27 final size:27
Alignment explanation
Indices: 5208--5275 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 27
5198 GGGTAATTAA
*
5208 GTAATT-CAGTAATCAACTTAATTCAGG
1 GTAATTAC-GTAATTAACTTAATTCAGG
*
5235 GTAATTAAGTAATTAACTTAATTCAGG
1 GTAATTACGTAATTAACTTAATTCAGG
5262 GTAATTACGTAATT
1 GTAATTACGTAATT
5276 TGGTAATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (27 bp):
GTAATTACGTAATTAACTTAATTCAGG
Found at i:8717 original size:100 final size:100
Alignment explanation
Indices: 8544--8744 Score: 402
Period size: 100 Copynumber: 2.0 Consensus size: 100
8534 ATTCATTCAA
8544 TCAAAAAGACTAGGAGTAAGAATGGGTTGATGGCTATCAAAATTGATTTGGAGAAGGCATATGAT
1 TCAAAAAGACTAGGAGTAAGAATGGGTTGATGGCTATCAAAATTGATTTGGAGAAGGCATATGAT
8609 CGAGTTCGATGGGATTTCTTACGGGAGACTTTGTT
66 CGAGTTCGATGGGATTTCTTACGGGAGACTTTGTT
8644 TCAAAAAGACTAGGAGTAAGAATGGGTTGATGGCTATCAAAATTGATTTGGAGAAGGCATATGAT
1 TCAAAAAGACTAGGAGTAAGAATGGGTTGATGGCTATCAAAATTGATTTGGAGAAGGCATATGAT
8709 CGAGTTCGATGGGATTTCTTACGGGAGACTTTGTT
66 CGAGTTCGATGGGATTTCTTACGGGAGACTTTGTT
8744 T
1 T
8745 GTTTTCGGAT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 101 1.00
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.30
Consensus pattern (100 bp):
TCAAAAAGACTAGGAGTAAGAATGGGTTGATGGCTATCAAAATTGATTTGGAGAAGGCATATGAT
CGAGTTCGATGGGATTTCTTACGGGAGACTTTGTT
Found at i:11695 original size:15 final size:16
Alignment explanation
Indices: 11655--11698 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
11645 AGTGAATACT
11655 CACCAGGTGAGTATTG
1 CACCAGGTGAGTATTG
*
11671 CACCAAGTGAGTATT-
1 CACCAGGTGAGTATTG
*
11686 TACCAGGTGAGTA
1 CACCAGGTGAGTA
11699 CTGTATTGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (16 bp):
CACCAGGTGAGTATTG
Found at i:12125 original size:23 final size:23
Alignment explanation
Indices: 12099--12158 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
12089 TTGAGGAGAG
*
12099 CTCCACGCAAGAGTTGGGTGAGC
1 CTCCACGCAAGAGCTGGGTGAGC
* *
12122 CTCCATGCGAGAGCTGGGTGAGC
1 CTCCACGCAAGAGCTGGGTGAGC
*
12145 CTCCGCGCAAGAGC
1 CTCCACGCAAGAGC
12159 AAGGGAGTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.30, G:0.35, T:0.15
Consensus pattern (23 bp):
CTCCACGCAAGAGCTGGGTGAGC
Found at i:12289 original size:4 final size:4
Alignment explanation
Indices: 12280--12305 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12270 TATGTATAAA
12280 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
12306 TACTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:12637 original size:25 final size:25
Alignment explanation
Indices: 12601--12658 Score: 91
Period size: 25 Copynumber: 2.3 Consensus size: 25
12591 TTTTTTTGTC
*
12601 CTAGCGCATATCAGGGGAGTCT-CT
1 CTAGCGCGTATCAGGGGAGTCTCCT
12625 CTTAGCGCGTATCAGGGGAGTCTCCT
1 C-TAGCGCGTATCAGGGGAGTCTCCT
12651 CTAGCGCG
1 CTAGCGCG
12659 GAGCAAGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
24 1 0.03
25 27 0.87
26 3 0.10
ACGTcount: A:0.17, C:0.28, G:0.31, T:0.24
Consensus pattern (25 bp):
CTAGCGCGTATCAGGGGAGTCTCCT
Found at i:12723 original size:15 final size:15
Alignment explanation
Indices: 12700--12729 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12690 TAACGCAGAG
12700 CAAGAGAGTCTCCCT
1 CAAGAGAGTCTCCCT
*
12715 CAAGGGAGTCTCCCT
1 CAAGAGAGTCTCCCT
12730 AACGCGGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.20
Consensus pattern (15 bp):
CAAGAGAGTCTCCCT
Found at i:12741 original size:39 final size:40
Alignment explanation
Indices: 12640--12790 Score: 193
Period size: 39 Copynumber: 3.9 Consensus size: 40
12630 CGCGTATCAG
*
12640 GGGAGTCTCCTCTAGCGCGGAGC-A-AGAGTCTCCCTC-A
1 GGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCCTCAA
* *
12677 GGGAAGTCTCCCCTAACGCAGAGCAAGAGAGTCTCCCTCAA
1 GGG-AGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCCTCAA
*
12718 GGGAGTCTCC-CTAACGCGGAGCAAGAGAGTCTCCCTCAG
1 GGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCCTCAA
* * * *
12757 GGGAGTCTCCTTTAACGCGCAGCAGGGGAGTCTC
1 GGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTC
12791 TCCCTAGCGC
Statistics
Matches: 100, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
37 3 0.03
38 17 0.17
39 38 0.38
40 38 0.38
41 4 0.04
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (40 bp):
GGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCCTCAA
Found at i:12788 original size:40 final size:40
Alignment explanation
Indices: 12636--12790 Score: 208
Period size: 40 Copynumber: 4.0 Consensus size: 40
12626 TTAGCGCGTA
*
12636 TCAGGGGAGTCTCCTCTAGCGCGGAGC-A-AGAGTCTCCC
1 TCAGGGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCC
* * *
12674 TCAGGGAAGTCTCCCCTAACGCAGAGCAAGAGAGTCTCCC
1 TCAGGGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCC
*
12714 TCAAGGGAGTCTCC-CTAACGCGGAGCAAGAGAGTCTCCC
1 TCAGGGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCC
* * * *
12753 TCAGGGGAGTCTCCTTTAACGCGCAGCAGGGGAGTCTC
1 TCAGGGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTC
12791 TCCCTAGCGC
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
38 23 0.23
39 38 0.37
40 41 0.40
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (40 bp):
TCAGGGGAGTCTCCTCTAACGCGGAGCAAGAGAGTCTCCC
Found at i:13147 original size:25 final size:25
Alignment explanation
Indices: 13119--13208 Score: 92
Period size: 25 Copynumber: 3.6 Consensus size: 25
13109 CGTGGTAAGG
13119 GAGTCTCCCCTAGCGCACAGCAGGT
1 GAGTCTCCCCTAGCGCACAGCAGGT
** *** *
13144 GAGTCTTGCCTAGCGTGTAGTA-GT
1 GAGTCTCCCCTAGCGCACAGCAGGT
*
13168 GGAGTCTCCCCTAGTGCACAGCAGGT
1 -GAGTCTCCCCTAGCGCACAGCAGGT
*
13194 GAGTCTCACCTAGCG
1 GAGTCTCCCCTAGCG
13209 TGTGGAGTCT
Statistics
Matches: 48, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
24 2 0.04
25 44 0.92
26 2 0.04
ACGTcount: A:0.19, C:0.29, G:0.30, T:0.22
Consensus pattern (25 bp):
GAGTCTCCCCTAGCGCACAGCAGGT
Found at i:13297 original size:9 final size:9
Alignment explanation
Indices: 13283--13317 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
13273 AATTAGGATT
13283 TTTTTTTAA
1 TTTTTTTAA
13292 TTTTTTTAA
1 TTTTTTTAA
*
13301 ATTTTTT-A
1 TTTTTTTAA
13309 TTTTTTTAA
1 TTTTTTTAA
13318 AAGATAGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:13305 original size:17 final size:17
Alignment explanation
Indices: 13285--13318 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
13275 TTAGGATTTT
13285 TTTTTAATTTTTTTAAA
1 TTTTTAATTTTTTTAAA
*
13302 TTTTTTATTTTTTTAAA
1 TTTTTAATTTTTTTAAA
13319 AGATAGGCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTAATTTTTTTAAA
Found at i:14391 original size:36 final size:36
Alignment explanation
Indices: 14347--14417 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
14337 GTATTAGGCG
* *
14347 ACTGAGGCCAGTGACGTTATAGCCAATCATTGGGCT
1 ACTGAGGCCAGCGACGTTATAGCCAAACATTGGGCT
**
14383 ACTGAGGCCAGCGGTGTTATAGCCAAACATTGGGC
1 ACTGAGGCCAGCGACGTTATAGCCAAACATTGGGC
14418 GACCAAGGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (36 bp):
ACTGAGGCCAGCGACGTTATAGCCAAACATTGGGCT
Found at i:14427 original size:36 final size:36
Alignment explanation
Indices: 14362--14430 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
14352 GGCCAGTGAC
* * **
14362 GTTATAGCCAATCATTGGGCTACTGAGGCCAGCGGT
1 GTTATAGCCAAACATTGGGCGACCAAGGCCAGCGGT
14398 GTTATAGCCAAACATTGGGCGACCAAGGCCAGC
1 GTTATAGCCAAACATTGGGCGACCAAGGCCAGC
14431 AGCATTACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.26, C:0.25, G:0.29, T:0.20
Consensus pattern (36 bp):
GTTATAGCCAAACATTGGGCGACCAAGGCCAGCGGT
Found at i:16548 original size:16 final size:15
Alignment explanation
Indices: 16522--16566 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
16512 AAGTAAATAC
*
16522 TCACCAGGTGAGTAT
1 TCACCAAGTGAGTAT
16537 TGCACCAAGTGAGTAT
1 T-CACCAAGTGAGTAT
* *
16553 TTACCACGTGAGTA
1 TCACCAAGTGAGTA
16567 CTGTATTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (15 bp):
TCACCAAGTGAGTAT
Found at i:16563 original size:15 final size:15
Alignment explanation
Indices: 16524--16599 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
16514 GTAAATACTC
*
16524 ACCAGGTGAGTATTGC
1 ACCAGGTGAGTATT-T
*
16540 ACCAAGTGAGTATTT
1 ACCAGGTGAGTATTT
* *
16555 ACCACGTGAGTACTGT
1 ACCAGGTGAGTA-TTT
***
16571 ATTGGGTGAGTATTT
1 ACCAGGTGAGTATTT
16586 ACCAGGTGAGTATT
1 ACCAGGTGAGTATT
16600 GTATTGGGTG
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
15 24 0.51
16 23 0.49
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (15 bp):
ACCAGGTGAGTATTT
Found at i:16580 original size:31 final size:31
Alignment explanation
Indices: 16545--16613 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
16535 ATTGCACCAA
16545 GTGAGTATTTACCACGTGAGTACTGTATTGG
1 GTGAGTATTTACCACGTGAGTACTGTATTGG
* *
16576 GTGAGTATTTACCAGGTGAGTATTGTATTGG
1 GTGAGTATTTACCACGTGAGTACTGTATTGG
16607 GTGAGTA
1 GTGAGTA
16614 GGGTAGGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (31 bp):
GTGAGTATTTACCACGTGAGTACTGTATTGG
Found at i:16581 original size:16 final size:15
Alignment explanation
Indices: 16560--16613 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
16550 TATTTACCAC
16560 GTGAGTACTGTATTGG
1 GTGAGTA-TGTATTGG
* ***
16576 GTGAGTATTTACCAG
1 GTGAGTATGTATTGG
16591 GTGAGTATTGTATTGG
1 GTGAGTA-TGTATTGG
16607 GTGAGTA
1 GTGAGTA
16614 GGGTAGGAAC
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.22, C:0.06, G:0.35, T:0.37
Consensus pattern (15 bp):
GTGAGTATGTATTGG
Found at i:27392 original size:198 final size:198
Alignment explanation
Indices: 27021--27444 Score: 575
Period size: 198 Copynumber: 2.1 Consensus size: 198
27011 AATCACTTTA
* * * *
27021 TATAATTTTAT-TTATAGGATTATTATATAATACACCTTTCAGTTAAATTTTACACTCCCTAAGC
1 TATAATTTT-TCTTATAGGATTATTATACAATACACCTATCAATTAAATTTTACACTCCATAAGC
**
27085 AGGTTAAGAAGTTGACATTTACCCCATTTCATAATCAATTAAATATTTAATATCAATACATATTC
65 AGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATCAATACATATTC
* * *
27150 CTTAAGGGGACACATGGCAACCTTAAACCCTGCATGTACAGTCTGCTAAATTCGACTGACGGTGT
130 CCTAAGGGGACACATGGCAACCTTAAACCCTGCACGTACAGTCTGCTAAACTCGACTGACGGTGT
27215 ATAG
195 ATAG
* * ** *
27219 TATAATTTTTCTTATAAGATTATTATACAATCCA-CTATCAATGTAAATTTTGGACTCCATAAGT
1 TATAATTTTTCTTATAGGATTATTATACAATACACCTATCAAT-TAAATTTTACACTCCATAAGC
* * * * *
27283 GGGTTAAGAAGTTGACGCATACGCCATTTCATAATTAATTAAATATTTAATATTAATACATATTC
65 AGGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATCAATACATATTC
* * * *
27348 CCTAAGGGGATACATGTCAACCCTTAAACCC-GCACGTGCAGTCTGCTAAACTCTACTGACGGTG
130 CCTAAGGGGACACATGGCAA-CCTTAAACCCTGCACGTACAGTCTGCTAAACTCGACTGACGGTG
*
27412 TATTG
194 TATAG
*
27417 TATAATTTTTCTTATAGGATAATTATAC
1 TATAATTTTTCTTATAGGATTATTATAC
27445 TGTCAAATTA
Statistics
Matches: 197, Mismatches: 26, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
197 7 0.04
198 180 0.91
199 10 0.05
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (198 bp):
TATAATTTTTCTTATAGGATTATTATACAATACACCTATCAATTAAATTTTACACTCCATAAGCA
GGTTAAGAAGTTGACACATACCCCATTTCATAATCAATTAAATATTTAATATCAATACATATTCC
CTAAGGGGACACATGGCAACCTTAAACCCTGCACGTACAGTCTGCTAAACTCGACTGACGGTGTA
TAG
Found at i:27538 original size:22 final size:20
Alignment explanation
Indices: 27513--27552 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
27503 GATTTTTAGC
27513 AACCTTATTAATCTTTTTAATA
1 AACCTTATT-AT-TTTTTAATA
27535 AACCTTATTATTTTTTAA
1 AACCTTATTATTTTTTAA
27553 AAAAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 2 0.11
22 9 0.50
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (20 bp):
AACCTTATTATTTTTTAATA
Done.