Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015269.1 Corchorus capsularis cultivar CVL-1 contig15290, 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: 37926
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--35 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1 AT AT AT AT 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 AT AT AT AT A
36 CACACACGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:551 original size:20 final size:20
Alignment explanation
Indices: 507--548 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
497 AAATATTATA
*
507 TTTATCTTATAATGGGTAGT
1 TTTATCTTAAAATGGGTAGT
527 TTTATC-TAAAATGGGTAGT
1 TTTATCTTAAAATGGGTAGT
546 TTT
1 TTT
549 TATTTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.26, C:0.05, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTATCTTAAAATGGGTAGT
Found at i:2505 original size:3 final size:3
Alignment explanation
Indices: 2497--2543 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
2487 ATTATATTAT
2497 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2544 CACTGCTAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5281 original size:3 final size:3
Alignment explanation
Indices: 5275--5303 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5265 TATATAATAA
5275 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5304 ATATGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6497 original size:32 final size:31
Alignment explanation
Indices: 6439--6499 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 31
6429 CCTGGAACCG
* *
6439 AAATGACCCGATCCTCAATTATCCGAACCTA
1 AAATGACCCGATCCTAAATTACCCGAACCTA
6470 AAATGACCCAGA-CCTAAAATTACCCGAACC
1 AAATGACCC-GATCCT-AAATTACCCGAACC
6500 AGATCAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (31 bp):
AAATGACCCGATCCTAAATTACCCGAACCTA
Found at i:7217 original size:119 final size:119
Alignment explanation
Indices: 7087--7317 Score: 349
Period size: 119 Copynumber: 1.9 Consensus size: 119
7077 TCAATAAAAA
* **
7087 ATATTGAATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATCAAAC-TATA-AAATTTTTTAAT
1 ATATTGAATTTAATTAAAAGAAAATAGAGTTTTTAGTAAAATCAAACATATATAAAAATTTTAAT
*
7150 ATATCCAAGTTTTTAACGAAAAATAGTAAAATGGTAAAAATAAAATAATTATAAAC
66 ATATCCAAGTTTTTAACAAAAAATAGT--AATGGTAAAAATAAAATAATTATAAAC
*
7206 ATATTGAATTTAATTAAAAGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTGAAAAATTTT
1 ATATTGAATTTAATTAAAAGAAAATAGAGTTTTTAGTAAAATCAAAC-ATATA-T-AAAAATTTT
*
7271 AATATATCCAAGTTTTTAATAAAAAATAGTAATGGTAAAAATAAAAT
63 AATATATCCAAGTTTTTAACAAAAAATAGTAATGGTAAAAATAAAAT
7318 TTTAAATTAA
Statistics
Matches: 101, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
119 45 0.45
121 4 0.04
122 17 0.17
124 35 0.35
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.35
Consensus pattern (119 bp):
ATATTGAATTTAATTAAAAGAAAATAGAGTTTTTAGTAAAATCAAACATATATAAAAATTTTAAT
ATATCCAAGTTTTTAACAAAAAATAGTAATGGTAAAAATAAAATAATTATAAAC
Found at i:7343 original size:119 final size:117
Alignment explanation
Indices: 7101--7343 Score: 278
Period size: 119 Copynumber: 2.0 Consensus size: 117
7091 TGAATTTAAT
* **
7101 TAAATGAAAATAGAGTTTTTAGTAAAATCAAACTATAAAATTTTTTAATATATCCAAGTTTTTAA
1 TAAAAGAAAATAGAGTTTTTAGTAAAATCAAACTATAAAAAATTTTAATATATCCAAGTTTTTAA
* * * ** *
7166 CGAAAAATAGTAAAATGGTAAAAATAAAATAATTATAAACATATTGAATTTAAT
66 CAAAAAATAGT-AAATGGTAAAAATAAAAT-ATTATAAACAAAATGAATAAAAA
*
7220 TAAAAGAAAATAGAGTTTTTAGTAGAATCAAACTATATATTGAAAAATTTTAATATATCCAAGTT
1 TAAAAGAAAATAGAGTTTTTAGTAAAATCAAAC--TATA---AAAAATTTTAATATATCCAAGTT
* *
7285 TTTAATAAAAAATAGT-AATGGTAAAAATAAAAT-TT-TAAATTAAAATG-ATAAAAA
61 TTTAACAAAAAATAGTAAATGGTAAAAATAAAATATTATAAA-CAAAATGAATAAAAA
7339 TAAAA
1 TAAAA
7344 TAATTATAAA
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
119 44 0.42
120 6 0.06
121 4 0.04
122 17 0.16
124 35 0.33
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.34
Consensus pattern (117 bp):
TAAAAGAAAATAGAGTTTTTAGTAAAATCAAACTATAAAAAATTTTAATATATCCAAGTTTTTAA
CAAAAAATAGTAAATGGTAAAAATAAAATATTATAAACAAAATGAATAAAAA
Found at i:7345 original size:149 final size:147
Alignment explanation
Indices: 7176--7463 Score: 461
Period size: 149 Copynumber: 1.9 Consensus size: 147
7166 CGAAAAATAG
* *
7176 TAAAATGGTAAAAATAAAATAATTATAAACATATTGAATTTAATTAAAAGAAAATAGAGTTTTTA
1 TAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTTA
*
7241 GTAGAATCAAACTATATATTGAAAAATTTTAATATATCCAAGTTTTTAATAAAAAATAGT-AATG
66 GTAGAATCAAAATATATATT-AAAAA-TTTAATATATCCAAGTTTTTAAT-AAAAATAGTAAATG
7305 GTAAAAATAAAATTTTAAAT
128 GTAAAAATAAAATTTTAAAT
* * **
7325 TAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAGTTAAATGAAAATATTGTTTTTA
1 TAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTTA
*
7390 GTAGAATCAAAATATATATTAAAAATTTAATATATCCAAGTTTTTAATAAAAATAGTAAAATTGT
66 GTAGAATCAAAATATATATTAAAAATTTAATATATCCAAGTTTTTAATAAAAATAGT-AAATGGT
7455 AAAAATAAA
130 AAAAATAAA
7464 GTAATTAAAA
Statistics
Matches: 129, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
146 9 0.07
147 23 0.18
148 19 0.15
149 78 0.60
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (147 bp):
TAAAATGATAAAAATAAAATAATTATAAAAATATTGAATTTAATTAAAAGAAAATAGAGTTTTTA
GTAGAATCAAAATATATATTAAAAATTTAATATATCCAAGTTTTTAATAAAAATAGTAAATGGTA
AAAATAAAATTTTAAAT
Found at i:7389 original size:23 final size:23
Alignment explanation
Indices: 7352--7404 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
7342 AATAATTATA
*
7352 AAAATATTGAATTTAGTTA-AATG
1 AAAATATTGAATTTAG-TAGAATC
**
7375 AAAATATTGTTTTTAGTAGAATC
1 AAAATATTGAATTTAGTAGAATC
7398 AAAATAT
1 AAAATAT
7405 ATATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (23 bp):
AAAATATTGAATTTAGTAGAATC
Found at i:8273 original size:23 final size:24
Alignment explanation
Indices: 8242--8286 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
8232 GATTTTGTTG
*
8242 TAGTTGAATAAAAATA-AAGTTTT
1 TAGTAGAATAAAAATATAAGTTTT
*
8265 TAGTAGAATAAAACTATAAGTT
1 TAGTAGAATAAAAATATAAGTT
8287 AAGCAATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (24 bp):
TAGTAGAATAAAAATATAAGTTTT
Found at i:8384 original size:4 final size:4
Alignment explanation
Indices: 8372--8415 Score: 79
Period size: 4 Copynumber: 10.8 Consensus size: 4
8362 ACTTTTATAT
8372 ATAG TATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG -ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
8416 TGGTTGCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (4 bp):
ATAG
Found at i:15181 original size:15 final size:15
Alignment explanation
Indices: 15161--15191 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15151 CAGATTTAAT
15161 TTCTTTTCAAATAAG
1 TTCTTTTCAAATAAG
*
15176 TTCTTTTCAATTAAG
1 TTCTTTTCAAATAAG
15191 T
1 T
15192 CCCTGAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (15 bp):
TTCTTTTCAAATAAG
Found at i:20285 original size:128 final size:128
Alignment explanation
Indices: 20057--20314 Score: 516
Period size: 128 Copynumber: 2.0 Consensus size: 128
20047 AAAGTTGAGG
20057 TTTTACACCCAAATTGATTATCTTAGCTTCATTGTTCTAGGTTGAGCAAACTTAGGGTTCTTCAA
1 TTTTACACCCAAATTGATTATCTTAGCTTCATTGTTCTAGGTTGAGCAAACTTAGGGTTCTTCAA
20122 TCTTGTAGAATCCTAGCAAGCAATTAGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATC
66 TCTTGTAGAATCCTAGCAAGCAATTAGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATC
20185 TTTTACACCCAAATTGATTATCTTAGCTTCATTGTTCTAGGTTGAGCAAACTTAGGGTTCTTCAA
1 TTTTACACCCAAATTGATTATCTTAGCTTCATTGTTCTAGGTTGAGCAAACTTAGGGTTCTTCAA
20250 TCTTGTAGAATCCTAGCAAGCAATTAGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATC
66 TCTTGTAGAATCCTAGCAAGCAATTAGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATC
20313 TT
1 TT
20315 GAGAGTTCAA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 130 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.41
Consensus pattern (128 bp):
TTTTACACCCAAATTGATTATCTTAGCTTCATTGTTCTAGGTTGAGCAAACTTAGGGTTCTTCAA
TCTTGTAGAATCCTAGCAAGCAATTAGGTTGTGATTGCTTAATTGTTTGTGAATCTTGTGATC
Found at i:20630 original size:26 final size:26
Alignment explanation
Indices: 20594--20656 Score: 126
Period size: 26 Copynumber: 2.4 Consensus size: 26
20584 CACCACCTTC
20594 TTGAAAATTCAAAAAAATCAGCAACT
1 TTGAAAATTCAAAAAAATCAGCAACT
20620 TTGAAAATTCAAAAAAATCAGCAACT
1 TTGAAAATTCAAAAAAATCAGCAACT
20646 TTGAAAATTCA
1 TTGAAAATTCA
20657 TAGCCGATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.25
Consensus pattern (26 bp):
TTGAAAATTCAAAAAAATCAGCAACT
Found at i:20749 original size:15 final size:15
Alignment explanation
Indices: 20729--20758 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20719 AGTTATATCG
*
20729 AAAAATATAAAAAAT
1 AAAAATAAAAAAAAT
20744 AAAAATAAAAAAAAT
1 AAAAATAAAAAAAAT
20759 TTTCGACCAG
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:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAAATAAAAAAAAT
Found at i:22447 original size:35 final size:35
Alignment explanation
Indices: 22408--22563 Score: 106
Period size: 35 Copynumber: 4.4 Consensus size: 35
22398 TTTTACTGAG
*
22408 TTACTGATTACCATTACTATTTTACTGATTATTCT
1 TTACTAATTACCATTACTATTTTACTGATTATTCT
** * * *
22443 TTACTCTTTACTGATTACTA-GTTACCAT-TTTATTCT
1 TTACTAATTAC-CATTACTATTTTA-C-TGATTATTCT
* *
22479 TTACTAATTGCCATTACT-TTTTACTTATTAATAT-T
1 TTACTAATTACCATTACTATTTTACTGATT-AT-TCT
** * * *
22514 TTACTCTTTACCATT-TTTTCTTTACTGATTACTCT
1 TTACTAATTACCATTACTAT-TTTACTGATTATTCT
22549 TTACTAATTACCATT
1 TTACTAATTACCATT
22564 TTTCTTTACT
Statistics
Matches: 92, Mismatches: 19, Indels: 20
0.70 0.15 0.15
Matches are distributed among these distances:
33 1 0.01
34 5 0.05
35 52 0.57
36 33 0.36
37 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.04, T:0.53
Consensus pattern (35 bp):
TTACTAATTACCATTACTATTTTACTGATTATTCT
Found at i:22467 original size:21 final size:21
Alignment explanation
Indices: 22408--22467 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
22398 TTTTACTGAG
* *
22408 TTACTGATTACCATTACTATT
1 TTACTGATTACTATTACTACT
22429 TTACTGATTATTCT-TTACT-CT
1 TTACTGATTA--CTATTACTACT
22450 TTACTGATTACTAGTTAC
1 TTACTGATTACTA-TTAC
22468 CATTTTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
21 25 0.76
22 5 0.15
23 1 0.03
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (21 bp):
TTACTGATTACTATTACTACT
Found at i:22549 original size:14 final size:14
Alignment explanation
Indices: 22532--22598 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 14
22522 TACCATTTTT
22532 TCTTTACTGATTAC
1 TCTTTACTGATTAC
*
22546 TCTTTACTAATTACC
1 TCTTTACTGATTA-C
*
22561 ATTTTTCTTTACTGGTTAC
1 -----TCTTTACTGATTAC
*
22580 TTTTTACTGATTAC
1 TCTTTACTGATTAC
22594 TCTTT
1 TCTTT
22599 TACTTTTCAC
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
14 28 0.68
15 1 0.02
19 1 0.02
20 11 0.27
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.55
Consensus pattern (14 bp):
TCTTTACTGATTAC
Found at i:22571 original size:34 final size:34
Alignment explanation
Indices: 22476--22593 Score: 112
Period size: 34 Copynumber: 3.4 Consensus size: 34
22466 ACCATTTTAT
* * * *
22476 TCTTTACTAATTGCCATTACTT-TTTACTTATTAA
1 TCTTTACTAATTACCATT-TTTCTTTACTGATTAC
* **
22510 TATTTTACTCTTTACCATTTTTTCTTTACTGATTAC
1 T-CTTTACTAATTACCA-TTTTTCTTTACTGATTAC
*
22546 TCTTTACTAATTACCATTTTTCTTTACTGGTTAC
1 TCTTTACTAATTACCATTTTTCTTTACTGATTAC
* *
22580 TTTTTACTGATTAC
1 TCTTTACTAATTAC
22594 TCTTTTACTT
Statistics
Matches: 68, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
34 30 0.44
35 25 0.37
36 13 0.19
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.55
Consensus pattern (34 bp):
TCTTTACTAATTACCATTTTTCTTTACTGATTAC
Found at i:22586 original size:7 final size:7
Alignment explanation
Indices: 22576--22696 Score: 50
Period size: 7 Copynumber: 16.7 Consensus size: 7
22566 TCTTTACTGG
22576 TTACTTT
1 TTACTTT
**
22583 TTACTGA
1 TTACTTT
22590 TTACTCTT
1 TTACT-TT
22598 TTACTTT
1 TTACTTT
*
22605 TCACTCTT
1 TTACT-TT
22613 TTA-TTAT
1 TTACTT-T
22620 TT--TTT
1 TTACTTT
**
22625 TTACTGA
1 TTACTTT
*
22632 TTACCATT
1 TTA-CTTT
*
22640 TTACTCT
1 TTACTTT
**
22647 TTACTAA
1 TTACTTT
22654 TTACCATTT
1 TTA-C-TTT
22663 TTACTTT
1 TTACTTT
**
22670 TTACTGA
1 TTACTTT
22677 TTACTCTT
1 TTACT-TT
*
22685 TTACTTG
1 TTACTTT
22692 TTACT
1 TTACT
22697 GATTACCATT
Statistics
Matches: 83, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
5 3 0.04
6 3 0.04
7 53 0.64
8 20 0.24
9 4 0.05
ACGTcount: A:0.20, C:0.18, G:0.03, T:0.59
Consensus pattern (7 bp):
TTACTTT
Found at i:22602 original size:22 final size:22
Alignment explanation
Indices: 22576--22872 Score: 197
Period size: 22 Copynumber: 13.8 Consensus size: 22
22566 TCTTTACTGG
22576 TTACTTTTTACTGATTACTC-TT
1 TTACTTTTTACTGATTAC-CATT
* * **
22598 TTACTTTTCACT-CTT-TTATT
1 TTACTTTTTACTGATTACCATT
*
22618 ATT-TTTTTTACTGATTACCATT
1 -TTACTTTTTACTGATTACCATT
* *
22640 TTACTCTTTACTAATTACCATTT
1 TTACTTTTTACTGATTACCA-TT
22663 TTACTTTTTACTGATTACTC-TT
1 TTACTTTTTACTGATTAC-CATT
*
22685 TTACTTGTTACTGATTACCATT
1 TTACTTTTTACTGATTACCATT
* * *
22707 TTACTCTTTATTAATTACCATT
1 TTACTTTTTACTGATTACCATT
* * *
22729 TTAC-CTTT-CAGA-TACCTTT
1 TTACTTTTTACTGATTACCATT
*
22748 TTACTTTTTTACTGATTACCTTT
1 TTAC-TTTTTACTGATTACCATT
* *
22771 TTACCTTTTTACTGTTTA-C-TA
1 TTA-CTTTTTACTGATTACCATT
* * *
22792 TTACTTCTTACTGATT-TC-TA
1 TTACTTTTTACTGATTACCATT
* * *
22812 TTACTCTTTA-TAGATTATCAGT
1 TTACTTTTTACT-GATTACCATT
* * *
22834 TTACTCTTTACTAATTGCCATT
1 TTACTTTTTACTGATTACCATT
*
22856 TTACCTTTTACTGATTA
1 TTACTTTTTACTGATTA
22873 TATCTTTCTT
Statistics
Matches: 216, Mismatches: 41, Indels: 36
0.74 0.14 0.12
Matches are distributed among these distances:
19 11 0.05
20 36 0.17
21 22 0.10
22 104 0.48
23 41 0.19
24 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.04, T:0.55
Consensus pattern (22 bp):
TTACTTTTTACTGATTACCATT
Found at i:22696 original size:15 final size:14
Alignment explanation
Indices: 22568--22689 Score: 61
Period size: 15 Copynumber: 8.4 Consensus size: 14
22558 ACCATTTTTC
*
22568 TTTACTGGTTACTT
1 TTTACTGATTACTT
22582 TTTACTGATTACTCT
1 TTTACTGATTACT-T
*
22597 TTTACT-TTTCACTCT
1 TTTACTGATT-ACT-T
* *
22612 TTTA-TTATT-TTT
1 TTTACTGATTACTT
*
22624 TTTACTGATTACCAT
1 TTTACTGATTA-CTT
** *
22639 TTTACTCTTTACTA
1 TTTACTGATTACTT
* **
22653 ATTACCATTTTTACTT
1 TTTA-C-TGATTACTT
22669 TTTACTGATTACTCT
1 TTTACTGATTACT-T
22684 TTTACT
1 TTTACT
22690 TGTTACTGAT
Statistics
Matches: 82, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
12 5 0.06
13 5 0.06
14 25 0.30
15 37 0.45
16 10 0.12
ACGTcount: A:0.20, C:0.18, G:0.04, T:0.58
Consensus pattern (14 bp):
TTTACTGATTACTT
Found at i:22758 original size:8 final size:8
Alignment explanation
Indices: 22741--22782 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
22731 ACCTTTCAGA
22741 TACCTTTT
1 TACCTTTT
*
22749 TACTTTTT
1 TACCTTTT
**
22757 TA-CTGAT
1 TACCTTTT
22764 TACCTTTT
1 TACCTTTT
22772 TACCTTTT
1 TACCTTTT
22780 TAC
1 TAC
22783 TGTTTACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
7 4 0.15
8 23 0.85
ACGTcount: A:0.17, C:0.21, G:0.02, T:0.60
Consensus pattern (8 bp):
TACCTTTT
Found at i:22804 original size:20 final size:20
Alignment explanation
Indices: 22779--22816 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
22769 TTTTACCTTT
22779 TTACTG-TTTACTATTACTTC
1 TTACTGATTT-CTATTACTTC
22799 TTACTGATTTCTATTACT
1 TTACTGATTTCTATTACT
22817 CTTTATAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.21, C:0.18, G:0.05, T:0.55
Consensus pattern (20 bp):
TTACTGATTTCTATTACTTC
Found at i:22956 original size:34 final size:31
Alignment explanation
Indices: 22884--22983 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 31
22874 ATCTTTCTTA
* * *
22884 TTGAACTTAATCACTGATTACTTTTT-CTTA
1 TTGAACTTAATTACTGATTCCTTTTTACTTT
22914 TTGAACTTAATTACTGATTGCCTTTTTTACTTT
1 TTGAACTTAATTACTGATT-CC-TTTTTACTTT
22947 TTGGAACTTAATTACTCTGATTACCCTTTTTACTTT
1 TT-GAACTTAATTA--CTGATT--CCTTTTTACTTT
22983 T
1 T
22984 CTGACTGATC
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
30 18 0.31
31 1 0.02
32 5 0.08
33 5 0.08
34 11 0.19
36 17 0.29
37 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (31 bp):
TTGAACTTAATTACTGATTCCTTTTTACTTT
Found at i:22977 original size:36 final size:33
Alignment explanation
Indices: 22884--22983 Score: 116
Period size: 36 Copynumber: 3.0 Consensus size: 33
22874 ATCTTTCTTA
* *
22884 TTGAACTTAATCACTGATTA--CTTTTT-CTTA
1 TTGAACTTAATTACTGATTACCCTTTTTACTTT
* *
22914 TTGAACTTAATTACTGATTGCCTTTTTTACTTT
1 TTGAACTTAATTACTGATTACCCTTTTTACTTT
22947 TTGGAACTTAATTACTCTGATTACCCTTTTTACTTT
1 TT-GAACTTAATTA--CTGATTACCCTTTTTACTTT
22983 T
1 T
22984 CTGACTGATC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
30 18 0.31
32 5 0.09
33 5 0.09
34 11 0.19
36 19 0.33
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (33 bp):
TTGAACTTAATTACTGATTACCCTTTTTACTTT
Found at i:26759 original size:27 final size:27
Alignment explanation
Indices: 26729--26803 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
26719 AAGTGAACTT
* *
26729 AAAATGACCAAAATACTCCTAAATGCA
1 AAAATGACCAAAATACCCCTAAACGCA
* * **
26756 AAAATGACCAAAATGCCCCTGAACGTG
1 AAAATGACCAAAATACCCCTAAACGCA
*
26783 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATACCCCTA
26804 TGTGACCCTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.47, C:0.25, G:0.12, T:0.16
Consensus pattern (27 bp):
AAAATGACCAAAATACCCCTAAACGCA
Found at i:31220 original size:12 final size:12
Alignment explanation
Indices: 31200--31239 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
31190 CATGACCGGC
31200 CAACGCATGGAG
1 CAACGCATGGAG
*
31212 CATCGCATGGAG
1 CAACGCATGGAG
*
31224 CAACGCATTGAG
1 CAACGCATGGAG
31236 CAAC
1 CAAC
31240 CGGCCACAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.12
Consensus pattern (12 bp):
CAACGCATGGAG
Found at i:31261 original size:42 final size:42
Alignment explanation
Indices: 31215--31297 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
31205 CATGGAGCAT
*
31215 CGCAT-GGAGCAACGCATTGAG-CAACCGGCCACAACCGGCCAA
1 CGCATGGGA-CAACGCA-CGAGCCAACCGGCCACAACCGGCCAA
* * *
31257 CGCATGGGACATCGCACGGGCCATCCGGCCACAACCGGCCA
1 CGCATGGGACAACGCACGAGCCAACCGGCCACAACCGGCCA
31298 TTTGATCCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 2 0.06
42 30 0.86
43 3 0.09
ACGTcount: A:0.27, C:0.39, G:0.28, T:0.07
Consensus pattern (42 bp):
CGCATGGGACAACGCACGAGCCAACCGGCCACAACCGGCCAA
Done.