Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010155.1 Corchorus capsularis cultivar CVL-1 contig10176, 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: 38599
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1708 original size:21 final size:22
Alignment explanation
Indices: 1683--1732 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
1673 TTGGTTAACG
1683 TATAACATTTT-TAATTAAGTA-
1 TATAAC-TTTTATAATTAAGTAC
1704 TATAACTTTTCAATAATTAAGTAC
1 TATAACTTTT--ATAATTAAGTAC
1728 TATAA
1 TATAA
1733 ATTAAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 6 0.24
23 10 0.40
24 5 0.20
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (22 bp):
TATAACTTTTATAATTAAGTAC
Found at i:4167 original size:90 final size:90
Alignment explanation
Indices: 4014--4194 Score: 344
Period size: 90 Copynumber: 2.0 Consensus size: 90
4004 CCTATTTAAC
4014 ATGTTGTATTTCTCTCAACTCTTTCAAATTCCCACTTTCATAATATATACTAAAAAACTTCTATG
1 ATGTTGTATTTCTCTCAACTCTTTCAAATTCCCACTTTCATAATATATACTAAAAAACTTCTATG
4079 TTATTCTAATCATATTTCTTGGGTA
66 TTATTCTAATCATATTTCTTGGGTA
*
4104 ATGTTGTATTTCTCTCAACTCTTTCAAATTCCTACTTTCATAATATATACTAAAAAACTTCTATG
1 ATGTTGTATTTCTCTCAACTCTTTCAAATTCCCACTTTCATAATATATACTAAAAAACTTCTATG
*
4169 TTATTCTTATCATATTTCTTGGGTA
66 TTATTCTAATCATATTTCTTGGGTA
4194 A
1 A
4195 AGAAAGATGG
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.45
Consensus pattern (90 bp):
ATGTTGTATTTCTCTCAACTCTTTCAAATTCCCACTTTCATAATATATACTAAAAAACTTCTATG
TTATTCTAATCATATTTCTTGGGTA
Found at i:5085 original size:7 final size:7
Alignment explanation
Indices: 5073--5280 Score: 81
Period size: 7 Copynumber: 31.3 Consensus size: 7
5063 CCTTTGATGA
5073 TTACTCT
1 TTACTCT
5080 TTACTC-
1 TTACTCT
5086 -TACTCT
1 TTACTCT
*
5092 TTACTTT
1 TTACTCT
5099 TTAC-CAT
1 TTACTC-T
*
5106 TT-TTCT
1 TTACTCT
**
5112 TTACTGA
1 TTACTCT
5119 TTACTCT
1 TTACTCT
5126 TT--TCT
1 TTACTCT
5131 TTACTCTT
1 TTACTC-T
5139 TTACTCT
1 TTACTCT
*
5146 TTGGCAT-T
1 TT-AC-TCT
5154 TT--TCT
1 TTACTCT
**
5159 TTACTGA
1 TTACTCT
5166 TTACTCT
1 TTACTCT
5173 TTA--CT
1 TTACTCT
*
5178 TTGCTCT
1 TTACTCT
*
5185 TTACTATT
1 TTACT-CT
5193 TTACT-T
1 TTACTCT
**
5199 TTTTTCT
1 TTACTCT
**
5206 TTACTGA
1 TTACTCT
5213 TTACTCT
1 TTACTCT
5220 TTA--CT
1 TTACTCT
5225 TTACTCT
1 TTACTCT
5232 TTACTCT
1 TTACTCT
5239 TTA-TCAT
1 TTACTC-T
*
5246 TT--TTT
1 TTACTCT
**
5251 TTACTAA
1 TTACTCT
5258 TTACTCT
1 TTACTCT
**
5265 TTACTGA
1 TTACTCT
5272 TTACTCT
1 TTACTCT
5279 TT
1 TT
5281 TACTTTTTAG
Statistics
Matches: 146, Mismatches: 33, Indels: 44
0.65 0.15 0.20
Matches are distributed among these distances:
4 1 0.01
5 25 0.17
6 10 0.07
7 92 0.63
8 17 0.12
9 1 0.01
ACGTcount: A:0.16, C:0.21, G:0.03, T:0.59
Consensus pattern (7 bp):
TTACTCT
Found at i:5094 original size:47 final size:46
Alignment explanation
Indices: 5043--5289 Score: 275
Period size: 47 Copynumber: 5.3 Consensus size: 46
5033 TTACTCTTTA
* * * *
5043 CTTTACTCTTCATTATTTTACCTTTGA-TGATTACTCTTTACTCTACT
1 CTTTACTCTTTATCATTTT-TCTTT-ACTGATTACTCTTTACTTTACT
* * *
5090 CTTTACTTTTTACCATTTTTCTTTACTGATTACTCTTTTCTTTACT
1 CTTTACTCTTTATCATTTTTCTTTACTGATTACTCTTTACTTTACT
** *
5136 CTTTTACTCTTTGGCATTTTTCTTTACTGATTACTCTTTACTTTGCT
1 C-TTTACTCTTTATCATTTTTCTTTACTGATTACTCTTTACTTTACT
* *
5183 CTTTACTATTT-TACTTTTTTTCTTTACTGATTACTCTTTACTTTACT
1 CTTTACTCTTTAT-C-ATTTTTCTTTACTGATTACTCTTTACTTTACT
*
5230 CTTTACTCTTTATCATTTTT-TTTACTAATTACTCTTTACTGATTACT
1 CTTTACTCTTTATCATTTTTCTTTACTGATTACTCTTTACT--TTACT
*
5277 CTTTTACTTTTTA
1 C-TTTACTCTTTA
5290 GTGATTGCCT
Statistics
Matches: 172, Mismatches: 20, Indels: 15
0.83 0.10 0.07
Matches are distributed among these distances:
45 20 0.12
46 38 0.22
47 103 0.60
48 11 0.06
ACGTcount: A:0.17, C:0.21, G:0.04, T:0.59
Consensus pattern (46 bp):
CTTTACTCTTTATCATTTTTCTTTACTGATTACTCTTTACTTTACT
Found at i:5114 original size:20 final size:20
Alignment explanation
Indices: 5089--5147 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
5079 TTTACTCTAC
5089 TCTTTACTTTTTACCAT-TTT
1 TCTTTACTTTTTACC-TCTTT
**
5109 TCTTTACTGATTA-CTCTTT
1 TCTTTACTTTTTACCTCTTT
5128 TCTTTACTCTTTTA-CTCTTT
1 TCTTTACT-TTTTACCTCTTT
5148 GGCATTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.03
19 12 0.36
20 20 0.61
ACGTcount: A:0.14, C:0.22, G:0.02, T:0.63
Consensus pattern (20 bp):
TCTTTACTTTTTACCTCTTT
Found at i:5171 original size:133 final size:138
Alignment explanation
Indices: 4990--5284 Score: 345
Period size: 140 Copynumber: 2.2 Consensus size: 138
4980 ATCATTTTTC
* * ** *
4990 CTTTACTGATTATTC-TTTACGCTTTACCATTCTTCTTTCCCGATTACTCTTTACTTTACTC-TT
1 CTTTACT-ATTACTCTTTTACTCTTTGGCATTCTTCTTTACCGATTACTCTTTACTTTACTCTTT
*
5053 -C-A-TTA-TTTTACCTTTGA-TGATTACTCTTTACTCTACTCTTTACTTTTTACCATTTTTCTT
65 ACTATTTACTTTTACCTTT-ACTGATTACTCTTTACTCTACTCTTTACTCTTTACCATTTTT-TT
*
5113 TACTGATTACT
128 TACTAATTACT
* * * *
5124 CTTTTCT-TTACTCTTTTACTCTTTGGCATTTTTCTTTACTGATTACTCTTTACTTTGCTCTTTA
1 CTTTACTATTACTCTTTTACTCTTTGGCATTCTTCTTTACCGATTACTCTTTACTTTACTCTTTA
** * *
5188 CTATTTTACTTTTTTTCTTTACTGATTACTCTTTACTTTACTCTTTACTCTTTATCATTTTTTTT
66 CTA-TTTAC-TTTTACCTTTACTGATTACTCTTTACTCTACTCTTTACTCTTTACCATTTTTTTT
5253 ACTAATTACT
129 ACTAATTACT
5263 CTTTACTGATTACTCTTTTACT
1 CTTTACT-ATTACTCTTTTACT
5285 TTTTAGTGAT
Statistics
Matches: 134, Mismatches: 16, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
132 5 0.04
133 39 0.29
134 8 0.06
135 1 0.01
136 1 0.01
138 3 0.02
139 19 0.14
140 45 0.34
141 13 0.10
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.57
Consensus pattern (138 bp):
CTTTACTATTACTCTTTTACTCTTTGGCATTCTTCTTTACCGATTACTCTTTACTTTACTCTTTA
CTATTTACTTTTACCTTTACTGATTACTCTTTACTCTACTCTTTACTCTTTACCATTTTTTTTAC
TAATTACT
Found at i:5230 original size:12 final size:12
Alignment explanation
Indices: 5156--5236 Score: 62
Period size: 12 Copynumber: 6.7 Consensus size: 12
5146 TTGGCATTTT
5156 TCTTTACTGATTAC
1 TCTTTACT--TTAC
*
5170 TCTTTACTTTGC
1 TCTTTACTTTAC
5182 TCTTTAC--TA-
1 TCTTTACTTTAC
**
5191 T-TTTACTTTTTT
1 TCTTTAC-TTTAC
5203 TCTTTACTGATTAC
1 TCTTTACT--TTAC
5217 TCTTTACTTTAC
1 TCTTTACTTTAC
5229 TCTTTACT
1 TCTTTACT
5237 CTTTATCATT
Statistics
Matches: 55, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
8 5 0.09
9 1 0.02
10 1 0.02
11 1 0.02
12 24 0.44
13 5 0.09
14 18 0.33
ACGTcount: A:0.16, C:0.21, G:0.04, T:0.59
Consensus pattern (12 bp):
TCTTTACTTTAC
Found at i:5309 original size:21 final size:21
Alignment explanation
Indices: 5258--5553 Score: 223
Period size: 21 Copynumber: 13.8 Consensus size: 21
5248 TTTTTACTAA
5258 TTACTCTTTACTGATTA-CTCTT
1 TTACT-TTTACTGATTACCT-TT
* *
5280 TTACTTTTTAGTGATTGCCTTT
1 TTAC-TTTTACTGATTACCTTT
*
5302 TTGCTTTTTACTGATTACC-TT
1 TTAC-TTTTACTGATTACCTTT
*
5323 TTACTTCTTACTGATTAGCTTT
1 TTACTT-TTACTGATTACCTTT
5345 TTACTCTTTACTGATTACCTTT
1 TTACT-TTTACTGATTACCTTT
*
5367 TTACTCTTACTGATTACC-TT
1 TTACTTTTACTGATTACCTTT
*
5387 TTACTTCTTACTGATT-GCTATT
1 TTACTT-TTACTGATTACCT-TT
* *
5409 TTACTCTTACTGATTA-CTAT
1 TTACTTTTACTGATTACCTTT
* * *
5429 TTACTTTTTGCCGATTA-TTATT
1 TTAC-TTTTACTGATTACCT-TT
* *
5451 TTACTCTTACTAATTACC-TT
1 TTACTTTTACTGATTACCTTT
*
5471 TTACTTTTTACTGACTA-CTATT
1 TTAC-TTTTACTGATTACCT-TT
* ** *
5493 TTACTCTTGTTGATTACCTTC
1 TTACTTTTACTGATTACCTTT
5514 TTACTTTCTACTGATTA-CTATT
1 TTACTTT-TACTGATTACCT-TT
5536 TTACTCTTTTACTGATTA
1 TTA--CTTTTACTGATTA
5554 TTTCTGCTCC
Statistics
Matches: 219, Mismatches: 35, Indels: 39
0.75 0.12 0.13
Matches are distributed among these distances:
20 22 0.10
21 92 0.42
22 88 0.40
23 13 0.06
24 4 0.02
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.54
Consensus pattern (21 bp):
TTACTTTTACTGATTACCTTT
Found at i:5338 original size:43 final size:43
Alignment explanation
Indices: 5258--5553 Score: 323
Period size: 42 Copynumber: 6.9 Consensus size: 43
5248 TTTTTACTAA
* * * * *
5258 TTACTCTTTACTGATTACTCTTTTACTTTTTAGTGATTGCCTTT
1 TTACTTTTTACTGATTACTATTTTAC-TCTTACTGATTACCTTT
* * *
5302 TTGCTTTTTACTGATTAC-CTTTTACTTCTTACTGATTAGCTTT
1 TTACTTTTTACTGATTACTATTTTAC-TCTTACTGATTACCTTT
*
5345 TTACTCTTTACTGATTACCT-TTTTACTCTTACTGATTACC-TT
1 TTACTTTTTACTGATTA-CTATTTTACTCTTACTGATTACCTTT
* * *
5387 TTACTTCTTACTGATTGCTATTTTACTCTTACTGATTA-CTAT
1 TTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTT
* * * *
5429 TTACTTTTTGCCGATTATTATTTTACTCTTACTAATTACC-TT
1 TTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTT
* ** *
5471 TTACTTTTTACTGACTACTATTTTACTCTTGTTGATTACCTTC
1 TTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTT
*
5514 TTACTTTCTACTGATTACTATTTTACTCTTTTACTGATTA
1 TTACTTTTTACTGATTACTATTTTACTC--TTACTGATTA
5554 TTTCTGCTCC
Statistics
Matches: 212, Mismatches: 32, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.01
42 101 0.48
43 77 0.36
44 23 0.11
45 8 0.04
ACGTcount: A:0.19, C:0.20, G:0.07, T:0.54
Consensus pattern (43 bp):
TTACTTTTTACTGATTACTATTTTACTCTTACTGATTACCTTT
Found at i:7065 original size:27 final size:27
Alignment explanation
Indices: 7034--7085 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
7024 CTCTTTCTAT
7034 TGTCTTTTTGAAAACTCTCCTCCTTAC
1 TGTCTTTTTGAAAACTCTCCTCCTTAC
7061 TGTCTTTTTGAAAACTCTCCTCCTT
1 TGTCTTTTTGAAAACTCTCCTCCTT
7086 TTTGCTATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.17, C:0.29, G:0.08, T:0.46
Consensus pattern (27 bp):
TGTCTTTTTGAAAACTCTCCTCCTTAC
Found at i:7809 original size:24 final size:22
Alignment explanation
Indices: 7767--7810 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
7757 GCTTGCTGTA
7767 ATTTACTTTGTGAATTGATTCT
1 ATTTACTTTGTGAATTGATTCT
7789 ATTTAACTGTTGT-AATGTGATT
1 ATTT-ACT-TTGTGAAT-TGATT
7811 TACTGTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 9 0.47
ACGTcount: A:0.25, C:0.07, G:0.16, T:0.52
Consensus pattern (22 bp):
ATTTACTTTGTGAATTGATTCT
Found at i:7817 original size:18 final size:19
Alignment explanation
Indices: 7789--7828 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
7779 AATTGATTCT
* *
7789 ATTTAACTGTTGTAATGTG
1 ATTTAACTGTTGAAATGAG
7808 ATTT-ACTGTTGAAATGAG
1 ATTTAACTGTTGAAATGAG
7826 ATT
1 ATT
7829 CTTGCGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (19 bp):
ATTTAACTGTTGAAATGAG
Found at i:9212 original size:50 final size:50
Alignment explanation
Indices: 9140--9472 Score: 344
Period size: 50 Copynumber: 6.5 Consensus size: 50
9130 GAATCAACTG
*
9140 CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGATTATC
* * * ** * * *
9190 CTTTGAAATGTCTTCCAATTCCATCTTTAGTGGATCGTCTTCCGATCAAC
1 CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGATTATC
* * *
9240 CTTCGAATTGTCTTCCAATTCCATCCATCTTGAAAGGACCGTCTTCCGAATCAACTT
1 CTTCGAATTGTCTTCCAA-T---TCCATCTTAAAAGGACCGTCTTCCG-AT-TA-TC
*
9297 CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGCTTATC
1 CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGATTATC
* * * * *
9347 CTTCGAACTGTCTTCCAATTCAATC-TAAAAGGATCATCTTCCGATTACC
1 CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGATTATC
** * * * * * *
9396 CTTTTAACTGTCTTCCAATTCAATCTTAAGAGAACCGTCTTCCGATCAAC
1 CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGATTATC
* *
9446 TTTCGAATTGTCTTCCAAATCCATCTT
1 CTTCGAATTGTCTTCCAATTCCATCTT
9473 GAGAAAATCT
Statistics
Matches: 233, Mismatches: 42, Indels: 16
0.80 0.14 0.05
Matches are distributed among these distances:
49 43 0.18
50 120 0.52
51 2 0.01
52 1 0.00
53 24 0.10
54 21 0.09
55 2 0.01
56 2 0.01
57 18 0.08
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (50 bp):
CTTCGAATTGTCTTCCAATTCCATCTTAAAAGGACCGTCTTCCGATTATC
Found at i:10099 original size:67 final size:67
Alignment explanation
Indices: 10002--10370 Score: 248
Period size: 67 Copynumber: 5.6 Consensus size: 67
9992 TCATCTTCTG
* * * * * * ** *
10002 ATCAACTTCTTAAAATTGTTTCTTGGAAACCGACTTCCGGTGTATTTCTTAATGAGATTGTCTTC
1 ATCAACTTCTAAAAACTCTTTCTAGCAAACCGACTTCCGGTCTATTTCTTAACAAGATCGTCTTC
10067 CA
66 CA
** * * * *
10069 ATCAACTTCTGCAAACTCTTTCTACCAAACCGTCTTCCGGTCAATTTCTGAACAAGATCGTCTTC
1 ATCAACTTCTAAAAACTCTTTCTAGCAAACCGACTTCCGGTCTATTTCTTAACAAGATCGTCTTC
*
10134 CG
66 CA
* * * * * *
10136 ATCAATTTCTAAAAACTC-TT-GA-TAAACC-ATCTTCTGGTCTACTTCTTGACAAGATCGTCTT
1 ATCAACTTCTAAAAACTCTTTCTAGCAAACCGA-CTTCCGGTCTATTTCTTAACAAGATCGTCTT
*
10197 CCG
65 CCA
* * * * ** * *** *
10200 ATCAACTTCTAAAAACTCTTTTTTGGAAACCGTCTTTTGGTGTATTTCTTAATGGGATTGTCTTC
1 ATCAACTTCTAAAAACTCTTTCTAGCAAACCGACTTCCGGTCTATTTCTTAACAAGATCGTCTTC
10265 CA
66 CA
* * * * * *
10267 ATCAACTTCTGAAAATTCTTTCTAGCAAACTGTCCTCCGGT-TAATTTCTTACCAAGATCGTCTT
1 ATCAACTTCTAAAAACTCTTTCTAGCAAACCGACTTCCGGTCT-ATTTCTTAACAAGATCGTCTT
**
10331 CTG
65 CCA
* * *
10334 ATTAAC-TCTTAAAAACTTTTTCTGAG-AAACCGTCTTC
1 ATCAACTTC-TAAAAACTCTTTCT-AGCAAACCGACTTC
10371 TGGATTACCT
Statistics
Matches: 232, Mismatches: 62, Indels: 16
0.75 0.20 0.05
Matches are distributed among these distances:
64 51 0.22
65 3 0.01
66 5 0.02
67 171 0.74
68 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (67 bp):
ATCAACTTCTAAAAACTCTTTCTAGCAAACCGACTTCCGGTCTATTTCTTAACAAGATCGTCTTC
CA
Found at i:10349 original size:198 final size:198
Alignment explanation
Indices: 9989--10350 Score: 519
Period size: 198 Copynumber: 1.8 Consensus size: 198
9979 ATTGTCTTCG
* * * *
9989 AGATCATCTTCTGATCAACTTCTTAAAATTGTTTCTTGGAAACCGACTTCCGGTGTATTTCTTAA
1 AGATCATCTTCCGATCAACTTCTAAAAACTCTTTCTTGGAAACCGACTTCCGGTGTATTTCTTAA
* *
10054 TGAGATTGTCTTCCAATCAACTTCTGCAAACTCTTTCTACCAAACCGTCTTCCGGTCAATTTCTG
66 TGAGATTGTCTTCCAATCAACTTCTGAAAACTCTTTCTACCAAACCGTCCTCCGGTCAATTTCTG
*
10119 AACAAGATCGTCTTCCGATCAATTTCTAAAAACTCTTGATAAACCATCTTCTGGTCTACTTCTTG
131 AACAAGATCGTCTTCCGATCAATCTCTAAAAACTCTTGATAAACCATCTTCTGGTCTACTTCTTG
10184 ACA
196 ACA
* * * **
10187 AGATCGTCTTCCGATCAACTTCTAAAAACTCTTTTTTGGAAACCGTCTTTTGGTGTATTTCTTAA
1 AGATCATCTTCCGATCAACTTCTAAAAACTCTTTCTTGGAAACCGACTTCCGGTGTATTTCTTAA
* * * * * *
10252 TGGGATTGTCTTCCAATCAACTTCTGAAAATTCTTTCTAGCAAACTGTCCTCCGGTTAATTTCTT
66 TGAGATTGTCTTCCAATCAACTTCTGAAAACTCTTTCTACCAAACCGTCCTCCGGTCAATTTCTG
* * *
10317 ACCAAGATCGTCTTCTGATTAA-CTCTTAAAAACT
131 AACAAGATCGTCTTCCGATCAATCTC-TAAAAACT
10351 TTTTCTGAGA
Statistics
Matches: 142, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
197 2 0.01
198 140 0.99
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (198 bp):
AGATCATCTTCCGATCAACTTCTAAAAACTCTTTCTTGGAAACCGACTTCCGGTGTATTTCTTAA
TGAGATTGTCTTCCAATCAACTTCTGAAAACTCTTTCTACCAAACCGTCCTCCGGTCAATTTCTG
AACAAGATCGTCTTCCGATCAATCTCTAAAAACTCTTGATAAACCATCTTCTGGTCTACTTCTTG
ACA
Found at i:11627 original size:7 final size:7
Alignment explanation
Indices: 11615--11662 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
11605 ACCCTAGAGC
11615 TTTTCTT
1 TTTTCTT
11622 TTTTCTT
1 TTTTCTT
11629 TCTTTC-T
1 T-TTTCTT
*
11636 TCTTCTT
1 TTTTCTT
11643 TTTTCTT
1 TTTTCTT
*
11650 TTTATTTT
1 TTT-TCTT
11658 TTTTC
1 TTTTC
11663 CAATTATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 3 0.09
7 21 0.62
8 10 0.29
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:12481 original size:15 final size:15
Alignment explanation
Indices: 12458--12493 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
12448 GGTGGACAAA
*
12458 ATAACCAGAGGTATG
1 ATAATCAGAGGTATG
12473 ATAATCAGAGGTATG
1 ATAATCAGAGGTATG
12488 ATAATC
1 ATAATC
12494 GTGATTCCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (15 bp):
ATAATCAGAGGTATG
Found at i:16061 original size:2 final size:2
Alignment explanation
Indices: 16054--16085 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
16044 ATGATAACAG
16054 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16086 GCCTGTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21260 original size:23 final size:23
Alignment explanation
Indices: 21229--21273 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
21219 ATTGGTTTGC
*
21229 AGAGGCCGAGCGAGAGTGCTCAT
1 AGAGACCGAGCGAGAGTGCTCAT
21252 AGAGACCGAGCGAGAGTGCTCA
1 AGAGACCGAGCGAGAGTGCTCA
21274 AGATTGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.22, G:0.38, T:0.11
Consensus pattern (23 bp):
AGAGACCGAGCGAGAGTGCTCAT
Found at i:22014 original size:2 final size:2
Alignment explanation
Indices: 22007--22035 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21997 TTTGCTAGTA
22007 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 A
22036 ATAACTACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24579 original size:15 final size:14
Alignment explanation
Indices: 24531--24582 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
24521 ATGATTTTCA
*
24531 ATTATTTATTAAATT
1 ATTATTT-TTAATTT
* *
24546 ATTAATTATACATTT
1 ATTATTTTTA-ATTT
24561 ATTATTTTTAATTT
1 ATTATTTTTAATTT
24575 AATTATTT
1 -ATTATTT
24583 ATTTTTATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 6 0.20
15 24 0.80
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTTTTAATTT
Found at i:27064 original size:11 final size:11
Alignment explanation
Indices: 27048--27073 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
27038 TGAGAAAATG
27048 AAATCATTAAA
1 AAATCATTAAA
27059 AAATCATTAAA
1 AAATCATTAAA
27070 AAAT
1 AAAT
27074 TTTGTTACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATCATTAAA
Found at i:33875 original size:66 final size:66
Alignment explanation
Indices: 33779--33916 Score: 181
Period size: 66 Copynumber: 2.1 Consensus size: 66
33769 ATTACTAGTA
**
33779 GGGG-TTTGCCTAATCATACTTTAAAGTTTCACCATACATGATTTGGGGTTTGACCATTACGCTT
1 GGGGTTTTGCCTAATCATACTTTAAAGTTTCACCATACATGATTTAAGGTTTGACCATTACGCTT
33843 T
66 T
* ** * *
33844 GGGGTTTTGCCTAATTATGTTTTACAA-TTTCACTATACATGATTTAAGGTTTGACTATTACGCT
1 GGGGTTTTGCCTAATCATACTTTA-AAGTTTCACCATACATGATTTAAGGTTTGACCATTACGCT
33908 TT
65 TT
*
33910 AGGGTTT
1 GGGGTTT
33917 GATCCCATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
65 4 0.06
66 57 0.90
67 2 0.03
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (66 bp):
GGGGTTTTGCCTAATCATACTTTAAAGTTTCACCATACATGATTTAAGGTTTGACCATTACGCTT
T
Found at i:34057 original size:87 final size:85
Alignment explanation
Indices: 33849--34365 Score: 274
Period size: 87 Copynumber: 6.0 Consensus size: 85
33839 GCTTTGGGGT
* * * * * *
33849 TTTGCCTAATTATGTTTTACAATTTC-ACTATACATGATTTAAGGTTTGACTATTACGCTTTAGG
1 TTTGCCTAATCATGCTTTACAATTTCAAC-ATACATGATTTTA-GTTTGACCATTAAGATTT-GG
* *
33913 GTTTGATCCCATTAGTAGTACTGG
63 GGTTGATCCCATTA-CAGTACTGG
* * * * * **
33937 CTTGCCTATTGATGCTTTACATTTTGATTATACATGATTTCTAGTTTGACCATTAAGATTTGGGG
1 TTTGCCTAATCATGCTTTACAATTTCAACATACATGATTT-TAGTTTGACCATTAAGATTTGGGG
*
34002 TTGATCCCATTACA-TCCCTGGG
65 TTGATCCCATTACAGT-ACT-GG
** * *
34024 TTTGCCTAATCATGCTTTACAATTTCAACATACATGATTTGGGGTTTTACCATTACA-CTTTGCG
1 TTTGCCTAATCATGCTTTACAATTTCAACATACATGATTT-TAGTTTGACCATTA-AGATTTG-G
** * **
34088 ATTTGATCTCATTACTAGTAGGGG
63 GGTTGATCCCATTAC-AGTACTGG
** * * * * *
34112 TTTAG-GGAATCATGCTTTA-AAGTTCACCGTACATGATTTTGGGTTTGACCATTATGATTTGGG
1 TTT-GCCTAATCATGCTTTACAATTTCAACATACATGATTTT-AGTTTGACCATTAAGATTTGGG
* *
34175 CTTCGATTCCATTACTAGTACTGG
64 GTT-GATCCCATTAC-AGTACTGG
* *
34199 TTTGCCTATTCATG-----C--TTT--ACATACATGATTTCTAGTTTGACCACTAAGATTTGGGG
1 TTTGCCTAATCATGCTTTACAATTTCAACATACATGATTT-TAGTTTGACCATTAAGATTTGGGG
*
34255 TTTGA-CCCTATTAATTACA-TCCTTAGG
65 -TTGATCCC-----ATTACAGTAC-T-GG
* ** * ** * *
34282 TTTGTCTAATCATATTTTACAATTTCACCATACATGATTTGGGGTTTGACCATTACGCTTTGGGG
1 TTTGCCTAATCATGCTTTACAATTTCAACATACATGATTT-TAGTTTGACCATTAAGATTTGGGG
34347 TTTGATCCCATTACTAGTA
65 -TTGATCCCATTAC-AGTA
34366 GGCATTTAAG
Statistics
Matches: 323, Mismatches: 71, Indels: 68
0.70 0.15 0.15
Matches are distributed among these distances:
78 2 0.01
79 32 0.10
80 3 0.01
81 4 0.01
82 2 0.01
83 18 0.06
85 1 0.00
86 7 0.02
87 123 0.38
88 83 0.26
89 4 0.01
90 5 0.02
92 36 0.11
93 3 0.01
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.41
Consensus pattern (85 bp):
TTTGCCTAATCATGCTTTACAATTTCAACATACATGATTTTAGTTTGACCATTAAGATTTGGGGT
TGATCCCATTACAGTACTGG
Found at i:34344 original size:21 final size:22
Alignment explanation
Indices: 34319--34360 Score: 68
Period size: 21 Copynumber: 1.9 Consensus size: 22
34309 CCATACATGA
34319 TTTGGGGTTTGA-CCATTACGC
1 TTTGGGGTTTGACCCATTACGC
34340 TTTGGGGTTTGATCCCATTAC
1 TTTGGGGTTTGA-CCCATTAC
34361 TAGTAGGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40
Consensus pattern (22 bp):
TTTGGGGTTTGACCCATTACGC
Found at i:36036 original size:31 final size:31
Alignment explanation
Indices: 36000--36067 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
35990 TTTTGTGCAC
*
36000 GTGGCATGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGCCACTTTTTGAAACAT
* **
36031 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGCCACTTTTTGAAACAT
36062 GTGGCA
1 GTGGCA
36068 CGACTTTTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (31 bp):
GTGGCATGCCACGTGCCACTTTTTGAAACAT
Found at i:36108 original size:31 final size:31
Alignment explanation
Indices: 36070--36157 Score: 167
Period size: 31 Copynumber: 2.8 Consensus size: 31
36060 ATGTGGCACG
36070 ACTTTTTGGTACATGTGGCGTGCCACATGTC
1 ACTTTTTGGTACATGTGGCGTGCCACATGTC
*
36101 ACTTTTTGGTACATATGGCGTGCCACATGTC
1 ACTTTTTGGTACATGTGGCGTGCCACATGTC
36132 ACTTTTTGGTACATGTGGCGTGCCAC
1 ACTTTTTGGTACATGTGGCGTGCCAC
36158 GTCAGACACC
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (31 bp):
ACTTTTTGGTACATGTGGCGTGCCACATGTC
Found at i:37645 original size:16 final size:16
Alignment explanation
Indices: 37624--37759 Score: 152
Period size: 16 Copynumber: 8.6 Consensus size: 16
37614 GAGAGTGTGA
37624 GTGAGTATCT-CACCAG
1 GTGAGTAT-TGCACCAG
*
37640 GTGAGTATTACACCAG
1 GTGAGTATTGCACCAG
* **
37656 GTGAGTATTGTACTGG
1 GTGAGTATTGCACCAG
* **
37672 GTGAGTATTGTACTGG
1 GTGAGTATTGCACCAG
37688 GTGAGTATCT-CACCAG
1 GTGAGTAT-TGCACCAG
37704 GTGAGTATTGCACCAG
1 GTGAGTATTGCACCAG
*
37720 GTGAGTATTGTACCAG
1 GTGAGTATTGCACCAG
*
37736 GTGAGTATT-TACCAG
1 GTGAGTATTGCACCAG
37751 GTGAGTATT
1 GTGAGTATT
37760 TGTTTTGGGT
Statistics
Matches: 109, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
15 17 0.16
16 91 0.83
17 1 0.01
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (16 bp):
GTGAGTATTGCACCAG
Found at i:37695 original size:48 final size:47
Alignment explanation
Indices: 37635--37759 Score: 178
Period size: 48 Copynumber: 2.6 Consensus size: 47
37625 TGAGTATCTC
* **
37635 ACCAGGTGAGTATTACACCAGGTGAGTATTGTACTGGGTGAGTATTGT
1 ACCAGGTGAGTATT-CACCAGGTGAGTATTGCACCAGGTGAGTATTGT
**
37683 ACTGGGTGAGTATCTCACCAGGTGAGTATTGCACCAGGTGAGTATTGT
1 ACCAGGTGAGTAT-TCACCAGGTGAGTATTGCACCAGGTGAGTATTGT
*
37731 ACCAGGTGAGTATTTACCAGGTGAGTATT
1 ACCAGGTGAGTATTCACCAGGTGAGTATT
37760 TGTTTTGGGT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 15 0.22
48 52 0.76
49 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.30, T:0.30
Consensus pattern (47 bp):
ACCAGGTGAGTATTCACCAGGTGAGTATTGCACCAGGTGAGTATTGT
Found at i:37701 original size:64 final size:63
Alignment explanation
Indices: 37624--37758 Score: 216
Period size: 64 Copynumber: 2.1 Consensus size: 63
37614 GAGAGTGTGA
** **
37624 GTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTGTACTGGGTGAGTATTGTACTGG
1 GTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTGTACCAGGTGAGTATT-TACCAG
*
37688 GTGAGTATCTCACCAGGTGAGTATTGCACCAGGTGAGTATTGTACCAGGTGAGTATTTACCAG
1 GTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTGTACCAGGTGAGTATTTACCAG
37751 GTGAGTAT
1 GTGAGTAT
37759 TTGTTTTGGG
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
63 12 0.18
64 54 0.82
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.30
Consensus pattern (63 bp):
GTGAGTATCTCACCAGGTGAGTATTACACCAGGTGAGTATTGTACCAGGTGAGTATTTACCAG
Found at i:38250 original size:46 final size:46
Alignment explanation
Indices: 38161--38251 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
38151 TTGACTTCTT
* * *
38161 GGAAAGCGCTCCACGCAGGAGTTAGGTGAGTCTCCATGTAAGAGCA
1 GGAAAGCGCTCCACGCAAGAGTTAGGTGAGTCTCCACGCAAGAGCA
* * * *
38207 GGAAAGTGCTCCGCGCAAGAGTTGGGTGAGTCTCCCCGCAAGAGC
1 GGAAAGCGCTCCACGCAAGAGTTAGGTGAGTCTCCACGCAAGAGC
38252 TGGGGAACAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.25, C:0.24, G:0.34, T:0.16
Consensus pattern (46 bp):
GGAAAGCGCTCCACGCAAGAGTTAGGTGAGTCTCCACGCAAGAGCA
Done.