Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018388.1 Corchorus olitorius cultivar O-4 contig18421, 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: 51112
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1179 original size:72 final size:72
Alignment explanation
Indices: 1093--1235 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 72
1083 GGTGCCTCTT
*
1093 TTTGTTATTTGAGTTAATTTAAAAGTTAATTTGGTGATTGAGGCATGTAAATGTTCTAAATTTAA
1 TTTGTTATTTGAGTTAAATTAAAAGTTAATTTGGTGATTGAGGCATGTAAATGTTCTAAATTTAA
1158 CTAATTG
66 CTAATTG
* * *
1165 TTTGTTATTTGAGTTAAATTAAAAGTTGATTTGGTGATTGATGCATGTAAATGTTCTAAATTTAT
1 TTTGTTATTTGAGTTAAATTAAAAGTTAATTTGGTGATTGAGGCATGTAAATGTTCTAAATTTAA
1230 CTAATT
66 CTAATT
1236 TATGAATACA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.31, C:0.04, G:0.17, T:0.47
Consensus pattern (72 bp):
TTTGTTATTTGAGTTAAATTAAAAGTTAATTTGGTGATTGAGGCATGTAAATGTTCTAAATTTAA
CTAATTG
Found at i:2738 original size:40 final size:40
Alignment explanation
Indices: 2665--2968 Score: 463
Period size: 39 Copynumber: 7.7 Consensus size: 40
2655 CCAAATTCCT
*
2665 AGTTTGCCCTTCCCCACC-GAAGGTGTTGTTTAAATACTC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
2704 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
*
2744 AGTTTGCCCTT-CCCACCGGAAGGTGTTGTCTAAATACCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
2783 AGTTTGCCCTT-CCCACCGGAAGGTGTTGTTTAAATACCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
* *
2822 AATTTGCCCTT-CCCACCGGAAGGTGTTGTTTAAATACTC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
* *
2861 GGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATACCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
* * *
2901 AGTTTGGCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCC
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
* ** *
2941 AGTTTGCCTTTCCCTGCCGGAAAGTGTT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTT
2969 CTCAGTTTGC
Statistics
Matches: 246, Mismatches: 17, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
39 129 0.52
40 117 0.48
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (40 bp):
AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCC
Found at i:2817 original size:118 final size:120
Alignment explanation
Indices: 2665--2968 Score: 481
Period size: 118 Copynumber: 2.6 Consensus size: 120
2655 CCAAATTCCT
*
2665 AGTTTGCCCTTCCCCACC-GAAGGTGTTGTTTAAATACTCAGTTTGCCCTTCCCCACCGGAAGGT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGT
2729 GTTGTTTAAATACCCAGTTTGCCCTT-CCCACCGGAAGGTGTTGTCTAAATACCC
66 GTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATACCC
*
2783 AGTTTGCCCTT-CCCACCGGAAGGTGTTGTTTAAATACCCAATTTGCCCTT-CCCACCGGAAGGT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGT
* *
2846 GTTGTTTAAATACTCGGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATACCC
66 GTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATACCC
* * * * ** *
2901 AGTTTGGCCTTCCCCACCGGAAGGTGTTGTCTAAATTCCCAGTTTGCCTTTCCCTGCCGGAAAGT
1 AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGT
2966 GTT
66 GTT
2969 CTCAGTTTGC
Statistics
Matches: 170, Mismatches: 12, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
117 43 0.25
118 79 0.46
119 35 0.21
120 13 0.08
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (120 bp):
AGTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGT
GTTGTTTAAATACCCAGTTTGCCCTTCCCCACCGGAAGGTGTTGTCTAAATACCC
Found at i:2978 original size:31 final size:31
Alignment explanation
Indices: 2940--2999 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2930 TCTAAATTCC
**
2940 CAGTTTGCCTTTCCCTGCCGGAAAGTGTTCT
1 CAGTTTGCCTTTCCCCACCGGAAAGTGTTCT
2971 CAGTTTGCCTTTCCCCACCGGAAAGTGTT
1 CAGTTTGCCTTTCCCCACCGGAAAGTGTT
3000 GTCTAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.15, C:0.30, G:0.22, T:0.33
Consensus pattern (31 bp):
CAGTTTGCCTTTCCCCACCGGAAAGTGTTCT
Found at i:6703 original size:8 final size:8
Alignment explanation
Indices: 6686--6737 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
6676 AATTTCCCTT
6686 AAAAAT-A
1 AAAAATGA
6693 AAAAATGA
1 AAAAATGA
6701 AAAAATGA
1 AAAAATGA
*
6709 TGAAAATGA
1 -AAAAATGA
6718 CGAAAAAT-A
1 --AAAAATGA
6727 AAAAATGA
1 AAAAATGA
6735 AAA
1 AAA
6738 CAAAGGCACT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
7 12 0.32
8 13 0.34
9 8 0.21
10 5 0.13
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (8 bp):
AAAAATGA
Found at i:6731 original size:17 final size:15
Alignment explanation
Indices: 6686--6737 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 15
6676 AATTTCCCTT
6686 AAAAATAAAAAATGA
1 AAAAATAAAAAATGA
*
6701 AAAAATGATGAAAATGA
1 AAAAAT-A-AAAAATGA
6718 CGAAAAATAAAAAATGA
1 --AAAAATAAAAAATGA
6735 AAA
1 AAA
6738 CAAAGGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 9 0.29
16 1 0.03
17 14 0.45
18 1 0.03
19 6 0.19
ACGTcount: A:0.73, C:0.02, G:0.12, T:0.13
Consensus pattern (15 bp):
AAAAATAAAAAATGA
Found at i:7141 original size:7 final size:7
Alignment explanation
Indices: 7120--7371 Score: 344
Period size: 7 Copynumber: 38.3 Consensus size: 7
7110 CAAGAAATTC
7120 AATCAAA
1 AATCAAA
7127 AA-CAAAA
1 AATC-AAA
7134 AATCAAA
1 AATCAAA
7141 AATCAAA
1 AATCAAA
7148 AATCAAA
1 AATCAAA
7155 AATCAAA
1 AATCAAA
7162 AATCAAA
1 AATCAAA
7169 AATCAAA
1 AATCAAA
7176 AATCAAA
1 AATCAAA
7183 AATCAAA
1 AATCAAA
7190 AATCAAA
1 AATCAAA
7197 AATCAAA
1 AATCAAA
7204 AATCAAA
1 AATCAAA
7211 AATCAAA
1 AATCAAA
7218 AATCAAA
1 AATCAAA
7225 AATCAAA
1 AATCAAA
7232 AATCAAA
1 AATCAAA
7239 AATCAAA
1 AATCAAA
7246 AATCAAAAA
1 AATC--AAA
7255 AATC-AA
1 AATCAAA
7261 AATC-AA
1 AATCAAA
7267 AATC-AA
1 AATCAAA
7273 AATC-AA
1 AATCAAA
7279 AATC-AA
1 AATCAAA
7285 AATC-AA
1 AATCAAA
7291 AATC-AA
1 AATCAAA
7297 AATC-AA
1 AATCAAA
7303 AATC-AA
1 AATCAAA
7309 AATC-AA
1 AATCAAA
7315 AATC-AA
1 AATCAAA
7321 AATC-AA
1 AATCAAA
7327 AATC-AA
1 AATCAAA
7333 AATC-AA
1 AATCAAA
7339 AATC-AA
1 AATCAAA
7345 AATC-AA
1 AATCAAA
7351 AATC-AA
1 AATCAAA
7357 AATC-AA
1 AATCAAA
7363 AATCAAA
1 AATCAAA
7370 AA
1 AA
7372 GGGAATTGAT
Statistics
Matches: 240, Mismatches: 0, Indels: 10
0.96 0.00 0.04
Matches are distributed among these distances:
6 109 0.45
7 123 0.51
8 1 0.00
9 7 0.03
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (7 bp):
AATCAAA
Found at i:15024 original size:16 final size:16
Alignment explanation
Indices: 14981--15015 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
14971 TTTGGCTTTA
*
14981 GGTCACTCGGGTTCTG
1 GGTCATTCGGGTTCTG
*
14997 GGTCATTCGGGTTTTG
1 GGTCATTCGGGTTCTG
15013 GGT
1 GGT
15016 TTTTCGGGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.17, G:0.40, T:0.37
Consensus pattern (16 bp):
GGTCATTCGGGTTCTG
Found at i:18014 original size:22 final size:22
Alignment explanation
Indices: 17989--18043 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
17979 TAATTCCCAA
17989 ATTCTCTCTTCCATTTTCTTCT
1 ATTCTCTCTTCCATTTTCTTCT
18011 ATTCTCTCTTCCATTTTCTTCT
1 ATTCTCTCTTCCATTTTCTTCT
18033 ATTCTCTCTTC
1 ATTCTCTCTTC
18044 GACCTATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.09, C:0.33, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTCTCTCTTCCATTTTCTTCT
Found at i:19000 original size:22 final size:22
Alignment explanation
Indices: 18972--19016 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
18962 TTTCTTTTTT
18972 TACATTCTTAACACAATTCCAA
1 TACATTCTTAACACAATTCCAA
*
18994 TACATTCTTAACATAATTCCAA
1 TACATTCTTAACACAATTCCAA
19016 T
1 T
19017 GTTGGGTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (22 bp):
TACATTCTTAACACAATTCCAA
Found at i:19172 original size:21 final size:21
Alignment explanation
Indices: 19147--19186 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19137 ATGTTGACAT
19147 CCACATCAGCATGTCAGAGTA
1 CCACATCAGCATGTCAGAGTA
19168 CCACATCAGCATGTCAGAG
1 CCACATCAGCATGTCAGAG
19187 CGCATGTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (21 bp):
CCACATCAGCATGTCAGAGTA
Found at i:20206 original size:32 final size:34
Alignment explanation
Indices: 20161--20235 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 34
20151 CGCCTTAGGA
* * *
20161 GGGCGGCACTGACCATGG-CGTGCCACCCTCCTT
1 GGGCAGCACTGACCATGGTCATGCCACCCTCATT
*
20194 GGGCAGCA-TGACCATGGTCATGCCTCCCTCATT
1 GGGCAGCACTGACCATGGTCATGCCACCCTCATT
*
20227 GGGCGGCAC
1 GGGCAGCAC
20236 CGGTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 9 0.26
33 26 0.74
ACGTcount: A:0.15, C:0.36, G:0.31, T:0.19
Consensus pattern (34 bp):
GGGCAGCACTGACCATGGTCATGCCACCCTCATT
Found at i:20276 original size:17 final size:17
Alignment explanation
Indices: 20254--20345 Score: 71
Period size: 17 Copynumber: 5.2 Consensus size: 17
20244 TTTTTGTTTT
*
20254 TTAATTATTAATTATTA
1 TTAATTATTAATTATAA
20271 TTAATTATTAATTATAA
1 TTAATTATTAATTATAA
**
20288 TTAATAATAACAATT-TAAA
1 TTAAT--TATTAATTAT-AA
*
20307 TTAA-TAATAATTAATAA
1 TTAATTATTAATT-ATAA
* *
20324 TTAAATAATTAATAATAA
1 TT-AATTATTAATTATAA
20342 TTAA
1 TTAA
20346 AAAATAAAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
16 7 0.11
17 27 0.44
18 10 0.16
19 17 0.28
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAATTATTAATTATAA
Found at i:20317 original size:22 final size:21
Alignment explanation
Indices: 20284--20341 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
20274 ATTATTAATT
20284 ATAATTAATAATAACAATTTAA
1 ATAATTAATAATAACAA-TTAA
*
20306 ATTAA-TAATAATTAATAATTAA
1 A-TAATTAATAA-TAACAATTAA
20328 ATAATTAATAATAA
1 ATAATTAATAATAA
20342 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 18 0.56
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATTAATAATAACAATTAA
Found at i:20323 original size:7 final size:7
Alignment explanation
Indices: 20254--20339 Score: 70
Period size: 7 Copynumber: 12.1 Consensus size: 7
20244 TTTTTGTTTT
*
20254 TTAATTA
1 TTAATAA
*
20261 TTAATTA
1 TTAATAA
*
20268 TTATTAA
1 TTAATAA
*
20275 TTATTAA
1 TTAATAA
20282 TT-ATAA
1 TTAATAA
20288 TTAATAA
1 TTAATAA
*
20295 -TAACAA
1 TTAATAA
20301 TTTAAATTAA
1 -TT-AA-TAA
20311 -TAATAA
1 TTAATAA
20317 TTAATAA
1 TTAATAA
20324 TTAAATAA
1 TT-AATAA
20332 TTAATAA
1 TTAATAA
20339 T
1 T
20340 AATTAAAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
6 13 0.19
7 41 0.61
8 9 0.13
9 2 0.03
10 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (7 bp):
TTAATAA
Found at i:20353 original size:25 final size:25
Alignment explanation
Indices: 20305--20353 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20295 TAACAATTTA
* *
20305 AATTAATAATAATTAATAATTAAAT
1 AATTAATAATAATTAAAAAATAAAT
20330 AATTAATAATAATTAAAAAATAAA
1 AATTAATAATAATTAAAAAATAAA
20354 AAAAAATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATTAATAATAATTAAAAAATAAAT
Found at i:20464 original size:12 final size:12
Alignment explanation
Indices: 20447--20471 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20437 CTACAAAATC
20447 CGACATGATTTT
1 CGACATGATTTT
20459 CGACATGATTTT
1 CGACATGATTTT
20471 C
1 C
20472 TTCAAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (12 bp):
CGACATGATTTT
Found at i:20651 original size:20 final size:20
Alignment explanation
Indices: 20626--20685 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
20616 TTCAGTAAAT
*
20626 AAAATTGCTATTATTATTGA
1 AAAATTGATATTATTATTGA
* *
20646 AAAATTTATATT-TTA-T-C
1 AAAATTGATATTATTATTGA
* *
20663 AAAATGGTTATTATTATTGA
1 AAAATTGATATTATTATTGA
20683 AAA
1 AAA
20686 TTTTCAAAGG
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
17 9 0.30
18 4 0.13
19 4 0.13
20 13 0.43
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (20 bp):
AAAATTGATATTATTATTGA
Found at i:20838 original size:2 final size:2
Alignment explanation
Indices: 20831--20862 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20821 TAGGCATGAT
20831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20863 CTAAATAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22866 original size:31 final size:31
Alignment explanation
Indices: 22813--22887 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
22803 TTTTCTTTGG
* *
22813 TTTCTTCAAAAAACTTGATTTTTAATTGTACCCA
1 TTTCTTC-AAAAAC-GGATTTTTAA-GGTACCCA
*
22847 TTTC-TCAAAAACGGATTTTTTAGGTACCCA
1 TTTCTTCAAAAACGGATTTTTAAGGTACCCA
22877 TTTCTTCAAAA
1 TTTCTTCAAAA
22888 TCGAATCCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
30 11 0.30
31 14 0.38
32 6 0.16
33 2 0.05
34 4 0.11
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (31 bp):
TTTCTTCAAAAACGGATTTTTAAGGTACCCA
Found at i:26970 original size:28 final size:28
Alignment explanation
Indices: 26938--26993 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
26928 CTCGAAAACC
26938 CTGCTTGCAAAGGTAGCAGCATATAAGT
1 CTGCTTGCAAAGGTAGCAGCATATAAGT
26966 CTGCTTGCAAAGGTAGCAGCATATAAGT
1 CTGCTTGCAAAGGTAGCAGCATATAAGT
26994 TTCCTTGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (28 bp):
CTGCTTGCAAAGGTAGCAGCATATAAGT
Found at i:27000 original size:28 final size:28
Alignment explanation
Indices: 26941--27000 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
26931 GAAAACCCTG
*
26941 CTTGCAAAGGTAGCAGCATATAAGTCTG
1 CTTGCAAAGGTAGCAGCATATAAGTCTC
*
26969 CTTGCAAAGGTAGCAGCATATAAGTTTC
1 CTTGCAAAGGTAGCAGCATATAAGTCTC
26997 CTTG
1 CTTG
27001 ACCCGGGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (28 bp):
CTTGCAAAGGTAGCAGCATATAAGTCTC
Found at i:30499 original size:74 final size:74
Alignment explanation
Indices: 30421--30568 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
30411 GATACCTTTC
30421 TTATTAAGATCCCATGATGATTGTATGATAATTATGGGGGGATTTGATCATTTGGTTGTGTGAAT
1 TTATTAAGATCCCATGATGATTGTATGATAATTATGGGGGGATTTGATCATTTGGTTGTGTGAAT
30486 GTAATCATA
66 GTAATCATA
30495 TTATTAAGATCCCATGATGATTGTATGATAATTATGGGGGGATTTGATCATTTGGTTGTGTGAAT
1 TTATTAAGATCCCATGATGATTGTATGATAATTATGGGGGGATTTGATCATTTGGTTGTGTGAAT
30560 GTAATCATA
66 GTAATCATA
30569 CGTAGAGAAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (74 bp):
TTATTAAGATCCCATGATGATTGTATGATAATTATGGGGGGATTTGATCATTTGGTTGTGTGAAT
GTAATCATA
Found at i:30680 original size:15 final size:15
Alignment explanation
Indices: 30660--30689 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
30650 GCTCCCTTTG
30660 TTAACACCGAGTTTA
1 TTAACACCGAGTTTA
30675 TTAACACCGAGTTTA
1 TTAACACCGAGTTTA
30690 AATTGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
TTAACACCGAGTTTA
Found at i:30915 original size:22 final size:22
Alignment explanation
Indices: 30887--30932 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
30877 TTAACTTGTA
30887 AATATACCAAAAAAAAATTATC
1 AATATACCAAAAAAAAATTATC
*
30909 AATATACCAAAAAATAATTATC
1 AATATACCAAAAAAAAATTATC
30931 AA
1 AA
30933 AGGACACTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.24
Consensus pattern (22 bp):
AATATACCAAAAAAAAATTATC
Found at i:33468 original size:24 final size:24
Alignment explanation
Indices: 33436--33484 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
33426 AGTGAACTTC
33436 CATTCTCCATTTCTAATTAGAAAT
1 CATTCTCCATTTCTAATTAGAAAT
*
33460 CATTCTCCATTTCTAATTAGTAAT
1 CATTCTCCATTTCTAATTAGAAAT
33484 C
1 C
33485 GGAAAGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.04, T:0.43
Consensus pattern (24 bp):
CATTCTCCATTTCTAATTAGAAAT
Found at i:38461 original size:5 final size:5
Alignment explanation
Indices: 38451--38497 Score: 71
Period size: 5 Copynumber: 9.6 Consensus size: 5
38441 AATAATAATA
38451 ATAAC ATAAC AATAAC AT-A- ATAAC ATAAC ATAAC ATAAC ATAAC ATA
1 ATAAC ATAAC -ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATA
38498 TGAACATATA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 30 0.77
6 5 0.13
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (5 bp):
ATAAC
Found at i:38465 original size:6 final size:6
Alignment explanation
Indices: 38403--38495 Score: 52
Period size: 6 Copynumber: 16.0 Consensus size: 6
38393 TATATCTATT
* * * * * * * * *
38403 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA GTAATA ATAATA
1 ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA ATAACA
38451 ATAAC- ATAACA ATAACATA ATAAC- ATAAC- ATAAC- ATAAC- ATAACA
1 ATAACA ATAACA ATAAC--A ATAACA ATAACA ATAACA ATAACA ATAACA
38496 TATGAACATA
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
5 25 0.31
6 49 0.61
8 6 0.08
ACGTcount: A:0.63, C:0.09, G:0.01, T:0.27
Consensus pattern (6 bp):
ATAACA
Found at i:38472 original size:19 final size:18
Alignment explanation
Indices: 38448--38488 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 18
38438 AGTAATAATA
38448 ATAATAACATAACAATAAC
1 ATAATAACATAAC-ATAAC
38467 ATAATAACATAACATAAC
1 ATAATAACATAACATAAC
38485 ATAA
1 ATAA
38489 CATAACATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (18 bp):
ATAATAACATAACATAAC
Found at i:38473 original size:3 final size:3
Alignment explanation
Indices: 38403--38454 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
38393 TATATCTATT
*
38403 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GTA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38451 ATA A
1 ATA A
38455 CATAACAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:38505 original size:23 final size:24
Alignment explanation
Indices: 38442--38493 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
38432 AATAATAGTA
*
38442 ATAATAATAATAACATAACAATAAC
1 ATAATAA-CATAACATAACAATAAC
38467 ATAATAACATAACATAAC-ATAAC
1 ATAATAACATAACATAACAATAAC
38490 ATAA
1 ATAA
38494 CATATGAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 9 0.35
24 10 0.38
25 7 0.27
ACGTcount: A:0.63, C:0.13, G:0.00, T:0.23
Consensus pattern (24 bp):
ATAATAACATAACATAACAATAAC
Found at i:41378 original size:21 final size:21
Alignment explanation
Indices: 41354--41399 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
41344 GTGGCACTGG
41354 CATCAGTAGCATCCAAAGTAT
1 CATCAGTAGCATCCAAAGTAT
*
41375 CATCAGTAGCATCCAAAGTGT
1 CATCAGTAGCATCCAAAGTAT
41396 CATC
1 CATC
41400 GTCATCCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (21 bp):
CATCAGTAGCATCCAAAGTAT
Found at i:41576 original size:18 final size:18
Alignment explanation
Indices: 41553--41587 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41543 TAATCATATA
41553 AGAAACCACAATAATGCT
1 AGAAACCACAATAATGCT
41571 AGAAACCACAATAATGC
1 AGAAACCACAATAATGC
41588 CTTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.23, G:0.11, T:0.14
Consensus pattern (18 bp):
AGAAACCACAATAATGCT
Found at i:44774 original size:28 final size:28
Alignment explanation
Indices: 44734--44802 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
44724 AAAGGAGGAG
44734 CAAGCTTAATTAAGCTTCACAATTGTAA
1 CAAGCTTAATTAAGCTTCACAATTGTAA
*
44762 CAAGCTTAATTAAGCTTTACAATTGTAA
1 CAAGCTTAATTAAGCTTCACAATTGTAA
44790 CAAGCTTAATTAA
1 CAAGCTTAATTAA
44803 AAAAATACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (28 bp):
CAAGCTTAATTAAGCTTCACAATTGTAA
Found at i:45484 original size:193 final size:192
Alignment explanation
Indices: 45148--45530 Score: 721
Period size: 193 Copynumber: 2.0 Consensus size: 192
45138 TGGCAAAAAA
* *
45148 AAAAGTAAGTCAAGAAGAGACATGATCCCTATGTTAATTAATATATGTGTTGTTAATTGTAGATC
1 AAAAGTAAGTCAAGAAGAGACATGATCCCTATGTTAATTAATATATATGTTGTTAACTGTAGATC
45213 TCAAATGGCAATACTTATACAAATAAGTTTGAAATTTGGAAGAGAACTAAAGACCAAATGGCATT
66 TCAAATGGCAATACTTATACAAATAAGTTTGAAATTTGGAAGAGAACTAAAGACCAAATGGCATT
* *
45278 CACCATGACATGCAATTTTCTTTTGCAGAGAAATTATGGTGATCTTATTCCACCATTATTAAT
131 CACCATAACATGCAATTTT-TTCTGCAGAGAAATTATGGTGATCTTATTCCACCATTATTAAT
45341 AAAAGTAAGTCAAGAAGAGACATGATCCCTATGTTAATTAATATATATGTTGTTAACTGTAGATC
1 AAAAGTAAGTCAAGAAGAGACATGATCCCTATGTTAATTAATATATATGTTGTTAACTGTAGATC
45406 TCAAATGGCAATACTTATACAAATAAGTTTGAAATTTGGAAGAGAACTAAAGACCAAATGGCATT
66 TCAAATGGCAATACTTATACAAATAAGTTTGAAATTTGGAAGAGAACTAAAGACCAAATGGCATT
45471 CACCATAACATGCAATTTTTTCTGCAGAGAAATTATGGTGATCTTATTCCACCATTATTA
131 CACCATAACATGCAATTTTTTCTGCAGAGAAATTATGGTGATCTTATTCCACCATTATTA
45531 GCTCCTCGGT
Statistics
Matches: 186, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
192 40 0.22
193 146 0.78
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (192 bp):
AAAAGTAAGTCAAGAAGAGACATGATCCCTATGTTAATTAATATATATGTTGTTAACTGTAGATC
TCAAATGGCAATACTTATACAAATAAGTTTGAAATTTGGAAGAGAACTAAAGACCAAATGGCATT
CACCATAACATGCAATTTTTTCTGCAGAGAAATTATGGTGATCTTATTCCACCATTATTAAT
Found at i:46553 original size:2 final size:2
Alignment explanation
Indices: 46546--46605 Score: 84
Period size: 2 Copynumber: 30.0 Consensus size: 2
46536 CAAGTATTAG
* * *
46546 TA TA TA TA TA TG TA TA TA TA TA TA TA TG TA TA TA CA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
46588 TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
46606 GAGGAGGAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
TA
Found at i:48966 original size:25 final size:25
Alignment explanation
Indices: 48920--48968 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
48910 TATTAAATAT
* *
48920 ATTTTAAAATGAATTAACAATAATC
1 ATTTTAAAATGAAATAAAAATAATC
48945 ATTTATAAAAT-AAATAAAAATAAT
1 ATTT-TAAAATGAAATAAAAATAAT
48969 ATAAAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (25 bp):
ATTTTAAAATGAAATAAAAATAATC
Found at i:51027 original size:29 final size:29
Alignment explanation
Indices: 50994--51052 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
50984 TTGAGTGTGG
50994 TATGGAAGGCGTAGAGCCAGATTAATAAA
1 TATGGAAGGCGTAGAGCCAGATTAATAAA
*
51023 TATGGAAGGTGTAGAGCCAGATTAATAAA
1 TATGGAAGGCGTAGAGCCAGATTAATAAA
51052 T
1 T
51053 GTATGCCTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (29 bp):
TATGGAAGGCGTAGAGCCAGATTAATAAA
Done.