Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015902.1 Corchorus capsularis cultivar CVL-1 contig15923, 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: 64264
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:514 original size:15 final size:15
Alignment explanation
Indices: 494--524 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
484 TTTGAATTCC
*
494 AATTCAATTCCAACA
1 AATTCAAATCCAACA
509 AATTCAAATCCAACA
1 AATTCAAATCCAACA
524 A
1 A
525 GATGATAAGA
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:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (15 bp):
AATTCAAATCCAACA
Found at i:2664 original size:29 final size:30
Alignment explanation
Indices: 2599--2664 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
2589 CACAGTTCCC
* *
2599 AAGAGAAAAAACCCTAGCAGACAGTTTCCAG
1 AAGA-AAAAAACCCTAGCAGACAGATTACAG
* *
2630 AA-AAAAAAACCCTAGCAGAGAGATTATA-
1 AAGAAAAAAACCCTAGCAGACAGATTACAG
2658 AAGAAAA
1 AAGAAAA
2665 CCCTAGTTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.07
29 25 0.83
30 1 0.03
31 2 0.07
ACGTcount: A:0.55, C:0.17, G:0.17, T:0.12
Consensus pattern (30 bp):
AAGAAAAAAACCCTAGCAGACAGATTACAG
Found at i:4947 original size:37 final size:37
Alignment explanation
Indices: 4904--5012 Score: 184
Period size: 36 Copynumber: 3.0 Consensus size: 37
4894 ATCAGGAATT
4904 AAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATC
1 AAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATC
4941 AAGTTTTCAAAGTTTTC-AATTGGGAAAGTTCCCATC
1 AAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATC
* * *
4977 AAGATTTCAAAGTTGTCAAGTTGGGAAAGTTCCCAT
1 AAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCAT
5013 TAGGTTTCAA
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 34 0.50
37 34 0.50
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (37 bp):
AAGTTTTCAAAGTTTTCAAATTGGGAAAGTTCCCATC
Found at i:5711 original size:15 final size:15
Alignment explanation
Indices: 5691--5720 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5681 AATTGGTTGT
*
5691 TTAATTGTTGTTTTC
1 TTAATTCTTGTTTTC
5706 TTAATTCTTGTTTTC
1 TTAATTCTTGTTTTC
5721 ATGATTTGTG
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:0.13, C:0.10, G:0.10, T:0.67
Consensus pattern (15 bp):
TTAATTCTTGTTTTC
Found at i:8325 original size:3 final size:3
Alignment explanation
Indices: 8317--8361 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
8307 GTTTTCAAAA
* *
8317 AAT AAT AAT AAT TAT AAT AAG AAT AAT AA- AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
8362 AGAATGGAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:9242 original size:13 final size:13
Alignment explanation
Indices: 9224--9250 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9214 CATCAAATAA
9224 TTCAAATCAAAAG
1 TTCAAATCAAAAG
9237 TTCAAATCAAAAG
1 TTCAAATCAAAAG
9250 T
1 T
9251 GAATGAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (13 bp):
TTCAAATCAAAAG
Found at i:9729 original size:95 final size:92
Alignment explanation
Indices: 9533--9718 Score: 254
Period size: 88 Copynumber: 2.0 Consensus size: 92
9523 TTGCAAACAC
9533 AAAAAAATGTTTTTCACAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTTCGAATGCAA
1 AAAAAAATGTTTTTCACAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTT---ATGCAA
* * *
9598 ATGCAAGTGCGTGGTGAAGCAACTAATAAA
63 ATGCAAGTGCATGGTGAAGCAACGAAAAAA
* *
9628 AAAAAAATGTTTTTCTCAAAAAGGTTTTTAGAT-AAAATTGGTTTCCAGAAG-TTT-T-CAAATG
1 AAAAAAATGTTTTTCACAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTTATGCAAATG
* *
9689 CAAGTGCATGGTGAAGCAACCAAGAAA
66 CAAGTGCATGGTGAAGCAACGAAAAAA
9716 AAA
1 AAA
9719 TGAATGAAAA
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
88 33 0.38
89 1 0.01
93 3 0.03
94 17 0.20
95 32 0.37
ACGTcount: A:0.42, C:0.11, G:0.18, T:0.28
Consensus pattern (92 bp):
AAAAAAATGTTTTTCACAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTTATGCAAATG
CAAGTGCATGGTGAAGCAACGAAAAAA
Found at i:9737 original size:88 final size:92
Alignment explanation
Indices: 9549--9737 Score: 206
Period size: 88 Copynumber: 2.1 Consensus size: 92
9539 ATGTTTTTCA
*
9549 CAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTTCGAATGCAAATGCAAGTGCGTGGTG
1 CAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTT---ATGCAAATGCAAGTGCATGGTG
* * ******
9614 AAGCAACTAATAAAAAAAAAATGTTTTTCT
63 AAGCAACCAAGAAAAAAAAAATGAAAAAAT
*
9644 CAAAAAGGTTTTTAGAT-AAAATTGGTTTCCAGAAG-TTT-T-CAAATGCAAGTGCATGGTGAAG
1 CAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTTATGCAAATGCAAGTGCATGGTGAAG
**
9705 CAACCAAGAAAAAATGAATGAAAAAAT
66 CAACCAAGAAAAAAAAAATGAAAAAAT
*
9732 GAAAAA
1 CAAAAA
9738 TGGAGAAGAA
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
88 43 0.53
89 1 0.01
93 3 0.04
94 17 0.21
95 17 0.21
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (92 bp):
CAAAAAGGTTTTTAGATAAAAATTGGTTTCCAAAAGCTTTATGCAAATGCAAGTGCATGGTGAAG
CAACCAAGAAAAAAAAAATGAAAAAAT
Found at i:10495 original size:21 final size:23
Alignment explanation
Indices: 10459--10511 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
10449 TGAATAGGTC
10459 CAAAAAAGAAGAAGAGAGAGAGA
1 CAAAAAAGAAGAAGAGAGAGAGA
*
10482 CAAAAAAG-AGAGAGAGTGAGAGA
1 CAAAAAAGAAGA-AGAGAGAGAGA
*
10505 AAAAAAA
1 CAAAAAA
10512 CAAAAAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 3 0.11
23 24 0.89
ACGTcount: A:0.66, C:0.04, G:0.28, T:0.02
Consensus pattern (23 bp):
CAAAAAAGAAGAAGAGAGAGAGA
Found at i:13684 original size:30 final size:30
Alignment explanation
Indices: 13650--13708 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
13640 CTCTGTTCTT
13650 TAACTTCTTCATTGTACATTGTTCCTAATA
1 TAACTTCTTCATTGTACATTGTTCCTAATA
13680 TAACTTCTTCATTGTACATTGTTCCTAAT
1 TAACTTCTTCATTGTACATTGTTCCTAAT
13709 GAGTTTCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (30 bp):
TAACTTCTTCATTGTACATTGTTCCTAATA
Found at i:17360 original size:87 final size:85
Alignment explanation
Indices: 17200--17360 Score: 234
Period size: 87 Copynumber: 1.9 Consensus size: 85
17190 GTTTCATGTC
* *
17200 ATAAATTATAAAGTTGAATAATAATGAAAATATTTTCTAAATCTTGCCAAATTGTGGAAGGTTTA
1 ATAAATCATAAAGTTGAATAATAATGAAAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTA
*
17265 GGAGATATTTTAAGAAATAA
66 GGAAATATTTTAAGAAATAA
* * *
17285 ATAAATCATAAAGATTGAATAATAATGAGAATATTTCTCTAAATCTTGCCAGATTGTGGGAGATT
1 ATAAATCATAAAG-TTGAATAATAATGAAAATATTT-TCTAAATCTTGCCAAATTGTGGAAGATT
17350 T-GGAAAATATT
64 TAGG-AAATATT
17361 AAATAATAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
85 12 0.18
86 23 0.34
87 32 0.48
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (85 bp):
ATAAATCATAAAGTTGAATAATAATGAAAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTTA
GGAAATATTTTAAGAAATAA
Found at i:28526 original size:26 final size:27
Alignment explanation
Indices: 28476--28540 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
28466 AAAGAAGGAG
28476 AAGAAAAGAAAAGAAAAGAAATTGAAA
1 AAGAAAAGAAAAGAAAAGAAATTGAAA
* * *
28503 AAGAAAAGGAAA-CAAAGAAGTTGAAA
1 AAGAAAAGAAAAGAAAAGAAATTGAAA
* *
28529 AAGTAAACAAAA
1 AAGAAAAGAAAA
28541 TGGAGGAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 21 0.66
27 11 0.34
ACGTcount: A:0.71, C:0.03, G:0.18, T:0.08
Consensus pattern (27 bp):
AAGAAAAGAAAAGAAAAGAAATTGAAA
Found at i:29970 original size:54 final size:53
Alignment explanation
Indices: 29888--30422 Score: 503
Period size: 54 Copynumber: 9.9 Consensus size: 53
29878 GTGTTTAAAG
* * *
29888 TGACCTAGTGTGGTCATTCCAAGAAGTTTCAAACGATCAGAGTTGATCTCTAGA
1 TGACCTAGTGCGGTCATTCCAAGAAGTTTC-AATGATCAGAGTTGATCTCCAGA
*
29942 TGACCTAGTGCGGTCATTCCAAGAAGTTTTCAATGATCACAGTTGATCTCCAGA
1 TGACCTAGTGCGGTCATTCCAAGAAG-TTTCAATGATCAGAGTTGATCTCCAGA
*
29996 TGA-CTAGTGCGGCCATTCCAAGAAGTTTTCAATGATCAGAGTTGATCTCCAGA
1 TGACCTAGTGCGGTCATTCCAAGAAG-TTTCAATGATCAGAGTTGATCTCCAGA
* * ** *
30049 TGACCCAGTGCGGTCATTCCACGAAGTTTCCAACCATCAAAGTTGATCTCCAGA
1 TGACCTAGTGCGGTCATTCCAAGAAGTTT-CAATGATCAGAGTTGATCTCCAGA
* * * *
30103 TGACCCAGTGCAGTCATTCCAAGAATTTTCCAATGATCAAAGTTGATC-CCAAGA
1 TGACCTAGTGCGGTCATTCCAAGAAGTTT-CAATGATCAGAGTTGATCTCC-AGA
* * * * * *
30157 TAATCTAGTGAGTTCATTCCAAGAAGTTTCCAACGATCAAAGTTGATCTCCAGA
1 TGACCTAGTGCGGTCATTCCAAGAAGTTT-CAATGATCAGAGTTGATCTCCAGA
* * * * * *
30211 TGACCCAGTGCGATCCTTTCAAGAAGTTTCAAATGATCA-ATGTTGATCCCCAAA
1 TGACCTAGTGCGGTCATTCCAAGAAGTTTC-AATGATCAGA-GTTGATCTCCAGA
* * * * * *
30265 TAATCC-AATGCGTTCATTTCAAGAAGTTTTTAGTGATCAGAGTTGAT-TCCCAGA
1 TGA-CCTAGTGCGGTCATTCCAAGAAG-TTTCAATGATCAGAGTTGATCT-CCAGA
* * *
30319 TGATCC-AGTGCGGTCATTTCAAGAAGTCTTTAGA-GATCAGAGTTGATCTCTA-A
1 TGA-CCTAGTGCGGTCATTCCAAGAAGT-TTCA-ATGATCAGAGTTGATCTCCAGA
* * *
30372 TTGATCC-AGTGCGGTCGTTCTAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 -TGA-CCTAGTGCGGTCATTCCAAGAAG-TTTCAATGATCAGAGTTGATCTC
30423 ATTTCAAGAA
Statistics
Matches: 411, Mismatches: 53, Indels: 34
0.83 0.11 0.07
Matches are distributed among these distances:
53 61 0.15
54 336 0.82
55 14 0.03
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (53 bp):
TGACCTAGTGCGGTCATTCCAAGAAGTTTCAATGATCAGAGTTGATCTCCAGA
Found at i:30432 original size:35 final size:35
Alignment explanation
Indices: 30393--30492 Score: 182
Period size: 35 Copynumber: 2.9 Consensus size: 35
30383 CGGTCGTTCT
30393 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
30428 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
* *
30463 AAGAAATTTTCGATGATCAGAGTTTATCTC
1 AAGAAGTTTTCGATGATCAGAGTTGATCTC
30493 TAATAGATCC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.37
Consensus pattern (35 bp):
AAGAAGTTTTCGATGATCAGAGTTGATCTCATTTC
Found at i:31213 original size:17 final size:17
Alignment explanation
Indices: 31191--31229 Score: 62
Period size: 17 Copynumber: 2.3 Consensus size: 17
31181 TGATGTTTGG
31191 TTTTTTTAT-ATATTATA
1 TTTTTTTATAATA-TATA
31208 TTTTTTTATAATATATA
1 TTTTTTTATAATATATA
31225 TTTTT
1 TTTTT
31230 CTTACCCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTTTATAATATATA
Found at i:31759 original size:87 final size:85
Alignment explanation
Indices: 31598--31759 Score: 202
Period size: 87 Copynumber: 1.9 Consensus size: 85
31588 GGTTTCATGT
* * *
31598 AATAAATTATAAAGTTGAATAAAAATGAGAATATTTTCTAAATCTTGCAAAATTGTGGAAGGTTT
1 AATAAATCATAAAGGTGAATAAAAATGAGAATATTTTCTAAATCTTGCAAAATTGTGGAAGATTT
*
31663 AGGAGATATTTTAAGAAATA
66 AGGAAATATTTTAAGAAATA
* * * *
31683 AATAAATCATAAAGAGTGAATAATACTGAGAATATTTCTCTAAATCTTG-ATAGATTGTGGGAGA
1 AATAAATCATAAAG-GTGAATAAAAATGAGAATATTT-TCTAAATCTTGCA-AAATTGTGGAAGA
31747 TTT-GGAAAATATT
63 TTTAGG-AAATATT
31760 AAATAATAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
85 13 0.20
86 22 0.34
87 30 0.46
ACGTcount: A:0.44, C:0.05, G:0.17, T:0.34
Consensus pattern (85 bp):
AATAAATCATAAAGGTGAATAAAAATGAGAATATTTTCTAAATCTTGCAAAATTGTGGAAGATTT
AGGAAATATTTTAAGAAATA
Found at i:37295 original size:163 final size:166
Alignment explanation
Indices: 36955--37296 Score: 530
Period size: 163 Copynumber: 2.1 Consensus size: 166
36945 TGGTAAGTAC
*
36955 ATTGAAAATGGTGATCATGCTTTATGTAATTGTATGTAATGCCTGTGGATTTTCAATTTTGTACC
1 ATTGAAAATGGTGATCATGCTTTATGTAATTGTATGTAATGCCTGTGGATTTTCAATTTTGTACA
* * *
37020 TTAAGAAGTTTCAAAACGTTAGTCAAAAAATGAGCTATTTGTATGGTATGTATGTCTCAATTCTT
66 TTAAGAAGATTCAAAACGTTAGTCAAAAAATGAGCTATATG-ATGGCATGTATGTCTCAATTCTT
*
37085 GTAGTGACATAGAGTCAAATTATAGGCAACTATATCA
130 GTAGTGACATAGAGACAAATTATAGGCAACTATATCA
**
37122 ATTGAAAATGGTGATTTTGCTTTATGTAATTGTATGTAATGCCTGTGGATTTTCAATTTTG-AGC
1 ATTGAAAATGGTGATCATGCTTTATGTAATTGTATGTAATGCCTGTGGATTTTCAATTTTGTA-C
* *
37186 ATTAA-AA-ATTCAAAACGTTAGTCAACAAATGATCTATATG-TGGCATGTATGTCTCAATTCTT
65 ATTAAGAAGATTCAAAACGTTAGTCAAAAAATGAGCTATATGATGGCATGTATGTCTCAATTCTT
* *
37248 GTAGTGACATGGAGACAAATTATGGGCAACTATATCA
130 GTAGTGACATAGAGACAAATTATAGGCAACTATATCA
*
37285 TTTGAAAATGGT
1 ATTGAAAATGGT
37297 TAATATCATC
Statistics
Matches: 162, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
163 66 0.41
165 29 0.18
166 3 0.02
167 64 0.40
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.37
Consensus pattern (166 bp):
ATTGAAAATGGTGATCATGCTTTATGTAATTGTATGTAATGCCTGTGGATTTTCAATTTTGTACA
TTAAGAAGATTCAAAACGTTAGTCAAAAAATGAGCTATATGATGGCATGTATGTCTCAATTCTTG
TAGTGACATAGAGACAAATTATAGGCAACTATATCA
Found at i:40167 original size:130 final size:131
Alignment explanation
Indices: 39916--40169 Score: 314
Period size: 129 Copynumber: 1.9 Consensus size: 131
39906 AATGACTTAA
* * * *
39916 AAAGTTTTTACGAATAGTTTATGATTTCGCAGCAACTTAAGAAGTTGTTACTACGAATACTATAA
1 AAAGTTGTTACGAATAGTTTATCATTTCGCAACAACTTAAGAAGTTGTTACTACGAAAACTATAA
* * **
39981 ACATTGGCAACAACTAAAAAAGTGTTGTGTAAAAGACCATCAAAATCACTTGGGCAACGTTTTTA
66 ACATTGGCAACAACTAAAAAAGTGTCGGGTAAAAGACCATCAAAATCACTAAGGCAACGTTTTTA
40046 T
131 T
* * ** * * *
40047 AAAGTTGTTACGAATAGTTTATCATTTCGCAACGACTT-TG-TTTTGTTATTACGAAAATTGTAA
1 AAAGTTGTTACGAATAGTTTATCATTTCGCAACAACTTAAGAAGTTGTTACTACGAAAACTATAA
* * * *
40110 GCATTGGCAACCACTAAAAAATTCGTCGGGTAAAATACCATCAAAATCACTAAGGCAACG
66 ACATTGGCAACAACTAAAAAAGT-GTCGGGTAAAAGACCATCAAAATCACTAAGGCAACG
40170 ACTTTTAGTT
Statistics
Matches: 103, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
129 37 0.36
130 32 0.31
131 34 0.33
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (131 bp):
AAAGTTGTTACGAATAGTTTATCATTTCGCAACAACTTAAGAAGTTGTTACTACGAAAACTATAA
ACATTGGCAACAACTAAAAAAGTGTCGGGTAAAAGACCATCAAAATCACTAAGGCAACGTTTTTA
T
Found at i:40185 original size:130 final size:131
Alignment explanation
Indices: 39916--40176 Score: 310
Period size: 131 Copynumber: 2.0 Consensus size: 131
39906 AATGACTTAA
* * * *
39916 AAAGTTTTTACGAATAGTTTATGATTTCGCAGCAACTTAAGAAGTTGTTACTACGAATACTATAA
1 AAAGTTGTTACGAATAGTTTATCATTTCGCAACAACTTAAGAAGTTGTTACTACGAAAACTATAA
* * ** *
39981 ACATTGGCAACAACTAAAAAAGTGTTGTGTAAAAGACCATCAAAATCACTTGGGCAACGTTTTTA
66 ACATTGGCAACAACTAAAAAAGTGTCGGGTAAAAGACCATCAAAATCACTAAGGCAACGCTTTTA
40046 T
131 T
* * ** * * *
40047 AAAGTTGTTACGAATAGTTTATCATTTCGCAACGACTT-TG-TTTTGTTATTACGAAAATTGTAA
1 AAAGTTGTTACGAATAGTTTATCATTTCGCAACAACTTAAGAAGTTGTTACTACGAAAACTATAA
* * * *
40110 GCATTGGCAACCACTAAAAAATTCGTCGGGTAAAATACCATCAAAATCACTAAGGCAACGACTTT
66 ACATTGGCAACAACTAAAAAAGT-GTCGGGTAAAAGACCATCAAAATCACTAAGGCAACG-CTTT
40175 TA
129 TA
40177 GTTATTGTTG
Statistics
Matches: 108, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
129 37 0.34
130 32 0.30
131 39 0.36
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (131 bp):
AAAGTTGTTACGAATAGTTTATCATTTCGCAACAACTTAAGAAGTTGTTACTACGAAAACTATAA
ACATTGGCAACAACTAAAAAAGTGTCGGGTAAAAGACCATCAAAATCACTAAGGCAACGCTTTTA
T
Found at i:47079 original size:14 final size:14
Alignment explanation
Indices: 47057--47086 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
47047 GGCTCCATAT
47057 GAAGCTTTGTATGG
1 GAAGCTTTGTATGG
*
47071 GAAGTTTTGTATGG
1 GAAGCTTTGTATGG
47085 GA
1 GA
47087 GGAAGTGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.03, G:0.37, T:0.37
Consensus pattern (14 bp):
GAAGCTTTGTATGG
Found at i:52412 original size:45 final size:45
Alignment explanation
Indices: 52361--52450 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
52351 TAATAGAGTA
*
52361 GTGGAATTACTAAAAGATTCTTACCCCAAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATTCCTACCCCAAATTAATGATAAGCTGG
** *
52406 GTGGAATTACTAAAAGATTCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATTCCTACCCCAAATTAATGATAAGCTGG
52451 AGAAGTAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATTCCTACCCCAAATTAATGATAAGCTGG
Found at i:52775 original size:165 final size:167
Alignment explanation
Indices: 52504--52833 Score: 434
Period size: 166 Copynumber: 2.0 Consensus size: 167
52494 AATGTCCTAA
* * * * ** * *
52504 ACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGATAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGCTGATGGAGCTAGAGAAC
* ** *
52569 GTATTTTTTTCATCTTTTTCTACTTGGCAGATTATTTAAATGTCCTAACTTTTGATTCTTGA-GG
66 GTAATTTTTTCATCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG
* * *
52633 GATTAAATAAGTAATCTTTTTTGTCATTTCTCAATGG
131 GATTAAATAACTAAACTTTTTGGTCATTTCTCAATGG
* *
52670 ACTTGAATAGAGTAGTGGAATTAATAAATGATCCCCATCAAGGATTGCTGAT-GAGCTAGAGAAC
1 ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGCTGATGGAGCTAGAGAAC
* * *
52734 -TAACATTTTTT-GTCTTTACCTACTTGGCAGATTACTTAAATGTCCTAATTTTTTATTCTTGAG
66 GT-A-ATTTTTTCATCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAG
52797 GGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
129 GGGATTAAATAACTAAACTTTTTGGTCATTTCTCAAT
52834 TGACAAATGA
Statistics
Matches: 141, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
164 1 0.01
165 56 0.40
166 84 0.60
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.40
Consensus pattern (167 bp):
ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCCACCAAGGATTGCTGATGGAGCTAGAGAAC
GTAATTTTTTCATCTTTACCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGG
GATTAAATAACTAAACTTTTTGGTCATTTCTCAATGG
Found at i:53420 original size:13 final size:13
Alignment explanation
Indices: 53402--53427 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53392 AAATTTTACG
53402 TCTTTTCTCACTT
1 TCTTTTCTCACTT
53415 TCTTTTCTCACTT
1 TCTTTTCTCACTT
53428 GACAGATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (13 bp):
TCTTTTCTCACTT
Found at i:55159 original size:41 final size:41
Alignment explanation
Indices: 55102--55187 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
55092 GGTGCAGAAC
55102 TGCACCCATTAGACACAATTTACATAGAATACAATAATAAA
1 TGCACCCATTAGACACAATTTACATAGAATACAATAATAAA
*
55143 TGCACCCATTAGACACAATTTACATAGAATGCAATAATAAA
1 TGCACCCATTAGACACAATTTACATAGAATACAATAATAAA
55184 TGCA
1 TGCA
55188 AGTGTGACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (41 bp):
TGCACCCATTAGACACAATTTACATAGAATACAATAATAAA
Found at i:55970 original size:27 final size:27
Alignment explanation
Indices: 55929--55983 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
55919 TGAATATTCT
55929 TTCTGCCAACAAAAACGTTGTTCATAA
1 TTCTGCCAACAAAAACGTTGTTCATAA
*
55956 TTCTGGCCAACAAAAACGTTGTTTATAA
1 TTCT-GCCAACAAAAACGTTGTTCATAA
55984 AGGCAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.31
Consensus pattern (27 bp):
TTCTGCCAACAAAAACGTTGTTCATAA
Found at i:59845 original size:87 final size:87
Alignment explanation
Indices: 59466--59837 Score: 539
Period size: 87 Copynumber: 4.3 Consensus size: 87
59456 TGAGAAGTTC
* * * * * * *
59466 ACTCCAAGGAGACTAGAGTTCAGGCAAAGAGTGCTTGTTGGGAAAAGAAATGCTGATAGCTCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
* *
59531 TGGCAAAGGCGATGATGATCAT
66 TGGCAAAGGTGACGATGATCAT
* * * **
59553 ACTCCAAGGAGGCTAAAGTTCAAGCCAAGGGTTCTTGTTGGCAACAGAATTGCTGATAATCCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
* *
59618 TGGAAAAGGTGACAATGATCAT
66 TGGCAAAGGTGACGATGATCAT
*
59640 ACTCCAAGGAGACTAAAGTTCAAGCCAATG-GTTATTGTTGGCAACAGAAATGCTGATAGCCCAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAA-GAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAA
59704 ATGGCAAAGGTGACGATGATCAT
65 ATGGCAAAGGTGACGATGATCAT
*
59727 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAATAGAAATGCTGATAGCCCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
*
59792 TGGCAAATGTGACGATGATCAT
66 TGGCAAAGGTGACGATGATCAT
* *
59814 ACTCCAAGGAGACTTACGTTCAAG
1 ACTCCAAGGAGACTAAAGTTCAAG
59838 AGAAGAGTGA
Statistics
Matches: 255, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
86 1 0.00
87 253 0.99
88 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (87 bp):
ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAACAGAAATGCTGATAGCCCAAA
TGGCAAAGGTGACGATGATCAT
Found at i:59891 original size:87 final size:87
Alignment explanation
Indices: 59466--59891 Score: 295
Period size: 87 Copynumber: 4.9 Consensus size: 87
59456 TGAGAAGTTC
* * * * ** * * *
59466 ACTCCAAGGAGACTAGAGTTC-AGGCAAAGAGTGCTTGTTGGGAAAAGAAATGCTGATAGCTC-A
1 ACTCCAAGGAGACTAAAGTTCAAGAC-AAGAGTGATTGATGACAATAGAAATGCTAAAAGC-CAA
* * *
59529 AATGGCAAAGGCGATGATGATCAT
64 AATAGCAAAGGTGACGATGATCAT
* * * ** * * * * * *
59553 ACTCCAAGGAGGCTAAAGTTCAAGCCAAGGGTTCTTGTTGGCAACAGAATTGCTGATAATCC-AA
1 ACTCCAAGGAGACTAAAGTTCAAGACAAGAGTGATTGATGACAATAGAAATGCT-AAAAGCCAAA
* * *
59617 ATGGAAAAGGTGACAATGATCAT
65 ATAGCAAAGGTGACGATGATCAT
* * * * * * * *
59640 ACTCCAAGGAGACTAAAGTTCAAGCCAATG-GTTATTGTTGGCAACAGAAATGCTGATAGCCCAA
1 ACTCCAAGGAGACTAAAGTTCAAGACAA-GAGTGATTGATGACAATAGAAATGCTAAAAGCCAAA
*
59704 ATGGCAAAGGTGACGATGATCAT
65 ATAGCAAAGGTGACGATGATCAT
* ** * * * * *
59727 ACTCCAAGGAGACTAAAGTTCAAGCCAAGAGTTCTTGTTGGCAATAGAAATGCTGATAGCCCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGACAAGAGTGATTGATGACAATAGAAATGCTAAAAGCCAAAA
* *
59792 TGGCAAATGTGACGATGATCAT
66 TAGCAAAGGTGACGATGATCAT
* * * * * *
59814 ACTCCAAGGAGACTTACGTTCAAGAGAAGAGTGATTGATGACAATA-AATCTGGTAAAATCCAAA
1 ACTCCAAGGAGACTAAAGTTCAAGACAAGAGTGATTGATGACAATAGAA-ATGCTAAAAGCCAAA
**
59878 ATAGTGAAGGTGAC
65 ATAGCAAAGGTGAC
59892 ACAAGCAAGA
Statistics
Matches: 287, Mismatches: 46, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
86 6 0.02
87 275 0.96
88 6 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.22
Consensus pattern (87 bp):
ACTCCAAGGAGACTAAAGTTCAAGACAAGAGTGATTGATGACAATAGAAATGCTAAAAGCCAAAA
TAGCAAAGGTGACGATGATCAT
Found at i:61331 original size:2 final size:2
Alignment explanation
Indices: 61324--61366 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
61314 TGGATAATTC
61324 TA TA TA TA TA 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 TA TA TA TA TA
61366 T
1 T
61367 GCTGTTTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63132 original size:2 final size:2
Alignment explanation
Indices: 63120--63153 Score: 50
Period size: 2 Copynumber: 16.0 Consensus size: 2
63110 AGCAAAAACT
63120 TA TA CTA TA TA TA TA TA TA TA TA TA TA CTA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
63154 AGTCTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 26 0.87
3 4 0.13
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:63483 original size:11 final size:11
Alignment explanation
Indices: 63440--63477 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
63430 TTCCTATATA
*
63440 AAATAAATTAT
1 AAATTAATTAT
63451 CAAA-TAATTAT
1 -AAATTAATTAT
63462 AAATTAATTAT
1 AAATTAATTAT
63473 AAATT
1 AAATT
63478 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:63696 original size:17 final size:17
Alignment explanation
Indices: 63666--63705 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
63656 AATGAGAACA
*
63666 ATTTCTCTTATTCTTCAT
1 ATTT-TCTTATTCTCCAT
*
63684 ATTTTCTTCTTCTCCAT
1 ATTTTCTTATTCTCCAT
63701 ATTTT
1 ATTTT
63706 ATTGTCTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTTTCTTATTCTCCAT
Done.