Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015656.1 Corchorus capsularis cultivar CVL-1 contig15677, 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: 95382
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:9 original size:2 final size:2
Alignment explanation
Indices: 3--32 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 CT
3 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
33 ATTTTTGCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1112 original size:2 final size:2
Alignment explanation
Indices: 1105--1132 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1095 TTATAGTATT
1105 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
1133 GTCTGGTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1501 original size:46 final size:48
Alignment explanation
Indices: 1418--1511 Score: 138
Period size: 46 Copynumber: 2.0 Consensus size: 48
1408 ATGTAAGATG
* *
1418 TTAACATAAAGGGATTATATAAACCTTTGTTTCTTGATAAAACTATGA
1 TTAACATAAAGGGATTATACAAACCTTTATTTCTTGATAAAACTATGA
**
1466 TTAACATAAAGGGA-T-TACAAACCTTTATTTCTTGATAGCACTATGA
1 TTAACATAAAGGGATTATACAAACCTTTATTTCTTGATAAAACTATGA
1512 CATTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
46 27 0.64
47 1 0.02
48 14 0.33
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (48 bp):
TTAACATAAAGGGATTATACAAACCTTTATTTCTTGATAAAACTATGA
Found at i:3672 original size:3 final size:3
Alignment explanation
Indices: 3664--3688 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3654 ATATATATAT
3664 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
3689 CAACAACGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:11908 original size:1 final size:1
Alignment explanation
Indices: 11902--11939 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
11892 TCGGTTAAGC
11902 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
11940 GGTTTTCGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:14980 original size:21 final size:21
Alignment explanation
Indices: 14954--15006 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
14944 GAATTAGTAT
*
14954 ACCTGGGAGAACCAATGGTAA
1 ACCTGGGAGAACCAAAGGTAA
* *
14975 ACCTGGGGGAACCAAAGTTAA
1 ACCTGGGAGAACCAAAGGTAA
*
14996 ACCGGGGAGAA
1 ACCTGGGAGAA
15007 TCACCAAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.32, T:0.11
Consensus pattern (21 bp):
ACCTGGGAGAACCAAAGGTAA
Found at i:17530 original size:18 final size:19
Alignment explanation
Indices: 17496--17532 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17486 CTTCATTCAA
*
17496 TATCAAATTTTAAAAAAAT
1 TATCAAATTTAAAAAAAAT
17515 TATCAAA-TTAAAAAAAAT
1 TATCAAATTTAAAAAAAAT
17533 GGATAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
TATCAAATTTAAAAAAAAT
Found at i:19587 original size:26 final size:27
Alignment explanation
Indices: 19557--19627 Score: 135
Period size: 26 Copynumber: 2.7 Consensus size: 27
19547 CTTAAAGGTT
19557 AAAAATATCATATTGATCCTTC-AAAA
1 AAAAATATCATATTGATCCTTCAAAAA
19583 AAAAATATCATATTGATCCTTCAAAAA
1 AAAAATATCATATTGATCCTTCAAAAA
19610 AAAAATATCATATTGATC
1 AAAAATATCATATTGATC
19628 AATTCAGGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 22 0.50
27 22 0.50
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.31
Consensus pattern (27 bp):
AAAAATATCATATTGATCCTTCAAAAA
Found at i:22269 original size:19 final size:19
Alignment explanation
Indices: 22245--22287 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
22235 TGGATTTAGC
*
22245 CAGTTT-TTTTAGTTCAGTT
1 CAGTTTCTTTGAG-TCAGTT
22264 CAGTTTCTTTGAGTCAGTT
1 CAGTTTCTTTGAGTCAGTT
22283 -AGTTT
1 CAGTTT
22288 GCGTCTGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 5 0.23
19 12 0.55
20 5 0.23
ACGTcount: A:0.16, C:0.12, G:0.19, T:0.53
Consensus pattern (19 bp):
CAGTTTCTTTGAGTCAGTT
Found at i:22753 original size:4 final size:4
Alignment explanation
Indices: 22746--22770 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
22736 TTACGGATTG
22746 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
22771 ATTTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:25213 original size:31 final size:31
Alignment explanation
Indices: 25176--25278 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 31
25166 TTTAATTTGG
25176 TCAAATAAGGGCCTAACGTTTGCCAAAATAC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATAC
* *
25207 TCAAATAAGGGCC---CGGTCTT--TAAATTTGAC
1 TCAAATAAGGGCCTAAC-GT-TTGCCAAA-AT-AC
* *
25237 -CAAATAAAGGCCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGCCTAACGTTTGCCAAAATAC
25267 TCAAATAAGGGC
1 TCAAATAAGGGC
25279 ATATTTCATA
Statistics
Matches: 55, Mismatches: 7, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
28 4 0.07
29 14 0.25
30 7 0.13
31 26 0.47
32 4 0.07
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.23
Consensus pattern (31 bp):
TCAAATAAGGGCCTAACGTTTGCCAAAATAC
Found at i:25276 original size:60 final size:60
Alignment explanation
Indices: 25117--25278 Score: 216
Period size: 60 Copynumber: 2.7 Consensus size: 60
25107 GCTAATTGCT
** * * * * * **
25117 CAAATAAGGGCCTAACGTTTGTTAAAATGTTTAAATAAGAGCCTGATCTTTTAATTTGGT
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTAAATTTGAC
* *
25177 CAAATAAGGGCCTAACGTTTGCCAAAATACTCAAATAAGGGCCCGGTCTTTAAATTTGAC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTAAATTTGAC
*
25237 CAAATAAAGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
1 CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
25279 ATATTTCATA
Statistics
Matches: 89, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
60 89 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTAAATTTGAC
Found at i:25348 original size:31 final size:31
Alignment explanation
Indices: 25308--25506 Score: 112
Period size: 31 Copynumber: 6.5 Consensus size: 31
25298 AACTGAAACC
* * *
25308 AGACCCTTATTTGAGTATTTTCGATAACGTT
1 AGACCCTTATTTGAGCATCTTCAATAACGTT
*
25339 AGACTCTTATTTGAGCATCTTCAATAACGTT
1 AGACCCTTATTTGAGCATCTTCAATAACGTT
* ** *
25370 AGGCCCTTATTTG-GCAAAATT-AA-AA-GAT
1 AGACCCTTATTTGAGC-ATCTTCAATAACGTT
* * * * *
25398 CGAGCTCTTATTTGAGCATTTTCGATAACATT
1 AGA-CCCTTATTTGAGCATCTTCAATAACGTT
** *
25430 AGACCCTTATTTG-GCCAAATT-AA-AA-GATC
1 AGACCCTTATTTGAG-CATCTTCAATAACG-TT
*
25459 AGACCCTTATTTGAGCATTTTGGC-A-AACGTT
1 AGACCCTTATTTGAGCATCTT--CAATAACGTT
*
25490 AGACTCTTATTTGAGCA
1 AGACCCTTATTTGAGCA
25507 GTTAGCCAGA
Statistics
Matches: 127, Mismatches: 28, Indels: 26
0.70 0.15 0.14
Matches are distributed among these distances:
28 3 0.02
29 34 0.27
30 10 0.08
31 76 0.60
32 4 0.03
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (31 bp):
AGACCCTTATTTGAGCATCTTCAATAACGTT
Found at i:25466 original size:29 final size:29
Alignment explanation
Indices: 25373--25471 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 29
25363 TAACGTTAGG
*
25373 CCCTTATTTGGCAAAATTAAAAGATC-GA
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
* ** * * *
25401 GCTCTTATTTGAG-CATTTTCGATAACATTAGA
1 -CCCTTATTTG-GCCAAATT--AAAAGATCAGA
25433 CCCTTATTTGGCCAAATTAAAAGATCAGA
1 CCCTTATTTGGCCAAATTAAAAGATCAGA
25462 CCCTTATTTG
1 CCCTTATTTG
25472 AGCATTTTGG
Statistics
Matches: 52, Mismatches: 13, Indels: 10
0.69 0.17 0.13
Matches are distributed among these distances:
29 30 0.58
30 2 0.04
31 18 0.35
32 2 0.04
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (29 bp):
CCCTTATTTGGCCAAATTAAAAGATCAGA
Found at i:25477 original size:60 final size:60
Alignment explanation
Indices: 25339--25502 Score: 224
Period size: 60 Copynumber: 2.7 Consensus size: 60
25329 CGATAACGTT
* * *
25339 AGACTCTTATTTGAGCATCTTCAATAACGTTAGGCCCTTATTTGGCAAAATTAAAAGATC
1 AGACTCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCAAAATTAAAAGATC
* *
25399 -GAGCTCTTATTTGAGCATTTTCGATAACATTAGACCCTTATTTGGCCAAATTAAAAGATC
1 AGA-CTCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCAAAATTAAAAGATC
* * *
25459 AGACCCTTATTTGAGCATTTTGGCA-AACGTTAGACTCTTATTTG
1 AGACTCTTATTTGAGCATTTTCG-ATAACGTTAGACCCTTATTTG
25503 AGCAGTTAGC
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
59 2 0.02
60 87 0.95
61 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (60 bp):
AGACTCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCAAAATTAAAAGATC
Found at i:29710 original size:27 final size:28
Alignment explanation
Indices: 29680--29745 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
29670 TTGATTAAAG
29680 ACACTGTTTAGATT-CATC-AAAAAAAAT
1 ACACTGTTTAGATTGCA-CAAAAAAAAAT
**
29707 ACACTGTTT-TTTTGGCACAAAAAAAAAT
1 ACACTGTTTAGATT-GCACAAAAAAAAAT
29735 ACACTGTTTAG
1 ACACTGTTTAG
29746 CATGGTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
26 2 0.06
27 10 0.31
28 20 0.62
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (28 bp):
ACACTGTTTAGATTGCACAAAAAAAAAT
Found at i:37499 original size:59 final size:58
Alignment explanation
Indices: 37397--37557 Score: 214
Period size: 59 Copynumber: 2.7 Consensus size: 58
37387 ACTGACACCA
* *
37397 GACCCTTATTTGAGCATTTTCGATAACGTTAGGTCCTTATTTGGCCAAAATCAAAGATCG
1 GACCCTTATTTGAGCATTTTGGA-AACGTTAGG-CCTTATTTGGCCAAAATAAAAGATCG
* * * *
37457 GACCCTTATTTGAGTATTTTGGCAACGTTAGGCCCTTATTTGGTCAAATTAAAAGATCG
1 GACCCTTATTTGAGCATTTTGGAAACGTTAGG-CCTTATTTGGCCAAAATAAAAGATCG
* *
37516 GACCCTTGTTTGAACATTTTGGTAAACGTTAGGCCTTATTTG
1 GACCCTTATTTGAGCATTTTGG-AAACGTTAGGCCTTATTTG
37558 AGCAATTAAC
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
59 60 0.67
60 29 0.33
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (58 bp):
GACCCTTATTTGAGCATTTTGGAAACGTTAGGCCTTATTTGGCCAAAATAAAAGATCG
Found at i:44320 original size:55 final size:54
Alignment explanation
Indices: 44231--44393 Score: 238
Period size: 55 Copynumber: 3.0 Consensus size: 54
44221 CAGGACTTTC
* *
44231 TTCAAGGAACA-TTGGGAGATTACGAAGATTTCAAGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTT-GGAGATCACG-AGATCTCAAGCGAGTGTCAGCATTGAAGCT
*
44286 TTCAAGGAACACTTGGAGACCACTGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
1 TTCAAGGAACACTTGGAGATCAC-GAGATCTCAAGCGAGTGTCAGCATTGAAGCT
* *
44341 TTCAAGGAACACTTGGAAATCACAGAGATCTCAGGCGAGTGTCAGCATTGAAG
1 TTCAAGGAACACTTGGAGATCAC-GAGATCTCAAGCGAGTGTCAGCATTGAAG
44394 ATTGATAAGA
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
55 96 0.97
56 3 0.03
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.23
Consensus pattern (54 bp):
TTCAAGGAACACTTGGAGATCACGAGATCTCAAGCGAGTGTCAGCATTGAAGCT
Found at i:44636 original size:21 final size:21
Alignment explanation
Indices: 44610--44649 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44600 ACTGGTGGGC
44610 TTTACTTACTGAGGAAGGCAT
1 TTTACTTACTGAGGAAGGCAT
*
44631 TTTACTTGCTGAGGAAGGC
1 TTTACTTACTGAGGAAGGC
44650 GAACTCTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
TTTACTTACTGAGGAAGGCAT
Found at i:44820 original size:17 final size:17
Alignment explanation
Indices: 44798--44830 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
44788 CCCATAATAC
44798 CTAGGTAGTATGAGGTA
1 CTAGGTAGTATGAGGTA
44815 CTAGGTAGTATGAGGT
1 CTAGGTAGTATGAGGT
44831 GATATGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.36, T:0.30
Consensus pattern (17 bp):
CTAGGTAGTATGAGGTA
Found at i:45489 original size:156 final size:156
Alignment explanation
Indices: 45182--45545 Score: 386
Period size: 156 Copynumber: 2.3 Consensus size: 156
45172 GAGCTTCTCA
* * *
45182 CCTCAAACTGTCCTTGAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTGAATGAGCTGAAA
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAA
* * *
45247 TTTCGCCAAGGGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTC
66 TTTCACCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTC
* * * *
45312 CCCTTGATGGTGAACTAGGTTTCTCT
131 CCCTAGATAGAGAACTAGGTTTCACT
****
45338 CC-CTGTGTTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAACGAAGCTG-
1 CCTC-AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACG-AGCTGA
* *
45400 ATTTTCTACC-AGTAGACTTA-TAT-TCTCACCATAA-AGCTATTGG-AAAAATTCTAAGTAAAA
64 AATTTC-ACCAAG-AGACTTAGAATATC-CA-CATAAGA-CTA-TGGAAAAAATTCTAAGTAAAA
* * * *
45460 CCGAACT-CTCTAGCATAGAGAAGTTGGTTTGACT
123 CCGAACTCCCCTAG-ATAGAGAACTAGGTTTCACT
* *
45494 CCTCAAACTGTCCTTAACTGAAAAACTAGCATAAGTTTTTCATACTAAGTCT
1 CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCT
45546 GTTTGAGATG
Statistics
Matches: 171, Mismatches: 26, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
154 2 0.01
155 20 0.12
156 145 0.85
157 4 0.02
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (156 bp):
CCTCAAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTCTCAACGAGCTGAAA
TTTCACCAAGAGACTTAGAATATCCACATAAGACTATGGAAAAAATTCTAAGTAAAACCGAACTC
CCCTAGATAGAGAACTAGGTTTCACT
Found at i:46164 original size:11 final size:11
Alignment explanation
Indices: 46150--46185 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
46140 TTTAGACCCG
46150 AAACCGACCGA
1 AAACCGACCGA
46161 AAACCGACCGA
1 AAACCGACCGA
46172 AAACCGACCGA
1 AAACCGACCGA
46183 AAA
1 AAA
46186 TATATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.33, G:0.17, T:0.00
Consensus pattern (11 bp):
AAACCGACCGA
Found at i:48542 original size:60 final size:60
Alignment explanation
Indices: 48449--48570 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
48439 CCCGGTTAAA
*
48449 GCCTTTTAATTGTACTAATTTTTTAGTAAAAGTTTTGCCAAATTTCAATGAAAAATAATT
1 GCCTTTTAATTGCACTAATTTTTTAGTAAAAGTTTTGCCAAATTTCAATGAAAAATAATT
48509 GCCTTTTAATTGCACTAATTTTTTAGTAAAAGTTTTGCCAAATTTCAATGAAAAATAATT
1 GCCTTTTAATTGCACTAATTTTTTAGTAAAAGTTTTGCCAAATTTCAATGAAAAATAATT
48569 GC
1 GC
48571 TAATGAGTGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (60 bp):
GCCTTTTAATTGCACTAATTTTTTAGTAAAAGTTTTGCCAAATTTCAATGAAAAATAATT
Found at i:50052 original size:26 final size:26
Alignment explanation
Indices: 50022--50073 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
50012 AAAACAAAAA
50022 CTAATCTACGAAAAAGAAAGAAGGGG
1 CTAATCTACGAAAAAGAAAGAAGGGG
50048 CTAATCTACGAAAAAGAAAGAAGGGG
1 CTAATCTACGAAAAAGAAAGAAGGGG
50074 ACCTGGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.27, T:0.12
Consensus pattern (26 bp):
CTAATCTACGAAAAAGAAAGAAGGGG
Found at i:51721 original size:7 final size:7
Alignment explanation
Indices: 51709--51773 Score: 85
Period size: 7 Copynumber: 9.0 Consensus size: 7
51699 AGAGCATGAT
51709 TAAAAAG
1 TAAAAAG
51716 TAAAAAG
1 TAAAAAG
51723 TAAAAAG
1 TAAAAAG
51730 TAAAAAG
1 TAAAAAG
51737 TAAAAAG
1 TAAAAAG
*
51744 TAAGAAGAA
1 TAA-AA-AG
* *
51753 TTAAAAT
1 TAAAAAG
51760 TAAAAAG
1 TAAAAAG
51767 TAAAAAG
1 TAAAAAG
51774 CAAGCGTGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
7 44 0.86
8 4 0.08
9 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (7 bp):
TAAAAAG
Found at i:51932 original size:36 final size:38
Alignment explanation
Indices: 51871--51942 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 38
51861 ATGACGAATT
51871 AAATAGAAAAATCGAAAACGGAATT-A-GAAATTGACC
1 AAATAGAAAAATCGAAAACGGAATTAAGGAAATTGACC
*
51907 AAATAGAAAAAT-TAAAA-GGCAAATTAAGGAAATTGA
1 AAATAGAAAAATCGAAAACGG--AATTAAGGAAATTGA
51943 TATACCTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
34 2 0.06
35 4 0.13
36 16 0.52
37 1 0.03
38 8 0.26
ACGTcount: A:0.58, C:0.07, G:0.17, T:0.18
Consensus pattern (38 bp):
AAATAGAAAAATCGAAAACGGAATTAAGGAAATTGACC
Found at i:53575 original size:16 final size:16
Alignment explanation
Indices: 53556--53587 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
53546 ATTTCCCTCT
53556 CCCTCAATTCTTGCCG
1 CCCTCAATTCTTGCCG
*
53572 CCCTCAGTTCTTGCCG
1 CCCTCAATTCTTGCCG
53588 TCGACGTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.09, C:0.44, G:0.16, T:0.31
Consensus pattern (16 bp):
CCCTCAATTCTTGCCG
Found at i:59355 original size:2 final size:2
Alignment explanation
Indices: 59348--59440 Score: 55
Period size: 2 Copynumber: 51.0 Consensus size: 2
59338 CTGATATTTA
* *
59348 AT AT AT AT AT AT AT AT AT AT CAT AT AC AT A- AT AT ACG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT A-T AT AT AT
* *
59391 A- AC AA AT -T AT AT A- AT A- AT A- AT A- AT A- AT -T AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59424 AT AT AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
59441 TTTTATTAGG
Statistics
Matches: 72, Mismatches: 6, Indels: 26
0.69 0.06 0.25
Matches are distributed among these distances:
1 11 0.15
2 58 0.81
3 3 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (2 bp):
AT
Found at i:59359 original size:6 final size:6
Alignment explanation
Indices: 59348--59440 Score: 55
Period size: 5 Copynumber: 17.0 Consensus size: 6
59338 CTGATATTTA
* * * *
59348 ATATAT ATATAT ATATAT ATCATAT ACATA- ATATACG ATATAT A-ACAA
1 ATATAT ATATAT ATATAT AT-ATAT ATATAT ATATA-T ATATAT ATATAT
59396 AT-TAT ATA-AT A-ATA- ATA-AT A-AT-T ATAT-T ATATAT ATA-AT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
59435 ATATAT
1 ATATAT
59441 TTTTATTAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
4 6 0.09
5 28 0.41
6 24 0.35
7 10 0.15
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (6 bp):
ATATAT
Found at i:59420 original size:20 final size:20
Alignment explanation
Indices: 59346--59435 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
59336 ATCTGATATT
59346 TAATATATAT-AT-A-TATA
1 TAATATATATAATAATTATA
59363 T-ATATCATATACATAA-TATA
1 TAATAT-ATATA-ATAATTATA
**
59383 CGATATATA-ACA-AATTATA
1 TAATATATATA-ATAATTATA
59402 TAATA-ATAATAATAATTATA
1 TAATATAT-ATAATAATTATA
*
59422 TTATATATATAATA
1 TAATATATATAATA
59436 TATATTTTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
16 4 0.07
17 5 0.08
18 4 0.07
19 14 0.24
20 26 0.44
21 6 0.10
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (20 bp):
TAATATATATAATAATTATA
Found at i:60018 original size:29 final size:30
Alignment explanation
Indices: 59970--60036 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
59960 ACATCCAACA
* * *
59970 GTCAAATAAGCTCATGAACT-TTTATTTTG
1 GTCAAATAAACTCATCAACTCTTAATTTTG
*
59999 GTCAAATAAACTCTTCAACTCTTAATTTTG
1 GTCAAATAAACTCATCAACTCTTAATTTTG
60029 GTCAAATA
1 GTCAAATA
60037 GGCCCTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (30 bp):
GTCAAATAAACTCATCAACTCTTAATTTTG
Found at i:60277 original size:19 final size:18
Alignment explanation
Indices: 60242--60283 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
60232 ATCAAATATT
60242 TTTTTTCCAAACAAATTAA
1 TTTTTTCCAAACAAATT-A
*
60261 TTTTTTCGAAA-ATAATTA
1 TTTTTTCCAAACA-AATTA
60279 TTTTT
1 TTTTT
60284 GCCGCATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTTTTCCAAACAAATTA
Found at i:64311 original size:25 final size:25
Alignment explanation
Indices: 64277--64325 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
64267 ACACCCTACC
*
64277 ACACCTAATTAAACCTTATGTTAAT
1 ACACCTAATTAAACCCTATGTTAAT
64302 ACACCTAATTAAACCCTATGTTAA
1 ACACCTAATTAAACCCTATGTTAA
64326 ACGTGATTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.04, T:0.33
Consensus pattern (25 bp):
ACACCTAATTAAACCCTATGTTAAT
Found at i:65235 original size:27 final size:27
Alignment explanation
Indices: 65161--65246 Score: 118
Period size: 27 Copynumber: 3.1 Consensus size: 27
65151 ACAAGTTCCT
*
65161 CTACTTACAAAAAGGGATCATTTTGGTCC
1 CTAC-TACAAAAAGGG-TCAATTTGGTCC
**
65190 CTTACTACAAAAACCGTCAATTTGGTCC
1 C-TACTACAAAAAGGGTCAATTTGGTCC
65218 CTACTACAAAAAGGGTCAATTTGGTCC
1 CTACTACAAAAAGGGTCAATTTGGTCC
65245 CT
1 CT
65247 CTAATTACAA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 26 0.51
28 12 0.24
29 10 0.20
30 3 0.06
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (27 bp):
CTACTACAAAAAGGGTCAATTTGGTCC
Found at i:66684 original size:12 final size:12
Alignment explanation
Indices: 66667--66691 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66657 TTTTTGCCTC
66667 TAGGGTTTGGCT
1 TAGGGTTTGGCT
66679 TAGGGTTTGGCT
1 TAGGGTTTGGCT
66691 T
1 T
66692 TCATGTCACA
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:0.08, C:0.08, G:0.40, T:0.44
Consensus pattern (12 bp):
TAGGGTTTGGCT
Found at i:67034 original size:193 final size:193
Alignment explanation
Indices: 66705--67053 Score: 608
Period size: 193 Copynumber: 1.8 Consensus size: 193
66695 TGTCACAACT
** * *
66705 TTTCAAATTTTGACTCTTCCACCGTTTTTTTTGACATAAAATATTGAAATTTAGACTATCTCACT
1 TTTCAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATATTAAAATTTAGACTATCTCACT
*
66770 TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATTTATTTTA
66 TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTA
*
66835 TCTCACTTAGGGTTTAGATTTTATGTCATGTCATTTTTTTGTCTCTCATAGCCATTTTTTTTA
131 TCTCACTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTGTCTCTCATAGCCATTTTTTTTA
* *
66898 TTTCAAATTTTGACTCTTCCACCACTTTTTATGACATAGAATGTTAAAATTTAGACTATCTCACT
1 TTTCAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATATTAAAATTTAGACTATCTCACT
* *
66963 TAGGGTTTGATATAGTTTTGGGGCATTTCTTTCTCTCACTTAGGGTTTATATATCATGTATTTTA
66 TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTA
67028 TCTCACTTAGGGTTTAGATTTCATGT
131 TCTCACTTAGGGTTTAGATTTCATGT
67054 GTCACAACTT
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
193 146 1.00
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (193 bp):
TTTCAAATTTTGACTCTTCCACCACTTTTTATGACATAAAATATTAAAATTTAGACTATCTCACT
TAGGGTTTAATATAGTTTTGGGGCATTTCTTTATCTCACTTAGGGTTTATATATCATGTATTTTA
TCTCACTTAGGGTTTAGATTTCATGTCATGTCATTTTTTTGTCTCTCATAGCCATTTTTTTTA
Found at i:71889 original size:24 final size:22
Alignment explanation
Indices: 71858--71903 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 22
71848 AAGAGGGAAG
71858 GATCAGAGAGAAGGAAGGGAGAA
1 GATCAGAGAGAAGGAA-GGAGAA
*
71881 GATCGAGAGATAAGGAAGGAGAA
1 GATC-AGAGAGAAGGAAGGAGAA
71904 AAAGAATGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.48, C:0.04, G:0.41, T:0.07
Consensus pattern (22 bp):
GATCAGAGAGAAGGAAGGAGAA
Found at i:87507 original size:2 final size:2
Alignment explanation
Indices: 87502--87526 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
87492 TTTAACTTTA
87502 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 A
87527 GTTTGAGAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.