Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009088.1 Corchorus capsularis cultivar CVL-1 contig09109, 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: 33071
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:473 original size:10 final size:10
Alignment explanation
Indices: 441--474 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
431 GGTCGAAATT
441 TTTTTTTATA
1 TTTTTTTATA
*
451 TTATTTTAT-
1 TTTTTTTATA
460 TTTTTTTATA
1 TTTTTTTATA
470 TTTTT
1 TTTTT
475 CGATATAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:581 original size:9 final size:8
Alignment explanation
Indices: 547--580 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
537 GAATCGGCTA
547 TGAATTTT
1 TGAATTTT
*
555 TGAAGTTTC
1 TGAA-TTTT
564 TGAATTTT
1 TGAATTTT
572 TGAATTTT
1 TGAATTTT
580 T
1 T
581 TAAGAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:2218 original size:33 final size:33
Alignment explanation
Indices: 2181--2251 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
2171 CCCTAAATTA
*
2181 TATTTAGGGGCGTTTCCTACAAATAAATGCCAC
1 TATTTAGGGGCGTTTCCTACAAATAAACGCCAC
** *
2214 TATTTAGGGGCGTTTTGTTCAAATAAACGCCAC
1 TATTTAGGGGCGTTTCCTACAAATAAACGCCAC
2247 TATTT
1 TATTT
2252 TGGGATGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (33 bp):
TATTTAGGGGCGTTTCCTACAAATAAACGCCAC
Found at i:3056 original size:30 final size:30
Alignment explanation
Indices: 3022--3097 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
3012 AGCCATGTGC
* *
3022 CCGGTCTTGTGCGGCT-ACTCCATGCAATGG
1 CCGGTCTTGTGC-GATGACTCCATCCAATGG
*
3052 CCGGTCTTGTGCGATGGCTCCATCCAATGG
1 CCGGTCTTGTGCGATGACTCCATCCAATGG
* *
3082 CCGGTCCTATGCGATG
1 CCGGTCTTGTGCGATG
3098 CCCTCATCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 2 0.05
30 38 0.95
ACGTcount: A:0.13, C:0.30, G:0.30, T:0.26
Consensus pattern (30 bp):
CCGGTCTTGTGCGATGACTCCATCCAATGG
Found at i:3854 original size:30 final size:30
Alignment explanation
Indices: 3820--3882 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
3810 CATCTTCAAG
3820 TCCATGATAAGTCCTT-CGCGCATCATTCCC
1 TCCATGATAAG-CCTTGCGCGCATCATTCCC
*
3850 TCCATGATAAGCCTTGGGCGCATCATTCCC
1 TCCATGATAAGCCTTGCGCGCATCATTCCC
3880 TCC
1 TCC
3883 TCCTTGAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.19, C:0.37, G:0.16, T:0.29
Consensus pattern (30 bp):
TCCATGATAAGCCTTGCGCGCATCATTCCC
Found at i:4240 original size:33 final size:33
Alignment explanation
Indices: 4203--4276 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
4193 TTCTTTTCAC
** *
4203 CCAAAACAGTCCTATTTTCAATGCTATGATCAA
1 CCAAAACAGAACTATTTGCAATGCTATGATCAA
*
4236 CCAAAACAGAATTATTTGCAATGCTATGATCAA
1 CCAAAACAGAACTATTTGCAATGCTATGATCAA
4269 CCAAAACA
1 CCAAAACA
4277 AATTTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (33 bp):
CCAAAACAGAACTATTTGCAATGCTATGATCAA
Found at i:4284 original size:33 final size:33
Alignment explanation
Indices: 4215--4285 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
4205 AAAACAGTCC
*
4215 TATTTTCAATGCTATGATCAACCAAAACAGAAT
1 TATTTGCAATGCTATGATCAACCAAAACAGAAT
4248 TATTTGCAATGCTATGATCAACCAAAACA-AATT
1 TATTTGCAATGCTATGATCAACCAAAACAGAA-T
4281 TATTT
1 TATTT
4286 TCATCATAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.06
33 34 0.94
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.34
Consensus pattern (33 bp):
TATTTGCAATGCTATGATCAACCAAAACAGAAT
Found at i:4341 original size:33 final size:32
Alignment explanation
Indices: 4304--4408 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 32
4294 ATTAGCATCC
* * *
4304 AAAACAGATTTTGTTTCATCACAAACAACACCT
1 AAAACAGATTTAGTATCATCGCAAACAACA-CT
* *
4337 AAAACAAATTTAGTGTCATCGCAAACAACACT
1 AAAACAGATTTAGTATCATCGCAAACAACACT
** *
4369 CAAATTAGGTTTAGTATCATCGCAAACAACATCT
1 -AAAACAGATTTAGTATCATCGCAAACAACA-CT
4403 AAAACA
1 AAAACA
4409 CTCTTTGCAA
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
32 2 0.03
33 55 0.93
34 2 0.03
ACGTcount: A:0.45, C:0.22, G:0.09, T:0.25
Consensus pattern (32 bp):
AAAACAGATTTAGTATCATCGCAAACAACACT
Found at i:10708 original size:45 final size:45
Alignment explanation
Indices: 10657--10745 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
10647 TAATAGAGTA
*
10657 GTGGAATTACTAAAAGATCCTTACCCCGAATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
*
10702 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTG
10746 CAGAAGTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATGAGCTGG
Found at i:11199 original size:35 final size:36
Alignment explanation
Indices: 11133--11204 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
11123 TTTTAATTGA
*
11133 ATATATATATATATATATATAAATGAAGAATTTGTTT
1 ATATATATATATATATATATAAAT-AAGAATTAGTTT
*
11170 ATATATATATATAT-TATATATAAT-TGAATTAGTTT
1 ATATATATATATATATATATA-AATAAGAATTAGTTT
11205 CAAATTATAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
35 9 0.28
36 6 0.19
37 17 0.53
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (36 bp):
ATATATATATATATATATATAAATAAGAATTAGTTT
Found at i:11719 original size:69 final size:69
Alignment explanation
Indices: 11601--11739 Score: 226
Period size: 69 Copynumber: 2.0 Consensus size: 69
11591 AAAACGAACA
* * *
11601 ACTAAGGAAAAAATGGTGGGAGCACCATTAATTACATCTCAATGCTAAAATTATATATAAAGACA
1 ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATCTCAATGCTAAAATTACATATAAAGACA
11666 ATGC
66 ATGC
*
11670 ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATC-CAAATGTTAAAATTACATATAAAGAC
1 ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATCTC-AATGCTAAAATTACATATAAAGAC
11734 AATGC
65 AATGC
11739 A
1 A
11740 TTTCAAGTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 64 0.98
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (69 bp):
ACTAAGGAAAAAATGGTAGGAACACCATTAATTACATCTCAATGCTAAAATTACATATAAAGACA
ATGC
Found at i:13450 original size:21 final size:21
Alignment explanation
Indices: 13418--13477 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
13408 GACAGCTAGC
*
13418 GGAGCTTGAAAAATCCGATTT
1 GGAGCTTGAAAAATCAGATTT
* *
13439 GGGGCTTCAAAAAAATCAGATTT
1 GGAGCTT--GAAAAATCAGATTT
13462 GGAGCTTGAAAAATCA
1 GGAGCTTGAAAAATCA
13478 AATCTGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 14 0.44
23 18 0.56
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.25
Consensus pattern (21 bp):
GGAGCTTGAAAAATCAGATTT
Found at i:20057 original size:15 final size:17
Alignment explanation
Indices: 20037--20069 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
20027 CGATGAAATG
20037 TCGGGTC-ATT-TGGGT
1 TCGGGTCAATTCTGGGT
20052 TCGGGTCAATTCTGGGT
1 TCGGGTCAATTCTGGGT
20069 T
1 T
20070 GAGTCGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.09, C:0.15, G:0.36, T:0.39
Consensus pattern (17 bp):
TCGGGTCAATTCTGGGT
Found at i:20456 original size:11 final size:11
Alignment explanation
Indices: 20440--20465 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
20430 GTCTCTGATT
20440 TATACTATATA
1 TATACTATATA
20451 TATACTATATA
1 TATACTATATA
20462 TATA
1 TATA
20466 TAATATAATA
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (11 bp):
TATACTATATA
Found at i:21237 original size:7 final size:7
Alignment explanation
Indices: 21225--21253 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
21215 AATGATATAG
21225 TTTCAAC
1 TTTCAAC
21232 TTTCAAC
1 TTTCAAC
21239 TTTCAAC
1 TTTCAAC
21246 TTTCAAC
1 TTTCAAC
21253 T
1 T
21254 AATGGAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTCAAC
Found at i:21524 original size:16 final size:16
Alignment explanation
Indices: 21497--21571 Score: 89
Period size: 16 Copynumber: 4.8 Consensus size: 16
21487 GTCGGGTTGA
21497 TCGGGTTCGGGTCATT
1 TCGGGTTCGGGTCATT
* *
21513 TTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCATT
*
21529 TCGGGTTCGGGTCGTT
1 TCGGGTTCGGGTCATT
* *
21545 T-GGATTCGGGTAATT
1 TCGGGTTCGGGTCATT
*
21560 TCGGGTTTGGGT
1 TCGGGTTCGGGT
21572 ATCCAAAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.25
16 36 0.75
ACGTcount: A:0.07, C:0.12, G:0.40, T:0.41
Consensus pattern (16 bp):
TCGGGTTCGGGTCATT
Found at i:21561 original size:31 final size:32
Alignment explanation
Indices: 21497--21571 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
21487 GTCGGGTTGA
* * * *
21497 TCGGGTTCGGGTCATTTTGGGTTTGGGTCATT
1 TCGGGTTCGGGTCAGTTTGGATTCGGGTAATT
21529 TCGGGTTCGGGTC-GTTTGGATTCGGGTAATT
1 TCGGGTTCGGGTCAGTTTGGATTCGGGTAATT
*
21560 TCGGGTTTGGGT
1 TCGGGTTCGGGT
21572 ATCCAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 25 0.66
32 13 0.34
ACGTcount: A:0.07, C:0.12, G:0.40, T:0.41
Consensus pattern (32 bp):
TCGGGTTCGGGTCAGTTTGGATTCGGGTAATT
Found at i:21841 original size:22 final size:22
Alignment explanation
Indices: 21733--21844 Score: 102
Period size: 22 Copynumber: 5.0 Consensus size: 22
21723 GCTCTATACT
*
21733 AGGTTAT-GAAAATTTCATTGTG
1 AGGTTATCG-AAATTTCATAGTG
* * *
21755 AGATTATCAAAATTTCATAATG
1 AGGTTATCGAAATTTCATAGTG
** *
21777 AGGTTATCGAAATTTTGTAGGG
1 AGGTTATCGAAATTTCATAGTG
* *
21799 AAGTTTATC-AAAGTTTTATAGTG
1 -AGGTTATCGAAA-TTTCATAGTG
21822 AGGTTATCGAAATTTCATAGTG
1 AGGTTATCGAAATTTCATAGTG
21844 A
1 A
21845 CCATTTCATA
Statistics
Matches: 71, Mismatches: 15, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
22 53 0.75
23 18 0.25
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (22 bp):
AGGTTATCGAAATTTCATAGTG
Found at i:21952 original size:23 final size:22
Alignment explanation
Indices: 21861--21939 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
21851 CATAGGGAGG
* ** *
21861 TATCAAAATTTGATAATATAAT
1 TATCAAAATTTCATAGGAAAAT
* **
21883 TATCAAAATTTTATACGG-AGTT
1 TATCAAAATTTCATA-GGAAAAT
21905 TATCAAAATTTCATAGGAAAAT
1 TATCAAAATTTCATAGGAAAAT
21927 TATCAAAACTTTC
1 TATCAAAA-TTTC
21940 TTAGTAAGGT
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
21 2 0.04
22 39 0.87
23 4 0.09
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAAAAT
Found at i:21980 original size:22 final size:22
Alignment explanation
Indices: 21882--22050 Score: 71
Period size: 22 Copynumber: 7.5 Consensus size: 22
21872 GATAATATAA
* *
21882 TTATCAAAATTTTATACGGA-GT
1 TTATCAAAATTTTATA-GAATGG
* **
21904 TTATCAAAATTTCATAGGAA-AA
1 TTATCAAAATTTTATA-GAATGG
21926 TTATCAAAACTTTCT-TAGTAA-GG
1 TTATCAAAA-TTT-TATAG-AATGG
** *
21949 TTATTGAAATTTTGTAGAATGG
1 TTATCAAAATTTTATAGAATGG
21971 TTATCAAAATTATATATAGAGGA-GG
1 TTATCAAAATT-T-TATAGA--ATGG
* * * ** *
21996 TTATAAAAATTTTGTTGTGTAG
1 TTATCAAAATTTTATAGAATGG
*
22018 TTATCAAAATTTTATAGGGAT-G
1 TTATCAAAATTTTATA-GAATGG
22040 TTATCAAAATT
1 TTATCAAAATT
22051 ACAAGTGTGA
Statistics
Matches: 112, Mismatches: 24, Indels: 22
0.71 0.15 0.14
Matches are distributed among these distances:
21 3 0.03
22 70 0.62
23 20 0.18
24 6 0.05
25 12 0.11
26 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTTATAGAATGG
Found at i:22006 original size:47 final size:44
Alignment explanation
Indices: 21847--22050 Score: 130
Period size: 44 Copynumber: 4.6 Consensus size: 44
21837 CATAGTGACC
* * *
21847 ATTTCATAGGGAGG-TATCAAAA-TTTGATA-ATATAATTATCAAA
1 ATTTTATAGGGAGGTTATAAAAATTTTG-TAGA-ATAGTTATCAAA
* * * ** *
21890 ATTTTATACGGAGTTTATCAAAATTTCATAGGAA-AATTATCAAA
1 ATTTTATAGGGAGGTTATAAAAATTTTGTA-GAATAGTTATCAAA
** ** *
21934 ACTTTCT-TAGTAAGGTTATTGAAATTTTGTAGAATGGTTATCAAA
1 A-TTT-TATAGGGAGGTTATAAAAATTTTGTAGAATAGTTATCAAA
* **
21979 ATTATATATAGAGGAGGTTATAAAAATTTTGTTGTGTAGTTATCAAA
1 ATT-T-TATAG-GGAGGTTATAAAAATTTTGTAGAATAGTTATCAAA
* *
22026 ATTTTATAGGGATGTTATCAAAATT
1 ATTTTATAGGGAGGTTATAAAAATT
22051 ACAAGTGTGA
Statistics
Matches: 125, Mismatches: 26, Indels: 19
0.74 0.15 0.11
Matches are distributed among these distances:
43 11 0.09
44 40 0.32
45 38 0.30
46 6 0.05
47 30 0.24
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (44 bp):
ATTTTATAGGGAGGTTATAAAAATTTTGTAGAATAGTTATCAAA
Found at i:22454 original size:16 final size:16
Alignment explanation
Indices: 22435--22570 Score: 102
Period size: 16 Copynumber: 8.6 Consensus size: 16
22425 GAACCCTCCC
*
22435 GACCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
22451 GACCC-ACAACCC-AGAT
1 GACCCGA-AACCCGA-AT
* *
22467 GTCCCGAGACCCGAAT
1 GACCCGAAACCCGAAT
* *
22483 GACCCGTAA-CCTAGAT
1 GACCCGAAACCCGA-AT
22499 GACCCGAAACCCGAAT
1 GACCCGAAACCCGAAT
* *
22515 GA-CCGTAACCCGAGT
1 GACCCGAAACCCGAAT
* *
22530 GACACGAGACCC-ATAT
1 GACCCGAAACCCGA-AT
*
22546 GACCCGAAACCAGAAT
1 GACCCGAAACCCGAAT
*
22562 AACCCGAAA
1 GACCCGAAA
22571 AGTTAACTCG
Statistics
Matches: 92, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
15 19 0.21
16 67 0.73
17 6 0.07
ACGTcount: A:0.35, C:0.35, G:0.20, T:0.10
Consensus pattern (16 bp):
GACCCGAAACCCGAAT
Found at i:23706 original size:175 final size:175
Alignment explanation
Indices: 23415--23764 Score: 700
Period size: 175 Copynumber: 2.0 Consensus size: 175
23405 GCTGAATGGA
23415 CACAAGATGATATTAAGAAGCTCCAACTGAACTACAAAGCCATCAATACCCTTCACTGTGCTTTG
1 CACAAGATGATATTAAGAAGCTCCAACTGAACTACAAAGCCATCAATACCCTTCACTGTGCTTTG
23480 AACATTACTGAGTTCAATAGGGTCTCTACTTGCACTAATGCAAAAGAGGTCTGGGAAAAACTCAG
66 AACATTACTGAGTTCAATAGGGTCTCTACTTGCACTAATGCAAAAGAGGTCTGGGAAAAACTCAG
23545 AGTTACTGATGAGGGTACTTCGCAAGTCAAGGAATCAAAGATCAG
131 AGTTACTGATGAGGGTACTTCGCAAGTCAAGGAATCAAAGATCAG
23590 CACAAGATGATATTAAGAAGCTCCAACTGAACTACAAAGCCATCAATACCCTTCACTGTGCTTTG
1 CACAAGATGATATTAAGAAGCTCCAACTGAACTACAAAGCCATCAATACCCTTCACTGTGCTTTG
23655 AACATTACTGAGTTCAATAGGGTCTCTACTTGCACTAATGCAAAAGAGGTCTGGGAAAAACTCAG
66 AACATTACTGAGTTCAATAGGGTCTCTACTTGCACTAATGCAAAAGAGGTCTGGGAAAAACTCAG
23720 AGTTACTGATGAGGGTACTTCGCAAGTCAAGGAATCAAAGATCAG
131 AGTTACTGATGAGGGTACTTCGCAAGTCAAGGAATCAAAGATCAG
23765 ACTGCAGCAA
Statistics
Matches: 175, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 175 1.00
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (175 bp):
CACAAGATGATATTAAGAAGCTCCAACTGAACTACAAAGCCATCAATACCCTTCACTGTGCTTTG
AACATTACTGAGTTCAATAGGGTCTCTACTTGCACTAATGCAAAAGAGGTCTGGGAAAAACTCAG
AGTTACTGATGAGGGTACTTCGCAAGTCAAGGAATCAAAGATCAG
Found at i:26080 original size:17 final size:17
Alignment explanation
Indices: 26058--26096 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
26048 AAATTAAATA
**
26058 TTTTTATTTTAATATAT
1 TTTTTATTGAAATATAT
*
26075 TTTTTATTGAAATTTAT
1 TTTTTATTGAAATATAT
26092 TTTTT
1 TTTTT
26097 TAATAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTATTGAAATATAT
Found at i:26713 original size:17 final size:17
Alignment explanation
Indices: 26691--26741 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
26681 AACCAAAACT
26691 AAAGCTTCTTTGAGCCA
1 AAAGCTTCTTTGAGCCA
26708 AAAGCTTCTTTGAGCCA
1 AAAGCTTCTTTGAGCCA
*
26725 AAAGCTTGTTTGAGCCA
1 AAAGCTTCTTTGAGCCA
26742 GACCAAAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (17 bp):
AAAGCTTCTTTGAGCCA
Found at i:27207 original size:15 final size:17
Alignment explanation
Indices: 27187--27224 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
27177 TTTTAATTAT
*
27187 TAAAAAATA-ATT-CAA
1 TAAAAAATATATTAAAA
27202 TAAAAAATATATTAAAA
1 TAAAAAATATATTAAAA
27219 TAAAAA
1 TAAAAA
27225 TATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 3 0.15
17 8 0.40
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAAATATATTAAAA
Found at i:30057 original size:13 final size:14
Alignment explanation
Indices: 30039--30067 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
30029 ATAAACCGGG
30039 TTTGCATTCAT-CA
1 TTTGCATTCATGCA
30052 TTTGCATTCATGCA
1 TTTGCATTCATGCA
30066 TT
1 TT
30068 AAGTAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.10, T:0.48
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:30368 original size:39 final size:39
Alignment explanation
Indices: 30274--30413 Score: 226
Period size: 39 Copynumber: 3.6 Consensus size: 39
30264 TTTAAGCAAT
* * * *
30274 TCCAAGAGAAGAGTTTTGGAAATTGAATGTTTTTAGTAA
1 TCCAAGAGAAGACTTTTGGAAAGTAAATGTTTTTAGGAA
30313 TTCCAAGAGAAGACTTTTGGAAAGTAAATGTTTTTAGGAA
1 -TCCAAGAGAAGACTTTTGGAAAGTAAATGTTTTTAGGAA
*
30353 TCCAAGAGAAGACTTTTGGAAAGTAATTGTTTTTAGGAA
1 TCCAAGAGAAGACTTTTGGAAAGTAAATGTTTTTAGGAA
30392 TCCAAGAGAAGACTTTTGGAAA
1 TCCAAGAGAAGACTTTTGGAAA
30414 TTAATAAAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 60 0.63
40 35 0.37
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (39 bp):
TCCAAGAGAAGACTTTTGGAAAGTAAATGTTTTTAGGAA
Found at i:30650 original size:33 final size:33
Alignment explanation
Indices: 30613--30719 Score: 126
Period size: 33 Copynumber: 3.2 Consensus size: 33
30603 AGCACTAGTG
* *
30613 ACCGGCCATGCGACTTGGAGAAGCCCGGCCAAC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* *
30646 ACCGGCCACGCGACTCGGAGATGCCCGGCCATC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
* * * *
30679 ACCCGCCACGCGACATGGACATGTCCGGCC-AC
1 ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
30711 AACCGGCCA
1 -ACCGGCCA
30720 TCGCTTGGTG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
32 1 0.02
33 61 0.98
ACGTcount: A:0.22, C:0.41, G:0.28, T:0.08
Consensus pattern (33 bp):
ACCGGCCACGCGACTTGGAGATGCCCGGCCAAC
Found at i:30740 original size:33 final size:33
Alignment explanation
Indices: 30703--30775 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
30693 ATGGACATGT
*
30703 CCGGCCACAACCGGCCATCGCTTGGTGCACCAA
1 CCGGCCACAACCGGCCATCGCTTGGCGCACCAA
30736 CCGGCCACAACCGGCCATCGCTTGGCGCACCAA
1 CCGGCCACAACCGGCCATCGCTTGGCGCACCAA
30769 CCGGCCA
1 CCGGCCA
30776 TCGATAGGGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.21, C:0.45, G:0.25, T:0.10
Consensus pattern (33 bp):
CCGGCCACAACCGGCCATCGCTTGGCGCACCAA
Found at i:31729 original size:17 final size:17
Alignment explanation
Indices: 31703--31736 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31693 CCACCCTTCT
31703 TGAAAATTCAAAAATTC
1 TGAAAATTCAAAAATTC
*
31720 TGAAACTTCAAAAATTC
1 TGAAAATTCAAAAATTC
31737 ATAGCCGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (17 bp):
TGAAAATTCAAAAATTC
Found at i:31830 original size:8 final size:9
Alignment explanation
Indices: 31810--31844 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
31800 ACTTATATCG
*
31810 AAAAATATA
1 AAAAAAATA
31819 AAAAAAATA
1 AAAAAAATA
31828 AAAAAAATA
1 AAAAAAATA
31837 AAAAAAAT
1 AAAAAAAT
31845 TTCGACCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (9 bp):
AAAAAAATA
Done.