Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006782.1 Corchorus capsularis cultivar CVL-1 contig06803, 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: 49938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:4490 original size:2 final size:2
Alignment explanation
Indices: 4483--4507 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4473 TTAAGGATAC
4483 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
4508 GTTTTCTCAA
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
Found at i:4809 original size:42 final size:43
Alignment explanation
Indices: 4737--4857 Score: 154
Period size: 42 Copynumber: 2.7 Consensus size: 43
4727 TAAGAGGCAC
* *
4737 AAGGAAGACGATACCTCTATTGTAATATGGAGTCTAGGAGAAGAA
1 AAGGAAGACAATACCTC--TTGAAATATGGAGTCTAGGAGAAGAA
* * *
4782 AATGAGGACAATACCTC-TGAAATATGGAGTCTGGGAGAAGAA
1 AAGGAAGACAATACCTCTTGAAATATGGAGTCTAGGAGAAGAA
4824 AAGGAAGACAATACCTCTATTGAAATATGGAGTC
1 AAGGAAGACAATACCTC--TTGAAATATGGAGTC
4858 CGGGGAATTC
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
42 38 0.58
45 28 0.42
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.21
Consensus pattern (43 bp):
AAGGAAGACAATACCTCTTGAAATATGGAGTCTAGGAGAAGAA
Found at i:8240 original size:28 final size:28
Alignment explanation
Indices: 8170--8241 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
8160 CTGGGACGTC
* * *
8170 TCCCTTTGATGTTTCAGGCGAAAAATCT
1 TCCCTCTGATGTATCAAGCGAAAAATCT
* * * *
8198 TCCTTCTGGTATATCAAGCGGAAAATCT
1 TCCCTCTGATGTATCAAGCGAAAAATCT
8226 TCCCTCTGATGTATCA
1 TCCCTCTGATGTATCA
8242 CACAGCAAGT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.35
Consensus pattern (28 bp):
TCCCTCTGATGTATCAAGCGAAAAATCT
Found at i:15580 original size:30 final size:30
Alignment explanation
Indices: 15506--15582 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
15496 GAGTATGACG
* *
15506 AGGAGGAAGATTCTAATCTCTTTATTTGTGT
1 AGGA-GAAGATTCTGATCTCTTTATTTGTGA
*
15537 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGAGAAGATTCTGATCTCTTTATTTGTGA
*
15567 AGGAGAAAATTCTGAT
1 AGGAGAAGATTCTGAT
15583 TTTGTTTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 38 0.90
31 4 0.10
ACGTcount: A:0.29, C:0.09, G:0.25, T:0.38
Consensus pattern (30 bp):
AGGAGAAGATTCTGATCTCTTTATTTGTGA
Found at i:15598 original size:30 final size:30
Alignment explanation
Indices: 15506--15600 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
15496 GAGTATGACG
* * * * *
15506 AGGAGGAAGATTCTAATCTCTTTATTTGTGT
1 AGGA-GAAAATTCTGATCTCTTTGTTTATGA
* *
15537 AGGAGAAGATTCTGATCTCTTTGTTTGTGA
1 AGGAGAAAATTCTGATCTCTTTGTTTATGA
* *
15567 AGGAGAAAATTCTGAT-TTTGTTTTTTATGA
1 AGGAGAAAATTCTGATCTCT-TTGTTTATGA
15597 AGGA
1 AGGA
15601 TTTGTTTGTG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
29 2 0.04
30 50 0.89
31 4 0.07
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.41
Consensus pattern (30 bp):
AGGAGAAAATTCTGATCTCTTTGTTTATGA
Found at i:26225 original size:3 final size:3
Alignment explanation
Indices: 26217--26260 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
26207 AATATAATCA
26217 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26261 GTTAAATAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:26237 original size:23 final size:23
Alignment explanation
Indices: 26210--26260 Score: 86
Period size: 23 Copynumber: 2.2 Consensus size: 23
26200 TTGAAAGAAT
26210 ATAATCAA-ATAATAATAATAATA
1 ATAAT-AATATAATAATAATAATA
26233 ATAATAATATAATAATAATAATA
1 ATAATAATATAATAATAATAATA
26256 ATAAT
1 ATAAT
26261 GTTAAATAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAATAATATAATAATAATAATA
Found at i:26244 original size:20 final size:20
Alignment explanation
Indices: 26221--26260 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
26211 TAATCAAATA
26221 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
26241 ATAATAATAATAATAATAAT
1 ATAATAATAATAATAATAAT
26261 GTTAAATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAATAATAATAATAATAAT
Found at i:26399 original size:6 final size:6
Alignment explanation
Indices: 26390--26418 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
26380 GTGATACTGA
26390 TGATAG TGATAG TGATAG TGATAG TGATA
1 TGATAG TGATAG TGATAG TGATAG TGATA
26419 TTTTCACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (6 bp):
TGATAG
Found at i:27079 original size:35 final size:35
Alignment explanation
Indices: 26981--27083 Score: 143
Period size: 35 Copynumber: 2.9 Consensus size: 35
26971 TAAGCCATTT
* **
26981 ATTTACTTAGTTACACCAAATTAGGCCAATTACTG
1 ATTTACTTAATTACACCAAATTAGGTTAATTACTG
* * *
27016 ATTTACTTATTTATACCAAATTAAGTTAATTACTG
1 ATTTACTTAATTACACCAAATTAGGTTAATTACTG
*
27051 ATTTACTTAATTACACCGAATTAGGTTAATTAC
1 ATTTACTTAATTACACCAAATTAGGTTAATTAC
27084 CAAGTTATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 59 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (35 bp):
ATTTACTTAATTACACCAAATTAGGTTAATTACTG
Found at i:27148 original size:52 final size:52
Alignment explanation
Indices: 27030--27149 Score: 136
Period size: 52 Copynumber: 2.3 Consensus size: 52
27020 ACTTATTTAT
* * **
27030 ACCAAATTAAGTTAA-TTACTGATTTACTTAATTACACCGAATTAGGTTAATT
1 ACCAAATT-ACTTAATTTAATGATTTACTTAATTACACCGAATTAGGTTAACC
* * * *
27082 ACCAAGTTATTTAATTTAATGGTTTACTTAATTGCACCGAATT-GAGTTAACC
1 ACCAAATTACTTAATTTAATGATTTACTTAATTACACCGAATTAG-GTTAACC
27134 ACCAAATTACTTAATT
1 ACCAAATTACTTAATT
27150 CCATTACCAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
51 6 0.11
52 51 0.89
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (52 bp):
ACCAAATTACTTAATTTAATGATTTACTTAATTACACCGAATTAGGTTAACC
Found at i:27180 original size:73 final size:73
Alignment explanation
Indices: 27077--27244 Score: 203
Period size: 73 Copynumber: 2.3 Consensus size: 73
27067 CGAATTAGGT
* * ** *
27077 TAATTACCAAGTTATTTAATTTAATGGTTTACTTAATTGCACCGAATTGAGTTAACCACCAAATT
1 TAATTACCAAATTACTTAATTTAACAGTTTACTTAATTGCACCGAATTAAGTTAACCACCAAATT
27142 ACTTAAT-
66 ACTTAATA
* * *** *
27149 TCCATTACCAAATTACTTAATTTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTTCCAGAT
1 T-AATTACCAAATTACTTAATTTAACAGTTTACTTAATTGCACCGAATTAAGTTAACCACCAAAT
*
27214 TACTTGATA
65 TACTTAATA
*
27223 TAATTACCAATTTACTTAATTT
1 TAATTACCAAATTACTTAATTT
27245 CACCGAATTA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
72 1 0.01
73 78 0.98
74 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (73 bp):
TAATTACCAAATTACTTAATTTAACAGTTTACTTAATTGCACCGAATTAAGTTAACCACCAAATT
ACTTAATA
Found at i:27198 original size:56 final size:54
Alignment explanation
Indices: 27152--27672 Score: 652
Period size: 56 Copynumber: 9.4 Consensus size: 54
27142 ACTTAATTCC
* *
27152 ATTACCAAATTACTTAA-T-TTACCAGTTTACTTAATTGCACCGAATTAAGTTA
1 ATTACCAAATTACTTAATTATTACCAGTTTACTTAATTACACCGAATTAAGTTG
* * * * *
27204 ATTTCCAGATTACTTGATATAATTACCAATTTACTTAATTTCACCGAATTAAG-TG
1 ATTACCAAATTACTT-A-ATTATTACCAGTTTACTTAATTACACCGAATTAAGTTG
* * * *
27259 AATTACCAAATTACTTAATCTAATTACCAATTTGCTTAATTTCACTGAATTAAGTTG
1 -ATTACCAAATTACTTAAT-T-ATTACCAGTTTACTTAATTACACCGAATTAAGTTG
*
27316 ACTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAA-TT-ATTACCAGTTTACTTAATTACACCGAATTAAGTTG
* * *
27372 ATTACCAAATTACTTAATTTAATTACCAATTTGCTTAATTACACCGGATTAAGTTG
1 ATTACCAAATTACTTAA-TT-ATTACCAGTTTACTTAATTACACCGAATTAAGTTG
27428 ATTACCAAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTG
1 ATTACC-AAATTACTTAA-TT-ATTACCAGTTTACTTAATTACACCGAATTAAGTTG
*
27485 ATTATCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAA-TT-ATTACCAGTTTACTTAATTACACCGAATTAAGTTG
* * *
27541 ACTACCAAATTACTTAATTTAATTACCAATGTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAA-TT-ATTACCAGTTTACTTAATTACACCGAATTAAGTTG
* * * *
27597 ACTACCAATTTACTTAATTTAATTACCAGTTTACTTAATTACACTGAATTAAGTTA
1 ATTACCAAATTACTTAA-TT-ATTACCAGTTTACTTAATTACACCGAATTAAGTTG
27653 ATTACCAAATTACTTAATTA
1 ATTACCAAATTACTTAATTA
27673 ATCCCTTTTA
Statistics
Matches: 424, Mismatches: 35, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
52 13 0.03
53 1 0.00
54 4 0.01
55 4 0.01
56 347 0.82
57 55 0.13
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.39
Consensus pattern (54 bp):
ATTACCAAATTACTTAATTATTACCAGTTTACTTAATTACACCGAATTAAGTTG
Found at i:27217 original size:35 final size:34
Alignment explanation
Indices: 27105--27218 Score: 102
Period size: 35 Copynumber: 3.2 Consensus size: 34
27095 ATTTAATGGT
*** *
27105 TTACTTAATTGCACCGAATTGAGTTAACCACCAAA
1 TTACTTAATTGCACCGAATT-AGTTAATTTCCAGA
* * * *
27140 TTACTTAATTCCATTACCAAATTACTTAATTTACCAGT
1 TTACTTAATTGC---ACCGAATTAGTTAATTT-CCAGA
27178 TTACTTAATTGCACCGAATTAAGTTAATTTCCAGA
1 TTACTTAATTGCACCGAATT-AGTTAATTTCCAGA
27213 TTACTT
1 TTACTT
27219 GATATAATTA
Statistics
Matches: 62, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
35 28 0.45
36 8 0.13
37 5 0.08
38 21 0.34
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (34 bp):
TTACTTAATTGCACCGAATTAGTTAATTTCCAGA
Found at i:27283 original size:21 final size:21
Alignment explanation
Indices: 27259--27298 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27249 GAATTAAGTG
27259 AATTACCAAATTACTTAATCT
1 AATTACCAAATTACTTAATCT
* *
27280 AATTACCAATTTGCTTAAT
1 AATTACCAAATTACTTAAT
27299 TTCACTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.03, T:0.40
Consensus pattern (21 bp):
AATTACCAAATTACTTAATCT
Found at i:27310 original size:112 final size:112
Alignment explanation
Indices: 27152--27671 Score: 762
Period size: 112 Copynumber: 4.7 Consensus size: 112
27142 ACTTAATTCC
* * * *
27152 ATTACCAAATTACTTAA--T--TTACCAGTTTACTTAATTGCACCGAATTAAGTTAATTTCCAGA
1 ATTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTGATTACCAAA
* * *
27213 TTACTTGATATAATTACCAATTTACTTAATTTCACCGAATTAAG-TG
66 TTACTTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTG
* * * * * *
27259 AATTACCAAATTACTTAATCTAATTACCAATTTGCTTAATTTCACTGAATTAAGTTGACTACCAA
1 -ATTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTGATTACCAA
*
27324 ATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTG
65 ATTACTTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTG
* * *
27372 ATTACCAAATTACTTAATTTAATTACCAATTTGCTTAATTACACCGGATTAAGTTGATTACCAAA
1 ATTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTGATTACC-AA
*
27437 ATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTG
65 ATTACTTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTG
* *
27485 ATTATCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTGACTACCAAA
1 ATTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTGATTACCAAA
*
27550 TTACTTAATTTAATTACCAATGTACTTAATTACACCGAATTAAGTTG
66 TTACTTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTG
* * * *
27597 ACTACCAATTTACTTAATTTAATTACCAGTTTACTTAATTACACTGAATTAAGTTAATTACCAAA
1 ATTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTGATTACCAAA
27662 TTACTTAATT
66 TTACTTAATT
27672 AATCCCTTTT
Statistics
Matches: 376, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
108 17 0.05
110 1 0.00
112 249 0.66
113 109 0.29
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.39
Consensus pattern (112 bp):
ATTACCAAATTACTTAATTTAATTACCAGTTTACTTAATTACACCGAATTAAGTTGATTACCAAA
TTACTTAATTTAATTACCAATTTACTTAATTACACCGAATTAAGTTG
Found at i:27342 original size:21 final size:21
Alignment explanation
Indices: 27318--27411 Score: 67
Period size: 21 Copynumber: 4.8 Consensus size: 21
27308 TTAAGTTGAC
27318 TACCAAATTACTTAATTTAAT
1 TACCAAATTACTTAATTTAAT
**
27339 TACCAGTTTACTTAA-TT-A-
1 TACCAAATTACTTAATTTAAT
* * * *
27357 CACC-GA--A-TTAAGTTGAT
1 TACCAAATTACTTAATTTAAT
27374 TACCAAATTACTTAATTTAAT
1 TACCAAATTACTTAATTTAAT
* *
27395 TACCAATTTGCTTAATT
1 TACCAAATTACTTAATT
27412 ACACCGGATT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 1 0.02
17 4 0.07
18 4 0.07
19 1 0.02
20 3 0.05
21 36 0.64
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.41
Consensus pattern (21 bp):
TACCAAATTACTTAATTTAAT
Found at i:27509 original size:21 final size:21
Alignment explanation
Indices: 27485--27524 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27475 AATTAAGTTG
*
27485 ATTATCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
**
27506 ATTACCAGTTTACTTAATT
1 ATTACCAAATTACTTAATT
27525 ACACCGAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:27557 original size:21 final size:20
Alignment explanation
Indices: 27533--27613 Score: 57
Period size: 21 Copynumber: 4.2 Consensus size: 20
27523 TTACACCGAA
27533 TTAAGTTGACTACCAAATTAC
1 TTAAGTTGACTACC-AATTAC
* * *
27554 TTAATTTAATTACCAATGTAC
1 TTAAGTTGACTACCAAT-TAC
*
27575 TTAA-TT-AC-ACCGA--A-
1 TTAAGTTGACTACCAATTAC
27589 TTAAGTTGACTACCAATTTAC
1 TTAAGTTGACTACCAA-TTAC
27610 TTAA
1 TTAA
27614 TTTAATTACC
Statistics
Matches: 46, Mismatches: 6, Indels: 16
0.68 0.09 0.24
Matches are distributed among these distances:
14 4 0.09
15 3 0.07
16 2 0.04
17 4 0.09
18 4 0.09
19 1 0.02
20 6 0.13
21 22 0.48
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.37
Consensus pattern (20 bp):
TTAAGTTGACTACCAATTAC
Found at i:27671 original size:16 final size:16
Alignment explanation
Indices: 27615--27672 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
27605 TTTACTTAAT
**
27615 TTAATTACCAGTTTAC
1 TTAATTACCAAATTAC
* *
27631 TTAATTACACTGAATTAAG
1 TTAATTAC-C-AAATT-AC
27650 TTAATTACCAAATTAC
1 TTAATTACCAAATTAC
27666 TTAATTA
1 TTAATTA
27673 ATCCCTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
16 16 0.48
17 5 0.15
18 3 0.09
19 9 0.27
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.41
Consensus pattern (16 bp):
TTAATTACCAAATTAC
Found at i:27823 original size:38 final size:37
Alignment explanation
Indices: 27746--27838 Score: 125
Period size: 38 Copynumber: 2.5 Consensus size: 37
27736 ATTAATCTTC
* *
27746 TTACTTTGACTCTTAATCATCAATTTACTTATTAATA
1 TTACTTTGACTCTTAATTATCAATTTACTGATTAATA
* *
27783 TTACTTTGACTCTTAATTA-CTAATTTTACTGGTTACTA
1 TTACTTTGACTCTTAATTATC-AA-TTTACTGATTAATA
27821 TTACTTTGACTCTTAATT
1 TTACTTTGACTCTTAATT
27839 TATTGGGGTA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.02
37 20 0.40
38 29 0.58
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (37 bp):
TTACTTTGACTCTTAATTATCAATTTACTGATTAATA
Found at i:32553 original size:168 final size:168
Alignment explanation
Indices: 32275--32601 Score: 654
Period size: 168 Copynumber: 1.9 Consensus size: 168
32265 TCTAAAAATA
32275 CAAGACTCATTCTTCCTGACATTGACATCACACTGGCAAAGGCCGCAGTGAATACAAGGCGGCAA
1 CAAGACTCATTCTTCCTGACATTGACATCACACTGGCAAAGGCCGCAGTGAATACAAGGCGGCAA
32340 ATGTGGTTCTGAAAGCTGGAACCAAGTTAGGTGATGCGCGTAGTCACTGAGAACTCAGCTTTTCC
66 ATGTGGTTCTGAAAGCTGGAACCAAGTTAGGTGATGCGCGTAGTCACTGAGAACTCAGCTTTTCC
32405 AGCTTGGATTTTGCCAGATCAAGTTGTTCCTGATCTGG
131 AGCTTGGATTTTGCCAGATCAAGTTGTTCCTGATCTGG
32443 CAAGACTCATTCTTCCTGACATTGACATCACACTGGCAAAGGCCGCAGTGAATACAAGGCGGCAA
1 CAAGACTCATTCTTCCTGACATTGACATCACACTGGCAAAGGCCGCAGTGAATACAAGGCGGCAA
32508 ATGTGGTTCTGAAAGCTGGAACCAAGTTAGGTGATGCGCGTAGTCACTGAGAACTCAGCTTTTCC
66 ATGTGGTTCTGAAAGCTGGAACCAAGTTAGGTGATGCGCGTAGTCACTGAGAACTCAGCTTTTCC
32573 AGCTTGGATTTTGCCAGATCAAGTTGTTC
131 AGCTTGGATTTTGCCAGATCAAGTTGTTC
32602 TGCAAGATAA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 159 1.00
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.26
Consensus pattern (168 bp):
CAAGACTCATTCTTCCTGACATTGACATCACACTGGCAAAGGCCGCAGTGAATACAAGGCGGCAA
ATGTGGTTCTGAAAGCTGGAACCAAGTTAGGTGATGCGCGTAGTCACTGAGAACTCAGCTTTTCC
AGCTTGGATTTTGCCAGATCAAGTTGTTCCTGATCTGG
Found at i:40169 original size:18 final size:20
Alignment explanation
Indices: 40129--40169 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
40119 CTTTACAAAC
*
40129 TGCAACTTGATTATTCTGTTA
1 TGCAACTTGA-TATTCTGCTA
40150 TGCAACTTGA-A-TCTGCTA
1 TGCAACTTGATATTCTGCTA
40168 TG
1 TG
40170 TCTGAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 8 0.42
19 1 0.05
21 10 0.53
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.41
Consensus pattern (20 bp):
TGCAACTTGATATTCTGCTA
Found at i:41855 original size:6 final size:6
Alignment explanation
Indices: 41844--41870 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41834 AACATATTAT
41844 ATATAA ATATAA ATATAA ATATAA ATA
1 ATATAA ATATAA ATATAA ATATAA ATA
41871 ATATTTCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAA
Found at i:45446 original size:3 final size:3
Alignment explanation
Indices: 45421--45465 Score: 54
Period size: 3 Copynumber: 14.0 Consensus size: 3
45411 TAATTCTTAC
*
45421 CTT CTTT CTT CTT ATT ACTTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT -C-TT CTT CTT CTT CTT CTT CTT CTT CTT
45466 ATTATTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
3 31 0.84
4 4 0.11
5 2 0.05
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:47340 original size:31 final size:31
Alignment explanation
Indices: 47274--47407 Score: 123
Period size: 31 Copynumber: 4.5 Consensus size: 31
47264 TTTTGTGCAC
* * * **
47274 GTGGCACGCCACGTGCCATTTTTTGAAACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
47305 GTGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* * * *
47336 GTGGCGTGACATGTTTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
*
47367 GT-G---GCCACATGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTGTCACTTTTTGGTACAT
* *
47394 GTGGCGTGCTACGT
1 GTGGCATGCCACGT
47408 CGGACACCGT
Statistics
Matches: 82, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
27 22 0.27
28 1 0.01
30 1 0.01
31 58 0.71
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.34
Consensus pattern (31 bp):
GTGGCATGCCACGTGTCACTTTTTGGTACAT
Found at i:47384 original size:27 final size:27
Alignment explanation
Indices: 47312--47398 Score: 111
Period size: 27 Copynumber: 3.1 Consensus size: 27
47302 CATGTGGCAT
* *
47312 GCCACGTGTCACTTTTTGGTACACGTG
1 GCCACATGTCACTTTTTGGTACATGTG
*
47339 GCGTGACATGTTTCACTTTTTGGTACATGTG
1 GC--CACATG--TCACTTTTTGGTACATGTG
47370 GCCACATGTCACTTTTTGGTACATGTG
1 GCCACATGTCACTTTTTGGTACATGTG
47397 GC
1 GC
47399 GTGCTACGTC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
27 23 0.44
29 9 0.17
31 20 0.38
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.37
Consensus pattern (27 bp):
GCCACATGTCACTTTTTGGTACATGTG
Found at i:47790 original size:15 final size:15
Alignment explanation
Indices: 47770--47801 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
47760 TATCGTGATT
47770 TGAAACTGGACAAAA
1 TGAAACTGGACAAAA
47785 TGAAACTGGACAAAA
1 TGAAACTGGACAAAA
47800 TG
1 TG
47802 TTCTTGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.22, T:0.16
Consensus pattern (15 bp):
TGAAACTGGACAAAA
Found at i:48776 original size:10 final size:10
Alignment explanation
Indices: 48758--48792 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
48748 ACAAAAATCA
48758 TCTTTTTTTCT
1 TCTTTTTTT-T
48769 TCTTTTTTTTT
1 TC-TTTTTTTT
48780 TCTTTTTTTT
1 TCTTTTTTTT
48790 TCT
1 TCT
48793 AGATCTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.48
11 5 0.22
12 7 0.30
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:48779 original size:14 final size:13
Alignment explanation
Indices: 48760--48790 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
48750 AAAAATCATC
48760 TTTTTTTCTTCTTT
1 TTTTTTTCTT-TTT
48774 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
48787 TTTT
1 TTTT
48791 CTAGATCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (13 bp):
TTTTTTTCTTTTT
Done.