Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012273.1 Corchorus capsularis cultivar CVL-1 contig12294, 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: 36560
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:368 original size:14 final size:14
Alignment explanation
Indices: 351--388 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
341 TTCAGTATTA
351 AATTTTCAGCACTC
1 AATTTTCAGCACTC
*
365 AATTTTTCAGCACTT
1 AA-TTTTCAGCACTC
380 AATTTTCAG
1 AATTTTCAG
389 TTTATCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.29, C:0.21, G:0.08, T:0.42
Consensus pattern (14 bp):
AATTTTCAGCACTC
Found at i:1162 original size:70 final size:70
Alignment explanation
Indices: 1080--1309 Score: 270
Period size: 70 Copynumber: 3.2 Consensus size: 70
1070 TTGTTTAGGT
* * *
1080 TTTTA-TAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
1144 ATTTTA
65 ATTTTA
1150 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
1215 TTATATTTTACCA
62 AT-TATTTT---A
* * * *
1228 TTTCACTATTTTACTCAACTAAAAACTCAATTTTTATGTAATTAAATCTAATA---TTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
1290 TTATA
66 TTTTA
1295 TTTTACTATTTTACT
1 TTTTACTATTTTACT
1310 ATTTTAGTTA
Statistics
Matches: 140, Mismatches: 11, Indels: 21
0.81 0.06 0.12
Matches are distributed among these distances:
67 15 0.11
70 53 0.38
71 7 0.05
72 2 0.01
73 2 0.01
74 4 0.03
75 6 0.04
78 51 0.36
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:1162 original size:78 final size:76
Alignment explanation
Indices: 1080--1315 Score: 310
Period size: 78 Copynumber: 3.2 Consensus size: 76
1070 TTGTTTAGGT
* * *
1080 TTTTA-TAGTTTTACTCAACTAAAAAATCTATTTTTATTTAATTAAATATAATATCTT-T-A-TA
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAACTA
*
1141 AT-TATTTT--A
65 TTATATTTTACA
1150 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTTATAACTA
1215 TTATATTTTACCA
65 TTATATTTTA-CA
* * *
1228 TTTCACTATTTTACTCAACTAAAAACTCAATTTTTATGTAATTAAATCTAATA--TTATAACTAT
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAACTAT
1291 TATATTTTACTA
66 TATATTTTAC-A
1303 TTTTACTATTTTA
1 TTTTACTATTTTA
1316 GTTAAAAAAC
Statistics
Matches: 148, Mismatches: 8, Indels: 15
0.87 0.05 0.09
Matches are distributed among these distances:
70 48 0.32
71 5 0.03
72 1 0.01
73 1 0.01
74 4 0.03
75 38 0.26
78 51 0.34
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (76 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTATAACTAT
TATATTTTACA
Found at i:4359 original size:19 final size:19
Alignment explanation
Indices: 4335--4375 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
4325 GAATTTAACA
4335 TTTTTTAT-ATATATTTAAT
1 TTTTTTATAATATATTT-AT
*
4354 TTTTTTATAATTTATTTAT
1 TTTTTTATAATATATTTAT
4373 TTT
1 TTT
4376 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTTATAATATATTTAT
Found at i:4366 original size:16 final size:16
Alignment explanation
Indices: 4334--4384 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
4324 TGAATTTAAC
4334 ATTTTTTATATATATTT
1 ATTTTTT-TATATATTT
4351 AATTTTTTTATA-ATTT
1 -ATTTTTTTATATATTT
*
4367 ATTTATTTTATATTTTT
1 ATTT-TTTTATATATTT
4384 A
1 A
4385 AAATTTTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 4 0.13
16 11 0.37
17 8 0.27
18 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTTATATATTT
Found at i:4369 original size:20 final size:18
Alignment explanation
Indices: 4335--4379 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
4325 GAATTTAACA
*
4335 TTTTTTATATATATTTAA
1 TTTTTTATATATATTTAT
4353 TTTTTT-TATA-ATTTAT
1 TTTTTTATATATATTTAT
4369 TTATTTTATAT
1 TT-TTTTATAT
4380 TTTTAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 8 0.33
18 9 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTATATATATTTAT
Found at i:4374 original size:24 final size:26
Alignment explanation
Indices: 4337--4399 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 26
4327 ATTTAACATT
* * *
4337 TTTTATATATATTTAATTTTTTTATAA
1 TTTTAT-TCTATTTAATATTTTTAAAA
*
4364 -TTTATT-TATTTTATATTTTTAAAA
1 TTTTATTCTATTTAATATTTTTAAAA
4388 TTTTATTCTATT
1 TTTTATTCTATT
4400 GAGAATATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 15 0.48
25 7 0.23
26 9 0.29
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTATTCTATTTAATATTTTTAAAA
Found at i:4381 original size:15 final size:15
Alignment explanation
Indices: 4344--4381 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
4334 ATTTTTTATA
4344 TATATTTAATTTTTT
1 TATATTTAATTTTTT
4359 TATAATTT-ATTTATTT
1 TAT-ATTTAATTT-TTT
4375 TATATTT
1 TATATTT
4382 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATATTTAATTTTTT
Found at i:4506 original size:21 final size:19
Alignment explanation
Indices: 4470--4511 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
4460 TATATAATGT
*
4470 ATATTTTATTTATATATTA
1 ATATTCTATTTATATATTA
4489 ATATTCTATATTATTATATTA
1 ATATTCTAT-TTA-TATATTA
4510 AT
1 AT
4512 TTATATAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATTCTATTTATATATTA
Found at i:4515 original size:10 final size:10
Alignment explanation
Indices: 4502--4539 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
4492 TTCTATATTA
4502 TTATATTAAT
1 TTATATTAAT
4512 TTATA-TAA-
1 TTATATTAAT
*
4520 GTATATTAAT
1 TTATATTAAT
4530 TTATATTAAT
1 TTATATTAAT
4540 AATACTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.17
9 6 0.25
10 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (10 bp):
TTATATTAAT
Found at i:4571 original size:17 final size:17
Alignment explanation
Indices: 4551--4591 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
4541 ATACTCTATT
4551 ATTATTA-ATACTATTAA
1 ATTATTACATA-TATTAA
*
4568 ATTATTACATATATTTA
1 ATTATTACATATATTAA
4585 ATTATTA
1 ATTATTA
4592 TTATATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 19 0.86
18 3 0.14
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTACATATATTAA
Found at i:4571 original size:20 final size:19
Alignment explanation
Indices: 4475--4594 Score: 70
Period size: 18 Copynumber: 6.3 Consensus size: 19
4465 AATGTATATT
* *
4475 TTATTTATATATTAATATTC
1 TTATTAATATATTAA-ATTA
* *
4495 TATATTATTATATTAATTTA
1 T-TATTAATATATTAAATTA
*
4515 -TA-TAAGTATATTAATTTA
1 TTATTAA-TATATTAAATTA
* **
4533 -TATTAATAATACTCTATTA
1 TTATTAAT-ATATTAAATTA
4552 TTATTAATACTATTAAATTA
1 TTATTAATA-TATTAAATTA
* *
4572 TTA--CATATATTTAATTA
1 TTATTAATATATTAAATTA
4589 TTATTA
1 TTATTA
4595 TATCTAATAT
Statistics
Matches: 77, Mismatches: 15, Indels: 17
0.71 0.14 0.16
Matches are distributed among these distances:
17 14 0.18
18 20 0.26
19 11 0.14
20 20 0.26
21 12 0.16
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (19 bp):
TTATTAATATATTAAATTA
Found at i:4582 original size:9 final size:8
Alignment explanation
Indices: 4495--4605 Score: 55
Period size: 9 Copynumber: 12.5 Consensus size: 8
4485 ATTAATATTC
*
4495 TATATTAT
1 TATATTAA
4503 TATATTAA
1 TATATTAA
*
4511 TTTATATAA
1 TATAT-TAA
4520 GTATATTAA
1 -TATATTAA
4529 TTTATATTAA
1 --TATATTAA
*
4539 TAATACTCTAT
1 T-ATA-T-TAA
4550 TATTATTAA
1 TA-TATTAA
4559 TACTATTAA
1 TA-TATTAA
4568 -ATTATTACA
1 TA-TATTA-A
4577 TATATTTAA
1 TATA-TTAA
*
4586 T-TATTAT
1 TATATTAA
4593 TATATCTAA
1 TATAT-TAA
4602 TATA
1 TATA
4606 ATATAATTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
7 4 0.05
8 23 0.28
9 30 0.37
10 19 0.23
11 5 0.06
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (8 bp):
TATATTAA
Found at i:5597 original size:32 final size:32
Alignment explanation
Indices: 5559--5632 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
5549 TTTTGAGTCA
*
5559 GGTTCGGGTTGGATTTAGGTCAGGTTAATTCG
1 GGTTCGGGTTGAATTTAGGTCAGGTTAATTCG
*
5591 GGTTCGGGTTGAATTTGGGTCAGGTTAATTCG
1 GGTTCGGGTTGAATTTAGGTCAGGTTAATTCG
5623 GGTTCGGGTT
1 GGTTCGGGTT
5633 CTGTTTGGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.14, C:0.09, G:0.39, T:0.38
Consensus pattern (32 bp):
GGTTCGGGTTGAATTTAGGTCAGGTTAATTCG
Found at i:5600 original size:16 final size:16
Alignment explanation
Indices: 5581--5632 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
5571 ATTTAGGTCA
5581 GGTTAATTCGGGTTCG
1 GGTTAATTCGGGTTCG
* *
5597 GGTTGAATTTGGG-TCA
1 GGTT-AATTCGGGTTCG
5613 GGTTAATTCGGGTTCG
1 GGTTAATTCGGGTTCG
5629 GGTT
1 GGTT
5633 CTGTTTGGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 7 0.23
16 16 0.53
17 7 0.23
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.38
Consensus pattern (16 bp):
GGTTAATTCGGGTTCG
Found at i:5640 original size:32 final size:31
Alignment explanation
Indices: 5559--5642 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 31
5549 TTTTGAGTCA
* *
5559 GGTTCGGGTTGGATTTAGGTCAGGTTAATTCG
1 GGTTCGGGTTAG-TTTGGGTCAGGTTAATTCG
*
5591 GGTTCGGGTTGAATTTGGGTCAGGTTAATTCG
1 GGTTCGGGTT-AGTTTGGGTCAGGTTAATTCG
*
5623 GGTTCGGGTTCTGTTTGGGT
1 GGTTCGGGTT-AGTTTGGGT
5643 TTTGGCCAGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.12, C:0.10, G:0.39, T:0.39
Consensus pattern (31 bp):
GGTTCGGGTTAGTTTGGGTCAGGTTAATTCG
Found at i:5809 original size:16 final size:16
Alignment explanation
Indices: 5788--5892 Score: 120
Period size: 16 Copynumber: 6.6 Consensus size: 16
5778 AATTTTCGGA
*
5788 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGAGCTTT
* *
5804 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGAGCTTT
*
5820 TTCGGGTTTGAGCTTT
1 TTCGGGTTCGAGCTTT
* *
5836 TTCGGGTTCGTGTTTT
1 TTCGGGTTCGAGCTTT
* *
5852 TTCGGGTTTGAACTTT
1 TTCGGGTTCGAGCTTT
* *
5868 TTCGGGTTCGGGTTTT
1 TTCGGGTTCGAGCTTT
5884 TTCGGGTTC
1 TTCGGGTTC
5893 AGGTTCAGGC
Statistics
Matches: 72, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 72 1.00
ACGTcount: A:0.04, C:0.13, G:0.32, T:0.50
Consensus pattern (16 bp):
TTCGGGTTCGAGCTTT
Found at i:5824 original size:32 final size:32
Alignment explanation
Indices: 5788--5891 Score: 190
Period size: 32 Copynumber: 3.2 Consensus size: 32
5778 AATTTTCGGA
5788 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
*
5820 TTCGGGTTTGAGCTTTTTCGGGTTCGTGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
*
5852 TTCGGGTTTGAACTTTTTCGGGTTCGGGTTTT
1 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
5884 TTCGGGTT
1 TTCGGGTT
5892 CAGGTTCAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.04, C:0.12, G:0.33, T:0.51
Consensus pattern (32 bp):
TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTT
Found at i:5906 original size:64 final size:64
Alignment explanation
Indices: 5788--5909 Score: 174
Period size: 64 Copynumber: 1.9 Consensus size: 64
5778 AATTTTCGGA
* * ***
5788 TTCGGGTTTGAGCTTTTTCGGGTTCGGGTTTTTTCGGGTTTGAGCTTTTTCGGGTTCGTGTTTT
1 TTCGGGTTTGAACTTTTTCGGGTTCGGGTTTTTTCGGGTTTCAGCTTAGGCGGGTTCGTGTTTT
*
5852 TTCGGGTTTGAACTTTTTCGGGTTCGGGTTTTTTCGGG-TTCAGGTTCAGGCGGGTTCG
1 TTCGGGTTTGAACTTTTTCGGGTTCGGGTTTTTTCGGGTTTCAGCTT-AGGCGGGTTCG
5910 GATAGTTAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
63 6 0.12
64 45 0.88
ACGTcount: A:0.05, C:0.14, G:0.34, T:0.47
Consensus pattern (64 bp):
TTCGGGTTTGAACTTTTTCGGGTTCGGGTTTTTTCGGGTTTCAGCTTAGGCGGGTTCGTGTTTT
Found at i:14071 original size:5 final size:6
Alignment explanation
Indices: 14059--14089 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
14049 TTCTTTTTCG
14059 TTATTT TTATTT TTA-TT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TT
14090 CGTTTTAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:14072 original size:17 final size:16
Alignment explanation
Indices: 14046--14093 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
14036 TACCCTTATC
*
14046 TTTTTCTTTTTCGTTA
1 TTTTTATTTTTCGTTA
**
14062 TTTTTATTTTTATTTTA
1 TTTTTATTTTT-CGTTA
14079 TTTTTATTTTTCGTT
1 TTTTTATTTTTCGTT
14094 TTAGTGCTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.10, C:0.06, G:0.04, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTTCGTTA
Found at i:14077 original size:11 final size:11
Alignment explanation
Indices: 14063--14088 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14053 TTTTCGTTAT
14063 TTTTATTTTTA
1 TTTTATTTTTA
14074 TTTTATTTTTA
1 TTTTATTTTTA
14085 TTTT
1 TTTT
14089 TCGTTTTAGT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:22831 original size:19 final size:20
Alignment explanation
Indices: 22792--22827 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
22782 ATTTTTAAGT
22792 AAAAATATAATATATAAATA
1 AAAAATATAATATATAAATA
22812 AAAAAT-TAATAT-TAAA
1 AAAAATATAATATATAAA
22828 ATAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 6 0.38
20 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATATAATATATAAATA
Found at i:24186 original size:17 final size:18
Alignment explanation
Indices: 24151--24186 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24141 CTCAACCTCA
24151 AACTAGAAGAAAAACTAG
1 AACTAGAAGAAAAACTAG
*
24169 AACTAGAGGAAAAA-TAG
1 AACTAGAAGAAAAACTAG
24186 A
1 A
24187 TGAAGAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.61, C:0.08, G:0.19, T:0.11
Consensus pattern (18 bp):
AACTAGAAGAAAAACTAG
Found at i:24815 original size:19 final size:18
Alignment explanation
Indices: 24778--24817 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
24768 TTCTTGAAAT
*
24778 AATTCTTCAATGGTCTTC
1 AATTCTTCAATGATCTTC
*
24796 AATTCTTCAAATTATCTTC
1 AATTCTTC-AATGATCTTC
24815 AAT
1 AAT
24818 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (18 bp):
AATTCTTCAATGATCTTC
Found at i:31867 original size:10 final size:10
Alignment explanation
Indices: 31852--31876 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
31842 GTTGCTGCTT
31852 AATTCCAGAA
1 AATTCCAGAA
31862 AATTCCAGAA
1 AATTCCAGAA
31872 AATTC
1 AATTC
31877 TAGAGTCCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.08, T:0.24
Consensus pattern (10 bp):
AATTCCAGAA
Found at i:32809 original size:13 final size:13
Alignment explanation
Indices: 32791--32823 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
32781 ATAATTATTG
32791 TTTGCTTTATTAA
1 TTTGCTTTATTAA
32804 TTTGCTTTATTAA
1 TTTGCTTTATTAA
*
32817 TCTGCTT
1 TTTGCTT
32824 AGATTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (13 bp):
TTTGCTTTATTAA
Found at i:33316 original size:42 final size:40
Alignment explanation
Indices: 33237--33316 Score: 97
Period size: 42 Copynumber: 1.9 Consensus size: 40
33227 AGATTTTCCT
* * * *
33237 TTAAACAAAATTAATTTTTCTTTTCCGTTTTTCCTTTTAA
1 TTAAAAAAAATTAATTTTTATTTTCCGTTTATACTTTTAA
*
33277 TTAAAAAAAATATATATTTTTATTTTCTGTTTATACTTTT
1 TTAAAAAAAAT-TA-ATTTTTATTTTCCGTTTATACTTTT
33317 TATTTTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 10 0.30
41 2 0.06
42 21 0.64
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.56
Consensus pattern (40 bp):
TTAAAAAAAATTAATTTTTATTTTCCGTTTATACTTTTAA
Found at i:34516 original size:15 final size:17
Alignment explanation
Indices: 34477--34520 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
34467 GGAACCAAGG
34477 TAATTTTCAAAGAAGGCC
1 TAATTTTCAAAGAA-GCC
*
34495 GAATTTTCAAAG-A-CC
1 TAATTTTCAAAGAAGCC
34510 TAATTTTCAAA
1 TAATTTTCAAA
34521 CTTCACAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 12 0.50
17 1 0.04
18 11 0.46
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (17 bp):
TAATTTTCAAAGAAGCC
Found at i:36167 original size:20 final size:20
Alignment explanation
Indices: 36134--36181 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
36124 TTTGCCATCA
36134 TTTTGGGCTTTAAACTTGGGC
1 TTTTGGG-TTTAAACTTGGGC
36155 TTTTGGGTTTAAACTTGGGC
1 TTTTGGGTTTAAACTTGGGC
36175 -TTTGGGT
1 TTTTGGGT
36182 AGTAGCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 7 0.26
20 13 0.48
21 7 0.26
ACGTcount: A:0.12, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
TTTTGGGTTTAAACTTGGGC
Done.