Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011527.1 Corchorus capsularis cultivar CVL-1 contig11548, 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: 40275
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:845 original size:2 final size:2
Alignment explanation
Indices: 838--862 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
828 TAACATAAGA
838 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
863 ATCTTCCCTA
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:1366 original size:21 final size:20
Alignment explanation
Indices: 1324--1367 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1314 TCTTGTAATC
*
1324 TAAAATTACTAAAAAAGTTA
1 TAAAATTACTAAAAAAGCTA
* *
1344 TAAAAGTTATTAAAATAGCTA
1 TAAAA-TTACTAAAAAAGCTA
1365 TAA
1 TAA
1368 TTCTTTCCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAATTACTAAAAAAGCTA
Found at i:4772 original size:31 final size:31
Alignment explanation
Indices: 4737--4802 Score: 107
Period size: 31 Copynumber: 2.1 Consensus size: 31
4727 AATTTTATGT
*
4737 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCCTT-TTCTTTAAAACATA
4768 TTTCCAATTGTACCCTTTTCTTTAAAACATA
1 TTTCCAATTGTACCCTTTTCTTTAAAACATA
4799 TTTC
1 TTTC
4803 TAAATTGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 2 0.06
31 31 0.94
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTCTTTAAAACATA
Found at i:5141 original size:19 final size:20
Alignment explanation
Indices: 5114--5151 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5104 TATTATTATT
5114 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
5134 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
5152 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:5374 original size:22 final size:22
Alignment explanation
Indices: 5317--5405 Score: 90
Period size: 22 Copynumber: 4.0 Consensus size: 22
5307 TGTCTCTATG
* *
5317 TGGTTATCAAAATTTCATAAGA
1 TGGTTACCAAAATTTCATAGGA
* ** *
5339 TAGTTATTATAATTTCATGAGGA
1 TGGTTACCAAAATTTCAT-AGGA
* *
5362 -GGTTACCAAAATTCCATAGTA
1 TGGTTACCAAAATTTCATAGGA
5383 TGGTTACCAAAATTTCATAGGA
1 TGGTTACCAAAATTTCATAGGA
5405 T
1 T
5406 CAAGTTATTA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
21 3 0.06
22 47 0.89
23 3 0.06
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTTACCAAAATTTCATAGGA
Found at i:5418 original size:24 final size:22
Alignment explanation
Indices: 5319--5449 Score: 61
Period size: 22 Copynumber: 5.9 Consensus size: 22
5309 TCTCTATGTG
* *
5319 GTTATCAAAATTTCATAAG-ATA
1 GTTATTAAAATTTCATAGGTA-A
* *
5341 GTTATTATAATTTCATGAGG-AG
1 GTTATTAAAATTTCAT-AGGTAA
** * *
5363 GTTACCAAAATTCCATA-GTATG
1 GTTATTAAAATTTCATAGGTA-A
**
5385 GTTACCAAAATTTCATAGGATCAA
1 GTTATTAAAATTTCATAGG-T-AA
* * **
5409 GTTATTAAAATCTCTTAGGTTG
1 GTTATTAAAATTTCATAGGTAA
*
5431 GTTATTGAAATTTCATAGG
1 GTTATTAAAATTTCATAGG
5450 GTGGTTAATT
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 59 0.70
23 5 0.06
24 16 0.19
25 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
GTTATTAAAATTTCATAGGTAA
Found at i:5441 original size:22 final size:22
Alignment explanation
Indices: 5409--5456 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
5399 ATAGGATCAA
* *
5409 GTTATTAAAATCTCTTAGGTTG
1 GTTATTAAAATCTCATAGGGTG
* *
5431 GTTATTGAAATTTCATAGGGTG
1 GTTATTAAAATCTCATAGGGTG
5453 GTTA
1 GTTA
5457 ATTATCACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (22 bp):
GTTATTAAAATCTCATAGGGTG
Found at i:5517 original size:22 final size:22
Alignment explanation
Indices: 5492--5550 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
5482 ATCAAAGAGA
*
5492 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGCGAGG
* *
5514 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAGCGAGG
*
5536 TTAACAAAATTTCAT
1 TTATCAAAATTTCAT
5551 TAAATATTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.06
22 27 0.87
23 2 0.06
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAGCGAGG
Found at i:5616 original size:22 final size:21
Alignment explanation
Indices: 5567--6578 Score: 197
Period size: 22 Copynumber: 46.9 Consensus size: 21
5557 TTTCATGGGG
*
5567 AGGTTATCAAAATTTTATAG-
1 AGGTTATCAAAATTTCATAGA
*
5587 TGTAGTTATCAAAATTTCATATGA
1 AG--GTTATCAAAATTTCATA-GA
* *
5611 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
5636 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
5658 AGGTTATC-AAATCTCATA-A
1 AGGTTATCAAAATTTCATAGA
*
5677 AGTGATTATCGAAATTTCATAGAA
1 AG-G-TTATCAAAATTTCATAG-A
5701 ATCGGATTATCAAAATTT-ATAGAA
1 A--GG-TTATCAAAATTTCATAG-A
*
5725 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * * *
5745 TGTTGTTATCAAAATTTTAAAGCG
1 AG--GTTATCAAAATTTCATAG-A
* *
5769 AGATTATCAAAATTGCATA-A
1 AGGTTATCAAAATTTCATAGA
* *
5789 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
5812 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
5834 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
5856 GAGGTTATCAAATTTTCA-A-A
1 -AGGTTATCAAAATTTCATAGA
*
5876 ATGTTATTACAAAAATTTCATAG-
1 AGGTTA-T-C-AAAATTTCATAGA
* * *
5899 -TGTTAT-----T-T-ATGGGG
1 AGGTTATCAAAATTTCAT-AGA
5913 AGGTTATCAAAATTTCATAGTA
1 AGGTTATCAAAATTTCATAG-A
* * *
5935 TGGTTA-CCAAA-TT-AGA-A
1 AGGTTATCAAAATTTCATAGA
* * * * *
5952 AGGATATTAAACTTTTATTA-T
1 AGGTTATCAAAATTTCA-TAGA
* *
5973 AGAGTAATCAAAATTTCA-AGG
1 AG-GTTATCAAAATTTCATAGA
* * *
5994 AGGATATCAAAA-TTCA-GGG
1 AGGTTATCAAAATTTCATAGA
*
6013 AGGATATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
6035 AGGTTATTAAAATTTCATAGTTT
1 AGGTTATCAAAATTTCATAG--A
* *
6058 A-GTTTTCAAAATTTCACAAGA
1 AGGTTATCAAAATTTCA-TAGA
*
6079 AGGTTATCAAAATTTCATAGT
1 AGGTTATCAAAATTTCATAGA
* * *
6100 ATGTAGATCAAAATTTCATAGGG
1 AGGT-TATCAAAATTTCATA-GA
* *
6123 AGATTAACAAAAATTTCATA-A
1 AGGTTATC-AAAATTTCATAGA
** *
6144 TGAGGTTATCAAAAAATCATAGGG
1 --AGGTTATCAAAATTTCATA-GA
*
6168 AGGTTATCAAAA-TT--T-GT
1 AGGTTATCAAAATTTCATAGA
* *
6185 A-GTTATCAAGATCTCATAAGA
1 AGGTTATCAAAATTTCAT-AGA
* * *
6206 AAGTTATCAAAATTTTATAGGG
1 AGGTTATCAAAATTTCATA-GA
* *
6228 AGGTTTATCAAAATTTTATGGGA
1 AGG-TTATCAAAATTTCAT-AGA
*
6251 AGATTTATCAAAATTTCATAACGA
1 AG-GTTATCAAAATTTCAT-A-GA
*
6275 A-GTTATCACAATTTCATA-A
1 AGGTTATCAAAATTTCATAGA
*
6294 TGTGATTATCAAAATTT--TAG-
1 AG-G-TTATCAAAATTTCATAGA
* *
6314 AGTGTGATTACTAACAA-TTCATATGG
1 AG-GTTA-T-C-AA-AATTTCATA-GA
* * *
6340 AGGTTTTTAAATTTTCATA-A
1 AGGTTATCAAAATTTCATAGA
* * * *
6360 CGTGGTTATCAATATATCATATGG
1 --AGGTTATCAAAATTTCATA-GA
* *
6384 AGGTTATCAACATTTCATAGTGT
1 AGGTTATCAAAATTTCATA--GA
* *
6407 TGGTTATCAAAATTTCATTGGGA
1 AGGTTATCAAAATTTCA-T-AGA
6430 A-GTTATCAAAATTTCATATTG-
1 AGGTTATCAAAATTTCATA--GA
* * * *
6451 AGATCT-TCAAAATTCCTTAGGG
1 AGGT-TATCAAAATTTCATA-GA
* *
6473 AGGTTAACCAAATTTCATAAGA
1 AGGTTATCAAAATTTCAT-AGA
** *
6495 AGGTTAAAAAAATTT-ATAAAA
1 AGGTTATCAAAATTTCAT-AGA
* *
6516 AGGTTCTCGAAA-TTCAATAGTA
1 AGGTTATCAAAATTTC-ATAG-A
** * * *
6538 TCGTCATTAAAAATTCATAGGA
1 AGGTTATCAAAATTTCATA-GA
6560 AGGTTATCAAAATTTCATA
1 AGGTTATCAAAATTTCATA
6579 ATGGGATCAT
Statistics
Matches: 721, Mismatches: 165, Indels: 210
0.66 0.15 0.19
Matches are distributed among these distances:
12 2 0.00
13 2 0.00
14 1 0.00
15 5 0.01
16 9 0.01
17 8 0.01
18 2 0.00
19 35 0.05
20 39 0.05
21 71 0.10
22 407 0.56
23 87 0.12
24 19 0.03
25 22 0.03
26 8 0.01
27 4 0.01
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:5731 original size:21 final size:23
Alignment explanation
Indices: 5680--5744 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 23
5670 CTCATAAAGT
*
5680 GATTATCGAAATTTCATAGAAATC
1 GATTATCAAAATTTCATAGAAA-C
5704 GGATTATCAAAATTT-ATAGAAA-
1 -GATTATCAAAATTTCATAGAAAC
5726 GATTATCAAAATTTCATAG
1 GATTATCAAAATTTCATAG
5745 TGTTGTTATC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 14 0.37
22 4 0.11
24 7 0.18
25 13 0.34
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.34
Consensus pattern (23 bp):
GATTATCAAAATTTCATAGAAAC
Found at i:6004 original size:20 final size:20
Alignment explanation
Indices: 5979--6029 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
5969 TTATAGAGTA
5979 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
5999 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
6018 ATCAAAATTTCA
1 ATCAAAATTTCA
6030 TATGAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:6239 original size:23 final size:23
Alignment explanation
Indices: 6209--6266 Score: 91
Period size: 23 Copynumber: 2.5 Consensus size: 23
6199 CATAAGAAAG
*
6209 TTATCAAAATTTTATAGGG-AGGT
1 TTATCAAAATTTTAT-GGGAAGAT
6232 TTATCAAAATTTTATGGGAAGAT
1 TTATCAAAATTTTATGGGAAGAT
6255 TTATCAAAATTT
1 TTATCAAAATTT
6267 CATAACGAAG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 3 0.09
23 30 0.91
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (23 bp):
TTATCAAAATTTTATGGGAAGAT
Found at i:6292 original size:128 final size:127
Alignment explanation
Indices: 6057--6310 Score: 278
Period size: 128 Copynumber: 2.0 Consensus size: 127
6047 TTTCATAGTT
* * * * *
6057 TAGTTTTCAAAATTTCACAAGAAGGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGG
1 TAGTTATCAAAATCTCACAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGG
* * * *
6122 GAGATTAACAAAAATTTCATAATGAGGTTATCAAAAAATCATAGGGAGGTTATCAAAATTTG
66 GAGATTAACAAAAATTTCATAACGAAGTTATCAAAAAATCATAAGGAGATTATCAAAATTTG
* * * ** *
6184 TAGTTATCAAGATCTCATAAGAAAGTTATCAAAATTTTATAGGGAGGTTTATCAAAATTTTAT-G
1 TAGTTATCAAAATCTCACAAGAAAGTTATCAAAATTTCATA-GGAGGTAGATCAAAATTTCATAG
* * ** * *
6248 GGAAGATTTATC-AAAATTTCATAACGAAGTTATCACAATTTCATAATGTGATTATCAAAATTT
65 GG-AGA-TTAACAAAAATTTCATAACGAAGTTATCAAAAAATCATAAGGAGATTATCAAAATTT
6311 TAGAGTGTGA
Statistics
Matches: 103, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
127 38 0.37
128 61 0.59
129 4 0.04
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (127 bp):
TAGTTATCAAAATCTCACAAGAAAGTTATCAAAATTTCATAGGAGGTAGATCAAAATTTCATAGG
GAGATTAACAAAAATTTCATAACGAAGTTATCAAAAAATCATAAGGAGATTATCAAAATTTG
Found at i:9492 original size:21 final size:23
Alignment explanation
Indices: 9441--9485 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
9431 AGCTTGCTAA
9441 GAAGCAGCTATCAGAGAAGGATG
1 GAAGCAGCTATCAGAGAAGGATG
9464 GAAGCAGCTATC-GA-AAGGATG
1 GAAGCAGCTATCAGAGAAGGATG
9485 G
1 G
9486 GCGCAGCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.36
22 2 0.09
23 12 0.55
ACGTcount: A:0.38, C:0.13, G:0.36, T:0.13
Consensus pattern (23 bp):
GAAGCAGCTATCAGAGAAGGATG
Found at i:21269 original size:3 final size:3
Alignment explanation
Indices: 21261--21293 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
21251 TTGGTAAAAA
21261 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
21294 TCTGATTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:23625 original size:31 final size:31
Alignment explanation
Indices: 23549--23652 Score: 158
Period size: 31 Copynumber: 3.4 Consensus size: 31
23539 TTATACAATT
*
23549 ATATATAAAATATATTTATGATATATATAAA
1 ATATATATAATATATTTATGATATATATAAA
* *
23580 AT-TGTCA-AATATATTTATGATATATAAAAA
1 ATATAT-ATAATATATTTATGATATATATAAA
23610 ATATATATAATATATTTATGATATATATAAA
1 ATATATATAATATATTTATGATATATATAAA
23641 ATATATATAATA
1 ATATATATAATA
23653 AATTATTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
30 27 0.41
31 39 0.59
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (31 bp):
ATATATATAATATATTTATGATATATATAAA
Found at i:23647 original size:11 final size:11
Alignment explanation
Indices: 23548--23650 Score: 63
Period size: 11 Copynumber: 9.8 Consensus size: 11
23538 ATTATACAAT
23548 TATATATAAAA
1 TATATATAAAA
* **
23559 TATATTTATGA
1 TATATATAAAA
23570 TATATAT-AAA
1 TATATATAAAA
* *
23580 -AT-TGTCAAA
1 TATATATAAAA
* **
23589 TATATTTATGA
1 TATATATAAAA
23600 TATATA-AAAA
1 TATATATAAAA
*
23610 -ATATATATAA
1 TATATATAAAA
* **
23620 TATATTTATGA
1 TATATATAAAA
23631 TATATATAAAA
1 TATATATAAAA
23642 TATATATAA
1 TATATATAA
23651 TAAATTATTT
Statistics
Matches: 67, Mismatches: 20, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
8 2 0.03
9 10 0.15
10 8 0.12
11 47 0.70
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (11 bp):
TATATATAAAA
Found at i:26015 original size:77 final size:77
Alignment explanation
Indices: 25923--26076 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
25913 CCACGTCAGC
25923 GCGTGTTATACACACACTCTAGCCATTTTCAATTGACACAACCCGATAACGTTTTATCCTCAATT
1 GCGTGTTATACACACACTCTAGCCATTTTCAATTGACACAACCCGATAACGTTTTATCCTCAATT
25988 GACACAAGAGGT
66 GACACAAGAGGT
26000 GCGTGTTATACACACACTCTAGCCATTTTCAATTGACACAACCCGATAACGTTTTATCCTCAATT
1 GCGTGTTATACACACACTCTAGCCATTTTCAATTGACACAACCCGATAACGTTTTATCCTCAATT
26065 GACACAAGAGGT
66 GACACAAGAGGT
26077 AACAGTGTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (77 bp):
GCGTGTTATACACACACTCTAGCCATTTTCAATTGACACAACCCGATAACGTTTTATCCTCAATT
GACACAAGAGGT
Found at i:28210 original size:23 final size:23
Alignment explanation
Indices: 28184--28229 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
28174 GCTAATGAAG
28184 TGTTTGT-GATCATTCTAATAGTA
1 TGTTTGTGGA-CATTCTAATAGTA
28207 TGTTTGTGGACATTCTAATAGTA
1 TGTTTGTGGACATTCTAATAGTA
28230 GCATCATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.46
Consensus pattern (23 bp):
TGTTTGTGGACATTCTAATAGTA
Found at i:28580 original size:60 final size:60
Alignment explanation
Indices: 28387--28580 Score: 180
Period size: 60 Copynumber: 3.2 Consensus size: 60
28377 TTATCATTAG
*
28387 GTGTAATGGTAAGTTAAAATTACCCCCAAAATGTAATGAGGTATCATTTGTCTAGATTTA
1 GTGTAAGGGTAAGTTAAAATTACCCCCAAAATGTAATGAGGTATCATTTGTCTAGATTTA
* * * * * * * * * * *
28447 GTGTAAGGGTAA---ACATATTTCCCTCTAAGTGTAATTA-GTTTTATGTGTTTTACTATCATTA
1 GTGTAAGGGTAAGTTA-AAATTACCCCCAAAATGTAATGAGGTATCATTTG-TCTA-GAT--TTA
* *
28508 GGTGTAATGGTAAGTTAAAATTACCCCCAAAATGTAACGAGGTATCATTTGTCTAGATTTA
1 -GTGTAAGGGTAAGTTAAAATTACCCCCAAAATGTAATGAGGTATCATTTGTCTAGATTTA
28569 GTGTAAGGGTAA
1 GTGTAAGGGTAA
28581 ACATATTTCC
Statistics
Matches: 98, Mismatches: 26, Indels: 20
0.68 0.18 0.14
Matches are distributed among these distances:
57 8 0.08
58 20 0.20
59 2 0.02
60 22 0.22
61 6 0.06
62 11 0.11
63 2 0.02
64 19 0.19
65 8 0.08
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (60 bp):
GTGTAAGGGTAAGTTAAAATTACCCCCAAAATGTAATGAGGTATCATTTGTCTAGATTTA
Found at i:28595 original size:122 final size:122
Alignment explanation
Indices: 28378--28621 Score: 479
Period size: 122 Copynumber: 2.0 Consensus size: 122
28368 ATGGGGCAAT
*
28378 TATCATTAGGTGTAATGGTAAGTTAAAATTACCCCCAAAATGTAATGAGGTATCATTTGTCTAGA
1 TATCATTAGGTGTAATGGTAAGTTAAAATTACCCCCAAAATGTAACGAGGTATCATTTGTCTAGA
28443 TTTAGTGTAAGGGTAAACATATTTCCCTCTAAGTGTAATTAGTTTTATGTGTTTTAC
66 TTTAGTGTAAGGGTAAACATATTTCCCTCTAAGTGTAATTAGTTTTATGTGTTTTAC
28500 TATCATTAGGTGTAATGGTAAGTTAAAATTACCCCCAAAATGTAACGAGGTATCATTTGTCTAGA
1 TATCATTAGGTGTAATGGTAAGTTAAAATTACCCCCAAAATGTAACGAGGTATCATTTGTCTAGA
28565 TTTAGTGTAAGGGTAAACATATTTCCCTCTAAGTGTAATTAGTTTTATGTGTTTTAC
66 TTTAGTGTAAGGGTAAACATATTTCCCTCTAAGTGTAATTAGTTTTATGTGTTTTAC
28622 CTATTTTACC
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
122 121 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (122 bp):
TATCATTAGGTGTAATGGTAAGTTAAAATTACCCCCAAAATGTAACGAGGTATCATTTGTCTAGA
TTTAGTGTAAGGGTAAACATATTTCCCTCTAAGTGTAATTAGTTTTATGTGTTTTAC
Found at i:33248 original size:18 final size:19
Alignment explanation
Indices: 33211--33248 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
33201 ACTCAACAAT
* *
33211 ATCTCCATGATTTTCATGC
1 ATCTCCATGACTTCCATGC
33230 ATCTCCATG-CTTCCATGC
1 ATCTCCATGACTTCCATGC
33248 A
1 A
33249 GCCCATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.37
Consensus pattern (19 bp):
ATCTCCATGACTTCCATGC
Found at i:37140 original size:19 final size:20
Alignment explanation
Indices: 37096--37137 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 20
37086 AGTATGCTAA
37096 AAACTAAACCAACCTTTATTTGT
1 AAACTAAACCAACCTTTA--T-T
37119 AAACTAAACCAACCTTTAT
1 AAACTAAACCAACCTTTAT
37138 AAATACAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 1 0.05
23 18 0.95
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (20 bp):
AAACTAAACCAACCTTTATT
Found at i:39786 original size:6 final size:6
Alignment explanation
Indices: 39758--39813 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
39748 AACACAACCT
** * * *
39758 AAAAGA AAAA-A AAAATT TAAAGA AGAAGA AGAA-A AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
39804 AAAAGA AAAA
1 AAAAGA AAAA
39814 AACAAAGCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
5 9 0.22
6 32 0.78
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:39787 original size:23 final size:23
Alignment explanation
Indices: 39758--39820 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
39748 AACACAACCT
***
39758 AAAAGAAAAAAAAAATTTAAAGA
1 AAAAGAAAAAAAAAAGAAAAAGA
* *
39781 AGAAGAAGAAAAAAAGAAAAAGA
1 AAAAGAAAAAAAAAAGAAAAAGA
39804 AAAAGAAAAAAACAAAG
1 AAAAGAAAAAAA-AAAG
39821 CCTGGTCGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 28 0.88
24 4 0.12
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (23 bp):
AAAAGAAAAAAAAAAGAAAAAGA
Done.