Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022130.1 Corchorus olitorius cultivar O-4 contig22163, 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: 90617
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1329 original size:10 final size:10
Alignment explanation
Indices: 1314--1350 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
1304 TAAAGAGAAT
1314 TATGTGAAGG
1 TATGTGAAGG
1324 TATGTGAAGG
1 TATGTGAAGG
1334 TATGTGAAGG
1 TATGTGAAGG
1344 TATGTGA
1 TATGTGA
1351 TTTGTGTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (10 bp):
TATGTGAAGG
Found at i:3798 original size:21 final size:21
Alignment explanation
Indices: 3770--3818 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
3760 TTGGAATGGC
*
3770 GATGGCACAGGCATAGCCGGT
1 GATGGCACAGGCATAACCGGT
* * *
3791 GGTGGCACGGGCTTAACCGGT
1 GATGGCACAGGCATAACCGGT
3812 GATGGCA
1 GATGGCA
3819 TGGTGAATGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.16
Consensus pattern (21 bp):
GATGGCACAGGCATAACCGGT
Found at i:7461 original size:15 final size:16
Alignment explanation
Indices: 7437--7476 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7427 AGAGGTTCAA
*
7437 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
7452 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
7468 AGAAAACAA
1 AGAAAACAA
7477 AACAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:21959 original size:13 final size:13
Alignment explanation
Indices: 21941--21966 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
21931 CTTGGCATGA
21941 GTGATGATTTTTG
1 GTGATGATTTTTG
21954 GTGATGATTTTTG
1 GTGATGATTTTTG
21967 TTGTTACCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.31, T:0.54
Consensus pattern (13 bp):
GTGATGATTTTTG
Found at i:22368 original size:19 final size:19
Alignment explanation
Indices: 22346--22392 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
22336 TAAGGGCTGG
22346 AATTAATTAATTAAATAAT
1 AATTAATTAATTAAATAAT
* * *
22365 AATTATTTTATTGAATAAT
1 AATTAATTAATTAAATAAT
*
22384 TATT-ATTAA
1 AATTAATTAA
22393 AAATCTTATG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
AATTAATTAATTAAATAAT
Found at i:25074 original size:22 final size:22
Alignment explanation
Indices: 25023--25076 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
25013 CGGGCATGGG
*
25023 CGGTGGTGGCTCGGTGATAGCT
1 CGGTAGTGGCTCGGTGATAGCT
25045 C-G-AGGTGGCTCGGTGAATAGC-
1 CGGTA-GTGGCTCGGTG-ATAGCT
25066 CGGTAGTGGCT
1 CGGTAGTGGCT
25077 TGCTGGTGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
21 13 0.48
22 13 0.48
23 1 0.04
ACGTcount: A:0.13, C:0.19, G:0.44, T:0.24
Consensus pattern (22 bp):
CGGTAGTGGCTCGGTGATAGCT
Found at i:28128 original size:32 final size:29
Alignment explanation
Indices: 28072--28141 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 29
28062 AAAATAAAGG
*
28072 AAACGCAAAAACAAGAATTTTTTTTTCAA
1 AAACGCAAAAACAACAATTTTTTTTTCAA
28101 AAACGCAAAACACAAAACAATTTTTTTTTCAA
1 AAACGCAAAA-AC--AACAATTTTTTTTTCAA
*
28133 AAATGCAAA
1 AAACGCAAA
28142 GAAGCAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 10 0.28
30 2 0.06
32 24 0.67
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (29 bp):
AAACGCAAAAACAACAATTTTTTTTTCAA
Found at i:30237 original size:37 final size:37
Alignment explanation
Indices: 30166--30477 Score: 290
Period size: 37 Copynumber: 8.4 Consensus size: 37
30156 CAGTGATTTC
** *
30166 TAAGGAGAGCTCTATGGTAAAGAAGGG-GCTGCCGCAG
1 TAAGGAGAGCTCTGCGGTAAAG-AGGGTGCTACCGCAG
* * **
30203 TAAGGAGAGCTCTGCGGTGAATAGGGTGCCGCCGCAG
1 TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAG
* * * * * *
30240 TAAGCAGAGCTCAGTGGTAAAGAAGGTGTTATCGCAG
1 TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAG
* * *
30277 TAAGAAGAGCTATGCAGTAAAGAGGGT-CGTACCGC-G
1 TAAGGAGAGCTCTGCGGTAAAGAGGGTGC-TACCGCAG
* * * *
30313 ATAAGGGGAGCTTTGCGGTAAAGAGGGGGCTACCGCGG
1 -TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAG
* * * *
30351 TAATGTGAGCTCTACGGTAAAGAGGGTGCTACCGCGG
1 TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAG
**
30388 TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGTGG
1 TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAG
* * * *
30425 TAAGGGGAGCTCTGCAGCAAATAGGGTGCTACCG-AGG
1 TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCA-G
30462 TAAGGAGAGCTCTGCG
1 TAAGGAGAGCTCTGCG
30478 ATGAGGAAGG
Statistics
Matches: 225, Mismatches: 44, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
36 5 0.02
37 218 0.97
38 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.38, T:0.18
Consensus pattern (37 bp):
TAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCAG
Found at i:30350 original size:20 final size:20
Alignment explanation
Indices: 30327--30435 Score: 72
Period size: 18 Copynumber: 5.8 Consensus size: 20
30317 GGGGAGCTTT
*
30327 GCGGTAAAGAGGGGGCTACC
1 GCGGTAAAGAGGGAGCTACC
* * *
30347 GCGGT-AA-TGTGAGCT-CT
1 GCGGTAAAGAGGGAGCTACC
* *
30364 ACGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGAGCTACC
* *
30384 GCGGT-AAG-GAGAGCT-CT
1 GCGGTAAAGAGGGAGCTACC
*
30401 GCGGTAAAGAGGGTGCTACC
1 GCGGTAAAGAGGGAGCTACC
*
30421 GTGGT-AAG-GGGAGCT
1 GCGGTAAAGAGGGAGCT
30436 CTGCAGCAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
17 11 0.17
18 21 0.32
19 18 0.28
20 15 0.23
ACGTcount: A:0.24, C:0.17, G:0.41, T:0.17
Consensus pattern (20 bp):
GCGGTAAAGAGGGAGCTACC
Found at i:35897 original size:15 final size:15
Alignment explanation
Indices: 35879--35938 Score: 50
Period size: 15 Copynumber: 4.0 Consensus size: 15
35869 ACCCAACTAT
35879 CTGCGACAGTATTTG
1 CTGCGACAGTATTTG
* * *
35894 CTGCGGCAATATTTA
1 CTGCGACAGTATTTG
* * *
35909 CTGTGGCAGTATTTC
1 CTGCGACAGTATTTG
35924 CTGC-AGCAGTATTTG
1 CTGCGA-CAGTATTTG
35939 TTGATTTGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (15 bp):
CTGCGACAGTATTTG
Found at i:36238 original size:84 final size:84
Alignment explanation
Indices: 36072--36230 Score: 257
Period size: 84 Copynumber: 1.9 Consensus size: 84
36062 TATTCCGCAG
* * *
36072 GTTTTTACGCCACCCCGCAGGATATCCAAGGATTTCATAACATTGGTCCTTTGTATGCCCCATCT
1 GTTTTTACGCCACCCCGCAAGATATCCAAGGATTTCATAACATCGGTCCTTGGTATGCCCCATCT
36137 TCTGGCAGTGACCACATCA
66 TCTGGCAGTGACCACATCA
* *
36156 GTTTTTACGCCA-CCTGACAAGATATCCAAGGATTTCATAACATCGGTCCTTGGTATGCCCCATT
1 GTTTTTACGCCACCCCG-CAAGATATCCAAGGATTTCATAACATCGGTCCTTGGTATGCCCCATC
36220 TTCTGGCAGTG
65 TTCTGGCAGTG
36231 GCTACATCTC
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
83 3 0.04
84 66 0.96
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (84 bp):
GTTTTTACGCCACCCCGCAAGATATCCAAGGATTTCATAACATCGGTCCTTGGTATGCCCCATCT
TCTGGCAGTGACCACATCA
Found at i:36486 original size:37 final size:37
Alignment explanation
Indices: 36419--36489 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
36409 TAGCTACCAG
*
36419 AGGATACAGATTCGCTGCTCTCTCTGTCAGATCTACC
1 AGGATACAGATTCGCTGCTCTCTCTATCAGATCTACC
* *
36456 AGGATGCAGATTTGCTGCTCTCAT-TATCAGATCT
1 AGGATACAGATTCGCTGCTCTC-TCTATCAGATCT
36490 CGCCATGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 29 0.97
38 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (37 bp):
AGGATACAGATTCGCTGCTCTCTCTATCAGATCTACC
Found at i:36562 original size:14 final size:15
Alignment explanation
Indices: 36543--36574 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
36533 TTTGGTGAAG
36543 AAAAAAGAAGAAA-A
1 AAAAAAGAAGAAAGA
36557 AAAAAAGAAGAAAGA
1 AAAAAAGAAGAAAGA
36572 AAA
1 AAA
36575 TTTTGATTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAGAAAGA
Found at i:36754 original size:22 final size:22
Alignment explanation
Indices: 36729--36771 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
36719 CATAATATGC
*
36729 GGTAGGTGGTAACACGGTTTGT
1 GGTAGGTGGTAACACGATTTGT
36751 GGTAGGTGGTAACACGATTTG
1 GGTAGGTGGTAACACGATTTG
36772 CGGCTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.09, G:0.40, T:0.30
Consensus pattern (22 bp):
GGTAGGTGGTAACACGATTTGT
Found at i:41928 original size:21 final size:20
Alignment explanation
Indices: 41904--41942 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
41894 GCATAAACTG
*
41904 TAAATGAAGAAAGTGAAAGTA
1 TAAAGGAAGAAAGT-AAAGTA
*
41925 TAAAGGAAGTAAGTAAAG
1 TAAAGGAAGAAAGTAAAG
41943 ATGTTAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.00, G:0.26, T:0.18
Consensus pattern (20 bp):
TAAAGGAAGAAAGTAAAGTA
Found at i:51867 original size:26 final size:26
Alignment explanation
Indices: 51827--51876 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
51817 AAAAATTTGT
51827 GGTTTTGGAGGTTATTTGGGGATTAG
1 GGTTTTGGAGGTTATTTGGGGATTAG
*
51853 GGTTTTGGAGTTTATTTGGGGATT
1 GGTTTTGGAGGTTATTTGGGGATT
51877 TCTTGATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.40, T:0.46
Consensus pattern (26 bp):
GGTTTTGGAGGTTATTTGGGGATTAG
Found at i:52534 original size:18 final size:18
Alignment explanation
Indices: 52498--52537 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52488 TTGAAGATTT
52498 ATTGAAGATAATTTGAAGA
1 ATTGAAGATAA-TTGAAGA
52517 ATTGAAGACTAA-TGAAGA
1 ATTGAAGA-TAATTGAAGA
52535 ATT
1 ATT
52538 TCAAGAGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 8 0.40
20 3 0.15
ACGTcount: A:0.47, C:0.03, G:0.20, T:0.30
Consensus pattern (18 bp):
ATTGAAGATAATTGAAGA
Found at i:64713 original size:14 final size:15
Alignment explanation
Indices: 64689--64719 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
64679 ACCTTTTTAC
64689 AACCACAAAGCTTCA
1 AACCACAAAGCTTCA
64704 AACC-CAAAGCTTCA
1 AACCACAAAGCTTCA
64718 AA
1 AA
64720 TACAAGTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.48, C:0.32, G:0.06, T:0.13
Consensus pattern (15 bp):
AACCACAAAGCTTCA
Found at i:65450 original size:38 final size:39
Alignment explanation
Indices: 65397--65470 Score: 132
Period size: 38 Copynumber: 1.9 Consensus size: 39
65387 ATTAGCTAAC
*
65397 ATACTTGGGTTTATTTTGTTATCATAAGAAACAACAAAT
1 ATACTTGGATTTATTTTGTTATCATAAGAAACAACAAAT
65436 ATACTT-GATTTATTTTGTTATCATAAGAAACAACA
1 ATACTTGGATTTATTTTGTTATCATAAGAAACAACA
65471 GGTTCAACAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 28 0.82
39 6 0.18
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (39 bp):
ATACTTGGATTTATTTTGTTATCATAAGAAACAACAAAT
Found at i:76359 original size:22 final size:23
Alignment explanation
Indices: 76313--76360 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
76303 TTGTAGCAAC
* *
76313 GAAAGAGGAAAAAAGCCGAATAA
1 GAAAGAGGAAAAAAGACGAAGAA
*
76336 GAAAGAGG-AAAGAGACGAAGAA
1 GAAAGAGGAAAAAAGACGAAGAA
76358 GAA
1 GAA
76361 CCTAAAACAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.60, C:0.06, G:0.31, T:0.02
Consensus pattern (23 bp):
GAAAGAGGAAAAAAGACGAAGAA
Found at i:77877 original size:209 final size:210
Alignment explanation
Indices: 77503--77920 Score: 721
Period size: 209 Copynumber: 2.0 Consensus size: 210
77493 TGAACTCAAG
* * * *
77503 AAGGTTTTTGGTGAAATGGATTTCTTTTCATTTTTGCGTTCTTCCATTGTTGAAGGATATTTAAG
1 AAGGTCTTTGGTAAAATGGATTTCATTTCATTTTTGCGTTCCTCCATTGTTGAAGGATATTTAAG
*
77568 AATGTATTTTTTAAAGGATTTATTTTTGAAGGATATATTATGATGATATATATTACATTACTATG
66 AATGTATTTTTTAAAGGATTTATTTTTGAAGGATATATTATGATAATATATATTACATTACTATG
*
77633 TGTGGAAAAAAGTATACACTTACAAAACAAATAACATGTACAAACAAGTTTACCCACATTAAAAA
131 TGTGGAAAAAAGTATACACTTACAAAACAAATAACAGGTACAAACAAGTTTACCCACATTAAAAA
77698 ATCCCCGTAGCGCAA
196 ATCCCCGTAGCGCAA
*
77713 AAGGTCTTTGGTAAAATGGATTTCATTTCATTTTTGCG-TCCTCCATTGTTGAATGATATTTAAG
1 AAGGTCTTTGGTAAAATGGATTTCATTTCATTTTTGCGTTCCTCCATTGTTGAAGGATATTTAAG
* * * *
77777 AATGTATTTTTTAAAGGATTTATTTTTTATGGATATATTATGATAATATATATTACGTTACTATT
66 AATGTATTTTTTAAAGGATTTATTTTTGAAGGATATATTATGATAATATATATTACATTACTATG
*
77842 TGTGGAAACAAGTATACACTTACAAAACAAATAACAGGTACAAACAAGTTTACCCACATTAAAAA
131 TGTGGAAAAAAGTATACACTTACAAAACAAATAACAGGTACAAACAAGTTTACCCACATTAAAAA
77907 ATCCCCGTAGCGCA
196 ATCCCCGTAGCGCA
77921 TATGATTAAA
Statistics
Matches: 196, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
209 161 0.82
210 35 0.18
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.37
Consensus pattern (210 bp):
AAGGTCTTTGGTAAAATGGATTTCATTTCATTTTTGCGTTCCTCCATTGTTGAAGGATATTTAAG
AATGTATTTTTTAAAGGATTTATTTTTGAAGGATATATTATGATAATATATATTACATTACTATG
TGTGGAAAAAAGTATACACTTACAAAACAAATAACAGGTACAAACAAGTTTACCCACATTAAAAA
ATCCCCGTAGCGCAA
Found at i:78577 original size:9 final size:9
Alignment explanation
Indices: 78563--78587 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
78553 GGAAAGGTAG
78563 AAATATACT
1 AAATATACT
78572 AAATATACT
1 AAATATACT
78581 AAATATA
1 AAATATA
78588 AGCAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (9 bp):
AAATATACT
Found at i:82642 original size:22 final size:22
Alignment explanation
Indices: 82593--82644 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
82583 GCATGGCACG
**
82593 GCACGACCCACGTGCCGGCACA
1 GCACGACCCACGTGCCAACACA
** *
82615 ATACGACCCACGTGCCAACGCA
1 GCACGACCCACGTGCCAACACA
82637 GCACGACC
1 GCACGACC
82645 AATTTTTAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.44, G:0.23, T:0.06
Consensus pattern (22 bp):
GCACGACCCACGTGCCAACACA
Found at i:83372 original size:105 final size:105
Alignment explanation
Indices: 83138--83505 Score: 621
Period size: 105 Copynumber: 3.5 Consensus size: 105
83128 AGTTTAGCCT
* * *
83138 TAATTTCACTATGTTTAGCCCTAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
* *
83203 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
66 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATATATAAC
83245 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
83310 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
83350 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
83415 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
66 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
* * ** *
83455 TAATTTCACTAAGTTTAG-CTCACATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
83506 TAAAAAAATA
Statistics
Matches: 251, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
104 28 0.11
105 156 0.62
107 67 0.27
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.42
Consensus pattern (105 bp):
TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAC
Found at i:86554 original size:20 final size:21
Alignment explanation
Indices: 86524--86562 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
86514 AATTTCTTTT
*
86524 CAATATTTACTATATCAATCC
1 CAATATTTACTAAATCAATCC
86545 CAAT-TTTACTAAATCAAT
1 CAATATTTACTAAATCAAT
86563 TAGCAAATCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
CAATATTTACTAAATCAATCC
Found at i:88402 original size:11 final size:11
Alignment explanation
Indices: 88388--88429 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
88378 ATTCATAACA
88388 AATTTATAATT
1 AATTTATAATT
88399 AATTTATAATT
1 AATTTATAATT
88410 -ATTTGATAATAT
1 AATTT-ATAAT-T
*
88422 ATTTTATA
1 AATTTATA
88430 TAGGAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 4 0.15
11 16 0.59
12 4 0.15
13 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (11 bp):
AATTTATAATT
Found at i:90077 original size:22 final size:21
Alignment explanation
Indices: 90010--90081 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
90000 AAATATGAAA
90010 GTCAAACTCCAAAT-ATCAATG
1 GTCAAACTCCAAATCAT-AATG
* *
90031 GTCAAACCCCAAATCTTAATG
1 GTCAAACTCCAAATCATAATG
*
90052 GTCAAACTACAAATCATATATG
1 GTCAAACTCCAAATCATA-ATG
90074 GTCAAACT
1 GTCAAACT
90082 GTAAAGCATG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
21 32 0.73
22 12 0.27
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.25
Consensus pattern (21 bp):
GTCAAACTCCAAATCATAATG
Found at i:90202 original size:87 final size:87
Alignment explanation
Indices: 90032--90498 Score: 556
Period size: 88 Copynumber: 5.4 Consensus size: 87
90022 ATATCAATGG
* ** * * *
90032 TCAAACCCCAAATCTTAATGGTCAAACTACAAATCATATATGGTCAAACTGTAAAGCATGATTAG
1 TCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAA-TTTAAAGCATGATTAG
* *
90097 TCAAGCCCCTACTAGTAATGGGA
65 GCAAACCCCTACTAGTAATGGGA
* * * * *
90120 TCAAATCTCGAATCGTAATTGTCAACCCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
1 TCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
* *
90185 CAAACCCTTACTAGTAATATGG-
66 CAAACCCCTACTAGTAAT-GGGA
*
90207 TCAAACCCCAAATCGTAATGGTCAAA-CCC---T--TGTATAGTGAAATTTAAACGCATGATTAG
1 TCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAA-GCATGATTAG
*
90266 GCAAACCCCTACTGGTAATGGGA
65 GCAAACCCCTACTAGTAATGGGA
* * * *
90289 TCAAACCCCAAAGT-GTAATGGTTAAACCCCAAATCATGTATGGTCAAGCTGTAAAGCATGATTA
1 TCAAACCCCAAA-TCGTAATGGTCAAACCCCAAATCATGTATGGTGAA-ATTTAAAGCATGATTA
* *
90353 GTCAAGCCCCTACTAGTAATGGGA
64 GGCAAACCCCTACTAGTAATGGGA
* * *
90377 TCAAACCTCAAATCGTAATTGTCAAACCCCAAATCATGTATCGTGAAATTTAAAGCATGATTAGG
1 TCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
* * *
90442 CAAAGCCTTACTAGTAATATGG-
66 CAAACCCCTACTAGTAAT-GGGA
90464 TCAAACCCCAAATCGTAATGGTCAAACCCCAAATC
1 TCAAACCCCAAATCGTAATGGTCAAACCCCAAATC
90499 GTAATGTTCA
Statistics
Matches: 320, Mismatches: 46, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
81 19 0.06
82 50 0.16
83 5 0.02
86 4 0.01
87 116 0.36
88 121 0.38
89 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (87 bp):
TCAAACCCCAAATCGTAATGGTCAAACCCCAAATCATGTATGGTGAAATTTAAAGCATGATTAGG
CAAACCCCTACTAGTAATGGGA
Found at i:90306 original size:23 final size:21
Alignment explanation
Indices: 90280--90321 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
90270 ACCCCTACTG
90280 GTAATGGGATCAAACCCCAAAGT
1 GTAAT-GG-TCAAACCCCAAAGT
*
90303 GTAATGGTTAAACCCCAAA
1 GTAATGGTCAAACCCCAAA
90322 TCATGTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (21 bp):
GTAATGGTCAAACCCCAAAGT
Found at i:90486 original size:21 final size:21
Alignment explanation
Indices: 90460--90521 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
90450 TACTAGTAAT
90460 ATGGTCAAACCCCAAATCGTA
1 ATGGTCAAACCCCAAATCGTA
90481 ATGGTCAAACCCCAAATCGTA
1 ATGGTCAAACCCCAAATCGTA
*
90502 ATGTTCAAACCCCAAATCGT
1 ATGGTCAAACCCCAAATCGT
90522 GAAATTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (21 bp):
ATGGTCAAACCCCAAATCGTA
Found at i:90488 original size:257 final size:263
Alignment explanation
Indices: 90032--90617 Score: 844
Period size: 257 Copynumber: 2.2 Consensus size: 263
90022 ATATCAATGG
* ** * *
90032 TCAAACCCCAAA-TCTTAATGGTCAAACTACAAATCATATATGGTCAAACTGTAAAGCATGATTA
1 TCAAACCCCAAAGT-GTAATGGTCAAACCCCAAATCATGTATGGTCAAGCTGTAAAGCATGATTA
* * *
90096 GTCAAGCCCCTACTAGTAATGGGATCAAATCTCGAATCGTAATTGTCAACCCCCAAATCATGTAT
65 GTCAAGCCCCTACTAGTAATGGGATCAAACCTCAAATCGTAATTGTCAAACCCCAAATCATGTAT
*
90161 GGTGAAATTTAAAGCATGATTAGGCAAACCCTTACTAGTAATATGGTCAAACCCCAAATCGTAAT
130 CGTGAAATTTAAAGCATGATTAGGCAAACCCTTACTAGTAATATGGTCAAACCCCAAATCGTAAT
*
90226 GGTCAAA-CC-C-T-TG-T-ATAGTGAAATTTAAACGCATGATTAGGCAAACCCCTACTGGTAAT
195 GGTCAAACCCACGTATGTTAATAGTGAAATTTAAAAGCATGATTAGGCAAACCCCTACTGGTAAT
90285 GGGA
260 GGGA
*
90289 TCAAACCCCAAAGTGTAATGGTTAAACCCCAAATCATGTATGGTCAAGCTGTAAAGCATGATTAG
1 TCAAACCCCAAAGTGTAATGGTCAAACCCCAAATCATGTATGGTCAAGCTGTAAAGCATGATTAG
90354 TCAAGCCCCTACTAGTAATGGGATCAAACCTCAAATCGTAATTGTCAAACCCCAAATCATGTATC
66 TCAAGCCCCTACTAGTAATGGGATCAAACCTCAAATCGTAATTGTCAAACCCCAAATCATGTATC
*
90419 GTGAAATTTAAAGCATGATTAGGCAAAGCCTTACTAGTAATATGGTCAAACCCCAAATCGTAATG
131 GTGAAATTTAAAGCATGATTAGGCAAACCCTTACTAGTAATATGGTCAAACCCCAAATCGTAATG
*
90484 GTCAAACCCCAAATCGTAATGTTCAAACCCCAAATCGTGAAATTTAAAAGCATGATTAGGCAAAC
196 GTCAAA-CCC--A-CGT-ATGTT---------AATAGTGAAATTTAAAAGCATGATTAGGCAAAC
90549 CCCTACTGGTAATGGGA
247 CCCTACTGGTAATGGGA
* * *
90566 TCAAACCCCAAAGTGTAATGGTCAAAGCCCAAATCATGTATGATGAAGCTGT
1 TCAAACCCCAAAGTGTAATGGTCAAACCCCAAATCATGTATGGTCAAGCTGT
Statistics
Matches: 291, Mismatches: 17, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
257 188 0.65
258 1 0.00
259 2 0.01
263 1 0.00
264 1 0.00
266 2 0.01
267 1 0.00
277 95 0.33
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (263 bp):
TCAAACCCCAAAGTGTAATGGTCAAACCCCAAATCATGTATGGTCAAGCTGTAAAGCATGATTAG
TCAAGCCCCTACTAGTAATGGGATCAAACCTCAAATCGTAATTGTCAAACCCCAAATCATGTATC
GTGAAATTTAAAGCATGATTAGGCAAACCCTTACTAGTAATATGGTCAAACCCCAAATCGTAATG
GTCAAACCCACGTATGTTAATAGTGAAATTTAAAAGCATGATTAGGCAAACCCCTACTGGTAATG
GGA
Found at i:90574 original size:102 final size:101
Alignment explanation
Indices: 90416--90600 Score: 284
Period size: 102 Copynumber: 1.8 Consensus size: 101
90406 CAAATCATGT
* * *
90416 ATCGTGAAATTTAAAGCATGATTAGGCAAAGCCTTACTAGTAATATGGTCAAACCCCAAA-TCGT
1 ATCGTGAAATTTAAAGCATGATTAGGCAAACCCCTACTAGTAATAGGGTCAAACCCCAAAGT-GT
90480 AATGGTCAAACCCCAAATCGTAATGTTCAAACCCCAA
65 AATGGTCAAACCCCAAATCGTAATGTTCAAACCCCAA
*
90517 ATCGTGAAATTTAAAAGCATGATTAGGCAAACCCCTACTGGTAAT-GGGATCAAACCCCAAAGTG
1 ATCGTGAAATTT-AAAGCATGATTAGGCAAACCCCTACTAGTAATAGGG-TCAAACCCCAAAGTG
*
90581 TAATGGTCAAAGCCCAAATC
64 TAATGGTCAAACCCCAAATC
90601 ATGTATGATG
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
101 14 0.18
102 61 0.80
103 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (101 bp):
ATCGTGAAATTTAAAGCATGATTAGGCAAACCCCTACTAGTAATAGGGTCAAACCCCAAAGTGTA
ATGGTCAAACCCCAAATCGTAATGTTCAAACCCCAA
Found at i:90596 original size:21 final size:23
Alignment explanation
Indices: 90557--90598 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
90547 ACCCCTACTG
90557 GTAATGGGATCAAACCCCAAAGT
1 GTAATGGGATCAAACCCCAAAGT
*
90580 GTAAT-GG-TCAAAGCCCAAA
1 GTAATGGGATCAAACCCCAAA
90599 TCATGTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (23 bp):
GTAATGGGATCAAACCCCAAAGT
Done.