Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014417.1 Corchorus capsularis cultivar CVL-1 contig14438, 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: 114708
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--32 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33 TNTACCCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4283 original size:16 final size:16
Alignment explanation
Indices: 4262--4292 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4252 AGGAATCTGA
4262 GAGAGCTTTTTTTTGT
1 GAGAGCTTTTTTTTGT
4278 GAGAGCTTTTTTTTG
1 GAGAGCTTTTTTTTG
4293 AATTGTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.13, C:0.06, G:0.26, T:0.55
Consensus pattern (16 bp):
GAGAGCTTTTTTTTGT
Found at i:4390 original size:26 final size:26
Alignment explanation
Indices: 4354--4412 Score: 109
Period size: 26 Copynumber: 2.2 Consensus size: 26
4344 TGGGAATGTT
4354 AGGAATTCAAATTCGAGAAGGAGAAA
1 AGGAATTCAAATTCGAGAAGGAGAAA
4380 AGGAATTCAAATTCGAGAAGGAGAAA
1 AGGAATTCAAATTCGAGAAGGAGAAA
4406 AGAGAAT
1 AG-GAAT
4413 CTGGAAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.51, C:0.07, G:0.27, T:0.15
Consensus pattern (26 bp):
AGGAATTCAAATTCGAGAAGGAGAAA
Found at i:4745 original size:18 final size:18
Alignment explanation
Indices: 4722--4759 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
4712 TGCGCACCTG
*
4722 GTTATGATGGGTGACAGA
1 GTTATGATAGGTGACAGA
4740 GTTATGATAGGTGACAGA
1 GTTATGATAGGTGACAGA
4758 GT
1 GT
4760 GAGTCTCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.37, T:0.29
Consensus pattern (18 bp):
GTTATGATAGGTGACAGA
Found at i:12963 original size:22 final size:22
Alignment explanation
Indices: 12935--12978 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12925 ATTAACAAAA
*
12935 GAACAGAAGGGTACAAGGCTAT
1 GAACAGAAAGGTACAAGGCTAT
*
12957 GAACAGAAAGGTATAAGGCTAT
1 GAACAGAAAGGTACAAGGCTAT
12979 AAGCTACTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.30, T:0.16
Consensus pattern (22 bp):
GAACAGAAAGGTACAAGGCTAT
Found at i:13109 original size:17 final size:17
Alignment explanation
Indices: 13087--13123 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
13077 TTAGTTATAA
*
13087 AACAATGTACTCACATT
1 AACAATGTACTCACACT
13104 AACAATGTACTCACACT
1 AACAATGTACTCACACT
13121 AAC
1 AAC
13124 TTACAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.24
Consensus pattern (17 bp):
AACAATGTACTCACACT
Found at i:28483 original size:29 final size:29
Alignment explanation
Indices: 28441--28544 Score: 199
Period size: 29 Copynumber: 3.6 Consensus size: 29
28431 TCTCTTTAGA
28441 AGCTTTCATTGTCGTTTACTATGAATCGG
1 AGCTTTCATTGTCGTTTACTATGAATCGG
28470 AGCTTTCATTGTCGTTTACTATGAATCGG
1 AGCTTTCATTGTCGTTTACTATGAATCGG
*
28499 AGCTTGCATTGTCGTTTACTATGAATCGG
1 AGCTTTCATTGTCGTTTACTATGAATCGG
28528 AGCTTTCATTGTCGTTT
1 AGCTTTCATTGTCGTTT
28545 GGAGTACCGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (29 bp):
AGCTTTCATTGTCGTTTACTATGAATCGG
Found at i:30089 original size:20 final size:19
Alignment explanation
Indices: 30064--30113 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
30054 AGGTTGATGG
30064 GAAAAAAGAGAGAAAGAAA-A
1 GAAAAAAGAG-G-AAGAAAGA
30084 GAAAAAAGAGGAAGAAAGA
1 GAAAAAAGAGGAAGAAAGA
30103 GAAAGAAAGAG
1 GAAA-AAAGAG
30114 CGGTGGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 16 0.57
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
GAAAAAAGAGGAAGAAAGA
Found at i:30090 original size:22 final size:23
Alignment explanation
Indices: 30065--30110 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
30055 GGTTGATGGG
30065 AAAAAA-GAGAGAAAGA-AAAGAA
1 AAAAAAGGA-AGAAAGAGAAAGAA
*
30087 AAAAGAGGAAGAAAGAGAAAGAA
1 AAAAAAGGAAGAAAGAGAAAGAA
30110 A
1 A
30111 GAGCGGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (23 bp):
AAAAAAGGAAGAAAGAGAAAGAA
Found at i:30103 original size:10 final size:10
Alignment explanation
Indices: 30072--30113 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
30062 GGGAAAAAAG
30072 AGAGAAAGAA
1 AGAGAAAGAA
30082 A-AGAAA-AA
1 AGAGAAAGAA
*
30090 AGAGGAAGAA
1 AGAGAAAGAA
30100 AGAGAAAGAA
1 AGAGAAAGAA
30110 AGAG
1 AGAG
30114 CGGTGGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 3 0.11
9 9 0.32
10 16 0.57
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (10 bp):
AGAGAAAGAA
Found at i:30623 original size:25 final size:24
Alignment explanation
Indices: 30579--30625 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
30569 TTAACCATAA
* *
30579 CTCAAAAAAAATATATTATGTTTC
1 CTCAAAAAAAAAATACTATGTTTC
30603 CTCAAAAAAAGAAATACTATGTT
1 CTCAAAAAAA-AAATACTATGTT
30626 AACCATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (24 bp):
CTCAAAAAAAAAATACTATGTTTC
Found at i:31146 original size:79 final size:79
Alignment explanation
Indices: 31054--31200 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 79
31044 ACAAAATCTA
* * *
31054 AAAAAATAATTTCATCGTACATACATGGTCACACAACAAAGGATGATAGTCAAACCGCAAAGTTT
1 AAAAAACAATTTCATCGTACATACATGGTCAAACAACAAAGGATGATAGTCAAACCCCAAAGTTT
31119 GATTCTCAAACCAC
66 GATTCTCAAACCAC
* * * ** ** * *
31133 AAAAAACATTTTCATTGTACATGCATGGTCAAACCCCAAAGTTTGATAGTCAATCCCCGAAGTTT
1 AAAAAACAATTTCATCGTACATACATGGTCAAACAACAAAGGATGATAGTCAAACCCCAAAGTTT
31198 GAT
66 GAT
31201 AGTCAATCCC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 56 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (79 bp):
AAAAAACAATTTCATCGTACATACATGGTCAAACAACAAAGGATGATAGTCAAACCCCAAAGTTT
GATTCTCAAACCAC
Found at i:31190 original size:21 final size:21
Alignment explanation
Indices: 31160--31306 Score: 186
Period size: 21 Copynumber: 7.0 Consensus size: 21
31150 TACATGCATG
31160 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
* *
31181 GTCAATCCCCGAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
* *
31202 GTCAATCCCCAAAATTTGATA
1 GTCAAACCCCAAAGTTTGATA
31223 GTCAAACCCCAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
* * *
31244 GTCAATCCCCAAAATTTGATT
1 GTCAAACCCCAAAGTTTGATA
** *
31265 GTCAAACCGAAAAGTTTGATT
1 GTCAAACCCCAAAGTTTGATA
* *
31286 GTTAAACCCTAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
31307 ATCCACACAT
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 109 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (21 bp):
GTCAAACCCCAAAGTTTGATA
Found at i:31233 original size:63 final size:63
Alignment explanation
Indices: 31160--31306 Score: 206
Period size: 63 Copynumber: 2.3 Consensus size: 63
31150 TACATGCATG
* * *
31160 GTCAAACCCCAAAGTTTGATAGTCAATCCCCGAAGTTTGATAGTCAATCCCCAAAA-TTTGATA
1 GTCAAACCCCAAAGTTTGATAGTCAATCCCCAAAATTTGATAGTCAA-ACCCAAAAGTTTGATA
* * *
31223 GTCAAACCCCAAAGTTTGATAGTCAATCCCCAAAATTTGATTGTCAAACCGAAAAGTTTGATT
1 GTCAAACCCCAAAGTTTGATAGTCAATCCCCAAAATTTGATAGTCAAACCCAAAAGTTTGATA
* *
31286 GTTAAACCCTAAAGTTTGATA
1 GTCAAACCCCAAAGTTTGATA
31307 ATCCACACAT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
62 6 0.08
63 69 0.92
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (63 bp):
GTCAAACCCCAAAGTTTGATAGTCAATCCCCAAAATTTGATAGTCAAACCCAAAAGTTTGATA
Found at i:32051 original size:16 final size:16
Alignment explanation
Indices: 32030--32064 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
32020 TTTATAATGA
32030 ATTTAATATTCAACAT
1 ATTTAATATTCAACAT
* *
32046 ATTTAATCTTCAATAT
1 ATTTAATATTCAACAT
32062 ATT
1 ATT
32065 GAATGACTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAATATTCAACAT
Found at i:32410 original size:3 final size:3
Alignment explanation
Indices: 32402--32449 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
32392 CTCCCATGTG
** *
32402 ATA ATA ATA ATA GCA AT- ATA ACA ATA ATA ATA TATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
32447 ATA
1 ATA
32450 GTCATTGAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:32438 original size:16 final size:16
Alignment explanation
Indices: 32417--32449 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
32407 AATAATAGCA
32417 ATATAACAATAATAAT
1 ATATAACAATAATAAT
*
32433 ATATAATAATAATAAT
1 ATATAACAATAATAAT
32449 A
1 A
32450 GTCATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
ATATAACAATAATAAT
Found at i:33551 original size:42 final size:42
Alignment explanation
Indices: 33503--33583 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
33493 CGTCAAAAAT
* *
33503 TTCATTTTTCTTAAATCGTCATCAAAATACGGTACGTTATCG
1 TTCATTTTTCTTAAATCGTCATCAAAATACAGCACGTTATCG
33545 TTCATTTTTCTTAAATCGTCATCAAAATACAGCACGTTA
1 TTCATTTTTCTTAAATCGTCATCAAAATACAGCACGTTA
33584 ACGCTATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.40
Consensus pattern (42 bp):
TTCATTTTTCTTAAATCGTCATCAAAATACAGCACGTTATCG
Found at i:40389 original size:2 final size:2
Alignment explanation
Indices: 40382--40415 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
40372 TATGTTTAGC
* *
40382 AT AT AT AT CT AC AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40416 TCATTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44512 original size:19 final size:19
Alignment explanation
Indices: 44488--44524 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44478 GACGACAGGA
44488 AATTAATATATGTTAGCAT
1 AATTAATATATGTTAGCAT
* *
44507 AATTAATGTATTTTAGCA
1 AATTAATATATGTTAGCA
44525 CCATCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (19 bp):
AATTAATATATGTTAGCAT
Found at i:50925 original size:2 final size:2
Alignment explanation
Indices: 50920--50956 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
50910 ATTAAAAAGG
50920 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50957 GATTGGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54196 original size:2 final size:2
Alignment explanation
Indices: 54189--54221 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54179 TATGTTAAAG
54189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54222 CAAGTTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56011 original size:17 final size:17
Alignment explanation
Indices: 55989--56022 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55979 GATTTTTCTG
55989 GAGCCGGATAGATTCAT
1 GAGCCGGATAGATTCAT
56006 GAGCCGGATAGATTCAT
1 GAGCCGGATAGATTCAT
56023 TATGATTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (17 bp):
GAGCCGGATAGATTCAT
Found at i:56196 original size:38 final size:38
Alignment explanation
Indices: 56145--56219 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
56135 TTTGGATTGT
*
56145 GAAATGAGATTTTGGAGCCCAACAAACCTCTAGACATA
1 GAAATGAGATTTTGAAGCCCAACAAACCTCTAGACATA
*
56183 GAAATGAGATTTTGAAGCCCAACAAACCTTTAGACAT
1 GAAATGAGATTTTGAAGCCCAACAAACCTCTAGACAT
56220 GTATACTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (38 bp):
GAAATGAGATTTTGAAGCCCAACAAACCTCTAGACATA
Found at i:56381 original size:15 final size:15
Alignment explanation
Indices: 56338--56382 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
56328 GAGGTGAGAG
*
56338 AATCTCACCATCACC
1 AATCTCACCATCACT
* **
56353 AATCACACTGTCACT
1 AATCTCACCATCACT
56368 AATCTCACCATCACT
1 AATCTCACCATCACT
56383 GCTGTTTCAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.24
Consensus pattern (15 bp):
AATCTCACCATCACT
Found at i:61207 original size:2 final size:2
Alignment explanation
Indices: 61164--61191 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
61154 GTTGTGGGTA
61164 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
61192 GCGGGTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:65962 original size:111 final size:112
Alignment explanation
Indices: 65752--65964 Score: 322
Period size: 112 Copynumber: 1.9 Consensus size: 112
65742 TCTTCCTCGC
* *
65752 CATCATCATTTCTATCATTCCCATCTTTCTTGTCCTCGAATTTATCCTTAAAAAAGTTTCCGGAA
1 CATCATCATTTCTATCATTCCCATCTTTCCTGTCCTCAAATTTATCCTTAAAAAAGTTTCCGGAA
*
65817 AAAACCATCCTTATCATCATCTTCAGCAGATTTTGAAATTCTTTCCT
66 AAAACCATCCTTATCATCATCTTCAACAGATTTTGAAATTCTTTCCT
* *
65864 CATCATCAATTT-TATCATTCCCGTCTTTCCTGTCTTCAAATTTATCCTTAAAAAA-TTTCCGGA
1 CATCATC-ATTTCTATCATTCCCATCTTTCCTGTCCTCAAATTTATCCTTAAAAAAGTTTCCGGA
* * * *
65927 AAAATCCATCTTTGTCATCATCTTCAACTGATTTTGAA
65 AAAAACCATCCTTATCATCATCTTCAACAGATTTTGAA
65965 GCTTTTTCTT
Statistics
Matches: 91, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
111 41 0.45
112 46 0.51
113 4 0.04
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (112 bp):
CATCATCATTTCTATCATTCCCATCTTTCCTGTCCTCAAATTTATCCTTAAAAAAGTTTCCGGAA
AAAACCATCCTTATCATCATCTTCAACAGATTTTGAAATTCTTTCCT
Found at i:68684 original size:51 final size:51
Alignment explanation
Indices: 68608--68709 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
68598 CTAAGACCTT
68608 TACTTTCCCAATCTTCACAATATATCTCATAATGACATTAGGCCTAAAAAA
1 TACTTTCCCAATCTTCACAATATATCTCATAATGACATTAGGCCTAAAAAA
68659 TACTTTCCCAATCTTCACAATATATCTCATAATGACATTAGGCCTAAAAAA
1 TACTTTCCCAATCTTCACAATATATCTCATAATGACATTAGGCCTAAAAAA
68710 ATCTTAGCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (51 bp):
TACTTTCCCAATCTTCACAATATATCTCATAATGACATTAGGCCTAAAAAA
Found at i:68735 original size:51 final size:51
Alignment explanation
Indices: 68608--68735 Score: 152
Period size: 51 Copynumber: 2.5 Consensus size: 51
68598 CTAAGACCTT
* * *
68608 TACTTTCCCAATCTTCACAATATATCTCATAATGACATTAGGCCTAAAAAA
1 TACTTACCAAATCTTCACAAAATATCTCATAATGACATTAGGCCTAAAAAA
* * *
68659 TACTTTCCCAATCTTCACAATATATCTCATAATGACATTAGGCCTAAAAAA
1 TACTTACCAAATCTTCACAAAATATCTCATAATGACATTAGGCCTAAAAAA
* *
68710 -ATCTTAGCAAATCCTT-ATAAAATATC
1 TA-CTTACCAAAT-CTTCACAAAATATC
68736 CAATATATAA
Statistics
Matches: 70, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 1 0.01
51 66 0.94
52 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (51 bp):
TACTTACCAAATCTTCACAAAATATCTCATAATGACATTAGGCCTAAAAAA
Found at i:70711 original size:3 final size:3
Alignment explanation
Indices: 70697--70795 Score: 171
Period size: 3 Copynumber: 33.0 Consensus size: 3
70687 TTTATCTTTT
*
70697 TTG TTA TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* *
70745 TTT TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG CTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
70793 TTG
1 TTG
70796 CTGGGTAGTT
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.01, C:0.01, G:0.31, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:72169 original size:2 final size:2
Alignment explanation
Indices: 72162--72208 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
72152 TTAAACCCCT
72162 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
72204 TC TC T
1 TC TC T
72209 ATATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:75024 original size:3 final size:3
Alignment explanation
Indices: 75016--75051 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
75006 ATTCAAGCAG
75016 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
75052 CTCTCTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:75056 original size:2 final size:2
Alignment explanation
Indices: 75049--75108 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
75039 TTCTTCTTCT
75049 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
75091 TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC
75109 CCCCCAAGTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:78398 original size:33 final size:34
Alignment explanation
Indices: 78331--78414 Score: 138
Period size: 33 Copynumber: 2.6 Consensus size: 34
78321 TGGACTAACT
78331 AAACTAATTTCAAGAAA--TAGTGCCAAAAAAAA
1 AAACTAATTTCAAGAAAGTTAGTGCCAAAAAAAA
*
78363 AAACTAATTTCAAGAAAGTTGGTGCC-AAAAAAA
1 AAACTAATTTCAAGAAAGTTAGTGCCAAAAAAAA
78396 AAACTAATTTCAAGAAAGT
1 AAACTAATTTCAAGAAAGT
78415 CATAAACTTT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
32 17 0.35
33 26 0.53
34 6 0.12
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.21
Consensus pattern (34 bp):
AAACTAATTTCAAGAAAGTTAGTGCCAAAAAAAA
Found at i:78461 original size:38 final size:38
Alignment explanation
Indices: 78419--78494 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
78409 GAAAGTCATA
78419 AACTTTATTAGCTAAAAATGTAAATATATTTATCCAAT
1 AACTTTATTAGCTAAAAATGTAAATATATTTATCCAAT
*
78457 AACTTTATTAGCTAAAAATGTAAATATATTTATTCAAT
1 AACTTTATTAGCTAAAAATGTAAATATATTTATCCAAT
78495 GAAATACTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (38 bp):
AACTTTATTAGCTAAAAATGTAAATATATTTATCCAAT
Found at i:81935 original size:23 final size:24
Alignment explanation
Indices: 81891--81942 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
81881 TGCAGCGCAT
** *
81891 TTTATTTAATTATTTCTGTTTTA-
1 TTTATTTAATTATGACTCTTTTAC
*
81914 TTTATTTAATTATGAGTCTTTTAC
1 TTTATTTAATTATGACTCTTTTAC
81938 TTTAT
1 TTTAT
81943 CCTTAAGTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (24 bp):
TTTATTTAATTATGACTCTTTTAC
Found at i:84419 original size:42 final size:42
Alignment explanation
Indices: 84356--84449 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 42
84346 GTTCTGCTCC
* *
84356 AGCCCCACCCTCAGAACCTGATCGCTGGGGTAGTGGCAGCAG
1 AGCCCCACCTTCACAACCTGATCGCTGGGGTAGTGGCAGCAG
*
84398 AGCCCCACCTTCACAATCTGATCGCTGGGGTAGTGGCAGCAG
1 AGCCCCACCTTCACAACCTGATCGCTGGGGTAGTGGCAGCAG
* *
84440 GGCTCCACCT
1 AGCCCCACCT
84450 CAGGATGGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.20, C:0.34, G:0.29, T:0.17
Consensus pattern (42 bp):
AGCCCCACCTTCACAACCTGATCGCTGGGGTAGTGGCAGCAG
Found at i:95929 original size:20 final size:20
Alignment explanation
Indices: 95906--95945 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
95896 AAGACATTGG
*
95906 TGGTTTTTTATCCATTTTTT
1 TGGTGTTTTATCCATTTTTT
* *
95926 TGGTGTTTTCTCCCTTTTTT
1 TGGTGTTTTATCCATTTTTT
95946 CTCTGGATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.15, G:0.12, T:0.68
Consensus pattern (20 bp):
TGGTGTTTTATCCATTTTTT
Found at i:98120 original size:65 final size:65
Alignment explanation
Indices: 98012--98133 Score: 199
Period size: 65 Copynumber: 1.9 Consensus size: 65
98002 TTTTGCTCCA
*
98012 AGTTTCATTTACATGAAGATAGTGGGAAGATACTAATTTTTTATATTATGAGCTAAGGTAAAAAT
1 AGTTTCATTTACATGAAGATAGTGGGAAGATACTAATTCTTTATATTATGAGCTAAGGTAAAAAT
* * * *
98077 AGTTTCATTTACGTGCAGATAGTGGGGAGATACTAATTCTTTATGTTATGAGCTAAG
1 AGTTTCATTTACATGAAGATAGTGGGAAGATACTAATTCTTTATATTATGAGCTAAG
98134 AGTATGTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 52 1.00
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (65 bp):
AGTTTCATTTACATGAAGATAGTGGGAAGATACTAATTCTTTATATTATGAGCTAAGGTAAAAAT
Found at i:101735 original size:45 final size:45
Alignment explanation
Indices: 101671--101763 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
101661 AATCAATGGA
101671 AAATTTGCTGTTGTTAGTGAGAATGATGGTTTAGATCCTTCTTGT
1 AAATTTGCTGTTGTTAGTGAGAATGATGGTTTAGATCCTTCTTGT
101716 AAATTTGCTGTTGTTAGTGAGAATGATGGTTTAGATCCTTCTTGT
1 AAATTTGCTGTTGTTAGTGAGAATGATGGTTTAGATCCTTCTTGT
101761 AAA
1 AAA
101764 GTTAGTATCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.25, C:0.09, G:0.24, T:0.43
Consensus pattern (45 bp):
AAATTTGCTGTTGTTAGTGAGAATGATGGTTTAGATCCTTCTTGT
Found at i:111145 original size:43 final size:43
Alignment explanation
Indices: 111096--111184 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
111086 AAAAATTAAT
*
111096 ATCAAGGCAACCATATAGGTAAAACCTATAAGCTTGCCCCTGA
1 ATCAAGGCAACCATATAGGTAAAACCTATAAGCTTGCCACTGA
111139 ATCAAGGCAACCATATAGGTAAAACCTATAAGCTTGCCACTGA
1 ATCAAGGCAACCATATAGGTAAAACCTATAAGCTTGCCACTGA
111182 ATC
1 ATC
111185 CGTAGGTTCG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (43 bp):
ATCAAGGCAACCATATAGGTAAAACCTATAAGCTTGCCACTGA
Done.