Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006004.1 Corchorus capsularis cultivar CVL-1 contig06022, 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: 44875
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Found at i:325 original size:26 final size:27
Alignment explanation
Indices: 296--349 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
286 TATTTATGAT
296 AATAATCTATACT-AATAATATAAAAA
1 AATAATCTATACTAAATAATATAAAAA
322 AATAATCTATACTAAAATAATATAAAAA
1 AATAATCTATACT-AAATAATATAAAAA
350 GTTAATTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 13 0.50
28 13 0.50
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (27 bp):
AATAATCTATACTAAATAATATAAAAA
Found at i:3514 original size:21 final size:21
Alignment explanation
Indices: 3467--3517 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
3457 AAAATTCAAA
* *
3467 ATAAAATAAAAACTACCTATT
1 ATAAGATAAAAACTACCCATT
*
3488 -TTAGATAAAAACTACCCATT
1 ATAAGATAAAAACTACCCATT
3508 ATAAGATAAA
1 ATAAGATAAA
3518 TATAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAGATAAAAACTACCCATT
Found at i:3948 original size:31 final size:31
Alignment explanation
Indices: 3906--3993 Score: 149
Period size: 31 Copynumber: 2.8 Consensus size: 31
3896 CATGATTACT
*
3906 CACCAAAAGGTATACCGTAAATACTCCCTACC
1 CACC-AAAGGTATACCGTAAATACTCCATACC
3938 CACCAAAGGTATACCGTAAATACTCCATACC
1 CACCAAAGGTATACCGTAAATACTCCATACC
*
3969 CACCAAAGGTATACCGTAAACACTC
1 CACCAAAGGTATACCGTAAATACTC
3994 ACCAAGTATT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
31 50 0.93
32 4 0.07
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (31 bp):
CACCAAAGGTATACCGTAAATACTCCATACC
Found at i:4966 original size:27 final size:28
Alignment explanation
Indices: 4927--4990 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
4917 GTGTGCTAGG
*
4927 GAGGCGACCCCCCTGTTGTGAGTAAGGT
1 GAGGCGACCCCCCTGGTGTGAGTAAGGT
* *
4955 GAGGCGA-TCCCCTGGTGTGAGTAAGGA
1 GAGGCGACCCCCCTGGTGTGAGTAAGGT
4982 G-GGCGACCC
1 GAGGCGACCC
4991 ATGGTGTGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 5 0.16
27 19 0.61
28 7 0.23
ACGTcount: A:0.19, C:0.25, G:0.39, T:0.17
Consensus pattern (28 bp):
GAGGCGACCCCCCTGGTGTGAGTAAGGT
Found at i:4995 original size:25 final size:27
Alignment explanation
Indices: 4943--4998 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
4933 ACCCCCCTGT
* *
4943 TGTGAGTAAGGTGAGGCGATCCCCTGG
1 TGTGAGTAAGGAGAGGCGATCCCATGG
4970 TGTGAGTAAGGAG-GGCGA-CCCATGG
1 TGTGAGTAAGGAGAGGCGATCCCATGG
4995 TGTG
1 TGTG
4999 CGTATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 10 0.37
26 5 0.19
27 12 0.44
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.21
Consensus pattern (27 bp):
TGTGAGTAAGGAGAGGCGATCCCATGG
Found at i:5264 original size:28 final size:29
Alignment explanation
Indices: 5233--5345 Score: 112
Period size: 28 Copynumber: 4.0 Consensus size: 29
5223 CCTTTGAGCT
*
5233 TTGCTATGCGCAAAGGGGGGCGA-CCCCC
1 TTGCTATGCGCAAAGGGGAGCGATCCCCC
*
5261 TTGCTATGCGTAAAGGGGAGCGATCCCCC
1 TTGCTATGCGCAAAGGGGAGCGATCCCCC
* *
5290 ---CTATGCGCACAAAGTGGGGGC-A-ACCCC
1 TTGCTATGCG--CAAAG-GGGAGCGATCCCCC
*
5317 TTACTATGCGCAAAGGGGAGCGATCCCCC
1 TTGCTATGCGCAAAGGGGAGCGATCCCCC
5346 CCTACGCGCA
Statistics
Matches: 69, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
26 7 0.10
27 9 0.13
28 32 0.46
29 14 0.20
30 7 0.10
ACGTcount: A:0.22, C:0.31, G:0.31, T:0.16
Consensus pattern (29 bp):
TTGCTATGCGCAAAGGGGAGCGATCCCCC
Found at i:5309 original size:57 final size:57
Alignment explanation
Indices: 5236--5373 Score: 176
Period size: 56 Copynumber: 2.5 Consensus size: 57
5226 TTGAGCTTTG
* *
5236 CTATGCG--CAAAGGGGGGCGACCCCCTTGCTATGCGTAAAGGGGAGCGAT-CCCCC
1 CTATGCGCACAAAGGGGGGCGACCCCCTTACTATGCGCAAAGGGGAGCGATCCCCCC
*
5290 CTATGCGCACAAAGTGGGGGC-AACCCCTTACTATGCGCAAAGGGGAGCGATCCCCCC
1 CTATGCGCACAAAG-GGGGGCGACCCCCTTACTATGCGCAAAGGGGAGCGATCCCCCC
* * *
5347 CTACGCGCATAAAGGAGGGCTGACCCC
1 CTATGCGCACAAAGGGGGGC-GACCCC
5374 TGACGATACA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
54 7 0.10
56 37 0.52
57 23 0.32
58 4 0.06
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.14
Consensus pattern (57 bp):
CTATGCGCACAAAGGGGGGCGACCCCCTTACTATGCGCAAAGGGGAGCGATCCCCCC
Found at i:5935 original size:35 final size:35
Alignment explanation
Indices: 5830--5958 Score: 136
Period size: 35 Copynumber: 3.7 Consensus size: 35
5820 GGGAGGTGTC
* *
5830 ACGCC-CCCCTTATCACATTTAATTAGGGAGGCATG
1 ACGCCTCCCCTTAACA-ATTTAATTAGGGAGGCATT
* * * *
5865 ACACCCACCCCTTAACATTTTAATTTGGGAGGCATT
1 AC-GCCTCCCCTTAACAATTTAATTAGGGAGGCATT
* * *
5901 ACGCCTCCCCTTGAGAATTTAATTACGGAGGCATT
1 ACGCCTCCCCTTAACAATTTAATTAGGGAGGCATT
*
5936 ACGCCT-CCCTTCACAATTTAATT
1 ACGCCTCCCCTTAACAATTTAATT
5959 GGGTATGCGT
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
34 15 0.19
35 34 0.44
36 20 0.26
37 9 0.12
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (35 bp):
ACGCCTCCCCTTAACAATTTAATTAGGGAGGCATT
Found at i:6242 original size:2 final size:2
Alignment explanation
Indices: 6235--6259 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6225 TATAGCCAAA
6235 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
6260 AATCTGAATT
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:6760 original size:45 final size:45
Alignment explanation
Indices: 6696--6781 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
6686 AAGCCAATAG
6696 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA
1 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA
*
6741 GCAGTTACTTCATCAAGAATGAGGTAACCACCCATGTTCTT
1 GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTT
6782 ATTTGAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (45 bp):
GCAGTTACTTCATCAAGAATGAGGTAACCACCCACGTTCTTCAAA
Found at i:7125 original size:2 final size:2
Alignment explanation
Indices: 7075--7106 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7065 AATCCTTGTT
7075 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7107 AATTAAATAT
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):
TA
Found at i:7488 original size:63 final size:63
Alignment explanation
Indices: 7389--7515 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
7379 AAGACATGGG
7389 TAATTGCATTCATACCCCTTTACTTTATCATTATTGTAAATAACACTACTTTAATTGTTATTT
1 TAATTGCATTCATACCCCTTTACTTTATCATTATTGTAAATAACACTACTTTAATTGTTATTT
7452 TAATTGCATTCATACCCCTTTACTTTATCATTATTGTAAATAACACTACTTTAATTGTTATTT
1 TAATTGCATTCATACCCCTTTACTTTATCATTATTGTAAATAACACTACTTTAATTGTTATTT
7515 T
1 T
7516 CATTTTAAAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.48
Consensus pattern (63 bp):
TAATTGCATTCATACCCCTTTACTTTATCATTATTGTAAATAACACTACTTTAATTGTTATTT
Found at i:12153 original size:9 final size:8
Alignment explanation
Indices: 12140--12173 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
12130 GGTAAAAGGG
12140 GAAAAAAA
1 GAAAAAAA
12148 GAAAAAAA
1 GAAAAAAA
12156 G-AAAAAA
1 GAAAAAAA
*
12163 GAAAAAGA
1 GAAAAAAA
12171 GAA
1 GAA
12174 CTCCAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:12162 original size:15 final size:15
Alignment explanation
Indices: 12142--12173 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12132 TAAAAGGGGA
12142 AAAAAAGAAAAAAAG
1 AAAAAAGAAAAAAAG
*
12157 AAAAAAGAAAAAGAG
1 AAAAAAGAAAAAAAG
12172 AA
1 AA
12174 CTCCAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:18308 original size:22 final size:22
Alignment explanation
Indices: 18264--18312 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
18254 AAAGCGAAAC
* *
18264 TGCAAATGAAATGAAACTCAAA
1 TGCAAATGAAATGAAAATAAAA
*
18286 TGCAATTGAAATGAAAATAAAA
1 TGCAAATGAAATGAAAATAAAA
18308 T-CAAA
1 TGCAAA
18313 GCGACTCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.20
Consensus pattern (22 bp):
TGCAAATGAAATGAAAATAAAA
Found at i:20364 original size:35 final size:35
Alignment explanation
Indices: 20316--20389 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
20306 TAGCTTTCAT
* *
20316 ATTGTTTTAGTTTTTACTATAATGTTATTATTGTG
1 ATTGTTTTAGTTTTTACTATAATATCATTATTGTG
* * *
20351 ATTGTTTTGGTTTTTACTTTAATATCATTATTTTG
1 ATTGTTTTAGTTTTTACTATAATATCATTATTGTG
20386 ATTG
1 ATTG
20390 CTTAAAGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.22, C:0.04, G:0.14, T:0.61
Consensus pattern (35 bp):
ATTGTTTTAGTTTTTACTATAATATCATTATTGTG
Found at i:33379 original size:44 final size:43
Alignment explanation
Indices: 33314--33399 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
33304 ACGCACAATA
* *
33314 AATACTCTTTTTCTTTTTTCTTTTTGGGTGAATAATAATAGTAT
1 AATACTCTTTTTCTTTCTTCTTTTT-GGTGAAAAATAATAGTAT
**
33358 AATACTCTTTCTTC-TTCTTCTTTTTTTTGAAAAATAATAGTA
1 AATACTCTTT-TTCTTTCTTCTTTTTGGTGAAAAATAATAGTA
33400 CTCTTTCTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 14 0.38
44 20 0.54
45 3 0.08
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.53
Consensus pattern (43 bp):
AATACTCTTTTTCTTTCTTCTTTTTGGTGAAAAATAATAGTAT
Found at i:33578 original size:14 final size:15
Alignment explanation
Indices: 33559--33587 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
33549 ACCAATAAAA
33559 ATATGGA-TATATTT
1 ATATGGAGTATATTT
33573 ATATGGAGTATATTT
1 ATATGGAGTATATTT
33588 TTTAAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (15 bp):
ATATGGAGTATATTT
Found at i:36892 original size:23 final size:22
Alignment explanation
Indices: 36864--36945 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 22
36854 AAAACCTCCA
36864 TATGAATTGTT-AGTAAATCACAC
1 TATGAATTGTTGA-T-AATCACAC
*
36887 TTTGAATT-TTGATAATCACAC
1 TATGAATTGTTGATAATCACAC
* *
36908 TATGAAATTG-TGATAACCTCAC
1 TATG-AATTGTTGATAATCACAC
36930 TATGAAATT-TTGATAA
1 TATG-AATTGTTGATAA
36946 ATCTTCCTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
21 11 0.22
22 32 0.63
23 8 0.16
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (22 bp):
TATGAATTGTTGATAATCACAC
Found at i:36921 original size:22 final size:22
Alignment explanation
Indices: 36879--36991 Score: 95
Period size: 23 Copynumber: 5.1 Consensus size: 22
36869 ATTGTTAGTA
*
36879 AATCACACTTTG-AATTTTGAT
1 AATCACACTATGAAATTTTGAT
*
36900 AATCACACTATGAAATTGTGAT
1 AATCACACTATGAAATTTTGAT
* *
36922 AACCTCACTATGAAATTTTGAT
1 AATCACACTATGAAATTTTGAT
* *
36944 AAATCTTC-CTATAAAATTTTGAT
1 -AATC-ACACTATGAAATTTTGAT
* * * *
36967 AAACCTCCCTATAAAATTTTGAT
1 -AATCACACTATGAAATTTTGAT
36990 AA
1 AA
36992 CTTTCTTATG
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
21 11 0.14
22 31 0.39
23 36 0.45
24 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (22 bp):
AATCACACTATGAAATTTTGAT
Found at i:36960 original size:23 final size:23
Alignment explanation
Indices: 36907--36991 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
36897 GATAATCACA
* * *
36907 CTATGAAATTGTGAT-AACCTCA
1 CTATAAAATTTTGATAAACCTCC
* * *
36929 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAACCTCC
36952 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAACCTCC
36975 CTATAAAATTTTGATAA
1 CTATAAAATTTTGATAA
36992 CTTTCTTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 14 0.25
23 41 0.75
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (23 bp):
CTATAAAATTTTGATAAACCTCC
Found at i:36984 original size:46 final size:45
Alignment explanation
Indices: 36891--36991 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 45
36881 TCACACTTTG
* *
36891 AATTTTGAT-AATCACACTATGAAATTGTGATAACCTCACTATGA
1 AATTTTGATAAATCACACTATAAAATTGTGATAACCTCACTATAA
* * *
36935 AATTTTGATAAATCTTC-CTATAAAATTTTGATAAACCTCCCTATAA
1 AATTTTGATAAATC-ACACTATAAAATTGTGAT-AACCTCACTATAA
36981 AATTTTGATAA
1 AATTTTGATAA
36992 CTTTCTTATG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
44 9 0.18
45 17 0.35
46 23 0.47
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.38
Consensus pattern (45 bp):
AATTTTGATAAATCACACTATAAAATTGTGATAACCTCACTATAA
Found at i:37068 original size:22 final size:22
Alignment explanation
Indices: 37018--37136 Score: 82
Period size: 22 Copynumber: 5.4 Consensus size: 22
37008 TTATAACTAC
* *
37018 AAATTTTGATGACCTCCCTATG
1 AAATTTTGATAACCTCTCTATG
**
37040 ATTTTTTGATAACCTCAT-TATG
1 AAATTTTGATAACCTC-TCTATG
* * *
37062 AACTTTTGTTAATCTCTCTATG
1 AAATTTTGATAACCTCTCTATG
* * *
37084 AAATTTTGATCTACAT-ACTATG
1 AAATTTTGAT-AACCTCTCTATG
* *
37106 AAATTGTGATAGCC-CTCTTATG
1 AAATTTTGATAACCTCTC-TATG
37128 AAATTTTGA
1 AAATTTTGA
37137 AAACTAAATT
Statistics
Matches: 72, Mismatches: 20, Indels: 10
0.71 0.20 0.10
Matches are distributed among these distances:
21 3 0.04
22 67 0.93
23 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (22 bp):
AAATTTTGATAACCTCTCTATG
Found at i:37449 original size:25 final size:24
Alignment explanation
Indices: 37394--37458 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 24
37384 GATAACAATG
37394 CTATGAAATTTTGATAA--TGTTC
1 CTATGAAATTTTGATAATCTGTTC
*
37416 CTAT-AAATTTTGATAATCTGATTT
1 CTATGAAATTTTGATAATCTG-TTC
*
37440 CTATGAAATTTCGATAATC
1 CTATGAAATTTTGATAATC
37459 ATTCTATGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 12 0.32
22 4 0.11
23 2 0.05
24 6 0.16
25 13 0.35
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (24 bp):
CTATGAAATTTTGATAATCTGTTC
Found at i:37658 original size:66 final size:65
Alignment explanation
Indices: 37517--37885 Score: 205
Period size: 66 Copynumber: 5.5 Consensus size: 65
37507 AAATTGAGAC
*
37517 TTTTATAACCTTCATATGAAATTTTGATAACTACACTATAAAATTTTGATAACCTCCCCATGAAA
1 TTTTATAACCTTCATATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCCATGAAA
* * * ***
37582 TATTAGTAACCTTC-TAATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCTCGTTATG
1 TTTTA-TAACCTTCAT-ATGAAATTTTGATAACCACACTATAAAATT-TTGATAACCTCCCCATG
*
37645 ACA
63 AAA
* * * **** * *
37648 TTTTGATAACC-TC-TTTGATAACATTT-CTAA-TTTTCTATAAAATTGTGATAATTAACCACCC
1 TTTT-ATAACCTTCATATGA-AA-TTTTGATAACCACACTATAAAATT-T--TGA-TAACCTCCC
*
37709 TATGAAA
59 CATGAAA
* ** * * * * * * * *
37716 TTTCAATAACCAACCTAAGAAATTTTAATAACCTGATC-CTATGAAATTTTGGTAACCACACAAT
1 TTT-TATAACCTTCATATGAAATTTTGATAACC--A-CACTATAAAATTTTGATAACCTCCCCAT
37780 GAAA
62 GAAA
* ** *
37784 TTTTGATAA-CTTCCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACCTCCTCATGA
1 TTTT-ATAACCTT-CATATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCCATGA
37848 AA
64 AA
* * *
37850 TTATAATAACCATCTTATGAAATTTTGATAACCACA
1 TT-TTATAACCTTCATATGAAATTTTGATAACCACA
37886 TAGAGACAAG
Statistics
Matches: 228, Mismatches: 53, Indels: 45
0.70 0.16 0.14
Matches are distributed among these distances:
64 13 0.06
65 14 0.06
66 112 0.49
67 8 0.04
68 61 0.27
69 7 0.03
70 3 0.01
71 1 0.00
72 9 0.04
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.36
Consensus pattern (65 bp):
TTTTATAACCTTCATATGAAATTTTGATAACCACACTATAAAATTTTGATAACCTCCCCATGAAA
Found at i:37772 original size:46 final size:44
Alignment explanation
Indices: 37707--37882 Score: 155
Period size: 44 Copynumber: 4.0 Consensus size: 44
37697 AATTAACCAC
*** *
37707 CCTATGAAATTTCAATAACCA-ACCTAAGAAATTTTAATAACCTGAT
1 CCTATGAAATTTTGGTAACCACA-CTAAGAAATTTTGATAACCT--T
37753 CCTATGAAATTTTGGTAACCACAC-AATGAAATTTTGATAA-CTT
1 CCTATGAAATTTTGGTAACCACACTAA-GAAATTTTGATAACCTT
* *
37796 CCATATGAAATTTTGGTAACCACACTATGGAATTTTGATAACC-T
1 CC-TATGAAATTTTGGTAACCACACTAAGAAATTTTGATAACCTT
* ** * *
37840 CCTCATGAAATTATAATAACCATC-TTATGAAATTTTGATAACC
1 CCT-ATGAAATTTTGGTAACCA-CACTAAGAAATTTTGATAACC
37883 ACATAGAGAC
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
43 4 0.04
44 69 0.62
45 7 0.06
46 31 0.28
47 1 0.01
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.34
Consensus pattern (44 bp):
CCTATGAAATTTTGGTAACCACACTAAGAAATTTTGATAACCTT
Found at i:37817 original size:44 final size:43
Alignment explanation
Indices: 37734--37882 Score: 156
Period size: 44 Copynumber: 3.3 Consensus size: 43
37724 ACCAACCTAA
*
37734 GAAATTTTAATAACCTGATCCTATGAAATTTTGGTAACCACACAAT
1 GAAATTTTGATAACC---TCCTATGAAATTTTGGTAACCACACAAT
* *
37780 GAAATTTTGATAACTTCCATATGAAATTTTGGTAACCACACTAT
1 GAAATTTTGATAACCTCC-TATGAAATTTTGGTAACCACACAAT
* * ** **
37824 GGAATTTTGATAACCTCCTCATGAAATTATAATAACCATC-TTAT
1 GAAATTTTGATAACCTCCT-ATGAAATTTTGGTAACCA-CACAAT
37868 GAAATTTTGATAACC
1 GAAATTTTGATAACC
37883 ACATAGAGAC
Statistics
Matches: 90, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
43 4 0.04
44 72 0.80
45 1 0.01
46 13 0.14
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.35
Consensus pattern (43 bp):
GAAATTTTGATAACCTCCTATGAAATTTTGGTAACCACACAAT
Found at i:37883 original size:22 final size:22
Alignment explanation
Indices: 37241--37883 Score: 130
Period size: 22 Copynumber: 28.9 Consensus size: 22
37231 GAAATACCAC
37241 TATGAAATTTTTG-TAATCACAT-T
1 TATGAAA-TTTTGATAA-C-CATCT
* *
37264 T-TGAAAATTTGACAACC-TCTT
1 TATGAAATTTTGATAACCATC-T
37285 TATGAAATTTTGATAACC-TCTT
1 TATGAAATTTTGATAACCATC-T
* * * *
37307 TATCAAATTTTGTTGATCCCT-T
1 TATGAAATTTTGAT-AACCATCT
*
37329 TATGAAATTCTT-ATAATCA-CAT
1 TATGAAATT-TTGATAACCATC-T
*
37351 TATGTAATTTTGATAACC-TCGCT
1 TATGAAATTTTGATAACCAT--CT
*
37374 T-TGAAATTTTGATAACAATGC-
1 TATGAAATTTTGATAACCAT-CT
*** *
37395 TATGAAATTTTGATAATGTTCC
1 TATGAAATTTTGATAACCATCT
* *
37417 TAT-AAATTTTGATAATCTGATTT
1 TATGAAATTTTGATAA-C-CATCT
* *
37440 CTATGAAATTTCGATAATCAT-T
1 -TATGAAATTTTGATAACCATCT
* * *
37462 CTATGAGA-TTTAATAACCTTC-
1 -TATGAAATTTTGATAACCATCT
*
37483 TATCAAATTTTTG-T-A-C-TCCT
1 TATGAAA-TTTTGATAACCAT-CT
* * *
37503 TATGAAATTGAGACTTTTATAACCTTCA
1 TATGAAA-T-----TTTGATAACCATCT
37531 TATGAAATTTTGATAACTACA-C-
1 TATGAAATTTTGATAAC--CATCT
* *
37553 TATAAAATTTTGATAACC-TCCC
1 TATGAAATTTTGATAACCAT-CT
* * *
37575 CATGAAATATT-AGTAACCTTCT
1 TATGAAATTTTGA-TAACCATCT
* * *
37597 AATGAAATTTTGTTAACCA-CAC
1 TATGAAATTTTGATAACCATC-T
37619 TATGAAATTCTT-ATAACC-TCGT
1 TATGAAATT-TTGATAACCATC-T
*
37641 TATGACATTTTGATAACC-TCT
1 TATGAAATTTTGATAACCATCT
* * ***
37662 T-TGATAACATTT-CTAATTTTC-
1 TATGA-AA-TTTTGATAACCATCT
* * * *
37683 TATAAAATTGTGATAATTAACCACCC
1 TATGAAATT-T--TGA-TAACCATCT
** * *
37709 TATGAAATTTCAATAACCAACC
1 TATGAAATTTTGATAACCATCT
* * *
37731 TAAGAAATTTTAATAACCTGATCC
1 TATGAAATTTTGATAACC--ATCT
* *
37755 TATGAAATTTTGGTAACCA-CAC
1 TATGAAATTTTGATAACCATC-T
* * *
37777 AATGAAATTTTGATAA-CTTCCA
1 TATGAAATTTTGATAACCAT-CT
* *
37799 TATGAAATTTTGGTAACCA-CAC
1 TATGAAATTTTGATAACCATC-T
*
37821 TATGGAATTTTGATAACC-TCCT
1 TATGAAATTTTGATAACCAT-CT
* * *
37843 CATGAAATTATAATAACCATCT
1 TATGAAATTTTGATAACCATCT
37865 TATGAAATTTTGATAACCA
1 TATGAAATTTTGATAACCA
37884 CATAGAGACA
Statistics
Matches: 461, Mismatches: 93, Indels: 133
0.67 0.14 0.19
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 20 0.04
21 52 0.11
22 297 0.64
23 24 0.05
24 24 0.05
25 19 0.04
26 9 0.02
27 2 0.00
28 9 0.02
29 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATCT
Found at i:37998 original size:19 final size:19
Alignment explanation
Indices: 37946--38001 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
37936 AAAATAATTT
37946 AATAA-GGAATAATTAAAAA
1 AATAATGGAATAATT-AAAA
** *
37965 AATAAT-TTATGATTAAAA
1 AATAATGGAATAATTAAAA
37983 AATAATGGAATAATTAAAA
1 AATAATGGAATAATTAAAA
38002 TATTATTTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
18 10 0.34
19 19 0.66
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (19 bp):
AATAATGGAATAATTAAAA
Found at i:38264 original size:22 final size:22
Alignment explanation
Indices: 38239--38291 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
38229 ATTACACTAT
*
38239 TTTTGATGA-CGTCCTTATGAAA
1 TTTTGATAACCGTCC-TATGAAA
*
38261 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAACCGTCCTATGAAA
*
38283 TTATGATAA
1 TTTTGATAA
38292 TTTCAATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 23 0.85
23 4 0.15
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (22 bp):
TTTTGATAACCGTCCTATGAAA
Found at i:38293 original size:62 final size:62
Alignment explanation
Indices: 38218--38346 Score: 213
Period size: 62 Copynumber: 2.1 Consensus size: 62
38208 ATTAAATTAA
* *
38218 AAATTATGATAATTACACTATTTTTGATGACGTCCTTATGAAATTTTGATAACCTTCCTATG
1 AAATTATGATAATTACAATATTTTTGATGACGTCCTTACGAAATTTTGATAACCTTCCTATG
* * *
38280 AAATTATGATAATTTCAATATTTTTTATGACGTCCTTACGAAATTTTGATAAGCTTCCTATG
1 AAATTATGATAATTACAATATTTTTGATGACGTCCTTACGAAATTTTGATAACCTTCCTATG
38342 AAATT
1 AAATT
38347 TCAATAGCGA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (62 bp):
AAATTATGATAATTACAATATTTTTGATGACGTCCTTACGAAATTTTGATAACCTTCCTATG
Found at i:38572 original size:22 final size:23
Alignment explanation
Indices: 38538--38594 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
38528 CCTCCATATG
*
38538 AATTGTCAGTAATCACACTC-TG-A
1 AATTGTGA-TAATCACAC-CATGAA
*
38561 AATTTTGATAATCACACCATGAA
1 AATTGTGATAATCACACCATGAA
38584 AATTGTGATAA
1 AATTGTGATAA
38595 CCTCGGTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 11 0.38
23 17 0.59
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (23 bp):
AATTGTGATAATCACACCATGAA
Found at i:38633 original size:23 final size:23
Alignment explanation
Indices: 38605--38662 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
38595 CCTCGGTATG
38605 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
38628 AAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
38651 AAATTTTGATAA
1 AAATTTTGATAA
38663 CCTCCTTATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.43
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:38676 original size:23 final size:21
Alignment explanation
Indices: 38401--38851 Score: 179
Period size: 22 Copynumber: 20.7 Consensus size: 21
38391 TTTTTAACCT
*
38401 TATGAAATTTTGTTAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
38422 TTAAGGAATTTTGA-AGACCTCAC
1 -TATGAAATTTTGATA-ACCTC-C
*
38445 TATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* * *
38468 CAT-AGGATGTTGATAACCTCC
1 TATGA-AATTTTGATAACCTCC
* * * *
38489 ATATGATATATTGATAACCACAT
1 -TATGAAATTTTGATAACCTC-C
* *
38512 TATGAAAATTT-AAAACCCTCC
1 TATGAAATTTTGATAA-CCTCC
* * * *
38533 ATATG-AATTGTCAGTAATCACAC
1 -TATGAAATTTTGA-TAACCTC-C
* *
38556 TCTGAAATTTTGATAATCACACC
1 TATGAAATTTTGATAA-C-CTCC
* *
38579 -ATGAAAATTGTGATAACCTCGG
1 TATG-AAATTTTGATAACCTC-C
*
38601 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
* *
38624 TATAAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
*
38647 TATAAAATTTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
38668 TTATGAAAATCTTAATAA----C
1 -TATG-AAATTTTGATAACCTCC
* *
38687 TA-CAAATTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
* * **
38708 TATGGAATTTTGTTAATTTCCC
1 TATGAAATTTTGATAACCT-CC
* * *
38730 TATGAAATTTTGATCTACATAC
1 TATGAAATTTTGAT-AACCTCC
*
38752 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
* *
38774 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
*
38796 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACC-TCC
*
38818 TATGAAATTTTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
*
38839 -CTGAAATTTTGAT
1 TATGAAATTTTGAT
38852 TACTCCATAA
Statistics
Matches: 322, Mismatches: 71, Indels: 74
0.69 0.15 0.16
Matches are distributed among these distances:
16 10 0.03
18 2 0.01
19 1 0.00
20 14 0.04
21 22 0.07
22 169 0.52
23 97 0.30
24 7 0.02
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:39032 original size:21 final size:22
Alignment explanation
Indices: 38957--39031 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
38947 TATCACATTT
* *
38957 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
* *
38979 TGAAATTTTGATAGCCTATCTA
1 TGAAATTTTGATAACCTCTCTA
* *
39001 TAAAATTTTG-TAACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
39022 TGAAATTTTG
1 TGAAATTTTG
39032 TCTCCTCTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
21 17 0.39
22 27 0.61
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:39363 original size:31 final size:31
Alignment explanation
Indices: 39332--39389 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
39322 TAATGGTAAT
*
39332 TTAGAAATATGTTTTTAAAA-AAGGGTATAA
1 TTAGAAATATGTTTTAAAAATAAGGGTATAA
*
39362 TTGGAAATATGTTTTAAAAATAAGGGTA
1 TTAGAAATATGTTTTAAAAATAAGGGTA
39390 CAATCGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.36
Consensus pattern (31 bp):
TTAGAAATATGTTTTAAAAATAAGGGTATAA
Found at i:39453 original size:16 final size:17
Alignment explanation
Indices: 39429--39467 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
39419 CGTACTTTAT
*
39429 TATATAATATAGATAG-
1 TATAGAATATAGATAGA
39445 TATAGAATATAGATAGA
1 TATAGAATATAGATAGA
39462 TATAGA
1 TATAGA
39468 TAGATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (17 bp):
TATAGAATATAGATAGA
Found at i:39466 original size:10 final size:10
Alignment explanation
Indices: 39435--39473 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
39425 TTATTATATA
39435 ATATAGATAG
1 ATATAGATAG
39445 -TATAG--A-
1 ATATAGATAG
39451 ATATAGATAG
1 ATATAGATAG
39461 ATATAGATAG
1 ATATAGATAG
39471 ATA
1 ATA
39474 ATTATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 6 0.24
9 6 0.24
10 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (10 bp):
ATATAGATAG
Found at i:40086 original size:37 final size:37
Alignment explanation
Indices: 40045--40119 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
40035 CTTTCTATTT
* * *
40045 CTTTTTCTTCCGTGCAGTTTCTTTTCTTCCTACAAAA
1 CTTTTCCTTCCATGCAATTTCTTTTCTTCCTACAAAA
*
40082 CTTTTCCTTCCATGCAATTTCTTTTCTTCCTACCAAA
1 CTTTTCCTTCCATGCAATTTCTTTTCTTCCTACAAAA
40119 C
1 C
40120 GTAGTGTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.17, C:0.31, G:0.05, T:0.47
Consensus pattern (37 bp):
CTTTTCCTTCCATGCAATTTCTTTTCTTCCTACAAAA
Done.