Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019507.1 Corchorus olitorius cultivar O-4 contig19540, 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: 93576
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1653 original size:2 final size:2
Alignment explanation
Indices: 1646--1692 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
1636 AAATAAATAA
* *
1646 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT GT 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 AT AT
1688 AT AT A
1 AT AT A
1693 GGCTTAAATC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9382 original size:33 final size:33
Alignment explanation
Indices: 9334--9405 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
9324 ATTGGGGGAA
9334 GTGG-GAGTCCCGCTGGTGTAGGTCCGAGAATT
1 GTGGAGAGTCCCGCTGGTGTAGGTCCGAGAATT
* * *
9366 GTGGAGAGTCCTGCTGGTTTAGGTCCGATAATT
1 GTGGAGAGTCCCGCTGGTGTAGGTCCGAGAATT
*
9399 GGGGAGA
1 GTGGAGA
9406 ATTCAGTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.18, C:0.15, G:0.40, T:0.26
Consensus pattern (33 bp):
GTGGAGAGTCCCGCTGGTGTAGGTCCGAGAATT
Found at i:14402 original size:3 final size:3
Alignment explanation
Indices: 14396--14431 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
14386 AATAAGTATA
14396 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
14432 GTTTGTGGAT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:15490 original size:24 final size:25
Alignment explanation
Indices: 15462--15512 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
15452 AAAAATGATC
*
15462 AATAAAATAAATAAACAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
15486 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
15511 AA
1 AA
15513 ATACTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:20509 original size:21 final size:21
Alignment explanation
Indices: 20485--20530 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
20475 CTAAGATGCA
*
20485 TAAAAA-AATAAATCTTAAATC
1 TAAAAACAAGAAAT-TTAAATC
20506 TAAAAACAAGAAATTTAAATC
1 TAAAAACAAGAAATTTAAATC
20527 TAAA
1 TAAA
20531 CCTAAATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.63, C:0.09, G:0.02, T:0.26
Consensus pattern (21 bp):
TAAAAACAAGAAATTTAAATC
Found at i:29503 original size:9 final size:9
Alignment explanation
Indices: 29489--29530 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
29479 TTATTGATTC
29489 TTTTTTCAT
1 TTTTTTCAT
29498 TTTTTTCAT
1 TTTTTTCAT
* *
29507 TTTCTTCTTT
1 TTTTTTC-AT
29517 TTTTTTCAT
1 TTTTTTCAT
29526 TTTTT
1 TTTTT
29531 CCTCAACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:35701 original size:30 final size:30
Alignment explanation
Indices: 35665--36145 Score: 691
Period size: 30 Copynumber: 16.0 Consensus size: 30
35655 ACTGATGAAA
*
35665 CAATGATCCTAAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
35695 CAATGATCCTCAAACAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* * *
35725 CAATGATCCTCAAACACGATTAAAAGAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
35755 CAATGATCCCCCAACCAGGA-TAATAATAAAG
1 CAATGAT-CCTCAACCAGGATTAA-AATAAAG
*
35786 CAACGATCCTCAACCAGGATTAAAAATAAAG
1 CAATGATCCTCAACCAGGATT-AAAATAAAG
35817 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
35847 CAATGATCCTCAACCAGGATTGAAAAATAAA-
1 CAATGATCCTCAACCAGGATT--AAAATAAAG
* *
35878 CAACGATCCTCAACCAGGATTAAAATAAAA
1 CAATGATCCTCAACCAGGATTAAAATAAAG
35908 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
35938 CAACGATCCTCAACCAGGATTAAAGTAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
35968 CAATGATCCTCAAACAGGACTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
35998 CAATGATCCTCAACCAGGATTAAAATAAAA
1 CAATGATCCTCAACCAGGATTAAAATAAAG
*
36028 CAATGATCATCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* ** *
36058 CAACGATCCTCAAATAGGATTAAAGTAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
36088 CAATGATCCTCAACCAGGATTAAAATAAAG
1 CAATGATCCTCAACCAGGATTAAAATAAAG
* *
36118 CACAT-AT-CTAAACCAGGATTGAAATAAA
1 CA-ATGATCCTCAACCAGGATTAAAATAAA
36146 CTCATAAAGC
Statistics
Matches: 407, Mismatches: 36, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
29 27 0.07
30 299 0.73
31 71 0.17
32 10 0.02
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.19
Consensus pattern (30 bp):
CAATGATCCTCAACCAGGATTAAAATAAAG
Found at i:36316 original size:39 final size:39
Alignment explanation
Indices: 36112--36305 Score: 225
Period size: 39 Copynumber: 5.0 Consensus size: 39
36102 CAGGATTAAA
*
36112 ATAAAGCACAT-AT-CTAAACCAGGATTGAAAT-AAACTC
1 ATAAAGCA-ATAATCCTAAACCAGGATTGAAATAAAACTG
* *
36149 ATAAAGCAA-AGATCCTAAACCAGGATCGAAATAAAGCTG
1 ATAAAGCAATA-ATCCTAAACCAGGATTGAAATAAAACTG
** * * *
36188 GCAAAGCAATAATCCTAAATCAGGATTGGAATAAGACTG
1 ATAAAGCAATAATCCTAAACCAGGATTGAAATAAAACTG
* *
36227 ATAAAGCGATAATCCTAAACCAGGATTGGAATAAAACTG
1 ATAAAGCAATAATCCTAAACCAGGATTGAAATAAAACTG
* * *
36266 ATAAGGCAATAATCCTAGATCAGGATTGAAATAAAACTG
1 ATAAAGCAATAATCCTAAACCAGGATTGAAATAAAACTG
36305 A
1 A
36306 CAACACAATA
Statistics
Matches: 132, Mismatches: 20, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
36 1 0.01
37 10 0.08
38 17 0.13
39 103 0.78
40 1 0.01
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.20
Consensus pattern (39 bp):
ATAAAGCAATAATCCTAAACCAGGATTGAAATAAAACTG
Found at i:36544 original size:36 final size:36
Alignment explanation
Indices: 36484--36556 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 36
36474 TACCCGGGAG
*
36484 TTTTAATCAATTGCCCGGAGGACTTAGCAAAATTAA
1 TTTTAATCAATTGCCCGGAAGACTTAGCAAAATTAA
* * * *
36520 TTTTGATCCATTGCCCGGAAGACTTATCAGAATTAA
1 TTTTAATCAATTGCCCGGAAGACTTAGCAAAATTAA
36556 T
1 T
36557 ACCCGGAGGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (36 bp):
TTTTAATCAATTGCCCGGAAGACTTAGCAAAATTAA
Found at i:37373 original size:169 final size:169
Alignment explanation
Indices: 36763--37369 Score: 950
Period size: 169 Copynumber: 3.6 Consensus size: 169
36753 GAGATTTTAA
* * * * ** *
36763 CAATGCAAACTCTGAATTGAAACCTTAAACAAGGATTTTAAACTTAATCATGAATCGTTGATGAA
1 CAATGCAAACTTTGAATAGAGACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAA
* *
36828 AAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCGATTGCCCGGAGGACTTATCAGAATTA
66 AAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCTGGAGGACTTATCAGAATTA
* *
36893 CTACCCGGAGGTTTTTGAATTTGTGCCCGGAGGACTTAC
131 ATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
* * *
36932 CAATGTAAACTCTGAATAGAGACCTTAAACAAGGATTTTAAACTTAAACATGAA-TTTTGATGAA
1 CAATGCAAACTTTGAATAGAGACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAA
*
36996 AAACTTGATGAAATGAAATGGTACCTGGAGGTTTTACCAATTGCCTGGAGGACTTATCAGAATTA
66 AAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCTGGAGGACTTATCAGAATTA
37061 ATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
131 ATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
* *
37100 CAATGCAAACTTTGAATTGAGACCTTGAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAA
1 CAATGCAAACTTTGAATAGAGACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAA
* *
37165 AAACTTGATAAAATGAAATGGTACCCGGAGGTTTTATCAATTGCCTGGAGGACTTATCAGAATTA
66 AAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCTGGAGGACTTATCAGAATTA
* *
37230 ATACCCTGAGGTTTCTGACTTTGTGCCCGGAGGACTTAC
131 ATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
* * * *
37269 CAATGCAAACTTTGAAAAAAGACCTTAAACAAGGATTTT-AACTTAAAATATGGATTTTTAATGA
1 CAATGCAAACTTTGAATAGAGACCTTAAACAAGGATTTTAAACTT-AAACATGAATTTTTAATGA
37333 AAAACTTGATGAAATGAAA-GGATACCCGGAGGTTTTA
65 AAAACTTGATGAAATGAAATGG-TACCCGGAGGTTTTA
37370 TCAAATGGAA
Statistics
Matches: 407, Mismatches: 28, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
168 164 0.40
169 243 0.60
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.29
Consensus pattern (169 bp):
CAATGCAAACTTTGAATAGAGACCTTAAACAAGGATTTTAAACTTAAACATGAATTTTTAATGAA
AAACTTGATGAAATGAAATGGTACCCGGAGGTTTTACCAATTGCCTGGAGGACTTATCAGAATTA
ATACCCGGAGGTTTCTGAATTTGTGCCCGGAGGACTTAC
Found at i:37503 original size:69 final size:69
Alignment explanation
Indices: 37422--37592 Score: 279
Period size: 69 Copynumber: 2.5 Consensus size: 69
37412 GCTTCACTTA
*
37422 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGTCTTGGATGGAACCAAAGCTTAAACTGA
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAAGCTTAAACTGA
37487 CTCG
66 CTCG
* * * *
37491 TATGGAAACGAGTTTGGCTTGTGGAAAAGCATATGTGGCTTGGATGGAAGCAAGGCTTAAACTGA
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAAGCTTAAACTGA
37556 CTCG
66 CTCG
* *
37560 TATGGAAACGATTTTGGCTTATGGAAAAGCCTA
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTA
37593 AAGCATTCGG
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 94 1.00
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.27
Consensus pattern (69 bp):
TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAAGCTTAAACTGA
CTCG
Found at i:38896 original size:15 final size:16
Alignment explanation
Indices: 38878--38914 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
38868 ATCCTTTCCT
38878 TTTTTTC-TCTTTTTC-
1 TTTTTTCAT-TTTTTCA
38893 TTTTTTCATTTTTTCA
1 TTTTTTCATTTTTTCA
38909 TTTTTT
1 TTTTTT
38915 TTGTGCACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTCATTTTTTCA
Found at i:39231 original size:18 final size:17
Alignment explanation
Indices: 39210--39278 Score: 90
Period size: 17 Copynumber: 4.1 Consensus size: 17
39200 CCCTTTTTGA
39210 TTTTGATTTGATTTT-TTT
1 TTTTGATTT--TTTTGTTT
39228 TTTTGATTTTTTTGTTT
1 TTTTGATTTTTTTGTTT
*
39245 TTTTTATTTTTTTG--T
1 TTTTGATTTTTTTGTTT
39260 TTTTGATTTTTTTGTTT
1 TTTTGATTTTTTTGTTT
39277 TT
1 TT
39279 GATTGAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
15 14 0.30
16 4 0.09
17 19 0.41
18 9 0.20
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (17 bp):
TTTTGATTTTTTTGTTT
Found at i:39239 original size:9 final size:8
Alignment explanation
Indices: 39221--39278 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
39211 TTTGATTTGA
39221 TTTT-TTT
1 TTTTGTTT
39228 TTTTGATTT
1 TTTTG-TTT
39237 TTTTGTTT
1 TTTTGTTT
39245 TTTT-TATT
1 TTTTGT-TT
*
39253 TTTT-TGT
1 TTTTGTTT
39260 TTTTGATTT
1 TTTTG-TTT
39269 TTTTGTTT
1 TTTTGTTT
39277 TT
1 TT
39279 GATTGAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
7 10 0.23
8 19 0.43
9 15 0.34
ACGTcount: A:0.05, C:0.00, G:0.09, T:0.86
Consensus pattern (8 bp):
TTTTGTTT
Found at i:39239 original size:15 final size:15
Alignment explanation
Indices: 39216--39282 Score: 93
Period size: 15 Copynumber: 4.5 Consensus size: 15
39206 TTGATTTTGA
39216 TTTGA-TTTTTT-TT
1 TTTGATTTTTTTGTT
39229 TTTGATTTTTTTGTTTT
1 TTTGATTTTTTTG--TT
*
39246 TTTTATTTTTTTGTT
1 TTTGATTTTTTTGTT
39261 TTTGATTTTTTTGTT
1 TTTGATTTTTTTGTT
39276 TTTGATT
1 TTTGATT
39283 GAATTTCTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
13 5 0.10
14 6 0.12
15 23 0.48
17 14 0.29
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.82
Consensus pattern (15 bp):
TTTGATTTTTTTGTT
Found at i:43597 original size:17 final size:18
Alignment explanation
Indices: 43552--43593 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 18
43542 GGTAGCTTCC
43552 TTTCCA-TTT-TTTCATT
1 TTTCCATTTTCTTTCATT
43568 TTTCCATTTTCTTTC-TT
1 TTTCCATTTTCTTTCATT
43585 TTT-CATTTT
1 TTTCCATTTT
43594 TCTTCAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 12 0.50
17 8 0.33
18 4 0.17
ACGTcount: A:0.10, C:0.19, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCCATTTTCTTTCATT
Found at i:50067 original size:27 final size:27
Alignment explanation
Indices: 50033--50084 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
50023 AAATGAACCT
* * *
50033 AAAATGACCAGAATGCCCCTGAATGCA
1 AAAATGACCAAAACGCCCCTAAATGCA
50060 AAAATGACCAAAACGCCCCTAAATG
1 AAAATGACCAAAACGCCCCTAAATG
50085 ACCGAAGTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.13
Consensus pattern (27 bp):
AAAATGACCAAAACGCCCCTAAATGCA
Found at i:52059 original size:19 final size:18
Alignment explanation
Indices: 52026--52061 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
52016 TTGAAATTAT
52026 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
52044 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
52062 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:65352 original size:22 final size:22
Alignment explanation
Indices: 65323--65425 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 22
65313 TGAATATTTT
65323 TATGAAATTTTGATAATCACCCA
1 TATGAAATTTTGATAATCA-CCA
* * *
65346 -ATTAAATTTTGATAACCATCA
1 TATGAAATTTTGATAATCACCA
*
65367 TATGAAATTTTGATAATTACC-
1 TATGAAATTTTGATAATCACCA
* * * *
65388 TATAAAATTGTGATAAACTCCA
1 TATGAAATTTTGATAATCACCA
*
65410 TAAT-AAACTTTGATAA
1 T-ATGAAATTTTGATAA
65426 CCTAATTATG
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
21 18 0.29
22 43 0.68
23 2 0.03
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACCA
Found at i:66872 original size:7 final size:8
Alignment explanation
Indices: 66855--66884 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
66845 TTTGGGTATT
66855 TTTTTTGG
1 TTTTTTGG
*
66863 TTTTTTGT
1 TTTTTTGG
66871 TTTTTTGG
1 TTTTTTGG
66879 TTTTTT
1 TTTTTT
66885 TTTACAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (8 bp):
TTTTTTGG
Found at i:66875 original size:16 final size:16
Alignment explanation
Indices: 66854--66884 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
66844 TTTTGGGTAT
66854 TTTTTTTGGTTTTTTG
1 TTTTTTTGGTTTTTTG
66870 TTTTTTTGGTTTTTT
1 TTTTTTTGGTTTTTT
66885 TTTACAATCT
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (16 bp):
TTTTTTTGGTTTTTTG
Found at i:68385 original size:3 final size:3
Alignment explanation
Indices: 68377--68405 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
68367 TAGTATAGAG
68377 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
68406 ATAAATAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:72951 original size:13 final size:14
Alignment explanation
Indices: 72933--72983 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
72923 AGTTAGTAAC
72933 AAAAATTCAAAA-T
1 AAAAATTCAAAATT
*
72946 AAAAATTGAAAATT
1 AAAAATTCAAAATT
*
72960 AAAAGTT-AAGAATT
1 AAAAATTCAA-AATT
*
72974 AGAAATTCAA
1 AAAAATTCAA
72984 TTGGGTTGCC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 13 0.42
14 16 0.52
15 2 0.06
ACGTcount: A:0.63, C:0.04, G:0.08, T:0.25
Consensus pattern (14 bp):
AAAAATTCAAAATT
Found at i:80469 original size:107 final size:104
Alignment explanation
Indices: 80231--80490 Score: 405
Period size: 107 Copynumber: 2.5 Consensus size: 104
80221 AATTTTTCTA
** *
80231 ACCCTTAAAATAAAATTTTAATTTTAATTTGGAGCTAAACTTAGTG-AATTAGTTATATATTTTA
1 ACCCTTAAAATAAAA-TAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
80295 TTTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
65 TTTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* *
80335 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAAT-AAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
80400 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
80442 ACCCTTAAAATAAATATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
1 ACCCTTAAAATAAA-ATAAAATTTTAATTTGGGGCTAAACTTAGTGAAA
80491 ATAAGGCTAA
Statistics
Matches: 144, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
104 38 0.26
105 41 0.28
106 3 0.02
107 62 0.43
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (104 bp):
ACCCTTAAAATAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:80535 original size:2 final size:2
Alignment explanation
Indices: 80528--80554 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
80518 AAAGTAGAAA
80528 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
80555 AGACACGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:81961 original size:21 final size:22
Alignment explanation
Indices: 81901--81962 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
81891 TATTTAATTG
*
81901 AATTAAATGATTATACAATTTTA
1 AATTAAATGATTACA-AATTTTA
* **
81924 AATT-ATTGACAATCAAATTTT-
1 AATTAAATGATTA-CAAATTTTA
81945 AATTAAATGATTACAAAT
1 AATTAAATGATTACAAAT
81963 ATACTCCGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
21 9 0.30
22 16 0.53
23 5 0.17
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (22 bp):
AATTAAATGATTACAAATTTTA
Found at i:83079 original size:18 final size:18
Alignment explanation
Indices: 83058--83115 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
83048 AAAATGAAAT
*
83058 TATAATAATAAATAATTA
1 TATAATAATAAAAAATTA
*
83076 TATAA-AAAAAAAGAATT-
1 TATAATAATAAAA-AATTA
* *
83093 TATAGTAATAAAAAAATA
1 TATAATAATAAAAAATTA
83111 TATAA
1 TATAA
83116 CATGACACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (18 bp):
TATAATAATAAAAAATTA
Found at i:83102 original size:35 final size:35
Alignment explanation
Indices: 83048--83115 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
83038 AGAAACGAAG
* * *
83048 AAAATGAAATTATAATAATAAATAATTATATAAAA
1 AAAAAGAAATTATAATAATAAAAAAATATATAAAA
* *
83083 AAAAAGAATTTATAGTAATAAAAAAATATATAA
1 AAAAAGAAATTATAATAATAAAAAAATATATAA
83116 CATGACACAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.29
Consensus pattern (35 bp):
AAAAAGAAATTATAATAATAAAAAAATATATAAAA
Found at i:83872 original size:2 final size:2
Alignment explanation
Indices: 83861--83897 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
83851 GCATTGCTAA
83861 AT AT -T 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 AT AT AT
83898 TGTAAAAATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:84537 original size:105 final size:105
Alignment explanation
Indices: 84357--84546 Score: 319
Period size: 106 Copynumber: 1.8 Consensus size: 105
84347 TAATCTCTAG
*
84357 CTAAGTCATCTCATATCTACTCCTGTTTTTTTTCTTGTTTTTTACTTACTCTATCCAATTATGGA
1 CTAAGTCATCTCATATCTACTCCTGTTTTTCTTCTTGTTTTTTACTTACTCTATCCAATTATGGA
84422 TGAATAAAAAATACTCAATTACCTAGTAGAGATCTAATCT
66 TGAATAAAAAATACTCAATTACCTAGTAGAGATCTAATCT
* * *
84462 CTAAGTCATCTCATATCTACTCCTGTTTTTCTTCTTTTTTTTTTA-TTCAGTCTATCCAATTATT
1 CTAAGTCATCTCATATCTACTCCTGTTTTTCTTC-TTGTTTTTTACTT-ACTCTATCCAATTATG
84526 GATGAATAAAAAATACTCAAT
64 GATGAATAAAAAATACTCAAT
84547 GCTACTTTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
105 35 0.44
106 44 0.56
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (105 bp):
CTAAGTCATCTCATATCTACTCCTGTTTTTCTTCTTGTTTTTTACTTACTCTATCCAATTATGGA
TGAATAAAAAATACTCAATTACCTAGTAGAGATCTAATCT
Found at i:86545 original size:26 final size:26
Alignment explanation
Indices: 86514--86571 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
86504 ACAGCCGCTA
86514 GCTCACTCTTCCTTACCCTCACCGCC
1 GCTCACTCTTCCTTACCCTCACCGCC
86540 GCTCACTCTTCCTTACCCTCACCGCC
1 GCTCACTCTTCCTTACCCTCACCGCC
86566 GCTCAC
1 GCTCAC
86572 ACTCAAACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.12, C:0.53, G:0.09, T:0.26
Consensus pattern (26 bp):
GCTCACTCTTCCTTACCCTCACCGCC
Found at i:87775 original size:20 final size:20
Alignment explanation
Indices: 87750--87803 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
87740 TTTCTTTTCT
87750 ATTATGAATGTTCAGCTTGG
1 ATTATGAATGTTCAGCTTGG
87770 ATTATGAATGTTCAGCTTGG
1 ATTATGAATGTTCAGCTTGG
87790 ATTATGAATGTTCA
1 ATTATGAATGTTCA
87804 TTGTCCAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTATGAATGTTCAGCTTGG
Found at i:90525 original size:21 final size:21
Alignment explanation
Indices: 90488--90536 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
90478 TATTCTTATA
90488 TGCTACGAGCTTATTTACAGT
1 TGCTACGAGCTTATTTACAGT
*
90509 TGCTACGAGCTTATTTACATT
1 TGCTACGAGCTTATTTACAGT
90530 TGCTACG
1 TGCTACG
90537 GACATTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.39
Consensus pattern (21 bp):
TGCTACGAGCTTATTTACAGT
Done.