Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021393.1 Corchorus olitorius cultivar O-4 contig21426, 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: 17529
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:159 original size:50 final size:50
Alignment explanation
Indices: 84--514 Score: 720
Period size: 50 Copynumber: 8.6 Consensus size: 50
74 TAATGCACCT
* *
84 TATGGAAACGGATGTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
134 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
* * *
184 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCATGTTGATAATTAACTCG
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
* * *
234 TATGGAAACGAGTTTGGCTTGTGGAAAAACCTATGTTGACAATTGACTCG
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
*
284 TATGGAAACGAATTTGACTTGTGGAAAAGCCTATGTTGATAATTGACTCG
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
334 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
*
384 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
* *
434 TATGGAAATGAGCTTT-GCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
1 TATGGAAACGA-ATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
**
484 TATGGAAACGAGCTTGGCTTGTGGAAAAGCC
1 TATGGAAACGAATTTGGCTTGTGGAAAAGCC
515 AAAGCTTTCG
Statistics
Matches: 359, Mismatches: 20, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
49 2 0.01
50 354 0.99
51 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (50 bp):
TATGGAAACGAATTTGGCTTGTGGAAAAGCCTATGTTGATAATTGACTCG
Found at i:798 original size:88 final size:87
Alignment explanation
Indices: 598--888 Score: 404
Period size: 88 Copynumber: 3.3 Consensus size: 87
588 AATACCTTTG
* * *
598 GAAAATAACTCTGAATCTTATGTTGTAACTGAAAACTCCTTGATTGATGATGAAAAAGGACCAAT
1 GAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAAT
* * * *
663 GTGCGGTCAA-CTAGAAAAACAACTT
66 TTGCGGTCAATTTTG----ATAACTT
* *
688 GAAAAATAACTCTGAGTCTGATGCTGTAACCGAAAACTTCTTGATTGATGATGAAAAAGGACCAA
1 G-AAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAA
753 TTTGCGGTCAATTTTGATAACTT
65 TTTGCGGTCAATTTTGATAACTT
*
776 GAAACATAACTCTGAGTCTGATGTTGCAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAA
1 GAAA-ATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAA
841 TTTGCGGTCAATTTTGATAACTT
65 TTTGCGGTCAATTTTGATAACTT
* *
864 GAAGAATAACTCAGTGTCTGATGTT
1 GAA-AATAACTCTGAGTCTGATGTT
889 ATGATTAAAA
Statistics
Matches: 183, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
87 3 0.02
88 108 0.59
89 1 0.01
90 1 0.01
91 68 0.37
92 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (87 bp):
GAAAATAACTCTGAGTCTGATGTTGTAACTGAAAACTTCTTGATTGATGATGAAAAAGGACCAAT
TTGCGGTCAATTTTGATAACTT
Found at i:1440 original size:50 final size:50
Alignment explanation
Indices: 1294--1443 Score: 221
Period size: 50 Copynumber: 3.0 Consensus size: 50
1284 CTTCGATGCC
* * * *
1294 CTTTAAAAAGCGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1344 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1 CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
* * *
1394 CTTTGAAACGC-AATTTTTGATCTTGAACTCATAAGTGGAAAGCAATTTTA
1 CTTTGAAAAGCGAA-TTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
1444 TTGTAAAACT
Statistics
Matches: 92, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
49 2 0.02
50 90 0.98
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (50 bp):
CTTTGAAAAGCGAATTTTGATCTTGAACTCACAAATGGAAAGCAATTTTA
Found at i:2060 original size:6 final size:6
Alignment explanation
Indices: 2049--2084 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
2039 ATCAATTCTC
2049 TTTTGA TTTTGA TTTTGA TTTTTGA TTTTTGA TTTT
1 TTTTGA TTTTGA TTTTGA -TTTTGA -TTTTGA TTTT
2085 TATGATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 16 0.55
7 13 0.45
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (6 bp):
TTTTGA
Found at i:2103 original size:7 final size:7
Alignment explanation
Indices: 2049--2085 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
2039 ATCAATTCTC
2049 TTTTGA-
1 TTTTGAT
2055 TTTTGA-
1 TTTTGAT
2061 TTTTGAT
1 TTTTGAT
2068 TTTTGAT
1 TTTTGAT
2075 TTTTGAT
1 TTTTGAT
2082 TTTT
1 TTTT
2086 ATGATTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 12 0.40
7 18 0.60
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.73
Consensus pattern (7 bp):
TTTTGAT
Found at i:2505 original size:14 final size:15
Alignment explanation
Indices: 2486--2525 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2476 AAGTGCCTTT
*
2486 ATTTTCCTTTTTTC-
1 ATTTTCATTTTTTCA
2500 ATTTTCATTTTTTCA
1 ATTTTCATTTTTTCA
2515 ATTTTTCATTT
1 A-TTTTCATTT
2526 ATTTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 1 0.04
16 9 0.39
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTCATTTTTTCA
Found at i:7320 original size:14 final size:13
Alignment explanation
Indices: 7303--7368 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 13
7293 ACAAAGGACG
7303 TTTTCCAAAAATGA
1 TTTT-CAAAAATGA
*
7317 TTTTAAAGAAACTG-
1 TTTTCAA-AAA-TGA
7331 TTTTCAAGAAATGA
1 TTTTCAA-AAATGA
7345 TTTTCAAAAATGA
1 TTTTCAAAAATGA
7358 GTTTTCGAAAA
1 -TTTTC-AAAA
7369 GGTTTTGATT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 10 0.22
14 29 0.64
15 6 0.13
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:7602 original size:12 final size:13
Alignment explanation
Indices: 7578--7609 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
7568 CGATGTGAAT
7578 AAAAA-AAAGAAG
1 AAAAAGAAAGAAG
7590 AAAAAGAAA-AAG
1 AAAAAGAAAGAAG
7602 AAAAAGAA
1 AAAAAGAA
7610 GATTGTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 16 0.84
13 3 0.16
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAGAAG
Found at i:7987 original size:6 final size:6
Alignment explanation
Indices: 7976--8011 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
7966 GAATCAATCT
*
7976 AAAGAA AAAGAA AAAG-C AAAGAA AAAGAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA A
8012 GAAAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:8023 original size:23 final size:22
Alignment explanation
Indices: 7976--8029 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
7966 GAATCAATCT
*
7976 AAAGAAAAAGAAAAAGCAAAGAA
1 AAAGAAAAAGAAAAA-CAAACAA
7999 AAAGAAAAAGAAAGAA-AAATCAA
1 AAAGAAAAAGAAA-AACAAA-CAA
*
8022 AAGGAAAA
1 AAAGAAAA
8030 GGTTCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 22 0.81
24 2 0.07
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAGAAAAACAAACAA
Found at i:8024 original size:16 final size:17
Alignment explanation
Indices: 7976--8017 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
7966 GAATCAATCT
7976 AAAGAAAAAGAAAAAGC
1 AAAGAAAAAGAAAAAGC
7993 AAAGAAAAAGAAAAAG-
1 AAAGAAAAAGAAAAAGC
8009 AAAGAAAAA
1 AAAGAAAAA
8018 TCAAAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAGAAAAAGC
Found at i:8028 original size:17 final size:16
Alignment explanation
Indices: 7976--8028 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
7966 GAATCAATCT
*
7976 AAAGAAAAAGAAAAAGC
1 AAAGAAAAA-AAAAAGG
7993 AAAGAAAAAGAAAAA-G
1 AAAGAAAAA-AAAAAGG
*
8009 AAAGAAAAATCAAAAGG
1 AAAGAAAAA-AAAAAGG
8026 AAA
1 AAA
8029 AGGTTCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 13 0.41
17 19 0.59
ACGTcount: A:0.77, C:0.04, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAGAAAAAAAAAAGG
Found at i:9037 original size:37 final size:38
Alignment explanation
Indices: 8982--9810 Score: 695
Period size: 37 Copynumber: 22.4 Consensus size: 38
8972 ACAAAATTCA
* * **
8982 GTCTCATCAAAA-CCTTATTCAAGATTTCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9019 GTCTTATC-AAATCCTTATTTAAGGTCCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* *
9056 AT-TTCATCAAAAT-CTTGTTCAAGAT-ACTGTTTAGGT
1 GTCTT-ATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9092 GTCTTATC-AAATCCTTGTTTAAGGTCCATGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9129 GTCTTATC-AAATCCTTATTTAAGGTCCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * ** *
9166 AAT-TCATTGAAATCC-GGTTCAAGATCCCTGTTTAGGT
1 -GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* *
9203 GTCTCATCAAAAT-CTTGTTCAAGATTCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * * * * *
9240 TTCTTAT-TAAATCTTTATTTAAGGTCCCTATTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9277 GTCTCATCGAAAT-CTGGTTCAAGATCCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
9314 GT-TTCATCAAAAT-CTTGTTCAAGATCCCTGTTTAGGT
1 GTCTT-ATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* *
9351 GTCTCATCAAAAT-CTTGTTCAAGATTCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * * * * *
9388 TTCTTAT-TAAATCTTTATTTAAGGTCCCTATTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9425 GTCTCATCGAAAT-CTGGTTCAAGATCCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
9462 GT-TTCATCAAAAT-CTTGTTCAAGATCCCTGTTTAGGT
1 GTCTT-ATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9499 GTCTCATCAAAAT-CTTGTTCAAGATTCATGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * * ** * *
9536 TTCTTAT-TAAATCTTTATTTGAGGTCCCTATTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9573 GTCTCATCAAAAT-CTTGTTTAAGATCCCTGTTTAGCT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * * *
9610 TTCTTATC-AAATCCTTATTTAAGGTGCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * ** *
9647 TTCTTGTCAAAATTTTTGTTTAAGATCCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * *
9685 TTCTTATC-AAATCCTTATTTAAGGTCCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * *
9722 GTCTCATCAAAAT-CTTGTTCAAAATTCCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
* * * * * *
9759 TTCTTAT-TAAATCCTTATTTAAGGTACCTGTTTAGGT
1 GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
9796 GTCTCT-TCAAAATCC
1 GTCT-TATCAAAATCC
9811 CAGTTTAGGT
Statistics
Matches: 636, Mismatches: 130, Indels: 51
0.78 0.16 0.06
Matches are distributed among these distances:
35 4 0.01
36 53 0.08
37 512 0.81
38 67 0.11
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (38 bp):
GTCTTATCAAAATCCTTGTTCAAGATCCCTGTTTAGGT
Found at i:9077 original size:74 final size:74
Alignment explanation
Indices: 8982--9809 Score: 988
Period size: 74 Copynumber: 11.2 Consensus size: 74
8972 ACAAAATTCA
* * * *
8982 GTCTCATCAAAACCTTATTCAAGATTTCTGTTTAGGTGTCTTATCAAATCCTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
9047 TGTTTAGGT
66 TGTTTAGGT
* * * * * *
9056 ATTTCATCAAAATCTTGTTCAAGA-TACTGTTTAGGTGTCTTATCAAATCCTTGTTTAAGGTCCA
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
9120 TGTTTAGGT
66 TGTTTAGGT
* * * * * * * ** * *
9129 GTCTTATC-AAATCCTTATTTAAGGTCCCTGTTTAGGTAATTCAT-TGAAATCC-GGTTCAAGAT
1 GTCTCATCAAAAT-CTTGTTCAAGATTCCTGTTTAGGT--TTCTTATCAAATCCTTATTTAAGGT
9191 CCCTGTTTAGGT
63 CCCTGTTTAGGT
* *
9203 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATTAAATCTTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
9268 TATTTAGGT
66 TGTTTAGGT
* * * * * * *
9277 GTCTCATCGAAATCTGGTTCAAGATCCCTGTTTAGGTGTT-TCATCAAAAT-CTTGTTCAAGATC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGT-TTCTTATC-AAATCCTTATTTAAGGTC
9340 CCTGTTTAGGT
64 CCTGTTTAGGT
* *
9351 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATTAAATCTTTATTTAAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
9416 TATTTAGGT
66 TGTTTAGGT
* * * * * * *
9425 GTCTCATCGAAATCTGGTTCAAGATCCCTGTTTAGGTGTT-TCATCAAAAT-CTTGTTCAAGATC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGT-TTCTTATC-AAATCCTTATTTAAGGTC
9488 CCTGTTTAGGT
64 CCTGTTTAGGT
* * * *
9499 GTCTCATCAAAATCTTGTTCAAGATTCATGTTTAGGTTTCTTATTAAATCTTTATTTGAGGTCCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
*
9564 TATTTAGGT
66 TGTTTAGGT
* * * *
9573 GTCTCATCAAAATCTTGTTTAAGATCCCTGTTTAGCTTTCTTATCAAATCCTTATTTAAGGTGCC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
9638 TGTTTAGGT
66 TGTTTAGGT
* ** * * *
9647 TTCTTGTCAAAATTTTTGTTTAAGATCCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
1 GTCTCATCAAAA-TCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCC
9712 CTGTTTAGGT
65 CTGTTTAGGT
* * *
9722 GTCTCATCAAAATCTTGTTCAAAATTCCTGTTTAGGTTTCTTATTAAATCCTTATTTAAGGTACC
1 GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
9787 TGTTTAGGT
66 TGTTTAGGT
*
9796 GTCTCTTCAAAATC
1 GTCTCATCAAAATC
9810 CCAGTTTAGG
Statistics
Matches: 636, Mismatches: 102, Indels: 32
0.83 0.13 0.04
Matches are distributed among these distances:
72 8 0.01
73 77 0.12
74 457 0.72
75 91 0.14
76 3 0.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (74 bp):
GTCTCATCAAAATCTTGTTCAAGATTCCTGTTTAGGTTTCTTATCAAATCCTTATTTAAGGTCCC
TGTTTAGGT
Found at i:9874 original size:18 final size:17
Alignment explanation
Indices: 9833--9874 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
9823 CTTATCAAAA
9833 TTTTGTTCAAAATCCAT
1 TTTTGTTCAAAATCCAT
*
9850 TTCTTGTTCAAAATTCAT
1 TT-TTGTTCAAAATCCAT
9868 GTTTTGT
1 -TTTTGT
9875 GTTAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 18 0.82
19 2 0.09
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.52
Consensus pattern (17 bp):
TTTTGTTCAAAATCCAT
Found at i:10067 original size:54 final size:53
Alignment explanation
Indices: 9906--10346 Score: 627
Period size: 54 Copynumber: 8.2 Consensus size: 53
9896 TCTCTCTAAA
*
9906 AAGTTGATCTTAAGTTGATCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
9960 AAGTTGATCTTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
10013 AAGTTGATCTTAAGATGACCTAGTGTGGTCTTTCATAGAAGTTTTGAGAAATCT
1 AAGTTGATCTTAAGATGACC-AGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
*
10067 AACTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
10121 AAGTTGATCTTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* *
10175 AAGTTGATCTTAAGATGGCCTAGTGTGGTCTTTCATAGAAGCTTTT-AGAGGTCT
1 AAGTTGATCTTAAGATGACC-AGTGTGGTCTTTCATAGAAG-TTTTCAGAGATCT
* * * * * *
10229 AAGTTGATCTTCAGATGACCCTGTGTGGTCTTCCATAGAAATTTTCAAATATCT
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
* * * *
10283 AAGTTGATCTTAAGTTGATCCAGTGTGGTCATTCCA-AGAAGTTTAC-GATGATCA
1 AAGTTGATCTTAAGATGA-CCAGTGTGGTC-TTTCATAGAAGTTTTCAGA-GATCT
10337 AAGTTGATCT
1 AAGTTGATCT
10347 CTAAATTGAC
Statistics
Matches: 353, Mismatches: 26, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
53 62 0.18
54 278 0.79
55 13 0.04
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (53 bp):
AAGTTGATCTTAAGATGACCAGTGTGGTCTTTCATAGAAGTTTTCAGAGATCT
Found at i:10368 original size:55 final size:55
Alignment explanation
Indices: 10283--10399 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
10273 TCAAATATCT
* *
10283 AAGTTGATCTTAAGTTGATCCAGTGTGGTCATTCCAAG-AA-GTTTACGATGATCA
1 AAGTTGATCTTAAATTGATCCAGTGCGGTCATTCCAAGAAAGGTTTAC-ATGATCA
10337 AAGTTGATCTCTAAATTGA-CACAGTGCGGTCATTCCAAGAAAGGTTTACATGATCA
1 AAGTTGATCT-TAAATTGATC-CAGTGCGGTCATTCCAAGAAAGGTTTACATGATCA
*
10393 AGGTTGA
1 AAGTTGA
10400 ATTCTTAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
54 11 0.20
55 24 0.43
56 15 0.27
57 6 0.11
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (55 bp):
AAGTTGATCTTAAATTGATCCAGTGCGGTCATTCCAAGAAAGGTTTACATGATCA
Found at i:10417 original size:55 final size:55
Alignment explanation
Indices: 10283--10419 Score: 149
Period size: 55 Copynumber: 2.5 Consensus size: 55
10273 TCAAATATCT
* * *
10283 AAGTTGATCT-TAAGTTGATCCAGTGTGGTCATTCCAAGAAGTTTACGATGATCA
1 AAGTTGATCTCTAAATTAATCCAGTGCGGTCATTCCAAGAAGTTTACGATGATCA
*
10337 AAGTTGATCTCTAAATTGA-CACAGTGCGGTCATTCCAAGAAAGGTTTAC-ATGATCA
1 AAGTTGATCTCTAAATTAATC-CAGTGCGGTCATTCCAAG-AA-GTTTACGATGATCA
* *
10393 AGGTTGAAT-TCTTAA-TAATCCAGTGCG
1 AAGTTG-ATCTCTAAATTAATCCAGTGCG
10420 ATTAATTAGG
Statistics
Matches: 72, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
54 11 0.15
55 33 0.46
56 20 0.28
57 8 0.11
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (55 bp):
AAGTTGATCTCTAAATTAATCCAGTGCGGTCATTCCAAGAAGTTTACGATGATCA
Found at i:10472 original size:33 final size:33
Alignment explanation
Indices: 10430--10507 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
10420 ATTAATTAGG
* * * *
10430 AAGTTCAAAATTTGCATTTCATTTCAAAATTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
10463 AAGTTCAAAATCTGCATATCATATCAAAACTCA
1 AAGTTCAAAATCTGCATATCATATCAAAACTCA
*
10496 AAATTCAAAATC
1 AAGTTCAAAATC
10508 CACAGTTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (33 bp):
AAGTTCAAAATCTGCATATCATATCAAAACTCA
Found at i:10651 original size:7 final size:7
Alignment explanation
Indices: 10639--11013 Score: 464
Period size: 7 Copynumber: 53.6 Consensus size: 7
10629 TTGTTTGCAT
10639 TTCAAAA
1 TTCAAAA
10646 TTCAAAA
1 TTCAAAA
10653 TTCAAAA
1 TTCAAAA
10660 TTCAAAA
1 TTCAAAA
10667 TTCAAAA
1 TTCAAAA
10674 TTCAAAA
1 TTCAAAA
10681 TTCAAAA
1 TTCAAAA
10688 TTCAAAA
1 TTCAAAA
10695 TTCAAAA
1 TTCAAAA
10702 TTCAAAA
1 TTCAAAA
10709 TTCAAAA
1 TTCAAAA
10716 TTCAAAA
1 TTCAAAA
10723 TTCAAAA
1 TTCAAAA
10730 TTCAAAA
1 TTCAAAA
10737 TTCAAAA
1 TTCAAAA
10744 TTCAAAA
1 TTCAAAA
10751 TTCAAAA
1 TTCAAAA
10758 TTCAAAA
1 TTCAAAA
10765 TTCAAAA
1 TTCAAAA
10772 TTCAAAA
1 TTCAAAA
10779 TTCAAAA
1 TTCAAAA
10786 TTCAAAA
1 TTCAAAA
10793 TTCAAAA
1 TTCAAAA
10800 TTCAAAA
1 TTCAAAA
10807 TTCAAAA
1 TTCAAAA
10814 TTCAAAA
1 TTCAAAA
*
10821 CTCAAAA
1 TTCAAAA
*
10828 CTCAAAA
1 TTCAAAA
*
10835 CTCAAAA
1 TTCAAAA
*
10842 CTCAAAA
1 TTCAAAA
*
10849 CTCAAAA
1 TTCAAAA
*
10856 CTCAAAA
1 TTCAAAA
*
10863 CTCAAAA
1 TTCAAAA
*
10870 CTCAAAA
1 TTCAAAA
*
10877 CTCAAAA
1 TTCAAAA
*
10884 CTCAAAA
1 TTCAAAA
*
10891 CTCAAAA
1 TTCAAAA
**
10898 CGCAAAA
1 TTCAAAA
**
10905 CGCAAAA
1 TTCAAAA
**
10912 CGCAAAA
1 TTCAAAA
**
10919 CGCAAAA
1 TTCAAAA
*
10926 CTCAAAA
1 TTCAAAA
*
10933 CTCAAAA
1 TTCAAAA
*
10940 CTCAAAA
1 TTCAAAA
*
10947 CTCAAAA
1 TTCAAAA
*
10954 CTCAAAA
1 TTCAAAA
*
10961 CTCAAAA
1 TTCAAAA
*
10968 CTCAAAA
1 TTCAAAA
*
10975 CTCAAAA
1 TTCAAAA
10982 CTT-AAAA
1 -TTCAAAA
* *
10989 CTCAAAC
1 TTCAAAA
*
10996 CTCAAAA
1 TTCAAAA
11003 TTCAAAA
1 TTCAAAA
11010 TTCA
1 TTCA
11014 TGGCTCAAAA
Statistics
Matches: 358, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
6 1 0.00
7 356 0.99
8 1 0.00
ACGTcount: A:0.57, C:0.21, G:0.01, T:0.21
Consensus pattern (7 bp):
TTCAAAA
Found at i:11077 original size:7 final size:7
Alignment explanation
Indices: 11061--11094 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
11051 ATATCATTCT
11061 TCAAAAG
1 TCAAAAG
*
11068 TCAAATG
1 TCAAAAG
11075 TCAAAAG
1 TCAAAAG
*
11082 TCAAAAT
1 TCAAAAG
11089 TCAAAA
1 TCAAAA
11095 TTTGCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.56, C:0.15, G:0.09, T:0.21
Consensus pattern (7 bp):
TCAAAAG
Found at i:13893 original size:21 final size:22
Alignment explanation
Indices: 13858--13898 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
13848 CTAAAGTTTA
*
13858 ATGGGATGCATGAATGAATGCC
1 ATGGCATGCATGAATGAATGCC
13880 ATGGCATG-ATGAATGAATG
1 ATGGCATGCATGAATGAATG
13899 TATGAGGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.34, C:0.10, G:0.32, T:0.24
Consensus pattern (22 bp):
ATGGCATGCATGAATGAATGCC
Done.