Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015867.1 Corchorus olitorius cultivar O-4 contig15900, 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: 79332
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:659 original size:27 final size:26
Alignment explanation
Indices: 624--719 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 26
614 AAAATGTACC
* * *
624 TGAAATGACTAAAATGTCCCTGGACG
1 TGAAATGACCAAAATGACCCTGGACA
650 TGAATATGACCAAAAT-ACCCTTGGACA
1 TGAA-ATGACCAAAATGACCC-TGGACA
*
677 TGCAAAATGACCAAAATGCCCCTGGACA
1 TG--AAATGACCAAAATGACCCTGGACA
*
705 TACAAATGACCAAAA
1 T-GAAATGACCAAAA
720 AAAGTAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
26 7 0.12
27 29 0.49
28 18 0.31
29 5 0.08
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.19
Consensus pattern (26 bp):
TGAAATGACCAAAATGACCCTGGACA
Found at i:720 original size:28 final size:28
Alignment explanation
Indices: 655--719 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
645 GGACGTGAAT
* *
655 ATGACCAAAATACCCTTGGACATGCAAA
1 ATGACCAAAATACCCCTGGACATACAAA
*
683 ATGACCAAAATGCCCCTGGACATAC-AA
1 ATGACCAAAATACCCCTGGACATACAAA
710 ATGACCAAAA
1 ATGACCAAAA
720 AAAGTAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.15
Consensus pattern (28 bp):
ATGACCAAAATACCCCTGGACATACAAA
Found at i:1121 original size:90 final size:90
Alignment explanation
Indices: 1007--1171 Score: 276
Period size: 90 Copynumber: 1.8 Consensus size: 90
997 TTTTGAAGGG
* *
1007 ATGCACTGCATCAACTTGATTCACCGAATCACCCTGATCTATTTGAAGATTTGCTGCACCGAGCT
1 ATGCACCGCATCAACTTGATTCACCGAATCACCCTGATCTATTTAAAGATTTGCTGCACCGAGCT
*
1072 CATTGAGTCCAGCATTGAAGAAATA
66 CACTGAGTCCAGCATTGAAGAAATA
* * *
1097 ATGCACCGCATTAGCTTGATTCACCGAATCACCCTGATTTATTTAAAGATTTGCTGCACCGAGCT
1 ATGCACCGCATCAACTTGATTCACCGAATCACCCTGATCTATTTAAAGATTTGCTGCACCGAGCT
1162 CACTGAGTCC
66 CACTGAGTCC
1172 GTATTAAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
90 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (90 bp):
ATGCACCGCATCAACTTGATTCACCGAATCACCCTGATCTATTTAAAGATTTGCTGCACCGAGCT
CACTGAGTCCAGCATTGAAGAAATA
Found at i:1219 original size:35 final size:35
Alignment explanation
Indices: 1178--1410 Score: 367
Period size: 35 Copynumber: 6.7 Consensus size: 35
1168 GTCCGTATTA
*
1178 AAGATGCTACACCGAGTCATCTGAATTCATCTTTG
1 AAGATGCTACACCGAGTCATCTGAATTCAACTTTG
* *
1213 AAGATGCCACACCGAGTCATCTGAATTCAACTTCG
1 AAGATGCTACACCGAGTCATCTGAATTCAACTTTG
* *
1248 AAGATGCTACACCGAGTCATCTGAGTTCATCTTTG
1 AAGATGCTACACCGAGTCATCTGAATTCAACTTTG
* *
1283 AAGATGCTACACCGAGACATCTGAATTCAACTTCG
1 AAGATGCTACACCGAGTCATCTGAATTCAACTTTG
* *
1318 AAGATGCTACACCGAGTCATCTGAGTTCATCTTTG
1 AAGATGCTACACCGAGTCATCTGAATTCAACTTTG
**
1353 AAGATGCTACACCGAGTCGCCTGAATTCAACTTTG
1 AAGATGCTACACCGAGTCATCTGAATTCAACTTTG
1388 AAGATGCTACACCGAGTCATCTG
1 AAGATGCTACACCGAGTCATCTG
1411 GATCCCTGAA
Statistics
Matches: 177, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 177 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (35 bp):
AAGATGCTACACCGAGTCATCTGAATTCAACTTTG
Found at i:1260 original size:70 final size:70
Alignment explanation
Indices: 1178--1410 Score: 412
Period size: 70 Copynumber: 3.3 Consensus size: 70
1168 GTCCGTATTA
* *
1178 AAGATGCTACACCGAGTCATCTGAATTCATCTTTGAAGATGCCACACCGAGTCATCTGAATTCAA
1 AAGATGCTACACCGAGTCATCTGAGTTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTCAA
1243 CTTCG
66 CTTCG
*
1248 AAGATGCTACACCGAGTCATCTGAGTTCATCTTTGAAGATGCTACACCGAGACATCTGAATTCAA
1 AAGATGCTACACCGAGTCATCTGAGTTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTCAA
1313 CTTCG
66 CTTCG
**
1318 AAGATGCTACACCGAGTCATCTGAGTTCATCTTTGAAGATGCTACACCGAGTCGCCTGAATTCAA
1 AAGATGCTACACCGAGTCATCTGAGTTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTCAA
*
1383 CTTTG
66 CTTCG
1388 AAGATGCTACACCGAGTCATCTG
1 AAGATGCTACACCGAGTCATCTG
1411 GATCCCTGAA
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 156 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (70 bp):
AAGATGCTACACCGAGTCATCTGAGTTCATCTTTGAAGATGCTACACCGAGTCATCTGAATTCAA
CTTCG
Found at i:1527 original size:25 final size:25
Alignment explanation
Indices: 1473--1527 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
1463 TTGGTGATGC
* *
1473 AATGCTGGATGTTAATGTAATGATA
1 AATGCTGGATGATAATGTAATGAGA
* *
1498 TATGCT-GATGATACATGTGATGAGA
1 AATGCTGGATGATA-ATGTAATGAGA
1523 AATGC
1 AATGC
1528 ATATGGTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (25 bp):
AATGCTGGATGATAATGTAATGAGA
Found at i:4423 original size:11 final size:10
Alignment explanation
Indices: 4407--4453 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
4397 AAGTTCGTGT
4407 TTGAAGACTCA
1 TTGAAGA-TCA
*
4418 TTGAAGATAA
1 TTGAAGATCA
4428 TTTGAAGAT--
1 -TTGAAGATCA
4437 TTGAAGATCA
1 TTGAAGATCA
4447 TTGAAGA
1 TTGAAGA
4454 ATTATTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 8 0.25
10 9 0.28
11 15 0.47
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.32
Consensus pattern (10 bp):
TTGAAGATCA
Found at i:4442 original size:19 final size:18
Alignment explanation
Indices: 4418--4453 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4408 TGAAGACTCA
4418 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
4437 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
4454 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:16434 original size:21 final size:21
Alignment explanation
Indices: 16410--16457 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
16400 AGAGTTTTCT
*
16410 GTGTGTGTATGGTTTGAATGG
1 GTGTGTGTATCGTTTGAATGG
* *
16431 GTGTGGGTGTCGTTTGAATGG
1 GTGTGTGTATCGTTTGAATGG
16452 GTGTGT
1 GTGTGT
16458 TTTTTCAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.10, C:0.02, G:0.46, T:0.42
Consensus pattern (21 bp):
GTGTGTGTATCGTTTGAATGG
Found at i:18515 original size:27 final size:27
Alignment explanation
Indices: 18484--18577 Score: 125
Period size: 27 Copynumber: 3.4 Consensus size: 27
18474 AATGTACCTG
* * **
18484 AAATGACTAAAATGTCCTTGGATGTGC
1 AAATGACCAAAATGCCCTTGGACATGC
* *
18511 AAATGACCAAAATACCCCTGGACATGC
1 AAATGACCAAAATGCCCTTGGACATGC
18538 TAAATGACCAAAATGCCCTTGGACATGC
1 -AAATGACCAAAATGCCCTTGGACATGC
18566 AAATGACCAAAA
1 AAATGACCAAAA
18578 GAAGTAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 33 0.57
28 25 0.43
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.20
Consensus pattern (27 bp):
AAATGACCAAAATGCCCTTGGACATGC
Found at i:18547 original size:28 final size:27
Alignment explanation
Indices: 18508--18577 Score: 113
Period size: 28 Copynumber: 2.6 Consensus size: 27
18498 TCCTTGGATG
18508 TGCAAATGACCAAAATACCCCTGGACA
1 TGCAAATGACCAAAATACCCCTGGACA
* *
18535 TGCTAAATGACCAAAATGCCCTTGGACA
1 TGC-AAATGACCAAAATACCCCTGGACA
18563 TGCAAATGACCAAAA
1 TGCAAATGACCAAAA
18578 GAAGTAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 15 0.38
28 25 0.62
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.17
Consensus pattern (27 bp):
TGCAAATGACCAAAATACCCCTGGACA
Found at i:21315 original size:10 final size:10
Alignment explanation
Indices: 21302--21336 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
21292 ATATATTATA
21302 TCCTTTCCAT
1 TCCTTTCCAT
21312 TCCTTTCCAT
1 TCCTTTCCAT
21322 TCCTTTCCAT
1 TCCTTTCCAT
21332 TCCTT
1 TCCTT
21337 AACCAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.09, C:0.40, G:0.00, T:0.51
Consensus pattern (10 bp):
TCCTTTCCAT
Found at i:21455 original size:5 final size:5
Alignment explanation
Indices: 21447--21476 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
21437 ACTTCCCTCC
*
21447 CCTTT CCTTT CCTTT CCTTC CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
21477 AATTACTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (5 bp):
CCTTT
Found at i:24664 original size:66 final size:66
Alignment explanation
Indices: 24586--24723 Score: 161
Period size: 66 Copynumber: 2.1 Consensus size: 66
24576 AGAAAATTTC
* * * * *
24586 TTTTCTTGGAAGAATTTTAGTAACAAAAACCTTGAAATAATTTAAAAGAATGAAA-TTTGATTCT
1 TTTTCTTAGAAGAATTCTAGCAACAAAAACCTTG-AAGAAGTTAAAAGAATGAAATTTTGATTCT
24650 TG
65 TG
* ** * * *
24652 TTTTCTTAGAAGAATTCTGGCAACAAAATTCTTGAAGGAGTTAGAAGGATGAAATTTTGATTCTT
1 TTTTCTTAGAAGAATTCTAGCAACAAAAACCTTGAAGAAGTTAAAAGAATGAAATTTTGATTCTT
24717 G
66 G
24718 TTTTCT
1 TTTTCT
24724 AAGGGTGTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
65 15 0.25
66 45 0.75
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.39
Consensus pattern (66 bp):
TTTTCTTAGAAGAATTCTAGCAACAAAAACCTTGAAGAAGTTAAAAGAATGAAATTTTGATTCTT
G
Found at i:25747 original size:14 final size:14
Alignment explanation
Indices: 25728--25754 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25718 TATCAAACGA
25728 TACATTACATTCAT
1 TACATTACATTCAT
25742 TACATTACATTCA
1 TACATTACATTCA
25755 GTACTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
TACATTACATTCAT
Found at i:26601 original size:2 final size:2
Alignment explanation
Indices: 26594--26625 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
26584 TTTATTCTTT
26594 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
26626 GAACACCTCC
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:27616 original size:2 final size:2
Alignment explanation
Indices: 27609--27643 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
27599 GACCCGTATT
27609 TA 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 TA T
27644 TCTATAAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32573 original size:2 final size:2
Alignment explanation
Indices: 32566--32590 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32556 TATTAGGATG
32566 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 T
32591 TGTAAAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33235 original size:42 final size:43
Alignment explanation
Indices: 33184--33277 Score: 129
Period size: 45 Copynumber: 2.2 Consensus size: 43
33174 AGTGCATTAC
** *
33184 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAAATAATTAATCAAAATAAAG
33225 CTAATATTCTACTCCTCCATCTCTAAATAATTAATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAAATAATTAATCAAAATAAAG
33270 CTAATATT
1 CTAATATT
33278 AATTGTTGCT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 36 0.78
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAAATAATTAATCAAAATAAAG
Found at i:35487 original size:46 final size:46
Alignment explanation
Indices: 35415--35508 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
35405 TTGGATCACG
* *
35415 TGCAACGTACGTGAAGGTGAGAACTAGTATATATAAAAGAAGAAAA
1 TGCAACGCACGTGAAGATGAGAACTAGTATATATAAAAGAAGAAAA
35461 TGCAACGCACGTGAAGATGATG-ACTAGTATATATAAAAGAAGAAAA
1 TGCAACGCACGTGAAGATGA-GAACTAGTATATATAAAAGAAGAAAA
35507 TG
1 TG
35509 GAGTAGCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (46 bp):
TGCAACGCACGTGAAGATGAGAACTAGTATATATAAAAGAAGAAAA
Found at i:41558 original size:19 final size:18
Alignment explanation
Indices: 41505--41559 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
41495 GGGTATCTTC
41505 TATGATTTGGGCTTTTAT
1 TATGATTTGGGCTTTTAT
* *
41523 TCT-ATTTTGGGC-ATTAT
1 TATGA-TTTGGGCTTTTAT
41540 TGATGATTTGGGCTTTTAT
1 T-ATGATTTGGGCTTTTAT
41559 T
1 T
41560 TATGCATTGG
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.21
18 17 0.59
19 6 0.21
ACGTcount: A:0.16, C:0.07, G:0.22, T:0.55
Consensus pattern (18 bp):
TATGATTTGGGCTTTTAT
Found at i:44736 original size:23 final size:24
Alignment explanation
Indices: 44710--44755 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
44700 GCGCCACCTC
*
44710 CTTC-TCCTTGTACGGAGTTTTCT
1 CTTCTTCCTTGTAAGGAGTTTTCT
*
44733 CTTCTTTCTTGTAAGGAGTTTTC
1 CTTCTTCCTTGTAAGGAGTTTTC
44756 CATGAGCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.11, C:0.22, G:0.17, T:0.50
Consensus pattern (24 bp):
CTTCTTCCTTGTAAGGAGTTTTCT
Found at i:47096 original size:14 final size:15
Alignment explanation
Indices: 47077--47106 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47067 AACTAGGAAA
47077 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
47091 AATAAATAAACAAGG
1 AATAAATAAACAAGG
47106 A
1 A
47107 TTGAACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:47704 original size:30 final size:30
Alignment explanation
Indices: 47648--47732 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 30
47638 CACCAATGAT
* ** **
47648 CAAATAAGCCCATAAACT-TTAATTTTGTC
1 CAAATAAGCCCATGAACTACCAATTTTGAA
* *
47677 CCAATAAGCCTATGAACTACCAATTTTGAA
1 CAAATAAGCCCATGAACTACCAATTTTGAA
*
47707 CAAATAAGCCCCTGAACTACCAATTT
1 CAAATAAGCCCATGAACTACCAATTT
47733 CGGCCAAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 15 0.33
30 30 0.67
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.28
Consensus pattern (30 bp):
CAAATAAGCCCATGAACTACCAATTTTGAA
Found at i:48376 original size:31 final size:31
Alignment explanation
Indices: 48334--48407 Score: 112
Period size: 31 Copynumber: 2.4 Consensus size: 31
48324 TTTTTTGAAA
* *
48334 AAAAAGTTAGAGGACTTATTTGGTCATTTTG
1 AAAAAGATAGAGGACTTATTTGGCCATTTTG
* *
48365 AAAAAGGTAGAGGGCTTATTTGGCCATTTTG
1 AAAAAGATAGAGGACTTATTTGGCCATTTTG
48396 AAAAAGATAGAG
1 AAAAAGATAGAG
48408 TCCAAAAGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.31
Consensus pattern (31 bp):
AAAAAGATAGAGGACTTATTTGGCCATTTTG
Found at i:48757 original size:13 final size:14
Alignment explanation
Indices: 48730--48764 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
48720 AATGATTTTA
48730 GTAATTATAATTGG
1 GTAATTATAATTGG
*
48744 GTATTTAT-ATTGG
1 GTAATTATAATTGG
48757 GTAATTAT
1 GTAATTAT
48765 TTGATAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
GTAATTATAATTGG
Found at i:50522 original size:32 final size:32
Alignment explanation
Indices: 50486--50551 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
50476 CGCCCGATAT
*
50486 TTGGAAGGATTTGGACAAAAATTTGAA-GCCCG
1 TTGGAAGGACTTGGAC-AAAATTTGAAGGCCCG
* * *
50518 TTGGATGGGCTTGGACAAAATTTTAAGGCCCG
1 TTGGAAGGACTTGGACAAAATTTGAAGGCCCG
50550 TT
1 TT
50552 TACAAAATGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (32 bp):
TTGGAAGGACTTGGACAAAATTTGAAGGCCCG
Found at i:75342 original size:42 final size:44
Alignment explanation
Indices: 75295--75384 Score: 139
Period size: 45 Copynumber: 2.1 Consensus size: 44
75285 CATTATCCAA
* *
75295 ATTCTACT-CT-ATCTCTAGGTAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCCTCATCTATAGATAATTCATCAAAATAAAGCTAAT
75337 ATTCTACTCCTCCATCTATAGATAATTCATCAAAATAAAGCTAAT
1 ATTCTACTCCT-CATCTATAGATAATTCATCAAAATAAAGCTAAT
75382 ATT
1 ATT
75385 AATTGTTGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
42 8 0.19
43 2 0.05
45 33 0.77
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.36
Consensus pattern (44 bp):
ATTCTACTCCTCATCTATAGATAATTCATCAAAATAAAGCTAAT
Found at i:76995 original size:2 final size:2
Alignment explanation
Indices: 76988--77036 Score: 70
Period size: 2 Copynumber: 26.5 Consensus size: 2
76978 TAATATTTAG
76988 TA TA TA TA -A TA TA TA TA TA TA TA TA T- TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
77027 TA TA TA -A TA T
1 TA TA TA TA TA T
77037 GTATTTTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
1 4 0.09
2 39 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:76998 original size:16 final size:15
Alignment explanation
Indices: 76977--77028 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
76967 GGTGTTTCAA
76977 ATAATATTTAGTATAT
1 ATAATATTTA-TATAT
76993 ATAATATATATATATAT
1 ATAATAT-T-TATATAT
*
77010 ATATTATTATATATAT
1 ATAATATT-TATATAT
77026 ATA
1 ATA
77029 TATAATATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
16 19 0.58
17 12 0.36
18 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATAATATTTATATAT
Found at i:77504 original size:22 final size:21
Alignment explanation
Indices: 77478--77518 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
77468 CCGCCCATAT
*
77478 ATAATTTTTTAAAATAATAATA
1 ATAATTTATTAAAA-AATAATA
77500 ATAATTTATTAAAAAATAA
1 ATAATTTATTAAAAAATAA
77519 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATTTATTAAAAAATAATA
Found at i:77521 original size:7 final size:7
Alignment explanation
Indices: 77507--77536 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
77497 ATAATAATTT
77507 ATTAAAA
1 ATTAAAA
*
77514 AATAAAA
1 ATTAAAA
77521 ATTAAAA
1 ATTAAAA
77528 ATTAAAA
1 ATTAAAA
77535 AT
1 AT
77537 AATAAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
ATTAAAA
Found at i:78013 original size:26 final size:27
Alignment explanation
Indices: 77949--78021 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 27
77939 AGGGTCATCT
77949 AGGGGCATTTTGGTCATTTTCACATTC
1 AGGGGCATTTTGGTCATTTTCACATTC
*
77976 AGGGGCATTTTGATCATTTGT-AC-TTC
1 AGGGGCATTTTGGTCATTT-TCACATTC
78002 AGGGGGCA-TTTGGTCATTTT
1 A-GGGGCATTTTGGTCATTTT
78022 TCTTCATTAC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
25 1 0.02
26 14 0.33
27 26 0.62
28 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTTCACATTC
Found at i:78367 original size:19 final size:19
Alignment explanation
Indices: 78328--78367 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
78318 GTATTTAGCT
* *
78328 TTGGGCTTGCACTTGGGCA
1 TTGGGCTTGCACTTAGACA
78347 TTGGGCTTGCACTTAGACA
1 TTGGGCTTGCACTTAGACA
78366 TT
1 TT
78368 TTAACTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.20, G:0.30, T:0.35
Consensus pattern (19 bp):
TTGGGCTTGCACTTAGACA
Done.