Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024015.1 Corchorus olitorius cultivar O-4 contig24048, 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: 67105
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1406 original size:25 final size:25
Alignment explanation
Indices: 1376--1423 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1366 ATGCAATGTC
1376 AAATTAGCTTTGAACTACATGAATG
1 AAATTAGCTTTGAACTACATGAATG
*
1401 AAATTAGCTTTGAGCTACATGAA
1 AAATTAGCTTTGAACTACATGAA
1424 CGCAAAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (25 bp):
AAATTAGCTTTGAACTACATGAATG
Found at i:1599 original size:27 final size:29
Alignment explanation
Indices: 1565--1640 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
1555 AAGTGGACTC
*
1565 AAAATGACCAACATGCCCCT-GA-ATATG
1 AAAATGACCAAAATGCCCCTGGATATATG
* * *
1592 CAAATGACCAAAATGCCCCTGGATTTTTG
1 AAAATGACCAAAATGCCCCTGGATATATG
1621 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
1641 AGGTGATCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 18 0.43
28 2 0.05
29 22 0.52
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGGATATATG
Found at i:2966 original size:78 final size:74
Alignment explanation
Indices: 2870--3124 Score: 263
Period size: 78 Copynumber: 3.4 Consensus size: 74
2860 TTTCATCAAC
*
2870 TTAGTTTTTCAAACTGGGAAAGTTCCCATCAAGTTTTTCAAGTTTTCAAATTGGGAAAGTTCCCA
1 TTAG-TTTTCAAATTGGGAAAGTTCCCATCAAG-TTTTCAAGTTTTCAAATTGGGAAAGTTCCCA
*
2935 TCAAGTTTTTTTT
64 TC-AG-TTTTGTT
* * * *
2948 TTAGGTTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGGTTTTCCAATTGGGAAAGCTCCCA
1 TTA-GTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCA-AGTTTTCAAATTGGGAAAGTTCCCA
3013 TCAG----GTT
64 TCAGTTTTGTT
* * * * *
3020 TTAGTTTTCAAATTGGGAAAATTCCCATCAGGTTTT--AGTTTTCAATTTAGGGAAAGTTCTCGT
1 TTAGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAGTTTTCAAATT-GGGAAAGTTCCCAT
3083 CA-TTTTCAGTT
65 CAGTTTT--GTT
* *
3094 TTAGTTTTCAAAGTCGGAAAGTTCCCATCAA
1 TTAGTTTTCAAATTGGGAAAGTTCCCATCAA
3125 AAACATTTTT
Statistics
Matches: 149, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
68 9 0.06
69 13 0.09
71 30 0.20
72 5 0.03
74 30 0.20
77 7 0.05
78 54 0.36
79 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (74 bp):
TTAGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTCAAGTTTTCAAATTGGGAAAGTTCCCATC
AGTTTTGTT
Found at i:3034 original size:34 final size:34
Alignment explanation
Indices: 2870--3123 Score: 213
Period size: 37 Copynumber: 6.9 Consensus size: 34
2860 TTTCATCAAC
* *
2870 TTAGTTTTTCAAACTGGGAAAGTTCCCATCAAGTTT
1 TTAG-TTTTCAAATTGGGAAAGTTCCCATC-AGGTT
*
2906 TTCAAGTTTTCAAATTGGGAAAGTTCCCATCAAGTTTTTTTT
1 TT--AGTTTTCAAATTGGGAAAGTTCCCATC-AG-----GTT
*
2948 TTAGGTTTTCAAATTGGGAAAGTTCCCATCAAGTCT
1 TTA-GTTTTCAAATTGGGAAAGTTCCCATCAGGT-T
* * *
2984 TCATGGTTTTCCAATTGGGAAAGCTCCCATCAGGTT
1 T--TAGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
*
3020 TTAGTTTTCAAATTGGGAAAATTCCCATCAGGTT
1 TTAGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
*
3054 TTAGTTTTCAATTTAGGGAAAGTTCTCGTCATTTTCA-GTT
1 TTAGTTTTCAAATT-GGGAAAGTTC-C--CA---TCAGGTT
* *
3094 TTAGTTTTCAAAGTCGGAAAGTTCCCATCA
1 TTAGTTTTCAAATTGGGAAAGTTCCCATCA
3124 AAAACATTTT
Statistics
Matches: 184, Mismatches: 16, Indels: 39
0.77 0.07 0.16
Matches are distributed among these distances:
33 3 0.02
34 42 0.23
35 10 0.05
36 9 0.05
37 54 0.29
38 6 0.03
39 9 0.05
40 17 0.09
41 29 0.16
42 5 0.03
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (34 bp):
TTAGTTTTCAAATTGGGAAAGTTCCCATCAGGTT
Found at i:5741 original size:17 final size:17
Alignment explanation
Indices: 5712--5754 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5702 TTCCCATCAT
*
5712 AAAAGAACAAAAA-GAA
1 AAAAGAAAAAAAAGGAA
5728 GAAAAGAAAAAAAAAGGAA
1 -AAAAG-AAAAAAAAGGAA
5747 AAAAGAAA
1 AAAAGAAA
5755 TGGAATTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 12 0.52
19 3 0.13
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAAGGAA
Found at i:5743 original size:18 final size:18
Alignment explanation
Indices: 5720--5754 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5710 ATAAAAGAAC
5720 AAAAA-GAAGAAAAGAAAA
1 AAAAAGGAA-AAAAGAAAA
5738 AAAAAGGAAAAAAGAAA
1 AAAAAGGAAAAAAGAAA
5755 TGGAATTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGGAAAAAAGAAAA
Found at i:5829 original size:14 final size:13
Alignment explanation
Indices: 5810--5860 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 13
5800 AACAAGAGGT
5810 TTTTCAAAAATATG
1 TTTTCAAAAATA-G
5824 TTTTCAAGAAA-AGG
1 TTTTCAA-AAATA-G
5838 TTTTCAAAAATGAG
1 TTTTCAAAAAT-AG
5852 TTTTCAAAA
1 TTTTCAAAA
5861 GATTTTTGAG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.09
14 26 0.79
15 4 0.12
ACGTcount: A:0.43, C:0.08, G:0.12, T:0.37
Consensus pattern (13 bp):
TTTTCAAAAATAG
Found at i:6455 original size:21 final size:21
Alignment explanation
Indices: 6431--6478 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
6421 GGATTGCTCA
*
6431 AAAAGAAGAAATTGATTTT-TC
1 AAAAGAA-AAAATGATTTTCTC
*
6452 AAAAGGAAAAAATGTTTTTCTC
1 AAAA-GAAAAAATGATTTTCTC
6474 AAAAG
1 AAAAG
6479 GTTTTAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (21 bp):
AAAAGAAAAAATGATTTTCTC
Found at i:6478 original size:22 final size:23
Alignment explanation
Indices: 6427--6479 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
6417 GAAAGGATTG
* *
6427 CTCAAAAAGAAGAAATTGATTTT
1 CTCAAAAGGAAGAAAATGATTTT
*
6450 -TCAAAAGGAA-AAAATGTTTTT
1 CTCAAAAGGAAGAAAATGATTTT
6471 CTCAAAAGG
1 CTCAAAAGG
6480 TTTTAGAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.35
22 17 0.65
ACGTcount: A:0.47, C:0.09, G:0.15, T:0.28
Consensus pattern (23 bp):
CTCAAAAGGAAGAAAATGATTTT
Found at i:8647 original size:21 final size:21
Alignment explanation
Indices: 8621--8662 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
8611 GCATCTTAGG
8621 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
8642 CAACTCCGATGAGCTTGAAAC
1 CAACTCCGATGAGCTTGAAAC
8663 TTCTTTGTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (21 bp):
CAACTCCGATGAGCTTGAAAC
Found at i:17789 original size:11 final size:11
Alignment explanation
Indices: 17773--17807 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
17763 TTTTTCTGTT
17773 TTTTGTTTTTG
1 TTTTGTTTTTG
*
17784 TTTTGTTTTCG
1 TTTTGTTTTTG
17795 TTTTGTTTTTG
1 TTTTGTTTTTG
17806 TT
1 TT
17808 GCGCTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.17, T:0.80
Consensus pattern (11 bp):
TTTTGTTTTTG
Found at i:18976 original size:14 final size:14
Alignment explanation
Indices: 18943--18969 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18933 GAGTTGAAGA
18943 AAAAAAGGAAAAAG
1 AAAAAAGGAAAAAG
18957 AAAAAAGGAAAAA
1 AAAAAAGGAAAAA
18970 ATTAAAAAAA
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAGGAAAAAG
Found at i:19030 original size:15 final size:16
Alignment explanation
Indices: 19010--19043 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
19000 AAGAGGCAAT
*
19010 AAAAAGGTGTTTT-TC
1 AAAAAGGTCTTTTCTC
19025 AAAAAGGTCTTTTCTC
1 AAAAAGGTCTTTTCTC
19041 AAA
1 AAA
19044 TCATGTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (16 bp):
AAAAAGGTCTTTTCTC
Found at i:21089 original size:15 final size:15
Alignment explanation
Indices: 21057--21102 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
21047 ACATGCTTTC
21057 AAAA-GATTTTTCGAAA
1 AAAATGATTTTTC--AA
21073 AAAATGATTTTTCAA
1 AAAATGATTTTTCAA
*
21088 AAAATG-GTTTTCAA
1 AAAATGATTTTTCAA
21102 A
1 A
21103 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 8 0.29
15 8 0.29
16 4 0.14
17 8 0.29
ACGTcount: A:0.48, C:0.07, G:0.11, T:0.35
Consensus pattern (15 bp):
AAAATGATTTTTCAA
Found at i:21089 original size:16 final size:16
Alignment explanation
Indices: 21057--21091 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
21047 ACATGCTTTC
21057 AAAAGATTTTTCGAAA
1 AAAAGATTTTTCGAAA
21073 AAAATGATTTTTC-AAA
1 AAAA-GATTTTTCGAAA
21089 AAA
1 AAA
21092 TGGTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (16 bp):
AAAAGATTTTTCGAAA
Found at i:28739 original size:22 final size:23
Alignment explanation
Indices: 28704--28746 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
28694 CTGTTTTCAG
28704 TTTTGCGTCGATAAAAAAAAAGT
1 TTTTGCGTCGATAAAAAAAAAGT
28727 TTTTGCGTC-ATAAAAAAAAA
1 TTTTGCGTCGATAAAAAAAAA
28747 TTTGTCCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (23 bp):
TTTTGCGTCGATAAAAAAAAAGT
Found at i:31901 original size:22 final size:21
Alignment explanation
Indices: 31865--31908 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
31855 CAAAAGTCGC
31865 GCCACTACCAAGCCACAACCG
1 GCCACTACCAAGCCACAACCG
* *
31886 GCCACTCACCATGCCACCACCG
1 GCCACT-ACCAAGCCACAACCG
31908 G
1 G
31909 TTATGCCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.27, C:0.50, G:0.16, T:0.07
Consensus pattern (21 bp):
GCCACTACCAAGCCACAACCG
Found at i:35257 original size:15 final size:16
Alignment explanation
Indices: 35224--35263 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
35214 TTACTTTGTT
35224 TTGTTTTCTAGTGTAA
1 TTGTTTTCTAGTGTAA
*
35240 TTGTTTTCT-GTTTAA
1 TTGTTTTCTAGTGTAA
*
35255 TTGCTTTCT
1 TTGTTTTCT
35264 TTCAACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.12, C:0.10, G:0.15, T:0.62
Consensus pattern (16 bp):
TTGTTTTCTAGTGTAA
Found at i:43263 original size:37 final size:35
Alignment explanation
Indices: 43212--43303 Score: 103
Period size: 37 Copynumber: 2.5 Consensus size: 35
43202 CCTAGGGTGG
* *
43212 TCTTTTTTTCAGTTTATTTAAATTGATCCAGGGCGA
1 TCTTTTCTT-AGTTTATTTAAATTGATCCAGAGCGA
* * *
43248 TCTCTTTGTATAGTTTATTTCAGTTGATCCAGAGCGA
1 TCT-TTTCT-TAGTTTATTTAAATTGATCCAGAGCGA
43285 TCTTTTCTTATGTTTATTT
1 TCTTTTCTTA-GTTTATTT
43304 GACCCAGGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
35 2 0.04
36 15 0.31
37 30 0.62
38 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.51
Consensus pattern (35 bp):
TCTTTTCTTAGTTTATTTAAATTGATCCAGAGCGA
Found at i:43330 original size:30 final size:30
Alignment explanation
Indices: 43296--43363 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
43286 CTTTTCTTAT
43296 GTTTATTTGACCCAGGG-TGGTCTTTCC-TCA
1 GTTTATTTGACCCAGGGCT-GTC-TTCCTTCA
* *
43326 GTTTATTCGACCCGGGGCTGTCTTCCTTCA
1 GTTTATTTGACCCAGGGCTGTCTTCCTTCA
*
43356 ATTTATTT
1 GTTTATTT
43364 TATTTAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 4 0.12
30 27 0.84
31 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (30 bp):
GTTTATTTGACCCAGGGCTGTCTTCCTTCA
Found at i:43454 original size:35 final size:33
Alignment explanation
Indices: 43370--43494 Score: 119
Period size: 35 Copynumber: 3.7 Consensus size: 33
43360 ATTTTATTTA
*
43370 AGTTGATCCAGGGTGATC-TTTCAATTTATTTC
1 AGTTGATCCAGGGTGATCTTTTCAATTTATGTC
* * *
43402 AATTGATCCAGGGTGATCTTCATTCAGTTTGTGTC
1 AGTTGATCCAGGGTGATCTT--TTCAATTTATGTC
* *
43437 AGTTGATCCAGGATGATCTCTCCTCAATTTACT-TC
1 AGTTGATCCAGGGTGATCT-T-TTCAATTTA-TGTC
* *
43472 AGTTGATCTAGGGCGATCTTTTC
1 AGTTGATCCAGGGTGATCTTTTC
43495 TGCAGTTTAT
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
32 17 0.23
33 3 0.04
34 1 0.01
35 51 0.69
36 2 0.03
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (33 bp):
AGTTGATCCAGGGTGATCTTTTCAATTTATGTC
Found at i:43936 original size:30 final size:30
Alignment explanation
Indices: 43895--44411 Score: 567
Period size: 30 Copynumber: 17.1 Consensus size: 30
43885 ACTCTGTCAG
* *
43895 TTTATTTTAATCCTGGTTTAGGATCACTAC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
43925 TTTACTTTAATCCTGATTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
** * *
43955 TCCATTTTAATCCTGGTTGAGGATCACTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * *
43985 TTCATTTTAGTCCTGGTTTAGGATCGTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * *
44015 TTCATGTCAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
44045 TTTATTTTTTAATCCTGGTTTAGGATCATTG-
1 TTTA--TTTTAATCCTGGTTTAGGATCATTGC
* *
44076 ATTATTTCTCAATCCTGGTTTAGGATCGTTG-
1 TTTATTT-T-AATCCTGGTTTAGGATCATTGC
*
44107 TTTATTTCTTAATCCTGGTTGAGGAT-AGTTGC
1 TTTA-TT-TTAATCCTGGTTTAGGATCA-TTGC
* *
44139 TTTATTTTAATCCTAGTTTAGGATCGTTG-
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
44168 TTTATTTCTTAATCCTGGTTGAGGATCGTTGC
1 TTTA-TT-TTAATCCTGGTTTAGGATCATTGC
* *
44200 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
44230 TTTATTTTAATCCTGGTTGAGGATCGTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* * * *
44260 -TTATTTTAATCATGGTTGACGATCTTTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* *
44289 CTTATTTTAATCCTGGTTTAGGATTATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
* ** **
44319 TCTATTTCGATCCTGGTTTAGGATCACCGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
**
44349 TTTATTTCGATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
*
44379 TTTATTCTAATCCTGGTTTAGGATCATTGC
1 TTTATTTTAATCCTGGTTTAGGATCATTGC
44409 TTT
1 TTT
44412 GTCAGTTAAT
Statistics
Matches: 421, Mismatches: 53, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
29 33 0.08
30 284 0.67
31 69 0.16
32 34 0.08
33 1 0.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.46
Consensus pattern (30 bp):
TTTATTTTAATCCTGGTTTAGGATCATTGC
Found at i:53625 original size:42 final size:42
Alignment explanation
Indices: 53540--53626 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
53530 CGCCCGGACT
* * * *
53540 CATCCGCGCCGCCTGCTCGGTCAAACCTGCCTTCCTCCGCGC
1 CATCCACGCCGCCTGCCCGGTCAAACCTGCCATCCTCCACGC
**
53582 CATCCACGCCGCCTGCCCGGTTGAACCTG-CATCCTTCCACGC
1 CATCCACGCCGCCTGCCCGGTCAAACCTGCCATCC-TCCACGC
53624 CAT
1 CAT
53627 TCCAGACTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 4 0.11
42 34 0.89
ACGTcount: A:0.13, C:0.48, G:0.20, T:0.20
Consensus pattern (42 bp):
CATCCACGCCGCCTGCCCGGTCAAACCTGCCATCCTCCACGC
Found at i:63047 original size:163 final size:160
Alignment explanation
Indices: 62766--63152 Score: 542
Period size: 163 Copynumber: 2.4 Consensus size: 160
62756 ATAGGCGAGT
* * *
62766 GAATTTTTCCCTCCAAAACACAGAAAAAAAAATTCTCTCACTCCATATATTACAATTGCGGCGTT
1 GAATTTTTCCCTCCAAAA-A-AGAAAAAAAAA-TCTCTCCCTCCATATATTAAAATGGCGGCGTT
* * *
62831 TCCTTTTCAAGACGCCACTAATCAGAGGCGTCTGATGTGAAAATGCCGCTATATATTATAGGCAT
63 TCCTTTTCAAGACGCCACTAATCAGAGGCGTCTGATGCGAAAACGCCGCTATATATTATAGACAT
* *
62896 AGAGTTGGAAACTTTCTTTGTTTTAGGGTTGAGG
128 AGAGATGGAAACTTTCTTTGTTTTAGGG-GGAGG
* *
62930 GAATTTTTCCCTCCGAAAAAAGGAAAAAAAAACCTCTCCCTCCATATATTAAAATGGTGGCGTTT
1 GAATTTTTCCCTCC-AAAAAA-GAAAAAAAAATCTCTCCCTCCATATATTAAAATGGCGGCGTTT
* ** * * *
62995 CCTTTTCTAGACGCCACTAATTGGCGGCGTCTGGTGCGAAAACGCTGCTATATATTATAGACATA
64 CCTTTTCAAGACGCCACTAATCAGAGGCGTCTGATGCGAAAACGCCGCTATATATTATAGACATA
63060 GAGATGGAAACTTTCTTTGTTTTAGGGGGAGG
129 GAGATGGAAACTTTCTTTGTTTTAGGGGGAGG
* *
63092 AAATTTTTCCCTCCAAAAAA-AAGAAAAAAATCTCTCCCTCCATATATTAATATGGCGGCGT
1 GAATTTTTCCCTCCAAAAAAGAA-AAAAAAATCTCTCCCTCCATATATTAAAATGGCGGCGT
63153 CTTTCTAGTG
Statistics
Matches: 200, Mismatches: 20, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
159 2 0.01
160 35 0.17
161 6 0.03
162 17 0.09
163 111 0.56
164 25 0.12
165 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (160 bp):
GAATTTTTCCCTCCAAAAAAGAAAAAAAAATCTCTCCCTCCATATATTAAAATGGCGGCGTTTCC
TTTTCAAGACGCCACTAATCAGAGGCGTCTGATGCGAAAACGCCGCTATATATTATAGACATAGA
GATGGAAACTTTCTTTGTTTTAGGGGGAGG
Found at i:63201 original size:31 final size:32
Alignment explanation
Indices: 63143--63204 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
63133 ATATATTAAT
*
63143 ATGGCGGCGTCTTTCTAGTGAAACGCCACTAA
1 ATGGCGGCGTCTTTCTAGTCAAACGCCACTAA
63175 ATGGCGGCGTC-TTC-ATGTCAAACGCCACTA
1 ATGGCGGCGTCTTTCTA-GTCAAACGCCACTA
63205 TATTCAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 1 0.04
31 16 0.57
32 11 0.39
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (32 bp):
ATGGCGGCGTCTTTCTAGTCAAACGCCACTAA
Found at i:64984 original size:16 final size:16
Alignment explanation
Indices: 64956--64988 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
64946 CACACACTAA
64956 ACACCATATCACAGTC
1 ACACCATATCACAGTC
64972 ACACACATA-CACAGTC
1 ACAC-CATATCACAGTC
64988 A
1 A
64989 TTCATCAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.36, G:0.06, T:0.15
Consensus pattern (16 bp):
ACACCATATCACAGTC
Found at i:66872 original size:26 final size:26
Alignment explanation
Indices: 66836--66912 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
66826 TGCACTTTTT
66836 GGCACAAGGGAGGAGCTAGCAGCGGC
1 GGCACAAGGGAGGAGCTAGCAGCGGC
66862 GGCACAAGGGAGGAGCTAGCAGCGGC
1 GGCACAAGGGAGGAGCTAGCAGCGGC
* *
66888 GGCACAA-GGAGGAGATAGCGGCGGC
1 GGCACAAGGGAGGAGCTAGCAGCGGC
66913 AGTAGCTAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
25 16 0.33
26 33 0.67
ACGTcount: A:0.27, C:0.22, G:0.47, T:0.04
Consensus pattern (26 bp):
GGCACAAGGGAGGAGCTAGCAGCGGC
Done.