Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010586.1 Corchorus capsularis cultivar CVL-1 contig10607, 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: 22072
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:230 original size:2 final size:2
Alignment explanation
Indices: 223--255 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
213 ATCCAGATAG
223 AT AT AT AT 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 AT AT AT AT A
256 ATTAAAAGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2501 original size:21 final size:21
Alignment explanation
Indices: 2477--2789 Score: 152
Period size: 21 Copynumber: 14.2 Consensus size: 21
2467 TTGATTACCT
2477 TCTTACTGATTACCATTTTAC
1 TCTTACTGATTACCATTTTAC
* *
2498 TCTTTTACTGATTACTATTTTCTGC
1 TC--TTACTGATTACCA-TTT-TAC
* **
2523 TCCTTTTTTACTGACTACTCTTTTAC
1 T-C----TTACTGATTACCATTTTAC
* * *
2549 TTTTTACTGATTGCC-TTTTGAT
1 -TCTTACTGATTACCATTTT-AC
*
2571 TTTTACTGATTA-CATTTTTAC
1 TCTTACTGATTACCA-TTTTAC
*
2592 TTCTTGCTGATTAGCC-TTTTAC
1 -TCTTACTGATTA-CCATTTTAC
* *
2614 TCTTTACTGATCACCTTTTTAC
1 TC-TTACTGATTACCATTTTAC
*
2636 TCTTACTGATTTCC-TTTTAC
1 TCTTACTGATTACCATTTTAC
* **
2656 TTCTTACTTATTACTTTTTTAC
1 -TCTTACTGATTACCATTTTAC
*
2678 TCTTACTGATTACTA-TTTAC
1 TCTTACTGATTACCATTTTAC
* * *
2698 TTTTTACTGACTACTATTTTAC
1 -TCTTACTGATTACCATTTTAC
**
2720 TCTTGTTGATTACC-TTCTTAC
1 TCTTACTGATTACCATT-TTAC
* *
2741 TTTTTACTGATTACTATTTTAC
1 -TCTTACTGATTACCATTTTAC
* * *
2763 TCTTTACTAATTTACCAATTTAA
1 TC-TTACTGA-TTACCATTTTAC
2786 TCTT
1 TCTT
2790 TCAGATACCT
Statistics
Matches: 228, Mismatches: 39, Indels: 49
0.72 0.12 0.16
Matches are distributed among these distances:
20 14 0.06
21 83 0.36
22 79 0.35
23 25 0.11
24 4 0.02
25 3 0.01
26 3 0.01
27 4 0.02
28 13 0.06
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.54
Consensus pattern (21 bp):
TCTTACTGATTACCATTTTAC
Found at i:2512 original size:15 final size:15
Alignment explanation
Indices: 2495--2549 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
2485 ATTACCATTT
*
2495 TACTCTTTTACTGAT
1 TACTCTTTTACTGAC
*
2510 TACTATTTT-CTG-C
1 TACTCTTTTACTGAC
* *
2523 TCCTTTTTTACTGAC
1 TACTCTTTTACTGAC
2538 TACTCTTTTACT
1 TACTCTTTTACT
2550 TTTTACTGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
13 7 0.22
14 6 0.19
15 19 0.59
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (15 bp):
TACTCTTTTACTGAC
Found at i:2555 original size:22 final size:22
Alignment explanation
Indices: 2527--2770 Score: 188
Period size: 22 Copynumber: 11.4 Consensus size: 22
2517 TTCTGCTCCT
*
2527 TTTTTACTGACTACTCTTTTAC
1 TTTTTACTGATTACTCTTTTAC
*
2549 TTTTTACTGATTGC-CTTTTGA-
1 TTTTTACTGATTACTCTTTT-AC
2570 TTTTTACTGATTACAT-TTTTAC
1 TTTTTACTGATTAC-TCTTTTAC
* *
2592 TTCTTGCTGATTAGC-CTTTTAC
1 TTTTTACTGATTA-CTCTTTTAC
* *
2614 TCTTTACTGATCAC-CTTTTTAC
1 TTTTTACTGATTACTC-TTTTAC
* *
2636 -TCTTACTGATTTC-CTTTTAC
1 TTTTTACTGATTACTCTTTTAC
* * *
2656 TTCTTACTTATTACTTTTTTAC
1 TTTTTACTGATTACTCTTTTAC
* *
2678 -TCTTACTGATTACT-ATTTAC
1 TTTTTACTGATTACTCTTTTAC
* *
2698 TTTTTACTGACTACTATTTTAC
1 TTTTTACTGATTACTCTTTTAC
*
2720 TCTTGT--TGATTAC-CTTCTTAC
1 T-TTTTACTGATTACTCTT-TTAC
*
2741 TTTTTACTGATTACTATTTTAC
1 TTTTTACTGATTACTCTTTTAC
*
2763 TCTTTACT
1 TTTTTACT
2771 AATTTACCAA
Statistics
Matches: 179, Mismatches: 27, Indels: 32
0.75 0.11 0.13
Matches are distributed among these distances:
20 16 0.09
21 78 0.44
22 79 0.44
23 6 0.03
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (22 bp):
TTTTTACTGATTACTCTTTTAC
Found at i:2574 original size:43 final size:43
Alignment explanation
Indices: 2527--2763 Score: 236
Period size: 42 Copynumber: 5.5 Consensus size: 43
2517 TTCTGCTCCT
* * *
2527 TTTTTACTGACTACTCTTTTACTTTTTACTGATTGCCTTTTGA-
1 TTTTTACTGATTACTATTTTACTTCTTACTGATTGCCTTTT-AC
*
2570 TTTTTACTGATTAC-ATTTTTACTTCTTGCTGATTAGCCTTTTAC
1 TTTTTACTGATTACTA-TTTTACTTCTTACTGATT-GCCTTTTAC
* * *
2614 TCTTTACTGATCACCT-TTTTAC-TCTTACTGATTTCCTTTTAC
1 TTTTTACTGATTA-CTATTTTACTTCTTACTGATTGCCTTTTAC
* * * *
2656 TTCTTACTTATTACTTTTTTAC-TCTTACTGATT-ACTATTTAC
1 TTTTTACTGATTACTATTTTACTTCTTACTGATTGCCT-TTTAC
* ** *
2698 TTTTTACTGACTACTATTTTAC-TCTTGTTGATTACCTTCTTAC
1 TTTTTACTGATTACTATTTTACTTCTTACTGATTGCCTT-TTAC
2741 TTTTTACTGATTACTATTTTACT
1 TTTTTACTGATTACTATTTTACT
2764 CTTTACTAAT
Statistics
Matches: 163, Mismatches: 21, Indels: 19
0.80 0.10 0.09
Matches are distributed among these distances:
41 4 0.02
42 67 0.41
43 67 0.41
44 24 0.15
45 1 0.01
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (43 bp):
TTTTTACTGATTACTATTTTACTTCTTACTGATTGCCTTTTAC
Found at i:2704 original size:14 final size:13
Alignment explanation
Indices: 2628--2705 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
2618 TACTGATCAC
*
2628 CTTTTTACTCTTA
1 CTTTTTACTTTTA
* *
2641 CTGATTTCCTTTTA
1 CT-TTTTACTTTTA
*
2655 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
2669 CTTTTTTACTCTTA
1 C-TTTTTACTTTTA
**
2683 CTGATTACTATTTA
1 CTTTTTACT-TTTA
2697 CTTTTTACT
1 CTTTTTACT
2706 GACTACTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 13 0.27
14 28 0.58
15 7 0.15
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:2764 original size:43 final size:42
Alignment explanation
Indices: 2441--2766 Score: 259
Period size: 43 Copynumber: 7.6 Consensus size: 42
2431 AGCATCACTA
**
2441 TTTTACTGATTACTATTTTACTCTTGTTGATTACCTTCTTACT
1 TTTTACTGATTACTATTTTACTCTTACTGATTACCTT-TTACT
** * * * ** ** *
2484 GATTACCAT-TTTACTCTTTTACTGATTACT-ATTTTCTGCTCCTT
1 TTTTA-C-TGATTACTATTTTACT-CTTACTGATTACCTTTTAC-T
* * * *
2528 TTTTACTGACTACTCTTTTACTTTTTACTGATTGCCTTTTGA-T
1 TTTTACTGATTACTATTTTAC-TCTTACTGATTACCTTTT-ACT
*
2571 TTTTACTGATTAC-ATTTTTACTTCTTGCTGATTAGCCTTTTACT
1 TTTTACTGATTACTA-TTTTAC-TCTTACTGATTA-CCTTTTACT
* * *
2615 CTTTACTGATCACCT-TTTTACTCTTACTGATTTCCTTTTACT
1 TTTTACTGATTA-CTATTTTACTCTTACTGATTACCTTTTACT
* * *
2657 TCTTACTTATTACTTTTTTACTCTTACTGATTA-CTATTTACT
1 TTTTACTGATTACTATTTTACTCTTACTGATTACCT-TTTACT
* **
2699 TTTTACTGACTACTATTTTACTCTTGTTGATTACCTTCTTACT
1 TTTTACTGATTACTATTTTACTCTTACTGATTACCTT-TTACT
2742 TTTTACTGATTACTATTTTACTCTT
1 TTTTACTGATTACTATTTTACTCTT
2767 TACTAATTTA
Statistics
Matches: 223, Mismatches: 43, Indels: 34
0.74 0.14 0.11
Matches are distributed among these distances:
41 4 0.02
42 69 0.31
43 93 0.42
44 52 0.23
45 5 0.02
ACGTcount: A:0.18, C:0.20, G:0.06, T:0.55
Consensus pattern (42 bp):
TTTTACTGATTACTATTTTACTCTTACTGATTACCTTTTACT
Found at i:3062 original size:55 final size:55
Alignment explanation
Indices: 3001--3333 Score: 560
Period size: 55 Copynumber: 6.1 Consensus size: 55
2991 CATTTTAACT
* *
3001 CTTAATTA-TCGATTTACCGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
* * *
3056 TTTAATTACTGATTTACTGATTACTACTACTTTGACTTTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
3111 CTTAATTACTTATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
3166 CTTAATTACTGATTCACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
**
3221 CTTTTTTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
*
3276 CTTAATTACTGATTTACTGATTACTGTTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
3331 CTT
1 CTT
3334 GAATGCGTGG
Statistics
Matches: 260, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
55 259 1.00
56 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.07, T:0.51
Consensus pattern (55 bp):
CTTAATTACTGATTTACTGATTACTATTACTTTGACTCTGATTAATCTCTTTTTA
Found at i:3996 original size:51 final size:50
Alignment explanation
Indices: 3962--4310 Score: 366
Period size: 51 Copynumber: 7.0 Consensus size: 50
3952 AACTTCTAAT
*
3962 TCAAAGGTGACA-TTTTATTTACTAATTACTTAAAAATTCAATCTTTTAG
1 TCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTAC
* * ** * *
4011 TCAAAGGTTAAAGCTTTATTTACTAATCACTCTAAAGATTCAATCTTTTAC
1 TCAAAGGTGACATTTTTATTTACTAATTACT-TAAAAATTCAATCTTTTAC
** * * * *
4062 -CTAAAGACGACATTTTTATTTACCAATTACTTAAAAATTTAATCTCTTAT
1 TC-AAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTAC
* *
4112 TCAAAGGTGAAATCTTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
1 TCAAAGGTGACATTTTTATTTACTAATTACT-TAAAAATTCAATCTTTTAC
* * * * * *
4163 TGAAAGATGACATTTTTATTTTCCAATTACTTAAAAATTCGATCTTTTAT
1 TCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTAC
* * * *
4213 TCAAAGGTTAAATCTTTATTTACTAGTTACTCTAAAAATTCAATCTTTTAC
1 TCAAAGGTGACATTTTTATTTACTAATTACT-TAAAAATTCAATCTTTTAC
* * *
4264 TCAAAGATGACATTTTTATTTA--AATTA-TTAAAAGCTTCAACCTTTTA
1 TCAAAGGTGACATTTTTATTTACTAATTACTTAAAA-ATTCAATCTTTTA
4311 TTTACAAGCT
Statistics
Matches: 242, Mismatches: 51, Indels: 15
0.79 0.17 0.05
Matches are distributed among these distances:
47 5 0.02
48 12 0.05
49 14 0.06
50 96 0.40
51 115 0.48
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.42
Consensus pattern (50 bp):
TCAAAGGTGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTAC
Found at i:4079 original size:101 final size:101
Alignment explanation
Indices: 3962--4312 Score: 505
Period size: 101 Copynumber: 3.5 Consensus size: 101
3952 AACTTCTAAT
* * * *
3962 TCAAAGGTGACA-TTTTATTTACTAATTACTTAAAAATTCAATCTTTTAGTCAAAGGTTAAAGCT
1 TCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCT
* *
4026 TTATTTACTAATCACTCTAAAGATTCAATCTTTTAC
66 TTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* * * *
4062 -CTAAAGACGACATTTTTATTTACCAATTACTTAAAAATTTAATCTCTTATTCAAAGGTGAAATC
1 TC-AAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
4126 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
65 TTTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* * *
4163 TGAAAGATGACATTTTTATTTTCCAATTACTTAAAAATTCGATCTTTTATTCAAAGGTTAAATCT
1 TCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCT
*
4228 TTATTTACTAGTTACTCTAAAAATTCAATCTTTTAC
66 TTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* *
4264 TCAAAGATGACATTTTTATTTA--AATTA-TTAAAAGCTTCAACCTTTTATT
1 TCAAAGATGACATTTTTATTTACCAATTACTTAAAA-ATTCAATCTTTTATT
4313 TACAAGCTAC
Statistics
Matches: 224, Mismatches: 23, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
98 6 0.03
99 18 0.08
100 8 0.04
101 192 0.86
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (101 bp):
TCAAAGATGACATTTTTATTTACCAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCT
TTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
Found at i:7658 original size:28 final size:27
Alignment explanation
Indices: 7622--7688 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
7612 TCTAAAAGTT
7622 ACCAAAATGTCCCTGACTGTGCAA-AATG
1 ACCAAAATGTCCCTGA--GTGCAAGAATG
* * *
7650 ACCAAAATGCCCCTTAGTGTAAGAATG
1 ACCAAAATGTCCCTGAGTGCAAGAATG
7677 ACCAAAAT-TCCC
1 ACCAAAATGTCCC
7689 CTTGATGACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 8 0.24
27 12 0.35
28 14 0.41
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (27 bp):
ACCAAAATGTCCCTGAGTGCAAGAATG
Found at i:12168 original size:23 final size:23
Alignment explanation
Indices: 12138--12306 Score: 70
Period size: 23 Copynumber: 7.3 Consensus size: 23
12128 ACAGCTTTGT
12138 AAGAAATTGGTTCTGATGGTGTG
1 AAGAAATTGGTTCTGATGGTGTG
** *
12161 AAGAAATTTATATCATCA-GGATGTG
1 AAGAAATTGGT-TC-TGATGG-TGTG
12186 AA-AAA-TGGTT-TGGATGGTGTG
1 AAGAAATTGGTTCT-GATGGTGTG
** * *
12207 AAGAAATTTATAC-CATCAGGATGT-
1 AAGAAATTGGTTCTGAT--GG-TGTG
*
12231 -AGAAATTAGTTCTGATGGTGTG
1 AAGAAATTGGTTCTGATGGTGTG
** * *
12253 AAGAAATTTATAC-CATCAGGATGT-
1 AAGAAATTGGTTCTGAT--GG-TGTG
12277 -AGAAATTGGTTCTGATGGTGTG
1 AAGAAATTGGTTCTGATGGTGTG
12299 AAGAAATT
1 AAGAAATT
12307 TATACCATCA
Statistics
Matches: 104, Mismatches: 22, Indels: 40
0.63 0.13 0.24
Matches are distributed among these distances:
20 1 0.01
21 13 0.12
22 14 0.13
23 47 0.45
24 15 0.14
25 14 0.13
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.33
Consensus pattern (23 bp):
AAGAAATTGGTTCTGATGGTGTG
Found at i:12212 original size:46 final size:45
Alignment explanation
Indices: 12141--12491 Score: 515
Period size: 46 Copynumber: 7.6 Consensus size: 45
12131 GCTTTGTAAG
* *
12141 AAATTGGTTCTGATGGTGTGAAGAAATTTATATCATCAGGATGTGA
1 AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGT-A
* *
12187 AAAATGGTT-TGGATGGTGTGAAGAAATTTATACCATCAGGATGTA
1 AAATTAGTTCT-GATGGTGTGAAGAAATTTATACCATCAGGATGTA
12232 GAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTA
1 -AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTA
*
12278 GAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTA
1 -AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTA
* * *
12324 GAAATCAGTTCTGATGGTGTGAAGAAATTTATACCATAAGGATGTGG
1 -AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGT-A
* *
12371 AAATCAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTGG
1 AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGT-A
*
12417 AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTTC
1 AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATG-TA
*
12463 AAATTGGTTCTGATGGTGTGAAGAAATTT
1 AAATTAGTTCTGATGGTGTGAAGAAATTT
12492 TCTCTTGGCC
Statistics
Matches: 287, Mismatches: 13, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
45 2 0.01
46 283 0.99
47 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (45 bp):
AAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTA
Found at i:12296 original size:92 final size:91
Alignment explanation
Indices: 12139--12491 Score: 573
Period size: 92 Copynumber: 3.8 Consensus size: 91
12129 CAGCTTTGTA
* * *
12139 AGAAATTGGTTCTGATGGTGTGAAGAAATTTATATCATCAGGATGTGAAAAATGGTT-TGGATGG
1 AGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTG-AAATTGGTTCT-GATGG
12203 TGTGAAGAAATTTATACCATCAGGATGT
64 TGTGAAGAAATTTATACCATCAGGATGT
12231 AGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTAGAAATTGGTTCTGATGGT
1 AGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGT-GAAATTGGTTCTGATGGT
12296 GTGAAGAAATTTATACCATCAGGATGT
65 GTGAAGAAATTTATACCATCAGGATGT
* * **
12323 AGAAATCAGTTCTGATGGTGTGAAGAAATTTATACCATAAGGATGTGGAAATCAGTTCTGATGGT
1 AGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGT-GAAATTGGTTCTGATGGT
12388 GTGAAGAAATTTATACCATCAGGATGT
65 GTGAAGAAATTTATACCATCAGGATGT
* *
12415 GGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTTCAAATTGGTTCTGATGGT
1 AGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATG-TGAAATTGGTTCTGATGGT
12480 GTGAAGAAATTT
65 GTGAAGAAATTT
12492 TCTCTTGGCC
Statistics
Matches: 244, Mismatches: 14, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
92 241 0.99
93 3 0.01
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (91 bp):
AGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTGAAATTGGTTCTGATGGTG
TGAAGAAATTTATACCATCAGGATGT
Found at i:12326 original size:23 final size:23
Alignment explanation
Indices: 12208--12328 Score: 76
Period size: 23 Copynumber: 5.3 Consensus size: 23
12198 GATGGTGTGA
12208 AGAAATTTATACCATCAGGATGT
1 AGAAATTTATACCATCAGGATGT
* *
12231 AGAAA-TTAGT-TC-TGATGG-TGT
1 AGAAATTTA-TACCATCA-GGATGT
12252 GAAGAAATTTATACCATCAGGATGT
1 --AGAAATTTATACCATCAGGATGT
** * *
12277 AGAAATTGGT-TC-TGATGG-TGT
1 AGAAATTTATACCATCA-GGATGT
12298 GAAGAAATTTATACCATCAGGATGT
1 --AGAAATTTATACCATCAGGATGT
12323 AGAAAT
1 AGAAAT
12329 CAGTTCTGAT
Statistics
Matches: 72, Mismatches: 12, Indels: 28
0.64 0.11 0.25
Matches are distributed among these distances:
21 10 0.14
22 9 0.12
23 34 0.47
24 9 0.12
25 10 0.14
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (23 bp):
AGAAATTTATACCATCAGGATGT
Found at i:12349 original size:23 final size:23
Alignment explanation
Indices: 12323--12397 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
12313 ATCAGGATGT
12323 AGAAATCAGTTCTGATGGTGTGA
1 AGAAATCAGTTCTGATGGTGTGA
* * *
12346 AGAAATTTA-TACCAT-AAGGATGTG-
1 AGAAA-TCAGT-TC-TGATGG-TGTGA
12370 -GAAATCAGTTCTGATGGTGTGA
1 AGAAATCAGTTCTGATGGTGTGA
12392 AGAAAT
1 AGAAAT
12398 TTATACCATC
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
21 5 0.13
22 6 0.16
23 16 0.42
24 6 0.16
25 5 0.13
ACGTcount: A:0.36, C:0.08, G:0.27, T:0.29
Consensus pattern (23 bp):
AGAAATCAGTTCTGATGGTGTGA
Found at i:12387 original size:138 final size:137
Alignment explanation
Indices: 12139--12491 Score: 573
Period size: 138 Copynumber: 2.6 Consensus size: 137
12129 CAGCTTTGTA
*
12139 AGAAATTGGTTCTGATGGTGTGAAGAAATTTATATCATCAGGATGTGAAAAATGGTT-TGGATGG
1 AGAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGT-AAAAATGGTTCT-GATGG
* *
12203 TGTGAAGAAATTTATACCATCAGGATGTAGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCA
64 TGTGAAGAAATTTATACCATAAGGATGTAGAAATCAGTTCTGATGGTGTGAAGAAATTTATACCA
12268 TCAGGATGT
129 TCAGGATGT
* *
12277 AGAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTAGAAATCAGTTCTGATGGT
1 AGAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTAAAAAT-GGTTCTGATGGT
*
12342 GTGAAGAAATTTATACCATAAGGATGTGGAAATCAGTTCTGATGGTGTGAAGAAATTTATACCAT
65 GTGAAGAAATTTATACCATAAGGATGTAGAAATCAGTTCTGATGGTGTGAAGAAATTTATACCAT
12407 CAGGATGT
130 CAGGATGT
* * * *
12415 GGAAATTAGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTTCAAATTGGTTCTGATGGT
1 AGAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATG-TAAAAATGGTTCTGATGGT
12480 GTGAAGAAATTT
65 GTGAAGAAATTT
12492 TCTCTTGGCC
Statistics
Matches: 200, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
137 5 0.03
138 190 0.95
139 5 0.03
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (137 bp):
AGAAATTGGTTCTGATGGTGTGAAGAAATTTATACCATCAGGATGTAAAAATGGTTCTGATGGTG
TGAAGAAATTTATACCATAAGGATGTAGAAATCAGTTCTGATGGTGTGAAGAAATTTATACCATC
AGGATGT
Found at i:14794 original size:18 final size:19
Alignment explanation
Indices: 14749--14794 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
14739 ATGGATTCCC
14749 TTGGAGAAATATTCAAAGAA
1 TTGGA-AAATATTCAAAGAA
* *
14769 AT-GCAAATATTCAAA-AA
1 TTGGAAAATATTCAAAGAA
14786 TTGGAAAAT
1 TTGGAAAAT
14795 GGACAATTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
17 3 0.14
18 16 0.76
19 1 0.05
20 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (19 bp):
TTGGAAAATATTCAAAGAA
Found at i:15017 original size:20 final size:20
Alignment explanation
Indices: 14992--15035 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
14982 TCAAAAGTGG
* *
14992 GAAAAGTGCTATAACGGCTA
1 GAAAAGAGCTACAACGGCTA
*
15012 GAAAAGAGCTCCAACGGCTA
1 GAAAAGAGCTACAACGGCTA
15032 GAAA
1 GAAA
15036 CTTGTGACAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (20 bp):
GAAAAGAGCTACAACGGCTA
Found at i:20287 original size:2 final size:2
Alignment explanation
Indices: 20280--20313 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20270 ATTTCACGAC
20280 AT 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
20314 TTGGTAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.