Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012492.1 Corchorus capsularis cultivar CVL-1 contig12513, 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: 6665
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:2741 original size:2 final size:2
Alignment explanation
Indices: 2734--2768 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
2724 AATAAATTTT
2734 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
2769 AAAGTACGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3368 original size:17 final size:16
Alignment explanation
Indices: 3328--3452 Score: 103
Period size: 16 Copynumber: 7.8 Consensus size: 16
3318 TTAGGCCGTT
3328 TTTGGGTTCGGGCTTAA
1 TTTGGGTTCGGG-TTAA
* *
3345 GTCGGGTTCGGGTTAAA
1 TTTGGGTTCGGGTT-AA
*
3362 TTTGGG-TCGGGTTGA
1 TTTGGGTTCGGGTTAA
*
3377 TTCGGGTTCGGGTTAAA
1 TTTGGGTTCGGGTT-AA
* *
3394 TTTGGG-TCAGGTTGA
1 TTTGGGTTCGGGTTAA
*
3409 TTTGGGTTCGGGTCAA
1 TTTGGGTTCGGGTTAA
*
3425 TTTTGGG-TCAGGTTAA
1 -TTTGGGTTCGGGTTAA
* *
3441 TTCGGATTCGGG
1 TTTGGGTTCGGG
3453 CTCGGATTGG
Statistics
Matches: 84, Mismatches: 18, Indels: 13
0.73 0.16 0.11
Matches are distributed among these distances:
15 17 0.20
16 39 0.46
17 28 0.33
ACGTcount: A:0.14, C:0.10, G:0.38, T:0.38
Consensus pattern (16 bp):
TTTGGGTTCGGGTTAA
Found at i:3384 original size:32 final size:32
Alignment explanation
Indices: 3341--3452 Score: 152
Period size: 32 Copynumber: 3.5 Consensus size: 32
3331 GGGTTCGGGC
* *
3341 TTAAGTCGGGTTCGGGTTAAATTTGGGTCGGG
1 TTAATTCGGGTTCGGGTTAAATTTGGGTCAGG
*
3373 TTGATTCGGGTTCGGGTTAAATTTGGGTCAGG
1 TTAATTCGGGTTCGGGTTAAATTTGGGTCAGG
* * * *
3405 TTGATTTGGGTTCGGGTCAATTTTGGGTCAGG
1 TTAATTCGGGTTCGGGTTAAATTTGGGTCAGG
*
3437 TTAATTCGGATTCGGG
1 TTAATTCGGGTTCGGG
3453 CTCGGATTGG
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 71 1.00
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (32 bp):
TTAATTCGGGTTCGGGTTAAATTTGGGTCAGG
Found at i:3697 original size:16 final size:16
Alignment explanation
Indices: 3678--3721 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
3668 TGGTTTCAGA
*
3678 TTTTTCGGGTTCTGA-T
1 TTTTTCGGGTT-TGAGC
3694 TTTTTCGGGTTTGAGC
1 TTTTTCGGGTTTGAGC
3710 TTTTTCGGGTTT
1 TTTTTCGGGTTT
3722 TTTTGGGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.05, C:0.11, G:0.27, T:0.57
Consensus pattern (16 bp):
TTTTTCGGGTTTGAGC
Found at i:4303 original size:171 final size:170
Alignment explanation
Indices: 4010--4327 Score: 480
Period size: 171 Copynumber: 1.9 Consensus size: 170
4000 TGGAAAATTT
* *
4010 TATGTTTTCCGATTGTACCCTTTTTTCAAATATATTTCTAAATTGAAATTATTAAAATTTATTAT
1 TATGTTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATTGAAATTATTAAAATTTAGTA-
4075 TTAAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTCATTG
65 TT-AAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTCATTG
*
4140 ATGAACATGCAAATTTCTACGAATGATAGGAAACTATGTCTA
129 ACGAACATGCAAATTTCTACGAATGATAGGAAACTATGTCTA
**
4182 TATGTTTTCCGATTGCACCCTTTTTTTCAAATATATTTCTAAATTGTCATTATTAAAATTTAGTA
1 TATGTTTTCCGATTGCACCC-TTTTTTCAAATATATTTCTAAATTGAAATTATTAAAATTTAGTA
* * * *
4247 -T-AATTTAATGTTTAAAAATTTCAATTTAGACCGAATTATAAG-TTGATCAAATTGATTTTCGT
65 TTAAAATTAAT-TAT-AAAATTTCAATTTAGACCGAATTATAAGTTTG-TAAAATTGATTTTCAT
4309 TGACGAACATGCAAATTTC
127 TGACGAACATGCAAATTTC
4328 CTTTACTATT
Statistics
Matches: 133, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
169 7 0.05
170 5 0.04
171 61 0.46
172 19 0.14
173 41 0.31
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (170 bp):
TATGTTTTCCGATTGCACCCTTTTTTCAAATATATTTCTAAATTGAAATTATTAAAATTTAGTAT
TAAAATTAATTATAAAATTTCAATTTAGACCGAATTATAAGTTTGTAAAATTGATTTTCATTGAC
GAACATGCAAATTTCTACGAATGATAGGAAACTATGTCTA
Found at i:4574 original size:22 final size:21
Alignment explanation
Indices: 4546--5545 Score: 165
Period size: 22 Copynumber: 46.8 Consensus size: 21
4536 TGTCTCCGTG
4546 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
* *
4568 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-A-GA
*
4591 -GGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
* *
4612 TGGTAACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA--GA
*
4635 -AGTTATCAAAATTTCATAG-
1 TGGTTATCAAAATTTCATAGA
*
4654 TGTAGTTACCAAAATTTCATAGGA
1 TG--GTTATCAAAATTTCATA-GA
*
4678 TCAGGTTATTAAAATTTCATAGTA
1 T--GGTTATCAAAATTTCATAG-A
4702 TGGTTATCACAAATTT-ATAGAA
1 TGGTTATCA-AAATTTCATAG-A
* ** *
4724 AGGTTATCAAAGAGATCATCAAAA
1 TGGTTATCAAA-ATTTCAT--AGA
* **
4748 T-GTCAT-AGCAAGGTT-ATA-A
1 TGGTTATCA--AAATTTCATAGA
*
4767 -GAATT-TC---A--T-AGT-G-
1 TG-GTTATCAAAATTTCA-TAGA
*
4780 TGGTTAACAAAATTTCATAAGGA
1 TGGTTATCAAAATTTCAT-A-GA
* *
4803 -GGTTA-CTAATATTTCATGGGGA
1 TGGTTATC-AAAATTTCAT--AGA
*
4825 -GGTTATCAAAATTTCATAGTG
1 TGGTTATCAAAATTTCATAG-A
4846 TGGTTATCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATA-GA
* *
4868 AGGTTATAAAAGTCTCAATTTCATA-A
1 TGGTTAT-CAA-----AATTTCATAGA
* * *
4894 -GGAGTACCAAAATTTGATAGA
1 TGG-TTATCAAAATTTCATAGA
* * *
4915 CGGTTATC-AGATCTCATAGA
1 TGGTTATCAAAATTTCATAGA
* *
4935 GTGATTATCGAAATTTCATAGAGA
1 -TGGTTATCAAAATTTCAT--AGA
4959 TCGGATTATCAAAATTT-ATAGGA
1 T-GG-TTATCAAAATTTCATA-GA
* * *
4982 AGATTATTAAAATTTCATA-A
1 TGGTTATCAAAATTTCATAGA
* * *
5002 TCTTGTTATCAAAATTTAAAAGCGA
1 --TGGTTATCAAAATTTCATA--GA
*
5027 -GGTTATCAAAATTACATA-A
1 TGGTTATCAAAATTTCATAGA
5046 TGTGATTATCAAAATTTCATAGA
1 TG-G-TTATCAAAATTTCATAGA
* * * *
5069 GGGGTCAACAAAATTTTATAGA
1 -TGGTTATCAAAATTTCATAGA
*
5091 GAGGTTATCAAAATTTCATA-A
1 -TGGTTATCAAAATTTCATAGA
* * * *
5112 AGAGTTACCAAATTTTCA-AAA
1 TG-GTTATCAAAATTTCATAGA
*
5133 TGTGATTACCAAAATTTCATAG-
1 TG-G-TTATCAAAATTTCATAGA
***
5155 TGG-TA-C-----TTCTGGGGA
1 TGGTTATCAAAATTTC-ATAGA
*
5170 -GGTTATCAAAATTTTATAGTA
1 TGGTTATCAAAATTTCATAG-A
* *
5191 TGGTTA-CCAAA-TT-A-GGA
1 TGGTTATCAAAATTTCATAGA
* * * *
5208 AGGTTATTAAAATTTTAT-TA
1 TGGTTATCAAAATTTCATAGA
*
5228 TGGAGTAATCAAAATTTCA-AGGA
1 T-G-GTTATCAAAATTTCATA-GA
*
5251 -GGATATCAAAATTTCATATGA
1 TGGTTATCAAAATTTCATA-GA
* * * *
5272 AGGTTATTAAAATTTTATAGTT
1 TGGTTATCAAAATTTCATAG-A
* * *
5294 TAGTTTTCAAATTTTCATAAGA
1 TGGTTATCAAAATTTCAT-AGA
*
5316 GGGTTATCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAG-A
*
5338 T-GTAGATCAAAATTTCATAGGGA
1 TGGT-TATCAAAATTTCATA--GA
* *
5361 -GATTAACAAAATTTCATAAAGA
1 TGGTTATCAAAATTTCAT--AGA
* **
5383 -AGTTATCAAAAAATCATATGA
1 TGGTTATCAAAATTTCATA-GA
*
5404 AGGTTATCAAAA-TT--T-G-
1 TGGTTATCAAAATTTCATAGA
* *
5420 TAGTTATCAAGATTTCATAAGGA
1 TGGTTATCAAAATTTCAT-A-GA
*
5443 -GGTTATCAAAATTTTATAGGGA
1 TGGTTATCAAAATTTCATA--GA
* *
5465 -GGTTTATCAAAATTTTATAACA
1 TGG-TTATCAAAATTTCAT-AGA
5487 T--TTATCAAAATTTCATAGCA
1 TGGTTATCAAAATTTCATAG-A
* **
5507 AGGTTATCGGAATTTCATAG-
1 TGGTTATCAAAATTTCATAGA
5527 TGTGATTATCAAAATTTCA
1 TG-G-TTATCAAAATTTCA
5546 GAGTGTGATT
Statistics
Matches: 710, Mismatches: 146, Indels: 244
0.65 0.13 0.22
Matches are distributed among these distances:
13 7 0.01
14 6 0.01
15 2 0.00
16 10 0.01
17 10 0.01
18 5 0.01
19 13 0.02
20 63 0.09
21 66 0.09
22 418 0.59
23 48 0.07
24 32 0.05
25 17 0.02
26 4 0.01
28 9 0.01
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TGGTTATCAAAATTTCATAGA
Found at i:4626 original size:44 final size:43
Alignment explanation
Indices: 4547--5720 Score: 244
Period size: 44 Copynumber: 27.3 Consensus size: 43
4537 GTCTCCGTGT
** *
4547 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGAGGA
1 GGTTATCAAAATTTCAT-AGTATGGTTACCAAAATTTCAT-AGGA
* *
4591 GGTTATCAAAATTTCATAGTGTGGTAACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATA-GGA
* * *
4635 AGTTATCAAAATTTCATAGTGTAGTTACCAAAATTTCATAGGATCA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGG---A
* * *
4681 GGTTATTAAAATTTCATAGTATGGTTATCACAAATTT-ATAGAAA
1 GGTTATCAAAATTTCATAGTATGGTTACCA-AAATTTCATAG-GA
* * * * *
4725 GGTTATC---A----A-AG-A-GATCATCAAAATGTCATAGCAA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAG-GA
* *
4759 GGTTAT-AAGAATTTCATAGTGTGGTTAACAAAATTTCATAAGGA
1 GGTTATCAA-AATTTCATAGTATGGTTACCAAAATTTCAT-AGGA
* * * * *
4803 GGTTA-CTAATATTTCATGGGGA-GGTTATCAAAATTTCATAGTGT
1 GGTTATC-AAAATTTCAT-AGTATGGTTACCAAAATTTCATAG-GA
* **
4847 GGTTATCAAAATTTCATA-TGAAGGTTATAAAAGTCTCAATTTCATAAGGA
1 GGTTATCAAAATTTCATAGT-ATGGTTA-CCAA-----AATTTCAT-AGGA
* * * * * *
4897 -G-TACCAAAATTTGATAG-ACGGTTATC-AGATCTCATA-GA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGA
* * *
4935 GTGATTATCGAAATTTCATAGAGATCGGATTATCAAAATTT-ATAGGAA
1 G-G-TTATCAAAATTTCATAG-TAT-GG-TTACCAAAATTTCATAGG-A
* * * * * * * *
4983 GATTATTAAAATTTCATAATCTTGTTATCAAAATTTAAAAGCGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAG-GA
* * * * * *
5027 GGTTATCAAAATTACATAATGTGATTATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAG-GA
* * * * * *
5071 GGTCAACAAAATTTTATAG-AGAGGTTATCAAAATTTCATA-AA
1 GGTTATCAAAATTTCATAGTA-TGGTTACCAAAATTTCATAGGA
* * * * * * *
5113 GAGTTACCAAATTTTCAAAATGTGATTACCAAAATTTCATA-GT
1 G-GTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGA
* * * * *
5156 GG-TA-C-----TTC-TGGGGA-GGTTATCAAAATTTTATAGTA
1 GGTTATCAAAATTTCAT-AGTATGGTTACCAAAATTTCATAGGA
* * * ** *
5191 TGGTTA-CCAAA--T--TAGGAAGGTTATTAAAATTTTATTATGGA
1 -GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCA-TA-GGA
* * * * *
5232 -GTAATCAAAATTTCA-AGGA-GGATATCAAAATTTCATATGAA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATA-GGA
* * * * ** * *
5273 GGTTATTAAAATTTTATAGTTTAGTTTTCAAATTTTCATAAGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGA
* *
5316 GGGTTATCAAAATTTCATAGTAT-GTAGATCAAAATTTCATAGGGA
1 -GGTTATCAAAATTTCATAGTATGGT-TACCAAAATTTCATA-GGA
* * * * ** *
5361 GATTAACAAAATTTCATAAAG-A-AGTTATCAAAAAATCATATGAA
1 GGTTATCAAAATTTCAT--AGTATGGTTACCAAAATTTCATA-GGA
* *
5405 GGTTATCAAAA-TT--T-GTA--GTTATCAAGATTTCATAAGGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCAT-AGGA
* * * * **
5443 GGTTATCAAAATTTTATAGGGA-GGTTTATCAAAATTTTATAACA
1 GGTTATCAAAATTTCATA-GTATGG-TTACCAAAATTTCATAGGA
* * * * ** *
5487 -TTTATCAAAATTTCATAGCAAGGTTATCGGAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAG-GA
* * * * * *
5530 GATTATCAAAATTTCAGAGTGTGATTACTAACAA-TTCGTATGGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAA-AATTTCATA-GGA
* * * *** * * * *
5574 GGTTTTTAAATTTTCATAACGTGGTAATCAATATGTCATATGGA
1 GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATA-GGA
* * * * *
5618 GGTTATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGA
1 GGTTATCAAAATTTCATAGT-ATGGTTACCAAAATTTCA-TAGGA
* ** * *
5663 AGTTATCAAAATTTCATAGTGA-GGTTTTCAAAATTCCTTAGGGA
1 GGTTATCAAAATTTCATAGT-ATGGTTACCAAAATTTCATA-GGA
*
5707 GGTTAACAAAATTT
1 GGTTATCAAAATTT
5721 TATAAGAAGG
Statistics
Matches: 834, Mismatches: 202, Indels: 188
0.68 0.17 0.15
Matches are distributed among these distances:
33 5 0.01
34 33 0.04
35 4 0.00
36 4 0.00
37 5 0.01
38 32 0.04
39 24 0.03
40 15 0.02
41 13 0.02
42 58 0.07
43 81 0.10
44 392 0.47
45 69 0.08
46 55 0.07
47 17 0.02
48 15 0.02
49 1 0.00
50 9 0.01
51 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGTATGGTTACCAAAATTTCATAGGA
Found at i:5657 original size:23 final size:22
Alignment explanation
Indices: 5235--5720 Score: 238
Period size: 22 Copynumber: 22.5 Consensus size: 22
5225 TTATGGAGTA
*
5235 ATCAAAATTTCA-AG-GAGGAT
1 ATCAAAATTTCATAGTGAGGTT
5255 ATCAAAATTTCATA-TGAAGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* * *
5277 ATTAAAATTTTATAGTTTA-GTT
1 ATCAAAATTTCATAG-TGAGGTT
* * *
5299 TTCAAATTTTCATA-AGAGGGTT
1 ATCAAAATTTCATAGTGA-GGTT
* *
5321 ATCAAAATTTCATAGT-ATGTAG
1 ATCAAAATTTCATAGTGAGGT-T
* *
5343 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGTGAGGTT
* ** *
5365 AACAAAATTTCATAAAGAAGTT
1 ATCAAAATTTCATAGTGAGGTT
**
5387 ATCAAAAAATCATA-TGAAGGTT
1 ATCAAAATTTCATAGTG-AGGTT
5409 ATCAAAA-TT--T-GT-A-GTT
1 ATCAAAATTTCATAGTGAGGTT
*
5425 ATCAAGATTTCATAAG-GAGGTT
1 ATCAAAATTTCAT-AGTGAGGTT
* *
5447 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGTGAGG-TT
* ** *
5470 ATCAAAATTTTATA-ACA-TTT
1 ATCAAAATTTCATAGTGAGGTT
**
5490 ATCAAAATTTCATAGCAAGGTT
1 ATCAAAATTTCATAGTGAGGTT
** * *
5512 ATCGGAATTTCATAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
* * *
5534 ATCAAAATTTCAGAGTGTGATT
1 ATCAAAATTTCATAGTGAGGTT
*
5556 A-CTAACAA-TTCGTA-TGGAGGTT
1 ATC-AA-AATTTCATAGT-GAGGTT
* * * ** * *
5578 TTTAAATTTTCATAACGTGGTA
1 ATCAAAATTTCATAGTGAGGTT
* *
5600 ATCAATATGTCATA-TGGAGGTT
1 ATCAAAATTTCATAGT-GAGGTT
* * *
5622 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAGTG-AGGTT
* * *
5645 ATCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAGTGAGGTT
5667 ATCAAAATTTCATAGTGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
* * * *
5689 TTCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATAGTGAGGTT
*
5711 AACAAAATTT
1 ATCAAAATTT
5721 TATAAGAAGG
Statistics
Matches: 347, Mismatches: 87, Indels: 62
0.70 0.18 0.12
Matches are distributed among these distances:
16 9 0.03
17 3 0.01
19 3 0.01
20 28 0.08
21 14 0.04
22 250 0.72
23 39 0.11
24 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATAGTGAGGTT
Found at i:5731 original size:22 final size:22
Alignment explanation
Indices: 5706--5754 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5696 TTCCTTAGGG
*
5706 AGGTTAACAAAAT-TTTATAAGA
1 AGGTTAA-AAAATATTTATAAAA
*
5728 AGGTTAAAATATATTTATAAAA
1 AGGTTAAAAAATATTTATAAAA
5750 AGGTT
1 AGGTT
5755 CTCGAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (22 bp):
AGGTTAAAAAATATTTATAAAA
Found at i:5732 original size:44 final size:44
Alignment explanation
Indices: 5641--5733 Score: 100
Period size: 44 Copynumber: 2.1 Consensus size: 44
5631 TCATAGTGTT
* *
5641 GGTTATCAAAATTTCATTGGGAAGTTATCAAAATTTCATAGTGA
1 GGTTATCAAAATTTCATTGGGAAGTTAACAAAATTTCATAGTAA
* * * *
5685 GGTTTTCAAAA-TTCCTTAGGGAGGTTAACAAAATTTTATAAG-AA
1 GGTTATCAAAATTTCATT-GGGAAGTTAACAAAATTTCAT-AGTAA
5729 GGTTA
1 GGTTA
5734 AAATATATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
43 5 0.12
44 33 0.82
45 2 0.05
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTTCATTGGGAAGTTAACAAAATTTCATAGTAA
Found at i:6545 original size:16 final size:16
Alignment explanation
Indices: 6524--6579 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
6514 GCCGCCCCAC
6524 TTGGGCGGCTTCACCA
1 TTGGGCGGCTTCACCA
** *
6540 TTGGGCAGGCCGCCCCA
1 TTGGGC-GGCTTCACCA
6557 CTTGGGCGGCTTCACCA
1 -TTGGGCGGCTTCACCA
6574 TTGGGC
1 TTGGGC
6580 AGGCCGCCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 12 0.38
17 14 0.44
18 6 0.19
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.21
Consensus pattern (16 bp):
TTGGGCGGCTTCACCA
Found at i:6550 original size:34 final size:33
Alignment explanation
Indices: 6450--6654 Score: 245
Period size: 34 Copynumber: 6.2 Consensus size: 33
6440 GATGACCCGT
**
6450 GCCGCCCCAAGAGGGCGGCTT-ACCATGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
** *
6482 GCCGCCCCAAGAGGACGGCTT-ACCATGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
*
6514 GCCGCCCCACTTGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCA-TGGGCAG
*
6548 GCCGCCCCACTTGGGCGGCTTCACCATTGGGCAG
1 GCCGCCCCACTAGGGCGGCTTCACCA-TGGGCAG
* * ***
6582 GCCGCCCCACTGGGGCGGCTTCACTATGAATAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
* *
6615 GCCGCCCCACTAGGGCGGCTTCGCCA-GGGTAG
1 GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
6647 GCCGCCCC
1 GCCGCCCC
6655 GGTGGGGGCG
Statistics
Matches: 156, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
32 60 0.38
33 31 0.20
34 65 0.42
ACGTcount: A:0.15, C:0.38, G:0.34, T:0.14
Consensus pattern (33 bp):
GCCGCCCCACTAGGGCGGCTTCACCATGGGCAG
Found at i:6631 original size:67 final size:67
Alignment explanation
Indices: 6462--6654 Score: 225
Period size: 67 Copynumber: 2.9 Consensus size: 67
6452 CGCCCCAAGA
** ** *
6462 GGGCGGCTT-ACCA-TGGGCAGGCCGCCCCAAGAGGACGGCTT-ACCATGGGCAGGCCGCCCCAC
1 GGGCGGCTTCACCATTGAACAGGCCGCCCCACTAGGGCGGCTTCACCATGGGCAGGCCGCCCCAC
*
6524 TT
66 TG
** *
6526 GGGCGGCTTCACCATTGGGCAGGCCGCCCCACTTGGGCGGCTTCACCATTGGGCAGGCCGCCCCA
1 GGGCGGCTTCACCATTGAACAGGCCGCCCCACTAGGGCGGCTTCACCA-TGGGCAGGCCGCCCCA
6591 CTG
65 CTG
* * * *
6594 GGGCGGCTTCACTA-TGAATAGGCCGCCCCACTAGGGCGGCTTCGCCA-GGGTAGGCCGCCCC
1 GGGCGGCTTCACCATTGAACAGGCCGCCCCACTAGGGCGGCTTCACCATGGGCAGGCCGCCCC
6655 GGTGGGGGCG
Statistics
Matches: 113, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
64 9 0.08
65 17 0.15
66 24 0.21
67 32 0.28
68 31 0.27
ACGTcount: A:0.15, C:0.37, G:0.34, T:0.15
Consensus pattern (67 bp):
GGGCGGCTTCACCATTGAACAGGCCGCCCCACTAGGGCGGCTTCACCATGGGCAGGCCGCCCCAC
TG
Done.