Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013257.1 Corchorus capsularis cultivar CVL-1 contig13278, 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: 14779
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:151 original size:26 final size:26
Alignment explanation
Indices: 85--152 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 26
75 TACTTAGTTT
85 ATTAGTTTATG-TTCAATTAGTATCTA
1 ATTAGTTTATGATT-AATTAGTATCTA
* *
111 ATTAGTTTATTATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATCTA
*
137 ATTAATTTATGATTAA
1 ATTAGTTTATGATTAA
153 AATGAAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 35 0.95
27 2 0.05
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATCTA
Found at i:200 original size:24 final size:25
Alignment explanation
Indices: 161--220 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
151 AAAATGAAGG
*
161 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
184 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
209 GAAATTAAGTTT
1 AAAATGAAGTTT
221 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:2202 original size:5 final size:5
Alignment explanation
Indices: 2192--2245 Score: 66
Period size: 5 Copynumber: 12.0 Consensus size: 5
2182 CACCATTAAT
2192 GAATG GAATG GAATG G-AT- GAAT- GAAT- GAAT- GAAT- GAATG GAATG
1 GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG GAATG
2236 GAATG GAATG
1 GAATG GAATG
2246 AGTTGCAAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 1 0.02
4 20 0.43
5 26 0.55
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (5 bp):
GAATG
Found at i:2215 original size:4 final size:4
Alignment explanation
Indices: 2189--2246 Score: 62
Period size: 4 Copynumber: 13.2 Consensus size: 4
2179 TTCCACCATT
*
2189 AATG AATGG AATGG AATG GATG AATG AATG AATG AATG AATGG AATGG
1 AATG AAT-G AAT-G AATG AATG AATG AATG AATG AATG AAT-G AAT-G
2237 AATGG AATG A
1 AAT-G AATG A
2247 GTTGCAAACA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 27 0.54
5 23 0.46
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.22
Consensus pattern (4 bp):
AATG
Found at i:4131 original size:31 final size:32
Alignment explanation
Indices: 4066--4133 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
4056 CGTCAATGAT
* *
4066 AAAATGTCTTGAATTTGGGAAGTTCAGGGAGC
1 AAAATATCCTGAATTTGGGAAGTTCAGGGAGC
*
4098 AAAATATCCTGAATTT-GGAAGTTTA-GGAGGC
1 AAAATATCCTGAATTTGGGAAGTTCAGGGA-GC
4129 AAAAT
1 AAAAT
4134 GTCATGATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 3 0.09
31 15 0.47
32 14 0.44
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (32 bp):
AAAATATCCTGAATTTGGGAAGTTCAGGGAGC
Found at i:9601 original size:45 final size:44
Alignment explanation
Indices: 9537--9623 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 44
9527 AAGTTACAGG
* *
9537 GAGTTTATCATAATTTTATAGTG-AGGTCTATCAAAATTTCATAAA
1 GAGTTCATCACAATTTTATAG-GAAGGT-TATCAAAATTTCATAAA
9582 GAGTTCATCACAATTTTATAGGAAGGTTATCAAAATTTCATA
1 GAGTTCATCACAATTTTATAGGAAGGTTATCAAAATTTCATA
9624 GTGTGGTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
44 16 0.41
45 23 0.59
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (44 bp):
GAGTTCATCACAATTTTATAGGAAGGTTATCAAAATTTCATAAA
Found at i:9631 original size:22 final size:22
Alignment explanation
Indices: 9541--10003 Score: 158
Period size: 22 Copynumber: 20.7 Consensus size: 22
9531 TACAGGGAGT
* *
9541 TTATCATAATTTTATAGTGAGG
1 TTATCAAAATTTCATAGTGAGG
**
9563 TCTATCAAAATTTCATAAAGA-G
1 T-TATCAAAATTTCATAGTGAGG
* *
9585 TTCATCACAATTTTATAG-GAAGG
1 TT-ATCAAAATTTCATAGTG-AGG
*
9608 TTATCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
9630 TTACCATTTACCAACATTTTATAGGGATG
1 TT---A--T--CAAAATTTCATAGTGAGG
*
9659 TTATCGAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
*
9681 -T-T-----TTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
9696 TTATCAAAATTTTATTGAGTGG
1 TTATCAAAATTTCATAGTGAGG
** * * * *
9718 AGATCCAAATTTCATTGGGAGA
1 TTATCAAAATTTCATAGTGAGG
* *
9740 TTATCAAAATTTCACATTGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
9762 TTATCAAAGTTTTATAGAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
9784 TTAACAAAATTTCATTGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* ** * *
9806 TTATCGATTTTTCATTGTCTGGAAGA
1 TTATCAAAATTTCATAG--T-G-AGG
* * *
9832 TTATCAAAATTTCATAATAAAG
1 TTATCAAAATTTCATAGTGAGG
* *
9854 TAATCAAAATTTTCATAGTGAAG
1 TTATCAAAA-TTTCATAGTGAGG
* *
9877 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * *
9899 TTATC-AAATTTTATAGGGAGA
1 TTATCAAAATTTCATAGTGAGG
* *
9920 TTATCAAAATTTTATAGTGTAGTAC
1 TTATCAAAATTTCATAGTG-AG--G
* * ** *
9945 TTACCATAATTTCAT-GAAAAG
1 TTATCAAAATTTCATAGTGAGG
***
9966 TTATCAAAATTTCATAGTGTTT
1 TTATCAAAATTTCATAGTGAGG
*
9988 TTATAAAAATTTCATA
1 TTATCAAAATTTCATA
10004 TGAATATTTA
Statistics
Matches: 319, Mismatches: 91, Indels: 62
0.68 0.19 0.13
Matches are distributed among these distances:
15 9 0.03
16 3 0.01
17 1 0.00
20 1 0.00
21 34 0.11
22 183 0.57
23 40 0.13
24 3 0.01
25 14 0.04
26 15 0.05
27 1 0.00
29 15 0.05
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:9869 original size:23 final size:22
Alignment explanation
Indices: 9834--9892 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 22
9824 CTGGAAGATT
9834 ATCAAAATTTCATAATAAAGTA
1 ATCAAAATTTCATAATAAAGTA
* * *
9856 ATCAAAATTTTCATAGTGAAGTT
1 ATCAAAA-TTTCATAATAAAGTA
*
9879 ATCGAAATTTCATA
1 ATCAAAATTTCATA
9893 GTGTGGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 14 0.44
23 18 0.56
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAATAAAGTA
Found at i:10187 original size:31 final size:31
Alignment explanation
Indices: 10146--10211 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
10136 AACTTTATAT
* *
10146 TTTCCGATTGTACCCTTATTTTT-GAAACATA
1 TTTCCAATTGTACCCTT-TTTTTAAAAACATA
10177 TTTCCAATTGTACCCTTTTTTTAAAAACATA
1 TTTCCAATTGTACCCTTTTTTTAAAAACATA
10208 TTTC
1 TTTC
10212 TAAATTACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.27, C:0.20, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTTTTTTAAAAACATA
Found at i:10408 original size:19 final size:20
Alignment explanation
Indices: 10381--10418 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
10371 TACTATTATT
10381 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
10401 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
10419 AATATCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:10660 original size:44 final size:43
Alignment explanation
Indices: 10591--10711 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 43
10581 ATCTCTATGT
* ** ** *
10591 GGTTATCAAAATTTCATAAGATGGTTATTATGATTTCATGA-GGA
1 GGTTATCAAAATTTCATATG-TGGTTACCAAAACTTCAT-ATGGA
*
10635 GGTTATCAAAATTCCATATTGTGGTTACCAAAACTTCATATGGA
1 GGTTATCAAAATTTCATA-TGTGGTTACCAAAACTTCATATGGA
*
10679 AGTTATCAAAATTTCATAGTGTGGTTACCAAAA
1 GGTTATCAAAATTTCATA-TGTGGTTACCAAAA
10712 TTTCTTAGAA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
43 1 0.02
44 63 0.97
45 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (43 bp):
GGTTATCAAAATTTCATATGTGGTTACCAAAACTTCATATGGA
Found at i:10753 original size:22 final size:23
Alignment explanation
Indices: 10591--10773 Score: 87
Period size: 22 Copynumber: 8.2 Consensus size: 23
10581 ATCTCTATGT
10591 GGTTATCAAAATTTCATA-AGAT-
1 GGTTATCAAAATTTCATAGAG-TC
* ** **
10613 GGTTATTATGATTTCAT-GAGGA
1 GGTTATCAAAATTTCATAGAGTC
* **
10635 GGTTATCAAAATTCCATATTGT-
1 GGTTATCAAAATTTCATAGAGTC
* * *
10657 GGTTACCAAAACTTCATATG-G-A
1 GGTTATCAAAATTTCATA-GAGTC
* *
10679 AGTTATCAAAATTTCATAGTGT-
1 GGTTATCAAAATTTCATAGAGTC
* * *
10701 GGTTACCAAAATTTCTTAGAATC
1 GGTTATCAAAATTTCATAGAGTC
* *
10724 AGGTTATTAAAATTTCTTAG-GTC
1 -GGTTATCAAAATTTCATAGAGTC
** *
10747 GGTTATTGAAATTTCATAGGGT-
1 GGTTATCAAAATTTCATAGAGTC
10769 GGTTA
1 GGTTA
10774 ATTGTCACAA
Statistics
Matches: 123, Mismatches: 28, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
21 1 0.01
22 100 0.81
23 5 0.04
24 17 0.14
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (23 bp):
GGTTATCAAAATTTCATAGAGTC
Found at i:10941 original size:44 final size:42
Alignment explanation
Indices: 10809--11560 Score: 193
Period size: 44 Copynumber: 17.8 Consensus size: 42
10799 ACCAAAGAGA
* * * *
10809 TTATCAAAATGTCATAGCGAGGTAATAAAAATTTCATATGTGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATATGAGG
* * **
10852 TTAACAAAATTTCATTAGGAGGTTA-CTAATATTTCATGGGGAGG
1 TTATCAAAATTTCA-TAGGAGGTTATC-AAAATTTCAT-ATGAGG
* *
10896 TTATCAAAATTTTATAGTGTGGTTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATATG-AGG
* * * * * *
10940 TTATAAAAGTCTCATTTTCATAAGAAG-TACCAAAATTTGATA-GAAGA
1 TTATCAAA-----A-TTTCATAGGAGGTTATCAAAATTTCATATG-AGG
* *
10987 TTATC-AAATCTCATA-GAGTGATTATCGAAATTTCATA-GAGATCAG
1 TTATCAAAATTTCATAGGAG-G-TTATCAAAATTTCATATGAG----G
* * **
11032 ATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTG
1 -TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCATA-TGAGG
* * * * * *
11076 TTATGAAAATTTCAAAGCGAGATTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCAT-ATGAGG
* * * * *
11120 TTATCAGAAA-TTCATAGAGGGGTCAACAAAATTTTATAAAGAGG
1 TTATCA-AAATTTCATAG-GAGGTTATCAAAATTTCAT-ATGAGG
* * * * *
11164 TTATCAAAATTTCAAAATGTGATTA-CAAAAATTTCATA-GTGG
1 TTATCAAAATTTC-ATAGGAGGTTATC-AAAATTTCATATGAGG
**
11206 -TAT-----TTTC-GGGGAGGTTATCAAAATTTCATA-GTATGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATATG-A-GG
* * * *
11242 TTA-CCAAA--T--TAGGAAGGTTATTAAACTTTTATTATG-GAG
1 TTATCAAAATTTCATAGG-AGGTTATCAAAATTTCA-TATGAG-G
* * * * **
11281 TAATCAGAATTTCA-AGGATGATATCAAAA-TTCA-GGGAGG
1 TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATATGAGG
* *
11320 ATATCAAAATTTCATATGAAGGTTATC-AAA----AT-T-A-G
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATATGAGG
* * *
11355 TTTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATA-GTATG
1 TTATCAAAATTTCATAGGA-GGTTATCAAAATTTCATATG-AGG
* * *
11398 TAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG
1 T-TATCAAAATTTCATA-GGAGGTTATCAAAATTTCAT-ATGAGG
* *
11443 TTATCAAAA-ATCATAGGGAGGTTATCAAAA-TT--TGT-A-G
1 TTATCAAAATTTCATA-GGAGGTTATCAAAATTTCATATGAGG
* * * * * *
11480 TTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCAT-AGGAGGTTATCAAAATTTCATATG-AG-G
* *
11525 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCA
1 TTATCAAAATTTCATAG-GAGGTTATCAAAATTTCA
11561 GAGTGTGACT
Statistics
Matches: 515, Mismatches: 117, Indels: 152
0.66 0.15 0.19
Matches are distributed among these distances:
34 18 0.03
35 23 0.04
36 10 0.02
37 12 0.02
38 20 0.04
39 37 0.07
40 20 0.04
41 18 0.03
42 28 0.05
43 71 0.14
44 154 0.30
45 40 0.08
46 26 0.05
47 13 0.03
48 16 0.03
49 3 0.01
50 6 0.01
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (42 bp):
TTATCAAAATTTCATAGGAGGTTATCAAAATTTCATATGAGG
Found at i:10943 original size:22 final size:22
Alignment explanation
Indices: 10809--10947 Score: 101
Period size: 22 Copynumber: 6.4 Consensus size: 22
10799 ACCAAAGAGA
*
10809 TTATCAAAATGTCATA-GCGAGG
1 TTATCAAAATTTCATATG-GAGG
* * *
10831 TAATAAAAATTTCATAT-GTGG
1 TTATCAAAATTTCATATGGAGG
*
10852 TTAACAAAATTTCAT-TAGGAGG
1 TTATCAAAATTTCATAT-GGAGG
* **
10874 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATATGGAGG
* *
10896 TTATCAAAATTTTATA-GTGTGG
1 TTATCAAAATTTCATATG-GAGG
*
10918 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATATGGAGG
10940 TTAT-AAAA
1 TTATCAAAA
10948 GTCTCATTTT
Statistics
Matches: 92, Mismatches: 17, Indels: 17
0.73 0.13 0.13
Matches are distributed among these distances:
20 1 0.01
21 21 0.23
22 68 0.74
23 2 0.02
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGAGG
Found at i:11022 original size:22 final size:22
Alignment explanation
Indices: 10970--11202 Score: 149
Period size: 22 Copynumber: 10.6 Consensus size: 22
10960 TAAGAAGTAC
* *
10970 CAAAATTTGATAGA-AGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
10991 C-AAATCTCATAGAGTGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
11012 CGAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAG-T--GATTAT
**
11037 CAAAATTT-ATAGAAAGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
11058 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAGAG-TGATTAT
* * * *
11080 GAAAATTTCAAAGCGAGATTAT
1 CAAAATTTCATAGAGTGATTAT
*
11102 CAAAATTACATA-ATGTGATTAT
1 CAAAATTTCATAGA-GTGATTAT
* * * *
11124 CAGAAA-TTCATAGAGGGGTCAA
1 CA-AAATTTCATAGAGTGATTAT
* * * *
11146 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAGAGTGATTAT
*
11168 CAAAATTTCA-AAATGTGATTA-
1 CAAAATTTCATAGA-GTGATTAT
11189 CAAAAATTTCATAG
1 C-AAAATTTCATAG
11203 TGGTATTTTC
Statistics
Matches: 164, Mismatches: 33, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
20 10 0.06
21 30 0.18
22 99 0.60
23 7 0.04
24 5 0.03
25 13 0.08
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAGAGTGATTAT
Found at i:11311 original size:20 final size:20
Alignment explanation
Indices: 11283--11352 Score: 70
Period size: 19 Copynumber: 3.5 Consensus size: 20
11273 TTATGGAGTA
* *
11283 ATCAGAATTTCAAGGATGAT
1 ATCAAAATTTCAAGGAGGAT
*
11303 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
* *
11322 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCA-A-GGAGGAT
11344 ATCAAAATT
1 ATCAAAATT
11353 AGTTTTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 17 0.41
20 10 0.24
22 14 0.34
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:11463 original size:21 final size:22
Alignment explanation
Indices: 11358--11560 Score: 136
Period size: 22 Copynumber: 9.5 Consensus size: 22
11348 AAATTAGTTT
*
11358 TCAAAATTTCATA-AGAGGGTTA
1 TCAAAATTTCATAGGGA-GGTTA
* * *
11380 TCAAAATTTCATA-GTATGTAGA
1 TCAAAATTTCATAGGGAGGT-TA
*
11402 TCAAAATTTCATAGGGAGATTA
1 TCAAAATTTCATAGGGAGGTTA
* **
11424 ACAAAATTTCATAATGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
11446 TCAAAA-ATCATAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
11467 TCAAAA-TT--T--GTA-GTTA
1 TCAAAATTTCATAGGGAGGTTA
* * * *
11483 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
11505 TCAAAATTTTATAGGAAGATTTA
1 TCAAAATTTCATAGGGAG-GTTA
* * *
11528 TCAAAATTTCATAGTGTGATTA
1 TCAAAATTTCATAGGGAGGTTA
11550 TCAAAATTTCA
1 TCAAAATTTCA
11561 GAGTGTGACT
Statistics
Matches: 142, Mismatches: 30, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
16 9 0.06
17 4 0.03
19 2 0.01
21 23 0.16
22 84 0.59
23 20 0.14
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTTA
Found at i:11505 original size:125 final size:124
Alignment explanation
Indices: 11316--11560 Score: 305
Period size: 125 Copynumber: 2.0 Consensus size: 124
11306 AAAATTCAGG
* * * **
11316 GAGGATATCAAAATTTCATATGAAGGTTATCAAAATTAGTTTTCAAAATTTCATAAGAGGGTTAT
1 GAGGATATCAAAATATCATAGGAAGGTTATCAAAATTAGTTATCAAAATTTCATAAGAAAGTTAT
* *
11381 CAAAATTTCATAGTATG-TAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
66 CAAAATTTCATAGGAAGATAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
* * *
11439 GAGGTTATCAAAA-ATCATAGGGAGGTTATCAAAATTTGTAGTTATCAAGATTTCATAAGAAAGT
1 GAGGATATCAAAATATCATAGGAAGGTTATCAAAA--T-TAGTTATCAAAATTTCATAAGAAAGT
* ** * * *
11503 TATCAAAATTTTATAGGAAGATTTATCAAAATTTCATAGTGTGATTATCAAAATTTCA
63 TATCAAAATTTCATAGGAAGATAGATCAAAATTTCATAGGGAGATTAACAAAATTTCA
11561 GAGTGTGACT
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
122 18 0.18
123 12 0.12
124 1 0.01
125 39 0.38
126 32 0.31
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (124 bp):
GAGGATATCAAAATATCATAGGAAGGTTATCAAAATTAGTTATCAAAATTTCATAAGAAAGTTAT
CAAAATTTCATAGGAAGATAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
Found at i:11565 original size:22 final size:22
Alignment explanation
Indices: 11525--11568 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
11515 ATAGGAAGAT
*
11525 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
11547 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTGTGA
11569 CTACTAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTGTGA
Found at i:11735 original size:22 final size:22
Alignment explanation
Indices: 11710--11816 Score: 74
Period size: 22 Copynumber: 4.9 Consensus size: 22
11700 TCCTTAGGGC
*
11710 GGTTAACAAAATTTCATAAGAA
1 GGTTATCAAAATTTCATAAGAA
** *
11732 GGTTAAAAAAAATTT-ATAAAAA
1 GGTT-ATCAAAATTTCATAAGAA
* ** * *
11754 GGTTCTTGAAATTCCAT-AGTAT
1 GGTTATCAAAATTTCATAAG-AA
* * *
11776 CGTTATTAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGAA
11798 GGTTATCAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
11817 TGGGATCATA
Statistics
Matches: 63, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
21 6 0.10
22 47 0.75
23 10 0.16
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGAA
Found at i:11858 original size:22 final size:22
Alignment explanation
Indices: 11830--11873 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
11820 GATCATAAAA
11830 AATAGTGTA-ATTATCATAATTT
1 AATAGTG-AGATTATCATAATTT
*
11852 AATAGTGAGTTTATCATAATTT
1 AATAGTGAGATTATCATAATTT
11874 CATATGAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 1 0.05
22 19 0.95
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (22 bp):
AATAGTGAGATTATCATAATTT
Done.