Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012067.1 Kokia drynarioides strain JFW-HI SEQ_127065, 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: 74724
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:108 original size:2 final size:2
Alignment explanation
Indices: 101--130 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
91 TTAATATGAT
101 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
131 CCAAAAGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:681 original size:103 final size:103
Alignment explanation
Indices: 492--682 Score: 233
Period size: 103 Copynumber: 1.9 Consensus size: 103
482 ATACATTGGA
* * * * * **
492 CCTTTTGATGCGAAATGAAATGACACCCGAGCACTCCATCCTGGTTACTCAGCCTAACATGCTCT
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCTAACACACTCT
* * *
557 CAATTTTTTCTTCTCTTTTTTTTGTAGAATGTGTTAGT
66 CAATTTTTTATTCTATATTTTTTGTAGAATGTGTTAGT
* * *
595 CCTTTTGACGCGAAGTGAAATGACAACTAAGCACTCCACCCCGGTTACTCAGTCTAACACACTC-
1 CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCTAACACACTCT
659 CGAATTTATTTATT-TATATTTTTT
66 C-AATTT-TTTATTCTATATTTTTT
683 TCTTTTTTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
102 1 0.01
103 67 0.92
104 5 0.07
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (103 bp):
CCTTTTGACGCGAAATGAAATGACAACCAAGCACTCCACCCCGGTTACTCAGCCTAACACACTCT
CAATTTTTTATTCTATATTTTTTGTAGAATGTGTTAGT
Found at i:1455 original size:13 final size:12
Alignment explanation
Indices: 1432--1496 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
1422 TTCCTGGAAA
1432 AAAATAAATAAAT
1 AAAATAAA-AAAT
1445 -AAAT--AAAAT
1 AAAATAAAAAAT
*
1454 AAGATAGAAAAAT
1 AAAATA-AAAAAT
1467 AAAATAAAAAATT
1 AAAATAAAAAA-T
*
1480 AAATTAAAAAAAT
1 AAAAT-AAAAAAT
1493 AAAA
1 AAAA
1497 ATAATTGGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.10
10 4 0.10
12 9 0.21
13 19 0.45
14 6 0.14
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:1466 original size:18 final size:17
Alignment explanation
Indices: 1432--1495 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 17
1422 TTCCTGGAAA
1432 AAAATAAATAAATAAAT
1 AAAATAAATAAATAAAT
1449 AAAATAAGATAGAA-AAAT
1 AAAATAA-ATA-AATAAAT
1467 AAAATAAA-AAATTAAATT
1 AAAATAAATAAA-TAAA-T
1485 AAAA-AAATAAA
1 AAAATAAATAAA
1496 AATAATTGGA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.05
16 1 0.02
17 14 0.34
18 22 0.54
19 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAATAAATAAATAAAT
Found at i:6438 original size:21 final size:22
Alignment explanation
Indices: 6414--6460 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
6404 CAATTTAAGG
6414 AAAAATAAAAGAA-ATAGAATT
1 AAAAATAAAAGAAGATAGAATT
6435 AAAAATAAAAGAAGATAGAATT
1 AAAAATAAAAGAAGATAGAATT
6457 AAAA
1 AAAA
6461 GAAATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAGATAGAATT
Found at i:6469 original size:15 final size:16
Alignment explanation
Indices: 6440--6469 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6430 GAATTAAAAA
6440 TAAAAGAAGATAGAAT
1 TAAAAGAAGATAGAAT
6456 TAAAAGAA-ATAGAA
1 TAAAAGAAGATAGAA
6470 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (16 bp):
TAAAAGAAGATAGAAT
Found at i:6469 original size:22 final size:19
Alignment explanation
Indices: 6415--6470 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 19
6405 AATTTAAGGA
6415 AAAATAAAAGAAATAGAATT
1 AAAA-AAAAGAAATAGAATT
6435 AAAAATAAAAGAAGATAGAATT
1 -AAAA-AAAAGAA-ATAGAATT
6457 AAAAGAAATAGAAA
1 AAAA-AAA-AGAAA
6471 ATAGGGAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 20 0.62
22 12 0.38
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.16
Consensus pattern (19 bp):
AAAAAAAAGAAATAGAATT
Found at i:6474 original size:22 final size:22
Alignment explanation
Indices: 6414--6474 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
6404 CAATTTAAGG
6414 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
6435 AAAAATAAAAGAAGATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
6457 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
6475 GGAAGTCGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 23 0.66
23 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:7547 original size:23 final size:24
Alignment explanation
Indices: 7521--7565 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
7511 ATGATCATAC
7521 TCTAAAAATATAT-ATATTTAATA
1 TCTAAAAATATATCATATTTAATA
* *
7544 TCTAAAAGTATGTCATATTTAA
1 TCTAAAAATATATCATATTTAA
7566 GCATTATCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (24 bp):
TCTAAAAATATATCATATTTAATA
Found at i:11298 original size:31 final size:31
Alignment explanation
Indices: 11262--11320 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
11252 ATAAAAAATG
*
11262 TATAAAAATATT-AAATATTAAAATAATATAA
1 TATAAAAATATTAAAAAATTAAAA-AATATAA
* *
11293 TATAAATATTTTAAAAAATTAAAAAATA
1 TATAAAAATATTAAAAAATTAAAAAATA
11321 ATATGGTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 14 0.58
32 10 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
TATAAAAATATTAAAAAATTAAAAAATATAA
Found at i:11615 original size:20 final size:20
Alignment explanation
Indices: 11592--11637 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
11582 TAATCAACGT
*
11592 AATAAATATT-TAATAAATAA
1 AATAAAT-TTCTAATAAAAAA
11612 AAT-AATTTCTAATAAAAAA
1 AATAAATTTCTAATAAAAAA
11631 ACATAAA
1 A-ATAAA
11638 ATAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
18 2 0.09
19 13 0.59
20 5 0.23
21 2 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAAATTTCTAATAAAAAA
Found at i:12336 original size:82 final size:82
Alignment explanation
Indices: 12199--12363 Score: 321
Period size: 82 Copynumber: 2.0 Consensus size: 82
12189 TTCGATATCT
*
12199 TTATGAGTTTCACTTTTCTTGTTTTTAATTACGAACTCTTATCTTCTTCAATTCTTCTTTAGGTC
1 TTATGAATTTCACTTTTCTTGTTTTTAATTACGAACTCTTATCTTCTTCAATTCTTCTTTAGGTC
12264 AACCTCTCAGTGTCTAC
66 AACCTCTCAGTGTCTAC
12281 TTATGAATTTCACTTTTCTTGTTTTTAATTACGAACTCTTATCTTCTTCAATTCTTCTTTAGGTC
1 TTATGAATTTCACTTTTCTTGTTTTTAATTACGAACTCTTATCTTCTTCAATTCTTCTTTAGGTC
12346 AACCTCTCAGTGTCTAC
66 AACCTCTCAGTGTCTAC
12363 T
1 T
12364 CCATTAATTT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.49
Consensus pattern (82 bp):
TTATGAATTTCACTTTTCTTGTTTTTAATTACGAACTCTTATCTTCTTCAATTCTTCTTTAGGTC
AACCTCTCAGTGTCTAC
Found at i:14674 original size:23 final size:23
Alignment explanation
Indices: 14648--14931 Score: 320
Period size: 23 Copynumber: 12.3 Consensus size: 23
14638 CTTATATTCA
14648 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
*
14671 TGCTCAAATATTAATGA-GATTTG
1 TGCTTAAATATTAAT-ATGATTTG
*
14694 TGCTCAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * * *
14717 CG-TTCACATATTAATGTGATTTA
1 TGCTT-AAATATTAATATGATTTG
*
14740 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
14763 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * * * *
14786 TTCTCAAATACTAATGTGACTTG
1 TGCTTAAATATTAATATGATTTG
* * *
14809 TGCTCAGATATTATTATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * * * *
14832 TACTCAAATATTAATGTAATTTA
1 TGCTTAAATATTAATATGATTTG
*
14855 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
14878 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
14901 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
14924 TGCTTAAA
1 TGCTTAAA
14932 AAATTAAGAT
Statistics
Matches: 220, Mismatches: 37, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
22 2 0.01
23 215 0.98
24 3 0.01
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTG
Found at i:14801 original size:115 final size:115
Alignment explanation
Indices: 14648--14927 Score: 434
Period size: 115 Copynumber: 2.4 Consensus size: 115
14638 CTTATATTCA
*
14648 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGAGATTTGTGCTCAAATATTAATATGA
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTGTGCTCAAATATTAATATGA
** * *
14713 TTTGCGTTCACATATTAATGTGATTTATGCTTAAATATTAATGTGATTTG
66 TTTGCACTCAAATATTAATGTAATTTATGCTTAAATATTAATGTGATTTG
* * * * *
14763 TGCTTAAATATTAATATGATTTGTTCTCAAATACTAATGTGACTTGTGCTCAGATATTATTATGA
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTGTGCTCAAATATTAATATGA
*
14828 TTTGTACTCAAATATTAATGTAATTTATGCTTAAATATTAATGTGATTTG
66 TTTGCACTCAAATATTAATGTAATTTATGCTTAAATATTAATGTGATTTG
* * *
14878 TGCTTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTGTGCT
1 TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTGTGCT
14928 TAAAAAATTA
Statistics
Matches: 148, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
115 148 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.45
Consensus pattern (115 bp):
TGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGTGATTTGTGCTCAAATATTAATATGA
TTTGCACTCAAATATTAATGTAATTTATGCTTAAATATTAATGTGATTTG
Found at i:16981 original size:15 final size:15
Alignment explanation
Indices: 16963--17009 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
16953 CAGCTAATTT
*
16963 TTTCTCAACATCTTC
1 TTTCTCAGCATCTTC
16978 TTTCTCAGCATCTTC
1 TTTCTCAGCATCTTC
*
16993 TTTTTCAGCATCTTC
1 TTTCTCAGCATCTTC
17008 TT
1 TT
17010 CCTCCTCCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.15, C:0.30, G:0.04, T:0.51
Consensus pattern (15 bp):
TTTCTCAGCATCTTC
Found at i:34892 original size:45 final size:44
Alignment explanation
Indices: 34841--34945 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 44
34831 TAATTGCATA
*
34841 TCGACATAAGTGAGTTATCGTTATCAGGCAACCCAAGGTTGCAAT
1 TCGACATAAGTGAGTT-TCGTTATCAGGCAACCCAAGGTAGCAAT
* * ** *
34886 TTGACATAAGTGAGCTTTTGTTATTGGGCAACCCAGGGTAGCAAT
1 TCGACATAAGTGAG-TTTCGTTATCAGGCAACCCAAGGTAGCAAT
* *
34931 TCAATATAAGTGAGT
1 TCGACATAAGTGAGT
34946 CATCTTTGCC
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
44 1 0.02
45 47 0.94
46 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (44 bp):
TCGACATAAGTGAGTTTCGTTATCAGGCAACCCAAGGTAGCAAT
Found at i:35228 original size:19 final size:19
Alignment explanation
Indices: 35186--35265 Score: 101
Period size: 19 Copynumber: 4.3 Consensus size: 19
35176 GAGATATTAA
*
35186 AATATGTGATATT--TGTG
1 AATATGTGAAATTGATGTG
35203 AAATATGTGAAATTGATGTG
1 -AATATGTGAAATTGATGTG
* * *
35223 AATATGAGACATTGATGAG
1 AATATGTGAAATTGATGTG
35242 AATATGTGAAATTGATGTG
1 AATATGTGAAATTGATGTG
35261 AATAT
1 AATAT
35266 CAAATGTGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
18 12 0.23
19 37 0.70
20 4 0.08
ACGTcount: A:0.39, C:0.01, G:0.24, T:0.36
Consensus pattern (19 bp):
AATATGTGAAATTGATGTG
Found at i:35262 original size:11 final size:9
Alignment explanation
Indices: 35185--35253 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
35175 TGAGATATTA
35185 AAATATGTG
1 AAATATGTG
* *
35194 ATATTTGTG
1 AAATATGTG
35203 AAATATGTG
1 AAATATGTG
35212 AAATTGATGTG
1 AAA-T-ATGTG
*
35223 -AATATGAG
1 AAATATGTG
*
35231 ACAT-TGATG
1 AAATATG-TG
35240 AGAATATGTG
1 A-AATATGTG
35250 AAAT
1 AAAT
35254 TGATGTGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
8 6 0.13
9 25 0.54
10 8 0.17
11 7 0.15
ACGTcount: A:0.41, C:0.01, G:0.23, T:0.35
Consensus pattern (9 bp):
AAATATGTG
Found at i:41269 original size:19 final size:18
Alignment explanation
Indices: 41245--41306 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
41235 ATATTTTTGG
41245 AATATGTGAAGTTGATGTA
1 AATATGTGAA-TTGATGTA
*
41264 AATATGTGGCATTGATGTA
1 AATATGT-GAATTGATGTA
* *
41283 AATATGTTAAATTGATGTG
1 AATATG-TGAATTGATGTA
41302 AATAT
1 AATAT
41307 CAAATGTGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 34 0.92
20 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.39
Consensus pattern (18 bp):
AATATGTGAATTGATGTA
Found at i:43838 original size:29 final size:29
Alignment explanation
Indices: 43774--43829 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
43764 TTTTTATTAC
* * * *
43774 AATAGAATTAATAAGTAAATACATATAAT
1 AATAAAATTAATAAATAAATACACAAAAT
43803 AATAAAATTAATAAATAAATACACAAA
1 AATAAAATTAATAAATAAATACACAAA
43830 CATTTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.04, T:0.27
Consensus pattern (29 bp):
AATAAAATTAATAAATAAATACACAAAAT
Found at i:46896 original size:17 final size:17
Alignment explanation
Indices: 46874--46907 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
46864 TGTTAGTAAG
*
46874 CATTGTCGTTGCATTTT
1 CATTGTCATTGCATTTT
46891 CATTGTCATTGCATTTT
1 CATTGTCATTGCATTTT
46908 AGTGTTAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.53
Consensus pattern (17 bp):
CATTGTCATTGCATTTT
Found at i:57479 original size:12 final size:12
Alignment explanation
Indices: 57462--57486 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57452 TGCTAAAGGG
57462 GGATTTATCTGA
1 GGATTTATCTGA
57474 GGATTTATCTGA
1 GGATTTATCTGA
57486 G
1 G
57487 TATCATAGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (12 bp):
GGATTTATCTGA
Found at i:61104 original size:30 final size:30
Alignment explanation
Indices: 61067--61134 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
61057 TGAACTTTCC
61067 CAAAAATTATGTTTTAACCCTCAAACTTTT
1 CAAAAATTATGTTTTAACCCTCAAACTTTT
* * *
61097 TAAAAATTATGTTTTGACCCTTAAACTTTT
1 CAAAAATTATGTTTTAACCCTCAAACTTTT
61127 CAAAAATT
1 CAAAAATT
61135 CAAAATTAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.41
Consensus pattern (30 bp):
CAAAAATTATGTTTTAACCCTCAAACTTTT
Found at i:65241 original size:18 final size:18
Alignment explanation
Indices: 65218--65253 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
65208 ATCATAAAAT
65218 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
65236 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
65254 TTTTTGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:69254 original size:68 final size:67
Alignment explanation
Indices: 69176--69388 Score: 266
Period size: 68 Copynumber: 3.1 Consensus size: 67
69166 TAGTCCAAAT
*
69176 ATGGTCTTATCATCAGAATGCCATAGC-CTAGCTATGGTCTTACATAAATACACTATCGTGGTCC
1 ATGGTCTTATCATCAGAATGCCATAGCTC-AGCTATGGTCTTACATATATACACT-TCGTGGTCC
69240 AACC
64 AACC
* * * *
69244 ATGGTCTTATCATCAAAATTCCATAGCTCAGCTATGGTCTTACCTATATACACTTCCATGGTCCA
1 ATGGTCTTATCATCAGAATGCCATAGCTCAGCTATGGTCTTACATATATACACTT-CGTGGTCCA
69309 ACC
65 ACC
* * * ** * **
69312 ATGGTCTTATCATCAGAATGTCGTAGCTGAATTATGGTCTTACATATATAAACCGCCGTGGTCCA
1 ATGGTCTTATCATCAGAATGCCATAGCTCAGCTATGGTCTTACATATATACA-CTTCGTGGTCCA
69377 ACC
65 ACC
69380 ATGGTCTTA
1 ATGGTCTTA
69389 CATTTGAATG
Statistics
Matches: 125, Mismatches: 17, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
67 1 0.01
68 122 0.98
69 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (67 bp):
ATGGTCTTATCATCAGAATGCCATAGCTCAGCTATGGTCTTACATATATACACTTCGTGGTCCAA
CC
Found at i:69316 original size:35 final size:35
Alignment explanation
Indices: 69209--69320 Score: 90
Period size: 35 Copynumber: 3.3 Consensus size: 35
69199 TAGCCTAGCT
* * *
69209 ATGGTCTTACATAAATACACTAT-CGTGGTCCAACC
1 ATGGTCTTACCTATATACACT-TCCATGGTCCAACC
* * * * *
69244 ATGGTCTTATC-ATCA-A-AATTCCATAG-CTCAGCT
1 ATGGTCTTACCTAT-ATACACTTCCATGGTC-CAACC
69277 ATGGTCTTACCTATATACACTTCCATGGTCCAACC
1 ATGGTCTTACCTATATACACTTCCATGGTCCAACC
69312 ATGGTCTTA
1 ATGGTCTTA
69321 TCATCAGAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
32 2 0.04
33 19 0.33
34 5 0.09
35 30 0.53
36 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (35 bp):
ATGGTCTTACCTATATACACTTCCATGGTCCAACC
Found at i:71412 original size:18 final size:18
Alignment explanation
Indices: 71391--71426 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
71381 ATTATATAAT
71391 ATTTAAATATATAGTTTA
1 ATTTAAATATATAGTTTA
* *
71409 ATTTAAATGTATATTTTA
1 ATTTAAATATATAGTTTA
71427 TTTTTAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTTAAATATATAGTTTA
Found at i:71548 original size:25 final size:26
Alignment explanation
Indices: 71484--71548 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
71474 TTTTTTTGTT
* * **
71484 TATTATTTATTTTTTAAAATTTTAAA
1 TATTATTTATATTTAAAAATTAAAAA
*
71510 TA-TATTTCTAATTTAAAAATTAAAAA
1 TATTATTTAT-ATTTAAAAATTAAAAA
71536 TATTATTT-TATTT
1 TATTATTTATATTT
71549 TGGTGGAGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 10 0.31
26 17 0.53
27 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TATTATTTATATTTAAAAATTAAAAA
Found at i:74577 original size:22 final size:22
Alignment explanation
Indices: 74536--74578 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
74526 ACATCTGTTT
*
74536 ACATAACACTTGAAATTATATG
1 ACATAACACATGAAATTATATG
74558 ACATAACACAT-AAATATATAT
1 ACATAACACATGAAAT-TATAT
74579 TTAATGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (22 bp):
ACATAACACATGAAATTATATG
Done.