Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011549.1 Kokia drynarioides strain JFW-HI SEQ_126535, 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: 194587
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Warning! 212 characters in sequence are not A, C, G, or T
Found at i:1516 original size:24 final size:24
Alignment explanation
Indices: 1484--1531 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1474 TCTGGGTTTA
1484 TGTATACAGTTTCTTTATTGTGAG
1 TGTATACAGTTTCTTTATTGTGAG
1508 TGTATACAGTTTCTTTATTGTGAG
1 TGTATACAGTTTCTTTATTGTGAG
1532 ACAAAGTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.50
Consensus pattern (24 bp):
TGTATACAGTTTCTTTATTGTGAG
Found at i:16203 original size:30 final size:31
Alignment explanation
Indices: 16169--16232 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
16159 AACGGATCAA
*
16169 TGACTTAAATAAAAAAATTT-AATAGTTCAG
1 TGACTTAAATAAAAAAATTTGAATAATTCAG
* * *
16199 TGACTTAAATGAGAAATTTTGAATAATTCAG
1 TGACTTAAATAAAAAAATTTGAATAATTCAG
16230 TGA
1 TGA
16233 TCAAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAAAATTTGAATAATTCAG
Found at i:17324 original size:23 final size:22
Alignment explanation
Indices: 17250--17351 Score: 91
Period size: 23 Copynumber: 4.5 Consensus size: 22
17240 AGTGCTAAGG
17250 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
* * * *
17272 AATCAGT-AGGAGCACATAGCGC
1 AAACAGTAAGCA-CACACAGTGC
*
17294 AAATCAGTAGGCACACGA-AGTGC
1 AAA-CAGTAAGCACAC-ACAGTGC
17317 GAAACAGTAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
*
17340 TTAACAGTAAGC
1 -AAACAGTAAGC
17352 GCGCTAGCGT
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
21 3 0.05
22 17 0.27
23 37 0.59
24 6 0.10
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.13
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:17452 original size:24 final size:26
Alignment explanation
Indices: 17414--17461 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
17404 TTTACATGGG
17414 CATAATCTCTCATAT-TCATCATTTTT
1 CATAATCTCTCATATATCA-CATTTTT
17440 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
17462 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.21, G:0.00, T:0.48
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTTT
Found at i:22194 original size:2 final size:2
Alignment explanation
Indices: 22187--22211 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
22177 ACCCTTTATG
22187 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
22212 TTATTAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23540 original size:27 final size:26
Alignment explanation
Indices: 23509--23567 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
23499 AAATAATGAT
*
23509 AAATATTTAAGTAAA-ATATTAATAAA
1 AAATATTTAACTAAATA-ATTAATAAA
*
23535 ATAATATTTAACTAATTAATTAATAAA
1 A-AATATTTAACTAAATAATTAATAAA
23562 AAATAT
1 AAATAT
23568 CTCCAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 6 0.21
27 22 0.76
28 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (26 bp):
AAATATTTAACTAAATAATTAATAAA
Found at i:32121 original size:35 final size:35
Alignment explanation
Indices: 32082--32148 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
32072 TATTTCAGTT
32082 CAATTCTTCTTTCGACTTGTTTCCCATCAGTACCA
1 CAATTCTTCTTTCGACTTGTTTCCCATCAGTACCA
**
32117 CAATTCTTCTTTTTACTTGTTTCCCATCAGTA
1 CAATTCTTCTTTCGACTTGTTTCCCATCAGTA
32149 TCAATGGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.19, C:0.28, G:0.07, T:0.45
Consensus pattern (35 bp):
CAATTCTTCTTTCGACTTGTTTCCCATCAGTACCA
Found at i:48042 original size:17 final size:18
Alignment explanation
Indices: 48020--48054 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
48010 ATTACAAAAG
48020 GTTTTCATCTTT-TTCTT
1 GTTTTCATCTTTGTTCTT
*
48037 GTTTTCATTTTTGTTCTT
1 GTTTTCATCTTTGTTCTT
48055 ATTATGTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.06, C:0.14, G:0.09, T:0.71
Consensus pattern (18 bp):
GTTTTCATCTTTGTTCTT
Found at i:56544 original size:16 final size:15
Alignment explanation
Indices: 56514--56556 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
56504 AGCAACTTTG
56514 ATAAATTTTTAATTT
1 ATAAATTTTTAATTT
*
56529 ATAATTTTTATAATTT
1 ATAAATTTT-TAATTT
*
56545 ATAAAATTTTAA
1 ATAAATTTTTAA
56557 ATTAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATAAATTTTTAATTT
Found at i:56559 original size:16 final size:16
Alignment explanation
Indices: 56516--56564 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
56506 CAACTTTGAT
*
56516 AAATTTTTAATTTAT-
1 AAATTTTAAATTTATA
*
56531 AATTTTTATAATTTATA
1 AAATTTTA-AATTTATA
*
56548 AAATTTTAAATTAATA
1 AAATTTTAAATTTATA
56564 A
1 A
56565 TGATAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 6 0.21
16 15 0.54
17 7 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTTTAAATTTATA
Found at i:56941 original size:16 final size:16
Alignment explanation
Indices: 56920--56954 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56910 ATTTTAAATA
*
56920 TTATTTTACTTTTACT
1 TTATTTTACTTTTAAT
*
56936 TTATTTTATTTTTAAT
1 TTATTTTACTTTTAAT
56952 TTA
1 TTA
56955 AAATAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTACTTTTAAT
Found at i:57983 original size:2 final size:2
Alignment explanation
Indices: 57976--58008 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
57966 AAATAGGCAC
*
57976 AG AG AG AG AG AG AG AG AG A- AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
58009 GGGATATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:69456 original size:17 final size:17
Alignment explanation
Indices: 69430--69463 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
69420 GCTTGGTCAC
* *
69430 ATTAATTAAAATATAAT
1 ATTAAATAAAAAATAAT
69447 ATTAAATAAAAAATAAT
1 ATTAAATAAAAAATAAT
69464 TAAATAATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATTAAATAAAAAATAAT
Found at i:80554 original size:14 final size:15
Alignment explanation
Indices: 80531--80575 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
80521 AATAAAATTT
80531 AATTTATTATTCTTA
1 AATTTATTATTCTTA
*
80546 AATTT-TTATT-TTT
1 AATTTATTATTCTTA
*
80559 AATTTATAATT-TTA
1 AATTTATTATTCTTA
80573 AAT
1 AAT
80576 GAAAGCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 7 0.27
14 14 0.54
15 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTATTATTCTTA
Found at i:81602 original size:12 final size:12
Alignment explanation
Indices: 81585--81611 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
81575 ACGGTTGTCA
81585 TTTCTTCTCTTG
1 TTTCTTCTCTTG
81597 TTTCTTCTCTTG
1 TTTCTTCTCTTG
81609 TTT
1 TTT
81612 AACATCTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTCTTCTCTTG
Found at i:81839 original size:2 final size:2
Alignment explanation
Indices: 81832--81869 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
81822 AATCAGTATA
81832 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
81870 TTGTTTTCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:89837 original size:32 final size:32
Alignment explanation
Indices: 89801--89871 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
89791 GTTAAATTTC
* * *
89801 TAATCATTCCTAATTTGTTCAAGGATTTGTAT
1 TAATCATTCCTAATCTCTTCAAGGATTTATAT
** *
89833 TAATCGGTCCTAATCTCTTTAAGGATTTATAT
1 TAATCATTCCTAATCTCTTCAAGGATTTATAT
89865 TAATCAT
1 TAATCAT
89872 CCTCTAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (32 bp):
TAATCATTCCTAATCTCTTCAAGGATTTATAT
Found at i:89968 original size:18 final size:18
Alignment explanation
Indices: 89936--89971 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
89926 CAAACCCTAA
**
89936 TTTTTTGTGGGATCAATT
1 TTTTTTGTGAAATCAATT
89954 TTTTTTGTGAAATCAATT
1 TTTTTTGTGAAATCAATT
89972 ATATAAAAAG
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:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (18 bp):
TTTTTTGTGAAATCAATT
Found at i:90937 original size:17 final size:18
Alignment explanation
Indices: 90917--90950 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
90907 CCTGCTCCGG
90917 GAAAA-GGTGGGCTCATC
1 GAAAAGGGTGGGCTCATC
*
90934 GAAAAGGGTGGGGTCAT
1 GAAAAGGGTGGGCTCAT
90951 GGTCATGGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.12, G:0.41, T:0.18
Consensus pattern (18 bp):
GAAAAGGGTGGGCTCATC
Found at i:91564 original size:21 final size:21
Alignment explanation
Indices: 91503--91560 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
91493 GAGTCGGGGT
*
91503 TGGGGTTGTCGGAGTTGTAAC
1 TGGGGTTGTCGGAGTTGTGAC
* * *
91524 TGGTGCTGTTGGAGTTGTGAC
1 TGGGGTTGTCGGAGTTGTGAC
91545 TGGGGTTGTCGG-GTTG
1 TGGGGTTGTCGGAGTTG
91561 GTGATCGGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.09, C:0.09, G:0.47, T:0.36
Consensus pattern (21 bp):
TGGGGTTGTCGGAGTTGTGAC
Found at i:101119 original size:60 final size:59
Alignment explanation
Indices: 101030--101190 Score: 148
Period size: 59 Copynumber: 2.6 Consensus size: 59
101020 TAATTAAGTA
* * * **
101030 TTAATTAGACAAAAAAAACTAAATTTAAATATCAATTTAAACCA-ATAAATCAAATTTAGGTAT
1 TTAATTAGACCAAAAAAAC---CTTTAAATATCAA-TTAAACCATA-AAATCAAATTCAAATAT
** * *
101093 TTAATT-GAACCGAATTAAACC-TTAAATACCAATTAAACCTTAAAATCAAATTCAAATAT
1 TTAATTAG-ACC-AAAAAAACCTTTAAATATCAATTAAACCATAAAATCAAATTCAAATAT
101152 TTAATTAGACCAAAAAAACCTTTAAATATCAAATTAAAC
1 TTAATTAGACCAAAAAAACCTTTAAATATC-AATTAAAC
101191 TTTGATACCA
Statistics
Matches: 80, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
58 7 0.09
59 38 0.47
60 20 0.25
62 1 0.01
63 8 0.10
64 6 0.08
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.30
Consensus pattern (59 bp):
TTAATTAGACCAAAAAAACCTTTAAATATCAATTAAACCATAAAATCAAATTCAAATAT
Found at i:116737 original size:12 final size:11
Alignment explanation
Indices: 116716--116749 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
116706 AAGACTTATT
116716 AAACAATAAAA
1 AAACAATAAAA
116727 AAACAAATAAAA
1 AAAC-AATAAAA
*
116739 AAACTATAAAA
1 AAACAATAAAA
116750 CTTACGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (11 bp):
AAACAATAAAA
Found at i:121315 original size:22 final size:22
Alignment explanation
Indices: 121285--121326 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
121275 AATTGGACTA
* *
121285 ATTTTTTTAATTATTTATTTTT
1 ATTTGTTTAATAATTTATTTTT
121307 ATTTGTTTAATAATTTATTT
1 ATTTGTTTAATAATTTATTT
121327 AATTGGACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
ATTTGTTTAATAATTTATTTTT
Found at i:122031 original size:47 final size:48
Alignment explanation
Indices: 121926--122033 Score: 157
Period size: 48 Copynumber: 2.3 Consensus size: 48
121916 GCCACATCAA
* *
121926 CAAATAGTTTTAAAATTATTAATTTTTTTTTTTAAATGTAAAATTATT
1 CAAATAATTTTAAAATTATTAATTTTTTTTTTTAAATATAAAATTATT
* *
121974 AAAATTATTTTAAAATTATTAA-TTTTTTTTTTAAATAATAAAATTA-T
1 CAAATAATTTTAAAATTATTAATTTTTTTTTTTAAAT-ATAAAATTATT
122021 CAAATAATTTTAA
1 CAAATAATTTTAA
122034 TTTTCAATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
47 26 0.49
48 27 0.51
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (48 bp):
CAAATAATTTTAAAATTATTAATTTTTTTTTTTAAATATAAAATTATT
Found at i:122801 original size:11 final size:10
Alignment explanation
Indices: 122785--122823 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 10
122775 AAAAAATAAT
122785 AATAATTTTGA
1 AATAATTTT-A
122796 AATAATTTT-
1 AATAATTTTA
122805 AATAATTTTAA
1 AATAATTTT-A
122816 AATAATTT
1 AATAATTT
122824 GTTGACGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.35
11 17 0.65
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (10 bp):
AATAATTTTA
Found at i:122809 original size:20 final size:20
Alignment explanation
Indices: 122759--122823 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
122749 AAAATTATTT
*
122759 AATAATTTT-ATTA-TTTAA
1 AATAATTTTAATAATTTTAA
** *
122777 AA-AATAATAATAATTTTGA
1 AATAATTTTAATAATTTTAA
122796 AATAATTTTAATAATTTTAA
1 AATAATTTTAATAATTTTAA
122816 AATAATTT
1 AATAATTT
122824 GTTGACGTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 4 0.11
18 5 0.14
19 6 0.16
20 22 0.59
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AATAATTTTAATAATTTTAA
Found at i:123340 original size:16 final size:17
Alignment explanation
Indices: 123305--123358 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
123295 TGAATAAAAA
123305 TGTAATTACTA--ATAT
1 TGTAATTACTACTATAT
*
123320 AGTAATTA-TACTATAT
1 TGTAATTACTACTATAT
*
123336 TGTAATTACAACTA-AT
1 TGTAATTACTACTATAT
123352 TGTAATT
1 TGTAATT
123359 TTTTAGATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 2 0.06
15 7 0.21
16 20 0.61
17 4 0.12
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (17 bp):
TGTAATTACTACTATAT
Found at i:123489 original size:16 final size:15
Alignment explanation
Indices: 123455--123519 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 15
123445 CATAATTTAT
123455 ATTAT-TAAAAAACTA
1 ATTATATAAAAAA-TA
*
123470 ATTACTATAAAAAATT
1 ATTA-TATAAAAAATA
123486 ATTAGTATGATAAAAATA
1 ATTA-TAT-A-AAAAATA
123504 ATT-TATAAAAAATA
1 ATTATATAAAAAATA
123518 AT
1 AT
123520 AATAATTTAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 9 0.21
15 5 0.12
16 12 0.28
17 8 0.19
18 9 0.21
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.35
Consensus pattern (15 bp):
ATTATATAAAAAATA
Found at i:135841 original size:15 final size:15
Alignment explanation
Indices: 135821--135849 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
135811 TATATTATAT
135821 ATACACTTTATGCAG
1 ATACACTTTATGCAG
135836 ATACACTTTATGCA
1 ATACACTTTATGCA
135850 TATCAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (15 bp):
ATACACTTTATGCAG
Found at i:139766 original size:33 final size:33
Alignment explanation
Indices: 139711--139779 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
139701 TCTAAAAATC
* * *
139711 AAAGTTAAAATTGATTCTTAAAGAATAAAGGCA
1 AAAGCTAAAATTGATTCCTAAAGAATAAAGACA
* *
139744 AAAGCTAAAGTTGATTCCTAAAGACTAAAGACA
1 AAAGCTAAAATTGATTCCTAAAGAATAAAGACA
139777 AAA
1 AAA
139780 TGTTAAACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.23
Consensus pattern (33 bp):
AAAGCTAAAATTGATTCCTAAAGAATAAAGACA
Found at i:143492 original size:117 final size:116
Alignment explanation
Indices: 143310--143522 Score: 257
Period size: 117 Copynumber: 1.8 Consensus size: 116
143300 TTTTTTTTTT
* * ** *
143310 AACTCCTTACATATAAAATATATCTAAATATAACATTAAGATTATTTTTGTGACGGAATTTGTTA
1 AACTCCTTACATATAAAATATATCTAAACATAACATTAAGATTATTTTTGCGACACAATTCGTTA
* * **
143375 TGTCCGTTCTTTTTTTATTACTTAAAAAAAATATTGTTAAAGCAAAATTAAA
66 T-ACCCTTCCCTTTTTATTACTTAAAAAAAATATTGTTAAAGCAAAATTAAA
* * * * * *
143427 AACTTCTTACATGTAAAATATAT-TCAAACATAATATTTATATTATTTTTGCGGCACAATTCGTT
1 AACTCCTTACATATAAAATATATCT-AAACATAACATTAAGATTATTTTTGCGACACAATTCGTT
*
143491 ATACCCTTCCCTTTTTATTCCTTAAAAAAAAT
65 ATACCCTTCCCTTTTTATTACTTAAAAAAAAT
143523 TTAATTATTT
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
116 26 0.33
117 53 0.67
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (116 bp):
AACTCCTTACATATAAAATATATCTAAACATAACATTAAGATTATTTTTGCGACACAATTCGTTA
TACCCTTCCCTTTTTATTACTTAAAAAAAATATTGTTAAAGCAAAATTAAA
Found at i:145763 original size:24 final size:22
Alignment explanation
Indices: 145734--145780 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
145724 AAAATTATTG
145734 TTTTGTTGTTG-TTTCTCACTA
1 TTTTGTTGTTGTTTTCTCACTA
*
145755 TTTTGTTGTTGTTTTCTCTCTA
1 TTTTGTTGTTGTTTTCTCACTA
145777 TTTT
1 TTTT
145781 ACTATCATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.06, C:0.13, G:0.13, T:0.68
Consensus pattern (22 bp):
TTTTGTTGTTGTTTTCTCACTA
Found at i:147872 original size:23 final size:22
Alignment explanation
Indices: 147836--147937 Score: 89
Period size: 23 Copynumber: 4.5 Consensus size: 22
147826 GCTGGAGAAA
*
147836 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
* *
147858 CCAATAGGCACACACAGTACAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
147881 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
*
147904 CAGTAGGCACACGA-AGTGCGAAA
1 CAGTAGGCACAC-ACAGTGC-AAT
*
147927 CAGTAAGCACA
1 CAGTAGGCACA
147938 TGAAGTGCGA
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
22 14 0.22
23 49 0.77
24 1 0.02
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:147942 original size:23 final size:23
Alignment explanation
Indices: 147904--147957 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
147894 TAGCGCAAAT
*
147904 CAGTAGGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
*
147927 CAGTAAGCACATGAAGTGCGAAA
1 CAGTAAGCACACGAAGTGCGAAA
147950 CAGTAAGC
1 CAGTAAGC
147958 GCGCTAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.28, T:0.11
Consensus pattern (23 bp):
CAGTAAGCACACGAAGTGCGAAA
Found at i:155084 original size:23 final size:23
Alignment explanation
Indices: 155053--155131 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
155043 TTGGGGAAAC
*
155053 AGTAAGCACACACAGTGCAATCT
1 AGTAGGCACACACAGTGCAATCT
155076 AGTAGGCACACACAGTGCAATC-
1 AGTAGGCACACACAGTGCAATCT
* * *
155098 AGTAGGCATATATAGTGCAAAT-T
1 AGTAGGCACACACAGTGC-AATCT
155121 AGTAGGCACAC
1 AGTAGGCACAC
155132 GAAGTGCGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
22 15 0.31
23 33 0.69
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.19
Consensus pattern (23 bp):
AGTAGGCACACACAGTGCAATCT
Found at i:155147 original size:23 final size:22
Alignment explanation
Indices: 155049--155147 Score: 92
Period size: 23 Copynumber: 4.4 Consensus size: 22
155039 AGTGTTGGGG
*
155049 AAACAGTAAGCACACACAGTGC
1 AAACAGTAGGCACACACAGTGC
*
155071 AATCTAGTAGGCACACACAGTGC
1 AAAC-AGTAGGCACACACAGTGC
* * * *
155094 AATCAGTAGGCATATATAGTGC
1 AAACAGTAGGCACACACAGTGC
*
155116 AAATTAGTAGGCACACGA-AGTGC
1 AAA-CAGTAGGCACAC-ACAGTGC
155139 GAAACAGTA
1 -AAACAGTA
155148 AGCGTGCTAG
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
22 20 0.32
23 39 0.62
24 4 0.06
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.17
Consensus pattern (22 bp):
AAACAGTAGGCACACACAGTGC
Found at i:157955 original size:22 final size:21
Alignment explanation
Indices: 157904--157974 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
157894 NNNNAATGGA
* * *
157904 TGTTTTGCTGTTATTTTTCAC
1 TGTTTTGTTGTTGTTTTTCAT
*
157925 TATTTTGTTGTTGTTTTCTCAT
1 TGTTTTGTTGTTGTTTT-TCAT
* *
157947 TGTTTTGTTATTGTTTTTTGAT
1 TGTTTTGTTGTTG-TTTTTCAT
157969 TGTTTT
1 TGTTTT
157975 ACTGTCATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 14 0.34
22 23 0.56
23 4 0.10
ACGTcount: A:0.08, C:0.07, G:0.15, T:0.69
Consensus pattern (21 bp):
TGTTTTGTTGTTGTTTTTCAT
Found at i:163144 original size:11 final size:12
Alignment explanation
Indices: 163119--163168 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
163109 GGAACCAACG
*
163119 AAAAATGAAGAA
1 AAAAATAAAGAA
163131 AAAAATAAAGAA
1 AAAAATAAAGAA
*
163143 AAAAGAGAAAGAA
1 AAAA-ATAAAGAA
* *
163156 AGAAAGAAAGAA
1 AAAAATAAAGAA
163168 A
1 A
163169 GAAGAAGGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 24 0.71
13 10 0.29
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (12 bp):
AAAAATAAAGAA
Found at i:163157 original size:4 final size:4
Alignment explanation
Indices: 163126--163171 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
163116 ACGAAAAATG
* * *
163126 AAGA AAAA AATA AAGA AAAA AGAGA AAGA AAGA AAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA A-AGA AAGA AAGA AAGA AAGA AAGA A
163172 GAAGGGGAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
4 33 0.92
5 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:163965 original size:15 final size:17
Alignment explanation
Indices: 163945--163987 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
163935 AAACACATTG
163945 TCTTTCTTTCCT-T-CT
1 TCTTTCTTTCCTCTCCT
163960 TCTTTCTTTCCTCTCCT
1 TCTTTCTTTCCTCTCCT
163977 TCCTTTCTTTC
1 T-CTTTCTTTC
163988 TTTCCCGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.48
16 1 0.04
17 3 0.12
18 9 0.36
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (17 bp):
TCTTTCTTTCCTCTCCT
Found at i:170425 original size:28 final size:32
Alignment explanation
Indices: 170362--170427 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
170352 GTACAAATCG
*
170362 TGACAAAATTGTCGTTATTTTCTTCTAAATTG
1 TGACAAAATTGTCGTTATTTTCTTCTAAATTA
*
170394 TGACAAAGTTGTCG-T-TTTTC-T-TAAATTA
1 TGACAAAATTGTCGTTATTTTCTTCTAAATTA
170422 TGACAA
1 TGACAA
170428 CGGGTCAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 12 0.38
29 1 0.03
30 5 0.16
31 1 0.03
32 13 0.41
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (32 bp):
TGACAAAATTGTCGTTATTTTCTTCTAAATTA
Found at i:170696 original size:18 final size:17
Alignment explanation
Indices: 170675--170708 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
170665 TAATCATTAA
170675 AATATAAATAATTAAACT
1 AATATAAAT-ATTAAACT
*
170693 AATATTAATATTAAAC
1 AATATAAATATTAAAC
170709 AATTTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
AATATAAATATTAAACT
Found at i:175335 original size:25 final size:25
Alignment explanation
Indices: 175307--175386 Score: 80
Period size: 23 Copynumber: 3.4 Consensus size: 25
175297 ATCACGTCTC
175307 GTGCTCTCTATTATTAGCA-TTGTGT
1 GTGCTCTCTATTATTAGCACTT-TGT
*
175332 GTGCTCTC--TGATTAGCACTTTGT
1 GTGCTCTCTATTATTAGCACTTTGT
* * *
175355 GTGCTCTC--TGATTAGTACTTTAT
1 GTGCTCTCTATTATTAGCACTTTGT
175378 GTGCTCTCT
1 GTGCTCTCT
175387 GTTGCCCAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
23 40 0.80
24 2 0.04
25 8 0.16
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (25 bp):
GTGCTCTCTATTATTAGCACTTTGT
Found at i:175345 original size:23 final size:23
Alignment explanation
Indices: 175319--175433 Score: 105
Period size: 23 Copynumber: 5.0 Consensus size: 23
175309 GCTCTCTATT
175319 ATTAGCA-TTGTGTGTGCTCTCTG
1 ATTAGCACTT-TGTGTGCTCTCTG
175342 ATTAGCACTTTGTGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
* *
175365 ATTAGTACTTTATGTGCTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
*
175388 -TTGCCCAGCAC-TTATGTGCTCTCTG
1 ATT----AGCACTTTGTGTGCTCTCTG
* *
175413 -TTAGTACTTTG-GTACTCTCTG
1 ATTAGCACTTTGTGTGCTCTCTG
175434 TTTGTTCCGT
Statistics
Matches: 80, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
21 13 0.16
22 4 0.05
23 41 0.51
24 2 0.03
25 16 0.20
26 4 0.05
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (23 bp):
ATTAGCACTTTGTGTGCTCTCTG
Found at i:176743 original size:103 final size:106
Alignment explanation
Indices: 176621--176830 Score: 293
Period size: 103 Copynumber: 2.0 Consensus size: 106
176611 AAAAATAACA
*
176621 TATAATAAACAATGAAGTGCAACATTTAAAATTAATAATTA-ACACACG-CAATATGTATTAA-A
1 TATAACAAACAATGAAGTGCAACATTTAAAATTAATAATTATACACACGTCAA-ATGTATTAATA
*
176683 TTAAAAT-AAAAATAATTTAAATTGTGAGTAAAATAAAATTT
65 TTAAAATAAAAAATAATTTAAATTGTGAATAAAATAAAATTT
* * * * * *
176724 TATAACAAATAATGAAGTGCAACGTTTAAAATTAATAATTATAGACATGTCGAATGTATTAATTT
1 TATAACAAACAATGAAGTGCAACATTTAAAATTAATAATTATACACACGTCAAATGTATTAATAT
*
176789 TAAAATAAAAAAATAGTTTAAATTGTGAATAAAATAAAATTT
66 TAAAAT-AAAAAATAATTTAAATTGTGAATAAAATAAAATTT
176831 AAATATTGTA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
103 38 0.41
104 14 0.15
105 9 0.10
107 32 0.34
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (106 bp):
TATAACAAACAATGAAGTGCAACATTTAAAATTAATAATTATACACACGTCAAATGTATTAATAT
TAAAATAAAAAATAATTTAAATTGTGAATAAAATAAAATTT
Found at i:177042 original size:18 final size:18
Alignment explanation
Indices: 177019--177055 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
177009 TGAAACTGTT
177019 TGTATAATAAA-ATTAAAA
1 TGTATAA-AAATATTAAAA
177037 TGTATAAAAATATTAAAA
1 TGTATAAAAATATTAAAA
177055 T
1 T
177056 AAAACTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.17
18 15 0.83
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
TGTATAAAAATATTAAAA
Found at i:192733 original size:251 final size:251
Alignment explanation
Indices: 192259--192909 Score: 1000
Period size: 251 Copynumber: 2.6 Consensus size: 251
192249 ACTTAACCTA
* * *
192259 TTCTAAAATTTACCGTAAATTGCAATGTAATAGATTTGATATCCATTATTTCTTTATATGCTTTT
1 TTCT-AAATTTACCATAATTTGCAATGTAATAGATTTGATATCTATTATTTCTTTATATGCTTTT
* * *
192324 GAAGCTTTCTTTCTTGACTTATTTAGAAGTCTTTCCTTTTTTGAATATTCTATTTGTTGTTTCAA
65 GGAGCTTTTTTTCTTGACTTATTTAGAAGTCTTTCCTTTTTTGAATATTCTATCTGTTGTTTCAA
* *
192389 GGTGTGCTTCTAATTTTTTTTTGAAATAACACTATCGATTTTCGATATTTTTTATCGTATAATTT
130 GGTGAGCCTCTAATTTTTTTTTGAAATAACACTATCGATTTTCGATATTTTTTATCGTATAATTT
* *
192454 ACTTAGAATGCACCATAATATTATGGATATTTTTTCATTCTTTGGTTGTACATCTTT
195 ACTTAGAATGCACCATAATATTATGGATATTTTTTCATTCTTTGGTAGTACATCTTG
* *
192511 TTCTGAAATTTACCATAATTTGCAATGTAATATATTTGATATATATTA-TT-TTTATATGCTTTT
1 TTCT-AAATTTACCATAATTTGCAATGTAATAGATTTGATATCTATTATTTCTTTATATGCTTTT
* * * *
192574 GGAGTTTTTTTTCTTGACTTATTTAGAAGTCTTTTCTTTTTTAAATATTCTATCTGTTGTTTCGA
65 GGAGCTTTTTTTCTTGACTTATTTAGAAGTCTTTCCTTTTTTGAATATTCTATCTGTTGTTTCAA
**
192639 GGTGAGCCTCTAATTTTTTTTTTGAAATAACACTATCGATTTTTTATATTTTTTATCGTATAATT
130 GGTGAGCCTCTAA-TTTTTTTTTGAAATAACACTATCGATTTTCGATATTTTTTATCGTATAATT
192704 TACTTAGAATGCACCATAATATTATGGATATTTTTTCATTCTTTGGTAGTACATCTTG
194 TACTTAGAATGCACCATAATATTATGGATATTTTTTCATTCTTTGGTAGTACATCTTG
* * *
192762 TTATAGAATTTACTATAATTTGCAATGCAATAGATTTGATATCTATTATTTCTTTATATGCTTTT
1 TTCTA-AATTTACCATAATTTGCAATGTAATAGATTTGATATCTATTATTTCTTTATATGCTTTT
* * * *
192827 GGAGCTTTTTTTCTTTATTTATTTAGAAGTCTTTCCTTTTTTGAATATTCTATCAGTTGTTCCAA
65 GGAGCTTTTTTTCTTGACTTATTTAGAAGTCTTTCCTTTTTTGAATATTCTATCTGTTGTTTCAA
** *
192892 GACGTGCCTCTAATTTTT
130 GGTGAGCCTCTAATTTTT
192910 CGGAATAACA
Statistics
Matches: 360, Mismatches: 35, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
250 83 0.23
251 148 0.41
252 49 0.14
253 80 0.22
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (251 bp):
TTCTAAATTTACCATAATTTGCAATGTAATAGATTTGATATCTATTATTTCTTTATATGCTTTTG
GAGCTTTTTTTCTTGACTTATTTAGAAGTCTTTCCTTTTTTGAATATTCTATCTGTTGTTTCAAG
GTGAGCCTCTAATTTTTTTTTGAAATAACACTATCGATTTTCGATATTTTTTATCGTATAATTTA
CTTAGAATGCACCATAATATTATGGATATTTTTTCATTCTTTGGTAGTACATCTTG
Done.