Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012588.1 Kokia drynarioides strain JFW-HI SEQ_127597, 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: 169585
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:9440 original size:82 final size:82
Alignment explanation
Indices: 9345--9508 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
9335 TGATTGTGGT
9345 GACATTTCTAATTGATACATTGTTAATTTTTGTTTACTTGAGGACAAGTAAAAACTCAAGTTTGG
1 GACATTTCTAATTGATACATTGTTAATTTTTGTTTACTTGAGGACAAGTAAAAACTCAAGTTTGG
*
9410 GGGTGTGATGGTATTAC
66 GGGTGTGAAGGTATTAC
9427 GACATTTCTAATTGATACATTGTTAATTTTTGTTTACTTGAGGACAAGTAAAAACTCAAGTTTGG
1 GACATTTCTAATTGATACATTGTTAATTTTTGTTTACTTGAGGACAAGTAAAAACTCAAGTTTGG
9492 GGGTGTGAAGGTATTAC
66 GGGTGTGAAGGTATTAC
9509 AAATGACATA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (82 bp):
GACATTTCTAATTGATACATTGTTAATTTTTGTTTACTTGAGGACAAGTAAAAACTCAAGTTTGG
GGGTGTGAAGGTATTAC
Found at i:32017 original size:18 final size:16
Alignment explanation
Indices: 31970--32017 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
31960 TTATAGATAG
31970 TTTTTCATGCATTTTT
1 TTTTTCATGCATTTTT
* *
31986 ATTGTCACTGCATTTTCT
1 TTTTTCA-TGCATTTT-T
32004 TTTTTCATTGCATT
1 TTTTTCA-TGCATT
32018 CATTTTGCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
16 5 0.20
17 8 0.32
18 12 0.48
ACGTcount: A:0.15, C:0.17, G:0.08, T:0.60
Consensus pattern (16 bp):
TTTTTCATGCATTTTT
Found at i:32604 original size:6 final size:6
Alignment explanation
Indices: 32593--32634 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
32583 TCAGTCACTT
*
32593 GAAAAA GAAAAA -AAAATGA GAAAAA GAAAGA GAAAAA GAAAA
1 GAAAAA GAAAAA GAAAA--A GAAAAA GAAAAA GAAAAA GAAAA
32635 GAAGAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
5 4 0.13
6 22 0.71
7 1 0.03
8 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:32625 original size:12 final size:12
Alignment explanation
Indices: 32593--32637 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
32583 TCAGTCACTT
*
32593 GAAAAAGAAAAA
1 GAAAGAGAAAAA
*
32605 AAAATGAGAAAAA
1 GAAA-GAGAAAAA
32618 GAAAGAGAAAAA
1 GAAAGAGAAAAA
32630 GAAA-AGAA
1 GAAAGAGAA
32638 GAAATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 4 0.14
12 15 0.52
13 10 0.34
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (12 bp):
GAAAGAGAAAAA
Found at i:36775 original size:19 final size:20
Alignment explanation
Indices: 36738--36775 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
36728 CTATAATATA
**
36738 AATGAACATAAAATTAAACC
1 AATGAACATAAAAGGAAACC
36758 AATGAA-ATAAAAGGAAAC
1 AATGAACATAAAAGGAAAC
36776 TTGAATTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.16
Consensus pattern (20 bp):
AATGAACATAAAAGGAAACC
Found at i:36877 original size:15 final size:16
Alignment explanation
Indices: 36844--36880 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
36834 CTCATTTCTA
36844 AAAAGGAATAATAAAG
1 AAAAGGAATAATAAAG
36860 AAAAGGAA-AACT-AAG
1 AAAAGGAATAA-TAAAG
36875 AAAAGG
1 AAAAGG
36881 TGTGTAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.68, C:0.03, G:0.22, T:0.08
Consensus pattern (16 bp):
AAAAGGAATAATAAAG
Found at i:39191 original size:23 final size:23
Alignment explanation
Indices: 39161--39421 Score: 342
Period size: 23 Copynumber: 11.3 Consensus size: 23
39151 CTTATATCCA
* *
39161 TGCTTAAATATTAATGTAATTTG
1 TGCTTAAATATTAATATGATTTG
*
39184 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* * *
39207 TGATTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
39230 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
39253 TGCTCAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* * *
39276 TGATTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
39299 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
*
39322 TGCTCAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * * *
39345 TGCTCAAATATTAATGTTATGTG
1 TGCTTAAATATTAATATGATTTG
* *
39368 TGCGTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
39391 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
39414 TGCTTAAA
1 TGCTTAAA
39422 GATTTAAGAT
Statistics
Matches: 207, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 207 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTG
Found at i:39271 original size:69 final size:69
Alignment explanation
Indices: 39160--39421 Score: 380
Period size: 69 Copynumber: 3.8 Consensus size: 69
39150 TCTTATATCC
* * *
39160 ATGCTTAAATATTAATGTAATTTGTGCTTAAATATTAATATGATTTATGATTAAATATTAATGTG
1 ATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAATGTG
39225 ATTT
66 ATTT
39229 ATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAATGTG
1 ATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAATGTG
39294 ATTT
66 ATTT
* * * *
39298 ATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTGTGCTCAAATATTAATGTT
1 ATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAATGTG
*
39363 ATGT
66 ATTT
* * * * * * * *
39367 GTGCGTAAATATTAATATGATTTATGATTAAATATTAATGTGATTTGTGCTTAAA
1 ATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAA
39422 GATTTAAGAT
Statistics
Matches: 178, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 178 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (69 bp):
ATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATATGATTTATGATTAAATATTAATGTG
ATTT
Found at i:41775 original size:21 final size:22
Alignment explanation
Indices: 41728--41779 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
41718 ATTAAATGGG
** *
41728 ATAAAAATAAATATGTAAGCAT
1 ATAAAAATAAATAAATAAGAAT
41750 A-AAAAATAAATAAATAA-AAT
1 ATAAAAATAAATAAATAAGAAT
41770 AT-AAAATAAA
1 ATAAAAATAAA
41780 GGAGTGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.42
21 14 0.54
22 1 0.04
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (22 bp):
ATAAAAATAAATAAATAAGAAT
Found at i:42852 original size:18 final size:18
Alignment explanation
Indices: 42812--42851 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
42802 GCCAGATTAC
*
42812 ATTTTATTTTTTTTGTAT
1 ATTTTATTTTTTTTCTAT
*
42830 ATTTTCTTTTTTTTCTAT
1 ATTTTATTTTTTTTCTAT
42848 -TTTT
1 ATTTT
42852 TTCCTGTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (18 bp):
ATTTTATTTTTTTTCTAT
Found at i:44400 original size:24 final size:25
Alignment explanation
Indices: 44368--44431 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
44358 TGGTTAAACT
44368 CTATTTGGGCTCGTAAGAGCTAA-C
1 CTATTTGGGCTCGTAAGAGCTAATC
*
44392 CTATTTGGGCTCGTAAGAGCTAATT
1 CTATTTGGGCTCGTAAGAGCTAATC
*
44417 CTATCTGGGCTCGTA
1 CTATTTGGGCTCGTA
44432 TAAATTAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
24 23 0.62
25 14 0.38
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (25 bp):
CTATTTGGGCTCGTAAGAGCTAATC
Found at i:44466 original size:26 final size:26
Alignment explanation
Indices: 44397--44471 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
44387 CTAACCTATT
* *
44397 TGGGCTCGTAAGAGCT-AATTCTATC
1 TGGGCTCGTATGAGCTAAATTCTACC
* **
44422 TGGGCTCGTATAAATTAAATTCTACC
1 TGGGCTCGTATGAGCTAAATTCTACC
*
44448 TGGGCTTGTATGAGCTAAATTCTA
1 TGGGCTCGTATGAGCTAAATTCTA
44472 GAGAACTTAA
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 12 0.30
26 28 0.70
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (26 bp):
TGGGCTCGTATGAGCTAAATTCTACC
Found at i:53064 original size:35 final size:33
Alignment explanation
Indices: 53011--53077 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 33
53001 TATGTGTGGC
*
53011 CTTTATTTTATGTAATATATATATATATGCATGGG
1 CTTTATTATATGTAATATATA-A-ATATGCATGGG
53046 CTTTATTATATAGT-ATATATAAATATGCATGG
1 CTTTATTATAT-GTAATATATAAATATGCATGG
53078 TTTTTGGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 10 0.33
34 1 0.03
35 17 0.57
36 2 0.07
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (33 bp):
CTTTATTATATGTAATATATAAATATGCATGGG
Found at i:58126 original size:29 final size:29
Alignment explanation
Indices: 58058--58139 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 29
58048 ACGCATGACA
**
58058 TTATTATATAGATATTATATATGTGTGGGCT
1 TTATTATATA-ATA-TATATATGCATGGGCT
58089 TTATTTTATATAATATATATATGCATGGGCT
1 TTA--TTATATAATATATATATGCATGGGCT
*
58120 TTATTATATAGTATATATAT
1 TTATTATATAATATATATAT
58140 TTTGGTGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
29 16 0.35
31 20 0.43
32 3 0.07
33 7 0.15
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.50
Consensus pattern (29 bp):
TTATTATATAATATATATATGCATGGGCT
Found at i:62627 original size:20 final size:19
Alignment explanation
Indices: 62582--62627 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
62572 ATTTTTGAAA
* *
62582 AATTAATTTTAAAGTAAGT
1 AATTAATTTTAAAGAAAAT
*
62601 AAATAATTATTAAAGAAAAT
1 AATTAATT-TTAAAGAAAAT
62621 AATTAAT
1 AATTAAT
62628 GGGTTGAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (19 bp):
AATTAATTTTAAAGAAAAT
Found at i:74442 original size:15 final size:15
Alignment explanation
Indices: 74416--74455 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
74406 TGAAGCTGAC
*
74416 GAAGAAGCAAGAGAA
1 GAAGAAGAAAGAGAA
*
74431 GAAGGAGAAAGAGAA
1 GAAGAAGAAAGAGAA
74446 GAAGAAGAAA
1 GAAGAAGAAA
74456 AAGAGGAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAGAAGAAAGAGAA
Found at i:86740 original size:15 final size:16
Alignment explanation
Indices: 86715--86746 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
86705 AGTACACATG
86715 CTCTCTTTTTCTTTTT
1 CTCTCTTTTTCTTTTT
86731 CTCT-TTTTTCTTTTT
1 CTCTCTTTTTCTTTTT
86746 C
1 C
86747 ATTTCTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (16 bp):
CTCTCTTTTTCTTTTT
Found at i:99430 original size:20 final size:21
Alignment explanation
Indices: 99405--99449 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
99395 TATATAGTCT
99405 ATAATTAAA-TTAAAAATAAA
1 ATAATTAAACTTAAAAATAAA
*
99425 ATAATTAAACTTTCAAAATAAA
1 ATAATTAAAC-TTAAAAATAAA
99447 ATA
1 ATA
99450 GGAAAATTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.41
22 13 0.59
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAATTAAACTTAAAAATAAA
Found at i:111836 original size:231 final size:234
Alignment explanation
Indices: 111428--111893 Score: 758
Period size: 231 Copynumber: 2.0 Consensus size: 234
111418 CTCCAAGGAT
111428 TTAAGCTTCCATGGTAGCTTGCTTAAGAAAAAAGTCAAAAATGGAATTTATTTGTCACGAGCTTG
1 TTAAGCTTCCATGGTAGCTTGCTTAAGAAAAAAGTCAAAAATGGAATTTATTTGTCACGAGCTTG
*
111493 ATGATAATCCCTTCTCTCTCTCCTCAGTATTTATCTTCACTAGCCAGTATAGGTATCCTTCTTTT
66 ATGATAATCCCTTCTCTCTCTCCTCAGTATTTATCTTCACTAGCCAGTATAGGTATCCTTATTTT
* * * * *
111558 CTCAGATCTAACTTCCTTGCACCTGTACAAGTTAGTTACTTCAGCTGTACACTCACGTAGATCTG
131 CTCAAATCTAACTTCCTTGCACCTATACAAGTCAGTTACTCCAGCTGTACACTCACGCAGATCTG
111623 GTGTACGCAGAAAGAAATTACAAGTTGTCGCGACATTTC
196 GTGTACGCAGAAAGAAATTACAAGTTGTCGCGACATTTC
*
111662 TTAAGCTTCCATGGTAGCTTGCTT-A-AAAAAA-TCAGAAATGGAATTTATTTGTCACGAGCTTG
1 TTAAGCTTCCATGGTAGCTTGCTTAAGAAAAAAGTCAAAAATGGAATTTATTTGTCACGAGCTTG
* * * *
111724 ATGATGATCCCTTCTCTCTCTCCTCAGTATTTATCTTTACTGGCTAGTATAGGTATCCTTATTTT
66 ATGATAATCCCTTCTCTCTCTCCTCAGTATTTATCTTCACTAGCCAGTATAGGTATCCTTATTTT
*
111789 CTCAAATCTAACTTCCTTGCAGCTATACAAGTCAGTTACTCCAGCTGTACACTCACGCAGATCTG
131 CTCAAATCTAACTTCCTTGCACCTATACAAGTCAGTTACTCCAGCTGTACACTCACGCAGATCTG
* * * * *
111854 GTGTATGCAGTAAGAAATTATAGGTTGTCTCGACATTTC
196 GTGTACGCAGAAAGAAATTACAAGTTGTCGCGACATTTC
111893 T
1 T
111894 GGATGCAAAT
Statistics
Matches: 215, Mismatches: 17, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
231 184 0.86
232 6 0.03
233 1 0.00
234 24 0.11
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (234 bp):
TTAAGCTTCCATGGTAGCTTGCTTAAGAAAAAAGTCAAAAATGGAATTTATTTGTCACGAGCTTG
ATGATAATCCCTTCTCTCTCTCCTCAGTATTTATCTTCACTAGCCAGTATAGGTATCCTTATTTT
CTCAAATCTAACTTCCTTGCACCTATACAAGTCAGTTACTCCAGCTGTACACTCACGCAGATCTG
GTGTACGCAGAAAGAAATTACAAGTTGTCGCGACATTTC
Found at i:125230 original size:30 final size:30
Alignment explanation
Indices: 125194--125252 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
125184 TTCACCACTT
*
125194 TTGGTTCTAGTAAAACTAGTTCTGGTTCTC
1 TTGGTTCTAGCAAAACTAGTTCTGGTTCTC
* *
125224 TTGGTTCTAGCAAAACTGGTTTTGGTTCT
1 TTGGTTCTAGCAAAACTAGTTCTGGTTCT
125253 GGCAAAGTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (30 bp):
TTGGTTCTAGCAAAACTAGTTCTGGTTCTC
Found at i:127954 original size:20 final size:20
Alignment explanation
Indices: 127917--127955 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
127907 CCGTGGTACC
**
127917 GATATTTTTACACGAGTATT
1 GATATTTTTACAAAAGTATT
*
127937 GATATTTTTATAAAAGTAT
1 GATATTTTTACAAAAGTAT
127956 CAATCATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (20 bp):
GATATTTTTACAAAAGTATT
Found at i:133336 original size:21 final size:21
Alignment explanation
Indices: 133312--133353 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
133302 AATCTATAGC
133312 TAATTCATCAAAGGCATATTG
1 TAATTCATCAAAGGCATATTG
* * *
133333 TAATTCTTCAAATGTATATTG
1 TAATTCATCAAAGGCATATTG
133354 ATTTAATTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (21 bp):
TAATTCATCAAAGGCATATTG
Found at i:135391 original size:20 final size:20
Alignment explanation
Indices: 135327--135413 Score: 61
Period size: 20 Copynumber: 4.3 Consensus size: 20
135317 GGAGCTATTC
*
135327 TGACTTGATTAAAAATCATTT
1 TGACTTGGTT-AAAATCATTT
* * *
135348 TGA--TGTATTAAAATGATAT
1 TGACTTG-GTTAAAATCATTT
* *
135367 CGACTTGGTTGAAATCATTT
1 TGACTTGGTTAAAATCATTT
* *
135387 TGACTTGTTTAAAATTATTT
1 TGACTTGGTTAAAATCATTT
*
135407 TAACTTG
1 TGACTTG
135414 ATTTTAAAAT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
19 12 0.24
20 34 0.67
21 5 0.10
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (20 bp):
TGACTTGGTTAAAATCATTT
Found at i:135422 original size:22 final size:20
Alignment explanation
Indices: 135378--135424 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
135368 GACTTGGTTG
* *
135378 AAATCATTTTGACTTGTTTA
1 AAATTATTTTAACTTGTTTA
135398 AAATTATTTTAACTTGATTTTA
1 AAATTATTTTAACTTG--TTTA
135420 AAATT
1 AAATT
135425 GTTTCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 14 0.61
22 9 0.39
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.51
Consensus pattern (20 bp):
AAATTATTTTAACTTGTTTA
Found at i:137017 original size:234 final size:234
Alignment explanation
Indices: 136608--137075 Score: 891
Period size: 234 Copynumber: 2.0 Consensus size: 234
136598 TGCGAAATTA
*
136608 TTTAAGATGTGGGTTGTTTTTAAACGCTTAAAAAATTTGTTAACATGGGTTCTCTTTTAAAAATG
1 TTTAAGATGTGGGTTGTTTTTAAACGCTTAAAAAAATTGTTAACATGGGTTCTCTTTTAAAAATG
*
136673 GTAAATTTCTAAGTTATAGGCCTAAAGACTAAATTGCATGAAAGTTAAAATGTTGGGGGCGATCC
66 GTAAATTTCTAAGTTATAGGCCTAAAGACTAAATTGCATGAAAGTTAAAATGTTGGGGGCAATCC
*
136738 TGTAAATTTACTTTAAGAGGGGTTGTAAGCTAGAATAAATTATTTTATACTTTTTGAATGATTAA
131 TGTAAATTTACTTTAAGAGGGGTTGTAAGCTAGAACAAATTATTTTATACTTTTTGAATGATTAA
*
136803 ATTGATGGAAATTATTATTAGATCGAGAAATGGGACAAT
196 ATTGATGGAAATTATTATCAGATCGAGAAATGGGACAAT
136842 TTTAAGATGTGGGTTGTTTTTAAACGCTTAAAAAAATTGTTAACATGGGTTCTCTTTTAAAAATG
1 TTTAAGATGTGGGTTGTTTTTAAACGCTTAAAAAAATTGTTAACATGGGTTCTCTTTTAAAAATG
*
136907 GTAAATTTCTAAGTTATAGGCCTAAAGACTAAATTGCATGAAAGTTAAAATGTTGGGGGCAATCT
66 GTAAATTTCTAAGTTATAGGCCTAAAGACTAAATTGCATGAAAGTTAAAATGTTGGGGGCAATCC
136972 TGTAAATTTACTTTAAGAGGGGTTGTAAGCTAGAACAAATTATTTTATACTTTTTGAATGATTAA
131 TGTAAATTTACTTTAAGAGGGGTTGTAAGCTAGAACAAATTATTTTATACTTTTTGAATGATTAA
137037 ATTGATGGAAATTATTATCAGATCGAGAAATGGGACAAT
196 ATTGATGGAAATTATTATCAGATCGAGAAATGGGACAAT
137076 CGGATTTAAT
Statistics
Matches: 229, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
234 229 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (234 bp):
TTTAAGATGTGGGTTGTTTTTAAACGCTTAAAAAAATTGTTAACATGGGTTCTCTTTTAAAAATG
GTAAATTTCTAAGTTATAGGCCTAAAGACTAAATTGCATGAAAGTTAAAATGTTGGGGGCAATCC
TGTAAATTTACTTTAAGAGGGGTTGTAAGCTAGAACAAATTATTTTATACTTTTTGAATGATTAA
ATTGATGGAAATTATTATCAGATCGAGAAATGGGACAAT
Found at i:138740 original size:232 final size:232
Alignment explanation
Indices: 138334--138792 Score: 855
Period size: 232 Copynumber: 2.0 Consensus size: 232
138324 AAATGTAAGT
138334 ATAACATATAATGAATCTTTATATGTTAAATGTATAAAATTTAGGTGTCAAATTTAATGAATCTT
1 ATAACATATAATGAATCTTTATATGTTAAATGTATAAAATTTAGGTGTCAAATTTAATGAATCTT
*
138399 TACATGAAAGAGTATGTGAATTTGTTATGTGAAAATATAAGTCATCGGTGTTTTTACGTCACAGC
66 TACATGAAAGAGTATGTGAATTTGTTATGTGAAAATATAAGTCATCGGTGTTTTTACGTCACAGA
138464 AAATGTGCAAGCAAACACACATTGATGCAAGTATAGTTGATAGACAATTCTATATTATATCGATC
131 AAATGTGCAAGCAAACACACATTGATGCAAGTATAGTTGATAGACAATTCTATATTATATCGATC
138529 CCGCGAGGAATGAGTTCTTGATGTTAACTGTCAGAGC
196 CCGCGAGGAATGAGTTCTTGATGTTAACTGTCAGAGC
*
138566 ATAACATATAATGAATCTTTATATGTTAAATGTATAAAATTTAGGTGTCAGATTTAATGAATCTT
1 ATAACATATAATGAATCTTTATATGTTAAATGTATAAAATTTAGGTGTCAAATTTAATGAATCTT
* *
138631 TACATGAAAGAGTATGTGAATTTGTTATGTGAAAATATATGTGATCGGTGTTTTTACGTCACAGA
66 TACATGAAAGAGTATGTGAATTTGTTATGTGAAAATATAAGTCATCGGTGTTTTTACGTCACAGA
**
138696 AAATGTGCAAGTGAACACACATTGATGCAAGTATAGTTGATAGACAATTCTATATTATATCGATC
131 AAATGTGCAAGCAAACACACATTGATGCAAGTATAGTTGATAGACAATTCTATATTATATCGATC
*
138761 CCGTGAGGAATGAGTTCTTGATGTTAACTGTC
196 CCGCGAGGAATGAGTTCTTGATGTTAACTGTC
138793 GAAGCAATTA
Statistics
Matches: 220, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
232 220 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (232 bp):
ATAACATATAATGAATCTTTATATGTTAAATGTATAAAATTTAGGTGTCAAATTTAATGAATCTT
TACATGAAAGAGTATGTGAATTTGTTATGTGAAAATATAAGTCATCGGTGTTTTTACGTCACAGA
AAATGTGCAAGCAAACACACATTGATGCAAGTATAGTTGATAGACAATTCTATATTATATCGATC
CCGCGAGGAATGAGTTCTTGATGTTAACTGTCAGAGC
Found at i:153590 original size:4 final size:4
Alignment explanation
Indices: 153574--153626 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
153564 CATTAGTTAA
* * * *
153574 AAAG AAA- AAAG AAAG AAAC AAAG AAAC AAAG AAAC AAAG AAATA AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAA-G AAAG
153622 AAAG A
1 AAAG A
153627 CATGAAATAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
3 3 0.08
4 33 0.85
5 3 0.08
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:153596 original size:8 final size:8
Alignment explanation
Indices: 153585--153615 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
153575 AAGAAAAAAG
153585 AAAGAAAC
1 AAAGAAAC
153593 AAAGAAAC
1 AAAGAAAC
153601 AAAGAAAC
1 AAAGAAAC
153609 AAAGAAA
1 AAAGAAA
153616 TAAAAGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAGAAAC
Found at i:154575 original size:21 final size:19
Alignment explanation
Indices: 154534--154584 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 19
154524 TGACAAAGAA
154534 ATAT-TTAATTATTATATG
1 ATATGTTAATTATTATATG
*
154552 ATATGTTAGTTATTATTCATG
1 ATATGTTAATTATTA-T-ATG
*
154573 ATATGTTGATTA
1 ATATGTTAATTA
154585 AATAAGGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.15
19 9 0.33
20 1 0.04
21 13 0.48
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (19 bp):
ATATGTTAATTATTATATG
Found at i:155055 original size:50 final size:51
Alignment explanation
Indices: 154976--155074 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 51
154966 AAAGGAGAGC
* * * * * *
154976 CTGACACGATTCATTCTGATTTTGTATAGCTGACGAGCTTAAATGTTCTAT
1 CTGACACGATTCATCCTGATCTTGAATAGCTGAAGAACTTAAACGTTCTAT
*
155027 CTGACATGATT-ATCCTGATCTTGAATAGCTGAAGAACTTAAACGTTCT
1 CTGACACGATTCATCCTGATCTTGAATAGCTGAAGAACTTAAACGTTCT
155075 GTAATCACGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
50 31 0.76
51 10 0.24
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (51 bp):
CTGACACGATTCATCCTGATCTTGAATAGCTGAAGAACTTAAACGTTCTAT
Found at i:162676 original size:6 final size:6
Alignment explanation
Indices: 162653--162712 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
162643 AATTAGTATA
* *
162653 TTTATT TTCATA TTTATT TTTATT TTTA-T TTTATT TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
162699 TTTATT TTCATT TT
1 TTTATT TTTATT TT
162713 AATTATGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 10 0.21
6 37 0.79
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:162687 original size:17 final size:17
Alignment explanation
Indices: 162653--162713 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
162643 AATTAGTATA
*
162653 TTTATTTTCATATTTATT
1 TTTATTTT-ATTTTTATT
162671 TTTATTTT-TATTTTATT
1 TTTATTTTAT-TTTTATT
162688 TTTATTTTATTTTTATT
1 TTTATTTTATTTTTATT
*
162705 TTCATTTTA
1 TTTATTTTA
162714 ATTATGCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.03
17 29 0.74
18 9 0.23
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTTTTATT
Found at i:162713 original size:11 final size:11
Alignment explanation
Indices: 162653--162712 Score: 84
Period size: 11 Copynumber: 5.2 Consensus size: 11
162643 AATTAGTATA
*
162653 TTTATTTTCATA
1 TTTATTTT-ATT
162665 TTTATTTTTATT
1 TTTA-TTTTATT
162677 TTTATTTTATT
1 TTTATTTTATT
162688 TTTATTTTATT
1 TTTATTTTATT
162699 TTTATTTTCATT
1 TTTATTTT-ATT
162711 TT
1 TT
162713 AATTATGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
11 26 0.58
12 15 0.33
13 4 0.09
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:163025 original size:43 final size:43
Alignment explanation
Indices: 162964--163050 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
162954 ACATCTTAAG
162964 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
1 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
163007 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
1 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
163050 T
1 T
163051 TATTGTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (43 bp):
TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
Found at i:163741 original size:12 final size:12
Alignment explanation
Indices: 163689--163742 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 12
163679 GAAAAAGAAG
163689 AAAAAA-GAAAA
1 AAAAAATGAAAA
163700 AAAAAAGTCGAAAA
1 AAAAAA-T-GAAAA
* *
163714 AAAAATTG-AGA
1 AAAAAATGAAAA
163725 AAAAAATGAAAA
1 AAAAAATGAAAA
163737 AAAAAA
1 AAAAAA
163743 AGACAAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 15 0.43
12 9 0.26
13 1 0.03
14 10 0.29
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (12 bp):
AAAAAATGAAAA
Found at i:168027 original size:6 final size:6
Alignment explanation
Indices: 168004--168063 Score: 79
Period size: 6 Copynumber: 10.3 Consensus size: 6
167994 AATTAGTATA
* *
168004 TTTATT TTCATA TTTATT TTTATT TTTA-T TTTATT TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
168050 TTTATT TTCATT TT
1 TTTATT TTTATT TT
168064 AATTATGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
5 10 0.21
6 37 0.79
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:168038 original size:17 final size:17
Alignment explanation
Indices: 168004--168064 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
167994 AATTAGTATA
*
168004 TTTATTTTCATATTTATT
1 TTTATTTT-ATTTTTATT
168022 TTTATTTT-TATTTTATT
1 TTTATTTTAT-TTTTATT
168039 TTTATTTTATTTTTATT
1 TTTATTTTATTTTTATT
*
168056 TTCATTTTA
1 TTTATTTTA
168065 ATTATGCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.03
17 29 0.74
18 9 0.23
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTATTTTTATT
Found at i:168064 original size:11 final size:11
Alignment explanation
Indices: 168004--168063 Score: 84
Period size: 11 Copynumber: 5.2 Consensus size: 11
167994 AATTAGTATA
*
168004 TTTATTTTCATA
1 TTTATTTT-ATT
168016 TTTATTTTTATT
1 TTTA-TTTTATT
168028 TTTATTTTATT
1 TTTATTTTATT
168039 TTTATTTTATT
1 TTTATTTTATT
168050 TTTATTTTCATT
1 TTTATTTT-ATT
168062 TT
1 TT
168064 AATTATGCAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
11 26 0.58
12 15 0.33
13 4 0.09
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:168376 original size:43 final size:43
Alignment explanation
Indices: 168315--168401 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
168305 ACATCTTAAG
168315 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
1 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
168358 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
1 TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
168401 T
1 T
168402 TATTGTGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (43 bp):
TGTGGGGAGGTTGATTGTGATTGTGATAAAATCCCTAAATTAT
Found at i:169092 original size:12 final size:12
Alignment explanation
Indices: 169040--169093 Score: 58
Period size: 11 Copynumber: 4.5 Consensus size: 12
169030 GAAAAAGAAG
169040 AAAAAA-GAAAA
1 AAAAAATGAAAA
169051 AAAAAAGTCGAAAA
1 AAAAAA-T-GAAAA
* *
169065 AAAAATTG-AGA
1 AAAAAATGAAAA
169076 AAAAAATGAAAA
1 AAAAAATGAAAA
169088 AAAAAA
1 AAAAAA
169094 AGACAAAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 15 0.43
12 9 0.26
13 1 0.03
14 10 0.29
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (12 bp):
AAAAAATGAAAA
Done.