Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012777.1 Kokia drynarioides strain JFW-HI SEQ_127789, 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: 649601
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 11 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:527885 original size:13 final size:13
Alignment explanation
Indices: 527867--527893 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
527857 TAAAGTACAC
527867 ATATCTAATACCT
1 ATATCTAATACCT
527880 ATATCTAATACCT
1 ATATCTAATACCT
527893 A
1 A
527894 CTCTCTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (13 bp):
ATATCTAATACCT
Found at i:537896 original size:23 final size:24
Alignment explanation
Indices: 537864--537911 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
537854 CAATCAATCT
* *
537864 ATTTTCTATTA-ATTTACTCTGAC
1 ATTTTATATTACATTTACACTGAC
*
537887 ATTTTATATTACATTTGCACTGAC
1 ATTTTATATTACATTTACACTGAC
537911 A
1 A
537912 AGGTTTAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTTTATATTACATTTACACTGAC
Found at i:552017 original size:21 final size:21
Alignment explanation
Indices: 551991--552030 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
551981 ATCCACAAAC
*
551991 ATACATTTAATTTCTATTCTT
1 ATACATTTAATCTCTATTCTT
552012 ATACATTTAATCTCTATTC
1 ATACATTTAATCTCTATTC
552031 AGAAACATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.00, T:0.53
Consensus pattern (21 bp):
ATACATTTAATCTCTATTCTT
Found at i:552038 original size:21 final size:21
Alignment explanation
Indices: 551993--552038 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
551983 CCACAAACAT
* ** *
551993 ACATTTAATTTCTATTCTTAT
1 ACATTTAATCTCTATTCAGAA
552014 ACATTTAATCTCTATTCAGAA
1 ACATTTAATCTCTATTCAGAA
552035 ACAT
1 ACAT
552039 CAATTCACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (21 bp):
ACATTTAATCTCTATTCAGAA
Found at i:559336 original size:21 final size:21
Alignment explanation
Indices: 559306--559345 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
559296 ATCTGCAAAC
*
559306 ATACATTTAAT-TACTATTCTT
1 ATACACTTAATAT-CTATTCTT
559327 ATACACTTAATATCTATTC
1 ATACACTTAATATCTATTC
559346 AAAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.47
Consensus pattern (21 bp):
ATACACTTAATATCTATTCTT
Found at i:563739 original size:12 final size:12
Alignment explanation
Indices: 563724--563757 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
563714 AAAAGAAAAA
563724 AAAAGAAAAGGG
1 AAAAGAAAAGGG
*
563736 AAAAGGAAAGGG
1 AAAAGAAAAGGG
563748 AAAAGGAAAA
1 AAAA-GAAAA
563758 AGTGATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAAAGAAAAGGG
Found at i:569085 original size:29 final size:29
Alignment explanation
Indices: 569044--569235 Score: 241
Period size: 29 Copynumber: 6.7 Consensus size: 29
569034 CCTTGAAGGT
569044 CCCT-AAACTTCCAAAAATTCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
569072 CCCTAAAACTTCCAAAAATTCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
569101 CCCCT-AAACTTCCAAAAATTCCATTTTTGA
1 -CCCTAAAACTTCCAAAAATTCCATTTTT-A
* *
569131 CCC-CAAACTTCTAAAAATTCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
* *
569159 CCC-AAAACTTCCAAAATTTCCAATTTTGA
1 CCCTAAAACTTCCAAAAATTCC-ATTTTTA
* * *
569188 CCCCAGAACTTCCAAAATTTCCATTTTTA
1 CCCTAAAACTTCCAAAAATTCCATTTTTA
**
569217 CCCCCAAACTT-CAAAAATT
1 CCCTAAAACTTCCAAAAATT
569236 ATCCTTTTAC
Statistics
Matches: 148, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
28 30 0.20
29 96 0.65
30 22 0.15
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.33
Consensus pattern (29 bp):
CCCTAAAACTTCCAAAAATTCCATTTTTA
Found at i:569139 original size:58 final size:58
Alignment explanation
Indices: 569044--569235 Score: 282
Period size: 58 Copynumber: 3.3 Consensus size: 58
569034 CCTTGAAGGT
*
569044 CCCTAAACTTCCAAAAATTCCATTTTT-ACCCTAAAACTTCCAAAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCC-CAAACTTCCAAAAATTCCATTTTTAC
*
569102 CCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTCTAAAAATTCCATTTTTA-
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTCCAAAAATTCCATTTTTAC
* * * *
569159 CCCAAAACTTCCAAAATTTCCAATTTTGACCCCAGAACTTCCAAAATTTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTGACCCCA-AACTTCCAAAAATTCCATTTTTAC
*
569218 CCCCAAACTT-CAAAAATT
1 CCCTAAACTTCCAAAAATT
569236 ATCCTTTTAC
Statistics
Matches: 122, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
57 31 0.25
58 78 0.64
59 13 0.11
ACGTcount: A:0.36, C:0.30, G:0.02, T:0.33
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTCCATTTTTGACCCCAAACTTCCAAAAATTCCATTTTTAC
Found at i:569198 original size:87 final size:86
Alignment explanation
Indices: 569048--569235 Score: 283
Period size: 87 Copynumber: 2.2 Consensus size: 86
569038 GAAGGTCCCT
*
569048 AAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTTACCCCTAAACTTC
1 AAACTT-CAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTGACCCCTAAACTTC
569113 CAAAAATTCCATTTTTGA-CCCC
65 CAAAAATTCCATTTTT-ACCCCC
*
569135 AAACTTCTAAAAATTCCATTTTTACCC-AAAACTTCCAAAATTTCCAATTTTGACCCC-AGAACT
1 AAACTTC-AAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCC-ATTTTGACCCCTA-AACT
*
569198 TCCAAAATTTCCATTTTTACCCCC
63 TCCAAAAATTCCATTTTTACCCCC
569222 AAACTTCAAAAATT
1 AAACTTCAAAAATT
569236 ATCCTTTTAC
Statistics
Matches: 94, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
86 27 0.29
87 67 0.71
ACGTcount: A:0.37, C:0.29, G:0.02, T:0.33
Consensus pattern (86 bp):
AAACTTCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCCATTTTGACCCCTAAACTTCC
AAAAATTCCATTTTTACCCCC
Found at i:569262 original size:87 final size:84
Alignment explanation
Indices: 569048--569306 Score: 260
Period size: 87 Copynumber: 3.0 Consensus size: 84
569038 GAAGGTCCCT
*
569048 AAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTCC-ATTTTTACCCCTAAACTT
1 AAACTTCTAAAAATTCCA-TTTTACCC-AAAACTTCC-AAAATTCCAATTTTTACCCC-AAACTT
*
569112 CCAAAAATTCCATTTTTGA-CCCC
62 CCAAAATTTCCATTTTT-ACCCCC
*
569135 AAACTTCTAAAAATTCCATTTTTACCCAAAACTTCCAAAATTTCCAATTTTGACCCCAGAACTTC
1 AAACTTCTAAAAATTCCA-TTTTACCCAAAACTTCCAAAA-TTCCAATTTTTACCCCA-AACTTC
569200 CAAAATTTCCATTTTTACCCCC
63 CAAAATTTCCATTTTTACCCCC
** * * * *
569222 AAACTTC-AAAAATTATCC-TTTTACCCTTGAA-TGTCTAAAATTCCATTTTTTTCTCCAAACTT
1 AAACTTCTAAAAA-T-TCCATTTTACCC-AAAACT-TCCAAAATTCCAATTTTTACCCCAAAC-T
*
569284 TCCGAAAATTACCA-TTTTACCCC
61 TCC-AAAATTTCCATTTTTACCCC
569307 TCGAGTATCC
Statistics
Matches: 151, Mismatches: 11, Indels: 21
0.83 0.06 0.11
Matches are distributed among these distances:
85 7 0.05
86 55 0.36
87 86 0.57
88 3 0.02
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (84 bp):
AAACTTCTAAAAATTCCATTTTACCCAAAACTTCCAAAATTCCAATTTTTACCCCAAACTTCCAA
AATTTCCATTTTTACCCCC
Found at i:580410 original size:30 final size:29
Alignment explanation
Indices: 580314--580574 Score: 275
Period size: 29 Copynumber: 8.9 Consensus size: 29
580304 GGATGTCCCT
*
580314 AAACTTCCAAAAATTCCA-TTTTGACCCT
1 AAACTTCCAAAAATTCCATTTTTGACCCC
580342 AAACTTCCAAAAATTCCATTTTT-ACCACC
1 AAACTTCCAAAAATTCCATTTTTGACC-CC
580371 AAACTTCCAAAAATTCCATTTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCC
580400 AAAGCTTCCAAAAATTCCATTTTT-ACCCTC
1 AAA-CTTCCAAAAATTCCATTTTTGACCC-C
* *
580430 GAACTTCCAAAAATTCCATTTTTGACCCTA
1 AAACTTCCAAAAATTCCATTTTTGACCC-C
580460 AAACTTCCAAAAAATT-CATTTTT-ACCCTC
1 AAACTTCC-AAAAATTCCATTTTTGACCC-C
* * * * *
580489 AAGCCTCCAAAATTTCCATTTTTAAACCCG
1 AAACTTCCAAAAATTCCATTTTT-GACCCC
* *
580519 AAACTTTCAAAAATTACCA-TTTTGCCCCC
1 AAACTTCCAAAAATT-CCATTTTTGACCCC
* * *
580548 AGA-TGTCCAAAAACTCCATTTTCGACC
1 AAACT-TCCAAAAATTCCATTTTTGACC
580575 TAGAAACTCT
Statistics
Matches: 199, Mismatches: 21, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
28 31 0.16
29 94 0.47
30 60 0.30
31 14 0.07
ACGTcount: A:0.35, C:0.30, G:0.04, T:0.31
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTGACCCC
Found at i:580425 original size:59 final size:58
Alignment explanation
Indices: 580310--580541 Score: 310
Period size: 59 Copynumber: 4.0 Consensus size: 58
580300 CCCTGGATGT
580310 CCCT-AAACTTCCAAAAATTCCA-TTTTGACCCTAAACTTCCAAAAATTCCATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTCCAAAAATTCCATTTTTA
*
580366 CCAC-CAAACTTCCAAAAATTCCATTTTTGACCCCAAAGCTTCCAAAAATTCCATTTTTA
1 CC-CTCAAACTTCCAAAAATTCCATTTTTGACCCTAAA-CTTCCAAAAATTCCATTTTTA
*
580425 CCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCAAAAAATT-CATTTTTA
1 CCCTCAAACTTCCAAAAATTCCATTTTTGACCCT-AAACTTCC-AAAAATTCCATTTTTA
* * * * * *
580484 CCCTCAAGCCTCCAAAATTTCCATTTTTAAACCCGAAACTTTCAAAAATTACCATTTT
1 CCCTCAAACTTCCAAAAATTCCATTTTT-GACCCTAAACTTCCAAAAATT-CCATTTT
580542 GCCCCCAGAT
Statistics
Matches: 156, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
56 2 0.01
57 19 0.12
58 20 0.13
59 95 0.61
60 20 0.13
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (58 bp):
CCCTCAAACTTCCAAAAATTCCATTTTTGACCCTAAACTTCCAAAAATTCCATTTTTA
Found at i:580684 original size:28 final size:30
Alignment explanation
Indices: 580643--580704 Score: 83
Period size: 28 Copynumber: 2.1 Consensus size: 30
580633 AAACTTTCCT
580643 AAAATTACCATTTTGCC-CTCGAGAATCC-
1 AAAATTACCATTTTGCCTCTCGAGAATCCG
* * *
580671 AAAATTATCGTTTTGCCTCTCGAGTATCCG
1 AAAATTACCATTTTGCCTCTCGAGAATCCG
580701 AAAA
1 AAAA
580705 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 15 0.52
29 10 0.34
30 4 0.14
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (30 bp):
AAAATTACCATTTTGCCTCTCGAGAATCCG
Found at i:592870 original size:200 final size:202
Alignment explanation
Indices: 592498--593013 Score: 711
Period size: 200 Copynumber: 2.5 Consensus size: 202
592488 CCAACTCAAG
* * *
592498 GCTCGATGTGAGCAAATATTCGAA-TCCCAGCTTCCTGATGAGATACTGAGAAGCAGGACGAAGT
1 GCTCGATGTGAGCAAATCTTCGAACT-CCAGCTTTCTGATGAGATACTGAGAAGCAGGTCGAAGT
* * *
592562 AATAAAA-GGTTAGCTTCATGATGAGATACTGAGAAGTGGACCAAATTTGTCTTTCTGATGAGGT
65 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA--TGTC--TATGATGAGAT
* * **
592626 ATAGAGAAGAAGATTGAAACAAACGATGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCA
126 ACAGAGAAGAAGATTGAAACAAACGATACGGTCATCCCCCTGATGAGATACTGAGAAGAAGACCA
592691 AATCAAA-CTCAC
191 AATCAAACCT-AC
* * * * *
592703 GCTCGATATGAGCAAATCTTCGAACTCCAGCTTTCTGATGAGATACTAAGAAGCATGTTGAAGCA
1 GCTCGATGTGAGCAAATCTTCGAACTCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCGAAGTA
592768 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAAT-TC-ATGATGAGATACAGA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATGTCTATGATGAGATACAGA
** * *
592831 GAAGCGGATTGAAACAAATGATATGGTCATCCCCCTGATGAGATACTGAGAAGAAGACCAAATCA
131 GAAGAAGATTGAAACAAACGATACGGTCATCCCCCTGATGAGATACTGAGAAGAAGACCAAATCA
592896 AACCTAC
196 AACCTAC
* * *
592903 GCTCGATGTGAGCAAATCTTTGAACCCCAGC-TTCTTGATGAGATACTGAGAAGCAGGTCGAGGT
1 GCTCGATGTGAGCAAATCTTCGAACTCCAGCTTTC-TGATGAGATACTGAGAAGCAGGTCGAAGT
* *
592967 AATAAAATGGTTAGCTTCCTGATGAGATACGGAGAAGTGAACCAAAT
65 AATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAAT
593014 CCGTCTTCCT
Statistics
Matches: 278, Mismatches: 29, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
199 3 0.01
200 171 0.62
201 2 0.01
203 2 0.01
204 1 0.00
205 61 0.22
206 38 0.14
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (202 bp):
GCTCGATGTGAGCAAATCTTCGAACTCCAGCTTTCTGATGAGATACTGAGAAGCAGGTCGAAGTA
ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATGTCTATGATGAGATACAGA
GAAGAAGATTGAAACAAACGATACGGTCATCCCCCTGATGAGATACTGAGAAGAAGACCAAATCA
AACCTAC
Found at i:593436 original size:11 final size:11
Alignment explanation
Indices: 593420--593464 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
593410 ACCGGGCCCC
593420 TTTTAAATTTA
1 TTTTAAATTTA
593431 TTTTAAATTTGA
1 TTTTAAATTT-A
* *
593443 ATTTAAATTAA
1 TTTTAAATTTA
*
593454 TCTTAAATTTA
1 TTTTAAATTTA
593465 AATTTATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:593445 original size:6 final size:6
Alignment explanation
Indices: 593421--593470 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
593411 CCGGGCCCCT
* *
593421 TTTAAA TTT-AT TTTAAA TTTGAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
593467 TTTA
1 TTTA
593471 TTTTCAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
4 2 0.06
5 6 0.17
6 25 0.69
7 3 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:593448 original size:23 final size:23
Alignment explanation
Indices: 593421--593470 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
593411 CCGGGCCCCT
* * *
593421 TTTAAATTTATTTTAAATTTGAA
1 TTTAAATTAATCTTAAATTTAAA
593444 TTTAAATTAATCTTAAATTTAAA
1 TTTAAATTAATCTTAAATTTAAA
593467 TTTA
1 TTTA
593471 TTTTCAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTAAATTAATCTTAAATTTAAA
Found at i:600998 original size:33 final size:33
Alignment explanation
Indices: 600961--601038 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 33
600951 AGTCGAATAG
**
600961 AATGATGAAGCTGTGTCGATAGATGTTCCAATC
1 AATGATGAAGCTGCCTCGATAGATGTTCCAATC
* * *
600994 AATGATGAAGTTGCCTTGATAGTTGTTCCAATC
1 AATGATGAAGCTGCCTCGATAGATGTTCCAATC
* *
601027 ATTCATGAAGCT
1 AATGATGAAGCT
601039 ACCCTTATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (33 bp):
AATGATGAAGCTGCCTCGATAGATGTTCCAATC
Found at i:601054 original size:33 final size:34
Alignment explanation
Indices: 600978--601060 Score: 84
Period size: 33 Copynumber: 2.5 Consensus size: 34
600968 AAGCTGTGTC
* **
600978 GATAG-ATGTTCCAATCAATGATGAAGTTGCCTT
1 GATAGTATGTTCCAATCAATCATGAAGTACCCTT
*
601011 GATAGT-TGTTCCAATCATTCATGAAGCTACCCTT
1 GATAGTATGTTCCAATCAATCATGAAG-TACCCTT
*
601045 -ATA-TATGTTCCCATCA
1 GATAGTATGTTCCAATCA
601061 CTTATGATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
32 1 0.02
33 36 0.86
34 5 0.12
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (34 bp):
GATAGTATGTTCCAATCAATCATGAAGTACCCTT
Found at i:602147 original size:37 final size:38
Alignment explanation
Indices: 602106--602203 Score: 119
Period size: 38 Copynumber: 2.6 Consensus size: 38
602096 GGACACTTTC
* * *
602106 ATGCAACGACATTCTTGGGTGCAA-TTGATGAATACTT
1 ATGCAGCGATATTCTTGGGTGCAATTTGAAGAATACTT
* *
602143 ATGCAGCGATAGTTC-TGGATGCAATTTGAAGAATATTT
1 ATGCAGCGATA-TTCTTGGGTGCAATTTGAAGAATACTT
*
602181 ATGCAGCGATAGTCTTGGGTGCA
1 ATGCAGCGATATTCTTGGGTGCA
602204 TTTCGAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 19 0.37
38 32 0.63
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.32
Consensus pattern (38 bp):
ATGCAGCGATATTCTTGGGTGCAATTTGAAGAATACTT
Found at i:603256 original size:49 final size:49
Alignment explanation
Indices: 603184--603318 Score: 243
Period size: 49 Copynumber: 2.8 Consensus size: 49
603174 ATTTTAGGAA
603184 ATTTTGAGATACTTACGAGGTACTACTGATGTTTGCTGCAGTTCAGGGG
1 ATTTTGAGATACTTACGAGGTACTACTGATGTTTGCTGCAGTTCAGGGG
* * *
603233 ATTTTGATATATTTACAAGGTACTACTGATGTTTGCTGCAGTTCAGGGG
1 ATTTTGAGATACTTACGAGGTACTACTGATGTTTGCTGCAGTTCAGGGG
603282 ATTTTGAGATACTTACGAGGTACTACTGATGTTTGCT
1 ATTTTGAGATACTTACGAGGTACTACTGATGTTTGCT
603319 TATAGTTTGG
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (49 bp):
ATTTTGAGATACTTACGAGGTACTACTGATGTTTGCTGCAGTTCAGGGG
Found at i:611160 original size:22 final size:22
Alignment explanation
Indices: 611135--611203 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
611125 ATTTTAAATA
611135 TATTGTTTTAGGTAAATTTACT
1 TATTGTTTTAGGTAAATTTACT
* * * * *
611157 TATTATTTT--CTATATTAAAT
1 TATTGTTTTAGGTAAATTTACT
611177 ATATTGTTTTAGGTAAAATTT-CT
1 -TATTGTTTTAGGT-AAATTTACT
611200 TATT
1 TATT
611204 CTTTCCTGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 12 0.36
23 2 0.06
24 4 0.12
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (22 bp):
TATTGTTTTAGGTAAATTTACT
Found at i:611219 original size:43 final size:42
Alignment explanation
Indices: 611115--611224 Score: 150
Period size: 43 Copynumber: 2.5 Consensus size: 42
611105 AACTTTCCTG
611115 ATTCTTTCCTATTTTAAATATATTGTTTTAGGTAAATTTACTT
1 ATTCTTTCCTA-TTTAAATATATTGTTTTAGGTAAATTTACTT
* *
611158 ATTATTTTCTATATTAAATATATTGTTTTAGGTAAAATTT-CTT
1 ATTCTTTCCTAT-TTAAATATATTGTTTTAGGT-AAATTTACTT
*
611201 ATTCTTTCCTGTTCTAAATATATT
1 ATTCTTTCCTATT-TAAATATATT
611225 CCAATATGTC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.03
43 51 0.86
44 6 0.10
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.55
Consensus pattern (42 bp):
ATTCTTTCCTATTTAAATATATTGTTTTAGGTAAATTTACTT
Found at i:612244 original size:100 final size:100
Alignment explanation
Indices: 612071--612271 Score: 393
Period size: 100 Copynumber: 2.0 Consensus size: 100
612061 TTATGTCTTG
612071 TTTGGATGCCATTATTTGACAAAAACATGTCTCATTTTGAAAGAGTAAAAAATACATATTTTCTT
1 TTTGGATGCCATTATTTGACAAAAACATGTCTCATTTTGAAAGAGTAAAAAATACATATTTTCTT
612136 ACTTATATTATGGGAATAAATTATATTAGGATGAT
66 ACTTATATTATGGGAATAAATTATATTAGGATGAT
612171 TTTGGATGCCATTATTTGACAAAAACATGTCTCATTTTGAAAGAGTAAAAAATACATATTTTCTT
1 TTTGGATGCCATTATTTGACAAAAACATGTCTCATTTTGAAAGAGTAAAAAATACATATTTTCTT
*
612236 ACTTATATTATGGGAATAAATTATATTCGGATGAT
66 ACTTATATTATGGGAATAAATTATATTAGGATGAT
612271 T
1 T
612272 CTAAAAAGCA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.39
Consensus pattern (100 bp):
TTTGGATGCCATTATTTGACAAAAACATGTCTCATTTTGAAAGAGTAAAAAATACATATTTTCTT
ACTTATATTATGGGAATAAATTATATTAGGATGAT
Found at i:613147 original size:43 final size:43
Alignment explanation
Indices: 613100--613222 Score: 124
Period size: 43 Copynumber: 2.9 Consensus size: 43
613090 AGGATTCCTT
*
613100 GGTAACTTTCTTGATTCTTTCCTATTTTAAATATATTGTTTTA
1 GGTAAATTTCTTGATTCTTTCCTATTTTAAATATATTGTTTTA
* ** *
613143 GGTAAATTTACTT-ATTATTTTGTATATTAAATATATTGTTTTA
1 GGTAAATTT-CTTGATTCTTTCCTATTTTAAATATATTGTTTTA
* * * **
613186 CGTAAAATTTCTTGTTTC-TTCCTGTTCAAAATATATT
1 GGT-AAATTTCTTGATTCTTTCCTATTTTAAATATATT
613223 CCAATATGTC
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
43 52 0.83
44 11 0.17
ACGTcount: A:0.28, C:0.10, G:0.09, T:0.54
Consensus pattern (43 bp):
GGTAAATTTCTTGATTCTTTCCTATTTTAAATATATTGTTTTA
Found at i:615781 original size:21 final size:21
Alignment explanation
Indices: 615757--615828 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
615747 GAGTTTGGGA
*
615757 TTTAGGGTTTGGGTTCATGGT
1 TTTAAGGTTTGGGTTCATGGT
* *
615778 TTTAAGGTTCTGAGTT--TGGGA
1 TTTAAGGTT-TGGGTTCAT-GGT
* *
615799 TTTAGGGTTTGGGCTCATGGT
1 TTTAAGGTTTGGGTTCATGGT
615820 TTTAAGGTT
1 TTTAAGGTT
615829 CTGAGTTTGG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
20 5 0.13
21 28 0.72
22 6 0.15
ACGTcount: A:0.14, C:0.06, G:0.35, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTGGGTTCATGGT
Found at i:615805 original size:42 final size:42
Alignment explanation
Indices: 615746--615852 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
615736 AAATAGTTTA
*
615746 TGAGTTTGGGATTTAGGGTTTGGGTTCATGGTTTTAAGGTTC
1 TGAGTTTGGGATTTAGGGTTTGGGCTCATGGTTTTAAGGTTC
615788 TGAGTTTGGGATTTAGGGTTTGGGCTCATGGTTTTAAGGTTC
1 TGAGTTTGGGATTTAGGGTTTGGGCTCATGGTTTTAAGGTTC
*
615830 TGAGTTTGGGATTTAGGATTTGG
1 TGAGTTTGGGATTTAGGGTTTGG
615853 TTTTGCTTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.15, C:0.05, G:0.36, T:0.44
Consensus pattern (42 bp):
TGAGTTTGGGATTTAGGGTTTGGGCTCATGGTTTTAAGGTTC
Found at i:616285 original size:43 final size:43
Alignment explanation
Indices: 616184--616270 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 43
616174 TGATTCTTTC
* * * *
616184 CTATTTTAAAAATATTGTTTTAGGTAAATTTATTTATTGTTGT
1 CTATATTAAATATATTGTTTTAGGTAAATTTACTTATTGCTGT
616227 CTATATTAAATATATTGTTTTAGGTAAAATTT-CTTATT-CTGT
1 CTATATTAAATATATTGTTTTAGGT-AAATTTACTTATTGCTGT
616269 CT
1 CT
616271 TGTTCTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
42 5 0.13
43 28 0.72
44 6 0.15
ACGTcount: A:0.30, C:0.06, G:0.10, T:0.54
Consensus pattern (43 bp):
CTATATTAAATATATTGTTTTAGGTAAATTTACTTATTGCTGT
Found at i:619266 original size:43 final size:42
Alignment explanation
Indices: 619192--619303 Score: 127
Period size: 43 Copynumber: 2.6 Consensus size: 42
619182 GGTAACTTTT
* *
619192 CTTATTCTTTCCTATTTAAGTATATTGTTTTAGGTAAATATA
1 CTTATTATTTCCTATTTAAATATATTGTTTTAGGTAAATATA
* * *
619234 CTTATTATTTTCTATATTAAATATATTTTTTTAGGTAAA-ATTT
1 CTTATTATTTCCTAT-TTAAATATATTGTTTTAGGTAAATA-TA
* *
619277 CTTTTTCTTTCCTATTCTAAATATATT
1 CTTATTATTTCCTATT-TAAATATATT
619304 CCAATTTGTC
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 15 0.25
43 44 0.75
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.56
Consensus pattern (42 bp):
CTTATTATTTCCTATTTAAATATATTGTTTTAGGTAAATATA
Found at i:622123 original size:25 final size:25
Alignment explanation
Indices: 622093--622164 Score: 126
Period size: 25 Copynumber: 2.8 Consensus size: 25
622083 CGAAGTACTG
622093 AACAGAGAGCACATAAGTGCTGGGT
1 AACAGAGAGCACATAAGTGCTGGGT
622118 AACAGAGAGCACATAAGTGCTGGGT
1 AACAGAGAGCACATAAGTGCTGGGT
*
622143 AACAGAGAGCACACAAAGTGCT
1 AACAGAGAGCACA-TAAGTGCT
622165 AAACTGAGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
25 38 0.84
26 7 0.16
ACGTcount: A:0.39, C:0.18, G:0.29, T:0.14
Consensus pattern (25 bp):
AACAGAGAGCACATAAGTGCTGGGT
Found at i:622203 original size:39 final size:39
Alignment explanation
Indices: 622149--622223 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
622139 GGGTAACAGA
* *
622149 GAGCACACAAAGTGCTAAACTGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
622188 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
622224 GCTAATCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:622218 original size:23 final size:23
Alignment explanation
Indices: 622188--622330 Score: 137
Period size: 23 Copynumber: 6.1 Consensus size: 23
622178 ACAAAGTACT
622188 GAGCACACAAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
*
622211 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* ** *
622234 GACCACATGAAGTGATAATAACAGA
1 GAGCACACAAAGTGCTAAT--CAGA
* * *
622259 GAGCACGA-GACGTGCTAAACAGA
1 GAGCAC-ACAAAGTGCTAATCAGA
*
622282 GAGCACACACAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAGA
* *
622305 GAGCGCACACAA-TGCTAATTAGA
1 GAGCACACA-AAGTGCTAATCAGA
622328 GAG
1 GAG
622331 TGTGCTAGTG
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
22 1 0.01
23 80 0.80
24 1 0.01
25 17 0.17
26 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.13
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCAGA
Found at i:625956 original size:17 final size:17
Alignment explanation
Indices: 625934--625972 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
625924 CTCCACCTTG
* *
625934 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
625951 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
625968 ACAAG
1 ACAAG
625973 TTTTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:630701 original size:13 final size:14
Alignment explanation
Indices: 630670--630706 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
630660 AAGTCATACA
630670 TTATGAGTTTGAGGT
1 TTATG-GTTTGAGGT
630685 TTATGGTTTGA-GT
1 TTATGGTTTGAGGT
630698 TTATGGTTT
1 TTATGGTTT
630707 TAGGGTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.50
14 6 0.27
15 5 0.23
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.54
Consensus pattern (14 bp):
TTATGGTTTGAGGT
Found at i:630741 original size:14 final size:14
Alignment explanation
Indices: 630719--630748 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
630709 GGGTTCGAGA
*
630719 TTAGGATTTTGGTT
1 TTAGCATTTTGGTT
630733 TTAGCATTTTGGTT
1 TTAGCATTTTGGTT
630747 TT
1 TT
630749 GGTTTTAGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.23, T:0.60
Consensus pattern (14 bp):
TTAGCATTTTGGTT
Found at i:631140 original size:43 final size:43
Alignment explanation
Indices: 631050--631157 Score: 119
Period size: 43 Copynumber: 2.5 Consensus size: 43
631040 CCTTTTTGAT
* * *
631050 TCTTTCTTGTTTTAAATATATTGATTTAGGTAAGTTTAATGAT
1 TCTTTCCTGTTTTAAATATATTGATTTAGGTAAATTTAATGAC
* * * *
631093 TCTTTCCTATTTTAAATATATTGTTTTAGGTAAAATTT-CTTAC
1 TCTTTCCTGTTTTAAATATATTGATTTAGGT-AAATTTAATGAC
* *
631136 TCTTTCCTGTTCTAAGTATATT
1 TCTTTCCTGTTTTAAATATATT
631158 CCAACGTGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 49 0.91
44 5 0.09
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.54
Consensus pattern (43 bp):
TCTTTCCTGTTTTAAATATATTGATTTAGGTAAATTTAATGAC
Found at i:631360 original size:14 final size:14
Alignment explanation
Indices: 631341--631368 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
631331 CAATTACCAA
631341 ATGGTTTAAAAATC
1 ATGGTTTAAAAATC
631355 ATGGTTTAAAAATC
1 ATGGTTTAAAAATC
631369 TTCTTAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
ATGGTTTAAAAATC
Found at i:632800 original size:22 final size:22
Alignment explanation
Indices: 632743--632801 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
632733 TGGTTATAGA
632743 TTATGAGTTTGAGG--TTTAGGG
1 TTATGAGTTTG-GGATTTTAGGG
**
632764 TT-TGAGTTTATGATTTTAGGG
1 TTATGAGTTTGGGATTTTAGGG
632785 TTATGAGTTTGGGATTT
1 TTATGAGTTTGGGATTT
632802 GGGATTTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 1 0.03
20 7 0.23
21 11 0.35
22 12 0.39
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (22 bp):
TTATGAGTTTGGGATTTTAGGG
Found at i:632817 original size:6 final size:6
Alignment explanation
Indices: 632806--632833 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
632796 GGATTTGGGA
632806 TTTTGG TTTTGG TTTTGG TTTTGG TTTT
1 TTTTGG TTTTGG TTTTGG TTTTGG TTTT
632834 AAGGGTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (6 bp):
TTTTGG
Found at i:633423 original size:20 final size:22
Alignment explanation
Indices: 633400--633441 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
633390 TCCAAAACCC
633400 TAAAA-ATAA-CTTAAAAATAA
1 TAAAAGATAATCTTAAAAATAA
633420 TAAAAGATAATTCTTAAAAATA
1 TAAAAGATAA-TCTTAAAAATA
633442 TTTAAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 4 0.21
23 10 0.53
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAAAGATAATCTTAAAAATAA
Found at i:634600 original size:23 final size:23
Alignment explanation
Indices: 634572--634625 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
634562 CGTCCATCCT
634572 TGCTGACTAGACCTTCTAAAAGC
1 TGCTGACTAGACCTTCTAAAAGC
* *
634595 TGCTGACTAGATCTTCTAGAAGC
1 TGCTGACTAGACCTTCTAAAAGC
634618 TGCTGACT
1 TGCTGACT
634626 GGATGCCATG
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:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (23 bp):
TGCTGACTAGACCTTCTAAAAGC
Found at i:635550 original size:25 final size:22
Alignment explanation
Indices: 635501--635552 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
635491 CTCTCTTTTC
635501 CTTATTTTTTGGTGGAACAAAT
1 CTTATTTTTTGGTGGAACAAAT
*
635523 CTTATTTTTTTGTGGAACAAAT
1 CTTATTTTTTGGTGGAACAAAT
*
635545 CTTCTTTT
1 CTTATTTT
635553 GTCTCGACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.52
Consensus pattern (22 bp):
CTTATTTTTTGGTGGAACAAAT
Found at i:640650 original size:23 final size:23
Alignment explanation
Indices: 640614--640668 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
640604 TCCATCCTTG
640614 CTGACTAGACCTTCT-GAAAGCTA
1 CTGACTAGACCTTCTAG-AAGCTA
* *
640637 CTGACTGGATCTTCTAGAAGCTA
1 CTGACTAGACCTTCTAGAAGCTA
640660 CTGACTAGA
1 CTGACTAGA
640669 TGTCACATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (23 bp):
CTGACTAGACCTTCTAGAAGCTA
Found at i:640947 original size:43 final size:43
Alignment explanation
Indices: 640895--641025 Score: 138
Period size: 43 Copynumber: 3.1 Consensus size: 43
640885 GCCCTGAACG
* *
640895 ATTA-TTTAGGTAACTTTTCTAATTCTTTCTTATTTTAAATAT
1 ATTACTTTAGGTAAATTTTCTAATTCTTTCCTATTTTAAATAT
** * ** *
640937 ATTGTTTTAGGTAAGTTTAATGATTCTTTCCTATTTTAAATAT
1 ATTACTTTAGGTAAATTTTCTAATTCTTTCCTATTTTAAATAT
* * * * *
640980 ATTACTTTAGGTAAAATTTCTTACTCTTTCCTGTTTTAAGTAT
1 ATTACTTTAGGTAAATTTTCTAATTCTTTCCTATTTTAAATAT
641023 ATT
1 ATT
641026 CCAATTTGTC
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
42 3 0.04
43 69 0.96
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.54
Consensus pattern (43 bp):
ATTACTTTAGGTAAATTTTCTAATTCTTTCCTATTTTAAATAT
Found at i:643912 original size:43 final size:43
Alignment explanation
Indices: 643864--643952 Score: 124
Period size: 43 Copynumber: 2.1 Consensus size: 43
643854 TGAATGATTG
** **
643864 TTTAGGTAACTTTTCTGATTCTTTTTTATTTTAAATATATTAT
1 TTTAGGTAACTTAACTGATTCTTTCCTATTTTAAATATATTAT
* *
643907 TTTAGGTAAGTTAAGTGATTCTTTCCTATTTTAAATATATTAT
1 TTTAGGTAACTTAACTGATTCTTTCCTATTTTAAATATATTAT
643950 TTT
1 TTT
643953 GGGAAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.27, C:0.07, G:0.09, T:0.57
Consensus pattern (43 bp):
TTTAGGTAACTTAACTGATTCTTTCCTATTTTAAATATATTAT
Found at i:646826 original size:43 final size:43
Alignment explanation
Indices: 646773--646871 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 43
646763 ACCCTGAATG
* *
646773 ATTG-TTTAGGTAACTTTTCTGATTCTTTCTTATTCCAAATAT
1 ATTGTTTTAGGTAACTTTACTGATTCTTTCCTATTCCAAATAT
* * **
646815 ATTGTTTTAGGTAAGTTTAGTGATTCTTTCCTATTTTAAATAT
1 ATTGTTTTAGGTAACTTTACTGATTCTTTCCTATTCCAAATAT
* *
646858 ATTATATTAGGTAA
1 ATTGTTTTAGGTAA
646872 AATTTCTTAC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (43 bp):
ATTGTTTTAGGTAACTTTACTGATTCTTTCCTATTCCAAATAT
Found at i:649183 original size:21 final size:21
Alignment explanation
Indices: 649139--649184 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
649129 AGTGATTACA
* *
649139 GATTATGAGTTTCGGGTTTAG
1 GATTATGAGTTTAGGATTTAG
*
649160 GATTATGAGTTTAGGATTTGG
1 GATTATGAGTTTAGGATTTAG
649181 GATT
1 GATT
649185 TTGGTTTTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (21 bp):
GATTATGAGTTTAGGATTTAG
Found at i:649550 original size:43 final size:43
Alignment explanation
Indices: 649497--649595 Score: 137
Period size: 43 Copynumber: 2.3 Consensus size: 43
649487 ACCCTGAACG
** * *
649497 ATTG-TTTAGGTAACTTTTTTTATTCTTTCTTATTTTAAATAT
1 ATTGTTTTAGGTAACTTTAGTGATTCTTTCCTATTTTAAATAT
*
649539 ATTGTTTTAGGTAAGTTTAGTGATTCTTTCCTATTTTAAATAT
1 ATTGTTTTAGGTAACTTTAGTGATTCTTTCCTATTTTAAATAT
*
649582 ATTATTTTAGGTAA
1 ATTGTTTTAGGTAA
649596 AATGTC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 4 0.08
43 46 0.92
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (43 bp):
ATTGTTTTAGGTAACTTTAGTGATTCTTTCCTATTTTAAATAT
Done.