Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold338
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: 543359
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.28
Warning! 76736 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:300526 original size:30 final size:32
Alignment explanation
Indices: 300461--300542 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 32
300451 CATACCTATG
**
300461 CAAATATATTATATATATATAACACCCATGCACC
1 CAAATATA-TAT-TATATATAACACCCATAAACC
300495 CAAATATATATTATATATAACA-CCA-AAACC
1 CAAATATATATTATATATAACACCCATAAACC
*
300525 C--ATATATATTGTATATAA
1 CAAATATATATTATATATAA
300543 ATAACAAAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 16 0.36
30 4 0.09
31 3 0.07
32 11 0.24
33 3 0.07
34 8 0.18
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (32 bp):
CAAATATATATTATATATAACACCCATAAACC
Found at i:310880 original size:34 final size:34
Alignment explanation
Indices: 310836--310911 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
310826 GAGTTAGTTT
*
310836 ATTAACTTTATTTCAGCTCAAATAAGTGTTAGTA
1 ATTAATTTTATTTCAGCTCAAATAAGTGTTAGTA
*
310870 ATTAATTTTATTTCAGCTTAAATAAGTGTTAGTA
1 ATTAATTTTATTTCAGCTCAAATAAGTGTTAGTA
310904 ATTAATTT
1 ATTAATTT
310912 GTTTAAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (34 bp):
ATTAATTTTATTTCAGCTCAAATAAGTGTTAGTA
Found at i:322433 original size:14 final size:14
Alignment explanation
Indices: 322414--322444 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
322404 TTTGGTTATA
*
322414 ATTGGACTTTGGAC
1 ATTGGACATTGGAC
322428 ATTGGACATTGGAC
1 ATTGGACATTGGAC
322442 ATT
1 ATT
322445 TTGATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (14 bp):
ATTGGACATTGGAC
Found at i:327210 original size:24 final size:21
Alignment explanation
Indices: 327181--327225 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 21
327171 ACTTATTAAG
327181 TTAAATATTAGATTAAATTTAATA
1 TTAAATATT--ATTAAA-TTAATA
327205 TTAAATATTATTAAATTAATA
1 TTAAATATTATTAAATTAATA
327226 GAATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
24 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAATATTATTAAATTAATA
Found at i:342185 original size:25 final size:24
Alignment explanation
Indices: 342121--342214 Score: 62
Period size: 25 Copynumber: 3.8 Consensus size: 24
342111 ATGTAATCGG
* *
342121 GAAGCTCTTTCGAGCCATATAATA
1 GAAGCTCTTACGAGCCATATAAAA
* * **
342145 GAAAGCTCATATGAGCTGTATAACAA
1 G-AAGCTCTTACGAGCCATATAA-AA
* ***
342171 GAAGCTCTTACGAGCCAAATATCGG
1 GAAGCTCTTACGAGCCATATA-AAA
*
342196 GAAGCTCATACGAGCCATA
1 GAAGCTCTTACGAGCCATA
342215 AACGAGAAGC
Statistics
Matches: 51, Mismatches: 16, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
24 1 0.02
25 48 0.94
26 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.22
Consensus pattern (24 bp):
GAAGCTCTTACGAGCCATATAAAA
Found at i:344485 original size:41 final size:41
Alignment explanation
Indices: 344428--344537 Score: 184
Period size: 41 Copynumber: 2.7 Consensus size: 41
344418 TAGCAACCCC
*
344428 TCGGGAAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
* * *
344469 TCGGGGAATTTGCACTTAGCAACCCTTTTTTTATCAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
344510 TCGGGGAATCTGCACTTAGCAACCCCTT
1 TCGGGGAATCTGCACTTAGCAACCCCTT
344538 ACATTCAATG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTGATCAGTGAT
Found at i:344628 original size:19 final size:20
Alignment explanation
Indices: 344579--344629 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 20
344569 TTCAATCTGG
* *
344579 AACCTTATTTTACAACATTT
1 AACCATATTTTTCAACATTT
*
344599 TACCA-ACTTTTTCAA-ATTT
1 AACCATA-TTTTTCAACATTT
344618 AACCATATTTTT
1 AACCATATTTTT
344630 TGTAATTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (20 bp):
AACCATATTTTTCAACATTT
Found at i:351039 original size:146 final size:147
Alignment explanation
Indices: 350840--351132 Score: 579
Period size: 146 Copynumber: 2.0 Consensus size: 147
350830 TTAAAAAATA
350840 ATTAAAATAAGAAAAAATAAAATATATACTATAATATAATACAAATACAAATATATATATTAAAA
1 ATTAAAATAAGAAAAAATAAAATATATACTATAATATAATACAAATACAAATATATATATTAAAA
350905 TATGTACAGTTAAAAGTTATGTAAATTTTTACTAAATATTTAATACTTTTAAAAAATAAATCAAA
66 TATGTACAGTTAAAAGTTATGTAAATTTTTACTAAATATTTAATACTTTTAAAAAATAAATCAAA
350970 CACTTTTTTTTTCTTTT
131 CACTTTTTTTTTCTTTT
350987 ATTAAAATAA-AAAAAATAAAATATATACTATAATATAATACAAATACAAATATATATATTAAAA
1 ATTAAAATAAGAAAAAATAAAATATATACTATAATATAATACAAATACAAATATATATATTAAAA
351051 TATGTACAGTTAAAAGTTATGTAAATTTTTACTAAATATTTAATACTTTTAAAAAATAAATCAAA
66 TATGTACAGTTAAAAGTTATGTAAATTTTTACTAAATATTTAATACTTTTAAAAAATAAATCAAA
351116 CACTTTTTTTTTCTTTT
131 CACTTTTTTTTTCTTTT
351133 TCCTTTTCTC
Statistics
Matches: 146, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
146 136 0.93
147 10 0.07
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.40
Consensus pattern (147 bp):
ATTAAAATAAGAAAAAATAAAATATATACTATAATATAATACAAATACAAATATATATATTAAAA
TATGTACAGTTAAAAGTTATGTAAATTTTTACTAAATATTTAATACTTTTAAAAAATAAATCAAA
CACTTTTTTTTTCTTTT
Found at i:358562 original size:16 final size:15
Alignment explanation
Indices: 358541--358580 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 15
358531 TTGGTGCTTT
358541 TGCTATATGTATATTA
1 TGCTATATGTATA-TA
358557 TGCTATATGTATATA
1 TGCTATATGTATATA
358572 TGCATATAT
1 TGC-TATAT
358581 ATCAATCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (15 bp):
TGCTATATGTATATA
Found at i:359239 original size:15 final size:15
Alignment explanation
Indices: 359219--359248 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
359209 TGTTGTCAAC
359219 GTTTGATTGCTACAA
1 GTTTGATTGCTACAA
359234 GTTTGATTGCTACAA
1 GTTTGATTGCTACAA
359249 CAAGAGTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
GTTTGATTGCTACAA
Found at i:361065 original size:61 final size:61
Alignment explanation
Indices: 360968--361090 Score: 192
Period size: 61 Copynumber: 2.0 Consensus size: 61
360958 TTAACAACTT
* *
360968 ACTTAATTTCACGATCGGACAATCTAAATGATTCGAATCAACAATGAACCGAGTTCCTATC
1 ACTTAATTTCACGATCGGACAATCTAAACGACTCGAATCAACAATGAACCGAGTTCCTATC
* * * *
361029 ACTTAATTTCATGATCGGGCAATCTAAACGACTCGAATCAACACTGAACCGAGTTCGTATC
1 ACTTAATTTCACGATCGGACAATCTAAACGACTCGAATCAACAATGAACCGAGTTCCTATC
361090 A
1 A
361091 TTTGGTATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.27
Consensus pattern (61 bp):
ACTTAATTTCACGATCGGACAATCTAAACGACTCGAATCAACAATGAACCGAGTTCCTATC
Found at i:361685 original size:46 final size:49
Alignment explanation
Indices: 361598--361693 Score: 135
Period size: 51 Copynumber: 2.0 Consensus size: 49
361588 GTTTAGTTAT
* *
361598 ATTAGTTTAATTAATTAAGTTGTTTTTTAAGTTTCTTTAGTTGCTTAAATC
1 ATTAGGTTAATGAATTAAGTTGTTTTTTAA--TTCTTTAGTTGCTTAAATC
361649 ATTAGGTTAATGAATTAAGTTG-TTTTTAA-T-TTTAGTTGCTTAAAT
1 ATTAGGTTAATGAATTAAGTTGTTTTTTAATTCTTTAGTTGCTTAAAT
361694 AATTTTGGCA
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
46 15 0.35
47 1 0.02
50 7 0.16
51 20 0.47
ACGTcount: A:0.29, C:0.04, G:0.14, T:0.53
Consensus pattern (49 bp):
ATTAGGTTAATGAATTAAGTTGTTTTTTAATTCTTTAGTTGCTTAAATC
Found at i:363941 original size:43 final size:43
Alignment explanation
Indices: 363892--363975 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
363882 AAGAAAGCAC
363892 GCATGGGACGACATT-AAAGGAGCTGTTGATTTCTCCTTTTCAT
1 GCATGGGACGACATTAAAAGGAGCTGTTGATTTCT-CTTTTCAT
* *
363935 GCATGGGGCGACATTAAAAGGAGCTGTTGTTTTCTCTTTTC
1 GCATGGGACGACATTAAAAGGAGCTGTTGATTTCTCTTTTC
363976 CATGTGCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 20 0.53
44 18 0.47
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.36
Consensus pattern (43 bp):
GCATGGGACGACATTAAAAGGAGCTGTTGATTTCTCTTTTCAT
Found at i:364248 original size:21 final size:21
Alignment explanation
Indices: 364224--364268 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 21
364214 TTTCCAACCA
364224 GCTATGAAAA-CATTCACATTT
1 GCTA-GAAAATCATTCACATTT
364245 GCTAGAAAATTCCATTCACATTT
1 GCTAGAAAA-T-CATTCACATTT
364268 G
1 G
364269 TGCCCATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
23 12 0.57
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (21 bp):
GCTAGAAAATCATTCACATTT
Found at i:370607 original size:21 final size:22
Alignment explanation
Indices: 370574--370628 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
370564 TGTTTCTCTC
*
370574 TCAC-TTTCCTTTTCGCCTTTT
1 TCACTTTTCATTTTCGCCTTTT
**
370595 TCA-TTTTCATTTTCTTCTTTT
1 TCACTTTTCATTTTCGCCTTTT
370616 TCACTTTT-ATTTT
1 TCACTTTTCATTTT
370629 TCTCTTCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.09, C:0.24, G:0.02, T:0.65
Consensus pattern (22 bp):
TCACTTTTCATTTTCGCCTTTT
Found at i:374212 original size:561 final size:561
Alignment explanation
Indices: 373150--374453 Score: 2295
Period size: 561 Copynumber: 2.3 Consensus size: 561
373140 TAAAAAAACA
* * * *
373150 ACCAAAATTGGTTCCTTAATGCTCGTAACTAAGATCCAATGCGCCTTAGCTACAATATTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTACAAGATTCGGTTT
*
373215 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCACTCAAAACAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
* *
373280 CAAAATTGGACCAAGATTCAGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAGTATTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATATTGATTTTCT
* * * *
373345 TTTTCCTTCGTTTACGCAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCCATTTAGTTTTGA
196 TTTTCCTTCGTATACACAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCAATTTACTTTTGA
373410 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
261 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
* *
373475 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGGATTTTTTTACATAGGA
326 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACACAGGA
373540 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
391 ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
* *
373605 CAATTTGGCCTGATTTTCAACTAAGTTTAAATTAAATTTCCTGATTGGGCTTGGAACGTCTTATT
456 CAATTTGGCCTGATTTTCAACTAAGTCTAAATTAAATTTCCTGATTGGGCTTGGAACATCTTATT
*
373670 GGGCCTTGCCTTCAAGAACTTGGGCTTGTAATCCATTTTCT
521 GGGCCTTGCCTTCAAGAACTTAGGCTTGTAATCCATTTTCT
* * *
373711 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGGTCCAATGCGCCTTAGCTACAGGACTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTACAAGATTCGGTTT
*
373776 CTTGGACCAAGATTTCCAAGAATTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
* * * *
373841 AAAAAATGGACTAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCT
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATATTGATTTTCT
373906 TTTTCCTTCGTATACACAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCAATTTACTTTTGA
196 TTTTCCTTCGTATACACAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCAATTTACTTTTGA
373971 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCT-AAAAAAAACCTAATTACTA
261 ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
374035 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTTACACAGG
326 ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAA-TTTTTTTACACAGG
374100 AATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTG
390 AATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTG
* * *
374165 ACAATTTGGCCTGATTTTCAACTAAGTCTAATTTATATTTCCTGATTGGGCTTGGAACATTTTAT
455 ACAATTTGGCCTGATTTTCAACTAAGTCTAAATTAAATTTCCTGATTGGGCTTGGAACATCTTAT
**
374230 TGGGCCTTGCCTTCAAGAACTTAGGCTTGTAATCTGTTTTCT
520 TGGGCCTTGCCTTCAAGAACTTAGGCTTGTAATCCATTTTCT
* * *
374272 ACCAAAATTGGTCCGTTGATGCTCGTAACTGAGATCCAATGTGCCTTAGCTGCAAGATTCGGTTT
1 ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTACAAGATTCGGTTT
*
374337 CTTGGACCAAGAATTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
66 CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
374402 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGA
131 CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGA
374454 NNNNNNNNNN
Statistics
Matches: 702, Mismatches: 40, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
560 68 0.10
561 634 0.90
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (561 bp):
ACCAAAATTGGTTCGTTGATGCTCGTAACTGAGATCCAATGCGCCTTAGCTACAAGATTCGGTTT
CTTGGACCAAGATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATCGCTCAAAACAG
CAAAATTGGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATATTGATTTTCT
TTTTCCTTCGTATACACAACTAAGGTCTTGCTAATAAATTCTTGAATGGTTCAATTTACTTTTGA
ACGCATAAGCCTCCTAACTATTTTCCTAACCCTATTAGGAAATCTAAAAAAAAACCTAATTACTA
ATTTCAAGGGGAAATTCGGCCAAGGCTTTTAATGGGCTGCTTGGGCTGAATTTTTTTACACAGGA
ATTAAATCATAAAGTCTAAAAATTAAAACTAGGTATTTAAAATTTTACAAATTGGGCCACTTTGA
CAATTTGGCCTGATTTTCAACTAAGTCTAAATTAAATTTCCTGATTGGGCTTGGAACATCTTATT
GGGCCTTGCCTTCAAGAACTTAGGCTTGTAATCCATTTTCT
Found at i:386550 original size:6 final size:6
Alignment explanation
Indices: 386539--386578 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
386529 AAAAAAGAAA
* * *
386539 AAAATC ATAATC AAAATC ATAATC AAAATC AAAAAC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
386579 AGAAGAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:386578 original size:12 final size:12
Alignment explanation
Indices: 386539--386569 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
386529 AAAAAAGAAA
386539 AAAATCATAATC
1 AAAATCATAATC
386551 AAAATCATAATC
1 AAAATCATAATC
386563 AAAATCA
1 AAAATCA
386570 AAAACAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAATCATAATC
Found at i:396873 original size:6 final size:7
Alignment explanation
Indices: 396847--396896 Score: 59
Period size: 8 Copynumber: 7.0 Consensus size: 7
396837 TGAGTCAGAA
396847 AAAATATG
1 AAAA-ATG
396855 AAAAATG
1 AAAAATG
396862 AAAAAATG
1 -AAAAATG
396870 AAAAA-G
1 AAAAATG
396876 AAAAATG
1 AAAAATG
396883 -AAAATG
1 AAAAATG
396889 TAAAAATG
1 -AAAAATG
396897 GAGAGGCTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 12 0.32
7 9 0.24
8 17 0.45
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:396878 original size:14 final size:14
Alignment explanation
Indices: 396846--396896 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
396836 TTGAGTCAGA
396846 AAAAATATGAAAAATG
1 AAAAA-ATGAAAAA-G
396862 AAAAAATGAAAAAG
1 AAAAAATGAAAAAG
*
396876 -AAAAATGAAAATG
1 AAAAAATGAAAAAG
*
396889 TAAAAATG
1 AAAAAATG
396897 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 12 0.36
14 8 0.24
15 8 0.24
16 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.16
Consensus pattern (14 bp):
AAAAAATGAAAAAG
Found at i:398402 original size:128 final size:127
Alignment explanation
Indices: 398130--398367 Score: 343
Period size: 128 Copynumber: 1.9 Consensus size: 127
398120 AACAGATCAG
* *
398130 TGAATATAACAGATCTGGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCT
1 TGAA-ATAATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCT
* * * *
398195 TCAAGTTTAAGGAAGCAGATTTAAGCCACAAGTCCTATGTCCCTGGTCAGTAGTGGAGTAGGT
65 TCAAGTGTAAGGAAGCAGATTGAAGCCACAAGTCCTATCTCCCTAGTCAGTAGTGGAGTAGGT
* * **
398258 TGGAAATTATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCGAAGACGGTGAATCTTATCT
1 T-GAAATAATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCT
*
398323 TCAAGTGTAAGGAAGCAGATTGAAGCCGATAA-TCCTATCTCCCTA
65 TCAAGTGTAAGGAAGCAGATTGAAGCC-ACAAGTCCTATCTCCCTA
398368 AAGTTGTAGT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
128 91 0.94
129 6 0.06
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (127 bp):
TGAAATAATAGATCTTGTCTCCCTAAGCAATAGCGGAGCAGATCAAAGACGACGAATCTTATCTT
CAAGTGTAAGGAAGCAGATTGAAGCCACAAGTCCTATCTCCCTAGTCAGTAGTGGAGTAGGT
Found at i:398596 original size:44 final size:44
Alignment explanation
Indices: 398336--399082 Score: 372
Period size: 44 Copynumber: 17.2 Consensus size: 44
398326 AGTGTAAGGA
* * * *
398336 AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * **
398380 AGCGGATTAAAGTA--ATAGATCTTATCTCTCTGATGTTGCAGCAG
1 AGCAGATTGAAG-ACGATA-ATCTTATCTCCCTGAAGTTGCAGTGG
** * * * ** * *
398424 AGTGGATCGCA-TC-A-GGTCTTTTCTCCCTGAAGTTGCAGCGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * ** *
398465 AGCAGACTG-AGTAAGCA-GGTCTTATCCCCCTGAAGTTGCAGTGG
1 AGCAGATTGAAG-ACG-ATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * **
398509 GGCAGATCGAAGATGACAAATCTTATCTCCCTGAAGTTATAGTGG
1 AGCAGATTGAAGACGA-TAATCTTATCTCCCTGAAGTTGCAGTGG
* * *
398554 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
398598 AG-AGGATTAAAGTA--ATAGATCTTATCTCTCTGAAGTTCCAGTAG
1 AGCA-GATTGAAG-ACGATA-ATCTTATCTCCCTGAAGTTGCAGTGG
** * * * ** * *
398642 AGTGGATCGCA-TC-A-GGTCTTATCTCCCTGAGGTTGTAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
** * * **
398683 AGCAGATTG-AGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGG
1 AGCAGATTGAAGACGATAA-TCTTATCTCCCTGAAGTTGCAGTGG
* * * *
398727 GGCAGACTGAAGAAGCA-AATCTTATCTCCCTGAGGTTGCAGTGG
1 AGCAGATTGAAGACG-ATAATCTTATCTCCCTGAAGTTGCAGTGG
* * *
398771 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGCAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * * *
398815 AGCGGATTAAAGTA--ATAGATCTTATCTCTCTGAAGTTCCAGTAG
1 AGCAGATTGAAG-ACGATA-ATCTTATCTCCCTGAAGTTGCAGTGG
** * * * ** * *
398859 AGTGGATCGCA-TC-A-GGTCTTATCTCCCTGAGGTTGTAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
** * * **
398900 AGCAGATTG-AGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGG
1 AGCAGATTGAAGACGATAA-TCTTATCTCCCTGAAGTTGCAGTGG
* * * *
398944 GGCAGACTGAAGAAGCA-AATCTTATCTCCCTGAGGTTGCAGTGG
1 AGCAGATTGAAGACG-ATAATCTTATCTCCCTGAAGTTGCAGTGG
* * *
398988 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGCAGTGG
1 AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
399032 AGCGGATTAAAGTA--ATAGATCTTATCTCTCTGAAGTTGCAGTAG
1 AGCAGATTGAAG-ACGATA-ATCTTATCTCCCTGAAGTTGCAGTGG
399076 AGCAGAT
1 AGCAGAT
399083 CGCATCAAGT
Statistics
Matches: 528, Mismatches: 141, Indels: 68
0.72 0.19 0.09
Matches are distributed among these distances:
40 3 0.01
41 78 0.15
42 2 0.00
43 19 0.04
44 376 0.71
45 48 0.09
46 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (44 bp):
AGCAGATTGAAGACGATAATCTTATCTCCCTGAAGTTGCAGTGG
Found at i:398848 original size:217 final size:217
Alignment explanation
Indices: 398336--399095 Score: 1234
Period size: 217 Copynumber: 3.5 Consensus size: 217
398326 AGTGTAAGGA
* *
398336 AGCAGATTGAAGCCGATAATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATC
* * * * * * *
398401 TTATCTCTCTGATGTTGCAGCAGAGTGGATCGCATCAGGTCTTTTCTCCCTGAAGTTGCAGCGGA
66 TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGTAGTGGA
* * * * ** *
398466 GCAGACTGAGTAAGCAGGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGA-TCGAAGATGACAAAT
131 GCAGATTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACT-GAAGAAG-CAAAT
* **
398530 CTTATCTCCCTGAAGTTATAGTGG
194 CTTATCTCCCTGAGGTTGCAGTGG
* *
398554 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGAGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATC
398619 TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGTAGTGGA
66 TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGTAGTGGA
398684 GCAGATTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCT
131 GCAGATTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCT
398749 TATCTCCCTGAGGTTGCAGTGG
196 TATCTCCCTGAGGTTGCAGTGG
* *
398771 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATC
398836 TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGTAGTGGA
66 TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGTAGTGGA
398901 GCAGATTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCT
131 GCAGATTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCT
398966 TATCTCCCTGAGGTTGCAGTGG
196 TATCTCCCTGAGGTTGCAGTGG
* *
398988 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATC
* ** *
399053 TTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTT
66 TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTT
399096 GCGGACTAGA
Statistics
Matches: 514, Mismatches: 27, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
217 343 0.67
218 170 0.33
219 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (217 bp):
AGCAGATTGAAGCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAGTAATAGATC
TTATCTCTCTGAAGTTCCAGTAGAGTGGATCGCATCAGGTCTTATCTCCCTGAGGTTGTAGTGGA
GCAGATTGAGAAAACAAGTCTTATCCCCCTGAAGTCACAGTGGGGCAGACTGAAGAAGCAAATCT
TATCTCCCTGAGGTTGCAGTGG
Found at i:403552 original size:7 final size:6
Alignment explanation
Indices: 403505--403548 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
403495 AAGAGACTGT
* *
403505 AGAAAA AGAAAA AGAACA AGAAAA A-AAGAG AGAAAA AGAAAA AG
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAA-AA AGAAAA AGAAAA AG
403549 GAAAGATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 2 0.06
6 28 0.88
7 2 0.06
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:406373 original size:22 final size:21
Alignment explanation
Indices: 406341--406382 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
406331 TTGGTATTTA
406341 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
406362 GGAATTTGGTACGAATTGGTA
1 GGAA-TTGGTACGAAATGGTA
406383 ATGGTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:407971 original size:49 final size:47
Alignment explanation
Indices: 407914--408008 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 47
407904 TTTAATGTGT
* *
407914 TTAGTTTAATTAATTCAATTGTTTTAATTTTCTTTAGTTGCTTAAATAC
1 TTAGTTTAATTAATTAAATTGTTTTAA-ATT-TTTAGTTGCTTAAATAC
407963 TTAGTTTAATTAATTAAATTGTTTTAAATTTTTAGTTGCTTAAATA
1 TTAGTTTAATTAATTAAATTGTTTTAAATTTTTAGTTGCTTAAATA
408009 ATTTCGACTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 16 0.36
48 2 0.05
49 26 0.59
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (47 bp):
TTAGTTTAATTAATTAAATTGTTTTAAATTTTTAGTTGCTTAAATAC
Found at i:409100 original size:61 final size:61
Alignment explanation
Indices: 409005--409127 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
408995 TTAGCAACTT
* * * * *
409005 ACTTAATTTTACGATCGGGCAATCTAAACGACTCGAATTAACACTGAACTGAGTTTGTATC
1 ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
409066 ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
1 ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
409127 A
1 A
409128 TAGCATTTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (61 bp):
ACTTAATTTCACGATCAGGCAATCTAAACGACTCGAATAAACACCGAACTGAGTTCGTATC
Found at i:411878 original size:30 final size:30
Alignment explanation
Indices: 411842--411903 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
411832 CCCTTTAAAG
*
411842 TAAAAAAAATTAGGTTTTTTTTAGTTTTCC
1 TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
411872 TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
1 TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
411902 TA
1 TA
411904 TTAGGACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (30 bp):
TAAAAAAAAATAGGTTTTTTTTAGTTTTCC
Found at i:415309 original size:24 final size:26
Alignment explanation
Indices: 415260--415323 Score: 78
Period size: 24 Copynumber: 2.5 Consensus size: 26
415250 AAGAAGGGTT
*
415260 GAAATTGGCTAAGTGAAATGATGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
*
415286 GAAA-TGGCTAGGTG-AATGAGGATG
1 GAAATTGGCTAAGTGAAATGAGGATG
*
415310 GAGATTTGGCTAAG
1 GA-AATTGGCTAAG
415324 GTTTTGAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 11 0.34
25 10 0.31
26 11 0.34
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (26 bp):
GAAATTGGCTAAGTGAAATGAGGATG
Found at i:416854 original size:36 final size:36
Alignment explanation
Indices: 416808--416910 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 36
416798 ATCAGGCACC
*
416808 CCACCACCACCAGCAATATTCCTTTCGGGACACACA
1 CCACCACCACCAGCATTATTCCTTTCGGGACACACA
** *
416844 CCACCACCACCAGCATTATTCCTTTCGGGACGTACG
1 CCACCACCACCAGCATTATTCCTTTCGGGACACACA
*
416880 CCACCACCACCAACATTACTTCCTTT-GGGAC
1 CCACCACCACCAGCATTA-TTCCTTTCGGGAC
416911 TTCGAGACAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
36 54 0.89
37 7 0.11
ACGTcount: A:0.26, C:0.41, G:0.13, T:0.20
Consensus pattern (36 bp):
CCACCACCACCAGCATTATTCCTTTCGGGACACACA
Found at i:417247 original size:20 final size:20
Alignment explanation
Indices: 417222--417262 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
417212 CAAGCTGAAC
*
417222 TAAGCTCAAACTTAGCTCAA
1 TAAGCTCAAACCTAGCTCAA
417242 TAAGCTCAAACCTAGCTCAA
1 TAAGCTCAAACCTAGCTCAA
417262 T
1 T
417263 TTAATTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.27, G:0.10, T:0.24
Consensus pattern (20 bp):
TAAGCTCAAACCTAGCTCAA
Found at i:417435 original size:27 final size:28
Alignment explanation
Indices: 417399--417475 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 28
417389 GTGTTTTAAT
*
417399 TTAATGCATGTTTTTAATATGTCCTAG-
1 TTAATACATGTTTTTAATATGTCCTAGC
* * *
417426 TTAATACATGTTATTAATTTGTCTTAGC
1 TTAATACATGTTTTTAATATGTCCTAGC
* * **
417454 CTATTACATAATTTTAATATGT
1 TTAATACATGTTTTTAATATGT
417476 TTTAGCTCCA
Statistics
Matches: 39, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.49
Consensus pattern (28 bp):
TTAATACATGTTTTTAATATGTCCTAGC
Found at i:420214 original size:43 final size:42
Alignment explanation
Indices: 420151--420236 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 42
420141 AAGGCACCTA
** * *
420151 GAAAAGAGAAATCAGTAGCTCTTTTAATGTCGTCCCTTGCAT
1 GAAAAGAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
420193 GAAAAGGAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
1 GAAAA-GAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
420236 G
1 G
420237 CTTTCTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
42 5 0.13
43 34 0.87
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
GAAAAGAGAAATCAACAGCTCCTTTAATGTCGTCCCATGCAT
Found at i:421456 original size:19 final size:21
Alignment explanation
Indices: 421424--421467 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
421414 TCAAAACAAA
421424 AAAAATCAAGAAAAAGAAAGG
1 AAAAATCAAGAAAAAGAAAGG
*
421445 AAAAAT-AA-AAAAAGAAAGT
1 AAAAATCAAGAAAAAGAAAGG
421464 AAAA
1 AAAA
421468 TAATTATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (21 bp):
AAAAATCAAGAAAAAGAAAGG
Found at i:426971 original size:42 final size:42
Alignment explanation
Indices: 426912--427746 Score: 1670
Period size: 42 Copynumber: 19.9 Consensus size: 42
426902 TGTGTGAAAC
426912 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
426954 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
426996 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427038 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427080 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427122 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427164 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427206 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427248 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427290 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427332 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427374 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427416 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427458 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427500 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427542 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427584 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427626 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427668 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
427710 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
1 GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCC
427747 CTTTGAATTT
Statistics
Matches: 793, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 793 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.41
Consensus pattern (42 bp):
GTTTGAAATTCAAACATTTGAACTCTTGTTCTTATCCAAAAT
Found at i:431640 original size:12 final size:12
Alignment explanation
Indices: 431623--431647 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
431613 AAAATCTGAT
431623 TTCAATGTGTAA
1 TTCAATGTGTAA
431635 TTCAATGTGTAA
1 TTCAATGTGTAA
431647 T
1 T
431648 GTGTATAAGG
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTCAATGTGTAA
Found at i:431836 original size:16 final size:16
Alignment explanation
Indices: 431815--431846 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
431805 ATTATAAAGT
431815 CTAAAAAATTAAAATA
1 CTAAAAAATTAAAATA
431831 CTAAAAAATTAAAATA
1 CTAAAAAATTAAAATA
431847 AGTATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (16 bp):
CTAAAAAATTAAAATA
Found at i:432260 original size:39 final size:40
Alignment explanation
Indices: 432198--432277 Score: 153
Period size: 39 Copynumber: 2.0 Consensus size: 40
432188 GAACGTTATA
432198 CCAAAGGTGATAAGTTCAGCAACAAAGAATAGATGGACGC
1 CCAAAGGTGATAAGTTCAGCAACAAAGAATAGATGGACGC
432238 CCAAAGGTGAT-AGTTCAGCAACAAAGAATAGATGGACGC
1 CCAAAGGTGATAAGTTCAGCAACAAAGAATAGATGGACGC
432277 C
1 C
432278 ACAAGCTATG
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 29 0.73
40 11 0.28
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (40 bp):
CCAAAGGTGATAAGTTCAGCAACAAAGAATAGATGGACGC
Found at i:432281 original size:20 final size:20
Alignment explanation
Indices: 432219--432281 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
432209 AAGTTCAGCA
432219 ACAAAGAATAGATGGACGCC
1 ACAAAGAATAGATGGACGCC
* ** *
432239 -CAAAG-GT-GATAGTTCAGCA
1 ACAAAGAATAGAT-GGAC-GCC
432258 ACAAAGAATAGATGGACGCC
1 ACAAAGAATAGATGGACGCC
432278 ACAA
1 ACAA
432282 GCTATGCTTG
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 7 0.23
20 11 0.37
21 3 0.10
22 3 0.10
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (20 bp):
ACAAAGAATAGATGGACGCC
Found at i:451772 original size:12 final size:12
Alignment explanation
Indices: 451701--451746 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
451691 GACTAGAAGA
*
451701 GAAAAATGAAAGT
1 GAAAAA-GAAATT
*
451714 GAAAAAGAGATT
1 GAAAAAGAAATT
451726 GAAAAAGAAATT
1 GAAAAAGAAATT
*
451738 GCAAAAGAA
1 GAAAAAGAA
451747 GAAAAAGCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
12 23 0.79
13 6 0.21
ACGTcount: A:0.63, C:0.02, G:0.22, T:0.13
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:458720 original size:21 final size:21
Alignment explanation
Indices: 458694--458743 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
458684 TGCTTTCTTA
*
458694 TTTTCTTCTTTTATTACTTCT
1 TTTTCTCCTTTTATTACTTCT
*
458715 TTTTCTCCTTTTATTATTTCT
1 TTTTCTCCTTTTATTACTTCT
458736 TTTTCTCC
1 TTTTCTCC
458744 ATAGAAGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCCTTTTATTACTTCT
Found at i:478758 original size:14 final size:14
Alignment explanation
Indices: 478739--478765 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
478729 TACATTGGGC
478739 AGATTCATGCATGT
1 AGATTCATGCATGT
478753 AGATTCATGCATG
1 AGATTCATGCATG
478766 GGGAGATGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (14 bp):
AGATTCATGCATGT
Found at i:485490 original size:20 final size:19
Alignment explanation
Indices: 485467--485531 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
485457 AAGCTCAAAC
485467 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
485487 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
485507 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
485527 GAGCT
1 GAGCT
485532 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:487035 original size:19 final size:18
Alignment explanation
Indices: 486999--487038 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
486989 TTTCCACTCG
*
486999 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
487017 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
487036 TTT
1 TTT
487039 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:492242 original size:219 final size:218
Alignment explanation
Indices: 491863--492305 Score: 681
Period size: 219 Copynumber: 2.0 Consensus size: 218
491853 GAAACACTTA
* * *
491863 ATGTCCCTCATTCGGTTGGAAGAAGACTCGGTTACCTTGCCTTTGTTGGTGTCGCCCAAAGGCTT
1 ATGTCCCTCATTCGGTTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
* *
491928 GCTTGTTTTGGACGGCACTATTTGCTTCTTGGCATGGATCAGTGGATTGTTTTTACTCGTGCTTT
66 GCTTGTTTTAGACGGCACTATTTGCTTCTTGGCATGGATCAGTGGATTGTTTTTACTCATGCTTT
* * *
491993 GGCCCCATTTTGTTGTGCCTACAGTGGTATAACCTCGAACGGCACCTTTTCGCTTGAGCTTCTTT
131 GGCCCCATTTTGTTATGCCTACAGTGGTATAACCTCGAACAG-ACCTTTTCGCTTGAGCTGCTTT
*
492058 TCCACCTTGATGGTCATGTGCACC
195 TCCACCTTGATGGCCATGTGCACC
* * *
492082 ATGTCCCTCGTTCGGTTGGAAGAAGACTCTATCGCCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
1 ATGTCCCTCATTCGGTTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
* * * *
492147 GTTTGTTTTAGATGGCACTATTTGC-TCATTGGCATGGATCGGTGGATTGTTTTTAGTCATGCTT
66 GCTTGTTTTAGACGGCACTATTTGCTTC-TTGGCATGGATCAGTGGATTGTTTTTACTCATGCTT
* * * *
492211 TGGCTCCATTTTGTTATGCCTGCGGTGGTATAACCTCGAACAGTCCTTTTCGCTTGAGCTGCTTT
130 TGGCCCCATTTTGTTATGCCTACAGTGGTATAACCTCGAACAGACCTTTTCGCTTGAGCTGCTTT
492276 TCCACCTTGATGGCCATGTGCACC
195 TCCACCTTGATGGCCATGTGCACC
492300 ATGTCC
1 ATGTCC
492306 ATGATTTCAA
Statistics
Matches: 203, Mismatches: 20, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
218 51 0.25
219 152 0.75
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (218 bp):
ATGTCCCTCATTCGGTTGGAAGAAGACTCGATCACCTTGCCTTTGTTGGTGTCACCCAAAGGCTT
GCTTGTTTTAGACGGCACTATTTGCTTCTTGGCATGGATCAGTGGATTGTTTTTACTCATGCTTT
GGCCCCATTTTGTTATGCCTACAGTGGTATAACCTCGAACAGACCTTTTCGCTTGAGCTGCTTTT
CCACCTTGATGGCCATGTGCACC
Found at i:495337 original size:20 final size:20
Alignment explanation
Indices: 495307--495344 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
495297 AAAAATATGC
495307 AAACTTATT-AATTTAAATA
1 AAACTTATTAAATTTAAATA
495326 AAACTATATTAAATTTAAA
1 AAACT-TATTAAATTTAAA
495345 AAGTCCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AAACTTATTAAATTTAAATA
Found at i:495986 original size:33 final size:33
Alignment explanation
Indices: 495949--496044 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 33
495939 TAAGTTAATG
495949 CATGACTTAATTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
* *
495982 CATGA---AAGTT-A-CAT---AA-TTAAACTAA
1 CATGACTTAATTTAATGATGCAAACTT-AACTAA
*
496007 CATGACTTTATTTAATGATGCAAACTTAACTAA
1 CATGACTTAATTTAATGATGCAAACTTAACTAA
496040 CATGA
1 CATGA
496045 AAGTTACATA
Statistics
Matches: 48, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
24 2 0.04
25 13 0.27
28 5 0.10
29 2 0.04
30 6 0.12
33 18 0.38
34 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (33 bp):
CATGACTTAATTTAATGATGCAAACTTAACTAA
Found at i:496682 original size:25 final size:28
Alignment explanation
Indices: 496653--496738 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
496643 GGTCAAACAA
496653 TAATTAG-ATA-T-TATTAAATATGTCC
1 TAATTAGTATAGTGTATTAAATATGTCC
* *
496678 TAATTAGTTTAGGTGTTTTAAATATGTCC
1 TAATTAGTATA-GTGTATTAAATATGTCC
*
496707 TAATTAGT-TCAAGTGTTTTAAATATGTCC
1 TAATTAGTAT--AGTGTATTAAATATGTCC
496736 TAA
1 TAA
496739 ACTAATACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
25 7 0.13
26 2 0.04
28 2 0.04
29 41 0.77
30 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (28 bp):
TAATTAGTATAGTGTATTAAATATGTCC
Found at i:496708 original size:29 final size:29
Alignment explanation
Indices: 496666--496738 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
496656 TTAGATATTA
* *
496666 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
496695 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
496724 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
496739 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:497847 original size:11 final size:11
Alignment explanation
Indices: 497831--497892 Score: 76
Period size: 11 Copynumber: 5.8 Consensus size: 11
497821 AGTAGACTCA
497831 TGAAAAAAAAT
1 TGAAAAAAAAT
497842 TGAAAACAAAAT
1 TGAAAA-AAAAT
*
497854 CGAAAAAAAAT
1 TGAAAAAAAAT
497865 TG-AAAAAAA-
1 TGAAAAAAAAT
*
497874 T-CAAAAAAAT
1 TGAAAAAAAAT
497884 TGAAAAAAA
1 TGAAAAAAA
497893 GAAAAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
9 8 0.18
10 8 0.18
11 18 0.41
12 10 0.23
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.15
Consensus pattern (11 bp):
TGAAAAAAAAT
Found at i:497862 original size:10 final size:10
Alignment explanation
Indices: 497834--497903 Score: 74
Period size: 10 Copynumber: 7.0 Consensus size: 10
497824 AGACTCATGA
497834 AAAAAAATTG
1 AAAAAAATTG
*
497844 AAAACAAAATCG
1 -AAA-AAAATTG
497856 AAAAAAAATTG
1 -AAAAAAATTG
*
497867 AAAAAAA-TC
1 AAAAAAATTG
497876 AAAAAAATTG
1 AAAAAAATTG
497886 AAAAAAA--G
1 AAAAAAATTG
497894 AAAAAAATTG
1 AAAAAAATTG
497904 TATACGGTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
8 8 0.16
9 8 0.16
10 16 0.31
11 9 0.18
12 10 0.20
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (10 bp):
AAAAAAATTG
Found at i:497871 original size:19 final size:20
Alignment explanation
Indices: 497832--497900 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 20
497822 GTAGACTCAT
497832 GAAAAAAAATTGAAAACAAAATC
1 GAAAAAAAATTG--AA-AAAATC
497855 GAAAAAAAATTGAAAAAAATC
1 GAAAAAAAATTG-AAAAAATC
*
497876 --AAAAAAATTGAAAAAA-A
1 GAAAAAAAATTGAAAAAATC
497893 GAAAAAAA
1 GAAAAAAA
497901 TTGTATACGG
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
18 6 0.14
19 16 0.37
21 6 0.14
22 3 0.07
23 12 0.28
ACGTcount: A:0.75, C:0.04, G:0.09, T:0.12
Consensus pattern (20 bp):
GAAAAAAAATTGAAAAAATC
Found at i:536694 original size:15 final size:16
Alignment explanation
Indices: 536676--536708 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
536666 CCTTTTCGCC
536676 TTTTTCATTTTCA-TT
1 TTTTTCATTTTCACTT
*
536691 TTTTTCTTTTTCACTT
1 TTTTTCATTTTCACTT
536707 TT
1 TT
536709 ATTTTTCTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCATTTTCACTT
Found at i:536699 original size:21 final size:21
Alignment explanation
Indices: 536675--536719 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
536665 TCCTTTTCGC
*
536675 CTTTTTCA-TTTTCATTTTTTT
1 CTTTTTCACTTTT-ATTTTTCT
536696 CTTTTTCACTTTTATTTTTCT
1 CTTTTTCACTTTTATTTTTCT
536717 CTT
1 CTT
536720 CTCTTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (21 bp):
CTTTTTCACTTTTATTTTTCT
Found at i:540342 original size:23 final size:23
Alignment explanation
Indices: 540313--540357 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
540303 TGCCGAATTG
540313 AGCTGAATTAAGCTGACACGAGA
1 AGCTGAATTAAGCTGACACGAGA
540336 AGCTGAATTAAGCTGACACGAG
1 AGCTGAATTAAGCTGACACGAG
540358 CTAACATCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (23 bp):
AGCTGAATTAAGCTGACACGAGA
Found at i:540856 original size:42 final size:42
Alignment explanation
Indices: 540809--540888 Score: 101
Period size: 42 Copynumber: 1.9 Consensus size: 42
540799 ACATCTTTTT
540809 CTTTTTCAATTT-TTTTCTCAATCT-CAATTTCTTTTTCTCTCA
1 CTTTTTCAATTTCTTTT-TC-ATCTGCAATTTCTTTTTCTCTCA
* * *
540851 CTTTTTCGATTTCTTTTTCTTTTGCAATTTCTTTTTCT
1 CTTTTTCAATTTCTTTTTCATCTGCAATTTCTTTTTCT
540889 TTTTCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 2 0.06
42 27 0.82
43 4 0.12
ACGTcount: A:0.12, C:0.21, G:0.03, T:0.64
Consensus pattern (42 bp):
CTTTTTCAATTTCTTTTTCATCTGCAATTTCTTTTTCTCTCA
Found at i:540872 original size:18 final size:18
Alignment explanation
Indices: 540851--540929 Score: 106
Period size: 18 Copynumber: 4.4 Consensus size: 18
540841 TTTTCTCTCA
540851 CTTTTTCGA-TTTCTTTTT
1 CTTTTTC-ACTTTCTTTTT
* *
540869 CTTTTGCAATTTCTTTTT
1 CTTTTTCACTTTCTTTTT
*
540887 CTTTTTCATTTTCTTTTT
1 CTTTTTCACTTTCTTTTT
*
540905 CTTCTTCACTTTCTTTTT
1 CTTTTTCACTTTCTTTTT
540923 CTTTTTC
1 CTTTTTC
540930 TTCTTTTTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
17 1 0.02
18 53 0.98
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (18 bp):
CTTTTTCACTTTCTTTTT
Found at i:540891 original size:36 final size:36
Alignment explanation
Indices: 540851--540929 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
540841 TTTTCTCTCA
540851 CTTTTTCGA-TTTCTTTTTCTT-TTGCAATTTCTTTTT
1 CTTTTTC-ATTTTCTTTTTCTTCTT-CAATTTCTTTTT
*
540887 CTTTTTCATTTTCTTTTTCTTCTTCACTTTCTTTTT
1 CTTTTTCATTTTCTTTTTCTTCTTCAATTTCTTTTT
540923 CTTTTTC
1 CTTTTTC
540930 TTCTTTTTCA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 1 0.03
36 37 0.93
37 2 0.05
ACGTcount: A:0.06, C:0.20, G:0.03, T:0.71
Consensus pattern (36 bp):
CTTTTTCATTTTCTTTTTCTTCTTCAATTTCTTTTT
Found at i:540943 original size:6 final size:6
Alignment explanation
Indices: 540836--540931 Score: 84
Period size: 6 Copynumber: 16.0 Consensus size: 6
540826 TCAATCTCAA
* ** ** * **
540836 TTTCTT TTTCTC TCACTT TTTCGA TTTCTT TTTCTT TTGCAA TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* * **
540884 TTTCTT TTTCAT TTTCTT TTTCTT CTTCAC TTTCTT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
540932 CTTTTTCATT
Statistics
Matches: 66, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (6 bp):
TTTCTT
Done.