Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 3 of 91
Found at i:542220 original size:2 final size:2
Alignment explanation
Indices: 542215--542279 Score: 121
Period size: 2 Copynumber: 32.0 Consensus size: 2
542205 TTCACACACA
542215 CT CT CT CT CT CT CT CT CT CT CT CT CT CT NCT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT -CT CT CT CT CT CT CT
542258 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
542280 TATATATATA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 60 0.97
3 2 0.03
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:542285 original size:2 final size:2
Alignment explanation
Indices: 542280--542324 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
542270 CTCTCTCTCT
542280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
542322 TA T
1 TA T
542325 CTGCCTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:557245 original size:45 final size:45
Alignment explanation
Indices: 557190--557295 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
557180 TTTTTTTCCA
* *
557190 ATATAACGTGTAACAACCTAA-C-TATGACGTATCACATATTTTTAT
1 ATATAGCGTGTAACAACATAATCATA-G-CGTATCACATATTTTTAT
* * * *
557235 ATATAGCGTGTAACAACATAATCATAGCGTGTCATATGTTTTTGT
1 ATATAGCGTGTAACAACATAATCATAGCGTATCACATATTTTTAT
*
557280 ATATAGTGTGTAACAA
1 ATATAGCGTGTAACAA
557296 GTGTAACAAC
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
45 48 0.92
46 2 0.04
47 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (45 bp):
ATATAGCGTGTAACAACATAATCATAGCGTATCACATATTTTTAT
Found at i:557322 original size:21 final size:21
Alignment explanation
Indices: 557296--557341 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
557286 TGTGTAACAA
*
557296 GTGTAACAACCTAACCATGTC
1 GTGTAACAACCTAACCATGAC
557317 GTGTAACAACCTAACCATGAC
1 GTGTAACAACCTAACCATGAC
557338 GTGT
1 GTGT
557342 TATATATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (21 bp):
GTGTAACAACCTAACCATGAC
Found at i:557360 original size:24 final size:24
Alignment explanation
Indices: 557332--557410 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
557322 ACAACCTAAC
*
557332 CATGACGTGTTATATATTTTTGTA
1 CATGACGTGTCATATATTTTTGTA
* * * **
557356 CATGACGTATCACA-A-CTTAAT-
1 CATGACGTGTCATATATTTTTGTA
*
557377 CATGATGTGTCATATATTTTTGTA
1 CATGACGTGTCATATATTTTTGTA
557401 CATGACGTGT
1 CATGACGTGT
557411 AACAACTTAA
Statistics
Matches: 39, Mismatches: 13, Indels: 6
0.67 0.22 0.10
Matches are distributed among these distances:
21 11 0.28
22 4 0.10
23 4 0.10
24 20 0.51
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (24 bp):
CATGACGTGTCATATATTTTTGTA
Found at i:557392 original size:45 final size:45
Alignment explanation
Indices: 557311--557465 Score: 175
Period size: 45 Copynumber: 3.4 Consensus size: 45
557301 ACAACCTAAC
* * * * * *
557311 CATGTCGTGTAACAACCTAACCATGACGTGTTATATATTTTTGTA
1 CATGACGTATAACAACTTAATCATGATGTGTCATATATTTTTGTA
*
557356 CATGACGTATCACAACTTAATCATGATGTGTCATATATTTTTGTA
1 CATGACGTATAACAACTTAATCATGATGTGTCATATATTTTTGTA
* * * * *
557401 CATGACGTGTAACAACTTAATCATGATATGTCACATGTTTTTATA
1 CATGACGTATAACAACTTAATCATGATGTGTCATATATTTTTGTA
* **
557446 CATGATGTGCAACAACTTAA
1 CATGACGTATAACAACTTAA
557466 CTATAACATG
Statistics
Matches: 95, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 95 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (45 bp):
CATGACGTATAACAACTTAATCATGATGTGTCATATATTTTTGTA
Found at i:557411 original size:120 final size:120
Alignment explanation
Indices: 557196--557415 Score: 275
Period size: 120 Copynumber: 1.8 Consensus size: 120
557186 TCCAATATAA
* * *
557196 CGTGTAACAACCTAACTATGACGTATCACATATTTTTATATATAGCGTGTAACAACATAATCATA
1 CGTGTAACAACCTAACCATGACGTATCACATATTTTTATACATAGCGTATAACAACATAATCATA
* * *
557261 GCGTGTCATATGTTTTTGTATATAGTGTGTAACAAGTGTAACAACCTAACCATGT
66 GCGTGTCATATATTTTTGTACATAGCGTGTAACAAGTGTAACAACCTAACCATGT
* * * * * *
557316 CGTGTAACAACCTAACCATGACGTGTTATATATTTTTGTACAT-GACGTATCACAACTTAATCAT
1 CGTGTAACAACCTAACCATGACGTATCACATATTTTTATACATAG-CGTATAACAACATAATCAT
*
557380 -GATGTGTCATATATTTTTGTACAT-GACGTGTAACAA
65 AG-CGTGTCATATATTTTTGTACATAG-CGTGTAACAA
557416 CTTAATCATG
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
119 3 0.04
120 81 0.96
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (120 bp):
CGTGTAACAACCTAACCATGACGTATCACATATTTTTATACATAGCGTATAACAACATAATCATA
GCGTGTCATATATTTTTGTACATAGCGTGTAACAAGTGTAACAACCTAACCATGT
Found at i:557487 original size:45 final size:45
Alignment explanation
Indices: 557345--557499 Score: 145
Period size: 45 Copynumber: 3.4 Consensus size: 45
557335 GACGTGTTAT
* * * ** *
557345 ATATTTTTGTACATGACGTATC-ACAACTTAATCATGATGTGTCAT
1 ATATTTTTATACATGACGT-GCAACAACTTAATCATAACATGTCAC
* * * *
557390 ATATTTTTGTACATGACGTGTAACAACTTAATCATGATATGTCAC
1 ATATTTTTATACATGACGTGCAACAACTTAATCATAACATGTCAC
* *
557435 ATGTTTTTATACATGATGTGCAACAACTTAA-CTATAACATG-CAAC
1 ATATTTTTATACATGACGTGCAACAACTTAATC-ATAACATGTC-AC
*
557480 ATATTTTTATACATAACGTG
1 ATATTTTTATACATGACGTG
557500 TAATATTATG
Statistics
Matches: 94, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
44 2 0.02
45 92 0.98
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.38
Consensus pattern (45 bp):
ATATTTTTATACATGACGTGCAACAACTTAATCATAACATGTCAC
Found at i:557610 original size:30 final size:31
Alignment explanation
Indices: 557575--557633 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
557565 TATAAAAAAA
* *
557575 GTTATTTTTGAAAACAT-CTTATCTATAAGG
1 GTTATTTTTAAAAACATCCTTATATATAAGG
*
557605 GTTATTTTTAAAAATATCCTTATATATAA
1 GTTATTTTTAAAAACATCCTTATATATAA
557634 TGACCCAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.46
Consensus pattern (31 bp):
GTTATTTTTAAAAACATCCTTATATATAAGG
Found at i:558457 original size:17 final size:17
Alignment explanation
Indices: 558431--558469 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
558421 GTAGTTAAAA
558431 AAAG-GAACTATAAGTT
1 AAAGTGAACTATAAGTT
558447 AAAGTGAACTATAAGTT
1 AAAGTGAACTATAAGTT
558464 AAAGTG
1 AAAGTG
558470 CAAGTTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.49, C:0.05, G:0.21, T:0.26
Consensus pattern (17 bp):
AAAGTGAACTATAAGTT
Found at i:563824 original size:21 final size:21
Alignment explanation
Indices: 563797--563855 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
563787 TTAAGTTTTA
563797 AAATTTTATTAATTGATTTGT
1 AAATTTTATTAATTGATTTGT
** * * *
563818 TTATTTTTTTAAATGAATTGT
1 AAATTTTATTAATTGATTTGT
563839 AAATTTTA-TAATTGATT
1 AAATTTTATTAATTGATT
563856 ATATTTATGA
Statistics
Matches: 28, Mismatches: 10, Indels: 1
0.72 0.26 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (21 bp):
AAATTTTATTAATTGATTTGT
Found at i:573042 original size:5 final size:5
Alignment explanation
Indices: 573032--573068 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
573022 CACACACCGG
*
573032 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AGGGA AA
1 AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AAGGA AA
573069 ACTCTTGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AAGGA
Found at i:575041 original size:11 final size:11
Alignment explanation
Indices: 575025--575077 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
575015 CAATAAGAAA
575025 TTAAAATTTAT
1 TTAAAATTTAT
575036 TTAAAATTT-T
1 TTAAAATTTAT
*
575046 TT-AAA-TAAT
1 TTAAAATTTAT
575055 TTCAAAATTT-T
1 TT-AAAATTTAT
575066 TTAAAATATTAT
1 TTAAAAT-TTAT
575078 GCATTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
8 1 0.03
9 6 0.18
10 8 0.24
11 17 0.50
12 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAAATTTAT
Found at i:575050 original size:10 final size:10
Alignment explanation
Indices: 575025--575072 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
575015 CAATAAGAAA
575025 TTAAAATTTAT
1 TTAAAATTT-T
575036 TTAAAATTTT
1 TTAAAATTTT
*
575046 TT-AAATAATT
1 TTAAAAT-TTT
*
575056 TCAAAATTTT
1 TTAAAATTTT
575066 TTAAAAT
1 TTAAAAT
575073 ATTATGCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
9 4 0.13
10 14 0.45
11 13 0.42
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAAATTTT
Found at i:584576 original size:22 final size:22
Alignment explanation
Indices: 584515--584579 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
584505 AATAATAATA
* *
584515 TTTTC-ATAAAATTTTGAAGAT
1 TTTTCTATCAAATTTTGAGGAT
584536 TTTTCTATCAAATTTTGAGGAT
1 TTTTCTATCAAATTTTGAGGAT
584558 TTTTCTATCAAATTTTGAGGAT
1 TTTTCTATCAAATTTTGAGGAT
584580 CTAAAAGGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
21 5 0.12
22 36 0.88
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (22 bp):
TTTTCTATCAAATTTTGAGGAT
Found at i:584885 original size:4 final size:4
Alignment explanation
Indices: 584876--584900 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
584866 TGTGGTCCAA
584876 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
584901 CATTATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:585492 original size:117 final size:117
Alignment explanation
Indices: 585354--585581 Score: 289
Period size: 124 Copynumber: 1.9 Consensus size: 117
585344 TCACATATAA
* **
585354 ACACCACAAGCAACATTGATAGTACTTTGGAGCACTTTAA-AGAAAATTTA-GATAAGATAACTA
1 ACACCACAAACAACATTGATAGTACTTTGGAGCA-TTTAATA-AAAAAATAGGATAAGATAACTA
* *
585417 TATATTACTCGGTTCTTGAATTAAGATGAGTCACGTCATAACACATTCACACAT
64 TAGATTACTCGGTTCTGGAATTAAGATGAGTCACGTCATAACACATTCACACAT
*
585471 ACACCACAAACAATATTGATAGTACTTTGGAGCATTTAATTTTTTTTAAAAAAATAGGATAAGAT
1 ACACCACAAACAACATTGATAGTACTTTGGAGCATTTAA-------TAAAAAAATAGGATAAGAT
* *
585536 AGCTATAGATTATTCGGTTCTGGAATTAAGATGAGTCACGTCATAA
59 AACTATAGATTACTCGGTTCTGGAATTAAGATGAGTCACGTCATAA
585582 TTTCATAAAA
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
116 5 0.05
117 32 0.34
123 6 0.06
124 51 0.54
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (117 bp):
ACACCACAAACAACATTGATAGTACTTTGGAGCATTTAATAAAAAAATAGGATAAGATAACTATA
GATTACTCGGTTCTGGAATTAAGATGAGTCACGTCATAACACATTCACACAT
Found at i:589663 original size:2 final size:2
Alignment explanation
Indices: 589656--589685 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
589646 TTTGAAAAAT
589656 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
589686 ACCGTGGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:589744 original size:2 final size:2
Alignment explanation
Indices: 589737--589767 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
589727 ANAAGTAAGA
589737 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
589768 AACCGTGGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:591775 original size:12 final size:12
Alignment explanation
Indices: 591753--591787 Score: 61
Period size: 12 Copynumber: 2.8 Consensus size: 12
591743 GCACGTGTAA
591753 TATATTATTATAT
1 TATA-TATTATAT
591766 TATATATTATAT
1 TATATATTATAT
591778 TATATATTAT
1 TATATATTAT
591788 TTAGTAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 18 0.82
13 4 0.18
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATATATTATAT
Found at i:591804 original size:71 final size:71
Alignment explanation
Indices: 591717--591857 Score: 257
Period size: 71 Copynumber: 2.0 Consensus size: 71
591707 TGGAATTAAC
591717 TTAGGAATGAAGAAGAAAGCATATCCGCACGTGTAATATATTATTATATTATA-TATTATATTAT
1 TTAGGAATGAAGAAGAAAGCATATCCGCACGTGTAATATATTATTATATTATATTA-TATATTAT
591781 ATATTAT
65 ATATTAT
*
591788 TTAGTAATGAAGAAGAAAGCATATCCGCACGTGTAATATATTATTATATTATATTATATATTATA
1 TTAGGAATGAAGAAGAAAGCATATCCGCACGTGTAATATATTATTATATTATATTATATATTATA
591853 TATTA
66 TATTA
591858 CATATCCATG
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
71 66 0.97
72 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (71 bp):
TTAGGAATGAAGAAGAAAGCATATCCGCACGTGTAATATATTATTATATTATATTATATATTATA
TATTAT
Found at i:594614 original size:161 final size:158
Alignment explanation
Indices: 594348--594659 Score: 416
Period size: 161 Copynumber: 1.9 Consensus size: 158
594338 TGGCAGGACT
*
594348 ACGAATACCCAGAAAGGACATAAATGAAATAATTACTTGATAGCGCAAGGACCTTGGAAGGGTGT
1 ACGAATACCCAAAAAGGACATAAATGAAATAATTACTTGATAGCGCAAGGACCTTGGAAGGGTGT
*
594413 CCATAGTGTTATCAAACATCGGTTTTAATTTGTGCATAAAAACAGCCATTCCCTGGTATGGATAA
66 CCATAATGTTATCAAACATCGG-TTT-ATTTGTGCATAAAAACAGCCATTCCCTGGTATGGATAA
*
594478 CATTGCTAT-TATTTCCTTATGGTAATGGCC
129 CATTGCGATAT-TTTCCTTATGGTAATGGCC
** *
594508 ACGAATACCCACAAAAGGATGTAAATGAAATAATTACTTGATAGCG-AAGGATCTTGGAAGAAAA
1 ACGAATACCCA-AAAAGGACATAAATGAAATAATTACTTGATAGCGCAAGGACCTT-G--G--AA
* * **
594572 GGGTGTCCATAATGTTATCAAACATTGG-TT-TTTGTTCATAAAAAGGGCCATTCCCTGGTATGG
60 GGGTGTCCATAATGTTATCAAACATCGGTTTATTTGTGCATAAAAACAGCCATTCCCTGGTATGG
*
594635 ATAAGATTGCGATATTTTCCTTATG
125 ATAACATTGCGATATTTTCCTTATG
594660 CTCATCTCCC
Statistics
Matches: 134, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
160 19 0.14
161 83 0.62
162 1 0.01
163 3 0.02
165 28 0.21
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.30
Consensus pattern (158 bp):
ACGAATACCCAAAAAGGACATAAATGAAATAATTACTTGATAGCGCAAGGACCTTGGAAGGGTGT
CCATAATGTTATCAAACATCGGTTTATTTGTGCATAAAAACAGCCATTCCCTGGTATGGATAACA
TTGCGATATTTTCCTTATGGTAATGGCC
Found at i:599044 original size:27 final size:26
Alignment explanation
Indices: 599013--599092 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 26
599003 GGAGATGACT
* *
599013 ATAATATTTTTTTCAATATGATATGTA
1 ATAAT-TTTTTTTCAATATGACATATA
*
599040 ATAATTTTTTTTTCAATATGACGTATA
1 ATAA-TTTTTTTTCAATATGACATATA
* *
599067 ATAACTTTTTTTTCAACATAACATAT
1 ATAA-TTTTTTTTCAATATGACATAT
599093 TGTCGTAACG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 44 0.98
28 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (26 bp):
ATAATTTTTTTTCAATATGACATATA
Found at i:599961 original size:12 final size:12
Alignment explanation
Indices: 599944--600000 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
599934 ATTATTTTTA
599944 TTTTATTATATT
1 TTTTATTATATT
599956 TTTTATTATCATAT
1 TTTTATTAT-AT-T
*
599970 TTTCTATTCTTATT
1 TTT-TATT-ATATT
*
599984 TCTTATTATTATT
1 TTTTATTA-TATT
599997 TTTT
1 TTTT
600001 CATACTTTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
12 9 0.25
13 13 0.36
14 7 0.19
15 6 0.17
16 1 0.03
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTATTATATT
Found at i:599983 original size:13 final size:14
Alignment explanation
Indices: 599918--599998 Score: 55
Period size: 14 Copynumber: 5.9 Consensus size: 14
599908 TATTTTTTAG
* **
599918 TTATTATTAATTAA
1 TTATTATTATTTTC
*
599932 TTATTATT-TTTATT
1 TTATTATTATTT-TC
599946 TTATTA-TATTTT-
1 TTATTATTATTTTC
599958 TTATTATCATATTTTC
1 TTATTAT--TATTTTC
*
599974 -TATTCTTA-TTTC
1 TTATTATTATTTTC
599986 TTATTATTATTTT
1 TTATTATTATTTT
599999 TTCATACTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
12 10 0.19
13 13 0.24
14 20 0.37
15 11 0.20
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATTATTATTTTC
Found at i:600122 original size:15 final size:15
Alignment explanation
Indices: 600096--600143 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
600086 AACAAAAATT
*
600096 TTATATATTTTTTTA
1 TTATATATTTTTATA
*
600111 TTATACTATTTTTATT
1 TTATA-TATTTTTATA
600127 TTATATATTTTTATA
1 TTATATATTTTTATA
600142 TT
1 TT
600144 TTTATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 16 0.55
16 13 0.45
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATATATTTTTATA
Found at i:600124 original size:14 final size:13
Alignment explanation
Indices: 600094--600163 Score: 63
Period size: 14 Copynumber: 5.3 Consensus size: 13
600084 TGAACAAAAA
*
600094 TTTTA-TATATTT
1 TTTTATTATATAT
600106 TTTTATTATACTAT
1 TTTTATTATA-TAT
*
600120 TTTTATTTTATAT
1 TTTTATTATATAT
* *
600133 ATTT-TTATATTT
1 TTTTATTATATAT
600145 TTATTATTATAATAT
1 TT-TTATTAT-ATAT
600160 TTTT
1 TTTT
600164 CATAGGCAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
12 12 0.26
13 12 0.26
14 17 0.37
15 5 0.11
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTATTATATAT
Found at i:600143 original size:8 final size:8
Alignment explanation
Indices: 600093--600163 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 8
600083 GTGAACAAAA
600093 ATTTTATAT
1 ATTTT-TAT
*
600102 ATTTTTTT
1 ATTTTTAT
*
600110 A-TTATACT
1 ATTTTTA-T
600118 ATTTTTAT
1 ATTTTTAT
*
600126 -TTTATAT
1 ATTTTTAT
600133 ATTTTTAT
1 ATTTTTAT
600141 ATTTTTATT
1 ATTTTTA-T
* *
600150 ATTATAAT
1 ATTTTTAT
600158 ATTTTT
1 ATTTTT
600164 CATAGGCAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
7 9 0.19
8 24 0.50
9 15 0.31
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (8 bp):
ATTTTTAT
Found at i:600143 original size:23 final size:25
Alignment explanation
Indices: 600117--600163 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 25
600107 TTTATTATAC
600117 TATTTTTATT-TTAT-ATATTTTTA
1 TATTTTTATTATTATAATATTTTTA
600140 TATTTTTATTATTATAATATTTTT
1 TATTTTTATTATTATAATATTTTT
600164 CATAGGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 10 0.45
24 4 0.18
25 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (25 bp):
TATTTTTATTATTATAATATTTTTA
Found at i:605413 original size:15 final size:15
Alignment explanation
Indices: 605388--605427 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
605378 CTCTCCACCC
*
605388 TTTTTTCATTTTT-T
1 TTTTTTAATTTTTAT
605402 TATTTTTAATTTTTAT
1 T-TTTTTAATTTTTAT
605418 TTTTTTAATT
1 TTTTTTAATT
605428 CATTTTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 20 0.87
16 2 0.09
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTAATTTTTAT
Found at i:605551 original size:28 final size:26
Alignment explanation
Indices: 605457--605557 Score: 114
Period size: 26 Copynumber: 3.8 Consensus size: 26
605447 TAGTGTCTAC
605457 ACATATAACAATTTTTTTTCCAACATG
1 ACATATAACAATTTTTTTT-CAACATG
* * *
605484 ACGTGTAATAATTTTTTTTCAACATG
1 ACATATAACAATTTTTTTTCAACATG
* *
605510 ACATATAACAATTTTTTTTTAATAT-
1 ACATATAACAATTTTTTTTCAACATG
*
605535 AGCATATAACAACATTTTTTTCA
1 A-CATATAACAA-TTTTTTTTCA
605558 CGTGCGCATA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
25 1 0.02
26 37 0.60
27 24 0.39
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.45
Consensus pattern (26 bp):
ACATATAACAATTTTTTTTCAACATG
Found at i:605656 original size:18 final size:18
Alignment explanation
Indices: 605621--605654 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
605611 TTCTCTTAAC
605621 TAAAAAAAAAGTTAAAAT
1 TAAAAAAAAAGTTAAAAT
605639 TAAAAAAAAA-TTAAAA
1 TAAAAAAAAAGTTAAAA
605655 ATACATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (18 bp):
TAAAAAAAAAGTTAAAAT
Found at i:610867 original size:21 final size:21
Alignment explanation
Indices: 610830--610879 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
610820 TGACAGAAAG
* *
610830 TTATTTTTGATAGAATTT-AA
1 TTATTTTTGAGAAAATTTCAA
610850 TTATTTTTGACGAAAATTTCAA
1 TTATTTTTGA-GAAAATTTCAA
*
610872 TTTTTTTT
1 TTATTTTT
610880 TTAATGAGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
21 6 0.24
22 9 0.36
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (21 bp):
TTATTTTTGAGAAAATTTCAA
Found at i:614864 original size:190 final size:190
Alignment explanation
Indices: 614508--614863 Score: 456
Period size: 190 Copynumber: 1.9 Consensus size: 190
614498 GAGATTCAAA
* * * *
614508 CAATGAACTTCACAAGTTCAAGAGATTTCTTATTTGCAAACTGTCTATCTATTCTTGATTTGTTT
1 CAATGAACTTCACAAGTTCAAGAGATGTATTATATGCAAAATGTCTATCTATTCTTGA-TTGTTT
*
614573 AGATAATTATTGGTTTAGGAATGATTTCAAGAAAAAAATTATCATGATTTGTACTCGATTAGTTG
65 AGATAATTATTAGTTTAGGAATGATTTCAAGAAAAAAATTATCATGATTTGTACTCGATTAGTTG
*
614638 TTTTCTCCACATTTCTTTCATCTTGGGGAAAAAAAATCACACTTACTTACACCTATTAAAT
130 TTTTCTACACATTTCTTTCATCTTGGGGAAAAAAAATCACACTTACTTACACCTATTAAAT
* *
614699 CAATGAAGTTGACAAGTT-AAGAGATGTATTATATGCAAAATGTCTATCTATTCTTGA-TGTATT
1 CAATGAACTTCACAAGTTCAAGAGATGTATTATATGCAAAATGTCTATCTATTCTTGATTGT-TT
* * * *
614762 ATGAT-ATATATTAGTTTAGGAACT-ATTGT-AATAAAAGAA-TATCATGATTTGTATTTGATTA
65 A-GATAAT-TATTAGTTTAGGAA-TGATT-TCAAGAAAAAAATTATCATGATTTGTACTCGATTA
* *
614823 TTTGTTTTTCTACACATTTTTTTTTCATCTT-GGGAAAAAAA
126 GTTG-TTTTCTACACA--TTTCTTTCATCTTGGGGAAAAAAA
614864 TGGACATCTA
Statistics
Matches: 143, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
188 3 0.02
189 28 0.20
190 72 0.50
191 28 0.20
192 12 0.08
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (190 bp):
CAATGAACTTCACAAGTTCAAGAGATGTATTATATGCAAAATGTCTATCTATTCTTGATTGTTTA
GATAATTATTAGTTTAGGAATGATTTCAAGAAAAAAATTATCATGATTTGTACTCGATTAGTTGT
TTTCTACACATTTCTTTCATCTTGGGGAAAAAAAATCACACTTACTTACACCTATTAAAT
Found at i:624882 original size:154 final size:158
Alignment explanation
Indices: 624604--624903 Score: 439
Period size: 154 Copynumber: 1.9 Consensus size: 158
624594 AAGCAATGCG
* **
624604 ATTGACACAGATCATATAGAAAACAAAAAACTAATACATATAATACTATGATGGGAAGCTTTCCA
1 ATTGACACAGATCATATAGAAAAAAAAAAACTAATACATATAATACTATGATAAGAAGCTTTCCA
*
624669 TGATATCACATCTGAAATTGTGCATGCAAATATTTCTTTTAATAGTCTGAAAACATATTAAATTG
66 TGATATCACATCTGAAATGGTGCATGCAAATATTTCTTTTAATAGTCTGAAAACATATTAAATTG
624734 TACAT-TT-TTGTTGTGGCATATGAGCA
131 TACATGTTGTTGTTGTGGCATATGAGCA
* ** * *
624760 ATTGACACAGGTTGTATAGAAAAAAAAAAAACTAATGCATCTAATACTATGATAAGAAGCTTTCC
1 ATTGACACAGATCATATAG-AAAAAAAAAAACTAATACATATAATACTATGATAAGAAGCTTTCC
* * * *
624825 ATGAT-TTACATCTG-AA-GGTGCTTGCAAATATTTCTTTTGATGGTCTGAAAACATATTAAATT
65 ATGATATCACATCTGAAATGGTGCATGCAAATATTTCTTTTAATAGTCTGAAAACATATTAAATT
624887 GTACATGTTGTTGTTGT
130 GTACATGTTGTTGTTGT
624904 CCAAAATAAA
Statistics
Matches: 128, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
154 48 0.38
155 4 0.03
156 31 0.24
157 45 0.35
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (158 bp):
ATTGACACAGATCATATAGAAAAAAAAAAACTAATACATATAATACTATGATAAGAAGCTTTCCA
TGATATCACATCTGAAATGGTGCATGCAAATATTTCTTTTAATAGTCTGAAAACATATTAAATTG
TACATGTTGTTGTTGTGGCATATGAGCA
Found at i:632359 original size:45 final size:45
Alignment explanation
Indices: 632309--632405 Score: 142
Period size: 45 Copynumber: 2.2 Consensus size: 45
632299 AAGGTAAAGA
*
632309 AAAAGCAGAAACTGATGG-GGTTCTCTTTTTGTTGTGTAAGCAGTG
1 AAAAGCAGAAACTGATGGAGATT-TCTTTTTGTTGTGTAAGCAGTG
* * *
632354 AAAAGCAGACATTGATGGAGATTTCTTTTTGTTGTTTAAGCAGTG
1 AAAAGCAGAAACTGATGGAGATTTCTTTTTGTTGTGTAAGCAGTG
632399 AAAAGCA
1 AAAAGCA
632406 TTGGATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
45 44 0.94
46 3 0.06
ACGTcount: A:0.31, C:0.10, G:0.26, T:0.33
Consensus pattern (45 bp):
AAAAGCAGAAACTGATGGAGATTTCTTTTTGTTGTGTAAGCAGTG
Found at i:632458 original size:7 final size:7
Alignment explanation
Indices: 632442--632471 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
632432 GCTTTACTTG
632442 TTTC-TT
1 TTTCATT
632448 TTTCATT
1 TTTCATT
632455 TTTCATT
1 TTTCATT
632462 TTTCATT
1 TTTCATT
632469 TTT
1 TTT
632472 TTTTTTGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTCATT
Found at i:632465 original size:14 final size:13
Alignment explanation
Indices: 632442--632476 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
632432 GCTTTACTTG
632442 TTTCTTTTTCATT
1 TTTCTTTTTCATT
632455 TTTCATTTTTCATT
1 TTTC-TTTTTCATT
632469 TTT-TTTTT
1 TTTCTTTTT
632477 TGGTATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.24
13 4 0.19
14 12 0.57
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTCATT
Found at i:632729 original size:42 final size:42
Alignment explanation
Indices: 632665--632745 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
632655 CCGTCGTCAA
* *
632665 ACTTAATACTAGCTTACATTTTTTATCAACGTGACATATGAC
1 ACTTAATACTAACTCACATTTTTTATCAACGTGACATATGAC
*
632707 ACTTGATACTAACTCACATTTTTTATCAACGTGACATAT
1 ACTTAATACTAACTCACATTTTTTATCAACGTGACATAT
632746 AGCGTGAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (42 bp):
ACTTAATACTAACTCACATTTTTTATCAACGTGACATATGAC
Found at i:633389 original size:19 final size:21
Alignment explanation
Indices: 633348--633394 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
633338 TTTTAAATAA
* *
633348 TAATAATTATTTTTTGGTTTT
1 TAATAATTATTTTTTGATATT
633369 TAATAATT-TTTTTT-ATATT
1 TAATAATTATTTTTTGATATT
*
633388 TATTAAT
1 TAATAAT
633395 AACAAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 9 0.39
20 6 0.26
21 8 0.35
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (21 bp):
TAATAATTATTTTTTGATATT
Found at i:635177 original size:145 final size:145
Alignment explanation
Indices: 634914--635177 Score: 519
Period size: 145 Copynumber: 1.8 Consensus size: 145
634904 CTCCATGGAT
*
634914 CAGGCAAGTTTTTGCATTTTAACTCTAATTGCAAATTACCCAACTTAGCTTTGATTGTTAGTTGT
1 CAGGCAAGTTTGTGCATTTTAACTCTAATTGCAAATTACCCAACTTAGCTTTGATTGTTAGTTGT
634979 TATCCCCCTCTGGCATTTGGAATTGGAGGTATTATATATATCAGAGTAAACTCTAATTGATGATT
66 TATCCCCCTCTGGCATTTGGAATTGGAGGTATTATATATATCAGAGTAAACTCTAATTGATGATT
635044 GATTAATGCATTTTA
131 GATTAATGCATTTTA
635059 CAGGCAAGTTTGTGCATTTTAACTCTAATTGCAAATTACCCAACTTAGCTTTGATTGTTAGTTGT
1 CAGGCAAGTTTGTGCATTTTAACTCTAATTGCAAATTACCCAACTTAGCTTTGATTGTTAGTTGT
635124 TATCCCCCTCTGGCATTTGGAATTGGAGGTATTATATATATCAGAGTAAACTCT
66 TATCCCCCTCTGGCATTTGGAATTGGAGGTATTATATATATCAGAGTAAACTCT
635178 TTCGTCCCTA
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
145 118 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.39
Consensus pattern (145 bp):
CAGGCAAGTTTGTGCATTTTAACTCTAATTGCAAATTACCCAACTTAGCTTTGATTGTTAGTTGT
TATCCCCCTCTGGCATTTGGAATTGGAGGTATTATATATATCAGAGTAAACTCTAATTGATGATT
GATTAATGCATTTTA
Found at i:651939 original size:16 final size:16
Alignment explanation
Indices: 651918--651948 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
651908 TGCATAATTT
651918 AAGAAAAAGAAAAGAA
1 AAGAAAAAGAAAAGAA
*
651934 AAGAAAAGGAAAAGA
1 AAGAAAAAGAAAAGA
651949 CATAAGTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAGAA
Found at i:656191 original size:14 final size:14
Alignment explanation
Indices: 656172--656199 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
656162 TGTGGTTGCT
656172 CTCTATTCCCCAAA
1 CTCTATTCCCCAAA
656186 CTCTATTCCCCAAA
1 CTCTATTCCCCAAA
656200 GCAGCTCAAA
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:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (14 bp):
CTCTATTCCCCAAA
Found at i:659853 original size:2 final size:2
Alignment explanation
Indices: 659846--659878 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
659836 CCGTCAGGTA
659846 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
659879 AAGTTTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:672943 original size:37 final size:37
Alignment explanation
Indices: 672893--672969 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
672883 TGGAAAAGTA
672893 AAATCCAATTTTATTAACAAGAACTGCAGCTTTTCTT
1 AAATCCAATTTTATTAACAAGAACTGCAGCTTTTCTT
672930 AAATCCAATTTTATTAACAAGAACTGCAGCTTTTCTT
1 AAATCCAATTTTATTAACAAGAACTGCAGCTTTTCTT
672967 AAA
1 AAA
672970 AAAAGGGTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (37 bp):
AAATCCAATTTTATTAACAAGAACTGCAGCTTTTCTT
Found at i:678535 original size:24 final size:22
Alignment explanation
Indices: 678489--678537 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
678479 ATTTTATCTT
678489 TTATTAATTTTAAAAATTATTA
1 TTATTAATTTTAAAAATTATTA
* *
678511 TTATATAATTTTATCAAATTTTTA
1 TTAT-TAATTTTA-AAAATTATTA
678535 TTA
1 TTA
678538 ATTTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 8 0.35
24 11 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTAATTTTAAAAATTATTA
Found at i:684688 original size:55 final size:56
Alignment explanation
Indices: 684618--684722 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 56
684608 ATTCACCAAT
*
684618 ATAAATAGACATAAAGCAGAAAGAAAAATTAATATTATATTTTCACATTAAGCATC
1 ATAAATAGACATAAAGCAGAAAGAAAAATTAATATTAGATTTTCACATTAAGCATC
* *
684674 ATAAA-AGATATAAAGTAGAAAGAAAAATTAATATTAGATTTTCACATTA
1 ATAAATAGACATAAAGCAGAAAGAAAAATTAATATTAGATTTTCACATTA
684723 GACATCGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 41 0.89
56 5 0.11
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.30
Consensus pattern (56 bp):
ATAAATAGACATAAAGCAGAAAGAAAAATTAATATTAGATTTTCACATTAAGCATC
Found at i:685001 original size:23 final size:22
Alignment explanation
Indices: 684975--685017 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
684965 AAGGAGAGAG
684975 AAAAAAGA-AAAAGACAAAAAGGT
1 AAAAAAGAGAAAA-A-AAAAAGGT
684998 AAAAAAGAGAAAAAAAAAAG
1 AAAAAAGAGAAAAAAAAAAG
685018 AAAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 6 0.32
23 9 0.47
24 4 0.21
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAAAAGAGAAAAAAAAAAGGT
Found at i:693473 original size:22 final size:23
Alignment explanation
Indices: 693438--693499 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
693428 CAAGACTAGA
**
693438 TATTGTAAAAGTCCAAGTCTAAG
1 TATTGTAAAAGTCCAAACCTAAG
*
693461 TATTGT-AAAGTCCAAACCTAGG
1 TATTGTAAAAGTCCAAACCTAAG
693483 TATTGTAAAAGTCCAAA
1 TATTGTAAAAGTCCAAA
693500 TCTTGGATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 19 0.54
23 16 0.46
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (23 bp):
TATTGTAAAAGTCCAAACCTAAG
Found at i:693499 original size:23 final size:22
Alignment explanation
Indices: 693418--693499 Score: 94
Period size: 23 Copynumber: 3.6 Consensus size: 22
693408 ATCTAGATAC
* *
693418 TGTAAAAGTTCAAGACTAGATAT
1 TGTAAAAGTCCAA-ACTAGGTAT
* *
693441 TGTAAAAGTCCAAGTCTAAGTAT
1 TGTAAAAGTCCAA-ACTAGGTAT
693464 TGT-AAAGTCCAAACCTAGGTAT
1 TGTAAAAGTCCAAA-CTAGGTAT
693486 TGTAAAAGTCCAAA
1 TGTAAAAGTCCAAA
693500 TCTTGGATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
22 19 0.37
23 32 0.63
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (22 bp):
TGTAAAAGTCCAAACTAGGTAT
Found at i:701416 original size:24 final size:23
Alignment explanation
Indices: 701388--701439 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
701378 CAACATTTTA
*
701388 TAAAAAAGTCTAAGCCTATATAT
1 TAAAAAAGTCTAAACCTATATAT
*
701411 TCAAAAAAGTCTAAACCTATGTAT
1 T-AAAAAAGTCTAAACCTATATAT
701435 TAAAA
1 TAAAA
701440 GTTCTAACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.50, C:0.13, G:0.08, T:0.29
Consensus pattern (23 bp):
TAAAAAAGTCTAAACCTATATAT
Found at i:701441 original size:21 final size:22
Alignment explanation
Indices: 701390--701452 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 22
701380 ACATTTTATA
* *
701390 AAAAAGTCTAAGCCTATATATT
1 AAAAAGTCTAAACCTATGTATT
701412 CAAAAAAGTCTAAACCTATGTATT
1 --AAAAAGTCTAAACCTATGTATT
701436 -AAAAGTTCT-AACCTATG
1 AAAAAG-TCTAAACCTATG
701453 ACTAAGATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
21 13 0.36
22 3 0.08
24 20 0.56
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (22 bp):
AAAAAGTCTAAACCTATGTATT
Found at i:703908 original size:35 final size:35
Alignment explanation
Indices: 703867--703943 Score: 145
Period size: 35 Copynumber: 2.2 Consensus size: 35
703857 TAAAAGAAGG
703867 TTTAGAAAGACATGATAAAGAAGAGAGATTTTTTT
1 TTTAGAAAGACATGATAAAGAAGAGAGATTTTTTT
703902 TTTAGAAAGACATGATAAAGAAGAGAGATTTTTTT
1 TTTAGAAAGACATGATAAAGAAGAGAGATTTTTTT
*
703937 TCTAGAA
1 TTTAGAA
703944 CTAAGATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (35 bp):
TTTAGAAAGACATGATAAAGAAGAGAGATTTTTTT
Found at i:704097 original size:24 final size:23
Alignment explanation
Indices: 704061--704112 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 23
704051 AGGCTAGGAC
704061 TTTTAATACATAGGCTTAGACTT
1 TTTTAATACATAGGCTTAGACTT
*
704084 TTTTGAATATATAGGCTTAGACTT
1 TTTT-AATACATAGGCTTAGACTT
704108 TTTTA
1 TTTTA
704113 TAAGATGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 5 0.19
24 22 0.81
ACGTcount: A:0.29, C:0.10, G:0.13, T:0.48
Consensus pattern (23 bp):
TTTTAATACATAGGCTTAGACTT
Found at i:708603 original size:45 final size:46
Alignment explanation
Indices: 708544--708638 Score: 129
Period size: 45 Copynumber: 2.1 Consensus size: 46
708534 GGTACTTAAA
*
708544 ATTTACTTCCATTGTGTATTTACATGTTTTTTTTTTACGTAATTTT
1 ATTTACTTCCATTGTGTATTTACATGTTCTTTTTTTACGTAATTTT
** * * *
708590 ATTTA-TTCCATTGTGTATTTATTTGTTCTTTTTTTGCTTTATTTT
1 ATTTACTTCCATTGTGTATTTACATGTTCTTTTTTTACGTAATTTT
708635 ATTT
1 ATTT
708639 TATTTTTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 38 0.88
46 5 0.12
ACGTcount: A:0.17, C:0.09, G:0.08, T:0.65
Consensus pattern (46 bp):
ATTTACTTCCATTGTGTATTTACATGTTCTTTTTTTACGTAATTTT
Found at i:726105 original size:18 final size:17
Alignment explanation
Indices: 726078--726122 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
726068 ATAAAAAATT
*
726078 AATTAATTATGATATAA
1 AATTAATTATAATATAA
726095 AATTAAATTATAATATAA
1 AATT-AATTATAATATAA
*
726113 TATTTAATTA
1 -AATTAATTA
726123 ACAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.17
18 17 0.71
19 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTAATTATAATATAA
Found at i:726511 original size:14 final size:15
Alignment explanation
Indices: 726492--726520 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
726482 GTATATTTAT
726492 AAAG-AAAAGAAAAA
1 AAAGAAAAAGAAAAA
726506 AAAGAAAAAGAAAAA
1 AAAGAAAAAGAAAAA
726521 TAATTTAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAAA
Found at i:756012 original size:2 final size:2
Alignment explanation
Indices: 756001--756031 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
755991 TATTTCGATA
756001 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
756032 TTGCTTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:756161 original size:3 final size:3
Alignment explanation
Indices: 756153--756180 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
756143 ATTTATCCCT
756153 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
756181 ATAAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:766586 original size:17 final size:20
Alignment explanation
Indices: 766556--766591 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
766546 TTGAAATCCA
766556 ACTTCCAAGAAAAT-TAAAC
1 ACTTCCAAGAAAATGTAAAC
766575 ACTT-CAAG-AAATGTAAA
1 ACTTCCAAGAAAATGTAAA
766592 ACCTGAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.25
18 8 0.50
19 4 0.25
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (20 bp):
ACTTCCAAGAAAATGTAAAC
Found at i:786079 original size:21 final size:22
Alignment explanation
Indices: 786049--786090 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
786039 TATTATATAT
786049 GGAAAAAACAA-C-GAACATAA
1 GGAAAAAACAACCAGAACATAA
786069 GGAAATAAACAACCAGAACATA
1 GGAAA-AAACAACCAGAACATA
786091 CTTCTCAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 1 0.05
23 7 0.37
ACGTcount: A:0.62, C:0.17, G:0.14, T:0.07
Consensus pattern (22 bp):
GGAAAAAACAACCAGAACATAA
Found at i:787344 original size:15 final size:15
Alignment explanation
Indices: 787324--787353 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
787314 ATCAAGTTAA
787324 GTGTTAAGATTTGAT
1 GTGTTAAGATTTGAT
*
787339 GTGTTAATATTTGAT
1 GTGTTAAGATTTGAT
787354 AATTAAGGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (15 bp):
GTGTTAAGATTTGAT
Found at i:789626 original size:2 final size:2
Alignment explanation
Indices: 789619--789826 Score: 416
Period size: 2 Copynumber: 104.0 Consensus size: 2
789609 GATGTTAAGG
789619 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
789661 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
789703 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
789745 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
789787 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
789827 ACACACACAC
Statistics
Matches: 206, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 206 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:800624 original size:2 final size:2
Alignment explanation
Indices: 800617--800648 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
800607 TCCACTAATT
800617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
800649 ATGTCACTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:807190 original size:251 final size:251
Alignment explanation
Indices: 806706--807379 Score: 659
Period size: 251 Copynumber: 2.7 Consensus size: 251
806696 AGGACTTCTT
* * * * * *
806706 AAAATATTAATATAAATGTGTGAAAGTTAACGTAATAAGATAATTAAG-TCAAATAAAGATAA-T
1 AAAATATTGATATAAATGTGTGAAATTTAACGTAAAAAGTTAATTAAGTTAAAATAAATATAATT
* * * *
806769 TTTTAAACAAATTAAACTTTTAAATTTGTATTCTCGAATTTAAAA-TATTTAACGGTTAACAAAT
66 TTTTAAA-AAATTAAA-TTTTAAATTTATATTATC-AAGTTAAAAGTATTTAA-GGTTTACAAAT
* * * * * ** * *
806833 TTTAATATATAAAAAAATAATAGTAAGGATAAAAACATTTTTAGTGAAAATTAGTAATTGAACAT
127 TTTAATTTATAAATAAATAATAATAAGGATAAAAACAATTATAGTGAAAATTAACAATTGAAAAA
** *
806898 TTTTGACGAAAAATTAAAAGAATTACTATAAAAAATTATAAACG-T-GAAAA-AGTATTGTG
192 ACTTGACGAAAAATTAAAAGAATTACTATAAAAAATTATAAA-GATGGAAAACA-TATTGTC
* * * * *
806957 GAAATATTGACATAAATTTGTGATATTTAACTTAAAAAGTTAATTAAGTTAAAATAAATATAATT
1 AAAATATTGATATAAATGTGTGAAATTTAACGTAAAAAGTTAATTAAGTTAAAATAAATATAATT
* *
807022 TTTTAAAAAATTAAATGTTTAAATTTATTTTATCAAGCTAAAAGTA-TTAATGGTTTACAAATTT
66 TTTTAAAAAATTAAAT-TTTAAATTTATATTATCAAGTTAAAAGTATTTAA-GGTTTACAAATTT
* * *
807086 TAATTTATAAATGAATAATAATAAGGATAAACACAATTATAGTGAAAATTAACAATTTAAAAAAC
129 TAATTTATAAATAAATAATAATAAGGATAAAAACAATTATAGTGAAAATTAACAATTGAAAAAAC
* * *
807151 TTGAC-ATAAAATTGTAAA-AATTAAC-GTAAAAATTTATAAAGATGGAAAACATATTGTC
194 TTGACGA-AAAATT-AAAAGAATT-ACTATAAAAAATTATAAAGATGGAAAACATATTGTC
* * * * * *
807209 AAAATATTGATGTAAATGTGTAAAATTTAACGTAACAAGTCAATTAAATCAAAATAAATATAATT
1 AAAATATTGATATAAATGTGTGAAATTTAACGTAAAAAGTTAATTAAGTTAAAATAAATATAATT
* * * ** ** * *
807274 TTTGT-GAAAATTAAACATCTAAATTTATATTATTGAGTTAAAAGTATTTGAAGGTTTTTAAGTA
66 TTT-TAAAAAATTAAA-TTTTAAATTTATATTATCAAGTTAAAAGTATTT-AAGGTTTACAAATT
* * * *
807338 TTAATTTATCAATAAACAATAATAAGAATAAAAATAATTATA
128 TTAATTTATAAATAAATAATAATAAGGATAAAAACAATTATA
807380 ATTAAAATAA
Statistics
Matches: 345, Mismatches: 64, Indels: 26
0.79 0.15 0.06
Matches are distributed among these distances:
250 2 0.01
251 143 0.41
252 142 0.41
253 56 0.16
254 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.36
Consensus pattern (251 bp):
AAAATATTGATATAAATGTGTGAAATTTAACGTAAAAAGTTAATTAAGTTAAAATAAATATAATT
TTTTAAAAAATTAAATTTTAAATTTATATTATCAAGTTAAAAGTATTTAAGGTTTACAAATTTTA
ATTTATAAATAAATAATAATAAGGATAAAAACAATTATAGTGAAAATTAACAATTGAAAAAACTT
GACGAAAAATTAAAAGAATTACTATAAAAAATTATAAAGATGGAAAACATATTGTC
Found at i:807375 original size:15 final size:15
Alignment explanation
Indices: 807348--807390 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
807338 TTAATTTATC
807348 AATAAACAATAATAAG
1 AATAAA-AATAATAAG
* *
807364 AATAAAAATAATTAT
1 AATAAAAATAATAAG
*
807379 AATTAAAATAAT
1 AATAAAAATAAT
807391 TAATTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (15 bp):
AATAAAAATAATAAG
Found at i:807401 original size:31 final size:31
Alignment explanation
Indices: 807365--807433 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
807355 AATAATAAGA
807365 ATAAAAATAATTATAATTAAAATAATTAATT
1 ATAAAAATAATTATAATTAAAATAATTAATT
* * * * * *
807396 ATAAAAGTAATTTTTATTATAATATTTATTT
1 ATAAAAATAATTATAATTAAAATAATTAATT
807427 A-AAAAAT
1 ATAAAAAT
807434 TTTCAATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
30 5 0.16
31 26 0.84
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (31 bp):
ATAAAAATAATTATAATTAAAATAATTAATT
Found at i:808210 original size:251 final size:245
Alignment explanation
Indices: 807685--808373 Score: 656
Period size: 251 Copynumber: 2.8 Consensus size: 245
807675 TTCACTTTTT
* * * *
807685 TATTTTTATCTTTATTATTATTCATTAAT-AATTGAAAATTTACT-AATCATTAAATACATTTAG
1 TATTTTTATCCTTA-TATTATTCATTTATAAATT-AAAATTTA-TAAATCGTTAAATACTTTTAG
* * * * * * * *
807748 CTTGGGAATATAAATTTAAGTGGTTAATTTTCACAAAA-AATTATTGTAACTTAGTTAACTTGTT
63 CTTGAGAATATAAATTTAAATGTTTAATTTTCACAAAATTATTTTTTTAACTTAATTGACTTGTT
* * * * * * *
807812 ATGGTAACTTTCACACA-TTTGTGTCAAAATTTTAATAATGCTTGATTTA-CTTTATAATTTTTT
128 AT-GTTA-TTTCTCACATTTTATGTTAATATTTTAATAATGTTTG-TTCACCTTTATAATTTTTT
** * * *
807875 ATGTTAATTCTTACAATTTTACGTGACAATTTTAAATTGCTAATTCCCACTATAAT
190 ACATTAATTCTTACAAATTTACGTGAAAATTTTAAATTGCTAATTCCCACTATAAC
*
807931 TA-TTTTATCCTTTATATTATTCATTTATAAATTAAAGTTTATAAATCGTTAAATACTTTTAGCT
1 TATTTTTATCC-TTATATTATTCATTTATAAATTAAAATTTATAAATCGTTAAATACTTTTAGCT
* *
807995 TGAAAATATACATTTAAATGTTTAATTTTCACTAAAATTAGTTTTTTTAACTTAATTGACTTGTT
65 TGAGAATATAAATTTAAATGTTTAATTTTCAC-AAAATTA-TTTTTTTAACTTAATTGACTTGTT
* * *
808060 ATATTATTTCTCACATGTTTATGTTAATATTTTAATAATATTTGTTGCACCTTTATAATTTTTTG
128 ATGTTATTTCTCACAT-TTTATGTTAATATTTTAATAATGTTTGTT-CACCTTTATAATTTTTTA
* * ***
808125 CATTAATTCTTATAAATTTACGT-AAAGATATTTTAATTGCTAATTTTTACTATAAC
191 CATTAATTCTTACAAATTTACGTGAAA-AT-TTTAAATTGCTAATTCCCACTATAAC
* * * *
808181 TATTTTTATCCTTACTATTATTAATTTATAAATTAAAATTTGTAAATTGTTAAATATTTTTAGCT
1 TATTTTTATCCTTA-TATTATTCATTTATAAATTAAAATTTATAAATCGTTAAATACTTTTAGCT
* * * * * * *
808246 CGAGAGTATATATTTAAATATTTAATTTTCACAAAAATCATATTTATGTTGACTTAATTGATTTG
65 TGAGAATATAAATTTAAATGTTTAATTTTCAC-AAAAT--TATTT-TTTTAACTTAATTGACTTG
* * * * * * *
808311 TTACGTTAACTT-TCACATATTTACGCTAATATTTTAATGATGTTTGTTCCACATTTATGATTT
126 TTATGTT-ATTTCTCACAT-TTTATGTTAATATTTTAATAATGTTTGTT-CACCTTTATAATTT
808374 CTTTTTTTAT
Statistics
Matches: 365, Mismatches: 60, Indels: 29
0.80 0.13 0.06
Matches are distributed among these distances:
244 1 0.00
245 73 0.20
246 21 0.06
247 5 0.01
248 47 0.13
249 35 0.10
250 26 0.07
251 85 0.23
252 3 0.01
253 66 0.18
254 3 0.01
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.49
Consensus pattern (245 bp):
TATTTTTATCCTTATATTATTCATTTATAAATTAAAATTTATAAATCGTTAAATACTTTTAGCTT
GAGAATATAAATTTAAATGTTTAATTTTCACAAAATTATTTTTTTAACTTAATTGACTTGTTATG
TTATTTCTCACATTTTATGTTAATATTTTAATAATGTTTGTTCACCTTTATAATTTTTTACATTA
ATTCTTACAAATTTACGTGAAAATTTTAAATTGCTAATTCCCACTATAAC
Found at i:811359 original size:94 final size:89
Alignment explanation
Indices: 811210--811396 Score: 223
Period size: 94 Copynumber: 2.0 Consensus size: 89
811200 TATTTACTTT
* * ** *
811210 AAAGAAAAAATTATTTGATTAATTTAAAAAAATAATAGGAAAATTAGTAAAAATTTTACAAAT-T
1 AAAGAAAAAAATATTTGATTAATTCAAAAAAATAATAACAAAAATAGTAAAAATTTTACAAATCT
*
811274 GTTTACAAAAGGAAATCAAAATAAAA
66 GTGTA-AAAAGGAAA-CAAAATAAAA
* *
811300 AAAGAAAAAAATATTTTATTAATTCACAGAAAAATAGAATAACAAAAATAGTAAAAATTTTGCAA
1 AAAGAAAAAAATATTTGATTAATTCA-A-AAAAAT--AATAACAAAAATAGTAAAAATTTTACAA
*
811365 ATCGTGTGTAAATAGGAAACAAAATAAAA
62 ATC-TGTGTAAAAAGGAAACAAAATAAAA
811394 AAA
1 AAA
811397 CAGTTACAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
90 23 0.28
91 1 0.01
92 6 0.07
94 39 0.48
95 8 0.10
96 5 0.06
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.26
Consensus pattern (89 bp):
AAAGAAAAAAATATTTGATTAATTCAAAAAAATAATAACAAAAATAGTAAAAATTTTACAAATCT
GTGTAAAAAGGAAACAAAATAAAA
Found at i:818029 original size:2 final size:2
Alignment explanation
Indices: 818024--818053 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
818014 CTTCAAATCT
818024 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
818054 GAGGAAGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:818944 original size:23 final size:23
Alignment explanation
Indices: 818914--818989 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
818904 ATTTGTAACG
*
818914 CAATGCCTAGTAAACTAGTCACA
1 CAATGCCTAATAAACTAGTCACA
818937 CAATGCCTAATAAACTAGTCACTA
1 CAATGCCTAATAAACTAGTCAC-A
* *
818961 -AATG-TTCAACAAACTAGTCACA
1 CAATGCCT-AATAAACTAGTCACA
818983 CAATGCC
1 CAATGCC
818990 ATCAAATTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
22 2 0.04
23 42 0.93
24 1 0.02
ACGTcount: A:0.41, C:0.26, G:0.11, T:0.22
Consensus pattern (23 bp):
CAATGCCTAATAAACTAGTCACA
Found at i:819000 original size:22 final size:22
Alignment explanation
Indices: 818925--819001 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 22
818915 AATGCCTAGT
818925 AAACTAGTCACACAATGCCTAAT-
1 AAACTAGTCACACAATGCC--ATC
* *
818948 AAACTAGTCACTA-AATGTTCAAC
1 AAACTAGTCAC-ACAATG-CCATC
818971 AAACTAGTCACACAATGCCATC
1 AAACTAGTCACACAATGCCATC
*
818993 AAATTAGTC
1 AAACTAGTC
819002 CCGCAATCCC
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
22 13 0.29
23 30 0.67
24 2 0.04
ACGTcount: A:0.43, C:0.25, G:0.09, T:0.23
Consensus pattern (22 bp):
AAACTAGTCACACAATGCCATC
Found at i:819156 original size:66 final size:66
Alignment explanation
Indices: 819003--819162 Score: 171
Period size: 66 Copynumber: 2.4 Consensus size: 66
818993 AAATTAGTCC
* * * * * *
819003 CGCAATCCCTACAA-CTCAGTCACGTAATCTTTACAACCTAGTATTACAATGTCTAAAAATCAAT
1 CGCAACCCCTACAATC-CAGTCACGCAATCCTTACAACCCAATATTACAATGCCTAAAAATCAAT
819067 CA
65 CA
* * *
819069 TGCAACCTCTACAATCCAGTCACGCAATCCTTACAACCCAATATTACAATGCCTAAAAATCAGTC
1 CGCAACCCCTACAATCCAGTCACGCAATCCTTACAACCCAATATTACAATGCCTAAAAATCAATC
819134 A
66 A
* * * *
819135 CGTATCCCCTAGAA-CCTAGTCATGCAAT
1 CGCAACCCCTACAATCC-AGTCACGCAAT
819163 GTCTAAAAAC
Statistics
Matches: 77, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
65 2 0.03
66 74 0.96
67 1 0.01
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (66 bp):
CGCAACCCCTACAATCCAGTCACGCAATCCTTACAACCCAATATTACAATGCCTAAAAATCAATC
A
Found at i:819163 original size:44 final size:44
Alignment explanation
Indices: 819115--819213 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 44
819105 CCCAATATTA
*
819115 CAATGCCTAAAAA-TCAGTCACGT-ATCCCCTAGAACCTAGTCATG
1 CAATGCCTAAAAACT-AGTCACGTAAT-CCCTACAACCTAGTCATG
* * *
819159 CAATGTCTAAAAACTAGTCATGTAATGCCTACAACCTAGTCATG
1 CAATGCCTAAAAACTAGTCACGTAATCCCTACAACCTAGTCATG
819203 CAACT-CCTAAA
1 CAA-TGCCTAAA
819214 TACCAGTCTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
44 43 0.91
45 4 0.09
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.24
Consensus pattern (44 bp):
CAATGCCTAAAAACTAGTCACGTAATCCCTACAACCTAGTCATG
Found at i:819175 original size:22 final size:22
Alignment explanation
Indices: 819150--819279 Score: 86
Period size: 22 Copynumber: 5.9 Consensus size: 22
819140 CCCCTAGAAC
*
819150 CTAGTCATGCAATGTCTAAAAA
1 CTAGTCATGCAATGCCTAAAAA
* * *
819172 CTAGTCATGTAATGCCTACAAC
1 CTAGTCATGCAATGCCTAAAAA
*
819194 CTAGTCATGCAACT-CCTAAATA
1 CTAGTCATGCAA-TGCCTAAAAA
* * *
819216 CCAGTC-TCACAATGCCTAAATA
1 CTAGTCAT-GCAATGCCTAAAAA
* * *
819238 CTAATC-TCGTAATGCCTACAAA
1 CTAGTCAT-GCAATGCCTAAAAA
* **
819260 CTAGTAACACAATGCCTAAA
1 CTAGTCATGCAATGCCTAAA
819280 TACCAATCTC
Statistics
Matches: 82, Mismatches: 22, Indels: 8
0.73 0.20 0.07
Matches are distributed among these distances:
21 2 0.02
22 79 0.96
23 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (22 bp):
CTAGTCATGCAATGCCTAAAAA
Found at i:819235 original size:66 final size:66
Alignment explanation
Indices: 819159--819296 Score: 163
Period size: 66 Copynumber: 2.1 Consensus size: 66
819149 CCTAGTCATG
* * * * ** *
819159 CAATGTCTAAAAACTAGTCAT-GTAATGCCTACAACCTAGTCATGCAACT-CCTAAATACCAGTC
1 CAATGCCTAAAAACTAATC-TCGTAATGCCTACAAACTAGTAACACAA-TGCCTAAATACCAATC
819222 TCA
64 TCA
*
819225 CAATGCCTAAATACTAATCTCGTAATGCCTACAAACTAGTAACACAATGCCTAAATACCAATCTC
1 CAATGCCTAAAAACTAATCTCGTAATGCCTACAAACTAGTAACACAATGCCTAAATACCAATCTC
*
819290 G
66 A
819291 CAATGC
1 CAATGC
819297 TTGCAAACAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
65 2 0.03
66 59 0.97
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.25
Consensus pattern (66 bp):
CAATGCCTAAAAACTAATCTCGTAATGCCTACAAACTAGTAACACAATGCCTAAATACCAATCTC
A
Found at i:819294 original size:22 final size:22
Alignment explanation
Indices: 819208--819296 Score: 81
Period size: 22 Copynumber: 4.0 Consensus size: 22
819198 TCATGCAACT
*
819208 CCTAAATACCAGTCTCACAATG
1 CCTAAATACCAATCTCACAATG
* **
819230 CCTAAATACTAATCTCGTAATG
1 CCTAAATACCAATCTCACAATG
* * **
819252 CCTACAA-ACTAGTAACACAATG
1 CCTA-AATACCAATCTCACAATG
*
819274 CCTAAATACCAATCTCGCAATG
1 CCTAAATACCAATCTCACAATG
819296 C
1 C
819297 TTGCAAACAT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
21 2 0.04
22 47 0.92
23 2 0.04
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (22 bp):
CCTAAATACCAATCTCACAATG
Found at i:824441 original size:17 final size:17
Alignment explanation
Indices: 824419--824453 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
824409 TTCCTCTTGT
824419 TCTTTTTTCTTTATTCA
1 TCTTTTTTCTTTATTCA
* *
824436 TCTTTTTTTTTTTTTCA
1 TCTTTTTTCTTTATTCA
824453 T
1 T
824454 TTTGAGAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTTTTCTTTATTCA
Found at i:828639 original size:19 final size:19
Alignment explanation
Indices: 828614--828656 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
828604 GCTAAATATA
828614 AAATTT-ATTTTGAATTAAT
1 AAATTTAATTTTG-ATTAAT
*
828633 TAATTTAATTTTGATTAAT
1 AAATTTAATTTTGATTAAT
828652 AAATT
1 AAATT
828657 ACATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
AAATTTAATTTTGATTAAT
Found at i:836941 original size:2 final size:2
Alignment explanation
Indices: 836934--836962 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
836924 TTGCTCACTT
836934 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
836963 GTAGGTTAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:850102 original size:21 final size:21
Alignment explanation
Indices: 850071--850122 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
850061 GCATAATATA
*
850071 TAAAAAA-TTTTTAAATTA-T
1 TAAAAAATTTTTTAAACTATT
850090 TAAAAAATTTTTTAAACTATT
1 TAAAAAATTTTTTAAACTATT
850111 TAAAAAATTTTT
1 TAAAAAATTTTT
850123 AAAAAGTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 7 0.23
20 10 0.33
21 13 0.43
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TAAAAAATTTTTTAAACTATT
Found at i:850123 original size:20 final size:19
Alignment explanation
Indices: 850071--850125 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
850061 GCATAATATA
*
850071 TAAAAAATTTTTAAATTAT
1 TAAAAAATTTTTAAACTAT
850090 TAAAAAATTTTTTAAACTATT
1 TAAAAAA-TTTTTAAACTA-T
850111 TAAAAAATTTTTAAA
1 TAAAAAATTTTTAAA
850126 AAGTTCTTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 7 0.21
20 18 0.55
21 8 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAAATTTTTAAACTAT
Found at i:850190 original size:30 final size:30
Alignment explanation
Indices: 850149--850219 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
850139 TTTATTACAT
*
850149 TCAATTAAGTTTTC-ATATTTTTATTGTGAG
1 TCAAATAAGTTTTCAAT-TTTTTATTGTGAG
* *
850179 TCAAATAAGTTTTTGAATTTTTTATTTTGAG
1 TCAAATAAG-TTTTCAATTTTTTATTGTGAG
*
850210 TCGAATAAGT
1 TCAAATAAGT
850220 CCTTATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 9 0.26
31 24 0.69
32 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.51
Consensus pattern (30 bp):
TCAAATAAGTTTTCAATTTTTTATTGTGAG
Found at i:853972 original size:29 final size:29
Alignment explanation
Indices: 853917--854010 Score: 120
Period size: 29 Copynumber: 3.3 Consensus size: 29
853907 AAACATTAAA
* * *
853917 GTGTAACAA-AAT-GTTTTTGAATATGAC
1 GTGTAACAATAATATTTTTTCAACATGAC
853944 GTGTAACAATAATATTTTTTCAACATGAC
1 GTGTAACAATAATATTTTTTCAACATGAC
* *
853973 GTGTAACAATAGTATTTTTTCAACATGGC
1 GTGTAACAATAATATTTTTTCAACATGAC
*
854002 TTGTAACAA
1 GTGTAACAA
854011 CCTAATCATA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 9 0.15
28 3 0.05
29 47 0.80
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (29 bp):
GTGTAACAATAATATTTTTTCAACATGAC
Found at i:854056 original size:24 final size:24
Alignment explanation
Indices: 854024--854074 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
854014 AATCATATGA
*
854024 TGTCACATGTTTTTATACATGGTG
1 TGTCACATGTTTCTATACATGGTG
*
854048 TGTCACATGTTTCTGTACATGGTG
1 TGTCACATGTTTCTATACATGGTG
854072 TGT
1 TGT
854075 AACAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.24, T:0.45
Consensus pattern (24 bp):
TGTCACATGTTTCTATACATGGTG
Found at i:854120 original size:45 final size:45
Alignment explanation
Indices: 854052--854168 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 45
854042 ATGGTGTGTC
* ** *
854052 ACATGTTTCTGTACATGGTGTGTAACAATTTAACTATTG-CGTATA
1 ACATGTTTTTGTACATGACGTGTAACAACTTAA-TATTGACGTATA
* * *
854097 ACATGTTTTTGCACATGACGTGTAACAACTTAATCTTGACGTGTA
1 ACATGTTTTTGTACATGACGTGTAACAACTTAATATTGACGTATA
* *
854142 ACATATTTTTGTACATGACTTGTAACA
1 ACATGTTTTTGTACATGACGTGTAACA
854169 TCATAGCGTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
44 4 0.07
45 57 0.93
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.38
Consensus pattern (45 bp):
ACATGTTTTTGTACATGACGTGTAACAACTTAATATTGACGTATA
Found at i:870582 original size:18 final size:19
Alignment explanation
Indices: 870556--870603 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
870546 GTGACGAGTG
*
870556 AAAAAAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
870574 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
870593 AAAATAATATT
1 AAAATAATATT
870604 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:870607 original size:35 final size:32
Alignment explanation
Indices: 870554--870621 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
870544 CGGTGACGAG
*
870554 TGAAAAAAATATTTTAAAATAAAATAATATTTTA
1 TGAAAAAAATATATTAAAAT--AATAATATTTTA
* *
870588 TGAATAAAATAATATTAAAATATTAATATTTTA
1 TGAAAAAAAT-ATATTAAAATAATAATATTTTA
870621 T
1 T
870622 TTATTATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 12 0.40
34 9 0.30
35 9 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (32 bp):
TGAAAAAAATATATTAAAATAATAATATTTTA
Found at i:871602 original size:4 final size:4
Alignment explanation
Indices: 871544--871645 Score: 84
Period size: 4 Copynumber: 24.8 Consensus size: 4
871534 AGAAGGACAA
* * * *
871544 AAAG AAA- AGAG AAAGG AGAAG AATG ACAG AAAG AAA- AGAG AAAGG AAAGG
1 AAAG AAAG AAAG AAA-G A-AAG AAAG AAAG AAAG AAAG AAAG AAA-G AAA-G
*
871594 AAAG AAAG AAA- AGAG AAAGG AAAGG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAA-G AAA-G AAAG AAAG AAAG AAAG AAAG AAAG
871643 AAA
1 AAA
871646 AAGAGAGAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
3 6 0.07
4 51 0.63
5 22 0.27
6 2 0.02
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:871603 original size:54 final size:54
Alignment explanation
Indices: 871516--871656 Score: 151
Period size: 54 Copynumber: 2.5 Consensus size: 54
871506 CATATCCAAG
* *
871516 AAGAAAAGAGAAAGGAGAAGAAGGACAA-AAAGAAAAGAGAAAGGAGAA-GAATGACAGA
1 AAGAAAAGAGAAA-G-G-A-AAGGA-AAGAAAGAAAAGAGAAAGGA-AAGGAAAGAAAGA
871574 AAGAAAAGAGAAAGGAAAGGAAAGAAAGAAAAGAGAAAGGAAAGGAAAGAAAGA
1 AAGAAAAGAGAAAGGAAAGGAAAGAAAGAAAAGAGAAAGGAAAGGAAAGAAAGA
* * * *
871628 AAGAAAGAAAGAAAGAAAAAGAGAGAAAG
1 AAGAAA-AGAGAAAGGAAAGGAAAGAAAG
871657 GAAGGAAGGT
Statistics
Matches: 74, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
53 4 0.05
54 36 0.49
55 19 0.26
56 1 0.01
57 1 0.01
58 13 0.18
ACGTcount: A:0.67, C:0.01, G:0.30, T:0.01
Consensus pattern (54 bp):
AAGAAAAGAGAAAGGAAAGGAAAGAAAGAAAAGAGAAAGGAAAGGAAAGAAAGA
Found at i:871615 original size:25 final size:25
Alignment explanation
Indices: 871516--871663 Score: 141
Period size: 25 Copynumber: 5.9 Consensus size: 25
871506 CATATCCAAG
871516 AAGAAAAGAGAAAGGAGAAGAAGGACAA-A
1 AAGAAAAGAGAAA-G-G-A-AAGGA-AAGA
*
871545 AAGAAAAGAGAAAGGAGAAGAATGACAGA
1 AAGAAAAGAGAAAGGA-AAG---GAAAGA
871574 AAGAAAAGAGAAAGGAAAGGAAAGA
1 AAGAAAAGAGAAAGGAAAGGAAAGA
871599 AAGAAAAGAGAAAGGAAAGGAAAGA
1 AAGAAAAGAGAAAGGAAAGGAAAGA
871624 AAG--AA-AGAAA-GAAA-GAAAGA
1 AAGAAAAGAGAAAGGAAAGGAAAGA
*
871644 AA-AAGAGAGAAAGG-AAGGAA
1 AAGAAAAGAGAAAGGAAAGGAA
871664 GGTTCAGTTG
Statistics
Matches: 107, Mismatches: 3, Indels: 24
0.80 0.02 0.18
Matches are distributed among these distances:
20 8 0.07
21 5 0.05
22 12 0.11
23 6 0.06
25 33 0.31
26 5 0.05
27 1 0.01
28 5 0.05
29 32 0.30
ACGTcount: A:0.67, C:0.01, G:0.31, T:0.01
Consensus pattern (25 bp):
AAGAAAAGAGAAAGGAAAGGAAAGA
Found at i:871645 original size:29 final size:29
Alignment explanation
Indices: 871516--871637 Score: 153
Period size: 29 Copynumber: 4.2 Consensus size: 29
871506 CATATCCAAG
*
871516 AAGAAAAGAGAAAGGAGAAGAAGGACAA-A
1 AAGAAAAGAGAAAGGAGAAGAAAGA-AAGA
* *
871545 AAGAAAAGAGAAAGGAGAAGAATGACAGA
1 AAGAAAAGAGAAAGGAGAAGAAAGAAAGA
871574 AAGAAAAGAGAAAGGA-AAGGAAAGAAAGAA
1 AAGAAAAGAGAAAGGAGAA-GAAAGAAAG-A
871604 AAGAGAAAG-GAAAGGA-AAGAAAGAAAGA
1 AAGA-AAAGAGAAAGGAGAAGAAAGAAAGA
871632 AAGAAA
1 AAGAAA
871638 GAAAGAAAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
27 2 0.02
28 8 0.09
29 57 0.67
30 14 0.16
31 4 0.05
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.01
Consensus pattern (29 bp):
AAGAAAAGAGAAAGGAGAAGAAAGAAAGA
Found at i:873094 original size:18 final size:18
Alignment explanation
Indices: 873067--873112 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
873057 TATCACGTAT
* *
873067 ACACGTTTAAACATGATA
1 ACACGATTAAACACGATA
873085 ACACGATTAAACACGATA
1 ACACGATTAAACACGATA
873103 ACACGATTAA
1 ACACGATTAA
873113 GTAAACGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.22
Consensus pattern (18 bp):
ACACGATTAAACACGATA
Found at i:874801 original size:32 final size:32
Alignment explanation
Indices: 874760--874859 Score: 200
Period size: 32 Copynumber: 3.1 Consensus size: 32
874750 TCTCTAGCTC
874760 TTCTAACCGAACCTTGCTTCCTTTCTCTTTTT
1 TTCTAACCGAACCTTGCTTCCTTTCTCTTTTT
874792 TTCTAACCGAACCTTGCTTCCTTTCTCTTTTT
1 TTCTAACCGAACCTTGCTTCCTTTCTCTTTTT
874824 TTCTAACCGAACCTTGCTTCCTTTCTCTTTTT
1 TTCTAACCGAACCTTGCTTCCTTTCTCTTTTT
874856 TTCT
1 TTCT
874860 TTTTTTCTTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 68 1.00
ACGTcount: A:0.12, C:0.31, G:0.06, T:0.51
Consensus pattern (32 bp):
TTCTAACCGAACCTTGCTTCCTTTCTCTTTTT
Found at i:874860 original size:8 final size:8
Alignment explanation
Indices: 874849--874905 Score: 51
Period size: 8 Copynumber: 6.5 Consensus size: 8
874839 GCTTCCTTTC
874849 TCTTTTTT
1 TCTTTTTT
874857 TCTTTTTT
1 TCTTTTTT
*
874865 TCTTTCTT
1 TCTTTTTT
*
874873 TCATTTCTT
1 TC-TTTTTT
874882 TCTTCTCTTT
1 TCTT-T-TTT
874892 TCTCTTTTCT
1 TCT-TTTT-T
874902 TCTT
1 TCTT
874906 GGATATGGGC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
8 19 0.45
9 12 0.29
10 10 0.24
11 1 0.02
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (8 bp):
TCTTTTTT
Found at i:874872 original size:4 final size:4
Alignment explanation
Indices: 874849--874891 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
874839 GCTTCCTTTC
* *
874849 TCTT TTTT TCTT TTTT TCTT TCTT TCATT TCTT TCTT CTCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT -TCTT T
874892 TCTCTTTTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 25 0.76
5 8 0.24
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (4 bp):
TCTT
Found at i:880172 original size:24 final size:24
Alignment explanation
Indices: 880140--880189 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
880130 GCTTCATGGT
880140 TCCCATTCGTTACTCTAGATGAAC
1 TCCCATTCGTTACTCTAGATGAAC
880164 TCCCATTCGTTACTCTAGATGAAC
1 TCCCATTCGTTACTCTAGATGAAC
880188 TC
1 TC
880190 ATTCTTTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.30, G:0.12, T:0.34
Consensus pattern (24 bp):
TCCCATTCGTTACTCTAGATGAAC
Found at i:893226 original size:12 final size:12
Alignment explanation
Indices: 893209--893233 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
893199 CCTGTTTGTT
893209 GTAGATATTGAA
1 GTAGATATTGAA
893221 GTAGATATTGAA
1 GTAGATATTGAA
893233 G
1 G
893234 AGGTACCACA
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:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GTAGATATTGAA
Found at i:904908 original size:19 final size:20
Alignment explanation
Indices: 904876--904915 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
904866 AAGTGAAAAA
904876 TTTTGGAATAAAAATAATAT
1 TTTTGGAATAAAAATAATAT
*
904896 TTTTTGAAT-AAAATAATAT
1 TTTTGGAATAAAAATAATAT
904915 T
1 T
904916 AAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTTGGAATAAAAATAATAT
Found at i:904918 original size:11 final size:11
Alignment explanation
Indices: 904904--904939 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
904894 ATTTTTTGAA
904904 TAAAATAATAT
1 TAAAATAATAT
904915 TAAAAATAATAT
1 T-AAAATAATAT
*
904927 TAAAATATTAT
1 TAAAATAATAT
904938 TA
1 TA
904940 CCATATTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAATAATAT
Found at i:904922 original size:12 final size:12
Alignment explanation
Indices: 904905--904931 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
904895 TTTTTTGAAT
904905 AAAATAATATTA
1 AAAATAATATTA
904917 AAAATAATATTA
1 AAAATAATATTA
904929 AAA
1 AAA
904932 TATTATTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATAATATTA
Found at i:905098 original size:19 final size:20
Alignment explanation
Indices: 905071--905110 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
905061 CGAATATAAT
905071 AATAATATTTTA-TTTGAAA
1 AATAATATTTTATTTTGAAA
*
905090 AATATTATTTTATTTTGAAA
1 AATAATATTTTATTTTGAAA
905110 A
1 A
905111 TTTTCATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
AATAATATTTTATTTTGAAA
Found at i:905659 original size:15 final size:15
Alignment explanation
Indices: 905639--905690 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 15
905629 GCTTTGTGGA
905639 ATCTGTTTTATCTAT
1 ATCTGTTTTATCTAT
* * *
905654 ATCTGTTTTTTTTTAA
1 ATCTG-TTTTATCTAT
*
905670 AGC-GTTTTATCTAT
1 ATCTGTTTTATCTAT
905684 ATCTGTT
1 ATCTGTT
905691 AAGACAGAGC
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
14 9 0.33
15 9 0.33
16 9 0.33
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.60
Consensus pattern (15 bp):
ATCTGTTTTATCTAT
Found at i:915192 original size:17 final size:17
Alignment explanation
Indices: 915170--915205 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
915160 GTTGATATCC
* *
915170 AAAAAGGAGGAAAAGAA
1 AAAAAGAAGAAAAAGAA
915187 AAAAAGAAGAAAAAGAA
1 AAAAAGAAGAAAAAGAA
915204 AA
1 AA
915206 GAGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (17 bp):
AAAAAGAAGAAAAAGAA
Found at i:915204 original size:22 final size:22
Alignment explanation
Indices: 915179--915220 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
915169 CAAAAAGGAG
915179 GAAAAGAAAAAAAGAAGAAAAA
1 GAAAAGAAAAAAAGAAGAAAAA
* *
915201 GAAAAGAGAAAAAGAGGAAA
1 GAAAAGAAAAAAAGAAGAAA
915221 TTAATCACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (22 bp):
GAAAAGAAAAAAAGAAGAAAAA
Found at i:916227 original size:15 final size:17
Alignment explanation
Indices: 916197--916229 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
916187 TATTTTGTGT
916197 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
916214 TAAC-TTAT-AAAATTA
1 TAACATTATAAAAATTA
916229 T
1 T
916230 TAATCATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:916275 original size:17 final size:17
Alignment explanation
Indices: 916249--916283 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
916239 TATATATACC
*
916249 ATTATTTATATAAACTT
1 ATTATATATATAAACTT
*
916266 ATTATATATATATACTT
1 ATTATATATATAAACTT
916283 A
1 A
916284 AAGAGAGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATATATATAAACTT
Found at i:916492 original size:58 final size:58
Alignment explanation
Indices: 916421--916537 Score: 182
Period size: 58 Copynumber: 2.0 Consensus size: 58
916411 ATGTCTTTCA
*
916421 ATATATGTAGTTTATATATTGTGTTAATTT-TAAAAAATATAATTACTATTATATATAT
1 ATATATATAGTTTATATATTGTGTTAATTTATAAAAAATATAATTACTATTATAT-TAT
* **
916479 ATATATATAGTTTATATATTGTGTTAATTTATTATGAATATAATTACTATTATATTAT
1 ATATATATAGTTTATATATTGTGTTAATTTATAAAAAATATAATTACTATTATATTAT
916537 A
1 A
916538 GGCTTTTAGT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 33 0.61
59 21 0.39
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (58 bp):
ATATATATAGTTTATATATTGTGTTAATTTATAAAAAATATAATTACTATTATATTAT
Found at i:924498 original size:30 final size:30
Alignment explanation
Indices: 924462--924557 Score: 158
Period size: 30 Copynumber: 3.2 Consensus size: 30
924452 CAATCAAACC
924462 TTTATATTTTTATTTTGAATCAAATAAATT
1 TTTATATTTTTATTTTGAATCAAATAAATT
*
924492 TTTATATTTTTATTTTGAA-CTAAATAAATC
1 TTTATATTTTTATTTTGAATC-AAATAAATT
*
924522 TTTGTATTTTTATTTTGAATCAAATAAATT
1 TTTATATTTTTATTTTGAATCAAATAAATT
924552 TTTATA
1 TTTATA
924558 ATTAATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.02
30 58 0.97
31 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTATATTTTTATTTTGAATCAAATAAATT
Found at i:925617 original size:16 final size:18
Alignment explanation
Indices: 925585--925640 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 18
925575 GATGATGAGG
925585 AGGAG-GAG-GAGA-AGA
1 AGGAGAGAGCGAGAGAGA
*
925600 AGGAGAGAG-GA-AGGGA
1 AGGAGAGAGCGAGAGAGA
925616 A-GAGGAGAGCGAGAGAGA
1 AGGA-GAGAGCGAGAGAGA
925634 AGGAGAG
1 AGGAGAG
925641 GAAATGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 8 0.24
16 13 0.39
17 2 0.06
18 8 0.24
19 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.54, T:0.00
Consensus pattern (18 bp):
AGGAGAGAGCGAGAGAGA
Found at i:925806 original size:3 final size:3
Alignment explanation
Indices: 925800--925846 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
925790 AGAAGACACT
* ** *
925800 GAA GAA GAG GAA GAA GGT GAA GAT GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
925847 TGATGATAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:929527 original size:33 final size:33
Alignment explanation
Indices: 929481--929550 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
929471 ATGCTTTTGC
* *
929481 TTTTTACTATTTGTTTTTGGTTTTCTGTTCATT
1 TTTTTACTATTTGTTTTTGCTTTTCTATTCATT
*
929514 TTTTTATCT-TTTGTTTTTTCTTTTCTATTCATT
1 TTTTTA-CTATTTGTTTTTGCTTTTCTATTCATT
929547 TTTT
1 TTTT
929551 GCAAAAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 31 0.94
34 2 0.06
ACGTcount: A:0.09, C:0.10, G:0.07, T:0.74
Consensus pattern (33 bp):
TTTTTACTATTTGTTTTTGCTTTTCTATTCATT
Found at i:934342 original size:22 final size:23
Alignment explanation
Indices: 934300--934344 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
934290 CGTGAATAAG
934300 TTTTATTCTTATAAAGATATTAA
1 TTTTATTCTTATAAAGATATTAA
*
934323 TTTTGTTC-TATAAA-ATTATTAA
1 TTTTATTCTTATAAAGA-TATTAA
934345 AAAATCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.60
23 7 0.35
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (23 bp):
TTTTATTCTTATAAAGATATTAA
Found at i:934585 original size:19 final size:19
Alignment explanation
Indices: 934563--934600 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
934553 TAATCATTAA
*
934563 ATAAATAATTAAA-AATTTT
1 ATAAA-AATAAAAGAATTTT
934582 ATAAAAATAAAAGAATTTT
1 ATAAAAATAAAAGAATTTT
934601 GACAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (19 bp):
ATAAAAATAAAAGAATTTT
Found at i:934666 original size:90 final size:90
Alignment explanation
Indices: 934567--934747 Score: 353
Period size: 90 Copynumber: 2.0 Consensus size: 90
934557 CATTAAATAA
934567 ATAATTAAAAATTTTATAAAAATAAAAGAATTTTGACAATTTTTAACAAATTAAGAAATCCTTCA
1 ATAATTAAAAATTTTATAAAAATAAAAGAATTTTGACAATTTTTAACAAATTAAGAAATCCTTCA
934632 ATATTCAAAGTAAGTAAGTAGGTGT
66 ATATTCAAAGTAAGTAAGTAGGTGT
*
934657 ATAANTAAAAATTTTATAAAAATAAAAGAATTTTGACAATTTTTAACAAATTAAGAAATCCTTCA
1 ATAATTAAAAATTTTATAAAAATAAAAGAATTTTGACAATTTTTAACAAATTAAGAAATCCTTCA
934722 ATATTCAAAGTAAGTAAGTAGGTGT
66 ATATTCAAAGTAAGTAAGTAGGTGT
934747 A
1 A
934748 ATAAATATAT
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 90 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (90 bp):
ATAATTAAAAATTTTATAAAAATAAAAGAATTTTGACAATTTTTAACAAATTAAGAAATCCTTCA
ATATTCAAAGTAAGTAAGTAGGTGT
Found at i:934759 original size:2 final size:2
Alignment explanation
Indices: 934752--934801 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
934742 GGTGTAATAA
* *
934752 AT AT AT AT -T AA AT AT A- AT AT AT AT -T AT AT AT CT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
934790 AT AT AT AT AT AT
1 AT AT AT AT AT AT
934802 TTGGGTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:934765 original size:11 final size:13
Alignment explanation
Indices: 934751--934800 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
934741 AGGTGTAATA
934751 AATATATAT-TA-
1 AATATATATATAT
934762 AATATA-ATATAT
1 AATATATATATAT
* *
934774 ATTATATATCTAT
1 AATATATATATAT
934787 AATATATATATAT
1 AATATATATATAT
934800 A
1 A
934801 TTTGGGTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 2 0.06
11 8 0.25
12 5 0.16
13 17 0.53
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATATATATAT
Found at i:934772 original size:16 final size:16
Alignment explanation
Indices: 934747--934782 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
934737 AAGTAGGTGT
934747 AATA-AATATATATTA
1 AATATAATATATATTA
934762 AATATAATATATATTA
1 AATATAATATATATTA
*
934778 TATAT
1 AATAT
934783 CTATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATAATATATATTA
Found at i:934775 original size:20 final size:21
Alignment explanation
Indices: 934746--934801 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
934736 TAAGTAGGTG
*
934746 TAATAAATATATAT-TAAATA
1 TAATATATATATATATAAATA
**
934766 TAATATATAT-TATATATCTA
1 TAATATATATATATATAAATA
934786 TAATATATATATATAT
1 TAATATATATATATAT
934802 TTGGGTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 3 0.10
20 23 0.74
21 5 0.16
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATATATATATATATAAATA
Found at i:940225 original size:1 final size:1
Alignment explanation
Indices: 940221--940259 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
940211 TTTTTTTTTT
* *
940221 GGGGGGGGGGGGGGGGTGGGGGTGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
940260 CGTGTGGTGN
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.95, T:0.05
Consensus pattern (1 bp):
G
Done.