Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 66 of 103
Found at i:24788105 original size:95 final size:95
Alignment explanation
Indices: 24787978--24788257 Score: 479
Period size: 95 Copynumber: 2.9 Consensus size: 95
24787968 TACTAACTCC
24787978 ACGCCACTCCACATTTATTACTCACGCGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAG
1 ACGCCACTCCACATTTATTACTCACGCGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAG
* *
24788043 TCATGTCACGCGCTTCCATATTAACTAGTA
66 TCGTGTCACGCGATTCCATATTAACTAGTA
* * * * *
24788073 ACGTCACTTCATATTTACTACTCACGTGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAG
1 ACGCCACTCCACATTTATTACTCACGCGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAG
*
24788138 TCGTGTCACGCTATTCCATATTAACTAGTA
66 TCGTGTCACGCGATTCCATATTAACTAGTA
*
24788168 ACGCCACTCCACATTTATTACTCACACGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAG
1 ACGCCACTCCACATTTATTACTCACGCGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAG
24788233 TCGTGTCACGCGATTCCATATTAAC
66 TCGTGTCACGCGATTCCATATTAAC
24788258 CACCGACGTG
Statistics
Matches: 170, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
95 170 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (95 bp):
ACGCCACTCCACATTTATTACTCACGCGAGTCAATATAAACTAGTGACGCGATTCCACGGAGAAG
TCGTGTCACGCGATTCCATATTAACTAGTA
Found at i:24788479 original size:26 final size:26
Alignment explanation
Indices: 24788448--24788499 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
24788438 ATGAATGAAT
* *
24788448 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGGAAAAGATACA
*
24788474 ACAAAGAGTAATATGGAAAAGATACA
1 ACAAAGAATAATATGGAAAAGATACA
24788500 GAATAATGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.19
Consensus pattern (26 bp):
ACAAAGAATAATATGGAAAAGATACA
Found at i:24790161 original size:24 final size:24
Alignment explanation
Indices: 24790134--24790227 Score: 136
Period size: 24 Copynumber: 3.9 Consensus size: 24
24790124 TGCATCGCCC
24790134 GCTGGATCTTCAACTGCATTGACT
1 GCTGGATCTTCAACTGCATTGACT
24790158 GCTGGATC-TCTAACTGCATTGACT
1 GCTGGATCTTC-AACTGCATTGACT
* * *
24790182 ACTGGATCTCCAATTGCATTGACT
1 GCTGGATCTTCAACTGCATTGACT
*
24790206 GCTGGATCTTCAATTGCATTGA
1 GCTGGATCTTCAACTGCATTGA
24790228 TTGCATCTGC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
23 2 0.03
24 60 0.95
25 1 0.02
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (24 bp):
GCTGGATCTTCAACTGCATTGACT
Found at i:24790274 original size:63 final size:63
Alignment explanation
Indices: 24790183--24790303 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 63
24790173 GCATTGACTA
* * * * *
24790183 CTGGATCTCCAATTGCATTGACTGCTGGATCTTCAATTGCATTGA-TTGCATCTGCATCGCTCG
1 CTGGATCTCCAACTACATTGACTACTGGATCTCCAACTGCATTGACTT-CATCTGCATCGCTCG
24790246 CTGGATCTCCAACTACATTGACTACTGGATCTCCAACTGCATTGACTTCATCTGCATC
1 CTGGATCTCCAACTACATTGACTACTGGATCTCCAACTGCATTGACTTCATCTGCATC
24790304 TGCATATTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
63 50 0.96
64 2 0.04
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.33
Consensus pattern (63 bp):
CTGGATCTCCAACTACATTGACTACTGGATCTCCAACTGCATTGACTTCATCTGCATCGCTCG
Found at i:24790278 original size:24 final size:24
Alignment explanation
Indices: 24790246--24790292 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
24790236 GCATCGCTCG
24790246 CTGGATCTCCAACTACATTGACTA
1 CTGGATCTCCAACTACATTGACTA
*
24790270 CTGGATCTCCAACTGCATTGACT
1 CTGGATCTCCAACTACATTGACT
24790293 TCATCTGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (24 bp):
CTGGATCTCCAACTACATTGACTA
Found at i:24790473 original size:24 final size:24
Alignment explanation
Indices: 24790422--24790481 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
24790412 GGCTCAGCAT
* * * *
24790422 GAGGGGCAGCACCTGAAGCAGGAA
1 GAGGGGCAGCAGCAGAAACAAGAA
*
24790446 GAGGGGCAGCAGCAGAAACAAGAG
1 GAGGGGCAGCAGCAGAAACAAGAA
*
24790470 GAGGAGCAGCAG
1 GAGGGGCAGCAG
24790482 GATAAACACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.43, T:0.02
Consensus pattern (24 bp):
GAGGGGCAGCAGCAGAAACAAGAA
Found at i:24792323 original size:23 final size:23
Alignment explanation
Indices: 24792297--24792348 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
24792287 TGAACAATAT
24792297 TCACGCAATAACATAGAAATCAG
1 TCACGCAATAACATAGAAATCAG
* * **
24792320 TCACGCAATGACCTATCAATCAG
1 TCACGCAATAACATAGAAATCAG
24792343 TCACGC
1 TCACGC
24792349 TAAGTTAAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.29, G:0.13, T:0.19
Consensus pattern (23 bp):
TCACGCAATAACATAGAAATCAG
Found at i:24801700 original size:3 final size:3
Alignment explanation
Indices: 24801694--24801719 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
24801684 CATAGAAGAA
24801694 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
24801720 CACCTCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:24806612 original size:35 final size:35
Alignment explanation
Indices: 24806562--24806631 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
24806552 TTATACATAT
24806562 AAAGTACATTCGGCTAAGATTGTCATATGGAAAAA
1 AAAGTACATTCGGCTAAGATTGTCATATGGAAAAA
* * *
24806597 AAAGTACATTTGGCTAGGATTTTCATATGGAAAAA
1 AAAGTACATTCGGCTAAGATTGTCATATGGAAAAA
24806632 CAGCTGGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (35 bp):
AAAGTACATTCGGCTAAGATTGTCATATGGAAAAA
Found at i:24813818 original size:19 final size:19
Alignment explanation
Indices: 24813794--24813833 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
24813784 AAAATGATTG
24813794 TATTTTTT-TAATATAATTT
1 TATTTTTTCT-ATATAATTT
*
24813813 TATTTTTTCTATATATTTT
1 TATTTTTTCTATATAATTT
24813832 TA
1 TA
24813834 ATGGCACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (19 bp):
TATTTTTTCTATATAATTT
Found at i:24814089 original size:41 final size:41
Alignment explanation
Indices: 24814043--24814123 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
24814033 AATATAAATT
*
24814043 TATCATAATATATTATATTTTAACAGTCCAACCCAATAACC
1 TATCATAACATATTATATTTTAACAGTCCAACCCAATAACC
* **
24814084 TATCATAACATATTATATTTTAATAGTTTAACCCAATAAC
1 TATCATAACATATTATATTTTAACAGTCCAACCCAATAAC
24814124 TCAACATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (41 bp):
TATCATAACATATTATATTTTAACAGTCCAACCCAATAACC
Found at i:24815431 original size:34 final size:34
Alignment explanation
Indices: 24815393--24815511 Score: 121
Period size: 34 Copynumber: 3.5 Consensus size: 34
24815383 AGGTCTGACC
* *
24815393 GATCGACGCGTAAGGAGAGATAGGAGGAAATACA
1 GATCGACGCGTAGGGAGAGAGAGGAGGAAATACA
*** * * **
24815427 GATCGGTTCATAGGGAGAGAGATGAGGAAATATT
1 GATCGACGCGTAGGGAGAGAGAGGAGGAAATACA
* * *
24815461 GATCGACGCTTAGGGAGAGAGAGGAAGAAATACC
1 GATCGACGCGTAGGGAGAGAGAGGAGGAAATACA
*
24815495 GATCGATGCGTAGGGAG
1 GATCGACGCGTAGGGAG
24815512 TTTAGAGTGA
Statistics
Matches: 66, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.36, C:0.11, G:0.37, T:0.16
Consensus pattern (34 bp):
GATCGACGCGTAGGGAGAGAGAGGAGGAAATACA
Found at i:24816411 original size:15 final size:15
Alignment explanation
Indices: 24816383--24816468 Score: 77
Period size: 15 Copynumber: 5.7 Consensus size: 15
24816373 AAAATCATTC
*
24816383 AAAA-AATAATTAAA
1 AAAATAATAAATAAA
24816397 AAAATAATAAATAAA
1 AAAATAATAAATAAA
* **
24816412 CAAATAATAGGTAAA
1 AAAATAATAAATAAA
*
24816427 AAAAT-ATAAAATATA
1 AAAATAAT-AAATAAA
*
24816442 AAAATAAATAAAAATAA
1 AAAAT-AATAAATA-AA
24816459 AAAATAATAA
1 AAAATAATAA
24816469 TAATGATTCA
Statistics
Matches: 57, Mismatches: 10, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
14 6 0.11
15 34 0.60
16 9 0.16
17 8 0.14
ACGTcount: A:0.76, C:0.01, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAATAAATAAA
Found at i:24816443 original size:17 final size:15
Alignment explanation
Indices: 24816394--24816468 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 15
24816384 AAAAATAATT
24816394 AAAAAAATAATAAAT-
1 AAAAAAATAA-AAATA
* **
24816409 AAACAAATAATAGGTA
1 AAAAAAATAA-AAATA
24816425 AAAAAATATAAAATATA
1 AAAAAA-ATAAAA-ATA
24816442 AAAATAAATAAAAATA
1 AAAA-AAATAAAAATA
24816458 AAAAATAATAA
1 AAAAA-AATAA
24816469 TAATGATTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
15 13 0.27
16 18 0.37
17 16 0.33
18 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.20
Consensus pattern (15 bp):
AAAAAAATAAAAATA
Found at i:24816449 original size:23 final size:23
Alignment explanation
Indices: 24816383--24816471 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 23
24816373 AAAATCATTC
*
24816383 AAAAAATAATTAAAAAAATAATAAAT
1 AAAAAATAA--AAATAAATAA-AAAT
**
24816409 AAACAAATAATAGGTAAA-AAAATAT
1 AAA-AAATAA-AAATAAATAAAA-AT
*
24816434 AAAATATAAAAATAAATAAAAAT
1 AAAAAATAAAAATAAATAAAAAT
*
24816457 AAAAAATAATAATAA
1 AAAAAATAAAAATAA
24816472 TGATTCAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
23 20 0.38
24 11 0.21
25 7 0.13
26 8 0.15
27 6 0.12
ACGTcount: A:0.75, C:0.01, G:0.02, T:0.21
Consensus pattern (23 bp):
AAAAAATAAAAATAAATAAAAAT
Found at i:24816776 original size:15 final size:17
Alignment explanation
Indices: 24816742--24816796 Score: 73
Period size: 16 Copynumber: 3.4 Consensus size: 17
24816732 TTGCTTACGA
24816742 AAAAATATAATAATAAT
1 AAAAATATAATAATAAT
24816759 AAAAATATAA-AA-AAT
1 AAAAATATAATAATAAT
24816774 AAAAATAGT-ATAATAA-
1 AAAAATA-TAATAATAAT
24816790 AAAAATA
1 AAAAATA
24816797 ATTTTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 11 0.31
16 12 0.34
17 12 0.34
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAAATATAATAATAAT
Found at i:24816780 original size:21 final size:21
Alignment explanation
Indices: 24816750--24816797 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
24816740 GAAAAAATAT
*
24816750 AATAATAATA-AAAATATAAAA
1 AATAAAAATAGAAAATA-AAAA
*
24816771 AATAAAAATAGTATAATAAAAA
1 AATAAAAATAG-AAAATAAAAA
24816793 AATAA
1 AATAA
24816798 TTTTTTTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (21 bp):
AATAAAAATAGAAAATAAAAA
Found at i:24816906 original size:22 final size:22
Alignment explanation
Indices: 24816878--24816933 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
24816868 TTAGAATATA
24816878 AAAAAATAAAATATAGGAGAAT
1 AAAAAATAAAATATAGGAGAAT
* *
24816900 AAAAAATAGAAA-ATATGATAAT
1 AAAAAATA-AAATATAGGAGAAT
**
24816922 ATGAAATAAAAT
1 AAAAAATAAAAT
24816934 GAAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.11
22 22 0.79
23 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (22 bp):
AAAAAATAAAATATAGGAGAAT
Found at i:24829972 original size:21 final size:21
Alignment explanation
Indices: 24829942--24829999 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
24829932 GGATATGTTC
*
24829942 ATACAATTCATGACAAAGATTA
1 ATAC-ATTCATGACAAAGACTA
*
24829964 ATACATTCATAACAAAGACTA
1 ATACATTCATGACAAAGACTA
* *
24829985 ATGCATTTATGACAA
1 ATACATTCATGACAA
24830000 GGATCGACGC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
21 27 0.87
22 4 0.13
ACGTcount: A:0.48, C:0.16, G:0.09, T:0.28
Consensus pattern (21 bp):
ATACATTCATGACAAAGACTA
Found at i:24831231 original size:39 final size:39
Alignment explanation
Indices: 24831141--24831356 Score: 285
Period size: 39 Copynumber: 5.6 Consensus size: 39
24831131 TCAACTCAGC
* * * * *
24831141 TCATGTGCACTCCCACACCACACATAGC-TA-A-GATCC
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
24831177 TCATGTGCACTCCCACACCGCACATGGCATATATTATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
*
24831216 TCATGTGCTCTCCCACACCGCATATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
*
24831255 TCATGTGCTCTCCCACACTGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
24831294 TCATGTACTCTCCCACACCGCACATGGCATATATCGTCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* * *
24831333 GCGTGTGCTCTCCCACACCACACA
1 TCATGTGCTCTCCCACACCGCACA
24831357 CTACCGGTAC
Statistics
Matches: 161, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
36 26 0.16
37 2 0.01
38 1 0.01
39 132 0.82
ACGTcount: A:0.26, C:0.36, G:0.13, T:0.25
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
Found at i:24839760 original size:4 final size:4
Alignment explanation
Indices: 24839751--24839794 Score: 56
Period size: 4 Copynumber: 11.2 Consensus size: 4
24839741 GTATTTTAAC
*
24839751 TTAT TTAT TTAT TTAT TTAT TTATT TTAA TTA- TT-T TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT TTAT T
24839795 GCATTATTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
3 4 0.11
4 28 0.78
5 4 0.11
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:24850365 original size:12 final size:12
Alignment explanation
Indices: 24850348--24850394 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
24850338 ATATATATGT
24850348 TTTTATTTTTTA
1 TTTTATTTTTTA
24850360 TTTTATTTTTTA
1 TTTTATTTTTTA
* *
24850372 TCTTGTTCATTTTA
1 TTTTATT--TTTTA
24850386 TTTTATTTT
1 TTTTATTTT
24850395 ATTGTTATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 19 0.66
14 10 0.34
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:24850895 original size:26 final size:26
Alignment explanation
Indices: 24850860--24850923 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
24850850 AAACTTTTTG
*
24850860 AAAACCCTAGAAACTCCTGCAAAGCA
1 AAAACCCTAGAAACTCCTGCAAAGAA
24850886 AAAACCCTAGAAACTCCTGCAAAGAA
1 AAAACCCTAGAAACTCCTGCAAAGAA
24850912 AAAACCCTAGAA
1 AAAACCCTAGAA
24850924 CAAATAGCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.50, C:0.28, G:0.11, T:0.11
Consensus pattern (26 bp):
AAAACCCTAGAAACTCCTGCAAAGAA
Found at i:24850933 original size:26 final size:26
Alignment explanation
Indices: 24850860--24850934 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 26
24850850 AAACTTTTTG
*** *
24850860 AAAACCCTAGAAACTCCTGCAAAGCA
1 AAAACCCTAGAAACAAATGCAAAGAA
***
24850886 AAAACCCTAGAAACTCCTGCAAAGAA
1 AAAACCCTAGAAACAAATGCAAAGAA
24850912 AAAACCCTAG-AACAAATAGCAAA
1 AAAACCCTAGAAACAAAT-GCAAA
24850935 ATTCTAGCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.09
26 40 0.91
ACGTcount: A:0.52, C:0.27, G:0.11, T:0.11
Consensus pattern (26 bp):
AAAACCCTAGAAACAAATGCAAAGAA
Found at i:24851618 original size:35 final size:34
Alignment explanation
Indices: 24851567--24851635 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 34
24851557 TTTCACCAAG
* *
24851567 CTTTACAATGGCTTTTACCAGGCTCAGCCAAAAC
1 CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
* *
24851601 CTTTCACAATGGTTTTTATCAGGATCAACCAAAAC
1 CTTT-ACAATGGCTTTTACCAGGATCAACCAAAAC
24851636 TCAACAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 4 0.13
35 26 0.87
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (34 bp):
CTTTACAATGGCTTTTACCAGGATCAACCAAAAC
Found at i:24854244 original size:15 final size:15
Alignment explanation
Indices: 24854224--24854277 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
24854214 TATTTCAGAC
24854224 TTGGAATTCTAGTAT
1 TTGGAATTCTAGTAT
* *
24854239 TTGGAATTTTA-CAT
1 TTGGAATTCTAGTAT
*
24854253 GCTTTGAATTCTAGTAT
1 --TTGGAATTCTAGTAT
24854270 TTGGAATT
1 TTGGAATT
24854278 TTACATGCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
14 2 0.07
15 17 0.57
16 9 0.30
17 2 0.07
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.48
Consensus pattern (15 bp):
TTGGAATTCTAGTAT
Found at i:24854262 original size:31 final size:31
Alignment explanation
Indices: 24854227--24854288 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
24854217 TTCAGACTTG
24854227 GAATTCTAGTATTTGGAATTTTACATGCTTT
1 GAATTCTAGTATTTGGAATTTTACATGCTTT
24854258 GAATTCTAGTATTTGGAATTTTACATGCTTT
1 GAATTCTAGTATTTGGAATTTTACATGCTTT
24854289 ATTCTGTTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.16, T:0.48
Consensus pattern (31 bp):
GAATTCTAGTATTTGGAATTTTACATGCTTT
Found at i:24854833 original size:31 final size:31
Alignment explanation
Indices: 24854779--24854854 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
24854769 AGTTATAAAC
24854779 AATTAATA-TA-TT-ATGCAAAATAGAACAA
1 AATTAATAGTATTTAATGCAAAATAGAACAA
*
24854807 AATTAATAGTATTTAATGGAAAATAGAACAA
1 AATTAATAGTATTTAATGCAAAATAGAACAA
24854838 AATTAATAGTATTTAAT
1 AATTAATAGTATTTAAT
24854855 AATAGAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 8 0.18
29 2 0.05
30 2 0.05
31 32 0.73
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (31 bp):
AATTAATAGTATTTAATGCAAAATAGAACAA
Found at i:24855322 original size:23 final size:23
Alignment explanation
Indices: 24855294--24855350 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
24855284 TGTAGATACG
24855294 TCTGTTGAAATACAACAAACACA
1 TCTGTTGAAATACAACAAACACA
* ** *
24855317 TCTGTTAAAAATAGTACAGACACA
1 TCTGTT-GAAATACAACAAACACA
24855341 TCTGTTGAAA
1 TCTGTTGAAA
24855351 ATAAAAAGGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (23 bp):
TCTGTTGAAATACAACAAACACA
Found at i:24860937 original size:25 final size:25
Alignment explanation
Indices: 24860901--24860954 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
24860891 CTTTTTAAAC
*
24860901 TAATGTTTATTTATT-CTATAAAGAT
1 TAATGTTAATTTATTAC-ATAAAGAT
*
24860926 TAATGTTAATTTATTACATGAAGAT
1 TAATGTTAATTTATTACATAAAGAT
24860951 TAAT
1 TAAT
24860955 ATTATTAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (25 bp):
TAATGTTAATTTATTACATAAAGAT
Found at i:24862473 original size:15 final size:14
Alignment explanation
Indices: 24862452--24862521 Score: 61
Period size: 15 Copynumber: 4.7 Consensus size: 14
24862442 CAAAATCATA
24862452 AAAAAATAATAAAT
1 AAAAAATAATAAAT
*
24862466 AAACAAATAATAGAT
1 AAA-AAATAATAAAT
*
24862481 AAAAAGA-AAAAAAT
1 AAAAA-ATAATAAAT
*
24862495 AGAAAATAAATAAAAT
1 AAAAAAT-AAT-AAAT
24862511 AAAAAAATAAT
1 -AAAAAATAAT
24862522 GATAATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
13 1 0.02
14 14 0.32
15 16 0.36
16 7 0.16
17 6 0.14
ACGTcount: A:0.77, C:0.01, G:0.04, T:0.17
Consensus pattern (14 bp):
AAAAAATAATAAAT
Found at i:24862495 original size:18 final size:18
Alignment explanation
Indices: 24862451--24862509 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
24862441 ACAAAATCAT
24862451 AAAAAAATA-ATAAATAA
1 AAAAAAATAGATAAATAA
*
24862468 ACAAATAATAGATAAA-AA
1 A-AAAAAATAGATAAATAA
24862486 GAAAAAAATAGA-AAATAA
1 -AAAAAAATAGATAAATAA
24862504 ATAAAA
1 A-AAAA
24862510 TAAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 5 0.14
18 24 0.69
19 6 0.17
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAAAAATAGATAAATAA
Found at i:24862516 original size:7 final size:7
Alignment explanation
Indices: 24862452--24862516 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
24862442 CAAAATCATA
24862452 AAAAAAT
1 AAAAAAT
*
24862459 AATAAAT
1 AAAAAAT
24862466 AAACAAAT
1 AAA-AAAT
* *
24862474 AATAGAT
1 AAAAAAT
24862481 AAAAAGA-
1 AAAAA-AT
24862488 AAAAAAT
1 AAAAAAT
*
24862495 AGAAAAT
1 AAAAAAT
24862502 AAATAAAAT
1 -AA-AAAAT
24862511 AAAAAA
1 AAAAAA
24862517 ATAATGATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 29 0.64
8 10 0.22
9 5 0.11
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:24862773 original size:22 final size:22
Alignment explanation
Indices: 24862746--24862803 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
24862736 AACTTAGAAT
24862746 ATAAAAAATAAAATATAGGAGA
1 ATAAAAAATAAAATATAGGAGA
* * *
24862768 ATAAAAAATAAAAAATATGATA
1 ATAAAAAATAAAATATAGGAGA
**
24862790 ATATGAAATAAAAT
1 ATAAAAAATAAAAT
24862804 GAAAATAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (22 bp):
ATAAAAAATAAAATATAGGAGA
Found at i:24874892 original size:37 final size:37
Alignment explanation
Indices: 24874830--24875252 Score: 404
Period size: 37 Copynumber: 11.3 Consensus size: 37
24874820 GGTTCTGTTA
* **
24874830 CCTCAGCTTTGAGGAGA-TCATATTTTAGAAGTTTTGTTG
1 CCTCAACTTTGAGGA-ATTCAT-TTTTA-AAGTTTCATTG
* *
24874869 CCTCAACTTTAAGGAATTCATTTTTAAAAGTGTCATTG
1 CCTCAACTTTGAGGAATTCATTTTT-AAAGTTTCATTG
* * *
24874907 CCTCAATTTTGAGGAGTTTATTTTTAAAGTTTCATTG
1 CCTCAACTTTGAGGAATTCATTTTTAAAGTTTCATTG
* * *
24874944 CCTCAATTTTGAGGATTTTATTTTTAAAGTTTCATTG
1 CCTCAACTTTGAGGAATTCATTTTTAAAGTTTCATTG
* * *
24874981 CCTCAATTTTGAGGAATTC-TATTTTAAAATCTCATTG
1 CCTCAACTTTGAGGAATTCAT-TTTTAAAGTTTCATTG
* * * * *
24875018 CCTCAATTTTGAGGATTTTATTTTGAAAGTTTCATTA
1 CCTCAACTTTGAGGAATTCATTTTTAAAGTTTCATTG
* * *
24875055 CCTCAGCTTTGAGGAGTTCATTTTTAAAGTTTCGTTG
1 CCTCAACTTTGAGGAATTCATTTTTAAAGTTTCATTG
* * *
24875092 CCCCAGCTTTG-GAGAGTTCATTTTTAAAGTTTCATTG
1 CCTCAACTTTGAG-GAATTCATTTTTAAAGTTTCATTG
* * * * ** *
24875129 CCTCAGCTTTGAAGATTTCATTTTAAAAGTTTTGTTA
1 CCTCAACTTTGAGGAATTCATTTTTAAAGTTTCATTG
* * *
24875166 CCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCATTG
1 CCTCAACTTTGAGGAATTCATTTTT-AAAGTTTCATTG
*
24875204 CCTCAACTTTGA-GAAGTTCATTTTAAAAGTTTCATTG
1 CCTCAACTTTGAGGAA-TTCATTTTTAAAGTTTCATTG
* *
24875241 CCACAGCTTTGA
1 CCTCAACTTTGA
24875253 AGAGTCACAT
Statistics
Matches: 326, Mismatches: 50, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
36 2 0.01
37 244 0.75
38 62 0.19
39 18 0.06
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (37 bp):
CCTCAACTTTGAGGAATTCATTTTTAAAGTTTCATTG
Found at i:24875050 original size:111 final size:112
Alignment explanation
Indices: 24874827--24875242 Score: 502
Period size: 111 Copynumber: 3.7 Consensus size: 112
24874817 AAAGGTTCTG
* ** *
24874827 TTACCTCAGCTTTGAGGAGATCATATTTTAGAAGTTTTGTTGCCTCAACTTTAAGGAATTCATTT
1 TTACCTCAGCTTTGAGGAGTTCAT-TTTTA-AAGTTTCATTGCCTCAACTTTGAGGAATTCATTT
* * *
24874892 TTAAAAGTGTCATTGCCTCAATTTTGAGGAGTTTATTTTTAAAGTTTCA
64 TTAAAAGTTTCATTGCCTCAATTTTGAGGATTTTATTTTAAAAGTTTCA
* ** * * *
24874941 TTGCCTCAATTTTGAGGATTTTATTTTTAAAGTTTCATTGCCTCAATTTTGAGGAATTC-TATTT
1 TTACCTCAGCTTTGAGGAGTTCATTTTTAAAGTTTCATTGCCTCAACTTTGAGGAATTCAT-TTT
* *
24875005 TAAAA-TCTCATTGCCTCAATTTTGAGGATTTTATTTTGAAAGTTTCA
65 TAAAAGTTTCATTGCCTCAATTTTGAGGATTTTATTTTAAAAGTTTCA
* * * *
24875052 TTACCTCAGCTTTGAGGAGTTCATTTTTAAAGTTTCGTTGCCCCAGCTTTG-GAGAGTTCATTTT
1 TTACCTCAGCTTTGAGGAGTTCATTTTTAAAGTTTCATTGCCTCAACTTTGAG-GAATTCATTTT
** * * **
24875116 T-AAAGTTTCATTGCCTCAGCTTTGAAGATTTCATTTTAAAAGTTTTG
65 TAAAAGTTTCATTGCCTCAATTTTGAGGATTTTATTTTAAAAGTTTCA
*
24875163 TTACCTCAGCTTTGAGGAGTTCATTTTTAAAAGTCTCATTGCCTCAACTTTGA-GAAGTTCA-TT
1 TTACCTCAGCTTTGAGGAGTTCATTTTT-AAAGTTTCATTGCCTCAACTTTGAGGAA-TTCATTT
24875226 TTAAAAGTTTCATTGCC
64 TTAAAAGTTTCATTGCC
24875243 ACAGCTTTGA
Statistics
Matches: 258, Mismatches: 36, Indels: 18
0.83 0.12 0.06
Matches are distributed among these distances:
110 4 0.02
111 159 0.62
112 72 0.28
113 5 0.02
114 18 0.07
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (112 bp):
TTACCTCAGCTTTGAGGAGTTCATTTTTAAAGTTTCATTGCCTCAACTTTGAGGAATTCATTTTT
AAAAGTTTCATTGCCTCAATTTTGAGGATTTTATTTTAAAAGTTTCA
Found at i:24875294 original size:8 final size:8
Alignment explanation
Indices: 24875281--24875385 Score: 74
Period size: 7 Copynumber: 14.5 Consensus size: 8
24875271 ACAAACCACA
24875281 AAAACAAC
1 AAAACAAC
24875289 AAAAC-AC
1 AAAACAAC
24875296 AAAAACAA-
1 -AAAACAAC
24875304 AAAA-AA-
1 AAAACAAC
24875310 AAAAC-AC
1 AAAACAAC
*
24875317 AAAACATC
1 AAAACAAC
24875325 AAAAC-AC
1 AAAACAAC
24875332 -AAA-AAC
1 AAAACAAC
24875338 AAAA-AA-
1 AAAACAAC
*
24875344 AAAACCAC
1 AAAACAAC
24875352 AAAAACAAC
1 -AAAACAAC
24875361 AAAACAA-
1 AAAACAAC
*
24875368 AAAA-AAA
1 AAAACAAC
24875375 AAAACAA-
1 AAAACAAC
24875382 AAAA
1 AAAA
24875386 AAAGGAAGAA
Statistics
Matches: 81, Mismatches: 4, Indels: 25
0.74 0.04 0.23
Matches are distributed among these distances:
6 18 0.22
7 30 0.37
8 25 0.31
9 8 0.10
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.01
Consensus pattern (8 bp):
AAAACAAC
Found at i:24875312 original size:28 final size:26
Alignment explanation
Indices: 24875280--24875388 Score: 112
Period size: 28 Copynumber: 4.0 Consensus size: 26
24875270 AACAAACCAC
* *
24875280 AAAAACAACAAAACACAAAAACAAAA
1 AAAAAAAAAAAAACACAAAAACAAAA
24875306 AAAAAAAACACAAAACATCAAAACACAAAA
1 AAAAAAAA-A-AAAACA-CAAAA-ACAAAA
* *
24875336 ACAAAAAAAAAACCACAAAAACAACAA
1 AAAAAAAAAAAAACACAAAAACAA-AA
*
24875363 AACAAAAAAAAAAAAACAAAAA-AAAA
1 AA-AAAAAAAAAAACACAAAAACAAAA
24875389 GGAAGAATAA
Statistics
Matches: 70, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
26 13 0.19
27 10 0.14
28 28 0.40
29 6 0.09
30 13 0.19
ACGTcount: A:0.82, C:0.17, G:0.00, T:0.01
Consensus pattern (26 bp):
AAAAAAAAAAAAACACAAAAACAAAA
Found at i:24875321 original size:36 final size:37
Alignment explanation
Indices: 24875265--24875386 Score: 167
Period size: 36 Copynumber: 3.3 Consensus size: 37
24875255 AGTCACATTT
* *
24875265 AAAAAAACAAACCACAAAAACAACAAAACACAAAAAC
1 AAAAAAAAAAAACACAAAAACAACAAAACACAAAAAC
*
24875302 AAAAAAAAAAAACAC-AAAACATCAAAACACAAAAAC
1 AAAAAAAAAAAACACAAAAACAACAAAACACAAAAAC
* * *
24875338 -AAAAAAAAAACCACAAAAACAACAAAACAAAAAAAA
1 AAAAAAAAAAAACACAAAAACAACAAAACACAAAAAC
24875374 AAAAACAAAAAAA
1 AAAAA-AAAAAAA
24875387 AAGGAAGAAT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
35 13 0.18
36 38 0.51
37 17 0.23
38 6 0.08
ACGTcount: A:0.80, C:0.19, G:0.00, T:0.01
Consensus pattern (37 bp):
AAAAAAAAAAAACACAAAAACAACAAAACACAAAAAC
Found at i:24875386 original size:8 final size:8
Alignment explanation
Indices: 24875280--24875386 Score: 87
Period size: 8 Copynumber: 13.6 Consensus size: 8
24875270 AACAAACCAC
24875280 AAAAACAA
1 AAAAACAA
* *
24875288 CAAAACAC
1 AAAAACAA
24875296 AAAAACAA
1 AAAAACAA
24875304 AAAAA-AA
1 AAAAACAA
*
24875311 AAACACAA
1 AAAAACAA
* *
24875319 AACATC-A
1 AAAAACAA
*
24875326 AAACACAA
1 AAAAACAA
*
24875334 AAACAAAAA
1 AAA-AACAA
*
24875343 AAAAACCAC
1 AAAAA-CAA
24875352 AAAAACAA
1 AAAAACAA
*
24875360 CAAAAC-A
1 AAAAACAA
24875367 AAAAA-AA
1 AAAAACAA
24875374 AAAAACAA
1 AAAAACAA
24875382 AAAAA
1 AAAAA
24875387 AAGGAAGAAT
Statistics
Matches: 75, Mismatches: 18, Indels: 12
0.71 0.17 0.11
Matches are distributed among these distances:
7 21 0.28
8 42 0.56
9 12 0.16
ACGTcount: A:0.81, C:0.18, G:0.00, T:0.01
Consensus pattern (8 bp):
AAAAACAA
Found at i:24876063 original size:41 final size:41
Alignment explanation
Indices: 24875953--24876063 Score: 123
Period size: 41 Copynumber: 2.7 Consensus size: 41
24875943 TTTTTTTTGG
* * * *
24875953 TGGGTCGACCGACGGTGGGCGAAGCAAAGAGGTTTGGGATC
1 TGGGTCGACCGCCGGTGAGCGAAGCAAGGAGGTTTGGGAGC
* * * * *
24875994 TGGGTTGATCGCTGGTGAACGAAGCAAGGATGTTTGGGAGC
1 TGGGTCGACCGCCGGTGAGCGAAGCAAGGAGGTTTGGGAGC
* *
24876035 TGGGTCGACCGCCGATGAGCGAACCAAGG
1 TGGGTCGACCGCCGGTGAGCGAAGCAAGG
24876064 CGGTAGGAGA
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.23, C:0.18, G:0.41, T:0.18
Consensus pattern (41 bp):
TGGGTCGACCGCCGGTGAGCGAAGCAAGGAGGTTTGGGAGC
Found at i:24877342 original size:15 final size:14
Alignment explanation
Indices: 24877319--24877388 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 14
24877309 CAAAATCATC
24877319 AAAAAATAATAAAT
1 AAAAAATAATAAAT
*
24877333 AAACAAATAATAGAT
1 AAA-AAATAATAAAT
*
24877348 -AAAAATAAAAAAAT
1 AAAAAAT-AATAAAT
24877362 AAAAAATAAATAAAAT
1 AAAAAAT-AAT-AAAT
24877378 AAAAAAATAAT
1 -AAAAAATAAT
24877389 GATAATAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
13 4 0.09
14 10 0.21
15 19 0.40
16 7 0.15
17 7 0.15
ACGTcount: A:0.79, C:0.01, G:0.01, T:0.19
Consensus pattern (14 bp):
AAAAAATAATAAAT
Found at i:24877383 original size:7 final size:7
Alignment explanation
Indices: 24877319--24877383 Score: 60
Period size: 7 Copynumber: 8.9 Consensus size: 7
24877309 CAAAATCATC
24877319 AAAAAAT
1 AAAAAAT
*
24877326 AATAAAT
1 AAAAAAT
24877333 AAACAAAT
1 AAA-AAAT
* *
24877341 AATAGAT
1 AAAAAAT
24877348 -AAAAAT
1 AAAAAAT
24877354 AAAAAAAT
1 -AAAAAAT
24877362 AAAAAAT
1 AAAAAAT
24877369 AAATAAAAT
1 -AA-AAAAT
24877378 AAAAAA
1 AAAAAA
24877384 ATAATGATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
6 4 0.09
7 22 0.47
8 16 0.34
9 5 0.11
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (7 bp):
AAAAAAT
Found at i:24877688 original size:17 final size:17
Alignment explanation
Indices: 24877645--24877689 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
24877635 ATAAAAAATA
*
24877645 AAAAAAATGATAATATG
1 AAAAAAATGAAAATATG
24877662 AAATAAAATGAAAATAAT-
1 AAA-AAAATGAAAAT-ATG
24877680 AAAAAAATGA
1 AAAAAAATGA
24877690 CAAAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 13 0.52
19 2 0.08
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (17 bp):
AAAAAAATGAAAATATG
Found at i:24883673 original size:24 final size:24
Alignment explanation
Indices: 24883640--24883693 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
24883630 ACTGAATTTT
* *
24883640 ATATT-AAATAGCCTCATTCTAGA
1 ATATTCAAATAACCTCATTCCAGA
*
24883663 ATATTCAAATAACCTTATTCCAGA
1 ATATTCAAATAACCTCATTCCAGA
*
24883687 ACATTCA
1 ATATTCA
24883694 GTGCAACTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (24 bp):
ATATTCAAATAACCTCATTCCAGA
Found at i:24885841 original size:30 final size:30
Alignment explanation
Indices: 24885798--24885888 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 30
24885788 CATTAAAGTG
*
24885798 CAACAA-ATTTTTTTTAAATATGACGTGTAA
1 CAACAATA-TTTTTTTAAACATGACGTGTAA
* * * *
24885828 TAATAATA-TTTTTTCAACATGGCGTGTAA
1 CAACAATATTTTTTTAAACATGACGTGTAA
* * *
24885857 CAACGATATTTTTTTTAACATTACGTGTAA
1 CAACAATATTTTTTTAAACATGACGTGTAA
24885887 CA
1 CA
24885889 TATTTTTGTA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
29 23 0.48
30 24 0.50
31 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (30 bp):
CAACAATATTTTTTTAAACATGACGTGTAA
Found at i:24885853 original size:29 final size:29
Alignment explanation
Indices: 24885798--24885888 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 29
24885788 CATTAAAGTG
* *
24885798 CAACAAATTTTTTTTAAATATGACGTGTAA
1 CAAC-AATATTTTTTAAACATGACGTGTAA
* * * *
24885828 TAATAATATTTTTTCAACATGGCGTGTAA
1 CAACAATATTTTTTAAACATGACGTGTAA
* * *
24885857 CAACGATATTTTTTTTAACATTACGTGTAA
1 CAACAATA-TTTTTTAAACATGACGTGTAA
24885887 CA
1 CA
24885889 TATTTTTGTA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
29 26 0.54
30 22 0.46
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (29 bp):
CAACAATATTTTTTAAACATGACGTGTAA
Found at i:24890286 original size:12 final size:13
Alignment explanation
Indices: 24890257--24890303 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
24890247 TATTTATTTT
24890257 AAATAAAATAAAA
1 AAATAAAATAAAA
*
24890270 AAATAAAAT-AGA
1 AAATAAAATAAAA
*
24890282 AAAT-AAGTAAAA
1 AAATAAAATAAAA
24890294 GAAATAAAAT
1 -AAATAAAAT
24890304 TGAATATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
13 13 0.48
14 3 0.11
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:24894048 original size:3 final size:3
Alignment explanation
Indices: 24894040--24894071 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
24894030 ATGAATACTT
24894040 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
24894072 TAGACGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:24895879 original size:14 final size:15
Alignment explanation
Indices: 24895841--24895879 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 15
24895831 TGAGGACAAA
24895841 GGGGAAATATATTAT
1 GGGGAAATATATTAT
24895856 --GG-AATATATTAT
1 GGGGAAATATATTAT
24895868 GGGGAAAT-TATT
1 GGGGAAATATATT
24895880 GAAAAGAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 6 0.29
15 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (15 bp):
GGGGAAATATATTAT
Found at i:24896351 original size:2 final size:2
Alignment explanation
Indices: 24896344--24896400 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
24896334 TAAATCTCAT
*
24896344 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA TN TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24896384 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
24896401 TTATGTCAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:24899476 original size:187 final size:185
Alignment explanation
Indices: 24899052--24899590 Score: 725
Period size: 187 Copynumber: 2.9 Consensus size: 185
24899042 ATAATGTTTC
* *
24899052 AATTTCCCAA-AAAG--AAGAGAAAAAAGGAAACGATGTATTTGACATTAAAATCATTTTTGGT-
1 AATTTCCCAAGAAAGAAAAGAAAAAAAAGGAAACGATGTATTTGACATTAAAATCTTTTTTGGTG
* * * * * *
24899113 AAAAGAGAGAGAAAACATTTAGATGATACCTAAATACAACTTTAAATTTTGGATCTTCTTTTCTC
66 AAGA-AGAGAGAAAACTTTTAAATGATA-CTAAATGCAACTTTGAATTTTGGATTTTCTTTTCTC
* * *
24899178 TTAATTTTTTTAA-TATAAAAAAATCTCAGATTTTGCTATTTTATTGTTGGGTCTTCT
129 TTAA-TTTTTTAATTACAAAAAAATCTCAGATTTTGCTATTCTATTGTTAGGTCTTCT
24899235 AATTTCCCAAGAAAGAAAAGAAAAAAAAGGAAACGATGTATTTGACATTAAAATCTTTTTTGGTG
1 AATTTCCCAAGAAAGAAAAGAAAAAAAAGGAAACGATGTATTTGACATTAAAATCTTTTTTGGTG
* * *
24899300 AAGAAGAGAGAAAACTTTTAAATGATACTTAAATGCAACTTTGAATTTTGGGTTTTCTTTTTTTT
66 AAGAAGAGAGAAAACTTTTAAATGATAC-TAAATGCAACTTTGAATTTTGGATTTTC-TTTTCTC
* *
24899365 TTAATTTTTTAATTACAAAAAAATCTTAAATTTTGCTATTCTATTGTTAGGTCTTCT
129 TTAATTTTTTAATTACAAAAAAATCTCAGATTTTGCTATTCTATTGTTAGGTCTTCT
* * *
24899422 -GTTTCCCCAAGAAAGAAAAGAAAAAAAAGGAAACGATGTATTTGACAGTAAAATCTTTTTTTGT
1 AATTT-CCCAAGAAAGAAAAGAAAAAAAAGGAAACGATGTATTTGACATTAAAATCTTTTTTGGT
* * * * * *
24899486 GAAGAACAGATAAAACTTTTAAAT-AGTAACTGAATGCAGCTTTGAATTTTAGAATTTCTTTTCT
65 GAAGAAGAGAGAAAACTTTTAAATGA-T-ACTAAATGCAACTTTGAATTTTGGATTTTCTTTTCT
24899550 CTTAATTTTTTAATTACAAAAAAA-CTCAGATTTTGCTATTC
128 CTTAATTTTTTAATTACAAAAAAATCTCAGATTTTGCTATTC
24899591 AATTAGTAGT
Statistics
Matches: 316, Mismatches: 30, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
183 10 0.03
184 4 0.01
185 16 0.05
186 130 0.41
187 154 0.49
188 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (185 bp):
AATTTCCCAAGAAAGAAAAGAAAAAAAAGGAAACGATGTATTTGACATTAAAATCTTTTTTGGTG
AAGAAGAGAGAAAACTTTTAAATGATACTAAATGCAACTTTGAATTTTGGATTTTCTTTTCTCTT
AATTTTTTAATTACAAAAAAATCTCAGATTTTGCTATTCTATTGTTAGGTCTTCT
Found at i:24900395 original size:127 final size:121
Alignment explanation
Indices: 24900258--24900486 Score: 291
Period size: 121 Copynumber: 1.8 Consensus size: 121
24900248 AGAAGAAGGG
* *
24900258 GAGATCGATTGAAAGAGAAGAATATTTAGTTAAAAAAAGCTAACATGTTTT-TTTTTT-TTAAAA
1 GAGATCGATTGAAAGAG--GAATACTT-CTT-AAAAAAGCTAACATGTTTTATTTTTTATTAAAA
* *
24900321 AAGAAAGTTTTTTGTTAGAGCTTTTCTTTAATTTTTTTTTTTAATTTGCAGAAAGAGGGTGAGT
62 AA-AAAGTTCTTT-TT-G-GCTTTTCTTTAAGTTTTTTTTTTAATTTGCAGAAAGAGGGTGAGT
* * **
24900385 GAGATCGATTGAAAGAGGAATACTTCTTGAAAGAGCTAACATGTTTTATTTTTTATTTTAAAAAA
1 GAGATCGATTGAAAGAGGAATACTTCTTAAAAAAGCTAACATGTTTTATTTTTTATTAAAAAAAA
*
24900450 AGTTCTTTTTGGGTTTTCTTTAAGTTTTTTTTTTAAT
66 AGTTCTTTTTGGCTTTTCTTTAAGTTTTTTTTTTAAT
24900487 AATTAAAAAA
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
121 24 0.26
122 1 0.01
123 19 0.21
124 17 0.19
125 13 0.14
127 17 0.19
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (121 bp):
GAGATCGATTGAAAGAGGAATACTTCTTAAAAAAGCTAACATGTTTTATTTTTTATTAAAAAAAA
AGTTCTTTTTGGCTTTTCTTTAAGTTTTTTTTTTAATTTGCAGAAAGAGGGTGAGT
Found at i:24900618 original size:25 final size:26
Alignment explanation
Indices: 24900590--24900638 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
24900580 TTGTTTTTCA
24900590 AAAAAATTAATTT-TTTTAAGAGTTT
1 AAAAAATTAATTTCTTTTAAGAGTTT
*
24900615 AAAAAATTACTTTCTTTTAAGAGT
1 AAAAAATTAATTTCTTTTAAGAGT
24900639 ATCTCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (26 bp):
AAAAAATTAATTTCTTTTAAGAGTTT
Found at i:24903970 original size:22 final size:22
Alignment explanation
Indices: 24903940--24903981 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
24903930 CTCATCATTC
24903940 TTTTCTTCTTCAT-TTTCTTTGT
1 TTTTCTTCTTC-TGTTTCTTTGT
*
24903962 TTTTTTTCTTCTGTTTCTTT
1 TTTTCTTCTTCTGTTTCTTT
24903982 TTACTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTTCTTCTTCTGTTTCTTTGT
Found at i:24904587 original size:23 final size:22
Alignment explanation
Indices: 24904561--24904613 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
24904551 TCCCTCTCCA
24904561 TTTCTTTTTAATTTTCCCTTCT-G
1 TTTCTTTTT-A-TTTCCCTTCTCG
* *
24904584 TTTCTCCTTTATTTCCCTTCTCT
1 TTTCT-TTTTATTTCCCTTCTCG
24904607 TTTCTTT
1 TTTCTTT
24904614 CTGTCTTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 11 0.44
23 11 0.44
24 3 0.12
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTCTTTTTATTTCCCTTCTCG
Found at i:24912734 original size:20 final size:22
Alignment explanation
Indices: 24912695--24912740 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
24912685 AGCATTTAAT
*
24912695 AAACCATGCTATTTTAGTTT-A
1 AAACCATGCAATTTTAGTTTGA
24912716 AAACCATGCAATTTT-GTTTGA
1 AAACCATGCAATTTTAGTTTGA
24912737 AAAC
1 AAAC
24912741 ATAAAACTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (22 bp):
AAACCATGCAATTTTAGTTTGA
Found at i:24913785 original size:24 final size:24
Alignment explanation
Indices: 24913758--24913804 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
24913748 TATCATAACA
*
24913758 TATCAAAAAAATATTGCATGCATT
1 TATCAAAAAAATATTACATGCATT
* *
24913782 TATCAAAAACATTTTACATGCAT
1 TATCAAAAAAATATTACATGCAT
24913805 ATCCCTCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (24 bp):
TATCAAAAAAATATTACATGCATT
Found at i:24913807 original size:22 final size:22
Alignment explanation
Indices: 24913739--24913807 Score: 59
Period size: 24 Copynumber: 3.0 Consensus size: 22
24913729 TTTTTTTTTA
*
24913739 AAAAACA-TTTATCATAACATATC
1 AAAAACATTTTA-CAT-GCATATC
* * *
24913762 AAAAAAATATTGCATGCATTTATC
1 AAAAACATTTTACATGCA--TATC
24913786 AAAAACATTTTACATGCATATC
1 AAAAACATTTTACATGCATATC
24913808 CCTCACTTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
22 6 0.17
23 9 0.25
24 21 0.58
ACGTcount: A:0.48, C:0.16, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAAACATTTTACATGCATATC
Found at i:24914788 original size:27 final size:27
Alignment explanation
Indices: 24914735--24914789 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
24914725 TTTTATATTC
*
24914735 ATCAAAATAATACATTGTTTTACTTTT
1 ATCAAAATAATACATTGTTATACTTTT
* *
24914762 ATCAAAATAATATATTGTATATATTTTT
1 ATCAAAATAATACATTGT-TATACTTTT
24914790 TGATGGAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (27 bp):
ATCAAAATAATACATTGTTATACTTTT
Found at i:24914969 original size:10 final size:10
Alignment explanation
Indices: 24914954--24914978 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
24914944 TTGGGTTTAA
24914954 TTTTTTTATT
1 TTTTTTTATT
24914964 TTTTTTTATT
1 TTTTTTTATT
24914974 TTTTT
1 TTTTT
24914979 GTCTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:24920407 original size:34 final size:33
Alignment explanation
Indices: 24920331--24920409 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
24920321 ATATTTGATG
* * * *
24920331 GTGAAGCTTTGACCTTGGCGTGTAACATTTGGT
1 GTGAAGCTTTGGCCTTGGCATGTAACATCTGCT
*
24920364 GTGAAGCTTTGGCCTTGGCATGTAGCATCTGCT
1 GTGAAGCTTTGGCCTTGGCATGTAACATCTGCT
24920397 GCTGAAGCTTTGG
1 G-TGAAGCTTTGG
24920410 TATGTAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 29 0.73
34 11 0.28
ACGTcount: A:0.16, C:0.18, G:0.32, T:0.34
Consensus pattern (33 bp):
GTGAAGCTTTGGCCTTGGCATGTAACATCTGCT
Found at i:24920860 original size:27 final size:29
Alignment explanation
Indices: 24920801--24920881 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 29
24920791 TACATGTCTG
*
24920801 CATGTGACAAC-AT-TTTTTTCAAA-ATAA
1 CATGTAACAACAATATTTTTT-AAACATAA
*
24920828 CATGTAGCAA-AA-ATTTTTTAAACATAA
1 CATGTAACAACAATATTTTTTAAACATAA
24920855 -AGTGTAACAACAATATTTTTTAAACAT
1 CA-TGTAACAACAATATTTTTTAAACAT
24920882 GGCGTGTAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 4 0.09
27 26 0.58
28 2 0.04
29 13 0.29
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.36
Consensus pattern (29 bp):
CATGTAACAACAATATTTTTTAAACATAA
Found at i:24939718 original size:14 final size:15
Alignment explanation
Indices: 24939686--24939724 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
24939676 AATATTAAAA
*
24939686 TAATAAAAAATATTT
1 TAATAAATAATATTT
*
24939701 TAATTAATAATA-TT
1 TAATAAATAATATTT
24939715 TAATAAATAA
1 TAATAAATAA
24939725 ATAATTATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAAATAATATTT
Found at i:24941529 original size:18 final size:18
Alignment explanation
Indices: 24941506--24941555 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
24941496 ATGTGTCACA
*
24941506 ATAACACGTTTAAACACG
1 ATAACACGATTAAACACG
24941524 ATAACACGATTAAACACG
1 ATAACACGATTAAACACG
24941542 ATAACACGATTAAA
1 ATAACACGATTAAA
24941556 TAAACGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.50, C:0.20, G:0.10, T:0.20
Consensus pattern (18 bp):
ATAACACGATTAAACACG
Found at i:24941531 original size:8 final size:8
Alignment explanation
Indices: 24941518--24941551 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
24941508 AACACGTTTA
24941518 AACACGAT
1 AACACGAT
24941526 AACACGATT
1 AACACGA-T
24941535 AAACACGAT
1 -AACACGAT
24941544 AACACGAT
1 AACACGAT
24941552 TAAATAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.62
9 2 0.08
10 7 0.29
ACGTcount: A:0.50, C:0.24, G:0.12, T:0.15
Consensus pattern (8 bp):
AACACGAT
Found at i:24945388 original size:27 final size:29
Alignment explanation
Indices: 24945351--24945410 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
24945341 GGACAAATGT
* *
24945351 CCTAGTGGTGG-AGAATTACAATTTTGCC
1 CCTAGTGGTGGTAAAATTACAATTTTACC
*
24945379 CCTAG-GGTGGTAAAATTACCATTTTACC
1 CCTAGTGGTGGTAAAATTACAATTTTACC
24945407 CCTA
1 CCTA
24945411 TACTCTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (29 bp):
CCTAGTGGTGGTAAAATTACAATTTTACC
Found at i:24945478 original size:19 final size:19
Alignment explanation
Indices: 24945454--24945491 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24945444 ACTTTTAAAC
24945454 CTCAAATCATACTCAAATA
1 CTCAAATCATACTCAAATA
*
24945473 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCAAATA
24945492 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCAAATA
Found at i:24946513 original size:28 final size:29
Alignment explanation
Indices: 24946472--24946531 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
24946462 GTCTATGGGC
*
24946472 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
24946500 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
24946530 AA
1 AA
24946532 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:24953990 original size:43 final size:44
Alignment explanation
Indices: 24953926--24954008 Score: 150
Period size: 43 Copynumber: 1.9 Consensus size: 44
24953916 CTTCAATATT
*
24953926 TTTTTTCTCTTTTAGCTTTCAATGATGTTTGATAAAGTTCCATA
1 TTTTTTCTCTTTTAGCATTCAATGATGTTTGATAAAGTTCCATA
24953970 TTTTTT-TCTTTTAGCATTCAATGATGTTTGATAAAGTTC
1 TTTTTTCTCTTTTAGCATTCAATGATGTTTGATAAAGTTC
24954009 AACAAGAAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
43 32 0.84
44 6 0.16
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (44 bp):
TTTTTTCTCTTTTAGCATTCAATGATGTTTGATAAAGTTCCATA
Found at i:24954183 original size:28 final size:28
Alignment explanation
Indices: 24954138--24954253 Score: 137
Period size: 28 Copynumber: 4.1 Consensus size: 28
24954128 ATCTCTTCAC
* * *
24954138 TATTCATCCACTTCTAGTGGATTAAAAG
1 TATTCATTCATTTTTAGTGGATTAAAAG
24954166 TATTCATTCATTTTTAGTGGATTAAAAG
1 TATTCATTCATTTTTAGTGGATTAAAAG
* *
24954194 TATTCA-TCATTTTCTGGTGGGTTAAAAG
1 TATTCATTCATTTT-TAGTGGATTAAAAG
*
24954222 TATTCATTCACTTCTGT-GTGGATTAAAAG
1 TATTCATTCA-TT-TTTAGTGGATTAAAAG
24954251 TAT
1 TAT
24954254 ACATCTACTT
Statistics
Matches: 77, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
27 7 0.09
28 49 0.64
29 17 0.22
30 3 0.04
31 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (28 bp):
TATTCATTCATTTTTAGTGGATTAAAAG
Found at i:24954271 original size:57 final size:57
Alignment explanation
Indices: 24954146--24954297 Score: 170
Period size: 56 Copynumber: 2.7 Consensus size: 57
24954136 ACTATTCATC
* * *
24954146 CACTTCTAGTGGATTAAAAGTATTCATTCA-TT-TTTAGTGGATTAAAAGTATTCAT
1 CACTTCTAGTGGGTTAAAAGTATTCATTCACTTCTGTAGTGGATTAAAAGTATACAT
* *
24954201 CATTTTCTGGTGGGTTAAAAGTATTCATTCACTTCTGT-GTGGATTAAAAGTATACAT
1 CA-CTTCTAGTGGGTTAAAAGTATTCATTCACTTCTGTAGTGGATTAAAAGTATACAT
* *
24954258 CTACTTCTTGTGGG-T-AAAGTTATACATTCACTTCTAGTAG
1 C-ACTTCTAGTGGGTTAAAAG-TATTCATTCACTTCT-GTAG
24954298 GTAAAGTTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
55 6 0.07
56 40 0.49
57 32 0.39
58 4 0.05
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (57 bp):
CACTTCTAGTGGGTTAAAAGTATTCATTCACTTCTGTAGTGGATTAAAAGTATACAT
Found at i:24954282 original size:27 final size:27
Alignment explanation
Indices: 24954247--24954307 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
24954237 GTGTGGATTA
* *
24954247 AAAG-TATACA-TCTACTTCTTGTGGGT
1 AAAGTTATACATTC-ACTTCTAGTAGGT
24954273 AAAGTTATACATTCACTTCTAGTAGGT
1 AAAGTTATACATTCACTTCTAGTAGGT
24954300 AAAGTTAT
1 AAAGTTAT
24954308 TATTGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 4 0.13
27 25 0.81
28 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (27 bp):
AAAGTTATACATTCACTTCTAGTAGGT
Found at i:24954684 original size:31 final size:31
Alignment explanation
Indices: 24954649--24954714 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
24954639 TTAGAAATCA
* *
24954649 AAGAATAACCATTGAAATCATTTGAACCTTG
1 AAGAATAACCATCGAAATCATTTGAACCTCG
* *
24954680 AAGAATAATCATCGAAATCTTTTGAACCTCG
1 AAGAATAACCATCGAAATCATTTGAACCTCG
24954711 AAGA
1 AAGA
24954715 TGATGAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (31 bp):
AAGAATAACCATCGAAATCATTTGAACCTCG
Found at i:24955114 original size:19 final size:20
Alignment explanation
Indices: 24955087--24955132 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
24955077 AGGAGACAAG
*
24955087 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
24955106 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
24955125 ATAATATT
1 ATAATATT
24955133 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:24955572 original size:20 final size:20
Alignment explanation
Indices: 24955527--24955564 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
24955517 TTTTGGCCTC
24955527 ATTTGACTTATTAGAGTATA
1 ATTTGACTTATTAGAGTATA
*
24955547 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTAGAGTA
24955565 AGATTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTAGAGTATA
Found at i:24955796 original size:23 final size:24
Alignment explanation
Indices: 24955762--24955807 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
24955752 TAAGAGCCCC
24955762 GATTTGCATTTTTCTGT-AGTGTT
1 GATTTGCATTTTTCTGTAAGTGTT
*
24955785 GATTTGCTTTTTTCTGTAAGTGT
1 GATTTGCATTTTTCTGTAAGTGT
24955808 GTTGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.13, C:0.09, G:0.22, T:0.57
Consensus pattern (24 bp):
GATTTGCATTTTTCTGTAAGTGTT
Found at i:24956091 original size:29 final size:30
Alignment explanation
Indices: 24956024--24956091 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
24956014 CTCATCTGTT
*
24956024 AAATCCAAGCAAAGAATTTTTACTAAAAAA
1 AAATCCAAGCAAAGAACTTTTACTAAAAAA
*
24956054 AAATCCAAGCAAAGAACTTTTA-TTAAAAA
1 AAATCCAAGCAAAGAACTTTTACTAAAAAA
24956083 AAATCCAAG
1 AAATCCAAG
24956092 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 15 0.42
30 21 0.58
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (30 bp):
AAATCCAAGCAAAGAACTTTTACTAAAAAA
Found at i:24956753 original size:46 final size:46
Alignment explanation
Indices: 24956701--24956792 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
24956691 TTAGGTAGAG
24956701 TCATCTCCATCCTTCAAAAATCTCATTACTCACAAAAGAGGAAGAA
1 TCATCTCCATCCTTCAAAAATCTCATTACTCACAAAAGAGGAAGAA
24956747 TCATCTCCATCCTTCAAAAATCTCATTACTCACAAAAGAGGAAGAA
1 TCATCTCCATCCTTCAAAAATCTCATTACTCACAAAAGAGGAAGAA
24956793 ATATCATGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.26, G:0.09, T:0.24
Consensus pattern (46 bp):
TCATCTCCATCCTTCAAAAATCTCATTACTCACAAAAGAGGAAGAA
Found at i:24963142 original size:8 final size:7
Alignment explanation
Indices: 24963114--24963144 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
24963104 CTCGTGTAAT
24963114 AATTTAA
1 AATTTAA
24963121 AATTTAA
1 AATTTAA
24963128 AATTTAA
1 AATTTAA
24963135 ATATTTAA
1 A-ATTTAA
24963143 AA
1 AA
24963145 AATTAACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:24964282 original size:16 final size:17
Alignment explanation
Indices: 24964250--24964282 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24964240 AATCAGAATG
24964250 GCAGAAACAGAGGAAGA
1 GCAGAAACAGAGGAAGA
*
24964267 GCAGAACCAG-GGAAGA
1 GCAGAAACAGAGGAAGA
24964283 AAATGAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.48, C:0.15, G:0.36, T:0.00
Consensus pattern (17 bp):
GCAGAAACAGAGGAAGA
Found at i:24971244 original size:2 final size:2
Alignment explanation
Indices: 24971228--24971259 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
24971218 ATATTATCAA
24971228 AT AT -T AT AT -T 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 AT
24971260 TAAAACGCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:24975199 original size:14 final size:14
Alignment explanation
Indices: 24975179--24975212 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
24975169 TATGTATATG
24975179 GTTAATAAAATTAAA
1 GTTAAT-AAATTAAA
24975194 -TTAATAAATTAAA
1 GTTAATAAATTAAA
24975207 GTTAAT
1 GTTAAT
24975213 TCATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (14 bp):
GTTAATAAATTAAA
Found at i:24981229 original size:18 final size:18
Alignment explanation
Indices: 24981206--24981246 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
24981196 GCTCGGGAGA
*
24981206 AGGAAAGAGTTCAAAAGG
1 AGGAAAAAGTTCAAAAGG
*
24981224 AGGAAAAAGTTCAAGAGG
1 AGGAAAAAGTTCAAAAGG
24981242 AGGAA
1 AGGAA
24981247 GGGGAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.34, T:0.10
Consensus pattern (18 bp):
AGGAAAAAGTTCAAAAGG
Found at i:24986402 original size:2 final size:2
Alignment explanation
Indices: 24986395--24986420 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24986385 TTAGATTAGT
24986395 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
24986421 GATAATATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:24986738 original size:19 final size:19
Alignment explanation
Indices: 24986706--24986750 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
24986696 ATATCAAGGG
* *
24986706 TTTGG-TCTAGAGGTTTAT
1 TTTGGCTCTACAGGTTCAT
24986724 TTTGGCTCTACAGGTTCAT
1 TTTGGCTCTACAGGTTCAT
*
24986743 TTTTGCTC
1 TTTGGCTC
24986751 CCTTACAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (19 bp):
TTTGGCTCTACAGGTTCAT
Found at i:24990380 original size:37 final size:37
Alignment explanation
Indices: 24990339--24990421 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
24990329 CAATAGAGAA
* * *
24990339 CAAATCACG-TCTAGTGCCGAAGCATTTGGCGGAGAGT
1 CAAATCACGTTC-AGAGCCGAAACATCTGGCGGAGAGT
**
24990376 CAAATCACGTTCAGAGTTGAAACATCTGGCGGAGAGT
1 CAAATCACGTTCAGAGCCGAAACATCTGGCGGAGAGT
24990413 CAAATCACG
1 CAAATCACG
24990422 CACAACATTG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 38 0.95
38 2 0.05
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (37 bp):
CAAATCACGTTCAGAGCCGAAACATCTGGCGGAGAGT
Found at i:24999361 original size:10 final size:10
Alignment explanation
Indices: 24999337--24999366 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
24999327 ACCAAACATC
24999337 AAATATCACTA
1 AAATATCA-TA
24999348 AAATATCATA
1 AAATATCATA
24999358 AAATATCAT
1 AAATATCAT
24999367 CAATTTCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (10 bp):
AAATATCATA
Found at i:25098044 original size:27 final size:27
Alignment explanation
Indices: 25098006--25098064 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
25097996 GGGTATTTCA
* *
25098006 GATACCTTTACTCATTAGAAGTGGATG
1 GATACCTGTACTCATCAGAAGTGGATG
* *
25098033 GATACCTGTACTTATCGGAAGTGGATG
1 GATACCTGTACTCATCAGAAGTGGATG
25098060 GATAC
1 GATAC
25098065 TTTCACCTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (27 bp):
GATACCTGTACTCATCAGAAGTGGATG
Found at i:25107108 original size:3 final size:3
Alignment explanation
Indices: 25107100--25107126 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
25107090 TACTTTTTTA
25107100 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
25107127 TCCCTCTTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25114647 original size:28 final size:29
Alignment explanation
Indices: 25114606--25114665 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
25114596 GTCTATGGGC
*
25114606 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCAGTTTTAGGGGGCAAAAATGT
* * *
25114634 AATTTTTGATTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAGTTTTA-GGGGGCAAAAATGT
25114664 AA
1 AA
25114666 ATATCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTCAGTTTTAGGGGGCAAAAATGT
Found at i:25120236 original size:23 final size:23
Alignment explanation
Indices: 25120209--25120270 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
25120199 AGTTATTACA
25120209 GAATCGTGTGACTAGTT-AT-TAT
1 GAATCGTGTGACTAGTTGATAT-T
* *
25120231 GAAATCGCGTTACTAGTTGATATT
1 G-AATCGTGTGACTAGTTGATATT
*
25120255 GAATCGTGTGAGTAGT
1 GAATCGTGTGACTAGT
25120271 ATCTATGGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 26 0.81
24 4 0.12
25 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (23 bp):
GAATCGTGTGACTAGTTGATATT
Found at i:25120287 original size:46 final size:45
Alignment explanation
Indices: 25120155--25120289 Score: 137
Period size: 46 Copynumber: 2.9 Consensus size: 45
25120145 CGTTGAGTAT
* * * *
25120155 TTGATATTGACTCGTGTGAGTAGTAAATATGGAGTGGTGTTAGTAG
1 TTGATATTGAATCGTGTGAGTAGT-ATTATGGAGTGGCGTTACTAG
** * * * *
25120201 TT-ATTACAGAATCGTGTGACTAGTTATTATGAAATCGCGTTACTAG
1 TTGA-TATTGAATCGTGTGAGTAG-TATTATGGAGTGGCGTTACTAG
25120247 TTGATATTGAATCGTGTGAGTAGTATCTATGGAGTGGCGTTAC
1 TTGATATTGAATCGTGTGAGTAGTAT-TATGGAGTGGCGTTAC
25120290 CACTTATTAT
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
45 4 0.06
46 63 0.91
47 2 0.03
ACGTcount: A:0.27, C:0.09, G:0.27, T:0.37
Consensus pattern (45 bp):
TTGATATTGAATCGTGTGAGTAGTATTATGGAGTGGCGTTACTAG
Found at i:25120312 original size:92 final size:92
Alignment explanation
Indices: 25120155--25120322 Score: 228
Period size: 92 Copynumber: 1.8 Consensus size: 92
25120145 CGTTGAGTAT
* * ** * *
25120155 TTGATATTGACTCGTGTGAGTAGTAAATATGGAGTGGTGTTAGTAGTTATTACAGAATCGTGTGA
1 TTGATATTGAATCGTGTGAGTAGTAAATATGGAGTGGCGTTACCACTTATTACAGAATCGCGTGA
25120220 CTAGTTATTATGAAATCGCGTTACTAG
66 CTAGTTATTATGAAATCGCGTTACTAG
** ** *
25120247 TTGATATTGAATCGTGTGAGTAGTATCTATGGAGTGGCGTTACCACTTATTATGGAATGGCGTGA
1 TTGATATTGAATCGTGTGAGTAGTAAATATGGAGTGGCGTTACCACTTATTACAGAATCGCGTGA
*
25120312 CTATTTATTAT
66 CTAGTTATTAT
25120323 AAGATTGTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
92 64 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.38
Consensus pattern (92 bp):
TTGATATTGAATCGTGTGAGTAGTAAATATGGAGTGGCGTTACCACTTATTACAGAATCGCGTGA
CTAGTTATTATGAAATCGCGTTACTAG
Found at i:25120319 original size:23 final size:23
Alignment explanation
Indices: 25120274--25120322 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
25120264 GAGTAGTATC
* *
25120274 TATGGAGTGGCGTTACCACTTAT
1 TATGGAATGGCGTGACCACTTAT
* *
25120297 TATGGAATGGCGTGACTATTTAT
1 TATGGAATGGCGTGACCACTTAT
25120320 TAT
1 TAT
25120323 AAGATTGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (23 bp):
TATGGAATGGCGTGACCACTTAT
Found at i:25120467 original size:138 final size:138
Alignment explanation
Indices: 25120211--25120472 Score: 339
Period size: 138 Copynumber: 1.9 Consensus size: 138
25120201 TTATTACAGA
* * *
25120211 ATCGTGTGACTAGTTATTATGAAATCGCGTTACTAGTTGATATTGAATCGTGTGAGTAGTATCTA
1 ATCGCGTGACTAGTTATTAAGAAATCGCGTTACTAGTTGATATTGAATCGCGTGAGTAGTATCTA
* ** * *
25120276 TGGAGTGGCGTTACCACTTATTATGGAATGGCGTGACTATTTATTATAAGATTGTGTGAGTAAAA
66 TGGAGTGGCGTTACCACTTATTATGAAATCACGTGACTATTGATTATAAGATTGCGTGAGTAAAA
25120341 AACATGGC
131 AACATGGC
* * *
25120349 ATCGCGTGACTGGTTATTACAG-AATCGCGTTACTAGTTTATATTGAGTCGCGTGAGTAGTATCT
1 ATCGCGTGACTAGTTATTA-AGAAATCGCGTTACTAGTTGATATTGAATCGCGTGAGTAGTATCT
* * * * **
25120413 ATGGATTGGTGTTACCATTTGTTATGAAATCACGTGACTAGTTGA-TATGGGATTGCGTGA
65 ATGGAGTGGCGTTACCACTTATTATGAAATCACGTGACTA-TTGATTATAAGATTGCGTGA
25120473 CTCATTTATT
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
138 101 0.96
139 4 0.04
ACGTcount: A:0.27, C:0.12, G:0.26, T:0.36
Consensus pattern (138 bp):
ATCGCGTGACTAGTTATTAAGAAATCGCGTTACTAGTTGATATTGAATCGCGTGAGTAGTATCTA
TGGAGTGGCGTTACCACTTATTATGAAATCACGTGACTATTGATTATAAGATTGCGTGAGTAAAA
AACATGGC
Found at i:25124092 original size:16 final size:15
Alignment explanation
Indices: 25124052--25124095 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
25124042 ATGAGTTGTG
*
25124052 AAGAAAAAAAAAACA
1 AAGAAAAAGAAAACA
* *
25124067 AAAAAAAAGAAAAGA
1 AAGAAAAAGAAAACA
25124082 AAGAAATAAGAAAA
1 AAGAAA-AAGAAAA
25124096 ATGAGAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.02
Consensus pattern (15 bp):
AAGAAAAAGAAAACA
Found at i:25124928 original size:14 final size:14
Alignment explanation
Indices: 25124911--25124937 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25124901 ATGAAATAGA
25124911 AAAAGAAAAATGAG
1 AAAAGAAAAATGAG
25124925 AAAAGAAAAATGA
1 AAAAGAAAAATGA
25124938 TGAAGCTTTA
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:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (14 bp):
AAAAGAAAAATGAG
Found at i:25126401 original size:21 final size:22
Alignment explanation
Indices: 25126351--25126401 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
25126341 TAGGTATATC
25126351 TCTAAAACGTCCGCGTACATTT
1 TCTAAAACGTCCGCGTACATTT
*
25126373 TCTAAAACTTCCG-GTTACATTT
1 TCTAAAACGTCCGCG-TACATTT
25126395 T-TAAAAC
1 TCTAAAAC
25126402 CTTTAGGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (22 bp):
TCTAAAACGTCCGCGTACATTT
Found at i:25126412 original size:21 final size:21
Alignment explanation
Indices: 25126351--25126414 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
25126341 TAGGTATATC
* *
25126351 TCTAAAACGTCCGCGTACATTT
1 TCTAAAACTTCAG-GTACATTT
*
25126373 TCTAAAACTTCCGGTTACATTT
1 TCTAAAACTTCAGG-TACATTT
*
25126395 T-TAAAACCTTTAGGTACATT
1 TCTAAAA-CTTCAGGTACATT
25126415 CTTATGACAC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 12 0.32
22 25 0.68
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (21 bp):
TCTAAAACTTCAGGTACATTT
Found at i:25126789 original size:22 final size:21
Alignment explanation
Indices: 25126761--25126811 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
25126751 ATTTTTTTAG
25126761 TATTATTT-TTTAAGTTTAATTC
1 TATTATTTATTT-AGTTTAA-TC
*
25126783 TATTATTTATTTATTTTAATC
1 TATTATTTATTTAGTTTAATC
25126804 TGATTATT
1 T-ATTATT
25126812 ATTACCATAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 3 0.12
22 20 0.77
23 3 0.12
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (21 bp):
TATTATTTATTTAGTTTAATC
Found at i:25128753 original size:15 final size:14
Alignment explanation
Indices: 25128733--25128774 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
25128723 AACTTTAATA
25128733 AAAAAATATAAGAAC
1 AAAAAATATAA-AAC
25128748 AAAAAATAATAAAAC
1 AAAAAAT-ATAAAAC
*
25128763 AAAATATATAAA
1 AAAAAATATAAA
25128775 TAAATTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 5 0.20
15 16 0.64
16 4 0.16
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAAAATATAAAAC
Found at i:25130848 original size:102 final size:103
Alignment explanation
Indices: 25130666--25130943 Score: 459
Period size: 102 Copynumber: 2.7 Consensus size: 103
25130656 ATTAGGTGCT
* *
25130666 TGAATATTTGTTGAGCATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAACA
1 TGAATATTTGTTGAACATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAGCA
25130731 TTGCGTGAGAGTTAATACGTGACTGAATATTACCTGAC
66 TTGCGTGAGAGTTAATACGTGACTGAATATTACCTGAC
* * *
25130769 TGAAT-TTTGTTGAACATTACGTGAGTTCTTTATAGGTATTATGTGACTGAATATATGTTGAGCA
1 TGAATATTTGTTGAACATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAGCA
25130833 TTGCGTGAGAGTTAATACGTGACTGAATATTACCTGAC
66 TTGCGTGAGAGTTAATACGTGACTGAATATTACCTGAC
* * * *
25130871 TAAATATTTGTTGAACATTGCGTGAGTTTTTTATAGGCGTTACGTGACTGAATATTTGTTGAGCA
1 TGAATATTTGTTGAACATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAGCA
*
25130936 TTGTGTGA
66 TTGCGTGA
25130944 CCTATTTGTA
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
102 96 0.60
103 65 0.40
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.38
Consensus pattern (103 bp):
TGAATATTTGTTGAACATTGCGTGAGTTCTTTATAGGCATTACGTGACTGAATATATGTTGAGCA
TTGCGTGAGAGTTAATACGTGACTGAATATTACCTGAC
Found at i:25130956 original size:48 final size:48
Alignment explanation
Indices: 25130862--25130956 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
25130852 TGACTGAATA
** *
25130862 TTACCTGACTAAATATTTGTTGAACATTGCGTGAGTTTTTTATAGGCG
1 TTACCTGACTAAATATTTGTTGAACATTGCGTGACCTATTTATAGGCG
* * * * *
25130910 TTACGTGACTGAATATTTGTTGAGCATTGTGTGACCTATTTGTAGGC
1 TTACCTGACTAAATATTTGTTGAACATTGCGTGACCTATTTATAGGC
25130957 ATTGCGTGTC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (48 bp):
TTACCTGACTAAATATTTGTTGAACATTGCGTGACCTATTTATAGGCG
Found at i:25131683 original size:21 final size:22
Alignment explanation
Indices: 25131658--25131698 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
25131648 CCTAGGTGGA
*
25131658 AAAATTCAAGGGAA-AAGTGTG
1 AAAATTCAAGGAAACAAGTGTG
25131679 AAAATTCAAGGAAACAAGTG
1 AAAATTCAAGGAAACAAGTG
25131699 AAAAAAGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.17
Consensus pattern (22 bp):
AAAATTCAAGGAAACAAGTGTG
Found at i:25131699 original size:20 final size:21
Alignment explanation
Indices: 25131658--25131702 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
25131648 CCTAGGTGGA
*
25131658 AAAATTCAAGGGAAAAGTGTG
1 AAAATTCAAGGGAAAAGAGTG
25131679 AAAATTCAA-GGAAACA-AGTG
1 AAAATTCAAGGGAAA-AGAGTG
25131699 AAAA
1 AAAA
25131703 AAGGTAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.56, C:0.07, G:0.22, T:0.16
Consensus pattern (21 bp):
AAAATTCAAGGGAAAAGAGTG
Found at i:25131703 original size:21 final size:20
Alignment explanation
Indices: 25131656--25131703 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
25131646 ACCCTAGGTG
*
25131656 GAAAAATTCAAGGGAAAAGT
1 GAAAAATTCAAGGAAAAAGT
*
25131676 GTGAAAATTCAAGGAAACAAGT
1 G-AAAAATTCAAGGAAA-AAGT
25131698 GAAAAA
1 GAAAAA
25131704 AGGTAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.56, C:0.06, G:0.23, T:0.15
Consensus pattern (20 bp):
GAAAAATTCAAGGAAAAAGT
Found at i:25134525 original size:30 final size:30
Alignment explanation
Indices: 25134489--25134549 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
25134479 GGAGGTGCCT
25134489 TTGAGTGTGAGGGACCAAATGCACATATTC
1 TTGAGTGTGAGGGACCAAATGCACATATTC
*
25134519 TTGAGTGTGAGGGACCAATTGCACATATTC
1 TTGAGTGTGAGGGACCAAATGCACATATTC
25134549 T
1 T
25134550 AGCAGGAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (30 bp):
TTGAGTGTGAGGGACCAAATGCACATATTC
Found at i:25137630 original size:30 final size:29
Alignment explanation
Indices: 25137560--25137632 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
25137550 AAGTAAATTT
*
25137560 AAATAAATTTTTAATTTTTTGTTATATTC
1 AAATAAATTTTTAATTTTTTGTTATAATC
* *
25137589 AATTAAGTTTTTATATTTTTAT-TT-TGAATC
1 AAATAAATTTTTA-ATTTTT-TGTTAT-AATC
25137619 AAATAAATTTTTAA
1 AAATAAATTTTTAA
25137633 ATAATTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
29 13 0.36
30 22 0.61
31 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (29 bp):
AAATAAATTTTTAATTTTTTGTTATAATC
Found at i:25147831 original size:13 final size:13
Alignment explanation
Indices: 25147813--25147837 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25147803 AGAAAATGAG
25147813 ATTTTATAAAATA
1 ATTTTATAAAATA
25147826 ATTTTATAAAAT
1 ATTTTATAAAAT
25147838 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:25153744 original size:20 final size:20
Alignment explanation
Indices: 25153688--25153745 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
25153678 CTCAAGAGTT
* * *
25153688 ATAACGTTTGATGAATAATG
1 ATAACCTTTAATGAATAATA
*
25153708 ATAACCCTTTCATGAATAATA
1 ATAA-CCTTTAATGAATAATA
*
25153729 ATAACTTTTAATGAATA
1 ATAACCTTTAATGAATA
25153746 GTTAGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (20 bp):
ATAACCTTTAATGAATAATA
Found at i:25153873 original size:30 final size:30
Alignment explanation
Indices: 25153839--25153902 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
25153829 AATCAAGTTA
* *
25153839 TTATATTTTTGTTTTGAA-CTAAATAAATTT
1 TTATACTTTTATTTTGAATC-AAATAAATTT
*
25153869 TTATACTTTTATTTTGAATCAAATGAATTT
1 TTATACTTTTATTTTGAATCAAATAAATTT
25153899 TTAT
1 TTAT
25153903 GATTAATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 29 0.97
31 1 0.03
ACGTcount: A:0.33, C:0.05, G:0.06, T:0.56
Consensus pattern (30 bp):
TTATACTTTTATTTTGAATCAAATAAATTT
Found at i:25157640 original size:39 final size:39
Alignment explanation
Indices: 25157565--25157640 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
25157555 AAGAAGCCGT
*
25157565 TTGAGAATTCTCCAAATTAGACTCATTATGCATACCCGC
1 TTGAGAATTCTCCAAATTAGACTCATTATCCATACCCGC
* *
25157604 TTGAGAATTTTCCAAATTGGACTCATTA-CCAGTACCC
1 TTGAGAATTCTCCAAATTAGACTCATTATCCA-TACCC
25157641 TCCCAATTGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.06
39 31 0.94
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (39 bp):
TTGAGAATTCTCCAAATTAGACTCATTATCCATACCCGC
Found at i:25167917 original size:19 final size:17
Alignment explanation
Indices: 25167888--25167922 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 17
25167878 ACCTATAAAA
25167888 TTTTTTCTTCTCATTTCC
1 TTTTTTCTTCTC-TTTCC
25167906 TTTTTTCTTTCTCTTTC
1 TTTTTTC-TTCTCTTTC
25167923 TTCTCACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTCTTCTCTTTCC
Found at i:25168356 original size:28 final size:26
Alignment explanation
Indices: 25168312--25168365 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
25168302 TTATTTGTAA
* *
25168312 AATTTAAAATATTAATATTTATATAT
1 AATTTAAAATATAAATATTAATATAT
25168338 AATTTAAACATTATAAATATTAATATAT
1 AATTTAAA-A-TATAAATATTAATATAT
25168366 TAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.33
27 1 0.04
28 15 0.62
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTTAAAATATAAATATTAATATAT
Found at i:25168367 original size:8 final size:8
Alignment explanation
Indices: 25168309--25168401 Score: 82
Period size: 8 Copynumber: 11.4 Consensus size: 8
25168299 AAATTATTTG
25168309 TAAAAT-T
1 TAAAATAT
25168316 TAAAATAT
1 TAAAATAT
*
25168324 TAATAT-T
1 TAAAATAT
*
25168331 TATATATAAT
1 TA-AAAT-AT
* *
25168341 TTAAACAT
1 TAAAATAT
25168349 TATAAATAT
1 TA-AAATAT
*
25168358 TAATATAT
1 TAAAATAT
25168366 TAAAATAT
1 TAAAATAT
*
25168374 TAANATGAT
1 TAAAAT-AT
25168383 TAAAATAT
1 TAAAATAT
25168391 TAAAATAT
1 TAAAATAT
25168399 TAA
1 TAA
25168402 TATTTTAGGG
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
7 9 0.13
8 43 0.61
9 16 0.23
10 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (8 bp):
TAAAATAT
Found at i:25168541 original size:15 final size:15
Alignment explanation
Indices: 25168516--25168554 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
25168506 ATATTAAATT
*
25168516 ATAAATAAAATATTA
1 ATAATTAAAATATTA
* *
25168531 TTAATTAAAATTTTA
1 ATAATTAAAATATTA
25168546 ATAATTAAA
1 ATAATTAAA
25168555 TTATACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATTAAAATATTA
Found at i:25168578 original size:25 final size:25
Alignment explanation
Indices: 25168536--25168583 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
25168526 TATTATTAAT
*
25168536 TAAAATTTTAATAATTAAATTATAC
1 TAAAATGTTAATAATTAAATTATAC
* *
25168561 TAAAATGTTGATATTTAAATTAT
1 TAAAATGTTAATAATTAAATTAT
25168584 TAATTATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (25 bp):
TAAAATGTTAATAATTAAATTATAC
Found at i:25168579 original size:40 final size:40
Alignment explanation
Indices: 25168504--25168593 Score: 96
Period size: 40 Copynumber: 2.2 Consensus size: 40
25168494 TTAATCACAA
25168504 TAATATTAAATTATAAATAAAATATTATTAATTAAAATT-T
1 TAATATTAAATTATAAATAAAATATTATTAATT-AAATTAT
* * *
25168544 TAATAATTAAATTAT-ACTAAAATGTTGA-TATTTAAATTAT
1 TAAT-ATTAAATTATAAATAAAATATT-ATTAATTAAATTAT
25168584 TAATTATTAA
1 TAA-TATTAA
25168594 TATTTTAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
39 5 0.12
40 26 0.60
41 12 0.28
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (40 bp):
TAATATTAAATTATAAATAAAATATTATTAATTAAATTAT
Found at i:25175866 original size:28 final size:28
Alignment explanation
Indices: 25175811--25175866 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
25175801 CAGAGCATAG
*
25175811 GGGTAAAATGGTAATTTTACCACCCCAA
1 GGGTAAAATGGTAATTTTACCACACCAA
*
25175839 GGGTAAAATTGTAATTTTA-CACAACCAA
1 GGGTAAAATGGTAATTTTACCAC-ACCAA
25175867 CACTTGTCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTACCACACCAA
Done.