Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 215 of 218
Found at i:64361468 original size:46 final size:46
Alignment explanation
Indices: 64361401--64361491 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
64361391 TCATATCTCG
* *
64361401 TCAATATTGGAATAAGAAGCTACTTGCAGGTGAAATCGATATTGTA
1 TCAATATTGGAATAAGAAGCTACTTGCAGATGAAATCAATATTGTA
*
64361447 TCAATATTGGAATAAGAAGCTACTTGTAGATGAAATCAATATTGT
1 TCAATATTGGAATAAGAAGCTACTTGCAGATGAAATCAATATTGT
64361492 GTCTCTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (46 bp):
TCAATATTGGAATAAGAAGCTACTTGCAGATGAAATCAATATTGTA
Found at i:64362424 original size:16 final size:16
Alignment explanation
Indices: 64362403--64362440 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
64362393 GACGAGGCAC
*
64362403 TGAATGTCTTCTTCGA
1 TGAATGTCTTCCTCGA
*
64362419 TGAATGTCTTCCTCGT
1 TGAATGTCTTCCTCGA
64362435 TGAATG
1 TGAATG
64362441 AAGACATGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (16 bp):
TGAATGTCTTCCTCGA
Found at i:64367191 original size:12 final size:12
Alignment explanation
Indices: 64367174--64367199 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
64367164 ATTATTAATT
64367174 ATTAACGGAAGC
1 ATTAACGGAAGC
64367186 ATTAACGGAAGC
1 ATTAACGGAAGC
64367198 AT
1 AT
64367200 GATAGGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (12 bp):
ATTAACGGAAGC
Found at i:64375022 original size:17 final size:17
Alignment explanation
Indices: 64375000--64375033 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
64374990 ATCCACTAAT
*
64375000 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
64375017 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
64375034 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:64379651 original size:17 final size:17
Alignment explanation
Indices: 64379629--64379662 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
64379619 ATCCACTAAT
*
64379629 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
64379646 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
64379663 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:64393445 original size:4 final size:4
Alignment explanation
Indices: 64393436--64393462 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
64393426 ATTTTCACTC
64393436 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
64393463 AGGGAAGCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:64403390 original size:27 final size:27
Alignment explanation
Indices: 64403352--64403416 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
64403342 AACCACTAGT
*
64403352 CCAATAACCCAATAGCCTACCCTTAGC
1 CCAATAACCCAATAGCCTACCCTCAGC
64403379 CCAATAACCCAATAGCCTACCCTCAGC
1 CCAATAACCCAATAGCCTACCCTCAGC
64403406 CCAA-AACCCAA
1 CCAATAACCCAA
64403417 AACAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 7 0.19
27 30 0.81
ACGTcount: A:0.37, C:0.43, G:0.06, T:0.14
Consensus pattern (27 bp):
CCAATAACCCAATAGCCTACCCTCAGC
Found at i:64404550 original size:3 final size:3
Alignment explanation
Indices: 64404544--64404575 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
64404534 TTGTTTATTC
64404544 TAT TAT TAT TAT TAT TAT TAT TAT TACT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT T
64404576 TGTTTGTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:64405126 original size:16 final size:16
Alignment explanation
Indices: 64405107--64405137 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64405097 TACACCCATA
*
64405107 TATATGTACATATTTT
1 TATATATACATATTTT
64405123 TATATATACATATTT
1 TATATATACATATTT
64405138 ATCGTTTCTT
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:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:64417506 original size:44 final size:44
Alignment explanation
Indices: 64417365--64417662 Score: 177
Period size: 44 Copynumber: 6.9 Consensus size: 44
64417355 ATTATACAGG
* * * *
64417365 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
* ** *
64417411 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAG-AGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGTAGA
64417455 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AGTAGA
* * ** * *
64417499 TCCTATCTCCTTGAGATTACAATGGAGCGGAT--TA-AAG--GA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
* * ** * * **
64417538 TCTTATCTCTCT-AAAGTTACAGTAGAGAAGATCACATCAG--G-
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAAGTAGA
* * * * * ** *
64417579 TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
*
64417625 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA
64417663 CACTATCCTA
Statistics
Matches: 192, Mismatches: 46, Indels: 28
0.72 0.17 0.11
Matches are distributed among these distances:
38 2 0.01
39 22 0.11
40 2 0.01
41 28 0.15
42 5 0.03
44 67 0.35
45 2 0.01
46 63 0.33
47 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
Found at i:64417728 original size:44 final size:44
Alignment explanation
Indices: 64417409--64417855 Score: 146
Period size: 44 Copynumber: 10.4 Consensus size: 44
64417399 AAGAATTTCA
* * * ***
64417409 GATCTTATCTCCCTGAGGTTACAGCGGAGCAGATT-GAAGCCAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* *
64417452 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCAAAGAT--AG
1 -GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAA-ATAAAG
* * * * *
64417496 TAATCCTATCTCCTTG-AGATTACAATGGAGCGGA-T----TAAAG
1 -GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATAAAG
* * * * * * *
64417536 GATCTTATCTCTCTAAAGTTACAGTAGAGAAGA-TCACAT-CAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * ** * **
64417578 G-TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGA--TTA-AAATAAAG
* ** * * *
64417623 GATCTTATCTCCCTG-AGATTACAGCGGAGCAGA-TCGAAGACAC
1 GATCTTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATAAAG
* * **
64417666 TATCCTATCTCCC-GAAGTTACAGTGGAGTGGATTAAAATAAAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * * *** *
64417709 GATCTTATCTCTCTGAAGTTACAATAGAGTAGA-TCGCAT-CAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * * * *
64417751 G-TCTTATTTCCCTGAGGTTACAGCGGAGCAGATTAAAGACATA-
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAA-ATAAAG
* *
64417794 -ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG
1 GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
* * *
64417837 AATTTTATCTCTCTGAAGT
1 GATCTTATCTCCCTGAAGT
64417856 GCAGTAGAGT
Statistics
Matches: 292, Mismatches: 84, Indels: 54
0.68 0.20 0.13
Matches are distributed among these distances:
38 1 0.00
39 22 0.08
40 4 0.01
41 49 0.17
42 26 0.09
43 65 0.22
44 92 0.32
45 5 0.02
46 28 0.10
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (44 bp):
GATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAG
Found at i:64417753 original size:173 final size:170
Alignment explanation
Indices: 64417452--64417778 Score: 480
Period size: 173 Copynumber: 1.9 Consensus size: 170
64417442 TTGAAGCCAG
* * *
64417452 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAGTAATCCTATCTCCTTGAGATT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCTCGAGATT
*
64417517 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGAAGATCACATCAGGTCT
66 ACAATGGAGCGGATTAAAGGATCTTATCTCTCTAAAGTTACAATAGAGAAGATCACATCAGGTCT
*
64417582 TATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTC
131 TATTTCCCTGAGGTTACAGCGGAGTAGACCGGAGAATTTC
*
64417622 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCC-CGA-AGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCTCGAGA-T
* * * * *
64417684 TACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGATCGCATC
65 TACAATGGAGCGGA-T----TAAAGGATCTTATCTCTCTAAAGTTACAATAGAGAAGATCACATC
64417749 AGGTCTTATTTCCCTGAGGTTACAGCGGAG
125 AGGTCTTATTTCCCTGAGGTTACAGCGGAG
64417779 CAGATTAAAG
Statistics
Matches: 140, Mismatches: 11, Indels: 9
0.88 0.07 0.06
Matches are distributed among these distances:
167 1 0.01
168 15 0.11
169 12 0.09
170 42 0.30
173 70 0.50
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (170 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACACTAATCCTATCTCCTCGAGATT
ACAATGGAGCGGATTAAAGGATCTTATCTCTCTAAAGTTACAATAGAGAAGATCACATCAGGTCT
TATTTCCCTGAGGTTACAGCGGAGTAGACCGGAGAATTTC
Found at i:64417772 original size:127 final size:127
Alignment explanation
Indices: 64417620--64417869 Score: 378
Period size: 127 Copynumber: 2.0 Consensus size: 127
64417610 CCGGAGAATT
*
64417620 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT-ATCCTATCTCCC-GAAG
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACA-TAATCCTATCTCCCTGAAG
* *
64417683 TTACAGTGGAGTGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAATAGAGTAGATCGCA
65 TTACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAG-TACAATAGAGTAGATCGCA
* * * *
64417747 TCAGGTCTTATTTCCCTGAGGTTACAGCGGAGCAGATTAAAGACATAATCCTATCTCCCTGAAGT
1 TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACATAATCCTATCTCCCTGAAGT
* * *
64417812 TACAGTGGAGCGGATTAAAATAAAGAATTTTATCTCTCTGAAGTGCAGTAGAGTAGAT
66 TACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTACAATAGAGTAGAT
64417870 TACATCCAAG
Statistics
Matches: 111, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 1 0.01
127 65 0.59
128 45 0.41
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (127 bp):
TCAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGACATAATCCTATCTCCCTGAAGT
TACAGTGGAGCGGATTAAAATAAAGAATCTTATCTCTCTGAAGTACAATAGAGTAGATCGCA
Found at i:64418184 original size:27 final size:27
Alignment explanation
Indices: 64418154--64418222 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
64418144 TCAGAACCAC
64418154 TAGCCCAATAACCCAATAGCCTACCCT
1 TAGCCCAATAACCCAATAGCCTACCCT
64418181 TAGCCCAATAACCCAATAGCCTACCCT
1 TAGCCCAATAACCCAATAGCCTACCCT
*
64418208 CAGCCCAA-AACCCAA
1 TAGCCCAATAACCCAA
64418223 AACAAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.36, C:0.42, G:0.07, T:0.14
Consensus pattern (27 bp):
TAGCCCAATAACCCAATAGCCTACCCT
Found at i:64419935 original size:18 final size:18
Alignment explanation
Indices: 64419914--64419948 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64419904 TATACACCCA
*
64419914 TATATATGTACATATTTT
1 TATATATATACATATTTT
64419932 TATATATATACATATTT
1 TATATATATACATATTT
64419949 ATCGTTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (18 bp):
TATATATATACATATTTT
Found at i:64423416 original size:14 final size:14
Alignment explanation
Indices: 64423397--64423445 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
64423387 TACTAAGGAA
64423397 GATTTTCTTAGCCT
1 GATTTTCTTAGCCT
*
64423411 GATTTTCTTTA---A
1 GATTTTC-TTAGCCT
*
64423423 GATTTTCTTGGCCT
1 GATTTTCTTAGCCT
64423437 GATTTTCTT
1 GATTTTCTT
64423446 TAGGCCAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
11 2 0.07
12 7 0.25
14 16 0.57
15 3 0.11
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.55
Consensus pattern (14 bp):
GATTTTCTTAGCCT
Found at i:64423431 original size:26 final size:26
Alignment explanation
Indices: 64423395--64423447 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
64423385 CATACTAAGG
64423395 AAGATTTTCTTAGCCTGATTTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
*
64423421 AAGATTTTCTTGGCCTGATTTTCTTT
1 AAGATTTTCTTAGCCTGATTTTCTTT
64423447 A
1 A
64423448 GGCCAAAGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (26 bp):
AAGATTTTCTTAGCCTGATTTTCTTT
Found at i:64424467 original size:24 final size:25
Alignment explanation
Indices: 64424427--64424488 Score: 99
Period size: 24 Copynumber: 2.5 Consensus size: 25
64424417 AACTTACATG
*
64424427 GCGATGCAGTAGAGGAGTGTCGACA
1 GCGATGCAGCAGAGGAGTGTCGACA
*
64424452 GCGATGC-GCAGAGGAGTGTCGACG
1 GCGATGCAGCAGAGGAGTGTCGACA
64424476 GCGATGCAGCAGA
1 GCGATGCAGCAGA
64424489 CGGTCGAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 22 0.65
25 12 0.35
ACGTcount: A:0.26, C:0.19, G:0.42, T:0.13
Consensus pattern (25 bp):
GCGATGCAGCAGAGGAGTGTCGACA
Found at i:64424995 original size:15 final size:15
Alignment explanation
Indices: 64424975--64425025 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
64424965 ATAAATCAAA
* *
64424975 TTTAATACTTAATAT
1 TTTAATATTTAATTT
64424990 TTTAATATTTTAATTT
1 TTTAATA-TTTAATTT
*
64425006 TTTAACATTTAATTT
1 TTTAATATTTAATTT
64425021 TTTAA
1 TTTAA
64425026 CTTATCATAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTAATATTTAATTT
Found at i:64424996 original size:8 final size:8
Alignment explanation
Indices: 64424983--64425025 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
64424973 AATTTAATAC
64424983 TTAATATT
1 TTAATATT
64424991 TTAATATT
1 TTAATATT
*
64424999 TTAATTTT
1 TTAATATT
*
64425007 TTAACA-T
1 TTAATATT
*
64425014 TTAATTTT
1 TTAATATT
64425022 TTAA
1 TTAA
64425026 CTTATCATAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
7 5 0.17
8 24 0.83
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (8 bp):
TTAATATT
Found at i:64427155 original size:25 final size:26
Alignment explanation
Indices: 64427125--64427176 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
64427115 AAACTCTTTT
* *
64427125 AAAAGAAA-CTACAGAGAATTTCTTA
1 AAAAGAAACCCACAGAGAATTTATTA
*
64427150 AAAAGAAACCCAGAGAGAATTTATTA
1 AAAAGAAACCCACAGAGAATTTATTA
64427176 A
1 A
64427177 CTCAAATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.54, C:0.12, G:0.13, T:0.21
Consensus pattern (26 bp):
AAAAGAAACCCACAGAGAATTTATTA
Found at i:64428979 original size:14 final size:16
Alignment explanation
Indices: 64428944--64428982 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
64428934 ATAGTAAAAG
64428944 TATAATTTCATCATTT
1 TATAATTTCATCATTT
64428960 TAATAATTT-AT-ATTT
1 T-ATAATTTCATCATTT
64428975 TATAATTT
1 TATAATTT
64428983 TTAAAGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 3 0.14
17 7 0.32
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAATTTCATCATTT
Found at i:64431386 original size:21 final size:22
Alignment explanation
Indices: 64431357--64431398 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
64431347 AATCTATTTA
64431357 ATTAGATATTGTTTTACAAGAC
1 ATTAGATATTGTTTTACAAGAC
* *
64431379 ATTA-ATATTTTTTTATAAGA
1 ATTAGATATTGTTTTACAAGA
64431399 ATTGTAGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.48
Consensus pattern (22 bp):
ATTAGATATTGTTTTACAAGAC
Found at i:64435415 original size:189 final size:188
Alignment explanation
Indices: 64435076--64435596 Score: 634
Period size: 189 Copynumber: 2.7 Consensus size: 188
64435066 TTCAAAGTTG
* * * * * *
64435076 GAATCACTTCATGATCTGGATCTTAGTCATTGCCCAATAGCCGAATTCCCAATAATCCCAAGAAG
1 GAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATAGACAAATTCCCGA-AATCCCAAGAAG
* * * * * * * *
64435141 CTTGACAGAATTTAACTTATCTGAAACTCAAATTGAAGATGTGTACTTGTCTCTCGACACTCCAA
65 CTTAACAAAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTCTCGACTCTCTAA
* *
64435206 GTAATCTTCAGACGTTAGATATGAGTGGCTCAAGGGTAAAAAATGTATCCATCAAGATA
130 GTAATCTTCAAACATTAGATATGAGTGGCTCAAGGGTAAAAAATGTATCCATCAAGATA
* *
64435265 GAATCCCTTCGTGACCTGAATCTTAGTCATTGCCCAATAGTCAAATTTCCCGAAATCCCAAGAA-
1 GAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATAGACAAA-TTCCCGAAATCCCAAGAAG
* *
64435329 CTTTAATAAAATTAAACTTATCTGGAACTCAAATTGAAGAGGTGTCCTTGTCTCTCGACTCTCTA
65 C-TTAACAAAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTCTCGACTCTCTA
* * *
64435394 GGTAATCTTCAAACATTAGATATGAGTGGCTCAAGGGTAAAAAATGTATCGATCAAGATG
129 AGTAATCTTCAAACATTAGATATGAGTGGCTCAAGGGTAAAAAATGTATCCATCAAGATA
*
64435454 GAAGCCGCCCTTCGTGATCTGAATCTTAGTCATTGCCCAAT-GACAGAATTCCCAGAAATCCCAA
1 GAA---TCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATAGACA-AATTCCC-GAAATCCCAA
* * * * * * * * *
64435518 GAAGCTTAAGAAAATTGAATTTATTTGGGACTCAAATT-AAGGAAGTGACTTTGTCTTTAGACTC
61 GAAGCTTAACAAAATTAAACTTATCTGGAACTCAAATTGAA-GAAGTGTCCTTGTCTCTCGACTC
*
64435582 TCTAAATAATCTTCA
125 TCTAAGTAATCTTCA
64435597 GATGTTAAAG
Statistics
Matches: 287, Mismatches: 36, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
188 1 0.00
189 162 0.56
190 6 0.02
191 10 0.03
192 107 0.37
193 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.29
Consensus pattern (188 bp):
GAATCCCTTCGTGATCTGAATCTTAGTCATTGCCCAATAGACAAATTCCCGAAATCCCAAGAAGC
TTAACAAAATTAAACTTATCTGGAACTCAAATTGAAGAAGTGTCCTTGTCTCTCGACTCTCTAAG
TAATCTTCAAACATTAGATATGAGTGGCTCAAGGGTAAAAAATGTATCCATCAAGATA
Found at i:64449545 original size:174 final size:174
Alignment explanation
Indices: 64449224--64449545 Score: 405
Period size: 174 Copynumber: 1.9 Consensus size: 174
64449214 TTTTACCCTT
* * *
64449224 GAGCCACTCATAACTAAAGTCTAAAGATCACTTGAAGGGTCGAGAGATAGACACACGTTTTCAAT
1 GAGCCACTCATAACTAAAGTCTAAAGATCACTTGAAGAGTCGAGAGATAGACACACCTCTTCAAT
** * * * * * *
64449289 TTGAGTTTCAGATAAGTTTAATCTTTTTAAGCTTTCTAGGATTTTTAGAAATTCGACTATTGGGC
66 TTGAGTCCCAGATAAGTTCAATATTATTAAGCTTTCTAGGAATTCTAGAAATTCGACAATTGGGC
*
64449354 AAGCACTTAGATTCAGATCACAAGGGGAATATTTTTTTACTATC
131 AAGCACTAAGATTCAGATCACAAGGGGAATATTTTTTTACTATC
* * * * *
64449398 GAGCCACTCATATCTAAAGTCTGAAGATTACTTGGAGAGTCGAGAGATAGGCACACCTCTTCAAT
1 GAGCCACTCATAACTAAAGTCTAAAGATCACTTGAAGAGTCGAGAGATAGACACACCTCTTCAAT
* * * *
64449463 TTGAGTCCCGGATAAGTTCAATATTATTAAGC-TTCTTGGGAATTCTGGAAATTTGACAATTGGG
66 TTGAGTCCCAGATAAGTTCAATATTATTAAGCTTTC-TAGGAATTCTAGAAATTCGACAATTGGG
* *
64449527 TAATCACTAA-AGTTCAGAT
130 CAAGCACTAAGA-TTCAGAT
64449546 TACGAAAAGA
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
173 4 0.03
174 119 0.97
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (174 bp):
GAGCCACTCATAACTAAAGTCTAAAGATCACTTGAAGAGTCGAGAGATAGACACACCTCTTCAAT
TTGAGTCCCAGATAAGTTCAATATTATTAAGCTTTCTAGGAATTCTAGAAATTCGACAATTGGGC
AAGCACTAAGATTCAGATCACAAGGGGAATATTTTTTTACTATC
Found at i:64456504 original size:30 final size:30
Alignment explanation
Indices: 64456443--64456517 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 30
64456433 CAACCATGCT
* * *
64456443 ATGGCGAGCACACAT-GGCAAATAGCGTAA
1 ATGGCGAACACACATGGGCAAACAGCGCAA
64456472 ATGGCGAACACACATGGGCAAACAGTC-CAA
1 ATGGCGAACACACATGGGCAAACAG-CGCAA
*
64456502 ATGGCGAACACTCATG
1 ATGGCGAACACACATG
64456518 ACGGATAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 14 0.35
30 25 0.62
31 1 0.03
ACGTcount: A:0.37, C:0.24, G:0.25, T:0.13
Consensus pattern (30 bp):
ATGGCGAACACACATGGGCAAACAGCGCAA
Found at i:64458312 original size:17 final size:18
Alignment explanation
Indices: 64458278--64458315 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
64458268 ATTTGGTCCT
64458278 AAATCTAAAAATAGAAAA
1 AAATCTAAAAATAGAAAA
* *
64458296 AAAT-TAAAATTATAAAA
1 AAATCTAAAAATAGAAAA
64458313 AAA
1 AAA
64458316 ATATTTCCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
AAATCTAAAAATAGAAAA
Found at i:64466067 original size:21 final size:22
Alignment explanation
Indices: 64466043--64466086 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
64466033 TTATTTCGAA
64466043 TATATAACATAGGTTTA-GACT
1 TATATAACATAGGTTTACGACT
*
64466064 TATATAGCATAGGTTTACGACT
1 TATATAACATAGGTTTACGACT
64466086 T
1 T
64466087 TCATAAGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
TATATAACATAGGTTTACGACT
Found at i:64471938 original size:17 final size:17
Alignment explanation
Indices: 64471904--64471941 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
64471894 CTAGATGTGA
*
64471904 TTTTTTTTTAAAGGTAT
1 TTTTTTTTTAAAGATAT
64471921 TTTTATTTTTAAA-ATAT
1 TTTT-TTTTTAAAGATAT
64471938 TTTT
1 TTTT
64471942 CGACATGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTTTTTTAAAGATAT
Found at i:64475263 original size:33 final size:32
Alignment explanation
Indices: 64475191--64475283 Score: 100
Period size: 31 Copynumber: 2.9 Consensus size: 32
64475181 ACAAGCTCTA
*
64475191 TCTGTGTTTATTGTCGC-GATGGACTATCTATT
1 TCTGTGTTTATTGTCCCAG-TGGACTATCTATT
* * *
64475223 T-TGTGTTTACTGTCCCAGTGAACTATCTTTGT
1 TCTGTGTTTATTGTCCCAGTGGACTATCTAT-T
* *
64475255 TCTGTGTTTATTGTCTCAGCGGACTATCT
1 TCTGTGTTTATTGTCCCAGTGGACTATCT
64475284 CTGTGGATGC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
31 23 0.46
32 4 0.08
33 23 0.46
ACGTcount: A:0.15, C:0.18, G:0.20, T:0.46
Consensus pattern (32 bp):
TCTGTGTTTATTGTCCCAGTGGACTATCTATT
Found at i:64488039 original size:20 final size:21
Alignment explanation
Indices: 64488016--64488062 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
64488006 AAATATATAA
64488016 ATTTTGAAATTTTT-ATAAA-T
1 ATTTTGAAATTTTTGA-AAATT
64488036 ATTTTG-AATTTTTGAAAATT
1 ATTTTGAAATTTTTGAAAATT
64488056 ATTTTGA
1 ATTTTGA
64488063 TTTCTTGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTTTGAAATTTTTGAAAATT
Found at i:64491548 original size:16 final size:16
Alignment explanation
Indices: 64491527--64491569 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
64491517 CAAATTTAAG
64491527 TCATTT-TAAGTTCAAA
1 TCATTTCTAA-TTCAAA
64491543 TCATTTCTAATTCAAA
1 TCATTTCTAATTCAAA
*
64491559 TCATCTCTAAT
1 TCATTTCTAAT
64491570 ATGACCAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (16 bp):
TCATTTCTAATTCAAA
Found at i:64491677 original size:2 final size:2
Alignment explanation
Indices: 64491670--64491702 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
64491660 ATAAGAACAA
64491670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
64491703 ATGGGGATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:64513407 original size:6 final size:6
Alignment explanation
Indices: 64513396--64513427 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
64513386 ACCCTATACC
64513396 CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA CC
1 CCTAAA CCTAAA CCTAAA CCTAAA CCTAAA CC
64513428 CTATAAGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.47, C:0.38, G:0.00, T:0.16
Consensus pattern (6 bp):
CCTAAA
Found at i:64532972 original size:17 final size:17
Alignment explanation
Indices: 64532936--64532968 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
64532926 AAGAATTTTT
64532936 TAAGTAAAAATATAATA
1 TAAGTAAAAATATAATA
64532953 TAAGT-AAAATATAATA
1 TAAGTAAAAATATAATA
64532969 ATAATTACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (17 bp):
TAAGTAAAAATATAATA
Found at i:64540180 original size:18 final size:19
Alignment explanation
Indices: 64540157--64540214 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
64540147 TCATAATTAG
* *
64540157 TTTAATTTTTTATTTCAA-
1 TTTAATTTTTTAATTAAAT
*
64540175 TTTAATATTTTAATTAAAT
1 TTTAATTTTTTAATTAAAT
*
64540194 TTTAATTTAATTAA-TAAAT
1 TTTAATTT-TTTAATTAAAT
64540213 TT
1 TT
64540215 ACTGATTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 15 0.45
19 14 0.42
20 4 0.12
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATTTTTTAATTAAAT
Found at i:64546577 original size:22 final size:22
Alignment explanation
Indices: 64546552--64546593 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
64546542 GATTGATACT
*
64546552 ATTAGAATACCTTAAATATTTA
1 ATTAAAATACCTTAAATATTTA
**
64546574 ATTAAAATATTTTAAATATT
1 ATTAAAATACCTTAAATATT
64546594 GACATCAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTAAAATACCTTAAATATTTA
Found at i:64549645 original size:6 final size:6
Alignment explanation
Indices: 64549634--64549659 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
64549624 CAGTTGAAAT
64549634 AAAAGA AAAAGA AAAAGA AAAAGA AA
1 AAAAGA AAAAGA AAAAGA AAAAGA AA
64549660 CAACAATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:64552489 original size:11 final size:11
Alignment explanation
Indices: 64552473--64552508 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
64552463 ATTTCTCAAA
64552473 TTTAATTAATT
1 TTTAATTAATT
64552484 TTTAATTAA-T
1 TTTAATTAATT
64552494 TTTAATTTAATT
1 TTTAA-TTAATT
64552506 TTT
1 TTT
64552509 GAAATGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.26
11 13 0.57
12 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTAATTAATT
Found at i:64567960 original size:19 final size:19
Alignment explanation
Indices: 64567919--64567961 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
64567909 ATTGAACCGA
*
64567919 ATTTA-AAATATTTTAATT
1 ATTTATAAATATTTTAATG
*
64567937 TTTTATAAATATTTTAATG
1 ATTTATAAATATTTTAATG
64567956 ATTTAT
1 ATTTAT
64567962 CTAATCAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
ATTTATAAATATTTTAATG
Found at i:64578136 original size:16 final size:17
Alignment explanation
Indices: 64578115--64578148 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
64578105 GTGTAATTTT
*
64578115 ATTTTTATTAA-TTTAA
1 ATTTTTATAAACTTTAA
64578131 ATTTTTATAAACTTTAA
1 ATTTTTATAAACTTTAA
64578148 A
1 A
64578149 GGAGTCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTTATAAACTTTAA
Found at i:64581728 original size:31 final size:31
Alignment explanation
Indices: 64581692--64581757 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
64581682 TTATAAAATG
64581692 GTCATTAAATTATTAGAAAGT-TTTCATTTAA
1 GTCATTAAATTATTAGAAAGTATTT-ATTTAA
* *
64581723 GTCATTGAATTATTCGAAAGTATTTATTTAA
1 GTCATTAAATTATTAGAAAGTATTTATTTAA
64581754 GTCA
1 GTCA
64581758 ATGGGCTGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 29 0.91
32 3 0.09
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (31 bp):
GTCATTAAATTATTAGAAAGTATTTATTTAA
Found at i:64591175 original size:24 final size:26
Alignment explanation
Indices: 64591148--64591196 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
64591138 TTTGCGAGGA
*
64591148 AAAT-GCAACTAAAA-AATTAAAAAT
1 AAATAGCAACAAAAATAATTAAAAAT
64591172 AAATGAGCAACAAAAATAATTAAAA
1 AAAT-AGCAACAAAAATAATTAAAA
64591197 TTTCAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
26 9 0.43
27 8 0.38
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.18
Consensus pattern (26 bp):
AAATAGCAACAAAAATAATTAAAAAT
Found at i:64591827 original size:24 final size:21
Alignment explanation
Indices: 64591766--64591814 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
64591756 AGTTAGACAA
*
64591766 AAAAAGAGAAGCAACTTGGAC
1 AAAAAGAGAAGTAACTTGGAC
*
64591787 AAAAAGAGAAGTAACTTGGAT
1 AAAAAGAGAAGTAACTTGGAC
64591808 AAAAAGA
1 AAAAAGA
64591815 AACGAAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.12
Consensus pattern (21 bp):
AAAAAGAGAAGTAACTTGGAC
Found at i:64597355 original size:21 final size:21
Alignment explanation
Indices: 64597326--64597365 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
64597316 CACATTTTGA
*
64597326 TTGTTTTGTTCCTATGTAACC
1 TTGTCTTGTTCCTATGTAACC
*
64597347 TTGTCTTGTTCCTTTGTAA
1 TTGTCTTGTTCCTATGTAA
64597366 TTTGATAGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.55
Consensus pattern (21 bp):
TTGTCTTGTTCCTATGTAACC
Found at i:64607150 original size:112 final size:112
Alignment explanation
Indices: 64606948--64607176 Score: 440
Period size: 112 Copynumber: 2.0 Consensus size: 112
64606938 AATCCATAAA
*
64606948 AACAAGCATTCAGCTTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
1 AACAGGCATTCAGCTTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
64607013 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
66 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
*
64607060 AACAGGCATTCAGCTTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATGC
1 AACAGGCATTCAGCTTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
64607125 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
66 ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
64607172 AACAG
1 AACAG
64607177 TTCAATCACC
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (112 bp):
AACAGGCATTCAGCTTGTCAAAATCAGTATATGGTCACCTAATCAATACCTACTACCACTAATAC
ATTGAAACTTGGTAAACCAAGCTTGTACACATAAACAAAGCTGAGTT
Found at i:64613744 original size:43 final size:43
Alignment explanation
Indices: 64613683--64613769 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
64613673 TATCTACGCT
64613683 TCAACTTGCCGTAAACGATTTGGGACATGGGAGAGAAGGTGAC
1 TCAACTTGCCGTAAACGATTTGGGACATGGGAGAGAAGGTGAC
64613726 TCAACTTGCCGTAAACGATTTGGGACATGGGAGAGAAGGTGAC
1 TCAACTTGCCGTAAACGATTTGGGACATGGGAGAGAAGGTGAC
64613769 T
1 T
64613770 TGAACTTTCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (43 bp):
TCAACTTGCCGTAAACGATTTGGGACATGGGAGAGAAGGTGAC
Found at i:64617309 original size:21 final size:21
Alignment explanation
Indices: 64617283--64617323 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
64617273 ATCTGCTCAA
* *
64617283 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
64617304 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
64617324 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:64627656 original size:65 final size:63
Alignment explanation
Indices: 64627587--64627710 Score: 140
Period size: 63 Copynumber: 1.9 Consensus size: 63
64627577 TTTTATAATT
* * *
64627587 TATTTATATATATATACGCATACTTATATATTTTTTATATTATACATAATTTATATATATATACA
1 TATTTATATATATATACACATACTTAT-T-TTTTTTAAAATATACATAATTTATATATATATACA
* * ** * **
64627652 TATTTTTATTTATATGTACATACTTATTTTTTTTAAAATCTTTATAATTTATATATATA
1 TATTTATATATATATACACATACTTATTTTTTTTAAAATATACATAATTTATATATATA
64627711 CATAAATATG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
63 26 0.53
64 1 0.02
65 22 0.45
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (63 bp):
TATTTATATATATATACACATACTTATTTTTTTTAAAATATACATAATTTATATATATATACA
Found at i:64627659 original size:20 final size:20
Alignment explanation
Indices: 64627614--64627673 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
64627604 GCATACTTAT
64627614 ATATTTTT-TATAT-TATAC
1 ATATTTTTATATATATATAC
*
64627632 ATA-ATTTATATATATATAC
1 ATATTTTTATATATATATAC
* *
64627651 ATATTTTTATTTATATGTAC
1 ATATTTTTATATATATATAC
64627671 ATA
1 ATA
64627674 CTTATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.09
18 8 0.23
19 8 0.23
20 16 0.46
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (20 bp):
ATATTTTTATATATATATAC
Found at i:64627662 original size:24 final size:24
Alignment explanation
Indices: 64627635--64627686 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
64627625 ATTATACATA
*
64627635 ATTTATATATATATACATATTTTT
1 ATTTATATATACATACATATTTTT
* *
64627659 ATTTATATGTACATACTTATTTTT
1 ATTTATATATACATACATATTTTT
64627683 -TTTA
1 ATTTA
64627687 AAATCTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTATATATACATACATATTTTT
Found at i:64631469 original size:16 final size:15
Alignment explanation
Indices: 64631433--64631470 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
64631423 AAGATATTTT
*
64631433 AACAAATGATATTAA
1 AACAAATGAAATTAA
64631448 AACAAATGAAATTAA
1 AACAAATGAAATTAA
64631463 CAACAAAT
1 -AACAAAT
64631471 ACAGTGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (15 bp):
AACAAATGAAATTAA
Found at i:64651131 original size:22 final size:22
Alignment explanation
Indices: 64651091--64651132 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
64651081 ATTAAATTAA
*
64651091 AAAATAAAAAGAAACGAATAGT
1 AAAATAAAAAGAAAAGAATAGT
* *
64651113 AAAATAATAATAAAAGAATA
1 AAAATAAAAAGAAAAGAATA
64651133 ATTTATTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (22 bp):
AAAATAAAAAGAAAAGAATAGT
Found at i:64651836 original size:15 final size:16
Alignment explanation
Indices: 64651818--64651855 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
64651808 AAGATATTTT
64651818 AACAAATGAAATTAA-
1 AACAAATGAAATTAAC
*
64651833 AACAAATGAATTTAAC
1 AACAAATGAAATTAAC
64651849 AACAAAT
1 AACAAAT
64651856 ACAGTGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.63, C:0.11, G:0.05, T:0.21
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:64665803 original size:16 final size:16
Alignment explanation
Indices: 64665782--64665817 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
64665772 AAGATATTTT
64665782 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
64665798 AACAAATGAAATTAAC
1 AACAAATGAAATTAAC
64665814 AACA
1 AACA
64665818 GATACGGTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.64, C:0.14, G:0.06, T:0.17
Consensus pattern (16 bp):
AACAAATGAAATTAAC
Found at i:64679066 original size:18 final size:18
Alignment explanation
Indices: 64679043--64679077 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
64679033 ATATTTTTTA
*
64679043 AATTCAGATATCAAAATG
1 AATTCAGATACCAAAATG
64679061 AATTCAGATACCAAAAT
1 AATTCAGATACCAAAAT
64679078 AAACCTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (18 bp):
AATTCAGATACCAAAATG
Found at i:64685193 original size:24 final size:24
Alignment explanation
Indices: 64685166--64685217 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
64685156 TTAGTAAGTC
*
64685166 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
64685190 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
64685214 AAAT
1 AAAT
64685218 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:64688112 original size:20 final size:19
Alignment explanation
Indices: 64688087--64688126 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
64688077 GAACACCTTT
64688087 TATATATA-GT-TGTATAGA
1 TATATATATGTGTGTATA-A
64688105 TATATATATGTGTGTATAA
1 TATATATATGTGTGTATAA
64688124 TAT
1 TAT
64688127 TAGTATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.40
19 6 0.30
20 6 0.30
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (19 bp):
TATATATATGTGTGTATAA
Found at i:64700231 original size:57 final size:58
Alignment explanation
Indices: 64700134--64700244 Score: 188
Period size: 57 Copynumber: 1.9 Consensus size: 58
64700124 TTTTTTTTCT
64700134 TCTTATCCATTTTAAAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAATGTTG
1 TCTTATCCATTTTAAAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAATGTTG
* * *
64700192 TCTT-TCCGTTTTATAATTTATATTCGAGATTTGTAGTTATTCCTCTCAACAAT
1 TCTTATCCATTTTAAAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAAT
64700245 ACTGTCTTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
57 46 0.92
58 4 0.08
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (58 bp):
TCTTATCCATTTTAAAATTTATATTCGAGATTTATAGTTATTCCTCTCAACAATGTTG
Found at i:64710949 original size:21 final size:21
Alignment explanation
Indices: 64710917--64710957 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
64710907 GAACAATTGG
64710917 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
64710938 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
64710958 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:64715683 original size:57 final size:58
Alignment explanation
Indices: 64715585--64715695 Score: 179
Period size: 57 Copynumber: 1.9 Consensus size: 58
64715575 TTTTTTTTCT
* *
64715585 TCTTATCCATTTTAAAATTTATATTCGGGATTTATAGTTATTCCTCTCAACAATATTA
1 TCTTATCCATTTTAAAATTTATATTCGAGATTTATAATTATTCCTCTCAACAATATTA
* *
64715643 TCTT-TCCATTTTATAATTTATATTCGAGATTTGTAATTATTCCTCTCAACAAT
1 TCTTATCCATTTTAAAATTTATATTCGAGATTTATAATTATTCCTCTCAACAAT
64715696 GTTGTCTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 45 0.92
58 4 0.08
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.48
Consensus pattern (58 bp):
TCTTATCCATTTTAAAATTTATATTCGAGATTTATAATTATTCCTCTCAACAATATTA
Found at i:64721460 original size:16 final size:16
Alignment explanation
Indices: 64721427--64721460 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
64721417 AGGGTATGTT
* *
64721427 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
64721443 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
64721459 AA
1 AA
64721461 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:64724285 original size:21 final size:21
Alignment explanation
Indices: 64724259--64724299 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
64724249 AGACGAGCAA
* *
64724259 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
64724280 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
64724300 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:64726237 original size:16 final size:16
Alignment explanation
Indices: 64726204--64726237 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
64726194 GGAGATTGTT
* *
64726204 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
64726220 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
64726236 AA
1 AA
64726238 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:64729568 original size:9 final size:8
Alignment explanation
Indices: 64729546--64729570 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
64729536 TAAGTTGTAT
64729546 TTAAAAAA
1 TTAAAAAA
64729554 TTAAAAAA
1 TTAAAAAA
64729562 TTAAAAAA
1 TTAAAAAA
64729570 T
1 T
64729571 ATATAAGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
TTAAAAAA
Found at i:64731881 original size:7 final size:7
Alignment explanation
Indices: 64731869--64731893 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
64731859 GGGGTCAAAA
64731869 TTAAATT
1 TTAAATT
64731876 TTAAATT
1 TTAAATT
64731883 TTAAATT
1 TTAAATT
64731890 TTAA
1 TTAA
64731894 TAGCTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTAAATT
Found at i:64738219 original size:3 final size:3
Alignment explanation
Indices: 64738211--64738249 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
64738201 ACAAATTCTA
*
64738211 TAT TAT TAT TGT TAT TGCAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T--AT TAT TAT TAT TAT TAT TAT T
64738250 GCTTTTATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 29 0.91
5 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:64738279 original size:22 final size:23
Alignment explanation
Indices: 64738254--64738299 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
64738244 ATTATTGCTT
64738254 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
64738276 TTATATATTTTTACATATACTTA
1 TTATAGATATATACATATACTTA
64738299 T
1 T
64738300 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:64738307 original size:22 final size:22
Alignment explanation
Indices: 64738265--64738309 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
64738255 TATAGATATA
* *
64738265 TACATATATTATTATATATTTT
1 TACATATATTATTACACATTTT
64738287 TACATATACTTA-TACACATTTT
1 TACATATA-TTATTACACATTTT
64738309 T
1 T
64738310 GTAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TACATATATTATTACACATTTT
Found at i:64750974 original size:46 final size:43
Alignment explanation
Indices: 64750892--64751271 Score: 228
Period size: 44 Copynumber: 8.8 Consensus size: 43
64750882 ATTATACAGG
* * *
64750892 TCTTATCTCCCTGAGATTACAGTAGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-A--TCAGA
* *
64750938 TCTTATCTCCCTGAGATTACAGCGGAGCGGATCAAAGAT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATCAG--A
* * * * *
64750982 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG----GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATCAGA
* ** * *
64751021 TCTTATCTCTCTGA-AGTTACAGCAGAGAAGATC--ACATCAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGATCA-GA
** *
64751063 -CTTATCTCCCTGAGATTACAGTGGAATAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG-A--TCAGA
* ** *
64751108 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA-GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAG--ATCAGA
* * * *
64751152 TCTTATCTCCCTGAGATTACAGCGGATCAGATCGAAGA-CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATCA-GA
* * * *
64751195 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA-ATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCAAAGAT-CA-GA
* * *
64751239 TCTTATCTCTCTGAGATTACAGTAGAGTAGATC
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATC
64751272 GCATCAAGTC
Statistics
Matches: 257, Mismatches: 56, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.09
41 25 0.10
42 9 0.04
43 31 0.12
44 97 0.38
45 4 0.02
46 65 0.25
47 1 0.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATCAAAGATCAGA
Found at i:64752883 original size:3 final size:3
Alignment explanation
Indices: 64752875--64752913 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
64752865 ACAAATTCTA
*
64752875 TAT TAT TAT TGT TAT TGCAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T--AT TAT TAT TAT TAT TAT TAT T
64752914 GCTTTTATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 29 0.91
5 3 0.09
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:64752943 original size:22 final size:23
Alignment explanation
Indices: 64752918--64752963 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
64752908 ATTATTGCTT
64752918 TTATAGATATATACATATA-TTA
1 TTATAGATATATACATATACTTA
* * *
64752940 TTATATATTTTTACATATACTTA
1 TTATAGATATATACATATACTTA
64752963 T
1 T
64752964 ACACATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATAGATATATACATATACTTA
Found at i:64752971 original size:22 final size:22
Alignment explanation
Indices: 64752929--64752973 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
64752919 TATAGATATA
* *
64752929 TACATATATTATTATATATTTT
1 TACATATATTATTACACATTTT
64752951 TACATATACTTA-TACACATTTT
1 TACATATA-TTATTACACATTTT
64752973 T
1 T
64752974 TGTAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TACATATATTATTACACATTTT
Found at i:64757449 original size:36 final size:36
Alignment explanation
Indices: 64757409--64757514 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
64757399 TGTAAAAAAC
64757409 GGTACTACGAATGAAGTGGTTTCATCTGATGTTGAT
1 GGTACTACGAATGAAGTGGTTTCATCTGATGTTGAT
* * *
64757445 GGTACAACAAATGAAGTGATTTCATCTGATGTTGAT
1 GGTACTACGAATGAAGTGGTTTCATCTGATGTTGAT
64757481 GGTACTACGAATGAAGTGGTTTCATCTGATGTTG
1 GGTACTACGAATGAAGTGGTTTCATCTGATGTTG
64757515 GTGGGGGTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (36 bp):
GGTACTACGAATGAAGTGGTTTCATCTGATGTTGAT
Found at i:64757725 original size:285 final size:285
Alignment explanation
Indices: 64757210--64757731 Score: 814
Period size: 285 Copynumber: 1.8 Consensus size: 285
64757200 CTACAAACAC
64757210 AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCCTGTTG
1 AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCCTGTTG
* * *
64757275 GGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTGGTTATGATTCTCAAAAG
66 AGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCAAAAG
* ** *
64757340 GATTCTTTTGATAATATTTCTGTGGGAAGTGAAGAGTCGCCTGCTAAAGAACCTCAAGATGTAAA
131 GATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGGCTAAAGAACCTCAAGATATAAA
* * *
64757405 AAACGGTACTACGAATGAAGTGGTTTCATCTGATGTTGATGGTACAACAAATGAAGTGATTTCAT
196 AAACGATAATACGAATGAAGTGGTTTCACCTGATGTTGATGGTACAACAAATGAAGTGATTTCAT
64757470 CTGATGTTGATGGTACTACGAATGA
261 CTGATGTTGATGGTACTACGAATGA
* * **
64757495 AGTGGTTTCATCTGATGTTGGTGGGGGTAATAGGATGACTTCAGACATC-AGAACTGTGCCTGTT
1 AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGAC-TCAAGAACCATGCCTGTT
*
64757559 GAGACTGATGACTT-GAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCCAA
65 GAGACTGATGA-TTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCAAA
* * * *
64757623 AGGATTCTTTTGATACTATTTCTGTGAGAAGTGAAGAGTTGCAGGCTAAGGAACCTCAGGATATA
129 AGGATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGGCTAAAGAACCTCAAGATATA
* * *
64757688 AAAGATGATAATACGAATGATGTGGTTTCACCTGATGTTGATGG
194 AAAAACGATAATACGAATGAAGTGGTTTCACCTGATGTTGATGG
64757732 GGGTAATAGG
Statistics
Matches: 213, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
285 209 0.98
286 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (285 bp):
AGTGGTTGCATCTGATGTTGGTGGGGGTAATAAGATGACTTCAGACTCAAGAACCATGCCTGTTG
AGACTGATGATTCGAGTACAGAGAAACAGGAATCTCAAGGATGCTCTAGCTATGATTCTCAAAAG
GATTCTTTTGATAATATTTCTGTGAGAAGTGAAGAGTCGCAGGCTAAAGAACCTCAAGATATAAA
AAACGATAATACGAATGAAGTGGTTTCACCTGATGTTGATGGTACAACAAATGAAGTGATTTCAT
CTGATGTTGATGGTACTACGAATGA
Found at i:64759669 original size:14 final size:13
Alignment explanation
Indices: 64759653--64759678 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64759643 TTGTTTTTAT
64759653 TTTTTTTTTCACC
1 TTTTTTTTTCACC
64759666 TTTTTTTTTCACC
1 TTTTTTTTTCACC
64759679 AATTCCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTTTTTCACC
Found at i:64761537 original size:30 final size:31
Alignment explanation
Indices: 64761502--64761559 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
64761492 TGTTTTTCTT
64761502 TTAATTTGTTAAATTTTT-TAAA-TATTTTTA
1 TTAATTT-TTAAATTTTTATAAATTATTTTTA
*
64761532 TTAATTTTTAAGTTTTTATAAATTATTT
1 TTAATTTTTAAATTTTTATAAATTATTT
64761560 ATAAACTGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 9 0.36
30 11 0.44
31 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (31 bp):
TTAATTTTTAAATTTTTATAAATTATTTTTA
Found at i:64773427 original size:19 final size:20
Alignment explanation
Indices: 64773385--64773427 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
64773375 ATTAAATAAG
* *
64773385 ATTTGCTTTGCCATTATTGT
1 ATTTGCTTTGACATTATAGT
64773405 ATTTGCTTTGACATT-TAGT
1 ATTTGCTTTGACATTATAGT
64773424 ATTT
1 ATTT
64773428 ATACAATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.19, C:0.12, G:0.14, T:0.56
Consensus pattern (20 bp):
ATTTGCTTTGACATTATAGT
Found at i:64775398 original size:16 final size:18
Alignment explanation
Indices: 64775379--64775415 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
64775369 TTTTTTGTGT
64775379 TATAAAT-T-ACATAATA
1 TATAAATATAACATAATA
*
64775395 TATAAATATAATATAATA
1 TATAAATATAACATAATA
64775413 TAT
1 TAT
64775416 CAGAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
TATAAATATAACATAATA
Found at i:64778337 original size:30 final size:30
Alignment explanation
Indices: 64778258--64778376 Score: 100
Period size: 30 Copynumber: 3.8 Consensus size: 30
64778248 CTAACACCCA
*
64778258 TTTCAAAAAAATTAAAAGGTTTAATTGAATT
1 TTTCAAAAAAATTAAGAGGTTTAA-TGAATT
*
64778289 TTT-ATTAAAAAAAT-AGAGGTTTAATGAATT
1 TTTCA--AAAAAATTAAGAGGTTTAATGAATT
* * *
64778319 TTTCAAAAAATTTAAGAGGATTAATAAAATCT
1 TTTCAAAAAAATTAAGAGGTTTAAT-GAAT-T
*
64778351 TTTGAAAAAGAATT-AGATGGTTTAAT
1 TTTCAAAAA-AATTAAGA-GGTTTAAT
64778377 TAAAATTTTT
Statistics
Matches: 71, Mismatches: 9, Indels: 14
0.76 0.10 0.15
Matches are distributed among these distances:
29 6 0.08
30 20 0.28
31 16 0.23
32 19 0.27
33 10 0.14
ACGTcount: A:0.47, C:0.03, G:0.13, T:0.38
Consensus pattern (30 bp):
TTTCAAAAAAATTAAGAGGTTTAATGAATT
Found at i:64785521 original size:44 final size:43
Alignment explanation
Indices: 64785422--64785523 Score: 102
Period size: 44 Copynumber: 2.3 Consensus size: 43
64785412 AATCAAGCCT
** * *
64785422 AATATTATTATATTAATAATAAGTTTTTAATTTTAATTTTTTA
1 AATATTAAAATATTAATAATAAGTTTATAATTTTAATTTATTA
64785465 AATATTTAAAATATTAATAGATAA-TATTATAATTTTTAATATTATTA
1 AATA-TTAAAATATTAATA-ATAAGT-TTATAA-TTTTAAT-TTATTA
64785512 AATA-T-AAATATT
1 AATATTAAAATATT
64785524 TAATTATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
43 4 0.08
44 20 0.40
45 10 0.20
46 7 0.14
47 9 0.18
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (43 bp):
AATATTAAAATATTAATAATAAGTTTATAATTTTAATTTATTA
Found at i:64785537 original size:30 final size:30
Alignment explanation
Indices: 64785461--64785538 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
64785451 ATTTTAATTT
* * *
64785461 TTTAAATATTTAAAATATTAATAGATAATA
1 TTTAATTATTTATATTATTAATAGATAATA
*
64785491 TTATAATT-TTTAATATTATTAA-ATATAAATA
1 TT-TAATTATTT-ATATTATTAATAGAT-AATA
64785522 TTTAATTATTTATATTA
1 TTTAATTATTTATATTA
64785539 AATAATATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
30 19 0.47
31 21 0.52
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TTTAATTATTTATATTATTAATAGATAATA
Found at i:64785546 original size:30 final size:31
Alignment explanation
Indices: 64785487--64785548 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 31
64785477 ATTAATAGAT
*
64785487 AATATTATAATTTTTAATATTATTAAATATA
1 AATATTATAATTTTTAATATTAATAAATATA
64785518 AATATT-TAATTATTT-ATATTAA-ATAATATA
1 AATATTATAATT-TTTAATATTAATA-AATATA
64785548 A
1 A
64785549 GAAAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
29 1 0.04
30 18 0.64
31 9 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (31 bp):
AATATTATAATTTTTAATATTAATAAATATA
Found at i:64787914 original size:11 final size:11
Alignment explanation
Indices: 64787884--64787926 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
64787874 ACACCAATTT
*
64787884 TTTTAAAAAAA
1 TTTTAAAAATA
*
64787895 TTTAAAAAAGTA
1 TTTTAAAAA-TA
64787907 TTTTAAAAATA
1 TTTTAAAAATA
64787918 TTTTAAAAA
1 TTTTAAAAA
64787927 ATAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:64787928 original size:12 final size:12
Alignment explanation
Indices: 64787884--64787929 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
64787874 ACACCAATTT
64787884 TTTTAAAAAA-A
1 TTTTAAAAAATA
64787895 -TTTAAAAAAGTA
1 TTTTAAAAAA-TA
64787907 TTTT-AAAAATA
1 TTTTAAAAAATA
64787918 TTTTAAAAAATA
1 TTTTAAAAAATA
64787930 AAAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.29
11 6 0.19
12 13 0.42
13 3 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
TTTTAAAAAATA
Found at i:64791827 original size:12 final size:14
Alignment explanation
Indices: 64791798--64791834 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
64791788 TCAAGATAGG
64791798 AAAATTGACACTAA
1 AAAATTGACACTAA
*
64791812 AAAATTGACATTAA
1 AAAATTGACACTAA
64791826 AAAATTGAC
1 AAAATTGAC
64791835 CTTTCTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.24
Consensus pattern (14 bp):
AAAATTGACACTAA
Found at i:64792740 original size:18 final size:19
Alignment explanation
Indices: 64792703--64792743 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
64792693 TGGGAGACAG
64792703 AAATGCCAGAAATAAAAAT
1 AAATGCCAGAAATAAAAAT
* *
64792722 AAATGCCTGGAAT-AAAAT
1 AAATGCCAGAAATAAAAAT
64792740 AAAT
1 AAAT
64792744 TGAGGTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.59, C:0.10, G:0.12, T:0.20
Consensus pattern (19 bp):
AAATGCCAGAAATAAAAAT
Found at i:64798444 original size:21 final size:23
Alignment explanation
Indices: 64798420--64798466 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
64798410 ACACAATTAG
* *
64798420 ATATT-ATAATTTTTAAAAAT-A
1 ATATTAATAATTATAAAAAATCA
64798441 ATATTAATAATTATAAAAAATCA
1 ATATTAATAATTATAAAAAATCA
64798464 ATA
1 ATA
64798467 ATACCTGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 13 0.59
23 4 0.18
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATTAATAATTATAAAAAATCA
Found at i:64800643 original size:16 final size:17
Alignment explanation
Indices: 64800622--64800653 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
64800612 TAATAATAAT
64800622 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
64800638 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
64800654 GCTTACCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:64801399 original size:21 final size:22
Alignment explanation
Indices: 64801365--64801405 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
64801355 TATTAGTTAA
64801365 TAATAATAACAATATATAATAT
1 TAATAATAACAATATATAATAT
* *
64801387 TAAT-ATAATAATATTTAAT
1 TAATAATAACAATATATAAT
64801406 TCACAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATAATAACAATATATAATAT
Found at i:64801568 original size:30 final size:27
Alignment explanation
Indices: 64801532--64801596 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
64801522 TTTCCTATAA
*
64801532 TATAATATCTTAACTTTAATTAATATAATT
1 TATAATATCTTAA--TTAAATAATAT-ATT
* *
64801562 TATAATATTTTAATTAAATAATATTTT
1 TATAATATCTTAATTAAATAATATATT
64801589 TATAATAT
1 TATAATAT
64801597 AATTCAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 10 0.31
30 12 0.38
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (27 bp):
TATAATATCTTAATTAAATAATATATT
Found at i:64801598 original size:16 final size:17
Alignment explanation
Indices: 64801562--64801599 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
64801552 TAATATAATT
64801562 TATAATATTTTAATTAA
1 TATAATATTTTAATTAA
*
64801579 -ATAATATTTTTA-TAA
1 TATAATATTTTAATTAA
64801594 TATAAT
1 TATAAT
64801600 TCAAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATAATATTTTAATTAA
Found at i:64806594 original size:12 final size:12
Alignment explanation
Indices: 64806577--64806604 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
64806567 AATTGAATCT
64806577 AAGGCCATGGTG
1 AAGGCCATGGTG
64806589 AAGGCCATGGTG
1 AAGGCCATGGTG
64806601 AAGG
1 AAGG
64806605 GGAAGGTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.43, T:0.14
Consensus pattern (12 bp):
AAGGCCATGGTG
Found at i:64808291 original size:42 final size:42
Alignment explanation
Indices: 64808244--64808323 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
64808234 AAAACACATC
*
64808244 ATCAATAAATTTGTAAATAATT-AGTTAAATTCTATTATGAGT
1 ATCAATAAATTAGTAAATAATTGA-TTAAATTCTATTATGAGT
64808286 ATCAATAAATTAGTAAATAATTGATTAAATTCTATTAT
1 ATCAATAAATTAGTAAATAATTGATTAAATTCTATTAT
64808324 TATTATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.42
Consensus pattern (42 bp):
ATCAATAAATTAGTAAATAATTGATTAAATTCTATTATGAGT
Found at i:64809450 original size:22 final size:23
Alignment explanation
Indices: 64809425--64809468 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
64809415 ATAGTAAGGA
64809425 TCGAAATTTAA-TTATAATTTTT
1 TCGAAATTTAATTTATAATTTTT
**
64809447 TCGAGTTTTAATTTATAATTTT
1 TCGAAATTTAATTTATAATTTT
64809469 ATATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.57
Consensus pattern (23 bp):
TCGAAATTTAATTTATAATTTTT
Found at i:64822555 original size:35 final size:36
Alignment explanation
Indices: 64822504--64822572 Score: 122
Period size: 35 Copynumber: 1.9 Consensus size: 36
64822494 ATATACATAC
*
64822504 ATATATGTATGTATGTGAACATGGATGAATGTGGAG
1 ATATATATATGTATGTGAACATGGATGAATGTGGAG
64822540 ATATATATAT-TATGTGAACATGGATGAATGTGG
1 ATATATATATGTATGTGAACATGGATGAATGTGG
64822573 GCACAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 23 0.72
36 9 0.28
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.35
Consensus pattern (36 bp):
ATATATATATGTATGTGAACATGGATGAATGTGGAG
Found at i:64829929 original size:7 final size:7
Alignment explanation
Indices: 64829919--64829954 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
64829909 AATCAAATAT
64829919 TAAAAGC
1 TAAAAGC
64829926 TAAAAGC
1 TAAAAGC
64829933 TAAAAGC
1 TAAAAGC
64829940 TAAAAGC
1 TAAAAGC
64829947 TAAAAGC
1 TAAAAGC
64829954 T
1 T
64829955 TATTTGAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.17
Consensus pattern (7 bp):
TAAAAGC
Found at i:64831975 original size:17 final size:18
Alignment explanation
Indices: 64831945--64831980 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
64831935 CACACAATAT
64831945 TTTTTTTCTTAATTTTTTA
1 TTTTTTTC-TAATTTTTTA
64831964 TTTTTTTC-AATTTTTTA
1 TTTTTTTCTAATTTTTTA
64831981 AAAATAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTCTAATTTTTTA
Found at i:64834181 original size:30 final size:30
Alignment explanation
Indices: 64834135--64834258 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
64834125 CTTTATTATG
*
64834135 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
64834166 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
64834196 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
64834226 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
64834256 CCA
1 CCA
64834259 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:64834190 original size:15 final size:15
Alignment explanation
Indices: 64834145--64834252 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
64834135 CCAATATCTC
64834145 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
64834160 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
64834175 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
64834190 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
64834205 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
64834220 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
64834235 GATACCCATATCTTT
1 GATACCCATATCTTT
64834250 GAT
1 GAT
64834253 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:64838867 original size:30 final size:30
Alignment explanation
Indices: 64838821--64838914 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
64838811 TTTTATTATG
*
64838821 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
64838852 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
64838882 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
64838912 CCA
1 CCA
64838915 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:64838876 original size:15 final size:15
Alignment explanation
Indices: 64838831--64838908 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
64838821 CCAATATCTC
64838831 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
64838846 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
64838861 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
64838876 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
64838891 GATACCCATATCTTT
1 GATACCCATATCTTT
64838906 GAT
1 GAT
64838909 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:64844529 original size:21 final size:21
Alignment explanation
Indices: 64844503--64844543 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
64844493 ATCTGCTCAA
* *
64844503 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
64844524 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
64844544 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:64859053 original size:16 final size:16
Alignment explanation
Indices: 64859028--64859058 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
64859018 ATTGTCTCTA
64859028 TTTTAGGATTTTTTAT
1 TTTTAGGATTTTTTAT
*
64859044 TTTTATGATTTTTTA
1 TTTTAGGATTTTTTA
64859059 ATAAATTTTA
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:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (16 bp):
TTTTAGGATTTTTTAT
Found at i:64859553 original size:31 final size:32
Alignment explanation
Indices: 64859495--64859558 Score: 78
Period size: 31 Copynumber: 2.0 Consensus size: 32
64859485 TATATTTAAA
* * *
64859495 GGTATTTAAACTTTACAATTTATACCT-ATTT
1 GGTATCTAAACTTGACAATTTAAACCTAATTT
64859526 GGTATCTAAACTTGA-AACTTTAAACCTAATTT
1 GGTATCTAAACTTGACAA-TTTAAACCTAATTT
64859558 G
1 G
64859559 ATTTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.07
31 21 0.75
32 5 0.18
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (32 bp):
GGTATCTAAACTTGACAATTTAAACCTAATTT
Found at i:64860071 original size:14 final size:14
Alignment explanation
Indices: 64860052--64860080 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
64860042 ATTTCAGGTC
64860052 GGGAGTATTACACA
1 GGGAGTATTACACA
64860066 GGGAGTATTACACA
1 GGGAGTATTACACA
64860080 G
1 G
64860081 CTTTCTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (14 bp):
GGGAGTATTACACA
Found at i:64860560 original size:33 final size:33
Alignment explanation
Indices: 64860488--64860560 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
64860478 ACCAGAACAA
*
64860488 CCTA-CAGATGCAACAGCACAAGTTATTCAAGC
1 CCTAGCAGACGCAACAGCACAAGTTATTCAAGC
* * *
64860520 CCCAGCAGACGCAACAGGAGAAGTTATTCAAAG-
1 CCTAGCAGACGCAACAGCACAAGTTATTC-AAGC
64860553 CCTAGCAG
1 CCTAGCAG
64860561 TCCTGCCGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 3 0.09
33 28 0.82
34 3 0.09
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (33 bp):
CCTAGCAGACGCAACAGCACAAGTTATTCAAGC
Found at i:64862651 original size:21 final size:22
Alignment explanation
Indices: 64862625--64862671 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
64862615 CTCTGCTCAA
*
64862625 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
64862646 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
64862668 ACTC
1 ACTC
64862672 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:64867911 original size:40 final size:40
Alignment explanation
Indices: 64867856--64867936 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
64867846 TTTAAGGGAG
64867856 ACTAAACCCCTACCAGCCCTTGACTCCGCCACTGATATAT
1 ACTAAACCCCTACCAGCCCTTGACTCCGCCACTGATATAT
*
64867896 ACTAAACCCCTACCAGCCCTTGACTCTGCCACTGATATAT
1 ACTAAACCCCTACCAGCCCTTGACTCCGCCACTGATATAT
64867936 A
1 A
64867937 AATAATCCTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.38, G:0.10, T:0.23
Consensus pattern (40 bp):
ACTAAACCCCTACCAGCCCTTGACTCCGCCACTGATATAT
Found at i:64882717 original size:42 final size:42
Alignment explanation
Indices: 64882666--64882763 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
64882656 GATCTTGGTA
* * * *
64882666 TCGCACACTTAGTGCCTGTTATTCGACATCGTCATTTT-CGTT
1 TCGCACACTTAGTGCCCGCTATTCAACATCATCATTTTAC-TT
64882708 TCGCACACTTAGTGCCCGCTATTCAACATCATCATTTTACTT
1 TCGCACACTTAGTGCCCGCTATTCAACATCATCATTTTACTT
*
64882750 TTGCACACTTAGTG
1 TCGCACACTTAGTG
64882764 TCATTCGTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
42 49 0.98
43 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.14, T:0.38
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCGCTATTCAACATCATCATTTTACTT
Found at i:64890598 original size:99 final size:99
Alignment explanation
Indices: 64890427--64890626 Score: 400
Period size: 99 Copynumber: 2.0 Consensus size: 99
64890417 CTATGCGGAG
64890427 GATTTTGTATCTGACTGTTAGTTGTAATATTGTTGCATTCTTGCTGTTCTTGAAAGAGTTGGTGG
1 GATTTTGTATCTGACTGTTAGTTGTAATATTGTTGCATTCTTGCTGTTCTTGAAAGAGTTGGTGG
64890492 TACCAACGTCTTTCTTGAATTATTTTATTTGACT
66 TACCAACGTCTTTCTTGAATTATTTTATTTGACT
64890526 GATTTTGTATCTGACTGTTAGTTGTAATATTGTTGCATTCTTGCTGTTCTTGAAAGAGTTGGTGG
1 GATTTTGTATCTGACTGTTAGTTGTAATATTGTTGCATTCTTGCTGTTCTTGAAAGAGTTGGTGG
64890591 TACCAACGTCTTTCTTGAATTATTTTATTTGACT
66 TACCAACGTCTTTCTTGAATTATTTTATTTGACT
64890625 GA
1 GA
64890627 GCTAAAAAAG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 101 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (99 bp):
GATTTTGTATCTGACTGTTAGTTGTAATATTGTTGCATTCTTGCTGTTCTTGAAAGAGTTGGTGG
TACCAACGTCTTTCTTGAATTATTTTATTTGACT
Found at i:64896905 original size:21 final size:20
Alignment explanation
Indices: 64896874--64896930 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 20
64896864 TTCTCAATCC
64896874 AATATGCATTTCAATATCACAAT
1 AATAT-CATTTCAAT-TCA-AAT
64896897 AAT-TCATTT-AATTCAAAT
1 AATATCATTTCAATTCAAAT
*
64896915 CATATCATTTGCAATT
1 AATATCATTT-CAATT
64896931 TCCATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
18 5 0.17
19 9 0.30
20 3 0.10
21 9 0.30
22 1 0.03
23 3 0.10
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (20 bp):
AATATCATTTCAATTCAAAT
Found at i:64898397 original size:23 final size:22
Alignment explanation
Indices: 64898354--64898397 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
64898344 TTCTAAGTCG
64898354 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
64898377 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
64898398 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:64898608 original size:51 final size:52
Alignment explanation
Indices: 64898489--64898680 Score: 164
Period size: 51 Copynumber: 3.8 Consensus size: 52
64898479 CAATGATGTT
* * * * ** *
64898489 TGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGGCCATTACCA-TC
1 TGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACGAACATCATTC
* * ** *
64898540 CGATACATGTAGCAGCCTGCACATAGTACTACACACGTGATCGAA-A-CTATTC
1 TGGTACACATAGTAGCCTGCACATAGTACTACACACGTGA-CGAACATC-ATTC
* * * **
64898592 -GGTACGCATAGTAGCCTACACATAGTACTACATA--T-ACGCCCATCATTC
1 TGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACGAACATCATTC
64898640 TGGTACACATAGTAGCCTGCACATAGTACTACACACGTGAC
1 TGGTACACATAGTAGCCTGCACATAGTACTACACACGTGAC
64898681 CATCACTTTC
Statistics
Matches: 110, Mismatches: 22, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
47 2 0.02
48 6 0.05
49 33 0.30
50 1 0.01
51 62 0.56
52 6 0.05
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (52 bp):
TGGTACACATAGTAGCCTGCACATAGTACTACACACGTGACGAACATCATTC
Found at i:64900490 original size:22 final size:22
Alignment explanation
Indices: 64900465--64900525 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
64900455 AAACTTAAAA
* *
64900465 TAAATAATAATAAAATAATTTT
1 TAAATAATAATAAAAAAAGTTT
*
64900487 TAAAAAATAATATAAAAAAGTTT
1 TAAATAATAATA-AAAAAAGTTT
*
64900510 AAAATAAATAAATAAA
1 TAAAT-AAT-AATAAA
64900526 TTAAATTGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 11 0.35
23 11 0.35
24 5 0.16
25 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAATAATAATAAAAAAAGTTT
Found at i:64900523 original size:25 final size:25
Alignment explanation
Indices: 64900459--64900525 Score: 86
Period size: 23 Copynumber: 2.8 Consensus size: 25
64900449 TGTGAAAAAC
*
64900459 TTAAAATAAATAATAATAAAATAATT
1 TTAAAATAAATAAT-ATAAAATAAGT
*
64900485 TTTAAA-AAATAATATAAAA-AAGT
1 TTAAAATAAATAATATAAAATAAGT
64900508 TTAAAATAAATAA-ATAAA
1 TTAAAATAAATAATATAAA
64900526 TTAAATTGCA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.35
24 12 0.32
25 7 0.19
26 5 0.14
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (25 bp):
TTAAAATAAATAATATAAAATAAGT
Found at i:64902905 original size:24 final size:24
Alignment explanation
Indices: 64902878--64902927 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
64902868 TTTCTATAAG
*
64902878 TTTAATAGTTATTAGTATAATATA
1 TTTAATAGTTATTAGCATAATATA
* * *
64902902 TTTAGTATTTATTAGCATAATTTA
1 TTTAATAGTTATTAGCATAATATA
64902926 TT
1 TT
64902928 GTACTTATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTAATAGTTATTAGCATAATATA
Found at i:64918932 original size:30 final size:32
Alignment explanation
Indices: 64918889--64918951 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
64918879 CCCCGCAAGG
**
64918889 ATTTAGTCGAATTTAATTTTTGTACTTTTTAA
1 ATTTAGTCGAATTTAATCCTTGTACTTTTTAA
64918921 ATTTA-TC-AATTTAATCCTTGTACTTTTTAA
1 ATTTAGTCGAATTTAATCCTTGTACTTTTTAA
64918951 A
1 A
64918952 ATTTGAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 22 0.76
31 2 0.07
32 5 0.17
ACGTcount: A:0.30, C:0.10, G:0.06, T:0.54
Consensus pattern (32 bp):
ATTTAGTCGAATTTAATCCTTGTACTTTTTAA
Found at i:64922818 original size:18 final size:18
Alignment explanation
Indices: 64922795--64922830 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
64922785 ACCTTGACGG
64922795 CGGACCGCTGTTCGAACC
1 CGGACCGCTGTTCGAACC
64922813 CGGACCGCTGTTCGAACC
1 CGGACCGCTGTTCGAACC
64922831 GGCTCGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.39, G:0.28, T:0.17
Consensus pattern (18 bp):
CGGACCGCTGTTCGAACC
Found at i:64925329 original size:82 final size:81
Alignment explanation
Indices: 64925171--64925327 Score: 248
Period size: 82 Copynumber: 1.9 Consensus size: 81
64925161 TAATTCTATC
* *
64925171 CTTTATATATTTTTCTCAATTTATATTAAATAACTTTAAATTTGAAATTTGAAACTCGCAAAGAA
1 CTTTATATATTTTTCTCAAATAATATTAAATAACTTTAAATTTGAAATTTGAAACTCGCAAAGAA
64925236 TATTTCTTTTTCCATA
66 TATTTCTTTTTCCATA
64925252 CTTTATATACATTTTT-TCAAATAATATTAAATAACTTTAAATTTGAAATTTGAAAC-C-CACAA
1 CTTTATAT--ATTTTTCTCAAATAATATTAAATAACTTTAAATTTGAAATTTGAAACTCGCA-AA
64925314 GAATATTTCTTTTT
63 GAATATTTCTTTTT
64925328 TCTTTTATTT
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
80 2 0.03
81 25 0.35
82 38 0.54
83 6 0.08
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.46
Consensus pattern (81 bp):
CTTTATATATTTTTCTCAAATAATATTAAATAACTTTAAATTTGAAATTTGAAACTCGCAAAGAA
TATTTCTTTTTCCATA
Done.