Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 80 of 82
Found at i:30292375 original size:13 final size:13
Alignment explanation
Indices: 30292357--30292387 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
30292347 TAATTAATAA
30292357 AAAATTTTTAATT
1 AAAATTTTTAATT
30292370 AAAATTTTTAATT
1 AAAATTTTTAATT
*
30292383 CAAAT
1 AAAAT
30292388 AAATCAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATTTTTAATT
Found at i:30303033 original size:2 final size:2
Alignment explanation
Indices: 30303026--30303054 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30303016 TTTTTGTTTA
30303026 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 A
30303055 ATAATTATNG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30303973 original size:16 final size:16
Alignment explanation
Indices: 30303948--30303981 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30303938 CTTCCTTCTC
*
30303948 TTTCTTTCTCAGACCT
1 TTTCTCTCTCAGACCT
30303964 TTTCTCTCTCAGACCT
1 TTTCTCTCTCAGACCT
30303980 TT
1 TT
30303982 ATACATAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.32, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTCTCTCTCAGACCT
Found at i:30305998 original size:2 final size:2
Alignment explanation
Indices: 30305991--30306039 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
30305981 TTGATTAGTT
30305991 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30306033 TA TA TA T
1 TA TA TA T
30306040 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30310686 original size:13 final size:13
Alignment explanation
Indices: 30310668--30310693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30310658 CGCACCCTTC
30310668 TCCTCTTCTCTCT
1 TCCTCTTCTCTCT
30310681 TCCTCTTCTCTCT
1 TCCTCTTCTCTCT
30310694 ACCGCCACAG
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:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (13 bp):
TCCTCTTCTCTCT
Found at i:30323211 original size:30 final size:30
Alignment explanation
Indices: 30323192--30323252 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
30323182 GTCTTATTTG
30323192 ATTTAAAATAAAAATATAATAATTTACTTA
1 ATTTAAAATAAAAATATAATAATTTACTTA
* *
30323222 ATTTAAAATAAAAATATAAAAATTTAATTA
1 ATTTAAAATAAAAATATAATAATTTACTTA
30323252 A
1 A
30323253 ATGTAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (30 bp):
ATTTAAAATAAAAATATAATAATTTACTTA
Found at i:30323290 original size:29 final size:30
Alignment explanation
Indices: 30323197--30323279 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
30323187 ATTTGATTTA
* * *
30323197 AAATAAAAATATAATAATTTACTT-AATTT
1 AAATAAAAATATAAAAATTTAATTAAATGT
30323226 AAAATAAAAATATAAAAATTTAATTAAATGT
1 -AAATAAAAATATAAAAATTTAATTAAATGT
30323257 -AATAAAAATA-AAAAATTTTAATT
1 AAATAAAAATATAAAAA-TTTAATT
30323280 TTTTTAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 5 0.10
29 17 0.35
30 22 0.46
31 4 0.08
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
AAATAAAAATATAAAAATTTAATTAAATGT
Found at i:30324989 original size:21 final size:20
Alignment explanation
Indices: 30324947--30324995 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
30324937 TAAATTTAAA
30324947 ATTATTTATTTTTAATTATT
1 ATTATTTATTTTTAATTATT
*
30324967 ATTATTTGTGTTTATAA-TATT
1 ATTATTTAT-TTT-TAATTATT
*
30324988 ATAATTTA
1 ATTATTTA
30324996 AACTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 8 0.33
21 13 0.54
22 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (20 bp):
ATTATTTATTTTTAATTATT
Found at i:30335889 original size:21 final size:20
Alignment explanation
Indices: 30335849--30335888 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
30335839 ATCATCATAC
30335849 ATATGATCCCATGGAATTTT
1 ATATGATCCCATGGAATTTT
*
30335869 ATATGTATCCTATGG-ATTTT
1 ATATG-ATCCCATGGAATTTT
30335889 TTTTTGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (20 bp):
ATATGATCCCATGGAATTTT
Found at i:30338707 original size:18 final size:18
Alignment explanation
Indices: 30338677--30338718 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
30338667 TCTTGTGTGA
*
30338677 TTTTTTGTATTAT-TACG
1 TTTTTTGGATTATATACG
*
30338694 TTTTTTGGATTTATATAGG
1 TTTTTTGGA-TTATATACG
30338713 TTTTTT
1 TTTTTT
30338719 TTATCTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 8 0.38
18 4 0.19
19 9 0.43
ACGTcount: A:0.17, C:0.02, G:0.14, T:0.67
Consensus pattern (18 bp):
TTTTTTGGATTATATACG
Found at i:30339434 original size:16 final size:16
Alignment explanation
Indices: 30339406--30339438 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30339396 GAATTTTAAC
30339406 TTATTTGGATTATGAAA
1 TTATTTGGATTAT-AAA
30339423 TTATTT-GATTATAAA
1 TTATTTGGATTATAAA
30339438 T
1 T
30339439 CATCATTCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 6 0.38
17 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (16 bp):
TTATTTGGATTATAAA
Found at i:30339974 original size:2 final size:2
Alignment explanation
Indices: 30339969--30339993 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30339959 CCTTTTTTTC
30339969 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30339994 TACTTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30353785 original size:21 final size:22
Alignment explanation
Indices: 30353746--30353789 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
30353736 ACGAGAAGGT
*
30353746 AAAGGAGAGAAAAAAAAAAGAA
1 AAAGAAGAGAAAAAAAAAAGAA
*
30353768 AAAGAAGAG-AAAAGAAAAGAA
1 AAAGAAGAGAAAAAAAAAAGAA
30353789 A
1 A
30353790 TGAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (22 bp):
AAAGAAGAGAAAAAAAAAAGAA
Found at i:30354580 original size:14 final size:14
Alignment explanation
Indices: 30354561--30354594 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
30354551 CAGATAAAAC
*
30354561 AATATTTTGTATTT
1 AATATTTTGTATGT
*
30354575 AATATTTTTTATGT
1 AATATTTTGTATGT
30354589 AATATT
1 AATATT
30354595 AAAACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (14 bp):
AATATTTTGTATGT
Found at i:30363398 original size:2 final size:2
Alignment explanation
Indices: 30363391--30363415 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30363381 TGTACCTTTC
30363391 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
30363416 CTGTTAGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30379512 original size:45 final size:45
Alignment explanation
Indices: 30379454--30379545 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
30379444 TTTCCACTAT
* *
30379454 AGTTCAACAAATATAAATTAATATTACATTTATTAGTTTATGAAA
1 AGTTCAACAAATATAAATTAATATTACATTTATTAATTTAGGAAA
* *
30379499 AGTTCAACTAATATAAATTAATATTGCATTTATTAATTTAGGAAA
1 AGTTCAACAAATATAAATTAATATTACATTTATTAATTTAGGAAA
30379544 AG
1 AG
30379546 ATAAGTTGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.39
Consensus pattern (45 bp):
AGTTCAACAAATATAAATTAATATTACATTTATTAATTTAGGAAA
Found at i:30388137 original size:2 final size:2
Alignment explanation
Indices: 30388124--30388162 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
30388114 GTGAATATGT
*
30388124 GA GA GT GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
30388163 GATGGTACCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.51, T:0.03
Consensus pattern (2 bp):
GA
Found at i:30396950 original size:6 final size:6
Alignment explanation
Indices: 30396906--30396949 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
30396896 TCTTTATCTC
* *
30396906 CTCCTC CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTTCTT CT
1 CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CTCCTT CT
30396950 TTAGGTGCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTCCTT
Found at i:30422358 original size:21 final size:19
Alignment explanation
Indices: 30422334--30422381 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
30422324 AATCCTATCT
30422334 ATATTAATATT-TGTAAATAAA
1 ATATTAATATTATG--AA-AAA
30422355 ATATTAAT-TTATGAAAAA
1 ATATTAATATTATGAAAAA
30422373 ATATTAATA
1 ATATTAATA
30422382 ATTAAATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 11 0.44
19 2 0.08
20 2 0.08
21 10 0.40
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
ATATTAATATTATGAAAAA
Found at i:30422403 original size:25 final size:25
Alignment explanation
Indices: 30422357--30422412 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
30422347 TAAATAAAAT
* *
30422357 ATTAATTTATGAAAAAATATTAATA
1 ATTAAATTATGAAAAAAAATTAATA
*
30422382 ATTAAATTAT-AAATAAAAATTAGTA
1 ATTAAATTATGAAA-AAAAATTAATA
*
30422407 TTTAAA
1 ATTAAA
30422413 AAATAAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTAAATTATGAAAAAAAATTAATA
Found at i:30422461 original size:37 final size:36
Alignment explanation
Indices: 30422423--30422511 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 36
30422413 AAATAAAATA
30422423 AAATAAAA-ATAAATAAC-CATAATATCA-TTAAATTAT
1 AAATAAAATATAAAT-ACTCATAA-A-CATTTAAATTAT
*
30422459 AAATAAAATATGAATACTTCATAAACATTTAAATTAT
1 AAATAAAATATAAATAC-TCATAAACATTTAAATTAT
*
30422496 AAATAAAATATTAATA
1 AAATAAAATATAAATA
30422512 TTTAAATGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
36 12 0.26
37 30 0.64
38 5 0.11
ACGTcount: A:0.60, C:0.07, G:0.01, T:0.33
Consensus pattern (36 bp):
AAATAAAATATAAATACTCATAAACATTTAAATTAT
Found at i:30422529 original size:22 final size:23
Alignment explanation
Indices: 30422498--30422541 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
30422488 TAAATTATAA
30422498 ATAAAATATTAATATT-TAAATG
1 ATAAAATATTAATATTATAAATG
*
30422520 ATAAATTATTAATATTATAAAT
1 ATAAAATATTAATATTATAAAT
30422542 AAATTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAAAATATTAATATTATAAATG
Found at i:30422537 original size:42 final size:41
Alignment explanation
Indices: 30422449--30422706 Score: 150
Period size: 42 Copynumber: 6.4 Consensus size: 41
30422439 CCATAATATC
* * *
30422449 ATTAAATTATAAATAAAATATGAATACTT-CAT-A-AACA-T
1 ATTAAATTATAAATAAAATATTAATATTTAAATGATAA-ATT
30422487 -TTAAATTATAAATAAAATATTAATATTTAAATGATAAATT
1 ATTAAATTATAAATAAAATATTAATATTTAAATGATAAATT
* * *
30422527 ATTAATATTATAAATAAATTATCAA-A-TTAAAT-ATTAA-T
1 ATTAA-ATTATAAATAAAATATTAATATTTAAATGATAAATT
* * ** * *
30422565 ATTTAAA-AATAAAATATAATAAAAATATTT-GATCATAATAATGT
1 A-TTAAATTAT-AAATAAAATATTAATATTTAAATGAT-A-AAT-T
* * * *
30422609 -TTAAA-T-TAAATAAAATGTTAATATTTTACGATG-TTAATG
1 ATTAAATTATAAATAAAATATTAATA-TTTA-AATGATAAATT
*
30422648 ATTAAATTATAAATAAAATATTAATATTTAAATGATCAATT
1 ATTAAATTATAAATAAAATATTAATATTTAAATGATAAATT
* *
30422689 ATTCATATTTTAAATAAA
1 ATT-AAATTATAAATAAA
30422707 TTATCAATTA
Statistics
Matches: 170, Mismatches: 27, Indels: 42
0.71 0.11 0.18
Matches are distributed among these distances:
37 28 0.16
38 15 0.09
39 13 0.08
40 36 0.21
41 21 0.12
42 53 0.31
43 3 0.02
44 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (41 bp):
ATTAAATTATAAATAAAATATTAATATTTAAATGATAAATT
Found at i:30422585 original size:26 final size:27
Alignment explanation
Indices: 30422485--30422594 Score: 84
Period size: 26 Copynumber: 4.1 Consensus size: 27
30422475 CTTCATAAAC
* *
30422485 ATTTAAATTAT-AAATAAAATATTAAT
1 ATTTAAATAATAAAATATAATATTAAT
* *
30422511 ATTTAAATGATAAATTATTAATATT-AT
1 ATTTAAATAATAAAATA-TAATATTAAT
** * *
30422538 AAATAAATTATCAAAT-TAAATATTAAT
1 ATTTAAATAATAAAATAT-AATATTAAT
**
30422565 ATTTAAA-AATAAAATATAATAAAAAT
1 ATTTAAATAATAAAATATAATATTAAT
30422591 ATTT
1 ATTT
30422595 GATCATAATA
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
25 1 0.02
26 33 0.51
27 25 0.38
28 6 0.09
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (27 bp):
ATTTAAATAATAAAATATAATATTAAT
Found at i:30422586 original size:158 final size:161
Alignment explanation
Indices: 30422372--30422744 Score: 419
Period size: 162 Copynumber: 2.3 Consensus size: 161
30422362 TTTATGAAAA
* * * *
30422372 AATATTAATAATTAAATTAT-AAA-TAAAAATTAGTATTTAAAAAATAAAATAAAATAAAAATAA
1 AATATT-ATAAATAAATTATCAAATTAAATATTAATATTT-AAAAATAAAATATAATAAAAATAA
30422435 ATAACCATAAT-ATCATTAAATTATAAATAAAATATGAATA-CTT-C-AT-AAACAT-TTAAATT
64 ATAACCATAATAATCATTAAA-T-TAAATAAAATATGAATATCTTACGATGAAA-ATATTAAATT
30422494 ATAAATAAAATATTAATATTTAAATGATAAATTATT
126 ATAAATAAAATATTAATATTTAAATGATAAATTATT
**
30422530 AATATTATAAATAAATTATCAAATTAAATATTAATATTTAAAAATAAAATATAATAAAAATATTT
1 AATATTATAAATAAATTATCAAATTAAATATTAATATTTAAAAATAAAATATAATAAAAATAAAT
* * ** * * * **
30422595 GATCATAATAATGTTTAAATTAAATAAAATGTTAATATTTTACGATGTTAATGATTAAATTATAA
66 AACCATAATAATCATTAAATTAAATAAAATATGAATATCTTACGATGAAAAT-ATTAAATTATAA
*
30422660 ATAAAATATTAATATTTAAATGATCAATTATT
130 ATAAAATATTAATATTTAAATGATAAATTATT
* * * *
30422692 CATATTTTAAATAAATTATC-AATT-ACTAAT-AT-TTTAAAAATAAAATATTAATA
1 AATATTATAAATAAATTATCAAATTAAATATTAATATTTAAAAATAAAATA-TAATA
30422745 TTTAAAATTT
Statistics
Matches: 185, Mismatches: 20, Indels: 19
0.83 0.09 0.08
Matches are distributed among these distances:
157 27 0.15
158 57 0.31
159 28 0.15
160 8 0.04
161 5 0.03
162 60 0.32
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (161 bp):
AATATTATAAATAAATTATCAAATTAAATATTAATATTTAAAAATAAAATATAATAAAAATAAAT
AACCATAATAATCATTAAATTAAATAAAATATGAATATCTTACGATGAAAATATTAAATTATAAA
TAAAATATTAATATTTAAATGATAAATTATT
Found at i:30422632 original size:40 final size:42
Alignment explanation
Indices: 30422588--30422676 Score: 103
Period size: 40 Copynumber: 2.2 Consensus size: 42
30422578 ATATAATAAA
* *
30422588 AATATTTGATC-ATAATAATGTTTAAA-T-TAAATAAAATGTT
1 AATATTTGA-CGATAATAATGATTAAATTATAAATAAAATATT
* **
30422628 AATATTTTACGATGTTAATGATTAAATTATAAATAAAATATT
1 AATATTTGACGATAATAATGATTAAATTATAAATAAAATATT
30422670 AATATTT
1 AATATTT
30422677 AAATGATCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 1 0.02
40 20 0.49
41 1 0.02
42 19 0.46
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (42 bp):
AATATTTGACGATAATAATGATTAAATTATAAATAAAATATT
Found at i:30422707 original size:27 final size:27
Alignment explanation
Indices: 30422676--30422729 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
30422666 TATTAATATT
* *
30422676 TAAATGATCAATTATTCATATTTTAAA
1 TAAATGATCAATTACTAATATTTTAAA
*
30422703 TAAATTATCAATTACTAATATTTTAAA
1 TAAATGATCAATTACTAATATTTTAAA
30422730 AATAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAATGATCAATTACTAATATTTTAAA
Found at i:30422746 original size:22 final size:21
Alignment explanation
Indices: 30422658--30422872 Score: 68
Period size: 22 Copynumber: 10.0 Consensus size: 21
30422648 ATTAAATTAT
30422658 AAATAAAATATTAATATTTAA
1 AAATAAAATATTAATATTTAA
* * * *
30422679 ATGATCAATTATTCATATTTTAAA
1 A-AATAAAATATTAATA-TTT-AA
* * *
30422703 TAAATTATCAATTACTAATATTTTA
1 -AAA-TA--AAATATTAATATTTAA
30422728 AAAATAAAATATTAATATTTAA
1 AAA-TAAAATATTAATATTTAA
* ** * *
30422750 AATTTCCATTATTAATATTCATA
1 AA-ATAAAATATTAATATTTA-A
* * *
30422773 AAATAAAA-AATAAAAATTAA
1 AAATAAAATATTAATATTTAA
**
30422793 CCATAATAATATTTAA-A-TT--
1 AAATAA-AATA-TTAATATTTAA
*
30422812 AAAT-AAATATTAATATTTTA
1 AAATAAAATATTAATATTTAA
* *
30422832 AAATATTAATGATTAA-A-TTAT
1 AAATA-AAAT-ATTAATATTTAA
30422853 AAATAAAATATTAATATTTA
1 AAATAAAATATTAATATTTA
30422873 GTTTAGAAAT
Statistics
Matches: 138, Mismatches: 35, Indels: 42
0.64 0.16 0.20
Matches are distributed among these distances:
16 4 0.03
17 5 0.04
18 3 0.02
19 7 0.05
20 13 0.09
21 22 0.16
22 47 0.34
23 14 0.10
24 8 0.06
25 3 0.02
26 3 0.02
27 9 0.07
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (21 bp):
AAATAAAATATTAATATTTAA
Found at i:30447588 original size:57 final size:58
Alignment explanation
Indices: 30447496--30447611 Score: 180
Period size: 57 Copynumber: 2.0 Consensus size: 58
30447486 CATGCACCTT
* * * * *
30447496 TGGCAAAGCATGTAGGTTTGTTTTCCCTCTGGTGGCATCCTATTGCCAATCATTGCAC
1 TGGCAAAGCATGTACGTTTGTATTCCCTCTGGTGGCAACCTACTGCCAACCATTGCAC
30447554 TGGCAAAGCATGTACGTTT-TATTCCCTCTGGTGGCAACCTACTGCCAACCATTGCAC
1 TGGCAAAGCATGTACGTTTGTATTCCCTCTGGTGGCAACCTACTGCCAACCATTGCAC
30447611 T
1 T
30447612 TCCTCATCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 35 0.66
58 18 0.34
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (58 bp):
TGGCAAAGCATGTACGTTTGTATTCCCTCTGGTGGCAACCTACTGCCAACCATTGCAC
Found at i:30456193 original size:15 final size:15
Alignment explanation
Indices: 30456173--30456201 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30456163 GAACTCCTTC
30456173 CAAAATTGTAAAAAA
1 CAAAATTGTAAAAAA
30456188 CAAAATTGTAAAAA
1 CAAAATTGTAAAAA
30456202 TTATGGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.07, T:0.21
Consensus pattern (15 bp):
CAAAATTGTAAAAAA
Found at i:30460428 original size:24 final size:24
Alignment explanation
Indices: 30460401--30460448 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
30460391 TCTGATTCTC
* *
30460401 TTCTTCTGACTTC-TTGTTGATCCT
1 TTCTTCCG-CTTCTTTGGTGATCCT
30460425 TTCTTCCGCTTCTTTGGTGATCCT
1 TTCTTCCGCTTCTTTGGTGATCCT
30460449 CGTTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.06, C:0.27, G:0.15, T:0.52
Consensus pattern (24 bp):
TTCTTCCGCTTCTTTGGTGATCCT
Found at i:30462445 original size:17 final size:18
Alignment explanation
Indices: 30462394--30462464 Score: 64
Period size: 17 Copynumber: 4.2 Consensus size: 18
30462384 TAATAATGTA
30462394 AAAAACTATTAATTT-ATT
1 AAAAA-TATTAATTTAATT
*
30462412 AACAAATA--AA-ATAATT
1 AA-AAATATTAATTTAATT
30462428 AAAAATATT-ATTTAATT
1 AAAAATATTAATTTAATT
*
30462445 AAAATTATTAATTT-ATT
1 AAAAATATTAATTTAATT
30462462 AAA
1 AAA
30462465 TATTAATATA
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
15 6 0.14
16 8 0.18
17 19 0.43
18 8 0.18
19 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATATTAATTTAATT
Found at i:30462469 original size:18 final size:17
Alignment explanation
Indices: 30462423--30462469 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
30462413 ACAAATAAAA
*
30462423 TAATTAAAAATATTATT
1 TAATTAAAATTATTATT
30462440 TAATTAAAATTATTAATT
1 TAATTAAAATTATT-ATT
30462458 T-ATTAAATATTA
1 TAATTAAA-ATTA
30462470 ATATATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATTAAAATTATTATT
Found at i:30469279 original size:19 final size:19
Alignment explanation
Indices: 30469252--30469297 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
30469242 ATTATTAATA
*
30469252 AAAAATAATT-TAATAAATT
1 AAAATTAATTATAA-AAATT
30469271 AAAATTAATTAGTAAAAATT
1 AAAATTAATTA-TAAAAATT
30469291 -AAATTAA
1 AAAATTAA
30469298 AATTTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 16 0.67
20 5 0.21
21 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTAATTATAAAAATT
Found at i:30469944 original size:49 final size:47
Alignment explanation
Indices: 30469851--30469946 Score: 131
Period size: 49 Copynumber: 2.0 Consensus size: 47
30469841 TTTGCTCAAT
* *
30469851 TTTTTATTTTCTTGCCATTCATTTCTGAAGTTGGAAATAGAATATAA
1 TTTTTATTTTCTTGCCATTCATTTCTGAAATTGAAAATAGAATATAA
*
30469898 TTTTTATTTTCTTGCCATATTCATTT-TAGAAATTGAAAATATAATATAA
1 TTTTTATTTTCTTGCC--ATTCATTTCT-GAAATTGAAAATAGAATATAA
30469947 CGCTAATGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 16 0.37
48 1 0.02
49 26 0.60
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.48
Consensus pattern (47 bp):
TTTTTATTTTCTTGCCATTCATTTCTGAAATTGAAAATAGAATATAA
Found at i:30495872 original size:19 final size:20
Alignment explanation
Indices: 30495840--30495877 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
30495830 TCTCTAGCCC
30495840 AATTAACAAAAAAAACCACA
1 AATTAACAAAAAAAACCACA
* *
30495860 AATT-ACAACAAAATCCAC
1 AATTAACAAAAAAAACCAC
30495878 CCCAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.63, C:0.24, G:0.00, T:0.13
Consensus pattern (20 bp):
AATTAACAAAAAAAACCACA
Found at i:30505879 original size:16 final size:16
Alignment explanation
Indices: 30505860--30505891 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30505850 ATTAAATATT
30505860 TATATAAACACACATA
1 TATATAAACACACATA
*
30505876 TATATATACACACATA
1 TATATAAACACACATA
30505892 AATACATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.19, G:0.00, T:0.28
Consensus pattern (16 bp):
TATATAAACACACATA
Found at i:30505881 original size:18 final size:18
Alignment explanation
Indices: 30505855--30505901 Score: 53
Period size: 16 Copynumber: 2.7 Consensus size: 18
30505845 TAATAATTAA
*
30505855 ATATTTATATAAACACAC
1 ATATATATATAAACACAC
30505873 ATATATATAT--ACACAC
1 ATATATATATAAACACAC
* *
30505889 ATAAATACATAAA
1 ATATATATATAAA
30505902 TTATATAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 14 0.58
18 10 0.42
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (18 bp):
ATATATATATAAACACAC
Found at i:30511703 original size:45 final size:45
Alignment explanation
Indices: 30511628--30511767 Score: 201
Period size: 45 Copynumber: 3.1 Consensus size: 45
30511618 TTCACGATGC
*
30511628 TACAC-TCTATGTACAAAAATATGTTACACGTCATGGTTAGGTTGT
1 TACACGTC-ATGTACAAAAACATGTTACACGTCATGGTTAGGTTGT
* * * *
30511673 TATACGTCATGTACAAAAACATGTTGCACGTCATGATTTGGTTGT
1 TACACGTCATGTACAAAAACATGTTACACGTCATGGTTAGGTTGT
* *
30511718 TACACGTCATGTACAAAAACATGTTACACGTCTTGGTTAGATTGT
1 TACACGTCATGTACAAAAACATGTTACACGTCATGGTTAGGTTGT
30511763 TACAC
1 TACAC
30511768 ACTAAATTAA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
45 81 0.98
46 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (45 bp):
TACACGTCATGTACAAAAACATGTTACACGTCATGGTTAGGTTGT
Found at i:30511879 original size:31 final size:29
Alignment explanation
Indices: 30511841--30511936 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
30511831 CTAAAAAAAA
**
30511841 GTTGTTACACTTCATGTTGAAAAAAAATATT
1 GTTGTTACACGCCATGTT--AAAAAAATATT
*
30511872 GTTGTTACAGGCCATGTTAAAAAAATATT
1 GTTGTTACACGCCATGTTAAAAAAATATT
* * * *
30511901 ATTATTACACGCCATATT-CAAAAATATT
1 GTTGTTACACGCCATGTTAAAAAAATATT
*
30511929 -TTATTACA
1 GTTGTTACA
30511937 TTTTAATGCC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
27 8 0.14
28 9 0.16
29 25 0.44
31 15 0.26
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
GTTGTTACACGCCATGTTAAAAAAATATT
Found at i:30511933 original size:30 final size:29
Alignment explanation
Indices: 30511861--30511936 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
30511851 TTCATGTTGA
* * * *
30511861 AAAAAAATATTGTTGTTACAGGCCATGTT
1 AAAAAAATATTATTATTACACGCCATATT
30511890 AAAAAAATATTATTATTACACGCCATATT
1 AAAAAAATATTATTATTACACGCCATATT
*
30511919 -CAAAAATATT-TTATTACA
1 AAAAAAATATTATTATTACA
30511937 TTTTAATGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 8 0.19
28 9 0.21
29 25 0.60
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.36
Consensus pattern (29 bp):
AAAAAAATATTATTATTACACGCCATATT
Found at i:30513011 original size:23 final size:25
Alignment explanation
Indices: 30512972--30513022 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
30512962 AATATAAATA
30512972 TTAATAAATTTTAAAATATTTA-TT
1 TTAATAAATTTTAAAATATTTACTT
* *
30512996 TTAA-AAATTTTTAAATTTTTACTT
1 TTAATAAATTTTAAAATATTTACTT
30513020 TTA
1 TTA
30513023 CTTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TTAATAAATTTTAAAATATTTACTT
Found at i:30514659 original size:17 final size:17
Alignment explanation
Indices: 30514637--30514677 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
30514627 TTTATACTTT
30514637 TTATAAAAAATAAAAAA
1 TTATAAAAAATAAAAAA
*
30514654 TTAT-AAAAATAAATAA
1 TTATAAAAAATAAAAAA
30514670 -TATAAAAA
1 TTATAAAAA
30514678 GAAAATATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 15 0.68
17 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
TTATAAAAAATAAAAAA
Found at i:30514673 original size:15 final size:16
Alignment explanation
Indices: 30514637--30514682 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
30514627 TTTATACTTT
30514637 TTATAAAAAATAAAAAA
1 TTAT-AAAAATAAAAAA
*
30514654 TTATAAAAATAAATAA
1 TTATAAAAATAAAAAA
*
30514670 -TATAAAAAGAAAA
1 TTATAAAAATAAAA
30514683 TATTCAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 11 0.42
16 11 0.42
17 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (16 bp):
TTATAAAAATAAAAAA
Found at i:30514683 original size:16 final size:16
Alignment explanation
Indices: 30514637--30514684 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
30514627 TTTATACTTT
*
30514637 TTATAAAAAATAAAAAA
1 TTATAAAAAA-AAATAA
*
30514654 TTATAAAAATAAATAA
1 TTATAAAAAAAAATAA
30514670 -TATAAAAAGAAAATA
1 TTATAAAAA-AAAATA
30514685 TTCAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 8 0.30
16 10 0.37
17 9 0.33
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (16 bp):
TTATAAAAAAAAATAA
Found at i:30517226 original size:22 final size:21
Alignment explanation
Indices: 30517191--30517253 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
30517181 TTCTTTGCTT
30517191 TTTTATTTTCTTGTTTTTATTGG
1 TTTT-TTTT-TTGTTTTTATTGG
* * *
30517214 TTTCTTTTTTTGTTATTGTTTG
1 TTT-TTTTTTTGTTTTTATTGG
*
30517236 TTTTTTTTAT-TTTTTATT
1 TTTTTTTTTTGTTTTTATT
30517254 TATTTTCGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
20 6 0.18
21 6 0.18
22 13 0.39
23 7 0.21
24 1 0.03
ACGTcount: A:0.08, C:0.03, G:0.10, T:0.79
Consensus pattern (21 bp):
TTTTTTTTTTGTTTTTATTGG
Found at i:30517239 original size:18 final size:19
Alignment explanation
Indices: 30517207--30517242 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
30517197 TTTCTTGTTT
30517207 TTATTGGTTTCTTTTTTTG
1 TTATTGGTTTCTTTTTTTG
*
30517226 TTATT-GTTTGTTTTTTT
1 TTATTGGTTTCTTTTTTT
30517243 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.06, C:0.03, G:0.14, T:0.78
Consensus pattern (19 bp):
TTATTGGTTTCTTTTTTTG
Found at i:30519393 original size:23 final size:24
Alignment explanation
Indices: 30519348--30519393 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
30519338 TTTTAGGAAG
*
30519348 CATTTTCTGCTTATGACTATATTAT
1 CATTTTC-GCTTATAACTATATTAT
*
30519373 CATTTTC-CTTATAACTTTATT
1 CATTTTCGCTTATAACTATATT
30519394 TTCCAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
25 7 0.37
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.54
Consensus pattern (24 bp):
CATTTTCGCTTATAACTATATTAT
Found at i:30532028 original size:72 final size:73
Alignment explanation
Indices: 30531910--30532107 Score: 380
Period size: 72 Copynumber: 2.7 Consensus size: 73
30531900 AGATGAAGTA
*
30531910 AAATTGTATCTGACTTGAAGTGCTGGTTGGGTTATGTGCCTATCCATCTCTGATGCCTTAGGACC
1 AAATTGTATATGACTTGAAGTGCTGGTTGGGTTATGTGCCTATCCATCTCTGATGCCTTAGGACC
30531975 AGATAGTG
66 AGATAGTG
30531983 AAATTGTAT-TGACTTGAAGTGCTGGTTGGGTTATGTGCCTATCCATCTCTGATGCCTTAGGACC
1 AAATTGTATATGACTTGAAGTGCTGGTTGGGTTATGTGCCTATCCATCTCTGATGCCTTAGGACC
30532047 AGATAGTG
66 AGATAGTG
30532055 AAATTGTATATGACTTGAAGTGCTGGTTGGGTTATGTGCCTATCCATCTCTGA
1 AAATTGTATATGACTTGAAGTGCTGGTTGGGTTATGTGCCTATCCATCTCTGA
30532108 AGGAAGCCAT
Statistics
Matches: 124, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
72 72 0.58
73 52 0.42
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (73 bp):
AAATTGTATATGACTTGAAGTGCTGGTTGGGTTATGTGCCTATCCATCTCTGATGCCTTAGGACC
AGATAGTG
Found at i:30539032 original size:22 final size:22
Alignment explanation
Indices: 30539007--30539050 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
30538997 TCTCTAAGTA
30539007 AACCTGATTATTGTTTCTGTGG
1 AACCTGATTATTGTTTCTGTGG
30539029 AACCTGATTATTGTTTCTGTGG
1 AACCTGATTATTGTTTCTGTGG
30539051 GATCTTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.23, T:0.45
Consensus pattern (22 bp):
AACCTGATTATTGTTTCTGTGG
Found at i:30545032 original size:6 final size:6
Alignment explanation
Indices: 30545021--30545049 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
30545011 CATTTTTCCC
30545021 ACAAAA ACAAAA ACAAAA ACAAAA ACAAA
1 ACAAAA ACAAAA ACAAAA ACAAAA ACAAA
30545050 GATTCCCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (6 bp):
ACAAAA
Found at i:30545834 original size:6 final size:6
Alignment explanation
Indices: 30545823--30545847 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
30545813 GTGTTCATCT
30545823 TCCTTC TCCTTC TCCTTC TCCTTC T
1 TCCTTC TCCTTC TCCTTC TCCTTC T
30545848 TTCTTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TCCTTC
Found at i:30549603 original size:6 final size:6
Alignment explanation
Indices: 30549592--30549619 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
30549582 CCTTACAATA
30549592 TGGGTG TGGGTG TGGGTG TGGGTG TGGG
1 TGGGTG TGGGTG TGGGTG TGGGTG TGGG
30549620 GTGAATTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (6 bp):
TGGGTG
Found at i:30554620 original size:18 final size:18
Alignment explanation
Indices: 30554573--30554618 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
30554563 TTGGAACACC
30554573 AAAGAAAGAAA--ATAGAG
1 AAAGAAAGAAAGGA-AGAG
30554590 AAAGAAAGAAAGGAAGAG
1 AAAGAAAGAAAGGAAGAG
*
30554608 AGAGAGAAGAA
1 AAAGA-AAGAA
30554619 GGGCTGTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 11 0.44
18 8 0.32
19 6 0.24
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (18 bp):
AAAGAAAGAAAGGAAGAG
Found at i:30556929 original size:2 final size:2
Alignment explanation
Indices: 30556922--30556982 Score: 74
Period size: 2 Copynumber: 31.5 Consensus size: 2
30556912 GGGAGGGTTT
* *
30556922 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AC AG AG -G
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30556963 AG AG A- AG -G AG ACG AG AG AG A
1 AG AG AG AG AG AG A-G AG AG AG A
30556983 AGGGAGACAG
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
1 3 0.06
2 46 0.90
3 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:30565803 original size:21 final size:21
Alignment explanation
Indices: 30565777--30565819 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
30565767 TAAAGGCAGG
30565777 ATAGTCAGATTACACAATTGA
1 ATAGTCAGATTACACAATTGA
30565798 ATAGTCAGATTACACAATTGA
1 ATAGTCAGATTACACAATTGA
30565819 A
1 A
30565820 GAAGATGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
ATAGTCAGATTACACAATTGA
Found at i:30570157 original size:4 final size:4
Alignment explanation
Indices: 30570148--30570174 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
30570138 GTCCTTGGAT
30570148 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
30570175 TCTCCTCTTC
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:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:30575767 original size:2 final size:2
Alignment explanation
Indices: 30575760--30575791 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
30575750 AATATAGTAA
30575760 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30575792 CGTATACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:30575881 original size:2 final size:2
Alignment explanation
Indices: 30575874--30575904 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
30575864 TGNTATAGTA
30575874 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30575905 CGAATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30592058 original size:16 final size:16
Alignment explanation
Indices: 30592024--30592058 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30592014 AAACAAAAAT
**
30592024 TCAGAGCCAGGATCTA
1 TCAGAGCCAGGATAGA
30592040 TCAGAGCCAGGATAGA
1 TCAGAGCCAGGATAGA
30592056 TCA
1 TCA
30592059 TCCTGAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (16 bp):
TCAGAGCCAGGATAGA
Found at i:30600134 original size:58 final size:58
Alignment explanation
Indices: 30600056--30600167 Score: 206
Period size: 58 Copynumber: 1.9 Consensus size: 58
30600046 TACCCACGCG
*
30600056 AACATGTTGTAGTGGTTGTGAAATGCTGCCACAAAAAATTTGTTACCAGTGTTTATCC
1 AACATGTTGTAGTGGCTGTGAAATGCTGCCACAAAAAATTTGTTACCAGTGTTTATCC
*
30600114 AACATGTTGTAGTGGCTGTGAAATGCTGCCACAAAAATTTTGTTACCAGTGTTT
1 AACATGTTGTAGTGGCTGTGAAATGCTGCCACAAAAAATTTGTTACCAGTGTTT
30600168 TTATTTAATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (58 bp):
AACATGTTGTAGTGGCTGTGAAATGCTGCCACAAAAAATTTGTTACCAGTGTTTATCC
Found at i:30622190 original size:14 final size:14
Alignment explanation
Indices: 30622171--30622200 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
30622161 GTGGCTCTGA
30622171 TTTTTTCTTTTTCT
1 TTTTTTCTTTTTCT
*
30622185 TTTTTTTTTTTTCT
1 TTTTTTCTTTTTCT
30622199 TT
1 TT
30622201 CTCTGATTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:30631142 original size:73 final size:73
Alignment explanation
Indices: 30631065--30631203 Score: 181
Period size: 73 Copynumber: 1.9 Consensus size: 73
30631055 TTTCCATTCA
* * * **
30631065 TACGATCTTTATTATAGAATAGAGGTAGA-GATTTCCTTTTTTTTTTTTGTTTTAATCGGTACTT
1 TACGATCTTTACTATAGAATAAAGATA-ATGATTTCCTTTTTCATTTTTGTTTTAATCGGTACTT
30631129 CTCCAAATG
65 CTCCAAATG
* * **
30631138 TACGATCTTTACTATAGATTAAAGATAATGATTTTCTTTTTCATTTTTGTTTTAATTTGTACTTC
1 TACGATCTTTACTATAGAATAAAGATAATGATTTCCTTTTTCATTTTTGTTTTAATCGGTACTTC
30631203 T
66 T
30631204 TTAAATATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 1 0.02
73 55 0.98
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (73 bp):
TACGATCTTTACTATAGAATAAAGATAATGATTTCCTTTTTCATTTTTGTTTTAATCGGTACTTC
TCCAAATG
Found at i:30631222 original size:73 final size:73
Alignment explanation
Indices: 30631094--30631231 Score: 168
Period size: 73 Copynumber: 1.9 Consensus size: 73
30631084 TAGAGGTAGA
** * * *
30631094 GATTTCCTTTTTTTTTTTTGTTTTAATCGGTACTTCTCCAAATGTACGATCTTTACTATAGATTA
1 GATTTCCTTTTTCATTTTTGTTTTAATCGGTACTTCTCCAAATATACGATATTTACAATAGATTA
30631159 AAGATAAT
66 AAGATAAT
* ** ** * *
30631167 GATTTTCTTTTTCATTTTTGTTTTAATTTGTACTTCTTTAAATATTCGATATTTACAATATATTA
1 GATTTCCTTTTTCATTTTTGTTTTAATCGGTACTTCTCCAAATATACGATATTTACAATAGATTA
30631232 TTTTCGATAT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 53 1.00
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.54
Consensus pattern (73 bp):
GATTTCCTTTTTCATTTTTGTTTTAATCGGTACTTCTCCAAATATACGATATTTACAATAGATTA
AAGATAAT
Found at i:30631758 original size:30 final size:30
Alignment explanation
Indices: 30631724--30631797 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
30631714 GCATTAGTGG
30631724 CAGATACACCTTCCATTTCAAGAATTGCAT
1 CAGATACACCTTCCATTTCAAGAATTGCAT
*
30631754 CAGATACATCTTCCATTTCAAGAATTGCAT
1 CAGATACACCTTCCATTTCAAGAATTGCAT
30631784 CAGATACACCTTCC
1 CAGATACACCTTCC
30631798 TTCCATGGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.30
Consensus pattern (30 bp):
CAGATACACCTTCCATTTCAAGAATTGCAT
Found at i:30631946 original size:37 final size:37
Alignment explanation
Indices: 30631891--30631961 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
30631881 ATCTGTGAGT
*
30631891 GAGTGAGTAAGAAGAAGAAAAAGAGAGACAAACAAAA
1 GAGTGAGTAAGAAGAAGAAAAAGAGAGAAAAACAAAA
30631928 GAGTGAGTAAG-AGAAAGAAAAAGAGAGAAAAACA
1 GAGTGAGTAAGAAG-AAGAAAAAGAGAGAAAAACA
30631962 GACATCAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
36 2 0.06
37 30 0.94
ACGTcount: A:0.62, C:0.04, G:0.28, T:0.06
Consensus pattern (37 bp):
GAGTGAGTAAGAAGAAGAAAAAGAGAGAAAAACAAAA
Found at i:30634963 original size:347 final size:348
Alignment explanation
Indices: 30634272--30634967 Score: 1038
Period size: 347 Copynumber: 2.0 Consensus size: 348
30634262 TCCAATGGGC
*
30634272 TTCGATTGGATCATGCAGGGTCGTCTTCATCACTACAAATTGGGTTTCCATTCCATGCATCATCA
1 TTCGATTGGATCATGCAGGGTCGTCTTCATCACTACAAACTGGGTTTCCATTCCATGCATCATCA
* * *
30634337 TCTGAACAGACTACGGACCTCTTCCATGAAAGCAACGCAGATTCTGCAGCTGAGCTAAGCAGGAA
66 TCTGAACAGACTACAGACCTCTTCCATGAAAGCAACGCAGATTCTACAGCTGAACTAAGCAGGAA
*** * * *
30634402 ATATGAACAGTGGCTTGCGGAACAATCCAGAGATTAATTTATTCCTTTGAACGTATGCGGCATAG
131 ATATGAACAGTGGCTTAAAGAACAATCCAGAGATTAATTTATTCCTTGGAACGCATGCAGCATAG
*
30634467 CCTGAAAGATATTGCTCAAAATCTTCCAGATGTGGCTTCCATGAGCATAGCCTCTCAGAATGAAA
196 CCTGAAAGATATTGCTCAAAATCTTCCAGACGTGGCTTCCATGAGCATAGCCTCTCAGAATGAAA
* * * * * * *
30634532 CCCAGGAAGCAATTGATTTAGCTCAACCTTCACAAGAAGGGGAATGGGATGTCGCTGTATCTAAT
261 CCCAAGAAGCAATTGATCTAACTCAACCTTCACAAAAAAGGGAAGGGGATGTCGCTGCATCTAAT
*
30634597 GAATATGCGTTGAGGGAGATGGA
326 GAATATGAGTTGAGGGAGATGGA
* * *
30634620 TTCGGTTGGATCATGCAGGGTCGTCTTCATCAGTACAGACTGGGTTTCCATTCCATGCATCATCA
1 TTCGATTGGATCATGCAGGGTCGTCTTCATCACTACAAACTGGGTTTCCATTCCATGCATCATCA
* * * *
30634685 TCTGAACAGACTACAGACCTCTTCCATGAAAGCAACGTAGATTCTATAGCTGAACTAAGTATGAA
66 TCTGAACAGACTACAGACCTCTTCCATGAAAGCAACGCAGATTCTACAGCTGAACTAAGCAGGAA
* * * *
30634750 ATATGAACAGTGGCTTAAAGAATAGTCCA-AGATTAATTTGTTCCTTGGGACGCATGCAGCATA-
131 ATATGAACAGTGGCTTAAAGAACAATCCAGAGATTAATTTATTCCTTGGAACGCATGCAGCATAG
** *
30634813 CCTAGAAAGATATTGCTCCGAATCTTTCAGACGTGGCTTCCATGAGCATAGCCTCTCAGAATG-A
196 CCT-GAAAGATATTGCTCAAAATCTTCCAGACGTGGCTTCCATGAGCATAGCCTCTCAGAATGAA
*
30634877 ACCACAATAAGCAATTGATCTAACTCAACCTTCACAAAAAAGGGAAGGGGATGTCGCTGCATCTA
260 ACC-CAAGAAGCAATTGATCTAACTCAACCTTCACAAAAAAGGGAAGGGGATGTCGCTGCATCTA
*
30634942 ATGAATATGAGTTGGGGGAGATGGA
324 ATGAATATGAGTTGAGGGAGATGGA
30634967 T
1 T
30634968 CCTTATTGTG
Statistics
Matches: 311, Mismatches: 35, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
346 7 0.02
347 161 0.52
348 143 0.46
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (348 bp):
TTCGATTGGATCATGCAGGGTCGTCTTCATCACTACAAACTGGGTTTCCATTCCATGCATCATCA
TCTGAACAGACTACAGACCTCTTCCATGAAAGCAACGCAGATTCTACAGCTGAACTAAGCAGGAA
ATATGAACAGTGGCTTAAAGAACAATCCAGAGATTAATTTATTCCTTGGAACGCATGCAGCATAG
CCTGAAAGATATTGCTCAAAATCTTCCAGACGTGGCTTCCATGAGCATAGCCTCTCAGAATGAAA
CCCAAGAAGCAATTGATCTAACTCAACCTTCACAAAAAAGGGAAGGGGATGTCGCTGCATCTAAT
GAATATGAGTTGAGGGAGATGGA
Found at i:30635301 original size:135 final size:136
Alignment explanation
Indices: 30635055--30635310 Score: 399
Period size: 135 Copynumber: 1.9 Consensus size: 136
30635045 GTTGCACACA
* *
30635055 CAATATACACAACAGGACTCCCCTAAGAATGTATCATTTGCTAGTTCAAATGGTCTTCATTGTTT
1 CAATATACACAACAGGACTCCCCTAAGAATGTATCATTTACTAGTTCAAATGGTCTCCATTGTTT
* * *
30635120 CCACAATCTTGATTCCTGAAGTAATATCCAAACCATTTGGTCAATTTATTAGCTTGCAACTTTGT
66 CCACAATCTCGATTCCTGAAGCAATATCCAAACCATTTGGTCAATTTATCAGCTTGCAACTTTGT
30635185 TTAAAG
131 TTAAAG
* *
30635191 CAATATACACAATAGGACT-CCTTACA-AATGTATCATTTACTAGTTCAAATGGTCTCCATTGTT
1 CAATATACACAACAGGACTCCCCTA-AGAATGTATCATTTACTAGTTCAAATGGTCTCCATTGTT
* * *
30635254 TCCACAATCTCGATTCTTGAAGCAATATCCCAACCATTTGGTGAATTTATCAGCTTG
65 TCCACAATCTCGATTCCTGAAGCAATATCCAAACCATTTGGTCAATTTATCAGCTTG
30635311 AAGCGATGTA
Statistics
Matches: 109, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
135 90 0.83
136 19 0.17
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (136 bp):
CAATATACACAACAGGACTCCCCTAAGAATGTATCATTTACTAGTTCAAATGGTCTCCATTGTTT
CCACAATCTCGATTCCTGAAGCAATATCCAAACCATTTGGTCAATTTATCAGCTTGCAACTTTGT
TTAAAG
Found at i:30651288 original size:18 final size:18
Alignment explanation
Indices: 30651265--30651300 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
30651255 ATTATTAATT
30651265 ATTTTTATATAATTTTAA
1 ATTTTTATATAATTTTAA
*
30651283 ATTTTTATATATTTTTAA
1 ATTTTTATATAATTTTAA
30651301 TATAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTTTTATATAATTTTAA
Found at i:30651376 original size:78 final size:77
Alignment explanation
Indices: 30651290--30651444 Score: 285
Period size: 78 Copynumber: 2.0 Consensus size: 77
30651280 TAAATTTTTA
30651290 TATATTTTTAATATAATTAAATTATATTATAAAATTATAAAACTTTTCTAAATTT-GAGGCCTCT
1 TATATTTTTAATATAATTAAATTATATTATAAAATTATAAAACTTTTCTAAATTTAG-GGCCTCT
30651354 CTAAATTGGGGGC
65 CTAAATTGGGGGC
30651367 NTATATTTTTAATATAATTAAATTATATTATAAAATTATAAAACTTTTCTAAATTTAGGGCCTCT
1 -TATATTTTTAATATAATTAAATTATATTATAAAATTATAAAACTTTTCTAAATTTAGGGCCTCT
30651432 CTAAATTGGGGGC
65 CTAAATTGGGGGC
30651445 CTAAAGTCCT
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
78 75 0.99
79 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.43
Consensus pattern (77 bp):
TATATTTTTAATATAATTAAATTATATTATAAAATTATAAAACTTTTCTAAATTTAGGGCCTCTC
TAAATTGGGGGC
Found at i:30653980 original size:2 final size:2
Alignment explanation
Indices: 30653973--30654016 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
30653963 GTTATTGTGT
30653973 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30654015 TA
1 TA
30654017 CTGTCATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:30654116 original size:2 final size:2
Alignment explanation
Indices: 30654109--30654147 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
30654099 GAGGGAGATN
30654109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30654148 GTCAACCACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30663249 original size:28 final size:27
Alignment explanation
Indices: 30663207--30663268 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
30663197 AAAGATATAT
*
30663207 TTAAATTAAAATAAAAATATAAAATTTAA
1 TTAAA-TAAAATAAAAATA-AAAAATTAA
* *
30663236 TTAAATACAATAAAAATAAAAAATTAT
1 TTAAATAAAATAAAAATAAAAAATTAA
30663263 TTAAAT
1 TTAAAT
30663269 TTTCTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 13 0.43
28 12 0.40
29 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (27 bp):
TTAAATAAAATAAAAATAAAAAATTAA
Found at i:30666052 original size:3 final size:3
Alignment explanation
Indices: 30666044--30666073 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
30666034 GGGCCCTTTC
30666044 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30666074 TTATTCTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:30684384 original size:13 final size:12
Alignment explanation
Indices: 30684360--30684397 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
30684350 GGTATCAAGC
*
30684360 TTTTAACACATT
1 TTTTAGCACATT
30684372 TTTTGAGCACATT
1 TTTT-AGCACATT
30684385 TTTTAGCACATT
1 TTTTAGCACATT
30684397 T
1 T
30684398 CTCCTTCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.50
Consensus pattern (12 bp):
TTTTAGCACATT
Found at i:30711399 original size:2 final size:2
Alignment explanation
Indices: 30711392--30711452 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
30711382 GTCCTACAGT
* *
30711392 TA TA TA TA TT TA TA TA TA TA TA AA TA TA TA TA TA CTA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
*
30711434 TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
30711453 TTAATATAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
1 1 0.02
2 48 0.94
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:30711437 original size:28 final size:26
Alignment explanation
Indices: 30711392--30711460 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 26
30711382 GTCCTACAGT
*
30711392 TATATATATTTATATATATATAAATA
1 TATATATATATATATATATATAAATA
30711418 TATATATACTATATATTATATATAAATA
1 TATATATA-TATATA-TATATATAAATA
*
30711446 TATATATTTA-ATATA
1 TATATATATATATATA
30711461 GAGAGGGAGT
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.05
26 11 0.28
27 7 0.18
28 19 0.49
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
TATATATATATATATATATATAAATA
Found at i:30713421 original size:15 final size:16
Alignment explanation
Indices: 30713384--30713423 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
30713374 CGACAAAATG
*
30713384 TTAATAAGATAAGAAAC
1 TTAATAA-AAAAGAAAC
30713401 TTAATAAAAAAGAAA-
1 TTAATAAAAAAGAAAC
30713416 TTAATAAA
1 TTAATAAA
30713424 CTATAACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 7 0.32
17 7 0.32
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (16 bp):
TTAATAAAAAAGAAAC
Found at i:30723858 original size:3 final size:3
Alignment explanation
Indices: 30723850--30723897 Score: 78
Period size: 3 Copynumber: 16.0 Consensus size: 3
30723840 ATGTTTCTTT
* *
30723850 ATA ATA ATA ATA ATA ATA ATT ATT ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30723898 TTATTATTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:30725699 original size:2 final size:2
Alignment explanation
Indices: 30725692--30725728 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
30725682 CTTAAGGAAT
30725692 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
30725729 TTCTCAGAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30732683 original size:34 final size:34
Alignment explanation
Indices: 30732615--30732682 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 34
30732605 GTAGGTAATA
30732615 TGAAGACTGAAGAGTAATTTTTATAATAATTTTT
1 TGAAGACTGAAGAGTAATTTTTATAATAATTTTT
*
30732649 TGAAGCCTGAAGAGTAA-TTTTATAATAATTTTT
1 TGAAGACTGAAGAGTAATTTTTATAATAATTTTT
30732682 T
1 T
30732683 TAATGTCACA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (34 bp):
TGAAGACTGAAGAGTAATTTTTATAATAATTTTT
Found at i:30740551 original size:9 final size:9
Alignment explanation
Indices: 30740537--30740583 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
30740527 TGCGGTGGCG
30740537 AGAAGCTGA
1 AGAAGCTGA
30740546 AGAAGCTGA
1 AGAAGCTGA
**
30740555 AGAAGGAGA
1 AGAAGCTGA
30740564 AGAAGCTGA
1 AGAAGCTGA
* *
30740573 GGAAGCGGA
1 AGAAGCTGA
30740582 AG
1 AG
30740584 GTTTCATGGC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.45, C:0.09, G:0.40, T:0.06
Consensus pattern (9 bp):
AGAAGCTGA
Found at i:30742750 original size:7 final size:7
Alignment explanation
Indices: 30742730--30742765 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
30742720 CATCAAACTC
30742730 TTTCTTT
1 TTTCTTT
30742737 CTTTCTTT
1 -TTTCTTT
30742745 TTTCTTT
1 TTTCTTT
30742752 TTTC-TT
1 TTTCTTT
30742758 TTTCTTT
1 TTTCTTT
30742765 T
1 T
30742766 CGGGTTGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.22
7 14 0.52
8 7 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTCTTT
Found at i:30742757 original size:14 final size:13
Alignment explanation
Indices: 30742730--30742765 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 13
30742720 CATCAAACTC
30742730 TTTCTTTCTTTCTTT
1 TTTCTTT-TTTC-TT
30742745 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
30742758 TTTCTTTT
1 TTTCTTTT
30742766 CGGGTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 10 0.48
14 4 0.19
15 7 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTTTCTT
Found at i:30743635 original size:19 final size:19
Alignment explanation
Indices: 30743598--30743636 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
30743588 ATTAAAAAGC
*
30743598 ATTAAATATTTCATAAAAA
1 ATTAAATATTTAATAAAAA
*
30743617 ATTAAATA-TTAATACAAA
1 ATTAAATATTTAATAAAAA
30743635 AT
1 AT
30743637 ACATCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAATATTTAATAAAAA
Found at i:30748923 original size:32 final size:32
Alignment explanation
Indices: 30748881--30748947 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
30748871 TTGTTTTTTT
30748881 TTTTGCCAGAGGGG-GGAAGAAGGTATTGGGTG
1 TTTTGCCAGAGGGGAGG-AGAAGGTATTGGGTG
*
30748913 TTTTGGCAGAGGGGAGGAGAAGGTATTGGGTG
1 TTTTGCCAGAGGGGAGGAGAAGGTATTGGGTG
30748945 TTT
1 TTT
30748948 AATATGATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
32 31 0.94
33 2 0.06
ACGTcount: A:0.21, C:0.04, G:0.46, T:0.28
Consensus pattern (32 bp):
TTTTGCCAGAGGGGAGGAGAAGGTATTGGGTG
Found at i:30752961 original size:2 final size:2
Alignment explanation
Indices: 30752954--30753005 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
30752944 TGAGGAAACT
30752954 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
30752996 GA GA GA GA GA
1 GA GA GA GA GA
30753006 TGTCAATTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30758371 original size:15 final size:15
Alignment explanation
Indices: 30758351--30758383 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
30758341 ATATATTATC
30758351 AATAAAAATTACATT
1 AATAAAAATTACATT
*
30758366 AATAAATATTACATT
1 AATAAAAATTACATT
30758381 AAT
1 AAT
30758384 TATAATTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AATAAAAATTACATT
Found at i:30782433 original size:73 final size:74
Alignment explanation
Indices: 30782312--30782452 Score: 214
Period size: 73 Copynumber: 1.9 Consensus size: 74
30782302 ATAAATAGAA
*
30782312 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTGATGAATACACACTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACACTTA
30782377 TAATAGAGT
66 TAATAGAGT
* * * *
30782386 TAAATCTTACTAATAATTATAAT-AAAAATGTTTCAAT-AGTCGTCATTTAATGAATACATATTT
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGA-TCATCATTTAATGAATACACACTT
30782449 ATAA
65 ATAA
30782453 GTGTAGGTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
72 1 0.02
73 37 0.61
74 23 0.38
ACGTcount: A:0.45, C:0.10, G:0.06, T:0.38
Consensus pattern (74 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTAATGAATACACACTTA
TAATAGAGT
Found at i:30795221 original size:16 final size:16
Alignment explanation
Indices: 30795202--30795250 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
30795192 ATCTTCATCT
30795202 TTAATTCTTTTTTAGA
1 TTAATTCTTTTTTAGA
* **
30795218 TTAACTAGTTTTT---
1 TTAATTCTTTTTTAGA
30795231 TTAATTCTTTTTTAGA
1 TTAATTCTTTTTTAGA
30795247 TTAA
1 TTAA
30795251 CTAGTTTTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 10 0.42
16 14 0.58
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TTAATTCTTTTTTAGA
Found at i:30795234 original size:29 final size:29
Alignment explanation
Indices: 30795201--30795258 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
30795191 TATCTTCATC
30795201 TTTAATTCTTTTTTAGATTAACTAGTTTT
1 TTTAATTCTTTTTTAGATTAACTAGTTTT
30795230 TTTAATTCTTTTTTAGATTAACTAGTTTT
1 TTTAATTCTTTTTTAGATTAACTAGTTTT
30795259 ATATCCTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (29 bp):
TTTAATTCTTTTTTAGATTAACTAGTTTT
Found at i:30795258 original size:16 final size:16
Alignment explanation
Indices: 30795210--30795258 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
30795200 CTTTAATTCT
30795210 TTTTTAGATTAACTAG
1 TTTTTAGATTAACTAG
* **
30795226 TTTTT---TTAATTCT
1 TTTTTAGATTAACTAG
30795239 TTTTTAGATTAACTAG
1 TTTTTAGATTAACTAG
30795255 TTTT
1 TTTT
30795259 ATATCCTAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
13 10 0.42
16 14 0.58
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.61
Consensus pattern (16 bp):
TTTTTAGATTAACTAG
Found at i:30795718 original size:209 final size:213
Alignment explanation
Indices: 30795329--30795729 Score: 491
Period size: 209 Copynumber: 1.9 Consensus size: 213
30795319 TATCCTTCAG
* *
30795329 CTTTAGTTCTTTTTTATATTAATTAAGTAATTTATTAATAAAAATAATAAATTTTATAATTAATA
1 CTTTAATTCTTTTTTATATTAATTAAGTAATTTATAAATAAAAATAATAAA--TTAT-ATTAATA
* * * *
30795394 ATTAATTAATTATATTTAATCAACATAATACTTATAATTTTATACTCTCATAACATTGACATGAC
63 ACTAATTAATTAGATTTAATCAAAATAATACTTATAATTTTATACTCTCATAACATTAACATGAC
30795459 ATTAATGTAAAGATAAAAAATATCATATGATCAAATCAATATATCATATCATTATTCATTATAAT
128 ATTAATGTAAAGATAAAAAATAT-ATATGATCAAATCAATATATCATATCATTATTCATTATAAT
30795524 ATCATTATATTTTTATTTTTAT
192 ATCATTATATTTTTATTTTTAT
30795546 CTTTAATT-TTTTTTATATTAATTAAGTAATTTATACAAATAAAAATAATAAA-T-T-TT-ATAA
1 CTTTAATTCTTTTTTATATTAATTAAGTAATTTAT--AAATAAAAATAATAAATTATATTAATAA
* ** * * * **
30795606 CTAA-TGATT-GATTTAATCAAAATAATACTTATTGTTTTATGCTCTCATGACATTAATATGATG
64 CTAATTAATTAGATTTAATCAAAATAATACTTATAATTTTATACTCTCATAACATTAACATGACA
*
30795669 TTAATGTGAAGATAAAAAATAT-TAT-A-CAAA-CATATTATATCGACATATCATTATTCATTAT
129 TTAATGTAAAGATAAAAAATATATATGATCAAATCA-A-TATAT---CATATCATTATTCATTAT
30795730 GACATATTAG
Statistics
Matches: 162, Mismatches: 15, Indels: 22
0.81 0.08 0.11
Matches are distributed among these distances:
204 2 0.01
205 5 0.03
206 6 0.04
207 3 0.02
209 83 0.51
210 4 0.02
211 7 0.04
212 2 0.01
214 1 0.01
215 1 0.01
216 26 0.16
217 7 0.04
218 15 0.09
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (213 bp):
CTTTAATTCTTTTTTATATTAATTAAGTAATTTATAAATAAAAATAATAAATTATATTAATAACT
AATTAATTAGATTTAATCAAAATAATACTTATAATTTTATACTCTCATAACATTAACATGACATT
AATGTAAAGATAAAAAATATATATGATCAAATCAATATATCATATCATTATTCATTATAATATCA
TTATATTTTTATTTTTAT
Found at i:30795871 original size:20 final size:20
Alignment explanation
Indices: 30795825--30795870 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
30795815 TATGACTCAA
* *
30795825 AATAAAA-ATATAAAAATTT
1 AATAAAATAAATAAAAATTC
30795844 AATAAAATAAATAAAAATTC
1 AATAAAATAAATAAAAATTC
30795864 ATATAAA
1 A-ATAAA
30795871 TTTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 7 0.30
20 11 0.48
21 5 0.22
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAAAATAAATAAAAATTC
Found at i:30812765 original size:31 final size:31
Alignment explanation
Indices: 30812727--30812823 Score: 135
Period size: 31 Copynumber: 3.1 Consensus size: 31
30812717 ATCATAACTT
30812727 AATTACAGTTTTCTTGATTAATTAAATTATA
1 AATTACAGTTTTCTTGATTAATTAAATTATA
*
30812758 AATTACAGTTTTCTTCATTAA--AAATTAATA
1 AATTACAGTTTTCTTGATTAATTAAATT-ATA
30812788 CTTAATTACAGTTTTCTTGATTAATTAAATTATA
1 ---AATTACAGTTTTCTTGATTAATTAAATTATA
30812822 AA
1 AA
30812824 CTAGCAACAC
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
29 5 0.09
30 3 0.05
31 22 0.38
33 20 0.34
34 3 0.05
35 5 0.09
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.46
Consensus pattern (31 bp):
AATTACAGTTTTCTTGATTAATTAAATTATA
Found at i:30813297 original size:66 final size:64
Alignment explanation
Indices: 30813192--30813328 Score: 168
Period size: 66 Copynumber: 2.1 Consensus size: 64
30813182 TAATGGCTAA
** * *
30813192 AATTTTTAGCAGTGTCCAATTATGATTAAATTTTGTTTATTTTGTAAGATAATATGC-CAAAATC
1 AATTTTTAGCAGTGTCCAATTATGATTAAATTTAATTTATTCTATAAGATAATAT-CTCAAAATC
** * *
30813256 AATTTTTAGCAGAGTGTTTAATTTTGATTAAATTTAATTTATTCTATACGATAATATCTCAAAAT
1 AATTTTTAGC--AGTGTCCAATTATGATTAAATTTAATTTATTCTATAAGATAATATCTCAAAAT
30813321 C
64 C
30813322 AATTTTT
1 AATTTTT
30813329 TGAGTTTTTC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
64 10 0.16
65 1 0.02
66 51 0.82
ACGTcount: A:0.35, C:0.09, G:0.10, T:0.46
Consensus pattern (64 bp):
AATTTTTAGCAGTGTCCAATTATGATTAAATTTAATTTATTCTATAAGATAATATCTCAAAATC
Found at i:30815943 original size:34 final size:34
Alignment explanation
Indices: 30815900--30815969 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
30815890 TTTATGAGTT
*
30815900 AAATTAATACTTATAATCATTTAACAGCAACATA
1 AAATTAATACTAATAATCATTTAACAGCAACATA
*
30815934 AAATTAATACTAATAATCATTTAACAGCAGCATA
1 AAATTAATACTAATAATCATTTAACAGCAACATA
30815968 AA
1 AA
30815970 GTTTATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.30
Consensus pattern (34 bp):
AAATTAATACTAATAATCATTTAACAGCAACATA
Found at i:30830081 original size:2 final size:2
Alignment explanation
Indices: 30830033--30830068 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
30830023 CATTTTTATG
*
30830033 AT AT AT TT AT AT AT AT AT AT AT AT AT GAT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A
30830069 AATGACTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30830192 original size:27 final size:28
Alignment explanation
Indices: 30830161--30830214 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
30830151 AATTTTCAAA
30830161 TTAATTAAATC-ATTTTAATCAAAATTT
1 TTAATTAAATCAATTTTAATCAAAATTT
* *
30830188 TTAATTAATTCAATTTTAATCGAAATT
1 TTAATTAAATCAATTTTAATCAAAATT
30830215 GTCTGTCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (28 bp):
TTAATTAAATCAATTTTAATCAAAATTT
Found at i:30840353 original size:99 final size:99
Alignment explanation
Indices: 30840180--30840365 Score: 270
Period size: 99 Copynumber: 1.9 Consensus size: 99
30840170 ATCCGTCTAG
* * *
30840180 CTCATTGTAAAAATATGTTAATACCCATTTTGAGAATATAAGTTATGATTAAGGAAAAAATATCC
1 CTCATTGTAAAAATATATTAATACCCATTCTGAGAATATAAGTTACGATTAAGGAAAAAATATCC
* *
30840245 ATGAGGTATTAATTAAGGAAAATCGTCCAATTAA
66 ATGAGGTATTAATCAAGAAAAATCGTCCAATTAA
*
30840279 CTCATTGTAAAAATATATTAATACCCATTCTGAGAATATAAGTTACGATTAA-GACAAGAATATC
1 CTCATTGTAAAAATATATTAATACCCATTCTGAGAATATAAGTTACGATTAAGGA-AAAAATAT-
30840343 CACAT-A-GTATTAATCAAGAAAAA
64 C-CATGAGGTATTAATCAAGAAAAA
30840366 ATATATAATA
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
98 2 0.03
99 71 0.91
100 2 0.03
101 3 0.04
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (99 bp):
CTCATTGTAAAAATATATTAATACCCATTCTGAGAATATAAGTTACGATTAAGGAAAAAATATCC
ATGAGGTATTAATCAAGAAAAATCGTCCAATTAA
Found at i:30843635 original size:14 final size:14
Alignment explanation
Indices: 30843616--30843654 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
30843606 AAAATTATTT
*
30843616 TAATTTTATATAAA
1 TAATTTTAAATAAA
30843630 TAATTTTAAAT-AA
1 TAATTTTAAATAAA
*
30843643 TTATTTTAAATA
1 TAATTTTAAATA
30843655 TTTTTTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TAATTTTAAATAAA
Found at i:30843740 original size:3 final size:3
Alignment explanation
Indices: 30843734--30843775 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
30843724 TCATTTGATG
* * *
30843734 TTA TTA TTA TTA TTA TT- TTA TTA TAA TTA TTT TTA TAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
30843776 AGATTTTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30843756 original size:14 final size:14
Alignment explanation
Indices: 30843737--30843775 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
30843727 TTTGATGTTA
*
30843737 TTATTATTATTATT
1 TTATTATAATTATT
30843751 TTATTATAATTA-T
1 TTATTATAATTATT
30843764 TT-TTATAATTAT
1 TTATTATAATTAT
30843776 AGATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 9 0.39
13 3 0.13
14 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATAATTATT
Found at i:30849523 original size:49 final size:49
Alignment explanation
Indices: 30849448--30849545 Score: 169
Period size: 49 Copynumber: 2.0 Consensus size: 49
30849438 GCATCCGGGG
* *
30849448 GCTGTAGGTATTGCTTGATTCAATTGAGTCATAAATCTTGTATCGGTTA
1 GCTGTAGGTATTGCTTGATTCAATTGAGTCATAAATCTTATATAGGTTA
*
30849497 GCTGTAGGTATTGCTTGATTCGATTGAGTCATAAATCTTATATAGGTTA
1 GCTGTAGGTATTGCTTGATTCAATTGAGTCATAAATCTTATATAGGTTA
30849546 TGTATTAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (49 bp):
GCTGTAGGTATTGCTTGATTCAATTGAGTCATAAATCTTATATAGGTTA
Found at i:30850105 original size:18 final size:18
Alignment explanation
Indices: 30850082--30850121 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
30850072 TTGATAGGTT
*
30850082 TAATTTAAAGAAT-TTATA
1 TAATTT-AAGAATATTAAA
30850100 TAATTTAAGAATATTAAA
1 TAATTTAAGAATATTAAA
30850118 TAAT
1 TAAT
30850122 ATTTCAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
TAATTTAAGAATATTAAA
Found at i:30864192 original size:40 final size:40
Alignment explanation
Indices: 30864137--30864214 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
30864127 TGAGGGAAAG
30864137 AAAGGATGGATTGTTATTAGTTCTTGATAGTGCTTCAAAT
1 AAAGGATGGATTGTTATTAGTTCTTGATAGTGCTTCAAAT
30864177 AAAGGATGGATTGTTATTAGTTCTTGATAGTGCTTCAA
1 AAAGGATGGATTGTTATTAGTTCTTGATAGTGCTTCAA
30864215 TGGTGTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (40 bp):
AAAGGATGGATTGTTATTAGTTCTTGATAGTGCTTCAAAT
Found at i:30898022 original size:2 final size:2
Alignment explanation
Indices: 30898015--30898064 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
30898005 TTATACATGC
30898015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30898057 AT AT AT AT
1 AT AT AT AT
30898065 GTTTCTTCTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30902047 original size:29 final size:29
Alignment explanation
Indices: 30902005--30902102 Score: 178
Period size: 29 Copynumber: 3.4 Consensus size: 29
30901995 ATCTTTATTC
30902005 ATAAGAGTTTAATTAAATGTAATAAAAGA
1 ATAAGAGTTTAATTAAATGTAATAAAAGA
30902034 ATAAGAGTTTAATTAAATGTAATAAAAGA
1 ATAAGAGTTTAATTAAATGTAATAAAAGA
* *
30902063 ATAAGAGTTTAATTAAACGTAATAAAGGA
1 ATAAGAGTTTAATTAAATGTAATAAAAGA
30902092 ATAAGAGTTTA
1 ATAAGAGTTTA
30902103 TTGAATTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.53, C:0.01, G:0.15, T:0.31
Consensus pattern (29 bp):
ATAAGAGTTTAATTAAATGTAATAAAAGA
Found at i:30903808 original size:53 final size:53
Alignment explanation
Indices: 30903740--30903845 Score: 185
Period size: 53 Copynumber: 2.0 Consensus size: 53
30903730 TTTTAGATAG
*
30903740 ACATTATGCACTCTGAAGAACTTATGAAGATACTGAATGTATTTTAATGAGCT
1 ACATTATGCACTCTGAAGAACTAATGAAGATACTGAATGTATTTTAATGAGCT
* *
30903793 ACATTTTGCACTCTGAAGAACTAATGAAGCTACTGAATGTATTTTAATGAGCT
1 ACATTATGCACTCTGAAGAACTAATGAAGATACTGAATGTATTTTAATGAGCT
30903846 CATGATGATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (53 bp):
ACATTATGCACTCTGAAGAACTAATGAAGATACTGAATGTATTTTAATGAGCT
Found at i:30907813 original size:6 final size:6
Alignment explanation
Indices: 30907804--30907836 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
30907794 TGGATGAAAG
30907804 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGA
1 TGAAGA TGAAGA TGAAGA TGAAGA TGAAGA TGA
30907837 TGTGGATGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.18
Consensus pattern (6 bp):
TGAAGA
Found at i:30907819 original size:18 final size:19
Alignment explanation
Indices: 30907796--30907836 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
30907786 TCACCAAATG
30907796 GATGAAAG-TGAAGATGAA
1 GATGAAAGATGAAGATGAA
30907814 GATG-AAGATGAAGATGAA
1 GATGAAAGATGAAGATGAA
30907832 GATGA
1 GATGA
30907837 TGTGGATGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (19 bp):
GATGAAAGATGAAGATGAA
Found at i:30938265 original size:23 final size:23
Alignment explanation
Indices: 30938231--30938274 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
30938221 TTGTTAATTA
30938231 TCCTTTTCTTTTTTCTATATTTT
1 TCCTTTTCTTTTTTCTATATTTT
* *
30938254 TCCTTTTTTTTTTTCTTTATT
1 TCCTTTTCTTTTTTCTATATT
30938275 CTTTATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (23 bp):
TCCTTTTCTTTTTTCTATATTTT
Found at i:30951756 original size:24 final size:24
Alignment explanation
Indices: 30951729--30951778 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
30951719 AACAAAGCTC
*
30951729 AATGGTTAAAGATACGAAACTCTA
1 AATGGTTAAAGATACAAAACTCTA
*
30951753 AATGGTTAAAGATTCAAAACTCTA
1 AATGGTTAAAGATACAAAACTCTA
30951777 AA
1 AA
30951779 ATGTGCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.14, T:0.26
Consensus pattern (24 bp):
AATGGTTAAAGATACAAAACTCTA
Found at i:30956858 original size:2 final size:2
Alignment explanation
Indices: 30956851--30956877 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30956841 AAATTAAATA
30956851 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
30956878 GTTTTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:30964409 original size:41 final size:41
Alignment explanation
Indices: 30964346--30964427 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
30964336 AATTGTTTAC
*
30964346 TTCACAACTCACAAGCCGAGTTCACAGACCAGCCTCCATTT
1 TTCACAACTCACAAGCAGAGTTCACAGACCAGCCTCCATTT
* * *
30964387 TTCACCACTCACAAGTATAGTTCACAGACCAGCCTCCATTT
1 TTCACAACTCACAAGCAGAGTTCACAGACCAGCCTCCATTT
30964428 CCTGCAACTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.29, C:0.35, G:0.11, T:0.24
Consensus pattern (41 bp):
TTCACAACTCACAAGCAGAGTTCACAGACCAGCCTCCATTT
Found at i:30970400 original size:5 final size:5
Alignment explanation
Indices: 30970390--30970414 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
30970380 TGGTGGGGTC
30970390 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
30970415 TTTAACGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:30974985 original size:4 final size:4
Alignment explanation
Indices: 30974978--30975010 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
30974968 TAAAAAAAAA
*
30974978 AAAG AAAG AAAG AAAG AAAT AAAG AAA- AAAG AA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AA
30975011 GTAAAAACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:30997176 original size:3 final size:3
Alignment explanation
Indices: 30997168--30997192 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
30997158 GAGGTAGTGT
30997168 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
30997193 AACCAGTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:30997574 original size:19 final size:19
Alignment explanation
Indices: 30997550--30997588 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
30997540 GGGACAAAGG
30997550 TACCAAGTACATAACATAC
1 TACCAAGTACATAACATAC
30997569 TACCAAGTACATAACATAC
1 TACCAAGTACATAACATAC
30997588 T
1 T
30997589 TGATTTGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.05, T:0.23
Consensus pattern (19 bp):
TACCAAGTACATAACATAC
Found at i:31007407 original size:8 final size:8
Alignment explanation
Indices: 31007394--31007420 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31007384 AAATTCTTTA
31007394 AAAAAAAT
1 AAAAAAAT
31007402 AAAAAAAT
1 AAAAAAAT
31007410 AAAAAAAT
1 AAAAAAAT
31007418 AAA
1 AAA
31007421 TTAAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAAAT
Done.