Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold21
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: 2821038
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 98422 characters in sequence are not A, C, G, or T
File 14 of 15
Found at i:2353149 original size:31 final size:32
Alignment explanation
Indices: 2353114--2353173 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
2353104 ATGTAATCAT
*
2353114 TAAATATTTATTAAAAAAT-TAA-TATATTTTA
1 TAAATATATA-TAAAAAATATAATTATATTTTA
*
2353145 TAAATATATATAATAAATATAATTATATT
1 TAAATATATATAAAAAATATAATTATATT
2353174 ATTTAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 12 0.48
32 6 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TAAATATATATAAAAAATATAATTATATTTTA
Found at i:2354113 original size:15 final size:17
Alignment explanation
Indices: 2354093--2354125 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2354083 ATTTATTGTT
2354093 TTTATTAT-TA-ATATA
1 TTTATTATATATATATA
2354108 TTTATTATATATATATA
1 TTTATTATATATATATA
2354125 T
1 T
2354126 GGAGAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 2 0.12
17 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTATTATATATATATA
Found at i:2356017 original size:17 final size:17
Alignment explanation
Indices: 2355997--2356045 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
2355987 TGTTTAAAAT
2355997 TTTAATATATTTAATAA
1 TTTAATATATTTAATAA
2356014 TTTATATAATATTT-AT-A
1 TTTA-AT-ATATTTAATAA
*
2356031 TTT-ATATAATTAATA
1 TTTAATATATTTAATA
2356046 TTAATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 9
0.73 0.03 0.24
Matches are distributed among these distances:
14 5 0.19
15 4 0.15
17 8 0.30
18 4 0.15
19 6 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATATATTTAATAA
Found at i:2356027 original size:19 final size:17
Alignment explanation
Indices: 2356003--2356040 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 17
2355993 AAATTTTAAT
2356003 ATATTTAATAATTTATATA
1 ATATTT-AT-ATTTATATA
2356022 ATATTTATATTTATATA
1 ATATTTATATTTATATA
2356039 AT
1 AT
2356041 TAATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.58
18 2 0.11
19 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATTTATATTTATATA
Found at i:2361380 original size:2 final size:2
Alignment explanation
Indices: 2361373--2361399 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2361363 GTTCTTTAAC
2361373 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 A
2361400 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2361831 original size:2 final size:2
Alignment explanation
Indices: 2361818--2361854 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2361808 AAAACAAATA
*
2361818 AT AT AT AA 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 AT AT AT
2361855 CAAAATTGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2362851 original size:6 final size:6
Alignment explanation
Indices: 2362840--2362864 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2362830 TTGGCCTAAA
2362840 TTTTGC TTTTGC TTTTGC TTTTGC T
1 TTTTGC TTTTGC TTTTGC TTTTGC T
2362865 AAAACAGATT
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:0.16, G:0.16, T:0.68
Consensus pattern (6 bp):
TTTTGC
Found at i:2368245 original size:24 final size:24
Alignment explanation
Indices: 2368215--2368261 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
2368205 CTGCAGTTGG
2368215 TGGCTTGACTGCG-AAAGTGTTTGT
1 TGGCTTGACTG-GTAAAGTGTTTGT
2368239 TGGCTTGACTGGTAAAGTGTTTG
1 TGGCTTGACTGGTAAAGTGTTTG
2368262 AGGTCTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.17, C:0.11, G:0.34, T:0.38
Consensus pattern (24 bp):
TGGCTTGACTGGTAAAGTGTTTGT
Found at i:2373266 original size:3 final size:3
Alignment explanation
Indices: 2373258--2373283 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2373248 CCATTTTTGC
2373258 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2373284 ATAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2373559 original size:23 final size:23
Alignment explanation
Indices: 2373533--2373589 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2373523 TATTTTTTTT
* *
2373533 ATATATTTTTTTAAAGTTAATTA
1 ATATATTATTTAAAAGTTAATTA
*
2373556 ATATATTATTTAAAATTTAATTA
1 ATATATTATTTAAAAGTTAATTA
*
2373579 AT-TAATATTTA
1 ATATATTATTTA
2373590 TAAAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 8 0.27
23 22 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (23 bp):
ATATATTATTTAAAAGTTAATTA
Found at i:2373587 original size:22 final size:23
Alignment explanation
Indices: 2373544--2373612 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
2373534 TATATTTTTT
* *
2373544 TAAAGTTAATTAATATATTATTTA
1 TAAAATTAATTAAT-TAATATTTA
*
2373568 -AAATTTAATTAATTAATATTTA
1 TAAAATTAATTAATTAATATTTA
* *
2373590 TAAAAAT-ATTAATTAAAATTTA
1 TAAAATTAATTAATTAATATTTA
2373612 T
1 T
2373613 TAACGAGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
22 23 0.59
23 16 0.41
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
TAAAATTAATTAATTAATATTTA
Found at i:2373626 original size:37 final size:36
Alignment explanation
Indices: 2373558--2373634 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 36
2373548 GTTAATTAAT
* **
2373558 ATATTATTTAAAATTTAATTAATTAATATTTATAAAA
1 ATATTAATTAAAATTTAATTAACGAATATTTA-AAAA
* *
2373595 ATATTAATTAAAATTT-ATTAACGAGTAATTTAAAAT
1 ATATTAATTAAAATTTAATTAACGAAT-ATTTAAAAA
2373631 ATAT
1 ATAT
2373635 ACAAAACTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 14 0.41
37 20 0.59
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (36 bp):
ATATTAATTAAAATTTAATTAACGAATATTTAAAAA
Found at i:2391825 original size:30 final size:32
Alignment explanation
Indices: 2391785--2391855 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
2391775 TATATATTTA
*
2391785 TTTAAGTTTTATTT-AATTTA-AAATATAAA-T
1 TTTAAATTTTATTTAAATTTATAAATA-AAATT
2391815 TTTAAATTTTATTTAAATTTATAAATAAAATT
1 TTTAAATTTTATTTAAATTTATAAATAAAATT
2391847 TTTAAATTT
1 TTTAAATTT
2391856 AATAATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
30 13 0.35
31 9 0.24
32 15 0.41
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (32 bp):
TTTAAATTTTATTTAAATTTATAAATAAAATT
Found at i:2391866 original size:31 final size:31
Alignment explanation
Indices: 2391785--2391874 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 31
2391775 TATATATTTA
* *
2391785 TTTAAGTTTTAT-TTAATTTAAAATATAAAT
1 TTTAAATTTTATATAAATTTAAAATATAAAT
*
2391815 TTTAAATTTTATTTAAATTTATAAATA-AAATT
1 TTTAAATTTTATATAAATTTA-AAATATAAA-T
2391847 TTTAAA-TTTA-ATAATATTTAAAAATATA
1 TTTAAATTTTATATAA-ATTT-AAAATATA
2391875 TAAAAATAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
30 14 0.27
31 23 0.45
32 14 0.27
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
TTTAAATTTTATATAAATTTAAAATATAAAT
Found at i:2391924 original size:21 final size:23
Alignment explanation
Indices: 2391880--2391924 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
2391870 ATATATAAAA
* *
2391880 ATAAAAATAATATATATTATATT
1 ATAAAAATAATATAAATTAAATT
2391903 ATAAAAAT-AT-TAAATTAAATT
1 ATAAAAATAATATAAATTAAATT
2391924 A
1 A
2391925 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 2 0.10
23 8 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATAAAAATAATATAAATTAAATT
Found at i:2392527 original size:15 final size:16
Alignment explanation
Indices: 2392507--2392536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2392497 ATTATTCACT
2392507 TATAAT-AAAATTATG
1 TATAATAAAAATTATG
2392522 TATAATAAAAATTAT
1 TATAATAAAAATTAT
2392537 TTATTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
TATAATAAAAATTATG
Found at i:2399567 original size:32 final size:32
Alignment explanation
Indices: 2399529--2399606 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 32
2399519 CAAAAATGAA
* * *
2399529 TATATATATATATATATATAAATATATTAAAATT
1 TATATA-ATATAAAT-TAAAAATATATTAAAACT
2399563 TATATAATATAAATTAAAAATATATTAAAACT
1 TATATAATATAAATTAAAAATATATTAAAACT
2399595 TATATAA-ATAAA
1 TATATAATATAAA
2399607 ACACATAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
31 5 0.12
32 23 0.56
33 7 0.17
34 6 0.15
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
TATATAATATAAATTAAAAATATATTAAAACT
Found at i:2399580 original size:21 final size:20
Alignment explanation
Indices: 2399543--2399581 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2399533 TATATATATA
*
2399543 TATATAAATATATTAAAATT
1 TATATAAATAAATTAAAATT
2399563 TATATAATATAAATTAAAA
1 TATATAA-ATAAATTAAAA
2399582 ATATATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATAAATAAATTAAAATT
Found at i:2399586 original size:20 final size:20
Alignment explanation
Indices: 2399540--2399587 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2399530 ATATATATAT
*
2399540 ATATATATAAATATATTAAA
1 ATATATATAAATAAATTAAA
*
2399560 ATTTATATAATATAAATTAAA
1 ATATATATAA-ATAAATTAAA
2399581 A-ATATAT
1 ATATATAT
2399588 TAAAACTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATATATAAATAAATTAAA
Found at i:2399603 original size:20 final size:19
Alignment explanation
Indices: 2399543--2399604 Score: 64
Period size: 15 Copynumber: 3.5 Consensus size: 19
2399533 TATATATATA
2399543 TATATAAATATATTAAAAT
1 TATATAAATATATTAAAAT
*
2399562 T-TATATA-ATA-T-AAAT
1 TATATAAATATATTAAAAT
2399577 TA-A-AAATATATTAAAACT
1 TATATAAATATATTAAAA-T
2399595 TATATAAATA
1 TATATAAATA
2399605 AAACACATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
14 2 0.06
15 9 0.26
16 2 0.06
17 6 0.18
18 8 0.24
19 2 0.06
20 5 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATAAATATATTAAAAT
Found at i:2410249 original size:21 final size:21
Alignment explanation
Indices: 2410172--2410332 Score: 110
Period size: 21 Copynumber: 7.7 Consensus size: 21
2410162 CACATCATCC
*
2410172 CCTGGTTACAGTCC-ATCATCT
1 CCTGGTTACAGTCCTA-CGTCT
* * * * *
2410193 CCAGGATACACTCCTTCGTCC
1 CCTGGTTACAGTCCTACGTCT
* *
2410214 CCTGGCTACAGTCCTACCTCT
1 CCTGGTTACAGTCCTACGTCT
2410235 CCTGGTTACAGTCCTACGTCT
1 CCTGGTTACAGTCCTACGTCT
* * * *
2410256 CCTGGATATAGTCCCACCTCT
1 CCTGGTTACAGTCCTACGTCT
* * * *
2410277 CCTGGGTACAGCCCCACGTCA
1 CCTGGTTACAGTCCTACGTCT
** *
2410298 CCTACTTACAGTCCTA-GTTCA
1 CCTGGTTACAGTCCTACG-TCT
*
2410319 CCAGGTTACAGTCC
1 CCTGGTTACAGTCC
2410333 AACAAGTCCA
Statistics
Matches: 107, Mismatches: 31, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
20 1 0.01
21 106 0.99
ACGTcount: A:0.19, C:0.38, G:0.16, T:0.27
Consensus pattern (21 bp):
CCTGGTTACAGTCCTACGTCT
Found at i:2410279 original size:42 final size:42
Alignment explanation
Indices: 2410169--2410296 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 42
2410159 TCCCACATCA
* * * * *
2410169 TCCCCTGGTTACAGT-CCATCATCTCCAGGATACACTCCTTCG
1 TCCCCTGGATACAGTCCCA-CCTCTCCTGGATACAGTCCTACG
* * *
2410211 TCCCCTGGCTACAGTCCTACCTCTCCTGGTTACAGTCCTACG
1 TCCCCTGGATACAGTCCCACCTCTCCTGGATACAGTCCTACG
* * * * *
2410253 TCTCCTGGATATAGTCCCACCTCTCCTGGGTACAGCCCCACG
1 TCCCCTGGATACAGTCCCACCTCTCCTGGATACAGTCCTACG
2410295 TC
1 TC
2410297 ACCTACTTAC
Statistics
Matches: 71, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 69 0.97
43 2 0.03
ACGTcount: A:0.16, C:0.40, G:0.16, T:0.27
Consensus pattern (42 bp):
TCCCCTGGATACAGTCCCACCTCTCCTGGATACAGTCCTACG
Found at i:2410484 original size:21 final size:21
Alignment explanation
Indices: 2410382--2410531 Score: 97
Period size: 21 Copynumber: 7.1 Consensus size: 21
2410372 TCCAACCTCA
* *
2410382 CCAAGCTATAGCCCTACCTCT
1 CCAAGCTATAGCCCCACTTCT
* * * *
2410403 CCAAGTTACAGTCCTACTTCT
1 CCAAGCTATAGCCCCACTTCT
* * *
2410424 CCAAGTTATAGTCCCACATCT
1 CCAAGCTATAGCCCCACTTCT
* *
2410445 CCCAGCTATAGCCCAACTTCT
1 CCAAGCTATAGCCCCACTTCT
* * *
2410466 CCTAGCTACAGCCCCACTTCA
1 CCAAGCTATAGCCCCACTTCT
* * * *
2410487 CC-CGTATATAGCCCAACTTCA
1 CCAAG-CTATAGCCCCACTTCT
*
2410508 CC-CGCATATAGCCCCACTTCT
1 CCAAGC-TATAGCCCCACTTCT
2410529 CCA
1 CCA
2410532 TCATACAGTC
Statistics
Matches: 103, Mismatches: 23, Indels: 5
0.79 0.18 0.04
Matches are distributed among these distances:
20 1 0.01
21 102 0.99
ACGTcount: A:0.25, C:0.41, G:0.09, T:0.25
Consensus pattern (21 bp):
CCAAGCTATAGCCCCACTTCT
Found at i:2410497 original size:63 final size:63
Alignment explanation
Indices: 2410373--2410531 Score: 153
Period size: 63 Copynumber: 2.5 Consensus size: 63
2410363 TTCTTATTCT
* * * * * * * *
2410373 CCAACCTCACCAAGCTATAGCCCTACCTCTCCAAGTTACAGTCCTACTTCTCCAAGTTATAGTC
1 CCAACATCACCCAGCTATAGCCCAACTTCTCCAAGCTACAGCCCCACTTCACCAAGTTATAG-C
* * *
2410437 CC-ACATCTCCCAGCTATAGCCCAACTTCTCCTAGCTACAGCCCCACTTCACC-CGTATATAGC
1 CCAACATCACCCAGCTATAGCCCAACTTCTCCAAGCTACAGCCCCACTTCACCAAGT-TATAGC
* *
2410499 CCAACTTCACCC-GCATATAGCCCCACTTCTCCA
1 CCAACATCACCCAGC-TATAGCCCAACTTCTCCA
2410532 TCATACAGTC
Statistics
Matches: 77, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
62 7 0.09
63 68 0.88
64 2 0.03
ACGTcount: A:0.25, C:0.42, G:0.09, T:0.24
Consensus pattern (63 bp):
CCAACATCACCCAGCTATAGCCCAACTTCTCCAAGCTACAGCCCCACTTCACCAAGTTATAGC
Found at i:2410536 original size:21 final size:21
Alignment explanation
Indices: 2410451--2410657 Score: 112
Period size: 21 Copynumber: 9.9 Consensus size: 21
2410441 ATCTCCCAGC
*
2410451 TATAGCCCAACTTCTCCTAGC-
1 TATAGCCCAACTTCTCC-ATCA
* * * *
2410472 TACAGCCCCACTTCACCCGT-A
1 TATAGCCCAACTTC-TCCATCA
* **
2410493 TATAGCCCAACTTCACCCGCA
1 TATAGCCCAACTTCTCCATCA
*
2410514 TATAGCCCCACTTCTCCATCA
1 TATAGCCCAACTTCTCCATCA
* * * *
2410535 TACAGTCCAACATCCCCATCA
1 TATAGCCCAACTTCTCCATCA
* * * *
2410556 TATAGCCCGACATCTCCTTCC
1 TATAGCCCAACTTCTCCATCA
* * * * *
2410577 TACAGCCCAACCTCACCCTCC
1 TATAGCCCAACTTCTCCATCA
* *
2410598 TATAGCCCTACATCTCCATCA
1 TATAGCCCAACTTCTCCATCA
* * * * *
2410619 TACAGCCCTACTTCACCAGCT
1 TATAGCCCAACTTCTCCATCA
*
2410640 TATAGCCCCACTTCTCCA
1 TATAGCCCAACTTCTCCA
2410658 GGGTACAGTC
Statistics
Matches: 139, Mismatches: 44, Indels: 6
0.74 0.23 0.03
Matches are distributed among these distances:
20 2 0.01
21 135 0.97
22 2 0.01
ACGTcount: A:0.25, C:0.44, G:0.07, T:0.24
Consensus pattern (21 bp):
TATAGCCCAACTTCTCCATCA
Found at i:2410644 original size:84 final size:84
Alignment explanation
Indices: 2410496--2410656 Score: 205
Period size: 84 Copynumber: 1.9 Consensus size: 84
2410486 ACCCGTATAT
* * * * *
2410496 AGCCCAACTTCACCCGCATATAGCCCCACTTCTCCATCATACAGTCCAACATCCCCATCATATAG
1 AGCCCAACCTCACCCGCATATAGCCCCACATCTCCATCATACAGCCCAACATCACCAGCATATAG
*
2410561 CCCGACATCTCCTTCCTAC
66 CCCCACATCTCCTTCCTAC
* * * * * *
2410580 AGCCCAACCTCACCCTCCTATAGCCCTACATCTCCATCATACAGCCCTACTTCACCAGCTTATAG
1 AGCCCAACCTCACCCGCATATAGCCCCACATCTCCATCATACAGCCCAACATCACCAGCATATAG
*
2410645 CCCCACTTCTCC
66 CCCCACATCTCC
2410657 AGGGTACAGT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
84 64 1.00
ACGTcount: A:0.25, C:0.45, G:0.07, T:0.23
Consensus pattern (84 bp):
AGCCCAACCTCACCCGCATATAGCCCCACATCTCCATCATACAGCCCAACATCACCAGCATATAG
CCCCACATCTCCTTCCTAC
Found at i:2410665 original size:42 final size:41
Alignment explanation
Indices: 2410373--2410699 Score: 174
Period size: 42 Copynumber: 7.8 Consensus size: 41
2410363 TTCTTATTCT
* * * *** *
2410373 CCAACCTCACCAAGCTATAGCCCTACCTCTCCAAGTTACAGT
1 CCAACTTCACC-AGCTATAGCCCCACATCTCCATCATACAGC
* * * * * *
2410415 CCTACTTCTCCAAGTTATAGTCCCACATCTCCCAGC-TATAGC
1 CCAACTTCACC-AGCTATAGCCCCACATCT-CCATCATACAGC
* * * * * *
2410457 CCAACTTCTCCTAGCTACAGCCCCACTTCACCCGT-ATATAGC
1 CCAACTTCACC-AGCTATAGCCCCACATC-TCCATCATACAGC
* * *
2410499 CCAACTTCACCCGCATATAGCCCCACTTCTCCATCATACAGT
1 CCAACTTCACCAGC-TATAGCCCCACATCTCCATCATACAGC
* * * * * *
2410541 CCAACATCCCCATCATATAGCCCGACATCTCCTTCCTACAGC
1 CCAACTTCACCAGC-TATAGCCCCACATCTCCATCATACAGC
* ** *
2410583 CCAACCTCACCCTCCTATAGCCCTACATCTCCATCATACAGC
1 CCAACTTCA-CCAGCTATAGCCCCACATCTCCATCATACAGC
* * ***
2410625 CCTACTTCACCAGCTTATAGCCCCACTTCTCCAGGGTACAGTC
1 CCAACTTCACCAGC-TATAGCCCCACATCTCCATCATACAG-C
* * *
2410668 CC-ACGTCACCCAGCTATAGCCCTACCTCTCCA
1 CCAACTTCA-CCAGCTATAGCCCCACATCTCCA
2410700 AGTTACAATC
Statistics
Matches: 221, Mismatches: 55, Indels: 18
0.75 0.19 0.06
Matches are distributed among these distances:
41 8 0.04
42 199 0.90
43 14 0.06
ACGTcount: A:0.25, C:0.43, G:0.09, T:0.23
Consensus pattern (41 bp):
CCAACTTCACCAGCTATAGCCCCACATCTCCATCATACAGC
Found at i:2410665 original size:84 final size:84
Alignment explanation
Indices: 2410496--2410699 Score: 203
Period size: 84 Copynumber: 2.4 Consensus size: 84
2410486 ACCCGTATAT
* * * * * * * *
2410496 AGCCCAACTTCACCCGCATATAGCCCCACTTCTCCATCATACAGTCCAACATCCCCATCATATAG
1 AGCCCAACCTCACCCACCTATAGCCCTACATCTCCATCATACAGCCCAACATCACCAGCATATAG
* **
2410561 CCCGACATCTCCTTCCTAC
66 CCCCACATCTCCAGCCTAC
* * * *
2410580 AGCCCAACCTCACCCTCCTATAGCCCTACATCTCCATCATACAGCCCTACTTCACCAGCTTATAG
1 AGCCCAACCTCACCCACCTATAGCCCTACATCTCCATCATACAGCCCAACATCACCAGCATATAG
* **
2410645 CCCCACTTCTCCAGGGTAC
66 CCCCACATCTCCAGCCTAC
* * *
2410664 AGTCCC-ACGTCACCCAGCTATAGCCCTACCTCTCCA
1 AG-CCCAACCTCACCCACCTATAGCCCTACATCTCCA
2410700 AGTTACAATC
Statistics
Matches: 98, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
84 95 0.97
85 3 0.03
ACGTcount: A:0.25, C:0.45, G:0.09, T:0.22
Consensus pattern (84 bp):
AGCCCAACCTCACCCACCTATAGCCCTACATCTCCATCATACAGCCCAACATCACCAGCATATAG
CCCCACATCTCCAGCCTAC
Found at i:2415104 original size:19 final size:20
Alignment explanation
Indices: 2415063--2415104 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2415053 ACGATTTTTT
* *
2415063 AATTAAGTAATATTTTTATA
1 AATTAAGTAATATTTTAAAA
*
2415083 AATTAATTAA-ATTTTAAAA
1 AATTAAGTAATATTTTAAAA
2415102 AAT
1 AAT
2415105 AATAAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
AATTAAGTAATATTTTAAAA
Found at i:2415178 original size:25 final size:25
Alignment explanation
Indices: 2415133--2415184 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
2415123 AATTATTATT
* *
2415133 TTTTAAAAAATATATATTTAATTAA
1 TTTTAAAAAAAATATATTTAATAAA
*
2415158 TTTTAAAAAAAAT-TGTATTAATAAA
1 TTTTAAAAAAAATATAT-TTAATAAA
2415183 TT
1 TT
2415185 AAAATGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
TTTTAAAAAAAATATATTTAATAAA
Found at i:2415266 original size:19 final size:21
Alignment explanation
Indices: 2415244--2415296 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
2415234 ATTATTATTT
2415244 TTTAATAAAATTAA-AT-TAA
1 TTTAATAAAATTAAGATATAA
* *
2415263 TTTAAAAAAATTAAGGTATAA
1 TTTAATAAAATTAAGATATAA
2415284 TTT-ATAAAATTAA
1 TTTAATAAAATTAA
2415297 TTGTTAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 13 0.45
20 10 0.34
21 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TTTAATAAAATTAAGATATAA
Found at i:2415411 original size:16 final size:16
Alignment explanation
Indices: 2415390--2415420 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2415380 TATAAAATTA
2415390 ATTTAATTTATTTTTT
1 ATTTAATTTATTTTTT
2415406 ATTTAATTTATTTTT
1 ATTTAATTTATTTTT
2415421 ACATGTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTAATTTATTTTTT
Found at i:2415607 original size:23 final size:23
Alignment explanation
Indices: 2415572--2415616 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2415562 TAAAAAAATT
*
2415572 TAAAATATAATTTATTTTTATTTA
1 TAAAATATAATTTA-ATTTATTTA
2415596 TAAAAT-TAATTTAATTTATTT
1 TAAAATATAATTTAATTTATTT
2415617 TTATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 7 0.35
24 6 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
TAAAATATAATTTAATTTATTTA
Found at i:2415612 original size:24 final size:24
Alignment explanation
Indices: 2415572--2415620 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 24
2415562 TAAAAAAATT
2415572 TAAAATATAATTTATTT-TTATTTA
1 TAAAATATAATTTATTTATT-TTTA
2415596 TAAAAT-TAATTTAATTTATTTTTA
1 TAAAATATAATTT-ATTTATTTTTA
2415620 T
1 T
2415621 TTATAAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.26
24 15 0.65
25 2 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TAAAATATAATTTATTTATTTTTA
Found at i:2415629 original size:23 final size:23
Alignment explanation
Indices: 2415569--2415630 Score: 63
Period size: 28 Copynumber: 2.5 Consensus size: 23
2415559 ATTTAAAAAA
*
2415569 ATTTA-AAATATAATTTATTTTT
1 ATTTATAAATTTAATTTATTTTT
2415591 ATTTATAAAATTAATTTAATTTATTTTT
1 ATTTAT---A--AATTTAATTTATTTTT
2415619 ATTTATAAATTT
1 ATTTATAAATTT
2415631 TTTTGGTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
22 5 0.15
23 5 0.15
25 1 0.03
26 1 0.03
28 21 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTATAAATTTAATTTATTTTT
Found at i:2419461 original size:24 final size:25
Alignment explanation
Indices: 2419434--2419497 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
2419424 AAATTTATAT
2419434 ATAATAAAATAAA-AAATAAATTTC
1 ATAATAAAATAAATAAATAAATTTC
* *
2419458 AT-A-AAAATAAATTAAATTAATTTT
1 ATAATAAAATAAA-TAAATAAATTTC
2419482 ATAAATAAAAATAAAT
1 AT-AAT-AAAATAAAT
2419498 TAGATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
22 8 0.25
23 1 0.03
24 13 0.41
26 1 0.03
27 1 0.03
28 8 0.25
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATAATAAAATAAATAAATAAATTTC
Found at i:2419487 original size:18 final size:18
Alignment explanation
Indices: 2419464--2419549 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 18
2419454 TTTCATAAAA
2419464 ATAAATTAAATTAATTTT
1 ATAAATTAAATTAATTTT
*
2419482 ATAAATAAAAATAAATTAGATTTA
1 ATAAAT-----TAAATTA-ATTTT
*
2419506 AAAAATTAAATT-ATTTT
1 ATAAATTAAATTAATTTT
* *
2419523 AAAAATTAAATTAAATTT
1 ATAAATTAAATTAATTTT
2419541 ATATAATTA
1 ATA-AATTA
2419550 TATCAAAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
17 16 0.29
18 12 0.22
19 11 0.20
23 7 0.13
24 9 0.16
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (18 bp):
ATAAATTAAATTAATTTT
Found at i:2419516 original size:23 final size:22
Alignment explanation
Indices: 2419439--2419516 Score: 54
Period size: 24 Copynumber: 3.5 Consensus size: 22
2419429 TATATATAAT
*
2419439 AAAA-TAAA-AAATAAATTTCATA
1 AAAATTAAATAAATTAATTT-A-A
*
2419461 AAAA-TAAATTAAATTAATTTTA
1 AAAATTAAA-TAAATTAATTTAA
* *
2419483 TAAATAAAAATAAATTAGATTTAA
1 AAAAT-TAAATAAATTA-ATTTAA
2419507 AAAATTAAAT
1 AAAATTAAAT
2419517 TATTTTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
22 12 0.27
23 11 0.25
24 21 0.48
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (22 bp):
AAAATTAAATAAATTAATTTAA
Found at i:2419549 original size:19 final size:18
Alignment explanation
Indices: 2419487--2419541 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
2419477 ATTTTATAAA
*
2419487 TAAAAA-TAAATTAGATT
1 TAAAAATTAAATTAAATT
*
2419504 TAAAAAATTAAATT-ATTT
1 T-AAAAATTAAATTAAATT
2419522 TAAAAATTAAATTAAATT
1 TAAAAATTAAATTAAATT
2419540 TA
1 TA
2419542 TATAATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 13 0.41
18 13 0.41
19 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
TAAAAATTAAATTAAATT
Found at i:2420122 original size:14 final size:14
Alignment explanation
Indices: 2420103--2420207 Score: 65
Period size: 14 Copynumber: 7.5 Consensus size: 14
2420093 AATATTCATA
2420103 AAAAAAATTTATTT
1 AAAAAAATTTATTT
2420117 AAAAAAATTTATTT
1 AAAAAAATTTATTT
* * **
2420131 TAGATGA-TTATTT
1 AAAAAAATTTATTT
** *
2420144 --TTAAATATATTCGT
1 AAAAAAATTTATT--T
2420158 AAAAAAATTTATTT
1 AAAAAAATTTATTT
* *
2420172 TAAAAAATAT-TTT
1 AAAAAAATTTATTT
2420185 ATAAAAAATTTATTT
1 A-AAAAAATTTATTT
2420200 ACAAAAAA
1 A-AAAAAA
2420208 AAAAATTAAC
Statistics
Matches: 67, Mismatches: 17, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
11 1 0.01
12 4 0.06
13 9 0.13
14 35 0.52
15 10 0.15
16 8 0.12
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (14 bp):
AAAAAAATTTATTT
Found at i:2420181 original size:28 final size:28
Alignment explanation
Indices: 2420138--2420199 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2420128 TTTTAGATGA
* *
2420138 TTATTTTTAAATATATTCGTA-AAAAAAT
1 TTATTTTAAAAAATATT-GTATAAAAAAT
*
2420166 TTATTTTAAAAAATATTTTATAAAAAAT
1 TTATTTTAAAAAATATTGTATAAAAAAT
2420194 TTATTT
1 TTATTT
2420200 ACAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 2 0.07
28 28 0.93
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (28 bp):
TTATTTTAAAAAATATTGTATAAAAAAT
Found at i:2420198 original size:56 final size:56
Alignment explanation
Indices: 2420094--2420199 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 56
2420084 TTCAACTATA
* * **
2420094 ATATTCATAAAAAAAATTTATTTAAAAAAATTTATTTTAGATGATTATTTTTAAAT
1 ATATTCATAAAAAAAATTTATTTAAAAAAATTTATTATAAAAAATTATTTTTAAAT
* *
2420150 ATATTCGT-AAAAAAATTTATTTTAAAAAATATT-TTATAAAAAATTTATTT
1 ATATTCATAAAAAAAATTTATTTAAAAAAAT-TTATTATAAAAAA-TTATTT
2420200 ACAAAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
55 27 0.64
56 15 0.36
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (56 bp):
ATATTCATAAAAAAAATTTATTTAAAAAAATTTATTATAAAAAATTATTTTTAAAT
Found at i:2427427 original size:2 final size:2
Alignment explanation
Indices: 2427420--2427450 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2427410 ATGGTAAGAC
2427420 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2427451 ATGTTTGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:2429062 original size:7 final size:7
Alignment explanation
Indices: 2429052--2429091 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
2429042 CATTCACTTC
*
2429052 CAACTTT
1 CAACTCT
*
2429059 CAACTTT
1 CAACTCT
2429066 CAACTCT
1 CAACTCT
2429073 CAACTCT
1 CAACTCT
2429080 CAACTCT
1 CAACTCT
2429087 CAACT
1 CAACT
2429092 AATCAACGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.33
Consensus pattern (7 bp):
CAACTCT
Found at i:2429069 original size:14 final size:14
Alignment explanation
Indices: 2429047--2429091 Score: 63
Period size: 14 Copynumber: 3.2 Consensus size: 14
2429037 CTCAGCATTC
* *
2429047 ACTTCCAACTTTCA
1 ACTTTCAACTCTCA
2429061 ACTTTCAACTCTCA
1 ACTTTCAACTCTCA
*
2429075 ACTCTCAACTCTCA
1 ACTTTCAACTCTCA
2429089 ACT
1 ACT
2429092 AATCAACGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.33
Consensus pattern (14 bp):
ACTTTCAACTCTCA
Found at i:2433551 original size:9 final size:9
Alignment explanation
Indices: 2433537--2433568 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
2433527 ATCAAGAGAA
2433537 TGTTTTGTT
1 TGTTTTGTT
2433546 TGTTTTGTT
1 TGTTTTGTT
2433555 TGTTTTGTT
1 TGTTTTGTT
2433564 TGTTT
1 TGTTT
2433569 CTGCACCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (9 bp):
TGTTTTGTT
Found at i:2433719 original size:2 final size:2
Alignment explanation
Indices: 2433673--2433702 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2433663 ATGTTTTCTT
2433673 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
2433703 GAGACACACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2437524 original size:20 final size:19
Alignment explanation
Indices: 2437481--2437524 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
2437471 TAAATATTAA
*
2437481 AAATATAATTTTTTTGTTTT
1 AAAT-TAATTTTTTTATTTT
2437501 -AATTAATTTTTTTATCTTT
1 AAATTAATTTTTTTAT-TTT
2437520 AAATT
1 AAATT
2437525 TTTTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 11 0.52
19 6 0.29
20 4 0.19
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
AAATTAATTTTTTTATTTT
Found at i:2437586 original size:25 final size:24
Alignment explanation
Indices: 2437553--2437614 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 24
2437543 AAATTTATTT
2437553 TTAAA-TAAAAATAATATA-ATAGA
1 TTAAATTAAAAATAATATATATA-A
**
2437576 TTAATATTAAAGTTAATATATATAA
1 TTAA-ATTAAAAATAATATATATAA
*
2437601 TTGAATTAAAAATA
1 TTAAATTAAAAATA
2437615 CGTATAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
23 4 0.13
24 9 0.29
25 15 0.48
26 3 0.10
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (24 bp):
TTAAATTAAAAATAATATATATAA
Found at i:2441361 original size:11 final size:10
Alignment explanation
Indices: 2441277--2441376 Score: 57
Period size: 11 Copynumber: 9.9 Consensus size: 10
2441267 ATTATATGAA
2441277 TAAAATATAT
1 TAAAATATAT
2441287 ATAAAATA-AT
1 -TAAAATATAT
*
2441297 TAAAATTTA-
1 TAAAATATAT
*
2441306 TATAATATTAAT
1 TAAAATA-T-AT
* *
2441318 TATTAATATTT
1 TA-AAATATAT
*
2441329 TAAAATCTA-
1 TAAAATATAT
*
2441338 TATAA-ATA-
1 TAAAATATAT
2441346 TAAAATATAT
1 TAAAATATAT
2441356 TAAAAATATGAT
1 T-AAAATAT-AT
2441368 TAAAATATA
1 TAAAATATA
2441377 ATGTACAAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
8 6 0.09
9 18 0.26
10 10 0.14
11 25 0.36
12 6 0.09
13 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (10 bp):
TAAAATATAT
Found at i:2442379 original size:2 final size:2
Alignment explanation
Indices: 2442374--2442398 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2442364 CGTGTAAAAT
2442374 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
2442399 GTTAATTCTA
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:2443381 original size:23 final size:21
Alignment explanation
Indices: 2443348--2443389 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
2443338 AGGAACATGG
*
2443348 ATGGGATGGGATGGGATGGGACT
1 ATGGGAAGGGA-GGGA-GGGACT
2443371 ATGGGAAGGGAGGGAGGGA
1 ATGGGAAGGGAGGGAGGGA
2443390 GAATGGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.26, C:0.02, G:0.57, T:0.14
Consensus pattern (21 bp):
ATGGGAAGGGAGGGAGGGACT
Found at i:2443537 original size:1 final size:1
Alignment explanation
Indices: 2443531--2443555 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2443521 ACAACAACTT
2443531 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
2443556 TTTTCAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:2446401 original size:27 final size:27
Alignment explanation
Indices: 2446371--2446422 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2446361 ATATATTTAT
2446371 TAAAAATAAAAA-ATAATAAATAATAAA
1 TAAAAATAAAAATA-AATAAATAATAAA
**
2446398 TAAAAATTTAAATAAATAAATAATA
1 TAAAAATAAAAATAAATAAATAATA
2446423 TTTTTAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (27 bp):
TAAAAATAAAAATAAATAAATAATAAA
Found at i:2449388 original size:2 final size:2
Alignment explanation
Indices: 2449381--2449430 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2449371 GAATGACATC
2449381 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
2449423 AT AT AT AT
1 AT AT AT AT
2449431 CTTTTGCTGT
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:2459750 original size:1 final size:1
Alignment explanation
Indices: 2459746--2459782 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
2459736 AAGAGGAACC
2459746 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2459783 TTATAAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2467716 original size:78 final size:78
Alignment explanation
Indices: 2467622--2467777 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
2467612 ATGCATGGAT
*
2467622 TTATGAAAAGTAAAAGAGTTAAAGACACCTCTGCAAATAAAGAAATATTGAATCATGGACCTGTC
1 TTATGAAAAGTAAAAGAGTTAAAGACACCCCTGCAAATAAAGAAATATTGAATCATGGACCTGTC
2467687 ACACATATACTAC
66 ACACATATACTAC
2467700 TTATGAAAAGTAAAAGAGTTAAAGACACCCCTGCAAATAAAGAAATATTGAATCATGGACCTGTC
1 TTATGAAAAGTAAAAGAGTTAAAGACACCCCTGCAAATAAAGAAATATTGAATCATGGACCTGTC
2467765 ACACATATACTAC
66 ACACATATACTAC
2467778 AAATAAAAGT
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (78 bp):
TTATGAAAAGTAAAAGAGTTAAAGACACCCCTGCAAATAAAGAAATATTGAATCATGGACCTGTC
ACACATATACTAC
Found at i:2470696 original size:2 final size:2
Alignment explanation
Indices: 2470686--2470715 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2470676 TGTGTGTGTG
*
2470686 TA TA CA 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
2470716 GTAATGGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2478225 original size:2 final size:2
Alignment explanation
Indices: 2478218--2478251 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2478208 CTTCTGCTTA
2478218 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
2478252 TGTACAGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2488761 original size:3 final size:3
Alignment explanation
Indices: 2488748--2488784 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
2488738 TTCAAAATTG
*
2488748 AGA AAA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2488785 CAATAGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2492006 original size:2 final size:2
Alignment explanation
Indices: 2491999--2492031 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2491989 GACTTTTGTT
2491999 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 T
2492032 CAAACTTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2492218 original size:1 final size:1
Alignment explanation
Indices: 2492212--2492242 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
2492202 TGTTGAAGAG
2492212 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2492243 CTGGATAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:2498973 original size:20 final size:19
Alignment explanation
Indices: 2498919--2498973 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
2498909 AAAACCATTA
*
2498919 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
2498939 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
2498959 AATGTATCGATACAT
1 AAAGTATCGATACAT
2498974 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:2499051 original size:13 final size:13
Alignment explanation
Indices: 2499033--2499058 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2499023 TACACCAAGT
2499033 ATGTATCGATACA
1 ATGTATCGATACA
2499046 ATGTATCGATACA
1 ATGTATCGATACA
2499059 CAAAAACTTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2503238 original size:23 final size:24
Alignment explanation
Indices: 2503211--2503279 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 24
2503201 AAATGCTATC
2503211 ATTTTTGTTTGTAAAAAATGAT-G
1 ATTTTTGTTTGTAAAAAATGATGG
* *
2503234 ATTTTTTTTTGTAAAAAATTATGG
1 ATTTTTGTTTGTAAAAAATGATGG
* * * *
2503258 CTTGTTGTTTGTTAAAATTGAT
1 ATTTTTGTTTGTAAAAAATGAT
2503280 AGTTATTTTT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 20 0.54
24 17 0.46
ACGTcount: A:0.30, C:0.01, G:0.16, T:0.52
Consensus pattern (24 bp):
ATTTTTGTTTGTAAAAAATGATGG
Found at i:2512738 original size:2 final size:2
Alignment explanation
Indices: 2512731--2512764 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2512721 CTTACCTTAC
2512731 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
2512765 CCTTATCGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2514407 original size:11 final size:12
Alignment explanation
Indices: 2514385--2514442 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 12
2514375 CGATTCATTT
2514385 TTAAATAAATTA
1 TTAAATAAATTA
2514397 TTAAA-AAATTA
1 TTAAATAAATTA
** *
2514408 TTATTTTAATT-
1 TTAAATAAATTA
2514419 TATAAA-AAATTA
1 T-TAAATAAATTA
*
2514431 TTAAATTAATTA
1 TTAAATAAATTA
2514443 ATTATTCATA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
11 18 0.51
12 17 0.49
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAAATAAATTA
Found at i:2514439 original size:23 final size:24
Alignment explanation
Indices: 2514385--2514446 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 24
2514375 CGATTCATTT
*
2514385 TTAAA-TAAATTATTAAAAAATTA
1 TTAAATTAATTTATTAAAAAATTA
**
2514408 TTATTTTAATTTA-TAAAAAATTA
1 TTAAATTAATTTATTAAAAAATTA
*
2514431 TTAAATTAATTAATTA
1 TTAAATTAATTTATTA
2514447 TTCATATAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAATTAATTTATTAAAAAATTA
Found at i:2514860 original size:16 final size:17
Alignment explanation
Indices: 2514833--2514866 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2514823 TAAAAGTTAT
2514833 ATTAATATATTTGATTA
1 ATTAATATATTTGATTA
*
2514850 ATTAA-ATATTTTATTA
1 ATTAATATATTTGATTA
2514866 A
1 A
2514867 AAATATGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTAATATATTTGATTA
Found at i:2514984 original size:20 final size:21
Alignment explanation
Indices: 2514943--2514988 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2514933 TCAATATTTT
2514943 TAAATA-T-ATTTATTATTAA
1 TAAATATTAATTTATTATTAA
2514962 TAAATATTAATTTATTA-TAA
1 TAAATATTAATTTATTATTAA
2514982 TAAATAT
1 TAAATAT
2514989 GTTATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.24
20 11 0.44
21 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAAATATTAATTTATTATTAA
Found at i:2514995 original size:21 final size:21
Alignment explanation
Indices: 2514949--2514996 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2514939 TTTTTAAATA
2514949 TATTTATTATTAATAAATATT
1 TATTTATTATTAATAAATATT
*
2514970 AATTTATTA-TAATAAATATGT
1 TATTTATTATTAATAAATAT-T
2514991 TATTTA
1 TATTTA
2514997 ATCAATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTTATTATTAATAAATATT
Found at i:2515056 original size:51 final size:52
Alignment explanation
Indices: 2514948--2515057 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 52
2514938 ATTTTTAAAT
* * * *
2514948 ATATTTATTATTAATAAATATTAATTTATTATAATAAATATGTTATTTAATC
1 ATATTTATTATTAAAAAATATTAATTTATTATAATAAATATATAATATAATC
* *
2515000 A-ATTTATTGTTAAAAAATAATTAATTTATTTTAAATAAA-A-ATAATATAA-C
1 ATATTTATTATTAAAAAAT-ATTAATTTATTAT-AATAAATATATAATATAATC
2515050 ATATTTAT
1 ATATTTAT
2515058 CTTAATTTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
50 2 0.04
51 27 0.55
52 14 0.29
53 6 0.12
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (52 bp):
ATATTTATTATTAAAAAATATTAATTTATTATAATAAATATATAATATAATC
Found at i:2515322 original size:14 final size:14
Alignment explanation
Indices: 2515305--2515376 Score: 54
Period size: 14 Copynumber: 4.9 Consensus size: 14
2515295 TTATATTCTT
*
2515305 ATAATTATAAGAAA
1 ATAATTATAAAAAA
*
2515319 ATAATTCTAAAAAA
1 ATAATTATAAAAAA
*
2515333 ATTAAATTCTTAAAAAA
1 A-T-AATT-ATAAAAAA
* *
2515350 ATAAATATAATAAA
1 ATAATTATAAAAAA
* *
2515364 TTAAATATAAAAA
1 ATAATTATAAAAA
2515377 TTTAACCTTC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 30 0.64
15 4 0.09
16 5 0.11
17 8 0.17
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (14 bp):
ATAATTATAAAAAA
Found at i:2515342 original size:16 final size:16
Alignment explanation
Indices: 2515316--2515355 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2515306 TAATTATAAG
2515316 AAAAT-AATTC-TAAA
1 AAAATAAATTCTTAAA
2515330 AAAATTAAATTCTTAAA
1 AAAA-TAAATTCTTAAA
2515347 AAAATAAAT
1 AAAATAAAT
2515356 ATAATAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 4 0.17
15 1 0.04
16 10 0.43
17 8 0.35
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATAAATTCTTAAA
Found at i:2515847 original size:26 final size:24
Alignment explanation
Indices: 2515810--2515863 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
2515800 AATTTTTATT
2515810 TATT-TTAATTTAAAATACATAAATA
1 TATTATTAATTTAAAATA-A-AAATA
*
2515835 TATTATTATTTTAAAATAAAAATA
1 TATTATTAATTTAAAATAAAAATA
2515859 -ATTAT
1 TATTAT
2515864 ATAAATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 5 0.19
24 5 0.19
25 5 0.19
26 12 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTATTAATTTAAAATAAAAATA
Found at i:2516034 original size:24 final size:24
Alignment explanation
Indices: 2515972--2516037 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
2515962 TAAATATATA
**
2515972 TATT-TTATTTTTAATTTTAATTTT
1 TATTATTATTTTTAA-TTTAATCAT
* **
2515996 TATTATAATACTTAATTTAATCAT
1 TATTATTATTTTTAATTTAATCAT
2516020 TATTATTATTTTTAATTT
1 TATTATTATTTTTAATTT
2516038 TATCGAAATT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
24 26 0.79
25 7 0.21
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTATTATTTTTAATTTAATCAT
Found at i:2520798 original size:2 final size:2
Alignment explanation
Indices: 2520791--2520817 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2520781 GAAAATTAAA
2520791 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 A
2520818 TGTTAGATAA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2527162 original size:23 final size:24
Alignment explanation
Indices: 2527117--2527164 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
2527107 TTTAAAAAAA
* **
2527117 TTATCAAAATATTATTATTTTAAT
1 TTATCAAAAAATTATTAAATTAAT
2527141 TTAT-AAAAAATTATTAAATTAAT
1 TTATCAAAAAATTATTAAATTAAT
2527164 T
1 T
2527165 AATATGTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTATCAAAAAATTATTAAATTAAT
Found at i:2527239 original size:17 final size:17
Alignment explanation
Indices: 2527217--2527296 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 17
2527207 ACATAGATTA
2527217 ATTATTATTATAATATT
1 ATTATTATTATAATATT
*
2527234 ATTATTTATTTAATAATTTT
1 ATTA-TTA-TT-ATAATATT
**
2527254 ATTAAGATTATAAT-TAT
1 ATTATTATTATAATAT-T
* *
2527271 ATTAGTATT-TTATATT
1 ATTATTATTATAATATT
2527287 A-TATTATTAT
1 ATTATTATTAT
2527297 GTTGATATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
15 6 0.12
16 7 0.14
17 18 0.36
18 5 0.10
19 3 0.06
20 11 0.22
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
ATTATTATTATAATATT
Found at i:2527285 original size:13 final size:13
Alignment explanation
Indices: 2527213--2527296 Score: 51
Period size: 11 Copynumber: 7.0 Consensus size: 13
2527203 TTTTACATAG
2527213 ATTA-ATTATTATT
1 ATTATATTATTA-T
*
2527226 ATAATATTATTAT
1 ATTATATTATTAT
*
2527239 -TTAT-TTAATA-
1 ATTATATTATTAT
* *
2527249 ATTTTATTA--AG
1 ATTATATTATTAT
2527260 ATTATA--ATTAT
1 ATTATATTATTAT
2527271 ATTAGTATT-TTAT
1 ATTA-TATTATTAT
2527284 ATTATATTATTAT
1 ATTATATTATTAT
2527297 GTTGATATGT
Statistics
Matches: 55, Mismatches: 6, Indels: 20
0.68 0.07 0.25
Matches are distributed among these distances:
9 1 0.02
10 1 0.02
11 18 0.33
12 12 0.22
13 16 0.29
14 7 0.13
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
ATTATATTATTAT
Found at i:2527338 original size:18 final size:18
Alignment explanation
Indices: 2527315--2527357 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
2527305 GTTTTTAAAT
* *
2527315 TAATAAAAGATTATATGA
1 TAATAAAAAATAATATGA
*
2527333 TAATAAAAAATAATATTA
1 TAATAAAAAATAATATGA
2527351 TAATAAA
1 TAATAAA
2527358 TATAATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
TAATAAAAAATAATATGA
Found at i:2527613 original size:18 final size:16
Alignment explanation
Indices: 2527561--2527632 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
2527551 GTTGTAATCA
2527561 TTTAATTATTTTAAA-
1 TTTAATTATTTTAAAT
* *
2527576 -TTAA-AATTTTTAAT
1 TTTAATTATTTTAAAT
2527590 CATTTAATTACTTTTTAAAT
1 --TTTAATTA--TTTTAAAT
2527610 TTTAATTATTTTAAAT
1 TTTAATTATTTTAAAT
2527626 TGTTAAT
1 T-TTAAT
2527633 CCGTAAGTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
13 7 0.16
14 4 0.09
16 9 0.20
17 9 0.20
18 9 0.20
20 7 0.16
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (16 bp):
TTTAATTATTTTAAAT
Found at i:2527615 original size:26 final size:29
Alignment explanation
Indices: 2527555--2527620 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
2527545 TTGTGAGTTG
*
2527555 TAATCATTTAATTATTTTAAATTAAAATTTT
1 TAATCATTTAATTACTTT--ATTAAAATTTT
2527586 TAATCATTTAATTACTTT-TT-AAA-TTT
1 TAATCATTTAATTACTTTATTAAAATTTT
*
2527612 TAATTATTT
1 TAATCATTT
2527621 TAAATTGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
26 11 0.33
27 3 0.09
28 2 0.06
31 17 0.52
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATCATTTAATTACTTTATTAAAATTTT
Found at i:2527880 original size:3 final size:3
Alignment explanation
Indices: 2527863--2527927 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
2527853 TTAATTTAAA
* ** * *
2527863 AAT ATT AAT -AT AAT AAT AAT TTT AAT AAT ATT ATT AAAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
*
2527907 AAG AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
2527928 TGATTAGCTA
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
2 4 0.08
3 43 0.88
4 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2528982 original size:2 final size:2
Alignment explanation
Indices: 2528977--2529013 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2528967 TTTTATCCTC
*
2528977 AT AT AT AT GT 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 AT AT A
2529014 CACAGACTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2530259 original size:2 final size:2
Alignment explanation
Indices: 2530252--2530276 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2530242 AGGAAGGCCA
2530252 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2530277 AAAGACAACA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2531933 original size:30 final size:30
Alignment explanation
Indices: 2531897--2531956 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
2531887 TTTTAAGAGA
2531897 TAAGAAATATAAAGGCTGTTAATAACTGTT
1 TAAGAAATATAAAGGCTGTTAATAACTGTT
2531927 TAAGAAATATAAAGGCTGTTAATAACTGTT
1 TAAGAAATATAAAGGCTGTTAATAACTGTT
2531957 GCGCATCCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.17, T:0.33
Consensus pattern (30 bp):
TAAGAAATATAAAGGCTGTTAATAACTGTT
Found at i:2536905 original size:3 final size:3
Alignment explanation
Indices: 2536897--2536927 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2536887 AAAAAGCGAA
*
2536897 TGC TGC TGC TGC TGC TGC TGC TGC TAC TGC T
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC T
2536928 CCAAAACCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.03, C:0.32, G:0.29, T:0.35
Consensus pattern (3 bp):
TGC
Found at i:2537973 original size:11 final size:11
Alignment explanation
Indices: 2537957--2537993 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
2537947 CAACAGCAAC
2537957 AAATCCTTAAT
1 AAATCCTTAAT
2537968 AAATCCTTAAT
1 AAATCCTTAAT
2537979 AAAATCCTTAAT
1 -AAATCCTTAAT
2537991 AAA
1 AAA
2537994 CTCATTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATCCTTAAT
Found at i:2537985 original size:12 final size:12
Alignment explanation
Indices: 2537957--2537993 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
2537947 CAACAGCAAC
2537957 AAATCCTTAAT-
1 AAATCCTTAATA
2537968 AAATCCTTAATA
1 AAATCCTTAATA
2537980 AAATCCTTAATA
1 AAATCCTTAATA
2537992 AA
1 AA
2537994 CTCATTTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATCCTTAATA
Found at i:2543163 original size:21 final size:21
Alignment explanation
Indices: 2543106--2543185 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 21
2543096 GTATGAGATG
* *
2543106 TAAAAAAATTAACATATAAATAT
1 TAAAATAATTAA-ATTTAAA-AT
2543129 TAAAAT-A--AAATTTAAAAT
1 TAAAATAATTAAATTTAAAAT
* * * *
2543147 TATAATAATTTAATTTATATT
1 TAAAATAATTAAATTTAAAAT
2543168 TAAAATAATTAAATTTAA
1 TAAAATAATTAAATTTAA
2543186 TAAAATAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
18 7 0.16
19 7 0.16
20 2 0.04
21 23 0.51
22 1 0.02
23 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATAATTAAATTTAAAAT
Found at i:2543195 original size:21 final size:22
Alignment explanation
Indices: 2543148--2543195 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
2543138 ATTTAAAATT
* **
2543148 ATAATAATTTAATTTATATTTA
1 ATAATAATTAAATTTATATAAA
2543170 A-AATAATTAAATTTA-ATAAA
1 ATAATAATTAAATTTATATAAA
2543190 ATAATA
1 ATAATA
2543196 TCATTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.18
21 17 0.77
22 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATAATTAAATTTATATAAA
Found at i:2543504 original size:3 final size:3
Alignment explanation
Indices: 2543496--2543530 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2543486 AATTTTTAAC
2543496 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2543531 GACAACAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2551535 original size:2 final size:2
Alignment explanation
Indices: 2551523--2551561 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2551513 CTCTTGTCTC
*
2551523 TA TA AA 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
2551562 GTTAGTTTTC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2551968 original size:2 final size:2
Alignment explanation
Indices: 2551963--2551990 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2551953 TGTGTGTGTG
2551963 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
2551991 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2551995 original size:2 final size:2
Alignment explanation
Indices: 2551990--2552026 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2551980 ATATATATAT
2551990 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
2552027 TCTCGAAAGA
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:2557864 original size:2 final size:2
Alignment explanation
Indices: 2557857--2557885 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2557847 TAATACTAGC
2557857 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
2557886 GTTAGCGTTT
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:2566515 original size:14 final size:15
Alignment explanation
Indices: 2566486--2566515 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2566476 AAAGTGTTAG
2566486 AAAGAAGAGTAAAGT
1 AAAGAAGAGTAAAGT
2566501 AAAGAAGAG-AAAGT
1 AAAGAAGAGTAAAGT
2566515 A
1 A
2566516 CATAGTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (15 bp):
AAAGAAGAGTAAAGT
Found at i:2569974 original size:1 final size:1
Alignment explanation
Indices: 2569968--2569992 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
2569958 ATCGAAACAT
2569968 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2569993 GGAAAACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2575562 original size:26 final size:26
Alignment explanation
Indices: 2575526--2575576 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2575516 TTGTTTACGC
2575526 CAAAAGCGTAAGCGTATAACATACAA
1 CAAAAGCGTAAGCGTATAACATACAA
* *
2575552 CAAAAGCGTAAGTGTATACCATACA
1 CAAAAGCGTAAGCGTATAACATACA
2575577 CCACGAGTCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.18
Consensus pattern (26 bp):
CAAAAGCGTAAGCGTATAACATACAA
Found at i:2576815 original size:2 final size:2
Alignment explanation
Indices: 2576808--2576836 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2576798 ACATTTCTAC
2576808 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
2576837 ATGACAAGTA
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:2580019 original size:3 final size:3
Alignment explanation
Indices: 2580011--2580039 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2580001 ACAACTCCAT
2580011 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2580040 GATGATCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2601926 original size:2 final size:2
Alignment explanation
Indices: 2601919--2601943 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2601909 CTTTTATTAA
2601919 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 T
2601944 AGCTTTCCTG
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2608378 original size:2 final size:2
Alignment explanation
Indices: 2608371--2608415 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2608361 AGTTTGCGAC
2608371 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
2608413 AT A
1 AT A
2608416 AAGGTTAAGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2610053 original size:22 final size:21
Alignment explanation
Indices: 2610028--2610071 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
2610018 AATAAGAAAT
2610028 AATGTAAAAAAAATATAGAGGG
1 AATG-AAAAAAAATATAGAGGG
*
2610050 AATGCAAAAAAATATAGAGGG
1 AATGAAAAAAAATATAGAGGG
2610071 A
1 A
2610072 TGCACAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.23, T:0.16
Consensus pattern (21 bp):
AATGAAAAAAAATATAGAGGG
Found at i:2610060 original size:20 final size:20
Alignment explanation
Indices: 2610034--2610075 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
2610024 AAATAATGTA
2610034 AAAAAAATATAGAGGGAATGC
1 AAAAAAATATAGAGGG-ATGC
2610055 AAAAAAATATAGAGGGATGC
1 AAAAAAATATAGAGGGATGC
2610075 A
1 A
2610076 CAGTCACTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.57, C:0.05, G:0.24, T:0.14
Consensus pattern (20 bp):
AAAAAAATATAGAGGGATGC
Found at i:2610271 original size:2 final size:2
Alignment explanation
Indices: 2610264--2610305 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2610254 CTTTTAACAC
2610264 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
2610306 CACAAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2610358 original size:2 final size:2
Alignment explanation
Indices: 2610353--2610384 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2610343 TCTCTCTCTC
*
2610353 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2610385 ACATATGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2612722 original size:44 final size:44
Alignment explanation
Indices: 2612659--2612745 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
2612649 TAAATATATT
*
2612659 ACCAACCAACCGATCATTGATGCTTAATTACCTGTTTTCCAATC
1 ACCAACCAACCGATCATTGATGCTTAATTACCTGTCTTCCAATC
* *
2612703 ACCAACCAACTGATCATTGATGCTTAATTATCTGTCTTCCAAT
1 ACCAACCAACCGATCATTGATGCTTAATTACCTGTCTTCCAAT
2612746 TAACAACAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.30, C:0.28, G:0.09, T:0.33
Consensus pattern (44 bp):
ACCAACCAACCGATCATTGATGCTTAATTACCTGTCTTCCAATC
Found at i:2615705 original size:2 final size:2
Alignment explanation
Indices: 2615698--2615733 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2615688 TTAACGATGG
*
2615698 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2615734 TGGGCTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2617505 original size:2 final size:2
Alignment explanation
Indices: 2617500--2617530 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2617490 ATATACTGCT
2617500 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 T
2617531 CTTAAACGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2618421 original size:2 final size:2
Alignment explanation
Indices: 2618416--2618459 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2618406 CTTTGGGGGG
2618416 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
2618458 GA
1 GA
2618460 ATCCTTAGAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2628351 original size:2 final size:2
Alignment explanation
Indices: 2628344--2628370 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2628334 TCTCAACACA
2628344 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
2628371 GCAATCCAAA
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:2629239 original size:6 final size:6
Alignment explanation
Indices: 2629230--2629276 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
2629220 ATCTCCTCCT
* ** *
2629230 CCTTCA CCTTCA CCTTCA CCTTCG CCTTTG CCTTCA CCCTCA CCTTC
1 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTC
2629277 TACTTCTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.11, C:0.51, G:0.04, T:0.34
Consensus pattern (6 bp):
CCTTCA
Found at i:2633506 original size:6 final size:6
Alignment explanation
Indices: 2633484--2633559 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
2633474 AGATTCACTT
* * *
2633484 TAATAA -AATTAA AAATAA TAATAA TAATAA TAA-AA TTAATTA TTATAA
1 TAATAA TAA-TAA TAATAA TAATAA TAATAA TAATAA -TAATAA TAATAA
* *
2633532 TAATAA CATTAA -AATTAA TAATAA -AATA
1 TAATAA TAATAA TAA-TAA TAATAA TAATA
2633560 TTTATTTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
5 9 0.16
6 42 0.75
7 5 0.09
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (6 bp):
TAATAA
Found at i:2633508 original size:21 final size:21
Alignment explanation
Indices: 2633485--2633558 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
2633475 GATTCACTTT
*
2633485 AATAA-AATTAAAAATAATAAT
1 AATAATAA-TAAAATTAATAAT
*
2633506 AATAATAATAAAATTAATTAT
1 AATAATAATAAAATTAATAAT
* *
2633527 TATAATAATAACATTAA-AAT
1 AATAATAATAAAATTAATAAT
2633547 --TAATAATAAAAT
1 AATAATAATAAAAT
2633559 ATTTATTTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
18 11 0.24
20 2 0.04
21 31 0.67
22 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAATAATAAAATTAATAAT
Found at i:2633696 original size:34 final size:36
Alignment explanation
Indices: 2633645--2633877 Score: 150
Period size: 35 Copynumber: 6.6 Consensus size: 36
2633635 AATTTATGTA
* *
2633645 TATAATAAATAATTAAAA-ATTAATAAAAATATATT
1 TATATTAAATAATTAAAATATAAATAAAAATATATT
* *
2633680 TATA-TAAATTAA-TAAAATATAAATAAAATTATAAT
1 TATATTAAA-TAATTAAAATATAAATAAAAATATATT
* *
2633715 TATATTAAATAA-T-AATTATAAATTATTAAATTATATT
1 TATATTAAATAATTAAAATATAAA-TA--AAAATATATT
*
2633752 CATATTAAATAA-TAAAATATAAAT-AAAATATATT
1 TATATTAAATAATTAAAATATAAATAAAAATATATT
* * * ** *
2633786 TATGTTGAATAATAATTAAAA-ATTATTAAATTTATTTT
1 TATATT--A-AATAATTAAAATATAAATAAAAATATATT
* * *
2633824 TATATTAAA-AA-T-AAAT-T-ATTAAAATTAAATT
1 TATATTAAATAATTAAAATATAAATAAAAATATATT
*
2633855 TATATTAAATAATAAAAAATATA
1 TATATTAAATAAT-TAAAATATA
2633878 TTAAAAACTA
Statistics
Matches: 159, Mismatches: 20, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
31 20 0.13
32 6 0.04
33 1 0.01
34 32 0.20
35 37 0.23
36 7 0.04
37 31 0.19
38 25 0.16
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (36 bp):
TATATTAAATAATTAAAATATAAATAAAAATATATT
Found at i:2633732 original size:42 final size:42
Alignment explanation
Indices: 2633686--2633781 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 42
2633676 TATTTATATA
2633686 AATTAATAAAATATAAATAAAATTATAATT-ATATTAAATAAT
1 AATTAATAAAATATAAATAAAATTAT-ATTCATATTAAATAAT
*
2633728 AATT-AT-AAAT-T--ATTAAATTATATTCATATTAAATAAT
1 AATTAATAAAATATAAATAAAATTATATTCATATTAAATAAT
2633765 AA--AATATAAATA-AAATA
1 AATTAATA-AAATATAAATA
2633782 TATTTATGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
36 5 0.11
37 23 0.51
38 4 0.09
39 1 0.02
40 6 0.13
41 2 0.04
42 4 0.09
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (42 bp):
AATTAATAAAATATAAATAAAATTATATTCATATTAAATAAT
Found at i:2633767 original size:31 final size:31
Alignment explanation
Indices: 2633732--2633870 Score: 118
Period size: 31 Copynumber: 4.2 Consensus size: 31
2633722 AATAATAATT
*
2633732 ATAAATTATTAAATTATATTCATATTAAATA
1 ATAAATTATTAAATTATATTTATATTAAATA
* * *
2633763 ATAAAATATAAATAAAATATATTTATGTTGAATAATA
1 AT-AAAT-T-ATTAAATTATATTTATATT--A-AATA
*
2633800 ATTAAAAATTATTAAATTTATTTTTATATTAAA-A
1 A-T--AAATTATTAAA-TTATATTTATATTAAATA
*
2633834 ATAAATTATTAAAATTAAATTTATATTAAATA
1 ATAAATTATT-AAATTATATTTATATTAAATA
2633866 ATAAA
1 ATAAA
2633871 AAATATATTA
Statistics
Matches: 87, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
31 24 0.28
32 13 0.15
33 2 0.02
34 17 0.20
35 2 0.02
36 2 0.02
37 10 0.11
38 12 0.14
39 5 0.06
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (31 bp):
ATAAATTATTAAATTATATTTATATTAAATA
Found at i:2633768 original size:72 final size:72
Alignment explanation
Indices: 2633652--2633869 Score: 270
Period size: 72 Copynumber: 3.1 Consensus size: 72
2633642 GTATATAATA
* *
2633652 AATAATTAAAAATTAATAAAAATATATTTATA-TAAATTAATAAAATATAAATAAAATTATAATT
1 AATAATTAAAAATT-ATTAAATTATATTTATATTAAA-TAATAAAATATAAATAAAATTATAATT
2633716 ATATTAAAT
64 ATATTAAAT
* * *
2633725 AATAATTATAAATTATTAAATTATATTCATATTAAATAATAAAATATAAATAAAA-TATATTTAT
1 AATAATTAAAAATTATTAAATTATATTTATATTAAATAATAAAATATAAATAAAATTATAATTAT
* *
2633789 GTTGAAT
66 ATTAAAT
* *
2633796 AATAATTAAAAATTATTAAATTTATTTTTATATTAAA-AAT-AAAT-T-ATTAAAATTA-AATTT
1 AATAATTAAAAATTATTAAA-TTATATTTATATTAAATAATAAAATATAAATAAAATTATAA-TT
2633856 ATATTAAAT
64 ATATTAAAT
2633865 AATAA
1 AATAA
2633870 AAAATATATT
Statistics
Matches: 127, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
68 7 0.06
69 17 0.13
70 4 0.03
71 35 0.28
72 47 0.37
73 17 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (72 bp):
AATAATTAAAAATTATTAAATTATATTTATATTAAATAATAAAATATAAATAAAATTATAATTAT
ATTAAAT
Done.