Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 6 of 240
Found at i:2263107 original size:21 final size:21
Alignment explanation
Indices: 2263083--2263123 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2263073 ATGTTTAAAG
2263083 TTTTGAAAATTTCTTT-TTATT
1 TTTTGAAAATTT-TTTGTTATT
*
2263104 TTTTGAACATTTTTTGTTAT
1 TTTTGAAAATTTTTTGTTAT
2263124 CTTGATGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.22, C:0.05, G:0.07, T:0.66
Consensus pattern (21 bp):
TTTTGAAAATTTTTTGTTATT
Found at i:2267031 original size:15 final size:18
Alignment explanation
Indices: 2266997--2267033 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
2266987 TATATTTAAA
2266997 AAATTATATATTATTTTT
1 AAATTATATATTATTTTT
2267015 AAATTAT-T-TTA-TTTT
1 AAATTATATATTATTTTT
2267030 AAAT
1 AAAT
2267034 ATAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.42
16 3 0.16
17 1 0.05
18 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
AAATTATATATTATTTTT
Found at i:2267067 original size:36 final size:37
Alignment explanation
Indices: 2267002--2267073 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 37
2266992 TTAAAAAATT
* * *
2267002 ATATATTATTTTTAAATTATTTTATTTTAAATATAAA
1 ATATATTATTTTTAAATAATTTAAATTTAAATATAAA
* *
2267039 ATAT-TTATTTTTACATAATTTAAATTTAATTATAA
1 ATATATTATTTTTAAATAATTTAAATTTAAATATAA
2267074 CTTTATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (37 bp):
ATATATTATTTTTAAATAATTTAAATTTAAATATAAA
Found at i:2280680 original size:19 final size:18
Alignment explanation
Indices: 2280633--2280682 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2280623 TCTATATAAA
2280633 TTATA-AAAAAATAGAAT
1 TTATATAAAAAATAGAAT
*
2280650 TTATTTAAAAAATAGAAAT
1 TTATATAAAAAATAG-AAT
*
2280669 TTGTATACAAAAAT
1 TTATATA-AAAAAT
2280683 TCTAAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 4 0.15
18 9 0.33
19 8 0.30
20 6 0.22
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (18 bp):
TTATATAAAAAATAGAAT
Found at i:2287893 original size:21 final size:21
Alignment explanation
Indices: 2287867--2287908 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2287857 ATATGAAATC
2287867 AAATCCTTGAAATTTTCGAGG
1 AAATCCTTGAAATTTTCGAGG
*
2287888 AAATCCTTGAAGTTTTCGAGG
1 AAATCCTTGAAATTTTCGAGG
2287909 TTTTAATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (21 bp):
AAATCCTTGAAATTTTCGAGG
Found at i:2288906 original size:20 final size:20
Alignment explanation
Indices: 2288881--2288920 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2288871 AATATTTTCT
*
2288881 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2288901 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2288921 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2288923 original size:34 final size:35
Alignment explanation
Indices: 2288869--2288935 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2288859 CAAACACCAG
* *
2288869 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2288904 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2288936 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2294420 original size:26 final size:26
Alignment explanation
Indices: 2294390--2294441 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
2294380 GACCATTAAG
2294390 TCAATACAT-GGGATTCTCAATCTAAT
1 TCAATACATAGGG-TTCTCAATCTAAT
2294416 TCAATACATAGGGTTCTCAATCTAAT
1 TCAATACATAGGGTTCTCAATCTAAT
2294442 ATTTATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (26 bp):
TCAATACATAGGGTTCTCAATCTAAT
Found at i:2302838 original size:26 final size:24
Alignment explanation
Indices: 2302808--2302872 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 24
2302798 AACACGTATT
2302808 TTATTTTTTTATATATTTCTTTTTAA
1 TTATTTTTTTATA-A-TTCTTTTTAA
*
2302834 TTATTTTTTTGGTCAATTCTTTTTAA
1 TTATTTTTTT-AT-AATTCTTTTTAA
*
2302860 TTATTTTATTATA
1 TTATTTTTTTATA
2302873 CTCTATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 1 0.03
25 1 0.03
26 29 0.85
27 2 0.06
28 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.69
Consensus pattern (24 bp):
TTATTTTTTTATAATTCTTTTTAA
Found at i:2307819 original size:14 final size:14
Alignment explanation
Indices: 2307800--2307827 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2307790 GAACTAGATT
2307800 ATAATCCAGTCATG
1 ATAATCCAGTCATG
2307814 ATAATCCAGTCATG
1 ATAATCCAGTCATG
2307828 CTTCGTGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (14 bp):
ATAATCCAGTCATG
Found at i:2310442 original size:12 final size:13
Alignment explanation
Indices: 2310425--2310468 Score: 54
Period size: 14 Copynumber: 3.4 Consensus size: 13
2310415 AATCAAAACC
2310425 AAAACCG-AAAAG
1 AAAACCGAAAAAG
2310437 AAAACCGAAAAAG
1 AAAACCGAAAAAG
**
2310450 AAAAAAGGAAAAAG
1 -AAAACCGAAAAAG
2310464 AAAAC
1 AAAAC
2310469 GGAAGAAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 7 0.26
13 9 0.33
14 11 0.41
ACGTcount: A:0.73, C:0.11, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAACCGAAAAAG
Found at i:2310472 original size:13 final size:13
Alignment explanation
Indices: 2310432--2310472 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2310422 ACCAAAACCG
*
2310432 AAAAGAAAACCGA
1 AAAAGAAAACGGA
*
2310445 AAAAGAAAAAAGGA
1 AAAAG-AAAACGGA
2310459 AAAAGAAAACGGA
1 AAAAGAAAACGGA
2310472 A
1 A
2310473 GAAGCAAGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.73, C:0.07, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAAACGGA
Found at i:2311553 original size:48 final size:48
Alignment explanation
Indices: 2311482--2311576 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
2311472 TTAGTTTTGT
2311482 CTATATTTTCATTTTTGATTTGAATATAACCAGGATTGAAAACACTAA
1 CTATATTTTCATTTTTGATTTGAATATAACCAGGATTGAAAACACTAA
*
2311530 CTATATTTTCATTTTTGATTTGAATATAACCAGGATTGAAAGCACTA
1 CTATATTTTCATTTTTGATTTGAATATAACCAGGATTGAAAACACTA
2311577 TTTTCATGTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (48 bp):
CTATATTTTCATTTTTGATTTGAATATAACCAGGATTGAAAACACTAA
Found at i:2316967 original size:11 final size:11
Alignment explanation
Indices: 2316951--2316975 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2316941 GTAACACTGA
2316951 TTATATATAAT
1 TTATATATAAT
2316962 TTATATATAAT
1 TTATATATAAT
2316973 TTA
1 TTA
2316976 GATCAGGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TTATATATAAT
Found at i:2341547 original size:39 final size:37
Alignment explanation
Indices: 2341480--2341572 Score: 89
Period size: 39 Copynumber: 2.5 Consensus size: 37
2341470 CACCAGATGG
* *
2341480 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
2341519 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* * *
2341556 TACCTAGTACCTCATCG
1 CACCCAGTGCCTCATCG
2341573 AATCTATCCG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.40
38 2 0.04
39 22 0.49
40 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:2342692 original size:17 final size:16
Alignment explanation
Indices: 2342660--2342693 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2342650 TTGGCTATTC
*
2342660 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
2342676 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
2342693 T
1 T
2342694 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:2342741 original size:14 final size:14
Alignment explanation
Indices: 2342682--2342732 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2342672 CTTTTGTTTC
*
2342682 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
2342695 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
2342710 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
2342724 TTTTATTTC
1 TTTTATTTC
2342733 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:2342901 original size:14 final size:17
Alignment explanation
Indices: 2342882--2342918 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
2342872 ATTTATTTCT
2342882 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
2342896 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
2342913 TAATAT
1 TAATAT
2342919 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:2343706 original size:23 final size:24
Alignment explanation
Indices: 2343674--2343720 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
2343664 GTCATTATAT
*
2343674 AATATGTGGATT-TTTTTTGAAAG
1 AATATATGGATTGTTTTTTGAAAG
*
2343697 AATATATGGATTGTTTTTTTAAAG
1 AATATATGGATTGTTTTTTGAAAG
2343721 GAAAATTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (24 bp):
AATATATGGATTGTTTTTTGAAAG
Found at i:2344270 original size:14 final size:14
Alignment explanation
Indices: 2344232--2344271 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
2344222 ATTGTTAACA
*
2344232 TTATTAAGTTTCTT
1 TTATTAAATTTCTT
*
2344246 TTATTATAATTTTTT
1 TTATTA-AATTTCTT
2344261 TTATTAAATTT
1 TTATTAAATTT
2344272 AAGTTTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (14 bp):
TTATTAAATTTCTT
Found at i:2349477 original size:25 final size:25
Alignment explanation
Indices: 2349444--2349494 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2349434 ATACTCAACT
2349444 TTTAGGCGCATTCATTTTGATCACC
1 TTTAGGCGCATTCATTTTGATCACC
2349469 TTTAGGCGCATTCATTTTGATCACC
1 TTTAGGCGCATTCATTTTGATCACC
2349494 T
1 T
2349495 AAAATGAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (25 bp):
TTTAGGCGCATTCATTTTGATCACC
Found at i:2354645 original size:23 final size:23
Alignment explanation
Indices: 2354619--2354662 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2354609 TAAAAATTAT
2354619 TTTATTAATATTTTACTTAGATG
1 TTTATTAATATTTTACTTAGATG
* *
2354642 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
2354663 AAATGGTAGC
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:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATG
Found at i:2361484 original size:21 final size:21
Alignment explanation
Indices: 2361460--2361505 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2361450 TCGAATAAAC
* *
2361460 AATATAAGAGAACTTAAAATA
1 AATATAAAACAACTTAAAATA
**
2361481 AATATAAAACATTTTAAAATA
1 AATATAAAACAACTTAAAATA
2361502 AATA
1 AATA
2361506 ATATTATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (21 bp):
AATATAAAACAACTTAAAATA
Found at i:2366345 original size:13 final size:13
Alignment explanation
Indices: 2366327--2366354 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2366317 TAATTTGGGT
2366327 TTTAATATGCTTG
1 TTTAATATGCTTG
2366340 TTTAATATGCTTG
1 TTTAATATGCTTG
2366353 TT
1 TT
2366355 GGGCTTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (13 bp):
TTTAATATGCTTG
Found at i:2370567 original size:21 final size:21
Alignment explanation
Indices: 2370541--2370581 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2370531 AGATGAGCAA
* *
2370541 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
2370562 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
2370582 TTAAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:2388509 original size:16 final size:16
Alignment explanation
Indices: 2388488--2388521 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2388478 ATTCATTTGA
*
2388488 TATATTTAATATTGTT
1 TATATTAAATATTGTT
*
2388504 TATATTAAATATTTTT
1 TATATTAAATATTGTT
2388520 TA
1 TA
2388522 AAAAAATTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATATTAAATATTGTT
Found at i:2388857 original size:17 final size:17
Alignment explanation
Indices: 2388835--2388867 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2388825 CAAAAAAGTA
2388835 TATATTTGAATAAAAAG
1 TATATTTGAATAAAAAG
*
2388852 TATATTTGATTAAAAA
1 TATATTTGAATAAAAA
2388868 TAAAAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (17 bp):
TATATTTGAATAAAAAG
Found at i:2391664 original size:24 final size:24
Alignment explanation
Indices: 2391627--2391699 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
2391617 GGTAAGACAT
2391627 TTTCCACAGCTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
* *
2391651 TTTCCACTGTTCCTCTCTTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
*
2391675 TTTCCACAGCTCCTCTATTCACCC
1 TTTCCACAGCTCCTCTCTTCACCC
2391699 T
1 T
2391700 ATCGATTGCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (24 bp):
TTTCCACAGCTCCTCTCTTCACCC
Found at i:2392512 original size:8 final size:8
Alignment explanation
Indices: 2392499--2392539 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
2392489 AATGCCGTTC
2392499 CTGTTGTT
1 CTGTTGTT
2392507 CTGTTGTT
1 CTGTTGTT
2392515 CTGTTGTT
1 CTGTTGTT
2392523 CTGTTGTT
1 CTGTTGTT
2392531 CTGTTGTT
1 CTGTTGTT
2392539 C
1 C
2392540 CTGGTAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.24, T:0.61
Consensus pattern (8 bp):
CTGTTGTT
Found at i:2396883 original size:34 final size:35
Alignment explanation
Indices: 2396825--2396891 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
2396815 CAAACACCAG
* * *
2396825 AAAATATTTTCCTGTAAGTCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2396860 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2396892 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2406152 original size:88 final size:87
Alignment explanation
Indices: 2406038--2406253 Score: 231
Period size: 86 Copynumber: 2.5 Consensus size: 87
2406028 TTTAAGGGTG
* ** ** * *
2406038 CAAAAA-GCCCTCAAACTTTTTCAAAAAACAATTAAGCCCCTGTGTTTTTTTTTGCACAT-ATTT
1 CAAAAAGGCCCTCAAACTCTTAAAAAAAACAATTAAGCCCCT-ACTTCTTTTTTG-AC-TCAATT
*
2406101 AGGTACTTGAACTTTCAAAATGCAT
63 AGGTACTCGAACTTTCAAAATGCAT
* *
2406126 CAAAAAGGCCCTCAAAC-CTTAAAAAAAGCAATTAAGCCCCTACTTCTTTTTTGACTCAATTGGG
1 CAAAAAGGCCCTCAAACTCTTAAAAAAAACAATTAAGCCCCTACTTCTTTTTTGACTCAATTAGG
2406190 TACTCGAACTTTCAAAATGCAT
66 TACTCGAACTTTCAAAATGCAT
* * * * *
2406212 CAAAAAGACCCTCAAGCTTTTTCAAGAAAAGCAATTAAGCCC
1 CAAAAAGGCCCTCAAAC-TCTT-AAAAAAAACAATTAAGCCC
2406254 AAACTAATTG
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
85 1 0.01
86 43 0.39
87 9 0.08
88 28 0.26
89 28 0.26
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (87 bp):
CAAAAAGGCCCTCAAACTCTTAAAAAAAACAATTAAGCCCCTACTTCTTTTTTGACTCAATTAGG
TACTCGAACTTTCAAAATGCAT
Found at i:2408809 original size:15 final size:15
Alignment explanation
Indices: 2408789--2408842 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
2408779 ATGCTTTACA
2408789 TTTTTTAAATTATAT
1 TTTTTTAAATTATAT
2408804 TTTTTTATAATTTATAT
1 TTTTTTA-AA-TTATAT
* *
2408821 GTTTTTAGATTATAT
1 TTTTTTAAATTATAT
*
2408836 ATTTTTA
1 TTTTTTA
2408843 TGAATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 19 0.56
16 3 0.09
17 12 0.35
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
TTTTTTAAATTATAT
Found at i:2408818 original size:17 final size:16
Alignment explanation
Indices: 2408789--2408841 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
2408779 ATGCTTTACA
2408789 TTTTTTAAA-TTATAT
1 TTTTTTAAATTTATAT
2408804 TTTTTTATAATTTATAT
1 TTTTTTA-AATTTATAT
* *
2408821 GTTTTTAGATTATATAT
1 TTTTTTAAATT-TATAT
2408838 TTTT
1 TTTT
2408842 ATGAATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 7 0.22
16 5 0.16
17 20 0.62
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (16 bp):
TTTTTTAAATTTATAT
Found at i:2417397 original size:30 final size:31
Alignment explanation
Indices: 2417339--2417396 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
2417329 CTTAAAAATT
*
2417339 TAAAATTTAAAATATATTTTTATATTTTTAA
1 TAAAATTTAAAATACATTTTTATATTTTTAA
*
2417370 TAAAA-TTAAAAT-CATTTTTATTTTTTT
1 TAAAATTTAAAATACATTTTTATATTTTT
2417397 TTCAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 13 0.52
30 7 0.28
31 5 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (31 bp):
TAAAATTTAAAATACATTTTTATATTTTTAA
Found at i:2417732 original size:21 final size:21
Alignment explanation
Indices: 2417708--2417747 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2417698 TTTTGAATCT
2417708 CAAATCTTAAACCTCAAACCC
1 CAAATCTTAAACCTCAAACCC
*
2417729 CAAATCTTAAATCTCAAAC
1 CAAATCTTAAACCTCAAAC
2417748 TCTAAACATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.23
Consensus pattern (21 bp):
CAAATCTTAAACCTCAAACCC
Found at i:2420637 original size:2 final size:2
Alignment explanation
Indices: 2420630--2420659 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2420620 TTATTTGCAA
2420630 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2420660 AAAATAGAGA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:2430396 original size:25 final size:25
Alignment explanation
Indices: 2430368--2430464 Score: 70
Period size: 25 Copynumber: 3.9 Consensus size: 25
2430358 AGAAGCTCTT
2430368 TCGAGCCATATAACAGGAAGCTTAA
1 TCGAGCCATATAACAGGAAGCTTAA
*** * * *
2430393 TCGAGATGTATATCTGGAAGCTCAA
1 TCGAGCCATATAACAGGAAGCTTAA
* * *
2430418 TCGAGCTATATATCGGGAAGCTTAA
1 TCGAGCCATATAACAGGAAGCTTAA
** *
2430443 GAGAGCCAT-TAATCAAGAAGCT
1 TCGAGCCATATAA-CAGGAAGCT
2430465 CGTGAGAGCC
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
24 2 0.04
25 53 0.96
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (25 bp):
TCGAGCCATATAACAGGAAGCTTAA
Found at i:2438687 original size:19 final size:18
Alignment explanation
Indices: 2438665--2438708 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2438655 TTTATGATTT
2438665 TTTTATAAGTTTATATAAA
1 TTTTATAAGTTTA-ATAAA
* *
2438684 TTTTAATGATTTTAATAAA
1 TTTT-ATAAGTTTAATAAA
2438703 TTTTAT
1 TTTTAT
2438709 TAACTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 13 0.59
20 7 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
TTTTATAAGTTTAATAAA
Found at i:2438770 original size:22 final size:22
Alignment explanation
Indices: 2438724--2438766 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
2438714 TTTTATTGTT
*
2438724 TATTATTTTTATAGAATTTTAA
1 TATTATTTTTATAAAATTTTAA
2438746 TATT-TTTTTATAAAATTTTAA
1 TATTATTTTTATAAAATTTTAA
2438767 ATATGCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATTATTTTTATAAAATTTTAA
Found at i:2438831 original size:16 final size:19
Alignment explanation
Indices: 2438796--2438835 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
2438786 TAGAAAAAAC
2438796 TATAATTTTACTAGATTTT
1 TATAATTTTACTAGATTTT
2438815 TATAA-TTTA-TA-ATTTT
1 TATAATTTTACTAGATTTT
2438831 TATAA
1 TATAA
2438836 GTTGATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 2 0.10
18 4 0.19
19 5 0.24
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (19 bp):
TATAATTTTACTAGATTTT
Found at i:2444475 original size:17 final size:16
Alignment explanation
Indices: 2444441--2444500 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
2444431 TAAAGTGACT
*
2444441 ATATATAAAA-ATTTA
1 ATATATAAAATATTAA
2444456 ATATATAAAATTATTAA
1 ATATATAAAA-TATTAA
*
2444473 ATAT-TAAAATA-AAA
1 ATATATAAAATATTAA
2444487 ATA-ATATAAATATT
1 ATATATA-AAATATT
2444501 TATTTTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 7 0.19
15 17 0.46
16 5 0.14
17 8 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATATAAAATATTAA
Found at i:2444479 original size:23 final size:23
Alignment explanation
Indices: 2444443--2444500 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2444433 AAGTGACTAT
* * *
2444443 ATATAAAAATTTAATATATAAAATT
1 ATATAAATA-TTAAAATA-AAAATA
2444468 AT-TAAATATTAAAATAAAAATA
1 ATATAAATATTAAAATAAAAATA
2444490 ATATAAATATT
1 ATATAAATATT
2444501 TATTTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 15 0.52
24 5 0.17
25 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATATAAATATTAAAATAAAAATA
Found at i:2481751 original size:51 final size:51
Alignment explanation
Indices: 2481687--2481868 Score: 203
Period size: 51 Copynumber: 3.6 Consensus size: 51
2481677 TATCGATGAA
* *
2481687 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTATATCGATAAATAATGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTATACCGATAAATATTGGT
* * *
2481738 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGTATACCGATAAA--TATTGGT
* * *
2481789 CACGTATGTAGTACTATGTGAAGGCTACTACGTGA-ACCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTAAGTGAAGGCTACTACGT-ATACCGATAAATA-TTGGT
* *
2481839 CACGTGCGTAGTACTATGTGAAGGCTACTA
1 CACGTGTGTAGTACTAAGTGAAGGCTACTA
2481869 TGTGTATCGA
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
50 35 0.31
51 76 0.68
52 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTAAGTGAAGGCTACTACGTATACCGATAAATATTGGT
Found at i:2483693 original size:19 final size:20
Alignment explanation
Indices: 2483671--2483723 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
2483661 AAGAAATATA
2483671 TAAAAATACATAAAT-ATTT
1 TAAAAATACATAAATAATTT
* *
2483690 TAAATATATATAAAATAATTT
1 TAAAAATACAT-AAATAATTT
*
2483711 TTAAAA-ACATAAA
1 TAAAAATACATAAA
2483724 AATAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 12 0.44
20 7 0.26
21 8 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATACATAAATAATTT
Found at i:2483713 original size:22 final size:22
Alignment explanation
Indices: 2483671--2483758 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 22
2483661 AAGAAATATA
*
2483671 TAAAAATACAT-AAAT-A-TTT
1 TAAAAATATATAAAATAATTTT
*
2483690 TAAATATATATAAAATAATTTT
1 TAAAAATATATAAAATAATTTT
*
2483712 TAAAAACATA-AAAATAAATATTT
1 TAAAAATATATAAAAT-AAT-TTT
* *
2483735 TCAAAAAAATATATTAATAATTTT
1 T-AAAAATATATA-AAATAATTTT
2483759 AAATATTTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
19 9 0.16
20 4 0.07
21 6 0.11
22 14 0.25
23 4 0.07
24 11 0.20
25 4 0.07
26 3 0.05
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAAATATATAAAATAATTTT
Found at i:2483740 original size:24 final size:24
Alignment explanation
Indices: 2483680--2483747 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 24
2483670 ATAAAAATAC
* *
2483680 ATAAATATTTTAAATATATATAAA
1 ATAAATATTTTAAAAACATATAAA
2483704 AT-AAT-TTTTAAAAACATA-AAA
1 ATAAATATTTTAAAAACATATAAA
*
2483725 ATAAATATTTTCAAAAAAATATA
1 ATAAATATTTT-AAAAACATATA
2483748 TTAATAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.14
22 14 0.38
23 7 0.19
24 10 0.27
25 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (24 bp):
ATAAATATTTTAAAAACATATAAA
Found at i:2486011 original size:7 final size:7
Alignment explanation
Indices: 2485999--2486038 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
2485989 AAATTGGGTT
2485999 GAATATA
1 GAATATA
2486006 GAATATA
1 GAATATA
2486013 GAATATA
1 GAATATA
2486020 GAATATA
1 GAATATA
2486027 GAATATA
1 GAATATA
2486034 GAATA
1 GAATA
2486039 AATGTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (7 bp):
GAATATA
Found at i:2497128 original size:19 final size:18
Alignment explanation
Indices: 2497104--2497150 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2497094 ATATATATTT
2497104 TATTTTTTTAATTTTAAAA
1 TATTTTTTT-ATTTTAAAA
*
2497123 TATTTTTATT-TTTTTAAA
1 TATTTTT-TTATTTTAAAA
*
2497141 TAATTTTTTA
1 TATTTTTTTA
2497151 GTATTTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 2 0.08
18 13 0.54
19 7 0.29
20 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TATTTTTTTATTTTAAAA
Found at i:2501310 original size:24 final size:24
Alignment explanation
Indices: 2501277--2501336 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
2501267 AATAAATAAA
*
2501277 TAAATAATTTTTTTATTAAT-TTAGT
1 TAAA-AATTTATTTATTAATATTA-T
**
2501302 TAAAAATTTATTTATTTGTATTAT
1 TAAAAATTTATTTATTAATATTAT
2501326 TAAAAATTTAT
1 TAAAAATTTAT
2501337 CTACTTAACG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (24 bp):
TAAAAATTTATTTATTAATATTAT
Found at i:2510811 original size:18 final size:21
Alignment explanation
Indices: 2510771--2510822 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2510761 ATTTATGGTT
*
2510771 TAATTTTTAGTTTTTTATAAA
1 TAATTTTTAGTTTTGTATAAA
2510792 TAATTTTTA-TTTTGT-T-AA
1 TAATTTTTAGTTTTGTATAAA
2510810 T-ATATTTTAGTTT
1 TAAT-TTTTAGTTT
2510823 GTTGACTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 2 0.07
18 8 0.29
19 4 0.14
20 5 0.18
21 9 0.32
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (21 bp):
TAATTTTTAGTTTTGTATAAA
Found at i:2511336 original size:23 final size:22
Alignment explanation
Indices: 2511296--2511338 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2511286 AATTTTAAAA
*
2511296 TATTTTTAAAATACTTTTTTTT
1 TATTTTTAAAATAATTTTTTTT
* *
2511318 TATTTTTTAAATAAATTTTTT
1 TATTTTTAAAATAATTTTTTT
2511339 GTGCTTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTTAAAATAATTTTTTTT
Found at i:2514340 original size:2 final size:2
Alignment explanation
Indices: 2514333--2514357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2514323 TAAACTCAAA
2514333 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
2514358 TTGCAACAAA
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:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2514522 original size:68 final size:68
Alignment explanation
Indices: 2514450--2514588 Score: 260
Period size: 68 Copynumber: 2.0 Consensus size: 68
2514440 TTTTTCAGCA
*
2514450 GCTAATTTTTTCATTTGCCTTTCGTCTTTCATTTCATTTAAATTTCATCTATAAATAATACCAGT
1 GCTAATTTATTCATTTGCCTTTCGTCTTTCATTTCATTTAAATTTCATCTATAAATAATACCAGT
2514515 TCT
66 TCT
*
2514518 GCTAATTTATTCATTTGCCTTTTGTCTTTCATTTCATTTAAATTTCATCTATAAATAATACCAGT
1 GCTAATTTATTCATTTGCCTTTCGTCTTTCATTTCATTTAAATTTCATCTATAAATAATACCAGT
2514583 TCT
66 TCT
2514586 GCT
1 GCT
2514589 TTGTGTTTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 69 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (68 bp):
GCTAATTTATTCATTTGCCTTTCGTCTTTCATTTCATTTAAATTTCATCTATAAATAATACCAGT
TCT
Found at i:2521361 original size:18 final size:18
Alignment explanation
Indices: 2521315--2521365 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2521305 AGCTCTCAGG
2521315 CATTCTTCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
* ***
2521333 CAGTAAGCTCCCTTCATC
1 CATTCTTCTCCCTTCATC
2521351 CATTCTTCTCCCTTC
1 CATTCTTCTCCCTTC
2521366 CTTCATTCCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.14, C:0.43, G:0.04, T:0.39
Consensus pattern (18 bp):
CATTCTTCTCCCTTCATC
Found at i:2524203 original size:20 final size:20
Alignment explanation
Indices: 2524178--2524217 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2524168 AATATTTTCC
*
2524178 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2524198 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2524218 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2524223 original size:34 final size:35
Alignment explanation
Indices: 2524166--2524232 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2524156 CAAACACTAG
*
2524166 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2524201 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2524233 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2524224 original size:14 final size:14
Alignment explanation
Indices: 2524201--2524240 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2524191 ACAGAAAAGT
*
2524201 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
2524215 AAATCATTTTACGG
1 AAAACATTTTACAG
2524229 AAAACATTTTAC
1 AAAACATTTTAC
2524241 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:2527842 original size:16 final size:16
Alignment explanation
Indices: 2527823--2527865 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2527813 AACCAATATT
* *
2527823 ATTTTGTTAGGATTAA
1 ATTTTGTAAGCATTAA
2527839 ATTTTAGTAAGCATTAA
1 ATTTT-GTAAGCATTAA
2527856 ATGTTTGTAA
1 AT-TTTGTAA
2527866 TAAAGAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 15 0.65
18 3 0.13
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (16 bp):
ATTTTGTAAGCATTAA
Found at i:2530360 original size:2 final size:2
Alignment explanation
Indices: 2530353--2530402 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2530343 GCAGCTTTAT
2530353 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2530395 AG AG AG AG
1 AG AG AG AG
2530403 GGGTGAAAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2531501 original size:31 final size:32
Alignment explanation
Indices: 2531441--2531502 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
2531431 TTCTAATAAA
*
2531441 TCCTAATTTCTTCAAGGGTTTGTACTAATCAG
1 TCCTAATTTCTTCAAGGATTTGTACTAATCAG
* *
2531473 TCCTAATTT-TTTAAGGATTTGTATTAATCA
1 TCCTAATTTCTTCAAGGATTTGTACTAATCA
2531503 ACCTCTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (32 bp):
TCCTAATTTCTTCAAGGATTTGTACTAATCAG
Found at i:2544226 original size:18 final size:18
Alignment explanation
Indices: 2544184--2544226 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2544174 ATGTGCTCCT
*
2544184 CCACCACTACCACCGCCG
1 CCACCGCTACCACCGCCG
2544202 CCACCGCTACCACCGCCG
1 CCACCGCTACCACCGCCG
*
2544220 CCGCCGC
1 CCACCGC
2544227 CACCGCTACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.63, G:0.16, T:0.05
Consensus pattern (18 bp):
CCACCGCTACCACCGCCG
Found at i:2544303 original size:21 final size:21
Alignment explanation
Indices: 2544270--2544309 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2544260 AGCCACTTCC
*
2544270 TCCTCCACTTCCACTTCCATA
1 TCCTCCACTTCCACCTCCATA
2544291 TCCTCCAGC-TCCACCTCCA
1 TCCTCCA-CTTCCACCTCCA
2544310 CCACCACCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.17, C:0.53, G:0.03, T:0.28
Consensus pattern (21 bp):
TCCTCCACTTCCACCTCCATA
Found at i:2544313 original size:9 final size:9
Alignment explanation
Indices: 2544301--2544388 Score: 60
Period size: 9 Copynumber: 10.1 Consensus size: 9
2544291 TCCTCCAGCT
2544301 CCACCTCCA
1 CCACCTCCA
*
2544310 CCACCACCA
1 CCACCTCCA
*
2544319 CC-GCTACCA
1 CCACCT-CCA
2544328 CCACCTCCA
1 CCACCTCCA
2544337 CCACCT---
1 CCACCTCCA
*
2544343 CCACGTCCA
1 CCACCTCCA
*
2544352 CCACC-CTTA
1 CCACCTC-CA
*
2544361 CCAGCTCCA
1 CCACCTCCA
*
2544370 CCACCTTCA
1 CCACCTCCA
*
2544379 CCACTTCCA
1 CCACCTCCA
2544388 C
1 C
2544389 TTCCACTTCC
Statistics
Matches: 59, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
6 5 0.08
8 2 0.03
9 49 0.83
10 3 0.05
ACGTcount: A:0.23, C:0.60, G:0.03, T:0.14
Consensus pattern (9 bp):
CCACCTCCA
Found at i:2544394 original size:12 final size:12
Alignment explanation
Indices: 2544379--2544411 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
2544369 ACCACCTTCA
2544379 CCACTTCCACTT
1 CCACTTCCACTT
2544391 CCACTTCCACTT
1 CCACTTCCACTT
2544403 CCACTTCCA
1 CCACTTCCA
2544412 AATCCTCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.52, G:0.00, T:0.30
Consensus pattern (12 bp):
CCACTTCCACTT
Found at i:2544461 original size:123 final size:129
Alignment explanation
Indices: 2544262--2544660 Score: 424
Period size: 129 Copynumber: 3.1 Consensus size: 129
2544252 ATACCCAGAG
* *
2544262 CCACTTCCTCCTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCACCGCTACC
1 CCACTTCCACTTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCA-C-C-ACC
* *
2544327 ACCACCTCCACCACCTCCACGTCCACCA-C-CC-TTACCAGCT-C-C-ACCACCTTCACCA-C-T
63 ACCACCACCACCACCTCCACGTCCACCACCACCATTACCAGCTCCGCTACCACCTCCACCACCTT
2544384 -T
128 CT
* * *
2544385 CCACTTCCACTTCCACTTCCACTTCCAAATCCTCCAGCTCCGCCTCCACCACCACCACTACCACC
1 CCACTTCCACTTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCACCACCACC
* * *
2544450 ACCTCCACCACCTCCATGTCCACCACCACCATTACCAGCTCCGCTACCAGCTCCACCACCTTCT
66 ACCACCACCACCTCCACGTCCACCACCACCATTACCAGCTCCGCTACCACCTCCACCACCTTCT
** * * * * *
2544514 CCACTTCCACTTCCACTTCCACTTCCATATCCTCCAGCTCCACCAGCACTACCGCCGCCTCCGCC
1 CCACTTCCACTTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCACCACCACC
* * * * * * *
2544579 ACCACC-CTTACCTCCACCTCCACCACCTCCTCCATTTCCAGCTCCACTACCAGCTCCACCTCCT
66 ACCACCAC-CACCTCCACGTCCACCA---CCACCATTACCAGCTCCGCTACCACCTCCACCACCT
*
2544643 TCA
127 TCT
2544646 CCAAC-TCCACTTCCA
1 CC-ACTTCCACTTCCA
2544661 TATCCAGAAG
Statistics
Matches: 235, Mismatches: 27, Indels: 19
0.84 0.10 0.07
Matches are distributed among these distances:
120 30 0.13
121 1 0.00
122 3 0.01
123 62 0.26
124 1 0.00
125 1 0.00
126 11 0.05
127 1 0.00
128 2 0.01
129 75 0.32
132 46 0.20
133 2 0.01
ACGTcount: A:0.20, C:0.55, G:0.04, T:0.20
Consensus pattern (129 bp):
CCACTTCCACTTCCACTTCCACTTCCATATCCTCCAGCTCCACCTCCACCACCACCACCACCACC
ACCACCACCACCTCCACGTCCACCACCACCATTACCAGCTCCGCTACCACCTCCACCACCTTCT
Found at i:2544471 original size:15 final size:15
Alignment explanation
Indices: 2544439--2544481 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2544429 TCCACCACCA
* **
2544439 CCACTACCACCACCT
1 CCACCACCACCATGT
*
2544454 CCACCACCTCCATGT
1 CCACCACCACCATGT
2544469 CCACCACCACCAT
1 CCACCACCACCAT
2544482 TACCAGCTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.26, C:0.58, G:0.02, T:0.14
Consensus pattern (15 bp):
CCACCACCACCATGT
Found at i:2544524 original size:6 final size:6
Alignment explanation
Indices: 2544513--2544540 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2544503 CACCACCTTC
2544513 TCCACT TCCACT TCCACT TCCACT TCCA
1 TCCACT TCCACT TCCACT TCCACT TCCA
2544541 TATCCTCCAG
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:0.18, C:0.50, G:0.00, T:0.32
Consensus pattern (6 bp):
TCCACT
Found at i:2544730 original size:18 final size:18
Alignment explanation
Indices: 2544709--2544755 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
2544699 ACTACCACTA
2544709 CCACCACCACCTCCATGT
1 CCACCACCACCTCCATGT
* *
2544727 CCACCAGCACCTCCATTT
1 CCACCACCACCTCCATGT
*
2544745 CCAACACCACC
1 CCACCACCACC
2544756 ACCTCCTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.55, G:0.04, T:0.15
Consensus pattern (18 bp):
CCACCACCACCTCCATGT
Found at i:2544732 original size:21 final size:21
Alignment explanation
Indices: 2544708--2544768 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
2544698 CACTACCACT
2544708 ACCACCACCACCTCCATGT--
1 ACCACCACCACCTCCATGTCC
* *
2544727 -CCACCAGCACCTCCATTTCC
1 ACCACCACCACCTCCATGTCC
* *
2544747 AACACCACCACCTCCTTGTCC
1 ACCACCACCACCTCCATGTCC
2544768 A
1 A
2544769 GCACTTACAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 16 0.48
21 17 0.52
ACGTcount: A:0.25, C:0.52, G:0.05, T:0.18
Consensus pattern (21 bp):
ACCACCACCACCTCCATGTCC
Found at i:2548282 original size:45 final size:45
Alignment explanation
Indices: 2548233--2548318 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
2548223 AGATTGAAAC
*
2548233 ACCTTATTCTAATCAATATCAAATAGATGGAGTTTAATAAATTCA
1 ACCTTATTCTAATCAATATCAAATAAATGGAGTTTAATAAATTCA
2548278 ACCTTATTCTAATCAATATCAAATAAATGGAGTTTAATAAA
1 ACCTTATTCTAATCAATATCAAATAAATGGAGTTTAATAAA
2548319 GTTTAAAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (45 bp):
ACCTTATTCTAATCAATATCAAATAAATGGAGTTTAATAAATTCA
Found at i:2548707 original size:21 final size:21
Alignment explanation
Indices: 2548683--2548744 Score: 53
Period size: 21 Copynumber: 3.1 Consensus size: 21
2548673 AAGGTCTTCA
2548683 TTGAGTTCACTAAAGAGTCCC
1 TTGAGTTCACTAAAGAGTCCC
* *
2548704 TTGA-TT---TGAAG-GTCTTCA
1 TTGAGTTCACTAAAGAGTC--CC
2548722 TTGAGTTCACTAAAGAGTCCC
1 TTGAGTTCACTAAAGAGTCCC
2548743 TT
1 TT
2548745 CAACCAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 14
0.62 0.08 0.29
Matches are distributed among these distances:
16 3 0.10
17 4 0.13
18 5 0.17
19 2 0.07
20 2 0.07
21 7 0.23
22 4 0.13
23 3 0.10
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (21 bp):
TTGAGTTCACTAAAGAGTCCC
Found at i:2548719 original size:39 final size:39
Alignment explanation
Indices: 2548665--2548744 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
2548655 AAATATTGTA
2548665 TTGATTTGAAGGTCTTCATTGAGTTCACTAAAGAGTCCC
1 TTGATTTGAAGGTCTTCATTGAGTTCACTAAAGAGTCCC
2548704 TTGATTTGAAGGTCTTCATTGAGTTCACTAAAGAGTCCC
1 TTGATTTGAAGGTCTTCATTGAGTTCACTAAAGAGTCCC
2548743 TT
1 TT
2548745 CAACCAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (39 bp):
TTGATTTGAAGGTCTTCATTGAGTTCACTAAAGAGTCCC
Found at i:2560751 original size:19 final size:20
Alignment explanation
Indices: 2560727--2560764 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2560717 ATTAGTATTT
2560727 TAAAAAAATT-AAATTCAAA
1 TAAAAAAATTAAAATTCAAA
*
2560746 TAAAAATATTAAAATTCAA
1 TAAAAAAATTAAAATTCAA
2560765 GATGAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAAATTAAAATTCAAA
Found at i:2566973 original size:12 final size:13
Alignment explanation
Indices: 2566955--2567001 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
2566945 TAAAACCTAT
2566955 AATAAAATTATTA
1 AATAAAATTATTA
**
2566968 AA-AAAAGAATTA
1 AATAAAATTATTA
*
2566980 AATAAAATTTTCTA
1 AATAAAATTAT-TA
2566994 AATAAAAT
1 AATAAAAT
2567002 AGAATTTACT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.37
13 7 0.26
14 10 0.37
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (13 bp):
AATAAAATTATTA
Found at i:2568154 original size:16 final size:16
Alignment explanation
Indices: 2568133--2568163 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2568123 TCATGCTACG
2568133 TCATCAATTTTTTACA
1 TCATCAATTTTTTACA
2568149 TCATCAATTTTTTAC
1 TCATCAATTTTTTAC
2568164 TGTAAAAATT
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:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (16 bp):
TCATCAATTTTTTACA
Found at i:2570842 original size:18 final size:18
Alignment explanation
Indices: 2570821--2570864 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2570811 TTTTAAAAAA
2570821 TAATTATTTTATTAGTAT
1 TAATTATTTTATTAGTAT
* *
2570839 TAATAATTTTATTAGTTT
1 TAATTATTTTATTAGTAT
*
2570857 TATTTATT
1 TAATTATT
2570865 GAATTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (18 bp):
TAATTATTTTATTAGTAT
Found at i:2571553 original size:19 final size:21
Alignment explanation
Indices: 2571505--2571553 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2571495 TTAGTCATTC
2571505 AATTTTAAAAAATTACAAAAT
1 AATTTTAAAAAATTACAAAAT
**
2571526 AATTATTAAATTATT-CAAAA-
1 AATT-TTAAAAAATTACAAAAT
2571546 AATTTTAA
1 AATTTTAA
2571554 TTAAGTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.16
20 4 0.16
21 9 0.36
22 8 0.32
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (21 bp):
AATTTTAAAAAATTACAAAAT
Found at i:2576440 original size:72 final size:72
Alignment explanation
Indices: 2576299--2576445 Score: 163
Period size: 72 Copynumber: 2.0 Consensus size: 72
2576289 TTACAATTAC
* ** * *
2576299 TCACTTTCTCAGCTTCCTCTTGTCTCCAAATACCTGCATATTCTTTTAGCATCTTCCTCCTTTCC
1 TCACCTTCTCAGCTTCCTCTTACCTCCAAATACCTGCATATTCTTTTAGCATCTACCTCCCTTCC
2576364 TTTAAAT
66 TTTAAAT
* * * *
2576371 TCACCTTCTCAGCTTCCTC-TACCTCCAAAATACCTTCCTGTTCTTTTGGCATC-ACCTCCCCTT
1 TCACCTTCTCAGCTTCCTCTTACCTCC-AAATACCTGCATATTCTTTTAGCATCTACCT-CCCTT
* *
2576434 CTTTTAATT
64 CCTTTAAAT
2576443 TCA
1 TCA
2576446 AATCTCCTGC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
71 8 0.13
72 54 0.87
ACGTcount: A:0.18, C:0.35, G:0.05, T:0.42
Consensus pattern (72 bp):
TCACCTTCTCAGCTTCCTCTTACCTCCAAATACCTGCATATTCTTTTAGCATCTACCTCCCTTCC
TTTAAAT
Found at i:2581744 original size:31 final size:30
Alignment explanation
Indices: 2581698--2581777 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
2581688 TAATGTAAAC
* * * *
2581698 TTTTGGTTCTGAACTTGGTAGTTATGTCTA
1 TTTTGGTTCTGAACTTGGCAATCAAGTCTA
*
2581728 TTTTGGTATTTGAACTTGGCAATCAAGTCTA
1 TTTTGGT-TCTGAACTTGGCAATCAAGTCTA
*
2581759 TTTTGGTCTCTAAACTTGG
1 TTTTGGT-TCTGAACTTGG
2581778 AAAAATATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 7 0.17
31 34 0.83
ACGTcount: A:0.20, C:0.12, G:0.21, T:0.46
Consensus pattern (30 bp):
TTTTGGTTCTGAACTTGGCAATCAAGTCTA
Found at i:2592723 original size:22 final size:22
Alignment explanation
Indices: 2592698--2592743 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
2592688 TTTTGAGCAA
*
2592698 TTTAATTTATTCTTTTATGTTT
1 TTTAACTTATTCTTTTATGTTT
*
2592720 TTTAACTTGTTCTTTTATGTTT
1 TTTAACTTATTCTTTTATGTTT
2592742 TT
1 TT
2592744 CTTTAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTAACTTATTCTTTTATGTTT
Found at i:2597181 original size:16 final size:17
Alignment explanation
Indices: 2597162--2597205 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 17
2597152 TAATCATTCA
2597162 AAAATTATAAAAATA-T
1 AAAATTATAAAAATATT
*
2597178 AAAA-TATTAAAATATT
1 AAAATTATAAAAATATT
*
2597194 AAAATGATAAAA
1 AAAATTATAAAA
2597206 TGATATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 9 0.39
16 9 0.39
17 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAATTATAAAAATATT
Found at i:2597206 original size:16 final size:16
Alignment explanation
Indices: 2597162--2597211 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 16
2597152 TAATCATTCA
2597162 AAAATTATAAAA-ATAT
1 AAAA-TATAAAATATAT
2597178 AAAATATTAAAATAT-T
1 AAAATA-TAAAATATAT
2597194 AAAATGATAAAATGATAT
1 AAAAT-ATAAAAT-ATAT
2597212 TTTTATTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 21 0.72
17 5 0.17
18 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (16 bp):
AAAATATAAAATATAT
Found at i:2609135 original size:29 final size:31
Alignment explanation
Indices: 2609070--2609126 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
2609060 AAAATTTATA
*
2609070 AAAAATATTTTTAAAATTATTTAAAAAGTAT
1 AAAAATATTTTTAAAATTATTTAAAAAATAT
*
2609101 AAAAATGTTTTT-AAA-TATTTAAAAAA
1 AAAAATATTTTTAAAATTATTTAAAAAA
2609127 ATTTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.42
30 3 0.12
31 11 0.46
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (31 bp):
AAAAATATTTTTAAAATTATTTAAAAAATAT
Found at i:2610509 original size:18 final size:18
Alignment explanation
Indices: 2610488--2610522 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2610478 TAATTAGAGT
*
2610488 AATTAAATTAATTAAAAA
1 AATTAAACTAATTAAAAA
2610506 AATTAAACTAATTAAAA
1 AATTAAACTAATTAAAA
2610523 TAGGAACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTAAACTAATTAAAAA
Found at i:2610982 original size:17 final size:17
Alignment explanation
Indices: 2610960--2610992 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2610950 GATGGCGCAA
*
2610960 AATACCCTTAAACCCTC
1 AATACCCTAAAACCCTC
2610977 AATACCCTAAAACCCT
1 AATACCCTAAAACCCT
2610993 TCTTCTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.39, G:0.00, T:0.21
Consensus pattern (17 bp):
AATACCCTAAAACCCTC
Found at i:2611018 original size:22 final size:22
Alignment explanation
Indices: 2610993--2611035 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
2610983 CTAAAACCCT
*
2610993 TCTTCTT-TTCTTTTTGTTTTTC
1 TCTTCTTCTT-TTTTTGGTTTTC
2611015 TCTTCTTCTTTTTTTGGTTTT
1 TCTTCTTCTTTTTTTGGTTTT
2611036 GAGAATCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (22 bp):
TCTTCTTCTTTTTTTGGTTTTC
Found at i:2617366 original size:25 final size:26
Alignment explanation
Indices: 2617329--2617387 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2617319 ATTATTTTAA
2617329 TTTTTTTATAA-TTTAAAAAATACTTT
1 TTTTTTTATAATTTTAAAAAATA-TTT
*
2617355 TTTTTTTA-AATTTTAAAAATTATTT
1 TTTTTTTATAATTTTAAAAAATATTT
2617380 TTATTTTT
1 TT-TTTTT
2617388 GTTTTTGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTTTTTATAATTTTAAAAAATATTT
Found at i:2622014 original size:13 final size:13
Alignment explanation
Indices: 2621977--2622014 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
2621967 ACACTTAAAT
2621977 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
2621990 TTTTCCACAGCAC
1 TTTTCAAAAGCAC
2622003 TTTTCAAAAGCA
1 TTTTCAAAAGCA
2622015 TTACCAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:2636522 original size:34 final size:34
Alignment explanation
Indices: 2636457--2636523 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
2636447 GCCTCCTCTG
**
2636457 TATAATGTTAAGAATCATAATGTCCTTTTTTTTT
1 TATAATGTTAAGAATCATAATGTCCAATTTTTTT
* * *
2636491 TATAATGTTACGAATCATAATTTTCAATTTTTT
1 TATAATGTTAAGAATCATAATGTCCAATTTTTT
2636524 ATATGCTCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (34 bp):
TATAATGTTAAGAATCATAATGTCCAATTTTTTT
Found at i:2640307 original size:14 final size:14
Alignment explanation
Indices: 2640261--2640309 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
2640251 TAAATTTATG
*
2640261 TTTTAATTAATTAT
1 TTTTAATTAAATAT
* * *
2640275 TTATTATTTTAATAA
1 TT-TTAATTAAATAT
2640290 TTTTAATTAAATAT
1 TTTTAATTAAATAT
2640304 TTTTAA
1 TTTTAA
2640310 ATAGTTTAAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 17 0.63
15 10 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTAATTAAATAT
Found at i:2659774 original size:14 final size:13
Alignment explanation
Indices: 2659732--2659776 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
2659722 TAAAATTCGA
2659732 AAAATATAAAAATT
1 AAAATAT-AAAATT
*
2659746 AAAATGATGAAATT
1 AAAAT-ATAAAATT
2659760 AAAATATAAAGATT
1 AAAATATAAA-ATT
2659774 AAA
1 AAA
2659777 TCTACAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 4 0.15
14 21 0.78
15 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.27
Consensus pattern (13 bp):
AAAATATAAAATT
Found at i:2670845 original size:36 final size:36
Alignment explanation
Indices: 2670778--2670847 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
2670768 GTTGTCTTGC
* **
2670778 TATTATTTCGCTATTATATTGCTACTATTTTGTTGT
1 TATTATTTCGATATTATATAACTACTATTTTGTTGT
* * *
2670814 TATTATTTGGATATTATATAACTATTGTTTTGTT
1 TATTATTTCGATATTATATAACTACTATTTTGTT
2670848 ATTAATTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.59
Consensus pattern (36 bp):
TATTATTTCGATATTATATAACTACTATTTTGTTGT
Found at i:2694369 original size:18 final size:18
Alignment explanation
Indices: 2694346--2694385 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2694336 AAAATTTATA
* *
2694346 ATTTATATATATTTCTTT
1 ATTTATATATATATATTT
2694364 ATTTATATATATATATTT
1 ATTTATATATATATATTT
2694382 ATTT
1 ATTT
2694386 CCATTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATATATATATATTT
Found at i:2696945 original size:18 final size:17
Alignment explanation
Indices: 2696922--2696959 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2696912 AATAGAAAGA
*
2696922 AAAAAAATCCTTAAATTT
1 AAAAAAAT-CATAAATTT
2696940 AAAAAAATCATAAATTT
1 AAAAAAATCATAAATTT
2696957 AAA
1 AAA
2696960 TAAACGAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAAATCATAAATTT
Found at i:2701436 original size:99 final size:95
Alignment explanation
Indices: 2701231--2701516 Score: 365
Period size: 99 Copynumber: 3.0 Consensus size: 95
2701221 AAAGGTTTAG
* * * * *
2701231 GGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTAAAAAATTAGATTAGAGTTTAGAGTTTA
1 GGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTGTTTA
* * * * *
2701296 TGATTTTTAATGAAAAATTAAATAAATTAG
66 GGGTTTTTAAGGAAAAATCAAATAAATTAA
* *
2701326 GGTTTAGGGTTACTTGAGTAAATTAATTATAATTTTTTTTAAAAAAATAGATTAGGGTTTAGTGT
1 GGTTTAGGGTTACTTGAGTAAATTAATTATAA---ATTTTAAAAAATTAGATTAGGGTTTAGTGT
2701391 TTAGGGTTTTTAAGGGAAAAATCAAATAAATTAA
63 TTAGGGTTTTTAA-GGAAAAATCAAATAAATTAA
* * * * *
2701425 GGTTTAAGGTTATTTGAGTAAATTAATTATAAAAATTTAAAAAATTAGATTGGGGTTTAGTATTT
1 GGTTTAGGGTTACTTGAGTAAATTAATTAT-AAATTTTAAAAAATTAGATTAGGGTTTAGTGTTT
*
2701490 AGAGTTTTTAAGGAAAAATCAAATAAA
65 AGGGTTTTTAAGGAAAAATCAAATAAA
2701517 ACTAGTTGTT
Statistics
Matches: 166, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
95 29 0.17
96 16 0.10
97 37 0.22
98 37 0.22
99 45 0.27
100 2 0.01
ACGTcount: A:0.41, C:0.01, G:0.17, T:0.41
Consensus pattern (95 bp):
GGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTTAAAAAATTAGATTAGGGTTTAGTGTTTA
GGGTTTTTAAGGAAAAATCAAATAAATTAA
Found at i:2702156 original size:11 final size:11
Alignment explanation
Indices: 2702140--2702188 Score: 54
Period size: 11 Copynumber: 4.9 Consensus size: 11
2702130 TTAGACTTAA
2702140 TAAATAATTTT
1 TAAATAATTTT
2702151 TAAATAATTTT
1 TAAATAATTTT
2702162 T-AAT--TTTT
1 TAAATAATTTT
2702170 T-AA-AATTTT
1 TAAATAATTTT
*
2702179 TAATTAATTT
1 TAAATAATTT
2702189 AATTAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 7 0.21
9 5 0.15
10 4 0.12
11 17 0.52
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TAAATAATTTT
Found at i:2702176 original size:17 final size:18
Alignment explanation
Indices: 2702144--2702183 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
2702134 ACTTAATAAA
2702144 TAATTTTTAAATAATTTT
1 TAATTTTTAAATAATTTT
*
2702162 TAATTTTTTAA-AATTTT
1 TAATTTTTAAATAATTTT
2702179 TAATT
1 TAATT
2702184 AATTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TAATTTTTAAATAATTTT
Found at i:2702380 original size:40 final size:40
Alignment explanation
Indices: 2702331--2702422 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
2702321 GCTTCTCAAG
*
2702331 GAAGCGTTTTCTGCCCACGTGGACAAAGCGCTTCCTTGAA
1 GAAGCGTTTTCTACCCACGTGGACAAAGCGCTTCCTTGAA
* * * *
2702371 GAAGAGTTTTTTTATCCACGTGGACAAAGCGCTTCCTTGAG
1 GAAGCG-TTTTCTACCCACGTGGACAAAGCGCTTCCTTGAA
2702412 GAAGCGTTTTC
1 GAAGCGTTTTC
2702423 CTGCTTTATC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 9 0.20
41 35 0.80
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.29
Consensus pattern (40 bp):
GAAGCGTTTTCTACCCACGTGGACAAAGCGCTTCCTTGAA
Found at i:2709090 original size:54 final size:54
Alignment explanation
Indices: 2709026--2709133 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
2709016 TCAATGGGTC
2709026 CTGGACTATGTCTATGTTATAGGAACAACGCATGGATAGTGCAAATTGAGGTTA
1 CTGGACTATGTCTATGTTATAGGAACAACGCATGGATAGTGCAAATTGAGGTTA
*
2709080 CTGGACTATGTCTATGTTATAGGAACAATGCATGGATAGTGCAAATTGAGGTTA
1 CTGGACTATGTCTATGTTATAGGAACAACGCATGGATAGTGCAAATTGAGGTTA
2709134 TTTGTAAATT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (54 bp):
CTGGACTATGTCTATGTTATAGGAACAACGCATGGATAGTGCAAATTGAGGTTA
Found at i:2710726 original size:22 final size:23
Alignment explanation
Indices: 2710700--2710746 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
2710690 ATAACATAGC
*
2710700 TTTAATAAAT-ATAGAAAAATCT
1 TTTAATAAATAAAAGAAAAATCT
2710722 TTTAATAAATGAAAAGAAAAATCT
1 TTTAATAAAT-AAAAGAAAAATCT
2710746 T
1 T
2710747 AAACTGTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
24 12 0.55
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (23 bp):
TTTAATAAATAAAAGAAAAATCT
Found at i:2711720 original size:42 final size:41
Alignment explanation
Indices: 2711680--2711818 Score: 156
Period size: 42 Copynumber: 3.3 Consensus size: 41
2711670 GTTTATACAG
* * *
2711680 AAAAGGAAGCAACTTGGGAAAGCAACATCTATGTCTATACAA
1 AAAAGGAAGCAACTTGGGAAAACAACATC-AAGTCTAGACAA
* *
2711722 AAAAGAAAGCAACTTGGAAAAACAACATGCAAG-CTCAGACAA
1 AAAAGGAAGCAACTTGGGAAAACAACAT-CAAGTCT-AGACAA
* *
2711764 AAAAGGAGGCAACTTGGGAAAACAACATCCAGGTGC-AGACAA
1 AAAAGGAAGCAACTTGGGAAAACAACAT-CAAGT-CTAGACAA
2711806 AAAAGGAAGCAAC
1 AAAAGGAAGCAAC
2711819 GTAGAAATAA
Statistics
Matches: 82, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
41 2 0.02
42 78 0.95
43 1 0.01
44 1 0.01
ACGTcount: A:0.50, C:0.18, G:0.21, T:0.12
Consensus pattern (41 bp):
AAAAGGAAGCAACTTGGGAAAACAACATCAAGTCTAGACAA
Found at i:2714271 original size:41 final size:41
Alignment explanation
Indices: 2714214--2714295 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
2714204 AATTCCCCTC
2714214 GAATTCAACATTGTTCTTTGCAAATTCATTCGATTAAACTA
1 GAATTCAACATTGTTCTTTGCAAATTCATTCGATTAAACTA
2714255 GAATTCAACATTGTTCTTTGCAAATTCATTCGATTAAACTA
1 GAATTCAACATTGTTCTTTGCAAATTCATTCGATTAAACTA
2714296 ACTAGTAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (41 bp):
GAATTCAACATTGTTCTTTGCAAATTCATTCGATTAAACTA
Found at i:2722765 original size:19 final size:20
Alignment explanation
Indices: 2722726--2722770 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2722716 GAAATAATTA
*
2722726 TTTTAATATATTTAGTGTTT
1 TTTTAATATATTTAGTATTT
*
2722746 TTTTAATATTTTTA-TATTT
1 TTTTAATATATTTAGTATTT
2722765 TTTTAA
1 TTTTAA
2722771 ATTAAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTAATATATTTAGTATTT
Found at i:2723820 original size:3 final size:3
Alignment explanation
Indices: 2723812--2723859 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
2723802 TCCACAAAGA
* * *
2723812 ATT ATT ATT ATT ATT ACT ATT ACT ATT ACT ATT ACTT -TT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
2723857 ATT
1 ATT
2723860 TTGGTCCTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:2733550 original size:7 final size:6
Alignment explanation
Indices: 2733534--2733576 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
2733524 TGCATAAATC
* *
2733534 TTTCTT TTTCTTT TTTCTT TTTCTT TTCCTT TTCCTCT TTTCT
1 TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TTTCT-T TTTCT
2733577 CCTTGTGCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 22 0.67
7 11 0.33
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:2733552 original size:13 final size:13
Alignment explanation
Indices: 2733534--2733560 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2733524 TGCATAAATC
2733534 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
2733547 TTTCTTTTTCTTT
1 TTTCTTTTTCTTT
2733560 T
1 T
2733561 CCTTTTCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTCTTTTTCTTT
Found at i:2733576 original size:19 final size:19
Alignment explanation
Indices: 2733534--2733574 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2733524 TGCATAAATC
* *
2733534 TTTCTTTTTCTTTTTTCTT
1 TTTCTTTTCCTTTTCTCTT
2733553 TTTCTTTTCCTTTTCCTCTT
1 TTTCTTTTCCTTTT-CTCTT
2733573 TT
1 TT
2733575 CTCCTTGTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTCTTTTCCTTTTCTCTT
Found at i:2736794 original size:20 final size:20
Alignment explanation
Indices: 2736769--2736808 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2736759 CTCATGCCTC
2736769 ATAACTTAGGCCATGTTCTA
1 ATAACTTAGGCCATGTTCTA
2736789 ATAACTTAGGCCATGTTCTA
1 ATAACTTAGGCCATGTTCTA
2736809 TAATGCTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (20 bp):
ATAACTTAGGCCATGTTCTA
Found at i:2747560 original size:16 final size:16
Alignment explanation
Indices: 2747539--2747571 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2747529 AATATTCAAA
*
2747539 TTTAAATTTAATATTT
1 TTTAAATGTAATATTT
2747555 TTTAAATGTAATATTT
1 TTTAAATGTAATATTT
2747571 T
1 T
2747572 ACATTGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TTTAAATGTAATATTT
Found at i:2753318 original size:27 final size:28
Alignment explanation
Indices: 2753239--2753318 Score: 67
Period size: 27 Copynumber: 2.9 Consensus size: 28
2753229 ATATATATAA
**
2753239 AATATTAATAATATTTTATTAAACGAGAAT
1 AATATTAATAATATTTT-TT-AATTAGAAT
* **
2753269 AATATTTGATAATA-TAATT-ATTAGAAT
1 AATA-TTAATAATATTTTTTAATTAGAAT
2753296 AATATT-ATAATATTTTTTAATTA
1 AATATTAATAATATTTTTTAATTA
2753319 TATATTTAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
25 6 0.15
26 5 0.12
27 14 0.35
29 2 0.05
30 5 0.12
31 8 0.20
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (28 bp):
AATATTAATAATATTTTTTAATTAGAAT
Found at i:2756418 original size:19 final size:20
Alignment explanation
Indices: 2756387--2756427 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
2756377 AATATTATGA
2756387 AATAAATTTTTTAATTCTAC
1 AATAAATTTTTTAATTCTAC
2756407 AATAAA-TTTTTAATTCTAC
1 AATAAATTTTTTAATTCTAC
2756426 AA
1 AA
2756428 ACAAAAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (20 bp):
AATAAATTTTTTAATTCTAC
Found at i:2763414 original size:48 final size:49
Alignment explanation
Indices: 2763360--2763455 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
2763350 TCAAGTTGAT
2763360 TTGAGAGTTAGTGTTGAAGATT-GAGAAGAAAGCAATTTATATTTTGGC
1 TTGAGAGTTAGTGTTGAAGATTGGAGAAGAAAGCAATTTATATTTTGGC
2763408 TTGAGAGTTAGTGTTGAAGATTGGAGAAGAAAGCAATTTATATTTTGG
1 TTGAGAGTTAGTGTTGAAGATTGGAGAAGAAAGCAATTTATATTTTGG
2763456 TTCGTAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 22 0.47
49 25 0.53
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.35
Consensus pattern (49 bp):
TTGAGAGTTAGTGTTGAAGATTGGAGAAGAAAGCAATTTATATTTTGGC
Found at i:2764798 original size:27 final size:27
Alignment explanation
Indices: 2764760--2764815 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
2764750 AGTATAATAT
2764760 CGTACCTAAGTTAAACCTGATCCAATC
1 CGTACCTAAGTTAAACCTGATCCAATC
*
2764787 CGTACCTAAGTTAAACTTGATCCAATC
1 CGTACCTAAGTTAAACCTGATCCAATC
2764814 CG
1 CG
2764816 GTTAACAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (27 bp):
CGTACCTAAGTTAAACCTGATCCAATC
Found at i:2774647 original size:33 final size:33
Alignment explanation
Indices: 2774605--2774681 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 33
2774595 TAAAAAAAAA
*
2774605 ATTGGTTCAATCTTGAACTAGTGTTCACGGTCC
1 ATTGGTTCAATCCTGAACTAGTGTTCACGGTCC
*
2774638 ATTGGTTCAATCCTGAATTAGTGTTCACGGTCC
1 ATTGGTTCAATCCTGAACTAGTGTTCACGGTCC
2774671 AGTTGGTTCAA
1 A-TTGGTTCAA
2774682 AACCATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 32 0.78
34 9 0.22
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (33 bp):
ATTGGTTCAATCCTGAACTAGTGTTCACGGTCC
Found at i:2776752 original size:16 final size:15
Alignment explanation
Indices: 2776716--2776751 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
2776706 CAAAATTAAG
2776716 ATTTTTACAATATCC
1 ATTTTTACAATATCC
2776731 ATTTTTACAATAGT-C
1 ATTTTTACAATA-TCC
2776746 ATTTTT
1 ATTTTT
2776752 TTAAAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.31, C:0.14, G:0.03, T:0.53
Consensus pattern (15 bp):
ATTTTTACAATATCC
Found at i:2780834 original size:15 final size:16
Alignment explanation
Indices: 2780814--2780857 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2780804 AAAATCCAAC
2780814 CCTAAAATCTTATA-T
1 CCTAAAATCTTATAGT
*
2780829 CCTAAAATCATATAGT
1 CCTAAAATCTTATAGT
*
2780845 CGCAAAAATCTTA
1 C-CTAAAATCTTA
2780858 AATATAACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 2 0.08
17 9 0.38
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (16 bp):
CCTAAAATCTTATAGT
Found at i:2781132 original size:39 final size:39
Alignment explanation
Indices: 2781077--2781154 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
2781067 TTACAATAAA
*
2781077 TTATTTTAATTCCCTTTTAAAAAATGGACCCATTTTAGG
1 TTATTTTAATTCCCTTTCAAAAAATGGACCCATTTTAGG
* * *
2781116 TTATTTTAATTTCCTTTCAAGAAATGGATCCATTTTAGG
1 TTATTTTAATTCCCTTTCAAAAAATGGACCCATTTTAGG
2781155 ATCGATTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (39 bp):
TTATTTTAATTCCCTTTCAAAAAATGGACCCATTTTAGG
Found at i:2784152 original size:24 final size:23
Alignment explanation
Indices: 2784120--2784164 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
2784110 GTATTTTTAC
*
2784120 ATATTTTAATATTTTATACCATTA
1 ATATTTTAATAATTTA-ACCATTA
2784144 ATATTTTAATAATTTAACCAT
1 ATATTTTAATAATTTAACCAT
2784165 CACATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (23 bp):
ATATTTTAATAATTTAACCATTA
Found at i:2784684 original size:27 final size:25
Alignment explanation
Indices: 2784636--2784702 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 25
2784626 TCCATTCGTA
*
2784636 TATTTAAAATTTAGTCCCCTACTTT
1 TATTTAAAAATTAGTCCCCTACTTT
*
2784661 TATTTAAGAAATTAGTCTCTCTACTTTTT
1 TATTTAA-AAATTAGTC-CCCTAC--TTT
2784690 TAATTTAAAAATT
1 T-ATTTAAAAATT
2784703 CAAGTGCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 7 0.20
26 8 0.23
27 5 0.14
29 9 0.26
30 6 0.17
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.49
Consensus pattern (25 bp):
TATTTAAAAATTAGTCCCCTACTTT
Found at i:2784814 original size:20 final size:20
Alignment explanation
Indices: 2784789--2784839 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
2784779 ATAATATTAA
2784789 ATCAAATTATAAAAGTAAAG-
1 ATCAAATTA-AAAAGTAAAGT
*
2784809 ATCAAA-TAAAAATTAAAGT
1 ATCAAATTAAAAAGTAAAGT
2784828 ATACAAATTAAA
1 AT-CAAATTAAA
2784840 TCTAAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.33
19 4 0.15
20 10 0.37
21 4 0.15
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (20 bp):
ATCAAATTAAAAAGTAAAGT
Done.