Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 21 of 226
Found at i:9549463 original size:18 final size:19
Alignment explanation
Indices: 9549432--9549469 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
9549422 GCTTTTGGTA
**
9549432 ACACCATCTTCAA-TTAGT
1 ACACCATCGCCAATTTAGT
9549450 ACACCATCGCCAATTTAGT
1 ACACCATCGCCAATTTAGT
9549469 A
1 A
9549470 TGCATTGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (19 bp):
ACACCATCGCCAATTTAGT
Found at i:9551066 original size:35 final size:35
Alignment explanation
Indices: 9551020--9551090 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
9551010 CGTTCAATTA
*
9551020 TGGCGAGAATAGAATCATGTGCCTTCTTGTTTGTT
1 TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
9551055 TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
1 TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
9551090 T
1 T
9551091 AGTAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.20, C:0.15, G:0.25, T:0.39
Consensus pattern (35 bp):
TGGCGAGAATAGAATCATGTGCCCTCTTGTTTGTT
Found at i:9557285 original size:27 final size:27
Alignment explanation
Indices: 9557235--9557303 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
9557225 GGACATGATG
* *
9557235 CCTATCTGATAGGCGGCACCAGTGACC
1 CCTATTTGATAGGTGGCACCAGTGACC
** ***
9557262 CCTATTTGATAGGTGGCATTAGTGGTG
1 CCTATTTGATAGGTGGCACCAGTGACC
9557289 CCTATTTGATAGGTG
1 CCTATTTGATAGGTG
9557304 ACATACCTAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.30
Consensus pattern (27 bp):
CCTATTTGATAGGTGGCACCAGTGACC
Found at i:9576063 original size:112 final size:110
Alignment explanation
Indices: 9575866--9576093 Score: 350
Period size: 112 Copynumber: 2.0 Consensus size: 110
9575856 AATATTTGAG
*
9575866 TATACAATTATAGATGGACCATAAGGAACCGTACATATTGACTAATAAAAACATTGCACGTTTTG
1 TATACAATTATAGATGGACCATAAGGAACCATACA-ATTGACTAATAAAAACATTGCACGTTTTG
* * *
9575931 TAGATAAATTAGACCACACTTTAGAGCTTAGTGTATGTCTTATGCTT
65 TAGATAAACTAAACCACACTTTAGAGCTTA-TATATGTCTTATGCTT
*
9575978 TATACATATATATAGATGGACCATAAGGAACCATAC-ATTGACTAATAAAAACATTGCATGTTTT
1 TATACA-AT-TATAGATGGACCATAAGGAACCATACAATTGACTAATAAAAACATTGCACGTTTT
* *
9576042 GTAGATAAACTAAACCACACTTTGGAGTTTATATATGTCTTATGCTT
64 GTAGATAAACTAAACCACACTTTAGAGCTTATATATGTCTTATGCTT
9576089 TATAC
1 TATAC
9576094 TGCAGTTTAC
Statistics
Matches: 107, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
111 20 0.19
112 60 0.56
113 2 0.02
114 25 0.23
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (110 bp):
TATACAATTATAGATGGACCATAAGGAACCATACAATTGACTAATAAAAACATTGCACGTTTTGT
AGATAAACTAAACCACACTTTAGAGCTTATATATGTCTTATGCTT
Found at i:9579557 original size:20 final size:19
Alignment explanation
Indices: 9579534--9579590 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 19
9579524 AAAAAATTTA
9579534 TTAAATTTTAATAAAAAAAT
1 TTAAATTTT-ATAAAAAAAT
*
9579554 TTAAATTTTGA-AAAAATAT
1 TTAAATTTT-ATAAAAAAAT
9579573 TGTAAAATTTTATAAAAA
1 T-T-AAATTTTATAAAAA
9579591 TCATATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 8 0.25
20 12 0.38
21 12 0.38
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TTAAATTTTATAAAAAAAT
Found at i:9579882 original size:9 final size:9
Alignment explanation
Indices: 9579781--9579930 Score: 67
Period size: 9 Copynumber: 15.9 Consensus size: 9
9579771 TGTTGGTACG
9579781 ATAATTTTT
1 ATAATTTTT
*
9579790 ATATTTCTTT
1 ATAATT-TTT
9579800 AT-ATTTTT
1 ATAATTTTT
9579808 ATAATTTTATT
1 ATAA-TTT-TT
* *
9579819 ACGAATTTAT
1 A-TAATTTTT
*
9579829 A-AAATTTT
1 ATAATTTTT
9579837 ATAAATTTTT
1 AT-AATTTTT
* *
9579847 CTACATTTCT
1 ATA-ATTTTT
9579857 ATATATTTTCT
1 ATA-ATTTT-T
9579868 AT--TTTTT
1 ATAATTTTT
9579875 ATAATTTTT
1 ATAATTTTT
9579884 A-ATATTTTT
1 ATA-ATTTTT
*
9579893 ATATTCTTTT
1 ATAAT-TTTT
* *
9579903 ATTAAAATTTA
1 A-T-AATTTTT
*
9579914 ATAACTTTT
1 ATAATTTTT
9579923 ATAATTTT
1 ATAATTTT
9579931 ATTTTTTTAT
Statistics
Matches: 106, Mismatches: 19, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
7 3 0.03
8 16 0.15
9 35 0.33
10 35 0.33
11 14 0.13
12 3 0.03
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.61
Consensus pattern (9 bp):
ATAATTTTT
Found at i:9580052 original size:16 final size:16
Alignment explanation
Indices: 9580024--9580088 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
9580014 GGTTCGCTTA
9580024 ATTGGATTAGAGGTGT
1 ATTGGATTAGAGGTGT
* *
9580040 ATTGAATTGGAGGTGT
1 ATTGGATTAGAGGTGT
9580056 ATTGGATTAGAGGTGT
1 ATTGGATTAGAGGTGT
9580072 ATTGGATTAGAGGTGT
1 ATTGGATTAGAGGTGT
9580088 A
1 A
9580089 ATAGCAAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
ATTGGATTAGAGGTGT
Found at i:9580336 original size:18 final size:17
Alignment explanation
Indices: 9580315--9580349 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9580305 TTATTATTAA
*
9580315 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
9580333 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
9580350 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:9580484 original size:157 final size:157
Alignment explanation
Indices: 9580211--9580673 Score: 809
Period size: 157 Copynumber: 3.0 Consensus size: 157
9580201 TAGAATACCC
* * *
9580211 TTAGCATAAATTTGTTTTAGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAG-------
1 TTAGCAAAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
9580269 --ATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
9580332 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
9580359 TTAGCAAAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
9580424 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
9580489 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
*
9580516 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAAAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
9580581 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
9580646 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
9580673 T
1 T
9580674 CAATATTCTT
Statistics
Matches: 300, Mismatches: 6, Indels: 9
0.95 0.02 0.03
Matches are distributed among these distances:
148 55 0.18
157 245 0.82
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAAAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:9580489 original size:16 final size:16
Alignment explanation
Indices: 9580452--9580493 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9580442 TTAATCATAT
*
9580452 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
9580468 TT-AAATATATTATAA
1 TTAAAATATATTATAA
9580483 TTAAAATATAT
1 TTAAAATATAT
9580494 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:9580500 original size:14 final size:15
Alignment explanation
Indices: 9580461--9580502 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9580451 TTTAAACATA
*
9580461 ATTATTATTAAATAT
1 ATTATAATTAAATAT
9580476 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
9580490 A-TATAATTTAATA
1 ATTATAATTAAATA
9580503 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:9580646 original size:16 final size:16
Alignment explanation
Indices: 9580609--9580650 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9580599 TTAATCATAT
*
9580609 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
9580625 TT-AAATATATTATAA
1 TTAAAATATATTATAA
9580640 TTAAAATATAT
1 TTAAAATATAT
9580651 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:9580657 original size:14 final size:15
Alignment explanation
Indices: 9580618--9580659 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9580608 TTTAAACATA
*
9580618 ATTATTATTAAATAT
1 ATTATAATTAAATAT
9580633 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
9580647 A-TATAATTTAATA
1 ATTATAATTAAATA
9580660 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:9584514 original size:38 final size:37
Alignment explanation
Indices: 9584464--9584647 Score: 140
Period size: 38 Copynumber: 4.7 Consensus size: 37
9584454 ATAGTATTAT
*
9584464 ATATTATG-ATTTTATTAAATTCATATAAGAATATTTA
1 ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
**** *
9584501 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATT
1 ATATTAAGAATTTTATTAAATTATATAAGAATATT---TA
* * * *
9584541 ATATTTAATAATAATTATTTTAAATTATATTA-TATAGTATTA
1 ATA-TTAAGAAT--TT-TATTAAATTATATAAGAATA-T-TTA
*
9584583 TATATTATG-ATTTTATTAAATTCATATAAGAATATTTA
1 -ATATTAAGAATTTTATTAAATT-ATATAAGAATATTTA
9584621 ATATTAAGAATTTTATTAAATTATATA
1 ATATTAAGAATTTTATTAAATTATATA
9584648 TTTTTATTAA
Statistics
Matches: 115, Mismatches: 18, Indels: 28
0.71 0.11 0.17
Matches are distributed among these distances:
37 28 0.24
38 37 0.32
39 8 0.07
40 7 0.06
41 9 0.08
42 4 0.03
43 8 0.07
44 13 0.11
45 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (37 bp):
ATATTAAGAATTTTATTAAATTATATAAGAATATTTA
Found at i:9584532 original size:18 final size:18
Alignment explanation
Indices: 9584511--9584664 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
9584501 ATATTAAGAA
9584511 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
9584529 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
* *
9584544 -TTTAAT-AATAAT-TAT
1 TTTTATTAAATTATATAT
* * *
9584559 TTTAAATTATATTATATAG
1 TTT-TATTAAATTATATAT
* * *
9584578 TATTA-TATATTAT-GA-
1 TTTTATTAAATTATATAT
*
9584593 TTTTATTAAATTCATATAA
1 TTTTATTAAATT-ATATAT
*** * *
9584612 GAATATTTAATATTA-AGAA
1 TTTTA-TTAA-ATTATATAT
9584631 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
9584649 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
9584665 TTAATAATAA
Statistics
Matches: 100, Mismatches: 22, Indels: 28
0.67 0.15 0.19
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 5 0.05
16 12 0.12
17 17 0.17
18 38 0.38
19 11 0.11
20 5 0.05
21 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:9584534 original size:56 final size:55
Alignment explanation
Indices: 9584473--9584664 Score: 208
Period size: 56 Copynumber: 3.3 Consensus size: 55
9584463 TATATTATGA
9584473 TTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
1 TTTTATTAAATT-ATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
* * * * *
9584529 TTTTATTAAATTATATTTAATAATAATT-ATTTTAA-ATTATATTATATAGTATTATATATTAT
1 TTTTATTAAATTATA--TAAGAATATTTAATATTAAGA--ATTTTAT-TA--AAT-TATA-TAT
9584591 GATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
1 --TTTTATTAAATT-ATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
9584649 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
9584665 TTAATAATAA
Statistics
Matches: 112, Mismatches: 10, Indels: 29
0.74 0.07 0.19
Matches are distributed among these distances:
55 8 0.07
56 30 0.27
57 15 0.13
58 5 0.04
59 4 0.04
60 4 0.04
61 4 0.04
62 5 0.04
63 15 0.13
64 18 0.16
65 4 0.04
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (55 bp):
TTTTATTAAATTATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATAT
Found at i:9584585 original size:120 final size:120
Alignment explanation
Indices: 9584446--9584691 Score: 483
Period size: 120 Copynumber: 2.0 Consensus size: 120
9584436 ATTATTAATC
9584446 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
*
9584511 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
9584566 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
9584631 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
9584686 TATATT
1 TATATT
9584692 TAACCTATCA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 125 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
Found at i:9584919 original size:16 final size:16
Alignment explanation
Indices: 9584882--9584923 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
9584872 TTAATCATAT
*
9584882 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
9584898 TT-AAATATATTATAA
1 TTAAAATATATTATAA
9584913 TTAAAATATAT
1 TTAAAATATAT
9584924 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:9584930 original size:14 final size:15
Alignment explanation
Indices: 9584891--9584932 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
9584881 TTTAAACATA
*
9584891 ATTATTATTAAATAT
1 ATTATAATTAAATAT
9584906 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
9584920 A-TATAATTTAATA
1 ATTATAATTAAATA
9584933 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:9592738 original size:31 final size:31
Alignment explanation
Indices: 9592703--9592770 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
9592693 TTAATAGCCC
* *
9592703 AGTGATTTAAATAAAAATTTTCGAATAATTT
1 AGTGATTTAAATAAAAACTTTCAAATAATTT
* *
9592734 AGTGACTTAAATGAAAACTTTCAAATAATTT
1 AGTGATTTAAATAAAAACTTTCAAATAATTT
*
9592765 AATGAT
1 AGTGAT
9592771 CAAATTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (31 bp):
AGTGATTTAAATAAAAACTTTCAAATAATTT
Found at i:9593315 original size:22 final size:23
Alignment explanation
Indices: 9593274--9593317 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
9593264 ACGAATAAGT
9593274 ATCACGTGTAAATCTTTAATTCC
1 ATCACGTGTAAATCTTTAATTCC
*
9593297 ATCATGTGTAAA-CTTTAATTC
1 ATCACGTGTAAATCTTTAATTC
9593318 GATGAGTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (23 bp):
ATCACGTGTAAATCTTTAATTCC
Found at i:9595619 original size:46 final size:46
Alignment explanation
Indices: 9595528--9595619 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
9595518 AAAATATTCT
* * *
9595528 CTATGAACTATAAAATAAATATGAAAGGCACCTTCATTCTAAAGAA
1 CTATGAACTATAAAATAAATATAAAAGACACCTTCATTCCAAAGAA
* * * * *
9595574 CTATGGACTATAAAATAGATATAAAAGATACCTTTATTCCGAAGAA
1 CTATGAACTATAAAATAAATATAAAAGACACCTTCATTCCAAAGAA
9595620 AATTGATGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (46 bp):
CTATGAACTATAAAATAAATATAAAAGACACCTTCATTCCAAAGAA
Found at i:9596780 original size:2 final size:2
Alignment explanation
Indices: 9596773--9596807 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9596763 CTAAAGTGAA
9596773 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9596808 AAGAAAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9599813 original size:183 final size:183
Alignment explanation
Indices: 9599512--9599862 Score: 549
Period size: 183 Copynumber: 1.9 Consensus size: 183
9599502 CATAAACCCA
*
9599512 TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAGACCTGACAGAC
1 TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAAACCTGACAGAC
* * * *
9599577 TGAGTAACAGGCCCCTTTCGCAACGCTTCCTGCTCTTCGAACTCACAGAGGGCATATTGAATTCC
66 TGAGTAACAGACCCCTTTCGCAACCCTTCCAGCTCTTCAAACTCACAGAGGGCATATTGAATTCC
* *
9599642 TTGGCCATGTTCCAAACTATCACTAGTCTTTGATAAATTGTCCCATGAACTGG
131 TTGGCCATATTCCAAACTATCACTAGTCTTTAATAAATTGTCCCATGAACTGG
* * *
9599695 TTCTGTCTTCTAAGGGGATCTTTGGTTGATTTGAAGTCTCAACTACATCTTGAAACCTGGCAGAC
1 TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAAACCTGACAGAC
* * * *
9599760 TGAGTAACAGACCCCTTTTGCAACCCTTGCAGCTCTTCAAACTCGCTGAGGGCATATTGAATTCC
66 TGAGTAACAGACCCCTTTCGCAACCCTTCCAGCTCTTCAAACTCACAGAGGGCATATTGAATTCC
** *
9599825 TTGGCCATATTCTGAGCTATCACTAGTCTTTAATAAAT
131 TTGGCCATATTCCAAACTATCACTAGTCTTTAATAAAT
9599863 GACTGATTCT
Statistics
Matches: 151, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
183 151 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (183 bp):
TTCTGTCTTCTAAGGGGATCTTTGGCTGATTTGAAGTCTCAACTACATCCTGAAACCTGACAGAC
TGAGTAACAGACCCCTTTCGCAACCCTTCCAGCTCTTCAAACTCACAGAGGGCATATTGAATTCC
TTGGCCATATTCCAAACTATCACTAGTCTTTAATAAATTGTCCCATGAACTGG
Found at i:9609015 original size:64 final size:64
Alignment explanation
Indices: 9608894--9609018 Score: 178
Period size: 64 Copynumber: 2.0 Consensus size: 64
9608884 CATCCCGATT
* * * * **
9608894 GGTATTGATCCTGCATATGTTGCGGACATACCGCAGCTCTTTGTGAGTGTATTGATATATGATC
1 GGTATTGATCCTGCATATATTGCGAACATACCGCAGCTCTTTATGAGCGTACCGATATATGATC
* *
9608958 GGTATTGATCCTGCATGTATTGCGAACATACCGCAGCTCTTTATGAGCGTCCCGATATATG
1 GGTATTGATCCTGCATATATTGCGAACATACCGCAGCTCTTTATGAGCGTACCGATATATG
9609019 GCTCTTCATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (64 bp):
GGTATTGATCCTGCATATATTGCGAACATACCGCAGCTCTTTATGAGCGTACCGATATATGATC
Found at i:9609549 original size:11 final size:11
Alignment explanation
Indices: 9609535--9609592 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
9609525 TAAATATTAG
9609535 TTTATTAATAT
1 TTTATTAATAT
*
9609546 TTTATT-TTAT
1 TTTATTAATAT
*
9609556 TTTAAATAATAT
1 TTT-ATTAATAT
9609568 TTTA-T--TAT
1 TTTATTAATAT
*
9609576 TTTATTAGTAT
1 TTTATTAATAT
9609587 TTTATT
1 TTTATT
9609593 TAGTATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 7 0.18
9 1 0.03
10 7 0.18
11 18 0.46
12 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:9611508 original size:25 final size:23
Alignment explanation
Indices: 9611463--9611520 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 23
9611453 TCTTACAAGT
9611463 TTCCTGTTATAGCCCAAATAAGC
1 TTCCTGTTATAGCCCAAATAAGC
* *
9611486 TTCCTGTTACATAGCTCACATAAGC
1 TTCCTGTT--ATAGCCCAAATAAGC
*
9611511 TTCCTATTAT
1 TTCCTGTTAT
9611521 GTGGCTCGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 10 0.33
25 20 0.67
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (23 bp):
TTCCTGTTATAGCCCAAATAAGC
Found at i:9613781 original size:25 final size:25
Alignment explanation
Indices: 9613703--9613783 Score: 87
Period size: 25 Copynumber: 3.3 Consensus size: 25
9613693 CTCTCAAGCA
*
9613703 CTATAACGGGAAGCTCAT--TGAGC
1 CTATAACGGGAAGCTCATCCGGAGC
*
9613726 CTTGTAACGGGAAGCTCATCCGGA-C
1 C-TATAACGGGAAGCTCATCCGGAGC
* *
9613751 AATATAACGGGAAGCTTATCCGGAGC
1 -CTATAACGGGAAGCTCATCCGGAGC
9613777 CTATAAC
1 CTATAAC
9613784 AAGTAGCTCC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.02
24 16 0.34
25 27 0.57
26 3 0.06
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.21
Consensus pattern (25 bp):
CTATAACGGGAAGCTCATCCGGAGC
Found at i:9613807 original size:24 final size:24
Alignment explanation
Indices: 9613780--9613832 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
9613770 CCGGAGCCTA
*
9613780 TAACAAGTAGCTCCAAAGAGCAAT
1 TAACAAGTAGCTCCAAAGAGCAAC
* * *
9613804 TAACGAGTAGTTCCGAAGAGCAAC
1 TAACAAGTAGCTCCAAAGAGCAAC
9613828 TAACA
1 TAACA
9613833 GGAAGCACCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (24 bp):
TAACAAGTAGCTCCAAAGAGCAAC
Found at i:9614424 original size:21 final size:21
Alignment explanation
Indices: 9614400--9614441 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9614390 AAATTTAACA
* *
9614400 TCAATTTAATACAAGTTACAT
1 TCAATTCAATACAAGTCACAT
*
9614421 TCAATTCAATCCAAGTCACAT
1 TCAATTCAATACAAGTCACAT
9614442 CTTAGGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.33
Consensus pattern (21 bp):
TCAATTCAATACAAGTCACAT
Found at i:9616822 original size:29 final size:29
Alignment explanation
Indices: 9616788--9616852 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
9616778 TAAATTTTAA
*
9616788 AAAAATATAAATA-ATAAATATTTAAGTT
1 AAAAATATAAAGACATAAATATTTAAGTT
*
9616816 AAGAAATA-AGAGACATAAATATTTAAGTT
1 AA-AAATATAAAGACATAAATATTTAAGTT
9616845 AAAAATAT
1 AAAAATAT
9616853 TATTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (29 bp):
AAAAATATAAAGACATAAATATTTAAGTT
Found at i:9617287 original size:2 final size:2
Alignment explanation
Indices: 9617275--9617312 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
9617265 CATACCTTGT
9617275 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TGA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA T
9617313 GGCATGATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 1 0.03
2 28 0.85
3 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9641955 original size:2 final size:2
Alignment explanation
Indices: 9641948--9641986 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
9641938 TTAAAAAGAA
*
9641948 AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
9641987 GGTCGTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:9648712 original size:2 final size:2
Alignment explanation
Indices: 9648705--9648738 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9648695 GTAAGGTCTC
9648705 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
9648739 TCATTGTTTT
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:9652461 original size:28 final size:28
Alignment explanation
Indices: 9652414--9652470 Score: 66
Period size: 28 Copynumber: 2.0 Consensus size: 28
9652404 TATTTTAACG
9652414 TTAACATTTTTTCTTCATAT-TATCATTT
1 TTAACATTTTTTCTTCATATATAT-ATTT
9652442 TTAACAGTTTTATT-TT-ATATATATATTT
1 TTAACA-TTTT-TTCTTCATATATATATTT
9652470 T
1 T
9652471 ATTTATTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
28 15 0.58
29 9 0.35
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.61
Consensus pattern (28 bp):
TTAACATTTTTTCTTCATATATATATTT
Found at i:9655799 original size:38 final size:39
Alignment explanation
Indices: 9655721--9655800 Score: 92
Period size: 39 Copynumber: 2.1 Consensus size: 39
9655711 TGATCCTAAA
** *
9655721 TTAAAAATATATAAAAATACATAAATATTTTGAATAATT
1 TTAAAAATATATAAAAATACATAAATATCATAAATAATT
*
9655760 TTAAAATATATATAAAAATA-A-AAATATGCATAAATATTT
1 TTAAAA-ATATATAAAAATACATAAATAT-CATAAATAATT
9655799 TT
1 TT
9655801 GTTATAACTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 6 0.17
39 16 0.46
40 13 0.37
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (39 bp):
TTAAAAATATATAAAAATACATAAATATCATAAATAATT
Found at i:9664861 original size:28 final size:28
Alignment explanation
Indices: 9664828--9664885 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
9664818 TCTTTTAATG
*
9664828 AATGAAATCATACAATTCAGAAGAAA-AA
1 AATGAAACCATACAATTCAG-AGAAAGAA
9664856 AATGAAACCATACAATTCAGAGAAAGAA
1 AATGAAACCATACAATTCAGAGAAAGAA
9664884 AA
1 AA
9664886 AATAGTAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (28 bp):
AATGAAACCATACAATTCAGAGAAAGAA
Found at i:9667326 original size:57 final size:57
Alignment explanation
Indices: 9667240--9667349 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
9667230 GAGTGATCCT
* *
9667240 ATCTTGATATAGCCCTCCCGAAGAGTATGTGTGAAAA-AGATCTAGCCCGGACGGGTG
1 ATCTTGATATAGCCCTCCCAAAGAATATGTG-GAAAATAGATCTAGCCCGGACGGGTG
*
9667297 ATCTTGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATTTAGCCCGGACG
1 ATCTTGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATCTAGCCCGGACG
9667350 ATAATCGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
56 5 0.10
57 44 0.90
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (57 bp):
ATCTTGATATAGCCCTCCCAAAGAATATGTGGAAAATAGATCTAGCCCGGACGGGTG
Found at i:9667589 original size:67 final size:67
Alignment explanation
Indices: 9667481--9667676 Score: 356
Period size: 67 Copynumber: 2.9 Consensus size: 67
9667471 TATATTACAA
*
9667481 GGGATTTAGCCTAGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
9667546 AG
66 AG
*
9667548 GGGATTTAGCCTGGACTGGTAATCCCGTTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
9667613 AG
66 AG
* *
9667615 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGAGAGTGTGCTCTCT
1 GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCT
9667677 GAATTGAAAA
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 124 1.00
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (67 bp):
GGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCTTGC
AG
Found at i:9669821 original size:4 final size:4
Alignment explanation
Indices: 9669812--9669837 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
9669802 TGTTTTAATT
9669812 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
9669838 AACAACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:9670859 original size:18 final size:18
Alignment explanation
Indices: 9670826--9670883 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
9670816 AAGACATTCT
9670826 TATTGATGATA-T--CGA
1 TATTGATGATAGTGACGA
9670841 TATTGATGATAGTGACGA
1 TATTGATGATAGTGACGA
* *
9670859 TATTGATGCTAGTGACGC
1 TATTGATGATAGTGACGA
9670877 TATTGAT
1 TATTGAT
9670884 CGTGACCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
15 11 0.29
16 1 0.03
18 26 0.68
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (18 bp):
TATTGATGATAGTGACGA
Found at i:9681492 original size:13 final size:13
Alignment explanation
Indices: 9681474--9681524 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
9681464 ACACTCAAAT
9681474 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
**
9681487 TTTTCAAAAATAC
1 TTTTCAAAAGCAC
*
9681500 TTTTCTACAA-CAC
1 TTTTC-AAAAGCAC
9681513 TTTTCAAAAGCA
1 TTTTCAAAAGCA
9681525 ATGACCCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 3 0.10
13 25 0.81
14 3 0.10
ACGTcount: A:0.39, C:0.22, G:0.04, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:9688636 original size:4 final size:4
Alignment explanation
Indices: 9688627--9688651 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
9688617 AACATATCTG
9688627 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
9688652 TATTTGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:9694614 original size:32 final size:32
Alignment explanation
Indices: 9694576--9694639 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
9694566 AATTAATCAA
9694576 CATGAGTTG-TCAAATTAAATTAATT-AATTTAT
1 CATGAGTTGCT-AAATTAAATT-ATTCAATTTAT
*
9694608 CATGAGTTGCTAAATTCAATTATTCAATTTAT
1 CATGAGTTGCTAAATTAAATTATTCAATTTAT
9694640 AAGTTTATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 3 0.10
32 25 0.86
33 1 0.03
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (32 bp):
CATGAGTTGCTAAATTAAATTATTCAATTTAT
Found at i:9695726 original size:21 final size:21
Alignment explanation
Indices: 9695698--9695761 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
9695688 AATCTTACTA
* *
9695698 CTACAGTATCCAATCTCATTG
1 CTACAGTAACCAATCTCATCG
* *
9695719 CTATAGTAACTAATCTCATCG
1 CTACAGTAACCAATCTCATCG
* *
9695740 CTACAGTAACTAATCTTATCG
1 CTACAGTAACCAATCTCATCG
9695761 C
1 C
9695762 CACCGCTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (21 bp):
CTACAGTAACCAATCTCATCG
Found at i:9699401 original size:18 final size:18
Alignment explanation
Indices: 9699358--9699392 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9699348 AATCCTTATG
*
9699358 ATTGAA-TTTGTTAATTA
1 ATTGAAGTTAGTTAATTA
9699375 ATTGAAGTTAGTTAATTA
1 ATTGAAGTTAGTTAATTA
9699393 GTTTGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (18 bp):
ATTGAAGTTAGTTAATTA
Found at i:9701549 original size:21 final size:22
Alignment explanation
Indices: 9701515--9701562 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
9701505 GTTTTTTTTT
9701515 TAAAAGTTACAAA-TATTGA-AA
1 TAAAAGTTACAAATTATT-ACAA
9701536 TAAAA-TTACTAAATTATTACAA
1 TAAAAGTTAC-AAATTATTACAA
9701558 TAAAA
1 TAAAA
9701563 AAAGTTGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.17
21 9 0.38
22 11 0.46
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAGTTACAAATTATTACAA
Found at i:9708699 original size:12 final size:11
Alignment explanation
Indices: 9708662--9708701 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
9708652 TCACAATAAT
9708662 AATAATAAA-G
1 AATAATAAATG
9708672 AATAAT-AAT-
1 AATAATAAATG
9708681 AATAATAAATG
1 AATAATAAATG
9708692 AATAAATAAA
1 AAT-AATAAA
9708702 AACAAGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 8 0.31
10 9 0.35
11 3 0.12
12 6 0.23
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (11 bp):
AATAATAAATG
Found at i:9709990 original size:15 final size:15
Alignment explanation
Indices: 9709966--9710000 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9709956 TATCGAAGAG
*
9709966 CTTCCGGCTCTTAAA
1 CTTCCGGCTCGTAAA
*
9709981 CTTCCTGCTCGTAAA
1 CTTCCGGCTCGTAAA
9709996 CTTCC
1 CTTCC
9710001 CCGTAAACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.17, C:0.37, G:0.11, T:0.34
Consensus pattern (15 bp):
CTTCCGGCTCGTAAA
Found at i:9711643 original size:22 final size:22
Alignment explanation
Indices: 9711617--9711660 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
9711607 GAATATCTTA
9711617 TTTTT-TAAAGATATTTTAATTC
1 TTTTTATAAAGA-ATTTTAATTC
*
9711639 TTTTTACTAAATAATTTTAATT
1 TTTTTA-TAAAGAATTTTAATT
9711661 TAAAGTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTTATAAAGAATTTTAATTC
Found at i:9714737 original size:50 final size:51
Alignment explanation
Indices: 9714662--9714769 Score: 164
Period size: 50 Copynumber: 2.1 Consensus size: 51
9714652 CTTACGTATG
* * *
9714662 ATCACTTATCACTTGTCCCTGATCAGATAAGTGCAGGT-AAGCTACCACTT
1 ATCACTTACCACTTGTCACTGATCAGATAAGTGCAGCTGAAGCTACCACTT
* *
9714712 ATCACTTACCACTTGTCACTGATCAGATAAGTGTAGCTGAAGCTACTACTT
1 ATCACTTACCACTTGTCACTGATCAGATAAGTGCAGCTGAAGCTACCACTT
9714763 ATCACTT
1 ATCACTT
9714770 GTCACTGATC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
50 34 0.65
51 18 0.35
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (51 bp):
ATCACTTACCACTTGTCACTGATCAGATAAGTGCAGCTGAAGCTACCACTT
Found at i:9726017 original size:23 final size:21
Alignment explanation
Indices: 9725968--9726018 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
9725958 CACATAAATA
9725968 TTAAATTAATTTTTAAATTTT
1 TTAAATTAATTTTTAAATTTT
** *
9725989 AAAAATTATATGTTTTTAATTTT
1 TTAAATTA-AT-TTTTAAATTTT
9726012 TTAAATT
1 TTAAATT
9726019 TTAAAAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
23 15 0.65
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAAATTAATTTTTAAATTTT
Found at i:9730938 original size:2 final size:2
Alignment explanation
Indices: 9730931--9730970 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9730921 TTAAATAATG
9730931 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
9730971 CATTAAAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9736304 original size:19 final size:22
Alignment explanation
Indices: 9736275--9736314 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
9736265 ATATTGCATC
9736275 AAAAATAAATA-TTT-ATATTA
1 AAAAATAAATACTTTAATATTA
9736295 AAAAAT-AATACTTTAATATT
1 AAAAATAAATACTTTAATATT
9736315 TGTTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATAAATACTTTAATATTA
Found at i:9740370 original size:19 final size:20
Alignment explanation
Indices: 9740342--9740385 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
9740332 TCAGAAAAAT
*
9740342 TATTAATTAT-TAATATTTA
1 TATTAATTATAAAATATTTA
*
9740361 TATTATTTATAAAATATTTA
1 TATTAATTATAAAATATTTA
9740381 -ATTAA
1 TATTAA
9740386 ATTGGTGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTAATTATAAAATATTTA
Found at i:9747663 original size:20 final size:21
Alignment explanation
Indices: 9747634--9747673 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
9747624 TTTGTTTTCT
*
9747634 AAAATTTTAAATAT-ATTAAA
1 AAAATGTTAAATATAATTAAA
*
9747654 AAAATGTTAAGTATAATTAA
1 AAAATGTTAAATATAATTAA
9747674 TTTTAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAATGTTAAATATAATTAAA
Found at i:9747856 original size:24 final size:23
Alignment explanation
Indices: 9747815--9747861 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
9747805 TTAAAATTTT
*
9747815 AATATATTCAATATATTTTTTAA
1 AATATATTCAATACATTTTTTAA
*
9747838 AATATATTTTAATACATTTTTTAA
1 AATATA-TTCAATACATTTTTTAA
9747862 TAGGTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATATTCAATACATTTTTTAA
Found at i:9747859 original size:12 final size:12
Alignment explanation
Indices: 9747824--9747863 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
9747814 TAATATATTC
9747824 AATATATTTTTT
1 AATATATTTTTT
* *
9747836 AAAATATATTTT
1 AATATATTTTTT
*
9747848 AATACATTTTTT
1 AATATATTTTTT
9747860 AATA
1 AATA
9747864 GGTAAAGAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (12 bp):
AATATATTTTTT
Found at i:9747941 original size:17 final size:17
Alignment explanation
Indices: 9747916--9747952 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
9747906 AAAAAACTTC
9747916 AAATATTTAAATATATT
1 AAATATTTAAATATATT
* *
9747933 AAATTTTTAAATATGTT
1 AAATATTTAAATATATT
9747950 AAA
1 AAA
9747953 GAAAATGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (17 bp):
AAATATTTAAATATATT
Found at i:9748051 original size:68 final size:71
Alignment explanation
Indices: 9747918--9748055 Score: 201
Period size: 68 Copynumber: 2.0 Consensus size: 71
9747908 AAAACTTCAA
* * * * *
9747918 ATATTTAAATATATTAAATTTTTAAATATGTTAAAGAAAATGTTGAGTATAACCAATTTTAAAAT
1 ATATTTAAATATATTAAAATTTTAAACATATTAAAGAAAATATTAAGTATAACCAATTTTAAAAT
9747983 TTTAAT
66 TTTAAT
*
9747989 ATATTT-AATATATTAAAATTTTGAACATATTAAA-AAAA-ATTAAGTATAACCAATTTTAAAAT
1 ATATTTAAATATATTAAAATTTTAAACATATTAAAGAAAATATTAAGTATAACCAATTTTAAAAT
9748051 TTTAA
66 TTTAA
9748056 AATTTCAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
68 27 0.44
69 4 0.07
70 24 0.39
71 6 0.10
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (71 bp):
ATATTTAAATATATTAAAATTTTAAACATATTAAAGAAAATATTAAGTATAACCAATTTTAAAAT
TTTAAT
Found at i:9750686 original size:14 final size:14
Alignment explanation
Indices: 9750650--9750689 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
9750640 AAAAACCCTA
9750650 TTTTTCCTT-TTTC
1 TTTTTCCTTCTTTC
*
9750663 -TTTTCTTTCTTTC
1 TTTTTCCTTCTTTC
9750676 TTTTTCCTTCTTTC
1 TTTTTCCTTCTTTC
9750690 CTTTCTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 12 0.52
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTCCTTCTTTC
Found at i:9750693 original size:23 final size:21
Alignment explanation
Indices: 9750660--9750702 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
9750650 TTTTTCCTTT
*
9750660 TTCTTTTCTTTCTTTCTTTTTCC
1 TTCTTTCCTTTC--TCTTTTTCC
9750683 TTCTTTCCTTTCTCTTTTTC
1 TTCTTTCCTTTCTCTTTTTC
9750703 GTTTGCCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTCTTTCCTTTCTCTTTTTCC
Found at i:9750785 original size:14 final size:14
Alignment explanation
Indices: 9750766--9750799 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
9750756 TTTATATTAA
9750766 AATAATAATA-ACAT
1 AATAATAATATA-AT
9750780 AATAATAATATAAT
1 AATAATAATATAAT
9750794 AATAAT
1 AATAAT
9750800 TTTACTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
AATAATAATATAAT
Found at i:9750799 original size:11 final size:11
Alignment explanation
Indices: 9750767--9750799 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9750757 TTATATTAAA
*
9750767 ATAATAATAAC
1 ATAATAATAAT
9750778 ATAATAATAAT
1 ATAATAATAAT
9750789 ATAATAATAAT
1 ATAATAATAAT
9750800 TTTACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:9751968 original size:29 final size:30
Alignment explanation
Indices: 9751912--9751983 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
9751902 TTTTTATATG
*
9751912 AATAATATAAAATAAATCAATATATACGAA
1 AATAAGATAAAATAAATCAATATATACGAA
* * * *
9751942 AATAAGATAACATGAAT-AATATTTACGAG
1 AATAAGATAAAATAAATCAATATATACGAA
9751971 AAT-AGATAAAATA
1 AATAAGATAAAATA
9751984 CACAGTAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
28 8 0.23
29 13 0.37
30 14 0.40
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (30 bp):
AATAAGATAAAATAAATCAATATATACGAA
Found at i:9754797 original size:22 final size:22
Alignment explanation
Indices: 9754765--9754876 Score: 152
Period size: 22 Copynumber: 5.1 Consensus size: 22
9754755 ACTTTCTAGC
9754765 TTAACGTACTAAGCTCTCATGT
1 TTAACGTACTAAGCTCTCATGT
* * * *
9754787 TTAACGAACTAAACCCTCATGG
1 TTAACGTACTAAGCTCTCATGT
* *
9754809 CTAACGTACTAAGCTCTCATGG
1 TTAACGTACTAAGCTCTCATGT
*
9754831 CTAACGTACTAAGCTCTCATGT
1 TTAACGTACTAAGCTCTCATGT
*
9754853 TTCACGTACTAAGCTCTCATGT
1 TTAACGTACTAAGCTCTCATGT
9754875 TT
1 TT
9754877 GAACAATAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 79 1.00
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (22 bp):
TTAACGTACTAAGCTCTCATGT
Found at i:9772171 original size:15 final size:15
Alignment explanation
Indices: 9772151--9772181 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
9772141 CCAACCTTCA
9772151 AATTTTACCTCAATT
1 AATTTTACCTCAATT
9772166 AATTTTACCTCAATT
1 AATTTTACCTCAATT
9772181 A
1 A
9772182 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:9774441 original size:11 final size:11
Alignment explanation
Indices: 9774425--9774451 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
9774415 TAGAAATTAG
9774425 TTTGTGAAACT
1 TTTGTGAAACT
9774436 TTTGTGAAACT
1 TTTGTGAAACT
9774447 TTTGT
1 TTTGT
9774452 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:9774884 original size:18 final size:17
Alignment explanation
Indices: 9774856--9774890 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9774846 ATTATTAAGA
*
9774856 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
9774873 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
9774891 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:9774983 original size:157 final size:155
Alignment explanation
Indices: 9774695--9775003 Score: 548
Period size: 157 Copynumber: 2.0 Consensus size: 155
9774685 NNNNNNNTTT
*
9774695 TTAAGAATTTTATTAAATTATATATTTTAATTATAATATTATTTAACAATAATTATGTTTAAATA
1 TTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTATTTAACAATAATTATGTTTAAATA
9774760 TGATTAAATTATTTATTATTGATATTAATCTTATTAAAATTTAAATAACAATAACAATAATAATT
66 TGATTAAATTATTTATTATTGATATTAATCTTATTAAAATTTAAATAACAATAACAATAATAATT
9774825 TACCAAAACAAATTTATGCTAATTA
131 TACCAAAACAAATTTATGCTAATTA
*
9774850 TTAAGAATTTTATTAAATTATATATTTTAATTAAAATA-TATTTAATAATAATTATGTTTAAATA
1 TTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTATTTAACAATAATTATGTTTAAATA
*
9774914 TGATTAAATTATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATC
66 TGATTAAATTATTTATTATTGAT-AT--TAATCTTATTAAAATTTAAATAACAATAACAATAATA
*
9774979 ATTTACCAAAACAAATTTCTGCTAA
128 ATTTACCAAAACAAATTTATGCTAA
9775004 GGGTATTCTA
Statistics
Matches: 147, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
154 48 0.33
155 39 0.27
157 60 0.41
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (155 bp):
TTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTATTTAACAATAATTATGTTTAAATA
TGATTAAATTATTTATTATTGATATTAATCTTATTAAAATTTAAATAACAATAACAATAATAATT
TACCAAAACAAATTTATGCTAATTA
Found at i:9775144 original size:16 final size:16
Alignment explanation
Indices: 9775123--9775161 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
9775113 TTGATTTGCT
*
9775123 ATTACACAGCTTTTCC
1 ATTACACAGCTATTCC
**
9775139 ATTACACCTCTATTCC
1 ATTACACAGCTATTCC
9775155 ATTACAC
1 ATTACAC
9775162 CTCTAATCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.36
Consensus pattern (16 bp):
ATTACACAGCTATTCC
Found at i:9775162 original size:16 final size:16
Alignment explanation
Indices: 9775135--9775176 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
9775125 TACACAGCTT
9775135 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
9775151 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
* *
9775167 ATCCAATACA
1 TTCCATTACA
9775177 GCGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:9776976 original size:2 final size:2
Alignment explanation
Indices: 9776969--9776994 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9776959 TTAACAAATG
9776969 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
9776995 TAAAAAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9779046 original size:2 final size:2
Alignment explanation
Indices: 9779039--9779067 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9779029 TACAATACTA
9779039 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
9779068 GAGAGAGAGA
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:9779072 original size:2 final size:2
Alignment explanation
Indices: 9779067--9779099 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
9779057 ATATATATAT
*
9779067 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9779100 ACAAAAAAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9781551 original size:52 final size:52
Alignment explanation
Indices: 9781486--9781590 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
9781476 CACTGCATGT
9781486 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
1 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
9781538 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
1 AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
9781590 A
1 A
9781591 TGCTTGCCAC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (52 bp):
AAGTTTATTTTTGGTTCTTTTAATCTGGTTTTGAAATAAGCACTATTTTGTA
Found at i:9795961 original size:3 final size:3
Alignment explanation
Indices: 9795953--9795984 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
9795943 AGGTTATTAA
9795953 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
9795985 AAAGATGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9814827 original size:17 final size:17
Alignment explanation
Indices: 9814805--9814843 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
9814795 AAATTTTAAT
9814805 AAAAATATAAAAA-ATAC
1 AAAAATA-AAAAATATAC
*
9814822 AAAAATAAAAAATATAT
1 AAAAATAAAAAATATAC
9814839 AAAAA
1 AAAAA
9814844 AGTGTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAAATAAAAAATATAC
Found at i:9814829 original size:15 final size:15
Alignment explanation
Indices: 9814802--9814835 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
9814792 ATTAAATTTT
9814802 AATAAAAATATAAAA
1 AATAAAAATATAAAA
9814817 AATACAAAA-ATAAAA
1 AATA-AAAATATAAAA
9814832 AATA
1 AATA
9814836 TATAAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAAAAATATAAAA
Found at i:9814832 original size:7 final size:7
Alignment explanation
Indices: 9814802--9814835 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
9814792 ATTAAATTTT
9814802 AATAAAA
1 AATAAAA
9814809 ATATAAAA
1 A-ATAAAA
9814817 AATACAAA
1 AATA-AAA
9814825 AATAAAA
1 AATAAAA
9814832 AATA
1 AATA
9814836 TATAAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (7 bp):
AATAAAA
Found at i:9814881 original size:9 final size:9
Alignment explanation
Indices: 9814761--9814843 Score: 52
Period size: 9 Copynumber: 9.6 Consensus size: 9
9814751 CATGTGATAA
9814761 AAAAATTAT
1 AAAAATTAT
9814770 AAAAA--AT
1 AAAAATTAT
*
9814777 AAAAATTGT
1 AAAAATTAT
9814786 -AAAATTATT
1 AAAAATTA-T
**
9814795 AAATTTTAAT
1 AAAAATT-AT
9814805 AAAAA-TAT
1 AAAAATTAT
* *
9814813 AAAAAATAC
1 AAAAATTAT
9814822 AAAAA-TA-
1 AAAAATTAT
9814829 AAAAATATAT
1 AAAAAT-TAT
9814839 AAAAA
1 AAAAA
9814844 AGTGTAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 17
0.71 0.09 0.21
Matches are distributed among these distances:
7 12 0.21
8 15 0.26
9 17 0.29
10 13 0.22
11 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:9815153 original size:14 final size:13
Alignment explanation
Indices: 9815126--9815151 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9815116 AACTTTAACG
9815126 GTCAATGGTTAAA
1 GTCAATGGTTAAA
9815139 GTCAATGGTTAAA
1 GTCAATGGTTAAA
9815152 AGACATTTTT
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:0.08, G:0.23, T:0.31
Consensus pattern (13 bp):
GTCAATGGTTAAA
Found at i:9815215 original size:39 final size:39
Alignment explanation
Indices: 9815167--9815248 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
9815157 TTTTTTTATA
*
9815167 TTTTTATGA-TTTTTATAAAATTTTCTAATTTTCTATATT
1 TTTTTATGATTTTTTAT-AAATTTTCTAATTTTCAATATT
** *
9815206 TTTTTATGATTTTTTATATTTTTTCTAATTTTCAATGTT
1 TTTTTATGATTTTTTATAAATTTTCTAATTTTCAATATT
9815245 TTTT
1 TTTT
9815249 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 31 0.82
40 7 0.18
ACGTcount: A:0.23, C:0.05, G:0.04, T:0.68
Consensus pattern (39 bp):
TTTTTATGATTTTTTATAAATTTTCTAATTTTCAATATT
Found at i:9815236 original size:10 final size:10
Alignment explanation
Indices: 9815158--9815277 Score: 72
Period size: 10 Copynumber: 12.5 Consensus size: 10
9815148 TAAAAGACAT
9815158 TTTTTTAT-A
1 TTTTTTATAA
*
9815167 -TTTTTATGA
1 TTTTTTATAA
9815176 -TTTTTATAA
1 TTTTTTATAA
** *
9815185 AATTTTCTAA
1 TTTTTTATAA
* *
9815195 TTTTCTATAT
1 TTTTTTATAA
*
9815205 TTTTTTATGA
1 TTTTTTATAA
9815215 TTTTTTAT-A
1 TTTTTTATAA
*
9815224 TTTTTTCTAA
1 TTTTTTATAA
** *
9815234 TTTTCAAT-G
1 TTTTTTATAA
9815243 TTTTTTATTAA
1 TTTTTTA-TAA
**
9815254 AATTTTATAA
1 TTTTTTATAA
9815264 -TTTTTATAA
1 TTTTTTATAA
9815273 TTTTT
1 TTTTT
9815278 ATTGATTTTT
Statistics
Matches: 83, Mismatches: 22, Indels: 11
0.72 0.19 0.09
Matches are distributed among these distances:
8 7 0.08
9 30 0.36
10 41 0.49
11 5 0.06
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:9815260 original size:39 final size:39
Alignment explanation
Indices: 9815177--9815276 Score: 105
Period size: 39 Copynumber: 2.5 Consensus size: 39
9815167 TTTTTATGAT
* * **
9815177 TTTTATAAAATTTTCTAATTTTCTATATTTTTTTATGATT
1 TTTTAT-AATTTTTCTAATTTTCTATATTTTTTTATAAAA
*
9815217 TTTTATATTTTTTCTAATTTTC-A-ATGTTTTTTATTAAAA
1 TTTTATAATTTTTCTAATTTTCTATAT-TTTTTTA-TAAAA
*
9815256 TTTTATAATTTTTATAATTTT
1 TTTTATAATTTTTCTAATTTT
9815277 TATTGATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 2 0.04
38 8 0.16
39 35 0.69
40 6 0.12
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (39 bp):
TTTTATAATTTTTCTAATTTTCTATATTTTTTTATAAAA
Found at i:9815288 original size:10 final size:9
Alignment explanation
Indices: 9815159--9815279 Score: 73
Period size: 9 Copynumber: 12.8 Consensus size: 9
9815149 AAAAGACATT
9815159 TTTTTAT-A
1 TTTTTATAA
*
9815167 TTTTTATGA
1 TTTTTATAA
9815176 TTTTTATAAA
1 TTTTTAT-AA
* *
9815186 ATTTTCTAA
1 TTTTTATAA
*
9815195 TTTTCTATATT
1 TTTT-TATA-A
*
9815206 TTTTTATGAT
1 TTTTTAT-AA
*
9815216 TTTTTATAT
1 TTTTTATAA
*
9815225 TTTTTCTAA
1 TTTTTATAA
* **
9815234 TTTTCAATGT
1 TTTT-TATAA
9815244 TTTTTATTAAA
1 TTTTTA-T-AA
*
9815255 ATTTTATAA
1 TTTTTATAA
9815264 TTTTTATAA
1 TTTTTATAA
9815273 TTTTTAT
1 TTTTTAT
9815280 TGATTTTTAA
Statistics
Matches: 88, Mismatches: 17, Indels: 15
0.73 0.14 0.12
Matches are distributed among these distances:
8 7 0.08
9 44 0.50
10 27 0.31
11 10 0.11
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:9815300 original size:9 final size:9
Alignment explanation
Indices: 9815253--9815302 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 9
9815243 TTTTTTATTA
9815253 AAATTTTAT
1 AAATTTTAT
*
9815262 AATTTTTAT
1 AAATTTTAT
*
9815271 AATTTTTAT
1 AAATTTTAT
**
9815280 TGATTTT-T
1 AAATTTTAT
9815288 -AATTTTAT
1 AAATTTTAT
9815296 AAATTTT
1 AAATTTT
9815303 TTGCTACATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 27 0.79
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (9 bp):
AAATTTTAT
Found at i:9815303 original size:17 final size:16
Alignment explanation
Indices: 9815254--9815304 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 16
9815244 TTTTTATTAA
9815254 AATTTTATAATTTTTAT
1 AATTTTATAATTTTT-T
*
9815271 AATTTT-TATTGATTTTT
1 AATTTTATAAT--TTTTT
9815288 AATTTTATAAATTTTTT
1 AATTTTAT-AATTTTTT
9815305 GCTACATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
16 3 0.11
17 18 0.64
18 5 0.18
19 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (16 bp):
AATTTTATAATTTTTT
Found at i:9815548 original size:91 final size:90
Alignment explanation
Indices: 9815453--9815639 Score: 198
Period size: 91 Copynumber: 2.1 Consensus size: 90
9815443 TCTTAGGGCT
* * * * * ***
9815453 TTTTTAATGTATTTTGATAGTTCAAATACTCAATTAAATGTAAAAAAA-AAAGGCAATGGCTTAA
1 TTTTTAATATATTTTAAAAGTTCAAATACCCAATTAAATGGAAAAAAACAAA--CAAAAACTTAA
**
9815517 TTACTTTT-TTGGAAAAATTTGAAAATC
64 TTACTTTTATTAAAAAAATTTGAAAA-C
* * * *
9815544 TTTTTTATATATTTTAAAATTTCAAATACCCAATTGAGTGGAAAAAAACAAACAAAAACTTAATT
1 TTTTTAATATATTTTAAAAGTTCAAATACCCAATTAAATGGAAAAAAACAAACAAAAACTTAATT
*
9815609 ACTTTTATTAAAAAAATTTGACAAC
66 ACTTTTATTAAAAAAATTTGAAAAC
9815634 TTTTTA
1 TTTTTA
9815640 CCCCTTAAAC
Statistics
Matches: 78, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
90 22 0.28
91 53 0.68
92 3 0.04
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (90 bp):
TTTTTAATATATTTTAAAAGTTCAAATACCCAATTAAATGGAAAAAAACAAACAAAAACTTAATT
ACTTTTATTAAAAAAATTTGAAAAC
Found at i:9819555 original size:5 final size:6
Alignment explanation
Indices: 9819530--9819554 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9819520 CATTAATAGC
9819530 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
9819555 TCTTTCAATT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:9820133 original size:46 final size:45
Alignment explanation
Indices: 9820063--9820181 Score: 193
Period size: 46 Copynumber: 2.6 Consensus size: 45
9820053 AATTTTTTTA
9820063 CTTCAAAATAAAAAATAAAACAATTAAAAAATATAATCTTAATTG
1 CTTCAAAATAAAAAATAAAACAATTAAAAAATATAATCTTAATTG
* * * *
9820108 CTTTAAAATAAAATAATAAAACAATTAACAAATATACTCTTATTTG
1 CTTCAAAATAAAA-AATAAAACAATTAAAAAATATAATCTTAATTG
9820154 CTTCAAAATAAAAAATAAAACAATTAAA
1 CTTCAAAATAAAAAATAAAACAATTAAA
9820182 CTAAATTCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
45 26 0.39
46 41 0.61
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (45 bp):
CTTCAAAATAAAAAATAAAACAATTAAAAAATATAATCTTAATTG
Found at i:9832105 original size:23 final size:22
Alignment explanation
Indices: 9832078--9832127 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 22
9832068 GCTAACTACA
9832078 AAATCAAATC-TCTAAGATTTAT
1 AAATCAAATCTTCTAAGA-TTAT
9832100 AGAATCAAATCTTCTAAGATTAT
1 A-AATCAAATCTTCTAAGATTAT
9832123 AAATC
1 AAATC
9832128 CTCTACGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.19
23 14 0.54
24 7 0.27
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (22 bp):
AAATCAAATCTTCTAAGATTAT
Found at i:9838945 original size:2 final size:2
Alignment explanation
Indices: 9838938--9838965 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9838928 GTCTCTTTAG
9838938 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
9838966 GTACTCTCCT
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):
AT
Found at i:9841214 original size:21 final size:21
Alignment explanation
Indices: 9841190--9841258 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 21
9841180 TTTGTGTATT
9841190 TTATAAAATTATATCAAAAAA
1 TTATAAAATTATATCAAAAAA
* * *
9841211 TTATATTATTTAAATCTTAAAAAA
1 TTATA-AAATTATATC--AAAAAA
*
9841235 -T-TAAAGTTATAGTCAAAAAA
1 TTATAAAATTATA-TCAAAAAA
9841255 TTAT
1 TTAT
9841259 TATAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
20 6 0.17
21 11 0.31
22 12 0.33
23 1 0.03
24 6 0.17
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (21 bp):
TTATAAAATTATATCAAAAAA
Found at i:9845301 original size:2 final size:2
Alignment explanation
Indices: 9845289--9845332 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
9845279 AATCAATCAA
*
9845289 AT AT GT 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
9845331 AT
1 AT
9845333 TGTTATGTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9855532 original size:6 final size:6
Alignment explanation
Indices: 9855521--9855551 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
9855511 TCCTCCTTGA
9855521 CAAACC CAAACC CAAACC CAAACC CAAACC C
1 CAAACC CAAACC CAAACC CAAACC CAAACC C
9855552 TGTCGAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACC
Found at i:9856814 original size:3 final size:3
Alignment explanation
Indices: 9856806--9856838 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
9856796 TTTGGGATGC
9856806 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
9856839 GCATAGCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:9858779 original size:12 final size:12
Alignment explanation
Indices: 9858757--9858789 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9858747 TTAAAAGTTG
9858757 TATAT-AAAAAA
1 TATATAAAAAAA
*
9858768 TATTTAAAAAAA
1 TATATAAAAAAA
9858780 TATATAAAAA
1 TATATAAAAA
9858790 TTATTGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TATATAAAAAAA
Found at i:9861686 original size:13 final size:13
Alignment explanation
Indices: 9861649--9861686 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
9861639 TTAATTTATA
9861649 AAAAATTAAA-AT
1 AAAAATTAAATAT
9861661 AATTAAATTAAATAT
1 AA--AAATTAAATAT
9861676 AAAAATTAAAT
1 AAAAATTAAAT
9861687 CCACAATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 8 0.35
15 4 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAATTAAATAT
Found at i:9868669 original size:19 final size:20
Alignment explanation
Indices: 9868620--9868669 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 20
9868610 ACCTGCAAGC
9868620 AACA-TGAAAAAGAAATAGA
1 AACAGTGAAAAAGAAATAGA
* * * *
9868639 AGCAGCGTAAAAGAGA-AGA
1 AACAGTGAAAAAGAAATAGA
9868658 AACAGTGAAAAA
1 AACAGTGAAAAA
9868670 ATAAAAAAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.62, C:0.08, G:0.22, T:0.08
Consensus pattern (20 bp):
AACAGTGAAAAAGAAATAGA
Found at i:9871736 original size:50 final size:50
Alignment explanation
Indices: 9871606--9871746 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
9871596 ATACCCGGTT
** * *
9871606 CACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGTTATTCGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCTAGTCATTCAGTA
* * *
9871657 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTA-TCATTCCAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAGTCATT-CAGTA
*
9871707 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCTAG
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAG
9871747 CAACTTCACT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
49 4 0.05
50 41 0.53
51 32 0.42
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCTAGTCATTCAGTA
Found at i:9871947 original size:15 final size:16
Alignment explanation
Indices: 9871903--9871950 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
9871893 ATCCAGTTCA
*
9871903 AAAATAACATTTTTGC
1 AAAATCACATTTTTGC
9871919 AAAATCACATTTTTGC
1 AAAATCACATTTTTGC
* *
9871935 AAAATTATATTTTTGC
1 AAAATCACATTTTTGC
9871951 CCCTAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
AAAATCACATTTTTGC
Found at i:9879281 original size:26 final size:26
Alignment explanation
Indices: 9879252--9879312 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
9879242 CCCGTTATAT
*
9879252 GGCTCTTCGTGAGCTTCTCGATTAAA
1 GGCTCTTCGGGAGCTTCTCGATTAAA
* * * * *
9879278 GGCTATTTGGGAGCTTTTTGATTAAT
1 GGCTCTTCGGGAGCTTCTCGATTAAA
9879304 GGCTCTTCG
1 GGCTCTTCG
9879313 AAGCTTCCTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (26 bp):
GGCTCTTCGGGAGCTTCTCGATTAAA
Found at i:9879367 original size:25 final size:25
Alignment explanation
Indices: 9879339--9879404 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 25
9879329 CTTGCTTGAA
9879339 CTTCCCGA-TACATGGCTATCCGAAG
1 CTTCCCGATTA-ATGGCTATCCGAAG
* * *
9879364 CTTCCTGATTAATGGCTCTTCGAAG
1 CTTCCCGATTAATGGCTATCCGAAG
* *
9879389 CTACCCG-TTATTGGCT
1 CTTCCCGATTAATGGCT
9879405 CACATGAGCT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 8 0.24
25 24 0.71
26 2 0.06
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (25 bp):
CTTCCCGATTAATGGCTATCCGAAG
Found at i:9885329 original size:13 final size:14
Alignment explanation
Indices: 9885313--9885341 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9885303 ATAATTTTAA
9885313 ATAAAAA-TTAAAT
1 ATAAAAATTTAAAT
9885326 ATAAAAATTTAAAT
1 ATAAAAATTTAAAT
9885340 AT
1 AT
9885342 TTGATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAAAAATTTAAAT
Found at i:9889936 original size:29 final size:29
Alignment explanation
Indices: 9889901--9889965 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
9889891 CTTAATATCC
9889901 AGCCCAATATTTTAAATCAATTTACGAAT
1 AGCCCAATATTTTAAATCAATTTACGAAT
* *
9889930 AGTCCAATATTTTAAATTAATTTACGAAT
1 AGCCCAATATTTTAAATCAATTTACGAAT
9889959 AGCCCAA
1 AGCCCAA
9889966 AACAGACCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.34
Consensus pattern (29 bp):
AGCCCAATATTTTAAATCAATTTACGAAT
Found at i:9898265 original size:175 final size:175
Alignment explanation
Indices: 9897974--9898317 Score: 688
Period size: 175 Copynumber: 2.0 Consensus size: 175
9897964 GGGGAATAGT
9897974 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
1 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
9898039 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
66 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
9898104 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATGCATCTA
131 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATGCATCTA
9898149 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
1 TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
9898214 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
66 GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
9898279 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATG
131 ATGCATCTATAACAGAAACAGGAGACACTTACTCATATG
9898318 TATTATCTAC
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
175 169 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (175 bp):
TCCTTACACTTTCATAGGAAACCTAAATCCTTAAAGAGCCTCAAAGTCCTATAGTTCAATTATTG
GAATTCAACACCTTGATCAGGATACAAGGCCTTGGTGAAACAAAACAAAGGATCTATCACATGGA
ATGCATCTATAACAGAAACAGGAGACACTTACTCATATGCATCTA
Found at i:9898763 original size:64 final size:64
Alignment explanation
Indices: 9898683--9898812 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 64
9898673 AAGACAATAC
9898683 TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
1 TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
* *
9898747 TGATAAATCATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATTATGTGCTT
1 TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
9898811 TG
1 TG
9898813 TTATGCATGT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (64 bp):
TGATAAATAATCTAAAACAGTACACATGATATTCCTGGTCCAAATTATAACACATCATGTGCTT
Found at i:9903445 original size:23 final size:22
Alignment explanation
Indices: 9903417--9903459 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
9903407 AATTATAATA
9903417 TTAAAATTAAAAATTTTAAAAGG
1 TTAAAA-TAAAAATTTTAAAAGG
* *
9903440 TTAAAATGAATATTTTAAAA
1 TTAAAATAAAAATTTTAAAA
9903460 TACAGCTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (22 bp):
TTAAAATAAAAATTTTAAAAGG
Found at i:9905016 original size:22 final size:21
Alignment explanation
Indices: 9904991--9905059 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
9904981 CAACAATGTT
9904991 ATTTTTTAATAAAATTTTTATA
1 ATTTTTT-ATAAAATTTTTATA
* * * *
9905013 ATTTTTGTTTATAATTTTTCTG
1 ATTTTT-TATAAAATTTTTATA
9905035 A-TTTTTATAATAATTTTTA-A
1 ATTTTTTATAA-AATTTTTATA
9905055 ATTTT
1 ATTTT
9905060 AAAGGGGCTT
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
20 4 0.11
21 14 0.39
22 17 0.47
23 1 0.03
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTTTTATAAAATTTTTATA
Found at i:9905023 original size:13 final size:13
Alignment explanation
Indices: 9905007--9905031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9904997 TAATAAAATT
9905007 TTTATAATTTTTG
1 TTTATAATTTTTG
9905020 TTTATAATTTTT
1 TTTATAATTTTT
9905032 CTGATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (13 bp):
TTTATAATTTTTG
Found at i:9940785 original size:29 final size:29
Alignment explanation
Indices: 9940741--9941227 Score: 614
Period size: 29 Copynumber: 16.7 Consensus size: 29
9940731 NNNNNNNNNN
* *
9940741 GGTTAGGGTTAGGGTTTTTAATTAAATTC
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
*
9940770 GATTAGGGTTAGGGTTTTTAATCAAATTCA
1 GGTTAGGGTTAGGGTTTTTAATCAAATT-A
*
9940800 -GTTAGGGTTAAGGTTTTTAATCAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
9940828 GGTTAGTTAGGGTTAGGGTTTTTAATCAAATTA
1 -G---GTTAGGGTTAGGGTTTTTAATCAAATTA
* * *
9940861 GGTTAGGGGTACGGTTTTT-ACCTAAATTA
1 GGTTAGGGTTAGGGTTTTTAATC-AAATTA
* * *
9940890 GGTTAGAGTTAAGGTTTTTAATTAAATTAGGTTA
1 GGTTAGGGTTAGGGTTTTTAA-TCAA--A--TTA
*
9940924 GGGTTAGGGTTAGGGTTTTTAATTAAATTA
1 -GGTTAGGGTTAGGGTTTTTAATCAAATTA
*
9940954 GGTTAGGGTTAGGGTTTTTAATCGAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
*
9940983 GGTTAGGGTTAGGGTTTTTAATGAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
* *
9941012 GGTTAGGGGTAGGGATTTTAATCAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
*
9941041 GGTTAGGGTTAGGGTTTTTAAT-TAA--A
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
9941067 --TTA-GGTTAGGGTTTTTAATCAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
9941093 GGTTAGGGTTAGGGTTTTTAATCAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
9941122 GGTTAGGGTTAGGGTTTTTAATCAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
*
9941151 GGTTAGGGTTAGGGCTTTTAATCAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
* *
9941180 GTTTAGGGTTAAGG-TTTTAATCAAATTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTA
* *
9941208 GGTTAGGGTTTGGGGTTTTA
1 GGTTAGGGTTAGGGTTTTTA
9941228 GGGTTTATGG
Statistics
Matches: 403, Mismatches: 34, Indels: 42
0.84 0.07 0.09
Matches are distributed among these distances:
23 16 0.04
24 5 0.01
26 2 0.00
28 33 0.08
29 286 0.71
30 6 0.01
32 3 0.01
33 27 0.07
34 6 0.01
35 19 0.05
ACGTcount: A:0.28, C:0.03, G:0.28, T:0.42
Consensus pattern (29 bp):
GGTTAGGGTTAGGGTTTTTAATCAAATTA
Found at i:9940986 original size:81 final size:79
Alignment explanation
Indices: 9940925--9941227 Score: 315
Period size: 81 Copynumber: 3.6 Consensus size: 79
9940915 ATTAGGTTAG
*
9940925 GGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATCGAATTAGGTTAGG
1 GGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATC-AA--A--TTA-G
*
9940990 GTTAGGGTTT-TTAATGAAATTA
60 GTT---GTTTATTAATCAAATTA
* * *
9941012 GGTTAGGGGTAGGGATTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTT---
9941077 GTTT-TTAATCAAATTA
63 GTTTATTAATCAAATTA
9941093 GGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGG
1 GGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTT---
*
9941158 GTTAGGGCTTTTAATCAAATTA
63 GTT-----TATTAATCAAATTA
* * * *
9941180 GTTTAGGGTTAAGG-TTTTAATCAAATTAGGTTAGGGTTTGGGGTTTTA
1 GGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTA
9941228 GGGTTTATGG
Statistics
Matches: 198, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
81 87 0.44
82 3 0.02
84 1 0.01
86 35 0.18
87 72 0.36
ACGTcount: A:0.27, C:0.03, G:0.29, T:0.42
Consensus pattern (79 bp):
GGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTGTT
TATTAATCAAATTA
Found at i:9941094 original size:110 final size:109
Alignment explanation
Indices: 9940838--9941227 Score: 474
Period size: 110 Copynumber: 3.4 Consensus size: 109
9940828 GGTTAGTTAG
* * * * *
9940838 GGTTAGGGTTTTTAATCAAATTAGGTTAGGGGTACGGTTTTTACCTAAATTAGGTTAGAGTTAAG
1 GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTA-ATAAATTAGGTTAGGGTTAGG
*
9940903 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA
65 GTTTTTAA-TCAA--A--TTA-GGTTAGGGTTAGGGTTTTTAATT-AA--A--TTA
* *
9940959 GGGTTAGGGTTTTTAATCGAATTAGGTTAGGGTTAGGGTTTTTAATGAAATTAGGTTAGGGGTAG
1 -GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAAT-AAATTAGGTTAGGGTTAG
*
9941024 GGATTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
64 GGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
9941070 GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGG
1 GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAAT-AAATTAGGTTAGGGTTAGG
* *
9941135 GTTTTTAATCAAATTAGGTTAGGGTTAGGGCTTTTAATCAAATTA
65 GTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
* * *
9941180 GTTTAGGGTTAAGGTTTTAATCAAATTAGGTTAGGGTTTGGGGTTTTA
1 GGTTAGGG-T----TTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTA
9941228 GGGTTTATGG
Statistics
Matches: 244, Mismatches: 18, Indels: 19
0.87 0.06 0.07
Matches are distributed among these distances:
110 111 0.45
111 4 0.02
113 1 0.00
115 34 0.14
116 23 0.09
117 3 0.01
119 1 0.00
121 4 0.02
122 63 0.26
ACGTcount: A:0.27, C:0.03, G:0.28, T:0.42
Consensus pattern (109 bp):
GGTTAGGGTTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATAAATTAGGTTAGGGTTAGGG
TTTTTAATCAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTA
Found at i:9941234 original size:7 final size:7
Alignment explanation
Indices: 9941210--9941249 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
9941200 TCAAATTAGG
9941210 TTAGGGT
1 TTAGGGT
*
9941217 TTGGGGTT
1 TTAGGG-T
9941225 TTAGGGT
1 TTAGGGT
*
9941232 TTATGGT
1 TTAGGGT
9941239 TTAGGGT
1 TTAGGGT
9941246 TTAG
1 TTAG
9941250 AATTCAGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:9941638 original size:18 final size:18
Alignment explanation
Indices: 9941615--9941649 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9941605 CGGAAAAGGA
*
9941615 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
9941633 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
9941650 AAACGCATCT
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:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:9943737 original size:29 final size:29
Alignment explanation
Indices: 9943705--9943788 Score: 92
Period size: 29 Copynumber: 3.1 Consensus size: 29
9943695 AATTGAAATT
*
9943705 AAATATGGATTTGAGAGAATTTTGGAAGG
1 AAATATGGATTTGAGAGAATTTTGAAAGG
**
9943734 AAAT-T-GA---GAG-GAA-TTTGAAATT
1 AAATATGGATTTGAGAGAATTTTGAAAGG
9943756 AAATATGGATTTGAGAGAATTTTGAAAGG
1 AAATATGGATTTGAGAGAATTTTGAAAGG
9943785 AAAT
1 AAAT
9943789 TGAGAGGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 14
0.69 0.08 0.23
Matches are distributed among these distances:
22 10 0.23
23 4 0.09
24 5 0.12
27 5 0.12
28 4 0.09
29 15 0.35
ACGTcount: A:0.43, C:0.00, G:0.26, T:0.31
Consensus pattern (29 bp):
AAATATGGATTTGAGAGAATTTTGAAAGG
Found at i:9943750 original size:22 final size:22
Alignment explanation
Indices: 9943715--9943822 Score: 78
Period size: 22 Copynumber: 4.6 Consensus size: 22
9943705 AAATATGGAT
*
9943715 TTGAGA-GAATTTTGGAAGGAAA
1 TTGAGAGGAA-TTTGAAAGGAAA
**
9943737 TTGAGAGGAATTTGAAATTAAA
1 TTGAGAGGAATTTGAAAGGAAA
9943759 TATGGATTTGAGAGAATTTTGAAAGGAAA
1 T-T-GA---GAG-GAA-TTTGAAAGGAAA
*
9943788 TTGAGAGGAA-TTGAGAGGAAA
1 TTGAGAGGAATTTGAAAGGAAA
9943809 TATGAGAGG-ATTTG
1 T-TGAGAGGAATTTG
9943823 TTTGTGAAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
21 12 0.17
22 26 0.37
23 7 0.10
24 5 0.07
27 5 0.07
28 4 0.06
29 11 0.16
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.29
Consensus pattern (22 bp):
TTGAGAGGAATTTGAAAGGAAA
Found at i:9943795 original size:51 final size:51
Alignment explanation
Indices: 9943678--9943799 Score: 217
Period size: 51 Copynumber: 2.4 Consensus size: 51
9943668 TTATTTTAAA
* *
9943678 AAAGGAAATTGAGAGCAAATTGAAATTAAATATGGATTTGAGAGAATTTTG
1 AAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
*
9943729 GAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
1 AAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
9943780 AAAGGAAATTGAGAGGAATT
1 AAAGGAAATTGAGAGGAATT
9943800 GAGAGGAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.44, C:0.01, G:0.26, T:0.29
Consensus pattern (51 bp):
AAAGGAAATTGAGAGGAATTTGAAATTAAATATGGATTTGAGAGAATTTTG
Found at i:9943806 original size:21 final size:22
Alignment explanation
Indices: 9943777--9943818 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
9943767 TGAGAGAATT
9943777 TTGAAAGGAAAT-TGAGAGGAA
1 TTGAAAGGAAATATGAGAGGAA
*
9943798 TTGAGAGGAAATATGAGAGGA
1 TTGAAAGGAAATATGAGAGGA
9943819 TTTGTTTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (22 bp):
TTGAAAGGAAATATGAGAGGAA
Done.