Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 31 of 182
Found at i:12130332 original size:23 final size:23
Alignment explanation
Indices: 12130297--12130390 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
12130287 CTTTGTGTGC
*
12130297 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
12130320 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
12130343 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
12130368 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
12130390 T
1 T
12130391 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:12131377 original size:11 final size:11
Alignment explanation
Indices: 12131354--12131386 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12131344 AATGTTCCTC
12131354 CTTTCATTTTT
1 CTTTCATTTTT
12131365 CTTTC-TTTGTT
1 CTTTCATTT-TT
12131376 CTTTCATTTTT
1 CTTTCATTTTT
12131387 ATTTTCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.15
11 14 0.70
12 3 0.15
ACGTcount: A:0.06, C:0.18, G:0.03, T:0.73
Consensus pattern (11 bp):
CTTTCATTTTT
Found at i:12132444 original size:14 final size:14
Alignment explanation
Indices: 12132395--12132444 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
12132385 TAATTGGGCC
12132395 TTTAATTTGGACCTT
1 TTTAATTTGGA-CTT
* *
12132410 TGTAA-ATGGACTT
1 TTTAATTTGGACTT
12132423 TGTT-ATTTGGACTT
1 T-TTAATTTGGACTT
12132437 TTTAATTT
1 TTTAATTT
12132445 AAATTTTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
13 7 0.25
14 17 0.61
15 4 0.14
ACGTcount: A:0.22, C:0.08, G:0.16, T:0.54
Consensus pattern (14 bp):
TTTAATTTGGACTT
Found at i:12132501 original size:17 final size:18
Alignment explanation
Indices: 12132479--12132519 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
12132469 TTTCAAATAT
*
12132479 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
12132496 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
12132514 TTTAAA
1 TTTAAA
12132520 CCTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:12133381 original size:32 final size:31
Alignment explanation
Indices: 12133345--12133441 Score: 89
Period size: 32 Copynumber: 3.2 Consensus size: 31
12133335 ACAATAATTA
12133345 TATTAAAAATATTATTAAATTATATATTATTT
1 TATT-AAAATATTATTAAATTATATATTATTT
* *
12133377 TATT-AAAT-TGTATTTAA-TA-ATA--ATTA
1 TATTAAAATAT-TATTAAATTATATATTATTT
* *
12133403 TATTAAAATATAATTAAATTATTTATTATTTT
1 TATTAAAATATTATTAAATTATATATTA-TTT
12133435 TATTAAA
1 TATTAAA
12133442 TTATATTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
26 7 0.14
27 9 0.18
28 6 0.12
29 5 0.10
30 10 0.20
31 1 0.02
32 13 0.25
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (31 bp):
TATTAAAATATTATTAAATTATATATTATTT
Found at i:12133423 original size:57 final size:59
Alignment explanation
Indices: 12133337--12133458 Score: 196
Period size: 58 Copynumber: 2.1 Consensus size: 59
12133327 TAACAATAAC
* *
12133337 AATAATTATATTAAAAATATTATTAAATTATATATTA-TTTTATTAAATTGTATTTAAT
1 AATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTATATTTAAT
*
12133395 AATAATTATATT-AAAATATAATTAAATTATTTATTATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTATATTTAAT
12133453 AA-AATT
1 AATAATT
12133459 TAATAATAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
57 26 0.43
58 34 0.57
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.52
Consensus pattern (59 bp):
AATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTATATTTAAT
Found at i:12133603 original size:16 final size:16
Alignment explanation
Indices: 12133583--12133629 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
12133573 GATTACAATC
*
12133583 CTATTCCATTACAGCAT
1 CTATTTCATTACAGC-T
*
12133600 -TATTTCATTACAACT
1 CTATTTCATTACAGCT
12133615 CTATTTCATTACAGC
1 CTATTTCATTACAGC
12133630 GAACTAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 1 0.04
16 25 0.96
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (16 bp):
CTATTTCATTACAGCT
Found at i:12133899 original size:12 final size:11
Alignment explanation
Indices: 12133868--12133892 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12133858 TAAAGGCTCA
12133868 ATTAATTTTTT
1 ATTAATTTTTT
12133879 ATTAATTTTTT
1 ATTAATTTTTT
12133890 ATT
1 ATT
12133893 TACTTTTGAA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTAATTTTTT
Found at i:12138665 original size:20 final size:20
Alignment explanation
Indices: 12138640--12138709 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
12138630 TTTTATAGGT
*
12138640 TAATTAATTTAGTTTAATCC
1 TAATTAATTTAGTTTAATCA
12138660 TAATTAA-TTAGTTTAAATCA
1 TAATTAATTTAGTTT-AATCA
** *
12138680 TGGTTTAACTTAGTTTAATCA
1 T-AATTAATTTAGTTTAATCA
12138701 TAATTAATT
1 TAATTAATT
12138710 AATCATCCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
19 7 0.17
20 17 0.41
21 10 0.24
22 7 0.17
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (20 bp):
TAATTAATTTAGTTTAATCA
Found at i:12145337 original size:7 final size:7
Alignment explanation
Indices: 12145325--12145349 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12145315 CCCTAATTTT
12145325 TTTTCCC
1 TTTTCCC
12145332 TTTTCCC
1 TTTTCCC
12145339 TTTTCCC
1 TTTTCCC
12145346 TTTT
1 TTTT
12145350 TAGTACTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTCCC
Found at i:12146655 original size:21 final size:20
Alignment explanation
Indices: 12146631--12146679 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
12146621 AATTCTAAAA
*
12146631 ATAAAAAATACATAAAAATG
1 ATAAAAAATACAAAAAAATG
* *
12146651 TATAAAATATTCAAAAAAATG
1 -ATAAAAAATACAAAAAAATG
12146672 ATAAAAAA
1 ATAAAAAA
12146680 AGATATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (20 bp):
ATAAAAAATACAAAAAAATG
Found at i:12153766 original size:29 final size:29
Alignment explanation
Indices: 12153723--12153780 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
12153713 TCCAACGGGC
*
12153723 AAAAACGCGTCCACGT-AGACGCTTTTTTA
1 AAAAACGCGTCCACGTCAG-CGCGTTTTTA
* *
12153752 AAAAACGCTTTCACGTCAGCGCGTTTTTA
1 AAAAACGCGTCCACGTCAGCGCGTTTTTA
12153781 CTTAACACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.92
30 2 0.08
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (29 bp):
AAAAACGCGTCCACGTCAGCGCGTTTTTA
Found at i:12156554 original size:256 final size:256
Alignment explanation
Indices: 12156099--12156562 Score: 910
Period size: 256 Copynumber: 1.8 Consensus size: 256
12156089 ATTTGATATT
12156099 GTATGTGTGTGTATGGAGGGATGGATGGAAGTTTTTTTTTGTAAAATATATGAAAGAGTGAAATA
1 GTATGTGTGTGTATGGAGGGATGGATGGAAGTTTTTTTTTGTAAAATATATGAAAGAGTGAAATA
12156164 CCATTACTCTTTGCTAGAGAACTAGCCATTAATCATAGGTAATCTTCATCCAGTTCCTCAACTTC
66 CCATTACTCTTTGCTAGAGAACTAGCCATTAATCATAGGTAATCTTCATCCAGTTCCTCAACTTC
*
12156229 CCCTTTCCAAAGATCCTAACCGAGGACCTCTAGTTTGAAAGTTTCAAATTTTAATTGTTGGACAT
131 CCCTTTCCAAAGATCCTAACCCAGGACCTCTAGTTTGAAAGTTTCAAATTTTAATTGTTGGACAT
12156294 ACCATTAATTAACCCAGTTCCTCAACTTCCCCTTTCCAAAGATCCTAACCCAGGACCTCTA
196 ACCATTAATTAACCCAGTTCCTCAACTTCCCCTTTCCAAAGATCCTAACCCAGGACCTCTA
12156355 GTATGTGTGTGTATGGAGGGATGGATGGAAGTTTTTTTTTGTAAAATATATGAAAGAGTGAAATA
1 GTATGTGTGTGTATGGAGGGATGGATGGAAGTTTTTTTTTGTAAAATATATGAAAGAGTGAAATA
*
12156420 CCATTACTCTTTGCTAGAGAACTAGCCATTAATCATAGGTAATCTTCATCTAGTTCCTCAACTTC
66 CCATTACTCTTTGCTAGAGAACTAGCCATTAATCATAGGTAATCTTCATCCAGTTCCTCAACTTC
12156485 CCCTTTCCAAAGATCCTAACCCAGGACCTCTAGTTTGAAAGTTTCAAATTTTAATTGTTGGACAT
131 CCCTTTCCAAAGATCCTAACCCAGGACCTCTAGTTTGAAAGTTTCAAATTTTAATTGTTGGACAT
12156550 ACCATTAATTAAC
196 ACCATTAATTAAC
12156563 TGCTGTGACT
Statistics
Matches: 206, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
256 206 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (256 bp):
GTATGTGTGTGTATGGAGGGATGGATGGAAGTTTTTTTTTGTAAAATATATGAAAGAGTGAAATA
CCATTACTCTTTGCTAGAGAACTAGCCATTAATCATAGGTAATCTTCATCCAGTTCCTCAACTTC
CCCTTTCCAAAGATCCTAACCCAGGACCTCTAGTTTGAAAGTTTCAAATTTTAATTGTTGGACAT
ACCATTAATTAACCCAGTTCCTCAACTTCCCCTTTCCAAAGATCCTAACCCAGGACCTCTA
Found at i:12158569 original size:30 final size:29
Alignment explanation
Indices: 12158475--12158579 Score: 72
Period size: 31 Copynumber: 3.5 Consensus size: 29
12158465 CCCGGGGAGG
*
12158475 TAAAATGGTAATTTTTGGTGAAATCAGGGTT
1 TAAAATGG-AATTTTTGGTGAAACCAGGG-T
* * ** *
12158506 TAAAAT-GAAATTTT--AGAAAGTTCGGGGGG
1 TAAAATGGAATTTTTGGTGAAA---CCAGGGT
12158535 TAAAATGGTAATTTTTGGTGAAACCAGGGT
1 TAAAATGG-AATTTTTGGTGAAACCAGGGT
12158565 TAAAAATGGAATTTT
1 T-AAAATGGAATTTT
12158580 AGAAGGTTTG
Statistics
Matches: 55, Mismatches: 11, Indels: 17
0.66 0.13 0.20
Matches are distributed among these distances:
27 4 0.07
29 12 0.22
30 16 0.29
31 19 0.35
33 4 0.07
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (29 bp):
TAAAATGGAATTTTTGGTGAAACCAGGGT
Found at i:12158605 original size:59 final size:60
Alignment explanation
Indices: 12158467--12158668 Score: 282
Period size: 59 Copynumber: 3.4 Consensus size: 60
12158457 TTTGGATACC
* *
12158467 CGGGGAGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTTAAAATGAAATTTTAGAAAGTT
1 CGGGG-GGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTT
* *
12158528 CGGGGGGTAAAATGGTAATTTTTGGTGAAACCAGGGTTAAAAATGGAATTTTAGAAGGTT
1 CGGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTT
* ** * * *
12158588 -TGGGGGTAAAACAGTAATTTTTGGTGAAATTAGGGTTAAAAATGGAATTTTGGGAAGTT
1 CGGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTT
*
12158647 C-GAGGGTAAAATGGTAATTTTT
1 CGGGGGGTAAAATGGTAATTTTT
12158669 AGATGTTTCG
Statistics
Matches: 125, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
59 69 0.55
60 51 0.41
61 5 0.04
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (60 bp):
CGGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTAGAAAGTT
Found at i:12158637 original size:30 final size:30
Alignment explanation
Indices: 12158476--12158638 Score: 86
Period size: 30 Copynumber: 5.4 Consensus size: 30
12158466 CCGGGGAGGT
* *
12158476 AAAATGGTAATTTTTGGTGAAATCAGGGTTT
1 AAAATGG-AATTTTTGGTGAAATTAGGGTTA
* * * *
12158507 AAAAT-GAAATTTT--AGAAAGTTCGGGGGGT-
1 AAAATGGAATTTTTGGTGAAA-TT--AGGGTTA
**
12158536 AAAATGGTAATTTTTGGTGAAACCAGGGTTA
1 AAAATGG-AATTTTTGGTGAAATTAGGGTTA
* ** ** * *
12158567 AAAATGGAATTTTAGAAG-GTTTGGGGGTA
1 AAAATGGAATTTTTGGTGAAATTAGGGTTA
*
12158596 AAACA-GTAATTTTTGGTGAAATTAGGGTTA
1 AAA-ATGGAATTTTTGGTGAAATTAGGGTTA
12158626 AAAATGGAATTTT
1 AAAATGGAATTTT
12158639 GGGAAGTTCG
Statistics
Matches: 92, Mismatches: 29, Indels: 23
0.64 0.20 0.16
Matches are distributed among these distances:
27 4 0.04
28 1 0.01
29 29 0.32
30 36 0.39
31 18 0.20
33 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (30 bp):
AAAATGGAATTTTTGGTGAAATTAGGGTTA
Found at i:12158653 original size:30 final size:30
Alignment explanation
Indices: 12158500--12158667 Score: 77
Period size: 29 Copynumber: 5.7 Consensus size: 30
12158490 TGGTGAAATC
* * * *
12158500 AGGGTTTAAAATGAAATTTTAGAAAGTTCG
1 AGGGTTAAAAATGGAATTTTGGGAAGTTCG
* * * *
12158530 GGGGGT-AAAATGGTAATTTTTGGTGAA--ACC
1 AGGGTTAAAAATGG-AA-TTTTGG-GAAGTTCG
* *
12158560 AGGGTTAAAAATGGAATTTT-AGAAGGTTTG
1 AGGGTTAAAAATGGAATTTTGGGAA-GTTCG
* * *
12158590 -GGGGTAAAACA-GTAATTTTTGGTGAAATT--
1 AGGGTTAAAA-ATGGAA-TTTTGG-GAAGTTCG
12158619 AGGGTTAAAAATGGAATTTTGGGAAGTTCG
1 AGGGTTAAAAATGGAATTTTGGGAAGTTCG
12158649 AGGG-T-AAAATGGTAATTTT
1 AGGGTTAAAAATGG-AATTTT
12158668 TAGATGTTTC
Statistics
Matches: 102, Mismatches: 20, Indels: 33
0.66 0.13 0.21
Matches are distributed among these distances:
27 3 0.03
28 12 0.12
29 35 0.34
30 33 0.32
31 14 0.14
32 5 0.05
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (30 bp):
AGGGTTAAAAATGGAATTTTGGGAAGTTCG
Found at i:12160559 original size:6 final size:6
Alignment explanation
Indices: 12160550--12160639 Score: 68
Period size: 6 Copynumber: 16.0 Consensus size: 6
12160540 TAATATCATT
* *
12160550 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -ATAAA TTTAAA TTTAGGA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
* * * *
12160596 --TAAC TTTAAA TTTAAA -TAAAA TTTAAA ATT-AA TTTAAA CTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12160640 AAAATCAAAA
Statistics
Matches: 65, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
4 2 0.03
5 18 0.28
6 44 0.68
7 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:12160584 original size:17 final size:17
Alignment explanation
Indices: 12160550--12160627 Score: 88
Period size: 17 Copynumber: 4.6 Consensus size: 17
12160540 TAATATCATT
*
12160550 TTTAAATTT-AATTAAA
1 TTTAAATTTAAAATAAA
12160566 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
** *
12160583 TTTAAATTTAGGATAAC
1 TTTAAATTTAAAATAAA
12160600 TTTAAATTT-AAATAAAA
1 TTTAAATTTAAAAT-AAA
*
12160617 TTTAAAATTAA
1 TTTAAATTTAA
12160628 TTTAAACTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 11 0.22
17 39 0.76
18 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:12160983 original size:57 final size:57
Alignment explanation
Indices: 12160902--12161014 Score: 174
Period size: 57 Copynumber: 2.0 Consensus size: 57
12160892 TTTAGGCTTC
* * *
12160902 ATCTTGCTCTTACTTCAATTTCAGAGATAATGACTTTTTATCCAACTCTACTTCAATG
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCC-ACTCTACTTCAATG
*
12160960 ATCTTGCTCTTA-TTCAATTTCAGAGATAAAGACGTATTATCCACTCTATTTCAAT
1 ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAAT
12161015 TTCAAGCGGA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
56 12 0.24
57 27 0.53
58 12 0.24
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.41
Consensus pattern (57 bp):
ATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTATTATCCACTCTACTTCAATG
Found at i:12161088 original size:75 final size:75
Alignment explanation
Indices: 12160956--12161584 Score: 958
Period size: 75 Copynumber: 8.4 Consensus size: 75
12160946 ACTCTACTTC
* *
12160956 AATGATCTTGCTCTTA-TTCAATTTCAGAGATAAAGACGTATTATCCACTCTATTTCAATTTCAA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
* *
12161020 GCGGACAGGA
66 GAGGATAGGA
*
12161030 GAA-GGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
1 -AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
12161094 AGAGGATAGGA
65 AGAGGATAGGA
* * * *
12161105 AATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGTTTTACTTCAATTTCA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCA
12161170 AGAGGATAGGA
65 AGAGGATAGGA
*
12161181 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTATTTCAATTTCAA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
* *
12161246 GCGGACAGGA
66 GAGGATAGGA
*
12161256 GAA-GGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
1 -AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
12161320 AGAGGATAGGA
65 AGAGGATAGGA
* * *
12161331 AATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTACTTCAATTTCA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCA
12161396 AGAGGATAGGA
65 AGAGGATAGGA
* * * *
12161407 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCATCTTTACTTCAATTTCG
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCA
12161472 AGAGGATAGGA
65 AGAGGATAGGA
* *
12161483 AATGATCTTGTTCCTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
* *
12161548 GCGGACAGGA
66 GAGGATAGGA
* *
12161558 AAAGATCTTGCTCCTACTTCAATTTCA
1 AATGATCTTGCTCTTACTTCAATTTCA
12161585 AGCGGACAGG
Statistics
Matches: 509, Mismatches: 39, Indels: 12
0.91 0.07 0.02
Matches are distributed among these distances:
74 16 0.03
75 278 0.55
76 215 0.42
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (75 bp):
AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
GAGGATAGGA
Found at i:12161245 original size:151 final size:150
Alignment explanation
Indices: 12160956--12161584 Score: 958
Period size: 151 Copynumber: 4.2 Consensus size: 150
12160946 ACTCTACTTC
* *
12160956 AATGATCTTGCTCTTA-TTCAATTTCAGAGATAAAGACGTATTATCCACTCTATTTCAATTTCAA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
* * *
12161020 GCGGACAGGAGAA-GGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTAC
66 GAGGATAGGA-AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTAC
*
12161084 TTCAATTTCAAGAGGATAGGA
130 TTCAATTTCAAGAGGACAGGA
* * * *
12161105 AATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGTTTTACTTCAATTTCA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCA
*
12161170 AGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTAT
65 AGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTAC
*
12161235 TTCAATTTCAAGCGGACAGGA
130 TTCAATTTCAAGAGGACAGGA
*
12161256 GAA-GGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
1 -AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCA
* * *
12161320 AGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAGCTTTA
65 AGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTA
*
12161385 CTTCAATTTCAAGAGGATAGGA
129 CTTCAATTTCAAGAGGACAGGA
* * * *
12161407 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCATCTTTACTTCAATTTCG
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTACTTCAATTTCA
* *
12161472 AGAGGATAGGAAATGATCTTGTTCCTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTAC
65 AGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTAC
*
12161537 TTCAATTTCAAGCGGACAGGA
130 TTCAATTTCAAGAGGACAGGA
* *
12161558 AAAGATCTTGCTCCTACTTCAATTTCA
1 AATGATCTTGCTCTTACTTCAATTTCA
12161585 AGCGGACAGG
Statistics
Matches: 436, Mismatches: 37, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
149 16 0.04
150 103 0.24
151 246 0.56
152 71 0.16
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (150 bp):
AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAA
GAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACT
TCAATTTCAAGAGGACAGGA
Found at i:12161366 original size:226 final size:226
Alignment explanation
Indices: 12160956--12161584 Score: 1082
Period size: 226 Copynumber: 2.8 Consensus size: 226
12160946 ACTCTACTTC
*
12160956 AATGATCTTGCTCTTA-TTCAATTTCAGAGATAAAGACGTATTATCCACTCTATTTCAATTTCAA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTATTTCAATTTCAA
12161020 GCGGACAGGAGAAGGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACT
66 GCGGACAGGAGAAGGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACT
12161085 TCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTAT
131 TCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTAT
*
12161150 CCAGTTTTACTTCAATTTCAAGAGGATAGGA
196 CCAGCTTTACTTCAATTTCAAGAGGATAGGA
12161181 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTATTTCAATTTCAA
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTATTTCAATTTCAA
12161246 GCGGACAGGAGAAGGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACT
66 GCGGACAGGAGAAGGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACT
12161311 TCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTAT
131 TCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTAT
12161376 CCAGCTTTACTTCAATTTCAAGAGGATAGGA
196 CCAGCTTTACTTCAATTTCAAGAGGATAGGA
* * * * *
12161407 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCATCTTTACTTCAATTTCG
1 AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCA-CTCTATTTCAATTTCA
* * * * *
12161472 AGAGGATAGGA-AATGATCTTGTTCCTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTA
65 AGCGGACAGGAGAA-GGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTA
* * * *
12161536 CTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCA
129 CTTCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCA
12161585 AGCGGACAGG
Statistics
Matches: 385, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
225 16 0.04
226 255 0.66
227 114 0.30
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (226 bp):
AATGATCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTATTTCAATTTCAA
GCGGACAGGAGAAGGTCTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACT
TCAATTTCAAGAGGATAGGAAATGATCTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTAT
CCAGCTTTACTTCAATTTCAAGAGGATAGGA
Found at i:12161584 original size:38 final size:38
Alignment explanation
Indices: 12161533--12161848 Score: 231
Period size: 38 Copynumber: 8.4 Consensus size: 38
12161523 GTTATCCACT
12161533 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
12161571 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
* * * *** ***
12161609 CTACTTCAATTTC-AG-AGATAAAGACGTGTTATCCAACT-
1 CTACTTCAATTTCAAGCGGA-CAGGAAAAG--ATCTTGCTC
* * *
12161647 CTACTTTAATTTCAAGAGGATAGGAAAAGATCTTGCTC
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
* * * * * * * *
12161685 CTACTTCAATTTC-AG-AGATAAAGACATGTTATT-CAC
1 CTACTTCAATTTCAAGCGGA-CAGGAAAAGATCTTGCTC
12161721 TCTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
1 -CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
* * * * * *
12161760 CTACTTCAATTTC-AG-AGATA--AAGACG-TGTTATCCAC
1 CTACTTCAATTTCAAGCGGACAGGAA-AAGAT-CT-TGCTC
*
12161796 TCTACTTCAATTTCAAACGGACAGGAAAAGATCTTGCTC
1 -CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
12161835 CTACTTCAATTTCA
1 CTACTTCAATTTCA
12161849 GAGATAAAGA
Statistics
Matches: 209, Mismatches: 49, Indels: 40
0.70 0.16 0.13
Matches are distributed among these distances:
34 3 0.01
35 3 0.01
36 12 0.06
37 49 0.23
38 113 0.54
39 21 0.10
40 5 0.02
41 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (38 bp):
CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTC
Found at i:12161767 original size:75 final size:75
Alignment explanation
Indices: 12161571--12161908 Score: 595
Period size: 75 Copynumber: 4.5 Consensus size: 75
12161561 GATCTTGCTC
12161571 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
12161636 GTTATCCAACT
66 GTTATCC-ACT
* * * *
12161647 CTACTTTAATTTCAAGAGGATAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACAT
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
*
12161712 GTTATTCACT
66 GTTATCCACT
12161722 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
12161787 GTTATCCACT
66 GTTATCCACT
*
12161797 CTACTTCAATTTCAAACGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
*
12161862 ATTATCCACT
66 GTTATCCACT
*
12161872 CTACTTCCATTTCAAGCGGACAGGAAAAGATCTTGCT
1 CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCT
12161909 GCGGTCTGAT
Statistics
Matches: 248, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
75 181 0.73
76 67 0.27
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (75 bp):
CTACTTCAATTTCAAGCGGACAGGAAAAGATCTTGCTCCTACTTCAATTTCAGAGATAAAGACGT
GTTATCCACT
Found at i:12174059 original size:60 final size:58
Alignment explanation
Indices: 12173874--12174190 Score: 318
Period size: 58 Copynumber: 5.4 Consensus size: 58
12173864 TTGGATACCC
* * * *
12173874 GGGGGCAAAATGGTAA-TTTTGGTGAAATCGAGGTTTAAAATGGAATTTTTGAGAGTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGA-AGTTT
* *
12173932 GGGGGT-AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAACTTT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAG-AAGTTT
* * * * *
12173990 GGGGGGTAAAACGGTAATTTTTGGTGATACTGGGGGTTAAAAAAGGAAATTTAGAAGGTTT
1 -GGGGGTAAAATGGTAATTTTTGGTGA-AATCGGGGTTAAAAATGGAATTTTAGAA-GTTT
* * * * * *
12174051 GGGAGTAAAATGGT-ATTCTTGGTGAAATTGGGGTTTAAAATGGAATTTTGGGAAGTTCG
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-AGAAGTT-T
* * * *
12174110 GGGGGTAAAAGGGTAATTTTTGGTGAAATCGGTGTT-AAAATGGAATTTTGGGAAGTTC
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTT-AGAAGTTT
* * *
12174168 GAGAGTAAAATTGTAATTTTTGG
1 GGGGGTAAAATGGTAATTTTTGG
12174191 ATGTTTCGGG
Statistics
Matches: 219, Mismatches: 31, Indels: 18
0.82 0.12 0.07
Matches are distributed among these distances:
57 9 0.04
58 83 0.38
59 53 0.24
60 50 0.23
61 24 0.11
ACGTcount: A:0.32, C:0.03, G:0.32, T:0.33
Consensus pattern (58 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGTTT
Found at i:12174090 original size:30 final size:28
Alignment explanation
Indices: 12174056--12174160 Score: 95
Period size: 30 Copynumber: 3.6 Consensus size: 28
12174046 GGTTTGGGAG
*
12174056 TAAAATGGTATTCTTGGTGAAATTGGGGTT
1 TAAAATGGAATT-TTGGTGAAATTGGGG-T
* *
12174086 TAAAATGGAATTTTGG-GAAGTTCGGGGGG
1 TAAAATGGAATTTTGGTGAAATT--GGGGT
* * *
12174115 TAAAAGGGTAATTTTTGGTGAAATCGGTGT
1 TAAAATGG-AA-TTTTGGTGAAATTGGGGT
12174145 TAAAATGGAATTTTGG
1 TAAAATGGAATTTTGG
12174161 GAAGTTCGAG
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
28 11 0.18
29 13 0.21
30 27 0.44
31 6 0.10
32 4 0.07
ACGTcount: A:0.30, C:0.03, G:0.32, T:0.35
Consensus pattern (28 bp):
TAAAATGGAATTTTGGTGAAATTGGGGT
Found at i:12176121 original size:6 final size:6
Alignment explanation
Indices: 12176112--12176156 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
12176102 TAATATCATT
* *
12176112 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA ATT-AA TTTAAA CTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
12176157 AAAATCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
4 2 0.06
5 8 0.24
6 23 0.70
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:12176146 original size:11 final size:11
Alignment explanation
Indices: 12176112--12176155 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
12176102 TAATATCATT
12176112 TTTAAATTTAA
1 TTTAAATTTAA
12176123 -TTAAATTTAAA
1 TTTAAATTT-AA
*
12176134 TTTAAAATTAA
1 TTTAAATTTAA
*
12176145 TTTAAACTTAA
1 TTTAAATTTAA
12176156 AAAAATCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 8 0.28
11 14 0.48
12 7 0.24
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:12176148 original size:17 final size:18
Alignment explanation
Indices: 12176112--12176157 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
12176102 TAATATCATT
12176112 TTTAAATTT--AATTAAA
1 TTTAAATTTAAAATTAAA
12176128 TTTAAATTTAAAATT-AA
1 TTTAAATTTAAAATTAAA
*
12176145 TTTAAACTTAAAA
1 TTTAAATTTAAAA
12176158 AAATCAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 9 0.33
17 14 0.52
18 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAAATTTAAAATTAAA
Found at i:12178836 original size:2 final size:2
Alignment explanation
Indices: 12178829--12178855 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12178819 ATATTTAACA
12178829 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12178856 AATTAGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12180087 original size:19 final size:18
Alignment explanation
Indices: 12180018--12180089 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
12180008 ATTACATTAA
*
12180018 ATTTGATATTAAATA-TT
1 ATTTAATATTAAATATTT
*
12180035 ATTAAATTAATTAAATATTT
1 ATTTAA-T-ATTAAATATTT
* * *
12180055 ATCTACAAAATAAATATTT
1 ATTTA-ATATTAAATATTT
12180074 AATTTAATATTAAATA
1 -ATTTAATATTAAATA
12180090 ATCACTTTAC
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
17 4 0.10
18 1 0.02
19 26 0.63
20 9 0.22
21 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (18 bp):
ATTTAATATTAAATATTT
Found at i:12188252 original size:44 final size:44
Alignment explanation
Indices: 12188188--12188309 Score: 113
Period size: 44 Copynumber: 2.7 Consensus size: 44
12188178 TATAGTACTA
* * *
12188188 ATTATGCACTTCGAAGATATTGTTGTTTTAATGTAATGTAACTT
1 ATTATGCACTTCGAAAATATTATTATTTTAATGTAATGTAACTT
* *
12188232 ATTATGCACTT-GAACAATATTATTATTTTGATGTGATGTATTA-TT
1 ATTATGCACTTCGAA-AATATTATTATTTTAATGTAATGTA--ACTT
* * * *
12188277 AATTATACACTTTGATAATATTATTACTTTAAT
1 -ATTATGCACTTCGAAAATATTATTATTTTAAT
12188310 ATGATGTAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
43 3 0.05
44 31 0.48
45 2 0.03
46 26 0.41
47 2 0.03
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (44 bp):
ATTATGCACTTCGAAAATATTATTATTTTAATGTAATGTAACTT
Found at i:12188288 original size:46 final size:46
Alignment explanation
Indices: 12188180--12188326 Score: 113
Period size: 46 Copynumber: 3.2 Consensus size: 46
12188170 TATTGTGGTA
* * * ** * *
12188180 TAGTACTAATTATGCACTTCGA-AGATATTGTTGTTTTAATGTAATG
1 TAGTACTAATTATACACTTTGACA-ATATTATTACTTTAATATGATG
* * * * *
12188226 TA--ACTTATTATGCAC-TTGAACAATATTATTATTTTGATGTGATG
1 TAGTACTAATTATACACTTTG-ACAATATTATTACTTTAATATGATG
* * *
12188270 TATTATTAATTATACACTTTGATAATATTATTACTTTAATATGATG
1 TAGTACTAATTATACACTTTGACAATATTATTACTTTAATATGATG
12188316 TAGTACTAATT
1 TAGTACTAATT
12188327 GTGTTCTATA
Statistics
Matches: 81, Mismatches: 15, Indels: 10
0.76 0.14 0.09
Matches are distributed among these distances:
43 2 0.02
44 33 0.41
45 1 0.01
46 42 0.52
47 3 0.04
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (46 bp):
TAGTACTAATTATACACTTTGACAATATTATTACTTTAATATGATG
Found at i:12189635 original size:20 final size:20
Alignment explanation
Indices: 12189591--12189682 Score: 96
Period size: 20 Copynumber: 4.6 Consensus size: 20
12189581 GTATTCAGGA
* * *
12189591 TTTATGCCGGTAAATCAGGC
1 TTTATGCCGGTGATTCAAGC
*
12189611 ATTATGCCGGTGATTCAAGC
1 TTTATGCCGGTGATTCAAGC
*
12189631 TTTATGCAGGTGATTCAAGC
1 TTTATGCCGGTGATTCAAGC
* *
12189651 TTTATGCAGGTGTATT-AGGC
1 TTTATGCCGGTG-ATTCAAGC
*
12189671 TTTGTGCCGGTG
1 TTTATGCCGGTG
12189683 TAACAGGCTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (20 bp):
TTTATGCCGGTGATTCAAGC
Found at i:12189683 original size:20 final size:20
Alignment explanation
Indices: 12189649--12189700 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
12189639 GGTGATTCAA
* **
12189649 GCTTTATGCAGGTGTATTAG
1 GCTTTGTGCAGGTGTAACAG
*
12189669 GCTTTGTGCCGGTGTAACAG
1 GCTTTGTGCAGGTGTAACAG
12189689 GCTTTGTGCAGG
1 GCTTTGTGCAGG
12189701 ATATACATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.35, T:0.35
Consensus pattern (20 bp):
GCTTTGTGCAGGTGTAACAG
Found at i:12190636 original size:16 final size:17
Alignment explanation
Indices: 12190604--12190637 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12190594 ATTGATTATT
12190604 TATATAAAAAAGTTGCAA
1 TATATAAAAAAG-TGCAA
12190622 TATATAAAAAA-TGCAA
1 TATATAAAAAAGTGCAA
12190638 AATGTAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.26
Consensus pattern (17 bp):
TATATAAAAAAGTGCAA
Found at i:12193685 original size:13 final size:13
Alignment explanation
Indices: 12193669--12193703 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12193659 TGTGGTGGAA
*
12193669 AAGTGCTTTTGAG
1 AAGTACTTTTGAG
12193682 AAGTACTTTTGAG
1 AAGTACTTTTGAG
12193695 AAGTACTTT
1 AAGTACTTT
12193704 AAAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.40
Consensus pattern (13 bp):
AAGTACTTTTGAG
Found at i:12193943 original size:24 final size:22
Alignment explanation
Indices: 12193887--12193949 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
12193877 TAACTTATTG
* *
12193887 TTAATATTTTAATATATGAAATA
1 TTAATA-TTAAATATTTGAAATA
*
12193910 TTAATTTTAAATATTTGTAAATAA
1 TTAATATTAAATATTTG-AAAT-A
*
12193934 TTAATATTAATTATTT
1 TTAATATTAAATATTT
12193950 AAAAATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 9 0.27
23 9 0.27
24 15 0.45
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (22 bp):
TTAATATTAAATATTTGAAATA
Found at i:12193955 original size:24 final size:23
Alignment explanation
Indices: 12193905--12193960 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
12193895 TTAATATATG
* **
12193905 AAATATTAATTTTAAATATTTGT
1 AAATATTAATATTAAATATTTAA
*
12193928 AAATAATTAATATTAATTATTTAA
1 AAAT-ATTAATATTAAATATTTAA
12193952 AAAT-TTAAT
1 AAATATTAAT
12193961 TACATTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.18
23 4 0.14
24 19 0.68
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTAA
Found at i:12197785 original size:15 final size:15
Alignment explanation
Indices: 12197767--12197797 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12197757 CATTAAAATA
*
12197767 TTAAAAATTATATAT
1 TTAAAAAATATATAT
12197782 TTAAAAAATATATAT
1 TTAAAAAATATATAT
12197797 T
1 T
12197798 ATTATTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAAAAATATATAT
Found at i:12199697 original size:21 final size:21
Alignment explanation
Indices: 12199659--12199698 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
12199649 GAGCCGACAG
*
12199659 TGCTTCTTCAGCTTTCTCCCT
1 TGCTTCTTCAGCTGTCTCCCT
12199680 TGCTTCTTC-GCATGTCTCC
1 TGCTTCTTCAGC-TGTCTCC
12199699 ATACCCGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.05, C:0.38, G:0.12, T:0.45
Consensus pattern (21 bp):
TGCTTCTTCAGCTGTCTCCCT
Found at i:12205981 original size:17 final size:17
Alignment explanation
Indices: 12205959--12205994 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
12205949 CTATTTAGAT
12205959 TTTTTTATAA-ATGTTTA
1 TTTTTTA-AATATGTTTA
12205976 TTTTTTAAATATGTTTA
1 TTTTTTAAATATGTTTA
12205993 TT
1 TT
12205995 ATATGTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTTTAAATATGTTTA
Found at i:12208381 original size:19 final size:18
Alignment explanation
Indices: 12208317--12208385 Score: 65
Period size: 19 Copynumber: 3.9 Consensus size: 18
12208307 CACGTGACAA
*
12208317 AAAAATTATAAAAATA--
1 AAAAATTAAAAAAATATT
12208333 AAAAA-T-AAAAAATATT
1 AAAAATTAAAAAAATATT
**
12208349 AAATTTTAATAAAAATATT
1 AAAAATTAA-AAAAATATT
12208368 AAAAATTAGAAAAAATAT
1 AAAAATTA-AAAAAATAT
12208386 AAATTCATAA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
14 7 0.17
15 1 0.02
16 8 0.19
17 1 0.02
18 1 0.02
19 23 0.55
20 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (18 bp):
AAAAATTAAAAAAATATT
Found at i:12208397 original size:16 final size:18
Alignment explanation
Indices: 12208337--12208417 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 18
12208327 AAAATAAAAA
* *
12208337 ATAAAAAATATTAAATTTT
1 ATAAAAAATA-TAAATATC
* *
12208356 A-ATAAAAATATTAAAAATT
1 ATA-AAAAATA-TAAATATC
*
12208375 AGAAAAAATATAAAT-TC
1 ATAAAAAATATAAATATC
12208392 ATAAAAAAGATATAAATATC
1 AT-AAAAA-ATATAAATATC
12208412 ATAAAA
1 ATAAAA
12208418 TATAAAATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
17 2 0.04
18 10 0.19
19 35 0.67
20 5 0.10
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAAAAAATATAAATATC
Found at i:12208399 original size:19 final size:20
Alignment explanation
Indices: 12208377--12208417 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
12208367 TAAAAATTAG
12208377 AAAAAATATAAAT-TCATAA
1 AAAAAATATAAATATCATAA
*
12208396 AAAAGATATAAATATCATAA
1 AAAAAATATAAATATCATAA
12208416 AA
1 AA
12208418 TATAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAATATAAATATCATAA
Found at i:12208547 original size:21 final size:22
Alignment explanation
Indices: 12208523--12208564 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12208513 CAGAGGAAGC
*
12208523 ATTTTA-TGATTTTTTTTTTAA
1 ATTTTATTGATTTTATTTTTAA
12208544 ATTTTATTGATTTTATTTTTA
1 ATTTTATTGATTTTATTTTTA
12208565 TTATTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (22 bp):
ATTTTATTGATTTTATTTTTAA
Found at i:12208709 original size:19 final size:18
Alignment explanation
Indices: 12208687--12208767 Score: 67
Period size: 19 Copynumber: 4.4 Consensus size: 18
12208677 TTTTAATGCA
12208687 TTTTATTATTTTTTATGAT
1 TTTTATTATTTTTTAT-AT
* **
12208706 TTTTATAAAATTTTACTAT
1 TTTTATTATTTTTTA-TAT
* *
12208725 TTTTA-TA-TTTTTACAA
1 TTTTATTATTTTTTATAT
*
12208741 TTTTAATATTTTTTATATT
1 TTTTATTATTTTTTATA-T
12208760 TTTTATTA
1 TTTTATTA
12208768 AAATTTAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
16 6 0.12
17 7 0.15
18 8 0.17
19 26 0.54
20 1 0.02
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.68
Consensus pattern (18 bp):
TTTTATTATTTTTTATAT
Found at i:12208738 original size:17 final size:17
Alignment explanation
Indices: 12208716--12208766 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
12208706 TTTTATAAAA
12208716 TTTTACTATTTTTATAT
1 TTTTACTATTTTTATAT
* *
12208733 TTTTACAATTTTAATATT
1 TTTTACTATTTTTATA-T
12208751 TTTTA-TATTTTT-TAT
1 TTTTACTATTTTTATAT
12208766 T
1 T
12208767 AAAATTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 19 0.66
18 6 0.21
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTACTATTTTTATAT
Found at i:12208766 original size:7 final size:8
Alignment explanation
Indices: 12208692--12208766 Score: 55
Period size: 9 Copynumber: 8.9 Consensus size: 8
12208682 ATGCATTTTA
12208692 TTAT-TTT
1 TTATATTT
12208699 TTATGATTT
1 TTAT-ATTT
*
12208708 TTATAAAATT
1 TTAT--ATTT
12208718 TTACTATTT
1 TTA-TATTT
12208727 TTATATTT
1 TTATATTT
*
12208735 TTACAATTT
1 TTA-TATTT
*
12208744 TAATATTTT
1 TTATA-TTT
12208753 TTATATTT
1 TTATATTT
12208761 TT-TATT
1 TTATATT
12208767 AAAATTTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
7 8 0.15
8 14 0.25
9 26 0.47
10 6 0.11
11 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (8 bp):
TTATATTT
Found at i:12210649 original size:6 final size:6
Alignment explanation
Indices: 12210638--12210664 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
12210628 TGATCAAAAT
12210638 TGAAAG TGAAAG TGAAAG TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGA
12210665 TATGAATTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (6 bp):
TGAAAG
Found at i:12214315 original size:31 final size:31
Alignment explanation
Indices: 12214279--12214343 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
12214269 CAACCCAATA
*
12214279 ACTTAAAT-ACAAACTTTTGAATAGCTTAGTG
1 ACTTAAATGA-AAACTTTTGAATAACTTAGTG
* * *
12214310 ACTTAAGTGAAAGCTTTTGAATAATTTAGTG
1 ACTTAAATGAAAACTTTTGAATAACTTAGTG
12214341 ACT
1 ACT
12214344 ATTTTGTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTTGAATAACTTAGTG
Found at i:12224524 original size:71 final size:70
Alignment explanation
Indices: 12224395--12224555 Score: 189
Period size: 71 Copynumber: 2.3 Consensus size: 70
12224385 TAAAATTCAA
* * * * *
12224395 TACTGACTGGAGTTGTTTTGGAACAACTCTACTAAGTATTAGTAGAAGTACAAAGGTATGGGACA
1 TACTGACTCGAGTTGTTTCGGAACAACTCTACAAAGTATTAGTAGAAGTACAAAGGTATAGAAC-
*
12224460 TTTGAC
65 CTTGAC
* * **
12224466 TACTGACTTGAGTTGTTTCGGAATAACTCTACAAAGTATT-GATAGAAGTACAGGGGTATAGAAC
1 TACTGACTCGAGTTGTTTCGGAACAACTCTACAAAGTATTAG-TAGAAGTACAAAGGTATAGAAC
*
12224530 CTTGGC
65 CTTGAC
*
12224536 TACTGACTCGAATTGTTTCG
1 TACTGACTCGAGTTGTTTCG
12224556 ATAGAAATAA
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
70 23 0.30
71 54 0.70
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (70 bp):
TACTGACTCGAGTTGTTTCGGAACAACTCTACAAAGTATTAGTAGAAGTACAAAGGTATAGAACC
TTGAC
Found at i:12224709 original size:21 final size:21
Alignment explanation
Indices: 12224661--12224716 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
12224651 TTAGAATCGG
*
12224661 TTGTATCGGTAGAAGTCTTGA
1 TTGTATCGGTAGAAGTCTTCA
12224682 -TGCTATCGGTAGAAG-CTGTCA
1 TTG-TATCGGTAGAAGTCT-TCA
*
12224703 TTGTATCTGTAGAA
1 TTGTATCGGTAGAA
12224717 CTCTGTGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.13
21 24 0.80
22 2 0.07
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.36
Consensus pattern (21 bp):
TTGTATCGGTAGAAGTCTTCA
Found at i:12232759 original size:21 final size:21
Alignment explanation
Indices: 12232733--12232775 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12232723 CTCCACTCTT
12232733 TATCACATTCAAATTCATCTG
1 TATCACATTCAAATTCATCTG
*
12232754 TATCACTTTCAAATTCATCTG
1 TATCACATTCAAATTCATCTG
12232775 T
1 T
12232776 TACCCACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (21 bp):
TATCACATTCAAATTCATCTG
Found at i:12234975 original size:3 final size:3
Alignment explanation
Indices: 12234969--12235003 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
12234959 TATCGATGAT
*
12234969 GAG GAG GTG GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GA
12235004 CGATGATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.66, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:12241241 original size:22 final size:23
Alignment explanation
Indices: 12241215--12241257 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12241205 AAAAATTATT
*
12241215 TTTAAATCAATAAATA-AATATA
1 TTTAAATAAATAAATACAATATA
*
12241237 TTTAAATAAATATATACAATA
1 TTTAAATAAATAAATACAATA
12241258 AACTCGTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
TTTAAATAAATAAATACAATATA
Found at i:12241244 original size:14 final size:14
Alignment explanation
Indices: 12241225--12241251 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12241215 TTTAAATCAA
12241225 TAAATAAATATATT
1 TAAATAAATATATT
12241239 TAAATAAATATAT
1 TAAATAAATATAT
12241252 ACAATAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATAAATATATT
Found at i:12242126 original size:7 final size:7
Alignment explanation
Indices: 12242110--12242160 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
12242100 AATAGGTTTA
*
12242110 ATTATTG
1 ATTATAG
12242117 ATTATAG
1 ATTATAG
*
12242124 ATTATAA
1 ATTATAG
12242131 ATTATAG
1 ATTATAG
12242138 ATTATAG
1 ATTATAG
* *
12242145 ATGACAG
1 ATTATAG
*
12242152 ATGATAG
1 ATTATAG
12242159 AT
1 AT
12242161 ATGATTTATA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (7 bp):
ATTATAG
Found at i:12242376 original size:29 final size:29
Alignment explanation
Indices: 12242321--12242376 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
12242311 TAATATTATT
* * * *
12242321 TTATATTTATATATTATATATAGAAATAA
1 TTATATTTATACAATATAAAAAGAAATAA
*
12242350 TTATATTTATACAATATAAAAATAAAT
1 TTATATTTATACAATATAAAAAGAAAT
12242377 TGATGTATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
TTATATTTATACAATATAAAAAGAAATAA
Found at i:12242806 original size:4 final size:4
Alignment explanation
Indices: 12242797--12242823 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12242787 ATCTAATTAT
12242797 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
12242824 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:12258152 original size:46 final size:44
Alignment explanation
Indices: 12258086--12258181 Score: 124
Period size: 44 Copynumber: 2.1 Consensus size: 44
12258076 GAAATAGGGT
12258086 TGTAATGGAATAGAGATGTAATTAATAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGATGTAA-TAAT-ATT-AATGTGTTTGGTTGAA
* *
12258132 TGTAATGGAATAGA-ACTGTAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGA-TGTAATAATATTAATGTGTTTGGTTGAA
12258176 TGTAAT
1 TGTAAT
12258182 AGATATTGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
43 2 0.04
44 21 0.46
45 4 0.09
46 19 0.41
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (44 bp):
TGTAATGGAATAGAGATGTAATAATATTAATGTGTTTGGTTGAA
Found at i:12258785 original size:15 final size:15
Alignment explanation
Indices: 12258765--12258796 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12258755 TCTATTAAAA
*
12258765 AAATTAAATAAATTT
1 AAATTAAATAAAATT
12258780 AAATTAAATAAAATT
1 AAATTAAATAAAATT
12258795 AA
1 AA
12258797 CATGTATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATTAAATAAAATT
Found at i:12259649 original size:18 final size:18
Alignment explanation
Indices: 12259626--12259681 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
12259616 ATTTTTAAAA
*
12259626 TATAAATTTTTGAGTTTT
1 TATAAATTTTTGAATTTT
12259644 TATAAATATTTTGAATTTT
1 TATAAAT-TTTTGAATTTT
*
12259663 TA-AAATTATTTTAATTTT
1 TATAAATT-TTTGAATTTT
12259681 T
1 T
12259682 TGTTGTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 1 0.03
18 21 0.62
19 12 0.35
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (18 bp):
TATAAATTTTTGAATTTT
Found at i:12259682 original size:19 final size:19
Alignment explanation
Indices: 12259626--12259681 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
12259616 ATTTTTAAAA
*
12259626 TATAAAT-TTTTGAGTTTT
1 TATAAATATTTTGAATTTT
12259644 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
12259663 TA-AAATTATTTT-AATTTT
1 TATAAA-TATTTTGAATTTT
12259681 T
1 T
12259682 TGTTGTAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
18 17 0.49
19 18 0.51
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:12265639 original size:30 final size:32
Alignment explanation
Indices: 12265605--12265663 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
12265595 TTTTTAATTA
*
12265605 AAATTT-ACCGTCAACCTTTT-AAAAAGAATC
1 AAATTTGACCGTCAACATTTTGAAAAAGAATC
*
12265635 AAATTTGACCTTCAACATTTTGAAAAAGA
1 AAATTTGACCGTCAACATTTTGAAAAAGA
12265664 GTTAAAATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 6 0.24
31 12 0.48
32 7 0.28
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (32 bp):
AAATTTGACCGTCAACATTTTGAAAAAGAATC
Found at i:12265775 original size:22 final size:22
Alignment explanation
Indices: 12265757--12265799 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12265747 AACTTTATGC
12265757 TATT-ATTTTGAATTTTTTATA
1 TATTGATTTTGAATTTTTTATA
* *
12265778 TTTTGATTTTGATTTTTTTATA
1 TATTGATTTTGAATTTTTTATA
12265800 ATTTTTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (22 bp):
TATTGATTTTGAATTTTTTATA
Found at i:12266019 original size:6 final size:6
Alignment explanation
Indices: 12266008--12266033 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12265998 ATATTTTTAA
12266008 TTTGAT TTTGAT TTTGAT TTTGAT TT
1 TTTGAT TTTGAT TTTGAT TTTGAT TT
12266034 ATATTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTGAT
Found at i:12266039 original size:18 final size:18
Alignment explanation
Indices: 12265983--12266039 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
12265973 TCTATGCTAT
12265983 TATTTTGAATTT--TTTA
1 TATTTTGAATTTGATTTA
*
12265999 TATTTTTAATTTGATTT-
1 TATTTTGAATTTGATTTA
*
12266016 TGATTTTGATTTTGATTTA
1 T-ATTTTGAATTTGATTTA
12266035 TATTT
1 TATTT
12266040 ATAATTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.32
17 1 0.03
18 21 0.62
19 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (18 bp):
TATTTTGAATTTGATTTA
Found at i:12270835 original size:15 final size:17
Alignment explanation
Indices: 12270805--12270836 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
12270795 TTATTTACGT
12270805 AAATAACTCTACTTAAA
1 AAATAACTCTACTTAAA
12270822 AAATAA-TC-ACTTAAA
1 AAATAACTCTACTTAAA
12270837 TAATCTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATAACTCTACTTAAA
Found at i:12274350 original size:48 final size:48
Alignment explanation
Indices: 12274279--12274558 Score: 416
Period size: 48 Copynumber: 5.8 Consensus size: 48
12274269 TGGAGGTGGT
*
12274279 TTCACAACGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
12274327 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
*
12274375 TTCACAATGGGAGGACTTGGGTATACAGGAGGTGTTGGTGTTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
* * *
12274423 TTCACAATGGGAGGACTTGGGTATACAGGAGGCTTTGGAGCTGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
* * * * *
12274471 TTCACAATGGGAGGACTGGGGTAGACGGGAGGCTTTGGTGATGGCGGC
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
* * * * * *
12274519 TTTACAATAGGAGGACTGGGGTAGACGGGAGGCTTTGGTG
1 TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTG
12274559 GTGGTGAAGT
Statistics
Matches: 219, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 219 1.00
ACGTcount: A:0.20, C:0.14, G:0.42, T:0.24
Consensus pattern (48 bp):
TTCACAATGGGAGGACTTGGGTATACAGGAGGCGTTGGTGTTGGCGGC
Found at i:12279367 original size:30 final size:30
Alignment explanation
Indices: 12279276--12279553 Score: 156
Period size: 30 Copynumber: 9.5 Consensus size: 30
12279266 GCATGGGGGC
* *
12279276 AAAATGGTAATTTTTGGTGAAACCGGGGTT
1 AAAATGGGAATTTTTGGTGAAATCGGGGTT
* *
12279306 AAAA-CGGAA-TTTT-G-GAAAGTTCGGGGGT
1 AAAATGGGAATTTTTGGTGAAA--TCGGGGTT
*
12279334 AAAATGGGAATTTTTGGTGAAATCAGGGTT
1 AAAATGGGAATTTTTGGTGAAATCGGGGTT
*
12279364 AAAAAT-GGAA-TTTT-G-GAAGGTTCGAGGG-T
1 -AAAATGGGAATTTTTGGTGAA--ATCG-GGGTT
* * *
12279393 ACAATGGGAATTTTTGGTGAAACCGAGGTT
1 AAAATGGGAATTTTTGGTGAAATCGGGGTT
* *
12279423 AAAAAT-GGAA-TTTT-G-GAAGGTTCGGGGGT
1 -AAAATGGGAATTTTTGGTGAA--ATCGGGGTT
*
12279452 AAAATGGTAATTTTTGGTGAAATCGGGGTT
1 AAAATGGGAATTTTTGGTGAAATCGGGGTT
* ** ** * *
12279482 AAAAAT-GGAATTTTAGAAG-GTTTGGGGGT
1 -AAAATGGGAATTTTTGGTGAAATCGGGGTT
* * *
12279511 AAAATGGTAGTTTTTGGTGAAATTGGGGTT
1 AAAATGGGAATTTTTGGTGAAATCGGGGTT
12279541 AAAAT-GGAATTTT
1 AAAATGGGAATTTT
12279554 GGAAAGTTTA
Statistics
Matches: 184, Mismatches: 39, Indels: 51
0.67 0.14 0.19
Matches are distributed among these distances:
26 4 0.02
27 7 0.04
28 30 0.16
29 52 0.28
30 64 0.35
31 17 0.09
32 10 0.05
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (30 bp):
AAAATGGGAATTTTTGGTGAAATCGGGGTT
Found at i:12279399 original size:59 final size:59
Alignment explanation
Indices: 12279248--12279585 Score: 457
Period size: 59 Copynumber: 5.8 Consensus size: 59
12279238 ACCCGAGGGT
* ** * *
12279248 AAAATGGTAATTTTGGACGCAT-GGGGGCAAAATGGTAATTTTTGGTGAAACCGGGGTT-
1 AAAATGG-AATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTA
* * * *
12279306 AAAACGGAATTTTGGAAAGTTCGGGGGTAAAATGGGAATTTTTGGTGAAATCAGGGTTA
1 AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTA
* * * * *
12279365 AAAATGGAATTTTGGAAGGTTCGAGGGTACAATGGGAATTTTTGGTGAAACCGAGGTTA
1 AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTA
12279424 AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTA
1 AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTA
* * * *
12279483 AAAATGGAATTTTAGAAGGTTTGGGGGTAAAATGGTAGTTTTTGGTGAAATTGGGGTT-
1 AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTA
* **
12279541 AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
1 AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGG
12279586 ACAGTCTAAG
Statistics
Matches: 249, Mismatches: 29, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
57 10 0.04
58 79 0.32
59 160 0.64
ACGTcount: A:0.32, C:0.04, G:0.33, T:0.32
Consensus pattern (59 bp):
AAAATGGAATTTTGGAAGGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTA
Found at i:12279586 original size:30 final size:28
Alignment explanation
Indices: 12279300--12279582 Score: 123
Period size: 30 Copynumber: 9.7 Consensus size: 28
12279290 TGGTGAAACC
* * *
12279300 GGGGTTAAAACGGAATTTTGGAAAGTTC
1 GGGGGTAAAATGGAATTTTGGAAAGTTT
*
12279328 GGGGGTAAAATGGGAATTTTTGGTGAAA--TC
1 GGGGGTAAAAT-GGAA-TTTT-G-GAAAGTTT
* * * *
12279358 AGGGTTAAAAATGGAATTTTGGAAGGTTC
1 GGGGGT-AAAATGGAATTTTGGAAAGTTT
* * **
12279387 GAGGGTACAATGGGAATTTTTGGTGAAA--CC
1 GGGGGTAAAAT-GGAA-TTTT-G-GAAAGTTT
* * * *
12279417 GAGGTTAAAAATGGAATTTTGGAAGGTTC
1 GGGGGT-AAAATGGAATTTTGGAAAGTTT
*
12279446 GGGGGTAAAATGGTAATTTTTGGTGAAA--TC
1 GGGGGTAAAATGG-AA-TTTT-G-GAAAGTTT
* * *
12279476 GGGGTTAAAAATGGAATTTTAGAAGGTTT
1 GGGGGT-AAAATGGAATTTTGGAAAGTTT
*
12279505 GGGGGTAAAATGGTAGTTTTTGGTGAAA--TT
1 GGGGGTAAAATGG-A-ATTTT-G-GAAAGTTT
*
12279535 GGGGTTAAAATGGAATTTTGGAAAGTTT
1 GGGGGTAAAATGGAATTTTGGAAAGTTT
*
12279563 AGGGGTAAAATGGTAATTTT
1 GGGGGTAAAATGG-AATTTT
12279583 TGGACAGTCT
Statistics
Matches: 197, Mismatches: 30, Indels: 55
0.70 0.11 0.20
Matches are distributed among these distances:
26 4 0.02
27 10 0.05
28 46 0.23
29 46 0.23
30 59 0.30
31 19 0.10
32 13 0.07
ACGTcount: A:0.32, C:0.03, G:0.33, T:0.32
Consensus pattern (28 bp):
GGGGGTAAAATGGAATTTTGGAAAGTTT
Found at i:12279825 original size:162 final size:162
Alignment explanation
Indices: 12279612--12279994 Score: 579
Period size: 162 Copynumber: 2.3 Consensus size: 162
12279602 TAAAATAATA
* * *
12279612 AAACCAAGAAAGGCTGACACGTGGTAGCCTCTGATGCAGTCAAACAGTCAAAGGGCTAATTTATA
1 AAACCAA-AAA-G-TGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGACTAATTTATA
* *
12279677 AATCTTGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAG-TTGATTTAAGGATTAAATTAA
63 AATCTTGAAAAATTCTTGGGCCAATTGTGTAATTAAATAAAAGTTTG-TTTAAAGATTAAATTAA
*
12279741 AACAAATTAAAAATGACAGGGATTAGATACATAAAT
127 AACAAATTAAAAATGACAGGGACTAGATACATAAAT
* *
12279777 AAACCAAAAAGTGACACGTGGCATCCTCTGGTGCAATCAAACAGTCAAAGGACTAATTTATAAAT
1 AAACCAAAAAGTGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGACTAATTTATAAAT
12279842 CTTGAAAAATTCTTGGGCCAATTGTGTAATTAAATAAAAGTTTGTTTAAAGATTAAATTAAAACA
66 CTTGAAAAATTCTTGGGCCAATTGTGTAATTAAATAAAAGTTTGTTTAAAGATTAAATTAAAACA
* *
12279907 AATTAAAAATTACAGGGACTAGGTACATAAAT
131 AATTAAAAATGACAGGGACTAGATACATAAAT
* * * ** *
12279939 AAGCCAAAAAATAATGCGTGGCAGCCTCTGGTGTAGTCAAACAGTCAAAGGACTAA
1 AAACCAAAAAGTGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGACTAA
12279995 ATTGAAAACT
Statistics
Matches: 199, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
162 185 0.93
163 4 0.02
164 3 0.02
165 7 0.04
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (162 bp):
AAACCAAAAAGTGACACGTGGCAGCCTCTGGTGCAGTCAAACAGTCAAAGGACTAATTTATAAAT
CTTGAAAAATTCTTGGGCCAATTGTGTAATTAAATAAAAGTTTGTTTAAAGATTAAATTAAAACA
AATTAAAAATGACAGGGACTAGATACATAAAT
Found at i:12280587 original size:16 final size:17
Alignment explanation
Indices: 12280566--12280600 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
12280556 TTTTGAAACC
*
12280566 AAATCCAGATCTGG-GA
1 AAATCCAAATCTGGAGA
12280582 AAATCCAAATCTGGAGA
1 AAATCCAAATCTGGAGA
12280599 AA
1 AA
12280601 TTTCGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (17 bp):
AAATCCAAATCTGGAGA
Found at i:12281625 original size:11 final size:12
Alignment explanation
Indices: 12281602--12281636 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
12281592 TTATTTGGAC
12281602 TTTTAATTTAAA
1 TTTTAATTTAAA
12281614 TTTTAA-TTAAA
1 TTTTAATTTAAA
12281625 TTTTAAATTTAA
1 TTTT-AATTTAA
12281637 TAATAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.43
12 8 0.38
13 4 0.19
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTAATTTAAA
Found at i:12281647 original size:18 final size:17
Alignment explanation
Indices: 12281606--12281649 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
12281596 TTGGACTTTT
12281606 AATTTAAATTTTAATTA
1 AATTTAAATTTTAATTA
12281623 AATTTTAAA-TTTAATAATA
1 AA-TTTAAATTTTAAT--TA
12281642 AATTTAAA
1 AATTTAAA
12281650 CCTAAAGATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 12 0.50
19 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTAAATTTTAATTA
Found at i:12288459 original size:41 final size:38
Alignment explanation
Indices: 12288359--12288462 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
12288349 TTCGAAGCAT
* *
12288359 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
12288396 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
12288434 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
12288463 CTCAAGGTTG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:12288574 original size:12 final size:12
Alignment explanation
Indices: 12288553--12288585 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12288543 GATTTTCAAT
12288553 TTTCAATTTCAC
1 TTTCAATTTCAC
*
12288565 TTTCACTTTCAC
1 TTTCAATTTCAC
12288577 TTTCAATTT
1 TTTCAATTT
12288586 TGATCACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (12 bp):
TTTCAATTTCAC
Found at i:12289916 original size:11 final size:11
Alignment explanation
Indices: 12289900--12289928 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
12289890 AGAAATTTAA
12289900 GAAGAAATGAT
1 GAAGAAATGAT
12289911 GAAGAAATGAT
1 GAAGAAATGAT
12289922 GAAGAAA
1 GAAGAAA
12289929 ATGAAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.14
Consensus pattern (11 bp):
GAAGAAATGAT
Found at i:12295228 original size:328 final size:328
Alignment explanation
Indices: 12294514--12295494 Score: 1820
Period size: 328 Copynumber: 3.0 Consensus size: 328
12294504 TCTATACTGA
12294514 TTGAAGTTGTTTGATTGTAATTTTTTTAAAGGGCACAATATCACTAAACTATTGGTGAATTTATA
1 TTGAAGTTGTTTGATTGTAATTTTTTTAAAGGGCACAATATCACTAAACTATTGGTGAATTTATA
12294579 TTTTGATCACTTAACTTTAAAAAGTTACAGAATGGTCATTAAATTATTCAAAAAAAAAATTTAAT
66 TTTTGATCACTTAACTTTAAAAAGTTACAGAATGGTCATTAAATTATTC-AAAAAAAAATTTAAT
12294644 TAGTTCATTGAACCATTAAAAAAAATTTATTTAAGTCATGAGTTGTTAAA-TTTTAAAAAAATAT
130 TAGTTCATTGAACCATTAAAAAAAATTTATTTAAGTCATGAGTTGTTAAATTTTTAAAAAAATAT
12294708 TTGGCTAGCAAACTCTAAGCGACAAATCAATGATTATTATGGTGGATCACTCATCGGTGGTGAGT
195 TTGGCTAGCAAACTCTAAGCGACAAATCAATGATTATTATGGTGGATCACTCATC---GGTGAGT
*
12294773 AGAATAATATACTTTAGATTCAAATCGATTTGACAATCGATGTCAAAGATCAGAGAAAAAAATTG
257 AGAATAACATACTTTAGATTCAAATCGATTTGACAATCGATGTCAAAGATCAGAGAAAAAAATTG
12294838 TAATTTT
322 TAATTTT
12294845 TTGAAGTTGTTTGATTGTAATTTTTTTAAAGGGCACAATATCACTAAACTATTGGTGAATTTATA
1 TTGAAGTTGTTTGATTGTAATTTTTTTAAAGGGCACAATATCACTAAACTATTGGTGAATTTATA
*
12294910 TTTTGATCACTTAACTTTAAAAAATTACAGAATGGTCATTAAATTATTCAAAAAAAAATTTAATT
66 TTTTGATCACTTAACTTTAAAAAGTTACAGAATGGTCATTAAATTATTCAAAAAAAAATTTAATT
**** *
12294975 AGTTCATTGAACCATTAAAATTTTTTTATTTAAGTCATGAGTTGTTAAATTTTTTAAAAAATATT
131 AGTTCATTGAACCATTAAAAAAAATTTATTTAAGTCATGAGTTGTTAAATTTTTAAAAAAATATT
*
12295040 TGGCTAGCAAACTCTAAGCGACAAACCAATGATTATTATGGTGGATCACTCATCGGTGAGTAGAA
196 TGGCTAGCAAACTCTAAGCGACAAATCAATGATTATTATGGTGGATCACTCATCGGTGAGTAGAA
12295105 TAACATACTTTAGATTCAAATCGATTTGACAATCGATGTCAAAGATCAGAGAAAAAAATTGTAAT
261 TAACATACTTTAGATTCAAATCGATTTGACAATCGATGTCAAAGATCAGAGAAAAAAATTGTAAT
12295170 TTT
326 TTT
12295173 TTGAAGTTGTTTGATTGTAATTTTTTTAAAGGGCACAATATCACTAAACTATTGGTGAATTTATA
1 TTGAAGTTGTTTGATTGTAATTTTTTTAAAGGGCACAATATCACTAAACTATTGGTGAATTTATA
* * *
12295238 TTTTAATCACTTAACTTTAAAAAGTTACAGAATGGTCATTAAATTATTCAAAAAAAAAATTAGTT
66 TTTTGATCACTTAACTTTAAAAAGTTACAGAATGGTCATTAAATTATTCAAAAAAAAATTTAATT
12295303 AGTTCATTGAACCATTAAAAAAAATTTATTTAAGTCATGAGTTGTTAAATTTTTAAAAAAATATT
131 AGTTCATTGAACCATTAAAAAAAATTTATTTAAGTCATGAGTTGTTAAATTTTTAAAAAAATATT
12295368 TGGCTAGCAAACTCTAAGCGACAAATCAATGATTATTATGGTGGATCACTCATCGGTGAGTAGAA
196 TGGCTAGCAAACTCTAAGCGACAAATCAATGATTATTATGGTGGATCACTCATCGGTGAGTAGAA
12295433 TAACATACTTTAGATTCAAATCGATTTGACAATCGATGTCAAAGATCAGAGAAAAAAATTGT
261 TAACATACTTTAGATTCAAATCGATTTGACAATCGATGTCAAAGATCAGAGAAAAAAATTGT
12295495 TTGAATTTTT
Statistics
Matches: 631, Mismatches: 18, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
328 390 0.62
330 61 0.10
331 180 0.29
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.36
Consensus pattern (328 bp):
TTGAAGTTGTTTGATTGTAATTTTTTTAAAGGGCACAATATCACTAAACTATTGGTGAATTTATA
TTTTGATCACTTAACTTTAAAAAGTTACAGAATGGTCATTAAATTATTCAAAAAAAAATTTAATT
AGTTCATTGAACCATTAAAAAAAATTTATTTAAGTCATGAGTTGTTAAATTTTTAAAAAAATATT
TGGCTAGCAAACTCTAAGCGACAAATCAATGATTATTATGGTGGATCACTCATCGGTGAGTAGAA
TAACATACTTTAGATTCAAATCGATTTGACAATCGATGTCAAAGATCAGAGAAAAAAATTGTAAT
TTT
Found at i:12304023 original size:12 final size:12
Alignment explanation
Indices: 12304004--12304040 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
12303994 GCACACAAAG
12304004 AACCAGAAAGAA
1 AACCAGAAAGAA
* *
12304016 AACTAGAAAAAA
1 AACCAGAAAGAA
12304028 AACCAGAAAGAA
1 AACCAGAAAGAA
12304040 A
1 A
12304041 CGTGCTAGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.70, C:0.14, G:0.14, T:0.03
Consensus pattern (12 bp):
AACCAGAAAGAA
Found at i:12304063 original size:22 final size:22
Alignment explanation
Indices: 12304038--12304079 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
12304028 AACCAGAAAG
*
12304038 AAACGTGCTAGACAGCAGAGGA
1 AAACGTGATAGACAGCAGAGGA
12304060 AAACGTGATAGACAGCAGAG
1 AAACGTGATAGACAGCAGAG
12304080 ATATAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.31, T:0.10
Consensus pattern (22 bp):
AAACGTGATAGACAGCAGAGGA
Found at i:12323980 original size:31 final size:30
Alignment explanation
Indices: 12323936--12324049 Score: 101
Period size: 31 Copynumber: 3.8 Consensus size: 30
12323926 TACCAACTTT
* *
12323936 AAAAAATGCCAAGTTTAGTTATCAAATTAGG
1 AAAAAATGTCAAGTTTAG-TACCAAATTAGG
*
12323967 AAAAAGTGTCAAGTTTGAGTACCAAATT-GG
1 AAAAAATGTCAAGTTT-AGTACCAAATTAGG
*
12323997 ACAAAAA---AAAGTTTAGGTACCAAATTAGG
1 A-AAAAATGTCAAGTTTA-GTACCAAATTAGG
* *
12324026 AAAAAATGTGAAGTTCAAGTACCA
1 AAAAAATGTCAAGTT-TAGTACCA
12324050 TATGTTATAT
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
27 1 0.01
28 21 0.31
29 3 0.04
30 3 0.04
31 37 0.54
32 3 0.04
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (30 bp):
AAAAAATGTCAAGTTTAGTACCAAATTAGG
Found at i:12324016 original size:28 final size:28
Alignment explanation
Indices: 12323977--12324031 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12323967 AAAAAGTGTC
12323977 AAGTTTGAGTACCAAATT-GGACAAAAAA
1 AAGTTTGAGTACCAAATTAGGA-AAAAAA
12324005 AAGTTT-AGGTACCAAATTAGGAAAAAA
1 AAGTTTGA-GTACCAAATTAGGAAAAAA
12324032 TGTGAAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.04
28 21 0.84
29 3 0.12
ACGTcount: A:0.51, C:0.09, G:0.18, T:0.22
Consensus pattern (28 bp):
AAGTTTGAGTACCAAATTAGGAAAAAAA
Found at i:12324965 original size:22 final size:20
Alignment explanation
Indices: 12324923--12324994 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 20
12324913 ATTATATTGT
12324923 TGTTTT-GTT-TTTTTTTAC
1 TGTTTTGGTTGTTTTTTTAC
*
12324941 TGTTTTGGTTGCTCTTTTTTGC
1 TGTTTTGGTTG-T-TTTTTTAC
*
12324963 TGTTTTTGTGTTGTATTTTTAC
1 TG-TTTTG-GTTGTTTTTTTAC
12324985 TGTTTTGGTT
1 TGTTTTGGTT
12324995 ACTGTTTTCG
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 6 0.13
19 3 0.07
20 3 0.07
21 6 0.13
22 17 0.38
23 6 0.13
24 4 0.09
ACGTcount: A:0.04, C:0.07, G:0.19, T:0.69
Consensus pattern (20 bp):
TGTTTTGGTTGTTTTTTTAC
Found at i:12325529 original size:43 final size:43
Alignment explanation
Indices: 12325457--12325540 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
12325447 TTTTCTATTT
* * *
12325457 AATTCTTTTATAAATATTTTTGCTATATAATTTTTTTTCACTTC
1 AATTCTTTTATAAATATATTTACTATATAA-TCTTTTTCACTTC
* *
12325501 AATT-TTTTATAAATATATTTATTGTATAATCTTTTTCACT
1 AATTCTTTTATAAATATATTTACTATATAATCTTTTTCACT
12325541 CACATAGTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 10 0.29
43 21 0.60
44 4 0.11
ACGTcount: A:0.30, C:0.10, G:0.02, T:0.58
Consensus pattern (43 bp):
AATTCTTTTATAAATATATTTACTATATAATCTTTTTCACTTC
Found at i:12329520 original size:5 final size:5
Alignment explanation
Indices: 12329510--12329534 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12329500 AACCAACTAA
12329510 AACCT AACCT AACCT AACCT AACCT
1 AACCT AACCT AACCT AACCT AACCT
12329535 TATTTGCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
AACCT
Found at i:12336650 original size:21 final size:20
Alignment explanation
Indices: 12336608--12336658 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
12336598 ATTCTTGCCC
12336608 TTTTCTTTTTATATTCAATTTT
1 TTTTC-TTTTATATTCAA-TTT
***
12336630 TTTTCTTTTATATTTTGTTT
1 TTTTCTTTTATATTCAATTT
12336650 TTTTCTTTT
1 TTTTCTTTT
12336659 GTAGTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 12 0.46
21 9 0.35
22 5 0.19
ACGTcount: A:0.12, C:0.08, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTATATTCAATTT
Found at i:12337023 original size:21 final size:20
Alignment explanation
Indices: 12336985--12337024 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12336975 TGATGTTTAA
**
12336985 TTATTTTTCTCTTTATTTTG
1 TTATTTTTCTCTACATTTTG
12337005 TTATTTTTCTGCTACATTTT
1 TTATTTTTCT-CTACATTTT
12337025 AATTTCGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.12, C:0.12, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTTTTCTCTACATTTTG
Found at i:12340450 original size:42 final size:42
Alignment explanation
Indices: 12340377--12340460 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
12340367 ACCTCAAGAA
* * *
12340377 ATCCTGCAAGCCAGCGATCAGCATTTTCCACCAACTCATTAC
1 ATCCGGCAACCCAGCGATCAGCATTTCCCACCAACTCATTAC
* * * *
12340419 ATCCGGCAACCCAGCGGTCAGCGTTTCCCACCCACTCGTTAC
1 ATCCGGCAACCCAGCGATCAGCATTTCCCACCAACTCATTAC
12340461 GATGCATAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.39, G:0.15, T:0.21
Consensus pattern (42 bp):
ATCCGGCAACCCAGCGATCAGCATTTCCCACCAACTCATTAC
Found at i:12341488 original size:21 final size:22
Alignment explanation
Indices: 12341432--12341490 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
12341422 TGAAAATTTT
*
12341432 TAATTATTACATAAATAATAAAA
1 TAATTAAT-CATAAATAATAAAA
**
12341455 TAATTTGTCATAATATAA-AAAA
1 TAATTAATCATAA-ATAATAAAA
12341477 TAATTAAT-ATAAAT
1 TAATTAATCATAAAT
12341491 TTAAACTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
20 2 0.06
21 4 0.13
22 15 0.48
23 10 0.32
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (22 bp):
TAATTAATCATAAATAATAAAA
Found at i:12344830 original size:21 final size:23
Alignment explanation
Indices: 12344800--12344848 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
12344790 TATTTATAAA
*
12344800 ATAA-AATAATAATATGTAATTAT
1 ATAATAATAATAATATAT-ATTAT
12344823 ATAATAATAATAATATATATTAT
1 ATAATAATAATAATATATATTAT
12344846 ATA
1 ATA
12344849 TATATATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
ATAATAATAATAATATATATTAT
Found at i:12344841 original size:18 final size:18
Alignment explanation
Indices: 12344805--12344854 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
12344795 ATAAAATAAA
*
12344805 ATAATAATATGTAATTAT
1 ATAATAATATATAATTAT
12344823 ATAATAATA-ATAATATAT
1 ATAATAATATATAAT-TAT
*
12344841 ATTATATATATATA
1 ATAATA-ATATATA
12344855 TCATTATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 17 0.63
19 3 0.11
20 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAATAATATATAATTAT
Found at i:12361959 original size:27 final size:28
Alignment explanation
Indices: 12361915--12361967 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
12361905 GTAATATTTT
12361915 TAATTAAAAAATTCATTTTATAATTATG
1 TAATTAAAAAATTCATTTTATAATTATG
*
12361943 TAATTAAAAAATT-ATTTTGTAATTA
1 TAATTAAAAAATTCATTTTATAATTA
12361968 ATTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (28 bp):
TAATTAAAAAATTCATTTTATAATTATG
Found at i:12363073 original size:26 final size:25
Alignment explanation
Indices: 12363044--12363105 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 25
12363034 AATAATAATG
* *
12363044 ATAATAAATAATTTAATCATATTTTA
1 ATAATAAATAATTAAAT-ATAATTTA
* *
12363070 ATAATATTATTATTAAATATAATTTA
1 ATAATA-AATAATTAAATATAATTTA
12363096 ATAA-AAATAA
1 ATAATAAATAA
12363106 AAATAATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 17 0.59
27 8 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATAATAAATAATTAAATATAATTTA
Found at i:12363082 original size:61 final size:59
Alignment explanation
Indices: 12363009--12363141 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 59
12362999 TATTAAATAT
*
12363009 ATAAGATTATTATTAAATATAATTTAATAATAATGATAATAAATAAT-T-TAATCATAT-TTTA
1 ATAATATTATTATTAAATATAATTTAATAA-AA--ATAA-AAATAATATATAAT-ATATATTTA
12363070 ATAATATTATTATTAAATATAATTTAATAAAAATAAAAATAATATATAATATATAATTTA
1 ATAATATTATTATTAAATATAATTTAATAAAAATAAAAATAATATATAATATAT-ATTTA
12363130 ATAATATTATTA
1 ATAATATTATTA
12363142 ATATAATTAT
Statistics
Matches: 67, Mismatches: 1, Indels: 9
0.87 0.01 0.12
Matches are distributed among these distances:
57 7 0.10
58 9 0.13
59 4 0.06
60 18 0.27
61 29 0.43
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (59 bp):
ATAATATTATTATTAAATATAATTTAATAAAAATAAAAATAATATATAATATATATTTA
Found at i:12363177 original size:18 final size:18
Alignment explanation
Indices: 12363156--12363212 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
12363146 AATTATTTTT
12363156 ATATTAAATTATATTAAA
1 ATATTAAATTATATTAAA
**
12363174 ATATTATTTTAGTATT---
1 ATATTAAATTA-TATTAAA
*
12363190 ATATTAAATTATAGTAAA
1 ATATTAAATTATATTAAA
12363208 ATATT
1 ATATT
12363213 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
15 3 0.10
16 9 0.30
18 14 0.47
19 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
ATATTAAATTATATTAAA
Found at i:12363193 original size:34 final size:34
Alignment explanation
Indices: 12363154--12363229 Score: 109
Period size: 34 Copynumber: 2.2 Consensus size: 34
12363144 ATAATTATTT
* *
12363154 TTATATTAAATTATATTAAAATA-TTATTTTAGTA
1 TTATATTAAATTATAGTAAAATATTTATTTTA-AA
12363188 TTATATTAAATTATAGTAAAATATTTTATTTTAAA
1 TTATATTAAATTATAGTAAAATA-TTTATTTTAAA
12363223 TTATATT
1 TTATATT
12363230 TTGGAATAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
34 22 0.58
35 8 0.21
36 8 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (34 bp):
TTATATTAAATTATAGTAAAATATTTATTTTAAA
Found at i:12363222 original size:15 final size:15
Alignment explanation
Indices: 12363198--12363260 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 15
12363188 TTATATTAAA
*
12363198 TTATAGTAAAATATT
1 TTATATTAAAATATT
*
12363213 TTATTTTAAATTATATT
1 TTATATTAAA--ATATT
** *
12363230 TTGGAATAAAATATT
1 TTATATTAAAATATT
12363245 TTATATTAAAATATT
1 TTATATTAAAATATT
12363260 T
1 T
12363261 CAAATATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
15 26 0.70
17 11 0.30
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
TTATATTAAAATATT
Found at i:12365823 original size:29 final size:29
Alignment explanation
Indices: 12365781--12365883 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 29
12365771 AGTTCAGGGG
*
12365781 TAAAATAGTAATTTTTGGTGAAATCGAGGT
1 TAAAAT-GGAATTTTTGGTGAAATCGAGGT
*
12365811 TAAAATGGAA-TTTT-G-GAAAGCTCGAGGG
1 TAAAATGGAATTTTTGGTGAAA--TCGAGGT
12365839 TAAAATGGTAATTTTTGGTGAAATCGAGGT
1 TAAAATGG-AATTTTTGGTGAAATCGAGGT
12365869 TAAAAATGGAATTTT
1 T-AAAATGGAATTTT
12365884 GAAAAGTTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
26 4 0.06
27 1 0.02
28 18 0.29
29 5 0.08
30 23 0.37
31 8 0.13
32 4 0.06
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
TAAAATGGAATTTTTGGTGAAATCGAGGT
Found at i:12365873 original size:118 final size:117
Alignment explanation
Indices: 12365659--12365903 Score: 291
Period size: 118 Copynumber: 2.1 Consensus size: 117
12365649 TTGACTTTCG
* * * * *
12365659 GGGGTAAAA-ATGTGATTTTTGGTGAAATTAGGGTCAAAATGGGATTTTGGAAAGCTTGCGGGTA
1 GGGGTAAAATATGTAATTTTTGGTGAAATGAGGGTCAAAATGGAATTTTGGAAAGCTCGAGGGTA
* * ** *
12365723 AAACGGTAATTTTTGATGAGACTGGGGCTAAAAAATGGGGTTTTGGAAAGTTC
66 AAACGGTAATTTTTGATGAAACTGAGGCT-AAAAATGGAATTTTGAAAAGTTC
*
12365776 AGGGGTAAAATA-GTAATTTTTGGTGAAATCGA-GGTTAAAATGGAATTTTGGAAAGCTCGAGGG
1 -GGGGTAAAATATGTAATTTTTGGTGAAAT-GAGGGTCAAAATGGAATTTTGGAAAGCTCGAGGG
* * *
12365839 TAAAATGGTAATTTTTGGTGAAA-TCGAGGTTAAAAATGGAATTTTGAAAAGTTC
64 TAAAACGGTAATTTTTGATGAAACT-GAGGCTAAAAATGGAATTTTGAAAAGTTC
12365893 GGGCGTAAAAT
1 GGG-GTAAAAT
12365904 GGTGATTTAT
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
116 3 0.03
117 28 0.26
118 76 0.70
119 2 0.02
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (117 bp):
GGGGTAAAATATGTAATTTTTGGTGAAATGAGGGTCAAAATGGAATTTTGGAAAGCTCGAGGGTA
AAACGGTAATTTTTGATGAAACTGAGGCTAAAAATGGAATTTTGAAAAGTTC
Found at i:12365904 original size:59 final size:58
Alignment explanation
Indices: 12365659--12365911 Score: 255
Period size: 58 Copynumber: 4.3 Consensus size: 58
12365649 TTGACTTTCG
* * * * *
12365659 GGGGTAAAAAT-GTGATTTTTGGTGAAAT-TAGGGTCAAAATGGGATTTTGGAAAGCTT-
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAG-TTC
* * * * * **
12365716 GCGGGTAAAACGGTAATTTTTGATGAGA-CTGGGGCTAAAAAATGGGGTTTTGGAAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGTGAAATC-GAGG-TTAAAAATGGAATTTTGGAAAGTTC
* *
12365776 AGGGGTAAAATAGTAATTTTTGGTGAAATCGAGGTT-AAAATGGAATTTTGGAAAGCTC
1 -GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
*
12365834 GAGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGAAAAGTTC
1 G-GGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
*
12365893 GGGCGTAAAATGGTGATTT
1 GGG-GTAAAATGGTAATTT
12365912 ATGAACAGTT
Statistics
Matches: 162, Mismatches: 23, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
57 6 0.04
58 71 0.44
59 40 0.25
60 43 0.27
61 2 0.01
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.31
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTC
Found at i:12366822 original size:21 final size:21
Alignment explanation
Indices: 12366774--12366823 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
12366764 TTTCATTCCT
* **
12366774 CTCCTTTTTATTTGTTTTTTA
1 CTCCTTTTCATTTCCTTTTTA
*
12366795 GTCCCTTTTCATTTCCTTTTTA
1 CT-CCTTTTCATTTCCTTTTTA
12366817 CTCCTTT
1 CTCCTTT
12366824 GTTTATCTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.08, C:0.24, G:0.04, T:0.64
Consensus pattern (21 bp):
CTCCTTTTCATTTCCTTTTTA
Found at i:12366980 original size:3 final size:3
Alignment explanation
Indices: 12366953--12367068 Score: 94
Period size: 3 Copynumber: 38.0 Consensus size: 3
12366943 TGGCTCTTCG
* **
12366953 ATT ATT -TT -TT ATT CATT ATTT ATT ATT AAT ATT AAAA ATT ATT ATT
1 ATT ATT ATT ATT ATT -ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * * *
12366999 A-A AGTT ATT ATT AAT ACT GTT ATT AAT ATT ACTT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
12367045 ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
12367069 CGACGTTTTC
Statistics
Matches: 91, Mismatches: 15, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.05
3 75 0.82
4 11 0.12
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:12367838 original size:23 final size:23
Alignment explanation
Indices: 12367781--12367841 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
12367771 ACCATAATAT
*
12367781 TAAATTTAAA-TTAAATTCAAAC
1 TAAATTTAAATTTAAATTCAAAA
*
12367803 TAAAATTAAATTTAAA-TCAAAAA
1 TAAATTTAAATTTAAATTC-AAAA
12367826 TAAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
12367842 ATAAATTTGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.32
23 23 0.68
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTCAAAA
Found at i:12367843 original size:7 final size:6
Alignment explanation
Indices: 12367780--12367858 Score: 58
Period size: 6 Copynumber: 13.8 Consensus size: 6
12367770 TACCATAATA
* * * * *
12367780 TTAAAT TTAAA- TTAAAT TCAAA- CTAAAA TTAAAT TTAAA- TCAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
12367825 ATAAAT TTAAAT TTAAA- ATAAAT TTGAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
12367859 ATAAACTTAA
Statistics
Matches: 55, Mismatches: 14, Indels: 8
0.71 0.18 0.10
Matches are distributed among these distances:
5 16 0.29
6 39 0.71
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:12367854 original size:17 final size:17
Alignment explanation
Indices: 12367780--12367886 Score: 101
Period size: 17 Copynumber: 6.3 Consensus size: 17
12367770 TACCATAATA
*
12367780 TTAAATTTAAATTAAAT
1 TTAAATTTAAAATAAAT
* *
12367797 TCAAA-CTAAAATTAAAT
1 TTAAATTTAAAA-TAAAT
**
12367814 TTAAATCAAAAATAAAT
1 TTAAATTTAAAATAAAT
12367831 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
12367848 TTGAATTTAAAATAAAC
1 TTAAATTTAAAATAAAT
**
12367865 TT-AATTTCAAAGCAAAT
1 TTAAATTT-AAAATAAAT
12367882 TTAAA
1 TTAAA
12367887 ATGATTTGGG
Statistics
Matches: 74, Mismatches: 12, Indels: 7
0.80 0.13 0.08
Matches are distributed among these distances:
16 9 0.12
17 58 0.78
18 7 0.09
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:12370594 original size:10 final size:10
Alignment explanation
Indices: 12370579--12370621 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
12370569 AAGACTCTTC
12370579 AAATGCATGG
1 AAATGCATGG
*
12370589 AAATGCTTGG
1 AAATGCATGG
12370599 AAATGCATGG
1 AAATGCATGG
**
12370609 AAAAACATGG
1 AAATGCATGG
12370619 AAA
1 AAA
12370622 GAATTGAACC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19
Consensus pattern (10 bp):
AAATGCATGG
Found at i:12371596 original size:121 final size:120
Alignment explanation
Indices: 12371406--12371650 Score: 375
Period size: 121 Copynumber: 2.0 Consensus size: 120
12371396 ATCTACTAAC
* * * * *
12371406 AAATTGGTTCTCAAACTTTTTTGATGAACTTCATTTTCTCTATCCATATTAAACTTTGAAATCAC
1 AAATTCGTTCTCAAACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACAC
* * *
12371471 CTCATCAATTTCAGTCTACGAAGAATTTGACTTAAAATTTGAGCTTTTCATCTTTT
66 CTCATCAATTTCAGCCTACAAAGAATGTGACTTAAAATTTGAGCTTTTCATC-TTT
12371527 AAATTCGTTC-CAAGACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACA
1 AAATTCGTTCTCAA-ACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACA
* *
12371591 CCTCATCAATTTGAGCCTTCAAAGAATGTGACTTAAAATTTGAGCTTTTCATCTTT
65 CCTCATCAATTTCAGCCTACAAAGAATGTGACTTAAAATTTGAGCTTTTCATCTTT
12371647 AAAT
1 AAAT
12371651 ATTGTGTATA
Statistics
Matches: 113, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
120 10 0.09
121 103 0.91
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.40
Consensus pattern (120 bp):
AAATTCGTTCTCAAACTTTCTTGACGAACTTCATTTTCTCTATCCATATTAAAATTTGAAAACAC
CTCATCAATTTCAGCCTACAAAGAATGTGACTTAAAATTTGAGCTTTTCATCTTT
Found at i:12377229 original size:28 final size:28
Alignment explanation
Indices: 12377176--12377232 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
12377166 TTCTATTTCC
*
12377176 TAAAATAAACATCTCAACTAATTTCTAA
1 TAAAATAAACATCTCAACCAATTTCTAA
* *
12377204 TAAAATAATCTTCTCAATCCAA-TTCTAA
1 TAAAATAAACATCTCAA-CCAATTTCTAA
12377232 T
1 T
12377233 TCCGTTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (28 bp):
TAAAATAAACATCTCAACCAATTTCTAA
Found at i:12380090 original size:36 final size:36
Alignment explanation
Indices: 12380041--12380119 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
12380031 ACTTACATTT
12380041 TAAAATATAAAAAATAAAGAGAT-TAAATTT-TTAAAAA
1 TAAAA-ATAAAAAATAAA-A-ATATAAATTTATTAAAAA
* *
12380078 TAAAAATAAAAAATTAAATTATAAATTTATTAAAAA
1 TAAAAATAAAAAATAAAAATATAAATTTATTAAAAA
12380114 TAAAAA
1 TAAAAA
12380120 ACTTACAGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 1 0.03
35 8 0.21
36 24 0.63
37 5 0.13
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (36 bp):
TAAAAATAAAAAATAAAAATATAAATTTATTAAAAA
Found at i:12382678 original size:21 final size:22
Alignment explanation
Indices: 12382654--12382705 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
12382644 TATTTTAAAT
12382654 ATTTTCT-ATAATTATTTATAA
1 ATTTTCTAATAATTATTTATAA
* * *
12382675 A-TTTCTAATATTTCTTTATGA
1 ATTTTCTAATAATTATTTATAA
*
12382696 ATTTTATAAT
1 ATTTTCTAAT
12382706 TTATATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
22 7 0.28
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (22 bp):
ATTTTCTAATAATTATTTATAA
Found at i:12386408 original size:31 final size:30
Alignment explanation
Indices: 12386370--12386455 Score: 79
Period size: 29 Copynumber: 2.9 Consensus size: 30
12386360 TTAACATAAT
12386370 ATTTGGTACCTGAACTTGATACTTTTTCCTA
1 ATTTGGTACCTGAACTTGATA-TTTTTCCTA
* * *
12386401 ATTTGGTATCTAAACTT--T-TTTTGGACCTA
1 ATTTGGTACCTGAACTTGATATTTT--TCCTA
* *
12386430 ATTTGGTACTTGAACTTGACATTTTT
1 ATTTGGTACCTGAACTTGATATTTTT
12386456 TTCTTAATTT
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
27 4 0.10
29 19 0.45
31 15 0.36
32 4 0.10
ACGTcount: A:0.23, C:0.15, G:0.14, T:0.48
Consensus pattern (30 bp):
ATTTGGTACCTGAACTTGATATTTTTCCTA
Found at i:12386481 original size:60 final size:60
Alignment explanation
Indices: 12386370--12386484 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 60
12386360 TTAACATAAT
*
12386370 ATTTGGTACCTGAACTTGATACTTTTTCCTAATTTGGTATCTAAACTTTTTTTGGACCTA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTTGGACCTA
* * * *
12386430 ATTTGGTACTTGAACTTGACATTTTTTTCTTAATTTGGT-TCTTAAGCTTTTTTTG
1 ATTTGGTACCTGAACTTGACA-CTTTTTCCTAATTTGGTATC-TAAACTTTTTTTG
12386485 AAGATTCAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 21 0.44
61 27 0.56
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTATCTAAACTTTTTTTGGACCTA
Found at i:12386751 original size:30 final size:30
Alignment explanation
Indices: 12386710--12386843 Score: 107
Period size: 31 Copynumber: 4.5 Consensus size: 30
12386700 TCCCAAAAAA
*
12386710 TTTAAGTACCAACTTA-AAAAAAGTGTCAAG
1 TTTAAGTACCAAATTAGAAAAAA-TGTCAAG
*
12386740 TTTAGGTACCAAATTATGAAAAAATGTCAAG
1 TTTAAGTACCAAATTA-GAAAAAATGTCAAG
* * *
12386771 TTTAAGTATCAAATTGGACCAAAAA----AAT
1 TTTAAGTACCAAATTAGA--AAAAATGTCAAG
* *
12386799 TTTAAGTACCAAATTAAGAAAAAGTGTTAAG
1 TTTAAGTACCAAATT-AGAAAAAATGTCAAG
* *
12386830 TTCAAGTGCCAAAT
1 TTTAAGTACCAAAT
12386844 GTTATATTAA
Statistics
Matches: 83, Mismatches: 12, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
27 4 0.05
28 16 0.19
29 2 0.02
30 16 0.19
31 34 0.41
32 11 0.13
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.28
Consensus pattern (30 bp):
TTTAAGTACCAAATTAGAAAAAATGTCAAG
Found at i:12386784 original size:89 final size:90
Alignment explanation
Indices: 12386652--12386831 Score: 240
Period size: 89 Copynumber: 2.0 Consensus size: 90
12386642 TTAAAAAAGA
* * *
12386652 TTAGGTACCAAATTAGGAAAAAGAGTTAAGTTCAGGTACCAAATTGAATCCCAAAAAA-TTTAAG
1 TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGAA-CCAAAAAAATTTTAAG
*
12386716 TACCAACTTAA-AAAAAGTGTCAAGT
65 TACCAAATTAAGAAAAAGTGTCAAGT
* * * *
12386741 TTAGGTACCAAATTATGAAAAA-ATGTCAAGTTTAAGTATCAAATTGGACCAAAAAAATTTTAAG
1 TTAGGTACCAAATTAGGAAAAAGA-GTCAAGTTCAAGTACCAAATTGAACCAAAAAAATTTTAAG
*
12386805 TACCAAATTAAGAAAAAGTGTTAAGT
65 TACCAAATTAAGAAAAAGTGTCAAGT
12386831 T
1 T
12386832 CAAGTGCCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
88 9 0.11
89 56 0.71
90 14 0.18
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (90 bp):
TTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAAGTACCAAATTGAACCAAAAAAATTTTAAGT
ACCAAATTAAGAAAAAGTGTCAAGT
Found at i:12387304 original size:20 final size:20
Alignment explanation
Indices: 12387279--12387339 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
12387269 CAACTACTAA
12387279 AACTATTA-ATATGTATATAT
1 AACTATTATATAT-TATATAT
*
12387299 AACTATTATAGATTATATAT
1 AACTATTATATATTATATAT
12387319 AACTATTATTATATTATATAT
1 AACTATTA-TATATTATATAT
12387340 TATAATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 23 0.62
21 14 0.38
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (20 bp):
AACTATTATATATTATATAT
Found at i:12403449 original size:6 final size:6
Alignment explanation
Indices: 12403441--12403479 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
12403431 CTTTACTTTT
*
12403441 TGCTTT TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGC
1 TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGCTTC TGC
12403480 ACTTTTAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.18, T:0.51
Consensus pattern (6 bp):
TGCTTC
Done.