Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 93 of 126
Found at i:28750573 original size:14 final size:14
Alignment explanation
Indices: 28750537--28750577 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28750527 CTTATTTAAA
28750537 TTTGTATTTA-CTT
1 TTTGTATTTATCTT
*
28750550 TATG--TTTATCTT
1 TTTGTATTTATCTT
28750562 TTTGTATTTATCTT
1 TTTGTATTTATCTT
28750576 TT
1 TT
28750578 AGAATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
13 3 0.13
14 10 0.43
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (14 bp):
TTTGTATTTATCTT
Found at i:28751399 original size:21 final size:22
Alignment explanation
Indices: 28751365--28751407 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
28751355 TATTTCTTCC
28751365 AATTCTGTTTTCTTTTATTTTT
1 AATTCTGTTTTCTTTTATTTTT
28751387 AATTCTG-TTTCTTTTATTTTT
1 AATTCTGTTTTCTTTTATTTTT
28751408 CCTCAAATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.72
Consensus pattern (22 bp):
AATTCTGTTTTCTTTTATTTTT
Found at i:28759814 original size:103 final size:102
Alignment explanation
Indices: 28759647--28759839 Score: 248
Period size: 103 Copynumber: 1.9 Consensus size: 102
28759637 GTGTGTTAGA
* *
28759647 CTGAGTAACCGGGGTGGAGTGCTTGGTTGTCATTTTACTTCGCGTCAAAAGGGCTAACACATTC-
1 CTGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTTACTTCGCGTCAAAAGGGCTAACACATTCT
*
28759711 TACAA-AAAAAGAGAAGAAAAAAATTGAGAGCATGTTGGG
66 TA-AAGAAAAA-AAAAG-AAAAAATTGAGAGCATGTTGGG
* * * ***
28759750 CTGAGTAACCGGGATGGAGTGTTTGGGTGTCATTTTATTTCGCGTCAAAA-GGTTCAATGTATTC
1 CTGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTTACTTCGCGTCAAAAGGGCT-AACACATTC
28759814 TTAAAGAAAAAAAAAGAAAAAATTGA
65 TTAAAGAAAAAAAAAGAAAAAATTGA
28759840 CAAAATAAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
102 13 0.17
103 58 0.74
104 7 0.09
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.27
Consensus pattern (102 bp):
CTGAGTAACCGGGATGGAGTGCTTGGGTGTCATTTTACTTCGCGTCAAAAGGGCTAACACATTCT
TAAAGAAAAAAAAAGAAAAAATTGAGAGCATGTTGGG
Found at i:28760460 original size:14 final size:14
Alignment explanation
Indices: 28760424--28760464 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28760414 ATTATTTAAA
28760424 TTTGTATTTA-CTT
1 TTTGTATTTATCTT
*
28760437 TATG--TTTATCTT
1 TTTGTATTTATCTT
28760449 TTTGTATTTATCTT
1 TTTGTATTTATCTT
28760463 TT
1 TT
28760465 AGAGTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
11 4 0.17
12 6 0.26
13 3 0.13
14 10 0.43
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.71
Consensus pattern (14 bp):
TTTGTATTTATCTT
Found at i:28763318 original size:30 final size:30
Alignment explanation
Indices: 28763279--28763352 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
28763269 GAACAACTTT
*
28763279 GAGGGAATCAAGGGGACAACACCTA-TAGAG
1 GAGGAAATCAAGGGGACAACACC-ACTAGAG
* * * *
28763309 GAGGAAATCAAAGGGACATCATCACTAGTG
1 GAGGAAATCAAGGGGACAACACCACTAGAG
28763339 GAGGAAATCAAGGG
1 GAGGAAATCAAGGG
28763353 ATTTTAGGCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 1 0.03
30 36 0.97
ACGTcount: A:0.41, C:0.15, G:0.32, T:0.12
Consensus pattern (30 bp):
GAGGAAATCAAGGGGACAACACCACTAGAG
Found at i:28764115 original size:24 final size:24
Alignment explanation
Indices: 28764065--28764116 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
28764055 TTCGTAGGTC
* **
28764065 AAATAAATTATGCTAATAAATGTT
1 AAATAAATTATACTAATAAATACT
*
28764089 AAATAGATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
28764113 AAAT
1 AAAT
28764117 CTTATAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:28765447 original size:30 final size:30
Alignment explanation
Indices: 28765411--28765474 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
28765401 TGCATAAAGA
28765411 GTTTCTAACATTTTCTACAAGAAGGATAAT
1 GTTTCTAACATTTTCTACAAGAAGGATAAT
*
28765441 GTTTCTAACCTTTTCTACAAGAAGGATAAT
1 GTTTCTAACATTTTCTACAAGAAGGATAAT
28765471 GTTT
1 GTTT
28765475 TCTCCATCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (30 bp):
GTTTCTAACATTTTCTACAAGAAGGATAAT
Found at i:28773680 original size:80 final size:80
Alignment explanation
Indices: 28773547--28773708 Score: 324
Period size: 80 Copynumber: 2.0 Consensus size: 80
28773537 ACAAGGTTAA
28773547 TCCTCATGCCTAGTTGTTTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTT
1 TCCTCATGCCTAGTTGTTTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTT
28773612 CACTATTTAGTTTGT
66 CACTATTTAGTTTGT
28773627 TCCTCATGCCTAGTTGTTTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTT
1 TCCTCATGCCTAGTTGTTTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTT
28773692 CACTATTTAGTTTGT
66 CACTATTTAGTTTGT
28773707 TC
1 TC
28773709 ATCCTCAAGA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.17, C:0.19, G:0.14, T:0.50
Consensus pattern (80 bp):
TCCTCATGCCTAGTTGTTTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTT
CACTATTTAGTTTGT
Found at i:28773704 original size:39 final size:39
Alignment explanation
Indices: 28773579--28773832 Score: 212
Period size: 39 Copynumber: 6.3 Consensus size: 39
28773569 TTGTTTCCTA
*
28773579 TTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
1 TTAGTTTGTTCATTCTCAAGATATTTCCAGGTTCACTAT
* * * * ** *
28773618 TTAGTTTGTTC-CTCATGCCTAGTTGTTTGTATTGTTTC-CTA-
1 TTAGTTTGTTCATTC-T--CAAGATATTTCCA--GGTTCACTAT
*
28773659 TTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
1 TTAGTTTGTTCATTCTCAAGATATTTCCAGGTTCACTAT
*
28773698 TTAGTTTGTTCATCCTCAAGATATTTCCAGGTTCACTAT
1 TTAGTTTGTTCATTCTCAAGATATTTCCAGGTTCACTAT
* * * ** *
28773737 TTAGTTTGTTCATCCTCATGCCTAGTTGTTTGTATTGTTTC-CTA-
1 TTAGTTTGTTCAT--TC-T--CAAGATATTTCCA--GGTTCACTAT
*
28773781 TTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
1 TTAGTTTGTTCATTCTCAAGATATTTCCAGGTTCACTAT
28773820 TTAGTTTGTTCAT
1 TTAGTTTGTTCAT
28773833 CCTGTTAGAT
Statistics
Matches: 165, Mismatches: 33, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
37 8 0.05
38 8 0.05
39 89 0.54
41 21 0.13
42 8 0.05
43 4 0.02
44 20 0.12
45 3 0.02
46 4 0.02
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (39 bp):
TTAGTTTGTTCATTCTCAAGATATTTCCAGGTTCACTAT
Found at i:28773796 original size:122 final size:119
Alignment explanation
Indices: 28773579--28773835 Score: 469
Period size: 122 Copynumber: 2.1 Consensus size: 119
28773569 TTGTTTCCTA
* *
28773579 TTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTATTTAGTTTGTTCCTCATGCCTAGTTGT
1 TTAGTTTGTTCATCCTCAAGATATTTCCAGGTTCACTATTTAGTTTGTTCCTCATGCCTAGTTGT
28773644 TTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
66 TTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
28773698 TTAGTTTGTTCATCCTCAAGATATTTCCAGGTTCACTATTTAGTTTGTTCATCCTCATGCCTAGT
1 TTAGTTTGTTCATCCTCAAGATATTTCCAGGTTCACTATTTAGTTTG-T--TCCTCATGCCTAGT
28773763 TGTTTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
63 TGTTTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
28773820 TTAGTTTGTTCATCCT
1 TTAGTTTGTTCATCCT
28773836 GTTAGATTGT
Statistics
Matches: 133, Mismatches: 2, Indels: 3
0.96 0.01 0.02
Matches are distributed among these distances:
119 45 0.34
120 1 0.01
122 87 0.65
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (119 bp):
TTAGTTTGTTCATCCTCAAGATATTTCCAGGTTCACTATTTAGTTTGTTCCTCATGCCTAGTTGT
TTGTATTGTTTCCTATTAGTTTCTTCATTCTCAAGATATTTCCAGGTTCACTAT
Found at i:28775455 original size:27 final size:27
Alignment explanation
Indices: 28775398--28775457 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
28775388 CAACAACACA
*
28775398 AAAAAACGTGATATTAGAAGCAGACTG
1 AAAAAACGTGATATTAGAAGCAGACTC
*
28775425 AAAAAACGTGCTATTAGAAGCA-ACCTC
1 AAAAAACGTGATATTAGAAGCAGA-CTC
28775452 AAAAAA
1 AAAAAA
28775458 ATTTCACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.03
27 29 0.97
ACGTcount: A:0.52, C:0.15, G:0.17, T:0.17
Consensus pattern (27 bp):
AAAAAACGTGATATTAGAAGCAGACTC
Found at i:28775650 original size:30 final size:30
Alignment explanation
Indices: 28775585--28775653 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
28775575 AATCACTAAT
* * *
28775585 AACCATTTTCCGTTACAGACTTAACGGAGC
1 AACCATTTTACGTTACAGACTTAACGAAAC
* * *
28775615 TACCATTTTATGTTACAGACTTAACTAAAC
1 AACCATTTTACGTTACAGACTTAACGAAAC
28775645 AACCATTTT
1 AACCATTTT
28775654 TCATCCCCCT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (30 bp):
AACCATTTTACGTTACAGACTTAACGAAAC
Found at i:28777450 original size:10 final size:9
Alignment explanation
Indices: 28777402--28777468 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
28777392 ATTTTTTCTA
*
28777402 ATTTTAATT
1 ATTTTTATT
28777411 -TTTTTA-T
1 ATTTTTATT
28777418 ATTTTTATT
1 ATTTTTATT
* *
28777427 AAATTTTAAT
1 -ATTTTTATT
28777437 ATTTTTATT
1 ATTTTTATT
28777446 GATTTTTA-T
1 -ATTTTTATT
*
28777455 -TTTTTATA
1 ATTTTTATT
28777463 ATTTTT
1 ATTTTT
28777469 TTGCCACATG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
7 7 0.15
8 11 0.24
9 14 0.30
10 14 0.30
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (9 bp):
ATTTTTATT
Found at i:28777452 original size:19 final size:18
Alignment explanation
Indices: 28777411--28777468 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 18
28777401 AATTTTAATT
28777411 TTTTTATATTTTTATTAAA
1 TTTTTATATTTTTATT-AA
* *
28777430 TTTTAATATTTTTATTGA
1 TTTTTATATTTTTATTAA
28777448 TTTTTAT-TTTTTA-TAA
1 TTTTTATATTTTTATTAA
28777464 TTTTT
1 TTTTT
28777469 TTGCCACATG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 7 0.20
17 6 0.17
18 7 0.20
19 15 0.43
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTTTATATTTTTATTAA
Found at i:28778623 original size:11 final size:11
Alignment explanation
Indices: 28778607--28778631 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28778597 TCAGAAATTT
28778607 TTTTATTTGTG
1 TTTTATTTGTG
28778618 TTTTATTTGTG
1 TTTTATTTGTG
28778629 TTT
1 TTT
28778632 ATAAGTCATA
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:0.08, C:0.00, G:0.16, T:0.76
Consensus pattern (11 bp):
TTTTATTTGTG
Found at i:28781618 original size:21 final size:19
Alignment explanation
Indices: 28781568--28781639 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 19
28781558 AAAAAAAAAC
28781568 TACTATTTTTTATTGTTTTCT
1 TACTATTTTTTATT-TTTT-T
** *
28781589 TGTTGTTTTTTATTATTTTGT
1 TACTATTTTTTATT-TTTT-T
*
28781610 TACTATTTTCTTGTTTTTTT
1 TACTATTTT-TTATTTTTTT
28781630 TCACTATTTT
1 T-ACTATTTT
28781640 GTTACATTTT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.05
21 34 0.85
22 4 0.10
ACGTcount: A:0.12, C:0.08, G:0.07, T:0.72
Consensus pattern (19 bp):
TACTATTTTTTATTTTTTT
Found at i:28781620 original size:32 final size:31
Alignment explanation
Indices: 28781583--28781649 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 31
28781573 TTTTTTATTG
*
28781583 TTTTCTTGTTGTTTTTT-ATTATTTTGTTACTA
1 TTTTCTTGTT-TTTTTTCACTATTTTGTTAC-A
28781615 TTTTCTTGTTTTTTTTCACTATTTTGTTACA
1 TTTTCTTGTTTTTTTTCACTATTTTGTTACA
28781646 TTTT
1 TTTT
28781650 ATTAGTATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 11 0.33
32 22 0.67
ACGTcount: A:0.12, C:0.09, G:0.07, T:0.72
Consensus pattern (31 bp):
TTTTCTTGTTTTTTTTCACTATTTTGTTACA
Found at i:28781649 original size:21 final size:22
Alignment explanation
Indices: 28781632--28781674 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
28781622 GTTTTTTTTC
*
28781632 ACTATTTTGTTAC-ATTTTATT
1 ACTATGTTGTTACTATTTTATT
*
28781653 AGTATGTTGTTACTATTTTATT
1 ACTATGTTGTTACTATTTTATT
28781675 GTTATCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (22 bp):
ACTATGTTGTTACTATTTTATT
Found at i:28781668 original size:32 final size:32
Alignment explanation
Indices: 28781569--28781671 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
28781559 AAAAAAAACT
* * * * *
28781569 ACTATTTT-TTATTGTTTTCTTGTTGTTTTTT
1 ACTATTTTGTTACTATTTTATTGTTGTTGTTC
* * * *
28781600 ATTATTTTGTTACTATTTTCTTGTTTTTTTTC
1 ACTATTTTGTTACTATTTTATTGTTGTTGTTC
28781632 ACTATTTTGTTAC-ATTTTATTAGTATGTTGTT-
1 ACTATTTTGTTACTATTTTATT-GT-TGTTGTTC
28781664 ACTATTTT
1 ACTATTTT
28781672 ATTGTTATCG
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
31 14 0.23
32 41 0.68
33 5 0.08
ACGTcount: A:0.16, C:0.08, G:0.09, T:0.68
Consensus pattern (32 bp):
ACTATTTTGTTACTATTTTATTGTTGTTGTTC
Found at i:28781831 original size:15 final size:15
Alignment explanation
Indices: 28781811--28781840 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28781801 ATGTATTATA
*
28781811 TATATATTAAAAATT
1 TATATATAAAAAATT
28781826 TATATATAAAAAATT
1 TATATATAAAAAATT
28781841 ATTATGGGCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TATATATAAAAAATT
Found at i:28781845 original size:17 final size:17
Alignment explanation
Indices: 28781805--28781845 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
28781795 TTTTTGATGT
*
28781805 ATTATATATATATTAAAA
1 ATTAT-TATATATAAAAA
28781823 A-T-TTATATATAAAAA
1 ATTATTATATATAAAAA
28781838 ATTATTAT
1 ATTATTAT
28781846 GGGCGGGCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 5 0.25
18 1 0.05
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTATTATATATAAAAA
Found at i:28798372 original size:20 final size:21
Alignment explanation
Indices: 28798338--28798376 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28798328 CATTTTTCTA
*
28798338 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
28798359 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
28798377 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:28815831 original size:28 final size:28
Alignment explanation
Indices: 28815800--28816057 Score: 213
Period size: 28 Copynumber: 9.3 Consensus size: 28
28815790 ATAGGGGCAT
*
28815800 CTTTAACAGAGCCAACCACAAAGGCTTC
1 CTTTAACAGAGTCAACCACAAAGGCTTC
*
28815828 CTTTAACAGAGT-AAGCCACAAAGGTTTC
1 CTTTAACAGAGTCAA-CCACAAAGGCTTC
* * * *
28815856 CTTTAACAAACTCAGCCACAAAGGCTCC
1 CTTTAACAGAGTCAACCACAAAGGCTTC
*
28815884 CTTTAACAGAGTCAGCCACAAAGGCTTC
1 CTTTAACAGAGTCAACCACAAAGGCTTC
* * * *
28815912 CTTTAATAGAGTCAGCCATAAAGGCTTT
1 CTTTAACAGAGTCAACCACAAAGGCTTC
* *
28815940 CTTTAACATAGTCAACCACAAAAGCTT-
1 CTTTAACAGAGTCAACCACAAAGGCTTC
* * *
28815967 TTTTAACATAGAT-AGA-CACAAAGGCTTA
1 CTTTAACAGAG-TCA-ACCACAAAGGCTTC
* *** * *
28815995 CTTT-ACAGAGATTAGTTACAAAGGTTTT
1 CTTTAACAGAG-TCAACCACAAAGGCTTC
* * *
28816023 CTTTAACAGAATCAATCACAAAGGCTTT
1 CTTTAACAGAGTCAACCACAAAGGCTTC
28816051 C-TTAACA
1 CTTTAACA
28816058 TAGATAGCCA
Statistics
Matches: 191, Mismatches: 31, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
27 36 0.19
28 149 0.78
29 6 0.03
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (28 bp):
CTTTAACAGAGTCAACCACAAAGGCTTC
Found at i:28815850 original size:84 final size:83
Alignment explanation
Indices: 28815735--28816048 Score: 237
Period size: 84 Copynumber: 3.7 Consensus size: 83
28815725 AATAGTCACG
* * * * **
28815735 AAGGCTTTCCTTTAATAGAGGTTGCCACAAAGGCATTCTTTAACAAAGATTCA-CCATAGGGGCA
1 AAGGC-TTCCTTTAATAGA-GTAGCCACAAAGGCTTTCTTTAACAAA-ACTCAGCCACAAAGGC-
28815799 T-CTTTAACAGAGCCAACCACA
62 TCCTTTAACAGAGCCAACCACA
*
28815820 AAGGCTTCCTTTAACAGAGTAAGCCACAAAGG-TTTCCTTTAAC-AAACTCAGCCACAAAGGCTC
1 AAGGCTTCCTTTAATAGAGT-AGCCACAAAGGCTTT-CTTTAACAAAACTCAGCCACAAAGGCT-
* *
28815883 CCTTTAACAGAGTCAGCCACA
63 CCTTTAACAGAGCCAACCACA
* * * * * **
28815904 AAGGCTTCCTTTAATAGAGTCAGCCATAAAGGCTTTCTTTAAC-ATAGTCAACCACAAAAGCTTT
1 AAGGCTTCCTTTAATAGAGT-AGCCACAAAGGCTTTCTTTAACAAAACTCAGCCACAAAGGCTCC
* **
28815968 TTTAACATAGATAGA-CACA
65 TTTAACAGAGCCA-ACCACA
* * * ** * * **
28815987 AAGGCTTACTTTACAGAGATTAGTTACAAAGGTTTTCTTTAACAGAA-TCAATCACAAAGGCT
1 AAGGCTTCCTTTA-ATAGAGTAGCCACAAAGGCTTTCTTTAACAAAACTCAGCCACAAAGGCT
28816049 TTCTTAACAT
Statistics
Matches: 187, Mismatches: 33, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
82 5 0.03
83 70 0.37
84 104 0.56
85 8 0.04
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (83 bp):
AAGGCTTCCTTTAATAGAGTAGCCACAAAGGCTTTCTTTAACAAAACTCAGCCACAAAGGCTCCT
TTAACAGAGCCAACCACA
Found at i:28815993 original size:27 final size:28
Alignment explanation
Indices: 28815816--28816114 Score: 142
Period size: 28 Copynumber: 10.8 Consensus size: 28
28815806 CAGAGCCAAC
* * *
28815816 CACAAAGGCTTCCTTTAACAGAG-TAAGC
1 CACAAAGGCTT-TTTTAACAGAGATCAGA
*
28815844 CACAAAGG-TTTCCTTTAACA-A-ACTCAGC
1 CACAAAGGCTTT--TTTAACAGAGA-TCAGA
** *
28815872 CACAAAGGCTCCCTTTAACAGAG-TCAGC
1 CACAAAGGCT-TTTTTAACAGAGATCAGA
* * *
28815900 CACAAAGGCTTCCTTTAATAGAG-TCAGC
1 CACAAAGGCTT-TTTTAACAGAGATCAGA
* *
28815928 CATAAAGGCTTTCTTTAACATAG-TCA-A
1 CACAAAGGCTTT-TTTAACAGAGATCAGA
* *
28815955 CCACAAAAGCTTTTTTAACATAGAT-AGA
1 -CACAAAGGCTTTTTTAACAGAGATCAGA
* * *
28815983 CACAAAGGCTTACTTT-ACAGAGATTAGT
1 CACAAAGGCTT-TTTTAACAGAGATCAGA
* *
28816011 TACAAAGGTTTTCTTTAACAGA-ATCA-A
1 CACAAAGGCTTT-TTTAACAGAGATCAGA
* * *
28816038 TCACAAAGGCTTTCTTAACATAGAT-AGC
1 -CACAAAGGCTTTTTTAACAGAGATCAGA
* * *
28816066 CATAAAGGCTCATTTT-ACAGAGATAAGA
1 CACAAAGGCT-TTTTTAACAGAGATCAGA
*
28816094 CACAAAGG-TTTTCTTTACAGA
1 CACAAAGGCTTTT-TTAACAGA
28816115 AATTGCCATA
Statistics
Matches: 213, Mismatches: 34, Indels: 48
0.72 0.12 0.16
Matches are distributed among these distances:
26 2 0.01
27 58 0.27
28 146 0.69
29 7 0.03
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (28 bp):
CACAAAGGCTTTTTTAACAGAGATCAGA
Found at i:28816018 original size:83 final size:83
Alignment explanation
Indices: 28815816--28816115 Score: 263
Period size: 83 Copynumber: 3.6 Consensus size: 83
28815806 CAGAGCCAAC
* * *
28815816 CACAAAGGCTTC-CTTTAACAGAG-TAAGCCACAAAGGTTTCCTTTAACA-AACTCAGCCACAAA
1 CACAAAGGC-TCACTTT-ACAGAGATAAGACACAAAGGTTTTCTTTAACAGAA-TCAACCACAAA
* ** * *
28815878 GGCTCCCTTTAACAGAG-TCAGC
63 AGCTTTC-TTAACATAGAT-AGA
* * * * * * *
28815900 CACAAAGGCTTC-CTTTA-ATAGAGTCAGCCATAAAGGCTTTCTTTAACATAGTCAACCACAAAA
1 CACAAAGGC-TCACTTTACAGAGA-TAAGACACAAAGGTTTTCTTTAACAGAATCAACCACAAAA
*
28815963 GCTTTTTTAACATAGATAGA
64 GCTTTCTTAACATAGATAGA
* * ** * *
28815983 CACAAAGGCTTACTTTACAGAGATTAGTTACAAAGGTTTTCTTTAACAGAATCAATCACAAAGGC
1 CACAAAGGCTCACTTTACAGAGATAAGACACAAAGGTTTTCTTTAACAGAATCAACCACAAAAGC
*
28816048 TTTCTTAACATAGATAGC
66 TTTCTTAACATAGATAGA
* *
28816066 CATAAAGGCTCATTTTACAGAGATAAGACACAAAGGTTTTCTTT-ACAGAA
1 CACAAAGGCTCACTTTACAGAGATAAGACACAAAGGTTTTCTTTAACAGAA
28816116 ATTGCCATAA
Statistics
Matches: 178, Mismatches: 32, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
82 10 0.06
83 112 0.63
84 55 0.31
85 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (83 bp):
CACAAAGGCTCACTTTACAGAGATAAGACACAAAGGTTTTCTTTAACAGAATCAACCACAAAAGC
TTTCTTAACATAGATAGA
Found at i:28816018 original size:111 final size:111
Alignment explanation
Indices: 28815901--28816114 Score: 254
Period size: 111 Copynumber: 1.9 Consensus size: 111
28815891 AGAGTCAGCC
* * * *
28815901 ACAAAGGCTTCCTTTAATAGAGTCAGCCATAAAGGCTTTCTTTAACATAG-TCAACCACAAAAGC
1 ACAAAGGCTTCCTTTAACAGAATCAACCACAAAGGCTTTC-TTAACATAGAT-AACCACAAAAGC
* *
28815965 T-TTTTTAACATAGAT-AGACACAAAGGCTTACTTTACAGAGATTAGTT
64 TCATTTT-ACAGAGATAAGACACAAAGGCTTACTTTACAGAGATTAGTT
* * * * * *
28816012 ACAAAGGTTTTCTTTAACAGAATCAATCACAAAGGCTTTCTTAACATAGATAGCCATAAAGGCTC
1 ACAAAGGCTTCCTTTAACAGAATCAACCACAAAGGCTTTCTTAACATAGATAACCACAAAAGCTC
* *
28816077 ATTTTACAGAGATAAGACACAAAGGTTTTCTTTACAGA
66 ATTTTACAGAGATAAGACACAAAGGCTTACTTTACAGA
28816115 AATTGCCATA
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
110 26 0.30
111 60 0.70
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (111 bp):
ACAAAGGCTTCCTTTAACAGAATCAACCACAAAGGCTTTCTTAACATAGATAACCACAAAAGCTC
ATTTTACAGAGATAAGACACAAAGGCTTACTTTACAGAGATTAGTT
Found at i:28819081 original size:15 final size:15
Alignment explanation
Indices: 28819043--28819086 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28819033 TTTCATTGTC
* *
28819043 ACTTGTTACATCTAT
1 ACTTGTTGCATCTTT
* *
28819058 ACCTATTGCATCTTT
1 ACTTGTTGCATCTTT
28819073 ACTTGTTGCATCTT
1 ACTTGTTGCATCTT
28819087 CGCCTGTTAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (15 bp):
ACTTGTTGCATCTTT
Found at i:28824216 original size:12 final size:11
Alignment explanation
Indices: 28824197--28824227 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
28824187 AGCAAACATT
28824197 TTTTTCTTTTC
1 TTTTTCTTTTC
28824208 TTTTCTCTTTTC
1 TTTT-TCTTTTC
28824220 TTTTTCTT
1 TTTTTCTT
28824228 ATTTTCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:28827193 original size:15 final size:15
Alignment explanation
Indices: 28827173--28827206 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
28827163 CATAAAATTT
*
28827173 AAAGTGAAACAAGTA
1 AAAGTGAAACAAATA
28827188 AAAGTGAAACAAATA
1 AAAGTGAAACAAATA
28827203 AAAG
1 AAAG
28827207 AAAATGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.18, T:0.12
Consensus pattern (15 bp):
AAAGTGAAACAAATA
Found at i:28834754 original size:2 final size:2
Alignment explanation
Indices: 28834747--28834803 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
28834737 GAAGGGAAAA
28834747 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
28834789 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
28834804 CTTTTATCAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:28836130 original size:38 final size:38
Alignment explanation
Indices: 28836035--28836138 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 38
28836025 ATACTACTAT
*
28836035 AAATAAAAT-ATAATTTTATTATATTAAAAACACAAAA
1 AAATAAAATAAAAATTTTATTATATTAAAAACACAAAA
* *
28836072 AAATAAAATAAAAATATTATTATATTAAAAACACAAAT
1 AAATAAAATAAAAATTTTATTATATTAAAAACACAAAA
* *** *
28836110 AAATATAATAATTGTTTTATTGTATTAAA
1 AAATAAAATAAAAATTTTATTATATTAAA
28836139 TATAATTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
37 9 0.16
38 48 0.84
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.36
Consensus pattern (38 bp):
AAATAAAATAAAAATTTTATTATATTAAAAACACAAAA
Found at i:28836262 original size:21 final size:22
Alignment explanation
Indices: 28836236--28836284 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
28836226 GGCTTTGTGG
28836236 TTTAATATAAAT-ATATAAT-TA
1 TTTAATATAAATAAT-TAATATA
*
28836257 TTTAATATATATAATTAATATA
1 TTTAATATAAATAATTAATATA
28836279 TTTAAT
1 TTTAAT
28836285 TTAGTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 15 0.60
22 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTAATATAAATAATTAATATA
Found at i:28836283 original size:22 final size:21
Alignment explanation
Indices: 28836236--28836303 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
28836226 GGCTTTGTGG
*
28836236 TTTAATATAAATATATAAT-TA
1 TTTAATATATATAT-TAATATA
28836257 TTTAATATATATAATTAATATA
1 TTTAATATATAT-ATTAATATA
*
28836279 TTTAATTTAGTAT-TATAATATA
1 TTTAATATA-TATAT-TAATATA
28836301 TTT
1 TTT
28836304 GGGTCAAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 16 0.39
22 22 0.54
23 3 0.07
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (21 bp):
TTTAATATATATATTAATATA
Found at i:28837532 original size:31 final size:35
Alignment explanation
Indices: 28837497--28837573 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
28837487 AAATAAAAAA
28837497 TAATTTAATAATTAT-CT-TA-AT-AATATTTTAT
1 TAATTTAATAATTATACTGTAGATAAATATTTTAT
* *
28837528 TAATTTAATATTTATATTGTAGATAAATATTTTAT
1 TAATTTAATAATTATACTGTAGATAAATATTTTAT
28837563 TAATTTAATAA
1 TAATTTAATAA
28837574 AATTTAATCT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 14 0.36
32 1 0.03
33 2 0.05
34 2 0.05
35 20 0.51
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TAATTTAATAATTATACTGTAGATAAATATTTTAT
Found at i:28837535 original size:19 final size:19
Alignment explanation
Indices: 28837513--28837578 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
28837503 AATAATTATC
28837513 TTAATAATATTTTATTAA-
1 TTAATAATATTTTATTAAT
28837531 TT--TAATA-TTTA-T-AT
1 TTAATAATATTTTATTAAT
28837545 TGTAGATAAATATTTTATTAAT
1 T-TA-AT-AATATTTTATTAAT
*
28837567 TTAATAAAATTT
1 TTAATAATATTT
28837579 AATCTAATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 17
0.68 0.02 0.30
Matches are distributed among these distances:
13 1 0.03
14 2 0.05
15 5 0.13
16 5 0.13
18 3 0.08
19 10 0.26
20 6 0.16
21 3 0.08
22 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TTAATAATATTTTATTAAT
Found at i:28837581 original size:50 final size:47
Alignment explanation
Indices: 28837527--28837619 Score: 123
Period size: 47 Copynumber: 1.9 Consensus size: 47
28837517 TAATATTTTA
* * *
28837527 TTAATTTAATATTTATATTGTAGATAAATATTTTATTAATTTAATAAAAT
1 TTAATCTAATATTTAT-CT-TA-ATAAATATTATATTAATTTAATAAAAT
*
28837577 TTAATCTAATATTTATCTTAATAAGTATTATATTAATTTAATA
1 TTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
28837620 TTAAAGTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
47 21 0.54
48 2 0.05
49 1 0.03
50 15 0.38
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (47 bp):
TTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATAAAAT
Found at i:28840160 original size:15 final size:15
Alignment explanation
Indices: 28840140--28840172 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28840130 GTCTCTCTAA
28840140 TTCTCATAAATTTAT
1 TTCTCATAAATTTAT
28840155 TTCTCATAAATTTAT
1 TTCTCATAAATTTAT
28840170 TTC
1 TTC
28840173 ATGTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCTCATAAATTTAT
Found at i:28840221 original size:19 final size:20
Alignment explanation
Indices: 28840176--28840221 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
28840166 TTATTTCATG
28840176 TTAATTTCTTTTTGAATCATT
1 TTAATTTCTTTTTGAAT-ATT
*
28840197 TT-ATTTCTTTTTGTAT-TT
1 TTAATTTCTTTTTGAATATT
28840215 TTAATTT
1 TTAATTT
28840222 TTAATACATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 13 0.57
21 2 0.09
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.70
Consensus pattern (20 bp):
TTAATTTCTTTTTGAATATT
Found at i:28840243 original size:28 final size:26
Alignment explanation
Indices: 28840212--28840280 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
28840202 TCTTTTTGTA
28840212 TTTTTAATTTTTAATACATATATTTT
1 TTTTTAATTTTTAATACATATATTTT
* * **
28840238 GGTTTTTTATTTATAATTTATATATTTT
1 --TTTTTAATTTTTAATACATATATTTT
28840266 TTTTTATATTTTTAA
1 TTTTTA-ATTTTTAA
28840281 ATCACTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
26 5 0.15
27 7 0.21
28 22 0.65
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTTTAATTTTTAATACATATATTTT
Found at i:28840828 original size:13 final size:13
Alignment explanation
Indices: 28840805--28840836 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
28840795 ATATGCATGA
28840805 TAAATACAAATATC
1 TAAA-ACAAATATC
28840819 TAAAACAAATATC
1 TAAAACAAATATC
28840832 TAAAA
1 TAAAA
28840837 ATTCAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (13 bp):
TAAAACAAATATC
Found at i:28844385 original size:31 final size:30
Alignment explanation
Indices: 28844315--28844385 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
28844305 CGATTACATT
* *
28844315 TAACAAAACAGTCACTCAACTTTGAAAATG
1 TAACAAAACAGTCACTAAAATTTGAAAATG
28844345 TAACAAAACAGTCACTAAAATTATCGAAAA-G
1 TAACAAAACAGTCACTAAAATT-T-GAAAATG
*
28844376 TGACAAAACA
1 TAACAAAACA
28844386 ATCCTTTGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 20 0.56
31 11 0.31
32 5 0.14
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (30 bp):
TAACAAAACAGTCACTAAAATTTGAAAATG
Found at i:28845246 original size:30 final size:31
Alignment explanation
Indices: 28845178--28845249 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
28845168 AAGCCAATAA
*
28845178 GATTGTTTTGTCACTTTTCGATAACTTTAGT
1 GATTGTTTTGTCACTTTTCGATAACTTGAGT
* *
28845209 GACTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GATTGTTTTGTCAC-TTTTCGATAACTTGAGT
28845239 GATTGTTTTGT
1 GATTGTTTTGT
28845250 TAAATGTAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 17 0.47
31 14 0.39
32 5 0.14
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.50
Consensus pattern (31 bp):
GATTGTTTTGTCACTTTTCGATAACTTGAGT
Found at i:28847020 original size:14 final size:14
Alignment explanation
Indices: 28847001--28847031 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28846991 GAATTTCTAA
28847001 TTATTCGAATCGAG
1 TTATTCGAATCGAG
28847015 TTATTCGAATCGAG
1 TTATTCGAATCGAG
28847029 TTA
1 TTA
28847032 AATTTTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (14 bp):
TTATTCGAATCGAG
Found at i:28847324 original size:42 final size:42
Alignment explanation
Indices: 28847246--28847329 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
28847236 CAAATATTTT
*
28847246 TAAACCCAAATATAATTTCATTCTTCAAAAACACTTATAAAC
1 TAAACCCAAATATAATTTCATTCCTCAAAAACACTTATAAAC
*
28847288 TAAACCCAAATATAATTGT-ATTCCT-AAATAATACTTATAAAC
1 TAAACCCAAATATAATT-TCATTCCTCAAA-AACACTTATAAAC
28847330 AACTCCTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 34 0.89
43 1 0.03
ACGTcount: A:0.48, C:0.19, G:0.01, T:0.32
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTCAAAAACACTTATAAAC
Found at i:28848163 original size:32 final size:32
Alignment explanation
Indices: 28848084--28848163 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 32
28848074 TAAATTACCT
*
28848084 ATATATAAA-ATTTTAATATTTTAATGAATGAA
1 ATATATAAATATTTTAA-ATTTTAATGAATAAA
* **
28848116 ATATAT-AAT-TATTAAATTTTAAT-TTTAAA
1 ATATATAAATATTTTAAATTTTAATGAATAAA
28848145 ATAATATAAATATTTTAAA
1 AT-ATATAAATATTTTAAA
28848164 AAATAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
29 5 0.13
30 12 0.31
31 10 0.26
32 12 0.31
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (32 bp):
ATATATAAATATTTTAAATTTTAATGAATAAA
Found at i:28848175 original size:19 final size:19
Alignment explanation
Indices: 28848137--28848172 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28848127 TTAAATTTTA
*
28848137 ATTTTAAAATAATATAAAT
1 ATTTTAAAATAATAAAAAT
28848156 ATTTTAAAA-AATAAAAA
1 ATTTTAAAATAATAAAAA
28848173 ATAATATGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTTTAAAATAATAAAAAT
Found at i:28851129 original size:41 final size:41
Alignment explanation
Indices: 28851063--28851272 Score: 296
Period size: 41 Copynumber: 5.1 Consensus size: 41
28851053 TATGCTCTAC
* **
28851063 CGAGTCATAAGTCTTCCTTTAAATATAATCTCATGCTCATCC
1 CGAGTCACAAGTCTTCCTTT-AATATAATCTCATGCTCATTT
*
28851105 CGAGTCACGAGTCTTCCTTTAATATAATCTCATGCTCATTT
1 CGAGTCACAAGTCTTCCTTTAATATAATCTCATGCTCATTT
* ** *
28851146 TGAGTCATTAGTCTTCCTTTAATATAACCTCATGCTCATTT
1 CGAGTCACAAGTCTTCCTTTAATATAATCTCATGCTCATTT
*
28851187 CGAGTCACAAGTCTTCATTTAATATAATCTCAT-CTTCATTT
1 CGAGTCACAAGTCTTCCTTTAATATAATCTCATGC-TCATTT
* *
28851228 CGAGTCACAAGTTTTCCTTTAATATAATCTCATGCTCATCT
1 CGAGTCACAAGTCTTCCTTTAATATAATCTCATGCTCATTT
28851269 CGAG
1 CGAG
28851273 ACATGAGTCT
Statistics
Matches: 150, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
40 1 0.01
41 130 0.87
42 19 0.13
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (41 bp):
CGAGTCACAAGTCTTCCTTTAATATAATCTCATGCTCATTT
Found at i:28851245 original size:123 final size:124
Alignment explanation
Indices: 28851063--28851285 Score: 333
Period size: 123 Copynumber: 1.8 Consensus size: 124
28851053 TATGCTCTAC
* * *
28851063 CGAGTCATAAGTCTTCCTTTAAATATAATCTCATGCTCATCCCGAGTCACGAGTCTTCCTTTAAT
1 CGAGTCACAAGTCTTCATTTAAATATAATCTCATGCTCATCCCGAGTCACAAGTCTTCCTTTAAT
* * * *
28851128 ATAATCTCATGCTCATTTTGAGTCATTAGTCTTCCTTTAATATAACCTCATGCTCATTT
66 ATAATCTCATGCTCATCTCGAGACATGAGTCTTCCTTTAATATAACCTCATGCTCATTT
** *
28851187 CGAGTCACAAGTCTTCATTT-AATATAATCTCAT-CTTCATTTCGAGTCACAAGTTTTCCTTTAA
1 CGAGTCACAAGTCTTCATTTAAATATAATCTCATGC-TCATCCCGAGTCACAAGTCTTCCTTTAA
28851250 TATAATCTCATGCTCATCTCGAGACATGAGTCTTCC
65 TATAATCTCATGCTCATCTCGAGACATGAGTCTTCC
28851286 ATATATACAT
Statistics
Matches: 88, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
122 1 0.01
123 69 0.78
124 18 0.20
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (124 bp):
CGAGTCACAAGTCTTCATTTAAATATAATCTCATGCTCATCCCGAGTCACAAGTCTTCCTTTAAT
ATAATCTCATGCTCATCTCGAGACATGAGTCTTCCTTTAATATAACCTCATGCTCATTT
Found at i:28854073 original size:21 final size:21
Alignment explanation
Indices: 28854039--28854078 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28854029 TACCCTGTAC
*
28854039 TTCTACCGATACAACCATGGG
1 TTCTACCGAAACAACCATGGG
* *
28854060 TTCTATCGAAACAAGCATG
1 TTCTACCGAAACAACCATG
28854079 CAGAATTCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (21 bp):
TTCTACCGAAACAACCATGGG
Found at i:28860965 original size:23 final size:22
Alignment explanation
Indices: 28860910--28860965 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
28860900 CTCAAACAAG
* *
28860910 TAATTCAAGTTTTAAGTTCGAA
1 TAATTCAAATTTTAAATTCGAA
28860932 TCAAGTT-AAATTTTACAATTCGAA
1 T-AA-TTCAAATTTTA-AATTCGAA
28860956 TAATTCAAAT
1 TAATTCAAAT
28860966 AATTCGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 3 0.11
23 15 0.54
24 10 0.36
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (22 bp):
TAATTCAAATTTTAAATTCGAA
Found at i:28861121 original size:10 final size:10
Alignment explanation
Indices: 28861108--28861161 Score: 51
Period size: 10 Copynumber: 5.7 Consensus size: 10
28861098 TTTTTAAATG
28861108 TTTATAAAAA
1 TTTATAAAAA
28861118 TTTATAAAAA
1 TTTATAAAAA
*
28861128 -TT-TCAAAA
1 TTTATAAAAA
* *
28861136 TTTATATATA
1 TTTATAAAAA
28861146 TTT-TAAAAA
1 TTTATAAAAA
*
28861155 ATTATAA
1 TTTATAA
28861162 TTTTTTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
8 5 0.15
9 10 0.29
10 19 0.56
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:28861130 original size:38 final size:38
Alignment explanation
Indices: 28861064--28861161 Score: 92
Period size: 38 Copynumber: 2.6 Consensus size: 38
28861054 AAATAATTCA
* ** *
28861064 AAATAATTTTCAAAAATTCA-AAATAATTTTTAAATTTTT
1 AAAT-ATTTT-AAAAATTTATAAATAATTTCAAAATTTAT
*
28861103 AAATGTTTATAAAAATTTATAAA-AATTTCAAAATTTAT
1 AAATATTT-TAAAAATTTATAAATAATTTCAAAATTTAT
* *
28861141 ATATATTTTAAAAAATTATAA
1 AAATATTTTAAAAATTTATAA
28861162 TTTTTTTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
37 12 0.24
38 29 0.59
39 8 0.16
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (38 bp):
AAATATTTTAAAAATTTATAAATAATTTCAAAATTTAT
Found at i:28861154 original size:19 final size:19
Alignment explanation
Indices: 28861112--28861176 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
28861102 TAAATGTTTA
* *
28861112 TAAAAATTTATA-AAAATT
1 TAAAAATTTATATATATTT
*
28861130 TCAAAATTTATATATATTT
1 TAAAAATTTATATATATTT
* * *
28861149 TAAAAAATTATAATTTTTTT
1 TAAAAATTTAT-ATATATTT
28861169 TAAAAATT
1 TAAAAATT
28861177 CTAAAGATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
18 11 0.30
19 13 0.35
20 13 0.35
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TAAAAATTTATATATATTT
Found at i:28863115 original size:59 final size:57
Alignment explanation
Indices: 28862864--28863165 Score: 252
Period size: 59 Copynumber: 5.1 Consensus size: 57
28862854 GCGGCCATTG
* *
28862864 CATGACCGACACCCCTTTTAATCTGATAAAAAAAATC-AATTTTTTGGGTGTTAGCCATGT
1 CATGACCGACACCCCTTTTTATCTGAT--AAAAAATCAAATTTTTT-GGTGTT-GCCATGC
* * * * * * *
28862924 AATGATCGATA-CCCTATTCATCTGATAAAAAATCAAAATTTTTGGTGTTGGTCATGC
1 CATGACCGACACCCCTTTTTATCTGATAAAAAATCAAATTTTTTGGTGTT-GCCATGC
* * * *
28862981 AATGACCGACA-CCCTTTTTTTCAGATAAAAAAATTTCAATATTTTTTGGTGTTGATCATTG-
1 CATGACCGACACCCCTTTTTATCTGAT-AAAAAA--TCAA-ATTTTTTGGTGTTG-CCA-TGC
**
28863042 CATGGGCGACACCCCTTTTTATCTGAATAAAAAATCAAATTTTTTGGTGTTAGCCATGC
1 CATGACCGACACCCCTTTTTATCTG-ATAAAAAATCAAATTTTTTGGTGTT-GCCATGC
* * * *
28863101 CATGGCCGACACCCCTTTTTGTCAGATAAAAAATTCGAATTTTTTTTGGTGTTGACCATGC
1 CATGACCGACACCCCTTTTTATCTGATAAAAAA-TC-AA-ATTTTTTGGTGTTG-CCATGC
28863162 CATG
1 CATG
28863166 CCATTGCATG
Statistics
Matches: 201, Mismatches: 26, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
57 39 0.19
58 23 0.11
59 52 0.26
60 21 0.10
61 45 0.22
62 19 0.09
63 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (57 bp):
CATGACCGACACCCCTTTTTATCTGATAAAAAATCAAATTTTTTGGTGTTGCCATGC
Found at i:28863304 original size:60 final size:56
Alignment explanation
Indices: 28863232--28863409 Score: 180
Period size: 60 Copynumber: 3.0 Consensus size: 56
28863222 TAATTCAGAT
* * *
28863232 AAAA-AGGAGTGTCGGCCATGCAATGGTCAATATCAAAAAAATTTGAAATTTTTTATCTG
1 AAAATAGGGGTGTCGGCCATGC-ATGGCCAACA-CAAAAAAA-TTG-AATTTTTTATCTG
* *
28863291 AAAATAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTGATTTTTTTAATCAG
1 AAAATAGGGGTGTCGGCCA-TGCATGGCCAACAC-AAAAAAATTGAATTTTTT-ATCTG
* *
28863350 ATAAAT-GGAGGTGTCGACCATGGCATGGCCAACACCAAAAAAATTGAATTTTTAATCTG
1 A-AAATAGG-GGTGTCGGCCAT-GCATGGCCAACA-CAAAAAAATTGAATTTTTTATCTG
28863409 A
1 A
28863410 CAAACCCAAA
Statistics
Matches: 102, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
58 7 0.07
59 21 0.21
60 70 0.69
61 4 0.04
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (56 bp):
AAAATAGGGGTGTCGGCCATGCATGGCCAACACAAAAAAATTGAATTTTTTATCTG
Found at i:28864716 original size:25 final size:26
Alignment explanation
Indices: 28864688--28864751 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
28864678 AAATTAAACA
* *
28864688 AAATAAATTTTTTGTTAT-AAAAATT
1 AAATAAAATTTTTATTATAAAAAATT
28864713 AAATAAAATTTTTATTATAAAAAATT
1 AAATAAAATTTTTATTATAAAAAATT
28864739 AATATAAAATTTT
1 AA-ATAAAATTTT
28864752 AAATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 16 0.46
26 9 0.26
27 10 0.29
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AAATAAAATTTTTATTATAAAAAATT
Found at i:28864972 original size:16 final size:16
Alignment explanation
Indices: 28864927--28864976 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
28864917 TAAATCAAGC
*
28864927 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
28864943 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
28864957 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
28864973 TAAT
1 TAAT
28864977 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:28865915 original size:6 final size:6
Alignment explanation
Indices: 28865904--28865930 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28865894 CCTTACAACT
28865904 AAACAA AAACAA AAACAA AAACAA AAA
1 AAACAA AAACAA AAACAA AAACAA AAA
28865931 GGGCCCTCTC
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAA
Found at i:28875664 original size:3 final size:3
Alignment explanation
Indices: 28875656--28875680 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28875646 CCAGCCATTC
28875656 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
28875681 TTCAATTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:28876912 original size:57 final size:58
Alignment explanation
Indices: 28876807--28876926 Score: 131
Period size: 57 Copynumber: 2.1 Consensus size: 58
28876797 TTAATGTAAT
* * *
28876807 ATTTCATATATTTTTTAATTTGATATTTAAATTATTTTTAATCCAATTTCG-TATTTAA
1 ATTTAATATATTTTTTAATTTGATATCTAAATTATTTTTAATCCAATTT-GATATCTAA
* **
28876865 ATTTAATAT-TTTTTTAATTTGGTATCT-AATT-TTCTTTATATTTAATTTGATATCTAA
1 ATTTAATATATTTTTTAATTTGATATCTAAATTATT-TTTA-ATCCAATTTGATATCTAA
28876922 ATTTA
1 ATTTA
28876927 TTAAATATTA
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
55 2 0.04
56 9 0.17
57 34 0.64
58 8 0.15
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (58 bp):
ATTTAATATATTTTTTAATTTGATATCTAAATTATTTTTAATCCAATTTGATATCTAA
Found at i:28876934 original size:29 final size:28
Alignment explanation
Indices: 28876877--28876935 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
28876867 TTAATATTTT
* * * *
28876877 TTTAATTTGGTATCTAATTTTCTTTATA
1 TTTAATTTGATATCTAAATTTATTAATA
28876905 TTTAATTTGATATCTAAATTTATTAAATA
1 TTTAATTTGATATCTAAATTTATT-AATA
28876934 TT
1 TT
28876936 ATAAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 21 0.81
29 5 0.19
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTAATTTGATATCTAAATTTATTAATA
Found at i:28877122 original size:28 final size:28
Alignment explanation
Indices: 28877071--28877181 Score: 109
Period size: 28 Copynumber: 3.9 Consensus size: 28
28877061 AAAAAATAGA
*
28877071 TACCAAATTAAAAAAAAATTAAATTTAAG
1 TACCAAATT-AAAAAAAATCAAATTTAAG
*
28877100 TACCAAATTAAAAAAAATCAAATTTGAG
1 TACCAAATTAAAAAAAATCAAATTTAAG
* * * *
28877128 TATCAAATTAAATTAAAA--AATTTTAAT
1 TACCAAATTAAA-AAAAATCAAATTTAAG
28877155 TACCAAATTTAAAAATAATATCAAATT
1 TACCAAA-TTAAAAA-AA-ATCAAATT
28877182 CATATACCAA
Statistics
Matches: 66, Mismatches: 10, Indels: 10
0.77 0.12 0.12
Matches are distributed among these distances:
27 13 0.20
28 35 0.53
29 14 0.21
31 4 0.06
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.32
Consensus pattern (28 bp):
TACCAAATTAAAAAAAATCAAATTTAAG
Found at i:28877698 original size:16 final size:15
Alignment explanation
Indices: 28877679--28877727 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
28877669 ATAAAATGAA
28877679 AATATATAAAAATATT
1 AATAT-TAAAAATATT
* *
28877695 AATATTAAATAAAAAT
1 AATATTAAA-AATATT
*
28877711 AATATTAAAAATTTT
1 AATATTAAAAATATT
28877726 AA
1 AA
28877728 AAAAAGTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
15 9 0.33
16 18 0.67
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATTAAAAATATT
Found at i:28877699 original size:29 final size:31
Alignment explanation
Indices: 28877667--28877727 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
28877657 GTTTGCTTAT
*
28877667 ATATAAAATGAAAAT-ATA-TAAAAATATTA
1 ATATAAAATAAAAATAATATTAAAAATATTA
* *
28877696 ATATTAAATAAAAATAATATTAAAAATTTTA
1 ATATAAAATAAAAATAATATTAAAAATATTA
28877727 A
1 A
28877728 AAAAAGTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
30 3 0.11
31 11 0.41
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (31 bp):
ATATAAAATAAAAATAATATTAAAAATATTA
Found at i:28877914 original size:80 final size:80
Alignment explanation
Indices: 28877828--28877984 Score: 242
Period size: 80 Copynumber: 2.0 Consensus size: 80
28877818 TTTTTCAATT
** * * * *
28877828 TTGTCTTTTTTGGTCAACCAACTATTTTGGATTTTTGGGTGTTTTTATTTTTAAATTAGTTAAAA
1 TTGTCTTTTTTAATCAACCAACTATATTGGATTTTTGGGTGTTTCTATATTTAAATTAGTCAAAA
28877893 AAGATAAAATTGCAA
66 AAGATAAAATTGCAA
* *
28877908 TTGTCTTTTTTAATCACCCAACTATATTGGATTTTTGGGTGTTTCTATATTTACATTAGTCAAAA
1 TTGTCTTTTTTAATCAACCAACTATATTGGATTTTTGGGTGTTTCTATATTTAAATTAGTCAAAA
28877973 AAGATAAAATTG
66 AAGATAAAATTG
28877985 AATAGTTGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.46
Consensus pattern (80 bp):
TTGTCTTTTTTAATCAACCAACTATATTGGATTTTTGGGTGTTTCTATATTTAAATTAGTCAAAA
AAGATAAAATTGCAA
Found at i:28881223 original size:24 final size:24
Alignment explanation
Indices: 28881195--28881245 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
28881185 CATTTTACTC
*
28881195 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
28881219 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
28881243 AAA
1 AAA
28881246 GATTATTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.57, C:0.10, G:0.12, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:28883453 original size:16 final size:17
Alignment explanation
Indices: 28883434--28883469 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28883424 GCTTTAGAGA
28883434 ATATG-CCAAAATATTC
1 ATATGTCCAAAATATTC
28883450 ATATGTCCAAAATATTC
1 ATATGTCCAAAATATTC
28883467 ATA
1 ATA
28883470 ATTGTTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (17 bp):
ATATGTCCAAAATATTC
Found at i:28884537 original size:443 final size:443
Alignment explanation
Indices: 28883711--28884595 Score: 1635
Period size: 443 Copynumber: 2.0 Consensus size: 443
28883701 CAATCCAATA
* **
28883711 AAAATTTATTGATAGCAAACTTTGAGAGTGAATCTTATTTTTTAAGTGTACAACAGGTACATAAC
1 AAAATTTATTAATAGCAAACTTTGAGAGTGAATCTTATTTTCCAAGTGTACAACAGGTACATAAC
28883776 CAATAACTTTTCACGCATAAGTTGTCTCTCTTCTTAAATAGTTCTTGGAAATTTTTGGTCTTTTC
66 CAATAACTTTTCACGCATAAGTTGTCTCTCTTCTTAAATAGTTCTTGGAAATTTTTGGTCTTTTC
28883841 TTACTTTCTTCATTTTTTCACTTTTGGTGGCGAGAAAAATTATCATGACCATCCCCGATGACTAT
131 TTACTTTCTTCATTTTTTCACTTTTGGTGGCGAGAAAAATTATCATGACCATCCCCGATGACTAT
*
28883906 TATTATAGTCCAATTTACTACATCCATGTCAAAGATTATGTCATTCGAATTTATCATATAATGTT
196 TATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCATTCGAATTTATCATATAATGTT
28883971 ACATTCTCTTCAGGGAATGATTAGGTTTCCTGGTTAAAAACTTTTATTCAACAATAAGTAAATTT
261 ACATTCTCTTCAGGGAATGATTAGGTTTCCTGGTTAAAAACTTTTATTCAACAATAAGTAAATTT
* *
28884036 TTTTTATGATATTGCTACTGTAAGAACACATTTGAATCATGAAAAGTTGAATAAGTTCTCTCTTG
326 TTTTCATGATATTGCTACTATAAGAACACATTTGAATCATGAAAAGTTGAATAAGTTCTCTCTTG
* *
28884101 CAAGGTTCTCATCAGTAATATTTTTTCATGTAATTTTAATTAAGAATTTATTG
391 CAAGGTTCTCATCAGTAATATTTTTCCATGTAATTTTAACTAAGAATTTATTG
*
28884154 AAAATTTATTAATAGCAAACTTTGAGAGTGAATCTTATTTTCCAAGTGTACAGCAGGTACATAAC
1 AAAATTTATTAATAGCAAACTTTGAGAGTGAATCTTATTTTCCAAGTGTACAACAGGTACATAAC
28884219 CAATAACTTTTCACGCATAAGTTGTCTCTCTTCTTAAATAGTTCTTGGAAATTTTTGGTCTTTTC
66 CAATAACTTTTCACGCATAAGTTGTCTCTCTTCTTAAATAGTTCTTGGAAATTTTTGGTCTTTTC
* *
28884284 TTACTTTTTTCATTTTTTCACTTTTGGTGGTGAGAAAAATTATCATGACCATCCCCGATGACTAT
131 TTACTTTCTTCATTTTTTCACTTTTGGTGGCGAGAAAAATTATCATGACCATCCCCGATGACTAT
28884349 TATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCATTCGAATTTATCATATAATGTT
196 TATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCATTCGAATTTATCATATAATGTT
28884414 ACATTCTCTTCAGGGAATGATTAGGTTTCCTGGTTAAAAACTTTTATTCAACAATAAGTAAATTT
261 ACATTCTCTTCAGGGAATGATTAGGTTTCCTGGTTAAAAACTTTTATTCAACAATAAGTAAATTT
* *
28884479 TTTTCATGATATTGCTACTATAGGAACACATTTGAATCATTAAAAGTTGAATAAGTTCTCTCTTG
326 TTTTCATGATATTGCTACTATAAGAACACATTTGAATCATGAAAAGTTGAATAAGTTCTCTCTTG
* *
28884544 CAAGGTTCTCATTAGTAATATTTTTCCATGTAATTTTAACTGAGAATTTATT
391 CAAGGTTCTCATCAGTAATATTTTTCCATGTAATTTTAACTAAGAATTTATT
28884596 TTGAATATTG
Statistics
Matches: 427, Mismatches: 15, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
443 427 1.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (443 bp):
AAAATTTATTAATAGCAAACTTTGAGAGTGAATCTTATTTTCCAAGTGTACAACAGGTACATAAC
CAATAACTTTTCACGCATAAGTTGTCTCTCTTCTTAAATAGTTCTTGGAAATTTTTGGTCTTTTC
TTACTTTCTTCATTTTTTCACTTTTGGTGGCGAGAAAAATTATCATGACCATCCCCGATGACTAT
TATTATAGTCCAATTTACTACATCCATGTCAAAGATTATATCATTCGAATTTATCATATAATGTT
ACATTCTCTTCAGGGAATGATTAGGTTTCCTGGTTAAAAACTTTTATTCAACAATAAGTAAATTT
TTTTCATGATATTGCTACTATAAGAACACATTTGAATCATGAAAAGTTGAATAAGTTCTCTCTTG
CAAGGTTCTCATCAGTAATATTTTTCCATGTAATTTTAACTAAGAATTTATTG
Found at i:28886239 original size:20 final size:20
Alignment explanation
Indices: 28886214--28886267 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
28886204 AGTCTTCAAG
28886214 GTATCGGTAGAAGTAGAGTT
1 GTATCGGTAGAAGTAGAGTT
*
28886234 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTAGAGTT
* * *
28886254 CTACCGATAGAAGT
1 GTATCGGTAGAAGT
28886268 CTCACTGGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.09, G:0.33, T:0.28
Consensus pattern (20 bp):
GTATCGGTAGAAGTAGAGTT
Found at i:28899053 original size:2 final size:2
Alignment explanation
Indices: 28899046--28899097 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
28899036 TCGTATATTC
28899046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28899088 AT AT AT AT AT
1 AT AT AT AT AT
28899098 CTTTTATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28905191 original size:9 final size:9
Alignment explanation
Indices: 28905166--28905215 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
28905156 AATTTCACCC
28905166 AAAAAAG-A
1 AAAAAAGAA
*
28905174 AAAAGAGAA
1 AAAAAAGAA
28905183 AAAAAAGAA
1 AAAAAAGAA
*
28905192 AGAAAAGAA
1 AAAAAAGAA
28905201 AGGAAAAAGAA
1 A--AAAAAGAA
28905212 AAAA
1 AAAA
28905216 GAAAAAGGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 6 0.17
9 21 0.60
11 8 0.23
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:28905199 original size:20 final size:21
Alignment explanation
Indices: 28905169--28905212 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28905159 TTCACCCAAA
28905169 AAAGAAAAAGAGAA-AAAAAAG
1 AAAGAAAAAGA-AAGAAAAAAG
*
28905190 AAAG-AAAAGAAAGGAAAAAG
1 AAAGAAAAAGAAAGAAAAAAG
28905210 AAA
1 AAA
28905213 AAAGAAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 15 0.71
21 4 0.19
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAGAAAGAAAAAAG
Found at i:28905220 original size:13 final size:13
Alignment explanation
Indices: 28905166--28905222 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 13
28905156 AATTTCACCC
28905166 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
*
28905179 AGAAAAAAAAGAAAG
1 A-AAAAAGAA-AAAG
28905194 AAAAGAAAGGAAAAAG
1 -AAA-AAA-GAAAAAG
28905210 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
28905223 GAGAGGTCGA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 8 0.22
14 10 0.27
15 9 0.24
16 8 0.22
17 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:28905222 original size:20 final size:19
Alignment explanation
Indices: 28905166--28905224 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 19
28905156 AATTTCACCC
28905166 AAAAAAGAAAAAGAGAAAAA
1 AAAAAAGAAAAAG-GAAAAA
28905186 AAAGAAAGAAAAGAAAGGAAAAA
1 AAA-AAAG--AA-AAAGGAAAAA
28905209 GAAAAAAGAAAAAGGA
1 -AAAAAAGAAAAAGGA
28905225 GAGGTCGAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
20 9 0.26
21 6 0.18
23 12 0.35
24 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAAGAAAAAGGAAAAA
Found at i:28906326 original size:49 final size:49
Alignment explanation
Indices: 28906180--28906771 Score: 624
Period size: 49 Copynumber: 12.1 Consensus size: 49
28906170 TTGAATCATG
* *
28906180 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCACAAC-AGGGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGA-CGAACCTTA
* * ** * * *
28906229 TACCTTAGAG-CGTGGAGGGAAATATTTAAGCTGCAACGACGAATCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
* * * *
28906277 TACCCTAGAGATATGGACGAAAAGGTTGAAGTCGCAACGACGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
* * * * * *
28906326 TACCCTAGAG-CGTGAAGGGAAAGATTTAAGCCGCAACGATGAATCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
* ** *
28906374 TACCCTAGAGATATAAAGGGAAAGGTTGAAGCCGCAATGACGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
* **
28906423 TACCCTAGAGATGTGGAGGAAAAGGTTGAAGCCGCAACGGTGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
* * *
28906472 TACCTTAGAGATGT-GATGGGAAAGATTGAAGCCGCAATGACGAACCTTA
1 TACCCTAGAGATGTGGA-GGGAAAGGTTGAAGCCGCAACGACGAACCTTA
* * * *
28906521 TACCCTAGAGATGTGGAGGAAAAGGTTAAAGCCGCAATGGCGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
* * * * *
28906570 TACCTTAGAGATGT-GATGGGAAAGATTGAAGCCGCAATGGA-GAATCTTG
1 TACCCTAGAGATGTGGA-GGGAAAGGTTGAAGCCGCAA-CGACGAACCTTA
* * *
28906619 TACCCTAGAGATATGAAGGGAAAGGTTAAAGCCGCAACGACGAACCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
*
28906668 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAA--ATGCAAGCCTTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACG-AA-CCTTA
* * * * * * **
28906717 TACCCTACAGATGTGAAGGGAAAGATTGAAGTCGAAACGATGAATATTA
1 TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
28906766 TACCCT
1 TACCCT
28906772 GAAGATGAAG
Statistics
Matches: 447, Mismatches: 83, Indels: 26
0.80 0.15 0.05
Matches are distributed among these distances:
47 2 0.00
48 83 0.19
49 353 0.79
50 6 0.01
51 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (49 bp):
TACCCTAGAGATGTGGAGGGAAAGGTTGAAGCCGCAACGACGAACCTTA
Found at i:28907143 original size:189 final size:189
Alignment explanation
Indices: 28906885--28907484 Score: 751
Period size: 189 Copynumber: 3.2 Consensus size: 189
28906875 AAGTGAAATA
* * *
28906885 AAGCACCAAAACCCTATACCCCTGAGTTGTAGTAGGTCGAATTAAAATAATGAAGCAGAGCTCAA
1 AAGCACCAAAATCCTATACCCCTGAGTTGTAGTGGGTCAAATTAAAATAATGAAGCAGAGCTCAA
* *
28906950 CATCCTTGAGGTTATAGTGAAGTGGAGTAAGACTTCAAATCCCATCTTCCTGGTGAGGTATAGAG
66 CATCCTTGAGGTTATAGTGGAGTGGAGTAAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAG
* * * * *
28907015 AAGTGGGTTAAAACAGGTCGTAGATCTTAAGGTCCCTGAGGTTACATTGGAGTGGAGTG
131 AAGTGGGTTAAAATAGGTCGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTG
** * *
28907074 AAGCGTCAAAATCTTATACCCCTGAGTTGTAGTGGGTCAAATTAAAACAACT-AAGCAGAGCTCA
1 AAGCACCAAAATCCTATACCCCTGAGTTGTAGTGGGTCAAATTAAAATAA-TGAAGCAGAGCTCA
* *
28907138 ACATCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGA
65 ACATCCTTGAGGTTATAGTGGAGTGGAGTAAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGA
* * * *
28907203 GACA-TGGGTTAAAATAGG-CAGCAGATCTCAATGTCCTTGAGGTTACAGTGAAGTGGAATG
130 GA-AGTGGGTTAAAATAGGTC-GCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTG
* * * ** * * *
28907263 AAGCACCAGATTCCTATACCCCTGATTTACAGTGGTTCAAATAAAAATAATGAAGCAAAGCTCAA
1 AAGCACCAAAATCCTATACCCCTGAGTTGTAGTGGGTCAAATTAAAATAATGAAGCAGAGCTCAA
* * * * * *
28907328 C-TCCCTGAGGTTATAATGGAGTGGAGTAAGACTTCAAATCTCATTTTCCTAGTG-GTGTACATA
66 CATCCTTGAGGTTATAGTGGAGTGGAGTAAGACTTCAAATCCCATCTTCCTGGTGAG-GTACAGA
* * * * * * *
28907391 GAAGTGTGTTAAAATAGGTAGCAGATCTCAACGTCTCTAAAGTTACAGTAGAGTAGAGTG
130 GAAGTGGGTTAAAATAGGTCGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTG
28907451 AAGCACCAAAATCCTATACCCACTGAGTTGTAGT
1 AAGCACCAAAATCCTATACCC-CTGAGTTGTAGT
28907485 AAGTCAGATG
Statistics
Matches: 348, Mismatches: 55, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
187 2 0.01
188 119 0.34
189 225 0.65
190 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (189 bp):
AAGCACCAAAATCCTATACCCCTGAGTTGTAGTGGGTCAAATTAAAATAATGAAGCAGAGCTCAA
CATCCTTGAGGTTATAGTGGAGTGGAGTAAGACTTCAAATCCCATCTTCCTGGTGAGGTACAGAG
AAGTGGGTTAAAATAGGTCGCAGATCTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTG
Found at i:28907248 original size:95 final size:95
Alignment explanation
Indices: 28906938--28907259 Score: 257
Period size: 95 Copynumber: 3.4 Consensus size: 95
28906928 AAAATAATGA
* *
28906938 AGCAGAGCTCAACATCCTTGAGGTTATAGTGAAGTGGAGTAAGACTTCAAATCCCATCTTCCTGG
1 AGCAGAGCTCAACATCCTTGAGGTTACAGTGAAGTGGAGTGAGACTTCAAATCCCATCTTCCTGG
*
28907003 TGAGGTATAGAGA-AGTGGGTTAAAACAGGTC
66 TGAGGTACAGAGACA-TGGGTTAAAACAGG-C
* * * ** * * * * ** *
28907034 -GTAGATCTTAAGGTCCCTGAGGTTACATTGGAGTGGAGTGA-AGCGTCAAAATCTTATAC-CCC
1 AGCAGAGCTCAACATCCTTGAGGTTACAGTGAAGTGGAGTGAGA-CTTC-AAATCCCAT-CTTCC
* ** * * ** *
28907096 TGAGT--TGTAGTGGGTCA--AATTAAAACA-AC
63 TG-GTGAGGTACAGAGACATGGGTTAAAACAGGC
*
28907125 TAAGCAGAGCTCAACATCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCATCTTCCT
1 --AGCAGAGCTCAACATCCTTGAGGTTACAGTGAAGTGGAGTGAGACTTCAAATCCCATCTTCCT
*
28907190 GGTGAGGTACAGAGACATGGGTTAAAATAGGC
64 GGTGAGGTACAGAGACATGGGTTAAAACAGGC
* **
28907222 AGCAGATCTCAATGTCCTTGAGGTTACAGTGAAGTGGA
1 AGCAGAGCTCAACATCCTTGAGGTTACAGTGAAGTGGA
28907260 ATGAAGCACC
Statistics
Matches: 165, Mismatches: 46, Indels: 31
0.68 0.19 0.13
Matches are distributed among these distances:
91 1 0.01
92 3 0.02
93 19 0.12
94 45 0.27
95 74 0.45
96 19 0.12
97 4 0.02
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (95 bp):
AGCAGAGCTCAACATCCTTGAGGTTACAGTGAAGTGGAGTGAGACTTCAAATCCCATCTTCCTGG
TGAGGTACAGAGACATGGGTTAAAACAGGC
Found at i:28907685 original size:233 final size:233
Alignment explanation
Indices: 28907267--28907733 Score: 801
Period size: 233 Copynumber: 2.0 Consensus size: 233
28907257 GGAATGAAGC
28907267 ACCAGATTCCTATACCCCTGATTTACAGTGGTTCAAATAAAAATAATGAAGCAAAGCTCAACTCC
1 ACCAGATTCCTATACCCCTGATTTACAGTGGTTCAAATAAAAATAATGAAGCAAAGCTCAACTCC
* * *
28907332 CTGAGGTTATAATGGAGTGGAGTAAGACTTCAAATCTCATTTTCCTAGTGGTGTACATAGAAGTG
66 CTGAGGTTACAATGGAGTGGAGTAAGACTTCAAATCTCATTTTCCTAGTGATGTACAAAGAAGTG
*
28907397 TGTTAAAATAGGTAGCAGATCTCAACGTCTCTAAAGTTACAGTAGAGTAGAGTGAAGCACCAAAA
131 TGTTAAAATAGGCAGCAGATCTCAACGTCTCTAAAGTTACAGTAGAGTAGAGTGAAGCACCAAAA
*
28907462 TCCTATACCCACTGAGTTGTAGTAAGTCAGATGAAAAT
196 TCCTACACCCACTGAGTTGTAGTAAGTCAGATGAAAAT
** *
28907500 ACCAGATTCCTATACCCCTGATTTACAGTAGG-TCGGATAAAAATAATGAAGCGAAGCTCAACTC
1 ACCAGATTCCTATACCCCTGATTTACAGT-GGTTCAAATAAAAATAATGAAGCAAAGCTCAACTC
*
28907564 TCTGAGGTTACAATGGAGTGGAGTAAGACTTCAAATCTCATTTTCCTAGTGATGTACAAAGAAGT
65 CCTGAGGTTACAATGGAGTGGAGTAAGACTTCAAATCTCATTTTCCTAGTGATGTACAAAGAAGT
* * *
28907629 GTGTTAAAATAGGCAGCAGATCTCAACGTCTTTAAAGTTACAGTGGAGTGGAGTGAAGCACCAAA
130 GTGTTAAAATAGGCAGCAGATCTCAACGTCTCTAAAGTTACAGTAGAGTAGAGTGAAGCACCAAA
*
28907694 ATCCTACACCCACTGAGTTGTAGTAGGTCAGATGAAAAT
195 ATCCTACACCCACTGAGTTGTAGTAAGTCAGATGAAAAT
28907733 A
1 A
28907734 ATGAAGTAGA
Statistics
Matches: 220, Mismatches: 13, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
233 218 0.99
234 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (233 bp):
ACCAGATTCCTATACCCCTGATTTACAGTGGTTCAAATAAAAATAATGAAGCAAAGCTCAACTCC
CTGAGGTTACAATGGAGTGGAGTAAGACTTCAAATCTCATTTTCCTAGTGATGTACAAAGAAGTG
TGTTAAAATAGGCAGCAGATCTCAACGTCTCTAAAGTTACAGTAGAGTAGAGTGAAGCACCAAAA
TCCTACACCCACTGAGTTGTAGTAAGTCAGATGAAAAT
Found at i:28909287 original size:17 final size:17
Alignment explanation
Indices: 28909267--28909301 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28909257 TTTTTAGTTT
*
28909267 TTTTACTTTAAACTTTA
1 TTTTAATTTAAACTTTA
*
28909284 TTTTAATTTAAATTTTA
1 TTTTAATTTAAACTTTA
28909301 T
1 T
28909302 CCATTCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTTAATTTAAACTTTA
Found at i:28912988 original size:3 final size:3
Alignment explanation
Indices: 28912980--28913042 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
28912970 TAGTTTATCC
28912980 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28913028 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
28913043 GGAGGAGGAG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:28913048 original size:3 final size:3
Alignment explanation
Indices: 28913042--28913071 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28913032 AATAATAATA
*
28913042 AGG AGG AGG AGG AGG AGG AGG AAG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
28913072 CCTGAGTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:28913575 original size:61 final size:61
Alignment explanation
Indices: 28913500--28913621 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
28913490 CAATCCTTAA
28913500 GGGAGGGTAAGAATTAAAGTAACCACACAAGTAAATACATCAAATCTAATTTTAAAAGATT
1 GGGAGGGTAAGAATTAAAGTAACCACACAAGTAAATACATCAAATCTAATTTTAAAAGATT
*
28913561 GGGAGGGTAAGAATTAAAGTAACCACACAAGTAATTACATCAAATCTAATTTTAAAAGATT
1 GGGAGGGTAAGAATTAAAGTAACCACACAAGTAAATACATCAAATCTAATTTTAAAAGATT
28913622 ATTTTATACA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.25
Consensus pattern (61 bp):
GGGAGGGTAAGAATTAAAGTAACCACACAAGTAAATACATCAAATCTAATTTTAAAAGATT
Found at i:28925593 original size:14 final size:14
Alignment explanation
Indices: 28925574--28925600 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28925564 CCGGTGTCTT
28925574 ACTGTTTATTTATC
1 ACTGTTTATTTATC
28925588 ACTGTTTATTTAT
1 ACTGTTTATTTAT
28925601 AACATCATGT
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:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (14 bp):
ACTGTTTATTTATC
Found at i:28925837 original size:21 final size:21
Alignment explanation
Indices: 28925799--28925849 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
28925789 GACCTCTATC
28925799 GATACAAGTGACAGTTCTACT
1 GATACAAGTGACAGTTCTACT
28925820 GATACAAGTGACTA-TTCTACT
1 GATACAAGTGAC-AGTTCTACT
*
28925841 GAAACAAGT
1 GATACAAGT
28925850 CTTACTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (21 bp):
GATACAAGTGACAGTTCTACT
Found at i:28926682 original size:52 final size:52
Alignment explanation
Indices: 28926593--28926826 Score: 312
Period size: 52 Copynumber: 4.6 Consensus size: 52
28926583 TTTCCTTTAG
* * * * *
28926593 TACTTACGATGATACATAGTCATTGGACCTCACAATCCGTAAAGGATTCACA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
* * *
28926645 TACTCACGATGACACGTAGTCATCGGACATCATAATCCATAAAGGATTCAGA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
* * * *
28926697 TACTCATGATGACATATAGTCATCGGACCT--T-ATCTGTAAAGGATTCATA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
*
28926746 TACTCACGAGGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
1 TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
* *
28926798 TACTCACGATGACACATACTTATCGGACC
1 TACTCACGATGACACATAGTCATCGGACC
28926827 CTTTTACATT
Statistics
Matches: 156, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
49 42 0.27
50 1 0.01
51 1 0.01
52 112 0.72
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.26
Consensus pattern (52 bp):
TACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAGA
Found at i:28926779 original size:101 final size:101
Alignment explanation
Indices: 28926631--28926826 Score: 311
Period size: 101 Copynumber: 1.9 Consensus size: 101
28926621 CTCACAATCC
* *
28926631 GTAAAGGATTCACATACTCACGATGACACGTAGTCATCGGACATCATAATCCATAAAGGATTCAG
1 GTAAAGGATTCACATACTCACGAGGACACATAGTCATCGGACATCATAATCCATAAAGGATTCAG
* * *
28926696 ATACTCATGATGACATATAGTCATCGGACCTTATCT
66 ATACTCACGATGACACATACTCATCGGACCTTATCT
* * *
28926732 GTAAAGGATTCATATACTCACGAGGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAG
1 GTAAAGGATTCACATACTCACGAGGACACATAGTCATCGGACATCATAATCCATAAAGGATTCAG
*
28926797 ATACTCACGATGACACATACTTATCGGACC
66 ATACTCACGATGACACATACTCATCGGACC
28926827 CTTTTACATT
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (101 bp):
GTAAAGGATTCACATACTCACGAGGACACATAGTCATCGGACATCATAATCCATAAAGGATTCAG
ATACTCACGATGACACATACTCATCGGACCTTATCT
Found at i:28931531 original size:24 final size:24
Alignment explanation
Indices: 28931470--28931532 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
28931460 TAGAGTAATA
* * *
28931470 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
28931494 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
28931518 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
28931533 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:28933168 original size:24 final size:26
Alignment explanation
Indices: 28933141--28933205 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 26
28933131 TGTAAACTGC
28933141 ATAATATATAAAAATAA-A-ATAAAA
1 ATAATATATAAAAATAATAGATAAAA
28933165 ATAAT-TCATAAAAA-AATAGATAAAA
1 ATAATAT-ATAAAAATAATAGATAAAA
28933190 AT-ATATTATAAAAATA
1 ATAATA-TATAAAAATA
28933206 TAAAATGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
23 3 0.09
24 15 0.43
25 15 0.43
26 2 0.06
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (26 bp):
ATAATATATAAAAATAATAGATAAAA
Found at i:28933175 original size:13 final size:12
Alignment explanation
Indices: 28933141--28933205 Score: 62
Period size: 13 Copynumber: 5.2 Consensus size: 12
28933131 TGTAAACTGC
28933141 ATAATATATAAAA
1 ATAAT-TATAAAA
*
28933154 ATAA-AATAAAA
1 ATAATTATAAAA
28933165 ATAATTCATAAAA
1 ATAATT-ATAAAA
*
28933178 A-AATAGATAAAA
1 ATAAT-TATAAAA
28933190 ATATATTATAAAA
1 ATA-ATTATAAAA
28933203 ATA
1 ATA
28933206 TAAAATGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 10 0.23
12 10 0.23
13 21 0.49
14 2 0.05
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (12 bp):
ATAATTATAAAA
Found at i:28933187 original size:25 final size:26
Alignment explanation
Indices: 28933145--28933211 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
28933135 AACTGCATAA
*
28933145 TATATAAAAATAAAATAAAAATA-AT
1 TATAAAAAAATAAAATAAAAATATAT
*
28933170 TCATAAAAAAAT-AGATAAAAATATAT
1 T-ATAAAAAAATAAAATAAAAATATAT
*
28933196 TATAAAAATATAAAAT
1 TATAAAAAAATAAAAT
28933212 GAATCAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 20 0.57
26 15 0.43
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (26 bp):
TATAAAAAAATAAAATAAAAATATAT
Found at i:28936396 original size:12 final size:12
Alignment explanation
Indices: 28936381--28936414 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
28936371 TAATTGTATT
28936381 AAAAATTATAAA
1 AAAAATTATAAA
* *
28936393 AAAAATTGTTAA
1 AAAAATTATAAA
28936405 AAAAATTATA
1 AAAAATTATA
28936415 GGTGATTATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (12 bp):
AAAAATTATAAA
Found at i:28941599 original size:22 final size:22
Alignment explanation
Indices: 28941573--28941614 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
28941563 TAGAGTCCGC
28941573 AGAGAATGTCAGTATTAGAGAT
1 AGAGAATGTCAGTATTAGAGAT
*
28941595 AGAGAATGTGAGTATTAGAG
1 AGAGAATGTCAGTATTAGAG
28941615 GCAGCGAAGT
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:0.40, C:0.02, G:0.31, T:0.26
Consensus pattern (22 bp):
AGAGAATGTCAGTATTAGAGAT
Found at i:28941819 original size:38 final size:38
Alignment explanation
Indices: 28941751--28941829 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
28941741 TTAAAATTTA
*
28941751 TAAATATTTAATATATTTTATTAAAATAAAAATCATAAT
1 TAAATATTTAATATATTTTATTAAAATAAAAAT-AAAAT
* **
28941790 TAAA-ATTTAAT-TTTTTTATTTAACTTAAAAATAAAAT
1 TAAATATTTAATATATTTTA-TTAAAATAAAAATAAAAT
28941827 TAA
1 TAA
28941830 TTTTACTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
37 13 0.37
38 18 0.51
39 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (38 bp):
TAAATATTTAATATATTTTATTAAAATAAAAATAAAAT
Found at i:28941944 original size:15 final size:15
Alignment explanation
Indices: 28941926--28941958 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
28941916 ACAACCGCCC
28941926 AAGGG-CCAACATTAG
1 AAGGGTCCAACATT-G
28941941 AAGGGTCCAACATTG
1 AAGGGTCCAACATTG
28941956 AAG
1 AAG
28941959 AGTCTGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.18, G:0.27, T:0.15
Consensus pattern (15 bp):
AAGGGTCCAACATTG
Found at i:28943696 original size:26 final size:25
Alignment explanation
Indices: 28943646--28943700 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
28943636 TAGCCTAAAT
*
28943646 TAAATAAATTGAAAATGTAATTGAAA
1 TAAATAAATTCAAAATGTAATTG-AA
28943672 TAAATAAA-TCAAAAT-TAAATATGAA
1 TAAATAAATTCAAAATGT-AAT-TGAA
28943697 TAAA
1 TAAA
28943701 CCATGAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (25 bp):
TAAATAAATTCAAAATGTAATTGAA
Found at i:28945552 original size:37 final size:37
Alignment explanation
Indices: 28945482--28945580 Score: 114
Period size: 37 Copynumber: 2.7 Consensus size: 37
28945472 AAAATATTCC
* *
28945482 TACGGCGACAGTTTT-GGTGTAATTTGAAAGTGCTCA
1 TACGGCGACAGTTTTGGGCGCAATTTGAAAGTGCTCA
28945518 TACGGCGACAGTTTTGGGCGCAATTT-AGAAGTGCTCA
1 TACGGCGACAGTTTTGGGCGCAATTTGA-AAGTGCTCA
* * *
28945555 TGCAGCAACA-TGTTTGGGCGCAATTT
1 TACGGCGACAGT-TTTGGGCGCAATTT
28945581 TGGATTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
36 17 0.31
37 38 0.69
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (37 bp):
TACGGCGACAGTTTTGGGCGCAATTTGAAAGTGCTCA
Found at i:28946285 original size:4 final size:4
Alignment explanation
Indices: 28946271--28946299 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
28946261 GGCTATCTAT
28946271 TCAC TCA- TCAC TCAC TCAC TCAC TCAC TC
1 TCAC TCAC TCAC TCAC TCAC TCAC TCAC TC
28946300 GCCATCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.28
Consensus pattern (4 bp):
TCAC
Found at i:28951560 original size:18 final size:18
Alignment explanation
Indices: 28951534--28951571 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28951524 GCATGCACAT
28951534 CATGATCATATGCAGTCA
1 CATGATCATATGCAGTCA
*
28951552 CATGCTCATATGCAGTCA
1 CATGATCATATGCAGTCA
28951570 CA
1 CA
28951572 GCAGACTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (18 bp):
CATGATCATATGCAGTCA
Found at i:28955174 original size:28 final size:28
Alignment explanation
Indices: 28955134--28955188 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
28955124 GGTACCATTT
**
28955134 CCCAATTCTTTTGGAGCTGTTTATATTA
1 CCCAATTCTTTTGGAAATGTTTATATTA
28955162 CCCAATTCTTTTGGAAATGTTTATATT
1 CCCAATTCTTTTGGAAATGTTTATATT
28955189 CTGGTCGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (28 bp):
CCCAATTCTTTTGGAAATGTTTATATTA
Found at i:28971256 original size:33 final size:33
Alignment explanation
Indices: 28971204--28971282 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
28971194 GAATATTATT
* * *
28971204 ATGAGATATTATATTTTAGCTATTTGATTCCTA
1 ATGAGATATTATATCTTAGCAATTTGATTCCAA
*
28971237 AT-AGGATATTATCTCTTAGCAATTTGATTCCAA
1 ATGA-GATATTATATCTTAGCAATTTGATTCCAA
28971270 ATGAGATATTATA
1 ATGAGATATTATA
28971283 GGATATTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 1 0.03
33 37 0.95
34 1 0.03
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (33 bp):
ATGAGATATTATATCTTAGCAATTTGATTCCAA
Found at i:28972434 original size:15 final size:15
Alignment explanation
Indices: 28972414--28972444 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28972404 GACTTAGTTT
28972414 AAATTTGGATTTGTA
1 AAATTTGGATTTGTA
*
28972429 AAATTTTGATTTGTA
1 AAATTTGGATTTGTA
28972444 A
1 A
28972445 CTCAAAGTTA
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:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (15 bp):
AAATTTGGATTTGTA
Found at i:28975273 original size:30 final size:31
Alignment explanation
Indices: 28975237--28975300 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
28975227 GTGGTGCCTC
*
28975237 TGTGCTTATGTTGCATCTGGAAAACTCAT-T
1 TGTGCTTATGCTGCATCTGGAAAACTCATCT
28975267 TGTGCTTATGCTGCATCTGGAAAACTCATCT
1 TGTGCTTATGCTGCATCTGGAAAACTCATCT
28975298 TGT
1 TGT
28975301 ATTCCTTCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (31 bp):
TGTGCTTATGCTGCATCTGGAAAACTCATCT
Found at i:28976957 original size:16 final size:18
Alignment explanation
Indices: 28976925--28976957 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28976915 TCCCATTATA
28976925 TCTTATCATAGGTTTTAC
1 TCTTATCATAGGTTTTAC
28976943 TCTTATC-TA-GTTTTA
1 TCTTATCATAGGTTTTA
28976958 GGGCGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (18 bp):
TCTTATCATAGGTTTTAC
Found at i:28981600 original size:18 final size:16
Alignment explanation
Indices: 28981579--28981613 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
28981569 TCTTTCAACA
28981579 AAAATTACAAAATAATTT
1 AAAATT-CAAAAT-ATTT
28981597 AAAATTCAAAATATTT
1 AAAATTCAAAATATTT
28981613 A
1 A
28981614 TAAAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 6 0.35
18 6 0.35
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATTCAAAATATTT
Found at i:28981608 original size:17 final size:18
Alignment explanation
Indices: 28981579--28981626 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28981569 TCTTTCAACA
28981579 AAAATTACAAAATAATT-T
1 AAAATT-CAAAATAATTAT
*
28981597 AAAATTCAAAATATTTAT
1 AAAATTCAAAATAATTAT
*
28981615 AAAAATCAAAAT
1 AAAATTCAAAAT
28981627 TTATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 9 0.33
18 18 0.67
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTCAAAATAATTAT
Found at i:28983483 original size:2 final size:2
Alignment explanation
Indices: 28983476--28983500 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28983466 ACGTGTATTC
28983476 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 A
28983501 GGGTGCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28989416 original size:23 final size:23
Alignment explanation
Indices: 28989385--28989558 Score: 166
Period size: 23 Copynumber: 7.8 Consensus size: 23
28989375 GAGAGTACCG
*
28989385 AAGTACTAAACAGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
28989408 AAGTGCTAATCAGAGAGTACACA
1 AAGTGCTAAACAGAGAGCACACA
*
28989431 AA--G-T--AC--TGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
28989447 AAGTGCTAATCAGAGAGCACACG
1 AAGTGCTAAACAGAGAGCACACA
*
28989470 AAGTGCTAATCAGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
* *
28989493 AAGTGCTAATAACAAAGAGCACGA-G
1 AAGTGCT-A-AACAGAGAGCAC-ACA
*
28989518 ATGTGCTAAACAGAGAGCACACA
1 AAGTGCTAAACAGAGAGCACACA
*
28989541 CAGTGCTAAACAGAGAGC
1 AAGTGCTAAACAGAGAGC
28989559 GTGCTAGTGT
Statistics
Matches: 122, Mismatches: 18, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
16 10 0.08
18 2 0.02
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 86 0.70
24 2 0.02
25 16 0.13
26 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACACA
Found at i:28989446 original size:39 final size:39
Alignment explanation
Indices: 28989399--28989473 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
28989389 ACTAAACAGA
*
28989399 GAGCACACAAAGTGCTAATCAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTACT
*
28989438 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGT
28989474 GCTAATCAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACAAAGTACT
Found at i:28989532 original size:48 final size:46
Alignment explanation
Indices: 28989438--28989558 Score: 154
Period size: 48 Copynumber: 2.6 Consensus size: 46
28989428 ACAAAGTACT
* *
28989438 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCAGA
1 GAGCACACAAAGTGCTAATCAAAGAGCACACGAAGTGCTAAACAGA
*
28989484 GAGCACACAAAGTGCTAATAACAAAGAGCACGA-GATGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAT--CAAAGAGCAC-ACGAAGTGCTAAACAGA
* * *
28989532 GAGCACACACAGTGCTAAACAGAGAGC
1 GAGCACACAAAGTGCTAATCAAAGAGC
28989559 GTGCTAGTGT
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
46 26 0.39
48 39 0.59
49 1 0.02
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (46 bp):
GAGCACACAAAGTGCTAATCAAAGAGCACACGAAGTGCTAAACAGA
Found at i:28998447 original size:41 final size:42
Alignment explanation
Indices: 28998355--28998449 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
28998345 GTTCGTAAAT
* * *
28998355 AATTTTTGTCAAGGTGGAGATTGTTCGAAATTGGTTGACTAG
1 AATTCTTGTTAAGGTGGAGATTGTTAGAAATTGGTTGACTAG
*
28998397 AATTCTTGTTAAGGTGGAGATTGTTAGAATTTGG-TGACTAG
1 AATTCTTGTTAAGGTGGAGATTGTTAGAAATTGGTTGACTAG
28998438 AATTCTTGTTAA
1 AATTCTTGTTAA
28998450 AATAAAATTC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 19 0.39
42 30 0.61
ACGTcount: A:0.27, C:0.06, G:0.26, T:0.40
Consensus pattern (42 bp):
AATTCTTGTTAAGGTGGAGATTGTTAGAAATTGGTTGACTAG
Found at i:29000665 original size:30 final size:28
Alignment explanation
Indices: 29000619--29000675 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 28
29000609 TAATTATACA
*
29000619 AAATCAAAATTTATGTATCAAATTATAATT
1 AAATCAAAATTCATGTAT-AAATT-TAATT
*
29000649 AAATTAAAATTCATGTATAAATTTAAT
1 AAATCAAAATTCATGTATAAATTTAAT
29000676 ATTTATTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.16
29 5 0.20
30 16 0.64
ACGTcount: A:0.51, C:0.05, G:0.04, T:0.40
Consensus pattern (28 bp):
AAATCAAAATTCATGTATAAATTTAATT
Found at i:29006361 original size:18 final size:18
Alignment explanation
Indices: 29006340--29006379 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
29006330 TCTTACATTG
29006340 ATTTATCATCTAACAAAC
1 ATTTATCATCTAACAAAC
*
29006358 ATTTATCATCTAACAAAG
1 ATTTATCATCTAACAAAC
29006376 ATTT
1 ATTT
29006380 TTCTGAAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTTATCATCTAACAAAC
Found at i:29007424 original size:17 final size:17
Alignment explanation
Indices: 29007397--29007434 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
29007387 ATATGTTAAA
*
29007397 ATTTTTAATTTTTTCGTT
1 ATTTTTAATTTATTCG-T
29007415 ATTTTT-ATTTATTCGT
1 ATTTTTAATTTATTCGT
29007431 ATTT
1 ATTT
29007435 AATCAAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (17 bp):
ATTTTTAATTTATTCGT
Found at i:29014363 original size:26 final size:27
Alignment explanation
Indices: 29014334--29014390 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 27
29014324 TAACACAATA
29014334 AAATAAAATA-ACATAATCATAGTAAT
1 AAATAAAATAGACATAATCATAGTAAT
*
29014360 AAATAAAATAGTGATATAATCATAGTAAT
1 AAATAAAATA--GACATAATCATAGTAAT
29014389 AA
1 AA
29014391 TGATAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.37
29 17 0.63
ACGTcount: A:0.60, C:0.05, G:0.07, T:0.28
Consensus pattern (27 bp):
AAATAAAATAGACATAATCATAGTAAT
Found at i:29015910 original size:15 final size:15
Alignment explanation
Indices: 29015890--29015930 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
29015880 TTAAAATAAA
29015890 TAATAATAATAACAT
1 TAATAATAATAACAT
* **
29015905 TAATAATATTATTAT
1 TAATAATAATAACAT
29015920 TAATAATAATA
1 TAATAATAATA
29015931 GTAGGAGCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAACAT
Found at i:29017038 original size:12 final size:12
Alignment explanation
Indices: 29017021--29017045 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29017011 GGCTTGCACT
29017021 TCCGGATACACC
1 TCCGGATACACC
29017033 TCCGGATACACC
1 TCCGGATACACC
29017045 T
1 T
29017046 TCAGATGCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.40, G:0.16, T:0.20
Consensus pattern (12 bp):
TCCGGATACACC
Found at i:29019228 original size:16 final size:16
Alignment explanation
Indices: 29019209--29019241 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29019199 TTTATGATAC
*
29019209 TTTATATTATGTTATT
1 TTTATATTATGTAATT
29019225 TTTATATTATGTAATT
1 TTTATATTATGTAATT
29019241 T
1 T
29019242 AAAACACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTATATTATGTAATT
Found at i:29022795 original size:17 final size:17
Alignment explanation
Indices: 29022775--29022816 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
29022765 TACTTTCATG
29022775 TTATTTTTTATTTAGT-T
1 TTATTTTTTATTTA-TAT
*
29022792 TTATATTTTATTTATAT
1 TTATTTTTTATTTATAT
29022809 TTATTTTT
1 TTATTTTT
29022817 ATAATTCTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (17 bp):
TTATTTTTTATTTATAT
Found at i:29022809 original size:23 final size:24
Alignment explanation
Indices: 29022783--29022834 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
29022773 TGTTATTTTT
*
29022783 TATTTAGTTTTAT-ATTTTATTTA
1 TATTTAGTTTTATAATTCTATTTA
* *
29022806 TATTTATTTTTATAATTCTATTTC
1 TATTTAGTTTTATAATTCTATTTA
29022830 TATTT
1 TATTT
29022835 CTATTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (24 bp):
TATTTAGTTTTATAATTCTATTTA
Done.