Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 172 of 193
Found at i:53574992 original size:30 final size:28
Alignment explanation
Indices: 53574958--53575049 Score: 78
Period size: 29 Copynumber: 3.2 Consensus size: 28
53574948 TCATCGAGGT
53574958 TAAAAATGGAATTTTAAAAGATTCGGGGGG
1 TAAAAATGGAATTTT-AAAGATTC-GGGGG
* * ** *
53574988 T-AAAATGGTAATTTTCGATGAAACCGGGG
1 TAAAAATGG-AATTTT-AAAGATTCGGGGG
* *
53575017 TTAAAATGGAATTTTAAAGATTCGAGGG
1 TAAAAATGGAATTTTAAAGATTCGGGGG
53575045 TAAAA
1 TAAAA
53575050 TGGTAAATTT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
28 11 0.23
29 18 0.38
30 18 0.38
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.28
Consensus pattern (28 bp):
TAAAAATGGAATTTTAAAGATTCGGGGG
Found at i:53575000 original size:59 final size:57
Alignment explanation
Indices: 53574931--53575088 Score: 194
Period size: 59 Copynumber: 2.7 Consensus size: 57
53574921 ACCCGGGGGC
** *
53574931 AAATGGTAATTTTGGTGTCATCGAGGTTAAAAATGGAATTTTAAAAGATTCGGGGGGTA
1 AAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTT-AAAGATTC-GAGGGTA
* * *
53574990 AAATGGTAATTTTCGATGAAACCGGGGTT-AAAATGGAATTTTAAAGATTCGAGGGTA
1 AAATGGTAATTTT-GGTGAAATCGAGGTTAAAAATGGAATTTTAAAGATTCGAGGGTA
*
53575047 AAATGGTAAATTTTGGTGAAATC-AGGGTTAAAAATGGGATTT
1 AAATGGT-AATTTTGGTGAAATCGA-GGTTAAAAATGGAATTT
53575089 AGGGAAGTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
57 24 0.28
58 25 0.29
59 26 0.31
60 10 0.12
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (57 bp):
AAATGGTAATTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAAAGATTCGAGGGTA
Found at i:53575132 original size:30 final size:30
Alignment explanation
Indices: 53575093--53575317 Score: 312
Period size: 30 Copynumber: 7.6 Consensus size: 30
53575083 GGATTTAGGG
* *
53575093 AAGTTTGGGGGT-AAAATGATAATTTTTG-A
1 AAGTTTTGGGGTCAAAATG-TAATTTTGGAA
* *
53575122 AAGTTTTGGGGTTAAAATGTGATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
53575152 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
53575182 AAGTTTTAGGGTTAAAATGTAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
53575212 AAGTTTTGGGGTCAAAATGTAATTTTAGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
53575242 AAGTTTTGGGGTCAAAATGTAA-CTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
* *
53575271 AAGTTTTGGGGTCGAAATATAATTTTGGAA
1 AAGTTTTGGGGTCAAAATGTAATTTTGGAA
*
53575301 AAGTTCTGGGGTCAAAA
1 AAGTTTTGGGGTCAAAA
53575318 CATGATTTCT
Statistics
Matches: 174, Mismatches: 19, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
29 43 0.25
30 131 0.75
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATGTAATTTTGGAA
Found at i:53576360 original size:7 final size:7
Alignment explanation
Indices: 53576350--53576410 Score: 67
Period size: 7 Copynumber: 9.3 Consensus size: 7
53576340 TTATTTCGAT
53576350 ATTATTA
1 ATTATTA
53576357 ATTATTA
1 ATTATTA
53576364 A-TATTA
1 ATTATTA
*
53576370 ACTA-TA
1 ATTATTA
*
53576376 ATCA-TA
1 ATTATTA
*
53576382 AATATTA
1 ATTATTA
53576389 ATTA-TA
1 ATTATTA
53576395 ATTATTA
1 ATTATTA
53576402 ATTATTA
1 ATTATTA
53576409 AT
1 AT
53576411 AATATTTTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
6 20 0.43
7 26 0.57
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (7 bp):
ATTATTA
Found at i:53576370 original size:13 final size:14
Alignment explanation
Indices: 53576350--53576410 Score: 67
Period size: 13 Copynumber: 4.6 Consensus size: 14
53576340 TTATTTCGAT
53576350 ATTATTAATTATTA
1 ATTATTAATTATTA
*
53576364 A-TATTAACTA-TA
1 ATTATTAATTATTA
* *
53576376 ATCA-TAAATATTA
1 ATTATTAATTATTA
53576389 ATTA-TAATTATTA
1 ATTATTAATTATTA
53576402 ATTATTAAT
1 ATTATTAAT
53576411 AATATTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 8 0.21
13 26 0.67
14 5 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATTAATTATTA
Found at i:53577095 original size:6 final size:6
Alignment explanation
Indices: 53577086--53577152 Score: 70
Period size: 6 Copynumber: 11.7 Consensus size: 6
53577076 GAATTTATAA
* *
53577086 TAAATT TAAATT TAAA-T TAAATC CAAATT TAAA-T TAAATT TAAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAA-TT
*
53577133 TAAA-- TAAATT TAATTT TAAA
1 TAAATT TAAATT TAAATT TAAA
53577153 ACAAATTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
4 4 0.08
5 10 0.20
6 30 0.60
7 6 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:53577097 original size:17 final size:17
Alignment explanation
Indices: 53577071--53577152 Score: 96
Period size: 17 Copynumber: 4.8 Consensus size: 17
53577061 TTGTATTTGG
*
53577071 AATTTGAATTTATAA-TA
1 AATTTAAATTTA-AATTA
53577088 AATTTAAATTTAAATTA
1 AATTTAAATTTAAATTA
**
53577105 AATCCAAATTTAAATTA
1 AATTTAAATTTAAATTA
53577122 AATTTAAATTTTAAA-TA
1 AATTTAAA-TTTAAATTA
*
53577139 AATTTAATTTTAAA
1 AATTTAAATTTAAA
53577153 ACAAATTCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
16 8 0.14
17 43 0.75
18 6 0.11
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTAAATTA
Found at i:53577097 original size:23 final size:22
Alignment explanation
Indices: 53577087--53577130 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
53577077 AATTTATAAT
53577087 AAATTTAAATTTAAATTAAATCC
1 AAATTTAAATTTAAATTAAAT-C
53577110 AAATTTAAA-TTAAATTTAAAT
1 AAATTTAAATTTAAA-TTAAAT
53577131 TTTAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AAATTTAAATTTAAATTAAATC
Found at i:53577105 original size:11 final size:11
Alignment explanation
Indices: 53577077--53577131 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
53577067 TTGGAATTTG
53577077 AATTTATAA-TA
1 AATTTA-AATTA
53577088 AATTTAAATTTA
1 AATTTAAA-TTA
*
53577100 AA-TTAAATCCA
1 AATTTAAAT-TA
53577111 AATTTAAATTA
1 AATTTAAATTA
53577122 AATTTAAATT
1 AATTTAAATT
53577132 TTAAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 3 0.08
11 25 0.66
12 10 0.26
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:53577158 original size:17 final size:17
Alignment explanation
Indices: 53577121--53577159 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
53577111 AATTTAAATT
*
53577121 AAATTTAAATTTTAAAT
1 AAATTTAAATTTTAAAC
53577138 AAATTT-AATTTTAAAAC
1 AAATTTAAATTTT-AAAC
53577155 AAATT
1 AAATT
53577160 CAAAATGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTAAATTTTAAAC
Found at i:53584647 original size:12 final size:12
Alignment explanation
Indices: 53584630--53584654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53584620 GAACTCAAAC
53584630 ATAAACAAAGAG
1 ATAAACAAAGAG
53584642 ATAAACAAAGAG
1 ATAAACAAAGAG
53584654 A
1 A
53584655 ACCAAACCTG
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:0.68, C:0.08, G:0.16, T:0.08
Consensus pattern (12 bp):
ATAAACAAAGAG
Found at i:53585668 original size:18 final size:19
Alignment explanation
Indices: 53585647--53585690 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
53585637 TAAATAAATT
*
53585647 TTAA-ATATAAAATATTCA
1 TTAATATATAAAATAATCA
53585665 TTAATTATATAAAATAATCA
1 TTAA-TATATAAAATAATCA
53585685 TTAATA
1 TTAATA
53585691 AACTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 2 0.09
20 17 0.74
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAATATATAAAATAATCA
Found at i:53585676 original size:20 final size:20
Alignment explanation
Indices: 53585651--53585689 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53585641 TAAATTTTAA
*
53585651 ATATAAAATATTCATTAATT
1 ATATAAAATAATCATTAATT
53585671 ATATAAAATAATCATTAAT
1 ATATAAAATAATCATTAAT
53585690 AAACTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATAAAATAATCATTAATT
Found at i:53591092 original size:35 final size:36
Alignment explanation
Indices: 53591046--53591122 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 36
53591036 TTATAATTTG
* *
53591046 AAAATTAATTAAAAAT-TTAAA-AAAATTATAAAAATA
1 AAAATTAATTAAAAATCATAAATAAAA-AAT-AAAATA
53591082 AAAATT-ATTAAAAATCATAAATAAAAAATAAAATA
1 AAAATTAATTAAAAATCATAAATAAAAAATAAAATA
53591117 AAAATT
1 AAAATT
53591123 GGGTTTCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
35 21 0.57
36 12 0.32
37 4 0.11
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (36 bp):
AAAATTAATTAAAAATCATAAATAAAAAATAAAATA
Found at i:53591093 original size:16 final size:15
Alignment explanation
Indices: 53591066--53591114 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
53591056 AAAAATTTAA
53591066 AAAAATTATAAAAAT
1 AAAAATTATAAAAAT
53591081 AAAAATTATTAAAAAT
1 AAAAATTA-TAAAAAT
*
53591097 CATAAA-TA-AAAAAT
1 -AAAAATTATAAAAAT
53591111 AAAA
1 AAAA
53591115 TAAAAATTGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 6 0.20
15 8 0.27
16 9 0.30
17 4 0.13
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTATAAAAAT
Found at i:53591095 original size:17 final size:18
Alignment explanation
Indices: 53591046--53591102 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 18
53591036 TTATAATTTG
*
53591046 AAAATTAATTAAAAATTTA
1 AAAATT-ATTAAAAATATA
*
53591065 AAAA-AATTATAAAA-ATA
1 AAAATTATTA-AAAATATA
53591082 AAAATTATTAAAAATCATA
1 AAAATTATTAAAAAT-ATA
53591101 AA
1 AA
53591103 TAAAAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
17 14 0.45
18 8 0.26
19 9 0.29
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATTATTAAAAATATA
Found at i:53594587 original size:18 final size:19
Alignment explanation
Indices: 53594561--53594597 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
53594551 ATCATTTTAC
53594561 TCAAATATCAT-AAAATAA
1 TCAAATATCATCAAAATAA
*
53594579 TCAAGTATCATCAAAATAA
1 TCAAATATCATCAAAATAA
53594598 CATTTATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.27
Consensus pattern (19 bp):
TCAAATATCATCAAAATAA
Found at i:53595401 original size:6 final size:6
Alignment explanation
Indices: 53595367--53595434 Score: 50
Period size: 6 Copynumber: 11.5 Consensus size: 6
53595357 TAATAGGGAT
* * * * *
53595367 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA CTTCAC TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* *
53595414 TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTT
53595435 TTATCACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
4 1 0.02
5 3 0.06
6 44 0.86
7 3 0.06
ACGTcount: A:0.26, C:0.25, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTCAA
Found at i:53595409 original size:18 final size:18
Alignment explanation
Indices: 53595386--53595434 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
53595376 ACAATTCATA
53595386 TCACTTTCAATTTCAAC-T
1 TCACTTTCAATTTC-ACTT
*
53595404 TCACTTTCACTTTCACTT
1 TCACTTTCAATTTCACTT
53595422 TCACTTTCAATTT
1 TCACTTTCAATTT
53595435 TTATCACAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTTCACTT
Found at i:53595411 original size:12 final size:13
Alignment explanation
Indices: 53595388--53595430 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
53595378 AATTCATATC
*
53595388 ACTTTCAATTTCA
1 ACTTTCACTTTCA
53595401 AC-TTCACTTTC-
1 ACTTTCACTTTCA
53595412 ACTTTCACTTTC-
1 ACTTTCACTTTCA
53595424 ACTTTCA
1 ACTTTCA
53595431 ATTTTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 2 0.07
12 24 0.86
13 2 0.07
ACGTcount: A:0.23, C:0.30, G:0.00, T:0.47
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:53601816 original size:2 final size:2
Alignment explanation
Indices: 53601805--53601840 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
53601795 TCCTTCTTAC
53601805 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53601841 TAATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53601878 original size:15 final size:15
Alignment explanation
Indices: 53601860--53601905 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 15
53601850 AATATTTATG
*
53601860 TTCAAAATATATGCA
1 TTCAAAATATATACA
53601875 TTC--AATATATACA
1 TTCAAAATATATACA
53601888 -T-AAAATATATACA
1 TTCAAAATATATACA
53601901 TTCAA
1 TTCAA
53601906 TACATACAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
12 1 0.04
13 19 0.73
14 1 0.04
15 5 0.19
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (15 bp):
TTCAAAATATATACA
Found at i:53601881 original size:13 final size:13
Alignment explanation
Indices: 53601865--53601913 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
53601855 TTATGTTCAA
*
53601865 AATATATGCATTC
1 AATATATACATTC
**
53601878 AATATATACATAA
1 AATATATACATTC
53601891 AATATATACATTC
1 AATATATACATTC
*
53601904 AATACATACA
1 AATATATACA
53601914 GATCTCAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (13 bp):
AATATATACATTC
Found at i:53601893 original size:26 final size:26
Alignment explanation
Indices: 53601863--53601913 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
53601853 ATTTATGTTC
* *
53601863 AAAATATATGCATTCAATATATACAT
1 AAAATATATACATTCAATACATACAT
53601889 AAAATATATACATTCAATACATACA
1 AAAATATATACATTCAATACATACA
53601914 GATCTCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATATATACATTCAATACATACAT
Found at i:53603453 original size:6 final size:6
Alignment explanation
Indices: 53603435--53603549 Score: 85
Period size: 6 Copynumber: 19.0 Consensus size: 6
53603425 TTAAATTGAT
* * *
53603435 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A
* ** *
53603482 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
*
53603530 TTTAACA TTAAAAA TTTAAA
1 TTTAA-A TT-TAAA TTTAAA
53603550 AGTCCAATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.09
6 52 0.60
7 21 0.24
8 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:53603465 original size:17 final size:17
Alignment explanation
Indices: 53603435--53603511 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
53603425 TTAAATTGAT
53603435 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
53603451 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
53603468 TTTAAAATTAAATATTTAAA
1 TTT-AAATT-TAT-TTTAAA
*
53603488 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
53603505 TTTAAAT
1 TTTAAAT
53603512 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 18 0.36
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:53603500 original size:11 final size:11
Alignment explanation
Indices: 53603425--53603511 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
53603415 GACTTTTGAG
* *
53603425 TTAAATTGATT
1 TTAAATTTAAT
53603436 TTAAATTT-AT
1 TTAAATTTAAT
53603446 TTAAATTTAGAT
1 TTAAATTTA-AT
*
53603458 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
53603469 TTAAAATTAAATAT
1 TT-AAATT-TA-AT
53603483 TTAAATTTAAT
1 TTAAATTTAAT
*
53603494 TTGAATTTAAAT
1 TTAAATTT-AAT
53603506 TTAAAT
1 TTAAAT
53603512 AAAAATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 24 0.40
12 14 0.23
13 9 0.15
14 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:53603532 original size:31 final size:30
Alignment explanation
Indices: 53603462--53603541 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
53603452 TTAGATTTAT
* *
53603462 TTTAAATTTAAAATTAAATATTTAAATTTAA
1 TTTAAATTTAAAATTAAATA-TAAAATTAAA
* *
53603493 TTTGAATTTAAATTTAAATA-AAAATTAAAA
1 TTTAAATTTAAAATTAAATATAAAATT-AAA
*
53603523 TATTAAATTTAACATTAAA
1 T-TTAAATTTAAAATTAAA
53603542 AATTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 5 0.12
30 3 0.08
31 32 0.80
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTAAATTTAAAATTAAATATAAAATTAAA
Found at i:53603532 original size:37 final size:37
Alignment explanation
Indices: 53603448--53603528 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
53603438 AAATTTATTT
* * *
53603448 AAATTTAGATTT-ATTTTAAATTTAAAATTAAATATTT
1 AAATTTA-ATTTGAATTTAAATTTAAAATTAAAAATTA
53603485 AAATTTAATTTGAATTTAAATTT-AAA-TAAAAATTA
1 AAATTTAATTTGAATTTAAATTTAAAATTAAAAATTA
53603520 AAATATTAA
1 AAAT-TTAA
53603529 ATTTAACATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 11 0.28
36 11 0.28
37 17 0.44
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (37 bp):
AAATTTAATTTGAATTTAAATTTAAAATTAAAAATTA
Found at i:53604275 original size:3 final size:3
Alignment explanation
Indices: 53604267--53604313 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
53604257 ATTAATTATG
* *
53604267 ATA ATA ATA ATA ATA ATA ATTA ATA ATA CTA ATA ATA TTA ATTA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA A-TA ATA
53604314 GATCTTTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:53604299 original size:22 final size:22
Alignment explanation
Indices: 53604267--53604313 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
53604257 ATTAATTATG
53604267 ATAATAATAATAATAATAATTA
1 ATAATAATAATAATAATAATTA
* *
53604289 ATAATACTAATAATATTAATTA
1 ATAATAATAATAATAATAATTA
53604311 ATA
1 ATA
53604314 GATCTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATAATAATAATAATAATTA
Found at i:53605351 original size:161 final size:162
Alignment explanation
Indices: 53605175--53605487 Score: 477
Period size: 161 Copynumber: 1.9 Consensus size: 162
53605165 CTTTTCAATT
* *
53605175 TAGTCCTTTGACTGTTTGACTGTACCATAGGCTGCCACGTATCACTTTTTAGATTATTTATGCAT
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTATCACTTTTTAGATTATTTATGCAT
* * *
53605240 TTAGTCCTTTTTATTTTTTTATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTAATTACGA
66 TTAGTCCTTTTTA-TTTTTAATTTGGTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAA
*
53605303 AATTGGCCCAATAATTTTTCAAGGTTTATAAAC
130 AATTGGCCCAAAAATTTTTCAAGGTTTATAAAC
* * * * *
53605336 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATTTTTTGGATTATTTCTGCAT
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTATCACTTTTTAGATTATTTATGCAT
* *
53605401 TTAGTCCTTTTTATTTTTAATTTGGTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAA
66 TTAGTCCTTTTTATTTTTAATTTGGTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAA
*
53605466 ATTGGTCCAAAAATTTTTCAAG
131 ATTGGCCCAAAAATTTTTCAAG
53605488 ATTTTCAAAT
Statistics
Matches: 136, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
160 23 0.17
161 78 0.57
162 35 0.26
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (162 bp):
TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTATCACTTTTTAGATTATTTATGCAT
TTAGTCCTTTTTATTTTTAATTTGGTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAA
ATTGGCCCAAAAATTTTTCAAGGTTTATAAAC
Found at i:53605621 original size:30 final size:30
Alignment explanation
Indices: 53605580--53605783 Score: 300
Period size: 30 Copynumber: 6.7 Consensus size: 30
53605570 CCCTAAATTG
*
53605580 TCCAGAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
53605611 CCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
53605641 TCCAAAATTATATTTTTGACCCTAAAACTTT
1 TCCAAAATTACA-TTTTGACCCCAAAACTTT
* * * *
53605672 ACTAAAATTACATTTTAACCCTAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
53605702 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
53605732 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
53605762 TCCAAAATTACATTTTAACCCC
1 TCCAAAATTACATTTTGACCCC
53605784 GATTTCACCG
Statistics
Matches: 156, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
30 127 0.81
31 29 0.19
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:53605740 original size:91 final size:90
Alignment explanation
Indices: 53605585--53605782 Score: 342
Period size: 91 Copynumber: 2.2 Consensus size: 90
53605575 AATTGTCCAG
*
53605585 AAATTACATTTTGACCCTAAAACTTTCCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCTAAAACTTTCCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
* *
53605650 ATATTTTTGACCCTAAAACTTTACTA
66 ATA-TTTTGACCCCAAAACTTTACCA
*
53605676 AAATTACATTTTAACCCTAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
1 AAATTACATTTTAACCCTAAAACTTTCCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
*
53605741 ATATTTTGACCCCAAAACTTTTCCA
66 ATATTTTGACCCCAAAACTTTACCA
53605766 AAATTACATTTTAACCC
1 AAATTACATTTTAACCC
53605783 CGATTTCACC
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
90 36 0.35
91 66 0.65
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (90 bp):
AAATTACATTTTAACCCTAAAACTTTCCCAAAATTACATTTTGACCCCAAAACTTTTCCAAAATT
ATATTTTGACCCCAAAACTTTACCA
Found at i:53605811 original size:29 final size:30
Alignment explanation
Indices: 53605765--53606042 Score: 184
Period size: 29 Copynumber: 9.5 Consensus size: 30
53605755 AAACTTTTCC
*
53605765 AAAATTA-CATTTTAACCCCGATTTCACCG
1 AAAATTACCATTTTAACCCCGATTTCACCT
* ***
53605794 AAAATTACCATTTT-ACCCTCGA-ATCTTTT
1 AAAATTACCATTTTAACCC-CGATTTCACCT
* *
53605823 AAAATT-TCATTTTTAACCCCGATTTCACCA
1 AAAATTACCA-TTTTAACCCCGATTTCACCT
* * ***
53605853 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCACCT
* *
53605882 AAAATT-CTATTTTCAACCCCGATTTCACCG
1 AAAATTACCATTTT-AACCCCGATTTCACCT
** **
53605912 AAAATTACCATTTT-ACCCTCGA-AGCTTCT
1 AAAATTACCATTTTAACCC-CGATTTCACCT
*
53605941 AAAATT-CCATTTTTAACCCCGATTTCACCG
1 AAAATTACCA-TTTTAACCCCGATTTCACCT
* * * ***
53605971 AAAATTATCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCACCT
*
53606000 AAAATT-CCATTTTTAACCCCGATTACACC-
1 AAAATTACCA-TTTTAACCCCGATTTCACCT
53606029 AAAATTACCATTTT
1 AAAATTACCATTTT
53606043 GCCCCGGGTA
Statistics
Matches: 182, Mismatches: 50, Indels: 34
0.68 0.19 0.13
Matches are distributed among these distances:
28 13 0.07
29 89 0.49
30 70 0.38
31 10 0.05
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCACCT
Found at i:53605840 original size:59 final size:59
Alignment explanation
Indices: 53605765--53606047 Score: 444
Period size: 59 Copynumber: 4.8 Consensus size: 59
53605755 AAACTTTTCC
* *
53605765 AAAATTACA-TTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* *
53605823 AAAATTTCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* * * * *
53605882 AAAATTCTATTTTCAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
*
53605941 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTATCATTTTACCCCCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
* *
53606000 AAAATTCCATTTTTAACCCCGATTACACC-AAAATTACCATTTTGCCCC
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCC
53606048 GGGTATCTAT
Statistics
Matches: 205, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
58 25 0.12
59 180 0.88
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
Found at i:53618260 original size:69 final size:69
Alignment explanation
Indices: 53618142--53618749 Score: 911
Period size: 69 Copynumber: 8.9 Consensus size: 69
53618132 ACCTTTTACT
* * *
53618142 ATCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCGTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
53618205 ACGTC
65 ACGTC
53618210 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
53618275 CGTC
66 CGTC
*
53618279 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
53618344 CGT-
66 CGTC
* *
53618347 -TCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
53618409 ACGTC
65 ACGTC
*
53618414 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
53618479 CGT-
66 CGTC
* *
53618482 -TCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
53618544 ACGTC
65 ACGTC
* *
53618549 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGCAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
53618614 CGT-
66 CGTC
* *
53618617 -TCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
53618679 GCGTC
65 ACGTC
* * * *
53618684 ATCATCTTTGAAATTGAAGTAAAGTTGAATGTCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTC-TTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
53618749 A
65 A
53618750 GATCATTTCC
Statistics
Matches: 493, Mismatches: 29, Indels: 34
0.89 0.05 0.06
Matches are distributed among these distances:
66 115 0.23
67 69 0.14
68 73 0.15
69 201 0.41
70 35 0.07
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (69 bp):
ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
CGTC
Found at i:53618407 original size:135 final size:135
Alignment explanation
Indices: 53618142--53618749 Score: 1024
Period size: 135 Copynumber: 4.5 Consensus size: 135
53618132 ACCTTTTACT
* * * *
53618142 ATCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCGTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCA
* *
53618205 ACGTCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGTAA
65 ACGT--TCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTAA
53618269 GAGCAACGTC
126 GAGCAACGTC
53618279 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
53618344 CGTTCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
66 CGTTCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
53618409 ACGTC
131 ACGTC
53618414 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
53618479 CGTTCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
66 CGTTCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
53618544 ACGTC
131 ACGTC
*
53618549 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGCAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
53618614 CGTTCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
66 CGTTCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
53618679 GCGTC
131 ACGTC
* * * * *
53618684 ATCATCTTTGAAATTGAAGTAAAGTTGAATGTCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCTC-TTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCA
53618749 A
65 A
53618750 GATCATTTCC
Statistics
Matches: 453, Mismatches: 14, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
135 314 0.69
136 77 0.17
137 24 0.05
138 38 0.08
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (135 bp):
ATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGAGCAA
CGTTCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
ACGTC
Found at i:53618589 original size:204 final size:204
Alignment explanation
Indices: 53618141--53618749 Score: 914
Period size: 204 Copynumber: 3.0 Consensus size: 204
53618131 GACCTTTTAC
*
53618141 TATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCGTTATCTCTGAAATTGAAGTAAGAGCAA
1 TATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
53618206 CGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGA
66 CGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGA
* *
53618271 GCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAGTTGAAG
131 GCAACGT-ATCCCCTTGAAATTGAAGTAGAG-TGGATAATCAAGTCTTTATCTCTGAAATTGAAG
53618335 TAAGAGCAACG
194 TAAGAGCAACG
53618346 T-TCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 TATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
53618410 CGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAGTTGAAGTAAGA
66 CGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGA
*
53618475 GCAACGT-TCCCCTTGAAATTGAAGTAGAGTGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTA
131 GCAACGTATCCCCTTGAAATTGAAGTAGAGTGGATAATCAAGTCTTTATCTCTGAAATTGAAGTA
53618538 AGAGCAACG
196 AGAGCAACG
* * * *
53618547 TCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAGTTGAAGCAAGAG
1 T-ATCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGTAAGAG
* *
53618611 CAACGT--TCCCCTTGAAATTGAAGTAGAG-TGGATAAT-ACGTCTTTATCTCTGAAATTGAAGT
63 CAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGAT-ATCAAGTCTTTATCTCTGAAATTGAAGT
* * * * * *
53618672 AAGAGCAGCGTCATCATCTTTGAAATTGAAGTAAAGTTGA-ATGTCAAGTCTTTATCTCTGAAAT
127 AAGAGCAACGT-ATC-CCCTTGAAATTGAAGTAGAGTGGATA-ATCAAGTCTTTATCTCTGAAAT
53618736 TGAAGTAAGAGCAA
189 TGAAGTAAGAGCAA
53618750 GATCATTTCC
Statistics
Matches: 374, Mismatches: 19, Indels: 22
0.90 0.05 0.05
Matches are distributed among these distances:
201 77 0.21
202 46 0.12
203 26 0.07
204 192 0.51
205 33 0.09
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (204 bp):
TATCCCCTTGAAATTGAAGTAGAGTGGATAATACGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
CGTCATCCTCTTGAAATTGAAGTAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGA
GCAACGTATCCCCTTGAAATTGAAGTAGAGTGGATAATCAAGTCTTTATCTCTGAAATTGAAGTA
AGAGCAACG
Found at i:53619095 original size:6 final size:6
Alignment explanation
Indices: 53619077--53619191 Score: 85
Period size: 6 Copynumber: 19.0 Consensus size: 6
53619067 TTAAATTGAT
* * *
53619077 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAA-A
* ** *
53619124 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
*
53619172 TTTAACA TTAAAAA TTTAAA
1 TTTAA-A TT-TAAA TTTAAA
53619192 AGTCCAATGT
Statistics
Matches: 87, Mismatches: 13, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.09
6 52 0.60
7 21 0.24
8 2 0.02
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (6 bp):
TTTAAA
Found at i:53619107 original size:17 final size:17
Alignment explanation
Indices: 53619077--53619153 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
53619067 TTAAATTGAT
53619077 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
53619093 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
53619110 TTTAAAATTAAATATTTAAA
1 TTT-AAATT-TAT-TTTAAA
*
53619130 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
53619147 TTTAAAT
1 TTTAAAT
53619154 AAAAATTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
16 9 0.18
17 18 0.36
18 12 0.24
19 2 0.04
20 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:53619142 original size:11 final size:11
Alignment explanation
Indices: 53619067--53619153 Score: 61
Period size: 11 Copynumber: 7.5 Consensus size: 11
53619057 GACTTTTGAG
* *
53619067 TTAAATTGATT
1 TTAAATTTAAT
53619078 TTAAATTT-AT
1 TTAAATTTAAT
53619088 TTAAATTTAGAT
1 TTAAATTTA-AT
*
53619100 TT-ATTTTAAAT
1 TTAAATTT-AAT
*
53619111 TTAAAATTAAATAT
1 TT-AAATT-TA-AT
53619125 TTAAATTTAAT
1 TTAAATTTAAT
*
53619136 TTGAATTTAAAT
1 TTAAATTT-AAT
53619148 TTAAAT
1 TTAAAT
53619154 AAAAATTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
10 9 0.15
11 24 0.40
12 14 0.23
13 9 0.15
14 4 0.07
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:53619174 original size:31 final size:30
Alignment explanation
Indices: 53619104--53619183 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
53619094 TTAGATTTAT
* *
53619104 TTTAAATTTAAAATTAAATATTTAAATTTAA
1 TTTAAATTTAAAATTAAATA-TAAAATTAAA
* *
53619135 TTTGAATTTAAATTTAAATA-AAAATTAAAA
1 TTTAAATTTAAAATTAAATATAAAATT-AAA
*
53619165 TATTAAATTTAACATTAAA
1 T-TTAAATTTAAAATTAAA
53619184 AATTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
29 5 0.12
30 3 0.08
31 32 0.80
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (30 bp):
TTTAAATTTAAAATTAAATATAAAATTAAA
Found at i:53619174 original size:37 final size:37
Alignment explanation
Indices: 53619090--53619170 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
53619080 AAATTTATTT
* * *
53619090 AAATTTAGATTT-ATTTTAAATTTAAAATTAAATATTT
1 AAATTTA-ATTTGAATTTAAATTTAAAATTAAAAATTA
53619127 AAATTTAATTTGAATTTAAATTT-AAA-TAAAAATTA
1 AAATTTAATTTGAATTTAAATTTAAAATTAAAAATTA
53619162 AAATATTAA
1 AAAT-TTAA
53619171 ATTTAACATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 11 0.28
36 11 0.28
37 17 0.44
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (37 bp):
AAATTTAATTTGAATTTAAATTTAAAATTAAAAATTA
Found at i:53619916 original size:3 final size:3
Alignment explanation
Indices: 53619908--53619957 Score: 64
Period size: 3 Copynumber: 16.0 Consensus size: 3
53619898 ATTAATTATG
* *
53619908 ATA ATA ATA ATA ATA ATA ATA ATTA ATA ATA CTA ATA ATA TTA ATTA
1 ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA A-TA
53619955 ATA
1 ATA
53619958 GATCTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 35 0.85
4 6 0.15
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:53619934 original size:22 final size:22
Alignment explanation
Indices: 53619909--53619957 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
53619899 TTAATTATGA
53619909 TAATAATAATAATAATAATAAT
1 TAATAATAATAATAATAATAAT
* *
53619931 TAATAATACTAATAATATTAAT
1 TAATAATAATAATAATAATAAT
53619953 TAATA
1 TAATA
53619958 GATCTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TAATAATAATAATAATAATAAT
Found at i:53620996 original size:162 final size:162
Alignment explanation
Indices: 53620818--53621131 Score: 470
Period size: 162 Copynumber: 1.9 Consensus size: 162
53620808 CTTTTCAATT
* * *
53620818 TAGTCCTTTGACTGTTTGACTGTACCATAGGCTGCCACGTGTCACTTTTCAGATTATTTCTGCAT
1 TAGTCCTTTAACTGTTTGACTGCACCAAAGGCTGCCACGTGTCACTTTTCAGATTATTTCTGCAT
* * *
53620883 TTAGTCCTTTTTATTTTTTTATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTACG
66 TTAGTCCTTTTTA-TTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTTTA-TTTAATTACA
*
53620946 AAATTGGCCCAATAATTTTTCAAGGTATATAAAC
129 AAATTGGCCCAAAAATTTTTCAAGGTATATAAAC
* * **
53620980 TAGTCCTTTAACTGTTTGACTGCACCAAAGGTTGCCACGTGTCATTTTTTGGATTATTTCTGCAT
1 TAGTCCTTTAACTGTTTGACTGCACCAAAGGCTGCCACGTGTCACTTTTCAGATTATTTCTGCAT
* *
53621045 TTAGTCCTTTTTATTTTTAATTTATTTTAATTTAATCCTTAAATCGACTTTTATTTAATTACAAA
66 TTAGTCCTTTTTATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAA
*
53621110 ATTGGTCCAAAAATTTTTCAAG
131 ATTGGCCCAAAAATTTTTCAAG
53621132 ATTTTCAAAT
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
161 23 0.17
162 109 0.80
163 4 0.03
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.46
Consensus pattern (162 bp):
TAGTCCTTTAACTGTTTGACTGCACCAAAGGCTGCCACGTGTCACTTTTCAGATTATTTCTGCAT
TTAGTCCTTTTTATTTTTAATTTATTTTAATTTAATCCTCAAATCAACTTTTATTTAATTACAAA
ATTGGCCCAAAAATTTTTCAAGGTATATAAAC
Found at i:53621262 original size:30 final size:30
Alignment explanation
Indices: 53621223--53621425 Score: 264
Period size: 30 Copynumber: 6.7 Consensus size: 30
53621213 CCCTAAATTA
53621223 TCCAGAAATTACATTTTGACCCCAAAAC-TT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
*
53621253 TCCTAAAATTACATTTTGACCCTAAAACTTT
1 TCC-AAAATTACATTTTGACCCCAAAACTTT
* *
53621284 TCCAAAATTATATTTTTGACCCCGAAACTTT
1 TCCAAAATTACA-TTTTGACCCCAAAACTTT
* * * *
53621315 ACTAAAAATACATTTTGACCTCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
53621345 TCCAAATTTACATTTTGATCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
53621375 TCCAAAATTATATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
53621405 TCCAAAATTACATTTTAACCC
1 TCCAAAATTACATTTTGACCC
53621426 TGATTTCACC
Statistics
Matches: 149, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
30 119 0.80
31 30 0.20
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.36
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:53621449 original size:30 final size:30
Alignment explanation
Indices: 53621408--53621722 Score: 164
Period size: 29 Copynumber: 10.5 Consensus size: 30
53621398 AAACTTTTCC
* *
53621408 AAAATTA-CATTTTAACCCTGATTTCACCG
1 AAAATTACCATTTTAACCCCGATTTCATCG
* * * **
53621437 AAAATTACCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCATCG
*
53621466 AAAATT-CCATTTTTAACCCCGGTTTCATCG
1 AAAATTACCA-TTTTAACCCCGATTTCATCG
* *
53621496 AAAATTACCATTTTACACCCGAAGCCTCGATTTCACCA
1 AAAATTACCATTTTA-A--C----CC-CGATTTCATCG
* ** * *
53621534 AAAATTACCATTTTACCCCCGA-AGCTTCT
1 AAAATTACCATTTTAACCCCGATTTCATCG
****
53621563 AAAATTTTGTTTTTAACCCCGATTTCATCG
1 AAAATTACCATTTTAACCCCGATTTCATCG
** * *
53621593 AAAATTACCATTTT-ACCCCGA-AGCTTCT
1 AAAATTACCATTTTAACCCCGATTTCATCG
*
53621621 AAAATT-CCGTTTTTAACCCCGATTTCATCG
1 AAAATTACC-ATTTTAACCCCGATTTCATCG
** * * * **
53621651 AAAATTGTCATTTTACCCCCGA-ATCTTTT
1 AAAATTACCATTTTAACCCCGATTTCATCG
* *
53621680 AAAATT-CCATTTTTAACCCCGATTACA-CC
1 AAAATTACCA-TTTTAACCCCGATTTCATCG
53621709 AAAATTACCATTTT
1 AAAATTACCATTTT
53621723 GCCCCGGGTA
Statistics
Matches: 208, Mismatches: 58, Indels: 40
0.68 0.19 0.13
Matches are distributed among these distances:
27 2 0.01
28 18 0.09
29 88 0.42
30 66 0.32
31 7 0.03
33 1 0.00
35 1 0.00
37 2 0.01
38 23 0.11
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCATCG
Found at i:53621450 original size:60 final size:60
Alignment explanation
Indices: 53621223--53621515 Score: 199
Period size: 60 Copynumber: 4.8 Consensus size: 60
53621213 CCCTAAATTA
* * * * *
53621223 TCCAGAAATTACA-TTTTGACCCCAAAACTTT-CCTAAAATTACATTTTGACCCTAAAACTTT
1 TCCA-AAATTACATTTTTAACCCC--GACTTTACCGAAAATTACATTTTAACCCCAAAACTTT
* * * * * *
53621284 TCCAAAATTATATTTTTGACCCCGAAACTTTA-CTAAAAATACATTTTGACCTCAAAACTTT
1 TCCAAAATTACATTTTTAACCCCG--ACTTTACCGAAAATTACATTTTAACCCCAAAACTTT
* * * ** * *
53621345 TCCAAATTTACATTTTGATCCCAAAACTTTTCC-AAAATTATATTTTAACCCCAAAACTTT
1 TCCAAAATTACATTTTTAACCC-CGACTTTACCGAAAATTACATTTTAACCCCAAAACTTT
* * * *
53621405 TCCAAAATTACA-TTTTAACCCTGA-TTTCACCGAAAATTACCATTTTACCCCCGAATCTTT
1 TCCAAAATTACATTTTTAACCCCGACTTT-ACCGAAAATTA-CATTTTAACCCCAAAACTTT
* * *
53621465 T--AAAATTCCATTTTTAACCCCG-GTTTCATCGAAAATTACCATTTTACACCC
1 TCCAAAATTACATTTTTAACCCCGACTTT-ACCGAAAATTA-CATTTTA-ACCC
53621516 GAAGCCTCGA
Statistics
Matches: 189, Mismatches: 31, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
57 3 0.02
58 11 0.06
59 46 0.24
60 66 0.35
61 63 0.33
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.36
Consensus pattern (60 bp):
TCCAAAATTACATTTTTAACCCCGACTTTACCGAAAATTACATTTTAACCCCAAAACTTT
Found at i:53621469 original size:29 final size:29
Alignment explanation
Indices: 53621437--53621518 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 29
53621427 GATTTCACCG
*
53621437 AAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTACCATTTTACCCCCGAATCTTCT
* ** * *
53621466 AAAATT-CCATTTTTAACCCCGGTTTCATCG
1 AAAATTACCA-TTTT-ACCCCCGAATCTTCT
*
53621496 AAAATTACCATTTTACACCCGAA
1 AAAATTACCATTTTACCCCCGAA
53621519 GCCTCGATTT
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
28 3 0.08
29 15 0.38
30 19 0.47
31 3 0.08
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGAATCTTCT
Found at i:53621480 original size:59 final size:58
Alignment explanation
Indices: 53621408--53621518 Score: 168
Period size: 59 Copynumber: 1.9 Consensus size: 58
53621398 AAACTTTTCC
* *
53621408 AAAATTACATTTTAACCCTGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTT
1 AAAATTACATTTTAACCCCGATTTCACCGAAAATTACCATTTTACACCCGAATCTTTT
* * *
53621466 AAAATTCCATTTTTAACCCCGGTTTCATCGAAAATTACCATTTTACACCCGAA
1 AAAATTACA-TTTTAACCCCGATTTCACCGAAAATTACCATTTTACACCCGAA
53621519 GCCTCGATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 8 0.17
59 39 0.83
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.34
Consensus pattern (58 bp):
AAAATTACATTTTAACCCCGATTTCACCGAAAATTACCATTTTACACCCGAATCTTTT
Found at i:53621538 original size:97 final size:96
Alignment explanation
Indices: 53621427--53621616 Score: 308
Period size: 97 Copynumber: 2.0 Consensus size: 96
53621417 TTTTAACCCT
* * * *
53621427 GATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGGTTTC
1 GATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTC
53621492 ATCGAAAATTACCATTTTACACCCGAAGCCTC
66 ATCGAAAATTACCATTTTAC-CCCGAAGCCTC
***
53621524 GATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTTTGTTTTTAACCCCGATTTC
1 GATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTC
53621589 ATCGAAAATTACCATTTTACCCCGAAGC
66 ATCGAAAATTACCATTTTACCCCGAAGC
53621617 TTCTAAAATT
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
96 8 0.09
97 78 0.91
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (96 bp):
GATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCATTTTTAACCCCGATTTC
ATCGAAAATTACCATTTTACCCCGAAGCCTC
Found at i:53621636 original size:58 final size:59
Alignment explanation
Indices: 53621523--53621727 Score: 288
Period size: 58 Copynumber: 3.5 Consensus size: 59
53621513 CCCGAAGCCT
* * **
53621523 CGATTTCACCAAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTTTGTTTTTAACCC
1 CGATTTCATCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCGTTTTTAACCC
53621582 CGATTTCATCGAAAATTACCATTTTA-CCCCGAAGCTTCTAAAATTCCGTTTTTAACCC
1 CGATTTCATCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCGTTTTTAACCC
** * * *
53621640 CGATTTCATCGAAAATTGTCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCC
1 CGATTTCATCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCGTTTTTAACCC
* * *
53621699 CGATTACA-CCAAAATTACCATTTTGCCCC
1 CGATTTCATCGAAAATTACCATTTTACCCC
53621728 GGGTATCCAT
Statistics
Matches: 131, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
58 71 0.54
59 60 0.46
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (59 bp):
CGATTTCATCGAAAATTACCATTTTACCCCCGAAGCTTCTAAAATTCCGTTTTTAACCC
Found at i:53621668 original size:29 final size:30
Alignment explanation
Indices: 53621573--53621672 Score: 91
Period size: 30 Copynumber: 3.4 Consensus size: 30
53621563 AAAATTTTGT
**
53621573 TTTTAACCCCGATTTCATCGAAAATTACCA
1 TTTTAACCCCGATTTCATCGAAAATTGTCA
** * *
53621603 TTTT-ACCCCGA-AGCTTCTAAAATTCCGT--
1 TTTTAACCCCGATTTCATCGAAAATT--GTCA
53621631 TTTTAACCCCGATTTCATCGAAAATTGTCA
1 TTTTAACCCCGATTTCATCGAAAATTGTCA
*
53621661 TTTTACCCCCGA
1 TTTTAACCCCGA
53621673 ATCTTTTAAA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
28 15 0.28
29 14 0.26
30 24 0.45
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (30 bp):
TTTTAACCCCGATTTCATCGAAAATTGTCA
Found at i:53626231 original size:115 final size:115
Alignment explanation
Indices: 53626079--53626302 Score: 367
Period size: 115 Copynumber: 1.9 Consensus size: 115
53626069 AATTCAGTTG
** * *
53626079 CTAAAATAGGATTTGTCAACTCGATTAACTCAAAATTTTTTGACTCGATTCAACTTGACTCAATC
1 CTAAAATAGGATTCATCAACTCGATCAACTCAAAATTTTTTGACTCAATTCAACTTGACTCAATC
53626144 GAATACTCACCCCTACCTTTGGGGTATCTTATATTAGTATCATACGGTTA
66 GAATACTCACCCCTACCTTTGGGGTATCTTATATTAGTATCATACGGTTA
* * ** *
53626194 CTAAAATAGGATTCATCAACTCGATCAACTTAAAATTTTTTTACTCAATTTGATTTGACTCAATC
1 CTAAAATAGGATTCATCAACTCGATCAACTCAAAATTTTTTGACTCAATTCAACTTGACTCAATC
53626259 GAATACTCACCCCTACCTTTGGGGTATCTTATATTAGTATCATA
66 GAATACTCACCCCTACCTTTGGGGTATCTTATATTAGTATCATA
53626303 TGGCTGACAG
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
115 100 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.37
Consensus pattern (115 bp):
CTAAAATAGGATTCATCAACTCGATCAACTCAAAATTTTTTGACTCAATTCAACTTGACTCAATC
GAATACTCACCCCTACCTTTGGGGTATCTTATATTAGTATCATACGGTTA
Found at i:53626619 original size:14 final size:14
Alignment explanation
Indices: 53626600--53626627 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53626590 AGAAAAGATT
53626600 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53626614 TTTAATTAATTAAA
1 TTTAATTAATTAAA
53626628 ATTTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:53628759 original size:31 final size:31
Alignment explanation
Indices: 53628724--53628784 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
53628714 AACAACCTAG
*
53628724 TGACTTAAATAAAAATTTTTAAATAGTTCAT
1 TGACTTAAATAAAAACTTTTAAATAGTTCAT
* *
53628755 TGACTTAAATGAAAACTTTTGAATAGTTCA
1 TGACTTAAATAAAAACTTTTAAATAGTTCA
53628785 ATGATCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTAAATAGTTCAT
Found at i:53634868 original size:22 final size:22
Alignment explanation
Indices: 53634826--53634868 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
53634816 TTTTTAAATA
* *
53634826 TTTATGAAAAATACTCTAAAAC
1 TTTATCAAAAATACTCCAAAAC
53634848 TTTATCAAATAATA-TCCAAAA
1 TTTATCAAA-AATACTCCAAAA
53634869 ATCATAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.14, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTATCAAAAATACTCCAAAAC
Found at i:53635532 original size:22 final size:22
Alignment explanation
Indices: 53635506--53635557 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
53635496 TGTTTCTTTG
*
53635506 TTATTTTGCTGTCATTTCACTTA
1 TTATTTTGCTATCATTTCA-TTA
* *
53635529 -TATTTTACTATCATTTTATTA
1 TTATTTTGCTATCATTTCATTA
53635550 TTATTTTG
1 TTATTTTG
53635558 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 21 0.88
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (22 bp):
TTATTTTGCTATCATTTCATTA
Found at i:53636654 original size:4 final size:4
Alignment explanation
Indices: 53636647--53636676 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
53636637 AAACATATAT
53636647 ATTG ATTG ATTG ATTG ATTG ATTG ATTG AT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG AT
53636677 GAGAAGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
ATTG
Found at i:53644772 original size:21 final size:21
Alignment explanation
Indices: 53644743--53644784 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
53644733 CCTTACACCG
*
53644743 CGTTGTGGATAAA-CTACTCAT
1 CGTTATGGATAAATC-ACTCAT
53644764 CGTTATGGATAAATCACTCAT
1 CGTTATGGATAAATCACTCAT
53644785 AGTTGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (21 bp):
CGTTATGGATAAATCACTCAT
Found at i:53646554 original size:31 final size:30
Alignment explanation
Indices: 53646484--53646563 Score: 81
Period size: 31 Copynumber: 2.7 Consensus size: 30
53646474 TGTGTAATTG
* * *
53646484 TATACATG-AATTTTAATTTGGTGCAATTA
1 TATACATGAAACTCTAATTTGGTGCAAATA
*
53646513 TATACATGAAACTCTAATTGTGGTTCAAATA
1 TATACATGAAACTCTAATT-TGGTGCAAATA
** *
53646544 TATATTTGAAACTTTAATTT
1 TATACATGAAACTCTAATTT
53646564 TGATTTAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 8 0.19
30 9 0.21
31 25 0.60
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (30 bp):
TATACATGAAACTCTAATTTGGTGCAAATA
Found at i:53646824 original size:30 final size:31
Alignment explanation
Indices: 53646759--53646843 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 31
53646749 ATTAAATTAA
* * * *
53646759 AATTAAAATTTTAAGTATACATTTGAATCAC
1 AATTAAAATTTCAAGTATATAATTGTATCAC
* * * *
53646790 AATTAGAGTTTCACGTGTATAATTGTATCA-
1 AATTAAAATTTCAAGTATATAATTGTATCAC
53646820 AATTAAAATTTCAAGTATATAATT
1 AATTAAAATTTCAAGTATATAATT
53646844 ACACATTAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
30 20 0.48
31 22 0.52
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.40
Consensus pattern (31 bp):
AATTAAAATTTCAAGTATATAATTGTATCAC
Found at i:53651512 original size:14 final size:14
Alignment explanation
Indices: 53651479--53651505 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53651469 GGGAATAGTA
53651479 AAATATTAAAAAAT
1 AAATATTAAAAAAT
53651493 AAATATTAAAAAA
1 AAATATTAAAAAA
53651506 AAGATATGTG
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATATTAAAAAAT
Found at i:53651669 original size:17 final size:17
Alignment explanation
Indices: 53651649--53651684 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
53651639 GTTCTTTGTT
*
53651649 GGTAATTGTTCATCGAA
1 GGTAATTGTTCATCAAA
53651666 GGTAATTGTTCATCAAA
1 GGTAATTGTTCATCAAA
53651683 GG
1 GG
53651685 AGGCTACGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (17 bp):
GGTAATTGTTCATCAAA
Found at i:53652662 original size:30 final size:30
Alignment explanation
Indices: 53652583--53652650 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
53652573 TTTTTGGTCA
*
53652583 AATTTTGTACTCAAACTTGAAAATTTTCCT
1 AATTTGGTACTCAAACTTGAAAATTTTCCT
53652613 AATTTGGTACTCAAACTTGAAAATTTTCCT
1 AATTTGGTACTCAAACTTGAAAATTTTCCT
53652643 AATTTGGT
1 AATTTGGT
53652651 GCCTAAACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (30 bp):
AATTTGGTACTCAAACTTGAAAATTTTCCT
Found at i:53686546 original size:21 final size:22
Alignment explanation
Indices: 53686502--53686549 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
53686492 TAATTGAAAA
* * *
53686502 AAATCGATTAAATTAAATAGTT
1 AAATTGATTAAATTAAAAAATT
53686524 AAATTGATTAAA-TAAAAAATT
1 AAATTGATTAAATTAAAAAATT
53686545 AAATT
1 AAATT
53686550 TTTAATAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.35
Consensus pattern (22 bp):
AAATTGATTAAATTAAAAAATT
Found at i:53690137 original size:258 final size:261
Alignment explanation
Indices: 53689669--53690195 Score: 738
Period size: 258 Copynumber: 2.0 Consensus size: 261
53689659 TGAAAAACTA
* * * * * *
53689669 AAGAATGGGAAGTACATTGTCAAAGTTTCGGGTGAAACTTATTCGTGCCCCTTTTGTCCTCAGAA
1 AAGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCTCAGAA
* * *
53689734 GAAAAAGCCAAATTACCGGTACATGGATCTCGTCCAGCATGCTTCTGCTGTGGCAAATACTAGTT
66 GAAAAA-CC--ATTACCGATACATAGACCTCGTCCAGCATGCTTCTGCTGTGGCAAATACTAGTT
* *
53689799 CTGCAAGAAGAACACCAATAGTGAAAGCCAATCACCTGGCTTTGTCGAAATATTTGGAAAAGGAT
128 CTGCAAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTTTGGCGAAATATTTGGAAAAGGAT
* * * *
53689864 CTTGCCCCTTTGGTTAGTTCATTGAAACCTG-TGACTCAGGAGGATCCTCTTAGTGGTTGTGACC
193 CTCGCCCCATTGGTTAGTTCATTGAAACCTGCAG-CTCAAGAGGATCCTCTTAGTGGTTGTGACC
*
53689928 ATGAT
257 ACGAT
*
53689933 AAGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCTGAGAA
1 AAGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCTCAGAA
* * * *
53689998 G-AAAA-C-TTACCGATACTTAGACCTCGTCCAGCATGCTTCTGGTGTGGGAAATAGTAGTTCTG
66 GAAAAACCATTACCGATACATAGACCTCGTCCAGCATGCTTCTGCTGTGGCAAATACTAGTTCTG
* * *
53690060 CAAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTTTGGCTAAGTATTTGGAAAAGGGTCTC
131 CAAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTTTGGCGAAATATTTGGAAAAGGATCTC
** *
53690125 GTGCCATTGGTTAGTTCATTGAAACCTGCAGCTCAAGTGGATCCTCTTAGTGGTTGTGACCACGA
196 GCCCCATTGGTTAGTTCATTGAAACCTGCAGCTCAAGAGGATCCTCTTAGTGGTTGTGACCACGA
53690190 T
261 T
*
53690191 GAGAA
1 AAGAA
53690196 ATTTGTTTGG
Statistics
Matches: 234, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
258 169 0.72
259 1 0.00
261 1 0.00
263 4 0.02
264 59 0.25
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (261 bp):
AAGAATGGGAAGCACATTGTCAAAGCTTCAGATGAAACTTATACGTGCCCCTATTGTCCTCAGAA
GAAAAACCATTACCGATACATAGACCTCGTCCAGCATGCTTCTGCTGTGGCAAATACTAGTTCTG
CAAGAAGAACACCAATAATGAAAGCCAATCACCTGGCTTTGGCGAAATATTTGGAAAAGGATCTC
GCCCCATTGGTTAGTTCATTGAAACCTGCAGCTCAAGAGGATCCTCTTAGTGGTTGTGACCACGA
T
Found at i:53694954 original size:21 final size:21
Alignment explanation
Indices: 53694911--53694954 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
53694901 ATTTAATTTT
* * * *
53694911 TATATAATATAAATTACATAA
1 TATATAAAATAAAATAAAAAA
53694932 TATATAAAATAAAATAAAAAA
1 TATATAAAATAAAATAAAAAA
53694953 TA
1 TA
53694955 ACATATCATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
TATATAAAATAAAATAAAAAA
Found at i:53702630 original size:14 final size:14
Alignment explanation
Indices: 53702588--53702630 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
53702578 AATGCAAGTG
53702588 ACTAAAATATAATA
1 ACTAAAATATAATA
** *
53702602 TTTTAAATATAAATA
1 ACTAAAATAT-AATA
53702617 ACTAAAATATAATA
1 ACTAAAATATAATA
53702631 TGAGAGAAAC
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (14 bp):
ACTAAAATATAATA
Found at i:53705069 original size:6 final size:6
Alignment explanation
Indices: 53705044--53705082 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
53705034 ACAATTCATA
* * *
53705044 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
53705083 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:53713214 original size:18 final size:16
Alignment explanation
Indices: 53713182--53713225 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
53713172 ATGGAATGAG
53713182 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
53713198 AATAAA--TTTAATTA
1 AATAAATTTTTAATTA
*
53713212 ATTAAAATTTTTAA
1 AAT-AAATTTTTAA
53713226 ACCCTAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 6 0.25
17 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:53720716 original size:31 final size:30
Alignment explanation
Indices: 53720678--53720804 Score: 92
Period size: 31 Copynumber: 4.1 Consensus size: 30
53720668 ATTGTGTTTT
**
53720678 GGGGTTTATTTAAAATTTTCAATAACTTTAA
1 GGGGTTTAACTAAAATTTTCAA-AACTTTAA
*
53720709 GGGGTTTAACTAAAATTTTCAAAACTTTTA
1 GGGGTTTAACTAAAATTTTCAAAACTTTAA
*** * * * *
53720739 GAATATTTGATTAAAATTTTTAAAAATTTTAA
1 G-GGGTTTAACTAAAA-TTTTCAAAACTTTAA
* * * * *
53720771 AGGATTTAACCAAAATTTTCCAAACTTTTA
1 GGGGTTTAACTAAAATTTTCAAAACTTTAA
53720801 GGGG
1 GGGG
53720805 CCAGGATACG
Statistics
Matches: 71, Mismatches: 23, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
30 21 0.30
31 38 0.54
32 12 0.17
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.41
Consensus pattern (30 bp):
GGGGTTTAACTAAAATTTTCAAAACTTTAA
Found at i:53727946 original size:20 final size:18
Alignment explanation
Indices: 53727910--53727970 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
53727900 TATTCCAAAC
* *
53727910 TAAAAAATAATATAAAAA
1 TAAAAATTAATACAAAAA
*
53727928 TAATAATATTAATACAAAAT
1 TAA-AA-ATTAATACAAAAA
53727948 TAAAAATTAAT-CAATAAA
1 TAAAAATTAATACAA-AAA
53727966 -AAAAA
1 TAAAAA
53727971 ACCTAAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
17 8 0.22
18 11 0.31
19 4 0.11
20 13 0.36
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAATTAATACAAAAA
Found at i:53728996 original size:21 final size:21
Alignment explanation
Indices: 53728970--53729011 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53728960 TATTTTAGAC
* *
53728970 ATACATTTTTAGTTTATATAT
1 ATACATATTTAATTTATATAT
*
53728991 ATACATATTTAATTTTTATAT
1 ATACATATTTAATTTATATAT
53729012 TATTATTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (21 bp):
ATACATATTTAATTTATATAT
Found at i:53729794 original size:16 final size:16
Alignment explanation
Indices: 53729773--53729805 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53729763 ATTTGATTTT
53729773 TTTTATA-ATTTATAAA
1 TTTTATATATTT-TAAA
53729789 TTTTATATATTTTAAA
1 TTTTATATATTTTAAA
53729805 T
1 T
53729806 GCATTTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATATATTTTAAA
Found at i:53730029 original size:90 final size:90
Alignment explanation
Indices: 53729925--53730101 Score: 345
Period size: 90 Copynumber: 2.0 Consensus size: 90
53729915 TCAATGTTAC
53729925 ATTAACTTATTTCAATGATGTTAGTGAAATATTAAAAAATAATTTATAATTTTTAAATTTTGATA
1 ATTAACTTATTTCAATGATGTTAGTGAAATATTAAAAAATAATTTATAATTTTTAAATTTTGATA
53729990 CCAATTGAACCTAAGTGAAAAAGAA
66 CCAATTGAACCTAAGTGAAAAAGAA
53730015 ATTAACTTATTTCAATGATGTTAGTGAAATATTAAAAAATAATTTATAATTTTTAAATTTTGATA
1 ATTAACTTATTTCAATGATGTTAGTGAAATATTAAAAAATAATTTATAATTTTTAAATTTTGATA
*
53730080 CCAATTGAATCTAAGTGAAAAA
66 CCAATTGAACCTAAGTGAAAAA
53730102 AAAAATGATG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (90 bp):
ATTAACTTATTTCAATGATGTTAGTGAAATATTAAAAAATAATTTATAATTTTTAAATTTTGATA
CCAATTGAACCTAAGTGAAAAAGAA
Found at i:53730135 original size:83 final size:87
Alignment explanation
Indices: 53729958--53730142 Score: 204
Period size: 90 Copynumber: 2.1 Consensus size: 87
53729948 GTGAAATATT
*
53729958 AAAAAATAATTTATAATTTTTAAATTTTGATACCAATTGAACCTAAGTGAAAAAGAAATTAACTT
1 AAAAAATAATTTATAATTTTTAAATTTTGATACCAATTGAACCTAAGTGAAAAAGAAA-TAACTG
* * * **
53730023 ATTTCAATGATGTTAGTGAAATATT
65 ATTTCAAT-ATATTAG-AAAAGAGA
*
53730048 AAAAAATAATTTATAATTTTTAAATTTTGATACCAATTGAATCTAAGTGAAAAA-AAA-AA-TGA
1 AAAAAATAATTTATAATTTTTAAATTTTGATACCAATTGAACCTAAGTGAAAAAGAAATAACTGA
*
53730110 TGTT-TAT-TATTA-AAAACGAGA
66 T-TTCAATATATTAGAAAA-GAGA
53730131 AAAAAA-AATTTA
1 AAAAAATAATTTA
53730143 AGTACCAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
82 9 0.11
83 7 0.08
84 4 0.05
86 5 0.06
87 4 0.05
89 3 0.04
90 53 0.62
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.36
Consensus pattern (87 bp):
AAAAAATAATTTATAATTTTTAAATTTTGATACCAATTGAACCTAAGTGAAAAAGAAATAACTGA
TTTCAATATATTAGAAAAGAGA
Found at i:53732403 original size:285 final size:286
Alignment explanation
Indices: 53731883--53732457 Score: 759
Period size: 285 Copynumber: 2.0 Consensus size: 286
53731873 GGACCCTAAC
*
53731883 TTGGATAAAATAGTAGTAAAAGATTTTGAGCCTTCTATCTTCAAGGTGATGCTTCCTTTTACTTT
1 TTGGATAAAATAGTAATAAAAGATTTTGAGCCTTCTATCTTCAAGGTGATGCTTCCTTTTACTTT
* * *
53731948 CTTTTGGTTTTGGACTTTGAAGAATAAACCAACAATTAAGTATATTGCATAAGGAAACCCTTGAA
66 C---T--TTTTGGACTTTGAAGAATAAACCAACAATAAAGCATATTGCATAAGCAAACCCTTGAA
* * * *
53732013 GTAAAAATATGATTCTTCTCAATTAATTGAAATAGAAATAGGGTTCAATAGATTGTAGTTCTTAT
126 G-AAAAATATGATTCTTCTCAATTAATTGAAATAGAAATAGGATTAAACAAATTGTAGTTCTTAT
* *
53732078 ATTTGTCTGGATGTGAAGATCCAAGTGTAGAGTTTAGTTATATAGATGTGCTTTTTCATTCATTG
190 ATTTGCCTGGATGTGAAGATCCAAGTATAGAGTTTAGTTATATAGATGTGCTTTTTCATTCATTG
53732143 GCTAATGAAAGGATCAACTCAAATGAGAATTCAT
255 GCTAATG-AA-GATCAACTCAAATGAGAATTCAT
* * *
53732177 TTGGATAAAGA-AGTAATGAAAGATTTTGAGCCTTCTATCTTCGAGGTGATGCTTCCTTTTAGTT
1 TTGGATAAA-ATAGTAATAAAAGATTTTGAGCCTTCTATCTTCAAGGTGATGCTTCCTTTTACTT
* *
53732241 TC-TTTTGGACTTTGAAGAATGAACCTTA-AATAAAGCATATTGCATAAGCAAACCCTTG-A-AA
65 TCTTTTTGGACTTTGAAGAATAAACC-AACAATAAAGCATATTGCATAAGCAAACCCTTGAAGAA
* * * * *
53732302 TAATGTGATTCTTCGT-AATTCATTTG-ATTAGAAATAGGATTAAACAAATTGTGGTTCTTATAT
129 AAATATGATTCTTC-TCAATT-AATTGAAATAGAAATAGGATTAAACAAATTGTAGTTCTTATAT
* * * *
53732365 TTGCCTGGATGTGAAGATCCAAGTATAGATTTTAGTTATGTTGATGTGCTTTTTCATTTATTGGC
192 TTGCCTGGATGTGAAGATCCAAGTATAGAGTTTAGTTATATAGATGTGCTTTTTCATTCATTGGC
**
53732430 TAATGAAGATCGTCTCAAATGAGAATTC
257 TAATGAAGATCAACTCAAATGAGAATTC
53732458 GTCATTACGC
Statistics
Matches: 251, Mismatches: 26, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
283 19 0.08
284 2 0.01
285 113 0.45
286 5 0.02
287 1 0.00
288 49 0.20
289 1 0.00
294 60 0.24
295 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (286 bp):
TTGGATAAAATAGTAATAAAAGATTTTGAGCCTTCTATCTTCAAGGTGATGCTTCCTTTTACTTT
CTTTTTGGACTTTGAAGAATAAACCAACAATAAAGCATATTGCATAAGCAAACCCTTGAAGAAAA
ATATGATTCTTCTCAATTAATTGAAATAGAAATAGGATTAAACAAATTGTAGTTCTTATATTTGC
CTGGATGTGAAGATCCAAGTATAGAGTTTAGTTATATAGATGTGCTTTTTCATTCATTGGCTAAT
GAAGATCAACTCAAATGAGAATTCAT
Found at i:53736148 original size:18 final size:18
Alignment explanation
Indices: 53736125--53736167 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
53736115 GAATAAGTTT
53736125 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
53736143 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
53736161 TTAATTA
1 TTAATTA
53736168 CTACTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:53737909 original size:4 final size:4
Alignment explanation
Indices: 53737900--53737926 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
53737890 GTAACTTATG
53737900 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
53737927 TTATATTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:53747485 original size:18 final size:17
Alignment explanation
Indices: 53747455--53747519 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 17
53747445 TTATGTTTTT
*
53747455 TTTTTAATT-TTTTAAA
1 TTTTAAATTATTTTAAA
*
53747471 TTTTAAATTTATTTT-TA
1 TTTTAAA-TTATTTTAAA
* *
53747488 TTTTTAATAATTTTATAA
1 TTTTAAATTATTTTA-AA
53747506 TTTTTAAATTATTT
1 -TTTTAAATTATTT
53747520 AGTGATGTAT
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
16 12 0.32
17 9 0.24
18 5 0.14
19 11 0.30
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAAATTATTTTAAA
Found at i:53747499 original size:27 final size:28
Alignment explanation
Indices: 53747455--53747508 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
53747445 TTATGTTTTT
*
53747455 TTTTTAATTTTTTAAATTTTA-AATTTA
1 TTTTTAATTTTTAAAATTTTATAATTTA
53747482 TTTTT-ATTTTTAATAATTTTATAATTT
1 TTTTTAATTTTTAA-AATTTTATAATTT
53747509 TTAAATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (28 bp):
TTTTTAATTTTTAAAATTTTATAATTTA
Found at i:53747499 original size:36 final size:33
Alignment explanation
Indices: 53747444--53747519 Score: 91
Period size: 36 Copynumber: 2.2 Consensus size: 33
53747434 GTAAGTGTAT
*
53747444 TTTATGTTTTTTTTTTAATTTTTTAAATTTTAAA
1 TTTAT-TTTTTTTTTTAATTTTATAAATTTTAAA
*
53747478 TTTATTTTTATTTTTAATAATTTTATAATTTTTAAA
1 TTTATTTTT-TTTTT--TAATTTTATAAATTTTAAA
53747514 -TTATTT
1 TTTATTT
53747520 AGTGATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 4 0.11
34 10 0.27
35 6 0.16
36 17 0.46
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (33 bp):
TTTATTTTTTTTTTTAATTTTATAAATTTTAAA
Found at i:53747508 original size:35 final size:34
Alignment explanation
Indices: 53747444--53747519 Score: 93
Period size: 33 Copynumber: 2.2 Consensus size: 34
53747434 GTAAGTGTAT
* *
53747444 TTTATGTTTTTTTTTTAATTTTTTAAA-TTTTAAA
1 TTTAT-TTTTATTTTTAATATTTTAAATTTTTAAA
53747478 TTTATTTTTATTTTTAATAATTTTATAATTTTTAAA
1 TTTATTTTTATTTTTAAT-ATTTTA-AATTTTTAAA
53747514 -TTATTT
1 TTTATTT
53747520 AGTGATGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 12 0.32
34 10 0.27
35 8 0.22
36 7 0.19
ACGTcount: A:0.29, C:0.00, G:0.01, T:0.70
Consensus pattern (34 bp):
TTTATTTTTATTTTTAATATTTTAAATTTTTAAA
Found at i:53759438 original size:16 final size:17
Alignment explanation
Indices: 53759403--53759446 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
53759393 TTTTCATATT
*
53759403 ATTTCGAATTTAAATTA
1 ATTTCGAATTTAAATCA
*
53759420 ATTT-GAATTTAAGTCA
1 ATTTCGAATTTAAATCA
*
53759436 ATTTCAAATTT
1 ATTTCGAATTT
53759447 GAATAATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (17 bp):
ATTTCGAATTTAAATCA
Found at i:53762109 original size:20 final size:20
Alignment explanation
Indices: 53762076--53762114 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
53762066 TTCGGATTTC
*
53762076 GATTTTTCATATTTAATTTTA
1 GATTTTTCAAATTT-ATTTTA
53762097 GATTTTT-AAATTTATTTT
1 GATTTTTCAAATTTATTTT
53762115 GACAAAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 5 0.29
21 7 0.41
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (20 bp):
GATTTTTCAAATTTATTTTA
Found at i:53774116 original size:61 final size:61
Alignment explanation
Indices: 53774018--53774135 Score: 148
Period size: 61 Copynumber: 1.9 Consensus size: 61
53774008 ATTTTGAATT
* * ** *
53774018 ATTAAAATAAAAGCGCCTTAAGAGTATGTTGAGAAAATTGCAAAAAATTT-ATTTTGGTGTG
1 ATTAAAATAAAAGCGCCATAAGAGTAAGACGACAAAATTGC-AAAAATTTCATTTTGGTGTG
* * *
53774079 ATTAAAATGAAAGCGCCATAAGATTAAGACGACAAAATTGCAAAGATTTCATTTTGG
1 ATTAAAATAAAAGCGCCATAAGAGTAAGACGACAAAATTGCAAAAATTTCATTTTGG
53774136 GAGGCCAAGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 7 0.15
61 41 0.85
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (61 bp):
ATTAAAATAAAAGCGCCATAAGAGTAAGACGACAAAATTGCAAAAATTTCATTTTGGTGTG
Found at i:53774836 original size:16 final size:18
Alignment explanation
Indices: 53774817--53774849 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
53774807 CGATTTTATT
53774817 TAATTTT-TATT-TTTCG
1 TAATTTTCTATTCTTTCG
53774833 TAATTTTCTATTCTTTC
1 TAATTTTCTATTCTTTC
53774850 TGAAATCGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.18, C:0.12, G:0.03, T:0.67
Consensus pattern (18 bp):
TAATTTTCTATTCTTTCG
Found at i:53774952 original size:17 final size:17
Alignment explanation
Indices: 53774923--53774955 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53774913 CGTGGTTGAT
53774923 GTTTGATAATATTTATC
1 GTTTGATAATATTTATC
53774940 GTTT-ATAAGTATTTAT
1 GTTTGATAA-TATTTAT
53774956 ATTTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (17 bp):
GTTTGATAATATTTATC
Found at i:53777557 original size:56 final size:57
Alignment explanation
Indices: 53777497--53777612 Score: 198
Period size: 57 Copynumber: 2.1 Consensus size: 57
53777487 TGATATTTAA
*
53777497 TATCTTGCACATTAAGAT-AAAAGGGATTAAGTCAACTCATACAGGTGATTTAATTG
1 TATCTTGCACATTAAGATAAAAAGGGATTAAATCAACTCATACAGGTGATTTAATTG
* *
53777553 TATCTTGCACATTAAGATAAAAAGGGATTAAATCAGCTCATACATGTGATTTAATTG
1 TATCTTGCACATTAAGATAAAAAGGGATTAAATCAACTCATACAGGTGATTTAATTG
53777610 TAT
1 TAT
53777613 TTGTTTCATG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
56 18 0.32
57 38 0.68
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (57 bp):
TATCTTGCACATTAAGATAAAAAGGGATTAAATCAACTCATACAGGTGATTTAATTG
Found at i:53778779 original size:14 final size:14
Alignment explanation
Indices: 53778760--53778786 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53778750 TCAATCAGCG
53778760 ATTTTAGTTTTTTT
1 ATTTTAGTTTTTTT
53778774 ATTTTAGTTTTTT
1 ATTTTAGTTTTTT
53778787 AAATTTGTAC
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:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (14 bp):
ATTTTAGTTTTTTT
Found at i:53779240 original size:32 final size:32
Alignment explanation
Indices: 53779203--53779270 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
53779193 TATATTTCGG
*
53779203 ATTTTC-AAGTTGATAATGGATTTTATT-TCAAT
1 ATTTTCAAAG-TGATAATGGATTTGATTATC-AT
*
53779235 ATTTTCAAAGTGATGATGGATTTGATTATCAT
1 ATTTTCAAAGTGATAATGGATTTGATTATCAT
53779267 ATTT
1 ATTT
53779271 CATTTACATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 27 0.84
33 5 0.16
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.49
Consensus pattern (32 bp):
ATTTTCAAAGTGATAATGGATTTGATTATCAT
Found at i:53780057 original size:21 final size:22
Alignment explanation
Indices: 53780026--53780066 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53780016 ATCAACCTCT
*
53780026 GATCAAATTAAATTAATTAACC
1 GATCAAATTAAATAAATTAACC
*
53780048 GATC-AATTAACTAAATTAA
1 GATCAAATTAAATAAATTAA
53780067 ATCGATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (22 bp):
GATCAAATTAAATAAATTAACC
Found at i:53810103 original size:59 final size:58
Alignment explanation
Indices: 53810016--53810164 Score: 203
Period size: 59 Copynumber: 2.6 Consensus size: 58
53810006 TATGTAATGG
* * * *
53810016 TATATATGAATTTT-AATTTGATTCAATTATAGTAAAACTTTAATTGTGATTTAAATT
1 TATATTTGAATTTTAAATTTGATTCAATTATAGTAAAACTCTAACTGTGATTCAAATT
*
53810073 TATATTTGAATTTTAAAATTTGATTCAATTATAGTGAAACTCTAACTGTGATTCAAATT
1 TATATTTGAATTTT-AAATTTGATTCAATTATAGTAAAACTCTAACTGTGATTCAAATT
*
53810132 TATATTTGAATTTTGAAACTTGATAT-AATTATA
1 TATATTTGAATTTT-AAATTTGAT-TCAATTATA
53810165 CACATTTACA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
57 13 0.16
59 68 0.83
60 1 0.01
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.47
Consensus pattern (58 bp):
TATATTTGAATTTTAAATTTGATTCAATTATAGTAAAACTCTAACTGTGATTCAAATT
Found at i:53817316 original size:14 final size:15
Alignment explanation
Indices: 53817283--53817319 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
53817273 TTTTGTTAAA
53817283 AAAAAAATTAAAGCT
1 AAAAAAATTAAAGCT
**
53817298 AAAAAAATTAAATTT
1 AAAAAAATTAAAGCT
53817313 AAAAAAA
1 AAAAAAA
53817320 ATGAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (15 bp):
AAAAAAATTAAAGCT
Found at i:53818734 original size:25 final size:26
Alignment explanation
Indices: 53818706--53818774 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
53818696 AAAGTAATCT
53818706 TAAAATCTAATTTAAAATA-AAACCC
1 TAAAATCTAATTTAAAATATAAACCC
* * **
53818731 TAAAAACTAA-TTAATATATAAATTC
1 TAAAATCTAATTTAAAATATAAACCC
*
53818756 TAAATTCTAATTTAAAATA
1 TAAAATCTAATTTAAAATA
53818775 CCTAATAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
24 7 0.20
25 21 0.60
26 7 0.20
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAATCTAATTTAAAATATAAACCC
Found at i:53819004 original size:20 final size:20
Alignment explanation
Indices: 53818960--53819000 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
53818950 AGAAGCAAAT
* *
53818960 CTAATTTCTAATATAAAATG
1 CTAATATCTAATATAAAAAG
53818980 CTAATATCTAAT-TAAAAAG
1 CTAATATCTAATATAAAAAG
53818999 CT
1 CT
53819001 TAATTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.37
Consensus pattern (20 bp):
CTAATATCTAATATAAAAAG
Found at i:53822737 original size:2 final size:2
Alignment explanation
Indices: 53822730--53822760 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
53822720 ATGTTTAATA
53822730 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53822761 AAGACTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:53823882 original size:58 final size:58
Alignment explanation
Indices: 53823792--53823910 Score: 238
Period size: 58 Copynumber: 2.1 Consensus size: 58
53823782 ATACAAACAA
53823792 AAGAAAATTACAAACAAACTTAAAAGGGTTGTTGGGTTTCTCTTTTTTCGTGTAACTT
1 AAGAAAATTACAAACAAACTTAAAAGGGTTGTTGGGTTTCTCTTTTTTCGTGTAACTT
53823850 AAGAAAATTACAAACAAACTTAAAAGGGTTGTTGGGTTTCTCTTTTTTCGTGTAACTT
1 AAGAAAATTACAAACAAACTTAAAAGGGTTGTTGGGTTTCTCTTTTTTCGTGTAACTT
53823908 AAG
1 AAG
53823911 CTCATAATCG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.37
Consensus pattern (58 bp):
AAGAAAATTACAAACAAACTTAAAAGGGTTGTTGGGTTTCTCTTTTTTCGTGTAACTT
Found at i:53826824 original size:11 final size:11
Alignment explanation
Indices: 53826808--53826850 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 11
53826798 GACTAACGTA
*
53826808 TATATATTTTT
1 TATATATTATT
53826819 TATATATTATT
1 TATATATTATT
*
53826830 TA-AAATTATT
1 TATATATTATT
53826840 TATA-ATTATT
1 TATATATTATT
53826850 T
1 T
53826851 TCTAACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 16 0.55
11 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (11 bp):
TATATATTATT
Found at i:53828984 original size:30 final size:29
Alignment explanation
Indices: 53828946--53829008 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 29
53828936 TTAAATTAAT
*
53828946 AAAA-ATAAAATTACATTTTAATCTTTTTA
1 AAAATATAAAATTACAATTTAATC-TTTTA
**
53828975 AAAATATAAAATTTTAATTTAATCTTTTA
1 AAAATATAAAATTACAATTTAATCTTTTA
53829004 AAAAT
1 AAAAT
53829009 TATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (29 bp):
AAAATATAAAATTACAATTTAATCTTTTA
Found at i:53837519 original size:21 final size:22
Alignment explanation
Indices: 53837476--53837523 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
53837466 ATTTTAGTGC
*
53837476 ATTTAATATTGTTTATCTGTTGT
1 ATTT-ATATTGTTTAACTGTTGT
*
53837499 ATTTATA-TGTTTAACTTTTGT
1 ATTTATATTGTTTAACTGTTGT
53837520 -TTTA
1 ATTTA
53837524 CTCATAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 12 0.52
22 3 0.13
23 4 0.17
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.62
Consensus pattern (22 bp):
ATTTATATTGTTTAACTGTTGT
Found at i:53845577 original size:5 final size:5
Alignment explanation
Indices: 53845567--53845608 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
53845557 AATAAATAAA
53845567 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA
53845609 ATAGATACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:53855678 original size:30 final size:31
Alignment explanation
Indices: 53855638--53855702 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
53855628 GATCAATTGC
*
53855638 AGTCCCTGTACT-TTCAAATTG-GTAAATTTT
1 AGTCCATGTACTGTTCAAATTGTG-AAATTTT
*
53855668 AGTCCATGTACTGTTCAAATTTTGAAATTTT
1 AGTCCATGTACTGTTCAAATTGTGAAATTTT
53855699 AGTC
1 AGTC
53855703 TTGACCAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 11 0.35
31 19 0.61
32 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (31 bp):
AGTCCATGTACTGTTCAAATTGTGAAATTTT
Found at i:53856795 original size:50 final size:53
Alignment explanation
Indices: 53856729--53856839 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 53
53856719 TTATAATTTG
*
53856729 TAAAATTTTAAATTAATAATGAT-AAAATTAT-AT-T-TTAACTATCAAAATAA
1 TAAAATTTTAAATTAATAAT-ATAAAAATTATAATATATAAACTATCAAAATAA
* * * * *
53856779 TAAAATTTTGATTTAATTATTTAAAAATTATAAATATATAAACTATTAAAATAA
1 TAAAATTTTAAATTAATAATATAAAAATTAT-AATATATAAACTATCAAAATAA
53856833 TAAAATT
1 TAAAATT
53856840 ATATTTTTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
49 1 0.02
50 25 0.50
52 2 0.04
53 1 0.02
54 21 0.42
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (53 bp):
TAAAATTTTAAATTAATAATATAAAAATTATAATATATAAACTATCAAAATAA
Found at i:53866760 original size:30 final size:31
Alignment explanation
Indices: 53866696--53866760 Score: 73
Period size: 30 Copynumber: 2.1 Consensus size: 31
53866686 AAAAGTTATT
* *
53866696 AAAATAGTAAATTTATATTTTTACTATCGTA
1 AAAATAGTAAATTTATATTTTAACTATCCTA
53866727 AAAATA-TATAATTTA-ATTTTAACT-TCCTCA
1 AAAATAGTA-AATTTATATTTTAACTATCCT-A
53866757 AAAA
1 AAAA
53866761 ATTTCTAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
29 3 0.10
30 15 0.50
31 12 0.40
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (31 bp):
AAAATAGTAAATTTATATTTTAACTATCCTA
Found at i:53869691 original size:16 final size:15
Alignment explanation
Indices: 53869648--53869694 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
53869638 TTAGTAGAGT
*
53869648 GAAAGATGAAAAATT
1 GAAAGATGAAAAATA
53869663 GAAAGGATAGAAAAATA
1 GAAA-GAT-GAAAAATA
*
53869680 GAAAGATGGAAAATA
1 GAAAGATGAAAAATA
53869695 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 11 0.39
16 6 0.21
17 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (15 bp):
GAAAGATGAAAAATA
Found at i:53871016 original size:22 final size:22
Alignment explanation
Indices: 53870991--53871070 Score: 70
Period size: 22 Copynumber: 3.5 Consensus size: 22
53870981 TAAACGAAAC
* * *
53870991 AAACGGAGAGTACCGAAGTGCT
1 AAACAGAGAGCACAGAAGTGCT
*
53871013 AAACAGAGAGCACATAAGTGCT
1 AAACAGAGAGCACAGAAGTGCT
*
53871035 AAGTAACAGAGAGCACATAAAGTGCT
1 -A--AACAGAGAGCACA-GAAGTGCT
*
53871061 AAACATAGAG
1 AAACAGAGAG
53871071 TACACAAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
22 18 0.38
23 9 0.19
25 14 0.29
26 7 0.15
ACGTcount: A:0.45, C:0.16, G:0.25, T:0.14
Consensus pattern (22 bp):
AAACAGAGAGCACAGAAGTGCT
Found at i:53871047 original size:25 final size:26
Alignment explanation
Indices: 53871014--53871062 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
53871004 CGAAGTGCTA
53871014 AACAGAGAGCACAT-AAGTGCTAAGT
1 AACAGAGAGCACATAAAGTGCTAAGT
53871039 AACAGAGAGCACATAAAGTGCTAA
1 AACAGAGAGCACATAAAGTGCTAA
53871063 ACATAGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 14 0.61
26 9 0.39
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.14
Consensus pattern (26 bp):
AACAGAGAGCACATAAAGTGCTAAGT
Found at i:53871065 original size:23 final size:23
Alignment explanation
Indices: 53871006--53871080 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
53870996 GAGAGTACCG
53871006 AAGTGCTAAACAGAGAGCACAT-
1 AAGTGCTAAACAGAGAGCACATA
53871028 AAGTGCTAAGTAACAGAGAGCACATA
1 AAGTGCT-A--AACAGAGAGCACATA
* * *
53871054 AAGTGCTAAACATAGAGTACACA
1 AAGTGCTAAACAGAGAGCACATA
53871077 AAGT
1 AAGT
53871081 ACTGAGCACA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
22 7 0.15
23 17 0.37
25 15 0.33
26 7 0.15
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (23 bp):
AAGTGCTAAACAGAGAGCACATA
Found at i:53871070 original size:25 final size:23
Alignment explanation
Indices: 53871006--53871070 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 23
53870996 GAGAGTACCG
53871006 AAGTGCTAAAC-AGAGAGCACAT
1 AAGTGCTAAACAAGAGAGCACAT
53871028 AAGTGCTAAGTA-ACAGAGAGCACAT
1 AAGTGCTAA--ACA-AGAGAGCACAT
53871053 AAAGTGCTAAACATAGAG
1 -AAGTGCTAAACA-AGAG
53871071 TACACAAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 9 0.25
24 2 0.06
25 16 0.44
26 9 0.25
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (23 bp):
AAGTGCTAAACAAGAGAGCACAT
Found at i:53871076 original size:25 final size:23
Alignment explanation
Indices: 53871006--53871080 Score: 66
Period size: 25 Copynumber: 3.2 Consensus size: 23
53870996 GAGAGTACCG
*
53871006 AAGTGCTAAACAGAGAG-CACAT
1 AAGTGCTAAACACAGAGACACAT
53871028 AAGTGCTAAGTA-ACAGAGAGCACAT
1 AAGTGCTAA--ACACAGAGA-CACAT
*
53871053 AAAGTGCTAAACATAGAGTACACA-
1 -AAGTGCTAAACACAGAG-ACACAT
53871077 AAGT
1 AAGT
53871081 ACTGAGCACA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
22 9 0.20
23 9 0.20
24 2 0.05
25 14 0.32
26 10 0.23
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (23 bp):
AAGTGCTAAACACAGAGACACAT
Found at i:53874956 original size:94 final size:96
Alignment explanation
Indices: 53874768--53874956 Score: 267
Period size: 94 Copynumber: 2.0 Consensus size: 96
53874758 CAGATTAAAC
* *
53874768 CCAAACCCAATTTTTTTAAAAATAAATAAAGAAAAAGCAATAGAAAAAGAAAAAGAAAAAAAACA
1 CCAAACCCAATTTTTTAAAAAATAAATAAAGAAAAAGCAAGAGAAAAAGAAAAAGAAAAAAAAC-
* *
53874833 ACAAAAGGCGGTAAATCATAGGAGAGTTATAG
65 ACAAAAGACGGTAAAACATAGGAGAGTTATAG
* * * *
53874865 CCAAACCCAATTTTTTAAAAAAGTAAATAAAGACAAGGCAAGGGAAAAA-AAAAA-ACAAAAAAC
1 CCAAACCCAATTTTTTAAAAAA-TAAATAAAGAAAAAGCAAGAGAAAAAGAAAAAGAAAAAAAAC
53874928 -CAAAAGACGGTAAAACATAGGAGAGTTAT
65 ACAAAAGACGGTAAAACATAGGAGAGTTAT
53874957 TTTCGCTCGC
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
94 27 0.33
96 8 0.10
97 26 0.31
98 22 0.27
ACGTcount: A:0.58, C:0.12, G:0.15, T:0.15
Consensus pattern (96 bp):
CCAAACCCAATTTTTTAAAAAATAAATAAAGAAAAAGCAAGAGAAAAAGAAAAAGAAAAAAAACA
CAAAAGACGGTAAAACATAGGAGAGTTATAG
Found at i:53883910 original size:35 final size:35
Alignment explanation
Indices: 53883871--53883946 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
53883861 TTGTAAACTA
*
53883871 TTTTTTTAAAGAATATTGTATATAGGCTTAATACCT
1 TTTTTTTAAAGAATATT-AATATAGGCTTAATACCT
*** *
53883907 TTTTTTTATTTATTATTAATATAGGCTTAATACCT
1 TTTTTTTAAAGAATATTAATATAGGCTTAATACCT
53883942 TTTTT
1 TTTTT
53883947 GCTCCTTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
35 22 0.63
36 13 0.37
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.55
Consensus pattern (35 bp):
TTTTTTTAAAGAATATTAATATAGGCTTAATACCT
Found at i:53885831 original size:16 final size:16
Alignment explanation
Indices: 53885787--53885836 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
53885777 TTTAAAATAG
53885787 TAAAATTTTAAA-TTA
1 TAAAATTTTAAATTTA
**
53885802 T-ACTTTTTATAATTTA
1 TAAAATTTTA-AATTTA
*
53885818 TAAAATTTTAAATTAA
1 TAAAATTTTAAATTTA
53885834 TAA
1 TAA
53885837 TAATAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 6 0.22
15 3 0.11
16 12 0.44
17 6 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:53889885 original size:8 final size:8
Alignment explanation
Indices: 53889872--53889899 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
53889862 AAATAATAAT
53889872 AAAATTAA
1 AAAATTAA
53889880 AAAATTAA
1 AAAATTAA
53889888 AAAATTAA
1 AAAATTAA
53889896 AAAA
1 AAAA
53889900 AAAAAAAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAATTAA
Found at i:53889905 original size:16 final size:16
Alignment explanation
Indices: 53889872--53889907 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
53889862 AAATAATAAT
**
53889872 AAAATTAAAAAATTAA
1 AAAATTAAAAAAAAAA
53889888 AAAATTAAAAAAAAAA
1 AAAATTAAAAAAAAAA
53889904 AAAA
1 AAAA
53889908 ACTCTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATTAAAAAAAAAA
Found at i:53893444 original size:31 final size:31
Alignment explanation
Indices: 53893398--53893461 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
53893388 AGTCCATGTA
53893398 TTTTAATTTGATCAATTTTAATCCTTGTACT
1 TTTTAATTTGATCAATTTTAATCCTTGTACT
* * *
53893429 TTTTGATTTGTTCAATTTTAGTCCTTGTACT
1 TTTTAATTTGATCAATTTTAATCCTTGTACT
53893460 TT
1 TT
53893462 CAATCTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.58
Consensus pattern (31 bp):
TTTTAATTTGATCAATTTTAATCCTTGTACT
Done.