Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 124 of 216
Found at i:39280233 original size:12 final size:13
Alignment explanation
Indices: 39280216--39280244 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39280206 AATTTTTACG
39280216 ATTT-AAAAAATA
1 ATTTAAAAAAATA
39280228 ATTTAAAAAAATA
1 ATTTAAAAAAATA
39280241 ATTT
1 ATTT
39280245 TTTTCAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATTTAAAAAAATA
Found at i:39280323 original size:51 final size:51
Alignment explanation
Indices: 39280262--39280361 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
39280252 AATTATTTAA
39280262 AAATAGGGATTTAAGAGAAATTTA-AGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * * * *
39280313 AAATATGGATTTCAGAGAAATTTGGAAGGAATTTGAGAGGAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
39280362 GGAAATTTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.27, T:0.26
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:39280353 original size:11 final size:11
Alignment explanation
Indices: 39280321--39280373 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
39280311 TTAAATATGG
* *
39280321 ATTTCAGAGAA
1 ATTTGAGAGGA
39280332 ATTTG-GAAGGA
1 ATTTGAG-AGGA
39280343 ATTTGAGAGGA
1 ATTTGAGAGGA
*
39280354 AATTGAGAGGAA
1 ATTTGAGAGG-A
39280366 ATTTGAGA
1 ATTTGAGA
39280374 AAAGATTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
10 1 0.03
11 25 0.71
12 9 0.26
ACGTcount: A:0.42, C:0.02, G:0.30, T:0.26
Consensus pattern (11 bp):
ATTTGAGAGGA
Found at i:39280371 original size:12 final size:12
Alignment explanation
Indices: 39280329--39280373 Score: 60
Period size: 11 Copynumber: 3.9 Consensus size: 12
39280319 GGATTTCAGA
39280329 GAAATTTG-GAAG
1 GAAATTTGAG-AG
39280341 G-AATTTGAGAG
1 GAAATTTGAGAG
39280352 GAAA-TTGAGAG
1 GAAATTTGAGAG
39280363 GAAATTTGAGA
1 GAAATTTGAGA
39280374 AAAGATTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 20 0.67
12 10 0.33
ACGTcount: A:0.42, C:0.00, G:0.33, T:0.24
Consensus pattern (12 bp):
GAAATTTGAGAG
Found at i:39281028 original size:27 final size:28
Alignment explanation
Indices: 39280975--39281027 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 28
39280965 TAAATTTATT
39280975 AGAAAATTTTAAATTATTTGATTATATA
1 AGAAAATTTTAAATTATTTGATTATATA
*
39281003 AGAAAA-TTT-AATTA-TTGAATATATA
1 AGAAAATTTTAAATTATTTGATTATATA
39281028 TTAATATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 10 0.42
26 5 0.21
27 3 0.12
28 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (28 bp):
AGAAAATTTTAAATTATTTGATTATATA
Found at i:39281293 original size:31 final size:31
Alignment explanation
Indices: 39281258--39281333 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
39281248 AAAATTTATT
*
39281258 ATTTTAGTCACTCTTGTTAGATAAATTGTCA
1 ATTTTAGTCACTCTTGTTAAATAAATTGTCA
* *
39281289 ATTTTAGTCACTCCTGTTAAATAAGTTGTCA
1 ATTTTAGTCACTCTTGTTAAATAAATTGTCA
39281320 ATTTTAGTCACTCT
1 ATTTTAGTCACTCT
39281334 ATGGTTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.45
Consensus pattern (31 bp):
ATTTTAGTCACTCTTGTTAAATAAATTGTCA
Found at i:39282587 original size:31 final size:31
Alignment explanation
Indices: 39282536--39282615 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
39282526 TTTTAACAGT
** *
39282536 AGAGTGGCT-AAATTGTCAACTTACCTAACG
1 AGAGTGGCTAAAATTAACAACTTACCTAACA
* *
39282566 GGAGTGGCTAAAATTAACAACTTATCTAACA
1 AGAGTGGCTAAAATTAACAACTTACCTAACA
*
39282597 AGAGTGACTAAAA-TAACAA
1 AGAGTGGCTAAAATTAACAA
39282616 ATTTTGTAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 14 0.33
31 28 0.67
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (31 bp):
AGAGTGGCTAAAATTAACAACTTACCTAACA
Found at i:39282763 original size:38 final size:37
Alignment explanation
Indices: 39282704--39282780 Score: 84
Period size: 38 Copynumber: 2.1 Consensus size: 37
39282694 AATTTTTAAA
* * *
39282704 TATATATTTTAAAATTTTTTGAGTATCTTATCTATTTT
1 TATAAATTTTAAAATTGTTTGAAT-TCTTATCTATTTT
* *
39282742 TATAAATTTTAATAA-TGTTTGAATTTTTATGTATTTT
1 TATAAATTTTAA-AATTGTTTGAATTCTTATCTATTTT
39282779 TA
1 TA
39282781 ATTTTAATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
37 13 0.39
38 18 0.55
39 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (37 bp):
TATAAATTTTAAAATTGTTTGAATTCTTATCTATTTT
Found at i:39283043 original size:31 final size:31
Alignment explanation
Indices: 39282975--39283051 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
39282965 AATGGTAAAA
* *
39282975 TGACTAAAATTGACTACTTATCTAATGGAAG
1 TGACTAAAATTAACAACTTATCTAATGGAAG
*
39283006 TAACTAAAATTAACAACTTATCTACCAT-G-AG
1 TGACTAAAATTAACAACTTATCTA--ATGGAAG
39283037 TGACTAAAA-TAACAA
1 TGACTAAAATTAACAA
39283052 TTTTTTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 6 0.15
31 31 0.77
32 1 0.03
33 2 0.05
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
TGACTAAAATTAACAACTTATCTAATGGAAG
Found at i:39287963 original size:22 final size:22
Alignment explanation
Indices: 39287938--39287982 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39287928 TTTTCTCAAC
39287938 CTTCAACTCCGGCACCGATCCA
1 CTTCAACTCCGGCACCGATCCA
* *
39287960 CTTCCAGTCCGGCACCGATCCA
1 CTTCAACTCCGGCACCGATCCA
39287982 C
1 C
39287983 CTTCGGTCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.47, G:0.16, T:0.18
Consensus pattern (22 bp):
CTTCAACTCCGGCACCGATCCA
Found at i:39289008 original size:15 final size:15
Alignment explanation
Indices: 39288985--39289016 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
39288975 GCTTATCCAA
39288985 TCATATTGGTAGAAC
1 TCATATTGGTAGAAC
*
39289000 TCATGTTGGTAGAAC
1 TCATATTGGTAGAAC
39289015 TC
1 TC
39289017 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (15 bp):
TCATATTGGTAGAAC
Found at i:39291675 original size:194 final size:194
Alignment explanation
Indices: 39291418--39291805 Score: 724
Period size: 194 Copynumber: 2.0 Consensus size: 194
39291408 AAATTTTTTC
*
39291418 TGTGTTTGCCAAAATATGGTACTGATATTTAAAAAAAAAAAATGATTGCTATCTTCTTTACATTA
1 TGTGTTCGCCAAAATATGGTACTGATATTTAAAAAAAAAAAATGATTGCTATCTTCTTTACATTA
39291483 AGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTGTGGTGAAGT
66 AGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTGTGGTGAAGT
*
39291548 GTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATTTAGTTTGACTTTTTTATT
131 GTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATATAGTTTGACTTTTTTATT
*
39291612 TGTGTTCGCCAAAATATGGTACTGATATTT-AAAAAAAAAAATGATTGCTGTCTTCTGTTACATT
1 TGTGTTCGCCAAAATATGGTACTGATATTTAAAAAAAAAAAATGATTGCTATCTTCT-TTACATT
*
39291676 AAGATCTTTACTATTAAATTTGATTGCAAAACCATTTGTGCATTTTCATTTTTGCTGTGGTGAAG
65 AAGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTGTGGTGAAG
39291741 TGTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATATAGTTTGACTTTTTTATT
130 TGTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATATAGTTTGACTTTTTTATT
39291806 GCTATTGTGT
Statistics
Matches: 189, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
193 25 0.13
194 164 0.87
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.46
Consensus pattern (194 bp):
TGTGTTCGCCAAAATATGGTACTGATATTTAAAAAAAAAAAATGATTGCTATCTTCTTTACATTA
AGATCTTTACTATTAAATTTGATCGCAAAACCATTTGTGCATTTTCATTTTTGCTGTGGTGAAGT
GTTGGTCATTGGCTTCTTGCGCTTTTTCACATTGTTTTCTTGAATATAGTTTGACTTTTTTATT
Found at i:39302357 original size:21 final size:21
Alignment explanation
Indices: 39302333--39302402 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
39302323 GAAAAATACT
39302333 AGGTGGGTTCGGGACTATTCC
1 AGGTGGGTTCGGGACTATTCC
* * ** *
39302354 AGGTGGG-CCTGGAAAATTACT
1 AGGTGGGTTCGGGACTATT-CC
39302375 AGGTGGGTTCGGGACTATTCC
1 AGGTGGGTTCGGGACTATTCC
*
39302396 GGGTGGG
1 AGGTGGG
39302403 CCTGGAAATA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
20 7 0.19
21 22 0.61
22 7 0.19
ACGTcount: A:0.17, C:0.16, G:0.41, T:0.26
Consensus pattern (21 bp):
AGGTGGGTTCGGGACTATTCC
Found at i:39302380 original size:42 final size:42
Alignment explanation
Indices: 39302316--39302444 Score: 179
Period size: 42 Copynumber: 3.1 Consensus size: 42
39302306 TGCTTGTGGA
* * *
39302316 GGGCTTGGAAAAATACTAGGTGGGTTCGGGACTATTCCAGGT
1 GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
39302358 GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
1 GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
* * * *
39302400 GGGCCTGG-AAATATAATCGGCGGGTTCGGAACTATTCCGGGT
1 GGGCCTGGAAAAT-TACTAGGTGGGTTCGGGACTATTCCGGGT
39302442 GGG
1 GGG
39302445 TTTGGTGGTG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 4 0.05
42 75 0.95
ACGTcount: A:0.21, C:0.16, G:0.38, T:0.25
Consensus pattern (42 bp):
GGGCCTGGAAAATTACTAGGTGGGTTCGGGACTATTCCGGGT
Found at i:39302445 original size:21 final size:21
Alignment explanation
Indices: 39302376--39302446 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
39302366 AAAATTACTA
*
39302376 GGTGGGTTCGGGACTATTCCG
1 GGTGGGTTCGGAACTATTCCG
* *
39302397 GGTGGG-CCTGGAAATATAAT-C-
1 GGTGGGTTC-GGAACTAT--TCCG
*
39302418 GGCGGGTTCGGAACTATTCCG
1 GGTGGGTTCGGAACTATTCCG
39302439 GGTGGGTT
1 GGTGGGTT
39302447 TGGTGGTGGG
Statistics
Matches: 37, Mismatches: 7, Indels: 12
0.66 0.12 0.21
Matches are distributed among these distances:
19 1 0.03
20 2 0.05
21 31 0.84
22 2 0.05
23 1 0.03
ACGTcount: A:0.15, C:0.17, G:0.41, T:0.27
Consensus pattern (21 bp):
GGTGGGTTCGGAACTATTCCG
Found at i:39307637 original size:39 final size:38
Alignment explanation
Indices: 39307583--39307714 Score: 201
Period size: 39 Copynumber: 3.4 Consensus size: 38
39307573 GTTTGTGTCC
39307583 TTAATTATGTCTTAGTTTAAACATCATTAATATATGTAT
1 TTAATTATGTCTTAGTTTAAACATCATTAATATATGT-T
39307622 TTAATTATGTCTTAGTTTAAACATCATTAATATATGTCT
1 TTAATTATGTCTTAGTTTAAACATCATTAATATATGT-T
* * *
39307661 TTAATTATGTCTTATTTTGAACATCATTAATATGTGTT
1 TTAATTATGTCTTAGTTTAAACATCATTAATATATGTT
39307699 TTAATTAAGTGTCTTA
1 TTAATT-A-TGTCTTA
39307715 CATTCTGACA
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
38 7 0.08
39 73 0.84
40 7 0.08
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (38 bp):
TTAATTATGTCTTAGTTTAAACATCATTAATATATGTT
Found at i:39308673 original size:29 final size:27
Alignment explanation
Indices: 39308640--39308694 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 27
39308630 GTGATTAAAT
39308640 AAAATTGACA-CAAGCAGAATTTAAAAGAA
1 AAAATTGACAGCAAG-A-AA-TTAAAAGAA
39308669 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATTGACAGCAAGAAATTAAAAGA
39308695 TAAGTCCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.32
28 2 0.08
29 11 0.44
30 4 0.16
ACGTcount: A:0.60, C:0.09, G:0.15, T:0.16
Consensus pattern (27 bp):
AAAATTGACAGCAAGAAATTAAAAGAA
Found at i:39315409 original size:29 final size:27
Alignment explanation
Indices: 39315376--39315430 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
39315366 GTGATTAAAT
39315376 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
39315405 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
39315431 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:39323693 original size:41 final size:41
Alignment explanation
Indices: 39323643--39323869 Score: 202
Period size: 41 Copynumber: 5.5 Consensus size: 41
39323633 CTTAATTATT
* *
39323643 CCCTAAATTGCACATATGTGCCCCTATTTGTAGTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* *
39323684 CCCTGAATTGCACATACGTGCCCCTATTTTTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * ***
39323725 CCCTAAATTGCATATATGTGCCCCTTTTTGTACTTCAAAAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * ** *
39323766 CCTTAAATTGCATATACGTGCCTTTGTTTGTACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * ** * * * *
39323807 CCATGAGTAACACCTATGTGCCCCTTTTTATACTTCGGTAC
1 CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
* * * *
39323848 CCTTGAATAGCACTTACGTGCC
1 CCCTAAATTGCACATACGTGCC
39323870 TTGTTACAAT
Statistics
Matches: 149, Mismatches: 37, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 149 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (41 bp):
CCCTAAATTGCACATACGTGCCCCTATTTGTACTTCGGTAC
Found at i:39323736 original size:82 final size:82
Alignment explanation
Indices: 39323643--39323869 Score: 256
Period size: 82 Copynumber: 2.8 Consensus size: 82
39323633 CTTAATTATT
* * *
39323643 CCCTAAATTGCACATATGTGCCCCTATTTGTAGTTCGGTACCCCTGAATTGCACATACGTGCCCC
1 CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCC
*
39323708 TATTTTTACTTCGGTAC
66 TATTTGTACTTCGGTAC
* *** * * **
39323725 CCCTAAATTGCATATATGTGCCCCTTTTTGTACTTCAAAACCCTTAAATTGCATATACGTGCCTT
1 CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCC
*
39323790 TGTTTGTACTTCGGTAC
66 TATTTGTACTTCGGTAC
* * * ** * * * *
39323807 CCATGAGTAACACCTATGTGCCCCTTTTTATACTTCGGTACCCTTGAATAGCACTTACGTGCC
1 CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCC
39323870 TTGTTACAAT
Statistics
Matches: 117, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 117 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (82 bp):
CCCTAAATTGCACATATGTGCCCCTTTTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCC
TATTTGTACTTCGGTAC
Found at i:39323869 original size:123 final size:123
Alignment explanation
Indices: 39323646--39323869 Score: 272
Period size: 123 Copynumber: 1.8 Consensus size: 123
39323636 AATTATTCCC
* * * **
39323646 TAAATTGCACATATGTGCCCCTATTTGTAGTTCGGTACCCCTGAATTGCACATACGTGCCCCTAT
1 TAAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCATGAATAACACATACGTGCCCCTAT
* *
39323711 TTTTACTTCGGTACCCCTAAATTGCATATATGTGCCCCTTTTTGTACTTCAAAACCCT
66 TTTTACTTCGGTACCCCTAAATAGCATATACGTGCCCCTTTTTGTACTTCAAAACCCT
* ** * * * *
39323769 TAAATTGCATATACGTGCCTTTGTTTGTACTTCGGTACCCATGAGTAACACCTATGTGCCCCT-T
1 TAAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCATGAATAACACATACGTGCCCCTAT
* *
39323833 TTTATACTTCGGTACCCTTGAATAGCACT-TACGTGCC
66 TTT-TACTTCGGTACCCCTAAATAGCA-TATACGTGCC
39323870 TTGTTACAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
122 4 0.05
123 78 0.94
124 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.36
Consensus pattern (123 bp):
TAAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCATGAATAACACATACGTGCCCCTAT
TTTTACTTCGGTACCCCTAAATAGCATATACGTGCCCCTTTTTGTACTTCAAAACCCT
Found at i:39331686 original size:5 final size:5
Alignment explanation
Indices: 39331676--39331705 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
39331666 AAAACAAAGT
39331676 AAATA AAATA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
39331706 GAGTTCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAATA
Found at i:39332685 original size:14 final size:14
Alignment explanation
Indices: 39332666--39332695 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39332656 AGTGAGAGAG
*
39332666 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
39332680 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
39332694 GA
1 GA
39332696 ATGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:39333516 original size:24 final size:25
Alignment explanation
Indices: 39333475--39333521 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
39333465 AAATTTCGGA
*
39333475 AAGAATTTCTCAGAAAC-ACTTTTG
1 AAGAATTCCTCAGAAACAACTTTTG
39333499 AAGAATTCCTTCAG-AACAACTTT
1 AAGAATTCC-TCAGAAACAACTTT
39333522 CTTCTCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (25 bp):
AAGAATTCCTCAGAAACAACTTTTG
Found at i:39338157 original size:51 final size:51
Alignment explanation
Indices: 39338081--39338264 Score: 160
Period size: 51 Copynumber: 3.6 Consensus size: 51
39338071 TATAAACACG
39338081 TGTGTAGTACTAA-GTGCAGGCTACTACGTGTA-TCGATA-GATAATGGTCACA
1 TGTGTAGTAC-AATGTGCAGGCTACTACGTGTACTCGA-AGGAT-ATGGTCACA
* * * * **
39338132 TGTGTAGTACAATGTGCAGGCTACTATGTGTACTGGAAGGCTTTGGTCATG
1 TGTGTAGTACAATGTGCAGGCTACTACGTGTACTCGAAGGATATGGTCACA
* * * * * * * *
39338183 TGTGTAGTACTATGTGCAGGCTACTACGTGAACTAGAAAG-TTTGATCTCG
1 TGTGTAGTACAATGTGCAGGCTACTACGTGTACTCGAAGGATATGGTCACA
* * *
39338233 TGTGTAGTACTATGTGAAAGCTACTACGTGTA
1 TGTGTAGTACAATGTGCAGGCTACTACGTGTA
39338265 TCAAAAGATG
Statistics
Matches: 113, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
50 38 0.34
51 70 0.62
52 5 0.04
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (51 bp):
TGTGTAGTACAATGTGCAGGCTACTACGTGTACTCGAAGGATATGGTCACA
Found at i:39345880 original size:5 final size:5
Alignment explanation
Indices: 39345870--39345916 Score: 94
Period size: 5 Copynumber: 9.4 Consensus size: 5
39345860 AAAACAAAGT
39345870 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAATA AA
39345917 GTTTTAATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:39347553 original size:20 final size:18
Alignment explanation
Indices: 39347515--39347550 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
39347505 TTAATACAAT
39347515 TTAATTATTTTATAAAAA
1 TTAATTATTTTATAAAAA
39347533 TTAATTATTTTATAAAAA
1 TTAATTATTTTATAAAAA
39347551 AATCTTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATTATTTTATAAAAA
Found at i:39348946 original size:18 final size:17
Alignment explanation
Indices: 39348919--39348954 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
39348909 GGTTTTGAGT
*
39348919 TGGAATCTAAGTTTAAA
1 TGGAATCTAAGCTTAAA
39348936 TGGATATCTAAGCTTAAA
1 TGGA-ATCTAAGCTTAAA
39348954 T
1 T
39348955 CATGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (17 bp):
TGGAATCTAAGCTTAAA
Found at i:39356764 original size:47 final size:47
Alignment explanation
Indices: 39356693--39357508 Score: 1416
Period size: 47 Copynumber: 17.3 Consensus size: 47
39356683 CCCTTCGGGA
* * * * * *
39356693 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
39356740 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39356787 CTTATCACATATATACACTTTCACATTCATAACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39356834 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39356881 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39356928 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39356975 CTTATCACATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39357022 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39357069 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39357116 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39357163 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39357210 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39357257 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
39357304 CTTATCACATATATATACACTTTCACATTCACCACATTGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39357353 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39357400 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
39357447 CTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
39357496 CTTATCACATATA
1 CTTATCACATATA
39357509 CTATCATGTA
Statistics
Matches: 736, Mismatches: 29, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
47 645 0.88
49 91 0.12
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:39356771 original size:25 final size:25
Alignment explanation
Indices: 39356743--39356821 Score: 67
Period size: 25 Copynumber: 3.3 Consensus size: 25
39356733 ACTCGGCCCT
39356743 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
39356768 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
39356790 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
*
39356815 ATAACAT
1 ATCACAT
39356822 CGGCCATTAG
Statistics
Matches: 38, Mismatches: 11, Indels: 10
0.64 0.19 0.17
Matches are distributed among these distances:
22 11 0.29
23 5 0.13
24 5 0.13
25 17 0.45
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:39364397 original size:157 final size:157
Alignment explanation
Indices: 39364111--39364430 Score: 595
Period size: 157 Copynumber: 2.0 Consensus size: 157
39364101 TCTCGTGAAC
*
39364111 TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGCACGACATTCTTCATTATCATTAGCGCATTA
1 TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGCACAACATTCTTCATTATCATTAGCGCATTA
39364176 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
66 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
39364241 TAAACTCCTATCTGTAGCAAGAAAAGG
131 TAAACTCCTATCTGTAGCAAGAAAAGG
*
39364268 TCTTCCTCCACTGCTACTCCTCTCAAGTCAATGGCACAACATTCTTCATTATCATTAGCGCATTA
1 TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGCACAACATTCTTCATTATCATTAGCGCATTA
39364333 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
66 AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
* * *
39364398 TAAAGTCCTGTTTGTAGCAAGAAAAGG
131 TAAACTCCTATCTGTAGCAAGAAAAGG
39364425 TCTTCC
1 TCTTCC
39364431 AAGAATAATT
Statistics
Matches: 158, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 158 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (157 bp):
TCTTCCTCCACTGCTACTCCTATCAAGTCAATGGCACAACATTCTTCATTATCATTAGCGCATTA
AAAACATTGAATGTGACATGCTGATCATTCATCCTCATAGTCAGTTCACCTTTCTGCACATCAAT
TAAACTCCTATCTGTAGCAAGAAAAGG
Found at i:39380191 original size:18 final size:18
Alignment explanation
Indices: 39380168--39380202 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39380158 CCGATCCTTT
*
39380168 TGTTGCCTCCATTGGAGG
1 TGTTGCCGCCATTGGAGG
*
39380186 TGTTGCCGCCCTTGGAG
1 TGTTGCCGCCATTGGAG
39380203 CACCATTGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.26, G:0.34, T:0.31
Consensus pattern (18 bp):
TGTTGCCGCCATTGGAGG
Found at i:39381838 original size:30 final size:31
Alignment explanation
Indices: 39381804--39381863 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
39381794 AACTACACTT
39381804 AGCTCAAATCAGCTCA-TTTCAGCTCGTTTG
1 AGCTCAAATCAGCTCACTTTCAGCTCGTTTG
* * * *
39381834 AGCTCAATTTAGCTTACTTTCATCTCGTTT
1 AGCTCAAATCAGCTCACTTTCAGCTCGTTT
39381864 CTTTTATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (31 bp):
AGCTCAAATCAGCTCACTTTCAGCTCGTTTG
Found at i:39383857 original size:17 final size:16
Alignment explanation
Indices: 39383837--39383896 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 16
39383827 AAAAAGAAGA
39383837 AAAAGAGAAAGAAATTG
1 AAAA-AGAAAGAAATTG
*
39383854 AAAAAGAGAAAAAAATTG
1 -AAAA-AGAAAGAAATTG
*
39383872 AAAAAGAAAAGAAATCG
1 AAAAAG-AAAGAAATTG
39383889 AAAAAGAA
1 AAAAAGAA
39383897 TTTGAGAAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 4 0.11
17 18 0.47
18 16 0.42
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.08
Consensus pattern (16 bp):
AAAAAGAAAGAAATTG
Found at i:39383858 original size:18 final size:18
Alignment explanation
Indices: 39383835--39383895 Score: 97
Period size: 18 Copynumber: 3.4 Consensus size: 18
39383825 TGAAAAAGAA
39383835 GAAAAAGAGAAAGAAATT
1 GAAAAAGAGAAAGAAATT
*
39383853 GAAAAAGAGAAAAAAATT
1 GAAAAAGAGAAAGAAATT
*
39383871 GAAAAAGA-AAAGAAATC
1 GAAAAAGAGAAAGAAATT
39383888 GAAAAAGA
1 GAAAAAGA
39383896 ATTTGAGAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.70, C:0.02, G:0.20, T:0.08
Consensus pattern (18 bp):
GAAAAAGAGAAAGAAATT
Found at i:39393710 original size:47 final size:47
Alignment explanation
Indices: 39393653--39393955 Score: 416
Period size: 47 Copynumber: 6.4 Consensus size: 47
39393643 ATTGATGTAC
* * *
39393653 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
39393700 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTGTATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
39393749 ACA-TGTGTATGTGTGATAAGGCCGAAT-GCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
39393795 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
39393842 ACA-TGCATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
39393889 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG
1 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
*
39393936 AAGTGTATAAATGTGATAAG
1 AAGTGTATATATGTGATAAG
39393956 TCCCGAAGGG
Statistics
Matches: 237, Mismatches: 14, Indels: 10
0.91 0.05 0.04
Matches are distributed among these distances:
46 47 0.20
47 149 0.63
49 40 0.17
50 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.27
Consensus pattern (47 bp):
AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:39393826 original size:93 final size:93
Alignment explanation
Indices: 39393659--39393934 Score: 401
Period size: 93 Copynumber: 2.9 Consensus size: 93
39393649 GTACAAGTAT
* * * *
39393659 ATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATGCGTGATAAGGC
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG-AA--ATGTATATGTGTGATAAGGC
*
39393724 CGAATGGCCAATGTGATGAATGTGAACATGT
63 CGAATGGCCAATGTGATGAATGTGAACATGC
* * *
39393755 GTATGTGTGATAAGGCCGAAT-GCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCG
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-ATGTATATGTGTGATAAGGCCG
39393819 AATGGCCAATGTGATGAATGTGAACATGC
65 AATGGCCAATGTGATGAATGTGAACATGC
* *
39393848 ATATATGAGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCG
1 ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA-TGTATATGTGTGATAAGGCCG
*
39393913 AATGGCCAATGTGATGGATGTG
65 AATGGCCAATGTGATGAATGTG
39393935 GAAGTGTATA
Statistics
Matches: 163, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
93 66 0.40
94 62 0.38
95 18 0.11
96 17 0.10
ACGTcount: A:0.32, C:0.11, G:0.31, T:0.27
Consensus pattern (93 bp):
ATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAATGTATATGTGTGATAAGGCCGA
ATGGCCAATGTGATGAATGTGAACATGC
Found at i:39393833 original size:22 final size:22
Alignment explanation
Indices: 39393806--39393927 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
39393796 CATGTGTATG
39393806 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * *
39393828 TGTGATGAATG-TGAACAT-GCATATA
1 TGTGAT-AAGGCCG-A-ATGGC-CA-A
*
39393853 TGAGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
* * ***
39393875 TGTGATGAATG-TGAAAGTGTATATA
1 TGTGAT-AAGGCCG-AA-TGGCCA-A
39393900 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGCCGAATGGCCAA
39393922 TGTGAT
1 TGTGAT
39393928 GGATGTGGAA
Statistics
Matches: 70, Mismatches: 18, Indels: 24
0.62 0.16 0.21
Matches are distributed among these distances:
22 21 0.30
23 17 0.24
24 17 0.24
25 15 0.21
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (22 bp):
TGTGATAAGGCCGAATGGCCAA
Found at i:39393914 original size:140 final size:142
Alignment explanation
Indices: 39393664--39393934 Score: 415
Period size: 140 Copynumber: 1.9 Consensus size: 142
39393654 AGTATATATA
* * * *
39393664 TGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGAAAGTATATATATGCGTGATAAGGCCGAAT
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTACATATAT-CGAGATAAGGCCGAAT
* *
39393729 GGCCAATGTGATGAATGTGAACATGTGTATGTGTGATAAGGCCGAAT-GCCAATGTGATGAATGT
65 GGCCAATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGT
39393793 GAACATGTGTATG
130 GAACATGTGTATG
*
39393806 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA-TGCATATAT-GAGATAAGGCCGAAT
1 TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-AGTACATATATCGAGATAAGGCCGAAT
*
39393869 GGCCAATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATG
65 GGCCAATGTGATGAATGTGAACA-TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATG
39393933 TG
129 TG
39393935 GAAGTGTATA
Statistics
Matches: 118, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
139 1 0.01
140 57 0.48
141 17 0.14
142 42 0.36
143 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (142 bp):
TGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTACATATATCGAGATAAGGCCGAATG
GCCAATGTGATGAATGTGAACATGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTG
AACATGTGTATG
Found at i:39399329 original size:2 final size:2
Alignment explanation
Indices: 39399322--39399365 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
39399312 AATGTGTATA
39399322 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
39399364 TG
1 TG
39399366 CATTTGTGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:39400762 original size:35 final size:35
Alignment explanation
Indices: 39400723--39400797 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 35
39400713 ATTTATTTAT
39400723 TTATTTCT-TATCTATTATT-TTTATTATTAGTTAG-A
1 TTATTT-TATATCT-TTATTGTTTATTATTA-TTAGTA
* *
39400758 TTATTTTATTTCTTTATTGTTTGTTATTATTAGTA
1 TTATTTTATATCTTTATTGTTTATTATTATTAGTA
39400793 TTATT
1 TTATT
39400798 ATTTGTCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.67
Consensus pattern (35 bp):
TTATTTTATATCTTTATTGTTTATTATTATTAGTA
Found at i:39402424 original size:6 final size:6
Alignment explanation
Indices: 39402403--39402445 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
39402393 AGTCCATTTG
* *
39402403 TTTTA- TTTTA- TTTTAT TTTTAT TTTTAT GTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
39402446 CTTAGACTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:39402437 original size:18 final size:17
Alignment explanation
Indices: 39402403--39402445 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
39402393 AGTCCATTTG
39402403 TTTTA-TTTTATTTTAT
1 TTTTATTTTTATTTTAT
39402419 TTTTATTTTTATGTTTAT
1 TTTTATTTTTAT-TTTAT
*
39402437 TGTTATTTT
1 TTTTATTTT
39402446 CTTAGACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 6 0.25
18 13 0.54
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTATTTTAT
Found at i:39407494 original size:16 final size:16
Alignment explanation
Indices: 39407473--39407540 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
39407463 TTTGGTTCGC
39407473 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
39407489 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
39407505 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
39407521 TGTATTAGATTAAAGG
1 TGTATTGGATTAGAGG
39407537 TGTA
1 TGTA
39407541 ATAGCAAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39407866 original size:157 final size:157
Alignment explanation
Indices: 39407670--39407979 Score: 548
Period size: 157 Copynumber: 2.0 Consensus size: 157
39407660 CCCTTAGCAT
*
39407670 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
39407735 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
39407800 TTTAATAAAATTCTTAATAATTACCAG
131 TTTAATAAAATTCTTAATAATTACCAG
* * *
39407827 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTGATAAGATTATTAATATGAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
39407892 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
39407957 TTTAATAAAATTCTTAATAATTA
131 TTTAATAAAATTCTTAATAATTA
39407980 ATATTCTTAT
Statistics
Matches: 145, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
157 145 1.00
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (157 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATATTATAATTAAAATATATAA
TTTAATAAAATTCTTAATAATTACCAG
Found at i:39407976 original size:82 final size:81
Alignment explanation
Indices: 39407733--39407982 Score: 186
Period size: 76 Copynumber: 3.1 Consensus size: 81
39407723 TATTATTATC
* * *
39407733 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTAT-ATTAAAATATAT
39407798 AATTTAATAAAATTCTT
65 AATTTAATAAAATTCTT
* * * * *
39407815 AATAATTACCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT-TTAAAT
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAATATATTATATTAAAA
* * * * *
39407869 TTTGATAAGATT-AT-TAA-TATG
60 TAT-ATAA-TTTAATAAAATTCTT
39407890 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATACTTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATA-TTAAAATATAT
39407955 AATTTAATAAAATTCTT
65 AATTTAATAAAATTCTT
*
39407972 AATAATTAATA
1 AATAATAAATA
39407983 TTCTTATATG
Statistics
Matches: 121, Mismatches: 24, Indels: 46
0.63 0.13 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 10 0.08
76 21 0.17
77 6 0.05
78 8 0.07
79 8 0.07
80 6 0.05
81 21 0.17
82 20 0.17
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (81 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATATTAAAATATATA
ATTTAATAAAATTCTT
Found at i:39408053 original size:157 final size:155
Alignment explanation
Indices: 39407716--39408037 Score: 349
Period size: 157 Copynumber: 2.0 Consensus size: 155
39407706 TTAAATTTTA
* * * *
39407716 ATAAGATTATTATTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAACATA
1 ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
* * * * * ** *
39407781 TTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTACCAGAAATTTGTTTTGGTAAATT
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATC
* * * * *
39407846 ATTATTGTTATTGTTATTTAAATTTTG
131 ATAATTATTATTGATATATAAA--TAG
* *
39407873 ATAAGATTATTAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATA
1 ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
* * **
39407938 TTATACTTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA
66 TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-A
39408003 AATCATAATATATTATATGATACTATAAA-AG
127 AATCATAAT-TATTAT-TGATA-TATAAATAG
39408034 ATAA
1 ATAA
39408038 TTTGAAATAA
Statistics
Matches: 137, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
157 102 0.74
159 4 0.03
160 4 0.03
161 13 0.09
162 5 0.04
163 4 0.03
164 5 0.04
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (155 bp):
ATAAGATTATGAATATGAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACATA
TTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATC
ATAATTATTATTGATATATAAATAG
Found at i:39408877 original size:13 final size:13
Alignment explanation
Indices: 39408859--39408888 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
39408849 CAATCAGCTA
39408859 AATTCAGAAAAAC
1 AATTCAGAAAAAC
39408872 AATTCAGAAAAAC
1 AATTCAGAAAAAC
39408885 AATT
1 AATT
39408889 ACATGACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.13, G:0.07, T:0.20
Consensus pattern (13 bp):
AATTCAGAAAAAC
Found at i:39413354 original size:39 final size:41
Alignment explanation
Indices: 39413295--39413393 Score: 116
Period size: 39 Copynumber: 2.4 Consensus size: 41
39413285 ATCACTATAA
39413295 ATATTTTATTGTTAATAATA-TT-CTTAATATAAAATTTT-G
1 ATATTTTATTGTTAATAATATTTACTTAAT-TAAAATTTTCG
* *
39413334 ATATTTTATTGTTACA-AATATTTATTTAATTTAAATTTTCG
1 ATATTTTATTGTTA-ATAATATTTACTTAATTAAAATTTTCG
*
39413375 ATATTGTTATTGTCAATAA
1 ATATT-TTATTGTTAATAA
39413394 CGTTATCTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
39 18 0.35
40 11 0.22
41 12 0.24
42 10 0.20
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (41 bp):
ATATTTTATTGTTAATAATATTTACTTAATTAAAATTTTCG
Found at i:39414309 original size:21 final size:20
Alignment explanation
Indices: 39414280--39414329 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
39414270 ATTTTTTAAA
39414280 TATA-AAATTCATAAA-ATAT
1 TATAGAAATTCATAAATA-AT
*
39414299 TATTAGAAATTTATAAATAAT
1 TA-TAGAAATTCATAAATAAT
39414320 TATAGAAATT
1 TATAGAAATT
39414330 ATAGAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 10 0.37
21 14 0.52
22 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
TATAGAAATTCATAAATAAT
Found at i:39414338 original size:10 final size:10
Alignment explanation
Indices: 39414283--39414377 Score: 54
Period size: 10 Copynumber: 9.4 Consensus size: 10
39414273 TTTTAAATAT
39414283 AAAATTCATA-
1 AAAATT-ATAG
39414293 AAATATTATTAG
1 AAA-ATTA-TAG
*
39414305 AAATTTATA-
1 AAAATTATAG
39414314 AATAATTATAG
1 AA-AATTATAG
39414325 -AAATTATAG
1 AAAATTATAG
*
39414334 AAAATTTTTA-
1 AAAA-TTATAG
** *
39414344 AATGTTATAA
1 AAAATTATAG
*
39414354 AAAATTTTAG
1 AAAATTATAG
*
39414364 AAAAATATAG
1 AAAATTATAG
39414374 AAAA
1 AAAA
39414378 AATATAAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
9 14 0.22
10 36 0.55
11 12 0.18
12 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.36
Consensus pattern (10 bp):
AAAATTATAG
Found at i:39414359 original size:30 final size:31
Alignment explanation
Indices: 39414285--39414398 Score: 83
Period size: 30 Copynumber: 3.7 Consensus size: 31
39414275 TTAAATATAA
*
39414285 AATTCATAAAATATTATTAG-AAATTTATAAAT
1 AATT-ATAAAAAATTA-TAGAAAATTTATAAAT
* *
39414317 AATTAT-AGAAATTATAGAAAATTTTTAAAT
1 AATTATAAAAAATTATAGAAAATTTATAAAT
* * * *
39414347 -GTTATAAAAAATTTTAGAAAA-ATATAGAAA
1 AATTATAAAAAATTATAGAAAATTTATA-AAT
* * *
39414377 AAATATAAAAAAATATAAAAAA
1 AATTATAAAAAATTATAGAAAA
39414399 AGGTATAGAA
Statistics
Matches: 64, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
29 10 0.16
30 32 0.50
31 18 0.28
32 4 0.06
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.33
Consensus pattern (31 bp):
AATTATAAAAAATTATAGAAAATTTATAAAT
Found at i:39414405 original size:12 final size:10
Alignment explanation
Indices: 39414349--39414399 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
39414339 TTTTAAATGT
*
39414349 TATAAAAAAT
1 TATAAAAAAA
* *
39414359 TTTAGAAAAA
1 TATAAAAAAA
39414369 TATAGAAAAAA
1 TATA-AAAAAA
39414380 TATAAAAAAA
1 TATAAAAAAA
39414390 TATAAAAAAA
1 TATAAAAAAA
39414400 GGTATAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 26 0.74
11 9 0.26
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (10 bp):
TATAAAAAAA
Found at i:39414410 original size:12 final size:11
Alignment explanation
Indices: 39414364--39414411 Score: 64
Period size: 10 Copynumber: 4.4 Consensus size: 11
39414354 AAAATTTTAG
39414364 AAAAATATAGA
1 AAAAATATAGA
39414375 AAAAATATA-A
1 AAAAATATAGA
39414385 AAAAATATA-A
1 AAAAATATAGA
39414395 AAAAAGGTATAGA
1 AAAAA--TATAGA
39414408 AAAA
1 AAAA
39414412 TCTTAAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 16 0.47
11 9 0.26
12 4 0.12
13 5 0.15
ACGTcount: A:0.75, C:0.00, G:0.08, T:0.17
Consensus pattern (11 bp):
AAAAATATAGA
Found at i:39415183 original size:23 final size:23
Alignment explanation
Indices: 39415139--39415184 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
39415129 ATATTTTTCC
*
39415139 ATATTATTCTAAAATATATTATA
1 ATATTATTCTAAAACATATTATA
*
39415162 ATATTTTTCTAAAAACAT-TTATA
1 ATATTATTCT-AAAACATATTATA
39415185 GCATTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATTATTCTAAAACATATTATA
Found at i:39415335 original size:27 final size:28
Alignment explanation
Indices: 39415305--39415361 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
39415295 TTACTTAAGT
39415305 AATCAATTAAGCCCTCGTAAAATAA-AA
1 AATCAATTAAGCCCTCGTAAAATAATAA
** *
39415332 AATCAATTAAGTTCTTGTAAAATAATAA
1 AATCAATTAAGCCCTCGTAAAATAATAA
39415360 AA
1 AA
39415362 AATCGTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (28 bp):
AATCAATTAAGCCCTCGTAAAATAATAA
Found at i:39420629 original size:44 final size:45
Alignment explanation
Indices: 39420361--39421079 Score: 303
Period size: 44 Copynumber: 16.6 Consensus size: 45
39420351 ATCTACTCTG
* *
39420361 CTGCAACTTCA-GAGAGATAATACTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
* * * * * *
39420405 CTACAACTTCAAG-GAGATAAGACTAG-ATGC--AATCTGCT-CT
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
* **
39420445 CTGCAACTTCA-GAGAGATAAGATCCAATG-TT--TTAATCCACTCCA
1 CTGCAACTTCAGGAGAGATAAGA--C-TTGCTTACTTAATCTGCTCCA
* * *
39420489 CTGCAACTTCAGGA-AGATAGGATTATCGGC-T--TTAACCTGCTCCA
1 CTGCAACTTCAGGAGAGATAAGACT-T--GCTTACTTAATCTGCTCCA
* * * *
39420533 CTACAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AATCTGCTC-CA
*
39420578 CTGCAACTTCAGGAG-GATAAGACTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
* * * * *
39420622 CTGCAACTTCAGG-GAGATAAGACTAG-ATGC--GATCTGCT-CT
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
** * **
39420662 CTGCAACTTCA-GAGAGATAAGATCCAAGGTT--TTAATCCACTCCA
1 CTGCAACTTCAGGAGAGATAAGA--CTTGCTTACTTAATCTGCTCCA
* * * * * *
39420706 CTGCAACTTCA-AAAAGATAGGATTATCGGC-T--TTAACCTACTCCA
1 CTGCAACTTCAGGAGAGATAAGACT-T--GCTTACTTAATCTGCTCCA
* * * * *
39420750 CTACAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGTCTGCTTCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AATCTGCTCCA
* * *
39420795 CTGCAACTTTAGGAG-GATAAGATTTGCTTACTTAGTCTGCTCCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
* * * * *
39420839 CTGCAACTTCAGGA-AGATAAGACTAG-ATGC--GATCTGCT-CT
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
* ** * **
39420879 CTGCAACTTTA-GAGAGATAAGATCCAAGGTT--TTAATCCACTCCA
1 CTGCAACTTCAGGAGAGATAAGA--CTTGCTTACTTAATCTGCTCCA
* * * * *
39420923 CTGCAACTTCA-GAAAGATAGGA-TT-ATCAGCTTTAACCTGCTCCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTA-C-TTAATCTGCTCCA
* * *
39420967 CTGCAACTTCAGG-GAGATAAGATTTGC-CATCTTCAGTCTGC-CTCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTA-CTT-AATCTGCTC-CA
* *
39421012 CTGCAACTTCAGGAG-GATAAGACTTGCTTACTTAGTCTGTTCCA
1 CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
*
39421056 CTGCAACTTCAGG-GAGAGAAGACT
1 CTGCAACTTCAGGAGAGATAAGACT
39421080 AGATGCGATC
Statistics
Matches: 517, Mismatches: 97, Indels: 122
0.70 0.13 0.17
Matches are distributed among these distances:
39 4 0.01
40 61 0.12
41 23 0.04
42 8 0.02
43 30 0.06
44 273 0.53
45 112 0.22
46 6 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (45 bp):
CTGCAACTTCAGGAGAGATAAGACTTGCTTACTTAATCTGCTCCA
Found at i:39420736 original size:217 final size:217
Alignment explanation
Indices: 39420361--39421103 Score: 1317
Period size: 217 Copynumber: 3.4 Consensus size: 217
39420351 ATCTACTCTG
* * *
39420361 CTGCAACTTCA-GAGAGATAATACTTGCTTACTTAGTCTGCTCCACTACAACTTCAAGGAGATAA
1 CTGCAACTTCAGGAG-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAA
* *
39420425 GACTAGATGCAATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAATGTTTTAATCCACTCCAC
65 GACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCAC
*
39420490 TGCAACTTCAGGAAGATAGGATTATCGGCTTTAACCTGCTCCACTACAACTTCAGGGAGATAAGA
130 TGCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTGCTCCACTACAACTTCAGGGAGATAAGA
39420555 TTTGCCATCTTCAGTCTGCCTCA
195 TTTGCCATCTTCAGTCTGCCTCA
39420578 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
39420643 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCACT
* *
39420708 GCAACTTCAAAAAGATAGGATTATCGGCTTTAACCTACTCCACTACAACTTCAGGGAGATAAGAT
131 GCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTGCTCCACTACAACTTCAGGGAGATAAGAT
*
39420773 TTGCCATCTTCAGTCTGCTTCA
196 TTGCCATCTTCAGTCTGCCTCA
* * *
39420795 CTGCAACTTTAGGAGGATAAGATTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGAAGATAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
*
39420860 ACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATAAGATCCAAGGTTTTAATCCACTCCACT
66 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCACT
* *
39420925 GCAACTTCAGAAAGATAGGATTATCAGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGAT
131 GCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTGCTCCACTACAACTTCAGGGAGATAAGAT
39420990 TTGCCATCTTCAGTCTGCCTCA
196 TTGCCATCTTCAGTCTGCCTCA
* *
39421012 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGTTCCACTGCAACTTCAGGGAGAGAAG
1 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
39421077 ACTAGATGCGATCTGCTCTCTGCAACT
66 ACTAGATGCGATCTGCTCTCTGCAACT
39421104 GCTCCACTAT
Statistics
Matches: 502, Mismatches: 23, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
217 499 0.99
218 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (217 bp):
CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAG
ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCACTCCACT
GCAACTTCAGAAAGATAGGATTATCGGCTTTAACCTGCTCCACTACAACTTCAGGGAGATAAGAT
TTGCCATCTTCAGTCTGCCTCA
Found at i:39421207 original size:44 final size:45
Alignment explanation
Indices: 39421102--39421222 Score: 151
Period size: 44 Copynumber: 2.7 Consensus size: 45
39421092 CTCTCTGCAA
** *
39421102 CTGCTCCACTATAACTTCAGGGAGATAAGATTTGCCATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGT
*
39421147 CTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTG-CTTACTT-AGT
1 CTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCCAT-CTTCAGT
39421191 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
39421223 AGATGCGATC
Statistics
Matches: 67, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
44 35 0.52
45 32 0.48
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCCATCTTCAGT
Found at i:39421221 original size:143 final size:143
Alignment explanation
Indices: 39420959--39421246 Score: 540
Period size: 143 Copynumber: 2.0 Consensus size: 143
39420949 CAGCTTTAAC
*
39420959 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
1 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
*
39421024 GAGGATAAGACTTGCTTACTTAGTCTGTTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
66 GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
39421089 CTGCTCTCTGCAA
131 CTGCTCTCTGCAA
*
39421102 CTGCTCCACTATAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
1 CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
*
39421167 GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGAT
66 GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
39421232 CTGCTCTCTGCAA
131 CTGCTCTCTGCAA
39421245 CT
1 CT
39421247 TCAGAGAGAT
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
143 141 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (143 bp):
CTGCTCCACTACAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAG
GAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGAGAAGACTAGATGCGAT
CTGCTCTCTGCAA
Found at i:39429360 original size:23 final size:25
Alignment explanation
Indices: 39429315--39429369 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
39429305 GCTGCTCATT
*
39429315 CATTTTCTTTTGAACCTGATTCT-G
1 CATTTCCTTTTGAACCTGATTCTAG
39429339 CATTTCCTTTTGAGA-CTG-TTCTAG
1 CATTTCCTTTTGA-ACCTGATTCTAG
*
39429363 CCTTTCC
1 CATTTCC
39429370 ATCCTTTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 4 0.15
24 22 0.81
25 1 0.04
ACGTcount: A:0.15, C:0.25, G:0.13, T:0.47
Consensus pattern (25 bp):
CATTTCCTTTTGAACCTGATTCTAG
Found at i:39433108 original size:15 final size:15
Alignment explanation
Indices: 39433072--39433110 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
39433062 GTAAATATCG
39433072 TGATAATAAATACAA
1 TGATAATAAATACAA
39433087 T-AGTAATAAATACAA
1 TGA-TAATAAATACAA
39433102 TGATAATAA
1 TGATAATAA
39433111 TTTTAACGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 20 0.91
16 1 0.05
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (15 bp):
TGATAATAAATACAA
Found at i:39437598 original size:20 final size:20
Alignment explanation
Indices: 39437570--39437618 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
39437560 ATATATCCTG
*
39437570 ATTTTATTTGATTCTAATCA
1 ATTTGATTTGATTCTAATCA
*
39437590 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTCTAATCA
*
39437610 AATTGATTT
1 ATTTGATTT
39437619 AATTGCCCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.55
Consensus pattern (20 bp):
ATTTGATTTGATTCTAATCA
Found at i:39448136 original size:23 final size:23
Alignment explanation
Indices: 39448101--39448221 Score: 165
Period size: 23 Copynumber: 5.3 Consensus size: 23
39448091 AGTGTTATTG
*
39448101 ATCAATGGTAGCTTCGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
*
39448123 ATTCAGTGGTAGCTACGG-TACAT
1 A-TCAGTGGTAGCTTCGGCTACAT
* *
39448146 ATCATTGGTAGCTTCGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
39448169 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39448192 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
39448215 ATCAGTG
1 ATCAGTG
39448222 TGGCATTTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.22
23 67 0.78
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:39448173 original size:45 final size:46
Alignment explanation
Indices: 39448101--39448221 Score: 190
Period size: 45 Copynumber: 2.7 Consensus size: 46
39448091 AGTGTTATTG
*
39448101 ATCAATGGTAGCTTCGGCTACAATTCAGTGGTAGCTACGG-TACAT
1 ATCAATGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
39448146 ATCATTGGTAGCTTCGGTTACATTTCAGTGGTAGCTACGGCTACAT
1 ATCAATGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
* *
39448192 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAATGGTAGCTTCGGCTACATTTCAGTG
39448222 TGGCATTTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 37 0.54
46 32 0.46
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAATGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGGCTACAT
Found at i:39448471 original size:23 final size:25
Alignment explanation
Indices: 39448425--39448472 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
39448415 GAAATTGCTA
* *
39448425 AGAAATGTTTGATTAGTTATATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
39448450 AGAAATG-TTAATT-GTTAAATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
39448473 TATTTATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (25 bp):
AGAAATGTTTAATTAGTTAAATGAG
Found at i:39450085 original size:19 final size:17
Alignment explanation
Indices: 39450061--39450108 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
39450051 TGGGCCTCAA
39450061 TGGGCCGAAATGGGCTGTG
1 TGGGCC-AAATGGGCT-TG
* *
39450080 TGGGCCCAGTGGGCTTG
1 TGGGCCAAATGGGCTTG
*
39450097 TGGGCCACATGG
1 TGGGCCAAATGG
39450109 ATAAAATGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 11 0.46
18 7 0.29
19 6 0.25
ACGTcount: A:0.12, C:0.21, G:0.46, T:0.21
Consensus pattern (17 bp):
TGGGCCAAATGGGCTTG
Found at i:39450439 original size:27 final size:27
Alignment explanation
Indices: 39450383--39450496 Score: 153
Period size: 27 Copynumber: 4.3 Consensus size: 27
39450373 CCAAAATTTA
*
39450383 TAAAATGATCGTAATG-CCCTGTAGGT
1 TAAAATGATCGTAATGCCCCTGTAGGG
*
39450409 TAAAATGATCGTAATACCCCTGTAGGG
1 TAAAATGATCGTAATGCCCCTGTAGGG
* * *
39450436 TAAAATAACCATAATGCCCCTGTAGGG
1 TAAAATGATCGTAATGCCCCTGTAGGG
39450463 TAAAATGA-CTGTAATGCCCCTGTA-GG
1 TAAAATGATC-GTAATGCCCCTGTAGGG
39450489 TAAAATGA
1 TAAAATGA
39450497 CTATAATACC
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
26 26 0.33
27 52 0.67
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (27 bp):
TAAAATGATCGTAATGCCCCTGTAGGG
Found at i:39450602 original size:24 final size:24
Alignment explanation
Indices: 39450570--39450664 Score: 127
Period size: 24 Copynumber: 4.0 Consensus size: 24
39450560 CCCTCGAGGT
* *
39450570 TAAATGATTGATTTGTTTGTGATG
1 TAAATGACTGATTTGTCTGTGATG
* * * *
39450594 TAAGTGATTGATTAGTCTGAGATG
1 TAAATGACTGATTTGTCTGTGATG
*
39450618 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATG
39450642 TAAATGACTGATTTGTCTGTGAT
1 TAAATGACTGATTTGTCTGTGAT
39450665 TGGTATAACT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.44
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATG
Found at i:39450679 original size:24 final size:23
Alignment explanation
Indices: 39450628--39450698 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 23
39450618 TAAATGACTG
* *
39450628 ATTTGTCTGTGATT-TAAATGACTG
1 ATTTGTCTGTGATTGT--ATAACTA
39450652 ATTTGTCTGTGATTGGTATAACTA
1 ATTTGTCTGTGATT-GTATAACTA
*
39450676 ATTTGTCTATGAATTGTATAACT
1 ATTTGTCTGTG-ATTGTATAACT
39450699 GATTCTGAGC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 37 0.90
25 3 0.07
26 1 0.02
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.46
Consensus pattern (23 bp):
ATTTGTCTGTGATTGTATAACTA
Found at i:39450805 original size:27 final size:27
Alignment explanation
Indices: 39450765--39450829 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
39450755 ATAGAGGAAG
*
39450765 TACTG-TACTGGTGGCTCT-GCCACA-A
1 TACTGTTACTAGTGGCT-TGGCCACATA
39450790 TCACTGTTACTAGTGGCTTGGCCACATA
1 T-ACTGTTACTAGTGGCTTGGCCACATA
39450818 TACTGTTACTAG
1 TACTGTTACTAG
39450830 CAGCTTTGCT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 27 0.77
28 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (27 bp):
TACTGTTACTAGTGGCTTGGCCACATA
Found at i:39450835 original size:27 final size:27
Alignment explanation
Indices: 39450783--39450835 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39450773 TGGTGGCTCT
**
39450783 GCCACAATCACTGTTACTAGTGGCTTG
1 GCCACAATCACTGTTACTAGCAGCTTG
39450810 GCCACATAT-ACTGTTACTAGCAGCTT
1 GCCACA-ATCACTGTTACTAGCAGCTT
39450836 TGCTACGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTGTTACTAGCAGCTTG
Found at i:39450897 original size:32 final size:33
Alignment explanation
Indices: 39450847--39451084 Score: 276
Period size: 32 Copynumber: 7.5 Consensus size: 33
39450837 GCTACGATGC
* *
39450847 TACTAATGGCTT-TGTGCCGGTCATATTACTGT
1 TACTGATGGCTTGTGTGCCGATCATATTACTGT
* *
39450879 TACTGATGG-TTGTGTGCCGATCATATCACTGC
1 TACTGATGGCTTGTGTGCCGATCATATTACTGT
*
39450911 TACTGATGGCTT-TGTGCCGATCATATTACCGT
1 TACTGATGGCTTGTGTGCCGATCATATTACTGT
* * * *
39450943 TATTGATGG-TTGTGTACCGATCATATCACTGC
1 TACTGATGGCTTGTGTGCCGATCATATTACTGT
39450975 TACTGATGGCTT-TGTGCCGATCATATTACTGT
1 TACTGATGGCTTGTGTGCCGATCATATTACTGT
* * * *
39451007 TACTGATGGC-TGTGTGCCGGTCATATCATTGC
1 TACTGATGGCTTGTGTGCCGATCATATTACTGT
* *
39451039 TACTGATGGCTT-TGTGCCAATCATATTAGT-T
1 TACTGATGGCTTGTGTGCCGATCATATTACTGT
*
39451070 TACTTATGGCTTGTG
1 TACTGATGGCTTGTG
39451085 GTCATTCTAT
Statistics
Matches: 173, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
31 16 0.09
32 152 0.88
33 5 0.03
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (33 bp):
TACTGATGGCTTGTGTGCCGATCATATTACTGT
Found at i:39450924 original size:64 final size:64
Alignment explanation
Indices: 39450844--39451084 Score: 367
Period size: 64 Copynumber: 3.8 Consensus size: 64
39450834 TTTGCTACGA
* *
39450844 TGCTACTAATGGCTTTGTGCCGGTCATATTACTGTTACTGATGGTTGTGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTACTGTTACTGATGGTTGTGTGCCGATCATATCAC
* * *
39450908 TGCTACTGATGGCTTTGTGCCGATCATATTACCGTTATTGATGGTTGTGTACCGATCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTACTGTTACTGATGGTTGTGTGCCGATCATATCAC
* * *
39450972 TGCTACTGATGGCTTTGTGCCGATCATATTACTGTTACTGATGGCTGTGTGCCGGTCATATCAT
1 TGCTACTGATGGCTTTGTGCCGATCATATTACTGTTACTGATGGTTGTGTGCCGATCATATCAC
* * *
39451036 TGCTACTGATGGCTTTGTGCCAATCATATTAGT-TTACTTATGGCTTGTG
1 TGCTACTGATGGCTTTGTGCCGATCATATTACTGTTACTGATGG-TTGTG
39451085 GTCATTCTAT
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
63 9 0.06
64 152 0.94
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTACTGTTACTGATGGTTGTGTGCCGATCATATCAC
Found at i:39451348 original size:34 final size:29
Alignment explanation
Indices: 39451321--39451408 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 29
39451311 CTGTTTCTGC
39451321 ATTGGGCTAAGGCCCACAATGTTACTG-T
1 ATTGGGCTAAGGCCCACAATGTTACTGTT
*
39451349 ATTGGGCTAAGGCCCACATTGTTACTG-T
1 ATTGGGCTAAGGCCCACAATGTTACTGTT
** *
39451377 ATTGGGCTGTGGCCCACACACTGATACTGTT
1 ATTGGGCTAAGGCCCACA-A-TGTTACTGTT
39451408 A
1 A
39451409 CTGTTAATAG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
28 43 0.83
30 7 0.13
31 2 0.04
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (29 bp):
ATTGGGCTAAGGCCCACAATGTTACTGTT
Found at i:39451353 original size:28 final size:28
Alignment explanation
Indices: 39451312--39451394 Score: 121
Period size: 28 Copynumber: 3.0 Consensus size: 28
39451302 TGACTGACAC
* *
39451312 TGTTTCTGCATTGGGCTAAGGCCCACAA
1 TGTTACTGTATTGGGCTAAGGCCCACAA
*
39451340 TGTTACTGTATTGGGCTAAGGCCCACAT
1 TGTTACTGTATTGGGCTAAGGCCCACAA
**
39451368 TGTTACTGTATTGGGCTGTGGCCCACA
1 TGTTACTGTATTGGGCTAAGGCCCACA
39451395 CACTGATACT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.31
Consensus pattern (28 bp):
TGTTACTGTATTGGGCTAAGGCCCACAA
Found at i:39452845 original size:15 final size:15
Alignment explanation
Indices: 39452825--39452853 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39452815 TCAAGTCAAT
39452825 AAAGAAAAAGAAAAC
1 AAAGAAAAAGAAAAC
39452840 AAAGAAAAAGAAAA
1 AAAGAAAAAGAAAA
39452854 GAAAAGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAGAAAAC
Found at i:39452855 original size:20 final size:21
Alignment explanation
Indices: 39452825--39452863 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
39452815 TCAAGTCAAT
39452825 AAAGAAAAAGAAAACAAAGAA
1 AAAGAAAAAGAAAACAAAGAA
*
39452846 AAAG-AAAAGAAAAGAAAG
1 AAAGAAAAAGAAAACAAAG
39452864 GGGAGGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAGAAAAAGAAAACAAAGAA
Found at i:39454743 original size:3 final size:3
Alignment explanation
Indices: 39454735--39454761 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39454725 GGGTGATGAA
39454735 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
39454762 GGTCTCATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:39455261 original size:27 final size:27
Alignment explanation
Indices: 39455227--39455402 Score: 201
Period size: 27 Copynumber: 6.5 Consensus size: 27
39455217 TAAATTGTAC
39455227 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39455254 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39455280 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39455308 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39455336 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39455363 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39455390 AGCACTGAGTGTG
1 AGCACTAAGTGTG
39455403 TGGACTCAAT
Statistics
Matches: 127, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 104 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39455341 original size:82 final size:81
Alignment explanation
Indices: 39455228--39455383 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
39455218 AAATTGTACA
* *
39455228 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
39455292 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
39455309 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
39455374 TGCGAGTTGA
65 TGCGAATTGA
39455384 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:39455395 original size:82 final size:81
Alignment explanation
Indices: 39455224--39455402 Score: 225
Period size: 82 Copynumber: 2.2 Consensus size: 81
39455214 AATTAAATTG
* *
39455224 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
39455289 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
39455305 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
39455369 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
39455387 TATAGCACTGAGTGTG
1 TACAGCACTAAGTGTG
39455403 TGGACTCAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.22
82 64 0.78
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:39465966 original size:27 final size:27
Alignment explanation
Indices: 39465935--39466139 Score: 232
Period size: 27 Copynumber: 7.6 Consensus size: 27
39465925 TAAATTGTAC
39465935 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
39465962 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39465988 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
39466016 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
39466044 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39466071 AGCACTAAGTGTGCGAGTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
39466098 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
39466125 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
39466140 GACTCAATAT
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 23 0.15
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:39466130 original size:109 final size:109
Alignment explanation
Indices: 39465935--39466139 Score: 268
Period size: 109 Copynumber: 1.9 Consensus size: 109
39465925 TAAATTGTAC
* * *
39465935 AGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTG
1 AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
* *
39466000 TGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
66 TGCGAATTGACCATACAGCACTAAGTGTGCGAGTTTGACTATGT
* ** *
39466044 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTACG-TAGCACTAAGT
1 AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGT
* ** * *
39466108 GTGCGAGTTGATTATATAGCACTGAGTGTGCG
65 GTGCGAATTGACCATACAGCACTAAGTGTGCG
39466140 GACTCAATAT
Statistics
Matches: 81, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
108 1 0.01
109 80 0.99
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (109 bp):
AGCACTAAGTGTGCGATTTGACTACGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTG
TGCGAATTGACCATACAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:39476763 original size:7 final size:7
Alignment explanation
Indices: 39476751--39476785 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
39476741 GAAACAAAAG
39476751 AATAAAT
1 AATAAAT
39476758 AATAAAT
1 AATAAAT
39476765 AATAAAT
1 AATAAAT
39476772 AAT-AAT
1 AATAAAT
39476778 AATAAAT
1 AATAAAT
39476785 A
1 A
39476786 TTCCCCACGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.22
7 21 0.78
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAAAT
Found at i:39481784 original size:28 final size:28
Alignment explanation
Indices: 39481754--39481891 Score: 161
Period size: 28 Copynumber: 4.9 Consensus size: 28
39481744 TAAGAGTTCG
*
39481754 CATGGACTATCATTCAAGCAAGAGTCTG
1 CATGGACTATCATTCAAGCAAGAGTCTA
* * *
39481782 CATGGACTATTC-TTCATGTAAGAGTCCA
1 CATGGACTA-TCATTCAAGCAAGAGTCTA
* **
39481810 CATGGACTATCATTCCAGCAAGAGTCCC
1 CATGGACTATCATTCAAGCAAGAGTCTA
** *
39481838 CATAAACTATCCTTCAAGCAAGAGTCTA
1 CATGGACTATCATTCAAGCAAGAGTCTA
*
39481866 CATGGACTATCTTTCAAGCAAGAGTC
1 CATGGACTATCATTCAAGCAAGAGTC
39481892 CTCAGGAACT
Statistics
Matches: 91, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
27 2 0.02
28 87 0.96
29 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (28 bp):
CATGGACTATCATTCAAGCAAGAGTCTA
Found at i:39481814 original size:56 final size:56
Alignment explanation
Indices: 39481721--39481891 Score: 202
Period size: 56 Copynumber: 3.1 Consensus size: 56
39481711 ATTTAGGTAT
* * *
39481721 GAGTCTACAAGGACTATTC--CATGTAAGAGTTCGCATGGACTATCATTCAAGCAA
1 GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
* *
39481775 GAGTCTGCATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCCAGCAA
1 GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
** ** * * * * *
39481831 GAGTCCCCATAAACTATCCTTCAAGCAAGAGTCTACATGGACTATCTTTCAAGCAA
1 GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
39481887 GAGTC
1 GAGTC
39481892 CTCAGGAACT
Statistics
Matches: 100, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
54 17 0.17
56 83 0.83
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (56 bp):
GAGTCTACATGGACTATTCTTCATGTAAGAGTCCACATGGACTATCATTCAAGCAA
Found at i:39482774 original size:31 final size:32
Alignment explanation
Indices: 39482737--39482806 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
39482727 GACCCCCAAA
* *
39482737 AAGTTTAAGTAC-CAACTTA-AGAAAAAGTGCC
1 AAGTTTAAGT-CTCAAATTAGAAAAAAAGTGCC
* *
39482768 AAGTTTAGGTCTCAAATTAGAAAAAAAGTGTC
1 AAGTTTAAGTCTCAAATTAGAAAAAAAGTGCC
39482800 AAGTTTA
1 AAGTTTA
39482807 CGTATCAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 15 0.45
32 17 0.52
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.27
Consensus pattern (32 bp):
AAGTTTAAGTCTCAAATTAGAAAAAAAGTGCC
Found at i:39485226 original size:13 final size:13
Alignment explanation
Indices: 39485208--39485237 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39485198 TGCCCGGCCC
*
39485208 ATAAACCAACAAA
1 ATAAACCAAAAAA
39485221 ATAAACCAAAAAA
1 ATAAACCAAAAAA
39485234 ATAA
1 ATAA
39485238 TAATAATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.17, G:0.00, T:0.10
Consensus pattern (13 bp):
ATAAACCAAAAAA
Found at i:39485514 original size:19 final size:18
Alignment explanation
Indices: 39485490--39485535 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
39485480 GCACATGTAG
39485490 CGCCTCCGCGCCAAAGCCA
1 CGCCTCCGCGCC-AAGCCA
* *
39485509 CGCCTCCGAGCCGAGCCA
1 CGCCTCCGCGCCAAGCCA
*
39485527 CGCCACCGC
1 CGCCTCCGC
39485536 CAGAGACCAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.17, C:0.54, G:0.24, T:0.04
Consensus pattern (18 bp):
CGCCTCCGCGCCAAGCCA
Found at i:39485527 original size:18 final size:19
Alignment explanation
Indices: 39485490--39485530 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39485480 GCACATGTAG
*
39485490 CGCCTCCGCGCCAAAGCCA
1 CGCCTCCGAGCCAAAGCCA
*
39485509 CGCCTCCGAGCC-GAGCCA
1 CGCCTCCGAGCCAAAGCCA
39485527 CGCC
1 CGCC
39485531 ACCGCCAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.17, C:0.54, G:0.24, T:0.05
Consensus pattern (19 bp):
CGCCTCCGAGCCAAAGCCA
Found at i:39486486 original size:30 final size:30
Alignment explanation
Indices: 39486452--39486509 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
39486442 TTTCCTTTTA
39486452 TCTATTTTGTTATTATTGCTAAAATTGTCC
1 TCTATTTTGTTATTATTGCTAAAATTGTCC
39486482 TCTATTTTGTTATTATTGCTAAAATTGT
1 TCTATTTTGTTATTATTGCTAAAATTGT
39486510 TCGGTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.55
Consensus pattern (30 bp):
TCTATTTTGTTATTATTGCTAAAATTGTCC
Found at i:39486533 original size:3 final size:3
Alignment explanation
Indices: 39486527--39486574 Score: 87
Period size: 3 Copynumber: 16.0 Consensus size: 3
39486517 ATTATCTTCT
*
39486527 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39486575 GTAGTAGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:39497461 original size:15 final size:15
Alignment explanation
Indices: 39497441--39497493 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
39497431 GGTGAAAAAG
*
39497441 ATAATATCTTTTAAA
1 ATAATATATTTTAAA
39497456 ATAATAATATTATTAAAA
1 ATAAT-ATATT-TT-AAA
*
39497474 ATAATTGTATTTTAAA
1 ATAA-TATATTTTAAA
39497490 ATAA
1 ATAA
39497494 AGATAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 5 0.16
16 11 0.34
17 4 0.12
18 11 0.34
19 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
ATAATATATTTTAAA
Found at i:39497484 original size:18 final size:17
Alignment explanation
Indices: 39497441--39497490 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
39497431 GGTGAAAAAG
*
39497441 ATAATATCTTTTAAAATA
1 ATAATAT-TTTAAAAATA
39497459 ATAATATTATTAAAAATA
1 ATAATATT-TTAAAAATA
**
39497477 ATTGTATTTTAAAA
1 ATAATATTTTAAAA
39497491 TAAAGATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.25
18 21 0.75
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATAATATTTTAAAAATA
Found at i:39497719 original size:7 final size:8
Alignment explanation
Indices: 39497709--39497743 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
39497699 AAAACAAAAT
39497709 ATTTT-GA
1 ATTTTAGA
39497716 ATTTT-GA
1 ATTTTAGA
39497723 ATTTTAGA
1 ATTTTAGA
39497731 ATTTTAGA
1 ATTTTAGA
39497739 ATTTT
1 ATTTT
39497744 TTTGTCAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 12 0.44
8 15 0.56
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (8 bp):
ATTTTAGA
Found at i:39497734 original size:15 final size:15
Alignment explanation
Indices: 39497709--39497743 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
39497699 AAAACAAAAT
39497709 ATTTT-GAATTTTGA
1 ATTTTAGAATTTTGA
39497723 ATTTTAGAATTTTAGA
1 ATTTTAGAATTTT-GA
39497739 ATTTT
1 ATTTT
39497744 TTTGTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 7 0.37
16 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (15 bp):
ATTTTAGAATTTTGA
Found at i:39500405 original size:20 final size:21
Alignment explanation
Indices: 39500366--39500405 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39500356 TCTAAACCAA
39500366 CAAGTATCGATACCTTTTTGGC
1 CAAGTATCGATA-CTTTTTGGC
*
39500388 CAAGTATTGATA-TTTTTG
1 CAAGTATCGATACTTTTTG
39500406 AATTATCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (21 bp):
CAAGTATCGATACTTTTTGGC
Found at i:39500504 original size:21 final size:21
Alignment explanation
Indices: 39500466--39500506 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39500456 CAAACCCTAA
*
39500466 TAAGTATCAATACCTTTTGAT
1 TAAGTATCAATAACTTTTGAT
* *
39500487 TAAGTATCGATAATTTTTGA
1 TAAGTATCAATAACTTTTGA
39500507 AATATTAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (21 bp):
TAAGTATCAATAACTTTTGAT
Found at i:39500586 original size:101 final size:99
Alignment explanation
Indices: 39500389--39500683 Score: 333
Period size: 101 Copynumber: 2.9 Consensus size: 99
39500379 CTTTTTGGCC
* * * * * *
39500389 AAGTATTGATATTTTTGAATTATCGATA-CCCTCTCTT-AAACGATACCAAAGTGGCATTCTATT
1 AAGTATCGATATTTTTGAATTATTGATACCCCT-TCTTAAAACGATACCAAAATGACATTATGTT
* * *
39500452 TTCACAAACCCTAATAAGTATCAATACCTTTTGATT
65 TT-TCAAACCCTAATAAGTATCGATACCATTTGATT
* * *
39500488 AAGTATCGATAATTTTTGAAATATTAATACCCCTTCTTAAAAGCGATACCAAAATGACATTTTGT
1 AAGTATCGAT-ATTTTTGAATTATTGATACCCCTTCTTAAAA-CGATACCAAAATGACATTATGT
39500553 TTTTCAAACCCTAATAAGTATCGATACCATTTGATT
64 TTTTCAAACCCTAATAAGTATCGATACCATTTGATT
* *
39500589 AAGTATCGATATTTTCTGAATTATTGATACCCCTTCTTAAAAACGATACTAAAAATAACATTATG
1 AAGTATCGATATTTT-TGAATTATTGATACCCCTTCTT-AAAACGATAC-CAAAATGACATTATG
* ** *
39500654 TTTCTCACAAAACTTATAAAGTATCGATAC
63 TTTTTCA-AACCCTAAT-AAGTATCGATAC
39500684 GATATCAATA
Statistics
Matches: 167, Mismatches: 20, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
99 9 0.05
100 24 0.14
101 73 0.44
102 43 0.26
103 6 0.04
104 12 0.07
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (99 bp):
AAGTATCGATATTTTTGAATTATTGATACCCCTTCTTAAAACGATACCAAAATGACATTATGTTT
TTCAAACCCTAATAAGTATCGATACCATTTGATT
Found at i:39501389 original size:6 final size:6
Alignment explanation
Indices: 39501378--39501403 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
39501368 GAGCTAACAA
39501378 ATAATT ATAATT ATAATT ATAATT AT
1 ATAATT ATAATT ATAATT ATAATT AT
39501404 TTTATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATAATT
Found at i:39501826 original size:21 final size:19
Alignment explanation
Indices: 39501770--39501826 Score: 55
Period size: 19 Copynumber: 3.0 Consensus size: 19
39501760 ATTAATTATT
*
39501770 ATCATATTTA-AAAT-AAA
1 ATCATATTTATAATTAAAA
*
39501787 ATCATATTTATATTTAAAA
1 ATCATATTTATAATTAAAA
*
39501806 ATTATATTTATTTAATTAAAA
1 ATCATATTTA--TAATTAAAA
39501827 TTTTGAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 10 0.31
18 2 0.06
19 12 0.38
21 8 0.25
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
ATCATATTTATAATTAAAA
Found at i:39502093 original size:11 final size:11
Alignment explanation
Indices: 39502077--39502143 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
39502067 CTTTTATAGA
39502077 ATTATAAATAT
1 ATTATAAATAT
39502088 ATTATAAATAT
1 ATTATAAATAT
39502099 AGATTATAAAT-T
1 --ATTATAAATAT
*
39502111 ATAGATAAATACT
1 AT-TATAAATA-T
*
39502124 ATTATAAAAAT
1 ATTATAAATAT
39502135 A-TATAAATA
1 ATTATAAATA
39502144 GCAAAATTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
10 9 0.19
11 19 0.40
12 7 0.15
13 12 0.26
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (11 bp):
ATTATAAATAT
Found at i:39502104 original size:24 final size:24
Alignment explanation
Indices: 39502071--39502143 Score: 73
Period size: 24 Copynumber: 3.1 Consensus size: 24
39502061 GTGGTGCTTT
39502071 TATAGAATTATAAATATATTATAAA
1 TATAG-ATTATAAATATATTATAAA
*
39502096 TATAGATTATAAAT-TATAGATAAA
1 TATAGATTATAAATATAT-TATAAA
*
39502120 TACT--ATTATAAAAATA-TATAAA
1 TA-TAGATTATAAATATATTATAAA
39502142 TA
1 TA
39502144 GCAAAATTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
22 7 0.17
23 11 0.26
24 18 0.43
25 6 0.14
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.38
Consensus pattern (24 bp):
TATAGATTATAAATATATTATAAA
Found at i:39502498 original size:19 final size:19
Alignment explanation
Indices: 39502470--39502512 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
39502460 TTATTTTTAA
39502470 TTTA-ATATTTAAT-AATT
1 TTTATATATTTAATAAATT
*
39502487 TTATATATATTTATTAAATT
1 TT-TATATATTTAATAAATT
39502507 TTTATA
1 TTTATA
39502513 GTTAGTTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.09
18 2 0.09
19 12 0.55
20 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATATATTTAATAAATT
Found at i:39502501 original size:23 final size:23
Alignment explanation
Indices: 39502475--39502534 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 23
39502465 TTTAATTTAA
* *
39502475 TATTTAATAATTTTATA-TATATT
1 TATTTAATATTTTTATAGT-TAGT
39502498 TA-TTAA-ATTTTTATAGTTAGT
1 TATTTAATATTTTTATAGTTAGT
39502519 TATCTTAATATTTTTA
1 TAT-TTAATATTTTTA
39502535 ATTTTTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 13 0.42
22 5 0.16
23 6 0.19
24 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (23 bp):
TATTTAATATTTTTATAGTTAGT
Found at i:39502559 original size:31 final size:32
Alignment explanation
Indices: 39502488--39502560 Score: 78
Period size: 31 Copynumber: 2.2 Consensus size: 32
39502478 TTAATAATTT
*
39502488 TATATATATTTATTAAATTTTTATAGTTAGTTA
1 TATA-ATATTTATTAAATTTTTATAGTTAGTAA
* *
39502521 TCTTAATATTT-TT-AATTTTTATATTATAGTAA
1 T-ATAATATTTATTAAATTTTTATAGT-TAGTAA
39502553 TATAATAT
1 TATAATAT
39502561 AAAACATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
31 17 0.50
32 8 0.24
33 7 0.21
34 2 0.06
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (32 bp):
TATAATATTTATTAAATTTTTATAGTTAGTAA
Found at i:39507179 original size:33 final size:33
Alignment explanation
Indices: 39507141--39507208 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
39507131 GTATCATTAC
39507141 TTAGTATTGTCATATGCATGAGCAAACAGTCAT
1 TTAGTATTGTCATATGCATGAGCAAACAGTCAT
39507174 TTAGTATTGTCATATGCATGAGCAAACAGTCAT
1 TTAGTATTGTCATATGCATGAGCAAACAGTCAT
39507207 TT
1 TT
39507209 GCTCTATGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
TTAGTATTGTCATATGCATGAGCAAACAGTCAT
Found at i:39516268 original size:24 final size:23
Alignment explanation
Indices: 39516225--39516594 Score: 434
Period size: 23 Copynumber: 15.8 Consensus size: 23
39516215 TAGATAGCTC
**
39516225 TTATACATAAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
***
39516248 TTATACATCCCGTTTGGACAGCAT
1 TTATACA-CCAAATTGGACAGCAT
* * *
39516272 ATAAACACCAAATTGAACAGCAT
1 TTATACACCAAATTGGACAGCAT
39516295 TTATACACCAAAATTGGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
*
39516319 TTATACACCAAATTGGGCAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
39516342 ATATATACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
*
39516365 TTTTACACCAAAATTGGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
*
39516389 ATATACACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
*
39516412 TTATACACCAAAATTGGATAGCAT
1 TTATACACC-AAATTGGACAGCAT
**
39516436 TTATACACCAAATTGGGTAGCAT
1 TTATACACCAAATTGGACAGCAT
* * *
39516459 ATATATACCAAATTGGACAACAT
1 TTATACACCAAATTGGACAGCAT
*
39516482 TTTTACACCAAAATTGGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
* * *
39516506 ATAGACACCAAATTGGGCAGCAT
1 TTATACACCAAATTGGACAGCAT
* * *
39516529 ATATATACCAAATTGGACAACAT
1 TTATACACCAAATTGGACAGCAT
*
39516552 TTTTACACCAAAATTGGACAGCAT
1 TTATACACC-AAATTGGACAGCAT
*
39516576 ATATACACCAAATTGGACA
1 TTATACACCAAATTGGACA
39516595 TGAATCGAAT
Statistics
Matches: 292, Mismatches: 49, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
23 172 0.59
24 120 0.41
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (23 bp):
TTATACACCAAATTGGACAGCAT
Found at i:39516312 original size:47 final size:46
Alignment explanation
Indices: 39516225--39516594 Score: 434
Period size: 47 Copynumber: 7.9 Consensus size: 46
39516215 TAGATAGCTC
** * ***
39516225 TTATACATAAAATTGGACAGCATTTATACATCCCGTTTGGACAGCAT
1 TTATACACCAAATTGGACAGCATATATACA-CCAAATTGGACAGCAT
* * * *
39516272 ATAAACACCAAATTGAACAGCATTTATACACCAAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCATATATACACC-AAATTGGACAGCAT
* *
39516319 TTATACACCAAATTGGGCAGCATATATATACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCAT
*
39516365 TTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACAGCAT
1 TTATACACC-AAATTGGACAGCATATATACACCAAATTGGACAGCAT
* * **
39516412 TTATACACCAAAATTGGATAGCATTTATACACCAAATTGGGTAGCAT
1 TTATACACC-AAATTGGACAGCATATATACACCAAATTGGACAGCAT
* * * * *
39516459 ATATATACCAAATTGGACAACATTTTTACACCAAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCATATATACACC-AAATTGGACAGCAT
* * * * *
39516506 ATAGACACCAAATTGGGCAGCATATATATACCAAATTGGACAACAT
1 TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCAT
*
39516552 TTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACA
1 TTATACACC-AAATTGGACAGCATATATACACCAAATTGGACA
39516595 TGAATCGAAT
Statistics
Matches: 277, Mismatches: 42, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
46 63 0.23
47 214 0.77
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (46 bp):
TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCAT
Found at i:39516353 original size:70 final size:70
Alignment explanation
Indices: 39516225--39516594 Score: 456
Period size: 70 Copynumber: 5.3 Consensus size: 70
39516215 TAGATAGCTC
** * *** * * *
39516225 TTATACATAAAATTGGACAGCATTTATACATCCCGTTTGGACAGCATATAAACACC-AAATTGAA
1 TTATACACCAAATTGGACAGCATATATACA-CCAAATTGGACAGCATTTATACACCAAAATTGGA
39516289 CAGCAT
65 CAGCAT
* * * *
39516295 TTATACACCAAAATTGGACAGCATTTATACACCAAATTGGGCAGCATATATATACC-AAATTGGA
1 TTATACACC-AAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAAATTGGA
39516359 CAGCAT
65 CAGCAT
*
39516365 TTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAAATTGGA
1 TTATACACC-AAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAAATTGGA
*
39516430 TAGCAT
65 CAGCAT
** * * *
39516436 TTATACACCAAATTGGGTAGCATATATATACCAAATTGGACAACATTTTTACACCAAAATTGGAC
1 TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAAATTGGAC
39516501 AGCAT
66 AGCAT
* * * * * *
39516506 ATAGACACCAAATTGGGCAGCATATATATACCAAATTGGACAACATTTTTACACCAAAATTGGAC
1 TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAAATTGGAC
39516571 AGCAT
66 AGCAT
*
39516576 ATATACACCAAATTGGACA
1 TTATACACCAAATTGGACA
39516595 TGAATCGAAT
Statistics
Matches: 271, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
70 229 0.85
71 42 0.15
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (70 bp):
TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAAATTGGAC
AGCAT
Found at i:39516440 original size:117 final size:117
Alignment explanation
Indices: 39516234--39516594 Score: 537
Period size: 117 Copynumber: 3.1 Consensus size: 117
39516224 CTTATACATA
* *** *
39516234 AAATTGGACAGCATTTATACATCC-CGTTTGGACAGCATATAAACACCAAATTGAACAGCATTTA
1 AAATTGGACAGCATTTTTACA-CCAAAATTGGACAGCATATAAACACCAAATTGGACAGCATTTA
39516298 TACACCAAAATTGGACAGCATTTATACACCAAATTGGGCAGCATATATATACC
65 TACACCAAAATTGGACAGCATTTATACACCAAATTGGGCAGCATATATATACC
*
39516351 AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATATACACCAAATTGGACAGCATTTAT
1 AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAAACACCAAATTGGACAGCATTTAT
* *
39516416 ACACCAAAATTGGATAGCATTTATACACCAAATTGGGTAGCATATATATACC
66 ACACCAAAATTGGACAGCATTTATACACCAAATTGGGCAGCATATATATACC
* * * *
39516468 AAATTGGACAACATTTTTACACCAAAATTGGACAGCATATAGACACCAAATTGGGCAGCATATAT
1 AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAAACACCAAATTGGACAGCATTTAT
* * * * *
39516533 ATACC-AAATTGGACAACATTTTTACACCAAAATTGGACAGCATATATACACC
66 ACACCAAAATTGGACAGCATTTATACACC-AAATTGGGCAGCATATATATACC
39516585 AAATTGGACA
1 AAATTGGACA
39516595 TGAATCGAAT
Statistics
Matches: 223, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
116 22 0.10
117 201 0.90
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.26
Consensus pattern (117 bp):
AAATTGGACAGCATTTTTACACCAAAATTGGACAGCATATAAACACCAAATTGGACAGCATTTAT
ACACCAAAATTGGACAGCATTTATACACCAAATTGGGCAGCATATATATACC
Found at i:39521150 original size:18 final size:18
Alignment explanation
Indices: 39521127--39521190 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
39521117 GTTGAAAATT
39521127 ATGTTGACAGAGGCACCA
1 ATGTTGACAGAGGCACCA
* ***
39521145 ATGTTGACACA-GCTTGAA
1 ATGTTGACAGAGGC-ACCA
*
39521163 TATGTTGATAGAGGCACCA
1 -ATGTTGACAGAGGCACCA
39521182 ATGTTGACA
1 ATGTTGACA
39521191 CAACTTGAAT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
17 2 0.06
18 19 0.58
19 10 0.30
20 2 0.06
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (18 bp):
ATGTTGACAGAGGCACCA
Found at i:39521176 original size:37 final size:37
Alignment explanation
Indices: 39521126--39521200 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
39521116 AGTTGAAAAT
*
39521126 TATGTTGACAGAGGCACCAATGTTGACACAGCTTGAA
1 TATGTTGACAGAGGCACCAATGTTGACACAACTTGAA
*
39521163 TATGTTGATAGAGGCACCAATGTTGACACAACTTGAA
1 TATGTTGACAGAGGCACCAATGTTGACACAACTTGAA
39521200 T
1 T
39521201 CTAGGAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (37 bp):
TATGTTGACAGAGGCACCAATGTTGACACAACTTGAA
Found at i:39527499 original size:3 final size:3
Alignment explanation
Indices: 39527491--39527524 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
39527481 TTAGGGTTAG
* *
39527491 AGA AGA AGA AAA AGA AGA AAA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
39527525 TGAGAAGAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:39527912 original size:36 final size:36
Alignment explanation
Indices: 39527872--39528010 Score: 145
Period size: 36 Copynumber: 3.9 Consensus size: 36
39527862 CTGAAAACCA
* *
39527872 GCTTATGTTTTGTA-ATATTGTTGTTGGTATATTGTT
1 GCTTATGTTGT-TACATATTGTTGCTGGTATATTGTT
* * *
39527908 GCTTATGTAGTTACATATTGTTGCTGATATATTGCT
1 GCTTATGTTGTTACATATTGTTGCTGGTATATTGTT
* * * *
39527944 GCTTATGTTGTTATACATGGTTACTGGTATATTGTT
1 GCTTATGTTGTTACATATTGTTGCTGGTATATTGTT
* * * *
39527980 GCTTATGTTGTTATACATGGCTGCTGGTATA
1 GCTTATGTTGTTACATATTGTTGCTGGTATA
39528011 CATGGCTAAC
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 2 0.02
36 86 0.98
ACGTcount: A:0.19, C:0.09, G:0.22, T:0.50
Consensus pattern (36 bp):
GCTTATGTTGTTACATATTGTTGCTGGTATATTGTT
Found at i:39528717 original size:24 final size:22
Alignment explanation
Indices: 39528690--39528743 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
39528680 AGCTTTTCTC
* *
39528690 TTGGGGCAGCGTCTTTTTGATGAG
1 TTGGGGCAG-G-CTTGTTAATGAG
39528714 TTGGGGCA-GCTTGTTAATGAG
1 TTGGGGCAGGCTTGTTAATGAG
39528735 TTGGGGCAG
1 TTGGGGCAG
39528744 TTTGTAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 18 0.67
22 1 0.04
24 8 0.30
ACGTcount: A:0.15, C:0.11, G:0.41, T:0.33
Consensus pattern (22 bp):
TTGGGGCAGGCTTGTTAATGAG
Found at i:39528735 original size:21 final size:21
Alignment explanation
Indices: 39528709--39528805 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
39528699 CGTCTTTTTG
39528709 ATGAGTTGGGGCAGCTTGTTA
1 ATGAGTTGGGGCAGCTTGTTA
*
39528730 ATGAGTTGGGGCAGTTTG-TA
1 ATGAGTTGGGGCAGCTTGTTA
* * * *
39528750 ACTAAGTTGGGGTA-CTCTCTTG
1 A-TGAGTTGGGGCAGCT-TGTTA
* * *
39528772 CTGATTTGGGGTAGCTTGTTA
1 ATGAGTTGGGGCAGCTTGTTA
* *
39528793 CTGAGTTGAGGCA
1 ATGAGTTGGGGCA
39528806 ACTACTTGGT
Statistics
Matches: 58, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 4 0.07
21 51 0.88
22 3 0.05
ACGTcount: A:0.19, C:0.11, G:0.35, T:0.35
Consensus pattern (21 bp):
ATGAGTTGGGGCAGCTTGTTA
Found at i:39529529 original size:27 final size:28
Alignment explanation
Indices: 39529471--39529530 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
39529461 TACACCCCCT
** *
39529471 AAAAAATAGTCACTATATGCATATTATTA
1 AAAAAATACACACTACATGCATATTA-TA
39529500 AAAAAATACACACTACATGCATATTA-A
1 AAAAAATACACACTACATGCATATTATA
39529527 AAAA
1 AAAA
39529531 TAGTCAACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 5 0.18
29 23 0.82
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAAAATACACACTACATGCATATTATA
Found at i:39529795 original size:2 final size:2
Alignment explanation
Indices: 39529790--39529824 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39529780 AAAAAACATT
39529790 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
39529825 TTAAAAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Done.