Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 122 of 235
Found at i:41540570 original size:17 final size:17
Alignment explanation
Indices: 41540548--41540587 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
41540538 AAACTAGTCC
41540548 TTCGTGAGGTTTTCACA
1 TTCGTGAGGTTTTCACA
*
41540565 TTCGTGAGGTTTTCACC
1 TTCGTGAGGTTTTCACA
41540582 TTCGTG
1 TTCGTG
41540588 CAGGGTAGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.42
Consensus pattern (17 bp):
TTCGTGAGGTTTTCACA
Found at i:41545622 original size:21 final size:21
Alignment explanation
Indices: 41545598--41545638 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41545588 TCATTGAAGT
* *
41545598 TGAAGTTCTTTCTCTTCGAGG
1 TGAAATTCGTTCTCTTCGAGG
41545619 TGAAATTCGTTCTCTTCGAG
1 TGAAATTCGTTCTCTTCGAG
41545639 TTTTAGCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (21 bp):
TGAAATTCGTTCTCTTCGAGG
Found at i:41546072 original size:8 final size:7
Alignment explanation
Indices: 41546037--41546071 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
41546027 AAAACTGATG
41546037 TGAAAAA
1 TGAAAAA
41546044 TGAAAAGA
1 TGAAAA-A
41546052 TG-AAAA
1 TGAAAAA
41546058 TGAAAAA
1 TGAAAAA
41546065 TGAAAAA
1 TGAAAAA
41546072 AGTAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.12
7 20 0.77
8 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:41546462 original size:13 final size:13
Alignment explanation
Indices: 41546444--41546468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41546434 TAAATTAATT
41546444 TCTTTGTTATCCA
1 TCTTTGTTATCCA
41546457 TCTTTGTTATCC
1 TCTTTGTTATCC
41546469 TCGACAATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTTGTTATCCA
Found at i:41548184 original size:89 final size:89
Alignment explanation
Indices: 41547431--41548178 Score: 1106
Period size: 89 Copynumber: 8.4 Consensus size: 89
41547421 TTGAATATAG
* * *
41547431 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGGTCAGAGAAAGCAGATCTTGTCTTCATGTAC
1 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
* * *
41547496 CGGCGTGAAGTAGATTAAAGATAA
66 TGGCGTGAAGTAGATCAGAGATAA
* * * * * **
41547520 TAGATCTTGTCTTCCCATACTGGTGGCGAAACAGATCGAAGAAAACAGATCTTGTCTTCATGTAC
1 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
*
41547585 TGGCGTGAAGTAGATCAGAGATAC
66 TGGCGTGAAGTAGATCAGAGATAA
41547609 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
1 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
*
41547674 TGGCGTGAAGTAGATCAGAGATAC
66 TGGCGTGAAGTAGATCAGAGATAA
41547698 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
1 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
*
41547763 TGGCGTGAAGTAGATCAGAGATAC
66 TGGCGTGAAGTAGATCAGAGATAA
41547787 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
1 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
*
41547852 TGGCGTGAAGTAGATCAGAGATAC
66 TGGCGTGAAGTAGATCAGAGATAA
41547876 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
1 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
*
41547941 TGGCGTAAAGTAGATCAGAGATAA
66 TGGCGTGAAGTAGATCAGAGATAA
* * * * * *
41547965 CAGATCTTGCATTCCCATACTGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTGTCTTTATGTAT
1 CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
*
41548030 TAGCGTGAAGTAGATC-GAAGA-AA
66 TGGCGTGAAGTAGATCAG-AGATAA
* * * * * *
41548053 GTAGGTCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATATA
1 -CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTA
* * *
41548118 TTGGCGTGAAGTAGATCAAAGACAA
65 CTGGCGTGAAGTAGATCAGAGATAA
* * * *
41548143 CAAATCTTGTCTTCCCATA-TCGGTGGCGAAGTAGAT
1 CAGATCTTGCCTTCCCATACT-GGTGGTGAAGCAGAT
41548179 TGAAGATACA
Statistics
Matches: 610, Mismatches: 44, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
88 4 0.01
89 604 0.99
90 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (89 bp):
CAGATCTTGCCTTCCCATACTGGTGGTGAAGCAGATCAAAGAAAGTAGATCTTGTCTTCATGTAC
TGGCGTGAAGTAGATCAGAGATAA
Found at i:41549919 original size:31 final size:31
Alignment explanation
Indices: 41549878--41549944 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
41549868 ATACTTCATA
* ** *
41549878 TTTTATATATACT-TATACATTTTTTTATTTT
1 TTTTAAATATA-TATATACATAATTTTATCTT
41549909 TTTTAAATATATATATACATAATTTTATCTT
1 TTTTAAATATATATATACATAATTTTATCTT
41549940 TTTTA
1 TTTTA
41549945 TTTTTTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (31 bp):
TTTTAAATATATATATACATAATTTTATCTT
Found at i:41555731 original size:37 final size:39
Alignment explanation
Indices: 41555676--41555748 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
41555666 CCGAATATAA
*
41555676 TAAATATATATTTTTTA-TTTTTAAATTTTAAAATACTT
1 TAAAAATATATTTTTTATTTTTTAAATTTTAAAATACTT
* *
41555714 TAAAAATAT-TTTTTTATTTTTTTATTTTTAAAATA
1 TAAAAATATATTTTTTATTTTTTAAATTTTAAAATA
41555749 TTTTTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
37 7 0.23
38 24 0.77
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (39 bp):
TAAAAATATATTTTTTATTTTTTAAATTTTAAAATACTT
Found at i:41555920 original size:14 final size:15
Alignment explanation
Indices: 41555892--41555924 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41555882 AGCAGAAGAG
41555892 AATGAGAAGTAAAAA
1 AATGAGAAGTAAAAA
41555907 AATGA-AAGTTAAAAA
1 AATGAGAAG-TAAAAA
41555922 AAT
1 AAT
41555925 ATAAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (15 bp):
AATGAGAAGTAAAAA
Found at i:41558370 original size:23 final size:21
Alignment explanation
Indices: 41558340--41558395 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
41558330 ATTATTTTTT
*
41558340 AAAATTTTAAATATAGTTTAAA
1 AAAATTTTAAATAT-CTTTAAA
*
41558362 AAAACTTTTGAATATCTTTAAA
1 AAAA-TTTTAAATATCTTTAAA
41558384 AATAATTTTAAA
1 AA-AATTTTAAA
41558396 AAATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (21 bp):
AAAATTTTAAATATCTTTAAA
Found at i:41558393 original size:12 final size:12
Alignment explanation
Indices: 41558378--41558419 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 12
41558368 TTTGAATATC
41558378 TTTAAAAATAAT
1 TTTAAAAATAAT
41558390 TTTAAAAAATAAT
1 TTT-AAAAATAAT
*
41558403 TTTTAAAAT--T
1 TTTAAAAATAAT
41558413 TTTAAAA
1 TTTAAAA
41558420 TATACATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.26
12 8 0.30
13 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TTTAAAAATAAT
Found at i:41558399 original size:13 final size:14
Alignment explanation
Indices: 41558381--41558410 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
41558371 GAATATCTTT
41558381 AAAAATAA-TTTTA
1 AAAAATAATTTTTA
41558394 AAAAATAATTTTTA
1 AAAAATAATTTTTA
41558408 AAA
1 AAA
41558411 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAATAATTTTTA
Found at i:41558430 original size:35 final size:34
Alignment explanation
Indices: 41558335--41558438 Score: 90
Period size: 35 Copynumber: 3.0 Consensus size: 34
41558325 AAAATATTAT
* *
41558335 TTTTTAAAA-TTTT-AAATATAGTTTAAAAAA-AC
1 TTTTTAAAATTTTTAAAATATA-ATTAAAAAATAA
* * *
41558367 TTTTGAATATCTTTAAAA-ATAATTTTAAAAAATAA
1 TTTTTAAAATTTTTAAAATATAA--TTAAAAAATAA
41558402 TTTTTAAAATTTTTAAAATATACATTAAAAATATAA
1 TTTTTAAAATTTTTAAAATATA-ATTAAAAA-ATAA
41558438 T
1 T
41558439 AAAACAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 12
0.74 0.11 0.16
Matches are distributed among these distances:
32 7 0.12
33 6 0.11
34 11 0.20
35 23 0.41
36 8 0.14
37 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (34 bp):
TTTTTAAAATTTTTAAAATATAATTAAAAAATAA
Found at i:41558469 original size:33 final size:32
Alignment explanation
Indices: 41558432--41558512 Score: 74
Period size: 31 Copynumber: 2.5 Consensus size: 32
41558422 TACATTAAAA
41558432 ATATAATAAAACAAATAATAAATTTGAAAGGTT
1 ATATAATAAAA-AAATAATAAATTTGAAAGGTT
** * * *
41558465 ATAT-ATTTAAAAATAATATATTTTAAATGTT
1 ATATAATAAAAAAATAATAAATTTGAAAGGTT
* *
41558496 TTATAATATTAAAAATA
1 ATATAATA-AAAAAATA
41558513 TGTTTGAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
31 21 0.54
32 6 0.15
33 12 0.31
ACGTcount: A:0.54, C:0.01, G:0.05, T:0.40
Consensus pattern (32 bp):
ATATAATAAAAAAATAATAAATTTGAAAGGTT
Found at i:41558479 original size:31 final size:33
Alignment explanation
Indices: 41558444--41558512 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 33
41558434 ATAATAAAAC
41558444 AAATAATAAATTTGAAAGGTTATAT-AT-TTAA
1 AAATAATAAATTTGAAAGGTTATATAATATTAA
* * * *
41558475 AAATAATATATTTTAAATGTTTTATAATATTAA
1 AAATAATAAATTTGAAAGGTTATATAATATTAA
41558508 AAATA
1 AAATA
41558513 TGTTTGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 21 0.66
32 2 0.06
33 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (33 bp):
AAATAATAAATTTGAAAGGTTATATAATATTAA
Found at i:41558534 original size:22 final size:22
Alignment explanation
Indices: 41558506--41558575 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
41558496 TTATAATATT
* * *
41558506 AAAAATATGTTTGAATTTTTAA
1 AAAAATATATTTAAAATTTTAA
41558528 AAAAATATATTTAAAATTTT-A
1 AAAAATATATTTAAAATTTTAA
* *
41558549 AAAAATAATATTTAAAATATTAT
1 AAAAAT-ATATTTAAAATTTTAA
41558572 AAAA
1 AAAA
41558576 CCAATAATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 7 0.17
22 30 0.73
23 4 0.10
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
AAAAATATATTTAAAATTTTAA
Found at i:41558614 original size:28 final size:27
Alignment explanation
Indices: 41558582--41558654 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 27
41558572 AAAACCAATA
41558582 ATAAACAAA-TAAATAAAGCAAATAAAGG
1 ATAAACAAACTAAA-AAAGCAAATAAA-G
* * *
41558610 ATAAAAAAACTGAAAAAGTAAATAAAG
1 ATAAACAAACTAAAAAAGCAAATAAAG
* *
41558637 AAAAACAAAATATAAAAA
1 ATAAACAAACTA-AAAAA
41558655 AAGAAAAAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
27 9 0.25
28 24 0.67
29 3 0.08
ACGTcount: A:0.73, C:0.05, G:0.08, T:0.14
Consensus pattern (27 bp):
ATAAACAAACTAAAAAAGCAAATAAAG
Found at i:41572437 original size:17 final size:17
Alignment explanation
Indices: 41572417--41572451 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41572407 AATAGCATAG
41572417 AAATAATAT-AAACAAAT
1 AAATAA-ATGAAACAAAT
41572434 AAATAAATGAAACAAAT
1 AAATAAATGAAACAAAT
41572451 A
1 A
41572452 TACATAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (17 bp):
AAATAAATGAAACAAAT
Found at i:41577950 original size:17 final size:17
Alignment explanation
Indices: 41577924--41577957 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41577914 TTAATTTAAA
*
41577924 TAAATCAATTTCTCAAT
1 TAAATAAATTTCTCAAT
41577941 TAAATAAATTTCTCAAT
1 TAAATAAATTTCTCAAT
41577958 CCAATTCTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATAAATTTCTCAAT
Found at i:41582100 original size:29 final size:29
Alignment explanation
Indices: 41582000--41582099 Score: 139
Period size: 29 Copynumber: 3.4 Consensus size: 29
41581990 ACAAACAACC
41582000 CTAAAT-CTCGAAAGAACAAAGCACTTTGG
1 CTAAATCCT-GAAAGAACAAAGCACTTTGG
* *
41582029 CTAAATCCCGAAAGAACAAAGCATTTTGG
1 CTAAATCCTGAAAGAACAAAGCACTTTGG
* *
41582058 CTAAATCCTGAAATAACAAAACACTTTGG
1 CTAAATCCTGAAAGAACAAAGCACTTTGG
*
41582087 CTAAAACCTGAAA
1 CTAAATCCTGAAA
41582100 TTCTCCAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 62 0.98
30 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.21
Consensus pattern (29 bp):
CTAAATCCTGAAAGAACAAAGCACTTTGG
Found at i:41583285 original size:18 final size:18
Alignment explanation
Indices: 41583262--41583297 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
41583252 AGATGCTCCA
41583262 TTATTACTACATTTTGAG
1 TTATTACTACATTTTGAG
41583280 TTATTACTACATTTTGAG
1 TTATTACTACATTTTGAG
41583298 CAACATATCC
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:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TTATTACTACATTTTGAG
Found at i:41589842 original size:30 final size:30
Alignment explanation
Indices: 41589806--41589873 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
41589796 ATCACACTAA
*
41589806 TCATTTTTTGTCACAGA-TATAACGAAGTTG
1 TCATTTTTTGTCACAAACT-TAACGAAGTTG
* *
41589836 TCATTTTTTGTTACAAACTTAACGGAGTTG
1 TCATTTTTTGTCACAAACTTAACGAAGTTG
41589866 TCATTTTT
1 TCATTTTT
41589874 CATCCCGCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (30 bp):
TCATTTTTTGTCACAAACTTAACGAAGTTG
Found at i:41596357 original size:46 final size:46
Alignment explanation
Indices: 41596267--41596455 Score: 292
Period size: 46 Copynumber: 4.1 Consensus size: 46
41596257 CTTGTCCCTA
* *
41596267 ATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTTACTTG
*
41596312 ATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTTACTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTTACTTG
* * *
41596358 ATCAGATAAGTGTAGTTAAAACTACCACTTATCACTTTGTCACTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTTACTTG
*
41596404 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCT-CTTG
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGT-TACTTG
41596450 ATCAGA
1 ATCAGA
41596456 AGTACTCAAA
Statistics
Matches: 131, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
45 17 0.13
46 114 0.87
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (46 bp):
ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTTACTTG
Found at i:41596529 original size:124 final size:124
Alignment explanation
Indices: 41596383--41596626 Score: 479
Period size: 124 Copynumber: 2.0 Consensus size: 124
41596373 TTAAAACTAC
41596383 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
41596448 TGATCAGAAGTACTCAAATCCGGTGTTCCGCTTAATTTGATCATTTATTCGATTTATAG
66 TGATCAGAAGTACTCAAATCCGGTGTTCCGCTTAATTTGATCATTTATTCGATTTATAG
*
41596507 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
41596572 TGATCAGAAGTACTCAAATCCGGTGTTCCGCTTAATTTGATCATTTATTCGATTT
66 TGATCAGAAGTACTCAAATCCGGTGTTCCGCTTAATTTGATCATTTATTCGATTT
41596627 TTTTCACATT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (124 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
TGATCAGAAGTACTCAAATCCGGTGTTCCGCTTAATTTGATCATTTATTCGATTTATAG
Found at i:41600377 original size:20 final size:20
Alignment explanation
Indices: 41600354--41600391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41600344 TGTGTATATT
41600354 ATTTGAATTTATGGATTTGA
1 ATTTGAATTTATGGATTTGA
* *
41600374 ATTTGGATTTTTGGATTT
1 ATTTGAATTTATGGATTT
41600392 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (20 bp):
ATTTGAATTTATGGATTTGA
Found at i:41613710 original size:30 final size:29
Alignment explanation
Indices: 41613665--41613726 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
41613655 TTGGACGGGT
*
41613665 AACCTGATATAATTTCAGCTTGTATGAGC
1 AACCTGATATAATTTCAACTTGTATGAGC
* *
41613694 AACCTTGATGTAATTTCAACTTGTGTGAGC
1 AACC-TGATATAATTTCAACTTGTATGAGC
41613724 AAC
1 AAC
41613727 TCAGTTCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (29 bp):
AACCTGATATAATTTCAACTTGTATGAGC
Found at i:41616184 original size:28 final size:27
Alignment explanation
Indices: 41616125--41616184 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
41616115 TTCAGCTCTG
**
41616125 ATAATTTCGAAGCACAAAAACTGTATC
1 ATAATTTCGAAGCACAAAAACTGTAGA
* *
41616152 GTAATCTTCGGAGCACAAAAACTGTAGA
1 ATAAT-TTCGAAGCACAAAAACTGTAGA
41616180 ATAAT
1 ATAAT
41616185 AAAAGAAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (27 bp):
ATAATTTCGAAGCACAAAAACTGTAGA
Found at i:41624699 original size:6 final size:6
Alignment explanation
Indices: 41624690--41624721 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
41624680 GGAAAAGAAA
*
41624690 TTCGAA TTCGAC TTCGAC TTCGAC TTCGAC TT
1 TTCGAC TTCGAC TTCGAC TTCGAC TTCGAC TT
41624722 GACCATTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.38
Consensus pattern (6 bp):
TTCGAC
Found at i:41624976 original size:13 final size:13
Alignment explanation
Indices: 41624958--41625024 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
41624948 TTTTCATTGT
41624958 TTTTGAAGAGTAC
1 TTTTGAAGAGTAC
*
41624971 TTTTGAA-AGTGC
1 TTTTGAAGAGTAC
* * *
41624983 TATGGAAAAGTAC
1 TTTTGAAGAGTAC
41624996 TTTTG-AGA--A-
1 TTTTGAAGAGTAC
*
41625005 TTTTGAGGAGTAC
1 TTTTGAAGAGTAC
41625018 TTTTGAA
1 TTTTGAA
41625025 AATTTAGATG
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
9 5 0.12
10 3 0.08
12 12 0.30
13 20 0.50
ACGTcount: A:0.31, C:0.06, G:0.24, T:0.39
Consensus pattern (13 bp):
TTTTGAAGAGTAC
Found at i:41625309 original size:21 final size:19
Alignment explanation
Indices: 41625253--41625313 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
41625243 TAATTATTTA
41625253 TTAAATT-TAATTAGAATAT
1 TTAAATTATAATTA-AATAT
* *
41625272 ATAAATTATATTTAAATAT
1 TTAAATTATAATTAAATAT
41625291 TTAAATATAATAATTAAATAT
1 TTAAAT-T-ATAATTAAATAT
41625312 TT
1 TT
41625314 GTAATTAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 6 0.17
21 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAAATTATAATTAAATAT
Found at i:41631501 original size:210 final size:211
Alignment explanation
Indices: 41631118--41631514 Score: 600
Period size: 210 Copynumber: 1.9 Consensus size: 211
41631108 GCGTCTTGAC
* * * * * *
41631118 AAGAAGAAACATCTTGTCACAATGACGCGATAGCTGGCATCCTGATGATGCGATGTGTTATGTAA
1 AAGAAGAAACATCTTGTCACAACGACGCGATAGCTAGCATCCTAACGAGGCGATGTGTTATGCAA
*
41631183 TTTCCTTGATTTTCTTCTCCCAGTCAAATTCTTATTATTTGTCTCAATCAAACTCTAATTAGTAT
66 TTTCCTTAATTTTCTTCTCCCAGTCAAATTCTTATTATTTGTCTCAATCAAACTCTAATTAGTAT
* *
41631248 AGGTTATTTTAATATTATTTGACCTATAAATTTAACATATAAATAAGCTCTTTTCCAAGATGCGA
131 AGGTTATTTTAATATTATTTGACCTACAAATTTAACATATAAATAAGCTATTTTCCAAGATGCGA
41631313 CCACTTGGATCCTAAT
196 CCACTTGGATCCTAAT
* *
41631329 AAGAAGAAACCT-TTGTCACAACGACGCGATAGCTAGCATCCTAACGAGGTGATGTGTTATGCAA
1 AAGAAGAAACATCTTGTCACAACGACGCGATAGCTAGCATCCTAACGAGGCGATGTGTTATGCAA
* * *
41631393 TTTCCTTAATTTTCTTCTTCCAGTCAAATTCTTATTATTTGTC-CTAATCAAACTCTGATTAGTG
66 TTTCCTTAATTTTCTTCTCCCAGTCAAATTCTTATTATTTGTCTC-AATCAAACTCTAATTAGTA
* * * * *
41631457 TAGGTTATTTTAGTATTATTTGATCTACGAATTTAGCCTATAAATAAGCTATTTTCCA
130 TAGGTTATTTTAATATTATTTGACCTACAAATTTAACATATAAATAAGCTATTTTCCA
41631515 CCTTAGAAAG
Statistics
Matches: 166, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
209 1 0.01
210 154 0.93
211 11 0.07
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (211 bp):
AAGAAGAAACATCTTGTCACAACGACGCGATAGCTAGCATCCTAACGAGGCGATGTGTTATGCAA
TTTCCTTAATTTTCTTCTCCCAGTCAAATTCTTATTATTTGTCTCAATCAAACTCTAATTAGTAT
AGGTTATTTTAATATTATTTGACCTACAAATTTAACATATAAATAAGCTATTTTCCAAGATGCGA
CCACTTGGATCCTAAT
Found at i:41646293 original size:75 final size:75
Alignment explanation
Indices: 41646170--41646326 Score: 314
Period size: 75 Copynumber: 2.1 Consensus size: 75
41646160 CCCCAAGCCT
41646170 AATTTTTTCATTTACGTTTATTGAATTTTTAACTGTGGAATTAAGATTATGACATATTATATTTA
1 AATTTTTTCATTTACGTTTATTGAATTTTTAACTGTGGAATTAAGATTATGACATATTATATTTA
41646235 TTTATTTTTA
66 TTTATTTTTA
41646245 AATTTTTTCATTTACGTTTATTGAATTTTTAACTGTGGAATTAAGATTATGACATATTATATTTA
1 AATTTTTTCATTTACGTTTATTGAATTTTTAACTGTGGAATTAAGATTATGACATATTATATTTA
41646310 TTTATTTTTA
66 TTTATTTTTA
41646320 AATTTTT
1 AATTTTT
41646327 GTAATTATTT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 82 1.00
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (75 bp):
AATTTTTTCATTTACGTTTATTGAATTTTTAACTGTGGAATTAAGATTATGACATATTATATTTA
TTTATTTTTA
Found at i:41647518 original size:22 final size:23
Alignment explanation
Indices: 41647492--41647560 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
41647482 GATATTTTGA
*
41647492 ATATTTTAT-TTAATTAAATAAT
1 ATATTTTATAATAATTAAATAAT
* *
41647514 ATA-TTAATAATAATTAAATTAT
1 ATATTTTATAATAATTAAATAAT
* *
41647536 ATATTTTTATAATATTTTAATAAT
1 ATA-TTTTATAATAATTAAATAAT
41647560 A
1 A
41647561 AAATGATAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
21 4 0.11
22 17 0.46
24 16 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTTTATAATAATTAAATAAT
Found at i:41652019 original size:67 final size:67
Alignment explanation
Indices: 41651911--41652106 Score: 302
Period size: 67 Copynumber: 2.9 Consensus size: 67
41651901 TTTCCAATTC
* **
41651911 AGAGAGCACACTCTCGCGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCTTCTG
1 AGAGAGCACACTCTCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
41651976 TA
66 TA
* * *
41651978 AGAGAGCACACTCTCGAGAACCTCATTTCTTACAGCGGGATTACCAATCTAGGCTAAATCCCCTG
1 AGAGAGCACACTCTCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
41652043 TA
66 TA
* * * *
41652045 AGAGAGCACACTCCCGCGAACTTTATTTCTTACAGCGGGATTACCAGTCCTGGCTAAATCCC
1 AGAGAGCACACTCTCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCC
41652107 TTATAATATA
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 116 1.00
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.24
Consensus pattern (67 bp):
AGAGAGCACACTCTCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
TA
Found at i:41652328 original size:57 final size:57
Alignment explanation
Indices: 41652240--41652492 Score: 364
Period size: 57 Copynumber: 4.3 Consensus size: 57
41652230 CATATTACCT
* * *
41652240 GTCCGGGCTAAATCCATTTTC-CACATATTCTTTGGGAGGGCTATATCAAGATCACCC
1 GTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGATCACCC
41652297 GTCCGGGCTAGATCTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGATCACCC
1 GTCCGGGCTAGATCTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGATCACCC
* *
41652354 ATCCGGGTTAGATCTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGATCACCC
1 GTCCGGGCTAGATCTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGATCACCC
* *
41652411 ATCCGGGTTAGATCTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATAGGATCACCC
1 GTCCGGGCTAGATCTTTTTCACACATATTCTTCGGGAGGGCTATATC---A-A-GATCACCC
*
41652473 GTCCGGGATAGATCCTTTTT
1 GTCCGGGCTAGAT-CTTTTT
41652493 ACAGTCAATT
Statistics
Matches: 182, Mismatches: 7, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
56 6 0.03
57 149 0.82
60 1 0.01
61 1 0.01
62 19 0.10
63 6 0.03
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (57 bp):
GTCCGGGCTAGATCTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGATCACCC
Found at i:41655700 original size:10 final size:10
Alignment explanation
Indices: 41655685--41655714 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
41655675 TAGTTTAACA
41655685 TTTAATTAAG
1 TTTAATTAAG
41655695 TTTAATTAAG
1 TTTAATTAAG
41655705 TTTAACTTAA
1 TTTAA-TTAA
41655715 TTAACTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (10 bp):
TTTAATTAAG
Found at i:41659042 original size:15 final size:16
Alignment explanation
Indices: 41659022--41659056 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
41659012 AATTTTTTTA
*
41659022 AATATTTTTATAA-TT
1 AATATTTTAATAATTT
41659037 AATATTTTAATAATTT
1 AATATTTTAATAATTT
41659053 AATA
1 AATA
41659057 AATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTTTAATAATTT
Found at i:41659052 original size:24 final size:25
Alignment explanation
Indices: 41659004--41659076 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 25
41658994 AAAACTTCAA
*
41659004 TTTATAA-TAATTTTTTTAA-ATATT
1 TTTATAATTAA-TATTTTAATATATT
41659028 TTTATAATTAATATTTTAATA-ATT
1 TTTATAATTAATATTTTAATATATT
* *
41659052 TAATAAATATTAATATTTATAATAT
1 T-TTATA-ATTAATATTT-TAATAT
41659077 CTATAAAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
24 18 0.45
25 7 0.17
26 10 0.25
27 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTATAATTAATATTTTAATATATT
Found at i:41659085 original size:26 final size:26
Alignment explanation
Indices: 41659034--41659083 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
41659024 TATTTTTATA
*
41659034 ATTAATATTTTAATAATTTAATAAAT
1 ATTAATATTTTAATAATCTAATAAAT
41659060 ATTAATATTTATAAT-ATCT-ATAAA
1 ATTAATATTT-TAATAATCTAATAAA
41659084 ATGAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 5 0.23
26 13 0.59
27 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTAATATTTTAATAATCTAATAAAT
Found at i:41670705 original size:91 final size:91
Alignment explanation
Indices: 41670550--41670826 Score: 545
Period size: 91 Copynumber: 3.0 Consensus size: 91
41670540 TATACATATA
*
41670550 TTAATATAAACAATATTTAGATTGATATTATAGAGATATTGTATTGATTCAAAATTTTACATACA
1 TTAATATAAACACTATTTAGATTGATATTATAGAGATATTGTATTGATTCAAAATTTTACATACA
41670615 TGATAAGTATAATTATATTGATAAAT
66 TGATAAGTATAATTATATTGATAAAT
41670641 TTAATATAAACACTATTTAGATTGATATTATAGAGATATTGTATTGATTCAAAATTTTACATACA
1 TTAATATAAACACTATTTAGATTGATATTATAGAGATATTGTATTGATTCAAAATTTTACATACA
41670706 TGATAAGTATAATTATATTGATAAAT
66 TGATAAGTATAATTATATTGATAAAT
41670732 TTAATATAAACACTATTTAGATTGATATTATAGAGATATTGTATTGATTCAAAATTTTACATACA
1 TTAATATAAACACTATTTAGATTGATATTATAGAGATATTGTATTGATTCAAAATTTTACATACA
41670797 TGATAAGTATAATTATATTGATAAAT
66 TGATAAGTATAATTATATTGATAAAT
41670823 TTAA
1 TTAA
41670827 CGATCGAACT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 185 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (91 bp):
TTAATATAAACACTATTTAGATTGATATTATAGAGATATTGTATTGATTCAAAATTTTACATACA
TGATAAGTATAATTATATTGATAAAT
Found at i:41670725 original size:44 final size:44
Alignment explanation
Indices: 41670585--41670816 Score: 146
Period size: 44 Copynumber: 5.1 Consensus size: 44
41670575 TATTATAGAG
41670585 ATATTGTATTGATTCAAAATTTTACATACATGATAAGTATAATT
1 ATATTGTATTGATTCAAAATTTTACATACATGATAAGTATAATT
* * * *
41670629 ATATTGATAAATTTAATAT-AAACACTATTTAGAT---TGAT-ATTATAGA-G
1 ATATTG-T--A-TTGAT-TCAAA-A-T-TTTACATACATGATAAGTATA-ATT
41670676 ATATTGTATTGATTCAAAATTTTACATACATGATAAGTATAATT
1 ATATTGTATTGATTCAAAATTTTACATACATGATAAGTATAATT
* * * *
41670720 ATATTGATAAATTTAATAT-AAACACTATTTAGAT---TGAT-ATTATAGA-G
1 ATATTG-T--A-TTGAT-TCAAA-A-T-TTTACATACATGATAAGTATA-ATT
41670767 ATATTGTATTGATTCAAAATTTTACATACATGATAAGTATAATT
1 ATATTGTATTGATTCAAAATTTTACATACATGATAAGTATAATT
41670811 ATATTG
1 ATATTG
41670817 ATAAATTTAA
Statistics
Matches: 142, Mismatches: 16, Indels: 60
0.65 0.07 0.28
Matches are distributed among these distances:
40 12 0.08
41 2 0.01
42 4 0.03
43 24 0.17
44 30 0.21
45 2 0.01
46 2 0.01
47 24 0.17
48 24 0.17
49 4 0.03
50 2 0.01
51 12 0.08
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (44 bp):
ATATTGTATTGATTCAAAATTTTACATACATGATAAGTATAATT
Found at i:41680394 original size:216 final size:216
Alignment explanation
Indices: 41680018--41680669 Score: 1205
Period size: 216 Copynumber: 3.0 Consensus size: 216
41680008 TTGAACCTGA
*
41680018 TCTAGTTTAGAGGAGTCATCTGTTTTCCATGTCATAAAACAATTAATTTATCATCTGTTCTCCAA
1 TCTAGTTTAGAGGAGTCATCTGTTTTCCATGTCATAAAACAATTAATTTATCATCTGTTTTCCAA
*
41680083 AAGACTTGATATTTTAACTTTGTGCCATTTAGTTATAGATGTATAAGTTGAGCATAATTCATTTT
66 AAGACTTAATATTTTAACTTTGTGCCATTTAGTTATAGATGTATAAGTTGAGCATAATTCATTTT
* *
41680148 ATTATCCTTCCAATCTAAATTAGGTTTAAATTTAAATAATTTTATGAAATGGCTTAGGTCAAATG
131 ATTATCCTTCCAATCTAAATTAGATTTAAATTTAAATAATTTTATGAAATGGCTTAGATCAAATG
41680213 TCTGAAACCTAAACTGATGTC
196 TCTGAAACCTAAACTGATGTC
41680234 TCTAGTTTAGAGGAGTCATCTGTTTTCCATGTCATAAAACAATTAATTTATCATCTGTTTTCCAA
1 TCTAGTTTAGAGGAGTCATCTGTTTTCCATGTCATAAAACAATTAATTTATCATCTGTTTTCCAA
41680299 AAGACTTAATATTTTAACTTTGTGCCATTTAGTTATAGATGTATAAGTTGAGCATAATTCATTTT
66 AAGACTTAATATTTTAACTTTGTGCCATTTAGTTATAGATGTATAAGTTGAGCATAATTCATTTT
*
41680364 ATTATCCTTCCAATCTAAATTAGATTTAAATTTAAATAATTTTATGAAACGGCTTAGATCAAATG
131 ATTATCCTTCCAATCTAAATTAGATTTAAATTTAAATAATTTTATGAAATGGCTTAGATCAAATG
*
41680429 TCTGAAACCAAAACTGATGTC
196 TCTGAAACCTAAACTGATGTC
**
41680450 TCTAGTTTAGAGGAGTCATCTGTTTAACATGTCATAAAACAATTAATTTATCATCTGTTTTCCAA
1 TCTAGTTTAGAGGAGTCATCTGTTTTCCATGTCATAAAACAATTAATTTATCATCTGTTTTCCAA
*
41680515 AAGACTTAATATTTTAACTTTGTGCCATGTAGTTATAGATGTATAAGTTGAGCATAATTCATTTT
66 AAGACTTAATATTTTAACTTTGTGCCATTTAGTTATAGATGTATAAGTTGAGCATAATTCATTTT
*
41680580 ATTATCCTTCCAATCTTAATTAGATTTAAATTTAAATAATTTTATGAAATGGCTTAGATCAAATG
131 ATTATCCTTCCAATCTAAATTAGATTTAAATTTAAATAATTTTATGAAATGGCTTAGATCAAATG
*
41680645 TTTGAAACCTAAACTGATGTC
196 TCTGAAACCTAAACTGATGTC
41680666 TCTA
1 TCTA
41680670 ATCTATTGGT
Statistics
Matches: 423, Mismatches: 13, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
216 423 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (216 bp):
TCTAGTTTAGAGGAGTCATCTGTTTTCCATGTCATAAAACAATTAATTTATCATCTGTTTTCCAA
AAGACTTAATATTTTAACTTTGTGCCATTTAGTTATAGATGTATAAGTTGAGCATAATTCATTTT
ATTATCCTTCCAATCTAAATTAGATTTAAATTTAAATAATTTTATGAAATGGCTTAGATCAAATG
TCTGAAACCTAAACTGATGTC
Found at i:41691374 original size:30 final size:31
Alignment explanation
Indices: 41691314--41691385 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
41691304 ACCAAAAATT
***
41691314 TATTTTAAAAATTAAAAAAGTATTTTAAAAA-
1 TATTTT-AAAATTAAAAAAGTATAAAAAAAAG
41691345 TATTTTAAAATTAAAAAA-TAATAAAAAAAAG
1 TATTTTAAAATTAAAAAAGT-ATAAAAAAAAG
41691376 TATTTTAAAA
1 TATTTTAAAA
41691386 ATATTTTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 1 0.03
30 19 0.53
31 16 0.44
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (31 bp):
TATTTTAAAATTAAAAAAGTATAAAAAAAAG
Found at i:41691374 original size:42 final size:42
Alignment explanation
Indices: 41691327--41691455 Score: 242
Period size: 42 Copynumber: 3.1 Consensus size: 42
41691317 TTTAAAAATT
41691327 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAA
41691369 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAA
*
41691411 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-ATTAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAA
41691452 AAAA
1 AAAA
41691456 TAAATATATT
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 8 0.09
42 78 0.91
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (42 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAATAA
Found at i:41702856 original size:26 final size:26
Alignment explanation
Indices: 41702827--41702900 Score: 112
Period size: 26 Copynumber: 2.8 Consensus size: 26
41702817 TACACCTTGT
41702827 GTGTGACCTTTATACTTATGTTCAAG
1 GTGTGACCTTTATACTTATGTTCAAG
* *
41702853 GTGTGACCTGTATATTTATGTTCAAG
1 GTGTGACCTTTATACTTATGTTCAAG
* *
41702879 GTGTAACCTTTATACGTATGTT
1 GTGTGACCTTTATACTTATGTT
41702901 GCAGTTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (26 bp):
GTGTGACCTTTATACTTATGTTCAAG
Found at i:41706929 original size:14 final size:14
Alignment explanation
Indices: 41706910--41706943 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41706900 CAATATTCAA
41706910 ATAATAACAACAAT
1 ATAATAACAACAAT
* *
41706924 ATAATAATAATAAT
1 ATAATAACAACAAT
41706938 ATAATA
1 ATAATA
41706944 GCAAAATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAATAACAACAAT
Found at i:41707516 original size:22 final size:23
Alignment explanation
Indices: 41707470--41707516 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
41707460 TATCCATGTT
* *
41707470 TAAAATTTTAATTAAAAAATTATA
1 TAAAATTATAATT-AAAAATAATA
41707494 TAAAATTATAATT-AAAATAATA
1 TAAAATTATAATTAAAAATAATA
41707516 T
1 T
41707517 TTTTTTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
24 12 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAATTATAATTAAAAATAATA
Found at i:41715033 original size:15 final size:17
Alignment explanation
Indices: 41714998--41715035 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
41714988 ATGAGATTAA
*
41714998 AAATAGTTGTAATGTTG
1 AAATAGTTGTAATGTTC
41715015 AAATA-TTGT-ATGTTC
1 AAATAGTTGTAATGTTC
41715030 AAATAG
1 AAATAG
41715036 AAAATTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 10 0.53
16 4 0.21
17 5 0.26
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.39
Consensus pattern (17 bp):
AAATAGTTGTAATGTTC
Found at i:41716052 original size:11 final size:11
Alignment explanation
Indices: 41716036--41716140 Score: 131
Period size: 11 Copynumber: 9.6 Consensus size: 11
41716026 AAAATTTTAA
41716036 ATTTTTTATAT
1 ATTTTTTATAT
* *
41716047 ATTTTTTAGAA
1 ATTTTTTATAT
41716058 ATTTTTTATAT
1 ATTTTTTATAT
* *
41716069 ATTTTTTAGAA
1 ATTTTTTATAT
41716080 ATTTTTTATAT
1 ATTTTTTATAT
* *
41716091 ATTTTTTAGAA
1 ATTTTTTATAT
41716102 ATTTTTTATAT
1 ATTTTTTATAT
*
41716113 ATTTTTTAGA-
1 ATTTTTTATAT
*
41716123 AATTTTTATAT
1 ATTTTTTATAT
41716134 ATTTTTT
1 ATTTTTT
41716141 TGAAATTATA
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
10 8 0.10
11 69 0.90
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (11 bp):
ATTTTTTATAT
Found at i:41716060 original size:22 final size:22
Alignment explanation
Indices: 41716034--41716147 Score: 212
Period size: 22 Copynumber: 5.2 Consensus size: 22
41716024 AGAAAATTTT
41716034 AAATTTTTTATATATTTTTTAG
1 AAATTTTTTATATATTTTTTAG
41716056 AAATTTTTTATATATTTTTTAG
1 AAATTTTTTATATATTTTTTAG
41716078 AAATTTTTTATATATTTTTTAG
1 AAATTTTTTATATATTTTTTAG
41716100 AAATTTTTTATATATTTTTTAG
1 AAATTTTTTATATATTTTTTAG
*
41716122 AAA-TTTTTATATATTTTTTTG
1 AAATTTTTTATATATTTTTTAG
41716143 AAATT
1 AAATT
41716148 ATAAATTTTG
Statistics
Matches: 90, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
21 20 0.22
22 70 0.78
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
AAATTTTTTATATATTTTTTAG
Found at i:41718586 original size:21 final size:20
Alignment explanation
Indices: 41718560--41718602 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41718550 AAAAAAAAAG
*
41718560 TTTAATTTACTTTTT-TTAATT
1 TTTAATATA-TTTTTATT-ATT
41718581 TTTAATATATTTTTATTATT
1 TTTAATATATTTTTATTATT
41718601 TT
1 TT
41718603 GATTTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTAATATATTTTTATTATT
Found at i:41721259 original size:15 final size:16
Alignment explanation
Indices: 41721238--41721284 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 16
41721228 ATACTACAAA
41721238 AATATTTATTATTAAT
1 AATATTTATTATTAAT
*
41721254 -ATATTTATAATTGTAAT
1 AATATTTATTA-T-TAAT
41721271 AAATATTTATTATT
1 -AATATTTATTATT
41721285 GAAGTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 9 0.36
16 1 0.04
17 5 0.20
18 1 0.04
19 9 0.36
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (16 bp):
AATATTTATTATTAAT
Found at i:41721343 original size:13 final size:13
Alignment explanation
Indices: 41721325--41721364 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
41721315 ATGTGAAGAA
41721325 TATTATTTAAAAT
1 TATTATTTAAAAT
41721338 TATTATTTTAAAATT
1 TATTA-TTTAAAA-T
41721353 TATTA-TTAAAAT
1 TATTATTTAAAAT
41721365 AAAATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.04
13 11 0.44
14 7 0.28
15 6 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATTTAAAAT
Found at i:41721357 original size:15 final size:14
Alignment explanation
Indices: 41721325--41721359 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41721315 ATGTGAAGAA
41721325 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
41721338 TATTATTTTAAAATT
1 TATTATTTTAAAA-T
41721353 TATTATT
1 TATTATT
41721360 AAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.25
14 7 0.35
15 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:41726985 original size:130 final size:130
Alignment explanation
Indices: 41726752--41727145 Score: 788
Period size: 130 Copynumber: 3.0 Consensus size: 130
41726742 TCTGGCAATT
41726752 GCATATAGTCTTTGCCATGAAGTTGTATTGTTAGTTTTACCTGATCATTTCAAAGTAACAAGAGA
1 GCATATAGTCTTTGCCATGAAGTTGTATTGTTAGTTTTACCTGATCATTTCAAAGTAACAAGAGA
41726817 TATCTATGGTTGTTCATACTGTCAAAATGACCTCTCTGCTCACTCTCATTTCTCGTGCCCTACAA
66 TATCTATGGTTGTTCATACTGTCAAAATGACCTCTCTGCTCACTCTCATTTCTCGTGCCCTACAA
41726882 GCATATAGTCTTTGCCATGAAGTTGTATTGTTAGTTTTACCTGATCATTTCAAAGTAACAAGAGA
1 GCATATAGTCTTTGCCATGAAGTTGTATTGTTAGTTTTACCTGATCATTTCAAAGTAACAAGAGA
41726947 TATCTATGGTTGTTCATACTGTCAAAATGACCTCTCTGCTCACTCTCATTTCTCGTGCCCTACAA
66 TATCTATGGTTGTTCATACTGTCAAAATGACCTCTCTGCTCACTCTCATTTCTCGTGCCCTACAA
41727012 GCATATAGTCTTTGCCATGAAGTTGTATTGTTAGTTTTACCTGATCATTTCAAAGTAACAAGAGA
1 GCATATAGTCTTTGCCATGAAGTTGTATTGTTAGTTTTACCTGATCATTTCAAAGTAACAAGAGA
41727077 TATCTATGGTTGTTCATACTGTCAAAATGACCTCTCTGCTCACTCTCATTTCTCGTGCCCTACAA
66 TATCTATGGTTGTTCATACTGTCAAAATGACCTCTCTGCTCACTCTCATTTCTCGTGCCCTACAA
41727142 GCAT
1 GCAT
41727146 GTAGAATATA
Statistics
Matches: 264, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
130 264 1.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (130 bp):
GCATATAGTCTTTGCCATGAAGTTGTATTGTTAGTTTTACCTGATCATTTCAAAGTAACAAGAGA
TATCTATGGTTGTTCATACTGTCAAAATGACCTCTCTGCTCACTCTCATTTCTCGTGCCCTACAA
Found at i:41730716 original size:71 final size:71
Alignment explanation
Indices: 41730625--41730772 Score: 271
Period size: 71 Copynumber: 2.1 Consensus size: 71
41730615 TCAACAGCAT
41730625 ATTT-CTCGATTTTTGCTTCCAAATTAGTTCCTCCTGATATAGAATCTCTTCAAGTTCAGCTCTA
1 ATTTCCTCGATTTTTGCTTCCAAATTAGTTCCTCCTGATATAGAATCTCTTCAAGTTCAGCTCTA
41730689 ACAATA
66 ACAATA
* *
41730695 ATTTCCTCGATTTTTGCTTCCAAATTAGTTCCTCCTGATATAGTATCTCTTCAAGTTTAGCTCTA
1 ATTTCCTCGATTTTTGCTTCCAAATTAGTTCCTCCTGATATAGAATCTCTTCAAGTTCAGCTCTA
41730760 ACAATA
66 ACAATA
41730766 ATTTCCT
1 ATTTCCT
41730773 GCAGACAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
70 4 0.05
71 71 0.95
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (71 bp):
ATTTCCTCGATTTTTGCTTCCAAATTAGTTCCTCCTGATATAGAATCTCTTCAAGTTCAGCTCTA
ACAATA
Found at i:41736095 original size:12 final size:12
Alignment explanation
Indices: 41736078--41736116 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
41736068 AATATGTAAT
41736078 TTTATTATTTTA
1 TTTATTATTTTA
*
41736090 TTTATT-TTTAA
1 TTTATTATTTTA
*
41736101 ATTATTATTTTA
1 TTTATTATTTTA
41736113 TTTA
1 TTTA
41736117 AATTTATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:41736133 original size:33 final size:32
Alignment explanation
Indices: 41736062--41736134 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 32
41736052 AAAATTGTAT
* *
41736062 TATTTAAATATGTAATTTTATTATTTTATTTA
1 TATTTAAATATGTAATTTTATTAATTTATTAA
*
41736094 TTTTTAAATTAT-T-ATTTTATTTAAATTTATTAA
1 TATTTAAA-TATGTAATTTTA-TT-AATTTATTAA
41736127 TATTTAAA
1 TATTTAAA
41736135 AATAAAATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
31 6 0.18
32 10 0.29
33 18 0.53
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (32 bp):
TATTTAAATATGTAATTTTATTAATTTATTAA
Found at i:41739805 original size:3 final size:3
Alignment explanation
Indices: 41739797--41739824 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41739787 TTAATTTTCC
41739797 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41739825 TAATTTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41740936 original size:63 final size:63
Alignment explanation
Indices: 41740835--41740957 Score: 192
Period size: 63 Copynumber: 2.0 Consensus size: 63
41740825 AAAGTTACAT
*
41740835 ATTTTATGTAATTAAATTAATTAATTTATGAGAATGCACCACTAATTTTGCCATATTTATTGA
1 ATTTTATGTAATGAAATTAATTAATTTATGAGAATGCACCACTAATTTTGCCATATTTATTGA
** * * *
41740898 ATTTTATGTAATGAAATTGGTTAATTTATGAGAGTGCACCACTAATTTTTCCATGTTTAT
1 ATTTTATGTAATGAAATTAATTAATTTATGAGAATGCACCACTAATTTTGCCATATTTAT
41740958 ATTAAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 54 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (63 bp):
ATTTTATGTAATGAAATTAATTAATTTATGAGAATGCACCACTAATTTTGCCATATTTATTGA
Found at i:41754673 original size:21 final size:21
Alignment explanation
Indices: 41754647--41754689 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41754637 AAATACGCCA
41754647 AATAGAAGCTCATAAGAGCTG
1 AATAGAAGCTCATAAGAGCTG
41754668 AATAGAAGCTCATAAGAGCTG
1 AATAGAAGCTCATAAGAGCTG
41754689 A
1 A
41754690 TCCACTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.19
Consensus pattern (21 bp):
AATAGAAGCTCATAAGAGCTG
Found at i:41755670 original size:187 final size:186
Alignment explanation
Indices: 41755346--41755726 Score: 654
Period size: 187 Copynumber: 2.0 Consensus size: 186
41755336 AAATTTATCA
*
41755346 AAAATCACTTAATAAAATACTTTTAAATAAAAAATAATATTTTAAATTCATCATTTAACATCTAA
1 AAAATCACATAATAAAATACTTTTAAATAAAAAATAATATTTTAAATTCATCATTTAACATCTAA
*
41755411 AATCACAAGGTTCGCTGATGGCAACATTCAAATTCTTTAACAGTTTCAAAATCGAAGGTACGAGC
66 AATCACAAGGTTCACTGATGGCAACATTCAAATTCTTTAACAGTTTCAAAATCGAAGGTACGAGC
* *
41755476 AAGCTGGACCTAGTTGTAACGATCTCTAAAACATAAAAATTATTAAAAACGGGGCC
131 AAGCTGGACATAGTTGTAACGATCTCCAAAACATAAAAATTATTAAAAACGGGGCC
41755532 AAAATCACATAATAAAATACTTTTAAATAAAAAAATAATATTTTAAATTCATCATTTAACATCTA
1 AAAATCACATAATAAAATACTTTTAAAT-AAAAAATAATATTTTAAATTCATCATTTAACATCTA
* * * *
41755597 ACATCACAAGGTTCATTGATGGCAACATTCAAATTCTTTGACAGTTTCAAAATCGAAGGTATGAG
65 AAATCACAAGGTTCACTGATGGCAACATTCAAATTCTTTAACAGTTTCAAAATCGAAGGTACGAG
** *
41755662 TTAGCTGGACATAGTTGTAACGATCTCCAAAACATAAAAATTATTAAAAATGGGGCC
130 CAAGCTGGACATAGTTGTAACGATCTCCAAAACATAAAAATTATTAAAAACGGGGCC
41755719 AAAATCAC
1 AAAATCAC
41755727 TCGGTTGTTG
Statistics
Matches: 183, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
186 27 0.15
187 156 0.85
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (186 bp):
AAAATCACATAATAAAATACTTTTAAATAAAAAATAATATTTTAAATTCATCATTTAACATCTAA
AATCACAAGGTTCACTGATGGCAACATTCAAATTCTTTAACAGTTTCAAAATCGAAGGTACGAGC
AAGCTGGACATAGTTGTAACGATCTCCAAAACATAAAAATTATTAAAAACGGGGCC
Found at i:41763495 original size:5 final size:5
Alignment explanation
Indices: 41763480--41763518 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
41763470 ACATAATGTT
*
41763480 ATATC ACATC ATATC ATATC ATATC ATATC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATATC ATAT
41763519 AGTATATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATC
Found at i:41764393 original size:16 final size:16
Alignment explanation
Indices: 41764355--41764408 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
41764345 GAGTTTGTTA
41764355 CGGGCTCAGGTTTTCT
1 CGGGCTCAGGTTTTCT
** *
41764371 CAAGCTCAGGTTTTGT
1 CGGGCTCAGGTTTTCT
**
41764387 CGGGCTCAAATTTTCT
1 CGGGCTCAGGTTTTCT
41764403 CGGGCT
1 CGGGCT
41764409 TGGATCTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.13, C:0.24, G:0.28, T:0.35
Consensus pattern (16 bp):
CGGGCTCAGGTTTTCT
Found at i:41766500 original size:23 final size:23
Alignment explanation
Indices: 41766474--41766595 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
41766464 ATAAGTGCCA
*
41766474 CACTGATATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41766497 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41766520 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
41766543 CACTGATATGTAGTCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
41766566 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
41766589 CACTGAT
1 CACTGAT
41766596 CAATAACACT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 87 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:41766541 original size:46 final size:46
Alignment explanation
Indices: 41766474--41766595 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
41766464 ATAAGTGCCA
* *
41766474 CACTGATATGTAGCTGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
*
41766520 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGTCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
*
41766566 CACTGAAATGTAGCCAAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
41766596 CAATAACACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:41773458 original size:24 final size:23
Alignment explanation
Indices: 41773410--41773458 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
41773400 TCACTCAACC
*
41773410 AAAATTTTATTTTTATATATTAT
1 AAAATTTTATTTTTATATATCAT
41773433 AAAATTTTATATTTTA-ATATACAT
1 AAAATTTTAT-TTTTATATAT-CAT
41773457 AA
1 AA
41773459 TTTATTATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
AAAATTTTATTTTTATATATCAT
Found at i:41777430 original size:18 final size:17
Alignment explanation
Indices: 41777403--41777440 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
41777393 TTTCAATGTA
41777403 ATTGATGAGATTACATT
1 ATTGATGAGATTACATT
41777420 ATTGCATGAGATTACATT
1 ATTG-ATGAGATTACATT
41777438 ATT
1 ATT
41777441 ACATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (17 bp):
ATTGATGAGATTACATT
Found at i:41787443 original size:30 final size:30
Alignment explanation
Indices: 41787407--41787468 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
41787397 CAAGCACTGT
41787407 CAGCAGGAAAAGGCAGTCTAGCCTGCTTAC
1 CAGCAGGAAAAGGCAGTCTAGCCTGCTTAC
41787437 CAGCAGGAAAAGGCAGTCTAGCCTGCTTAC
1 CAGCAGGAAAAGGCAGTCTAGCCTGCTTAC
41787467 CA
1 CA
41787469 AGCTGACAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.27, G:0.26, T:0.16
Consensus pattern (30 bp):
CAGCAGGAAAAGGCAGTCTAGCCTGCTTAC
Found at i:41808052 original size:12 final size:13
Alignment explanation
Indices: 41808036--41808065 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
41808026 ATACAACTAC
41808036 TAATAAAAATAAA
1 TAATAAAAATAAA
41808049 -AATAAAAATAAA
1 TAATAAAAATAAA
41808061 TAATA
1 TAATA
41808066 TTTGTTGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAATAAAAATAAA
Found at i:41809474 original size:22 final size:23
Alignment explanation
Indices: 41809449--41809492 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
41809439 TAATTAATCC
*
41809449 TTTTTAAAATT-TTAAAATTATT
1 TTTTTAAAATTATAAAAATTATT
41809471 TTTTTAAAATTATAAAAATTAT
1 TTTTTAAAATTATAAAAATTAT
41809493 AAACAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTTTAAAATTATAAAAATTATT
Found at i:41810061 original size:12 final size:12
Alignment explanation
Indices: 41810046--41810079 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
41810036 TATAACTTTT
41810046 TTTTTTTATAAA
1 TTTTTTTATAAA
41810058 TTTTGTTTATAAA
1 TTTT-TTTATAAA
*
41810071 TTTTATTAT
1 TTTTTTTAT
41810080 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTTTTATAAA
Found at i:41810061 original size:13 final size:13
Alignment explanation
Indices: 41810045--41810074 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41810035 TTATAACTTT
*
41810045 TTTTTTTTATAAA
1 TTTTGTTTATAAA
41810058 TTTTGTTTATAAA
1 TTTTGTTTATAAA
41810071 TTTT
1 TTTT
41810075 ATTATTTTTT
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:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTGTTTATAAA
Found at i:41810101 original size:20 final size:21
Alignment explanation
Indices: 41810048--41810101 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
41810038 TAACTTTTTT
*
41810048 TTTTTATAAATTTTGTTTATAA
1 TTTTTA-AAATTTTGTTAATAA
* **
41810070 ATTTTATTATTTT-TTAATAA
1 TTTTTAAAATTTTGTTAATAA
41810090 TTTTTAAAATTT
1 TTTTTAAAATTT
41810102 AGAACAGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
20 15 0.60
21 5 0.20
22 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTAAAATTTTGTTAATAA
Found at i:41811493 original size:16 final size:18
Alignment explanation
Indices: 41811474--41811512 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
41811464 TTAAGTTATT
41811474 AAAATT-TTAAAAAT-TA
1 AAAATTATTAAAAATATA
*
41811490 AAAATTATTAAAATTATA
1 AAAATTATTAAAAATATA
41811508 AAAAT
1 AAAAT
41811513 ATGTTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 7 0.35
18 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATTATTAAAAATATA
Found at i:41822568 original size:18 final size:17
Alignment explanation
Indices: 41822545--41822582 Score: 67
Period size: 18 Copynumber: 2.2 Consensus size: 17
41822535 AAAAAAATGT
41822545 AATAATGTAATCTCATGC
1 AATAATGTAATCTCAT-C
41822563 AATAATGTAATCTCATC
1 AATAATGTAATCTCATC
41822580 AAT
1 AAT
41822583 TACATTGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.34
Consensus pattern (17 bp):
AATAATGTAATCTCATC
Found at i:41827691 original size:17 final size:17
Alignment explanation
Indices: 41827671--41827704 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41827661 AAATCCGAAT
41827671 ATTTATTAAAAAAATAA
1 ATTTATTAAAAAAATAA
* *
41827688 ATTTATTTAAAATATAA
1 ATTTATTAAAAAAATAA
41827705 CTCAATTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTATTAAAAAAATAA
Found at i:41857221 original size:40 final size:40
Alignment explanation
Indices: 41857166--41857350 Score: 282
Period size: 40 Copynumber: 4.7 Consensus size: 40
41857156 ATTGTTTGAT
* *
41857166 TGCACATACGTGCCCCTATTTGTACTTCAGTATCCCTGAA
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
*
41857206 TGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC-GAA
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
* * * *
41857245 TGCACATACATGCCCTTGTTTGTACTTCGGTACCCCTGAT
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
*
41857285 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAG
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
*
41857325 TGCACATACGTGCCCCTGTTTATACT
1 TGCACATACGTGCCCCTGTTTGTACT
41857351 CTGGTAACTC
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 37 0.28
40 96 0.72
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.32
Consensus pattern (40 bp):
TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAA
Found at i:41857297 original size:79 final size:80
Alignment explanation
Indices: 41857166--41857350 Score: 282
Period size: 79 Copynumber: 2.3 Consensus size: 80
41857156 ATTGTTTGAT
* *
41857166 TGCACATACGTGCCCCTATTTGTACTTCAGTATCCCTGAATGCACATACGTGCCCCTGTTTGTAC
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAATGCACATACGTGCCCCTGTTTGTAC
*
41857231 TTCGGTACCCC-GAA
66 TTCAGTACCCCTGAA
* * * *
41857245 TGCACATACATGCCCTTGTTTGTACTTCGGTACCCCTGATTGCACATACGTGCCCCTGTTTGTAC
1 TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAATGCACATACGTGCCCCTGTTTGTAC
*
41857310 TTCAGTACCCCTGAG
66 TTCAGTACCCCTGAA
*
41857325 TGCACATACGTGCCCCTGTTTATACT
1 TGCACATACGTGCCCCTGTTTGTACT
41857351 CTGGTAACTC
Statistics
Matches: 94, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 69 0.73
80 25 0.27
ACGTcount: A:0.19, C:0.31, G:0.18, T:0.32
Consensus pattern (80 bp):
TGCACATACGTGCCCCTGTTTGTACTTCAGTACCCCTGAATGCACATACGTGCCCCTGTTTGTAC
TTCAGTACCCCTGAA
Found at i:41860262 original size:42 final size:43
Alignment explanation
Indices: 41860154--41860267 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 43
41860144 AGCTCGTACA
* * * *
41860154 ATGCCAAC-GTCCCAGACGTGGTCTTACATGTATTCAAATAACG
1 ATGCC-ACTGTCCCAGACATGGTCTTACACGAAATCAAATAACG
* * * *
41860197 ATGCCACTGTCCCGGACAAGGTCTTACACGAAATCATAT-ATG
1 ATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATAACG
41860239 ATGCCTA-TGTCCCAGACATGGTCTTACAC
1 ATGCC-ACTGTCCCAGACATGGTCTTACAC
41860268 ATAAATCTCA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
42 29 0.49
43 30 0.51
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACACGAAATCAAATAACG
Found at i:41861285 original size:19 final size:19
Alignment explanation
Indices: 41861263--41861307 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
41861253 AAATGTCCAC
41861263 TAACCTTATAATGGCATAA
1 TAACCTTATAATGGCATAA
41861282 TAACCTTATAATGGCATAA
1 TAACCTTATAATGGCATAA
41861301 TAACCTT
1 TAACCTT
41861308 TTAAGGACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (19 bp):
TAACCTTATAATGGCATAA
Found at i:41862838 original size:24 final size:24
Alignment explanation
Indices: 41862811--41862857 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41862801 AGCCTATAAT
41862811 GGGTAGCTCCAAAAAGCAATTAAC
1 GGGTAGCTCCAAAAAGCAATTAAC
* *
41862835 GGGTAGCTCCGAAGAGCAATTAA
1 GGGTAGCTCCAAAAAGCAATTAA
41862858 TGGGAAGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.26, T:0.17
Consensus pattern (24 bp):
GGGTAGCTCCAAAAAGCAATTAAC
Found at i:41862917 original size:26 final size:24
Alignment explanation
Indices: 41862878--41862950 Score: 83
Period size: 26 Copynumber: 2.9 Consensus size: 24
41862868 AAGCTAGCAC
* *
41862878 TAACGGGAAGCTCATAAAGAGCCTT
1 TAACGGGAAGCTCAT-AAGAGCATA
41862903 TAATCGGGAAGCTCATGAAGAGTCATA
1 TAA-CGGGAAGCTCAT-AAGAG-CATA
*
41862930 TAACGGGACGCTCATAAGAGC
1 TAACGGGAAGCTCATAAGAGC
41862951 TGCGGTGTGC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.02
25 8 0.19
26 28 0.67
27 5 0.12
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
TAACGGGAAGCTCATAAGAGCATA
Found at i:41873911 original size:4 final size:4
Alignment explanation
Indices: 41873902--41873936 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
41873892 TGTGTTTTGA
41873902 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
1 ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATTG ATT
41873937 TTCTTTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
ATTG
Found at i:41889089 original size:48 final size:48
Alignment explanation
Indices: 41889018--41889114 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
41889008 CCTGTTATCC
*
41889018 TTTGGGTGGGGTTCCTAAGAACTTTACTAGGACATTATTATGGATTCT
1 TTTGGGTGGGGTTCCTAAGAACTTTACTAGGACATTATTATAGATTCT
*
41889066 TTTGGGTGGTGTTCCTAAGAACTTTACTAGGACATTATTATAGATTCT
1 TTTGGGTGGGGTTCCTAAGAACTTTACTAGGACATTATTATAGATTCT
41889114 T
1 T
41889115 AGGGTTGATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.24, C:0.12, G:0.23, T:0.41
Consensus pattern (48 bp):
TTTGGGTGGGGTTCCTAAGAACTTTACTAGGACATTATTATAGATTCT
Found at i:41895999 original size:31 final size:31
Alignment explanation
Indices: 41895961--41896032 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
41895951 TTCAAAAAAA
*
41895961 TGGGCTCACACACCTATGTGGCCTGCCTGTG
1 TGGGCTCACACACCCATGTGGCCTGCCTGTG
* *
41895992 TGGGCTCACACGCCCATGTGGCCTGCCTTTG
1 TGGGCTCACACACCCATGTGGCCTGCCTGTG
*
41896023 TGGGCCCACA
1 TGGGCTCACA
41896033 TGACTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.12, C:0.35, G:0.29, T:0.24
Consensus pattern (31 bp):
TGGGCTCACACACCCATGTGGCCTGCCTGTG
Found at i:41897344 original size:31 final size:31
Alignment explanation
Indices: 41897299--41897363 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
41897289 TTCAATCTCA
*
41897299 ACATATACTGGGCCGAAGCCTTTTCATAAATC
1 ACATATACTAGGCCGAAGCCTTTT-ATAAATC
*
41897331 ACAT-TACTAGGCCGAAGCCTTTTATAATTC
1 ACATATACTAGGCCGAAGCCTTTTATAAATC
41897361 ACA
1 ACA
41897364 ACTCATATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.29
31 18 0.58
32 4 0.13
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (31 bp):
ACATATACTAGGCCGAAGCCTTTTATAAATC
Found at i:41897644 original size:25 final size:25
Alignment explanation
Indices: 41897610--41897679 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41897600 CTCTTTTAAT
*
41897610 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41897635 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41897660 AACTGGGGCAAAGGCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41897680 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41897752 original size:20 final size:21
Alignment explanation
Indices: 41897727--41897774 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
41897717 AAATGAATAC
*
41897727 ATCATGTGCATATCATA-CAT
1 ATCATGTGCATATCATATCAA
*
41897747 ATCATGTGTATATCATATCAA
1 ATCATGTGCATATCATATCAA
41897768 ATCATGT
1 ATCATGT
41897775 ATATCAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAA
Found at i:41905598 original size:25 final size:25
Alignment explanation
Indices: 41905564--41905633 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
41905554 CTCTTTTAAT
*
41905564 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41905589 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
41905614 AACTGCGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
41905634 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:41905706 original size:20 final size:21
Alignment explanation
Indices: 41905681--41905728 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
41905671 AAATGAATAC
*
41905681 ATCATGTGCATATCATA-CAT
1 ATCATGTGCATATCATATCAA
41905701 ATCATGTGCATATCATATCAA
1 ATCATGTGCATATCATATCAA
41905722 ATCATGT
1 ATCATGT
41905729 ATATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (21 bp):
ATCATGTGCATATCATATCAA
Found at i:41908414 original size:45 final size:45
Alignment explanation
Indices: 41908353--41908551 Score: 175
Period size: 45 Copynumber: 4.6 Consensus size: 45
41908343 GTTTTCGTGC
* * *
41908353 AAGACCAAGTCCGGGACATTGGCATCGATATATG-GGTTTTCGA-GT
1 AAGACCATGTCTGGGACATTGGCATCGATATATGTGG-TTAC-ATGT
* *
41908398 AAGACCATGTTTGGGACGTTGGCATCGATATATGTGGTTACATGT
1 AAGACCATGTCTGGGACATTGGCATCGATATATGTGGTTACATGT
* * * *
41908443 AAGACCATGTCTAGGACATCGACATCG-TAT-T-TGATTA-ATGT
1 AAGACCATGTCTGGGACATTGGCATCGATATATGTGGTTACATGT
* * *
41908484 AAGACTC-TGTCTGGGACAATGGCATCG--ATATG-AGATAGCATGT
1 AAGAC-CATGTCTGGGACATTGGCATCGATATATGTGGTTA-CATGT
*
41908527 AAGACCACGTCTGGGACATTGGCAT
1 AAGACCATGTCTGGGACATTGGCAT
41908552 TGTTCGATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
40 2 0.02
41 28 0.22
42 7 0.06
43 26 0.21
44 4 0.03
45 57 0.45
46 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (45 bp):
AAGACCATGTCTGGGACATTGGCATCGATATATGTGGTTACATGT
Found at i:41913129 original size:45 final size:45
Alignment explanation
Indices: 41913007--41913121 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
41912997 CTAGGAATTT
*
41913007 AGAAATCTGAGCTAGTTGAGTTGGTCCAAGTTCGTGATATATGTG
1 AGAAATCCGAGCTAGTTGAGTTGGTCCAAGTTCGTGATATATGTG
* * * *
41913052 AGAAATCCAAACTTGTTGAGTTAGTCCAAGTTCGTGATATATGTG
1 AGAAATCCGAGCTAGTTGAGTTGGTCCAAGTTCGTGATATATGTG
* *
41913097 A-AGCATCCGAGCTCGTTGAGTTGGT
1 AGA-AATCCGAGCTAGTTGAGTTGGT
41913122 TTTAGTTCAT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 1 0.02
45 58 0.98
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (45 bp):
AGAAATCCGAGCTAGTTGAGTTGGTCCAAGTTCGTGATATATGTG
Found at i:41914585 original size:93 final size:93
Alignment explanation
Indices: 41914478--41914648 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
41914468 GCCCCTAAGT
* *
41914478 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
41914543 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
41914571 GAACTCGGACTCAACTCCACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
41914636 TGAGTTCGGATGC
66 CGAGTTCGGATGC
41914649 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:41914645 original size:46 final size:46
Alignment explanation
Indices: 41914473--41914645 Score: 192
Period size: 46 Copynumber: 3.7 Consensus size: 46
41914463 AACCCGCCCC
* * *
41914473 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
41914519 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* * *
41914567 TCA-CGAACTCGGACTCAACTCCACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
41914612 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41914646 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 14, Indels: 18
0.76 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 59 0.57
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:41919119 original size:47 final size:47
Alignment explanation
Indices: 41919027--41919776 Score: 1038
Period size: 47 Copynumber: 15.7 Consensus size: 47
41919017 TCTGTACATG
* *
41919027 ATGTGATGAATGTGAAAGTGCATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCA
41919076 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
41919123 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCA
* *
41919172 ATGTGATGAATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCA
* * *
41919219 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* * * * *
41919266 ACGTGATGGATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* * * * *
41919313 ACGTGATGGATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* * * *
41919360 ACGTGATGGATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCA
* *
41919409 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCA
* * *
41919458 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* * *
41919505 ATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* *
41919552 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCA
41919601 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* * *
41919648 ATGTGATGAATGTGAACA-TGCATATATGAGATAAGGTCGAATGGCCA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCA
41919695 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
* *
41919742 ATGTGATGGATGT-AGAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGA-AAGTGTATATATGTGATAAG
41919777 TCCCGAAGGG
Statistics
Matches: 658, Mismatches: 32, Indels: 24
0.92 0.04 0.03
Matches are distributed among these distances:
46 3 0.00
47 453 0.69
48 1 0.00
49 200 0.30
50 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCA
Found at i:41919202 original size:96 final size:94
Alignment explanation
Indices: 41919027--41919776 Score: 1038
Period size: 96 Copynumber: 7.9 Consensus size: 94
41919017 TCTGTACATG
* *
41919027 ATGTGATGAATGTGAAAGTGCATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
41919092 AGTGTATATATGTGATAAGGCCGAATGGCCA
64 AGTGTATATATGTGATAAGGCCGAATGGCCA
41919123 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* *
41919188 CA-TGTGTATGTGTGATAAGGCCGAATGGCCA
64 -AGTGTATATATGTGATAAGGCCGAATGGCCA
* * * * *
41919219 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* * *
41919284 TGTATATATGTGACAGGGCCGAGTGGCCA
66 TGTATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
41919313 ACGTGATGGATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* *
41919378 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TG--TATATATGTGATAAGGCCGAATGGCCA
* *
41919409 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
* * *
41919474 AGTGTATATATGTGATAAGGCCTAATAGCCG
64 AGTGTATATATGTGATAAGGCCGAATGGCCA
* * *
41919505 ATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* *
41919570 TGTATATATATGTGATAAGGCCTAATGGCCG
66 TG--TATATATGTGATAAGGCCGAATGGCCA
41919601 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-A
* * *
41919666 -TGCATATATGAGATAAGGTCGAATGGCCA
65 GTGTATATATGTGATAAGGCCGAATGGCCA
*
41919695 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGT-AGAA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA-AA
*
41919759 GTGTATAAATGTGATAAG
65 GTGTATATATGTGATAAG
41919777 TCCCGAAGGG
Statistics
Matches: 597, Mismatches: 46, Indels: 24
0.90 0.07 0.04
Matches are distributed among these distances:
93 3 0.01
94 269 0.45
96 283 0.47
97 2 0.00
98 40 0.07
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCGAATGGCCA
Found at i:41919224 original size:143 final size:143
Alignment explanation
Indices: 41919027--41919776 Score: 1064
Period size: 143 Copynumber: 5.2 Consensus size: 143
41919017 TCTGTACATG
* *
41919027 ATGTGATGAATGTGAAAGTGCATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA
41919092 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGAT
64 AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGAT
41919157 AAGGCCGAATGGCCA
129 AAGGCCGAATGGCCA
* *
41919172 ATGTGATGAATGTGAACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * *
41919236 GTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG--TATATATGTGACA
65 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATA
* *
41919299 GGGCCGAGTGGCCA
130 AGGCCGAATGGCCA
* * * * * * *
41919313 ACGTGATGGATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* *
41919378 TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
66 TG--TATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGAT
* *
41919443 AAGGCCTAATGGCCG
129 AAGGCCGAATGGCCA
* * *
41919458 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
* * *
41919523 TGTATATATGTGATGAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
66 TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAA
* *
41919588 GGCCTAATGGCCG
131 GGCCGAATGGCCA
41919601 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAA-A
* * *
41919666 -TGCATATATGAGATAAGGTCGAATGGCCAATGTGATGAATGTGAAAGTG--TATATATGTGATA
65 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATA
41919728 AGGCCGAATGGCCA
130 AGGCCGAATGGCCA
* *
41919742 ATGTGATGGATGT-AGAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGA-AAGTGTATATATGTGATAAG
41919777 TCCCGAAGGG
Statistics
Matches: 540, Mismatches: 57, Indels: 20
0.88 0.09 0.03
Matches are distributed among these distances:
140 2 0.00
141 136 0.25
143 303 0.56
144 1 0.00
145 97 0.18
146 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (143 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATGTGATAA
GGCCGAATGGCCA
Found at i:41940124 original size:24 final size:22
Alignment explanation
Indices: 41940086--41940143 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 22
41940076 ATGGTCTGGT
*
41940086 TAAACCACTCAAATGGTATAGA
1 TAAAACACTCAAATGGTATAGA
*
41940108 TAAAAGCTACTCAAATGGTATGGA
1 TAAAA-C-ACTCAAATGGTATAGA
41940132 TAAAACACTCAA
1 TAAAACACTCAA
41940144 TGATGCTGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 10 0.31
23 2 0.06
24 20 0.62
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (22 bp):
TAAAACACTCAAATGGTATAGA
Found at i:41941633 original size:14 final size:14
Alignment explanation
Indices: 41941614--41941645 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
41941604 AACCATTTAC
41941614 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
41941628 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
41941642 AAAA
1 AAAA
41941646 TTAGTGCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:41943691 original size:23 final size:21
Alignment explanation
Indices: 41943629--41943701 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 21
41943619 GAAAAGACGA
* *
41943629 ATGAACAATAAAATTCTTTGGC
1 ATGAACAGTAAAATTCTCT-GC
*
41943651 ATGAACAGTGAAATTCTCTGAC
1 ATGAACAGTAAAATTCTCTG-C
*
41943673 ATGAATAGTAAATATTCTCTGC
1 ATGAACAGTAAA-ATTCTCTGC
41943695 ATGAACA
1 ATGAACA
41943702 ATGAAAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.02
22 34 0.79
23 8 0.19
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (21 bp):
ATGAACAGTAAAATTCTCTGC
Found at i:41976045 original size:43 final size:42
Alignment explanation
Indices: 41975928--41976045 Score: 105
Period size: 43 Copynumber: 2.8 Consensus size: 42
41975918 GATTTGAGAT
* * * * *
41975928 TTACGTGTAAGACCATGTCTGGGACATGGGAATCATATCTGA
1 TTACATGTAAGACCACGTCTGGGACATAGGCATCATATCTAA
* * *
41975970 TTTCATGTAAGACC-CTGTCTAGGACAGAGGCATCGATA-CTAAA
1 TTACATGTAAGACCAC-GTCTGGGACATAGGCATC-ATATCT-AA
* *
41976013 TTACATGTAAAACCACGTCTGGGACATCGGCAT
1 TTACATGTAAGACCACGTCTGGGACATAGGCAT
41976046 TGTACTCGTT
Statistics
Matches: 59, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
42 28 0.47
43 30 0.51
44 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (42 bp):
TTACATGTAAGACCACGTCTGGGACATAGGCATCATATCTAA
Found at i:41977095 original size:36 final size:36
Alignment explanation
Indices: 41977043--41977115 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
41977033 GGTCACACTG
41977043 GCATGTGACCTCAACAGAATTGAAAAATTTTTCTAA
1 GCATGTGACCTCAACAGAATTGAAAAATTTTTCTAA
*
41977079 GCATGTGACCTGAACAGAATTGAAAAATTTTTCTAA
1 GCATGTGACCTCAACAGAATTGAAAAATTTTTCTAA
41977115 G
1 G
41977116 TTTTGAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (36 bp):
GCATGTGACCTCAACAGAATTGAAAAATTTTTCTAA
Found at i:41979708 original size:47 final size:46
Alignment explanation
Indices: 41979536--41979804 Score: 169
Period size: 47 Copynumber: 5.8 Consensus size: 46
41979526 ATGGGGTTAT
* * * *
41979536 GTGAGAGCCAGTATAAGACCATGTCTGGGGCATGACATCGGCATTGAG
1 GTGAGTGCCAGTGTAAGACCATGTCTGGGACATG-CATCGGC-TAGAG
* * * * * *
41979584 ATGAGGGCTAGTGTAAGA-CGTGTCTGGGACATGCATCAGCT-GCATC
1 GTGAGTGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTAG-A-G
* * * * *
41979630 ATGA-TAGCCCGTGTAGGACCACGTCTTGGACATGGCATCGGCGTAGAG
1 GTGAGT-GCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGC-TAGAG
*
41979678 GTGAGTGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGCCTCGA-
1 GTGAGTGCCAGTGTAAGACCATGTCTGGGACATGCATCGG-CTAGAG
* *
41979723 -TGATGTTAGCCAGTGTAAGA-CGTGTCTGGGACATGCATCGACTA-AG
1 GTGA-G-T-GCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTAGAG
* ** * *
41979769 TTTTGTGCTAGTGTAAGA-CATGTCTAGGACATGCAT
1 GTGAGTGCCAGTGTAAGACCATGTCTGGGACATGCAT
41979805 TAGCAAGTAT
Statistics
Matches: 176, Mismatches: 31, Indels: 32
0.74 0.13 0.13
Matches are distributed among these distances:
44 31 0.18
45 5 0.03
46 33 0.19
47 69 0.39
48 34 0.19
49 3 0.02
50 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.25
Consensus pattern (46 bp):
GTGAGTGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCTAGAG
Found at i:41979755 original size:94 final size:93
Alignment explanation
Indices: 41979541--41979855 Score: 278
Period size: 94 Copynumber: 3.4 Consensus size: 93
41979531 GTTATGTGAG
* * * * * *
41979541 AGCCAGTATAAGACCATGTCTGGGGCATGACATCGGCATTGAGATGAGGGCTAGTGTAAGACGTG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TAGAGATGAGTGCTAGTGTAAGACATG
41979606 TCTGGGACATGCATCAGCTGCATCATGAT
65 TCTGGGACATGCATCAGCTGCATCATGAT
* * * * * *
41979635 AGCCCGTGTAGGACCACGTCTTGGACATGGCATCGGCGTAGAGGTGAGTGCCAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC-TAGAGATGAGTGCTAGTGTAAGACATG
* * *
41979700 TCTGGGACATGCATCGGCCT-CGATGATGTT
65 TCTGGGACATGCATCAG-CTGC-ATCATGAT
* * * **
41979730 AGCCAGTGTAAGA-CGTGTCTGGGACAT-GCATCGACTA-AGTTTTGTGCTAGTGTAAGACATGT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAGAGATGAGTGCTAGTGTAAGACATGT
* * * * * **
41979792 CTAGGACATGCATTAGCAAGTATACACGGG
66 CTGGGACATGCATCAGC-TGCAT-CATGAT
** *
41979822 AGTTAGTGTAAGATCATGTCTGGGACATGGCATC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATC
41979856 AGCCTCGATG
Statistics
Matches: 176, Mismatches: 38, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
90 1 0.01
91 36 0.20
92 15 0.09
93 20 0.11
94 85 0.48
95 19 0.11
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (93 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCTAGAGATGAGTGCTAGTGTAAGACATGT
CTGGGACATGCATCAGCTGCATCATGAT
Found at i:41980781 original size:55 final size:55
Alignment explanation
Indices: 41980672--41980784 Score: 138
Period size: 55 Copynumber: 2.1 Consensus size: 55
41980662 CTTTTAAATT
* * * * *
41980672 AGTATTGTCCACGGTTAGGCCACACGGGCGCGTGCCATAGCGGTGTCTATAAGTC
1 AGTATTGCCCACGGGTAGGCCACACGGGCGCGCGCCATAGCCGTGCCTATAAGTC
* * *
41980727 AGTATTGCCCACGGGTAGGCCACACGGGCGTGCGTCATGGCCGTGCCCTA-AAGTC
1 AGTATTGCCCACGGGTAGGCCACACGGGCGCGCGCCATAGCCGTG-CCTATAAGTC
41980782 AGT
1 AGT
41980785 GTCGCACACG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 46 0.94
56 3 0.06
ACGTcount: A:0.19, C:0.27, G:0.32, T:0.21
Consensus pattern (55 bp):
AGTATTGCCCACGGGTAGGCCACACGGGCGCGCGCCATAGCCGTGCCTATAAGTC
Found at i:41980795 original size:55 final size:55
Alignment explanation
Indices: 41980681--41980797 Score: 128
Period size: 55 Copynumber: 2.1 Consensus size: 55
41980671 TAGTATTGTC
* * * * * *
41980681 CACGGTTAGGCCACACGGGCGCGTGCCATAGCGGTGTCTATAAGTCAGTATTGCC
1 CACGGGTAGGCCACACGGGCGCGCGCCATAGCCGTGCCTATAAGTCAGTATCGCA
* * * *
41980736 CACGGGTAGGCCACACGGGCGTGCGTCATGGCCGTGCCCTA-AAGTCAGTGTCGCA
1 CACGGGTAGGCCACACGGGCGCGCGCCATAGCCGTG-CCTATAAGTCAGTATCGCA
41980791 CACGGGT
1 CACGGGT
41980798 TGAGGACGTG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 48 0.94
56 3 0.06
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (55 bp):
CACGGGTAGGCCACACGGGCGCGCGCCATAGCCGTGCCTATAAGTCAGTATCGCA
Found at i:41982740 original size:158 final size:158
Alignment explanation
Indices: 41982444--41982763 Score: 586
Period size: 158 Copynumber: 2.0 Consensus size: 158
41982434 TTTTAAGCAA
*
41982444 TTCATACTATTAAGGCTTATCATTAAAATTGAACATTGAGTATCACAAAACTTGTATTCTAATTG
1 TTCATACTATTAAGGCTTATCATTAAAATTGAACATTGAGTATCACAAAACTTGTATTCTAATTA
* * *
41982509 TAATTCACTTGACCAAATATACACCCGTACATTAGTTACAAAACCCATTGGCCGAATATGTGTGT
66 TAATTCACTTGACCAAATATACACCAGTACATTAGTTACAAAACCCATTGGCCGAATATGTATAT
41982574 ATGAATACACAAGACTTCTTGCACATAT
131 ATGAATACACAAGACTTCTTGCACATAT
41982602 TTCATACTATTAAGGCTTATCATTAAAATTGAACATTGAGTATCACAAAACTTGTATTCTAATTA
1 TTCATACTATTAAGGCTTATCATTAAAATTGAACATTGAGTATCACAAAACTTGTATTCTAATTA
*
41982667 TAATTCACTTGACCAAATATACACCAGTACATTAGTTACAAAACCCCTTGGCCGAATATGTATAT
66 TAATTCACTTGACCAAATATACACCAGTACATTAGTTACAAAACCCATTGGCCGAATATGTATAT
*
41982732 ATGTATACACAAGACTTCTTGCACATAT
131 ATGAATACACAAGACTTCTTGCACATAT
41982760 TTCA
1 TTCA
41982764 CTATTTACAT
Statistics
Matches: 156, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
158 156 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (158 bp):
TTCATACTATTAAGGCTTATCATTAAAATTGAACATTGAGTATCACAAAACTTGTATTCTAATTA
TAATTCACTTGACCAAATATACACCAGTACATTAGTTACAAAACCCATTGGCCGAATATGTATAT
ATGAATACACAAGACTTCTTGCACATAT
Found at i:41983137 original size:39 final size:39
Alignment explanation
Indices: 41983094--41983260 Score: 262
Period size: 39 Copynumber: 4.3 Consensus size: 39
41983084 GGTCTTTAAC
** *
41983094 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* *
41983133 CCGGATATATTTCTAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
41983172 CCAGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* *
41983211 CCGAATATTTTTCCAACATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
41983250 CCGGATATTTT
1 CCGGATATTTT
41983261 CAATCTCATA
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 116 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:41986400 original size:20 final size:20
Alignment explanation
Indices: 41986363--41986401 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41986353 GAACACAAGC
*
41986363 TGTCCAATCAGCTCACTTAG
1 TGTCCAATCAGCTAACTTAG
* *
41986383 TGTCCATTCGGCTAACTTA
1 TGTCCAATCAGCTAACTTA
41986402 TGTAGTGAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTCCAATCAGCTAACTTAG
Found at i:41992620 original size:31 final size:32
Alignment explanation
Indices: 41992582--41992648 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
41992572 GAAATAGGGT
* *
41992582 CACACGCCCGTGTGGG-TAGGCCGTGTGGTCA
1 CACACGCCCATGTGGGTTAGGCCGTATGGTCA
41992613 CACACGCCCATGTGGGTTAGGCCGTATGGTCA
1 CACACGCCCATGTGGGTTAGGCCGTATGGTCA
41992645 CACA
1 CACA
41992649 TGCTCGTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.18, C:0.30, G:0.33, T:0.19
Consensus pattern (32 bp):
CACACGCCCATGTGGGTTAGGCCGTATGGTCA
Found at i:41994399 original size:28 final size:28
Alignment explanation
Indices: 41994357--41994433 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
41994347 ATCTTCGATG
41994357 TCTCGCACACTAAGTGCCATACCCAATA
1 TCTCGCACACTAAGTGCCATACCCAATA
* ** * *
41994385 TCTCGCACACCAAGTGTTATTCTCAATA
1 TCTCGCACACTAAGTGCCATACCCAATA
*
41994413 TTTCGCACACTAAGTGCCATA
1 TCTCGCACACTAAGTGCCATA
41994434 TATATATATA
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.30, C:0.31, G:0.12, T:0.27
Consensus pattern (28 bp):
TCTCGCACACTAAGTGCCATACCCAATA
Found at i:41994506 original size:40 final size:40
Alignment explanation
Indices: 41994448--41994523 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
41994438 TATATATATA
41994448 TAGCCGAAGCTATCTCAAATC-GCACATC-AAGTGCCACATT
1 TAGCCGAAGCTATCTCAAA-CAGCACA-CGAAGTGCCACATT
*
41994488 TAGCCGAAGCTATTTCAAACAGCACACGAAGTGCCA
1 TAGCCGAAGCTATCTCAAACAGCACACGAAGTGCCA
41994524 TTCTTAACCG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (40 bp):
TAGCCGAAGCTATCTCAAACAGCACACGAAGTGCCACATT
Found at i:41995757 original size:15 final size:15
Alignment explanation
Indices: 41995737--41995767 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41995727 TTAACATCAC
41995737 TTAATTTCCATATTA
1 TTAATTTCCATATTA
41995752 TTAATTTCCATATTA
1 TTAATTTCCATATTA
41995767 T
1 T
41995768 ATCATAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTCCATATTA
Found at i:41997798 original size:20 final size:20
Alignment explanation
Indices: 41997769--41997809 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41997759 TGCTTGCTCT
*
41997769 GTTTCTTTCCTATAAAAATA
1 GTTTCCTTCCTATAAAAATA
41997789 GTTTCCTTCCTATAAAAATA
1 GTTTCCTTCCTATAAAAATA
41997809 G
1 G
41997810 ACTTAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (20 bp):
GTTTCCTTCCTATAAAAATA
Found at i:42003584 original size:38 final size:38
Alignment explanation
Indices: 42003533--42003610 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
42003523 ACATAAAATG
* * * *
42003533 TTGTTTTAGAAATT-TTATCTTTTTTTTTACTCTTTAAT
1 TTGTTATAGAAATTATT-TATTTTTTATTACTCATTAAT
* *
42003571 TTGTTATATAAATTATTTATTTTTTATTATTCATTAAT
1 TTGTTATAGAAATTATTTATTTTTTATTACTCATTAAT
42003609 TT
1 TT
42003611 TTTACTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 31 0.94
39 2 0.06
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (38 bp):
TTGTTATAGAAATTATTTATTTTTTATTACTCATTAAT
Found at i:42010162 original size:21 final size:22
Alignment explanation
Indices: 42010138--42010221 Score: 82
Period size: 21 Copynumber: 3.8 Consensus size: 22
42010128 CTACCAAATA
*
42010138 AAATATTTTTTAAAA-AATTTT
1 AAATATATTTTAAAAGAATTTT
*
42010159 AAATATAATTTAAAAGAA-TTT
1 AAATATATTTTAAAAGAATTTT
* * *
42010180 AAATATATTTAAAAATAATTTAA
1 AAATATATTTTAAAAGAATTT-T
42010203 AAATAATAATTTTAAAAGA
1 AAAT-AT-ATTTTAAAAGA
42010222 TTATATTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 31 0.62
22 4 0.08
23 4 0.08
24 2 0.04
25 9 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AAATATATTTTAAAAGAATTTT
Found at i:42010170 original size:11 final size:11
Alignment explanation
Indices: 42010146--42010209 Score: 71
Period size: 10 Copynumber: 6.1 Consensus size: 11
42010136 TAAAATATTT
*
42010146 TTTAAAAA-AT
1 TTTAAAAATAA
*
42010156 TTTAAATATAA
1 TTTAAAAATAA
*
42010167 TTT-AAAAGAA
1 TTTAAAAATAA
*
42010177 TTTAAATAT-A
1 TTTAAAAATAA
42010187 TTTAAAAATAA
1 TTTAAAAATAA
42010198 TTTAAAAATAA
1 TTTAAAAATAA
42010209 T
1 T
42010210 AATTTTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
10 24 0.55
11 20 0.45
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TTTAAAAATAA
Found at i:42010212 original size:14 final size:15
Alignment explanation
Indices: 42010193--42010233 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
42010183 TATATTTAAA
42010193 AATAATTTAAAA-AT
1 AATAATTTAAAAGAT
42010207 AATAATTTTAAAAGAT
1 AATAA-TTTAAAAGAT
*
42010223 TAT-ATTTAAAA
1 AATAATTTAAAA
42010234 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 12 0.50
15 8 0.33
16 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (15 bp):
AATAATTTAAAAGAT
Found at i:42010256 original size:23 final size:22
Alignment explanation
Indices: 42010210--42010290 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 22
42010200 TAAAAATAAT
* *
42010210 AATTTTAAAAGATTATATTTAA
1 AATTTTAAAAAATAATATTTAA
42010232 AATTTTAAAAAATAATATTTAAA
1 AATTTTAAAAAATAATATTT-AA
* ** *
42010255 AATGTTAAAGTAT-ACATTTAA
1 AATTTTAAAAAATAATATTTAA
* *
42010276 AATATTATAAAATAA
1 AATTTTAAAAAATAA
42010291 ATAATAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 11 0.23
22 24 0.51
23 12 0.26
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.40
Consensus pattern (22 bp):
AATTTTAAAAAATAATATTTAA
Found at i:42010347 original size:20 final size:20
Alignment explanation
Indices: 42010322--42010393 Score: 117
Period size: 20 Copynumber: 3.5 Consensus size: 20
42010312 ATAATTTTAA
42010322 AAAAATATATTTAAATTTTT
1 AAAAATATATTTAAATTTTT
*
42010342 AAAAATATGTTTAAATTTTT
1 AAAAATATATTTAAATTTTT
*
42010362 AAAAATATGTTTAAATTTTT
1 AAAAATATATTTAAATTTTT
42010382 AAAAATAATATT
1 AAAAAT-ATATT
42010394 AGGAATTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 45 0.92
21 4 0.08
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
AAAAATATATTTAAATTTTT
Done.