Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 135 of 208
Found at i:41439385 original size:21 final size:22
Alignment explanation
Indices: 41439352--41439407 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
41439342 AAAATATTTC
*
41439352 AAAAAA-ATGAAAATGACAA-AA
1 AAAAAAGAAGAAAA-GACAAGAA
*
41439373 AAAAAAGAA-AAAAGAGAAGAA
1 AAAAAAGAAGAAAAGACAAGAA
*
41439394 AAACAAGAAGAAAA
1 AAAAAAGAAGAAAA
41439408 AAAGGAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 4 0.14
21 20 0.69
22 5 0.17
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.04
Consensus pattern (22 bp):
AAAAAAGAAGAAAAGACAAGAA
Found at i:41440828 original size:51 final size:51
Alignment explanation
Indices: 41440747--41440993 Score: 305
Period size: 51 Copynumber: 4.8 Consensus size: 51
41440737 CTGCAGACAA
* ** * * *
41440747 CGAATCTTATTTCCCTAACTTTGCAGTGGAACAAATTAAAGCTAAAGGTAG
1 CGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTAAAGGTAG
* * *
41440798 CGAATCTTGTTTCCCTGGCATTGCAATGGAATAGATTAAAGCTAAAGGCAA
1 CGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTAAAGGTAG
* * * * * * *
41440849 CGAATCCTATCTCCTTGGCGTTACAGTGGAATAGATTAAACCTAAAGGTAG
1 CGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTAAAGGTAG
* *
41440900 CGAATCTTGTTTCCCTGGCATTGCAGTGGAACAGATTAAGGCTAAAGGTAG
1 CGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTAAAGGTAG
* * *
41440951 CGAATCTTGTTTCCATGGCGTTCCAGTGGAATAGATTAAAGCT
1 CGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCT
41440994 GAAGTGGAGC
Statistics
Matches: 163, Mismatches: 33, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 163 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (51 bp):
CGAATCTTGTTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTAAAGGTAG
Found at i:41441001 original size:21 final size:21
Alignment explanation
Indices: 41440975--41441018 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
41440965 ATGGCGTTCC
* *
41440975 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAAATTAAAGCTGA
*
41440996 AGTGGAGCAAATTAAAGCTGA
1 AGTGGAACAAATTAAAGCTGA
41441017 AG
1 AG
41441019 GCAGTGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (21 bp):
AGTGGAACAAATTAAAGCTGA
Found at i:41441199 original size:51 final size:51
Alignment explanation
Indices: 41441094--41441200 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
41441084 TTCCCTGGCG
* * * *
41441094 TTAAAGCTGAAGACAGCGAATCTTATTTCCCTGGCTTTGCAGTGGAACAAA
1 TTAAAGCTAAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGAAACAAA
** * * *
41441145 TTAAAGCTAAAGGTAGCGAATCTTGTTTCCCTGGCATTACAGTGAAATAGA
1 TTAAAGCTAAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGAAACAAA
41441196 TTAAA
1 TTAAA
41441201 TCGAAGTGGA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (51 bp):
TTAAAGCTAAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGAAACAAA
Found at i:41441288 original size:51 final size:51
Alignment explanation
Indices: 41441205--41441356 Score: 205
Period size: 51 Copynumber: 3.0 Consensus size: 51
41441195 ATTAAATCGA
* * *
41441205 AGTGGAGCGGATTAAAGCTGAAGGCAGTGAATCCTATCTCCTTGGCGTTAC
1 AGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATCTCCTTGGCGTTAC
* * * * **
41441256 AGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCTTGGCGTTGT
1 AGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATCTCCTTGGCGTTAC
* *
41441307 AGCGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATCTCCCTGGCGTTA
1 AGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATCTCCTTGGCGTTA
41441357 AAGCTGAAGA
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 85 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (51 bp):
AGTGGAACAGATTAAAGCTGAAGGCAGTGAATCTTATCTCCTTGGCGTTAC
Found at i:41441304 original size:209 final size:210
Alignment explanation
Indices: 41440898--41441304 Score: 636
Period size: 209 Copynumber: 1.9 Consensus size: 210
41440888 ACCTAAAGGT
* * *
41440898 AGCGAATCTTGTTTCCCTGGCATTGCAGTGGAACAGATTAAGGCTAAAGGTAGCGAATCTTGTTT
1 AGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAAATTAAAGCTAAAGGTAGCGAATCTTGTTT
* * *
41440963 CCATGGCGTTCCAGTGGAATAGATTAAAGCTGAAGTGGAGCAAATTAAAGCTGAAGGCAGTGAAT
66 CCATGGCATTACAGTGAAATAGATTAAAGCTGAAGTGGAGCAAATTAAAGCTGAAGGCAGTGAAT
* * * * *
41441028 CCCATCTTCTTGGCGTTACAGTGGAATAGATTAAAGTTAAAAGTAGTGAATCTTGTTTCCCTGGC
131 CCCATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAAGTAGCGAATCTTATTTCCCTGGC
41441093 GTTAAAGCTGAAGAC
196 GTTAAAGCTGAAGAC
*
41441108 AGCGAATCTTATTTCCCTGGCTTTGCAGTGGAACAAATTAAAGCTAAAGGTAGCGAATCTTGTTT
1 AGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAAATTAAAGCTAAAGGTAGCGAATCTTGTTT
* * **
41441173 CCCTGGCATTACAGTGAAATAGATTAAATC-GAAGTGGAGCGGATTAAAGCTGAAGGCAGTGAAT
66 CCATGGCATTACAGTGAAATAGATTAAAGCTGAAGTGGAGCAAATTAAAGCTGAAGGCAGTGAAT
* * *
41441237 CCTATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAATCTTATTTCCTTGGC
131 CCCATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAAGTAGCGAATCTTATTTCCCTGGC
41441302 GTT
196 GTT
41441305 GTAGCGGAAC
Statistics
Matches: 178, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
209 92 0.52
210 86 0.48
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (210 bp):
AGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAAATTAAAGCTAAAGGTAGCGAATCTTGTTT
CCATGGCATTACAGTGAAATAGATTAAAGCTGAAGTGGAGCAAATTAAAGCTGAAGGCAGTGAAT
CCCATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAAGTAGCGAATCTTATTTCCCTGGC
GTTAAAGCTGAAGAC
Found at i:41441319 original size:122 final size:122
Alignment explanation
Indices: 41441094--41441322 Score: 314
Period size: 122 Copynumber: 1.9 Consensus size: 122
41441084 TTCCCTGGCG
* * * *
41441094 TTAAAGCTGAAGACAGCGAATCTTATTTCCCTGGCTTTGCAGTGGAACAAATTAAAGCTAAAGGT
1 TTAAAGCTGAAGACAGCGAATCCTATCTCCCTGGCGTTACAGTGGAACAAATTAAAGCTAAAGGT
* * *
41441159 AGCGAATCTTGTTTCCCTGGCATTACAGTGAAATAGATTAAATCGAAGTGGAGCGGA
66 AGCGAATCTTATTTCCCTGGCATTACAGCGAAACAGATTAAATCGAAGTGGAGCGGA
* * * *
41441216 TTAAAGCTGAAGGCAGTGAATCCTATCTCCTTGGCGTTACAGTGGAACAGATTAAAGCTAAAGGT
1 TTAAAGCTGAAGACAGCGAATCCTATCTCCCTGGCGTTACAGTGGAACAAATTAAAGCTAAAGGT
* * ** *
41441281 AGCGAATCTTATTTCCTTGGCGTTGTAGCGGAACAGATTAAA
66 AGCGAATCTTATTTCCCTGGCATTACAGCGAAACAGATTAAA
41441323 GCTGAAGGCA
Statistics
Matches: 91, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
122 91 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.28
Consensus pattern (122 bp):
TTAAAGCTGAAGACAGCGAATCCTATCTCCCTGGCGTTACAGTGGAACAAATTAAAGCTAAAGGT
AGCGAATCTTATTTCCCTGGCATTACAGCGAAACAGATTAAATCGAAGTGGAGCGGA
Found at i:41441365 original size:36 final size:36
Alignment explanation
Indices: 41441318--41441391 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
41441308 GCGGAACAGA
*
41441318 TTAAAGCTGAAGGCAGTGAATCTTATCTCCCTGGCG
1 TTAAAGCTGAAGACAGTGAATCTTATCTCCCTGGCG
*
41441354 TTAAAGCTGAAGACAGTGAATCTTATTTCCCTGGCG
1 TTAAAGCTGAAGACAGTGAATCTTATCTCCCTGGCG
41441390 TT
1 TT
41441392 GCAATGAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (36 bp):
TTAAAGCTGAAGACAGTGAATCTTATCTCCCTGGCG
Found at i:41441528 original size:143 final size:143
Alignment explanation
Indices: 41441360--41441709 Score: 468
Period size: 143 Copynumber: 2.4 Consensus size: 143
41441350 GGCGTTAAAG
* * * * *
41441360 CTGAAGACAGTGAATCTTATTTCCCTGGCGTTGCAAT-GAACAGATTAAAGCTAGAATTTATGGC
1 CTGAAGACAGCGAATATTATTTCCCTGACGTTGCAATGGAACAGATTAAAGCTACAAATTATGGC
* * * * * *
41441424 AGATCTTATCTTCCTGAAGTTTCAATGGAGTAGACTGAATACAGCGAATCTTATTTCCCTAAAGT
66 AGATCTTATCTTCCTGAAGTTACAATGGAGTAGACTGAAGACA-CCAACCTTATCTACCTAAAGT
41441489 TGCAGCGGAGCAGA
130 TGCAGCGGAGCAGA
* * *
41441503 CTGAAGACAGCGAATTTTATTTCCCTGACGTTGTAGTGGAACAGATTAAAGCTACAAATTATGGC
1 CTGAAGACAGCGAATATTATTTCCCTGACGTTGCAATGGAACAGATTAAAGCTACAAATTATGGC
* * * * * *
41441568 AGATCTTATCTTCCTGAAGTTACAGTGGCGTAGATTGAAGCCACCAGCCTTATCTACCTGAAGTT
66 AGATCTTATCTTCCTGAAGTTACAATGGAGTAGACTGAAGACACCAACCTTATCTACCTAAAGTT
41441633 GCAGCGGAGCAGA
131 GCAGCGGAGCAGA
* * * *
41441646 CTGAAGAGAGCGAATATTATTTCTCTGAAGTTGCAATGGAACAGATTAAAGCTATAAATTATGG
1 CTGAAGACAGCGAATATTATTTCCCTGACGTTGCAATGGAACAGATTAAAGCTACAAATTATGG
41441710 ATATTATCTC
Statistics
Matches: 180, Mismatches: 26, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
143 118 0.66
144 62 0.34
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (143 bp):
CTGAAGACAGCGAATATTATTTCCCTGACGTTGCAATGGAACAGATTAAAGCTACAAATTATGGC
AGATCTTATCTTCCTGAAGTTACAATGGAGTAGACTGAAGACACCAACCTTATCTACCTAAAGTT
GCAGCGGAGCAGA
Found at i:41441820 original size:180 final size:179
Alignment explanation
Indices: 41441578--41441927 Score: 511
Period size: 180 Copynumber: 1.9 Consensus size: 179
41441568 AGATCTTATC
* * *
41441578 TTCCTGAAGTTACAGTGGCGTAGATTGAAGCCACCAGCCTTATCTACCTGAAGTTGCAGCGGAGC
1 TTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTACCTAAAGTTGCAGCGGAGC
*
41441643 AGACTGAAGAGAGCGAATATTATTTCTCTGAAGTTGCAATGGAACAGATTAAAGCTATAAATTAT
66 AGACTGAAGAGAGCGAATATTATTTCTCTGAAGTTGCAATGGAACAGATTAAAGCTATAAATTAC
* *
41441708 GGATATTATCTCTCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTTA
131 AGATATTATCTCTCTGAAGTTGCAATAGAGCAGATCATATCAAACCTTA
* * ** * *
41441757 TTCCTTGAAGTTCCAGTGGAGCAGGTTGAAGTTACTAGCCTTATCTTCCTAAAGTTGCAGCGGAG
1 TTCC-TGAAGTTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTACCTAAAGTTGCAGCGGAG
* * * * * *
41441822 CAGACTGAAGATAGCGGATCTTATTTCTCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTG
65 CAGACTGAAGAGAGCGAATATTATTTCTCTGAAGTTGCAATGGAACAGATTAAAGCTATAAATTA
* *
41441887 CAGATCTTATCTCTTTGAAGTTGCAATAGAGCAGATCATAT
130 CAGATATTATCTCTCTGAAGTTGCAATAGAGCAGATCATAT
41441928 TAAGTCGTAT
Statistics
Matches: 150, Mismatches: 20, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
179 4 0.03
180 146 0.97
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (179 bp):
TTCCTGAAGTTACAGTGGAGCAGATTGAAGCCACCAGCCTTATCTACCTAAAGTTGCAGCGGAGC
AGACTGAAGAGAGCGAATATTATTTCTCTGAAGTTGCAATGGAACAGATTAAAGCTATAAATTAC
AGATATTATCTCTCTGAAGTTGCAATAGAGCAGATCATATCAAACCTTA
Found at i:41442416 original size:22 final size:22
Alignment explanation
Indices: 41442388--41442534 Score: 213
Period size: 22 Copynumber: 6.7 Consensus size: 22
41442378 TTTATTGTTC
*
41442388 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
41442410 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
41442432 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
41442454 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
41442476 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
41442498 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
41442520 AAACATGAGAGCTTA
1 AAACATGAGAGCTTA
41442535 TATACATATA
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 113 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:41442570 original size:17 final size:17
Alignment explanation
Indices: 41442548--41442582 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41442538 ACATATATAA
*
41442548 ATACATATTTAATTTAT
1 ATACATATATAATTTAT
*
41442565 ATACATATATATTTTAT
1 ATACATATATAATTTAT
41442582 A
1 A
41442583 GTTTTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
ATACATATATAATTTAT
Found at i:41442639 original size:43 final size:43
Alignment explanation
Indices: 41442592--41442674 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
41442582 AGTTTTAAAA
* * *
41442592 TATATATACGTACATATAT-TTTTCATATTTTTATAATTTTATG
1 TATATACACATACATATATATATT-ATATTTTTATAATTTTATG
41442635 TATATACACATACATATATATATTATATTTTTATAATTTT
1 TATATACACATACATATATATATTATATTTTTATAATTTT
41442675 TATTTATTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 33 0.92
44 3 0.08
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.54
Consensus pattern (43 bp):
TATATACACATACATATATATATTATATTTTTATAATTTTATG
Found at i:41444271 original size:5 final size:5
Alignment explanation
Indices: 41444263--41444293 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
41444253 AATTGCTTGG
41444263 AATCA AATCA AATCA AATCA AATCA AATCA A
1 AATCA AATCA AATCA AATCA AATCA AATCA A
41444294 GATATTTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AATCA
Found at i:41445745 original size:17 final size:17
Alignment explanation
Indices: 41445723--41445756 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41445713 AATTAAGATT
41445723 TATAAAGGTGAGGCCAA
1 TATAAAGGTGAGGCCAA
41445740 TATAAAGGTGAGGCCAA
1 TATAAAGGTGAGGCCAA
41445757 CCTTTACCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.29, T:0.18
Consensus pattern (17 bp):
TATAAAGGTGAGGCCAA
Found at i:41446535 original size:27 final size:27
Alignment explanation
Indices: 41446500--41446559 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
41446490 TTAACTTAAA
*
41446500 AACCCTAACCCTTGACTTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCT
* *
41446527 AACCGTAACCCTTAATTTAAAAACCCT
1 AACCCTAACCCTTAACTTAAAAACCCT
41446554 AACCCT
1 AACCCT
41446560 TAACTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.35, G:0.03, T:0.23
Consensus pattern (27 bp):
AACCCTAACCCTTAACTTAAAAACCCT
Found at i:41446547 original size:48 final size:45
Alignment explanation
Indices: 41446486--41447042 Score: 495
Period size: 43 Copynumber: 12.8 Consensus size: 45
41446476 GATCTTAAAG
*
41446486 ACCCTTAACTTAAAAACCCTAACCCTTGACTTAAAAACCCTAACCGTA
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAA-C--A
* *
41446534 ACCCTTAATTTAAAAACCCTAACCCTTAACTTAAAAA-CCTTA-A
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACA
41446577 ACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT---A
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACA
* ** * *
41446620 ACTCTTAACTTTTAAACCCTAAATCCTTAACTT-AAAACCAT-A-A
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACA
* * * *
41446663 ACCCTTAACCTAAAAATCATAAACCCTTAACTTAAAAA-CC--ATA
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACA
* * * * *
41446706 ACTCTTAACTTTAAAACCTTAAACCCTTAACTTTAAAGCCCT-A-A
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACA
41446750 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCC---CTA
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAAC-A
* * *** *
41446793 ACCTTTAACTTTAAAACCCTAAAATTTAACTTTAAAACCCT-A-A
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACA
* *
41446836 ACTCTTAACTTAAAACCCCTAACCCTTAACTTAAAAACCCT-A-A
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACA
* * * * *
41446879 ACCCTAAACTTGAAAGCCAT-ACCCTTAACTTTAAAACCCT-A-A
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACA
* * * * *
41446921 ACCCTTAACTTAAAAACCATAAATCCTTGACCTAAAAACACT-A-A
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACA
* *
41446965 ACCCTTAACTTAAAAACCCTAACCTTTAACTTTAAAACCCT---A
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACA
*
41447007 ACCCTTAACTTTAAAACCCTAACCCTTAACTTAAAA
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAA
41447043 TATAATTTGA
Statistics
Matches: 429, Mismatches: 67, Indels: 32
0.81 0.13 0.06
Matches are distributed among these distances:
42 80 0.19
43 229 0.53
44 77 0.18
45 4 0.01
47 4 0.01
48 35 0.08
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.27
Consensus pattern (45 bp):
ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACA
Found at i:41446579 original size:22 final size:22
Alignment explanation
Indices: 41446486--41447042 Score: 629
Period size: 22 Copynumber: 25.7 Consensus size: 22
41446476 GATCTTAAAG
41446486 ACCCTTAACTTAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
*
41446507 ACCCTTGACTTAAAAACCCTAACCGTA
1 ACCCTTAACTTAAAAACCCT-A----A
*
41446534 ACCCTTAATTTAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
*
41446555 ACCCTTAACTTAAAAACCTTAA
1 ACCCTTAACTTAAAAACCCTAA
41446577 ACCCTTAACTTAAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
41446599 ACCCTTAACTTAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
* **
41446620 ACTCTTAACTTTTAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
* *
41446642 ATCCTTAACTT-AAAACCATAA
1 ACCCTTAACTTAAAAACCCTAA
* * *
41446663 ACCCTTAACCTAAAAATCATAA
1 ACCCTTAACTTAAAAACCCTAA
*
41446685 ACCCTTAACTTAAAAACCAT-A
1 ACCCTTAACTTAAAAACCCTAA
* * *
41446706 ACTCTTAACTTTAAAACCTTAA
1 ACCCTTAACTTAAAAACCCTAA
* *
41446728 ACCCTTAACTTTAAAGCCCTAA
1 ACCCTTAACTTAAAAACCCTAA
41446750 ACCCTTAACTTAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
41446771 ACCCTTAACTTAAAAACCCCT-A
1 ACCCTTAACTTAAAAA-CCCTAA
* *
41446793 ACCTTTAACTTTAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
** *
41446815 A-ATTTAACTTTAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
* *
41446836 ACTCTTAACTTAAAACCCCT-A
1 ACCCTTAACTTAAAAACCCTAA
41446857 ACCCTTAACTTAAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
* * * *
41446879 ACCCTAAACTT-GAAAGCC-AT
1 ACCCTTAACTTAAAAACCCTAA
*
41446899 ACCCTTAACTTTAAAACCCTAA
1 ACCCTTAACTTAAAAACCCTAA
*
41446921 ACCCTTAACTTAAAAACCATAA
1 ACCCTTAACTTAAAAACCCTAA
* * * *
41446943 ATCCTTGACCTAAAAACACTAA
1 ACCCTTAACTTAAAAACCCTAA
41446965 ACCCTTAACTTAAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
* *
41446986 ACCTTTAACTTTAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
*
41447007 ACCCTTAACTTTAAAACCCT-A
1 ACCCTTAACTTAAAAACCCTAA
41447028 ACCCTTAACTTAAAA
1 ACCCTTAACTTAAAA
41447043 TATAATTTGA
Statistics
Matches: 462, Mismatches: 58, Indels: 32
0.84 0.11 0.06
Matches are distributed among these distances:
20 11 0.02
21 215 0.47
22 217 0.47
27 19 0.04
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.27
Consensus pattern (22 bp):
ACCCTTAACTTAAAAACCCTAA
Found at i:41446664 original size:86 final size:86
Alignment explanation
Indices: 41446486--41447042 Score: 655
Period size: 86 Copynumber: 6.4 Consensus size: 86
41446476 GATCTTAAAG
*
41446486 ACCCTTAACTTAAAAACCCTAACCCTTGACTTAAAAACCCTAACCGTAACCCTTAA-TTTAAAAA
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAA-C-T----CTTAACTTT-AAAA
* *
41446550 CCCT-AACCCTTAACTTAAAAACCTTAA
59 CCCTAAACCCTTAACTTTAAAACCCTAA
*
41446577 ACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACTCTTAACTTTTAAACCCTAA
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACTCTTAACTTTAAAACCCTAA
* *
41446642 ATCCTTAAC-TTAAAACCATAA
65 ACCCTTAACTTTAAAACCCTAA
* * * * *
41446663 ACCCTTAACCTAAAAATCATAAACCCTTAACTTAAAAACCATAACTCTTAACTTTAAAACCTTAA
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACTCTTAACTTTAAAACCCTAA
*
41446728 ACCCTTAACTTTAAAGCCCTAA
65 ACCCTTAACTTTAAAACCCTAA
41446750 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCCTAAC-CTTTAACTTTAAAACCCTA
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAA-CCCTAACTC-TTAACTTTAAAACCCTA
**
41446814 AA-ATTTAACTTTAAAACCCTAA
64 AACCCTTAACTTTAAAACCCTAA
* * * * * * *
41446836 ACTCTTAACTTAAAACCCCTAACCCTTAACTTAAAAACCCTAAACCCTAAAC-TTGAAAGCC-AT
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCT-AACTCTTAACTTTAAAACCCTAA
41446899 ACCCTTAACTTTAAAACCCTAA
65 ACCCTTAACTTTAAAACCCTAA
* * * * * * *
41446921 ACCCTTAACTTAAAAACCATAAATCCTTGACCTAAAAACACTAAACCCTTAACTTAAAAACCCT-
1 ACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCT-AACTCTTAACTTTAAAACCCTA
*
41446985 AACCTTTAACTTTAAAACCCT-A
64 AACCCTTAACTTTAAAACCCTAA
*
41447007 ACCCTTAACTTTAAAACCCTAACCCTTAACTTAAAA
1 ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAA
41447043 TATAATTTGA
Statistics
Matches: 406, Mismatches: 48, Indels: 30
0.84 0.10 0.06
Matches are distributed among these distances:
84 2 0.00
85 59 0.15
86 212 0.52
87 89 0.22
90 1 0.00
91 21 0.05
92 22 0.05
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.27
Consensus pattern (86 bp):
ACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACTCTTAACTTTAAAACCCTAAA
CCCTTAACTTTAAAACCCTAA
Found at i:41447178 original size:37 final size:38
Alignment explanation
Indices: 41447136--41447304 Score: 107
Period size: 37 Copynumber: 4.4 Consensus size: 38
41447126 TTTTGACTGG
41447136 TACTAACAATTAATA-ATTTGATATAATTTGATAATTT
1 TACTAACAATTAATACATTTGATATAATTTGATAATTT
* * * *
41447173 TACTAACCATTAATACAATT-AT-CAA-TTAATAATTT
1 TACTAACAATTAATACATTTGATATAATTTGATAATTT
* * ** * * * * * **
41447208 TACATTCACATAATGTTAGATTTGAAAAAAATGTT-TTGACTGG
1 TAC--TAACA-ATTAATACATTTG-ATATAAT-TTGAT-AATTT
41447251 TACTAACAATTAATA-ATTTGATATAATTTGATAATTT
1 TACTAACAATTAATACATTTGATATAATTTGATAATTT
41447288 TACTAACAATTAATACA
1 TACTAACAATTAATACA
41447305 ATTATCAATT
Statistics
Matches: 93, Mismatches: 27, Indels: 23
0.65 0.19 0.16
Matches are distributed among these distances:
35 12 0.13
36 2 0.02
37 38 0.41
38 17 0.18
39 5 0.05
40 5 0.05
41 6 0.06
42 1 0.01
43 7 0.08
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (38 bp):
TACTAACAATTAATACATTTGATATAATTTGATAATTT
Found at i:41447313 original size:115 final size:114
Alignment explanation
Indices: 41447042--41447321 Score: 524
Period size: 115 Copynumber: 2.4 Consensus size: 114
41447032 TTAACTTAAA
*
41447042 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATGATTTTAAATTCACATAA
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTAAATTCACATAA
41447107 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
66 TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
*
41447156 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTACATTCACATAA
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTAAATTCACATAA
41447221 TGTTAGATTTGAAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
66 TGTTAGATTTG-AAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
*
41447271 ATATAATTTGATAATTTTACTAACAATTAATACAATTATCAATTAATAATT
1 ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATT
41447322 GAAAAAAATA
Statistics
Matches: 162, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
114 74 0.46
115 88 0.54
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.41
Consensus pattern (114 bp):
ATATAATTTGATAATTTTACTAACCATTAATACAATTATCAATTAATAATTTTAAATTCACATAA
TGTTAGATTTGAAAAAATGTTTTGACTGGTACTAACAATTAATAATTTG
Found at i:41450629 original size:125 final size:125
Alignment explanation
Indices: 41450343--41450807 Score: 670
Period size: 125 Copynumber: 3.7 Consensus size: 125
41450333 CTAGAAGCGT
* *
41450343 TTTTTTAAAC-ATTTGCTCA-AAAAGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAGC-AA
1 TTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACCTACTGTAGCAAA
** * *
41450405 AGCATGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCAGCTTGAAGCA
66 AGCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGCTTGAAGCA
*
41450465 TTTTTTTAAACTGTTTGCTCAGAAACGTCAACTCAAAATTATTTCTTCCAAGACCTACTGTAGCA
1 -TTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTT-TTCCAAGACCTACTGTAGCA
* *
41450530 AAAGCGCGTCCACGAGGGCGCGATTTC-TAATTTCTTCTCAAATAGCATCCTGTTTGAAGCA
64 AAAGCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGCTTGAAGCA
* * *
41450591 TTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTCTTCCAGGACCTAGTGTAGCAA
1 TTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTT-TTCCAAGACCTACTGTAGCAA
41450656 AAGCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCACAA-AGCATCCTGCTTGAAGCA
65 AAGCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCA-AATAGCATCCTGCTTGAAGCA
* * * * * *
41450717 TTTTTTATAGTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCGAAGGCCTACTGTAGCAAA
1 TTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACCTACTGTAGCAAA
* * *
41450782 AGCGCGTACACGTGGGCGCGACTTCA
66 AGCGCGTCCACGAGGGCGCGATTTCA
41450808 AAACTCCTTC
Statistics
Matches: 311, Mismatches: 25, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
123 10 0.03
124 8 0.03
125 149 0.48
126 117 0.38
127 27 0.09
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (125 bp):
TTTTTTAAACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTCCAAGACCTACTGTAGCAAA
AGCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGCTTGAAGCA
Found at i:41451900 original size:25 final size:25
Alignment explanation
Indices: 41451872--41451919 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41451862 GGAGTTTAGC
41451872 GTGCTCTCTGATTATTAGCACATCG
1 GTGCTCTCTGATTATTAGCACATCG
41451897 GTGCTCTCTGATTATTAGCACAT
1 GTGCTCTCTGATTATTAGCACAT
41451920 TTATGTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.38
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCG
Found at i:41452654 original size:30 final size:31
Alignment explanation
Indices: 41452630--41452688 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
41452620 GTAAATACTC
**
41452630 AAAATTTGAAGGGTTAA-AGTGTAAATATGA
1 AAAATTTGAAGGACTAATAGTGTAAATATGA
41452660 AAAATTTGAAGGACTAATAGTGTAAATAT
1 AAAATTTGAAGGACTAATAGTGTAAATAT
41452689 TTTAAGAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.47, C:0.02, G:0.20, T:0.31
Consensus pattern (31 bp):
AAAATTTGAAGGACTAATAGTGTAAATATGA
Found at i:41456490 original size:14 final size:16
Alignment explanation
Indices: 41456459--41456496 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41456449 TTTAATAGTA
41456459 ATATAAATAATAACAT
1 ATATAAATAATAACAT
* *
41456475 ATATACATAATAATAT
1 ATATAAATAATAACAT
41456491 AT-TAAA
1 ATATAAA
41456497 GTTGAAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATAATAACAT
Found at i:41456810 original size:3 final size:3
Alignment explanation
Indices: 41456748--41456795 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
41456738 AACTAATATA
* * * *
41456748 AAT AAT AAC ACT AGT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41456796 GGTAGTAGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41461174 original size:41 final size:41
Alignment explanation
Indices: 41461070--41461179 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
41461060 GTTAATTATT
* *
41461070 CCCTGAATTGCAGACACGTGCCCCTGTTTGTACTTCAGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTAC
* * ** **
41461111 CCATAAATTGCACATATATGCCCCTGTTTGTACTTTGGTAC
1 CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTAC
41461152 CCCTGAATTGCACATACGTG-CCCTGTTT
1 CCCTGAATTGCACATACGTGCCCCTGTTT
41461180 ACACTTCGGT
Statistics
Matches: 57, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
40 8 0.14
41 49 0.86
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (41 bp):
CCCTGAATTGCACATACGTGCCCCTGTTTGTACTTCAGTAC
Found at i:41462063 original size:12 final size:12
Alignment explanation
Indices: 41462046--41462075 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41462036 TCAAGCAATT
41462046 ACACGGCCTAGC
1 ACACGGCCTAGC
*
41462058 ACACGGCCTGGC
1 ACACGGCCTAGC
41462070 ACACGG
1 ACACGG
41462076 GCGTGTGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:41464695 original size:126 final size:124
Alignment explanation
Indices: 41464510--41464861 Score: 546
Period size: 126 Copynumber: 2.8 Consensus size: 124
41464500 ATATTTTGAG
** * *
41464510 TTGACGTTTCTGATAAAATAGTATAAAATCGCTTATAGCAGGATGTTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
41464575 AAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGTAGGTCACGGAAGAAATAA-T-TTTTT
*
41464636 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGAATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * *
41464701 AAATCGCGGCCTCGT-CA-GTGCGCTTTTGCTATAGTAGGTCATGTAAGAAATAATTTTTT
66 AAATCGCGCCCTCGTGGACGT--GCTTTTGCTACAGTAGGTCACGGAAGAAATAATTTTTT
*
41464760 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
*
41464825 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGTAG
41464862 CATGTTTGGG
Statistics
Matches: 206, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
124 99 0.48
125 3 0.01
126 104 0.50
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTTTTT
Found at i:41468086 original size:23 final size:23
Alignment explanation
Indices: 41468076--41468454 Score: 164
Period size: 23 Copynumber: 14.9 Consensus size: 23
41468066 TTTTTAATTA
*
41468076 AATTAAGTTAGGGTTAGGGTTTTTT
1 AATTAAATTA-GGTTAGGG-TTTTT
41468101 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATT-AA--A--TTA-GGTTAGGGTTTTT
*
41468130 AATTAAATTAGGTTAAGGTTAGGGTTT
1 AATTAAATTAGGTTAGGGTT----TTT
*
41468157 --TTAAGTTAAGGGTTTAGGGTTTTT
1 AATTAAATT-A-GG-TTAGGGTTTTT
41468181 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
41468204 AATTAAATTAGGTTAAGGTTAGGGTTTTT
1 AATT-AA--A--TT-AGGTTAGGGTTTTT
*
41468233 AAGTTAAGGGTTTAGGGTT--GGTTTTT
1 AA-TTAA---ATTA-GGTTAGGGTTTTT
* *
41468259 AATTTTAAGTTAAGGGTTTAGAGTTTTT
1 AA--TTAAATT-A-GG-TTAGGGTTTTT
41468287 AATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
* *
41468310 AAGTT-CA--GGGTTTAGGGTTTTT
1 AA-TTAAATTAGG-TTAGGGTTTTT
*
41468332 AATTAAATTAAGTTAGGGTTAGGGTTTGT
1 AATT--A--AA-TTA-GGTTAGGGTTTTT
*
41468361 AATTAATTTAGGTTAGGGTTTTT
1 AATTAAATTAGGTTAGGGTTTTT
*
41468384 AATTAAATTAGGTTAAGGTTAGGATTT
1 AATTAAATTAGGTTAGGGTT----TTT
*
41468411 --TTAAGTTCAGGGTTTAGGGTTTTT
1 AATTAAATT-A-GG-TTAGGGTTTTT
*
41468435 AATTAAATTAGATTAGGGTT
1 AATTAAATTAGGTTAGGGTT
41468455 AGGGTTTGTA
Statistics
Matches: 280, Mismatches: 26, Indels: 98
0.69 0.06 0.24
Matches are distributed among these distances:
21 4 0.01
22 13 0.05
23 75 0.27
24 23 0.08
25 24 0.09
26 36 0.13
27 16 0.06
28 32 0.11
29 41 0.15
30 16 0.06
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.46
Consensus pattern (23 bp):
AATTAAATTAGGTTAGGGTTTTT
Found at i:41468100 original size:30 final size:29
Alignment explanation
Indices: 41468047--41468306 Score: 211
Period size: 29 Copynumber: 9.4 Consensus size: 29
41468037 GTTAGGGTTT
41468047 TTAAGTTAAGGGTTTAGGGTTTTTAATTAAA
1 TTAAGTT-AGGG-TTAGGGTTTTTAATTAAA
41468078 TTAAGTTAGGGTTAGGGTTTTTTAATTAAA
1 TTAAGTTAGGGTTAGGG-TTTTTAATTAAA
*
41468108 TTAGGTTAGGGTTAGGGTTTTTAATTAAA
1 TTAAGTTAGGGTTAGGGTTTTTAATTAAA
* * *
41468137 TTAGGTTAAGGTTAGGG--TTT--TTAAG
1 TTAAGTTAGGGTTAGGGTTTTTAATTAAA
*
41468162 TTAAG---GGTTTAGGGTTTTTAATT--A
1 TTAAGTTAGGGTTAGGGTTTTTAATTAAA
41468186 --AA-TTA-GGTTAGGGTTTTTAATTAAA
1 TTAAGTTAGGGTTAGGGTTTTTAATTAAA
* *
41468211 TTAGGTTAAGGTTAGGGTTTTTAAGTT-AA
1 TTAAGTTAGGGTTAGGGTTTTTAA-TTAAA
**
41468240 --GGGTTTAGGGTT--GGTTTTTAATT---
1 TTAAG-TTAGGGTTAGGGTTTTTAATTAAA
*
41468263 TTAAGTTAAGGGTTTAGAGTTTTTAATTAAA
1 TTAAGTT-AGGG-TTAGGGTTTTTAATTAAA
*
41468294 TTAGGTTAGGGTT
1 TTAAGTTAGGGTT
41468307 TTTAAGTTCA
Statistics
Matches: 189, Mismatches: 15, Indels: 52
0.74 0.06 0.20
Matches are distributed among these distances:
22 9 0.05
23 16 0.08
24 5 0.03
25 16 0.08
26 13 0.07
27 6 0.03
28 20 0.11
29 53 0.28
30 38 0.20
31 13 0.07
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (29 bp):
TTAAGTTAGGGTTAGGGTTTTTAATTAAA
Found at i:41468212 original size:74 final size:75
Alignment explanation
Indices: 41468078--41468380 Score: 318
Period size: 74 Copynumber: 3.9 Consensus size: 75
41468068 TTTAATTAAA
41468078 TTAAGTT-AGGG-TTAGGGTTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAG
1 TTAAGTTAAGGGTTTAGGG-TTTTTAATT-AA--A--TTAGGGTTAGGGTTTTTAATTAAATTAG
41468141 GTTAAGGTTAGGGTTT
60 GTTAAGGTTAGGGTTT
41468157 TTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTAAG
1 TTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAAG
41468221 GTTAGGGTTT
66 GTTAGGGTTT
* *
41468231 TTAAGTTAAGGGTTTAGGGTTGGTTTTTAATTTTAAGTTAAGGGTTTAGAGTTTTTAATT-AA--
1 TTAAGTTAAGGGTTTA--G--GGTTTTTAA--TTAAATT-AGGG-TTAGGGTTTTTAATTAAATT
41468293 A--TT-AGGTTAGGGTTT
58 AGGTTAAGGTTAGGGTTT
* * *
41468308 TTAAGTTCAGGGTTTAGGGTTTTTAATTAAATTAAGTTAGGGTTAGGGTTTGTAATTAATTTAGG
1 TTAAGTTAAGGGTTTAGGGTTTTTAATT--A--AA-TTAGGGTTAGGGTTTTTAATTAAATTAGG
*
41468373 TTAGGGTT
61 TTAAGGTT
41468381 TTTAATTAAA
Statistics
Matches: 194, Mismatches: 8, Indels: 43
0.79 0.03 0.18
Matches are distributed among these distances:
71 2 0.01
73 10 0.05
74 69 0.36
75 10 0.05
76 3 0.02
77 29 0.15
78 11 0.06
79 11 0.06
80 24 0.12
81 7 0.04
82 4 0.02
83 14 0.07
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (75 bp):
TTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGGTTAGGGTTTTTAATTAAATTAGGTTAAG
GTTAGGGTTT
Found at i:41468292 original size:21 final size:22
Alignment explanation
Indices: 41468261--41468337 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
41468251 TGGTTTTTAA
*
41468261 TTTTAAGTTAAGGGTTTAGAGT
1 TTTTAAGTTAAGGGTTTAGGGT
*
41468283 TTTTAA-TTAAATTAGG-TTAGGGT
1 TTTTAAGTT-AA--GGGTTTAGGGT
*
41468306 TTTTAAGTTCAGGGTTTAGGGT
1 TTTTAAGTTAAGGGTTTAGGGT
41468328 TTTTAA-TTAA
1 TTTTAAGTTAA
41468338 ATTAAGTTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
21 7 0.16
22 21 0.47
23 13 0.29
24 4 0.09
ACGTcount: A:0.27, C:0.01, G:0.23, T:0.48
Consensus pattern (22 bp):
TTTTAAGTTAAGGGTTTAGGGT
Found at i:41468356 original size:29 final size:29
Alignment explanation
Indices: 41468316--41468567 Score: 136
Period size: 29 Copynumber: 9.2 Consensus size: 29
41468306 TTTTAAGTTC
*
41468316 AGGGTTTAGGGTTTTTAATTAAATTAAGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
*
41468346 AGGGTTAGGGTTTGTAATT-AA-T---TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
41468370 A-GGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* * * *
41468398 AAGGTTAGGATTTTTAAGTT-CA--GGGTTT
1 AGGGTTAGGGTTTTTAA-TTAAATTAGG-TT
*
41468426 AGGGTT----TTTAATTAAATT--A-GA--TT
1 AGGGTTAGGGTTT--TT-AATTAAATTAGGTT
* *
41468449 AGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
****
41468478 AGGGGTTAGGG---TT-A-GGGGTTAGGGTT
1 A-GGGTTAGGGTTTTTAATTAAATTA-GGTT
41468504 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
* *
41468533 AGGGTTAAGGTTTTTAATTAATTTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
41468562 AGGGTT
1 AGGGTT
41468568 TAGAGTTAAA
Statistics
Matches: 173, Mismatches: 21, Indels: 57
0.69 0.08 0.23
Matches are distributed among these distances:
23 24 0.14
24 12 0.07
25 15 0.09
26 10 0.06
27 10 0.06
28 14 0.08
29 70 0.40
30 18 0.10
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.44
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:41468417 original size:103 final size:103
Alignment explanation
Indices: 41468115--41468481 Score: 354
Period size: 103 Copynumber: 3.6 Consensus size: 103
41468105 AAATTAGGTT
* * * *
41468115 AGGG-TTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTTTTTAAGTTAA---GGGTTTAGGG
1 AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTGTAA-TTAATTTAGG-TTAGGG
* *** * *
41468176 TTTTTAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTT-
64 TTTTTAATTAAATTAGGTTAAGG-TTAGGATT--TTTAAGTTC
* ** * * *
41468218 AAGG-TTAGGGTTTTTAAGTT-AA-GGGTTTAGGGTT--GGTTTTTAATTTTAAGTTAAGGGTTT
1 AGGGTTTAGGGTTTTTAA-TTAAATTAGATTAGGGTTAGGGTTTGTAA--TTAA-TTTA-GG-TT
*
41468278 AGAGTTTTTAATTAAATTAGGTT-A-G---GG-TTTTTAAGTTC
60 AGGGTTTTTAATTAAATTAGGTTAAGGTTAGGATTTTTAAGTTC
41468316 AGGGTTTAGGGTTTTTAATTAAATTA-AGTTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGT
1 AGGGTTTAGGGTTTTTAATTAAATTAGA-TTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGT
41468380 TTTTAATTAAATTAGGTTAAGGTTAGGATTTTTAAGTTC
65 TTTTAATTAAATTAGGTTAAGGTTAGGATTTTTAAGTTC
41468419 AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGG
1 AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGG
41468482 GTTAGGGTTA
Statistics
Matches: 223, Mismatches: 20, Indels: 42
0.78 0.07 0.15
Matches are distributed among these distances:
97 30 0.13
98 8 0.04
99 21 0.09
100 21 0.09
101 4 0.02
102 18 0.08
103 90 0.40
104 4 0.02
106 27 0.12
ACGTcount: A:0.27, C:0.01, G:0.27, T:0.46
Consensus pattern (103 bp):
AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGTT
TTTAATTAAATTAGGTTAAGGTTAGGATTTTTAAGTTC
Found at i:41468491 original size:6 final size:6
Alignment explanation
Indices: 41468474--41468515 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
41468464 AATTAATTTA
41468474 GGTTAGG GGTTAG GGTTAGG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTA-G GGTTAG GGTTA-G GGTTAG GGTTAG GGTTAG GGTT
41468516 TTTAATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 23 0.68
7 11 0.32
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTTAG
Found at i:41468492 original size:13 final size:13
Alignment explanation
Indices: 41468474--41468515 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
41468464 AATTAATTTA
41468474 GGTTAGGGGTTAG
1 GGTTAGGGGTTAG
41468487 GGTTAGGGGTTAG
1 GGTTAGGGGTTAG
41468500 GGTTA-GGGTTAG
1 GGTTAGGGGTTAG
41468512 GGTT
1 GGTT
41468516 TTTAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.14, C:0.00, G:0.52, T:0.33
Consensus pattern (13 bp):
GGTTAGGGGTTAG
Found at i:41468504 original size:19 final size:20
Alignment explanation
Indices: 41468474--41468513 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
41468464 AATTAATTTA
41468474 GGTTAGGGGTTAGGGTTAGG
1 GGTTAGGGGTTAGGGTTAGG
41468494 GGTTA-GGGTTAGGGTTAGG
1 GGTTAGGGGTTAGGGTTAGG
41468513 G
1 G
41468514 TTTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.15, C:0.00, G:0.55, T:0.30
Consensus pattern (20 bp):
GGTTAGGGGTTAGGGTTAGG
Found at i:41468527 original size:84 final size:85
Alignment explanation
Indices: 41468419--41468575 Score: 262
Period size: 84 Copynumber: 1.9 Consensus size: 85
41468409 TTTTAAGTTC
*
41468419 AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAGGGTTTGTAATTAATTTAGGTTAGGGGT
1 AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAAGGTTTGTAATTAATTTAGGTTAGGGGT
*
41468484 TAGGGTTAGGGGTTAGGGTT
66 TAGAGTTAGGGGTTAGGGTT
* * *
41468504 AGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAATTTAGGTTAGGGTT
1 AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAAGGTTTGTAATTAATTTAGGTTAGGGGT
41468568 TAGAGTTA
66 TAGAGTTA
41468576 AATTAGGTTA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
84 63 0.94
85 4 0.06
ACGTcount: A:0.25, C:0.00, G:0.32, T:0.43
Consensus pattern (85 bp):
AGGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTAAGGTTTGTAATTAATTTAGGTTAGGGGT
TAGAGTTAGGGGTTAGGGTT
Found at i:41468536 original size:23 final size:23
Alignment explanation
Indices: 41468506--41468594 Score: 88
Period size: 23 Copynumber: 3.6 Consensus size: 23
41468496 TTAGGGTTAG
41468506 GGTTAGGGTTTTTAATTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
*
41468529 GGTTAGGGTTAAGGTTTTTAATTAATTTA
1 GGTTA--G----GGTTTTTAATTAAATTA
** *
41468558 GGTTAGGGTTTAGAGTTAAATTA
1 GGTTAGGGTTTTTAATTAAATTA
41468581 GGTTAGGGTTTTTA
1 GGTTAGGGTTTTTA
41468595 TTACATCAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
23 30 0.57
25 1 0.02
27 1 0.02
29 21 0.40
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (23 bp):
GGTTAGGGTTTTTAATTAAATTA
Found at i:41468590 original size:29 final size:28
Alignment explanation
Indices: 41468419--41468590 Score: 110
Period size: 29 Copynumber: 6.2 Consensus size: 28
41468409 TTTTAAGTTC
* *
41468419 AGGGTTTAGGGTTTTTAATTAAATTAGATT
1 AGGG-TTAGGG-TTTGAATTAAATTAGGTT
*
41468449 AGGGTTAGGGTTTGTAATTAATTTAGGTT
1 AGGGTTAGGGTTTG-AATTAAATTAGGTT
* ** *
41468478 AGGGGTTAGGGTTAGGGGTT--A--GGGTT
1 A-GGGTTAGGGTT-TGAATTAAATTAGGTT
*
41468504 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGG-TTTGAATTAAATTAGGTT
* **
41468533 AGGGTTAAGGTTT---TT-AATTAATTT
1 AGGGTTAGGGTTTGAATTAAATTAGGTT
*
41468557 A-GGTTAGGGTTTAGAGTTAAATTAGGTT
1 AGGGTTAGGGTTT-GAATTAAATTAGGTT
41468585 AGGGTT
1 AGGGTT
41468591 TTTATTACAT
Statistics
Matches: 109, Mismatches: 19, Indels: 29
0.69 0.12 0.18
Matches are distributed among these distances:
23 10 0.09
24 8 0.07
25 13 0.12
26 7 0.06
27 3 0.03
28 14 0.13
29 36 0.33
30 17 0.16
31 1 0.01
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (28 bp):
AGGGTTAGGGTTTGAATTAAATTAGGTT
Found at i:41468618 original size:25 final size:25
Alignment explanation
Indices: 41468590--41468702 Score: 94
Period size: 25 Copynumber: 4.7 Consensus size: 25
41468580 AGGTTAGGGT
41468590 TTTTATTACATCAAATAAACTTTTA
1 TTTTATTACATCAAATAAACTTTTA
* *
41468615 TTTTATTACATCAAAT-AA-TATCA
1 TTTTATTACATCAAATAAACTTTTA
** * ***
41468638 --AAATAAC-TCGAAAT-TTTTTTTA
1 TTTTATTACATC-AAATAAACTTTTA
*
41468660 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTTTA
41468685 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
41468703 TATCAAAATA
Statistics
Matches: 66, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
20 2 0.03
21 8 0.12
22 3 0.05
23 3 0.05
24 10 0.15
25 40 0.61
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.45
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTTTA
Found at i:41468708 original size:35 final size:35
Alignment explanation
Indices: 41468599--41468709 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 35
41468589 TTTTTATTAC
*
41468599 ATCAAATAAACTTTTATTTTATTACATCAAATAAT
1 ATCAAATAAACTTCTATTTTATTACATCAAATAAT
* ** *** * *
41468634 ATCAAA-ATAAC-TCGAAATTTT-TTTTATTTTATTAC
1 ATCAAATA-AACTTC--TATTTTATTACATCAAATAAT
41468669 ATCAAATAAACTTCTATTTTATTACATCAAATAAT
1 ATCAAATAAACTTCTATTTTATTACATCAAATAAT
41468704 ATCAAA
1 ATCAAA
41468710 ATAACTCAAA
Statistics
Matches: 53, Mismatches: 17, Indels: 12
0.65 0.21 0.15
Matches are distributed among these distances:
34 7 0.13
35 38 0.72
36 8 0.15
ACGTcount: A:0.44, C:0.13, G:0.01, T:0.42
Consensus pattern (35 bp):
ATCAAATAAACTTCTATTTTATTACATCAAATAAT
Found at i:41468744 original size:43 final size:45
Alignment explanation
Indices: 41468670--41468755 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 45
41468660 TTTTATTACA
*
41468670 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
*
41468715 TCAAA-AAATTTCTATTTT-TTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATA
41468756 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
43 22 0.56
44 12 0.31
45 5 0.13
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:41469871 original size:7 final size:7
Alignment explanation
Indices: 41469861--41469885 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41469851 TTATATACAT
41469861 AATACTA
1 AATACTA
41469868 AATACTA
1 AATACTA
41469875 AATACTA
1 AATACTA
41469882 AATA
1 AATA
41469886 TCAATCGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:41471078 original size:22 final size:22
Alignment explanation
Indices: 41471053--41471109 Score: 96
Period size: 22 Copynumber: 2.5 Consensus size: 22
41471043 AAATATGAAT
*
41471053 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTGTGGAAGGAAA
41471075 TTGAGAGAATTGTGGAAGGAAA
1 TTGAGAGAATTGTGGAAGGAAA
41471097 TTGAGAGGAATTG
1 TTGAGA-GAATTG
41471110 AGAGGAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 27 0.82
23 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.35, T:0.26
Consensus pattern (22 bp):
TTGAGAGAATTGTGGAAGGAAA
Found at i:41471368 original size:42 final size:42
Alignment explanation
Indices: 41471261--41471368 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
41471251 CGTCAGCAAC
* *
41471261 TCGCGCTGACATGGACGCGATTTCCTGGCGCGTACCCTAACA
1 TCGCGCTGACGTGGACGCGATTTTCTGGCGCGTACCCTAACA
* *
41471303 TCGCGCTGACGTGGACGCAATTTTCTGGCGCGTACCCTGACA
1 TCGCGCTGACGTGGACGCGATTTTCTGGCGCGTACCCTAACA
* *
41471345 TCGTGCTGACGTGGACACGATTTT
1 TCGCGCTGACGTGGACGCGATTTT
41471369 GCGGAAAAGG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (42 bp):
TCGCGCTGACGTGGACGCGATTTTCTGGCGCGTACCCTAACA
Found at i:41473720 original size:6 final size:6
Alignment explanation
Indices: 41473709--41473741 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
41473699 AAATAAACAA
41473709 GGGTAG GGGTAG GGGTAG GGGTAGG GGGTAG GG
1 GGGTAG GGGTAG GGGTAG GGGTA-G GGGTAG GG
41473742 CCAGTGGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.15, C:0.00, G:0.70, T:0.15
Consensus pattern (6 bp):
GGGTAG
Found at i:41477265 original size:16 final size:15
Alignment explanation
Indices: 41477244--41477275 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41477234 CGTTTTTTGA
41477244 ATTTTTTTGAATTTTT
1 ATTTTTTT-AATTTTT
41477260 ATTTTTTTAATTTTT
1 ATTTTTTTAATTTTT
41477275 A
1 A
41477276 AATTATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
ATTTTTTTAATTTTT
Found at i:41480512 original size:12 final size:12
Alignment explanation
Indices: 41480495--41480520 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41480485 TGGATATTCT
41480495 CCCTCATAATCC
1 CCCTCATAATCC
41480507 CCCTCATAATCC
1 CCCTCATAATCC
41480519 CC
1 CC
41480521 TAATTCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (12 bp):
CCCTCATAATCC
Found at i:41480941 original size:14 final size:14
Alignment explanation
Indices: 41480922--41480949 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41480912 CCTCACAGTC
41480922 CAAACCGAATTGGG
1 CAAACCGAATTGGG
41480936 CAAACCGAATTGGG
1 CAAACCGAATTGGG
41480950 GTAAGGTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.29, T:0.14
Consensus pattern (14 bp):
CAAACCGAATTGGG
Found at i:41482975 original size:16 final size:19
Alignment explanation
Indices: 41482933--41482975 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
41482923 AGAGATTGTG
41482933 ATAATAT-TTAGTATACTT
1 ATAATATGTTAGTATACTT
41482951 ATAAT-TGTTA-TA-ACTT
1 ATAATATGTTAGTATACTT
41482967 -TAATATGTT
1 ATAATATGTT
41482976 TGATGATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.17
16 8 0.35
17 3 0.13
18 8 0.35
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (19 bp):
ATAATATGTTAGTATACTT
Found at i:41491487 original size:51 final size:51
Alignment explanation
Indices: 41491411--41491525 Score: 212
Period size: 51 Copynumber: 2.3 Consensus size: 51
41491401 TCCTCTCTAA
41491411 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
41491462 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCAATT
1 TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
*
41491513 TCCCCTCAATTTC
1 TCCTCTCAATTTC
41491526 ATTTTTTAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.42
Consensus pattern (51 bp):
TCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATTTCAATT
Found at i:41491561 original size:10 final size:10
Alignment explanation
Indices: 41491548--41491591 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
41491538 AATTTTATAT
*
41491548 TTTTTTTTAA
1 TTTTTTTAAA
41491558 TTTTTTTAAA
1 TTTTTTTAAA
**
41491568 TAATTTTAAA
1 TTTTTTTAAA
*
41491578 TTTTTTTATA
1 TTTTTTTAAA
41491588 TTTT
1 TTTT
41491592 CATCAATGAC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:41491569 original size:31 final size:31
Alignment explanation
Indices: 41491526--41491584 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
41491516 CCTCAATTTC
*
41491526 ATTTTTTAAAATAATTTTATATTTTTTTTTA
1 ATTTTTTAAAATAATTTTAAATTTTTTTTTA
*
41491557 ATTTTTTTAAATAATTTTAAATTTTTTT
1 ATTTTTTAAAATAATTTTAAATTTTTTT
41491585 ATATTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (31 bp):
ATTTTTTAAAATAATTTTAAATTTTTTTTTA
Found at i:41492685 original size:7 final size:7
Alignment explanation
Indices: 41492673--41492697 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41492663 AGTCGATTGA
41492673 TATTTAG
1 TATTTAG
41492680 TATTTAG
1 TATTTAG
41492687 TATTTAG
1 TATTTAG
41492694 TATT
1 TATT
41492698 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:41493796 original size:25 final size:25
Alignment explanation
Indices: 41493768--41493836 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 25
41493758 TTTAAATTTA
* *
41493768 TTATCTGATGTAATAAAATATAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
41493793 TTATTTAATATAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
*
41493818 TCAATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
41493837 ACCCTAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
25 22 0.61
26 14 0.39
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:41493860 original size:18 final size:17
Alignment explanation
Indices: 41493832--41493880 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
41493822 TTTGATGTAA
* *
41493832 TAAAAACCCTAATTTATT
1 TAAAAA-CCTAACTTAAT
41493850 TAAATAACCTAACTTAAT
1 TAAA-AACCTAACTTAAT
41493868 TAAAAACCCTAAC
1 TAAAAA-CCTAAC
41493881 CCTAACCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (17 bp):
TAAAAACCTAACTTAAT
Found at i:41493896 original size:29 final size:29
Alignment explanation
Indices: 41493854--41493977 Score: 196
Period size: 29 Copynumber: 4.3 Consensus size: 29
41493844 TTTATTTAAA
41493854 TAACCTAACTTAATTAAAAACCCTAACCC
1 TAACCTAACTTAATTAAAAACCCTAACCC
* *
41493883 TAACCGAACCTAATTAAAAACCCTAACCC
1 TAACCTAACTTAATTAAAAACCCTAACCC
41493912 TAA-CTCAACTTAATTAAAAACCCTAACCC
1 TAACCT-AACTTAATTAAAAACCCTAACCC
*
41493941 TAACCTAACTTAATTAAAAACCCCAACCC
1 TAACCTAACTTAATTAAAAACCCTAACCC
*
41493970 TAATCTAA
1 TAACCTAA
41493978 TTTTACATAA
Statistics
Matches: 87, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
28 1 0.01
29 84 0.97
30 2 0.02
ACGTcount: A:0.45, C:0.31, G:0.01, T:0.23
Consensus pattern (29 bp):
TAACCTAACTTAATTAAAAACCCTAACCC
Found at i:41494036 original size:55 final size:55
Alignment explanation
Indices: 41493975--41494211 Score: 316
Period size: 55 Copynumber: 4.3 Consensus size: 55
41493965 AACCCTAATC
*
41493975 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTGTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
*
41494030 TAATTTTACATAATTTAATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
* * ** * * *
41494085 TAATTTTACCTAATTTGATAATTTTTCCTAATTTAATTAA-A-ATTTTTTTGTCTTAA
1 TAATTTTACATAATTTGATAA-TTTTACTAA--CCATTAACACAATTTTTGGACTTAA
* * * *
41494141 TAATTTTACATAATTTGAAAATTTTACTAACCATTAACAAAATTTTGGGACCTAA
1 TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
41494196 TAATTTTACATAATTT
1 TAATTTTACATAATTT
41494212 TACATAATGT
Statistics
Matches: 157, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
53 5 0.03
54 1 0.01
55 106 0.68
56 39 0.25
57 1 0.01
58 5 0.03
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (55 bp):
TAATTTTACATAATTTGATAATTTTACTAACCATTAACACAATTTTTGGACTTAA
Found at i:41494107 original size:18 final size:18
Alignment explanation
Indices: 41494084--41494118 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41494074 TTTGGACTTA
41494084 ATAATTTTACCTAATTTG
1 ATAATTTTACCTAATTTG
*
41494102 ATAATTTTTCCTAATTT
1 ATAATTTTACCTAATTT
41494119 AATTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.54
Consensus pattern (18 bp):
ATAATTTTACCTAATTTG
Found at i:41494210 original size:10 final size:10
Alignment explanation
Indices: 41494195--41494219 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41494185 TTGGGACCTA
41494195 ATAATTTTAC
1 ATAATTTTAC
41494205 ATAATTTTAC
1 ATAATTTTAC
41494215 ATAAT
1 ATAAT
41494220 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:41497609 original size:123 final size:123
Alignment explanation
Indices: 41497334--41497666 Score: 551
Period size: 123 Copynumber: 2.7 Consensus size: 123
41497324 GTACTGTAGT
* * * *
41497334 GCGTCCACGAGGGCGCGATTTCACAATATCTTCCCAAATAGCATCCTGGTAAAGGCGATTTTATA
1 GCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAGCCGATTTTATA
* *
41497399 CTATTTTCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCTACTGTAGCAAAATC
66 CTATTTGCTCAGAAACGTC-AAAAAAATTATTTCTTACATGACCTACTATAGCAAAATC
*
41497458 GCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAGCCAATTTTATA
1 GCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAGCCGATTTTATA
*
41497523 CTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCTACTATAGCGAAATC
66 CTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCTACTATAGCAAAATC
* *
41497581 GCGTCCACAAGGGCGCGATTTCAGAATTTCTTCTCAAATAGCATCCTGGTAGAGCCGATTTTATA
1 GCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAGCCGATTTTATA
41497646 CTATTTGAC-CAGAAACGTCAA
66 CTATTTG-CTCAGAAACGTCAA
41497667 CTCAAAATAA
Statistics
Matches: 197, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
123 118 0.60
124 79 0.40
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (123 bp):
GCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAGCCGATTTTATA
CTATTTGCTCAGAAACGTCAAAAAAATTATTTCTTACATGACCTACTATAGCAAAATC
Found at i:41500071 original size:16 final size:15
Alignment explanation
Indices: 41500050--41500102 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
41500040 TTAGATTATC
*
41500050 AATTAAATCCTAAATT
1 AATTAAAT-ATAAATT
41500066 AATTAATATATAAATT
1 AATTAA-ATATAAATT
*
41500082 AAATAAATATATAATAT
1 AATTAAATATA-AAT-T
41500099 AATT
1 AATT
41500103 CAATTAATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 5 0.16
16 20 0.65
17 6 0.19
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
AATTAAATATAAATT
Found at i:41500092 original size:17 final size:16
Alignment explanation
Indices: 41500060--41500095 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
41500050 AATTAAATCC
*
41500060 TAAATTAATTAATATA
1 TAAATTAATAAATATA
41500076 TAAATTAAATAAATATA
1 TAAATT-AATAAATATA
41500093 TAA
1 TAA
41500096 TATAATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATTAATAAATATA
Found at i:41501353 original size:3 final size:3
Alignment explanation
Indices: 41501345--41501385 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
41501335 AATTAATCAA
41501345 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
41501386 AAATATACAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:41503318 original size:87 final size:87
Alignment explanation
Indices: 41503165--41503333 Score: 268
Period size: 87 Copynumber: 1.9 Consensus size: 87
41503155 CCTTTCAAAT
* *
41503165 TTAAGTTCGGTGAATTCATCAAGTCCATCTCAATATGATCACCCAAACTCTGGGATATGAACTCA
1 TTAAGTTCGGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCA
41503230 TTAAGAGTAATAAACTCAACCTC
66 TTAAGAGTAA-AAACTCAACCTC
* * * *
41503253 TTAAG-TCGGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAATTTTGGGCTATGAATTCA
1 TTAAGTTCGGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCA
41503317 TTAAGAGTAAAAACTCA
66 TTAAGAGTAAAAACTCA
41503334 TTTTTATACA
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
86 7 0.09
87 63 0.84
88 5 0.07
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (87 bp):
TTAAGTTCGGTGAATTCATCAAGTCCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCA
TTAAGAGTAAAAACTCAACCTC
Found at i:41507195 original size:23 final size:23
Alignment explanation
Indices: 41507153--41507196 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41507143 TAGTTATTAT
*
41507153 TTTATTAATATTTTGCTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
41507176 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
41507197 AAAATGGTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:41508535 original size:2 final size:2
Alignment explanation
Indices: 41508530--41508564 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41508520 AAAAATATGA
41508530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41508565 GTAGATGAAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:41510172 original size:17 final size:17
Alignment explanation
Indices: 41510126--41510172 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
41510116 TACATGTAAA
41510126 TATATTTATATATTTTTT
1 TATATTTATATA-TTTTT
* * *
41510144 TCTAATGA-ATATTTTT
1 TATATTTATATATTTTT
41510160 TATATTTATATAT
1 TATATTTATATAT
41510173 ATATATATGT
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
16 10 0.45
17 7 0.32
18 5 0.23
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
TATATTTATATATTTTT
Found at i:41518252 original size:50 final size:50
Alignment explanation
Indices: 41518196--41518302 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
41518186 ATTATCGCTT
* *
41518196 TGGCGTTGCAATGGAAAAGATTGAAGCAAC-ATCGACGAATCTTATTTCCC
1 TGGCGTTGCAACGGAAAAGATTGAAGCAACGA-CGACGAATCTTATCTCCC
* * ** * *
41518246 TGGCGTTGTAGCGGAGCAGATTGAAGCCACGACGGCGAATCTTATCTCCC
1 TGGCGTTGCAACGGAAAAGATTGAAGCAACGACGACGAATCTTATCTCCC
41518296 TGGCGTT
1 TGGCGTT
41518303 AAGGCTTGGA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 47 0.98
51 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (50 bp):
TGGCGTTGCAACGGAAAAGATTGAAGCAACGACGACGAATCTTATCTCCC
Found at i:41518452 original size:50 final size:50
Alignment explanation
Indices: 41518370--41518653 Score: 205
Period size: 50 Copynumber: 5.7 Consensus size: 50
41518360 TTTGGCATTA
* ** *
41518370 TAGTGGAGCAGATTGAAGCCT-CAACGATGAATCTTACTCCCCTGGCGGTG
1 TAGTGGAACAGATTGAAG-CTACAACGGCGAATCTTACTTCCCTGGCGGTG
* ** *** **
41518420 TAGTGGAACAGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTG
1 TAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
* * ** * ** *
41518470 CAATTAAAAAGATT-AAGGCCGCAACGGCGAATCTTAATTCCCTGGCGGTG
1 TAGTGGAACAGATTGAA-GCTACAACGGCGAATCTTACTTCCCTGGCGGTG
** ** ** **
41518520 TAGTGGAACAGATTGAAGCTATGACGGCGAATCTTGTTTCCC-AACATTG
1 TAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
* * ** * **
41518569 CAATTAAAAAGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTG
1 TAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
*
41518619 TAGTGGAACAGATTGAAGCTACGACGGCGAATCTT
1 TAGTGGAACAGATTGAAGCTACAACGGCGAATCTT
41518654 GTTTCCCAAC
Statistics
Matches: 165, Mismatches: 65, Indels: 8
0.69 0.27 0.03
Matches are distributed among these distances:
49 38 0.23
50 125 0.76
51 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (50 bp):
TAGTGGAACAGATTGAAGCTACAACGGCGAATCTTACTTCCCTGGCGGTG
Found at i:41518598 original size:49 final size:49
Alignment explanation
Indices: 41518429--41518702 Score: 217
Period size: 50 Copynumber: 5.5 Consensus size: 49
41518419 GTAGTGGAAC
* *
41518429 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTT-CCCAACATTGCAATTAAAA
* ** ** ** * * ** *
41518479 AGATT-AAGGCCGCAACGGCGAATCTTAATTCCCTGGCGGTGTAGTGGAAC
1 AGATTGAA-GCCACAACGGCGAATCTTGTTTCCC-AACATTGCAATTAAAA
* **
41518529 AGATTGAAGCTATGACGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
* ** ** ** * * ** *
41518578 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCC-AACATTGCAATTAAAA
* *
41518628 AGATTGAAGCTACGACGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
1 AGATTGAAGCCACAACGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
*
41518677 AGATTGAAGCCGCAACGGCGAATCTT
1 AGATTGAAGCCACAACGGCGAATCTT
41518703 ACTTCNNNNN
Statistics
Matches: 159, Mismatches: 61, Indels: 9
0.69 0.27 0.04
Matches are distributed among these distances:
49 69 0.43
50 88 0.55
51 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (49 bp):
AGATTGAAGCCACAACGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
Found at i:41518614 original size:99 final size:99
Alignment explanation
Indices: 41518379--41518707 Score: 579
Period size: 99 Copynumber: 3.3 Consensus size: 99
41518369 ATAGTGGAGC
* ** *
41518379 AGATTGAAGCCTCAACGATGAATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
41518444 CGGCGAATCTTGTTTCCCCAACATTGCAATTAAAA
66 CGGCGAATCTTGTTT-CCCAACATTGCAATTAAAA
* *
41518479 AGATT-AAGGCCGCAACGGCGAATCTTAATTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTATG
1 AGATTGAA-GCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACG
41518543 ACGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
65 ACGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
41518578 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
41518643 CGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
66 CGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
41518677 AGATTGAAGCCGCAACGGCGAATCTTACTTC
1 AGATTGAAGCCGCAACGGCGAATCTTACTTC
41518708 NNNNNNNNNN
Statistics
Matches: 219, Mismatches: 8, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
99 146 0.67
100 73 0.33
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (99 bp):
AGATTGAAGCCGCAACGGCGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
CGGCGAATCTTGTTTCCCAACATTGCAATTAAAA
Found at i:41521208 original size:24 final size:27
Alignment explanation
Indices: 41521181--41521231 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
41521171 TTTTAAATTA
41521181 ATTAAT-TTCA-ATA-ATGTAATTATT
1 ATTAATCTTCATATATATGTAATTATT
* *
41521205 ATTATTCTTTATATATATGTAATTATT
1 ATTAATCTTCATATATATGTAATTATT
41521232 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 5 0.23
25 3 0.14
26 3 0.14
27 11 0.50
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (27 bp):
ATTAATCTTCATATATATGTAATTATT
Found at i:41521224 original size:27 final size:28
Alignment explanation
Indices: 41521194--41521264 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
41521184 AATTTCAATA
**
41521194 ATGTAATTA-TTATTATTCTTTATATAT
1 ATGTAATTATTTATTATAATTTATATAT
*
41521221 ATGTAATTATTTTTTTATAATTTATATAT
1 ATGTAATTA-TTTATTATAATTTATATAT
41521250 ATGT-ATATATTTATT
1 ATGTAAT-TATTTATT
41521265 TTTTTTATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 9 0.24
28 7 0.19
29 21 0.57
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (28 bp):
ATGTAATTATTTATTATAATTTATATAT
Found at i:41525149 original size:15 final size:15
Alignment explanation
Indices: 41525129--41525161 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
41525119 CAAAGATTAA
*
41525129 CAATGATGAAACACT
1 CAATGACGAAACACT
41525144 CAATGACGAAACACT
1 CAATGACGAAACACT
41525159 CAA
1 CAA
41525162 ACACACCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.15
Consensus pattern (15 bp):
CAATGACGAAACACT
Found at i:41529524 original size:24 final size:24
Alignment explanation
Indices: 41529497--41529542 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
41529487 TTTTTTTTAT
*
41529497 TTTTGGAAAAAAAACAAAAATTAA
1 TTTTCGAAAAAAAACAAAAATTAA
*
41529521 TTTTCGAAAAAAAATAAAAATT
1 TTTTCGAAAAAAAACAAAAATT
41529543 GGGAGTCGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (24 bp):
TTTTCGAAAAAAAACAAAAATTAA
Found at i:41530259 original size:15 final size:15
Alignment explanation
Indices: 41530241--41530275 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
41530231 CAAATGCCAT
41530241 AATAATAAATACAAC
1 AATAATAAATACAAC
* *
41530256 AATAGTAAATACATC
1 AATAATAAATACAAC
41530271 AATAA
1 AATAA
41530276 CATAGAAATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.23
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:41532603 original size:44 final size:44
Alignment explanation
Indices: 41532487--41533174 Score: 380
Period size: 44 Copynumber: 15.7 Consensus size: 44
41532477 CAGCTTTAAC
** *
41532487 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGC-AATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA-CTT-AGT
*
41532532 CTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTATT
1 CTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGT
* * * * * *
41532576 CTACTCCACTGCAACTTTAGGGAGATAAGACTAG-AT-GTGA-T
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGT
* * ** * ** * *
41532617 CTACT-CTCTGCAACTTCAAAGAAATAAGATCCAAGGTT--TTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCTTACTTAGT
* * * * *
41532660 CCGTTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTT--TAACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTTACTTAGT
* ** *
41532705 -TGCTTCACTGCAACTTCAGGGAGATAAGGTTTGC-TATCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTA-CTT-AGT
* *
41532749 CTGCCCCACTGCAACTTCA-GGAGGATAAGACTTACTTACTTAGT
1 CTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGT
* *
41532793 CTGCCCCACTGCAACTTCA-GGAGGATAAGACTTACTTACTTAGT
1 CTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGT
* * **
41532837 CTGCTCCACTGCAACTTTAGGGAGATAAGACTAG---A-TGGGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAG-T
* * * * ** * *
41532878 CTGCT-CTCTGCGACTTCAGAGAAATAAGATCCAAGGTT--TTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCTTACTTAGT
* * * **
41532921 CTGTTCCACTGCAACTTCAGGGAGATAGGATTATCGGC-T--TTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTTACTTAGT
* *
41532965 CTGCTCCACTGCAACTTCAGGGAGATAAG-GTCTGC-AATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCTTA-CTT-AGT
* *
41533010 CTGC-CTCACTGCAACTTTA-GTACGATAAGACTTGCTTACTTAGT
1 CTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGT
* *
41533054 CTGCTCCACTGCAACTTCAGGGAGATAAG-GTCTGC-AATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGCTTA-CTT-AGT
*
41533099 CTGC-CTCACTGCAACTTTA-GGAGGATAAGACTTGCTTACTTAGT
1 CTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTTACTTAGT
41533143 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
41533175 AGATGGGATC
Statistics
Matches: 505, Mismatches: 88, Indels: 101
0.73 0.13 0.15
Matches are distributed among these distances:
40 41 0.08
41 17 0.03
42 10 0.02
43 16 0.03
44 275 0.54
45 139 0.28
46 7 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTTAGT
Found at i:41532714 original size:128 final size:128
Alignment explanation
Indices: 41532579--41532993 Score: 412
Period size: 128 Copynumber: 3.2 Consensus size: 128
41532569 ACTTATTCTA
*
41532579 CTCCACTGCAACTTTAGGGAGATAAGACTAGATGTGATCTACTCTCTGCAACTTCAAAGAAATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTACTCTCTGCAACTTCAAAGAAATAA
*
41532644 GATCCAAGGTTTTAATCCGTTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACTTG
66 GATCCAAGGTTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACTTG
* ** * * * * * * *
41532707 CTTCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAATCTGCCCCACTGCAACTTC-AGGA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAG--AT-GT-GATCT-ACTCTCTGCAACTTCAAAGA
* ** * * ** **
41532771 GGATAAGA-CTTA-CTTACTTAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTA-CTTAC
61 -AATAAGATCCAAGGTT--TTAATCTGTTCCACTGCAACTTCAGGGA-GATAAGA-TTATC-GGC
*
41532832 -TT-AGTCTG
120 TTTAACT-TG
* * * * *
41532840 CTCCACTGCAACTTTAGGGAGATAAGACTAGATGGGATCTGCTCTCTGCGACTTCAGAGAAATAA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTACTCTCTGCAACTTCAAAGAAATAA
* *
41532905 GATCCAAGGTTTTAATCTGTTCCACTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTG
66 GATCCAAGGTTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACTTG
41532968 CTCCACTGCAACTTCAGGGAGATAAG
1 CTCCACTGCAACTTCAGGGAGATAAG
41532994 GTCTGCAATC
Statistics
Matches: 219, Mismatches: 49, Indels: 38
0.72 0.16 0.12
Matches are distributed among these distances:
127 4 0.02
128 100 0.46
129 12 0.05
130 4 0.02
131 5 0.02
132 14 0.06
133 76 0.35
134 4 0.02
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (128 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATCTACTCTCTGCAACTTCAAAGAAATAA
GATCCAAGGTTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACTTG
Found at i:41532738 original size:217 final size:216
Alignment explanation
Indices: 41532363--41532824 Score: 726
Period size: 217 Copynumber: 2.1 Consensus size: 216
41532353 ATCAGTCTGT
* * * *
41532363 TCCACTGCAACTTTAAGGAGATAAGAGTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAG
1 TCCACTGCAACTTT-AGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAAATAAG
* *
41532428 ATCCAAGGTTTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTATCAGCTTTAACCTGCTC
65 ATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCAGCTTTAACCTGCTC
* *
41532493 CACTGCAACTTCAGGGAGATAAGGTTTGCAATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGAT
130 CACTGCAACTTCAGGGAGATAAGGTTTGCAATCTTCAATCTGCCCCACTGCAACTTCAGGAGGAT
* *
41532558 AAGACTTGCTTACTTATTCTAC
195 AAGACTTACTTACTTAGTCTAC
*
41532580 TCCACTGCAACTTTAGGGAGATAAGACTAGATGTGATCTACTCTCTGCAACTTCAAAGAAATAAG
1 TCCACTGCAACTTTA-GGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAAATAAG
* * * *
41532645 ATCCAAGGTTTTAATCCGTTCCACTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACTTGCTT
65 ATCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCAGCTTTAACCTGCTC
*
41532710 CACTGCAACTTCAGGGAGATAAGGTTTGCTATCTTCAATCTGCCCCACTGCAACTTCAGGAGGAT
130 CACTGCAACTTCAGGGAGATAAGGTTTGCAATCTTCAATCTGCCCCACTGCAACTTCAGGAGGAT
*
41532775 AAGACTTACTTACTTAGTCTGC
195 AAGACTTACTTACTTAGTCTAC
* *
41532797 CCCACTGCAACTTCAGGAGGATAAGACT
1 TCCACTGCAACTTTAGGA-GATAAGACT
41532825 TACTTACTTA
Statistics
Matches: 224, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
216 4 0.02
217 220 0.98
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (216 bp):
TCCACTGCAACTTTAGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAAAGAAATAAGA
TCCAAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGATTATCAGCTTTAACCTGCTCC
ACTGCAACTTCAGGGAGATAAGGTTTGCAATCTTCAATCTGCCCCACTGCAACTTCAGGAGGATA
AGACTTACTTACTTAGTCTAC
Found at i:41532769 original size:89 final size:89
Alignment explanation
Indices: 41532665--41533171 Score: 356
Period size: 89 Copynumber: 5.8 Consensus size: 89
41532655 TTAATCCGTT
*
41532665 CCACTGCAACTTCAGG-GAGATAAGATTATCGGCTTTAACT-TGCTTCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGAG-GATAAGATTAT-GGCTTTAACTCTGCTCCACTGCAACTTCAGGGAG
* * *
41532728 ATAAGGTTTGCTATCTTCAATCTGCC
64 ATAAGGTCTGCAATCTTCAGTCTGCC
** * *
41532754 CCACTGCAACTTCAGGAGGATAAGACTTACTTAC-TT-AGTCTGCCCCACTGCAACTTCA-GGAG
1 CCACTGCAACTTCAGGAGGATAAGA-TTA-TGGCTTTAACTCTGCTCCACTGCAACTTCAGGGA-
* * * *
41532816 GATAA-GACT-TACTTACTT-AGTCTGCT
63 GATAAGGTCTGCA-AT-CTTCAGTCTGCC
* * * *** * * * *
41532842 CCACTGCAACTTTAGG-GAGATAAGACTA--GATGGGA-TCTGCT-CTCTGCGACTTCAGAGAAA
1 CCACTGCAACTTCAGGAG-GATAAGATTATGGCTTTAACTCTGCTCCACTGCAACTTCAGGGAGA
* * * **
41532902 TAAGATC--CAAGGT-TTTAATCTGTT
65 TAAGGTCTGCAA--TCTTCAGTCTGCC
*
41532926 CCACTGCAACTTCAGG-GAGATAGGATTATCGGCTTTAAC-CTGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGAG-GATAAGATTAT-GGCTTTAACTCTGCTCCACTGCAACTTCAGGGAG
41532989 ATAAGGTCTGCAATCTTCAGTCTGCC
64 ATAAGGTCTGCAATCTTCAGTCTGCC
* * * * * * *
41533015 TCACTGCAACTTTAGTACGATAAGACT-T-GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGAGGATAAGATTATGGCTT--TAACTCTGCTCCACTGCAACTTCAGGGAG
41533078 ATAAGGTCTGCAATCTTCAGTCTGCC
64 ATAAGGTCTGCAATCTTCAGTCTGCC
* * * * *
41533104 TCACTGCAACTTTAGGAGGATAAGACT-T-GCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGAGGATAAGATTATGGCTT--TAACTCTGCTCCACTGCAACTTCAGGGAG
41533167 ATAAG
64 ATAAG
41533172 ACTAGATGGG
Statistics
Matches: 336, Mismatches: 55, Indels: 54
0.76 0.12 0.12
Matches are distributed among these distances:
83 2 0.01
84 47 0.14
85 9 0.03
86 5 0.01
87 11 0.03
88 61 0.18
89 192 0.57
90 8 0.02
91 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.29
Consensus pattern (89 bp):
CCACTGCAACTTCAGGAGGATAAGATTATGGCTTTAACTCTGCTCCACTGCAACTTCAGGGAGAT
AAGGTCTGCAATCTTCAGTCTGCC
Found at i:41532871 original size:261 final size:260
Alignment explanation
Indices: 41532407--41533082 Score: 925
Period size: 261 Copynumber: 2.6 Consensus size: 260
41532397 GATCTGCTCT
* * * * *
41532407 CTGCAACTTCAGAGAGATAAGATCCA-AGGTTTTAATCC-GCTCCATTGCAACTTCAGGGAGAT-
1 CTGCAACTTCAGGGAGATAAGAT-TATCGGCTTTAA-CCTGCTCCACTGCAACTTCAGGGAGATA
* * * * ** *
41532469 AGGATTAT-CAGCTTTAACCTGCTCCACTGCAACTTCAGG-GAGATAAGGTTTGC-AATCTTCAG
64 AGG-TT-TGCATCTTCAATCTGCCCCACTGCAACTTCAGGAG-GATAAGACTTGCTTA-CTT-AG
* * *
41532531 TCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTATTCTACTCCACTGCAACTTTAG
124 TCTGCCCCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTCTACTCCACTGCAACTTTAG
*
41532596 GGAGATAAGACTAGATGTGATCTACTCTCTGCAACTTCAAAGAAATAAGATCCAAGGTTTTAATC
189 GGAGATAAGACTAGATGGGATCTACTCTCTGCAACTTCAAAGAAATAAGATCCAAGGTTTTAATC
41532661 CGTTCCA
254 CGTTCCA
* *
41532668 CTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACTTGCTTCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAG
*
41532733 GTTTGCTATCTTCAATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCC
66 GTTTGC-ATCTTCAATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCC
*
41532798 CCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCTCCACTGCAACTTTAGGGAGAT
130 CCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTCTACTCCACTGCAACTTTAGGGAGAT
* * * *
41532863 AAGACTAGATGGGATCTGCTCTCTGCGACTTCAGAGAAATAAGATCCAAGGTTTTAATCTGTTCC
195 AAGACTAGATGGGATCTACTCTCTGCAACTTCAAAGAAATAAGATCCAAGGTTTTAATCCGTTCC
41532928 A
260 A
*
41532929 CTGCAACTTCAGGGAGATAGGATTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAG
1 CTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAG
* * * * * * *
41532994 GTCTGCAATCTTCAGTCTGCCTCACTGCAACTTTAGTACGATAAGACTTGCTTACTTAGTCTGCT
66 GTTTGC-ATCTTCAATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCC
41533059 CCACTGCAACTTCAGG-GAGATAAG
130 CCACTGCAACTTCAGGAG-GATAAG
41533083 GTCTGCAATC
Statistics
Matches: 371, Mismatches: 36, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
260 4 0.01
261 324 0.87
262 41 0.11
263 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (260 bp):
CTGCAACTTCAGGGAGATAAGATTATCGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAG
GTTTGCATCTTCAATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCCC
CACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTCTACTCCACTGCAACTTTAGGGAGATA
AGACTAGATGGGATCTACTCTCTGCAACTTCAAAGAAATAAGATCCAAGGTTTTAATCCGTTCCA
Found at i:41532896 original size:217 final size:219
Alignment explanation
Indices: 41532399--41533082 Score: 655
Period size: 217 Copynumber: 3.1 Consensus size: 219
41532389 GTAGATGCGA
* * * ** *
41532399 TCTGCT-CTCTGCAACTTCAGAGAGATAAGATCCAAGGTTTTAATCCGCTCCATTGCAACTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCAAGGATGGAATCCGCTCCACTGCAACTTCAG
* * * *
41532463 GGAGATAGGATTATCAGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGCAATCTT
65 GGAGATAAGATTATCGGCTTTAACTTGCTTCACTGCAACTTCAGGGAGATAAGGTTTGC-ATCTT
* * * * *
41532528 CAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTATTCTACTCCACTGCAACTT
129 CAATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCCCCACTGCAACTT
** * *
41532593 TAGG-GAGATAAGAC-TAGAT-GTGA-
194 TAGGAG-GATAAGACTTACTTACTTAG
* * ** * * ** *
41532616 TCTACT-CTCTGCAACTTCAAAGAAATAAGATCCAAGGTTTTAATCCGTTCCACTGCAACTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCAAGGATGGAATCCGCTCCACTGCAACTTCAG
41532680 GGAGATAAGATTATCGGCTTTAACTTGCTTCACTGCAACTTCAGGGAGATAAGGTTTGCTATCTT
65 GGAGATAAGATTATCGGCTTTAACTTGCTTCACTGCAACTTCAGGGAGATAAGGTTTGC-ATCTT
*
41532745 CAATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTACTTACTTAGTCTGCCCCACTGCAACTT
129 CAATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCCCCACTGCAACTT
*
41532810 CAGGAGGATAAGACTTACTTACTTAG
194 TAGGAGGATAAGACTTACTTACTTAG
* * * * * * *
41532836 TCTGCTCCACTGCAACTTTAGGGAGATAAGA-CTA-GATGGGATCTGCT-CTCTGCGACTTCAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAAGGATGGAATCCGCTCCACTGCAACTTCAGG
* * * * **
41532898 GAAATAAGATCCA-AGGTTTTAA-TCTG-TTCCACTGCAACTTCAGGGAGAT-AGGATTAT-CGG
66 GAGATAAGAT-TATCGGCTTTAACT-TGCTT-CACTGCAACTTCAGGGAGATAAGG-TT-TGCAT
* * * * * *
41532958 CTTTAACCTGCTCCACTGCAACTTCAGG-GAGATAAG-GTCTGC-AATCTTCAGTCTGCCTCACT
126 CTTCAATCTGCCCCACTGCAACTTCAGGAG-GATAAGACT-TGCTTA-CTT-AGTCTGCCCCACT
* * *
41533020 GCAACTTTAGTACGATAAGACTTGCTTACTTAG
187 GCAACTTTAGGAGGATAAGACTTACTTACTTAG
41533053 TCTGCTCCACTGCAACTTCAGGGAGATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
41533083 GTCTGCAATC
Statistics
Matches: 398, Mismatches: 55, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
215 3 0.01
216 42 0.11
217 312 0.78
218 13 0.03
219 4 0.01
220 5 0.01
221 19 0.05
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (219 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCAAGGATGGAATCCGCTCCACTGCAACTTCAGG
GAGATAAGATTATCGGCTTTAACTTGCTTCACTGCAACTTCAGGGAGATAAGGTTTGCATCTTCA
ATCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCCCCACTGCAACTTTA
GGAGGATAAGACTTACTTACTTAG
Found at i:41539992 original size:20 final size:20
Alignment explanation
Indices: 41539967--41540010 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
41539957 CGATACCCAT
41539967 GCTTATGAGTCTTTCTACCA
1 GCTTATGAGTCTTTCTACCA
41539987 GCTTATGAGTCTTTCTACCA
1 GCTTATGAGTCTTTCTACCA
41540007 GCTT
1 GCTT
41540011 CTTGAACGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (20 bp):
GCTTATGAGTCTTTCTACCA
Found at i:41544375 original size:25 final size:25
Alignment explanation
Indices: 41544327--41544375 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41544317 TTATTTTTGG
**
41544327 AAAAAAAACAAAAATTAGTTGTCGA
1 AAAAAAAACAAAAATTAGGAGTCGA
*
41544352 AAAAAAAACAAAAATTGGGAGTCG
1 AAAAAAAACAAAAATTAGGAGTCG
41544376 CCACCAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.59, C:0.08, G:0.16, T:0.16
Consensus pattern (25 bp):
AAAAAAAACAAAAATTAGGAGTCGA
Found at i:41547218 original size:39 final size:40
Alignment explanation
Indices: 41547164--41547246 Score: 150
Period size: 39 Copynumber: 2.1 Consensus size: 40
41547154 TTCCGGTTCT
*
41547164 TTCATAACAACCAACACATTATA-GGAAAAAAATATACCA
1 TTCATAACAACCAACACATTATAGGGAAAAAAATACACCA
41547203 TTCATAACAACCAACACATTATAGGGAAAAAAATACACCA
1 TTCATAACAACCAACACATTATAGGGAAAAAAATACACCA
41547243 TTCA
1 TTCA
41547247 AAATCTTGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 23 0.55
40 19 0.45
ACGTcount: A:0.52, C:0.22, G:0.06, T:0.20
Consensus pattern (40 bp):
TTCATAACAACCAACACATTATAGGGAAAAAAATACACCA
Found at i:41549309 original size:33 final size:33
Alignment explanation
Indices: 41549272--41549340 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
41549262 ACTGCGAGTT
41549272 GAAGAATTTCATTCTCAAGTAGTAACAATTCGA
1 GAAGAATTTCATTCTCAAGTAGTAACAATTCGA
41549305 GAAGAATTTCATTCTCAAGTAGTAACAATTCGA
1 GAAGAATTTCATTCTCAAGTAGTAACAATTCGA
41549338 GAA
1 GAA
41549341 ATTTCCCCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (33 bp):
GAAGAATTTCATTCTCAAGTAGTAACAATTCGA
Found at i:41555994 original size:175 final size:173
Alignment explanation
Indices: 41555681--41556002 Score: 493
Period size: 175 Copynumber: 1.8 Consensus size: 173
41555671 ACTATTCATA
* *
41555681 GACTAAACTGAATAAATCATGGATTTTGGGCAAAATCGTAAAGTAAGGGTCACATAGTGGTGTGG
1 GACTAAACTAAATAAATCATGGATTTTGGGCAAAATCGTAAAGTAAGGGTCACATAATGGTGTGG
* ** * *
41555746 CCAGGCCATGTGAAAGGCTATAGGCCATGTGGAAGGGTTACACAACTGTGTGGCAAGGTCGTGTA
66 CCAAGCCATGTGAAAGGCTATAGGCCATGTGGAAGGGTTACACAACCATGTGGCAAGGCCATGTA
41555811 ACAGACTGTGGTCATGTCTAATACAATTTGAGGATTATTTAGG
131 ACAGACTGTGGTCATGTCTAATACAATTTGAGGATTATTTAGG
*
41555854 GACTAAACTAAATAAATCATGGATTTTTGGGCAAAATCGTAAAGTAGGGGTCACATAATGGTGTG
1 GACTAAACTAAATAAATCATGGA-TTTTGGGCAAAATCGTAAAGTAAGGGTCACATAATGGTGTG
* ** *
41555919 GCCAAAGCCATGTGAGAGGCTATAGGCTGTGTGGAAGGGTTACACAGCCATGTGGCCAA-GCCAT
65 GCC-AAGCCATGTGAAAGGCTATAGGCCATGTGGAAGGGTTACACAACCATGTGG-CAAGGCCAT
*
41555983 GTAATAGACTGTGGTCATGT
128 GTAACAGACTGTGGTCATGT
41556003 GACAATTGCA
Statistics
Matches: 133, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
173 22 0.17
174 42 0.32
175 66 0.50
176 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.26
Consensus pattern (173 bp):
GACTAAACTAAATAAATCATGGATTTTGGGCAAAATCGTAAAGTAAGGGTCACATAATGGTGTGG
CCAAGCCATGTGAAAGGCTATAGGCCATGTGGAAGGGTTACACAACCATGTGGCAAGGCCATGTA
ACAGACTGTGGTCATGTCTAATACAATTTGAGGATTATTTAGG
Found at i:41558731 original size:23 final size:22
Alignment explanation
Indices: 41558690--41558747 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
41558680 AAAAGCTATC
* *
41558690 TACAAATCAAATC-CCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
41558711 TACAGAATCATATCTTCTAAGCT
1 TACA-AATCATATCTTCTAAGAT
*
41558734 TACATATCATATCT
1 TACAAATCATATCT
41558748 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 4 0.13
22 17 0.55
23 10 0.32
ACGTcount: A:0.40, C:0.22, G:0.05, T:0.33
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:41562074 original size:17 final size:19
Alignment explanation
Indices: 41562035--41562074 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41562025 AATACATACA
41562035 TTAATCCAATCAAGAAAAC
1 TTAATCCAATCAAGAAAAC
*
41562054 TTAATCCAA-CAA-AAAAG
1 TTAATCCAATCAAGAAAAC
41562071 TTAA
1 TTAA
41562075 ATTCATCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 3 0.15
19 9 0.45
ACGTcount: A:0.55, C:0.17, G:0.05, T:0.23
Consensus pattern (19 bp):
TTAATCCAATCAAGAAAAC
Found at i:41564183 original size:2 final size:2
Alignment explanation
Indices: 41564176--41564206 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41564166 CTAAAAATAG
41564176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41564207 AATGAGAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41564909 original size:54 final size:54
Alignment explanation
Indices: 41564850--41564952 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
41564840 TTGCTGTTAT
* * *
41564850 CATTTTATTGTAATTAC-CTGTGCAATTTAATTGATGCACCATAATTACTATTAC
1 CATTTTATTGTAATTACTC-ATGCAATTTAATCGATGCACCACAATTACTATTAC
*
41564904 CATTTTATTGTAATTACTCATGCAATTTAATCGATGCATCACAATTACT
1 CATTTTATTGTAATTACTCATGCAATTTAATCGATGCACCACAATTACT
41564953 TTTAATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 43 0.98
55 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.42
Consensus pattern (54 bp):
CATTTTATTGTAATTACTCATGCAATTTAATCGATGCACCACAATTACTATTAC
Found at i:41565021 original size:135 final size:135
Alignment explanation
Indices: 41564779--41565084 Score: 447
Period size: 135 Copynumber: 2.3 Consensus size: 135
41564769 ATTTTTGTGA
* * *
41564779 TAATTAATCATGCAATTTAATTGATGCACCACAATTGTTGTTAATTTTAAAAAACGATCAATTGC
1 TAATTACTCATGCAATTTAATTGATGCACCACAATTCTTGTTAATTTTAAAAAAAGATCAATTGC
* ** *
41564844 TGTTATCATTTTATTGTAATTACCTGTGCAATTTAATTGATGCACCATAATTACTATTACCATTT
66 TGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATTACTATTACCATTT
41564909 TATTG
131 TATTG
* * *
41564914 TAATTACTCATGCAATTTAATCGATGCATCACAATTACTT-TTAATTTTAAAAACAAG-TCTATT
1 TAATTACTCATGCAATTTAATTGATGCACCACAATT-CTTGTTAATTTTAAAAA-AAGATCAATT
* * *
41564977 -CTTGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATTATTGTTATCA
64 GC-TGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATTACTATTACCA
41565041 TTTTATTG
128 TTTTATTG
41565049 TAATTACTCATGCAATTTAATTGATGCACCACAATT
1 TAATTACTCATGCAATTTAATTGATGCACCACAATT
41565085 TAATTAAAAG
Statistics
Matches: 153, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
134 1 0.01
135 148 0.97
136 4 0.03
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (135 bp):
TAATTACTCATGCAATTTAATTGATGCACCACAATTCTTGTTAATTTTAAAAAAAGATCAATTGC
TGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATTACTATTACCATTT
TATTG
Found at i:41565038 original size:54 final size:54
Alignment explanation
Indices: 41564978--41565084 Score: 196
Period size: 54 Copynumber: 2.0 Consensus size: 54
41564968 AAGTCTATTC
41564978 TTGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATTA
1 TTGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATTA
* *
41565032 TTGTTATCATTTTATTGTAATTACTCATGCAATTTAATTGATGCACCACAATT
1 TTGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATT
41565085 TAATTAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (54 bp):
TTGTTATCACTTTATTGTAATTACCCATGCAATTTAATTGATGCACCACAATTA
Found at i:41567938 original size:5 final size:5
Alignment explanation
Indices: 41567923--41567956 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
41567913 TTTTAAAACA
41567923 AAAAT ATAAAT AAAAT AAAAT AAAAT -AAAT AAAA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAA
41567957 AATAAGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.67
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:41576001 original size:86 final size:87
Alignment explanation
Indices: 41575784--41576041 Score: 349
Period size: 86 Copynumber: 3.0 Consensus size: 87
41575774 GCTTATTTGC
* * *
41575784 AGTTATTGCCACTTGTTGTGGGTGCACAACATATTTGTAGATTAAACAAACTGCCACTTGGTTCA
1 AGTTACTGCCACTTGTTGTGAGTGCACAACATATTTGTAGATTAAACAAACTGCTACTTGGTTCA
* * *
41575849 TGATCGAACAACATATATTT-TA
66 TAATCGAACCACAT-TGTTTGTA
* * * * * *
41575871 AGTTACTACCACTTGTTGTGAGTGCACAAAATATTTGCAGATTAAATAAACTGTTGCTTGGTTCA
1 AGTTACTGCCACTTGTTGTGAGTGCACAACATATTTGTAGATTAAACAAACTGCTACTTGGTTCA
*
41575936 TAATCTAACCACATTGTTTGTA
66 TAATCGAACCACATTGTTTGTA
* * *
41575958 A-TTACTGCCACTTGTTGTGAGTGCATAACATATTTGTAAATTAAACAAACTGCTACTTGGTTAA
1 AGTTACTGCCACTTGTTGTGAGTGCACAACATATTTGTAGATTAAACAAACTGCTACTTGGTTCA
41576022 TAATCGAACCACATTGTTTG
66 TAATCGAACCACATTGTTTG
41576042 CATATTAAAC
Statistics
Matches: 147, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
86 77 0.52
87 70 0.48
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (87 bp):
AGTTACTGCCACTTGTTGTGAGTGCACAACATATTTGTAGATTAAACAAACTGCTACTTGGTTCA
TAATCGAACCACATTGTTTGTA
Found at i:41576557 original size:19 final size:20
Alignment explanation
Indices: 41576530--41576567 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
41576520 AGGTACTAAA
41576530 TTGGACAAAA-TATAAAATT
1 TTGGACAAAATTATAAAATT
*
41576549 TTGGGCAAAATTATAAAAT
1 TTGGACAAAATTATAAAAT
41576568 CTAAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.05, G:0.13, T:0.32
Consensus pattern (20 bp):
TTGGACAAAATTATAAAATT
Found at i:41576622 original size:27 final size:28
Alignment explanation
Indices: 41576551--41576622 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
41576541 ATAAAATTTT
*
41576551 GGGCAAAATTATAAAATCTAAAAAATAG
1 GGGCAAAATTGTAAAATCTAAAAAATAG
* * * *
41576579 AGGCAAATTTGTCAAATC-CAAAAATAG
1 GGGCAAAATTGTAAAATCTAAAAAATAG
*
41576606 GGGCAAAACTGTAAAAT
1 GGGCAAAATTGTAAAAT
41576623 TTGGAAAACA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 21 0.60
28 14 0.40
ACGTcount: A:0.51, C:0.11, G:0.17, T:0.21
Consensus pattern (28 bp):
GGGCAAAATTGTAAAATCTAAAAAATAG
Found at i:41581535 original size:2 final size:2
Alignment explanation
Indices: 41581528--41581568 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
41581518 ATCTCATGGA
41581528 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
41581569 TATCATGGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:41583415 original size:13 final size:15
Alignment explanation
Indices: 41583386--41583418 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
41583376 TTGGGTACCA
41583386 AAATTGCAACACAAC
1 AAATTGCAACACAAC
41583401 AAATTGC-AC-CAAC
1 AAATTGCAACACAAC
41583414 AAATT
1 AAATT
41583419 TGTCTACCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 2 0.11
15 7 0.39
ACGTcount: A:0.52, C:0.24, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATTGCAACACAAC
Found at i:41583534 original size:11 final size:11
Alignment explanation
Indices: 41583518--41583556 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
41583508 TTTTTGGGAA
41583518 AAAAATAAAAT
1 AAAAATAAAAT
41583529 AAAAATAAAAT
1 AAAAATAAAAT
*
41583540 -AAACTCAAAAT
1 AAAAAT-AAAAT
41583551 AAAAAT
1 AAAAAT
41583557 CCCACTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.17
11 16 0.67
12 4 0.17
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:41583538 original size:16 final size:16
Alignment explanation
Indices: 41583519--41583554 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41583509 TTTTGGGAAA
41583519 AAAATAAAATAAAAAT
1 AAAATAAAATAAAAAT
* *
41583535 AAAATAAACTCAAAAT
1 AAAATAAAATAAAAAT
41583551 AAAA
1 AAAA
41583555 ATCCCACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAAAAT
Found at i:41585530 original size:23 final size:24
Alignment explanation
Indices: 41585487--41585547 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 24
41585477 TATTGATGAT
* **
41585487 ATAAATATAT-TTATTTTAAAT-A
1 ATAAATAAATATTATTAAAAATAA
41585509 ATAAATAAATATTATTAAAAATAA
1 ATAAATAAATATTATTAAAAATAA
*
41585533 ATAGATAAA-ATTATT
1 ATAAATAAATATTATT
41585548 TTCTTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 9 0.27
23 15 0.45
24 9 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (24 bp):
ATAAATAAATATTATTAAAAATAA
Found at i:41585531 original size:20 final size:20
Alignment explanation
Indices: 41585498--41585535 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41585488 TAAATATATT
41585498 TATTTTAAATAATAAATAAA
1 TATTTTAAATAATAAATAAA
41585518 TATTATTAAA-AATAAATA
1 TATT-TTAAATAATAAATA
41585536 GATAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TATTTTAAATAATAAATAAA
Found at i:41585545 original size:20 final size:21
Alignment explanation
Indices: 41585502--41585545 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
41585492 TATATTTATT
**
41585502 TTAAATAATAAATAAATATTA
1 TTAAATAATAAATAAATAAAA
*
41585523 TTAAA-AATAAATAGATAAAA
1 TTAAATAATAAATAAATAAAA
41585543 TTA
1 TTA
41585546 TTTTCTTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TTAAATAATAAATAAATAAAA
Found at i:41589017 original size:14 final size:14
Alignment explanation
Indices: 41588998--41589035 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
41588988 GTTTGGCAGT
41588998 AAAATGTTTTCCGG
1 AAAATGTTTTCCGG
* *
41589012 AAAATGATTTCTGG
1 AAAATGTTTTCCGG
41589026 AAAATGTTTT
1 AAAATGTTTT
41589036 ACTTTTCTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (14 bp):
AAAATGTTTTCCGG
Found at i:41589044 original size:20 final size:20
Alignment explanation
Indices: 41589019--41589058 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41589009 CGGAAAATGA
*
41589019 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
41589039 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
41589059 GGAAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:41589048 original size:34 final size:35
Alignment explanation
Indices: 41589004--41589070 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41588994 CAGTAAAATG
*
41589004 TTTTCCGGAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGGAAAATGATTTACTGGAAAATATTTTAC
*
41589038 TTTTCTGGAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGGAAAATGATTTACTGGAAAATATTTT
41589071 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.43
Consensus pattern (35 bp):
TTTTCCGGAAAATGATTTACTGGAAAATATTTTAC
Found at i:41589241 original size:73 final size:71
Alignment explanation
Indices: 41589144--41589287 Score: 245
Period size: 74 Copynumber: 2.0 Consensus size: 71
41589134 TTCCAAAAAA
*
41589144 GTTGTTTTTACATATATATATTAAT-AATTTTTATATTTTAAATTGTTTTTACATATATTGCAAT
1 GTTGTTTTTACATATATATATTAATAAATTTTTATATTTTAAATTATTTTTACATATATTGCAAT
41589208 GATTTT
66 GATTTT
41589214 GTTGTTTTTACATAATATATATATTAATAAATTTTTATATTTTAAATTATTTTTACATATATTGC
1 GTTGTTTTTAC---ATATATATATTAATAAATTTTTATATTTTAAATTATTTTTACATATATTGC
41589279 AATGATTTT
63 AATGATTTT
41589288 ATAATCAAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
70 11 0.16
73 14 0.20
74 44 0.64
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.56
Consensus pattern (71 bp):
GTTGTTTTTACATATATATATTAATAAATTTTTATATTTTAAATTATTTTTACATATATTGCAAT
GATTTT
Found at i:41589288 original size:38 final size:38
Alignment explanation
Indices: 41589172--41589290 Score: 102
Period size: 34 Copynumber: 3.2 Consensus size: 38
41589162 TATTAATAAT
*
41589172 TTTTATATTTTAAATTGTTTTTACATATATTGCAATGA
1 TTTTATATTTTAAATTATTTTTACATATATTGCAATGA
* * * * * * * * *
41589210 TTTTGTTGTTTTTACATAATATATATAT-TAAT-AAAT--
1 TTTT-AT-ATTTTAAATTATTTTTACATATATTGCAATGA
41589246 TTTTATATTTTAAATTATTTTTACATATATTGCAATGA
1 TTTTATATTTTAAATTATTTTTACATATATTGCAATGA
41589284 TTTTATA
1 TTTTATA
41589291 ATCAAATTAA
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
34 14 0.25
35 4 0.07
36 7 0.12
38 14 0.25
39 4 0.07
40 13 0.23
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (38 bp):
TTTTATATTTTAAATTATTTTTACATATATTGCAATGA
Found at i:41589408 original size:34 final size:32
Alignment explanation
Indices: 41589360--41589422 Score: 108
Period size: 34 Copynumber: 1.9 Consensus size: 32
41589350 TGAAAACAAC
41589360 TAATATCAATATTTGTAATTGTGTTAAAATAA
1 TAATATCAATATTTGTAATTGTGTTAAAATAA
41589392 TAATACTCAATTATTTGTAATTGTGTTAAAA
1 TAATA-TCAA-TATTTGTAATTGTGTTAAAA
41589423 ACAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 5 0.17
33 4 0.14
34 20 0.69
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (32 bp):
TAATATCAATATTTGTAATTGTGTTAAAATAA
Found at i:41591896 original size:19 final size:19
Alignment explanation
Indices: 41591872--41591908 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41591862 CAGATCAAGA
*
41591872 GAGAACGAAAGGGAGAACG
1 GAGAACGAAAAGGAGAACG
41591891 GAGAACGAAAAGGAGAAC
1 GAGAACGAAAAGGAGAAC
41591909 AAAACCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.38, T:0.00
Consensus pattern (19 bp):
GAGAACGAAAAGGAGAACG
Found at i:41600500 original size:38 final size:38
Alignment explanation
Indices: 41600449--41600536 Score: 167
Period size: 38 Copynumber: 2.3 Consensus size: 38
41600439 CGGTACTATT
41600449 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
1 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
*
41600487 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCTCACA
1 TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
41600525 TGGAGTGTAGGG
1 TGGAGTGTAGGG
41600537 TTGGATGGAG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.20, C:0.10, G:0.40, T:0.30
Consensus pattern (38 bp):
TGGAGTGTAGGGATGGGTGGGTTGATTATATCCCCACA
Found at i:41601763 original size:58 final size:59
Alignment explanation
Indices: 41601692--41601805 Score: 185
Period size: 58 Copynumber: 1.9 Consensus size: 59
41601682 TTTTAAATGA
*
41601692 GTTTTGTTTTAAAAATAAATAAAATCAAGTAATTAATATATGATGTTTTAT-CTTTTTG
1 GTTTTGTTTTAAAAATAAATAAAATAAAGTAATTAATATATGATGTTTTATGCTTTTTG
* * *
41601750 GTTTTGTTTTAAAAATAAATAAAATAAAGTATTTAATATATGTTTTTTTATGCTTT
1 GTTTTGTTTTAAAAATAAATAAAATAAAGTAATTAATATATGATGTTTTATGCTTT
41601806 CCTTTTTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
58 47 0.92
59 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.50
Consensus pattern (59 bp):
GTTTTGTTTTAAAAATAAATAAAATAAAGTAATTAATATATGATGTTTTATGCTTTTTG
Found at i:41605994 original size:2 final size:2
Alignment explanation
Indices: 41605987--41606015 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
41605977 ATTTTTATTT
41605987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41606016 CTTACATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41608214 original size:23 final size:24
Alignment explanation
Indices: 41608187--41608239 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
41608177 CTAGCATGTA
**
41608187 TATATATATACATTTTTA-ATTTT
1 TATATATATACATACTTATATTTT
* *
41608210 TATATATGTACGTACTTATATTTT
1 TATATATATACATACTTATATTTT
41608234 TATATA
1 TATATA
41608240 CTTTAATATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TATATATATACATACTTATATTTT
Found at i:41615348 original size:44 final size:44
Alignment explanation
Indices: 41615242--41615341 Score: 173
Period size: 44 Copynumber: 2.3 Consensus size: 44
41615232 AAATAAAAAA
*
41615242 CCTAGATCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
*
41615286 CTTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
1 CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
*
41615330 CCTATCTCCCTG
1 CCTAGCTCCCTG
41615342 GTCAGCAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 52 1.00
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (44 bp):
CCTAGCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
Found at i:41615504 original size:128 final size:129
Alignment explanation
Indices: 41615325--41615597 Score: 399
Period size: 128 Copynumber: 2.1 Consensus size: 129
41615315 TTGAAGATTG
*
41615325 CAAGTCCTATCTCCCTGGTCAGCAATGGAGTGGGTGCAAAATTACAAATCTTGTCTCCCTAAGCA
1 CAAGTCCTATCTCCCTGGTCAGCAATGGAATGGGTGCAAAATTACAAATCTTGTCTCCCTAAGCA
* * *
41615390 GTAGCGGAGCAGATCGAAGACGGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC-A
66 GTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGA
* * * * * * *
41615453 CAAGTCCTATATCCCTGGTCAGCAGTGGAATATGTTG-GAAATTACAGATCTTGTCTCCCTAGGC
1 CAAGTCCTATCTCCCTGGTCAGCAATGGAAT-GGGTGCAAAATTACAAATCTTGTCTCCCTAAGC
*
41615517 AGTAGTGGAGCAGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGA
65 AGTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGA
*
41615582 TAA-TCCTATCTCCCTG
1 CAAGTCCTATCTCCCTG
41615598 AAGTTGTAGT
Statistics
Matches: 129, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
128 123 0.95
129 6 0.05
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (129 bp):
CAAGTCCTATCTCCCTGGTCAGCAATGGAATGGGTGCAAAATTACAAATCTTGTCTCCCTAAGCA
GTAGCGGAGCAGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGA
Done.