Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold138
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: 1735418
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 2489 characters in sequence are not A, C, G, or T
File 10 of 11
Found at i:1381017 original size:85 final size:85
Alignment explanation
Indices: 1380868--1381525 Score: 493
Period size: 85 Copynumber: 7.7 Consensus size: 85
1380858 ATACCCTCAA
* * * * * * *
1380868 TCTGCTTGTCGGCTTTGACCTTGGGGACTATCCCATCTAAAGTCTACCTGTCGACTTTGACCCTA
1 TCTGCCTGTCGACTTTGACCTTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTA
1380933 GAGACTTTTCTATCCCTTAG
66 GAGACTTTTCTATCCCTTAG
* * * * * * * *
1380953 TTTACCTATCGACTTTGACCCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCAGC-TTCATCCCT
1 TCTGCCTGTCGACTTTGACCTTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGA-CCCT
* * *
1381017 AGAGACTTTCCTATACCTAAG
65 AGAGACTTTTCTATCCCTTAG
* * * ** * *
1381038 TCTGCCTGTC-AGCTTTGACCCTAGAGACT-TTTCTATTCTTTAGTCTGCCTGTTGACTTTGACC
1 TCTGCCTGTCGA-CTTTGACCTTGGAGACTGTCTC-A-TCTAAAGTCTGCCTGTCGGCTTTGACC
* **
1381101 CTGGAGAC-TGCCTCAT---TTAAAG
63 CTAGAGACTTTTCT-ATCCCTT--AG
* * * *
1381123 TCTGCCTGTCGGC-TTCATCCTTGGAGACT-TTTCTATCCCT-AAGTCTACCTGTCGGCTTTGAC
1 TCTGCCTGTCGACTTTGA-CCTTGGAGACTGTCTC-AT--CTAAAGTCTGCCTGTCGGCTTTGAC
*
1381185 CCTAAAGACTTTTCTATCCCTTAG
62 CCTAGAGACTTTTCTATCCCTTAG
* * * * * *
1381209 TATGTCTGTCGGCTTTGACCTTGGAGACTGTCTTATTTAAAGTCTGCCTGTCGGC-TTCATCCCT
1 TCTGCCTGTCGACTTTGACCTTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGA-CCCT
* *
1381273 GGAGACTTTTCTATCCCTAAG
65 AGAGACTTTTCTATCCCTTAG
* * * * * * *
1381294 TCTGCCTATCGGCTTTGTCCTTGGAGACTTTCT-ATCCCTAAA-TCTGTCTATCGACTTTGACCC
1 TCTGCCTGTCGACTTTGACCTTGGAGACTGTCTCAT--CTAAAGTCTGCCTGTCGGCTTTGACCC
*
1381357 TGGAGACTTTTCTAT-CCTTCAG
64 TAGAGACTTTTCTATCCCTT-AG
* * * * *
1381379 TCTGCCTGTC-AGCTTTGACCTTGGAGACTGCCTTATCTAAGGTCTGTCTGTTGGCTTTGACCCT
1 TCTGCCTGTCGA-CTTTGACCTTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCT
* * *
1381443 AGAAACTTTCCTATCCCTCAG
65 AGAGACTTTTCTATCCCTTAG
* * * * *
1381464 TCTGCCTATC-AGCTTTGACCCTGGAGACTGGCTCATCTAAAGTTTGCCTATCGGCTTTGACC
1 TCTGCCTGTCGA-CTTTGACCTTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACC
1381526 TGAGAGAATT
Statistics
Matches: 455, Mismatches: 90, Indels: 56
0.76 0.15 0.09
Matches are distributed among these distances:
83 1 0.00
84 23 0.05
85 353 0.78
86 68 0.15
87 8 0.02
88 2 0.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (85 bp):
TCTGCCTGTCGACTTTGACCTTGGAGACTGTCTCATCTAAAGTCTGCCTGTCGGCTTTGACCCTA
GAGACTTTTCTATCCCTTAG
Found at i:1381040 original size:43 final size:43
Alignment explanation
Indices: 1380992--1381492 Score: 398
Period size: 43 Copynumber: 11.7 Consensus size: 43
1380982 GCCTCATTTA
* * * * *
1380992 AAGTCTGCCTGTCAGC-TTCATCCCTAGAGACTTTCCTATACCT
1 AAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTCTATCCCT
* * * *
1381035 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTTCTATTCTT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCCT
* * * ** *
1381078 TAGTCTGCCTGTTGACTTTGACCCTGGAGAC-TGCCTCAT--TT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCT-ATCCCT
* *
1381119 AAAGTCTGCCTGTCGGC-TTCATCCTTGGAGACTTTTCTATCCCT
1 -AAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTCTATCCCT
* **
1381163 AAGTCTACCTGTCGGCTTTGACCCTAAAGACTTTTCTATCCCT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCCT
* * * * * *
1381206 TAGTATGTCTGTCGGCTTTGACCTTGGAGAC-TGTCTTAT--TT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TATCCCT
*
1381247 AAAGTCTGCCTGTCGGC-TTCATCCCTGGAGACTTTTCTATCCCT
1 -AAGTCTGCCTGTCGGCTTTGA-CCCTGGAGACTTTTCTATCCCT
* * *
1381291 AAGTCTGCCTATCGGCTTTGTCCTTGGAGAC-TTTCTATCCCT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCCT
* * * * *
1381333 AAATCTGTCTATCGACTTTGACCCTGGAGACTTTTCTATCCTT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCCT
* * * **
1381376 CAGTCTGCCTGTCAGCTTTGACCTTGGAGAC-TGCCTTAT--CT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTC-TATCCCT
* * * * *
1381417 AAGGTCTGTCTGTTGGCTTTGACCCTAGAAACTTTCCTATCCCT
1 AA-GTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCCT
* * *
1381461 CAGTCTGCCTATCAGCTTTGACCCTGGAGACT
1 AAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
1381493 GGCTCATCTA
Statistics
Matches: 362, Mismatches: 75, Indels: 42
0.76 0.16 0.09
Matches are distributed among these distances:
41 11 0.03
42 120 0.33
43 218 0.60
44 13 0.04
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (43 bp):
AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTTTTCTATCCCT
Found at i:1381138 original size:128 final size:128
Alignment explanation
Indices: 1380907--1381520 Score: 684
Period size: 128 Copynumber: 4.8 Consensus size: 128
1380897 ATCCCATCTA
* * * *
1380907 AAGTCTACCTGTCGACTTTGACCCTAGAGACTTTTCTATCCCTTAGTTTACCTATCGACTTTGAC
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTATCCCTTAGTCTGCCTATCGACTTTGAC
* *
1380972 CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCAGCTTCATCCCTAGAGACTTTCCTATACCT
66 CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTCATCCCTGGAGACTTTCCTATACCT
* * * * *
1381035 AAGTCTGCCTGTCAGCTTTGACCCTAGAGACTTTTCTATTCTTTAGTCTGCCTGTTGACTTTGAC
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTATCCCTTAGTCTGCCTATCGACTTTGAC
* * *
1381100 CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTCATCCTTGGAGACTTTTCTATCCCT
66 CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTCATCCCTGGAGACTTTCCTATACCT
* * * * * *
1381163 AAGTCTACCTGTCGGCTTTGACCCTAAAGACTTTTCTATCCCTTAGTATGTCTGTCGGCTTTGAC
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTATCCCTTAGTCTGCCTATCGACTTTGAC
* * * * *
1381228 CTTGGAGACTGTCTTATTTAAAGTCTGCCTGTCGGCTTCATCCCTGGAGACTTTTCTATCCCT
66 CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTCATCCCTGGAGACTTTCCTATACCT
* * * * * * *
1381291 AAGTCTGCCTATCGGCTTTGTCCTTGGAGAC-TTTCTATCCCTAAATCTGTCTATCGACTTTGAC
1 AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTATCCCTTAGTCTGCCTATCGACTTTGAC
** * * * * * *
1381355 CCTGGAGACT-TTTCTATCCTT-CAGTCTGCCTGTCAGCTTTGA-CCTTGGAGAC-TGCCT-TAT
66 CCTGGAGACTGCCTC-AT--TTAAAGTCTGCCTGTCGGC-TTCATCCCTGGAGACTTTCCTATAC
1381415 CT
127 CT
* * * * *
1381417 AAGGTCTGTCTGTTGGCTTTGACCCTAGAAACTTTCCTATCCCTCAGTCTGCCTATC-AGCTTTG
1 AA-GTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTATCCCTTAGTCTGCCTATCGA-CTTTG
* * * *
1381481 ACCCTGGAGACTGGCTCATCTAAAGTTTGCCTATCGGCTT
64 ACCCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTT
1381521 TGACCTGAGA
Statistics
Matches: 410, Mismatches: 67, Indels: 20
0.82 0.13 0.04
Matches are distributed among these distances:
126 10 0.02
127 77 0.19
128 316 0.77
129 7 0.02
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (128 bp):
AAGTCTGCCTGTCGGCTTTGACCCTAGAGACTTTTCTATCCCTTAGTCTGCCTATCGACTTTGAC
CCTGGAGACTGCCTCATTTAAAGTCTGCCTGTCGGCTTCATCCCTGGAGACTTTCCTATACCT
Found at i:1381521 original size:42 final size:43
Alignment explanation
Indices: 1380876--1381525 Score: 288
Period size: 43 Copynumber: 15.3 Consensus size: 43
1380866 AATCTGCTTG
* * * * * *
1380876 TCGGCTTTGACCTTGGGGACTATCCCAT-CTAAAGTCTACCTG
1 TCGGCTTTGACCCTGGAGACTGTCTCATCCTAAAGTCTGCCTA
* * * * * *
1380918 TCGACTTTGACCCTAGAGACT-TTTCTATCCCT-TAGTTTACCTA
1 TCGGCTTTGACCCTGGAGACTGTCTC-AT-CCTAAAGTCTGCCTA
* * * *
1380961 TCGACTTTGACCCTGGAGACTGCCTCAT-TTAAAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTGTCTCATCCTAAAGTCTGCCTA
* * * * *
1381003 TCAGC-TTCATCCCTAGAGACTTTC-CTATACCT-AAGTCTGCCTG
1 TCGGCTTTGA-CCCTGGAGACTGTCTC-AT-CCTAAAGTCTGCCTA
* * * * ** *
1381046 TCAGCTTTGACCCTAGAGACT-TTTCTATTCTTTAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTGTCTC-ATCCTAAAGTCTGCCTA
* * * * *
1381089 TTGACTTTGACCCTGGAGACTGCCTCAT-TTAAAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTGTCTCATCCTAAAGTCTGCCTA
* * * * *
1381131 TCGGC-TTCATCCTTGGAGACT-TTTCTATCCCT-AAGTCTACCTG
1 TCGGCTTTGA-CCCTGGAGACTGTCTC-AT-CCTAAAGTCTGCCTA
** * * * * *
1381174 TCGGCTTTGACCCTAAAGACT-TTTCTATCCCT-TAGTATGTCTG
1 TCGGCTTTGACCCTGGAGACTGTCTC-AT-CCTAAAGTCTGCCTA
* * * *
1381217 TCGGCTTTGACCTTGGAGACTGTCTTAT-TTAAAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTGTCTCATCCTAAAGTCTGCCTA
* *
1381259 TCGGC-TTCATCCCTGGAGACT-TTTCTATCCCT-AAGTCTGCCTA
1 TCGGCTTTGA-CCCTGGAGACTGTCTC-AT-CCTAAAGTCTGCCTA
* * * *
1381302 TCGGCTTTGTCCTTGGAGACTTTCT-ATCCCTAAA-TCTGTCTA
1 TCGGCTTTGACCCTGGAGACTGTCTCAT-CCTAAAGTCTGCCTA
* * ** *
1381344 TCGACTTTGACCCTGGAGACT-TTTCTATCCTTCAGTCTGCCTG
1 TCGGCTTTGACCCTGGAGACTGTCTC-ATCCTAAAGTCTGCCTA
* * * * * * *
1381387 TCAGCTTTGACCTTGGAGACTGCCTTAT-CTAAGGTCTGTCTG
1 TCGGCTTTGACCCTGGAGACTGTCTCATCCTAAAGTCTGCCTA
* * * * *
1381429 TTGGCTTTGACCCTAGAAACTTTC-CTATCCCT-CAGTCTGCCTA
1 TCGGCTTTGACCCTGGAGACTGTCTC-AT-CCTAAAGTCTGCCTA
* * *
1381472 TCAGCTTTGACCCTGGAGACTGGCTCAT-CTAAAGTTTGCCTA
1 TCGGCTTTGACCCTGGAGACTGTCTCATCCTAAAGTCTGCCTA
1381514 TCGGCTTTGACC
1 TCGGCTTTGACC
1381526 TGAGAGAATT
Statistics
Matches: 460, Mismatches: 112, Indels: 72
0.71 0.17 0.11
Matches are distributed among these distances:
41 22 0.05
42 180 0.39
43 233 0.51
44 25 0.05
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (43 bp):
TCGGCTTTGACCCTGGAGACTGTCTCATCCTAAAGTCTGCCTA
Found at i:1382014 original size:8 final size:8
Alignment explanation
Indices: 1382010--1382054 Score: 58
Period size: 7 Copynumber: 5.6 Consensus size: 8
1382000 AGTAAAAATC
1382010 AAAAATTA
1 AAAAATTA
1382018 AAAAATT-
1 AAAAATTA
1382025 AAAAATT-
1 AAAAATTA
1382032 AAAAATTAA
1 AAAAATT-A
1382041 TAAAAATTA
1 -AAAAATTA
1382050 AAAAA
1 AAAAA
1382055 ATCATGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 14 0.41
8 12 0.35
9 1 0.03
10 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATTA
Found at i:1382028 original size:22 final size:24
Alignment explanation
Indices: 1381986--1382053 Score: 86
Period size: 22 Copynumber: 2.9 Consensus size: 24
1381976 TATTCAATAT
* *
1381986 AAAATATAATAATAAGTAAAAATCA
1 AAAAT-TAATAAAAATTAAAAATCA
*
1382011 AAAATT-A-AAAAATTAAAAATTA
1 AAAATTAATAAAAATTAAAAATCA
1382033 AAAATTAATAAAAATTAAAAA
1 AAAATTAATAAAAATTAAAAA
1382054 AATCATGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 18 0.47
23 2 0.05
24 13 0.34
25 5 0.13
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (24 bp):
AAAATTAATAAAAATTAAAAATCA
Found at i:1382046 original size:17 final size:15
Alignment explanation
Indices: 1382003--1382056 Score: 72
Period size: 15 Copynumber: 3.4 Consensus size: 15
1381993 AATAATAAGT
1382003 AAAAATCAAAAATTAA
1 AAAAAT-AAAAATTAA
*
1382019 AAAATTAAAAATTAA
1 AAAAATAAAAATTAA
1382034 AAATTAATAAAAATTAA
1 AAA--AATAAAAATTAA
1382051 AAAAAT
1 AAAAAT
1382057 CATGAAATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
15 15 0.44
16 5 0.15
17 14 0.41
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAAAATTAA
Found at i:1382053 original size:7 final size:7
Alignment explanation
Indices: 1382002--1382040 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
1381992 TAATAATAAG
1382002 TAAAAAT
1 TAAAAAT
*
1382009 CAAAAAT
1 TAAAAAT
1382016 TAAAAAAT
1 T-AAAAAT
1382024 TAAAAAT
1 TAAAAAT
1382031 TAAAAAT
1 TAAAAAT
1382038 TAA
1 TAA
1382041 TAAAAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (7 bp):
TAAAAAT
Found at i:1382543 original size:55 final size:55
Alignment explanation
Indices: 1382458--1382712 Score: 321
Period size: 55 Copynumber: 4.6 Consensus size: 55
1382448 TCAAAGGAAA
* *
1382458 AATAGCACGAACAGCAACCTCCAGCAATCAAGAAACTCCAGCCAGCAGCTTCCAC
1 AATAGCACGAACAACAACCTCCAGCAATCAAAAAACTCCAGCCAGCAGCTTCCAC
* * ** * *
1382513 GATAGCACAAACTGCAACCTCCAGCAATCAAGAAATTCCAGCCAGCAGCTTCCAC
1 AATAGCACGAACAACAACCTCCAGCAATCAAAAAACTCCAGCCAGCAGCTTCCAC
* * ** * *
1382568 GATAGCATGAACAACAACCTCCAATAATAAAAAAACTCCAGCCAGCAACTTCCAC
1 AATAGCACGAACAACAACCTCCAGCAATCAAAAAACTCCAGCCAGCAGCTTCCAC
* * * *
1382623 AATAGCATGAACAACAACCTCCAGCAATCAAAAAAACTCCAACTAGTAGCTTCCAC
1 AATAGCACGAACAACAACCTCCAGCAATC-AAAAAACTCCAGCCAGCAGCTTCCAC
* *
1382679 AATAGCACGAACAACAACCTCTAGCAATCGAAAA
1 AATAGCACGAACAACAACCTCCAGCAATCAAAAA
1382713 CAACCAGCCA
Statistics
Matches: 174, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
55 125 0.72
56 49 0.28
ACGTcount: A:0.42, C:0.32, G:0.12, T:0.14
Consensus pattern (55 bp):
AATAGCACGAACAACAACCTCCAGCAATCAAAAAACTCCAGCCAGCAGCTTCCAC
Found at i:1383416 original size:65 final size:66
Alignment explanation
Indices: 1383341--1383469 Score: 215
Period size: 66 Copynumber: 2.0 Consensus size: 66
1383331 AAACAAAATT
* *
1383341 ATGGATGCGAATATGAAATTTGC-TGAGTTGTTAAACCCTATCATGTGTATGTGATGACCTTGTT
1 ATGGATGCGAATATGAAATTTGCATGAGTTGTTAAACCCCATCATGTGTACGTGATGACCTTGTT
1383405 C
66 C
* *
1383406 ATGGATGCGAATATGAAATTTGCATGAGTTGTTGAACCCCATCATGTGTACGTGGTGACCTTGT
1 ATGGATGCGAATATGAAATTTGCATGAGTTGTTAAACCCCATCATGTGTACGTGATGACCTTGT
1383470 CTTTCTTGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 23 0.39
66 36 0.61
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.35
Consensus pattern (66 bp):
ATGGATGCGAATATGAAATTTGCATGAGTTGTTAAACCCCATCATGTGTACGTGATGACCTTGTT
C
Found at i:1385742 original size:51 final size:51
Alignment explanation
Indices: 1385608--1385722 Score: 171
Period size: 51 Copynumber: 2.3 Consensus size: 51
1385598 AATTAACTAG
*
1385608 ATGTATCGATACATTAAAAAATATATCGATACATCTGGGTAAAAAAACAGA
1 ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAAAACAGA
* * *
1385659 ATGTATCGATATATTGAAAAATGTATCGATACATCCT-GGT-AAAAAACATA
1 ATGTATCGATACATTGAAAAATATATCGATACAT-CTGGGTAAAAAAACAGA
1385709 ATGTATCGATACAT
1 ATGTATCGATACAT
1385723 GTACAGTTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
50 22 0.38
51 34 0.59
52 2 0.03
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATATATCGATACATCTGGGTAAAAAAACAGA
Found at i:1388153 original size:79 final size:80
Alignment explanation
Indices: 1388020--1388299 Score: 316
Period size: 79 Copynumber: 3.5 Consensus size: 80
1388010 ACCATCGAAA
* ** * * ** * *
1388020 ATACTCTAACCCCATTTTTACTTTTAAAATATGAAAATTTTCATC-TTAGGGATACCCCAACCCA
1 ATACTCAAACCCCATTTTTACTTCCAAAATATCAAAATTTTCACCATCCGAGATACTCCAACCCA
*
1388084 GTTATTTCTGAGAGG
66 GTTATTTTTGAGAGG
* * * * *
1388099 ATACTCCAACCCCATTTTTATTTCCAAAATAT-AGATTTTTCACCATCCGAGATACTCCAACCCC
1 ATACTCAAACCCCATTTTTACTTCCAAAATATCAAAATTTTCACCATCCGAGATACTCCAACCCA
*
1388163 GTTATTTTTGAGGGG
66 GTTATTTTTGAGAGG
* * *
1388178 ATACTCAAACCTCGTTTTTACTTCCAAAATATCAAAATTTTCACCATCTGAGATACTCCAACCCT
1 ATACTCAAACCCCATTTTTACTTCCAAAATATCAAAATTTTCACCATCCGAGATACTCCAACCC-
*
1388243 A-TTATTTTTGAAAGG
65 AGTTATTTTTGAGAGG
* * *
1388258 ATACTCTAACCCTATTTTTACTTCC-AAATATTAAAATTTTCA
1 ATACTCAAACCCCATTTTTACTTCCAAAATATCAAAATTTTCA
1388300 TTTCGGGGAT
Statistics
Matches: 169, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
78 9 0.05
79 99 0.59
80 61 0.36
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.36
Consensus pattern (80 bp):
ATACTCAAACCCCATTTTTACTTCCAAAATATCAAAATTTTCACCATCCGAGATACTCCAACCCA
GTTATTTTTGAGAGG
Found at i:1388335 original size:158 final size:156
Alignment explanation
Indices: 1388020--1388475 Score: 415
Period size: 158 Copynumber: 2.9 Consensus size: 156
1388010 ACCATCGAAA
* * * * ** *
1388020 ATACTCTAACCCCATTTTTACTTTTAAAATATGAAAATTTTCATCTTAGGGATACCCCAACCCAG
1 ATACTCTAACCTC-TTTTTACTTTTAAAATATCAAAATTTTCACCATCTGGATACTCCAACCCA-
* * * * * *
1388085 TTATTTCTGAGAGGATACTCCAACCCCATTTTTATTTCCAAAATATAGATTTTTCACCATCCGAG
64 TTATTTTTGAAAGGATACTCCAACCCTATTTTTACTTCCAAAATATAAAATTTTCACCATCCGAG
* * ***
1388150 ATACTCCAACCCCGTTATTTTTGAGGGG
129 ATACTCAAACCCCATTATTTCCAAGGGG
* **
1388178 ATACTCAAACCTCGTTTTTACTTCCAAAATATCAAAATTTTCACCATCTGAGATACTCCAACCCT
1 ATACTCTAACCTC-TTTTTACTTTTAAAATATCAAAATTTTCACCATCTG-GATACTCCAACCC-
* ** *
1388243 ATTATTTTTGAAAGGATACTCTAACCCTATTTTTACTTCC-AAATATTAAAATTTTCA-TTTCGG
63 ATTATTTTTGAAAGGATACTCCAACCCTATTTTTACTTCCAAAATA-TAAAATTTTCACCATCCG
* *
1388306 GGATACTCAAATCCCATTATTTCCAAGGGG
127 AGATACTCAAACCCCATTATTTCCAAGGGG
* * * *
1388336 ATACTCTAACCTCATTTTATTTTTGAAATATTAAAATTTTCATCTCA-C-GGATACTCCAACCCC
1 ATACTCTAACCTCTTTTTACTTTTAAAATATCAAAATTTTCA-C-CATCTGGATACTCCAA-CCC
* * * * *
1388399 ATT-TTTTTCAAAGGGATACTCCAACCTTATTTTT--TTCAAAAATATCAATTTTTCACCAT-CG
63 ATTATTTTTGAAA-GGATACTCCAACCCTATTTTTACTTCCAAAATATAAAATTTTCACCATCCG
* *
1388460 GGAATACTCTAACCCC
127 AG-ATACTCAAACCCC
1388476 GTTTTTATTT
Statistics
Matches: 242, Mismatches: 46, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
154 15 0.06
155 25 0.10
156 32 0.13
157 27 0.11
158 85 0.35
159 57 0.24
160 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (156 bp):
ATACTCTAACCTCTTTTTACTTTTAAAATATCAAAATTTTCACCATCTGGATACTCCAACCCATT
ATTTTTGAAAGGATACTCCAACCCTATTTTTACTTCCAAAATATAAAATTTTCACCATCCGAGAT
ACTCAAACCCCATTATTTCCAAGGGG
Found at i:1388341 original size:78 final size:77
Alignment explanation
Indices: 1388020--1388432 Score: 280
Period size: 78 Copynumber: 5.2 Consensus size: 77
1388010 ACCATCGAAA
* ** * * * *
1388020 ATACTCTAACCCCATTTTTACTTTTAAAATATGAAAATTTTCATCTTAGGGATACCCCAACCCAG
1 ATACTCTAACCCTATTTTTAC-TTCCAAATATTAAAATTTTCATATCAGGGATACTCCAACCCA-
* *
1388085 TTA-TTTCTGAGAGG
64 TTATTTTC-AAGGGG
* * * * * * * *
1388099 ATACTCCAACCCCATTTTTATTTCCAAA-ATATAGATTTTTCACCATCCGAGATACTCCAACCCC
1 ATACTCTAACCCTATTTTTACTTCCAAATAT-TAAAATTTTCA-TATCAGGGATACTCCAA-CCC
* **
1388163 GTTATTTTTGAGGGG
63 ATTATTTTCAAGGGG
* * * * * *
1388178 ATACTC-AAACCTCGTTTTTACTTCCAAAATATCAAAATTTTCACCATCTGAGATACTCCAACCC
1 ATACTCTAACCCT-ATTTTTACTTCC-AAATATTAAAATTTTCA-TATCAGGGATACTCCAACCC
* *
1388242 TATTATTTTTGAA-AGG
63 -ATTA-TTTTCAAGGGG
* * *
1388258 ATACTCTAACCCTATTTTTACTTCCAAATATTAAAATTTTCATTTCGGGGATACTCAAATCCCAT
1 ATACTCTAACCCTATTTTTACTTCCAAATATTAAAATTTTCATATCAGGGATACTCCAA-CCCAT
*
1388323 TATTTCCAAGGGG
65 TATTTTCAAGGGG
* ** * *
1388336 ATACTCTAA-CCTCA-TTTTATTTTTGAAATATTAAAATTTTCATCTCACGGATACTCCAACCCC
1 ATACTCTAACCCT-ATTTTTA-CTTCCAAATATTAAAATTTTCATATCAGGGATACTCCAA-CCC
* *
1388399 ATTTTTTTCAAAGGG
63 ATTATTTTCAAGGGG
* *
1388414 ATACTCCAACCTTATTTTT
1 ATACTCTAACCCTATTTTT
1388433 TTCAAAAATA
Statistics
Matches: 266, Mismatches: 52, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
77 15 0.06
78 101 0.38
79 82 0.31
80 56 0.21
81 12 0.05
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (77 bp):
ATACTCTAACCCTATTTTTACTTCCAAATATTAAAATTTTCATATCAGGGATACTCCAACCCATT
ATTTTCAAGGGG
Found at i:1388415 original size:28 final size:28
Alignment explanation
Indices: 1388384--1388438 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
1388374 TTCATCTCAC
1388384 GGATACTCCAACCCCATTTTTTTCAAAG
1 GGATACTCCAACCCCATTTTTTTCAAAG
**
1388412 GGATACTCCAACCTTATTTTTTTCAAA
1 GGATACTCCAACCCCATTTTTTTCAAA
1388439 AATATCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (28 bp):
GGATACTCCAACCCCATTTTTTTCAAAG
Found at i:1388482 original size:128 final size:129
Alignment explanation
Indices: 1388336--1388604 Score: 350
Period size: 128 Copynumber: 2.1 Consensus size: 129
1388326 TTCCAAGGGG
*
1388336 ATACTCTAACCTCATTTTATTTTT-GAAATATTAAAATTTTCATCTCACGGATACTCCAACCCCA
1 ATACTCTAACCCCATTTTATTTTTAG-AATATTAAAATTTTCATCTCACGGATACTCCAACCCCA
*
1388400 TT-TTTTTCAAAGGGATACTCCAA-CCT-TATTTT-TTTCAAAAATATCAATTTTTCACCATCGG
65 TTATTTCT-AAAGGGATACTCCAATCCTAT-TTTTATTTCAAAAATATCAATTTTTCACCATCGG
1388461 GA
128 GA
* * * **
1388463 ATACTCTAACCCCGTTTTTATTTTTAGAATATTAAAGTTTTCATTTCGGGGATACTCCAACCCCA
1 ATACTCTAACCCC-ATTTTATTTTTAGAATATTAAAATTTTCATCTCACGGATACTCCAACCCCA
* * * * *
1388528 TTATTTCTGAGGGGATACTCCAATCCTATTTTTATTTCCAAACTATCAATTTTTCACCATCGGGG
65 TTATTTCTAAAGGGATACTCCAATCCTATTTTTATTTCAAAAATATCAATTTTTCACCATCGGGA
*
1388593 ATACTCCAACCC
1 ATACTCTAACCC
1388605 TATTATTTCT
Statistics
Matches: 123, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
127 12 0.10
128 59 0.48
129 12 0.10
130 40 0.33
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.38
Consensus pattern (129 bp):
ATACTCTAACCCCATTTTATTTTTAGAATATTAAAATTTTCATCTCACGGATACTCCAACCCCAT
TATTTCTAAAGGGATACTCCAATCCTATTTTTATTTCAAAAATATCAATTTTTCACCATCGGGA
Found at i:1388638 original size:79 final size:79
Alignment explanation
Indices: 1388508--1388682 Score: 219
Period size: 79 Copynumber: 2.2 Consensus size: 79
1388498 AGTTTTCATT
* * * *
1388508 TCGGGGATACTCCAACCCCATTATTTCTGAGGGGATACTCCAATCCTATTTTTATTTCCAAACTA
1 TCGGGGATACTCCAACCCCATTATTTCTAAGGGGATACTCCAATCCTATTTTCACTACCAAACTA
1388573 TCAA-TTTTTCACC
66 TCAATTTTTTCACC
* * *
1388586 ATCGGGGATACTCCAACCCTATTATTTCTAAGGGGATACTCTAA-CCTCATTTTCACTACCAAAG
1 -TCGGGGATACTCCAACCCCATTATTTCTAAGGGGATACTCCAATCCT-ATTTTCACTACCAAAC
*
1388650 TATTAATTTTTTTCACC
64 TATCAA-TTTTTTCACC
* *
1388667 TCAGCGATACTCCAAC
1 TCGGGGATACTCCAAC
1388683 TTCGATTTTC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
78 3 0.04
79 57 0.69
80 14 0.17
81 9 0.11
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.34
Consensus pattern (79 bp):
TCGGGGATACTCCAACCCCATTATTTCTAAGGGGATACTCCAATCCTATTTTCACTACCAAACTA
TCAATTTTTTCACC
Found at i:1392995 original size:13 final size:13
Alignment explanation
Indices: 1392977--1393002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1392967 TACACCAAGT
1392977 ATGTATCGATACA
1 ATGTATCGATACA
1392990 ATGTATCGATACA
1 ATGTATCGATACA
1393003 CCAAAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1393021 original size:34 final size:32
Alignment explanation
Indices: 1392959--1393023 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1392949 TAGCCAAACT
**
1392959 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAAATGTATCGATACAA
1392991 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACC-AAAAA-TGTATCGATACA
1393024 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 14 0.48
33 3 0.10
34 12 0.41
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAAAATGTATCGATACAA
Found at i:1397092 original size:16 final size:16
Alignment explanation
Indices: 1397056--1397092 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
1397046 GATAAAAATG
*
1397056 TCCAAATTGAAGAAGC
1 TCCAAAATGAAGAAGC
1397072 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
1397087 TCCAAA
1 TCCAAA
1397093 CGAAATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:1399091 original size:13 final size:13
Alignment explanation
Indices: 1399073--1399108 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1399063 TTTTTCTTTG
*
1399073 TATCGATACATTA
1 TATCGATACACTA
*
1399086 TATCGATACACTG
1 TATCGATACACTA
1399099 TATCGATACA
1 TATCGATACA
1399109 GAGGGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.33
Consensus pattern (13 bp):
TATCGATACACTA
Found at i:1399272 original size:20 final size:20
Alignment explanation
Indices: 1399229--1399274 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1399219 AAATCTTTTG
1399229 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1399250 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1399270 CAAAA
1 CAAAA
1399275 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1399572 original size:20 final size:20
Alignment explanation
Indices: 1399549--1399603 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1399539 GGTAGCACCA
1399549 CCAGGTCGCGACCGGCACTC
1 CCAGGTCGCGACCGGCACTC
1399569 CCAGGTCGCGACCGGCACTC
1 CCAGGTCGCGACCGGCACTC
*
1399589 CCAGGTCGCAACCGG
1 CCAGGTCGCGACCGG
1399604 GCAGTCCCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.16, C:0.44, G:0.31, T:0.09
Consensus pattern (20 bp):
CCAGGTCGCGACCGGCACTC
Found at i:1401628 original size:13 final size:13
Alignment explanation
Indices: 1401610--1401635 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1401600 CAATTTTTTG
1401610 TGTATCGATACAT
1 TGTATCGATACAT
1401623 TGTATCGATACAT
1 TGTATCGATACAT
1401636 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1404187 original size:13 final size:13
Alignment explanation
Indices: 1404169--1404207 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1404159 ATAATCACCC
1404169 TGTATCGATACAA
1 TGTATCGATACAA
1404182 TGTATCGATACAA
1 TGTATCGATACAA
1404195 TGTATCGATACAA
1 TGTATCGATACAA
1404208 AGAAAAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1406307 original size:15 final size:15
Alignment explanation
Indices: 1406287--1406316 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1406277 ATTTCGTTTG
*
1406287 GAGCTTCTTCATTTT
1 GAGCTTCGTCATTTT
1406302 GAGCTTCGTCATTTT
1 GAGCTTCGTCATTTT
1406317 CGACATTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.20, G:0.17, T:0.50
Consensus pattern (15 bp):
GAGCTTCGTCATTTT
Found at i:1408150 original size:21 final size:21
Alignment explanation
Indices: 1408121--1408165 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1408111 AAGTTTTCAT
*
1408121 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1408141 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1408163 TTT
1 TTT
1408166 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1410391 original size:13 final size:13
Alignment explanation
Indices: 1410373--1410398 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1410363 CAATTTTTTG
1410373 TGTATCGATACAT
1 TGTATCGATACAT
1410386 TGTATCGATACAT
1 TGTATCGATACAT
1410399 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1411001 original size:49 final size:49
Alignment explanation
Indices: 1410924--1411025 Score: 186
Period size: 49 Copynumber: 2.1 Consensus size: 49
1410914 AGAATGCGTG
*
1410924 AATTTGCTAAAAATACCTTATTAAGGGGGAGAATGTACGAATCTGTTAA
1 AATTCGCTAAAAATACCTTATTAAGGGGGAGAATGTACGAATCTGTTAA
*
1410973 AATTCGCTAAAATTACCTTATTAAGGGGGAGAATGTACGAATCTGTTAA
1 AATTCGCTAAAAATACCTTATTAAGGGGGAGAATGTACGAATCTGTTAA
1411022 AATT
1 AATT
1411026 ATTTTGATTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (49 bp):
AATTCGCTAAAAATACCTTATTAAGGGGGAGAATGTACGAATCTGTTAA
Found at i:1411702 original size:13 final size:13
Alignment explanation
Indices: 1411684--1411710 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1411674 ATACACCAAG
1411684 AATGTATCGATAC
1 AATGTATCGATAC
1411697 AATGTATCGATAC
1 AATGTATCGATAC
1411710 A
1 A
1411711 CCAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1411786 original size:20 final size:21
Alignment explanation
Indices: 1411756--1411794 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1411746 CTATATTTTC
1411756 AAATATGTATCGATACATTAA
1 AAATATGTATCGATACATTAA
1411777 AAAT-TGTATCGATACATT
1 AAATATGTATCGATACATT
1411795 TACATGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAATATGTATCGATACATTAA
Found at i:1418335 original size:21 final size:21
Alignment explanation
Indices: 1418311--1418357 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1418301 TTTGAGGCTG
1418311 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
*
1418331 AATTTGAAGTGAAAAACAAGT
1 ATTTTGAAGTGAAAAACAAGT
1418352 ATTTTG
1 ATTTTG
1418358 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 5 0.22
21 10 0.43
22 8 0.35
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1424634 original size:21 final size:20
Alignment explanation
Indices: 1424609--1424661 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
1424599 TACAAGCCTA
**
1424609 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA-TACTTGG
1424630 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
1424649 TGTATCGATACAA
1 TGTATCGATACAA
1424662 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:1424667 original size:19 final size:18
Alignment explanation
Indices: 1424609--1424667 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 18
1424599 TACAAGCCTA
1424609 TGTATCGATACAATTTTTTGG
1 TGTATCGATACAA---TTTGG
*
1424630 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1424649 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1424668 CTACTGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 1 0.03
19 20 0.59
21 12 0.35
22 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1428399 original size:169 final size:170
Alignment explanation
Indices: 1428119--1428451 Score: 605
Period size: 169 Copynumber: 2.0 Consensus size: 170
1428109 TCGGTCACTT
*
1428119 CGTAGTGACCATTGAAGATCAATTAGATAGGCGATCCATCTATTGATCTTCCCCTTTTAATCAAC
1 CGTAGTGACCATTGAAGATCAATTAGATAGGCGATCCATCTACTGATCTTCCCCTTTTAATCAAC
* *
1428184 ATACTTTTCGTCATGCCATAGAAATCTCCAATAGCGAGGGATATTAAGTCGAGCGCTCCTCATTT
66 ATACTTTTCGTCATGCCACAGAAATCTCCAATAGCGAGGGATATTAAGTCGAGCGCGCCTCATTT
1428249 GCCCTATCGCCGGGGTCGAGCGCACGTTGCGACAGTTTGG
131 GCCCTATCGCCGGGGTCGAGCGCACGTTGCGACAGTTTGG
* *
1428289 CGTAGTGACCATTGAAGATCAATTAGATGGGCGATTCATCTACTGATCTTCCCC-TTTAATCAAC
1 CGTAGTGACCATTGAAGATCAATTAGATAGGCGATCCATCTACTGATCTTCCCCTTTTAATCAAC
1428353 ATACTTTTCGTCATGCCACAGAAATCTCCAATAGCGAGGGATATTAAGTCGAGCGCGCCTCATTT
66 ATACTTTTCGTCATGCCACAGAAATCTCCAATAGCGAGGGATATTAAGTCGAGCGCGCCTCATTT
*
1428418 GCCCTATCGCCGGGGTCGAGCGCACGTTGTGACA
131 GCCCTATCGCCGGGGTCGAGCGCACGTTGCGACA
1428452 TTAACGAACT
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
169 106 0.68
170 51 0.32
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (170 bp):
CGTAGTGACCATTGAAGATCAATTAGATAGGCGATCCATCTACTGATCTTCCCCTTTTAATCAAC
ATACTTTTCGTCATGCCACAGAAATCTCCAATAGCGAGGGATATTAAGTCGAGCGCGCCTCATTT
GCCCTATCGCCGGGGTCGAGCGCACGTTGCGACAGTTTGG
Found at i:1440309 original size:13 final size:13
Alignment explanation
Indices: 1440291--1440318 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1440281 ATACAAAGAT
1440291 CAATGTATCGATA
1 CAATGTATCGATA
1440304 CAATGTATCGATA
1 CAATGTATCGATA
1440317 CA
1 CA
1440319 TTGAGTAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1440315 original size:33 final size:33
Alignment explanation
Indices: 1440273--1440338 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1440263 AAATTCCCAG
1440273 ATGTATCGATACAAAGA-TCAATGTATCGATACA
1 ATGTATCGATACAAAGAGT-AATGTATCGATACA
**
1440306 ATGTATCGATACATTGAGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
1440339 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:1440378 original size:13 final size:13
Alignment explanation
Indices: 1440356--1440413 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1440346 GGCAGTAGCT
*
1440356 TTGTAGCGATACA
1 TTGTATCGATACA
1440369 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
1440385 CTTATGTATCGATACA
1 --T-TGTATCGATACA
1440401 TTGTATCGATACA
1 TTGTATCGATACA
1440414 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1440394 original size:19 final size:19
Alignment explanation
Indices: 1440370--1440432 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
1440360 AGCGATACAT
1440370 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1440389 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1440402 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1440421 TGTATCGATACA
1 TGTATCGATACA
1440433 GTTACTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1440403 original size:32 final size:32
Alignment explanation
Indices: 1440357--1440432 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
1440347 GCAGTAGCTT
*
1440357 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1440389 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
1440421 TGTATCGATACA
1 TGTATCGATACA
1440433 GTTACTGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:1443002 original size:22 final size:22
Alignment explanation
Indices: 1442975--1443016 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1442965 TATTGTTTAA
*
1442975 AATA-TTATAATATTTTTATATT
1 AATATTTAT-ATATTGTTATATT
1442997 AATATTTATATATTGTTATA
1 AATATTTATATATTGTTATA
1443017 ATCAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AATATTTATATATTGTTATATT
Found at i:1443025 original size:22 final size:22
Alignment explanation
Indices: 1442974--1443026 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 22
1442964 TTATTGTTTA
* *
1442974 AAATATTATAATATTTTTATATT
1 AAAT-TTATAATATTGTTATATC
1442997 AATATTTAT-ATATTGTTATAATC
1 AA-ATTTATAATATTGTTAT-ATC
1443020 AAATTTA
1 AAATTTA
1443027 AAAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 14 0.54
23 10 0.38
24 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
AAATTTATAATATTGTTATATC
Found at i:1444100 original size:12 final size:12
Alignment explanation
Indices: 1444083--1444107 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1444073 GACTCTGTGC
1444083 TGCTGGCGTTGG
1 TGCTGGCGTTGG
1444095 TGCTGGCGTTGG
1 TGCTGGCGTTGG
1444107 T
1 T
1444108 CATAGCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (12 bp):
TGCTGGCGTTGG
Found at i:1444624 original size:26 final size:26
Alignment explanation
Indices: 1444594--1444650 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
1444584 AAGGAAAAAG
1444594 AAAATTAAGAAATTTAACCAAATGCT
1 AAAATTAAGAAATTTAACCAAATGCT
*
1444620 AAAATTAAGAAATTTAACCTAATGCT
1 AAAATTAAGAAATTTAACCAAATGCT
*
1444646 CAAAT
1 AAAAT
1444651 ATCTCTGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (26 bp):
AAAATTAAGAAATTTAACCAAATGCT
Found at i:1449064 original size:17 final size:17
Alignment explanation
Indices: 1449042--1449076 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1449032 ACAATTCTAG
1449042 TGCATTTTCATTTTTTT
1 TGCATTTTCATTTTTTT
1449059 TGCATTTTCATTTTTTT
1 TGCATTTTCATTTTTTT
1449076 T
1 T
1449077 TCTTAATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.71
Consensus pattern (17 bp):
TGCATTTTCATTTTTTT
Found at i:1449404 original size:15 final size:15
Alignment explanation
Indices: 1449384--1449416 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1449374 GATATGAATT
1449384 TTTAAATATT-TATTA
1 TTTAAAT-TTATATTA
1449399 TTTAAATTTATATTA
1 TTTAAATTTATATTA
1449414 TTT
1 TTT
1449417 TTATTGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 2 0.12
15 15 0.88
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTAAATTTATATTA
Found at i:1449460 original size:25 final size:24
Alignment explanation
Indices: 1449392--1449460 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 24
1449382 TTTTTAAATA
*
1449392 TTTATTATTTAAATTTATATTATT
1 TTTATTATTTAAATTGATATTATT
1449416 TTTATTGATATTAAATTTGA-A-TATT
1 TTTATT-AT-TTAAA-TTGATATTATT
1449441 TGAATTATTATTTAAATTGA
1 T---TTATTATTTAAATTGA
1449461 CATTTAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
24 6 0.16
25 11 0.29
26 11 0.29
27 5 0.13
28 5 0.13
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (24 bp):
TTTATTATTTAAATTGATATTATT
Found at i:1450209 original size:13 final size:13
Alignment explanation
Indices: 1450191--1450215 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1450181 ATATTGCTTG
1450191 GTATCGATACATT
1 GTATCGATACATT
1450204 GTATCGATACAT
1 GTATCGATACAT
1450216 GTTCATTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1450212 original size:33 final size:32
Alignment explanation
Indices: 1450170--1450231 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
1450160 CACACCCAGA
1450170 TGTATCGATACATATTGC-TTGGTATCGATACAT
1 TGTATCGATACATATT-CATT-GTATCGATACAT
*
1450203 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATATTCATTGTATCGATA
1450232 TACTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATATTCATTGTATCGATACAT
Found at i:1450383 original size:20 final size:20
Alignment explanation
Indices: 1450337--1450375 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1450327 TTTCAAATGC
*
1450337 ATTGTATCGATATATTATGA
1 ATTGTATCGATATATTAGGA
1450357 ATTGTATCGATATA-TAGGA
1 ATTGTATCGATATATTAGGA
1450376 GTGTGTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTGTATCGATATATTAGGA
Found at i:1454349 original size:3 final size:3
Alignment explanation
Indices: 1454341--1454371 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1454331 CATTAAAGAC
1454341 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1454372 GTGACTCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1462882 original size:11 final size:11
Alignment explanation
Indices: 1462867--1462902 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1462857 AAAATATGAT
1462867 TAAAAATAA-A
1 TAAAAATAATA
1462877 TAAAAATAATA
1 TAAAAATAATA
*
1462888 TAAATATAATA
1 TAAAAATAATA
1462899 TAAA
1 TAAA
1462903 TATTTGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:1462903 original size:11 final size:11
Alignment explanation
Indices: 1462858--1462905 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1462848 ATAATATTTA
*
1462858 AAATATGAT-T
1 AAATATAATAT
*
1462868 AAAAATAA-AT
1 AAATATAATAT
*
1462878 AAAAATAATAT
1 AAATATAATAT
1462889 AAATATAATAT
1 AAATATAATAT
1462900 AAATAT
1 AAATAT
1462906 TTGAATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 15 0.45
11 18 0.55
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1465232 original size:26 final size:26
Alignment explanation
Indices: 1465185--1465254 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
1465175 GAAATGGTCA
*
1465185 TCAAGAAAT-TATCGTCAAGAACTTCTG
1 TCAAGAAATGT-TTGTCAAGAACTT-TG
* *
1465212 TCGAG-AATGTTTGTCAGGAACTTTG
1 TCAAGAAATGTTTGTCAAGAACTTTG
*
1465237 TCAAGAAATTTTTGTCAA
1 TCAAGAAATGTTTGTCAA
1465255 TACGAAAGCC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
25 6 0.17
26 24 0.69
27 5 0.14
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (26 bp):
TCAAGAAATGTTTGTCAAGAACTTTG
Found at i:1465495 original size:89 final size:88
Alignment explanation
Indices: 1465259--1465910 Score: 648
Period size: 89 Copynumber: 7.4 Consensus size: 88
1465249 TGTCAATACG
* * * * * * **
1465259 AAAGCCCACAAGTCAGTGACATCCTTCTCATAGCCCACAAGTCAATGG-CA-TTTTTTCAAAGCC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTAACTCCTTTCAAAGCC
* * *
1465322 CATAAGTCAGTGGCATCC-TTTC
66 CACAAGTCGGTGGCACCCTTTTC
* * * * * *
1465344 AAAGCCCACAAGTTAGTGGCATCC-TTTCAAAGTCCACAAGTCAATGGCATAC-CCTTTTAAAGC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTA-ACTCCTTTCAAAGC
*
1465407 CCACAAGTCAGTGGCACCCTTTTC
65 CCACAAGTCGGTGGCACCCTTTTC
* * * * * *
1465431 AAAGCCAACAAGTCAGTGGTAACTCTTTTCAAAGTCCACACATGTCGGTGG-CAC-CCTTTCAAA
1 AAAGCCCACAAGTCAGTGG-CACCCTTTTCAAAG-CC-CACAAGTCAGTGGTAACTCCTTTCAAA
* * *
1465494 GCTCACAAGTCAGTGGTACCC-TTTC
63 GCCCACAAGTCGGTGGCACCCTTTTC
* *
1465519 AAAGCCCACAAGTCAGTAGCACCCTTTTCAAAGCCCACAAGTCAGTGGTAACTCTTTTCAAAGTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTAACTCCTTTCAAAG-C
*
1465584 CACACAAGTTGGTGGCACCC-TTTC
65 C-CACAAGTCGGTGGCACCCTTTTC
* * * *
1465608 AAAGCCCATAAGTCTGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGATAACTCTTTTCAAAGTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTAACTCCTTTCAAAG-C
* *
1465673 CACACAAGTTGGTAGCACCCTTTT-
65 C-CACAAGTCGGTGGCACCCTTTTC
* *
1465697 AAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTAACTCTTTTCAAAGTC
1 AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTAACTCCTTTCAAAG-C
* *
1465762 CACACAAGTCGGTGGCAACTTTGTTC
65 C-CACAAGTCGGTGGCACCCTT-TTC
* *
1465788 AAAGCCCACACAAGTCAATGGCACCC-TTTCAAAGCCCACAAGTCAGTGGCACAC-CCTTTCAAA
1 AAAG-CC-CACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTA-ACTCCTTTCAAA
*
1465851 GCTCACAAGTCGGTGGCA-CCTTTTC
63 GCCCACAAGTCGGTGGCACCCTTTTC
*
1465876 AAAGCCCATACAAGTC-GATGGCAACTCTTTTCAAA
1 AAAGCCC--ACAAGTCAG-TGGC-ACCCTTTTCAAA
1465911 TCACCACTTT
Statistics
Matches: 487, Mismatches: 57, Indels: 41
0.83 0.10 0.07
Matches are distributed among these distances:
84 20 0.04
85 33 0.07
86 31 0.06
87 44 0.09
88 42 0.09
89 221 0.45
90 28 0.06
91 15 0.03
92 35 0.07
93 18 0.04
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (88 bp):
AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGTAACTCCTTTCAAAGCC
CACAAGTCGGTGGCACCCTTTTC
Found at i:1465889 original size:30 final size:28
Alignment explanation
Indices: 1465259--1465910 Score: 576
Period size: 28 Copynumber: 22.1 Consensus size: 28
1465249 TGTCAATACG
* *
1465259 AAAGCCCACAAGTCAGTGACATCCTTCTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* * **
1465288 ATAGCCCACAAGTCAATGGCATTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
*
1465316 AAAGCCCATAAGTCAGTGGCATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
*
1465344 AAAGCCCACAAGTTAGTGGCATCC-TTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* *
1465372 AAAGTCCACAAGTCAATGGCATACCCTTTT-
1 AAAGCCCACAAGTCAGTGGC--A-CCTTTTC
1465402 AAAGCCCACAAGTCAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
* *
1465431 AAAGCCAACAAGTCAGTGGTAACTCTTTTC
1 AAAGCCCACAAGTCAGTGG-CAC-CTTTTC
* * *
1465461 AAAGTCCACACATGTCGGTGGCACCCTTTC
1 AAAG-CC-CACAAGTCAGTGGCACCTTTTC
* * *
1465491 AAAGCTCACAAGTCAGTGGTACCCTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
*
1465519 AAAGCCCACAAGTCAGTAGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
*
1465548 AAAGCCCACAAGTCAGTGGTAACTCTTTTC
1 AAAGCCCACAAGTCAGTGG-CAC-CTTTTC
** *
1465578 AAAGTCCACACAAGTTGGTGGCACCCTTTC
1 AAAG-CC-CACAAGTCAGTGGCACCTTTTC
* *
1465608 AAAGCCCATAAGTCTGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
**
1465637 AAAGCCCACAAGTCAGTGATAACTCTTTTC
1 AAAGCCCACAAGTCAGTG-GCAC-CTTTTC
** *
1465667 AAAGTCCACACAAGTTGGTAGCACCCTTTT-
1 AAAG-CC-CACAAGTCAGTGGCA-CCTTTTC
*
1465697 AAAGCCCACAAGTTAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CCTTTTC
*
1465726 AAAGCCCACAAGTCAGTGGTAACTCTTTTC
1 AAAGCCCACAAGTCAGTGG-CAC-CTTTTC
* *
1465756 AAAGTCCACACAAGTCGGTGGCAACTTTGTTC
1 AAAG-CC-CACAAGTCAGTGGC-ACCTT-TTC
* *
1465788 AAAGCCCACACAAGTCAATGGCACCCTTTC
1 AAAG-CC-CACAAGTCAGTGGCACCTTTTC
*
1465818 AAAGCCCACAAGTCAGTGGCACACCCTTTC
1 AAAGCCCACAAGTCAGTGG--CACCTTTTC
* *
1465848 AAAGCTCACAAGTCGGTGGCACCTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTC
1465876 AAAGCCCATACAAGTC-GATGGCAACTCTTTTC
1 AAAGCCC--ACAAGTCAG-TGGC-AC-CTTTTC
1465908 AAA
1 AAA
1465911 TCACCACTTT
Statistics
Matches: 519, Mismatches: 70, Indels: 65
0.79 0.11 0.10
Matches are distributed among these distances:
28 172 0.33
29 112 0.22
30 131 0.25
31 28 0.05
32 76 0.15
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTC
Found at i:1466047 original size:49 final size:49
Alignment explanation
Indices: 1465943--1466109 Score: 182
Period size: 49 Copynumber: 3.5 Consensus size: 49
1465933 GTCCGATATT
* * * *
1465943 GCTGGCATTGAATCAGCATATTGG--CACCTTT--ATTAGCCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTC
*
1465988 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAACGTC
1 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTC
* * * *
1466037 ACTAGCCTTGAATCAGCACGTTAGTCCACTTTTCCCTATA-CCCAATGTC
1 GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCT-TAGCCCAATGTC
* * *
1466086 GTTGGCCCTGAATTAGCACATTGG
1 GCTGGCCTTGAATCAGCACATTGG
1466110 CTCCCTTCTT
Statistics
Matches: 100, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
45 22 0.22
47 6 0.06
49 70 0.70
50 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.30
Consensus pattern (49 bp):
GCTGGCCTTGAATCAGCACATTGGTCCACTTTTCCCTTAGCCCAATGTC
Found at i:1466799 original size:20 final size:20
Alignment explanation
Indices: 1466741--1466799 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
1466731 ATTTTTACCC
*
1466741 CAATGTATCGATACATGT-GT
1 CAATGTATCGATACAT-TCTT
* *
1466761 GAATGTAACGATACATTCTT
1 CAATGTATCGATACATTCTT
1466781 CAATGTATCGATACATTCT
1 CAATGTATCGATACATTCT
1466800 GTCTTTTTAC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (20 bp):
CAATGTATCGATACATTCTT
Found at i:1466865 original size:91 final size:91
Alignment explanation
Indices: 1466741--1466961 Score: 370
Period size: 91 Copynumber: 2.4 Consensus size: 91
1466731 ATTTTTACCC
* * *
1466741 CAATGTATCGATACATGTGTGAATGTAACGATACATTCTTCAATGTATCGATACATTCTGTCTTT
1 CAATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATCTATCGATACATTCTGTCTTT
*
1466806 TTACCCAGATATATCGATAAATTTTT
66 TCACCCAGATATATCGATAAATTTTT
* *
1466832 CAATGTATCAATATATGTATGAATGTATCGATACATTCTTCAATCTATCGATACATTCTGTCTTT
1 CAATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATCTATCGATACATTCTGTCTTT
* *
1466897 TCACCCAGATGTATCGATACATTTTT
66 TCACCCAGATATATCGATAAATTTTT
1466923 CAATGTATCGATACATGTATGAATGTATCGATACATTCT
1 CAATGTATCGATACATGTATGAATGTATCGATACATTCT
1466962 ATCTTTTTAC
Statistics
Matches: 120, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 120 1.00
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (91 bp):
CAATGTATCGATACATGTATGAATGTATCGATACATTCTTCAATCTATCGATACATTCTGTCTTT
TCACCCAGATATATCGATAAATTTTT
Found at i:1466909 original size:71 final size:70
Alignment explanation
Indices: 1466834--1467012 Score: 216
Period size: 71 Copynumber: 2.5 Consensus size: 70
1466824 AAATTTTTCA
* * * *
1466834 ATGTATCAATATATGTATGAATGTATCGATACATTCTTCAATCTATCGATACATTCTGTCTTTTC
1 ATGTATCGATACAT-TATCAATGTATCGATACATTCTTCAATCTATCGATACATTCTATCTTTTC
1466899 ACCCAG
65 ACCCAG
* * * *
1466905 ATGTATCGATACATTTTTCAATGTATCGATACATGT-ATGAATGTATCGATACATTCTATCTTTT
1 ATGTATCGATACA-TTATCAATGTATCGATACAT-TCTTCAATCTATCGATACATTCTATCTTTT
* *
1466969 TACCTAG
64 CACCCAG
*
1466976 ATATATCGATACATTATTCAATGTATCGATACATTCT
1 ATGTATCGATACATTA-TCAATGTATCGATACATTCT
1467013 GCCTTTTCAC
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
70 3 0.03
71 86 0.95
72 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (70 bp):
ATGTATCGATACATTATCAATGTATCGATACATTCTTCAATCTATCGATACATTCTATCTTTTCA
CCCAG
Found at i:1466930 original size:20 final size:20
Alignment explanation
Indices: 1466905--1466964 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
1466895 TTTCACCCAG
*
1466905 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTATCA
* *
1466925 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTATCA
1466945 ATGTATCGATACATTCTATC
1 ATGTATCGATACATT-TATC
1466965 TTTTTACCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 31 0.91
21 3 0.09
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTATCA
Found at i:1466983 original size:51 final size:51
Alignment explanation
Indices: 1466928--1467060 Score: 205
Period size: 51 Copynumber: 2.6 Consensus size: 51
1466918 TTTTTCAATG
* * *
1466928 TATCGATACATGTA-TGAATGTATCGATACATTCTATCTTTTTACCTAGATA
1 TATCGATACAT-TATTCAATGTATCGATACATTCTACCTTTTCACCTAGATA
* *
1466979 TATCGATACATTATTCAATGTATCGATACATTCTGCCTTTTCACCTAGATG
1 TATCGATACATTATTCAATGTATCGATACATTCTACCTTTTCACCTAGATA
1467030 TATCGATACATTATTCAATGTATCGATACAT
1 TATCGATACATTATTCAATGTATCGATACAT
1467061 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 2 0.03
51 74 0.97
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.40
Consensus pattern (51 bp):
TATCGATACATTATTCAATGTATCGATACATTCTACCTTTTCACCTAGATA
Found at i:1470975 original size:16 final size:15
Alignment explanation
Indices: 1470956--1471004 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
1470946 CACATTTATT
1470956 TTTTTTCTCTTATTTC
1 TTTTTTC-CTTATTTC
*
1470972 --TTTTCCTTATTGC
1 TTTTTTCCTTATTTC
1470985 TTATTTTCCTT-TTTC
1 TT-TTTTCCTTATTTC
1471000 TTTTT
1 TTTTT
1471005 CCTCCATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 7 0.25
14 8 0.29
15 5 0.18
16 8 0.29
ACGTcount: A:0.06, C:0.18, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTTTCCTTATTTC
Found at i:1471006 original size:13 final size:14
Alignment explanation
Indices: 1470951--1471007 Score: 57
Period size: 13 Copynumber: 4.1 Consensus size: 14
1470941 CTTTTCACAT
1470951 TTATTT-TTTTTCTC
1 TTATTTCTTTTTC-C
1470965 TTATTTC-TTTTCC
1 TTATTTCTTTTTCC
*
1470978 TTATTGCTTATTTTCC
1 TTATTTC-T-TTTTCC
1470994 TT-TTTCTTTTTCC
1 TTATTTCTTTTTCC
1471007 T
1 T
1471008 CCATTCTGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 14 0.38
14 12 0.32
15 3 0.08
16 8 0.22
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.72
Consensus pattern (14 bp):
TTATTTCTTTTTCC
Found at i:1471888 original size:18 final size:17
Alignment explanation
Indices: 1471831--1471889 Score: 68
Period size: 16 Copynumber: 3.5 Consensus size: 17
1471821 AATTTAATAA
* *
1471831 AAAATATTAAAT-AATT
1 AAAATATAAAATAAAGT
1471847 AAAA-ATAAAATAAAGT
1 AAAATATAAAATAAAGT
1471863 AAAATATAAAATAAAGTT
1 AAAATATAAAATAAAG-T
*
1471881 ACAATATAA
1 AAAATATAA
1471890 CTTTCTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 6 0.16
16 11 0.30
17 11 0.30
18 9 0.24
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAATATAAAATAAAGT
Found at i:1478017 original size:16 final size:15
Alignment explanation
Indices: 1477996--1478026 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1477986 TCGATACATC
1477996 ACTGTTCATCACTGTT
1 ACTGTTCAT-ACTGTT
1478012 ACTGTTCATACTGTT
1 ACTGTTCATACTGTT
1478027 CACGTATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTGTTCATACTGTT
Found at i:1478630 original size:34 final size:35
Alignment explanation
Indices: 1478567--1478633 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1478557 TTAAGTGATT
1478567 GAGAGGTTCTATCTTAGCCTTCGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTCG-AAAAGATAGAGA
1478603 GAGAGGTTTCTATCTTAGCCTT-G-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTCGAAAAGATAG
1478634 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 7 0.23
37 15 0.50
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTCGAAAAGATAGAGA
Found at i:1481873 original size:13 final size:13
Alignment explanation
Indices: 1481855--1481879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1481845 TTTTCTAGAT
1481855 TGTATCGATACAA
1 TGTATCGATACAA
1481868 TGTATCGATACA
1 TGTATCGATACA
1481880 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1482738 original size:21 final size:21
Alignment explanation
Indices: 1482713--1482764 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1482703 TTGTATAAAT
1482713 TTTGTATTAAAGGGAAGAACA
1 TTTGTATTAAAGGGAAGAACA
*
1482734 TTTGTATTAAAGGGAAGAACG
1 TTTGTATTAAAGGGAAGAACA
1482755 TTTGTATTAA
1 TTTGTATTAA
1482765 GGGGGAGAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (21 bp):
TTTGTATTAAAGGGAAGAACA
Found at i:1483617 original size:16 final size:15
Alignment explanation
Indices: 1483596--1483626 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1483586 TCGATACATC
1483596 ACTGTTCATCACTGTT
1 ACTGTTCAT-ACTGTT
1483612 ACTGTTCATACTGTT
1 ACTGTTCATACTGTT
1483627 CACGTATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTGTTCATACTGTT
Found at i:1484230 original size:34 final size:35
Alignment explanation
Indices: 1484167--1484233 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1484157 TTAAGTGATT
1484167 GAGAGGTTCTATCTTAGCCTTCGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTCG-AAAAGATAGAGA
1484203 GAGAGGTTTCTATCTTAGCCTT-G-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTCGAAAAGATAG
1484234 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 7 0.23
37 15 0.50
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTCGAAAAGATAGAGA
Found at i:1484916 original size:13 final size:13
Alignment explanation
Indices: 1484898--1484924 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1484888 ACATGCTGCT
1484898 TTGTATCGATACA
1 TTGTATCGATACA
1484911 TTGTATCGATACA
1 TTGTATCGATACA
1484924 T
1 T
1484925 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1484921 original size:33 final size:32
Alignment explanation
Indices: 1484879--1484943 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
1484869 CACACCCAGA
*
1484879 TGTATCGATACATGCTGCTTTGTATCGATACAT
1 TGTATCGATACATG-TGCATTGTATCGATACAT
*
1484912 TGTATCGATACATGTTCATTGTATCGATACAT
1 TGTATCGATACATGTGCATTGTATCGATACAT
1484944 GGCCAAATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATGTGCATTGTATCGATACAT
Found at i:1484955 original size:21 final size:19
Alignment explanation
Indices: 1484909--1484965 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1484899 TGTATCGATA
**
1484909 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGGC
1484928 CATTGTATCGATACATGGC
1 CATTGTATCGATACATGGC
1484947 CAAATTGTATCGATACATG
1 C--ATTGTATCGATACATG
1484966 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGGC
Found at i:1485020 original size:20 final size:19
Alignment explanation
Indices: 1484995--1485047 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1484985 TATCACTATT
1484995 TGTATCGATACATG-GTACAA
1 TGTATCGATACATGAG-A-AA
1485015 TGTATCGATACATGAAGAAA
1 TGTATCGATACATG-AGAAA
1485035 TGTATCGATACAT
1 TGTATCGATACAT
1485048 AGCATGTAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 29 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (19 bp):
TGTATCGATACATGAGAAA
Found at i:1493119 original size:19 final size:19
Alignment explanation
Indices: 1493063--1493120 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 19
1493053 AAGGGGGAGA
*
1493063 AGATAATCGTTTAAGGGAG
1 AGATAATCGTTTAAGGGGG
* ** *
1493082 AGAT-TTTTTTTAA-GAGG
1 AGATAATCGTTTAAGGGGG
1493099 AGATAATCGTTTAAGGGGG
1 AGATAATCGTTTAAGGGGG
1493118 AGA
1 AGA
1493121 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 10 0.36
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.31
Consensus pattern (19 bp):
AGATAATCGTTTAAGGGGG
Found at i:1493699 original size:13 final size:13
Alignment explanation
Indices: 1493681--1493707 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1493671 ACATGCTGCT
1493681 TTGTATCGATACA
1 TTGTATCGATACA
1493694 TTGTATCGATACA
1 TTGTATCGATACA
1493707 T
1 T
1493708 GGCCAAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1493784 original size:20 final size:20
Alignment explanation
Indices: 1493759--1493811 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1493749 TATCACTATT
** *
1493759 TGTATCGATACATGGTACAA
1 TGTATCGATACATGAAAAAA
1493779 TGTATCGATACATGAAAAAA
1 TGTATCGATACATGAAAAAA
1493799 TGTATCGATACAT
1 TGTATCGATACAT
1493812 AGCATGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATGAAAAAA
Found at i:1494497 original size:13 final size:13
Alignment explanation
Indices: 1494479--1494504 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1494469 TACAGCAAGT
1494479 ATGTATCGATACA
1 ATGTATCGATACA
1494492 ATGTATCGATACA
1 ATGTATCGATACA
1494505 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1496720 original size:20 final size:20
Alignment explanation
Indices: 1496695--1496747 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1496685 ATTTGCCTGC
* *
1496695 ATGTATCGATACATTGAATA
1 ATGTATCAATACATGGAATA
*
1496715 ATGTATTAATACATGGAATA
1 ATGTATCAATACATGGAATA
*
1496735 ATGTATCTATACA
1 ATGTATCAATACA
1496748 AAACTTATGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGTATCAATACATGGAATA
Found at i:1501087 original size:32 final size:33
Alignment explanation
Indices: 1501046--1501123 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
1501036 TATAGCCGTT
*
1501046 ATGTATCGATACAATGTATCGATACATTTTG-G
1 ATGTATCGATACAATGTATCGATACATCTTGTG
*
1501078 ATGTATCGATACATTGTATCGATACATCTTGTG
1 ATGTATCGATACAATGTATCGATACATCTTGTG
1501111 -TGTATCGATACAA
1 ATGTATCGATACAA
1501124 ACAATTAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
32 41 0.98
33 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACAATGTATCGATACATCTTGTG
Found at i:1501104 original size:13 final size:13
Alignment explanation
Indices: 1501047--1501104 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
1501037 ATAGCCGTTA
*
1501047 TGTATCGATACAA
1 TGTATCGATACAT
1501060 TGTATCGATACATTTT
1 TGTATCGATACA---T
1501076 GGATGTATCGATACAT
1 ---TGTATCGATACAT
1501092 TGTATCGATACAT
1 TGTATCGATACAT
1501105 CTTGTGTGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 25 0.66
16 1 0.03
19 12 0.32
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1501211 original size:13 final size:13
Alignment explanation
Indices: 1501193--1501217 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1501183 ACATTTGGTC
1501193 ATGTATCGATACA
1 ATGTATCGATACA
1501206 ATGTATCGATAC
1 ATGTATCGATAC
1501218 TGTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1503701 original size:13 final size:13
Alignment explanation
Indices: 1503683--1503746 Score: 101
Period size: 13 Copynumber: 4.9 Consensus size: 13
1503673 ATAAACCCTT
*
1503683 TGTATCGATACAC
1 TGTATCGATACAA
1503696 TGTATCGATACAA
1 TGTATCGATACAA
*
1503709 TGTATCGATACAC
1 TGTATCGATACAA
*
1503722 TCTATCGATACAA
1 TGTATCGATACAA
1503735 TGTATCGATACA
1 TGTATCGATACA
1503747 GAGAATGCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1503712 original size:26 final size:26
Alignment explanation
Indices: 1503683--1503746 Score: 119
Period size: 26 Copynumber: 2.5 Consensus size: 26
1503673 ATAAACCCTT
*
1503683 TGTATCGATACACTGTATCGATACAA
1 TGTATCGATACACTCTATCGATACAA
1503709 TGTATCGATACACTCTATCGATACAA
1 TGTATCGATACACTCTATCGATACAA
1503735 TGTATCGATACA
1 TGTATCGATACA
1503747 GAGAATGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.31
Consensus pattern (26 bp):
TGTATCGATACACTCTATCGATACAA
Found at i:1503961 original size:8 final size:8
Alignment explanation
Indices: 1503948--1503973 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1503938 AACATTAAAC
1503948 ATCACAAA
1 ATCACAAA
1503956 ATCACAAA
1 ATCACAAA
1503964 ATCACAAA
1 ATCACAAA
1503972 AT
1 AT
1503974 TTAATCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (8 bp):
ATCACAAA
Found at i:1509920 original size:13 final size:13
Alignment explanation
Indices: 1509902--1509937 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1509892 CATTTTGGGA
1509902 TGTATCGATACAT
1 TGTATCGATACAT
1509915 TGTATCGATACAT
1 TGTATCGATACAT
1509928 TGTATCGATA
1 TGTATCGATA
1509938 TATCTTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1510058 original size:13 final size:13
Alignment explanation
Indices: 1510040--1510064 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1510030 ACATTTGGTC
1510040 ATGTATCGATACA
1 ATGTATCGATACA
1510053 ATGTATCGATAC
1 ATGTATCGATAC
1510065 TGTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1514158 original size:52 final size:51
Alignment explanation
Indices: 1514080--1514209 Score: 199
Period size: 52 Copynumber: 2.5 Consensus size: 51
1514070 CTCGAAATAT
* *
1514080 GAAAAGTTGCTTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGG
1514132 GAAAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
1 GAAAA-TTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
*
1514184 GTAAATTGCCTGCATGTATCGATACA
1 GAAAATTGCCTGCATGTATCGATACA
1514210 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 21 0.29
52 47 0.64
53 5 0.07
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (51 bp):
GAAAATTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGG
Found at i:1514222 original size:51 final size:50
Alignment explanation
Indices: 1514080--1514229 Score: 162
Period size: 52 Copynumber: 2.9 Consensus size: 50
1514070 CTCGAAATAT
* * *
1514080 GAAAAGTTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGG
1514132 GAAAATTTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGG
* *
1514184 GTAAA-TTGCCTGCATGTATCGATACAAAGATCAGTGTATTGATACA
1 GAAAATTTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
1514230 ATGTATCGAT
Statistics
Matches: 87, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 32 0.37
52 46 0.53
53 1 0.01
54 4 0.05
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (50 bp):
GAAAATTTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGG
Found at i:1514320 original size:33 final size:33
Alignment explanation
Indices: 1514283--1514349 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1514273 AGTGGCTTAA
1514283 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1514316 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1514349 A
1 A
1514350 ACATTTTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1514323 original size:13 final size:13
Alignment explanation
Indices: 1514305--1514329 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1514295 CAAAAAAATA
1514305 TGTATCGATACAT
1 TGTATCGATACAT
1514318 TGTATCGATACA
1 TGTATCGATACA
1514330 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1514343 original size:20 final size:20
Alignment explanation
Indices: 1514318--1514370 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1514308 ATCGATACAT
1514318 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
1514338 TGTATCGATACAACATTTTA
1 TGTATCGATACAACATTTTA
1514358 TGTATCGATACAA
1 TGTATCGATACAA
1514371 ATCGTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
TGTATCGATACAACATTTTA
Found at i:1515940 original size:16 final size:16
Alignment explanation
Indices: 1515921--1515996 Score: 55
Period size: 16 Copynumber: 4.8 Consensus size: 16
1515911 GAAATTACCA
*
1515921 AAACCCGAAATAGCCC
1 AAACCCGAAAAAGCCC
** * *
1515937 AAACTTGAGACAGCCC
1 AAACCCGAAAAAGCCC
*
1515953 GAACCC-AAGAAAGCCC
1 AAACCCGAA-AAAGCCC
** *
1515969 AAACCAAAAAAAGCCT
1 AAACCCGAAAAAGCCC
1515985 AAACCCGAAAAA
1 AAACCCGAAAAA
1515997 ATTTGAAACC
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
15 1 0.02
16 41 0.93
17 2 0.05
ACGTcount: A:0.50, C:0.32, G:0.13, T:0.05
Consensus pattern (16 bp):
AAACCCGAAAAAGCCC
Found at i:1517317 original size:16 final size:17
Alignment explanation
Indices: 1517291--1517336 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
1517281 ATCCCAAATA
1517291 AGCCCGAACCCGAAA-G
1 AGCCCGAACCCGAAACG
**
1517307 AGCTTGAACCC-AAACG
1 AGCCCGAACCCGAAACG
1517323 AGCCCGAACCCGAA
1 AGCCCGAACCCGAA
1517337 CCTGCCCAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.12
16 19 0.79
17 2 0.08
ACGTcount: A:0.37, C:0.37, G:0.22, T:0.04
Consensus pattern (17 bp):
AGCCCGAACCCGAAACG
Found at i:1519507 original size:17 final size:17
Alignment explanation
Indices: 1519485--1519535 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
1519475 ATTTTTGTAT
*
1519485 TATTTATTTAAGATATA
1 TATTTATTTAAGATAAA
*
1519502 TATTTAATTTGA-ATAAA
1 TATTT-ATTTAAGATAAA
1519519 TATTTATTTAAGATAAA
1 TATTTATTTAAGATAAA
1519536 AATAAGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 5 0.17
17 19 0.66
18 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (17 bp):
TATTTATTTAAGATAAA
Found at i:1525142 original size:20 final size:19
Alignment explanation
Indices: 1525119--1525192 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 19
1525109 CACACCCAGA
*
1525119 TGTATCGATACATGCTGCTT
1 TGTATCGATACATG-TGCAT
*
1525139 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTGCAT
1525158 TGTATCGATACATG-GACAAAT
1 TGTATCGATACATGTG-C--AT
1525179 TGTATCGATACATG
1 TGTATCGATACATG
1525193 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.38
20 14 0.29
21 16 0.33
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATGTGCAT
Found at i:1525258 original size:13 final size:13
Alignment explanation
Indices: 1525237--1525267 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1525227 CGATACATGG
*
1525237 TACAATGTATCGA
1 TACATTGTATCGA
1525250 TACATTGTATCGA
1 TACATTGTATCGA
1525263 TACAT
1 TACAT
1525268 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1525263 original size:33 final size:32
Alignment explanation
Indices: 1525221--1525287 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
1525211 TTATCACTAT
1525221 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
1525254 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
1525287 T
1 T
1525288 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:1531279 original size:21 final size:19
Alignment explanation
Indices: 1531241--1531279 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1531231 TTATATTGAA
*
1531241 TGATTGAATTATGTCTATT
1 TGATTGAATTAGGTCTATT
1531260 TGATATGAATTAGGGTCTAT
1 TGAT-TGAATTA-GGTCTAT
1531280 AGGATAGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 7 0.41
21 6 0.35
ACGTcount: A:0.28, C:0.05, G:0.21, T:0.46
Consensus pattern (19 bp):
TGATTGAATTAGGTCTATT
Found at i:1531413 original size:13 final size:13
Alignment explanation
Indices: 1531395--1531437 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
1531385 ATACAACACT
1531395 CATTGTATCGATA
1 CATTGTATCGATA
1531408 CATTGTATCGATA
1 CATTGTATCGATA
*
1531421 CAATGTATCGATA
1 CATTGTATCGATA
1531434 CATT
1 CATT
1531438 AGGTACTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:1533293 original size:19 final size:19
Alignment explanation
Indices: 1533266--1533331 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
1533256 TTTTTTATAA
1533266 AAGGAGGAGATAATCGTTT
1 AAGGAGGAGATAATCGTTT
* **
1533285 AAGG-GG-GAGAATTTTTT
1 AAGGAGGAGATAATCGTTT
*
1533302 AAAGGAGGAGATAATCGCTT
1 -AAGGAGGAGATAATCGTTT
*
1533322 AAGGGGGAGA
1 AAGGAGGAGA
1533332 ATTTCTTAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
17 8 0.22
18 6 0.17
19 15 0.42
20 7 0.19
ACGTcount: A:0.36, C:0.05, G:0.36, T:0.23
Consensus pattern (19 bp):
AAGGAGGAGATAATCGTTT
Found at i:1533298 original size:40 final size:38
Alignment explanation
Indices: 1533254--1533343 Score: 130
Period size: 37 Copynumber: 2.4 Consensus size: 38
1533244 TGTGAAAATA
*
1533254 AATTTTTTATAAAAGGAGGAGATAATCGTTTAAGGGGGAG
1 AATTTTTT-T-AAAGGAGGAGATAATCGCTTAAGGGGGAG
1533294 AA-TTTTTTAAAGGAGGAGATAATCGCTTAAGGGGGAG
1 AATTTTTTTAAAGGAGGAGATAATCGCTTAAGGGGGAG
*
1533331 AA-TTTCTTAAAGG
1 AATTTTTTTAAAGG
1533344 GAGAAAAATG
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
37 40 0.83
38 1 0.02
39 5 0.10
40 2 0.04
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.30
Consensus pattern (38 bp):
AATTTTTTTAAAGGAGGAGATAATCGCTTAAGGGGGAG
Found at i:1533310 original size:37 final size:37
Alignment explanation
Indices: 1533265--1533343 Score: 140
Period size: 37 Copynumber: 2.1 Consensus size: 37
1533255 ATTTTTTATA
* *
1533265 AAAGGAGGAGATAATCGTTTAAGGGGGAGAATTTTTT
1 AAAGGAGGAGATAATCGCTTAAGGGGGAGAATTTCTT
1533302 AAAGGAGGAGATAATCGCTTAAGGGGGAGAATTTCTT
1 AAAGGAGGAGATAATCGCTTAAGGGGGAGAATTTCTT
1533339 AAAGG
1 AAAGG
1533344 GAGAAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.37, C:0.05, G:0.33, T:0.25
Consensus pattern (37 bp):
AAAGGAGGAGATAATCGCTTAAGGGGGAGAATTTCTT
Found at i:1533989 original size:13 final size:13
Alignment explanation
Indices: 1533968--1533997 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1533958 CGATACATGG
1533968 TACAATGTATCGA
1 TACAATGTATCGA
*
1533981 TACATTGTATCGA
1 TACAATGTATCGA
1533994 TACA
1 TACA
1533998 GGAAGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:1534012 original size:33 final size:33
Alignment explanation
Indices: 1533952--1534018 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
1533942 CTATCACTAT
* * *
1533952 TTGTATCGATACATGGTACAATGTATCGATACA
1 TTGTATCGATACATGGAAAAATATATCGATACA
1533985 TTGTATCGATACA-GGAAGAAATATATCGATACA
1 TTGTATCGATACATGGAA-AAATATATCGATACA
1534018 T
1 T
1534019 AGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.31
Consensus pattern (33 bp):
TTGTATCGATACATGGAAAAATATATCGATACA
Found at i:1534811 original size:26 final size:26
Alignment explanation
Indices: 1534781--1534844 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 26
1534771 TTAAACTTAA
*
1534781 GAATATATTAATAAAGCTTATTGCAT
1 GAATATGTTAATAAAGCTTATTGCAT
*
1534807 GAATACGTTAAATAAAGCTTATTGCAT
1 GAATATGTT-AATAAAGCTTATTGCAT
1534834 GAATATGTTAA
1 GAATATGTTAA
1534845 GGATATCTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (26 bp):
GAATATGTTAATAAAGCTTATTGCAT
Found at i:1539596 original size:30 final size:30
Alignment explanation
Indices: 1539560--1539627 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
1539550 TTAGGACCAC
1539560 TAAAATGATGATAAATGCATGAATAGAAAA
1 TAAAATGATGATAAATGCATGAATAGAAAA
1539590 TAAAATGATGATAAATGCATGAATAGAAAA
1 TAAAATGATGATAAATGCATGAATAGAAAA
1539620 TAAAATGA
1 TAAAATGA
1539628 CAAAGTTAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.57, C:0.03, G:0.16, T:0.24
Consensus pattern (30 bp):
TAAAATGATGATAAATGCATGAATAGAAAA
Found at i:1540782 original size:13 final size:13
Alignment explanation
Indices: 1540764--1540789 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1540754 CATTTTGGGA
1540764 TGTATCGATACAT
1 TGTATCGATACAT
1540777 TGTATCGATACAT
1 TGTATCGATACAT
1540790 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1540786 original size:33 final size:32
Alignment explanation
Indices: 1540744--1540807 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1540734 TACAAGCTAA
*
1540744 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
1540777 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
1540808 AACAGTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:1540956 original size:20 final size:21
Alignment explanation
Indices: 1540902--1540957 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
1540892 TATCGATATA
*
1540902 ATGTATCGATAC-TGTGCAAT
1 ATGTATCGATACATTTGCAAT
1540922 ATGTATCGATACATTTG-AAT
1 ATGTATCGATACATTTGCAAT
*
1540942 GTGTATCGATACATTT
1 ATGTATCGATACATTT
1540958 AAGGGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (21 bp):
ATGTATCGATACATTTGCAAT
Found at i:1541580 original size:41 final size:41
Alignment explanation
Indices: 1541484--1541566 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
1541474 CCCCTTAATC
1541484 AAAAAATTTCTCCCCCTTAATAAAGCAATTGAACAATTACA
1 AAAAAATTTCTCCCCCTTAATAAAGCAATTGAACAATTACA
*
1541525 AAAAAATTTCTCCCCCTTAATAAAGCAATTTAACAATTACA
1 AAAAAATTTCTCCCCCTTAATAAAGCAATTGAACAATTACA
1541566 A
1 A
1541567 GTTTCTTTCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.47, C:0.22, G:0.04, T:0.28
Consensus pattern (41 bp):
AAAAAATTTCTCCCCCTTAATAAAGCAATTGAACAATTACA
Found at i:1542966 original size:20 final size:22
Alignment explanation
Indices: 1542924--1542968 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1542914 GCTGTGAGTA
* *
1542924 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTGCCCGGTCGCAACC
1542946 TGGGGG-TG-CCGGTCGCAACC
1 TGGGGGCTGCCCGGTCGCAACC
1542966 TGG
1 TGG
1542969 TGAGTGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.07, C:0.29, G:0.47, T:0.18
Consensus pattern (22 bp):
TGGGGGCTGCCCGGTCGCAACC
Found at i:1543428 original size:13 final size:13
Alignment explanation
Indices: 1543410--1543445 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1543400 ATAAACCCTT
*
1543410 TGTATCGATACAC
1 TGTATCGATACAA
1543423 TGTATCGATACAA
1 TGTATCGATACAA
1543436 TGTATCGATA
1 TGTATCGATA
1543446 TAGAGAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1543662 original size:8 final size:8
Alignment explanation
Indices: 1543644--1543674 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1543634 TTTTCAACAT
1543644 CAAACATCA
1 CAAA-ATCA
1543653 CAAAATCA
1 CAAAATCA
1543661 CAAAATCA
1 CAAAATCA
1543669 CAAAAT
1 CAAAAT
1543675 TTAATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 18 0.82
9 4 0.18
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (8 bp):
CAAAATCA
Found at i:1548239 original size:19 final size:20
Alignment explanation
Indices: 1548194--1548245 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1548184 TTACAAGCCA
*
1548194 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATCTTGGG
*
1548214 ATGTATCGATACATCTTGTG
1 ATGTATCGATACATCTTGGG
1548234 -TGTATCGATACA
1 ATGTATCGATACA
1548246 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCTTGGG
Found at i:1548345 original size:13 final size:13
Alignment explanation
Indices: 1548327--1548351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1548317 ACATTTGGTC
1548327 ATGTATCGATACA
1 ATGTATCGATACA
1548340 ATGTATCGATAC
1 ATGTATCGATAC
1548352 TGTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1556154 original size:34 final size:34
Alignment explanation
Indices: 1556082--1556161 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
1556072 TGAATCATAT
* * *
1556082 CCTTAAAAG-AGGCTTTTGAAATCTCTTAAAACA
1 CCTTCAAAGAAGGCTTATGAAATCTCTCAAAACA
* *
1556115 TCTTCAAAGAAGGCTTATGAAATTTCTCAAAA-A
1 CCTTCAAAGAAGGCTTATGAAATCTCTCAAAACA
*
1556148 GCCTTCAAAAAAGG
1 -CCTTCAAAGAAGG
1556162 GTCTTGAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
33 8 0.21
34 30 0.79
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (34 bp):
CCTTCAAAGAAGGCTTATGAAATCTCTCAAAACA
Found at i:1560952 original size:13 final size:13
Alignment explanation
Indices: 1560934--1560973 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
1560924 GGTATATATA
1560934 TCAAGATATTAGT
1 TCAAGATATTAGT
1560947 TCAAGATA-TA--
1 TCAAGATATTAGT
*
1560957 TCGAGATATTAGT
1 TCAAGATATTAGT
1560970 TCAA
1 TCAA
1560974 TAAGAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
10 7 0.32
11 2 0.09
12 2 0.09
13 11 0.50
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (13 bp):
TCAAGATATTAGT
Found at i:1560963 original size:23 final size:23
Alignment explanation
Indices: 1560929--1560973 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1560919 CTATGGGTAT
1560929 ATATATCAAGATATTAGTTCAAG
1 ATATATCAAGATATTAGTTCAAG
*
1560952 ATATATCGAGATATTAGTTCAA
1 ATATATCAAGATATTAGTTCAA
1560974 TAAGAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (23 bp):
ATATATCAAGATATTAGTTCAAG
Done.