Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000002.1 Hibiscus syriacus cultivar Beakdansim tig00000003_pilon, whole genome shotgun sequence
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: 2131600
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1729790 original size:95 final size:93
Alignment explanation
Indices: 1729655--1729863 Score: 219
Period size: 95 Copynumber: 2.2 Consensus size: 93
1729645 GTATTGATAC
* * * *
1729655 CCCTACTATGGTATCGATACTACCCTATTATGGTATCGATA-ACCTCTTCCA-GTATTAATACCA
1 CCCTACTATGGTATCGATAC-ACACTATTATGGTACCGATACACCCCTT--AGGTATCAATACCA
*
1729718 AAATTAGCTTCGATGTAGT-CTGATATCAATA
63 AAATTAGATTCGATGT-GTACTGATATCAATA
* *
1729749 CCCTCACTATGGTATCGATAC-CACTATGCTATGGTACCGATACCCCCCTTAGGTATCGATACCA
1 CCCT-ACTATGGTATCGATACACACTAT--TATGGTACCGATACACCCCTTAGGTATCAATACCA
* * *
1729813 AAATTAGATTCGATGTTTACTGGTATCGATA
63 AAATTAGATTCGATGTGTACTGATATCAATA
* *
1729844 CCTTACCATGGTATCGATAC
1 CCCTACTATGGTATCGATAC
1729864 TAAATCACTT
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
93 5 0.05
94 21 0.22
95 66 0.68
96 5 0.05
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (93 bp):
CCCTACTATGGTATCGATACACACTATTATGGTACCGATACACCCCTTAGGTATCAATACCAAAA
TTAGATTCGATGTGTACTGATATCAATA
Found at i:1734068 original size:16 final size:16
Alignment explanation
Indices: 1734047--1734093 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
1734037 AATAAATAGA
1734047 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1734063 GAACATAAACGAACAC
1 GAACATAAACGAACAC
1734079 GAACATAAACGAACA
1 GAACATAAACGAACA
1734094 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.57, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:1734174 original size:10 final size:10
Alignment explanation
Indices: 1734159--1734217 Score: 62
Period size: 10 Copynumber: 6.7 Consensus size: 10
1734149 CATTTAATAA
1734159 ATAAACGAAC
1 ATAAACGAAC
1734169 ATAAACGAAC
1 ATAAACGAAC
1734179 ----ACGAAC
1 ATAAACGAAC
1734185 ATAAACGAAC
1 ATAAACGAAC
1734195 ----ACGAAC
1 ATAAACGAAC
1734201 ATAAACGAAC
1 ATAAACGAAC
1734211 ATAAACG
1 ATAAACG
1734218 TTGGAGACCC
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
6 12 0.29
10 29 0.71
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1734184 original size:16 final size:16
Alignment explanation
Indices: 1734163--1734211 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
1734153 TAATAAATAA
1734163 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1734179 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1734195 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1734211 A
1 A
1734212 TAAACGTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.57, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1734195 original size:26 final size:26
Alignment explanation
Indices: 1734159--1734217 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1734149 CATTTAATAA
* *
1734159 ATAAACGAACATAAACGA-ACACGAAC
1 ATAAACGAACACAAAC-ATAAACGAAC
*
1734185 ATAAACGAACACGAACATAAACGAAC
1 ATAAACGAACACAAACATAAACGAAC
1734211 ATAAACG
1 ATAAACG
1734218 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.08
Consensus pattern (26 bp):
ATAAACGAACACAAACATAAACGAAC
Found at i:1734978 original size:14 final size:14
Alignment explanation
Indices: 1734961--1735016 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
1734951 AATGAACATA
1734961 AACGAACATAATCG
1 AACGAACATAATCG
1734975 AACGAACAT-A---
1 AACGAACATAATCG
*
1734985 AACAAACATAATCG
1 AACGAACATAATCG
1734999 AACGAACATAATCG
1 AACGAACATAATCG
1735013 AACG
1 AACG
1735017 TTCATGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.54, C:0.21, G:0.12, T:0.12
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:1734981 original size:24 final size:24
Alignment explanation
Indices: 1734954--1735015 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
1734944 ATAAATGAAT
1734954 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAATCGAAC
*
1734978 GAACATAAACAAACATAATCGAAC
1 GAACATAAACGAACATAATCGAAC
*
1735002 GAACATAATCGAAC
1 GAACATAAACGAAC
1735016 GTTCATGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.55, C:0.21, G:0.11, T:0.13
Consensus pattern (24 bp):
GAACATAAACGAACATAATCGAAC
Found at i:1736973 original size:20 final size:20
Alignment explanation
Indices: 1736948--1736993 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1736938 GGACTAAGGG
1736948 AGTCAATAAACATTTGTTTT
1 AGTCAATAAACATTTGTTTT
1736968 AGTCAATAAACATTTGTTTT
1 AGTCAATAAACATTTGTTTT
1736988 AGTCAA
1 AGTCAA
1736994 CAACACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (20 bp):
AGTCAATAAACATTTGTTTT
Found at i:1747407 original size:18 final size:16
Alignment explanation
Indices: 1747365--1747404 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1747355 GGAATAGTAT
1747365 TGTGTATAACCAAGAG
1 TGTGTATAACCAAGAG
1747381 TGTGTATAACCAAGAG
1 TGTGTATAACCAAGAG
1747397 TGTGTATA
1 TGTGTATA
1747405 TAATAAGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (16 bp):
TGTGTATAACCAAGAG
Found at i:1749911 original size:64 final size:65
Alignment explanation
Indices: 1749734--1749892 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 65
1749724 GAATTAATTG
* * ** *
1749734 AACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCAAACTCCATGCATCGATGCACTCAGAATATTTTCAA
* * **
1749799 AACATCGAATGCATTTGATGCATCGATGCAAAATCCATGCATCGATGCAC-CAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCAAACTCCATGCATCGATGCACTCAGAATA-TTTTCA
1749862 A
65 A
1749863 AACATCGAATGCATTTCATGCATCGATGCA
1 AACATCGAATGCATTTCATGCATCGATGCA
1749893 CACTTGGTGC
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
64 34 0.41
65 49 0.59
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCAAACTCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1755445 original size:20 final size:21
Alignment explanation
Indices: 1755416--1755471 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1755406 CTTGTGCTTC
*
1755416 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1755436 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1755458 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1755472 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1758174 original size:65 final size:64
Alignment explanation
Indices: 1758057--1758266 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
1758047 TATTCAAAGG
* * **
1758057 CATGCA-CTGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT-AAACATCGAATGCA
1 CATGCATC-GATGCA-CAATCCATGCATCGATGCA-CCA-GAATATTTTTCAAACATCGAATGCA
*
1758119 TTC
62 TTT
* *** *
1758122 CATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATA-TTTTCAAAACATCGAATGCATT
1 CATGCATCGATGCACAATCCATGCATCGATGCAC-CAGAATATTTTTC-AAACATCGAATGCATT
1758186 T
64 T
* **
1758187 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
1758251 CATGCATCGATGCACA
1 CATGCATCGATGCACA
1758267 CTTGGTGCAC
Statistics
Matches: 122, Mismatches: 17, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
63 7 0.06
64 52 0.43
65 62 0.51
66 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (64 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACCAGAATATTTTTCAAACATCGAATGCATTT
Found at i:1758283 original size:64 final size:65
Alignment explanation
Indices: 1758105--1758268 Score: 224
Period size: 65 Copynumber: 2.5 Consensus size: 65
1758095 TGAATTAATT
* * ** *
1758105 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
* * **
1758170 AAACATCGAATGCATTTGATGCATCGATGCACAATCCATGCATCGATGCAC-CAGGCTATTTTTC
1 AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATA-TTTTC
1758234 -
65 A
1758234 AAACATCGAATGCATTTCATGCATCGATGCACACT
1 AAACATCGAATGCATTTCATGCATCGATGCACACT
1758269 TGGTGCACCG
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 37 0.43
65 50 0.57
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:1760271 original size:18 final size:18
Alignment explanation
Indices: 1760244--1760296 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
1760234 AGGGATTTTC
*
1760244 AGTGGCCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1760262 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1760280 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1760297 AATATTCAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.17, C:0.25, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1764108 original size:21 final size:19
Alignment explanation
Indices: 1764061--1764113 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
1764051 CATTCATGTA
*
1764061 TTTTATTATTTGCTTAATT
1 TTTTATTATTTACTTAATT
*
1764080 TTTATATTAATTTACTTTATCT
1 TTT-TATT-ATTTACTTAAT-T
*
1764102 TTTTATTCTTTA
1 TTTTATTATTTA
1764114 ATAGTGATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.11
20 8 0.29
21 13 0.46
22 4 0.14
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTATTATTTACTTAATT
Found at i:1766749 original size:26 final size:26
Alignment explanation
Indices: 1766713--1766767 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
1766703 TCTATATAAA
*
1766713 CAGTTATTCAAATTAGCTAATCAAAT
1 CAGTTATTCAAATCAGCTAATCAAAT
* * *
1766739 CAGTTGTTCAAATCAGCTATTGAAAT
1 CAGTTATTCAAATCAGCTAATCAAAT
1766765 CAG
1 CAG
1766768 CTACCAGCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (26 bp):
CAGTTATTCAAATCAGCTAATCAAAT
Found at i:1772266 original size:15 final size:15
Alignment explanation
Indices: 1772246--1772275 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1772236 CCCGGGAAGA
1772246 AAGCAGGGGTGACTG
1 AAGCAGGGGTGACTG
1772261 AAGCAGGGGTGACTG
1 AAGCAGGGGTGACTG
1772276 CGGGTTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.47, T:0.13
Consensus pattern (15 bp):
AAGCAGGGGTGACTG
Found at i:1781076 original size:32 final size:32
Alignment explanation
Indices: 1781040--1781102 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
1781030 AATTTTAGCC
* * *
1781040 AACCAAAAGTAACCTGAATCGAAAGCAACCCT
1 AACCAAAACTAACCCGAACCGAAAGCAACCCT
*
1781072 AACCAAAACTAACCCGAACCGAAAGTAACCC
1 AACCAAAACTAACCCGAACCGAAAGCAACCC
1781103 GAATTTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.32, G:0.11, T:0.10
Consensus pattern (32 bp):
AACCAAAACTAACCCGAACCGAAAGCAACCCT
Found at i:1781085 original size:16 final size:16
Alignment explanation
Indices: 1781066--1781105 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1781056 AATCGAAAGC
*
1781066 AACCCTAACCAAAACT
1 AACCCGAACCAAAACT
* *
1781082 AACCCGAACCGAAAGT
1 AACCCGAACCAAAACT
1781098 AACCCGAA
1 AACCCGAA
1781106 TTTAATTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.35, G:0.10, T:0.07
Consensus pattern (16 bp):
AACCCGAACCAAAACT
Found at i:1781343 original size:21 final size:20
Alignment explanation
Indices: 1781276--1781414 Score: 82
Period size: 21 Copynumber: 6.8 Consensus size: 20
1781266 AAATGACCAA
***
1781276 CAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1781296 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1781316 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1781337 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1781358 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1781378 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1781399 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1781415 ACACATAAAT
Statistics
Matches: 90, Mismatches: 24, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
19 1 0.01
20 42 0.47
21 47 0.52
ACGTcount: A:0.37, C:0.26, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1781476 original size:20 final size:20
Alignment explanation
Indices: 1781381--1781610 Score: 223
Period size: 20 Copynumber: 11.5 Consensus size: 20
1781371 CGATTTTCCA
* ** *
1781381 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1781401 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1781421 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
1781441 AAATCGCAACGTGTATCTGT
1 AAATCGCAACGCGTATCCGT
**
1781461 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1781481 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1781501 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1781521 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1781541 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1781561 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1781581 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1781601 AAATCACAAC
1 AAATCGCAAC
1781611 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 29, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1782331 original size:24 final size:24
Alignment explanation
Indices: 1782292--1782338 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1782282 AAATTTGGTC
1782292 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1782316 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1782339 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1782531 original size:13 final size:13
Alignment explanation
Indices: 1782513--1782537 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1782503 ATATAATCCT
1782513 GAAGAAGAAAAAA
1 GAAGAAGAAAAAA
1782526 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1782538 GTCCCCGAAG
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAGAAGAAAAAA
Found at i:1784868 original size:33 final size:33
Alignment explanation
Indices: 1784817--1784995 Score: 252
Period size: 33 Copynumber: 5.2 Consensus size: 33
1784807 CGGAAATTAC
*
1784817 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
1784850 AATCCCAAC-ATGAAAATCGCAATGCAGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
1784884 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
1784917 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
*
1784955 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
1784988 AATCGCAA
1 AATCGCAA
1784996 TGCGAAATGA
Statistics
Matches: 132, Mismatches: 6, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
32 1 0.01
33 66 0.50
34 30 0.23
35 3 0.02
36 2 0.02
37 1 0.01
38 29 0.22
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:1784922 original size:19 final size:19
Alignment explanation
Indices: 1784831--1785013 Score: 218
Period size: 19 Copynumber: 10.4 Consensus size: 19
1784821 GCAACGAGAG
1784831 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1784850 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1784864 AATCGCAATGCAGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1784884 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1784898 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1784917 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1784936 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1784955 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1784969 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1784988 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
1785006 AATCGCAA
1 AATCGCAA
1785014 CGAGAGAATC
Statistics
Matches: 142, Mismatches: 6, Indels: 33
0.78 0.03 0.18
Matches are distributed among these distances:
14 32 0.23
15 2 0.01
16 5 0.04
17 4 0.03
18 12 0.08
19 74 0.52
20 13 0.09
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1784974 original size:14 final size:15
Alignment explanation
Indices: 1784955--1785032 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
1784945 GCGAAATGAA
1784955 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
1784969 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCG--A-GAG
*
1784988 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
1785005 AAATCGCAA-CGAGAG
1 -AATCGCAAGCGAGAG
1785020 AATCGCAATGCGA
1 AATCGCAA-GCGA
1785033 AATTATAAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 16 0.31
15 1 0.02
16 10 0.20
17 1 0.02
18 9 0.18
19 14 0.27
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:1784983 original size:71 final size:72
Alignment explanation
Indices: 1784817--1785013 Score: 336
Period size: 71 Copynumber: 2.8 Consensus size: 72
1784807 CGGAAATTAC
*
1784817 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCAG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCAG
1784877 AAATGAA
66 AAATGAA
1784884 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-G
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCAG
1784948 AAATGAA
66 AAATGAA
1784955 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG-AAATCGCAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1785014 CGAGAGAATC
Statistics
Matches: 124, Mismatches: 1, Indels: 7
0.94 0.01 0.05
Matches are distributed among these distances:
67 40 0.32
69 1 0.01
70 9 0.07
71 58 0.47
72 16 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (72 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCAG
AAATGAA
Found at i:1785051 original size:51 final size:52
Alignment explanation
Indices: 1784831--1785035 Score: 267
Period size: 52 Copynumber: 3.9 Consensus size: 52
1784821 GCAACGAGAG
* *
1784831 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCAGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
* * * * *
1784884 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
1 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1784936 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1784988 AATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1785036 TATAAACGCA
Statistics
Matches: 134, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
50 7 0.05
51 38 0.28
52 55 0.41
53 22 0.16
54 7 0.05
55 4 0.03
56 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1785154 original size:52 final size:53
Alignment explanation
Indices: 1785042--1785157 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
1785032 AAATTATAAA
*
1785042 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1785095 CGCATTGCGATTATCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1785147 CGCATTGCGAT
1 CGCATTGCGAT
1785158 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTATCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:1785165 original size:19 final size:19
Alignment explanation
Indices: 1785060--1785157 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1785050 GATTCTCTCG
1785060 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1785080 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1785099 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
1785113 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1785132 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1785151 TTGCGAT
1 TTGCGAT
1785158 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1785283 original size:14 final size:13
Alignment explanation
Indices: 1785255--1785312 Score: 55
Period size: 14 Copynumber: 4.4 Consensus size: 13
1785245 TTATGTTCGC
*
1785255 ATCAATTACACAA
1 ATCAATTATACAA
1785268 ATCAACTTATACAA
1 ATCAA-TTATACAA
* *
1785282 ATCATCTTTTACAA
1 ATCA-ATTATACAA
*
1785296 ATCAATTAAAC-A
1 ATCAATTATACAA
1785308 ATCAA
1 ATCAA
1785313 AAATAAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
12 6 0.16
13 9 0.24
14 22 0.59
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (13 bp):
ATCAATTATACAA
Found at i:1787301 original size:33 final size:33
Alignment explanation
Indices: 1787254--1787346 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1787244 GCGAAACCAA
*
1787254 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1787287 AATCACAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1787320 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1787347 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1787314 original size:19 final size:19
Alignment explanation
Indices: 1787217--1787351 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1787207 TAGTTTACTT
* *
1787217 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1787237 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1787256 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1787275 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1787289 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1787308 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1787322 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1787341 TCGCAATGCGA
1 TCGCAACGCGA
1787352 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1787325 original size:14 final size:14
Alignment explanation
Indices: 1787273--1787329 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1787263 GCGAAATGAA
*
1787273 AATCGCAACGACAG
1 AATCGCAACGAAAG
*
1787287 AATCACAACGCGAAATG
1 AATCGCAA--CGAAA-G
1787304 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1787320 AATCGCAACG
1 AATCGCAACG
1787330 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.47, C:0.25, G:0.19, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1787369 original size:19 final size:19
Alignment explanation
Indices: 1787347--1787475 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1787337 AAAATCGCAA
1787347 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1787366 TGCGA-TCT--TAT--CGT
1 TGCGATTTTGGTTTCGCGT
1787380 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1787399 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1787413 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1787432 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1787451 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1787471 TGCGA
1 TGCGA
1787476 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 3 0.03
19 45 0.51
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1787389 original size:33 final size:33
Alignment explanation
Indices: 1787347--1787438 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1787337 AAAATCGCAA
1787347 TGCGATTTTGGTTTCGCGTTGCGA-TCTTATCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TATCGT
*
1787380 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
**
1787413 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1787439 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 53 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTATCGT
Found at i:1787676 original size:93 final size:93
Alignment explanation
Indices: 1787523--1788170 Score: 1222
Period size: 93 Copynumber: 7.1 Consensus size: 93
1787513 ATGGATTGCA
1787523 TTAC-TTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787586 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1787614 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787679 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1787707 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787772 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1787800 TTACTTTCAACCAAAAGACAAAAC-AA-ACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787863 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1787891 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787955 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1787983 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1788048 TAGCAGAATTGTCAGCAACCGAACAAA-
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1788075 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1788139 TAGCAGAATTGGCAGCAACCGAA-TAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
1788166 TTACT
1 TTACT
1788171 AAGCAATCTA
Statistics
Matches: 548, Mismatches: 3, Indels: 12
0.97 0.01 0.02
Matches are distributed among these distances:
90 6 0.01
91 157 0.29
92 135 0.25
93 250 0.46
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1788046 original size:276 final size:276
Alignment explanation
Indices: 1787522--1788170 Score: 1223
Period size: 276 Copynumber: 2.4 Consensus size: 276
1787512 AATGGATTGC
*
1787522 ATTAC-TTCAACCAAAAGACAAAACAAAGACAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 ATTACTTTCAACCAAAAGACAAAACAAACA-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1787586 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
65 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1787651 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
130 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
1787716 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
195 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
1787781 TGGCAGCAACCGAACAA
260 TGGCAGCAACCGAACAA
1787798 ATTTACTTTCAACCAAAAGACAAAACAAACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 A-TTACTTTCAACCAAAAGACAAAACAAACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787863 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACT
65 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1787927 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
130 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCA
1787992 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
195 ACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAAT
*
1788057 TGTCAGCAACCGAACAA
260 TGGCAGCAACCGAACAA
1788074 ATTACTTTCAACCAAAAGACAAAACAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 ATTACTTTCAACCAAAAGACAAAACAA-ACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1788139 TAGCAGAATTGGCAGCAACCGAA-TAATTTACT
65 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
1788171 AAGCAATCTA
Statistics
Matches: 367, Mismatches: 3, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
275 34 0.09
276 225 0.61
277 85 0.23
278 23 0.06
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (276 bp):
ATTACTTTCAACCAAAAGACAAAACAAACAAATACTATTTCACAGTGTTAAAGAATACACAGTTT
AGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA
TTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAA
CCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATT
GGCAGCAACCGAACAA
Found at i:1788081 original size:184 final size:186
Alignment explanation
Indices: 1787523--1788170 Score: 1222
Period size: 184 Copynumber: 3.5 Consensus size: 186
1787513 ATGGATTGCA
1787523 TTAC-TTCAACCAAAAGACAAAACAAAGAC-AATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787586 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1787651 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1787707 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787772 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAAC-AA-ACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
1787835 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1787891 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1787955 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
1788020 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGTCAGCAACCGAACAAA-
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
1788075 TTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1788139 TAGCAGAATTGGCAGCAACCGAA-TAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
1788171 AAGCAATCTA
Statistics
Matches: 457, Mismatches: 2, Indels: 11
0.97 0.00 0.02
Matches are distributed among these distances:
183 105 0.23
184 172 0.38
185 94 0.21
186 86 0.19
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1789887 original size:14 final size:14
Alignment explanation
Indices: 1789868--1789924 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1789858 TTGAAATGAA
*
1789868 AATCGCAACGAGAG
1 AATCGCAACGAGAC
1789882 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAC
*
1789901 AATCGCAACGAGAT
1 AATCGCAACGAGAC
1789915 AATCGCAACG
1 AATCGCAACG
1789925 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAC
Found at i:1789905 original size:33 final size:33
Alignment explanation
Indices: 1789860--1789943 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
1789850 TCTTTTGGTT
1789860 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1789893 GAAATGACAATCGCAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1789926 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1789944 CGAAATGAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1789906 original size:19 final size:19
Alignment explanation
Indices: 1789882--1789965 Score: 106
Period size: 19 Copynumber: 4.7 Consensus size: 19
1789872 GCAACGAGAG
*
1789882 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
1789901 AATCGCAA--CG--A-GAT
1 AATCGCAACGCGAAATGAA
1789915 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1789934 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1789953 AATCGCAATGCGA
1 AATCGCAACGCGA
1789966 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1789996 original size:14 final size:14
Alignment explanation
Indices: 1789977--1790033 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1789967 TTTGGTTTCG
1789977 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1789991 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1790010 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1790024 CGTTGCGATT
1 CGTTGCGATT
1790034 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1790009 original size:33 final size:33
Alignment explanation
Indices: 1789961--1790041 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1789951 AAAATCGCAA
**
1789961 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1789994 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1790027 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1790042 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1790044 original size:21 final size:21
Alignment explanation
Indices: 1790018--1790093 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1790008 CGCGTTGCGA
1790018 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1790039 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
1790059 TTCTATCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1790080 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1790094 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1790074 original size:41 final size:41
Alignment explanation
Indices: 1790017--1790094 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1790007 TCGCGTTGCG
* *
1790017 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTATCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1790058 ATTCTATCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTATCGTTGCGATTTTCATTTATCTCGTTGCGAC
1790095 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTATCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1790079 original size:20 final size:20
Alignment explanation
Indices: 1790017--1790084 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1790007 TCGCGTTGCG
*
1790017 ATTCTCTCGTTGCGATTTTC
1 ATTCTATCGTTGCGATTTTC
* ***
1790037 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTATCGTTGCGATTTTC
1790058 ATTCTATCGTTGCGATTTTC
1 ATTCTATCGTTGCGATTTTC
1790078 ATT-TATC
1 ATTCTATC
1790085 TCGTTGCGAC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
19 4 0.10
20 19 0.47
21 17 0.43
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.47
Consensus pattern (20 bp):
ATTCTATCGTTGCGATTTTC
Found at i:1790215 original size:33 final size:33
Alignment explanation
Indices: 1790173--1790243 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1790163 AATACTAACT
*
1790173 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1790206 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1790239 TGAAA
1 TGAAA
1790244 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1790477 original size:22 final size:22
Alignment explanation
Indices: 1790425--1790478 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1790415 TGGTTGTGAG
**
1790425 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1790447 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1790469 GGATTTCTTC
1 GGATTTCTTC
1790479 TCCGTAGAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1790651 original size:20 final size:20
Alignment explanation
Indices: 1790626--1790776 Score: 184
Period size: 20 Copynumber: 7.7 Consensus size: 20
1790616 CTTTAAATAT
1790626 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1790646 CGCGTTGCGATTTTA---TTA
1 CGCGTTGCGA-TTTACGGATA
*
1790664 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1790683 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1790703 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
*
1790723 CGTGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1790743 CACGTTGTGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
1790763 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
1790777 TGTGTTCACG
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
16 4 0.04
17 8 0.07
18 2 0.02
19 2 0.02
20 88 0.81
21 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1790774 original size:40 final size:40
Alignment explanation
Indices: 1790628--1790815 Score: 188
Period size: 40 Copynumber: 4.8 Consensus size: 40
1790618 TTAAATATCG
* *
1790628 CGTTGCGATTTACGGATACGCGTTGCGATTTTA---TTA-T
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACA
* *
1790665 CGTTGCGATTTACGGATACGCGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACA
* ** *
1790705 CATTGCGATTTACCCATACGTGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACA
* * *
1790745 CGTTGTGATTTACGGATACGCGTTGCGATTTATGTG-TTCA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACG-GATACA
* ** *
1790785 CGTTGCGATTTTCATATTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTT
1790816 TGGAAAATCG
Statistics
Matches: 125, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
36 3 0.02
37 28 0.22
39 2 0.02
40 91 0.73
41 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACA
Found at i:1790808 original size:20 final size:19
Alignment explanation
Indices: 1790763--1790816 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1790753 TTTACGGATA
* *
1790763 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTT-TATATT
*
1790783 CACGTTGCGATTTTCATATT
1 CGCGTTGCGATTTT-ATATT
1790803 CGCGTTGCGATTTT
1 CGCGTTGCGATTTT
1790817 GGAAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.13, C:0.19, G:0.24, T:0.44
Consensus pattern (19 bp):
CGCGTTGCGATTTTATATT
Found at i:1790809 original size:60 final size:59
Alignment explanation
Indices: 1790626--1790815 Score: 206
Period size: 60 Copynumber: 3.2 Consensus size: 59
1790616 CTTTAAATAT
1790626 CGCGTTGCGATTTACGGATACGCGTTGCGA-TT-TTATT-ATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATTATTCA-CGTTGCGATTTACGGATA
* * ** * **
1790683 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGTGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTA-TTATTCACGTTGCGATTTACGGATA
* * * * ** *
1790743 CACGTTGTGATTTACGGATACGCGTTGCGATTTATGTGTTCACGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTAT-TATTCACGTTGCGATTTACGGATA
1790803 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1790816 TGGAAAATCG
Statistics
Matches: 105, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
57 28 0.27
58 2 0.02
60 75 0.71
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.36
Consensus pattern (59 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATTATTCACGTTGCGATTTACGGATA
Found at i:1790832 original size:21 final size:21
Alignment explanation
Indices: 1790802--1790884 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1790792 ATTTTCATAT
*
1790802 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1790823 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1790844 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1790865 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1790885 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1791072 original size:2 final size:2
Alignment explanation
Indices: 1791065--1791097 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1791055 AAAATCCAAG
1791065 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1791098 TAATTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1792979 original size:2 final size:2
Alignment explanation
Indices: 1792972--1792997 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1792962 AAACCAATGA
1792972 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1792998 TAAATTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1793506 original size:23 final size:23
Alignment explanation
Indices: 1793476--1793525 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1793466 GGGCCTGAGA
*
1793476 GCCTACCCAAGAAAGTCCTCGGG
1 GCCTACCCAAGAAAGTCCCCGGG
1793499 GCCTACCCAAGAAAGTCCCCGGG
1 GCCTACCCAAGAAAGTCCCCGGG
1793522 GCCT
1 GCCT
1793526 TAGAGCTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (23 bp):
GCCTACCCAAGAAAGTCCCCGGG
Found at i:1794217 original size:3 final size:3
Alignment explanation
Indices: 1794209--1794250 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
1794199 GTGATACTTC
*
1794209 ATT ATT ATT ATT ATT ATT ATT ATT ATT CACTT CTT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -A-TT ATT ATT ATT A
1794251 ACTACATAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 32 0.91
4 1 0.03
5 2 0.06
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1795748 original size:31 final size:30
Alignment explanation
Indices: 1795705--1795796 Score: 91
Period size: 30 Copynumber: 3.0 Consensus size: 30
1795695 AGAGTCGAGG
*
1795705 GTTATCTATGTCTTTCGAGACATATGGATA
1 GTTACCTATGTCTTTCGAGACATATGGATA
* * *
1795735 GTTTCCCTATGTCTTTC-AGGACATATGTACA
1 G-TTACCTATGTCTTTCGA-GACATATGGATA
1795766 GTTACCTATGT-TCTTCG-GAACATATGGATA
1 GTTACCTATGTCT-TTCGAG-ACATATGGATA
1795796 G
1 G
1795797 GTCCTTCGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
29 2 0.04
30 24 0.48
31 24 0.48
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (30 bp):
GTTACCTATGTCTTTCGAGACATATGGATA
Found at i:1795776 original size:30 final size:30
Alignment explanation
Indices: 1795705--1795793 Score: 85
Period size: 31 Copynumber: 2.9 Consensus size: 30
1795695 AGAGTCGAGG
* *
1795705 GTTATCTATGTCTTTCGAGACATATGGATA
1 GTTACCTATGTCTTTCGAGACATATGGACA
* *
1795735 GTTTCCCTATGTCTTTC-AGGACATATGTACA
1 G-TTACCTATGTCTTTCGA-GACATATGGACA
1795766 GTTACCTATGT-TCTTCG-GAACATATGGA
1 GTTACCTATGTCT-TTCGAG-ACATATGGA
1795794 TAGGTCCTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
29 2 0.04
30 22 0.46
31 24 0.50
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (30 bp):
GTTACCTATGTCTTTCGAGACATATGGACA
Found at i:1800811 original size:31 final size:32
Alignment explanation
Indices: 1800755--1800848 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 32
1800745 AGAGTCAAGG
* * *
1800755 GTTATCTATGTCTTTCGAGACATATGGATAGT
1 GTTACCTATGTCCTTCGAGAAATATGGATAGT
* * *
1800787 -TTGCCTATGTCCTTCGGGAAATATGGACAGT
1 GTTACCTATGTCCTTCGAGAAATATGGATAGT
*
1800818 GTTACCTATGTTCTTC-AGAACATATGGATAG
1 GTTACCTATGTCCTTCGAGAA-ATATGGATAG
1800849 GTCCTTCGGG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 28 0.56
32 22 0.44
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (32 bp):
GTTACCTATGTCCTTCGAGAAATATGGATAGT
Found at i:1803359 original size:18 final size:18
Alignment explanation
Indices: 1803336--1803370 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1803326 ACTGAATATT
1803336 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1803354 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
1803371 GATAATCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.23, T:0.17
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1804113 original size:2 final size:2
Alignment explanation
Indices: 1804108--1804138 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1804098 ATACTTAAAC
1804108 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
1804139 CCACTTCTAT
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:1805132 original size:19 final size:19
Alignment explanation
Indices: 1805091--1805132 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1805081 TGATCGGCTT
*
1805091 GACCGGTCCAAACCGATCT
1 GACCGGTCCAAACCGATCC
*
1805110 GACCGGTCCGAAA-CGGTCC
1 GACCGGTCC-AAACCGATCC
1805129 GACC
1 GACC
1805133 CGTTGACCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.24, C:0.38, G:0.26, T:0.12
Consensus pattern (19 bp):
GACCGGTCCAAACCGATCC
Found at i:1805227 original size:28 final size:29
Alignment explanation
Indices: 1805146--1805357 Score: 179
Period size: 29 Copynumber: 7.4 Consensus size: 29
1805136 TGACCGACCC
*
1805146 GGTGATATTTT-GGAATTTATTTTGAAAAA
1 GGTGACATTTTGGGAA-TTATTTTGAAAAA
1805175 GGTGACATTTTGGGAATTATTTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
1805204 GGTGACATTTTGGGAATTA-TTTGAAAAA
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* *
1805232 TGAGACATTTTGGGAATT-TTTT-AAAACA
1 GGTGACATTTTGGGAATTATTTTGAAAA-A
* * * * * *
1805260 -GTGACGTTCTAGTAATTATTTTTAAAAC
1 GGTGACATTTTGGGAATTATTTTGAAAAA
* *
1805288 GATGACATTTTGGAAATTATTTAT-AAAACTA
1 GGTGACATTTTGGGAATTATTT-TGAAAA--A
* * *
1805319 -G-GATATTTTGGTAATTATTTTTAATAAA
1 GGTGACATTTTGGGAATTATTTTGAA-AAA
*
1805347 GGTGATATTTT
1 GGTGACATTTT
1805358 TGTAATTTTC
Statistics
Matches: 152, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
27 16 0.11
28 35 0.23
29 86 0.57
30 15 0.10
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (29 bp):
GGTGACATTTTGGGAATTATTTTGAAAAA
Found at i:1813606 original size:20 final size:19
Alignment explanation
Indices: 1813558--1813608 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
1813548 AAATGACCAA
*
1813558 CAAATTCACAACGCGAACT
1 CAAATTCGCAACGCGAACT
1813577 CAAATTCGCAACGCGAACT
1 CAAATTCGCAACGCGAACT
1813596 CAAATTTCGCAAC
1 CAAA-TTCGCAAC
1813609 CCAGTTTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 22 0.73
20 8 0.27
ACGTcount: A:0.39, C:0.31, G:0.12, T:0.18
Consensus pattern (19 bp):
CAAATTCGCAACGCGAACT
Found at i:1813727 original size:19 final size:19
Alignment explanation
Indices: 1813703--1813768 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
1813693 TTTTGCCAAT
1813703 TTCGCAACTGAATTTCAAA
1 TTCGCAACTGAATTTCAAA
*
1813722 TTCGCAACTAAATTTCAAA
1 TTCGCAACTGAATTTCAAA
* *
1813741 TTCGCAACTCGATTTTCGAA
1 TTCGCAACT-GAATTTCAAA
1813761 TTCGCAAC
1 TTCGCAAC
1813769 ACAAATTTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 27 0.64
20 15 0.36
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.32
Consensus pattern (19 bp):
TTCGCAACTGAATTTCAAA
Found at i:1813963 original size:14 final size:15
Alignment explanation
Indices: 1813944--1813981 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1813934 TCTCCATCTC
1813944 TAATTTTTTT-TACA
1 TAATTTTTTTATACA
*
1813958 TAATTTTATTTATATA
1 TAATTTT-TTTATACA
1813974 TAATTTTT
1 TAATTTTT
1813982 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTATACA
Found at i:1814752 original size:24 final size:24
Alignment explanation
Indices: 1814724--1814777 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1814714 GTATTAGAAA
1814724 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* * *
1814748 TTTGATCTTTGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1814772 TTTGAT
1 TTTGAT
1814778 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1817245 original size:43 final size:43
Alignment explanation
Indices: 1817196--1817290 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 43
1817186 TTATCACTTA
* * *** *
1817196 TCAAATTCACATTGCGATTTTTTTGTTGTGATTGATGCGAAAG
1 TCAAATTCACAATGCGATTATCGCGTTGCGATTGATGCGAAAG
* * *
1817239 TCAAATTCGCAATGTGATTATCGCGTTGCGATTGTTGCGAAAG
1 TCAAATTCACAATGCGATTATCGCGTTGCGATTGATGCGAAAG
1817282 TCAAATTCA
1 TCAAATTCA
1817291 AAACGCGAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (43 bp):
TCAAATTCACAATGCGATTATCGCGTTGCGATTGATGCGAAAG
Found at i:1817500 original size:64 final size:65
Alignment explanation
Indices: 1817393--1817543 Score: 225
Period size: 64 Copynumber: 2.3 Consensus size: 65
1817383 AACAACAATA
*
1817393 AACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTCTTATTTACAT-ATCAATTAAACAAAT
1 AACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTATTATTT-CATCATCAATTAAACAAAT
1817457 C
65 C
* *
1817458 AACTTTTACAAATCAATTAAACAAG-TAAAAAATAATTATTATTTCCTCATCAATTAAACAAATC
1 AACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTATTATTTCATCATCAATTAAACAAATC
* *
1817522 AACATTTATAAATCAATGTAAA
1 AACTTTTACAAATCAAT-TAAA
1817544 ATTCAATTAA
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
63 2 0.03
64 48 0.61
65 29 0.37
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.32
Consensus pattern (65 bp):
AACTTTTACAAATCAATTAAACAAGAAAAAAAATAATTATTATTTCATCATCAATTAAACAAATC
Found at i:1820999 original size:21 final size:19
Alignment explanation
Indices: 1820968--1821010 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
1820958 TATGAGAAAT
1820968 TGATTTTAAAATAT-AAAAA
1 TGATTTTAAAAT-TGAAAAA
1820987 TGATGTTTCAAAATTGAAAAA
1 TGAT-TTT-AAAATTGAAAAA
1821008 TGA
1 TGA
1821011 AAATAAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (19 bp):
TGATTTTAAAATTGAAAAA
Found at i:1824497 original size:47 final size:45
Alignment explanation
Indices: 1824427--1824552 Score: 182
Period size: 47 Copynumber: 2.8 Consensus size: 45
1824417 TATAAAATCT
*
1824427 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1824472 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
1824519 CTTGCCA-TTATTCCGTAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
1824553 GCATGGTTAC
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 38 0.51
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:1830726 original size:20 final size:20
Alignment explanation
Indices: 1830701--1830739 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1830691 TTTTCAAGGG
1830701 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
1830721 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
1830740 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:1830808 original size:45 final size:46
Alignment explanation
Indices: 1830759--1830849 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
1830749 GAACATCGAA
* * *
1830759 TGCATTTTATGCATCGATGC-ACATACCATGCATCAATGCACTCAG
1 TGCATTTGATGCATCGATGCAAAAGACCATGCATCAATGCACTCAG
*
1830804 TGCATTTGATGCATCGATGCAAAAGACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCAAAAGACCATGCATCAATGCACTCAG
1830850 GCTTTTTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 19 0.46
46 22 0.54
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCAAAAGACCATGCATCAATGCACTCAG
Found at i:1831771 original size:21 final size:21
Alignment explanation
Indices: 1831745--1831859 Score: 122
Period size: 21 Copynumber: 5.5 Consensus size: 21
1831735 AATCGGGCTT
* *
1831745 TTGAACGGTGGGAGGGACCTC
1 TTGAACGATGGGAGGGGCCTC
** *
1831766 TTGAACGATGACAAGGGCCTC
1 TTGAACGATGGGAGGGGCCTC
*
1831787 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGGGAGGGGCCTC
* *
1831808 TTGAATGATGAGAGGGGCCTC
1 TTGAACGATGGGAGGGGCCTC
* * *
1831829 TTGAATGATAGGAGGCGCCTC
1 TTGAACGATGGGAGGGGCCTC
*
1831850 TTGAATGATG
1 TTGAACGATG
1831860 ATAGGTACAT
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 78 1.00
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.23
Consensus pattern (21 bp):
TTGAACGATGGGAGGGGCCTC
Found at i:1831808 original size:42 final size:42
Alignment explanation
Indices: 1831745--1831860 Score: 160
Period size: 42 Copynumber: 2.8 Consensus size: 42
1831735 AATCGGGCTT
* *
1831745 TTGAACGGTGGGAGGGACCTCTTGAACGATGACAAGGGCCTC
1 TTGAACGGTGGGAGGGGCCTCTTGAATGATGACAAGGGCCTC
* *
1831787 TTGAACGGTGGGAGGGGCCTCTTGAATGATGAGAGGGGCCTC
1 TTGAACGGTGGGAGGGGCCTCTTGAATGATGACAAGGGCCTC
* * * *
1831829 TTGAATGATAGGAGGCGCCTCTTGAATGATGA
1 TTGAACGGTGGGAGGGGCCTCTTGAATGATGA
1831861 TAGGTACATT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (42 bp):
TTGAACGGTGGGAGGGGCCTCTTGAATGATGACAAGGGCCTC
Found at i:1832287 original size:63 final size:64
Alignment explanation
Indices: 1832177--1832316 Score: 162
Period size: 63 Copynumber: 2.2 Consensus size: 64
1832167 GTAAACTAGA
* * * *
1832177 TACCTCACCACGTAGTGCACCATTGTTATCGCGTAAAACATCCACCTCACCACGTAAAG-ACCG
1 TACCTCATCACGTAGTGCACCATTGTTATCACATAAAACATCCACCTCACCACGCAAAGCACCG
** **
1832240 TACCTCATCACGTAGTGCACCATTGTCT-TCACATAAAGTA-CCGACCTCATGACGCAAAGCACC
1 TACCTCATCACGTAGTGCACCATTGT-TATCACATAAAACATCC-ACCTCACCACGCAAAGCACC
1832303 G
64 G
1832304 -ACCTCATCACGTA
1 TACCTCATCACGTA
1832317 ACTCCCCTAG
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
62 2 0.03
63 59 0.89
64 5 0.08
ACGTcount: A:0.30, C:0.34, G:0.14, T:0.21
Consensus pattern (64 bp):
TACCTCATCACGTAGTGCACCATTGTTATCACATAAAACATCCACCTCACCACGCAAAGCACCG
Found at i:1834066 original size:14 final size:14
Alignment explanation
Indices: 1834049--1834079 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1834039 CGAAACTAAA
1834049 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
*
1834063 TTCGTGTTGCGATT
1 TTCGCGTTGCGATT
1834077 TTC
1 TTC
1834080 ATTTTCGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.19, G:0.26, T:0.48
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:1834105 original size:20 final size:20
Alignment explanation
Indices: 1834062--1834105 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1834052 GCGTTGCGAT
** * *
1834062 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGAAATTAAG
1834082 TTTCGTGTTGCGAAATTAAG
1 TTTCGTGTTGCGAAATTAAG
1834102 TTTC
1 TTTC
1834106 AAAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTTGCGAAATTAAG
Found at i:1834613 original size:20 final size:20
Alignment explanation
Indices: 1834588--1834629 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1834578 ATAAACGCGC
**
1834588 TTTGACTTCTGTGTTGCGAA
1 TTTGACTTAGGTGTTGCGAA
*
1834608 TTTGACTTAGGTGTTGTGAA
1 TTTGACTTAGGTGTTGCGAA
1834628 TT
1 TT
1834630 ACAAATTTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.48
Consensus pattern (20 bp):
TTTGACTTAGGTGTTGCGAA
Found at i:1834863 original size:22 final size:22
Alignment explanation
Indices: 1834817--1834856 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1834807 AAAATTAAAA
1834817 AAATACATCAATAGTTAGATAT
1 AAATACATCAATAGTTAGATAT
*
1834839 AAATATAT-AATA-TTAGAT
1 AAATACATCAATAGTTAGAT
1834857 GACTAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (22 bp):
AAATACATCAATAGTTAGATAT
Found at i:1838205 original size:21 final size:21
Alignment explanation
Indices: 1838166--1838206 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1838156 GTCTGCTGAA
* *
1838166 GCTCCACCTATTTTAGAGTAT
1 GCTCCACCTACTGTAGAGTAT
*
1838187 GCTCCACCTACTGTGGAGTA
1 GCTCCACCTACTGTAGAGTA
1838207 CTACTTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.32
Consensus pattern (21 bp):
GCTCCACCTACTGTAGAGTAT
Found at i:1841866 original size:21 final size:21
Alignment explanation
Indices: 1841842--1841884 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1841832 CATTAAGACC
* *
1841842 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCATAAAATCT
*
1841863 TTTGTCGAGGCCATAAAATCT
1 TTTGTCGAAGCCATAAAATCT
1841884 T
1 T
1841885 GTAGTGAAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (21 bp):
TTTGTCGAAGCCATAAAATCT
Found at i:1843228 original size:14 final size:15
Alignment explanation
Indices: 1843204--1843232 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1843194 TATATCGAAT
1843204 AAATCAATAAAGAAA
1 AAATCAATAAAGAAA
1843219 AAAT-AATAAAGAAA
1 AAATCAATAAAGAAA
1843233 CAAGATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATCAATAAAGAAA
Found at i:1851895 original size:5 final size:5
Alignment explanation
Indices: 1851885--1851925 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
1851875 AAAGATATAT
*
1851885 TAAAA TAAAA TAAAA TAAAA TAAAAA TAATA TAATAA TAAA
1 TAAAA TAAAA TAAAA TAAAA T-AAAA TAAAA TAA-AA TAAA
1851926 TATTAATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 23 0.72
6 9 0.28
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:1851912 original size:11 final size:11
Alignment explanation
Indices: 1851886--1851925 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1851876 AAGATATATT
1851886 AAAATAAAAT-
1 AAAATAAAATA
1851896 AAAATAAAATA
1 AAAATAAAATA
*
1851907 AAAATAATATA
1 AAAATAAAATA
*
1851918 ATAATAAA
1 AAAATAAA
1851926 TATTAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 10 0.38
11 16 0.62
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1851997 original size:18 final size:18
Alignment explanation
Indices: 1851976--1852018 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1851966 GTTGTTTTTA
*
1851976 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1851994 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1852012 AAATAAA
1 AAATAAA
1852019 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1852800 original size:64 final size:64
Alignment explanation
Indices: 1852611--1852781 Score: 308
Period size: 64 Copynumber: 2.7 Consensus size: 64
1852601 GAAAACATCT
*
1852611 TAAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
*
1852675 TAAATCCTAATTAAAATACTTAAAACTATTTAAAATAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1852739 TAAATCCTAATTAAAATAC-TAAAATCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTTAAAA-CTATTTAAACTAAAATAC
1852782 AAAGATAAAG
Statistics
Matches: 103, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
63 5 0.05
64 98 0.95
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (64 bp):
TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
Found at i:1852850 original size:76 final size:75
Alignment explanation
Indices: 1852730--1852893 Score: 222
Period size: 76 Copynumber: 2.2 Consensus size: 75
1852720 AAAAAATAAT
* * * *
1852730 ATAATATTCTAAATCCTAATTAAAATACTAAAATCTATTTAAACTAAAATACAAAGATAAAGATA
1 ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGA-AAAAATA
1852795 AAAT-ATAAAA
65 AAATGATAAAA
*
1852805 ATAATATCCTAAAACTTAATTAAAATACTAAAAACCTATTTAAACTAAAATACAAAGAAAAAATA
1 ATAATATCCTAAAACCTAATTAAAATACT-AAAACCTATTTAAACTAAAATACAAAGAAAAAATA
* * *
1852870 TAATGTTTAAA
65 AAATGATAAAA
*
1852881 ATATTATCCTAAA
1 ATAATATCCTAAA
1852894 TTTGAGTTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 35 0.45
76 43 0.55
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.30
Consensus pattern (75 bp):
ATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGAAAAAATAA
AATGATAAAA
Found at i:1855686 original size:28 final size:28
Alignment explanation
Indices: 1855646--1855705 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
1855636 GACTCTTGCT
*
1855646 TTGAAGAGTTGAAGCATCAGGGAGGATG
1 TTGAAGAGTTGAAGCAGCAGGGAGGATG
1855674 TTGAAGAGTTGAAGCAGCAGGGAGGATG
1 TTGAAGAGTTGAAGCAGCAGGGAGGATG
1855702 TTGA
1 TTGA
1855706 GCATATTCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.07, G:0.40, T:0.22
Consensus pattern (28 bp):
TTGAAGAGTTGAAGCAGCAGGGAGGATG
Found at i:1856409 original size:22 final size:23
Alignment explanation
Indices: 1856382--1856435 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
1856372 CGAAATAAAA
1856382 TTAAAATATATTAAATAT-ATTT
1 TTAAAATATATTAAATATAATTT
*
1856404 TTAAAAAAT-TTAAATATAATTT
1 TTAAAATATATTAAATATAATTT
*
1856426 TGAAAATATA
1 TTAAAATATA
1856436 GTGAATTACT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAAAATATATTAAATATAATTT
Found at i:1856418 original size:21 final size:22
Alignment explanation
Indices: 1856382--1856431 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
1856372 CGAAATAAAA
* *
1856382 TTAAAATATATTAAATATATTT
1 TTAAAAAATATTAAATATAATT
1856404 TTAAAAAAT-TTAAATATAATT
1 TTAAAAAATATTAAATATAATT
*
1856425 TTGAAAA
1 TTAAAAA
1856432 TATAGTGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTAAAAAATATTAAATATAATT
Found at i:1863332 original size:37 final size:37
Alignment explanation
Indices: 1863260--1863334 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
1863250 GTTGAAAAAT
*
1863260 ATTTATATATTTTCTTTAAAAAAATTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAATATATAAA
* *
1863297 ATTTATATAATTTT-TTTTACAAAATTGAAA-ATATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAATATATAAA
1863334 A
1 A
1863335 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 25 0.76
38 8 0.24
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAATATATAAA
Found at i:1872504 original size:124 final size:124
Alignment explanation
Indices: 1872374--1872623 Score: 500
Period size: 124 Copynumber: 2.0 Consensus size: 124
1872364 TAAAACATTC
1872374 TTATATTGTGCAATAAAATACCATATAAAAGTGTATTGTGTAATTCATACCCAAAATCATTTAAT
1 TTATATTGTGCAATAAAATACCATATAAAAGTGTATTGTGTAATTCATACCCAAAATCATTTAAT
1872439 AAATAAATCAATATAAAAATATATCATAAAATAATTTAAATCATTTTCATTCAAAAACA
66 AAATAAATCAATATAAAAATATATCATAAAATAATTTAAATCATTTTCATTCAAAAACA
1872498 TTATATTGTGCAATAAAATACCATATAAAAGTGTATTGTGTAATTCATACCCAAAATCATTTAAT
1 TTATATTGTGCAATAAAATACCATATAAAAGTGTATTGTGTAATTCATACCCAAAATCATTTAAT
1872563 AAATAAATCAATATAAAAATATATCATAAAATAATTTAAATCATTTTCATTCAAAAACA
66 AAATAAATCAATATAAAAATATATCATAAAATAATTTAAATCATTTTCATTCAAAAACA
1872622 TT
1 TT
1872624 CGAGGTTGGC
Statistics
Matches: 126, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 126 1.00
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (124 bp):
TTATATTGTGCAATAAAATACCATATAAAAGTGTATTGTGTAATTCATACCCAAAATCATTTAAT
AAATAAATCAATATAAAAATATATCATAAAATAATTTAAATCATTTTCATTCAAAAACA
Found at i:1875002 original size:21 final size:22
Alignment explanation
Indices: 1874977--1875027 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
1874967 ATTGAAACTC
1874977 GACTTGAATTC-AAAAAACTTA
1 GACTTGAATTCAAAAAAACTTA
1874998 GACTTGAATTCAAAAAAACTTA
1 GACTTGAATTCAAAAAAACTTA
*
1875020 AACTTGAA
1 GACTTGAA
1875028 ACAATCTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (22 bp):
GACTTGAATTCAAAAAAACTTA
Found at i:1884325 original size:31 final size:32
Alignment explanation
Indices: 1884290--1884357 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
1884280 ATTTTTGTAA
*
1884290 ATTTTGAATAAATTCAATT-AAGTCCAAATA-C
1 ATTTTG-ATAAATTCAATTCAAGTCCAAAAACC
* *
1884321 ATTTT-TTAAATTCAGTTCAAGTCCAAAAACC
1 ATTTTGATAAATTCAATTCAAGTCCAAAAACC
1884352 ATTTTG
1 ATTTTG
1884358 CCTTAAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
29 10 0.32
30 10 0.32
31 11 0.35
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (32 bp):
ATTTTGATAAATTCAATTCAAGTCCAAAAACC
Found at i:1884330 original size:29 final size:31
Alignment explanation
Indices: 1884298--1884356 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
1884288 AAATTTTGAA
*
1884298 TAAATTCAATT-AAGTCCAAATA-CATTTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTTT
*
1884327 TAAATTCAGTTCAAGTCCAAAAACCATTTT
1 TAAATTCAATTCAAGTCCAAAAACCATTTT
1884357 GCCTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 10 0.38
31 6 0.23
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTT
Found at i:1885110 original size:27 final size:28
Alignment explanation
Indices: 1885048--1885112 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
1885038 AGGAAGAAGA
*
1885048 TAAATAAATGAGAGAGAAAAAGAAAAAGC
1 TAAA-AAATGAAAGAGAAAAAGAAAAAGC
*
1885077 T-ACAAATGAAAGAGAAAAATG-AAAAG-
1 TAAAAAATGAAAGAGAAAAA-GAAAAAGC
1885103 TAAAAAATGA
1 TAAAAAATGA
1885113 GAGATAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 27 0.87
28 2 0.06
29 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.18, T:0.12
Consensus pattern (28 bp):
TAAAAAATGAAAGAGAAAAAGAAAAAGC
Found at i:1893137 original size:2 final size:2
Alignment explanation
Indices: 1893132--1893156 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1893122 TATATATATA
1893132 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
1893157 AAGTATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1894964 original size:23 final size:23
Alignment explanation
Indices: 1894932--1894997 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 23
1894922 ACCTCATGTA
*
1894932 TGTCCCGAAAAACCTGTGTACTG
1 TGTCCCGAAAAACCTATGTACTG
* * *
1894955 TGTCCTGAAAGACCTATGTACTA
1 TGTCCCGAAAAACCTATGTACTG
* **
1894978 TATCCCGAAGGACCTATGTA
1 TGTCCCGAAAAACCTATGTA
1894998 ACCCTCAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (23 bp):
TGTCCCGAAAAACCTATGTACTG
Found at i:1895653 original size:25 final size:25
Alignment explanation
Indices: 1895625--1895678 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
1895615 ACATATAATT
1895625 TATATCACTTATCTCACATTATTTA
1 TATATCACTTATCTCACATTATTTA
1895650 TATATCACTTATCTCACATTATTTA
1 TATATCACTTATCTCACATTATTTA
1895675 TATA
1 TATA
1895679 CTAAGTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATCACTTATCTCACATTATTTA
Found at i:1898138 original size:36 final size:36
Alignment explanation
Indices: 1897847--1898205 Score: 181
Period size: 36 Copynumber: 9.6 Consensus size: 36
1897837 AAATATTTAG
* * *
1897847 AACAAAATTGATCTCACATGAGATAGTTTTCC-TAA
1 AACAAATTTTATCTCACTTGAGATAGTTTTCCTTAA
* * * * * *
1897882 TAACAAATTTTGTCTCGCTGGAAACAATTTTCCTTAA
1 -AACAAATTTTATCTCACTTGAGATAGTTTTCCTTAA
* * * *
1897919 AACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAAAA
1 AACAAATTTTATCTCACTTGAGATAGTTTTC-CT--TAA
* * * **
1897958 AACAAATTTTGTCTCACTTGAGACA-TCTTCCACCCAA
1 AACAAATTTTATCTCACTTGAGATAGT-TTTC-CTTAA
* * *
1897995 AACAAATTTTATCTCGCTTGAGACA-TTATTCCAAAATTTTA
1 AACAAATTTTATCTCACTTGAGATAGTT-TTCC-----TTAA
* * *
1898036 AACAAAATTGATCTCACATGAGATAGTTTTCC-TAA
1 AACAAATTTTATCTCACTTGAGATAGTTTTCCTTAA
* * * *
1898071 GAACAAATTTTGTCTTA-TTGGAGAAAATTTTCCTTAA
1 -AACAAATTTTATCTCACTT-GAGATAGTTTTCCTTAA
* * * *
1898108 AACAAAATTAATCTCACTTGAGATTGTTTTCTCTAAAA
1 AACAAATTTTATCTCACTTGAGATAGTTTTC-CT-TAA
* * *
1898146 AACAAATTTTGTCTCACTTGAGACA-TCTTCCTCCTAA
1 AACAAATTTTATCTCACTTGAGATAGTTTTCCT--TAA
* *
1898183 AACAAATTTTGTCTCGCTTGAGA
1 AACAAATTTTATCTCACTTGAGA
1898206 CATTATTTCA
Statistics
Matches: 240, Mismatches: 64, Indels: 37
0.70 0.19 0.11
Matches are distributed among these distances:
35 3 0.01
36 93 0.39
37 68 0.28
38 23 0.10
39 26 0.11
41 25 0.10
42 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (36 bp):
AACAAATTTTATCTCACTTGAGATAGTTTTCCTTAA
Found at i:1898221 original size:37 final size:37
Alignment explanation
Indices: 1897956--1898208 Score: 139
Period size: 37 Copynumber: 6.8 Consensus size: 37
1897946 TTTCTCTAAA
* *
1897956 AAAACAAATTTTGTCTCACTTGAGACATCTTCCACCC
1 AAAACAAATTTTGTCTCACTTGAGACATCTTCCTCCT
* * * *
1897993 AAAACAAATTTTATCTCGCTTGAGACATTATTCCAAAAT-TT
1 AAAACAAATTTTGTCTCACTTGAGACA-TCTTCC----TCCT
* * * *
1898034 TAAACAAA-ATTGATCTCACATGAGATAGT-TT--TCCT
1 AAAACAAATTTTG-TCTCACTTGAGACA-TCTTCCTCCT
* * *
1898069 AAGAACAAATTTTGTCTTA-TTGGAGAAAATTTTCCT--T
1 AA-AACAAATTTTGTCTCACTT-GAG-ACATCTTCCTCCT
* ** * * *
1898106 AAAACAAAATTAATCTCACTTGAGA-TTGTT-TTCTCT
1 AAAACAAATTTTGTCTCACTTGAGACATCTTCCTC-CT
1898142 AAAAAACAAATTTTGTCTCACTTGAGACATCTTCCTCCT
1 --AAAACAAATTTTGTCTCACTTGAGACATCTTCCTCCT
*
1898181 AAAACAAATTTTGTCTCGCTTGAGACAT
1 AAAACAAATTTTGTCTCACTTGAGACAT
1898209 TATTTCATTA
Statistics
Matches: 161, Mismatches: 33, Indels: 44
0.68 0.14 0.18
Matches are distributed among these distances:
33 1 0.01
34 4 0.02
35 4 0.02
36 30 0.19
37 64 0.40
38 27 0.17
39 6 0.04
40 6 0.04
41 19 0.12
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (37 bp):
AAAACAAATTTTGTCTCACTTGAGACATCTTCCTCCT
Found at i:1898391 original size:36 final size:36
Alignment explanation
Indices: 1898344--1898672 Score: 295
Period size: 36 Copynumber: 9.4 Consensus size: 36
1898334 TTTGAATTTC
*
1898344 TTTCCCTTGAAACATATTTTGTCTCTCTTGAGACTG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
* * **
1898380 TTTCCCTTGAAAC-AA-GTTGTCTCCCTTGAGAGAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
* ** *
1898414 ATTCCCTTGAAA-AAA-----AATAT-TTGAGA-TCG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACT-G
* ** *
1898443 TTTCCTTTGAAATTAATTTTGTCTCTCTT-AGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
*
1898478 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGA-TG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
* * *
1898513 ATTTCCTTTGAAACAAATTTTGTCTCCCTTGAGACATT
1 -TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGAC-TG
* * *
1898551 TTTCCCTTGAAAAAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
*
1898587 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACTG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
* * * * * *
1898623 TTTCCCTTAAAACAAAGTTTGTCTCCCTTTATACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
*
1898659 CTTCCCTTGAAACA
1 TTTCCCTTGAAACA
1898673 TAAAATATTT
Statistics
Matches: 235, Mismatches: 44, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
29 17 0.07
30 3 0.01
34 28 0.12
35 33 0.14
36 123 0.52
37 30 0.13
38 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACTG
Found at i:1898453 original size:99 final size:100
Alignment explanation
Indices: 1898274--1898529 Score: 272
Period size: 99 Copynumber: 2.5 Consensus size: 100
1898264 ACTTTGGGAA
* *** *
1898274 TGTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACAGTTTTTTTTCGAAACAAAAATCTTTGA
1 TGTTTCCCTTGAAACAAAG--TTGTCTCTCTTGAGACAGATTCCCTTCGAAACAAAAATATTTGA
1898339 ATTTCTTTCCCTTGAAACAT-ATTTTGTCTCTCTTGAGAC
64 A-TTCTTTCCCTTGAAA-ATAATTTTGTCTCTCTT-AGAC
* *
1898378 TGTTTCCCTTGAAAC-AAGTTGTCTCCCTTGAGAGAGATTCCCTT-GAAA-AAAAATATTTGAGA
1 TGTTTCCCTTGAAACAAAGTTGTCTCTCTTGAGACAGATTCCCTTCGAAACAAAAATATTTGA-A
* *
1898440 -TCGTTTCCTTTGAAATTAATTTTGTCTCTCTTAGAC
65 TTC-TTTCCCTTGAAAATAATTTTGTCTCTCTTAGAC
* * * * *
1898476 AGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGA-TGATTTCCTTTGAAACAAA
1 TGTTTCCCTTGAAACAAAGTT-GTCTCTCTTGAGACAGATTCCCTTCGAAACAAA
1898530 TTTTGTCTCC
Statistics
Matches: 131, Mismatches: 14, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
98 21 0.16
99 48 0.37
100 21 0.16
101 23 0.18
103 3 0.02
104 15 0.11
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (100 bp):
TGTTTCCCTTGAAACAAAGTTGTCTCTCTTGAGACAGATTCCCTTCGAAACAAAAATATTTGAAT
TCTTTCCCTTGAAAATAATTTTGTCTCTCTTAGAC
Found at i:1898544 original size:21 final size:21
Alignment explanation
Indices: 1898520--1898581 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
1898510 ATGATTTCCT
1898520 TTGAAACAAATTTTGTCTCCC
1 TTGAAACAAATTTTGTCTCCC
*
1898541 TTGAGAC--A-TTT-T-TCCC
1 TTGAAACAAATTTTGTCTCCC
* * *
1898557 TTGAAAAAAATTTCGTCTCTC
1 TTGAAACAAATTTTGTCTCCC
1898578 TTGA
1 TTGA
1898582 GACAGTTTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
16 9 0.29
17 1 0.03
18 4 0.13
19 3 0.10
20 1 0.03
21 13 0.42
ACGTcount: A:0.27, C:0.21, G:0.11, T:0.40
Consensus pattern (21 bp):
TTGAAACAAATTTTGTCTCCC
Found at i:1898582 original size:73 final size:73
Alignment explanation
Indices: 1898434--1898647 Score: 271
Period size: 73 Copynumber: 3.0 Consensus size: 73
1898424 AAAAAAATAT
** *
1898434 TTGAGATCG-TTTCCTTTGAAATTAATTTTGTCTCTCTT-AGACA-GTTTCCCTTGAAACAAATT
1 TTGAGAT-GATTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACATGTTTCCCTTGAAAAAAATT
1898496 TCGTCTCTC
65 TCGTCTCTC
* *
1898505 TTGAGATGATTTCCTTTGAAACAAATTTTGTCTCCCTTGAGACATTTTTCCCTTGAAAAAAATTT
1 TTGAGATGATTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACATGTTTCCCTTGAAAAAAATTT
1898570 CGTCTCTC
66 CGTCTCTC
* * *
1898578 TTGAGA-CAGTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGAC-TGTTTCCCTT-AAAACAAAG
1 TTGAGATGA-TTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACATGTTTCCCTTGAAAA-AAA-
1898640 TTT-GTCTC
63 TTTCGTCTC
1898648 CCTTTATACA
Statistics
Matches: 127, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
70 1 0.01
71 37 0.29
72 23 0.18
73 66 0.52
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.41
Consensus pattern (73 bp):
TTGAGATGATTTCCTTTGAAACAAATTTTGTCTCTCTTGAGACATGTTTCCCTTGAAAAAAATTT
CGTCTCTC
Found at i:1898636 original size:109 final size:108
Alignment explanation
Indices: 1898443--1898651 Score: 330
Period size: 109 Copynumber: 1.9 Consensus size: 108
1898433 TTTGAGATCG
* ** *
1898443 TTTCCTTTGAAATTAATTTTGTCTCTCTTAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTG
1 TTTCCCTTGAAAAAAATTTCGTCTCTCTTAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTG
* * *
1898508 AGATGATTTCCTTTGAAACAAATTTTGTCTCCCTTGAGACATT
66 AGATGATTTCCCTTAAAACAAAGTTTGTCTCCCTTGAGACATT
1898551 TTTCCCTTGAAAAAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTT
1 TTTCCCTTGAAAAAAATTTCGTCTCTCTT-AGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTT
1898616 GAGACTG-TTTCCCTTAAAACAAAGTTTGTCTCCCTT
65 GAGA-TGATTTCCCTTAAAACAAAGTTTGTCTCCCTT
1898652 TATACAGCTT
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
108 25 0.27
109 65 0.71
110 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (108 bp):
TTTCCCTTGAAAAAAATTTCGTCTCTCTTAGACAGTTTCCCTTGAAACAAATTTCGTCTCTCTTG
AGATGATTTCCCTTAAAACAAAGTTTGTCTCCCTTGAGACATT
Found at i:1898780 original size:66 final size:67
Alignment explanation
Indices: 1898622--1898803 Score: 181
Period size: 66 Copynumber: 2.7 Consensus size: 67
1898612 TCTTGAGACT
* *
1898622 GTTTCCCTTAAAACAAAGTTTGTCTCCCTTTATACAGCTTCCCTTGAAACATAAAATATTTGAAT
1 GTTTCCCTTGAAACAAAGTTTGTCTCCCTTTAGACAGCTTCCCTTGAAACATAAAATATTTGAAT
*
1898687 TT
66 TC
* * * * ** *
1898689 GTTTCCCTTGAAACAAAGTTCGTCTCCCTTTAGATAGTTTCTCTTGAAACA-CCAATCTTTGACA
1 GTTTCCCTTGAAACAAAGTTTGTCTCCCTTTAGACAGCTTCCCTTGAAACATAAAATATTTGA-A
1898753 -TC
65 TTC
** * * * *
1898755 GTTTCCCTTGAAATGAATTTTGTCTCTCTCGT-GACAGTTTCCCTTGAAA
1 GTTTCCCTTGAAACAAAGTTTGTCTCCCT-TTAGACAGCTTCCCTTGAAA
1898804 AATGTATCTC
Statistics
Matches: 95, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
66 48 0.51
67 47 0.49
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.38
Consensus pattern (67 bp):
GTTTCCCTTGAAACAAAGTTTGTCTCCCTTTAGACAGCTTCCCTTGAAACATAAAATATTTGAAT
TC
Found at i:1899542 original size:19 final size:20
Alignment explanation
Indices: 1899518--1899564 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1899508 CAAAATTTTT
* *
1899518 AACCCGACCTAGTTTGAC-C
1 AACCCGACCCAGTTCGACTC
1899537 AACCCGACCCAGTTCGACTC
1 AACCCGACCCAGTTCGACTC
*
1899557 GACCCGAC
1 AACCCGAC
1899565 TGCCCAACCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.26, C:0.43, G:0.17, T:0.15
Consensus pattern (20 bp):
AACCCGACCCAGTTCGACTC
Found at i:1899580 original size:13 final size:13
Alignment explanation
Indices: 1899558--1899590 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1899548 GTTCGACTCG
1899558 ACCCGACTGCCCA
1 ACCCGACTGCCCA
*
1899571 ACCCGTCTGCCCA
1 ACCCGACTGCCCA
1899584 ACCCGAC
1 ACCCGAC
1899591 CCATTGATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.21, C:0.55, G:0.15, T:0.09
Consensus pattern (13 bp):
ACCCGACTGCCCA
Found at i:1899636 original size:17 final size:17
Alignment explanation
Indices: 1899614--1899668 Score: 110
Period size: 17 Copynumber: 3.2 Consensus size: 17
1899604 ACTTTGACCA
1899614 AAAAGTCAAAATTTTTG
1 AAAAGTCAAAATTTTTG
1899631 AAAAGTCAAAATTTTTG
1 AAAAGTCAAAATTTTTG
1899648 AAAAGTCAAAATTTTTG
1 AAAAGTCAAAATTTTTG
1899665 AAAA
1 AAAA
1899669 TTCATACTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (17 bp):
AAAAGTCAAAATTTTTG
Found at i:1906864 original size:134 final size:135
Alignment explanation
Indices: 1906610--1906865 Score: 327
Period size: 134 Copynumber: 1.9 Consensus size: 135
1906600 CCATTGACCG
* * * * *
1906610 TTGACTTTGACCAAAAAGTCAAAATTTTTGAAAAGTCGTATTCTATGTTTTTTGACGTCATGAGT
1 TTGACTTTGACCAAAAAATAAAAAATTTTGAAAAGTCATATTCTATGTTTTTCGACGTCATGAGT
* * * * * *
1906675 CTGATTACGAAGTTCGTTTTGCCAAATTCAAACCCGAAAGACTGAAAAATGTCAGTCAAACCCGT
66 CTGAATACGAAGTCCGTTTTCCCAAATTCAAACCCAAAAGACTCAAAAATATCAGTCAAACCCGT
1906740 TAACT
131 TAACT
* * *
1906745 TTGACTTTGACCAAAAAATAAAAAATTTTGAAAAGTCATATTTTATG-TTTTCGGCGTCTTGAGT
1 TTGACTTTGACCAAAAAATAAAAAATTTTGAAAAGTCATATTCTATGTTTTTCGACGTCATGAGT
* * * *
1906809 CTGAAT-CTGAAGTCCGTTTTCCCAAATTCAAACTCAAAAGCCTCCAAATTATCAGTC
66 CTGAATAC-GAAGTCCGTTTTCCCAAATTCAAACCCAAAAGACTCAAAAATATCAGTC
1906866 TAACATGAAC
Statistics
Matches: 102, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
133 1 0.01
134 59 0.58
135 42 0.41
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (135 bp):
TTGACTTTGACCAAAAAATAAAAAATTTTGAAAAGTCATATTCTATGTTTTTCGACGTCATGAGT
CTGAATACGAAGTCCGTTTTCCCAAATTCAAACCCAAAAGACTCAAAAATATCAGTCAAACCCGT
TAACT
Found at i:1907737 original size:16 final size:16
Alignment explanation
Indices: 1907716--1907753 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
1907706 TTAGATACCC
1907716 AGGATCAAGCACTTGG
1 AGGATCAAGCACTTGG
1907732 AGGATCAAGCACTTGG
1 AGGATCAAGCACTTGG
1907748 AGGATC
1 AGGATC
1907754 GACACATTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (16 bp):
AGGATCAAGCACTTGG
Found at i:1908853 original size:39 final size:39
Alignment explanation
Indices: 1908799--1908962 Score: 238
Period size: 39 Copynumber: 4.2 Consensus size: 39
1908789 TCTGCTACAA
*
1908799 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAGCAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
*
1908838 AAGATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
* * ** **
1908877 AGGATTTTATCTCGCTTAAGATTCTTTTACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
* *
1908916 AAGATTTTATCTCGCTTGAGATAGTTTCGCTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
1908955 AAGATTTT
1 AAGATTTT
1908963 TAGAAACTAA
Statistics
Matches: 109, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 109 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAG
Found at i:1909103 original size:53 final size:52
Alignment explanation
Indices: 1909019--1909216 Score: 193
Period size: 52 Copynumber: 3.7 Consensus size: 52
1909009 TGAGTTTTTA
* *
1909019 AAAGAAAACTGAGCCTAA-TTTTAGGGGTTTCTTGATGTTTTCAAATGAATTT
1 AAAG-AAACTAAGCCTAATTTTTAGGGATTTCTTGATGTTTTCAAATGAATTT
* * * *
1909071 CAAAGAAATTAAGCCTAATATTTAGGGATTTCTTGATGTTGTCAAATGAGTTT
1 -AAAGAAACTAAGCCTAATTTTTAGGGATTTCTTGATGTTTTCAAATGAATTT
** * * *
1909124 TTAGAAACTAAGCCTGATTTTTAGAGATTTCTTGATGATGATTTTC-AATGAGTTTT
1 AAAGAAACTAAGCCTAATTTTTAGGGATTTC-T--TGATG-TTTTCAAATGA-ATTT
*
1909180 AAAAGGAAACTAAGCCTAATTTTTAGGGTTTTCTTGA
1 -AAA-GAAACTAAGCCTAATTTTTAGGGATTTCTTGA
1909217 CAACTAAGAA
Statistics
Matches: 118, Mismatches: 19, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
52 36 0.31
53 35 0.30
55 13 0.11
56 7 0.06
57 2 0.02
58 25 0.21
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (52 bp):
AAAGAAACTAAGCCTAATTTTTAGGGATTTCTTGATGTTTTCAAATGAATTT
Found at i:1909202 original size:58 final size:57
Alignment explanation
Indices: 1908964--1909216 Score: 237
Period size: 58 Copynumber: 4.6 Consensus size: 57
1908954 AAAGATTTTT
**
1908964 AGAAACTAAGCCT-GGTTTTAGTGG-TTTCTTGATGATGATTTTC-AATGAGTTTTTAAA
1 AGAAACTAAGCCTAATTTTTAG-GGATTTCTTGATGATG-TTTTCAAATGAG-TTTTAAA
* * * *
1909021 AGAAAACTGAGCCTAA-TTTTAGGGGTTTC-T--TGATGTTTTCAAATGA-ATTTCAA
1 AG-AAACTAAGCCTAATTTTTAGGGATTTCTTGATGATGTTTTCAAATGAGTTTTAAA
* * * *
1909074 AGAAATTAAGCCTAATATTTAGGGATTTC-T--TGATGTTGTCAAATGAGTTTT--T
1 AGAAACTAAGCCTAATTTTTAGGGATTTCTTGATGATGTTTTCAAATGAGTTTTAAA
* *
1909126 AGAAACTAAGCCTGATTTTTAGAGATTTCTTGATGATGATTTTC-AATGAGTTTTAAA
1 AGAAACTAAGCCTAATTTTTAGGGATTTCTTGATGATG-TTTTCAAATGAGTTTTAAA
*
1909183 AGGAAACTAAGCCTAATTTTTAGGGTTTTCTTGA
1 A-GAAACTAAGCCTAATTTTTAGGGATTTCTTGA
1909217 CAACTAAGAA
Statistics
Matches: 163, Mismatches: 20, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
52 36 0.22
53 35 0.21
54 8 0.05
55 25 0.15
56 4 0.02
57 6 0.04
58 49 0.30
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (57 bp):
AGAAACTAAGCCTAATTTTTAGGGATTTCTTGATGATGTTTTCAAATGAGTTTTAAA
Found at i:1909447 original size:83 final size:83
Alignment explanation
Indices: 1909343--1909593 Score: 369
Period size: 84 Copynumber: 3.0 Consensus size: 83
1909333 AGCAAGGTGA
* * *
1909343 TAAGTCCTTCAGGCCATCTATAAGACCTTCGGGCAGATTTTTTAAACATTTCATTTGCTCGATTC
1 TAAGTCCTTCAGGCCATCTATAAGACCTTCGGGCAGATGTTTTCAACATTTCCTTTGCTCGATTC
1909408 ACACACTTTGAATCAGCT
66 ACACACTTTGAATCAGCT
*
1909426 TAAGTCCTTC-GAGCCATCTATAAGAACTTCGGGCAGGATGTTTTCAACATTTCCTTTGCTCGAT
1 TAAGTCCTTCAG-GCCATCTATAAGACCTTCGGGCA-GATGTTTTCAACATTTCCTTTGCTCGAT
* ** *
1909490 TCACATACTTCAAATTAGCT
64 TCACACACTTTGAATCAGCT
* *
1909510 TAAGTCCTTCAGGCCATCCATAAGACCTTCGGGCAAGATGTTTTCAGCATTTCCTTTGCTCGATT
1 TAAGTCCTTCAGGCCATCTATAAGACCTTCGGGC-AGATGTTTTCAACATTTCCTTTGCTCGATT
1909575 CACAACACTTTGAATCAGC
65 CAC-ACACTTTGAATCAGC
1909594 AACGCCCTAC
Statistics
Matches: 148, Mismatches: 15, Indels: 8
0.87 0.09 0.05
Matches are distributed among these distances:
82 1 0.01
83 32 0.22
84 102 0.69
85 13 0.09
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (83 bp):
TAAGTCCTTCAGGCCATCTATAAGACCTTCGGGCAGATGTTTTCAACATTTCCTTTGCTCGATTC
ACACACTTTGAATCAGCT
Found at i:1909712 original size:42 final size:42
Alignment explanation
Indices: 1909656--1909803 Score: 174
Period size: 42 Copynumber: 3.5 Consensus size: 42
1909646 GAATCAGCTG
*
1909656 AAGTCCTTCAGGCCATCAATAAGTCTTTCGAGAATGATGTGT
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAATGATGTGT
* * * *
1909698 AAGTCATTCGGGCCATCAGTAAGTCTTTCAAGCATGATGTGT
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAATGATGTGT
* * * **
1909740 AAGTCCTTCGGGCCATCTATGAGTCTTTTGAGCAA-GAT-AAT
1 AAGTCCTTCGGGCCATCAATAAGTCTTTCGAG-AATGATGTGT
*
1909781 AAGTCCTTCGGGCCATCCATAAG
1 AAGTCCTTCGGGCCATCAATAAG
1909804 ACCTTCGGAC
Statistics
Matches: 89, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
41 22 0.25
42 66 0.74
43 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (42 bp):
AAGTCCTTCGGGCCATCAATAAGTCTTTCGAGAATGATGTGT
Done.