Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 18
Found at i:1811718 original size:11 final size:10
Alignment explanation
Indices: 1811698--1811777 Score: 56
Period size: 11 Copynumber: 7.7 Consensus size: 10
1811688 AGTTTAAAAA
*
1811698 ATTATAAAAT
1 ATTATTAAAT
1811708 ACTTATTAAAT
1 A-TTATTAAAT
1811719 -TTATTAAAAT
1 ATTATT-AAAT
*
1811729 ATTATAAAATT
1 ATTATTAAA-T
*
1811740 ATTAATAAAT
1 ATTATTAAAT
1811750 -TTATCTAAAT
1 ATTAT-TAAAT
* *
1811760 ACTATAAAAT
1 ATTATTAAAT
1811770 AATTATTA
1 -ATTATTA
1811778 TATTATCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.15
10 18 0.33
11 28 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:1811726 original size:31 final size:30
Alignment explanation
Indices: 1811691--1811777 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 30
1811681 TCAATAAAGT
*
1811691 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
*
1811722 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAATATTATAAAA-TATTATTAAATTTA
*
1811753 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAATATTATAAAAT-ATTATTA
1811778 TATTATCGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:1811736 original size:19 final size:21
Alignment explanation
Indices: 1811695--1811744 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
1811685 TAAAGTTTAA
1811695 AAAATTA-TAAAATACTTATT
1 AAAATTATTAAAATACTTATT
*
1811715 AAATTTATTAAAATA-TTA-T
1 AAAATTATTAAAATACTTATT
1811734 AAAATTATTAA
1 AAAATTATTAA
1811745 TAAATTTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 11 0.41
20 9 0.33
21 7 0.26
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATTATTAAAATACTTATT
Found at i:1815004 original size:9 final size:9
Alignment explanation
Indices: 1814990--1815058 Score: 66
Period size: 9 Copynumber: 7.3 Consensus size: 9
1814980 GCTACTGGAA
1814990 ACCGGTTTG
1 ACCGGTTTG
*
1814999 ACCGGTTTCA
1 ACCGGTTT-G
*
1815009 ACCGGTTCG
1 ACCGGTTTG
*
1815018 AAACGGTTTG
1 -ACCGGTTTG
*
1815028 ACCGGTCTG
1 ACCGGTTTG
1815037 AACCGGTTTG
1 -ACCGGTTTG
*
1815047 ACCGGTCTG
1 ACCGGTTTG
1815056 ACC
1 ACC
1815059 CGACCCGACC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
9 26 0.54
10 22 0.46
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1815030 original size:29 final size:30
Alignment explanation
Indices: 1814987--1815044 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
1814977 GTGGCTACTG
*
1814987 GAAACCGGTTTGACCGGTTTCAACCGGTTC
1 GAAACCGGTTTGACCGGTCTCAACCGGTTC
*
1815017 GAAA-CGGTTTGACCGGTCTGAACCGGTT
1 GAAACCGGTTTGACCGGTCTCAACCGGTT
1815045 TGACCGGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (30 bp):
GAAACCGGTTTGACCGGTCTCAACCGGTTC
Found at i:1815031 original size:19 final size:20
Alignment explanation
Indices: 1815009--1815056 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
1814999 ACCGGTTTCA
1815009 ACCGGTTC-GAAACGGTTTG
1 ACCGGTTCTGAAACGGTTTG
*
1815028 ACCGG-TCTGAACCGGTTTG
1 ACCGGTTCTGAAACGGTTTG
1815047 ACCGG-TCTGA
1 ACCGGTTCTGA
1815057 CCCGACCCGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 2 0.07
19 25 0.93
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (20 bp):
ACCGGTTCTGAAACGGTTTG
Found at i:1815076 original size:17 final size:17
Alignment explanation
Indices: 1815054--1815109 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
1815044 TTGACCGGTC
*
1815054 TGACCCGACCCGACCGG
1 TGACCCGACCCGACCGT
1815071 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1815088 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1815105 TGACC
1 TGACC
1815110 GTTGACTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.18, C:0.46, G:0.25, T:0.11
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1822148 original size:11 final size:11
Alignment explanation
Indices: 1822132--1822181 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
1822122 AAACCGATTT
1822132 AACCGGTTTTC
1 AACCGGTTTTC
*
1822143 AACCGGTTCT-
1 AACCGGTTTTC
*
1822153 GACCGG-TTTC
1 AACCGGTTTTC
*
1822163 AACCGG-TTTG
1 AACCGGTTTTC
1822173 AACCGGTTT
1 AACCGGTTT
1822182 GACCGGTCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 2 0.06
10 19 0.59
11 11 0.34
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (11 bp):
AACCGGTTTTC
Found at i:1822159 original size:10 final size:9
Alignment explanation
Indices: 1822144--1822205 Score: 70
Period size: 10 Copynumber: 6.4 Consensus size: 9
1822134 CCGGTTTTCA
1822144 ACCGGTTCTG
1 ACCGGTT-TG
*
1822154 ACCGGTTTCA
1 ACCGGTTT-G
1822164 ACCGGTTTG
1 ACCGGTTTG
1822173 AACCGGTTTG
1 -ACCGGTTTG
*
1822183 ACCGGTCTG
1 ACCGGTTTG
1822192 AACCGGTTTG
1 -ACCGGTTTG
1822202 ACCG
1 ACCG
1822206 ATCTGACCCG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
9 13 0.29
10 32 0.71
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1822162 original size:20 final size:21
Alignment explanation
Indices: 1822132--1822200 Score: 92
Period size: 20 Copynumber: 3.4 Consensus size: 21
1822122 AAACCGATTT
1822132 AACCGGTTTTCAACCGGTTCTG
1 AACCGG-TTTCAACCGGTTCTG
1822154 -ACCGGTTTCAACCGGTT-TG
1 AACCGGTTTCAACCGGTTCTG
*
1822173 AACCGGTTT-GACCGG-TCTG
1 AACCGGTTTCAACCGGTTCTG
1822192 AACCGGTTT
1 AACCGGTTT
1822201 GACCGATCTG
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
18 1 0.02
19 18 0.41
20 20 0.45
21 5 0.11
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
AACCGGTTTCAACCGGTTCTG
Found at i:1822188 original size:19 final size:19
Alignment explanation
Indices: 1822144--1822205 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
1822134 CCGGTTTTCA
*
1822144 ACCGGTTCTG-ACCGGTTTCA
1 ACCGGTT-TGAACCGGTTT-G
1822164 ACCGGTTTGAACCGGTTTG
1 ACCGGTTTGAACCGGTTTG
*
1822183 ACCGGTCTGAACCGGTTTG
1 ACCGGTTTGAACCGGTTTG
1822202 ACCG
1 ACCG
1822206 ATCTGACCCG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
19 24 0.62
20 15 0.38
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.27
Consensus pattern (19 bp):
ACCGGTTTGAACCGGTTTG
Found at i:1822210 original size:19 final size:19
Alignment explanation
Indices: 1822171--1822211 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1822161 TCAACCGGTT
*
1822171 TGAACCGGTTTGACCGGTC
1 TGAACCGGTTTGACCGATC
1822190 TGAACCGGTTTGACCGATC
1 TGAACCGGTTTGACCGATC
1822209 TGA
1 TGA
1822212 CCCGACCCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (19 bp):
TGAACCGGTTTGACCGATC
Found at i:1822212 original size:9 final size:9
Alignment explanation
Indices: 1822144--1822213 Score: 50
Period size: 10 Copynumber: 7.3 Consensus size: 9
1822134 CCGGTTTTCA
1822144 ACCGGTTCTG
1 ACCGG-TCTG
* *
1822154 ACCGGTTTCA
1 ACCGGTCT-G
*
1822164 ACCGGTTTG
1 ACCGGTCTG
*
1822173 AACCGGTTTG
1 -ACCGGTCTG
1822183 ACCGGTCTG
1 ACCGGTCTG
*
1822192 AACCGGTTTG
1 -ACCGGTCTG
*
1822202 ACCGATCTG
1 ACCGGTCTG
1822211 ACC
1 ACC
1822214 CGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
9 20 0.40
10 30 0.60
ACGTcount: A:0.17, C:0.29, G:0.27, T:0.27
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:1822231 original size:17 final size:17
Alignment explanation
Indices: 1822209--1822247 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1822199 TTGACCGATC
1822209 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1822226 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
1822243 TGACC
1 TGACC
1822248 GTTGACTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:1825691 original size:24 final size:23
Alignment explanation
Indices: 1825668--1825751 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 23
1825658 TATTTTTTTA
1825668 AATTAAGTTAATAAAAAATATTT
1 AATTAAGTTAATAAAAAATATTT
*
1825691 AA-TAAGTTAATGTAAAAATATTT
1 AATTAAGTTAAT-AAAAAATATTT
*
1825714 -TTTAAGTTAATATAAAAAATATTAT
1 AATTAAGTT-A-ATAAAAAATATT-T
1825739 GAATTTAAGTTAA
1 -AA-TTAAGTTAA
1825752 ATATTTATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
22 9 0.18
23 18 0.37
24 10 0.20
25 3 0.06
26 1 0.02
27 1 0.02
28 7 0.14
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (23 bp):
AATTAAGTTAATAAAAAATATTT
Found at i:1825973 original size:51 final size:51
Alignment explanation
Indices: 1825906--1826002 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
1825896 GGCGTGGCCA
* * *
1825906 ATGCACCGCGCCTTACGCTAATGTGGCGCCACGTAGGGTAAGGCGCAACCC
1 ATGCACCACGCATTACGCTAATGTGGCGCCACGCAGGGTAAGGCGCAACCC
*
1825957 ATGCACCACGCATTACGCTGATGTGGCGCCACGCAGGGTAAGGCGC
1 ATGCACCACGCATTACGCTAATGTGGCGCCACGCAGGGTAAGGCGC
1826003 GATGCATGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.22, C:0.32, G:0.31, T:0.15
Consensus pattern (51 bp):
ATGCACCACGCATTACGCTAATGTGGCGCCACGCAGGGTAAGGCGCAACCC
Found at i:1826039 original size:40 final size:40
Alignment explanation
Indices: 1825984--1826061 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
1825974 CTGATGTGGC
*
1825984 GCCACGCAGGGTAAGGCGCGATGCATGGGTCGCACCTTAT
1 GCCACGCAGGGTAAGGCGCGATGCATGGGCCGCACCTTAT
* * * *
1826024 GCCACGTAGGGTAAGGTGCGGTGCATGGGCCGCGCCTT
1 GCCACGCAGGGTAAGGCGCGATGCATGGGCCGCACCTT
1826062 TCTGCCAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.17, C:0.27, G:0.38, T:0.18
Consensus pattern (40 bp):
GCCACGCAGGGTAAGGCGCGATGCATGGGCCGCACCTTAT
Found at i:1826325 original size:21 final size:20
Alignment explanation
Indices: 1826265--1826325 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
1826255 TAATATTTTG
1826265 TTAGTATTTTATTTAATTA-
1 TTAGTATTTTATTTAATTAT
* *
1826284 -TA-TA-ATTATTTAAATTTT
1 TTAGTATTTTATTT-AATTAT
1826302 TTAGTATTTTATTTAATTAAT
1 TTAGTATTTTATTTAATT-AT
1826323 TTA
1 TTA
1826326 TTTTTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
16 6 0.19
17 6 0.19
18 2 0.06
19 2 0.06
20 6 0.19
21 10 0.31
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTAGTATTTTATTTAATTAT
Found at i:1831519 original size:27 final size:28
Alignment explanation
Indices: 1831470--1831530 Score: 97
Period size: 27 Copynumber: 2.2 Consensus size: 28
1831460 AGTTAATGGG
*
1831470 ATGGCTCCATTGAAGTGGATTTCCCATT
1 ATGGCACCATTGAAGTGGATTTCCCATT
*
1831498 ATGGCACCA-TGATGTGGATTTCCCATT
1 ATGGCACCATTGAAGTGGATTTCCCATT
1831525 ATGGCA
1 ATGGCA
1831531 TTAAAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (28 bp):
ATGGCACCATTGAAGTGGATTTCCCATT
Found at i:1832365 original size:29 final size:29
Alignment explanation
Indices: 1832295--1832367 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
1832285 TCGGGTGATA
* * *
1832295 TTTACGGGTTGAAAGGTTTGTTGTGTGAT
1 TTTACGGGTTGAGAGGATTGTTGTGTAAT
*
1832324 TTTTCGGGTTGAGAGGATTGTTGTG-AAT
1 TTTACGGGTTGAGAGGATTGTTGTGTAAT
1832352 GTTTACGGGTTGAGAG
1 -TTTACGGGTTGAGAG
1832368 TGTATTTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 2 0.05
29 36 0.95
ACGTcount: A:0.18, C:0.04, G:0.37, T:0.41
Consensus pattern (29 bp):
TTTACGGGTTGAGAGGATTGTTGTGTAAT
Found at i:1832525 original size:40 final size:40
Alignment explanation
Indices: 1832474--1832551 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
1832464 AGTTGGCAGA
*
1832474 AAGGCGCGACTCATGCACCGCGCCTTACCCTACGTGGCAT
1 AAGGCGCGACTCATGCACCGCACCTTACCCTACGTGGCAT
* *
1832514 AAGGCGTGACTCATGCACCGCACCTTACCCTGCGTGGC
1 AAGGCGCGACTCATGCACCGCACCTTACCCTACGTGGC
1832552 GCCACATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.19, C:0.37, G:0.26, T:0.18
Consensus pattern (40 bp):
AAGGCGCGACTCATGCACCGCACCTTACCCTACGTGGCAT
Found at i:1835503 original size:2 final size:2
Alignment explanation
Indices: 1835496--1835526 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1835486 ATTATATCGT
1835496 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 T
1835527 TAATGATTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1838975 original size:21 final size:21
Alignment explanation
Indices: 1838931--1838976 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1838921 GATTTCTGGG
* * *
1838931 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
1838952 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
1838973 CAAG
1 CAAG
1838977 CGAACCAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:1839048 original size:23 final size:22
Alignment explanation
Indices: 1839000--1839048 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1838990 ATAGAATGTC
1839000 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
1839021 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
1839044 AAGGA
1 AAGGA
1839049 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.13
22 15 0.65
23 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.29, T:0.08
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:1839444 original size:20 final size:22
Alignment explanation
Indices: 1839404--1839460 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
1839394 TGAATATGTG
*
1839404 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
1839426 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
1839446 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
1839461 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:1840027 original size:31 final size:31
Alignment explanation
Indices: 1839989--1840237 Score: 410
Period size: 31 Copynumber: 8.0 Consensus size: 31
1839979 AGGGTCGAGG
1839989 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1840020 GTTTACCTATGTTCTTCAGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1840051 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1840082 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1840113 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1840144 GTTTACCTATGTTATTCGTGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1840175 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1840206 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1840237 G
1 G
1840238 GTCCTTCGGG
Statistics
Matches: 204, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
31 203 1.00
32 1 0.00
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1854687 original size:212 final size:210
Alignment explanation
Indices: 1854321--1854742 Score: 810
Period size: 212 Copynumber: 2.0 Consensus size: 210
1854311 TGGAAGTAAC
1854321 CTGTAGAACAAAATCTAATCTTATTCACCTTGGAGATTGGATTGAGCGGAATAGACTTAGATAAG
1 CTGTAGAACAAAATCTAATCTTATTCACCTTGGAGATTGGATTGAGCGGAATAGACTTAGATAAG
1854386 TGGTTATTCCGAAAAGAAAATGAGATTTTAATGTGGCTCATCATTGCTCTTGAAGAAAAAGAAGC
66 TGGTTATTCCGAAAAGAAAATGAGATTTTAATGTGGCTCATCATTGCTCTTGAAGAAAAAGAAGC
1854451 TGAAGATATACAGAAATAAGTAGTACCTCTGCACTTTCCGATCCTCCTTTGCTTGCACCTG-TTT
131 TGAAGATATACAGAAATAAGTAGTACCTCTGCACTTTCCGATCCTCCTTTGCTTGCACCTGTTTT
1854515 AAGGTTAGTCACAAG
196 AAGGTTAGTCACAAG
1854530 CTGTAGAACAAAATCTAATCTTATTCACCTTGGAGATTGGATTGAGCGGAATAGACTTAGATAAG
1 CTGTAGAACAAAATCTAATCTTATTCACCTTGGAGATTGGATTGAGCGGAATAGACTTAGATAAG
1854595 TGGTTTATTCCGAAAAGAAAAGCTGAGATTTTAATGTGGCTCATCATTGCTCTTGAAGAAAAAGA
66 TGG-TTATTCCGAAAAGAAAA--TGAGATTTTAATGTGGCTCATCATTGCTCTTGAAGAAAAAGA
1854660 AGCTGAAGATATACAGAAATAAGTAGTACCTCTGCACTTTCCGATCCTCCTTTGCTTGCACCTGT
128 AGCTGAAGATATACAGAAATAAGTAGTACCTCTGCACTTTCCGATCCTCCTTTGCTTGCACCTGT
1854725 TTTAAGGTTAGTCACAAG
193 TTTAAGGTTAGTCACAAG
1854743 AACAGATCCG
Statistics
Matches: 209, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
209 68 0.33
210 17 0.08
212 106 0.51
213 18 0.09
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (210 bp):
CTGTAGAACAAAATCTAATCTTATTCACCTTGGAGATTGGATTGAGCGGAATAGACTTAGATAAG
TGGTTATTCCGAAAAGAAAATGAGATTTTAATGTGGCTCATCATTGCTCTTGAAGAAAAAGAAGC
TGAAGATATACAGAAATAAGTAGTACCTCTGCACTTTCCGATCCTCCTTTGCTTGCACCTGTTTT
AAGGTTAGTCACAAG
Found at i:1859807 original size:21 final size:21
Alignment explanation
Indices: 1859774--1859814 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1859764 TTCTGGGCAA
* *
1859774 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1859795 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1859815 ACGAACAAGA
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:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:1861602 original size:149 final size:149
Alignment explanation
Indices: 1861275--1861712 Score: 753
Period size: 149 Copynumber: 3.0 Consensus size: 149
1861265 GAGTCGAGGG
*
1861275 TCTACGCGGTTCTTCGGGACATATG-TTATTCTTTGGAA-ATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGCATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1861338 ACTTGATCCCTAGCATATG--TATGA-TC-TAAAGAATTCTA--T-GTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
1861396 TATGGCACTAC-GTGCAAT
131 TATGGCACTACGGTGCAAT
1861414 TCTACGCGGTTCTTCGGGACATATGCATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGCATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1861479 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
1861544 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1861563 TCTACGCGGTTCTTCGGGACATATGCATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACAC--
1 TCTACGCGGTTCTTCGGGACATATGCATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1861626 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
1861691 TA---CACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1861707 TCTACG
1 TCTACG
1861713 GGGCACTTCG
Statistics
Matches: 287, Mismatches: 2, Indels: 15
0.94 0.01 0.05
Matches are distributed among these distances:
139 25 0.09
140 12 0.04
141 44 0.15
143 5 0.02
144 22 0.08
145 12 0.04
147 67 0.23
148 30 0.10
149 70 0.24
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGCATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:1864746 original size:21 final size:21
Alignment explanation
Indices: 1864720--1864764 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1864710 GATTTCTGGG
* *
1864720 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1864741 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1864762 CAA
1 CAA
1864765 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1866435 original size:149 final size:149
Alignment explanation
Indices: 1866255--1866558 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1866245 GAGTCGAGGG
1866255 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
1866320 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1866385 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1866404 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1866469 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
1866534 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1866553 TCTACG
1 TCTACG
1866559 GGGCACTTCG
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:1866581 original size:23 final size:23
Alignment explanation
Indices: 1866537--1866581 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1866527 ATCATTATAT
*
1866537 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
1866560 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1866582 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:1877164 original size:32 final size:32
Alignment explanation
Indices: 1877046--1877163 Score: 148
Period size: 32 Copynumber: 3.7 Consensus size: 32
1877036 GTTCCTTAGA
* *
1877046 ACATAGGT-ATACTGTCCATATGCCCCGAAAG
1 ACATAGGTAATTCTATCCATATGCCCCGAAAG
* *
1877077 ACGTAGGTAATTCTATCCATATGCCCCAAAAG
1 ACATAGGTAATTCTATCCATATGCCCCGAAAG
* * *
1877109 AAATAGGTAATTCTATACATATGTCCCGAAAG
1 ACATAGGTAATTCTATCCATATGCCCCGAAAG
* *
1877141 ACATAGGTAATTTTGTCCATATG
1 ACATAGGTAATTCTATCCATATG
1877164 TTCCGTAGAA
Statistics
Matches: 73, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
31 7 0.10
32 66 0.90
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (32 bp):
ACATAGGTAATTCTATCCATATGCCCCGAAAG
Found at i:1877177 original size:32 final size:31
Alignment explanation
Indices: 1877043--1877182 Score: 113
Period size: 32 Copynumber: 4.4 Consensus size: 31
1877033 TATGTTCCTT
* * *
1877043 AGAACATAGGT-ATACTGTCCATATGCCCCG
1 AGAACATAGGTAATTCTATCCATATGTCCCG
* * * *
1877073 AAAGACGTAGGTAATTCTATCCATATGCCCCAAA
1 AGA-ACATAGGTAATTCTATCCATATGTCCC--G
*
1877107 AGAA-ATAGGTAATTCTATACATATGTCCCG
1 AGAACATAGGTAATTCTATCCATATGTCCCG
* * * *
1877137 AAAGACATAGGTAATTTTGTCCATATGTTCCG
1 AGA-ACATAGGTAATTCTATCCATATGTCCCG
1877169 TAGAACATAGGTAA
1 -AGAACATAGGTAA
1877183 ACCCTCGACT
Statistics
Matches: 87, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
30 4 0.05
31 8 0.09
32 70 0.80
33 3 0.03
34 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (31 bp):
AGAACATAGGTAATTCTATCCATATGTCCCG
Found at i:1877179 original size:64 final size:64
Alignment explanation
Indices: 1877031--1877182 Score: 173
Period size: 64 Copynumber: 2.4 Consensus size: 64
1877021 GTAAACTGTT
* * * *
1877031 CATATGTTCCTTAGAACATAGGT-ATACTGTCCATATGCCCCGAAAGACGTAGGTAATTCTATC
1 CATATGTTCCATAGAACATAGGTAATACTATACATATGCCCCGAAAGACATAGGTAATTCTATC
** * * * * *
1877094 CATATGCCCCAAAAGAA-ATAGGTAATTCTATACATATGTCCCGAAAGACATAGGTAATTTTGTC
1 CATATGTTCC-ATAGAACATAGGTAATACTATACATATGCCCCGAAAGACATAGGTAATTCTATC
*
1877158 CATATGTTCCGTAGAACATAGGTAA
1 CATATGTTCCATAGAACATAGGTAA
1877183 ACCCTCGACT
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
63 18 0.25
64 53 0.75
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (64 bp):
CATATGTTCCATAGAACATAGGTAATACTATACATATGCCCCGAAAGACATAGGTAATTCTATC
Found at i:1877384 original size:28 final size:28
Alignment explanation
Indices: 1877335--1877389 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1877325 CATATCATAT
*
1877335 CATATCATATCACATGTATCACGTATTG
1 CATATCATATCACATGTATCACATATTG
1877363 CATATTCATATTCACA-GT-TCACATATT
1 CATA-TCATA-TCACATGTATCACATATT
1877390 CACATATGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.50
29 7 0.29
30 5 0.21
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (28 bp):
CATATCATATCACATGTATCACATATTG
Found at i:1881899 original size:40 final size:39
Alignment explanation
Indices: 1881854--1881933 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 39
1881844 TCTTTTTTCC
* *
1881854 CATCTCTTCTTCGTTCTGGGTTCTTCGT-TTTTTTGGGGTT
1 CATCTCTCCTTCGTCCT-GGTT-TTCGTATTTTTTGGGGTT
**
1881894 CATCTCTCCTTCGTCCTGGTTTTTTTATTTTTTGGGGTT
1 CATCTCTCCTTCGTCCTGGTTTTCGTATTTTTTGGGGTT
1881933 C
1 C
1881934 CTTTCTTGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 3 0.09
39 17 0.49
40 15 0.43
ACGTcount: A:0.04, C:0.21, G:0.20, T:0.55
Consensus pattern (39 bp):
CATCTCTCCTTCGTCCTGGTTTTCGTATTTTTTGGGGTT
Found at i:1887672 original size:11 final size:11
Alignment explanation
Indices: 1887658--1887755 Score: 79
Period size: 11 Copynumber: 8.5 Consensus size: 11
1887648 AAATTTCAAG
*
1887658 AGCTCGATTGA
1 AGCTCGATTCA
* *
1887669 AGCTCTAGACTCG
1 AGCTC--GATTCA
*
1887682 AGCTCGATTGA
1 AGCTCGATTCA
*
1887693 AGCTCGAGACTCA
1 AGCTC--GATTCA
1887706 AGCTCGATTCA
1 AGCTCGATTCA
1887717 AGCTCGATTCA
1 AGCTCGATTCA
**
1887728 AGCTCGATTTTG
1 AGCTCGA-TTCA
*
1887740 AGCTCAATTCA
1 AGCTCGATTCA
1887751 AGCTC
1 AGCTC
1887756 AAGACTGCTA
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
11 43 0.63
12 8 0.12
13 17 0.25
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:1887686 original size:24 final size:24
Alignment explanation
Indices: 1887657--1887723 Score: 107
Period size: 24 Copynumber: 2.8 Consensus size: 24
1887647 AAAATTTCAA
*
1887657 GAGCTCGATTGAAGCTCTAGACTC
1 GAGCTCGATTGAAGCTCGAGACTC
1887681 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGAGACTC
* *
1887705 AAGCTCGATTCAAGCTCGA
1 GAGCTCGATTGAAGCTCGA
1887724 TTCAAGCTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (24 bp):
GAGCTCGATTGAAGCTCGAGACTC
Found at i:1887749 original size:23 final size:22
Alignment explanation
Indices: 1887658--1887755 Score: 79
Period size: 24 Copynumber: 4.2 Consensus size: 22
1887648 AAATTTCAAG
* * *
1887658 AGCTCGATTGAAGCTCTAGACTCG
1 AGCTCGATTCAAGCTC-A-ATTCA
* *
1887682 AGCTCGATTGAAGCTCGAGACTCA
1 AGCTCGATTCAAGCTC-A-ATTCA
*
1887706 AGCTCGATTCAAGCTCGATTCA
1 AGCTCGATTCAAGCTCAATTCA
**
1887728 AGCTCGATTTTGAGCTCAATTCA
1 AGCTCGA-TTCAAGCTCAATTCA
1887751 AGCTC
1 AGCTC
1887756 AAGACTGCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
22 11 0.17
23 17 0.26
24 37 0.57
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (22 bp):
AGCTCGATTCAAGCTCAATTCA
Found at i:1889580 original size:5 final size:5
Alignment explanation
Indices: 1889567--1892188 Score: 4146
Period size: 5 Copynumber: 537.8 Consensus size: 5
1889557 AATTGAATCA
*
1889567 TATTT TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1889617 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1889667 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1889717 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1889767 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1889817 TATTG TATTG TATTG TATTG TATTG TATTG TATTG T-TTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1889866 TATTG TATTG TATTG TATTGTG TATTG TATTG TATTG TATTG TATTG T-TTG
1 TATTG TATTG TATTG TA-T-TG TATTG TATTG TATTG TATTG TATTG TATTG
1889917 TATTG TATTG TATTG TATTG TATTG TATTG --TTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1889965 TATTG TATTG TATTG TATTG TA-TG TATTG TATTG TATTG TATTG TA-TG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
* *
1890013 GATTG --TTG TATTG TATTG TATTG TATTG TATTG --TGG TATTG TA-TG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890058 TATTG TATTG T-TTG TATTG TATTG TATTG TATTG TATTG T-TTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890106 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
*
1890156 TA-TG TA-TG TA-TG TATTG TATGG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890203 TATTG TATTG TATATTG TA-TG TATTG TATTG TATTG TATTG TA-TG TATTG
1 TATTG TATTG --TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890253 TATTG TATTG TATTG TATTG TATTG TATTG TA-TG TATTG TA-TG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890301 TA-TG TATTG TATTG TATTG TATTG TATTG TA-TG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890349 TATTG TATTG TA-TG TA-TG -ATTG TA--G TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890394 TATTG TATTG TA-TG -ATTG TATTG TA-TG TATTG TATTG TATTTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-TTG TATTG
1890442 TATTG TA-TG TA-TG TATTG TA-TG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890489 TATTG TA-TG TATTG TATTG TATTG TATTG --TTG TATTG TATTG TA-TG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
*
1890535 TATTG TA-TG GATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890584 TATTG TATTG TATTG TATTG TATTG -A-TG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890632 TA-TG TATTG TATTG TATTG --TTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890679 TATTG TA-TG TATTG TATTG TATTG TATTG TATTG TA--G TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890726 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890776 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890826 TATTG TATTG TATTG TATTGTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TA-T-TG TATTG TATTG TATTG TATTG TATTG TATTG
1890878 TATTG TATTG TA-TG TA-TG TATTG TATTG TATTG TA-TG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890925 -ATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1890974 TATTG T-TTG TATTG TATTG TATTG TA-TG -ATTG TATTG TATATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG --TATTG TATTG
1891023 TATTG TATTG TA-TG TATTG TATTG TATTTG TATTG TATTG TA-TG TATT-
1 TATTG TATTG TATTG TATTG TATTG TA-TTG TATTG TATTG TATTG TATTG
1891071 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-TG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
*
1891120 TA-TG TATTG TTGTTG TATTG TATTG TATTG TATTG TA-T- TATTG TATTG
1 TATTG TATTG -TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891168 TATTG TA-TG TATTG TATTG TA-TG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
*
1891216 TA-TG -ATTG TATTG TATTG --TTG TATTG TATTG TGTATG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TAT-TG TATTG TATTG
1891263 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-TG T-TTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891311 TATTG TATTG TATTG TATTG TATTG TATTGG TATATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATT-G --TATTG TATTG TATTG
1891359 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTGTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-T-TG TATTG TATTG
1891411 TATTG TATTG TATTG TATTG TATTG TA-TG TATTG TATTTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-TTG TATTG TATTG
*
1891461 TATTG TATTG TATTG TATTG TATTG TATTG TA-TG TA-GG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891509 TA-TG TATTG TATTG TATTG TATTG TATTG TATTG -A-TG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891556 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891606 TA--G TATTG TATTG TATTG TATTG TATTG TATTG TATTG --TTG TA-TG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891651 TATTG --TTG TATTG TATTG -AGTATG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TA-T-TG TATTG TATTG TATTG TATTG TATTG
1891700 TATTG TATTG TATTG --TTG TATTG TATTG TATATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG --TATTG TATTG TATTG TATTG
1891750 --TTG TATTGTG TATTG TATTG TA-TG TATTG TATTG TATATTG TATTG
1 TATTG TA-T-TG TATTG TATTG TATTG TATTG TATTG --TATTG TATTG
*
1891796 TATTG TATTG TA-TG TATTG TATTG TATTG TATTG TATTG TATGG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891845 TATTG TATTG TATTG TATTG TATTG TATTG TA-TG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891894 TA-TG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TA-TG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
*
1891942 TATTG TAGTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1891992 TATTG TATTG TATTGTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1 TATTG TATTG TA-T-TG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1892044 TATTG --TTG TATTG TA-TG TA-TG TATTG TATTG TATTG TATTG TA-TG
1 TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG TATTG
1892089 TATTG TATTG TA-TG TATTG TATTGTG TATTG TATTG TATTG TATTTG
1 TATTG TATTG TATTG TATTG TA-T-TG TATTG TATTG TATTG TA-TTG
* * *
1892136 TATTG TATTG TATTG TATTTG TA-TG TATTG TATTA TATTA TATTA TATT-
1 TATTG TATTG TATTG TA-TTG TATTG TATTG TATTG TATTG TATTG TATTG
1892185 TATT
1 TATT
1892189 ATCAAATAAA
Statistics
Matches: 2475, Mismatches: 19, Indels: 247
0.90 0.01 0.09
Matches are distributed among these distances:
3 51 0.02
4 242 0.10
5 2083 0.84
6 49 0.02
7 46 0.02
8 4 0.00
ACGTcount: A:0.20, C:0.00, G:0.21, T:0.59
Consensus pattern (5 bp):
TATTG
Found at i:1892484 original size:24 final size:23
Alignment explanation
Indices: 1892439--1892484 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1892429 TATAATTATC
* *
1892439 AATAATGTATTTTAATATATTTT
1 AATAATGTATTTTAAAAAATTTT
1892462 AATAATGTAATTTTAAAAAATTT
1 AATAATGT-ATTTTAAAAAATTT
1892485 AAAATTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (23 bp):
AATAATGTATTTTAAAAAATTTT
Found at i:1892485 original size:23 final size:23
Alignment explanation
Indices: 1892439--1892486 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1892429 TATAATTATC
* *
1892439 AATAATGTATTTTAATATATTTT
1 AATAATGTATTTTAATAAAATTT
1892462 AATAATGTAATTTTAA-AAAATTT
1 AATAATGT-ATTTTAATAAAATTT
1892485 AA
1 AA
1892487 AATTATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (23 bp):
AATAATGTATTTTAATAAAATTT
Found at i:1894978 original size:25 final size:25
Alignment explanation
Indices: 1894944--1894991 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1894934 TTGAGGTGAT
1894944 AAGTTTTAATAAATATTACTATTAC
1 AAGTTTTAATAAATATTACTATTAC
*
1894969 AAGTTTTAATAAATATTATTATT
1 AAGTTTTAATAAATATTACTATT
1894992 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
AAGTTTTAATAAATATTACTATTAC
Found at i:1896905 original size:14 final size:14
Alignment explanation
Indices: 1896886--1896914 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1896876 TATTATAAAG
1896886 TATAAATTTATTAA
1 TATAAATTTATTAA
1896900 TATAAATTTATTAA
1 TATAAATTTATTAA
1896914 T
1 T
1896915 GAATAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TATAAATTTATTAA
Found at i:1902217 original size:15 final size:15
Alignment explanation
Indices: 1902193--1902237 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
1902183 AAATTTATAA
*
1902193 TTATAATTTATATTT
1 TTATATTTTATATTT
*
1902208 TTATATTTTATACTT
1 TTATATTTTATATTT
*
1902223 TTAAATTTTAT-TTT
1 TTATATTTTATATTT
1902237 T
1 T
1902238 AGATTATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 3 0.12
15 23 0.88
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATATTTTATATTT
Found at i:1902219 original size:28 final size:28
Alignment explanation
Indices: 1902186--1902250 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
1902176 TAGTTGTAAA
*
1902186 TTTATAATTAT-AATTTATATTTTTATAT
1 TTTATAATTATAAATTT-TATTTTTAGAT
* *
1902214 TTTATACTTTTAAATTTTATTTTTAGAT
1 TTTATAATTATAAATTTTATTTTTAGAT
*
1902242 TATATAATT
1 TTTATAATT
1902251 TGCATTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTATAATTATAAATTTTATTTTTAGAT
Found at i:1905922 original size:19 final size:18
Alignment explanation
Indices: 1905885--1905925 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
1905875 AAAGTTGTTT
* *
1905885 TTAAAATAAAAATAATAA
1 TTAAAAGAAAAAAAATAA
1905903 TTAAAAGAAAAGAAAATAA
1 TTAAAAGAAAA-AAAATAA
1905922 TTAA
1 TTAA
1905926 TTAAATAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
TTAAAAGAAAAAAAATAA
Found at i:1909639 original size:50 final size:49
Alignment explanation
Indices: 1909564--1909660 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 49
1909554 TAAAAATACA
* *
1909564 ATTTTCTAGAAAAATGATCGATCCCTTTG-AGAAAAGGATCGATCCCTTGC
1 ATTTTCCAGAAAAAGGATCGATCCCTTTGCA-AAAA-GATCGATCCCTTGC
* *
1909614 ATTTTCCATAAAAAGGATTGATCCCTTTGCAAAAAGATCGATCCCTT
1 ATTTTCCAGAAAAAGGATCGATCCCTTTGCAAAAAGATCGATCCCTT
1909661 TTTGTGAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 12 0.29
50 29 0.69
51 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (49 bp):
ATTTTCCAGAAAAAGGATCGATCCCTTTGCAAAAAGATCGATCCCTTGC
Found at i:1909656 original size:20 final size:21
Alignment explanation
Indices: 1909623--1909661 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1909613 CATTTTCCAT
*
1909623 AAAAAGGATTGATCCCTTTGC
1 AAAAAGGATCGATCCCTTTGC
1909644 AAAAA-GATCGATCCCTTT
1 AAAAAGGATCGATCCCTTT
1909662 TTGTGAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAAAGGATCGATCCCTTTGC
Found at i:1910533 original size:54 final size:54
Alignment explanation
Indices: 1910449--1910701 Score: 311
Period size: 54 Copynumber: 4.7 Consensus size: 54
1910439 TGCCCATACG
* * * * * *
1910449 TCATAAACATATTACGAATTTCGTGGTTTGCACACATAGTGCCGAAACGATTAT
1 TCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTACCGAAACGATTAT
* * * * *
1910503 TCATTAACCTATGATGAATTTCGT-ACTTTGCACACTTAGTGCTGAAACGGTTA-
1 TCATCAACATATGATGAATTTCGTGA-TTTGCACACTTAGTACCGAAACGATTAT
1910556 T--TCAACATATGATGAATTTCGTGATTTGCACACTTAGTACCGAAAC-AGTTAT
1 TCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTACCGAAACGA-TTAT
* *
1910608 TCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTACCAAAACGGTTAT
1 TCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTACCGAAACGATTAT
*
1910662 TCATCAACATATGATGAA-TTCTATGATTTGCACACTTAGT
1 TCATCAACATATGATGAATTTC-GTGATTTGCACACTTAGT
1910702 GCCTATTTGG
Statistics
Matches: 175, Mismatches: 16, Indels: 16
0.85 0.08 0.08
Matches are distributed among these distances:
51 42 0.24
52 2 0.01
53 4 0.02
54 127 0.73
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (54 bp):
TCATCAACATATGATGAATTTCGTGATTTGCACACTTAGTACCGAAACGATTAT
Found at i:1910575 original size:105 final size:107
Alignment explanation
Indices: 1910454--1910704 Score: 332
Period size: 105 Copynumber: 2.4 Consensus size: 107
1910444 ATACGTCATA
* * * * * *
1910454 AACATATTACGAATTTCGTGGTTTGCACACATAGTGCCGAAAC-GATTATTCATTAACCTATGAT
1 AACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACAG-TTATTCATCAACATATGAT
* **
1910518 GAATTTCGT-ACTTTGCACACTTAGTGCTGAAACGGTTA-T-TC
65 GAATTTCGTGA-TTTGCACACTTAGTACCAAAACGGTTATTATC
*
1910559 AACATATGATGAATTTCGTGATTTGCACACTTAGTACCGAAACAGTTATTCATCAACATATGATG
1 AACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACAGTTATTCATCAACATATGATG
1910624 AATTTCGTGATTTGCACACTTAGTACCAAAACGGTTATTCATC
66 AATTTCGTGATTTGCACACTTAGTACCAAAACGGTTATT-ATC
*
1910667 AACATATGATGAA-TTCTATGATTTGCACACTTAGTGCC
1 AACATATGATGAATTTC-GTGATTTGCACACTTAGTGCC
1910705 TATTTGGTAA
Statistics
Matches: 128, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
105 88 0.69
106 3 0.02
107 3 0.02
108 34 0.27
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (107 bp):
AACATATGATGAATTTCGTGATTTGCACACTTAGTGCCGAAACAGTTATTCATCAACATATGATG
AATTTCGTGATTTGCACACTTAGTACCAAAACGGTTATTATC
Found at i:1910775 original size:15 final size:15
Alignment explanation
Indices: 1910755--1910783 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1910745 ACTAGTATAA
1910755 CATATAGTTACACAC
1 CATATAGTTACACAC
1910770 CATATAGTTACACA
1 CATATAGTTACACA
1910784 ATTAAATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (15 bp):
CATATAGTTACACAC
Found at i:1911154 original size:20 final size:20
Alignment explanation
Indices: 1911129--1911179 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1911119 GATCCATGGC
*
1911129 ATCGATACCATCCTCATAGT
1 ATCGATACCACCCTCATAGT
* *
1911149 ATCGATACTC-CCCTCTTGGT
1 ATCGATAC-CACCCTCATAGT
1911169 ATCGATACCAC
1 ATCGATACCAC
1911180 TTGAATCGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.29
Consensus pattern (20 bp):
ATCGATACCACCCTCATAGT
Found at i:1913313 original size:71 final size:73
Alignment explanation
Indices: 1913216--1913354 Score: 194
Period size: 72 Copynumber: 1.9 Consensus size: 73
1913206 GTTTTAGGTA
* *
1913216 TTTTAGTTTAAATATGTTTTAGTA-TTTAATTAAGTTTTAGGATAATATTTTAAATA-TTATATT
1 TTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGGATAATATTTT-AATAGTTATATT
1913279 TTATATATT
65 TTATATATT
* * * *
1913288 TTTTAGTTT-AATAGGTTTTAGTATTTTAATTAGGATTTATGATATTATTTTAATAGTTTTATTT
1 TTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGGATAATATTTTAATAGTTATATTT
1913352 TAT
66 TAT
1913355 CTTGTTTTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
71 17 0.29
72 42 0.71
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.58
Consensus pattern (73 bp):
TTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGGATAATATTTTAATAGTTATATTT
TATATATT
Found at i:1914047 original size:17 final size:18
Alignment explanation
Indices: 1914025--1914065 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
1914015 TCTTAAATTA
*
1914025 TTTATTTAATTATTTTC-
1 TTTATTTAATTATTGTCT
*
1914042 TTTA-TTAATTCTTGTCT
1 TTTATTTAATTATTGTCT
1914059 TTTATTT
1 TTTATTT
1914066 TAAAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 10 0.50
17 8 0.40
18 2 0.10
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTGTCT
Found at i:1914120 original size:25 final size:25
Alignment explanation
Indices: 1914091--1914142 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1914081 AAAACCCCTT
1914091 TTTATCTTTATT-ACTATTATTATTA
1 TTTAT-TTTATTCACTATTATTATTA
* * *
1914116 TTTATTTTTTTCCCTTTTATTATTA
1 TTTATTTTATTCACTATTATTATTA
1914141 TT
1 TT
1914143 ATTATTTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTATTTTATTCACTATTATTATTA
Found at i:1919017 original size:2 final size:2
Alignment explanation
Indices: 1919012--1919038 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1919002 TTTTTTCTCT
1919012 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 T
1919039 GAACAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1926508 original size:16 final size:17
Alignment explanation
Indices: 1926487--1926520 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1926477 TAATTATGAT
1926487 TATTTTAAAT-ATTAAA
1 TATTTTAAATAATTAAA
1926503 TATTTTAAATAATTAAA
1 TATTTTAAATAATTAAA
1926520 T
1 T
1926521 TTTATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTTAAATAATTAAA
Found at i:1928779 original size:147 final size:147
Alignment explanation
Indices: 1928512--1928809 Score: 560
Period size: 147 Copynumber: 2.0 Consensus size: 147
1928502 TCCCACTAAT
1928512 CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATATATCATAT
1 CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATATATCATAT
*
1928577 AAAAATTTTGTCAAAATTTAAGGGCATCAGTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
66 AAAAATTTTGTCAAAATTTAAGGGCATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
1928642 AGTATGTGTGTATTGTC
131 AGTATGTGTGTATTGTC
*
1928659 CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATGTATCATAT
1 CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATATATCATAT
* *
1928724 AAAAATTTTGTCAAAATTTAAGGGTATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGTA
66 AAAAATTTTGTCAAAATTTAAGGGCATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
1928789 AGTATGTGTGTATTGTC
131 AGTATGTGTGTATTGTC
1928806 CATA
1 CATA
1928810 TTTCACATAA
Statistics
Matches: 147, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (147 bp):
CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATATATCATAT
AAAAATTTTGTCAAAATTTAAGGGCATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
AGTATGTGTGTATTGTC
Found at i:1931196 original size:36 final size:36
Alignment explanation
Indices: 1931126--1931196 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
1931116 CTCGTTTATT
* * **
1931126 AGCTCATTTATTGACTCGCTTATAAGTTTGTTTACG
1 AGCTCATTTATCGACTCACTTATAAGTTCATTTACG
* *
1931162 AGCTCATTTATCGACTCATTTATAGGTTCATTTAC
1 AGCTCATTTATCGACTCACTTATAAGTTCATTTAC
1931197 TCGGTTGACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (36 bp):
AGCTCATTTATCGACTCACTTATAAGTTCATTTACG
Found at i:1931216 original size:29 final size:29
Alignment explanation
Indices: 1931174--1931231 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1931164 CTCATTTATC
1931174 GACTCATTTATAGGTTCATTTACTCGGTT
1 GACTCATTTATAGGTTCATTTACTCGGTT
1931203 GACTCATTTATAGGTTCATTTACTCGGTT
1 GACTCATTTATAGGTTCATTTACTCGGTT
1931232 CTCTATGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (29 bp):
GACTCATTTATAGGTTCATTTACTCGGTT
Found at i:1945459 original size:24 final size:24
Alignment explanation
Indices: 1945411--1945459 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1945401 GTCAATCTTC
* * **
1945411 GGAGGTAATGTCTAAAGCAGTTAT
1 GGAGGTAATGTATAAAACAACTAT
1945435 GGAGGTAATGTATAAAACAACTAT
1 GGAGGTAATGTATAAAACAACTAT
1945459 G
1 G
1945460 AAGTAAGTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.27
Consensus pattern (24 bp):
GGAGGTAATGTATAAAACAACTAT
Found at i:1946497 original size:15 final size:15
Alignment explanation
Indices: 1946477--1946507 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1946467 TTTTCATGAT
1946477 GCTGTTACTAGTCAG
1 GCTGTTACTAGTCAG
1946492 GCTGTTACTAGTCAG
1 GCTGTTACTAGTCAG
1946507 G
1 G
1946508 AAAACGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (15 bp):
GCTGTTACTAGTCAG
Found at i:1951199 original size:18 final size:18
Alignment explanation
Indices: 1951168--1951210 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
1951158 GATATAAGAA
*
1951168 AAATAAAAAAAAAT-ATT
1 AAATAAAAAAAAATAATG
*
1951185 AAATAAAAATGAAATAATG
1 AAATAAAAA-AAAATAATG
1951204 AAATAAA
1 AAATAAA
1951211 GAAATAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 9 0.41
18 4 0.18
19 9 0.41
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAAAAAATAATG
Found at i:1952337 original size:9 final size:10
Alignment explanation
Indices: 1952325--1952382 Score: 54
Period size: 9 Copynumber: 6.2 Consensus size: 10
1952315 CATGAAAAAA
1952325 AAGTAA-AAT
1 AAGTAATAAT
1952334 AAGTAATAAT
1 AAGTAATAAT
1952344 AA-TAATAAT
1 AAGTAATAAT
* *
1952353 AA-TTATAGT
1 AAGTAATAAT
1952362 AA-TAATAAAT
1 AAGTAAT-AAT
1952372 AA-TAATAAT
1 AAGTAATAAT
1952381 AA
1 AA
1952383 ATATAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
9 30 0.70
10 13 0.30
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (10 bp):
AAGTAATAAT
Found at i:1952343 original size:3 final size:3
Alignment explanation
Indices: 1952331--1952382 Score: 68
Period size: 3 Copynumber: 16.7 Consensus size: 3
1952321 AAAAAAGTAA
* *
1952331 AAT AAGT AAT AAT AAT AAT AAT AAT TAT AGT AAT AAT AAAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
1952378 AAT AA
1 AAT AA
1952383 ATATAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1952532 original size:29 final size:29
Alignment explanation
Indices: 1952455--1952538 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 29
1952445 TATAAATTGC
*
1952455 CAAAAATATTTTAAAAAACTATATAATTTT
1 CAAAAATATTTTAAAAATC-ATATAATTTT
*
1952485 CAAAAATGTCTTTAAAAATCATATAATTTT
1 CAAAAATAT-TTTAAAAATCATATAATTTT
*
1952515 CAAAAATATTTTAAAAATTATATA
1 CAAAAATATTTTAAAAATCATATA
1952539 TTATATATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 14 0.29
30 26 0.53
31 9 0.18
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (29 bp):
CAAAAATATTTTAAAAATCATATAATTTT
Found at i:1952576 original size:40 final size:38
Alignment explanation
Indices: 1952505--1952780 Score: 203
Period size: 37 Copynumber: 7.1 Consensus size: 38
1952495 TTTAAAAATC
*
1952505 ATATA-ATTTTCAAAAATATTTT-AAAAATTATATAT-T
1 ATATATATTTTC-AAAATGTTTTAAAAAATTATATATAT
* *
1952541 ATATATGTTTTCAAAATGTTTTTCAAAAAAATTATATATTCT
1 ATATATATTTTCAAAATG-TTTT--AAAAAATTATATA-TAT
*
1952583 ATATTTATTTTCAAAATGTTTTTAAAAAAATATATTATATATAT
1 ATATATATTTTCAAAATG-TTTT---AAAA-A-ATTATATATAT
* *
1952627 ATATATATTTTCAAAAATGTCTT-GAAAATTATATAT-T
1 ATATATATTTTC-AAAATGTTTTAAAAAATTATATATAT
* * *
1952664 ATATTTATTTTCAAAAACGTTTTAAAAAACTATATAATAT
1 ATATATATTTTC-AAAATGTTTTAAAAAATTATAT-ATAT
* * * *
1952704 ATAAATGTTTTTCAAAATGTTTT-AAAAACTATATAT-C
1 ATATAT-ATTTTCAAAATGTTTTAAAAAATTATATATAT
***
1952741 AT-T-TATTTTCAAAATGTTTTTTTAAATTATATA-AT
1 ATATATATTTTCAAAATGTTTTAAAAAATTATATATAT
1952776 ATATA
1 ATATA
1952781 AATTAAAAAT
Statistics
Matches: 196, Mismatches: 25, Indels: 37
0.76 0.10 0.14
Matches are distributed among these distances:
34 15 0.08
35 12 0.06
36 11 0.06
37 32 0.16
38 20 0.10
39 14 0.07
40 28 0.14
41 6 0.03
42 22 0.11
43 5 0.03
44 17 0.09
45 14 0.07
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (38 bp):
ATATATATTTTCAAAATGTTTTAAAAAATTATATATAT
Found at i:1952594 original size:42 final size:39
Alignment explanation
Indices: 1952527--1952761 Score: 184
Period size: 40 Copynumber: 5.9 Consensus size: 39
1952517 AAAATATTTT
*
1952527 AAAAATTATATATTATATATGTTTTCAAAATGTTTTTCAA
1 AAAAATTATATATTATATATATTTTCAAAATGTTTTT-AA
*
1952567 AAAAATTATATATTCTATATTTATTTTCAAAATGTTTTTAAAA
1 AAAAATTATATA-T-TATATATATTTTCAAAATGTTTTT--AA
*
1952610 AAATATATTATATATATATATATATTTTCAAAAATG-TCTT--
1 AAA-A-ATTATATAT-TATATATATTTTC-AAAATGTTTTTAA
* * *
1952650 GAAAATTATATATTATATTTATTTTCAAAAACG-TTTT-A
1 AAAAATTATATATTATATATATTTTC-AAAATGTTTTTAA
* * *
1952688 AAAAACTATATAATATATAAATGTTTTTCAAAATG-TTTT--
1 AAAAATTATAT-AT-TATATAT-ATTTTCAAAATGTTTTTAA
* *
1952727 AAAAACTATATATCAT-T-TATTTTCAAAATGTTTTT
1 AAAAATTATATATTATATATATTTTCAAAATGTTTTT
1952762 TTAAATTATA
Statistics
Matches: 165, Mismatches: 19, Indels: 27
0.78 0.09 0.13
Matches are distributed among these distances:
34 11 0.07
35 5 0.03
37 23 0.14
38 20 0.12
39 14 0.08
40 28 0.17
41 6 0.04
42 22 0.13
43 5 0.03
44 17 0.10
45 14 0.08
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (39 bp):
AAAAATTATATATTATATATATTTTCAAAATGTTTTTAA
Found at i:1952670 original size:81 final size:77
Alignment explanation
Indices: 1952567--1952783 Score: 244
Period size: 81 Copynumber: 2.8 Consensus size: 77
1952557 TGTTTTTCAA
*
1952567 AAAAATTATATATTCTATATTTATTTTCAAAATGTTTTTAAAAAAATATATTATATATATATATA
1 AAAAATTATATA-T-TATATTTATTTTCAAAATGTTTTTAAAAAAATATA-TA-ATATATAAATA
1952632 TATTTTCAAAAATGTCTT
62 T-TTTTC-AAAATGTCTT
* * * *
1952650 GAAAATTATATATTATATTTATTTTCAAAAACG-TTTTAAAAAACTATATAATATATAAATGTTT
1 AAAAATTATATATTATATTTATTTTC-AAAATGTTTTTAAAAAAATATATAATATATAAATATTT
*
1952714 TTCAAAATGTTTT
65 TTCAAAATGTCTT
* * ** *
1952727 AAAAACTATATA-T-CATTTATTTTCAAAATGTTTTT-TTAAATTATATAATATATAAAT
1 AAAAATTATATATTATATTTATTTTCAAAATGTTTTTAAAAAAATATATAATATATAAAT
1952784 TAAAAATAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
74 24 0.20
75 14 0.12
76 1 0.01
77 19 0.16
78 5 0.04
79 10 0.08
80 2 0.02
81 27 0.23
82 6 0.05
83 11 0.09
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (77 bp):
AAAAATTATATATTATATTTATTTTCAAAATGTTTTTAAAAAAATATATAATATATAAATATTTT
TCAAAATGTCTT
Found at i:1953630 original size:81 final size:81
Alignment explanation
Indices: 1953407--1953997 Score: 559
Period size: 81 Copynumber: 7.2 Consensus size: 81
1953397 TTGAATATAA
* * * * *
1953407 TCGAACTCGAATGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CC
1 TCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCC
1953471 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * * * * *
1953487 TCAAACTCATAGGTCTTTGGTCACAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCAAAGGTCTTTGG---CAGATAGCCCTTCTCA-ACTTAAGCTATGCTGCAAATGATGT
* * * *
1953551 GCCCTCGAAGCTGAGTGTAA
62 GCCCTTGGAGCTGAGCGTAG
* *** *
1953571 TTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTG-CC
1 TCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCC
1953635 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * * *
1953651 TCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCT-AGACTTAAGTTGTGCTGCAAATGATA
1 TCGAACTCAAAGGTC--T--TTGGCAGATAGCCCTTCTCA-ACTTAAGCTATGCTGCAAATGATG
*
1953715 TGCCCTCGGAGCTGAGCGTAG
61 TGCCCTTGGAGCTGAGCGTAG
* * * * *
1953736 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACGTAAGCTATGTTGCAAATGATGTGCCG
1 TCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCC
1953801 TT-GAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * * * * ** *
1953816 TCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATTTTA
1 TCGAACTCAAAGGTC-TTTG---GCAGATAGCCCTTCTCA-ACTTAAGCTATGCTGCAAATGATG
* * *
1953880 TGCCCTTGAAGCTGAGTGTAA
61 TGCCCTTGGAGCTGAGCGTAG
* * * * *
1953901 TCGAACTCGAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CC
1 TCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCC
1953965 TT-GAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
1953980 TCGAACTCAAAGGTCTTT
1 TCGAACTCAAAGGTCTTT
1953998 TGCTAACAGA
Statistics
Matches: 402, Mismatches: 89, Indels: 41
0.76 0.17 0.08
Matches are distributed among these distances:
79 26 0.06
80 71 0.18
81 108 0.27
82 2 0.00
83 36 0.09
84 105 0.26
85 54 0.13
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (81 bp):
TCGAACTCAAAGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCC
TTGGAGCTGAGCGTAG
Found at i:1953769 original size:165 final size:164
Alignment explanation
Indices: 1953404--1954039 Score: 950
Period size: 165 Copynumber: 3.9 Consensus size: 164
1953394 AAGTTGAATA
* *
1953404 TAATCGAACTCGAATGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
* * *
1953469 CCTTGGAGCTGAGCGTAGTCAAACTCATAGGTCTTTGG-TCACAGATAACCCTTCTAGCCTTGAG
66 CCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGCCTTGAG
* *
1953533 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
130 TTATGCTGCAAATGATATGCCCTCGAAGCTGAGTG
* ** *
1953568 TAATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
* ** * * *
1953633 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAG
66 CCTT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGCCTTGAG
* * *
1953698 TTGTGCTGCAAATGATATGCCCTCGGAGCTGAGCG
130 TTATGCTGCAAATGATATGCCCTCGAAGCTGAGTG
* * **
1953733 TAGTCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACGTAAGCTATGTTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
*
1953798 CCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAG
66 CC-TTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGCCTTGAG
* ** *
1953863 TTATGCTGTAAATTTTATGCCCTTGAAGCTGAGTG
130 TTATGCTGCAAATGATATGCCCTCGAAGCTGAGTG
* *
1953898 TAATCGAACTCGAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTG
1 TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
*
1953963 CCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
66 CCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGCCTTGAGT
1954028 TATGCTGCAAAT
131 TATGCTGCAAAT
1954040 AGTTTGTTTA
Statistics
Matches: 423, Mismatches: 47, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
164 169 0.40
165 252 0.60
166 2 0.00
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (164 bp):
TAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG
CCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGCTAACAGATAACCCTTCTAGCCTTGAGT
TATGCTGCAAATGATATGCCCTCGAAGCTGAGTG
Found at i:1954015 original size:329 final size:329
Alignment explanation
Indices: 1953407--1954039 Score: 1009
Period size: 329 Copynumber: 1.9 Consensus size: 329
1953397 TTGAATATAA
* *
1953407 TCGAACTCGAATGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACGTAAGCTATACTGCAAATGATGTGCCT
* * *
1953472 TGGAGCTGAGCGTAGTCAAACTCATAGGTCTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTAT
66 TGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
* * *
1953537 GCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGTCTTTGGCAGATAGCCCT
131 GCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCT
1953602 TCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
196 TCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
* ** *
1953667 TTGGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCCTCGGAGCTGAGC
261 TTGGCTAACAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGGAGCTGAGC
1953732 GTAG
326 GTAG
* **
1953736 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACGTAAGCTATGTTGCAAATGATGTGCCG
1 TCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACGTAAGCTATACTGCAAATGATGTGCC-
*
1953801 TT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTT
65 TTGGAGCTGAGCGTAGTCAAACTCAAAGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAGTT
** * *
1953865 ATGCTGTAAATTTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCT
129 ATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCC
*
1953930 CTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCAAAGGT
194 CTTCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT
* * * *
1953994 CTTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
259 CTTTGGCTAACAGACAACCCTTCTAGACTTAAGTTATGCTGCAAAT
1954040 AGTTTGTTTA
Statistics
Matches: 277, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
329 150 0.54
330 127 0.46
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.30
Consensus pattern (329 bp):
TCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACGTAAGCTATACTGCAAATGATGTGCCT
TGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTAT
GCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCT
TCTCAACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCT
TTGGCTAACAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGGAGCTGAGC
GTAG
Found at i:1954239 original size:23 final size:23
Alignment explanation
Indices: 1954205--1954265 Score: 115
Period size: 23 Copynumber: 2.7 Consensus size: 23
1954195 ACTGAATTTG
1954205 ATCTG-AATTGGTTCTCGAACCC
1 ATCTGAAATTGGTTCTCGAACCC
1954227 ATCTGAAATTGGTTCTCGAACCC
1 ATCTGAAATTGGTTCTCGAACCC
1954250 ATCTGAAATTGGTTCT
1 ATCTGAAATTGGTTCT
1954266 GAGATCTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.13
23 33 0.87
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (23 bp):
ATCTGAAATTGGTTCTCGAACCC
Found at i:1960345 original size:9 final size:10
Alignment explanation
Indices: 1960333--1960390 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 10
1960323 TGAAAAAAAA
1960333 AAGTAA-AAT
1 AAGTAATAAT
1960342 AAGTAATAAT
1 AAGTAATAAT
1960352 AA-TAATAAT
1 AAGTAATAAT
*
1960361 AA-TAATAGT
1 AAGTAATAAT
1960370 AA-TAATAAAT
1 AAGTAAT-AAT
1960380 AA-TAATAAT
1 AAGTAATAAT
1960389 AA
1 AA
1960391 ATATAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
9 32 0.71
10 13 0.29
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (10 bp):
AAGTAATAAT
Found at i:1960351 original size:3 final size:3
Alignment explanation
Indices: 1960339--1960390 Score: 77
Period size: 3 Copynumber: 16.7 Consensus size: 3
1960329 AAAAAAGTAA
*
1960339 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
1960386 AAT AA
1 AAT AA
1960391 ATATAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1960396 original size:9 final size:8
Alignment explanation
Indices: 1960340--1960396 Score: 53
Period size: 9 Copynumber: 6.5 Consensus size: 8
1960330 AAAAAGTAAA
1960340 ATAAGTAAT
1 ATAA-TAAT
1960349 AATAATAAT
1 -ATAATAAT
1960358 AATAATAAT
1 -ATAATAAT
1960367 AGTAATAAT
1 A-TAATAAT
1960376 A-AATAAT
1 ATAATAAT
1960383 AATAATAAAT
1 -ATAAT-AAT
1960393 ATAA
1 ATAA
1960397 AAAACTATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
7 6 0.14
8 2 0.05
9 28 0.65
10 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (8 bp):
ATAATAAT
Found at i:1960409 original size:34 final size:34
Alignment explanation
Indices: 1960331--1960410 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
1960321 CCTGAAAAAA
* *
1960331 AAAAGTAA-AATAAGTAATAATAATAATAATAAT
1 AAAACTAATAATAAATAATAATAATAATAATAAT
* *
1960364 AATAGTAATAATAAATAATAATAATAA-ATATAA-
1 AAAACTAATAATAAATAATAATAATAATA-ATAAT
1960397 AAAACTATATAATA
1 AAAACTA-ATAATA
1960411 TACATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
33 13 0.32
34 27 0.68
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (34 bp):
AAAACTAATAATAAATAATAATAATAATAATAAT
Found at i:1960540 original size:29 final size:29
Alignment explanation
Indices: 1960463--1960546 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 29
1960453 TATAAATTGC
*
1960463 CAAAAATATTTTAAAAAACTATATAATTTT
1 CAAAAATATTTTAAAAATC-ATATAATTTT
*
1960493 CAAAAATGTCTTTAAAAATCATATAATTTT
1 CAAAAATAT-TTTAAAAATCATATAATTTT
*
1960523 CAAAAATATTTTAAAAATTATATA
1 CAAAAATATTTTAAAAATCATATA
1960547 TTATATATGT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
29 14 0.29
30 26 0.53
31 9 0.18
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.39
Consensus pattern (29 bp):
CAAAAATATTTTAAAAATCATATAATTTT
Found at i:1960584 original size:40 final size:39
Alignment explanation
Indices: 1960513--1960766 Score: 201
Period size: 42 Copynumber: 6.6 Consensus size: 39
1960503 TTTAAAAATC
*
1960513 ATATA-ATTTTCAAAAATATTTT--AAAAATTATATAT-T
1 ATATATATTTTC-AAAATGTTTTAAAAAAATTATATATAT
* *
1960549 ATATATGTTTTCAAAATGTTTTTCAAAAAAATTATATATTCT
1 ATATATATTTTCAAAATG-TTTT-AAAAAAATTATATA-TAT
*
1960591 ATATTTATTTTCAAAATGTTTTTAAAAAAATATATAATATAT
1 ATATATATTTTCAAAATG-TTTTAAAAAAAT-TAT-ATATAT
* *
1960633 ATATATATTTTCAAAAATGTCTT--GAAAATTATATAT-T
1 ATATATATTTTC-AAAATGTTTTAAAAAAATTATATATAT
* * *
1960670 ATATTTATTTTCAAAAACGTTTT-AAAAAACTATATAATAT
1 ATATATATTTTC-AAAATGTTTTAAAAAAATTATAT-ATAT
* * * *
1960710 AAAAATATTTTTCAAAATGTTTT--AAAAACTATATAT-C
1 ATATATA-TTTTCAAAATGTTTTAAAAAAATTATATATAT
1960747 AT-T-TATTTTCAAAATGTTTT
1 ATATATATTTTCAAAATGTTTT
1960767 TTTAAATTAT
Statistics
Matches: 184, Mismatches: 20, Indels: 30
0.79 0.09 0.13
Matches are distributed among these distances:
34 15 0.08
35 2 0.01
36 10 0.05
37 31 0.17
38 15 0.08
39 16 0.09
40 31 0.17
41 14 0.08
42 41 0.22
43 9 0.05
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (39 bp):
ATATATATTTTCAAAATGTTTTAAAAAAATTATATATAT
Found at i:1960601 original size:79 final size:77
Alignment explanation
Indices: 1960518--1960786 Score: 243
Period size: 79 Copynumber: 3.5 Consensus size: 77
1960508 AAATCATATA
1960518 ATTTTCAAAAATATTTT-AAAAAT-TAT-ATAT-TATATATGTTTTCAAAATGTTTTTCAAAAAA
1 ATTTTCAAAAATATTTTAAAAAATATATAATATATATATAT-TTTTCAAAATGTTTTT---AAAA
1960579 ATTATATATTCTATATTT
62 ATTATATA-T-TATATTT
* * *
1960597 ATTTTC-AAAATGTTTTTAAAAAAATATATAATATATATATATATTTTCAAAAATG-TCTTGAAA
1 ATTTTCAAAAAT-ATTTT-AAAAAATATATAATATATATATAT-TTTTC-AAAATGTTTTTAAAA
1960660 ATTATATATTATATTT
62 ATTATATATTATATTT
** * * *
1960676 ATTTTCAAAAACGTTTTAAAAAACTATATAATATAAAAATATTTTTCAAAATG-TTTTAAAAACT
1 ATTTTCAAAAATATTTTAAAAAA-TATATAATATATATATATTTTTCAAAATGTTTTTAAAAATT
*
1960740 ATATA-T-CATTT
65 ATATATTATATTT
* ** *
1960751 ATTTTC-AAAATGTTTTTTTAAATTATATAATATATA
1 ATTTTCAAAAAT-ATTTTAAAAAATATATAATATATA
1960787 AATAAAAAAT
Statistics
Matches: 162, Mismatches: 18, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
74 16 0.10
75 17 0.10
76 1 0.01
77 19 0.12
78 16 0.10
79 43 0.27
80 5 0.03
81 17 0.10
82 3 0.02
83 4 0.02
84 15 0.09
85 6 0.04
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (77 bp):
ATTTTCAAAAATATTTTAAAAAATATATAATATATATATATTTTTCAAAATGTTTTTAAAAATTA
TATATTATATTT
Found at i:1961617 original size:10 final size:9
Alignment explanation
Indices: 1961586--1961618 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1961576 AAGTCCATTA
1961586 TTTTTCTCT
1 TTTTTCTCT
1961595 TTTTT-TCT
1 TTTTTCTCT
*
1961603 TTTTCCTCT
1 TTTTTCTCT
1961612 TTTTTCT
1 TTTTTCT
1961619 AACACAGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:1963811 original size:96 final size:96
Alignment explanation
Indices: 1963636--1963813 Score: 259
Period size: 96 Copynumber: 1.9 Consensus size: 96
1963626 CGACTCAACT
* * * *
1963636 TTGAAAACTAATGAACTAAAAATTATCAAATTCAACTCGAACTCAAAATAAAATATTAAAACTTG
1 TTGAAAACTAATAAACTAAAAATTATCAAACTCAACTCAAACTCAAAATAAAATATTAAAAATTG
*
1963701 AATCGAACTCGAAAAGGCTCGAACTTGAAAC
66 AATCAAACTCGAAAAGGCTCGAACTTGAAAC
* **
1963732 TTGAAAACTCATAAACTAAAAATTATCAAACTCAGTTCAAACTCAAAATAAAATATTAAAAATT-
1 TTGAAAACTAATAAACTAAAAATTATCAAACTCAACTCAAACTCAAAATAAAATATTAAAAATTG
*
1963796 AACTCAAACTTGAAAAGG
66 AA-TCAAACTCGAAAAGG
1963814 TTCAAACTCA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
95 2 0.03
96 70 0.97
ACGTcount: A:0.51, C:0.16, G:0.08, T:0.25
Consensus pattern (96 bp):
TTGAAAACTAATAAACTAAAAATTATCAAACTCAACTCAAACTCAAAATAAAATATTAAAAATTG
AATCAAACTCGAAAAGGCTCGAACTTGAAAC
Found at i:1963904 original size:11 final size:12
Alignment explanation
Indices: 1963882--1963919 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1963872 GCTCGATTCA
*
1963882 AGCTCAATTTTG
1 AGCTCGATTTTG
*
1963894 AGCTCTA-TTTG
1 AGCTCGATTTTG
1963905 AGCTCGATTTTG
1 AGCTCGATTTTG
1963917 AGC
1 AGC
1963920 GTGAGGCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.39
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:1965287 original size:7 final size:7
Alignment explanation
Indices: 1965264--1965324 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
1965254 CAGAATTAGA
1965264 TTAAGGGT
1 TTAA-GGT
1965272 TT-AGAGT
1 TTAAG-GT
1965279 TTAAGGT
1 TTAAGGT
* *
1965286 TTAGGGC
1 TTAAGGT
*
1965293 TTAAGGC
1 TTAAGGT
1965300 TTAAGGT
1 TTAAGGT
*
1965307 TTAGGGTT
1 TTAAGG-T
1965315 TTAAGGT
1 TTAAGGT
1965322 TTA
1 TTA
1965325 GGGTGTAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
6 1 0.02
7 33 0.75
8 10 0.23
ACGTcount: A:0.25, C:0.03, G:0.31, T:0.41
Consensus pattern (7 bp):
TTAAGGT
Found at i:1965320 original size:15 final size:15
Alignment explanation
Indices: 1965300--1965328 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1965290 GGCTTAAGGC
1965300 TTAAGGTTTAGGGTT
1 TTAAGGTTTAGGGTT
1965315 TTAAGGTTTAGGGT
1 TTAAGGTTTAGGGT
1965329 GTAATCTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (15 bp):
TTAAGGTTTAGGGTT
Found at i:1965439 original size:8 final size:7
Alignment explanation
Indices: 1965399--1965486 Score: 65
Period size: 7 Copynumber: 12.7 Consensus size: 7
1965389 AATCAGATTA
1965399 AGGGTTT
1 AGGGTTT
* *
1965406 AGTGCTT
1 AGGGTTT
*
1965413 AGGG-CT
1 AGGGTTT
*
1965419 ATGGTTT
1 AGGGTTT
1965426 AGGGTTT
1 AGGGTTT
1965433 AAGGGTTT
1 -AGGGTTT
*
1965441 -GAGATTT
1 AG-GGTTT
1965448 AGGGTTT
1 AGGGTTT
*
1965455 AGAGTTT
1 AGGGTTT
**
1965462 AGAATTT
1 AGGGTTT
1965469 AGGGTTT
1 AGGGTTT
1965476 A-GGTTT
1 AGGGTTT
1965482 AGGGT
1 AGGGT
1965487 GTAATCTAAC
Statistics
Matches: 63, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
6 11 0.17
7 44 0.70
8 8 0.13
ACGTcount: A:0.20, C:0.02, G:0.36, T:0.41
Consensus pattern (7 bp):
AGGGTTT
Found at i:1965468 original size:21 final size:21
Alignment explanation
Indices: 1965423--1965483 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
1965413 AGGGCTATGG
1965423 TTTAGGGTTTAAGGGTTT-GAGA
1 TTTAGGGTTT-A-GGTTTAGAGA
1965445 TTTAGGGTTTAGAGTTTAGA-A
1 TTTAGGGTTTAG-GTTTAGAGA
1965466 TTTAGGGTTTAGGTTTAG
1 TTTAGGGTTTAGGTTTAG
1965484 GGTGTAATCT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.19
21 18 0.49
22 12 0.32
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.44
Consensus pattern (21 bp):
TTTAGGGTTTAGGTTTAGAGA
Found at i:1969874 original size:45 final size:45
Alignment explanation
Indices: 1969825--1969977 Score: 252
Period size: 45 Copynumber: 3.4 Consensus size: 45
1969815 TGTATGAATT
*
1969825 GGCATAAAATGTGCCACTAATGAAAATGCATAACGGTGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
* *
1969870 GGCATAAAAGATGCCACTAATGAAAATGCATAAAGGTGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
* * *
1969915 GGCATAAAAGGTTCCACTAATAAAAATGCATAACGATGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
1969960 GGCATAAAAGGTGCCACT
1 GGCATAAAAGGTGCCACT
1969978 CATGGTATTC
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 99 1.00
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.23
Consensus pattern (45 bp):
GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
Found at i:1976874 original size:44 final size:45
Alignment explanation
Indices: 1976826--1976926 Score: 168
Period size: 44 Copynumber: 2.3 Consensus size: 45
1976816 TGTATGAATT
1976826 GGCATAAAAGGTGCCACTAATGAAAATGCAT-ACGGTGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
***
1976870 GGCATAAAATACGCCACTAATGAAAATGCATAACGGTGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
1976915 GGCATAAAAGGT
1 GGCATAAAAGGT
1976927 TCCATTCATG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
44 28 0.56
45 22 0.44
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (45 bp):
GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
Found at i:1976921 original size:45 final size:44
Alignment explanation
Indices: 1976838--1976923 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 44
1976828 CATAAAAGGT
1976838 GCCACTAATGAAAATGCATACGGTGCATTATCGGCATAAAATAC
1 GCCACTAATGAAAATGCATACGGTGCATTATCGGCATAAAATAC
1976882 GCCACTAATGAAAATGCATAACGGTGCATTATCGGCATAAAA
1 GCCACTAATGAAAATGCAT-ACGGTGCATTATCGGCATAAAA
1976924 GGTTCCATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 19 0.46
45 22 0.54
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22
Consensus pattern (44 bp):
GCCACTAATGAAAATGCATACGGTGCATTATCGGCATAAAATAC
Found at i:1980295 original size:14 final size:14
Alignment explanation
Indices: 1980255--1980295 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1980245 AATTCAACAT
* *
1980255 GTTGGCTCAGACGA
1 GTTGACTCAGTCGA
1980269 GTTGACTCAGTCGA
1 GTTGACTCAGTCGA
*
1980283 GTTGACTCGGTCG
1 GTTGACTCAGTCG
1980296 GGTCAAATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.17, C:0.22, G:0.34, T:0.27
Consensus pattern (14 bp):
GTTGACTCAGTCGA
Found at i:1980757 original size:18 final size:18
Alignment explanation
Indices: 1980734--1980770 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1980724 ATTGGGGTCA
*
1980734 TTGACGGCTGAAGACTGG
1 TTGACGGCTAAAGACTGG
*
1980752 TTGACGGTTAAAGACTGG
1 TTGACGGCTAAAGACTGG
1980770 T
1 T
1980771 AGTCGAAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.35, T:0.27
Consensus pattern (18 bp):
TTGACGGCTAAAGACTGG
Found at i:1984915 original size:14 final size:14
Alignment explanation
Indices: 1984896--1984961 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
1984886 GAGTCAACGG
*
1984896 GTTGACTCAGACGA
1 GTTGACTCAGACAA
1984910 GTTGACTCAGACAA
1 GTTGACTCAGACAA
* * *
1984924 ATTAACTC-GATCGA
1 GTTGACTCAGA-CAA
** *
1984938 GTTGAAGCAGTCAA
1 GTTGACTCAGACAA
1984952 GTTGACTCAG
1 GTTGACTCAG
1984962 TCAGGTAAAA
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
13 2 0.05
14 35 0.92
15 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGACAA
Found at i:1984959 original size:28 final size:28
Alignment explanation
Indices: 1984896--1984961 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
1984886 GAGTCAACGG
**
1984896 GTTGACTCAGACGAGTTGACTCAGACAA
1 GTTGACTCAGACGAGTTGAAGCAGACAA
* * *
1984924 ATTAACTC-GATCGAGTTGAAGCAGTCAA
1 GTTGACTCAGA-CGAGTTGAAGCAGACAA
1984952 GTTGACTCAG
1 GTTGACTCAG
1984962 TCAGGTAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
27 2 0.07
28 26 0.90
29 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (28 bp):
GTTGACTCAGACGAGTTGAAGCAGACAA
Found at i:1998383 original size:14 final size:13
Alignment explanation
Indices: 1998331--1998383 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
1998321 TTAAATTTTT
*
1998331 GGTCAAAGTCAAT
1 GGTCAAAGTCAAC
*
1998344 GGTAAAAGTCAAC
1 GGTCAAAGTCAAC
1998357 GGGTC-AAGTTCAAC
1 -GGTCAAAG-TCAAC
1998371 GGATCAAAGTCAA
1 GG-TCAAAGTCAA
1998384 TGAGTTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 16 0.48
14 14 0.42
15 3 0.09
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.19
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:2001671 original size:15 final size:15
Alignment explanation
Indices: 2001651--2001687 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
2001641 TGAGACATTA
*
2001651 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
2001666 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
2001681 CCCGCCC
1 CCCGCCC
2001688 AGCTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:2002848 original size:22 final size:22
Alignment explanation
Indices: 2002823--2002892 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
2002813 TATTTTATAA
* *
2002823 TTATGTCTCTATGATATATTTT
1 TTATATCTCTATGACATATTTT
*
2002845 TTATATCTTTATGACATATTTT
1 TTATATCTCTATGACATATTTT
* *
2002867 TTTTATCT-TCATGACACATTTT
1 TTATATCTCT-ATGACATATTTT
2002889 TTAT
1 TTAT
2002893 CATTTGACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 1 0.02
22 40 0.98
ACGTcount: A:0.24, C:0.11, G:0.06, T:0.59
Consensus pattern (22 bp):
TTATATCTCTATGACATATTTT
Found at i:2008694 original size:26 final size:26
Alignment explanation
Indices: 2008664--2008715 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2008654 TGAATTTTAC
2008664 AAACCTCATATTTAATGGAAATTTCA
1 AAACCTCATATTTAATGGAAATTTCA
2008690 AAACCTCATATTTAATGGAAATTTCA
1 AAACCTCATATTTAATGGAAATTTCA
2008716 TATCCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (26 bp):
AAACCTCATATTTAATGGAAATTTCA
Found at i:2012991 original size:24 final size:24
Alignment explanation
Indices: 2012939--2013005 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
2012929 AGGATTGTGT
2012939 CACAAGAGCTGAGAAAACGAGTGC
1 CACAAGAGCTGAGAAAACGAGTGC
*
2012963 AACAAGAGCAT-AGAAAAC-ACGTGC
1 CACAAGAGC-TGAGAAAACGA-GTGC
* * *
2012987 CACAAAAACAGAGAAAACG
1 CACAAGAGCTGAGAAAACG
2013006 TGTCACAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
23 1 0.03
24 32 0.94
25 1 0.03
ACGTcount: A:0.51, C:0.21, G:0.22, T:0.06
Consensus pattern (24 bp):
CACAAGAGCTGAGAAAACGAGTGC
Found at i:2013554 original size:5 final size:5
Alignment explanation
Indices: 2013546--2013570 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2013536 TGGCCCAAAA
2013546 ACCCG ACCCG ACCCG ACCCG ACCCG
1 ACCCG ACCCG ACCCG ACCCG ACCCG
2013571 TTGCCATCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:2018289 original size:15 final size:16
Alignment explanation
Indices: 2018265--2018297 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2018255 GTTCTTTTCT
2018265 TTGATATT-AATAAAA
1 TTGATATTAAATAAAA
*
2018280 TTGATTTTAAATAAAA
1 TTGATATTAAATAAAA
2018296 TT
1 TT
2018298 AAATAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTGATATTAAATAAAA
Found at i:2027015 original size:10 final size:10
Alignment explanation
Indices: 2026983--2027049 Score: 93
Period size: 11 Copynumber: 6.7 Consensus size: 10
2026973 GGAAAATCGG
2026983 TTTGACCGGT
1 TTTGACCGGT
2026993 TTTGAACCGGT
1 TTTG-ACCGGT
*
2027004 TTTGACCAG-
1 TTTGACCGGT
2027013 TTTGACCGGT
1 TTTGACCGGT
2027023 TTTGAACCGGT
1 TTTG-ACCGGT
2027034 TTTGACCGG-
1 TTTGACCGGT
2027043 TTTGACC
1 TTTGACC
2027050 CGACCCGACC
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
9 15 0.29
10 17 0.33
11 20 0.38
ACGTcount: A:0.15, C:0.21, G:0.27, T:0.37
Consensus pattern (10 bp):
TTTGACCGGT
Found at i:2027016 original size:30 final size:30
Alignment explanation
Indices: 2026982--2027049 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
2026972 TGGAAAATCG
2026982 GTTTGACCGGTTTTGAACCGGTTTTGACCA
1 GTTTGACCGGTTTTGAACCGGTTTTGACCA
*
2027012 GTTTGACCGGTTTTGAACCGGTTTTGACCG
1 GTTTGACCGGTTTTGAACCGGTTTTGACCA
2027042 GTTTGACC
1 GTTTGACC
2027050 CGACCCGACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.37
Consensus pattern (30 bp):
GTTTGACCGGTTTTGAACCGGTTTTGACCA
Found at i:2027066 original size:17 final size:17
Alignment explanation
Indices: 2027044--2027083 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
2027034 TTTGACCGGT
2027044 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
2027061 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACCG
2027078 TTGACC
1 TTGACC
2027084 GTTGACTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.45, G:0.23, T:0.15
Consensus pattern (17 bp):
TTGACCCGACCCGACCG
Found at i:2028656 original size:36 final size:36
Alignment explanation
Indices: 2028616--2028685 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2028606 AGGGGTTACA
* *
2028616 GAGACTATTCAAAGAGTTCACAAAACATTTACCATT
1 GAGACTACTCAAAGAGTTCACAAAACATTAACCATT
*
2028652 GAGACTACTCAATGAGTTCACAAAACATTAACCA
1 GAGACTACTCAAAGAGTTCACAAAACATTAACCA
2028686 CTTATATATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.24
Consensus pattern (36 bp):
GAGACTACTCAAAGAGTTCACAAAACATTAACCATT
Found at i:2035503 original size:30 final size:29
Alignment explanation
Indices: 2035464--2035522 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
2035454 TTTATTGTTG
2035464 TGAGCTATATCATAAATA-TTTTATAATAAT
1 TGAGCTATAT-A-AAATATTTTTATAATAAT
* *
2035494 TGAGTTATATAAAATATTTTTATACTAAT
1 TGAGCTATATAAAATATTTTTATAATAAT
2035523 ATATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 5 0.19
29 12 0.46
30 9 0.35
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.46
Consensus pattern (29 bp):
TGAGCTATATAAAATATTTTTATAATAAT
Found at i:2035530 original size:29 final size:31
Alignment explanation
Indices: 2035475--2035541 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 31
2035465 GAGCTATATC
2035475 ATAAATA-TTTTATAATAATTGAGTTAT-AT
1 ATAAATATTTTTATAATAATTGAGTTATAAT
* *
2035504 A-AAATATTTTTATACTAATAT-ATTTATAAT
1 ATAAATATTTTTATAATAAT-TGAGTTATAAT
2035534 ATAAATAT
1 ATAAATAT
2035542 CAGTATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 5 0.16
29 17 0.53
30 4 0.12
31 6 0.19
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (31 bp):
ATAAATATTTTTATAATAATTGAGTTATAAT
Found at i:2039311 original size:18 final size:18
Alignment explanation
Indices: 2039262--2039314 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
2039252 GGTGAAGTAT
* *
2039262 AAATGGCGTTGTCATGGC
1 AAATGGTGTTGTCGTGGC
2039280 AAATGGTGTTGTCGTGGC
1 AAATGGTGTTGTCGTGGC
2039298 AAATGGTGTTGTCGTGG
1 AAATGGTGTTGTCGTGG
2039315 TAAGTGTACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.19, C:0.11, G:0.38, T:0.32
Consensus pattern (18 bp):
AAATGGTGTTGTCGTGGC
Found at i:2040512 original size:17 final size:17
Alignment explanation
Indices: 2040487--2040559 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
2040477 AACATATAAA
2040487 GAACTAGTTTAATTAAT
1 GAACTAGTTTAATTAAT
* *
2040504 GAACCAGTTTAAATGAAT
1 GAACTAGTTT-AATTAAT
*
2040522 GAACTAGTTTAATTAGT
1 GAACTAGTTTAATTAAT
2040539 GAACTAGCTTT-ATTGAAT
1 GAACTAG-TTTAATT-AAT
2040557 GAA
1 GAA
2040560 AGAGGATACT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
17 24 0.51
18 23 0.49
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTAATTAAT
Found at i:2040524 original size:18 final size:18
Alignment explanation
Indices: 2040487--2040559 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 18
2040477 AACATATAAA
*
2040487 GAACTAGTTT-AATTAAT
1 GAACTAGTTTAAATGAAT
*
2040504 GAACCAGTTTAAATGAAT
1 GAACTAGTTTAAATGAAT
* *
2040522 GAACTAGTTT-AATTAGT
1 GAACTAGTTTAAATGAAT
*
2040539 GAACTAGCTTT-ATTGAAT
1 GAACTAG-TTTAAATGAAT
2040557 GAA
1 GAA
2040560 AGAGGATACT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
17 21 0.46
18 25 0.54
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (18 bp):
GAACTAGTTTAAATGAAT
Found at i:2040533 original size:35 final size:35
Alignment explanation
Indices: 2040487--2040559 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
2040477 AACATATAAA
2040487 GAACTAGTTTAATTAATGAACCAG-TTTAAATGAAT
1 GAACTAGTTTAATTAATGAACCAGCTTT-AATGAAT
* * *
2040522 GAACTAGTTTAATTAGTGAACTAGCTTTATTGAAT
1 GAACTAGTTTAATTAATGAACCAGCTTTAATGAAT
2040557 GAA
1 GAA
2040560 AGAGGATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 31 0.91
36 3 0.09
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (35 bp):
GAACTAGTTTAATTAATGAACCAGCTTTAATGAAT
Found at i:2040697 original size:20 final size:20
Alignment explanation
Indices: 2040659--2040697 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2040649 CAACTTAATG
* *
2040659 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATAAACAC
2040679 TCATGCAAATTCATAAACA
1 TCATGCAAATTCATAAACA
2040698 AGTAAAAGAT
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:0.44, C:0.21, G:0.05, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATAAACAC
Found at i:2042232 original size:16 final size:16
Alignment explanation
Indices: 2042211--2042241 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2042201 TGAAAAATAG
2042211 ACCTCACCAACACAAA
1 ACCTCACCAACACAAA
*
2042227 ACCTCACCAATACAA
1 ACCTCACCAACACAA
2042242 TCCAAAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.42, G:0.00, T:0.10
Consensus pattern (16 bp):
ACCTCACCAACACAAA
Found at i:2042591 original size:20 final size:20
Alignment explanation
Indices: 2042557--2042608 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2042547 CTCTTTAAAT
* *
2042557 TTTTTTCTTTCTTTTTATTTA
1 TTTTTTATTT-TTTTGATTTA
*
2042578 TTTTTTATTTTTTTGATTTG
1 TTTTTTATTTTTTTGATTTA
*
2042598 TTTTTGATTTT
1 TTTTTTATTTT
2042609 GTACTGACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.10, C:0.04, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTTATTTTTTTGATTTA
Found at i:2042936 original size:18 final size:18
Alignment explanation
Indices: 2042909--2042960 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
2042899 GTGAAGTATG
*
2042909 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
2042927 AATGGTGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
2042945 AATGGTGTTGTCGTGG
1 AATGGTGTTGTCGTGG
2042961 TAAGTGTGTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.15, C:0.12, G:0.40, T:0.33
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:2044159 original size:17 final size:17
Alignment explanation
Indices: 2044134--2044206 Score: 85
Period size: 17 Copynumber: 4.2 Consensus size: 17
2044124 AACATATAAA
2044134 GAACTAGTTTAATTAAT
1 GAACTAGTTTAATTAAT
* *
2044151 GAACGAGTTTAAATGAAT
1 GAACTAGTTT-AATTAAT
*
2044169 GAACTAGTTTAATTAGT
1 GAACTAGTTTAATTAAT
2044186 GAACTAGCTTT-ATTGAAT
1 GAACTAG-TTTAATT-AAT
2044204 GAA
1 GAA
2044207 AGAGGATACT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
17 24 0.51
18 23 0.49
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (17 bp):
GAACTAGTTTAATTAAT
Found at i:2044171 original size:18 final size:18
Alignment explanation
Indices: 2044134--2044206 Score: 71
Period size: 18 Copynumber: 4.2 Consensus size: 18
2044124 AACATATAAA
*
2044134 GAACTAGTTT-AATTAAT
1 GAACTAGTTTAAATGAAT
*
2044151 GAACGAGTTTAAATGAAT
1 GAACTAGTTTAAATGAAT
* *
2044169 GAACTAGTTT-AATTAGT
1 GAACTAGTTTAAATGAAT
*
2044186 GAACTAGCTTT-ATTGAAT
1 GAACTAG-TTTAAATGAAT
2044204 GAA
1 GAA
2044207 AGAGGATACT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
17 21 0.46
18 25 0.54
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (18 bp):
GAACTAGTTTAAATGAAT
Found at i:2044180 original size:35 final size:35
Alignment explanation
Indices: 2044134--2044206 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
2044124 AACATATAAA
2044134 GAACTAGTTTAATTAATGAACGAG-TTTAAATGAAT
1 GAACTAGTTTAATTAATGAACGAGCTTT-AATGAAT
* * *
2044169 GAACTAGTTTAATTAGTGAACTAGCTTTATTGAAT
1 GAACTAGTTTAATTAATGAACGAGCTTTAATGAAT
2044204 GAA
1 GAA
2044207 AGAGGATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 31 0.91
36 3 0.09
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (35 bp):
GAACTAGTTTAATTAATGAACGAGCTTTAATGAAT
Done.