Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 16
Found at i:1418182 original size:30 final size:30
Alignment explanation
Indices: 1418121--1418212 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 30
1418111 CTAAGGAACA
* * ***
1418121 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
1418152 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* * *
1418182 TCTGGATAGTTACCGAGGATCTTTATAACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
1418212 T
1 T
1418213 CTGAATAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 44 0.83
31 9 0.17
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:1418213 original size:30 final size:30
Alignment explanation
Indices: 1418149--1418220 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
1418139 GTTCTTCGGG
* * *
1418149 ACCTATGGACAGTTACCGAGGATCTTTATG
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
1418179 ACCTCTGGATAGTTACCGAGGATCTTTATA
1 ACCTCTGGATAGTTACCGAGGATCTTTATA
*
1418209 ACCTCTGAATAG
1 ACCTCTGGATAG
1418221 GTCCTTCGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCGAGGATCTTTATA
Found at i:1427896 original size:15 final size:15
Alignment explanation
Indices: 1427873--1427902 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1427863 TTTCTTTATC
*
1427873 AATAGTATTAATAAT
1 AATAATATTAATAAT
1427888 AATAATATTAATAAT
1 AATAATATTAATAAT
1427903 CAAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AATAATATTAATAAT
Found at i:1428515 original size:19 final size:16
Alignment explanation
Indices: 1428494--1428527 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1428484 TAATATGAAT
*
1428494 AATAGTTTTTATAATC
1 AATAATTTTTATAATC
1428510 AATAATTTTTATAATC
1 AATAATTTTTATAATC
1428526 AA
1 AA
1428528 CAAATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
AATAATTTTTATAATC
Found at i:1428533 original size:17 final size:16
Alignment explanation
Indices: 1428499--1428533 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1428489 TGAATAATAG
*
1428499 TTTTTATAATCAATAA
1 TTTTTATAATCAAAAA
1428515 TTTTTATAATCAACAAA
1 TTTTTATAATCAA-AAA
1428532 TT
1 TT
1428534 CAAAACGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TTTTTATAATCAAAAA
Found at i:1444275 original size:177 final size:182
Alignment explanation
Indices: 1443955--1444321 Score: 651
Period size: 177 Copynumber: 2.0 Consensus size: 182
1443945 TTATTACTTG
1443955 ATTATTTAAAAATAAATATAATTTAAATTTTATATTTAATATAATTTATTACTTAATAATTTAAT
1 ATTATTTAAAAATAAATATAATTTAAATTTTATATTTAATATAATTTATTACTTAATAATTTAAT
1444020 ATTAACATCATCAAAAAAAATTATTACTTAATAATTATTTTATATTTTTATTATAATTTAAGTGA
66 ATTAACATCATCAAAAAAAATTATTACTTAATAATTATTTTATATTTTTATTATAATTTAAGTGA
1444085 TATATTATAAAAATCATAATATTAATAAGTGT-AA-A-AATTTAAA-TTTAT
131 TATATTATAAAAATCATAATATTAATAAGTGTAAATATAATTTAAATTTTAT
*
1444133 ATTATTTAAACAT-AATGAATAATTTAAA-TTTATATTTAATATAATTTATTACTTAATAATTTA
1 ATTATTTAAAAATAAAT--ATAATTTAAATTTTATATTTAATATAATTTATTACTTAATAATTTA
1444196 ATATTAACATCATC-AAAAAAATTATTACTTAATAATTATTTTATATTTTTATTATAATTTAAGT
64 ATATTAACATCATCAAAAAAAATTATTACTTAATAATTATTTTATATTTTTATTATAATTTAAGT
1444260 GATATATTATAAAAATCATAATATTAATAAGTGTAAATATAATTTAAATTTTAT
129 GATATATTATAAAAATCATAATATTAATAAGTGTAAATATAATTTAAATTTTAT
1444314 ATT-TTTAA
1 ATTATTTAA
1444322 TTTACAACAT
Statistics
Matches: 182, Mismatches: 1, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
177 87 0.48
178 63 0.35
179 11 0.06
180 13 0.07
181 8 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (182 bp):
ATTATTTAAAAATAAATATAATTTAAATTTTATATTTAATATAATTTATTACTTAATAATTTAAT
ATTAACATCATCAAAAAAAATTATTACTTAATAATTATTTTATATTTTTATTATAATTTAAGTGA
TATATTATAAAAATCATAATATTAATAAGTGTAAATATAATTTAAATTTTAT
Found at i:1446401 original size:20 final size:20
Alignment explanation
Indices: 1446376--1446425 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1446366 ATGTAAGCAA
*
1446376 GGTATCTATACCATAGGCAG
1 GGTATCTATACCATAGACAG
*
1446396 GGTATCTATGCCATAGACAG
1 GGTATCTATACCATAGACAG
1446416 GGTATCTATA
1 GGTATCTATA
1446426 TCTCAGTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (20 bp):
GGTATCTATACCATAGACAG
Found at i:1446984 original size:22 final size:22
Alignment explanation
Indices: 1446956--1447018 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1446946 GAGGGTTTAT
*
1446956 AGTGGTCATTCGGGACGTAT-C
1 AGTGGTCCTTCGGGACGTATAC
1446977 AAGTGGTCCTTCGGGACGTATAC
1 -AGTGGTCCTTCGGGACGTATAC
1447000 AGTGGTCCTTCGGGACGTA
1 AGTGGTCCTTCGGGACGTA
1447019 GTGGTCCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 38 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATAC
Found at i:1447842 original size:22 final size:22
Alignment explanation
Indices: 1447814--1447876 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1447804 AGAGGGTTTT
*
1447814 AGTGGTCATTCGGGACGTAT-C
1 AGTGGTCCTTCGGGACGTATAC
1447835 AAGTGGTCCTTCGGGACGTATAC
1 -AGTGGTCCTTCGGGACGTATAC
1447858 AGTGGTCCTTCGGGACGTA
1 AGTGGTCCTTCGGGACGTA
1447877 GTGGTCCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 38 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.33, T:0.27
Consensus pattern (22 bp):
AGTGGTCCTTCGGGACGTATAC
Found at i:1448308 original size:24 final size:23
Alignment explanation
Indices: 1448281--1448326 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1448271 CAAACCATTT
1448281 CATATAACA-TAATGCATACTTATG
1 CATATAACATTAAT--ATACTTATG
*
1448305 CATATATCATTAATATACTTAT
1 CATATAACATTAATATACTTAT
1448327 CAGTACTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 8 0.40
25 4 0.20
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39
Consensus pattern (23 bp):
CATATAACATTAATATACTTATG
Found at i:1448653 original size:31 final size:31
Alignment explanation
Indices: 1448604--1448728 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
1448594 CCAGAAGGAC
*
1448604 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
* * * *
1448635 CAGTACATATGTCCCGAAGAATATATGTAAG
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1448666 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1448697 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1448728 C
1 C
1448729 CCTCGACCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
31 83 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1449385 original size:64 final size:64
Alignment explanation
Indices: 1449247--1449408 Score: 182
Period size: 64 Copynumber: 2.5 Consensus size: 64
1449237 TCTTTCAATG
* * *
1449247 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTA
1 AAAGCATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTA
*** * * * * *
1449311 CTGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTTTTTATT-TTA
1 AAAGCATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATG-TTGTATTATTA
* * *
1449375 AAAGCGTGCATCAATGCACTACAAATGCATCGAT
1 AAAGCATGCATCGATGCACTACTAATGCATCGAT
1449409 ATACCTTCAA
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 75 0.93
65 6 0.07
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (64 bp):
AAAGCATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTA
Found at i:1452601 original size:31 final size:31
Alignment explanation
Indices: 1452563--1452687 Score: 216
Period size: 31 Copynumber: 4.0 Consensus size: 31
1452553 CCAGAAGGAC
*
1452563 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1452594 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1452625 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1452656 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1452687 C
1 C
1452688 CCTCGACCCT
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 90 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1453460 original size:64 final size:64
Alignment explanation
Indices: 1453322--1453471 Score: 180
Period size: 64 Copynumber: 2.3 Consensus size: 64
1453312 TCTTTCAATG
* *
1453322 AAAGTATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTA
1 AAAGTATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGACGTTGTATTATTA
*** * * *
1453386 CCGGTATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGACGTT-T-TTACTTT
1 AAAGTATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGACGTTGTATTA--TT
1453449 A
64 A
1453450 AAAG-AGTGCATCGATGCACTAC
1 AAAGTA-TGCATCGATGCACTAC
1453472 CAATGCATTG
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
62 3 0.04
63 2 0.03
64 67 0.93
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (64 bp):
AAAGTATGCATCGATGCACTACTGATGCATCGATGCATAAAATGCATTCGACGTTGTATTATTA
Found at i:1458861 original size:21 final size:21
Alignment explanation
Indices: 1458837--1459055 Score: 186
Period size: 21 Copynumber: 10.3 Consensus size: 21
1458827 CATATTCGCA
*
1458837 TTGCGA-TAGTCCAAGTTCGCG
1 TTGCGATTATTCCAAGTT-GCG
1458858 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA-TTATTCCAAGTTGCG
* *
1458879 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT-GCG
1458900 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA-TTATTCCAAGTTGCG
* *
1458921 TTGCGA-TAGTCGAAGTTCGCG
1 TTGCGATTATTCCAAGTT-GCG
*
1458942 TTGCGATTTATTCCAAATT-CG
1 TTGCGA-TTATTCCAAGTTGCG
*
1458963 TTGCGATTTATTCTAAGTTCGCG
1 TTGCGA-TTATTCCAAGTT-GCG
*
1458986 TTGCGATTTATTCCAAATT-CG
1 TTGCGA-TTATTCCAAGTTGCG
* *
1459007 TTGCGA-TAGTCGAAGTTTGCG
1 TTGCGATTATTCCAAG-TTGCG
1459028 TTGCGATTTATTCCAAGTT-CG
1 TTGCGA-TTATTCCAAGTTGCG
1459049 TTGCGAT
1 TTGCGAT
1459056 AGTCCAAAAT
Statistics
Matches: 163, Mismatches: 19, Indels: 33
0.76 0.09 0.15
Matches are distributed among these distances:
19 24 0.15
20 3 0.02
21 81 0.50
22 2 0.01
23 53 0.33
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (21 bp):
TTGCGATTATTCCAAGTTGCG
Found at i:1458888 original size:42 final size:42
Alignment explanation
Indices: 1458837--1459059 Score: 374
Period size: 42 Copynumber: 5.3 Consensus size: 42
1458827 CATATTCGCA
*
1458837 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1458879 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
1458921 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
1458963 TTGCGATTTATTCTAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
1459007 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1459049 TTGCGATAGTC
1 TTGCGATAGTC
1459060 CAAAATTGCA
Statistics
Matches: 171, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
42 131 0.77
44 40 0.23
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:1459015 original size:86 final size:85
Alignment explanation
Indices: 1458837--1459059 Score: 369
Period size: 86 Copynumber: 2.6 Consensus size: 85
1458827 CATATTCGCA
*
1458837 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA-TAGTCGAAGTTCGCGT
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTAGTCGAAGTTCGCGT
*
1458901 TGCGATTTATTCCAAGTTCG
66 TGCGATTTATTCCAAATTCG
* * *
1458921 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCTAAGTTCGCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGA-TTAGTCGAAGTTCGCG
1458986 TTGCGATTTATTCCAAATTCG
65 TTGCGATTTATTCCAAATTCG
*
1459007 TTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAGTTCGTTGCGA-TAGTC
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTAGTC
1459060 CAAAATTGCA
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 50 0.39
86 79 0.61
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (85 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATTAGTCGAAGTTCGCGT
TGCGATTTATTCCAAATTCG
Found at i:1459179 original size:10 final size:11
Alignment explanation
Indices: 1459148--1459181 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
1459138 GACACGTATT
1459148 ACCACGACCACG
1 ACCACGACC-CG
1459160 ACCACGACCCG
1 ACCACGACCCG
1459171 ACC-CGACCCG
1 ACCACGACCCG
1459181 A
1 A
1459182 GACGAGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.36
11 5 0.23
12 9 0.41
ACGTcount: A:0.29, C:0.53, G:0.18, T:0.00
Consensus pattern (11 bp):
ACCACGACCCG
Found at i:1459694 original size:6 final size:6
Alignment explanation
Indices: 1459683--1459709 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1459673 TCTCGTCTCG
1459683 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
1459710 AATACGTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.15, G:0.52, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1459855 original size:21 final size:21
Alignment explanation
Indices: 1459825--1460001 Score: 177
Period size: 21 Copynumber: 8.5 Consensus size: 21
1459815 AATATGTAAA
*
1459825 TCGCAATGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
1459846 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
1459866 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
* *
1459887 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
1459907 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
1459928 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
1459949 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
1459970 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
1459991 TCGCGTTGCGA
1 TCGCATTGCGA
1460002 ATGGAAACTG
Statistics
Matches: 133, Mismatches: 13, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.01
20 32 0.24
21 98 0.74
22 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:1459869 original size:62 final size:62
Alignment explanation
Indices: 1459800--1459987 Score: 185
Period size: 62 Copynumber: 3.0 Consensus size: 62
1459790 TGCGATTTTG
* *
1459800 GACTATCGCAATGCGAATATGTAA-ATCGCAATGCGATAGTCCAAGTTCGCATTGCGATAGTC
1 GACTATCGCATTGCG-ATATGTAAGATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
* * *
1459862 GACTATCGCATTGCGAT-T-TACATATTCGCATTGCGATAGT-CGACTATCGCATTGCGAT--T-
1 GACTATCGCATTGCGATATGTA-AGA-TCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTC
* *
1459921 TACATATTCGCATTGCGATA-GTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT
1 GAC-TA-TCGCATTGCGATATGT--AAGATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT
1459985 C
62 C
1459986 GA
1 GA
1459988 AGTTCGCGTT
Statistics
Matches: 102, Mismatches: 10, Indels: 25
0.74 0.07 0.18
Matches are distributed among these distances:
59 4 0.04
60 5 0.05
61 18 0.18
62 68 0.67
63 4 0.04
64 2 0.02
65 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (62 bp):
GACTATCGCATTGCGATATGTAAGATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC
Found at i:1459890 original size:41 final size:41
Alignment explanation
Indices: 1459845--1459987 Score: 209
Period size: 41 Copynumber: 3.5 Consensus size: 41
1459835 ATAGTCCAAG
1459845 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1459886 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
* * * *
1459927 TTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCCA-A
1 TTCGCATTGCGATAGT-CGACTATCGCATTGCGAT-TTACATA
1459968 GTTCGCATTGCGATAGTCGA
1 -TTCGCATTGCGATAGTCGA
1459988 AGTTCGCGTT
Statistics
Matches: 94, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
41 72 0.77
42 22 0.23
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (41 bp):
TTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
Found at i:1459892 original size:20 final size:20
Alignment explanation
Indices: 1459867--1459939 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1459857 TAGTCGACTA
1459867 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
1459887 TCGCATTGCGATAGT-CGACTA-
1 TCGCATTGCGAT-TTAC-A-TAT
1459908 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1459928 TCGCATTGCGAT
1 TCGCATTGCGAT
1459940 AGTCCAAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
19 2 0.04
20 27 0.59
21 15 0.33
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1460202 original size:167 final size:171
Alignment explanation
Indices: 1460003--1460336 Score: 640
Period size: 170 Copynumber: 2.0 Consensus size: 171
1459993 GCGTTGCGAA
1460003 TGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAA-T-TCGATCGCATTGCGATTTAGTTGG
1 TGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAGTTGG
1460066 TCATTTTGGAAAATCCAAAAAAAAG-TGGTTAAAATCGTATATTATAAGACATTTTTTGTCAATG
66 TCATTTTGGAAAATCCAAAAAAAAGTTGGTTAAAATCGTATATTATAAGACATTTTTTGTCAATG
1460130 AGGTTATTTTCT-TAAATTTTAAACTAAAAATCACTTAATC
131 AGGTTATTTTCTCTAAATTTTAAACTAAAAATCACTTAATC
1460170 TGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAGTTGG
1 TGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAGTTGG
1460235 TCATTTTGGAAAATCCAAAAAAAAGTTGGTTAAAATCGTATATTATAAGACATTTTTTGTCAATG
66 TCATTTTGGAAAATCCAAAAAAAAGTTGGTTAAAATCGTATATTATAAGACATTTTTTGTCAATG
1460300 AGGTTATTTTCTCTAAATTTTAAACTAAAAATCACTT
131 AGGTTATTTTCTCTAAATTTTAAACTAAAAATCACTT
1460337 TTAAAAGTTT
Statistics
Matches: 163, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
167 38 0.23
168 1 0.01
169 49 0.30
170 51 0.31
171 24 0.15
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (171 bp):
TGGAAACTGATTTGCGATACCGGAGATCGCGTTGCGAATTATCGATCGCATTGCGATTTAGTTGG
TCATTTTGGAAAATCCAAAAAAAAGTTGGTTAAAATCGTATATTATAAGACATTTTTTGTCAATG
AGGTTATTTTCTCTAAATTTTAAACTAAAAATCACTTAATC
Found at i:1468231 original size:32 final size:32
Alignment explanation
Indices: 1468188--1468251 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1468178 ATAACTACAA
1468188 TAATAAATTATTTAAAATAAATCAATACATAC
1 TAATAAATTATTTAAAATAAATCAATACATAC
* *
1468220 TAATTAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATACATAC
1468252 AACTGCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAATCAATACATAC
Found at i:1468291 original size:80 final size:79
Alignment explanation
Indices: 1468198--1468658 Score: 469
Period size: 80 Copynumber: 5.7 Consensus size: 79
1468188 TAATAAATTA
* **
1468198 TTTAAAATAAATCAATACATACTAATTAATTATTTAAAATAAATCAATCCATACAACTGCAATAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAA-TAAAATAA
1468263 TAAATCAATCCATAT
65 TAAATCAATCCATAT
* * * *
1468278 TTTAAAATAAATCATTCCATACTAATAAATTATTTAAAATAAATCAATCCATGCAAATACAATAA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAC-AATAAAATAA
1468343 TAAATCAATCCATAT
65 TAAATCAATCCATAT
* *
1468358 TTTAAAATAAATCAAT-CTATACAAATAAATTATTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATAC-ATACTAATAAATTATTTAAAATAAATCAATCCATAC-AATAAA--A
*
1468422 TTTAAAATAAATCAATCTATAT
62 --T--AATAAATCAATCCATAT
* *
1468444 TTTAAAATAAATC---A-AT--TAAT--A-T-TTTAAAATAAATAAATCTATACTAATAAATTAT
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATAC-AATAAA--A-
1468499 TTAAAATAAATCAATCCATAT
62 -T--AATAAATCAATCCATAT
* * *
1468520 TTTAAAATAAATTAATCCATA-TAAATAAATTATTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATACATACT-AATAAATTATTTAAAATAAATCAATCCATA-CAATAAA--A
1468584 TTTAAAATAAATCAATCCATAT
62 --T--AATAAATCAATCCATAT
*
1468606 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATA
1468659 TTTTAAAATA
Statistics
Matches: 337, Mismatches: 23, Indels: 36
0.85 0.06 0.09
Matches are distributed among these distances:
76 64 0.19
77 1 0.00
78 1 0.00
79 1 0.00
80 130 0.39
81 3 0.01
82 6 0.02
84 2 0.01
85 1 0.00
86 127 0.38
87 1 0.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (79 bp):
TTTAAAATAAATCAATACATACTAATAAATTATTTAAAATAAATCAATCCATACAATAAAATAAT
AAATCAATCCATAT
Found at i:1468325 original size:54 final size:54
Alignment explanation
Indices: 1468261--1468712 Score: 379
Period size: 54 Copynumber: 8.3 Consensus size: 54
1468251 CAACTGCAAT
*
1468261 AATAAATCAATCCATATTTTAAAATAAATCATTCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** * * *
1468315 AATAAATCAATCCATGCAAATACAATAATAAATCAATCCATATTTTAAAATAAATCAATCT-A
1 AATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATA--CT--AATAAAT-TATTTAA
* * * *
1468377 TACAAATAAAT---TA-TTTAAAATAAATCAATCTATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
* ** ** * **
1468427 AATAAATCAATCTATATTTTAAAATAAATCAATTAATA-TTTTAAAATAAAT-A
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
** ** * * **
1468479 AATCTATACTAATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAATTAATCCA
1 AATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATA--CT--AATAAATTATTTAA
* * *
1468539 TATAAATAAAT---TA-TTTAAAATAAATCAATCCATATTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1468589 AATAAATCAATCCATATTTTAAAATAAATCAATACATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1468643 AATAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1468697 AATAAATCAATTCATA
1 AATAAATCAATCCATA
1468713 CAACTACAAT
Statistics
Matches: 320, Mismatches: 50, Indels: 56
0.75 0.12 0.13
Matches are distributed among these distances:
49 3 0.01
50 36 0.11
52 9 0.03
53 14 0.04
54 197 0.62
55 4 0.01
56 1 0.00
57 5 0.02
58 18 0.06
59 8 0.03
60 6 0.02
62 16 0.05
63 3 0.01
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1468394 original size:32 final size:32
Alignment explanation
Indices: 1468358--1468442 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
1468348 CAATCCATAT
1468358 TTTAAAATAAATCAATCTATACAAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
*
1468390 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACAAATAAATTA
1468422 TTTAAAATAAATCAATCTATA
1 TTTAAAATAAATCAATCTATA
1468443 TTTTAAAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACAAATAAATTA
Found at i:1468397 original size:14 final size:14
Alignment explanation
Indices: 1468380--1468433 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
1468370 CAATCTATAC
1468380 AAATAAATTATTTA
1 AAATAAATTATTTA
*
1468394 AAATAAATCAATCTATA
1 AAATAAAT-TAT-T-TA
*
1468411 CTAATAAATTATTTA
1 -AAATAAATTATTTA
1468426 AAATAAAT
1 AAATAAAT
1468434 CAATCTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 15 0.47
15 4 0.12
16 2 0.06
17 4 0.12
18 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATAAATTATTTA
Found at i:1468448 original size:22 final size:22
Alignment explanation
Indices: 1468422--1468486 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1468412 TAATAAATTA
1468422 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
1468444 TTTAAAATAAATCAAT-TAATAT
1 TTTAAAATAAATCAATCT-ATAT
*
1468466 TTTAAAATAAATAAATCTATA
1 TTTAAAATAAATCAATCTATA
1468487 CTAATAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:1468545 original size:18 final size:18
Alignment explanation
Indices: 1468524--1468583 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
1468514 CCATATTTTA
1468524 AAATAAATTAATCCATAT
1 AAATAAATTAATCCATAT
*
1468542 AAATAAATT-AT--TTA-
1 AAATAAATTAATCCATAT
*
1468556 AAATAAATCAATCCATAT
1 AAATAAATTAATCCATAT
*
1468574 TAATAAATTA
1 AAATAAATTA
1468584 TTTAAAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 8 0.24
15 4 0.12
17 4 0.12
18 17 0.52
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATAAATTAATCCATAT
Found at i:1468549 original size:22 final size:22
Alignment explanation
Indices: 1468500--1468548 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1468490 ATAAATTATT
**
1468500 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
1468522 TAAAATAAATTAATCCATATAAA
1 TAAAATAAATCAATCCATAT-AA
1468545 TAAA
1 TAAA
1468549 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1468561 original size:32 final size:32
Alignment explanation
Indices: 1468520--1468712 Score: 169
Period size: 32 Copynumber: 6.7 Consensus size: 32
1468510 CAATCCATAT
*
1468520 TTTAAAATAAATTAATCCATATAAATAAATTA
1 TTTAAAATAAATCAATCCATATAAATAAATTA
*
1468552 TTTAAAATAAATCAATCCATATTAATAAATTA
1 TTTAAAATAAATCAATCCATATAAATAAATTA
1468584 TTTAAAATAAATCAATCC------AT--A-T-
1 TTTAAAATAAATCAATCCATATAAATAAATTA
*
1468606 TTTAAAATAAATCAATACATACT-AATAAATTA
1 TTTAAAATAAATCAATCCATA-TAAATAAATTA
*
1468638 TTTAAAATAAATC-A---AT-T-CAT--A-T-
1 TTTAAAATAAATCAATCCATATAAATAAATTA
1468660 TTTAAAATAAATCAATCCATACT-AATAAATTA
1 TTTAAAATAAATCAATCCATA-TAAATAAATTA
*
1468692 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
1468713 CAACTACAAT
Statistics
Matches: 135, Mismatches: 6, Indels: 40
0.75 0.03 0.22
Matches are distributed among these distances:
22 30 0.22
23 3 0.02
24 2 0.01
26 7 0.05
28 7 0.05
30 2 0.01
31 3 0.02
32 81 0.60
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATATAAATAAATTA
Found at i:1468610 original size:22 final size:22
Alignment explanation
Indices: 1468584--1468626 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1468574 TAATAAATTA
*
1468584 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
1468606 TTTAAAATAAATCAATACATA
1 TTTAAAATAAATCAATACATA
1468627 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:1468635 original size:22 final size:22
Alignment explanation
Indices: 1468586--1468634 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1468576 ATAAATTATT
* **
1468586 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATACATATAA
1468608 TAAAATAAATCAATACATACTAA
1 TAAAATAAATCAATACATA-TAA
1468631 TAAA
1 TAAA
1468635 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATACATATAA
Found at i:1468664 original size:22 final size:22
Alignment explanation
Indices: 1468638--1468680 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1468628 TAATAAATTA
*
1468638 TTTAAAATAAATCAATTCATAT
1 TTTAAAATAAATCAATCCATAT
1468660 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
1468681 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1468689 original size:22 final size:22
Alignment explanation
Indices: 1468640--1468688 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1468630 ATAAATTATT
* **
1468640 TAAAATAAATCAATTCATATTT
1 TAAAATAAATCAATCCATATAA
1468662 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1468685 TAAA
1 TAAA
1468689 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1468779 original size:32 final size:31
Alignment explanation
Indices: 1468740--1468837 Score: 115
Period size: 32 Copynumber: 3.4 Consensus size: 31
1468730 CAATCTATAT
1468740 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAAT-CATACTAATAAATTA
1468772 TTTAAAATAAATC-A--AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCATACTAATAAATTA
1468794 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAA-TCATACTAATAAATTA
1468826 TTTAAAATAAAT
1 TTTAAAATAAAT
1468838 TATTTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 13 0.23
23 2 0.04
24 1 0.02
26 4 0.07
27 4 0.07
28 4 0.07
30 1 0.02
31 2 0.04
32 25 0.45
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (31 bp):
TTTAAAATAAATCAATCATACTAATAAATTA
Found at i:1468787 original size:54 final size:54
Alignment explanation
Indices: 1468723--1468837 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 54
1468713 CAACTACAAT
*
1468723 AATAATTCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1468777 AATAAATCAATCTATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAA
1 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1468831 AATAAAT
1 AATAAAT
1468838 TATTTTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (54 bp):
AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1468798 original size:22 final size:22
Alignment explanation
Indices: 1468772--1468873 Score: 82
Period size: 22 Copynumber: 4.5 Consensus size: 22
1468762 TAATAAATTA
1468772 TTTAAAATAAATCAATCTATAT
1 TTTAAAATAAATCAATCTATAT
1468794 TTTAAAATAAATCAAT-TCATACT
1 TTTAAAATAAATCAATCT-ATA-T
** * ** * **
1468817 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCTA-TAT
1468841 TTTAAAATAAATCAATCT-TAT
1 TTTAAAATAAATCAATCTATAT
1468862 TTTAAAATAAAT
1 TTTAAAATAAAT
1468874 AACCTTATTA
Statistics
Matches: 60, Mismatches: 15, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
21 16 0.27
22 19 0.32
23 11 0.18
24 12 0.20
25 2 0.03
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
TTTAAAATAAATCAATCTATAT
Found at i:1468834 original size:14 final size:15
Alignment explanation
Indices: 1468817--1468852 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1468807 AATTCATACT
1468817 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1468831 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1468846 AATAAAT
1 AATAAAT
1468853 CAATCTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1468882 original size:20 final size:21
Alignment explanation
Indices: 1468837--1468882 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1468827 TTAAAATAAA
*
1468837 TTATTTTAAAATAAATCAATC
1 TTATTTTAAAATAAATCAACC
1468858 TTATTTTAAAATAAAT-AACC
1 TTATTTTAAAATAAATCAACC
1468878 TTATT
1 TTATT
1468883 AAATTATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (21 bp):
TTATTTTAAAATAAATCAACC
Found at i:1469916 original size:9 final size:10
Alignment explanation
Indices: 1469899--1469923 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1469889 TTATTATTTG
1469899 AATTTTTTTA
1 AATTTTTTTA
1469909 AATTTTTTTA
1 AATTTTTTTA
1469919 AATTT
1 AATTT
1469924 ATAAAATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
AATTTTTTTA
Found at i:1470064 original size:2 final size:2
Alignment explanation
Indices: 1470057--1470116 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1470047 ACCTAGTATG
1470057 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
1470099 -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1470117 ATGTGTAAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1470366 original size:73 final size:71
Alignment explanation
Indices: 1470289--1470430 Score: 232
Period size: 73 Copynumber: 2.0 Consensus size: 71
1470279 TTACATTCGA
1470289 ATAATTAAATTGAATAAAATAAAAGTTGAATGAATAAATT-AAAAATTTAAAAAGAAAGGAGAAA
1 ATAATTAAATTGAATAAAATAAAAGTTGAATGAATAAATTGAAAAATTTAAAAAG--A-GAGAAA
1470353 TTCAAATGT
63 TTCAAATGT
* *
1470362 ATAATTAAATTGAATAAAATAAAAGTTGAATGATTAAATTGAAAAATTTTAAAAGAGAGAAATTC
1 ATAATTAAATTGAATAAAATAAAAGTTGAATGAATAAATTGAAAAATTTAAAAAGAGAGAAATTC
1470427 AAAT
66 AAAT
1470431 TTTATATATA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
71 13 0.20
72 1 0.02
73 39 0.59
74 13 0.20
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.29
Consensus pattern (71 bp):
ATAATTAAATTGAATAAAATAAAAGTTGAATGAATAAATTGAAAAATTTAAAAAGAGAGAAATTC
AAATGT
Found at i:1473318 original size:2 final size:2
Alignment explanation
Indices: 1473313--1473360 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1473303 CATGGGTTAT
1473313 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1473355 TA TA TA
1 TA TA TA
1473361 AAGAACCACT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1475052 original size:29 final size:28
Alignment explanation
Indices: 1474996--1475052 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1474986 AAGTGAGATC
* *
1474996 AATTTTGCTTCAAGTGAAACAATTTCAA
1 AATTTTGCTTCAAGGGAAACAATCTCAA
* *
1475024 AATTTATGTTTCAAGGGAAACTATCTCAA
1 AATTT-TGCTTCAAGGGAAACAATCTCAA
1475053 GCGAGACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (28 bp):
AATTTTGCTTCAAGGGAAACAATCTCAA
Found at i:1475082 original size:102 final size:101
Alignment explanation
Indices: 1474852--1475089 Score: 282
Period size: 102 Copynumber: 2.3 Consensus size: 101
1474842 ATAAATGAGT
* * * * * ** *
1474852 GAGAAGAAAATTGTTTCAGGAGAAGCTATCTCAGGTGAGATAAATTTTTTTTCGAGTGAAACAAT
1 GAGACGAAATTTGTTTCA-GAGAAACAATCTCAAGTGAGATAAATTTTGCTTCAAGTGAAACAAT
* *
1474917 TTTAAAATTTGCGTTTCAAGGGAAAACTATCTCAAGC
65 TTCAAAATTTACGTTTCAAGGGAAAACTATCTCAAGC
* * * *
1474954 GAGGCGAAATTTATTTTTAG-GAAAACAATCTCAAGTGAGATCAATTTTGCTTCAAGTGAAACAA
1 GAGACGAAATTT-GTTTCAGAG-AAACAATCTCAAGTGAGATAAATTTTGCTTCAAGTGAAACAA
*
1475018 TTTCAAAATTTATGTTTCAAGGG-AAACTATCTCAAGC
64 TTTCAAAATTTACGTTTCAAGGGAAAACTATCTCAAGC
1475055 GAGACGAAACTTTGTTTCGAGAGAAACAATCTCAA
1 GAGACGAAA-TTTGTTTC-AGAGAAACAATCTCAA
1475090 AGGTTTATGT
Statistics
Matches: 113, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
101 26 0.23
102 82 0.73
103 5 0.04
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (101 bp):
GAGACGAAATTTGTTTCAGAGAAACAATCTCAAGTGAGATAAATTTTGCTTCAAGTGAAACAATT
TCAAAATTTACGTTTCAAGGGAAAACTATCTCAAGC
Found at i:1475108 original size:30 final size:30
Alignment explanation
Indices: 1475067--1475252 Score: 135
Period size: 30 Copynumber: 5.8 Consensus size: 30
1475057 GACGAAACTT
*
1475067 TGTTTCGAGAGAAACAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
** *
1475097 TGTTTCAAGAGAAACTGTCTCAAACGAGACAAAATT-
1 TGTTTCAAGAGAAACAATCTCAAA-G-G-----TTTA
*
1475133 TGTTTCAAGAGAAACAATCTCAAATGTTTA
1 TGTTTCAAGAGAAACAATCTCAAAGGTTTA
* *
1475163 TGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTTA
1 TGTTTCAAGAGAAACAATCTCAA---AG-----GTTTA
1475201 --TTTCAAGAGAAACAAATCTCAAAGGTTTA
1 TGTTTCAAGAGAAAC-AATCTCAAAGGTTTA
*
1475230 TGTTTCAAGAGAAACTATCTCAA
1 TGTTTCAAGAGAAACAATCTCAA
1475253 GCAAGATGAA
Statistics
Matches: 123, Mismatches: 14, Indels: 38
0.70 0.08 0.22
Matches are distributed among these distances:
29 6 0.05
30 50 0.41
31 14 0.11
32 1 0.01
33 1 0.01
34 3 0.02
36 35 0.28
37 9 0.07
38 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (30 bp):
TGTTTCAAGAGAAACAATCTCAAAGGTTTA
Found at i:1475144 original size:36 final size:36
Alignment explanation
Indices: 1475097--1475325 Score: 180
Period size: 36 Copynumber: 6.6 Consensus size: 36
1475087 CAAAGGTTTA
*
1475097 TGTTTCAAGAGAAACTGTCTCAAACGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAACGAGACAAAATT
* * *
1475133 TGTTTCAAGAGAAACAATCTCAAA--TG-----TTT
1 TGTTTCAAGAGAAACTATCTCAAACGAGACAAAATT
*
1475162 ATGTTTCAAGAGAAACTATCTCAAGCGAGACAAAATT
1 -TGTTTCAAGAGAAACTATCTCAAACGAGACAAAATT
* * *
1475199 TATTTCAAGAGAAACAAATCTCAAA-G-G-----TTT
1 TGTTTCAAGAGAAAC-TATCTCAAACGAGACAAAATT
* * * *
1475229 ATGTTTCAAGAGAAACTATCTCAAGCAAGATGAAACTT
1 -TGTTTCAAGAGAAACTATCTCAAACGAGA-CAAAATT
* **
1475267 TGTTTCAAGAGAAACTGTCTCAATTGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAACGAGACAAAATT
*
1475303 TTTTTCAAGAGAAACTATCTCAA
1 TGTTTCAAGAGAAACTATCTCAA
1475326 GGGAGATAGA
Statistics
Matches: 150, Mismatches: 25, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
29 2 0.01
30 31 0.21
31 14 0.09
32 2 0.01
34 1 0.01
35 1 0.01
36 63 0.42
37 34 0.23
38 2 0.01
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTATCTCAAACGAGACAAAATT
Found at i:1475219 original size:133 final size:133
Alignment explanation
Indices: 1474991--1475281 Score: 417
Period size: 133 Copynumber: 2.2 Consensus size: 133
1474981 ATCTCAAGTG
* * * * *
1474991 AGATC-AATTTTGCTTCAAGTGAAACAATTTCAAAATTTATGTTTCAAGGGAAACTATCTCAAGC
1 AGATCAAAATTTGTTTCAAGAGAAACAATCTCAAAATTTATGTTTCAAGAGAAACTATCTCAAGC
* * * *
1475055 GAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTGTCTCAA
66 GAGACGAAAATTTATTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAA
*
1475120 ACG
131 ACA
*
1475123 AGA-CAAAATTTGTTTCAAGAGAAACAATCTCAAATGTTTATGTTTCAAGAGAAACTATCTCAAG
1 AGATCAAAATTTGTTTCAAGAGAAACAATCTCAAA-ATTTATGTTTCAAGAGAAACTATCTCAAG
1475187 CGAGAC-AAAATTTATTTCAAGAGAAACAAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTC
65 CGAGACGAAAATTTATTTCAAGAGAAAC-AATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTC
*
1475251 AAGCA
129 AAACA
* *
1475256 AGATGAAACTTTGTTTCAAGAGAAAC
1 AGATCAAAATTTGTTTCAAGAGAAAC
1475282 TGTCTCAATT
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
131 1 0.01
132 46 0.33
133 74 0.52
134 20 0.14
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (133 bp):
AGATCAAAATTTGTTTCAAGAGAAACAATCTCAAAATTTATGTTTCAAGAGAAACTATCTCAAGC
GAGACGAAAATTTATTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAA
ACA
Found at i:1475289 original size:67 final size:66
Alignment explanation
Indices: 1474976--1475281 Score: 409
Period size: 66 Copynumber: 4.6 Consensus size: 66
1474966 ATTTTTAGGA
* * * * * * *
1474976 AAACAATCTCAAGTGAGATC-AATTTTGCTTCAAGTGAAACAATTTCAAA-ATTTATGTTTCAAG
1 AAACTATCTCAAGCGAGA-CAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAG
*
1475039 GG
65 AG
* *
1475041 AAACTATCTCAAGCGAGACGAAACTTTGTTTCGAGAGAAACAATCTCAAAGGTTTATGTTTCAAG
1 AAACTATCTCAAGCGAGAC-AAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAG
1475106 AG
65 AG
* * *
1475108 AAACTGTCTCAAACGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAATGTTTATGTTTCAAGA
1 AAACTATCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGA
1475173 G
66 G
*
1475174 AAACTATCTCAAGCGAGACAAAATTTATTTCAAGAGAAACAAATCTCAAAGGTTTATGTTTCAAG
1 AAACTATCTCAAGCGAGACAAAATTTGTTTCAAGAGAAAC-AATCTCAAAGGTTTATGTTTCAAG
1475239 AG
65 AG
* * *
1475241 AAACTATCTCAAGCAAGATGAAACTTTGTTTCAAGAGAAAC
1 AAACTATCTCAAGCGAGA-CAAAATTTGTTTCAAGAGAAAC
1475282 TGTCTCAATT
Statistics
Matches: 214, Mismatches: 22, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
64 1 0.00
65 16 0.07
66 105 0.49
67 73 0.34
68 19 0.09
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (66 bp):
AAACTATCTCAAGCGAGACAAAATTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGA
G
Found at i:1476730 original size:18 final size:19
Alignment explanation
Indices: 1476696--1476732 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1476686 TTAATTTGAA
*
1476696 CCTTGAACTTTTGTTGTTT
1 CCTTGAACTTTTATTGTTT
1476715 CCTTGAA-TTTTATTGTTT
1 CCTTGAACTTTTATTGTTT
1476733 TGATTTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (19 bp):
CCTTGAACTTTTATTGTTT
Found at i:1477932 original size:18 final size:18
Alignment explanation
Indices: 1477898--1477931 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1477888 CCCCATTGTG
1477898 TTAATCTCAGCTATTTTC
1 TTAATCTCAGCTATTTTC
*
1477916 TTAATGTCAG-TATTTT
1 TTAATCTCAGCTATTTT
1477932 TAGTGTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.53
Consensus pattern (18 bp):
TTAATCTCAGCTATTTTC
Found at i:1481172 original size:2 final size:2
Alignment explanation
Indices: 1481167--1481220 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1481157 AAACATGGGT
1481167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1481209 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1481221 AAGAACCACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1481321 original size:17 final size:17
Alignment explanation
Indices: 1481292--1481324 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1481282 AAGTAACCAA
1481292 ATTAGAAATAATGAATG
1 ATTAGAAATAATGAATG
1481309 ATTA-AAATGAATGAAT
1 ATTAGAAAT-AATGAAT
1481325 TATAACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (17 bp):
ATTAGAAATAATGAATG
Found at i:1482200 original size:22 final size:22
Alignment explanation
Indices: 1482168--1482214 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1482158 AGAAAAGAAA
*
1482168 GATCATTCCCCCTTGACATTAT
1 GATCATCCCCCCTTGACATTAT
* *
1482190 GATCATCCCCCCTTGATATTCT
1 GATCATCCCCCCTTGACATTAT
1482212 GAT
1 GAT
1482215 TTTTAAGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.32, G:0.11, T:0.36
Consensus pattern (22 bp):
GATCATCCCCCCTTGACATTAT
Found at i:1493896 original size:19 final size:18
Alignment explanation
Indices: 1493837--1493902 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
1493827 ATGACTTTTT
* *
1493837 GGTCAAATTCAACGATTAA
1 GGTCAAAGTCAAC-ATGAA
*
1493856 CGGTCAAAGTCAACATGTA
1 -GGTCAAAGTCAACATGAA
1493875 GGTCAACAGTCAAC-TGGAA
1 GGTCAA-AGTCAACAT-GAA
1493894 GGTCAAAGT
1 GGTCAAAGT
1493903 TAACGGTTCG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 10 0.25
19 18 0.45
20 12 0.30
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (18 bp):
GGTCAAAGTCAACATGAA
Found at i:1493956 original size:20 final size:20
Alignment explanation
Indices: 1493929--1493979 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1493919 GTTCAACGGG
*
1493929 TCAGATCGGTTCGGGTTGAC
1 TCAGATCGGTTCGAGTTGAC
* *
1493949 TTAGATCGATTCGAGTTGAC
1 TCAGATCGGTTCGAGTTGAC
1493969 TCAGATCGGTT
1 TCAGATCGGTT
1493980 TGGTTCGAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (20 bp):
TCAGATCGGTTCGAGTTGAC
Found at i:1508473 original size:20 final size:20
Alignment explanation
Indices: 1508448--1508519 Score: 72
Period size: 20 Copynumber: 3.3 Consensus size: 20
1508438 AAGTCAAAAC
1508448 ATAATCTGAATCAATTAATA
1 ATAATCTGAATCAATTAATA
* *
1508468 ATAATCATAGTTCGAATCAAATACTA
1 ATAATC-----T-GAATCAATTAATA
1508494 ATAATCTGAATCAATTAATA
1 ATAATCTGAATCAATTAATA
1508514 ATAATC
1 ATAATC
1508520 ATAGTCTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 23 0.55
21 1 0.02
25 1 0.02
26 17 0.40
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (20 bp):
ATAATCTGAATCAATTAATA
Found at i:1508484 original size:26 final size:25
Alignment explanation
Indices: 1508455--1508547 Score: 97
Period size: 26 Copynumber: 3.8 Consensus size: 25
1508445 AACATAATCT
*
1508455 GAATCAATTAATAATAATCATAGTTC
1 GAATCAAATAATAATAATCATAG-TC
*
1508481 GAATCAAATACTAATAATC----T-
1 GAATCAAATAATAATAATCATAGTC
*
1508501 GAATCAATTAATAATAATCATAGTC
1 GAATCAAATAATAATAATCATAGTC
*
1508526 TGAATCAAATACTAATAATCAT
1 -GAATCAAATAATAATAATCAT
1508548 TGATTTGAAC
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
20 17 0.31
21 1 0.02
24 1 0.02
26 36 0.65
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.32
Consensus pattern (25 bp):
GAATCAAATAATAATAATCATAGTC
Found at i:1508505 original size:46 final size:46
Alignment explanation
Indices: 1508448--1508545 Score: 180
Period size: 46 Copynumber: 2.1 Consensus size: 46
1508438 AAGTCAAAAC
1508448 ATAATCTGAATCAATTAATAATAATCATAGT-TCGAATCAAATACTA
1 ATAATCTGAATCAATTAATAATAATCATAGTCT-GAATCAAATACTA
1508494 ATAATCTGAATCAATTAATAATAATCATAGTCTGAATCAAATACTA
1 ATAATCTGAATCAATTAATAATAATCATAGTCTGAATCAAATACTA
1508540 ATAATC
1 ATAATC
1508546 ATTGATTTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 50 0.98
47 1 0.02
ACGTcount: A:0.48, C:0.13, G:0.06, T:0.33
Consensus pattern (46 bp):
ATAATCTGAATCAATTAATAATAATCATAGTCTGAATCAAATACTA
Found at i:1509443 original size:19 final size:19
Alignment explanation
Indices: 1509419--1509607 Score: 103
Period size: 19 Copynumber: 10.0 Consensus size: 19
1509409 ACCATAATAT
*
1509419 TTAGATTTTAGGTTGGAAG
1 TTAGATTTTAGGTTGGAAA
* *
1509438 TTAGATTTTAAGTTGAAAA
1 TTAGATTTTAGGTTGGAAA
1509457 TTAGATTTTAGGTTGGAAA
1 TTAGATTTTAGGTTGGAAA
** *** ***
1509476 CAAGATTTTCTATCAAAAA
1 TTAGATTTTAGGTTGGAAA
** *
1509495 CAAGATTTCAGGTTGGAAA
1 TTAGATTTTAGGTTGGAAA
** *
1509514 CCAGATTTTATGTT-GAAA
1 TTAGATTTTAGGTTGGAAA
** * *
1509532 CCAAATTTTCA-ATTGGAAA
1 TTAGATTTT-AGGTTGGAAA
* *
1509551 CTAGATTTTAAGTTGGAAA
1 TTAGATTTTAGGTTGGAAA
* *
1509570 CTAGATTTTCGGTTGGAAA
1 TTAGATTTTAGGTTGGAAA
* **
1509589 TCAGATCCTAGGTTGGAAA
1 TTAGATTTTAGGTTGGAAA
1509608 CCATATTTTC
Statistics
Matches: 132, Mismatches: 35, Indels: 6
0.76 0.20 0.03
Matches are distributed among these distances:
18 15 0.11
19 117 0.89
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.35
Consensus pattern (19 bp):
TTAGATTTTAGGTTGGAAA
Found at i:1509482 original size:38 final size:38
Alignment explanation
Indices: 1509420--1509588 Score: 155
Period size: 38 Copynumber: 4.5 Consensus size: 38
1509410 CCATAATATT
** *
1509420 TAGATTTTAGGTTGGAAGTTAGATTTTAAGTTGAAAAT
1 TAGATTTTAGGTTGGAAACTAGATTTTAAGTTGAAAAC
* * **
1509458 TAGATTTTAGGTTGGAAACAAGATTTTCTA-TCAAAAAC
1 TAGATTTTAGGTTGGAAACTAGATTTT-AAGTTGAAAAC
* * * *
1509496 AAGATTTCAGGTTGGAAACCAGATTTTATGTTG-AAAC
1 TAGATTTTAGGTTGGAAACTAGATTTTAAGTTGAAAAC
* * * *
1509533 CAAATTTTCA-ATTGGAAACTAGATTTTAAGTTGGAAAC
1 TAGATTTT-AGGTTGGAAACTAGATTTTAAGTTGAAAAC
*
1509571 TAGATTTTCGGTTGGAAA
1 TAGATTTTAGGTTGGAAA
1509589 TCAGATCCTA
Statistics
Matches: 102, Mismatches: 24, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
37 29 0.28
38 72 0.71
39 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (38 bp):
TAGATTTTAGGTTGGAAACTAGATTTTAAGTTGAAAAC
Found at i:1509557 original size:37 final size:38
Alignment explanation
Indices: 1509507--1509617 Score: 116
Period size: 38 Copynumber: 2.9 Consensus size: 38
1509497 AGATTTCAGG
*
1509507 TTGGAAACCAGATTTTATGTT-GAAACCAAATTTTCAA
1 TTGGAAACCAGATTTTAAGTTGGAAACCAAATTTTCAA
* * * **
1509544 TTGGAAACTAGATTTTAAGTTGGAAACTAGATTTTCGG
1 TTGGAAACCAGATTTTAAGTTGGAAACCAAATTTTCAA
* ** * *
1509582 TTGGAAATCAGATCCTAGGTTGGAAACCATATTTTC
1 TTGGAAACCAGATTTTAAGTTGGAAACCAAATTTTC
1509618 TTATATGAAC
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
37 19 0.32
38 41 0.68
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (38 bp):
TTGGAAACCAGATTTTAAGTTGGAAACCAAATTTTCAA
Found at i:1509784 original size:40 final size:40
Alignment explanation
Indices: 1509719--1510070 Score: 216
Period size: 40 Copynumber: 8.8 Consensus size: 40
1509709 CACAAGCAAT
* * * *
1509719 GTGATGTATCGTACGGGGTATACACCTAAATATGAGAGTG
1 GTGATGTATTGTACGAGATACACACCTAAATATGAGAGTG
* * * ** **
1509759 GTGATGTATTGCATGAGATACACACCTAATTACAAGCA-AC
1 GTGATGTATTGTACGAGATACACACCTAAATATGAG-AGTG
* * * * *
1509799 GTTATGTATCGTAC-AAAGCACACACCAAAATATGAGAGTG
1 GTGATGTATTGTACGAGA-TACACACCTAAATATGAGAGTG
* ** *
1509839 GTGATGTATTGTAC-AGGATACACACCCT-ATTACAAGCA-AG
1 GTGATGTATTGTACGA-GATACACA-CCTAAATATGAG-AGTG
* * *
1509879 GTAATGTATTGTACGAGGTACACACCTAAATATGAGAGTA
1 GTGATGTATTGTACGAGATACACACCTAAATATGAGAGTG
** * * * *
1509919 GTGACATATTTGTACGAGATACACACCCAATTATAAGTAAT-
1 GTGATGTA-TTGTACGAGATACACACCTAAATATGAG-AGTG
* * * *
1509960 GTGATGTATTGTATGGGGTACACACCTAAACATGAGAGTG
1 GTGATGTATTGTACGAGATACACACCTAAATATGAGAGTG
* ** *
1510000 ATGATGTATTGTACGAGATACACACCT-AATCACAAGCA-AG
1 GTGATGTATTGTACGAGATACACACCTAAAT-ATGAG-AGTG
* *
1510040 GTGATGTATTGTACGTGATACACCCCTAAAT
1 GTGATGTATTGTACGAGATACACACCTAAAT
1510071 GAGTGATGAG
Statistics
Matches: 229, Mismatches: 68, Indels: 29
0.70 0.21 0.09
Matches are distributed among these distances:
39 11 0.05
40 176 0.77
41 40 0.17
42 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (40 bp):
GTGATGTATTGTACGAGATACACACCTAAATATGAGAGTG
Found at i:1509843 original size:80 final size:80
Alignment explanation
Indices: 1509710--1510070 Score: 402
Period size: 80 Copynumber: 4.5 Consensus size: 80
1509700 GATACCAATC
* * * * *
1509710 ACAAGCAATGTGATGTATCGTACGGGGTATACACCTAAATATGAGAGTGGTGATGTATTGCATGA
1 ACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTGGTGATGTATTGCACGA
1509775 GATACACACCTAATT
66 GATACACACCTAATT
* * * * * * * *
1509790 ACAAGCAACGTTATGTATCGTACAAAGCACACACCAAAATATGAGAGTGGTGATGTATTGTAC-A
1 ACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTGGTGATGTATTGCACGA
1509854 GGATACACACCCT-ATT
66 -GATACACA-CCTAATT
* * ** *
1509870 ACAAGCAAGGTAATGTATTGTACGAGGTACACACCTAAATATGAGAGTAGTGACATATTTGTACG
1 ACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTGGTGATGTA-TTGCACG
*
1509935 AGATACACACCCAATT
65 AGATACACACCTAATT
* * * * * * * *
1509951 ATAAGTAATGTGATGTATTGTATGGGGTACACACCTAAACATGAGAGTGATGATGTATTGTACGA
1 ACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTGGTGATGTATTGCACGA
*
1510016 GATACACACCTAATC
66 GATACACACCTAATT
* * *
1510031 ACAAGCAAGGTGATGTATTGTACGTGATACACCCCTAAAT
1 ACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAAT
1510071 GAGTGATGAG
Statistics
Matches: 234, Mismatches: 42, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
79 1 0.00
80 166 0.71
81 66 0.28
82 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (80 bp):
ACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTGGTGATGTATTGCACGA
GATACACACCTAATT
Found at i:1509997 original size:161 final size:160
Alignment explanation
Indices: 1509706--1510070 Score: 437
Period size: 161 Copynumber: 2.3 Consensus size: 160
1509696 TATTGATACC
* * * * * **
1509706 AATCACAAGCAATGTGATGTATCGTACGGGGTATACACCTAAATATGAGAGTGGTGATGTATTGC
1 AATCACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTAGTGACATATTGC
* * * *
1509771 ATGAGATACACACCTAATTACAAGCAACGTTATGTATCGTACAAAGCACACACCAAAATATGAGA
66 ACGAGATACACACCCAATTACAAGCAACGTGATGTATCGTACAAAGCACACACCAAAACATGAGA
*
1509836 GTGGTGATGTATTGTAC-AGGATACACACCCT
131 GTGATGATGTATTGTACGA-GATACACA-CCT
* *
1509867 -ATTACAAGCAAGGTAATGTATTGTACGAGGTACACACCTAAATATGAGAGTAGTGACATATTTG
1 AATCACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTAGTGACATA-TTG
* * * * * **** * *
1509931 TACGAGATACACACCCAATTATAAGTAATGTGATGTATTGTATGGGGTACACACCTAAACATGAG
65 CACGAGATACACACCCAATTACAAGCAACGTGATGTATCGTACAAAGCACACACCAAAACATGAG
1509996 AGTGATGATGTATTGTACGAGATACACACCT
130 AGTGATGATGTATTGTACGAGATACACACCT
* * *
1510027 AATCACAAGCAAGGTGATGTATTGTACGTGATACACCCCTAAAT
1 AATCACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAAT
1510071 GAGTGATGAG
Statistics
Matches: 171, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
160 54 0.32
161 116 0.68
162 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (160 bp):
AATCACAAGCAAGGTGATGTATTGTACGAGGTACACACCTAAATATGAGAGTAGTGACATATTGC
ACGAGATACACACCCAATTACAAGCAACGTGATGTATCGTACAAAGCACACACCAAAACATGAGA
GTGATGATGTATTGTACGAGATACACACCT
Found at i:1515732 original size:97 final size:97
Alignment explanation
Indices: 1515620--1515805 Score: 327
Period size: 97 Copynumber: 1.9 Consensus size: 97
1515610 GTGGTTCGAC
*
1515620 TTTATCAATCAAAGTTAACATCCACTACCTTAGCATCCACACTAATGATTTTTCAAATTCTCTAG
1 TTTATCAATCAAAGTTAACATCCACTACCTTAGCATCCACACTAAGGATTTTTCAAATTCTCTAG
*
1515685 ATTTTCTTACCTTTGAGGGAAAATCTAGAGAA
66 ATTTGCTTACCTTTGAGGGAAAATCTAGAGAA
**
1515717 TTTATCAATTGAAGTTAACATCCACTACCTTAGCATCCACACTAAGGATTTTTCAAATTCTCTAG
1 TTTATCAATCAAAGTTAACATCCACTACCTTAGCATCCACACTAAGGATTTTTCAAATTCTCTAG
*
1515782 ATTTGCTTACCTTTGAGGGCAAAT
66 ATTTGCTTACCTTTGAGGGAAAAT
1515806 TTTAGCCTTA
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 84 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (97 bp):
TTTATCAATCAAAGTTAACATCCACTACCTTAGCATCCACACTAAGGATTTTTCAAATTCTCTAG
ATTTGCTTACCTTTGAGGGAAAATCTAGAGAA
Found at i:1516285 original size:21 final size:21
Alignment explanation
Indices: 1516261--1516335 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1516251 CCTTTAAGGG
*
1516261 AAGGGATCGATCCTTTTCATC
1 AAGGGATCAATCCTTTTCATC
* ** *
1516282 AAGGGATCAAT-TTTTTGGTG
1 AAGGGATCAATCCTTTTCATC
* *
1516302 AATGGATCAATCCTTTTCCTC
1 AAGGGATCAATCCTTTTCATC
* *
1516323 GAGGGATCGATCC
1 AAGGGATCAATCC
1516336 CAAACCTATT
Statistics
Matches: 40, Mismatches: 13, Indels: 2
0.73 0.24 0.04
Matches are distributed among these distances:
20 15 0.38
21 25 0.62
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
AAGGGATCAATCCTTTTCATC
Found at i:1516952 original size:20 final size:21
Alignment explanation
Indices: 1516929--1517004 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
1516919 TTTCATCGAT
*
1516929 GGATCAAT-ATTTTTGTGAAG
1 GGATCAATCATTTTTGTAAAG
*
1516949 GGATCGATCATTTTTGTAAAG
1 GGATCAATCATTTTTGTAAAG
* * *
1516970 GGATCTATC-CTTTGGTCAAAG
1 GGATCAATCATTTTTGT-AAAG
*
1516991 GGATCAATCCTTTT
1 GGATCAATCATTTT
1517005 AAAAAGGGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 12 0.26
21 31 0.67
22 3 0.07
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (21 bp):
GGATCAATCATTTTTGTAAAG
Found at i:1520860 original size:16 final size:15
Alignment explanation
Indices: 1520834--1520863 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1520824 GCCAACATCC
1520834 TTTTTCTTCTTCTTT
1 TTTTTCTTCTTCTTT
1520849 TTTTTCTCTCTTCTT
1 TTTTTCT-TCTTCTT
1520864 CTATCATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTCTTCTTT
Found at i:1522411 original size:21 final size:21
Alignment explanation
Indices: 1522387--1522462 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
1522377 TCAAGAAAGA
1522387 GATCGATCATTTTCATCGAGG
1 GATCGATCATTTTCATCGAGG
* *
1522408 GATCGATCATTTT-GTTGAAGG
1 GATCGATCATTTTCATCG-AGG
1522429 GATCGATCATTTTCCA-CGAGG
1 GATCGATCATTTT-CATCGAGG
*
1522450 GATCTATCATTTT
1 GATCGATCATTTT
1522463 TGTAAAGGGA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
20 2 0.04
21 44 0.94
22 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (21 bp):
GATCGATCATTTTCATCGAGG
Found at i:1522449 original size:42 final size:42
Alignment explanation
Indices: 1522382--1522477 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
1522372 CCGTTTCAAG
*
1522382 AAAGAGATCGATCATTTTCATCGAGGGATCGATCA-TTTTGTT
1 AAAGGGATCGATCATTTTCATCGAGGGATCGATCATTTTTG-T
* *
1522424 GAAGGGATCGATCATTTTCCA-CGAGGGATCTATCATTTTTGT
1 AAAGGGATCGATCATTTT-CATCGAGGGATCGATCATTTTTGT
1522466 AAAGGGATCGAT
1 AAAGGGATCGAT
1522478 TCCAAACCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 41 0.85
43 7 0.15
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (42 bp):
AAAGGGATCGATCATTTTCATCGAGGGATCGATCATTTTTGT
Found at i:1523813 original size:19 final size:19
Alignment explanation
Indices: 1523791--1523834 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1523781 GTTGGAAGTA
*
1523791 AGATTTTAGGCTGGAAACC
1 AGATTTTAGACTGGAAACC
*
1523810 AGA-TTTAGATTGGAAACC
1 AGATTTTAGACTGGAAACC
1523828 AGATTTT
1 AGATTTT
1523835 TCGTTCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (19 bp):
AGATTTTAGACTGGAAACC
Found at i:1523864 original size:19 final size:18
Alignment explanation
Indices: 1523802--1523871 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
1523792 GATTTTAGGC
*
1523802 TGGAAACCAGATTTAGAT
1 TGGAAACCAGATTTCGAT
1523820 TGGAAACCAGATTTTTCG-T
1 TGGAAACCAGA--TTTCGAT
** *
1523839 TCAAAACTAGATTCTCGAT
1 TGGAAACCAGATT-TCGAT
*
1523858 TGGAAACCATATTT
1 TGGAAACCAGATTT
1523872 TTGGTTGAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
17 2 0.05
18 15 0.38
19 19 0.47
20 4 0.10
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (18 bp):
TGGAAACCAGATTTCGAT
Found at i:1524114 original size:80 final size:80
Alignment explanation
Indices: 1523981--1524616 Score: 650
Period size: 80 Copynumber: 8.0 Consensus size: 80
1523971 TATTAATACT
* ** *
1523981 AATCACAAGCAATATGATGTATCGTATAGGGTACACGCCTAAATATGAGAGTGGTGATGTATTGT
1 AATCATAAGCAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTGT
* *
1524046 ATGGGATATACACCC
66 ACGGGATACACACCC
* * * * *
1524061 AATCATAAGCAAGGTGACGTATCGTATATGGTATACACCTAAATATTAGAGTGGTAATGTATTGT
1 AATCATAAGCAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTGT
*
1524126 ACGGGATATACACCC
66 ACGGGATACACACCC
* * ** * * *
1524141 AATCATAAGAAAGGTGATTTATATTACAAGGTACACACCTAAATATGAGAGTGGTGATATATTGT
1 AATCATAAGCAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTGT
* * *
1524206 ACGAGATACAAACCT
66 ACGGGATACACACCC
* * * * * * *
1524221 AATTACAAGCAACGTTATTTATCGTA-CGGATTACACACCTAAATATGAGAGTGGTGATGTATTG
1 AATCATAAGCAAGGTGATGTATCGTATAGG-GTACACACCTAAATATGAGAGTGGTGATGTATTG
1524285 TACGGGATACACACCC
65 TACGGGATACACACCC
* * * * * * * * * * *
1524301 AATTATAAGTAAGGTGATATATTGTACAAGATATACACCTAATTATGAGATTGGTAATGTATTGT
1 AATCATAAGCAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTGT
* *
1524366 ACGGGATACATACTC
66 ACGGGATACACACCC
* * * *
1524381 AATCAT-AGACAAGGTGATGTATCGAATAGGGTATACACCTAAATATGAGA--GGTGATATATTA
1 AATCATAAG-CAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTG
1524443 TACGGGATACACACCC
65 TACGGGATACACACCC
* * * * * * *
1524459 AATTATAAGCAAGGTGATGTATTGTACATGGTAAAGACTTAAATATGAGAGTGGTGATGTATTGT
1 AATCATAAGCAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTGT
** *
1524524 ATAGGATACGCACCC
66 ACGGGATACACACCC
* * * * * *
1524539 AATCACAAGCAATGTGATGTATTGTATGGGGTACACACCTAAATATGAGAGTGCTGATGTATTAT
1 AATCATAAGCAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTGT
* *
1524604 ATGAGATACACAC
66 ACGGGATACACAC
1524617 TTAATTAATA
Statistics
Matches: 455, Mismatches: 95, Indels: 12
0.81 0.17 0.02
Matches are distributed among these distances:
78 62 0.14
79 5 0.01
80 387 0.85
81 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (80 bp):
AATCATAAGCAAGGTGATGTATCGTATAGGGTACACACCTAAATATGAGAGTGGTGATGTATTGT
ACGGGATACACACCC
Found at i:1524601 original size:40 final size:39
Alignment explanation
Indices: 1523995--1524616 Score: 252
Period size: 40 Copynumber: 15.6 Consensus size: 39
1523985 ACAAGCAATA
* * *
1523995 TGATGTATCGTATAGGG-TACACGCCTAAATATGAGAGTGG
1 TGATGTATTGTA-CGGGATACACACCTAAATATGAGAGT-G
* * * *
1524035 TGATGTATTGTATGGGATATACACC-CAATCATAAGCAAG-G
1 TGATGTATTGTACGGGATACACACCTAAAT-ATGAG--AGTG
* * ** * *
1524075 TGACGTATCGTATATGG-TATACACCTAAATATTAGAGTGG
1 TGATGTATTGTA-CGGGATACACACCTAAATATGAGAGT-G
* * * * *
1524115 TAATGTATTGTACGGGATATACACCCAATCATAAGAAAG-G
1 TGATGTATTGTACGGGATACACACCTAA--ATATGAGAGTG
* *
1524155 TGATTTATAT-TACAAGG-TACACACCTAAATATGAGAGTGG
1 TGATGTAT-TGTAC-GGGATACACACCTAAATATGAGAGT-G
* * * * ** **
1524195 TGATATATTGTACGAGATACAAACCTAATTACAAGCAACG
1 TGATGTATTGTACGGGATACACACCTAAATATGAG-AGTG
* * *
1524235 TTATTTATCGTAC-GGATTACACACCTAAATATGAGAGTGG
1 TGATGTATTGTACGGGA-TACACACCTAAATATGAGAGT-G
* * *
1524275 TGATGTATTGTACGGGATACACACCCAATTATAAGTAAG-G
1 TGATGTATTGTACGGGATACACACCTAAATATGAG--AGTG
* ** * * *
1524315 TGATATATTGTACAAGATATACACCTAATTATGAGATTGG
1 TGATGTATTGTACGGGATACACACCTAAATATGAGAGT-G
* * * *
1524355 TAATGTATTGTACGGGATACATA-CTCAATCATAGACAAG-G
1 TGATGTATTGTACGGGATACACACCTAAAT-AT-GA-GAGTG
* *
1524395 TGATGTATCGAATA-GGG-TATACACCTAAATATGAGAG-G
1 TGATGTATTG--TACGGGATACACACCTAAATATGAGAGTG
* * * * *
1524433 TGATATATTATACGGGATACACACCCAATTATAAGCAAG-G
1 TGATGTATTGTACGGGATACACACCTAAATATGAG--AGTG
* * * *
1524473 TGATGTATTGTACATGG-TAAAGACTTAAATATGAGAGTGG
1 TGATGTATTGTAC-GGGATACACACCTAAATATGAGAGT-G
** * * ** *
1524513 TGATGTATTGTATAGGATACGCACC-CAATCACAAGCAATG
1 TGATGTATTGTACGGGATACACACCTAAAT-ATGAG-AGTG
* *
1524553 TGATGTATTGTATGGGGTACACACCTAAATATGAGAGTG
1 TGATGTATTGTACGGGATACACACCTAAATATGAGAGTG
* * *
1524592 CTGATGTATTATATGAGATACACAC
1 -TGATGTATTGTACGGGATACACAC
1524617 TTAATTAATA
Statistics
Matches: 427, Mismatches: 112, Indels: 86
0.68 0.18 0.14
Matches are distributed among these distances:
36 2 0.00
37 3 0.01
38 36 0.08
39 27 0.06
40 317 0.74
41 29 0.07
42 13 0.03
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.29
Consensus pattern (39 bp):
TGATGTATTGTACGGGATACACACCTAAATATGAGAGTG
Found at i:1524668 original size:2 final size:2
Alignment explanation
Indices: 1524657--1524729 Score: 139
Period size: 2 Copynumber: 37.0 Consensus size: 2
1524647 GAGTAGTGAA
1524657 AT AT -T AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
1524698 AT AT AT 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 AT AT AT
1524730 CTGTAGAATT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 69 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1531101 original size:2 final size:2
Alignment explanation
Indices: 1531094--1531136 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1531084 AAATATTTAT
1531094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1531136 T
1 T
1531137 GCATGATCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1531187 original size:20 final size:20
Alignment explanation
Indices: 1531162--1531200 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1531152 CAACCATATA
*
1531162 TGTTCATTTTTATTTATTTC
1 TGTTCAGTTTTATTTATTTC
1531182 TGTTCAGTTTTATTTATTT
1 TGTTCAGTTTTATTTATTT
1531201 GCCATGGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (20 bp):
TGTTCAGTTTTATTTATTTC
Found at i:1537239 original size:41 final size:41
Alignment explanation
Indices: 1537206--1537382 Score: 291
Period size: 41 Copynumber: 4.3 Consensus size: 41
1537196 GAATAAATGC
1537206 ATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
1 ATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
1537247 ATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
1 ATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
*
1537288 ATGCTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
1 ATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
* * * * *
1537329 ATGCTATCATTATCGAATCAAGTTGAATGGTGAAGTATTGC
1 ATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
*
1537370 ATGTTTCCATGAT
1 ATGTTACCATGAT
1537383 TTAATTGAAT
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 127 1.00
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.36
Consensus pattern (41 bp):
ATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGT
Found at i:1537239 original size:82 final size:82
Alignment explanation
Indices: 1537153--1537362 Score: 213
Period size: 82 Copynumber: 2.6 Consensus size: 82
1537143 GAATTGGTTT
* * * ** * *
1537153 GTGAATTAATACATGTTATCAAGATCTAATTAAATTGGTTTGTGAATAAATGCATGTTACCATGA
1 GTGAATTAATACATGTTACCAAGATCGAATCAAATTGAATGGTGAATAAATGCATGCTACCATGA
1537218 TCGAATCAAGTTGAATG
66 TCGAATCAAGTTGAATG
* ** * * * * *
1537235 GTGAATTATTGTATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGCTACCATGA
1 GTGAATTAATACATGTTACCAAGATCGAATCAAATTGAATGGTGAATAAATGCATGCTACCATGA
1537300 TCGAATCAAGTTGAATG
66 TCGAATCAAGTTGAATG
* ** * * ** *
1537317 GTGAATTATTGTATGCTATCATTATCGAATCAAGTTGAATGGTGAA
1 GTGAATTAATACATGTTACCAAGATCGAATCAAATTGAATGGTGAA
1537363 GTATTGCATG
Statistics
Matches: 110, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
82 110 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (82 bp):
GTGAATTAATACATGTTACCAAGATCGAATCAAATTGAATGGTGAATAAATGCATGCTACCATGA
TCGAATCAAGTTGAATG
Found at i:1537398 original size:82 final size:82
Alignment explanation
Indices: 1537203--1537408 Score: 270
Period size: 82 Copynumber: 2.5 Consensus size: 82
1537193 TGTGAATAAA
* * *
1537203 TGCATGTTACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGTTACCATGATCGAATCAA
1 TGCATGCTACCATGATCGAATCAAGTCGAATGGTGAATTATTGTATGCTACCATGATCGAATCAA
*
1537268 GTTGAATGGTGAATTAT
66 GTTGAATGGTGAAGTAT
* * * *
1537285 TGTATGCTACCATGATCGAATCAAGTTGAATGGTGAATTATTGTATGCTATCATTATCGAATCAA
1 TGCATGCTACCATGATCGAATCAAGTCGAATGGTGAATTATTGTATGCTACCATGATCGAATCAA
1537350 GTTGAATGGTGAAGTAT
66 GTTGAATGGTGAAGTAT
* * ** * *
1537367 TGCATGTTTCCATGATTTAATTGAA-TCGAATGGTGAAATATT
1 TGCATGCTACCATGATCGAA-TCAAGTCGAATGGTGAATTATT
1537409 TCATGATTGA
Statistics
Matches: 109, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
82 106 0.97
83 3 0.03
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (82 bp):
TGCATGCTACCATGATCGAATCAAGTCGAATGGTGAATTATTGTATGCTACCATGATCGAATCAA
GTTGAATGGTGAAGTAT
Found at i:1537447 original size:33 final size:33
Alignment explanation
Indices: 1537377--1537448 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
1537367 TGCATGTTTC
* * *
1537377 CATGATTTAATTGAATCGAATGGTGAAATATTT
1 CATGATTGAATTGAATCGAATGGTGAAATAGTA
* * *
1537410 CATGATTGAATTGAATTGAATTGTGAATTAGTA
1 CATGATTGAATTGAATCGAATGGTGAAATAGTA
1537443 CATGAT
1 CATGAT
1537449 GCCAAGATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (33 bp):
CATGATTGAATTGAATCGAATGGTGAAATAGTA
Found at i:1544665 original size:37 final size:37
Alignment explanation
Indices: 1544615--1544688 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1544605 TGTAGGTGAG
1544615 GCATTGGTAGAATAAGTAGAACCGGACAGTTCTGGAA
1 GCATTGGTAGAATAAGTAGAACCGGACAGTTCTGGAA
1544652 GCATTGGTAGAATAAGTAGAACCGGACAGTTCTGGAA
1 GCATTGGTAGAATAAGTAGAACCGGACAGTTCTGGAA
1544689 AACTCGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.14, G:0.30, T:0.22
Consensus pattern (37 bp):
GCATTGGTAGAATAAGTAGAACCGGACAGTTCTGGAA
Found at i:1545478 original size:40 final size:40
Alignment explanation
Indices: 1545432--1545518 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
1545422 TGAATTGGTT
** * *
1545432 TGTGAATTAATACATGTTATTATGATTGAATCAAGTTGAA
1 TGTGAATTAATACATGTTACAATGATCGAATCAAGCTGAA
* **
1545472 TGTGAATTATTGTATGTTACAATGATCGAATCAAGCTGAA
1 TGTGAATTAATACATGTTACAATGATCGAATCAAGCTGAA
1545512 TGGTGAA
1 T-GTGAA
1545519 GTATTGCATT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 34 0.87
41 5 0.13
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.37
Consensus pattern (40 bp):
TGTGAATTAATACATGTTACAATGATCGAATCAAGCTGAA
Found at i:1545538 original size:41 final size:41
Alignment explanation
Indices: 1545444--1545584 Score: 137
Period size: 41 Copynumber: 3.5 Consensus size: 41
1545434 TGAATTAATA
** *
1545444 CATGTTATTATGATTGAATCAAGTTGAAT-GTGAATTATTG
1 CATGTTACAATGATTGAATCAAGTTGAATGGTGAAGTATTG
* * *
1545484 TATGTTACAATGATCGAATCAAGCTGAATGGTGAAGTATTG
1 CATGTTACAATGATTGAATCAAGTTGAATGGTGAAGTATTG
* * *
1545525 CAT-TATGCCATGATTGAATTGAA-TTGAATGGTGAAGTATTG
1 CATGT-TACAATGATTGAA-TCAAGTTGAATGGTGAAGTATTG
*
1545566 CATGTTGTC-ATGATTGAAT
1 CATGTT-ACAATGATTGAAT
1545585 TGAATTGAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 10
0.78 0.12 0.09
Matches are distributed among these distances:
40 26 0.31
41 52 0.63
42 5 0.06
ACGTcount: A:0.32, C:0.08, G:0.23, T:0.38
Consensus pattern (41 bp):
CATGTTACAATGATTGAATCAAGTTGAATGGTGAAGTATTG
Found at i:1545585 original size:41 final size:41
Alignment explanation
Indices: 1545508--1545600 Score: 152
Period size: 41 Copynumber: 2.3 Consensus size: 41
1545498 CGAATCAAGC
1545508 TGAATGGTGAAGTATTGCATTATGCCATGATTGAATTGAAT
1 TGAATGGTGAAGTATTGCATTATGCCATGATTGAATTGAAT
*
1545549 TGAATGGTGAAGTATTGCATGT-TGTCATGATTGAATTGAAT
1 TGAATGGTGAAGTATTGCAT-TATGCCATGATTGAATTGAAT
*
1545590 TGAATTGTGAA
1 TGAATGGTGAA
1545601 TTAGTACATT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 48 0.98
42 1 0.02
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (41 bp):
TGAATGGTGAAGTATTGCATTATGCCATGATTGAATTGAAT
Found at i:1553962 original size:22 final size:21
Alignment explanation
Indices: 1553912--1553962 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
1553902 TATATGAAGG
*
1553912 AAAATGATGAAAAAATAAATA
1 AAAATGACGAAAAAATAAATA
*
1553933 AATGATGACGAAAAAAGTGAAA-A
1 AA-AATGACGAAAAAA-T-AAATA
1553956 AAAATGA
1 AAAATGA
1553963 AAAGGGGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
21 2 0.08
22 15 0.62
23 4 0.17
24 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.16, T:0.16
Consensus pattern (21 bp):
AAAATGACGAAAAAATAAATA
Found at i:1558334 original size:21 final size:23
Alignment explanation
Indices: 1558310--1558361 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
1558300 AGTCATTGAT
*
1558310 ATAATTTACCTTT-TA-TTTTAA
1 ATAATTTACCTTTAAAGTTTTAA
1558331 ATAATTTACCTTTAAAGTTTTAA
1 ATAATTTACCTTTAAAGTTTTAA
*
1558354 CTAATTTA
1 ATAATTTA
1558362 TAATTATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 13 0.48
22 1 0.04
23 13 0.48
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.52
Consensus pattern (23 bp):
ATAATTTACCTTTAAAGTTTTAA
Found at i:1571915 original size:21 final size:21
Alignment explanation
Indices: 1571874--1571915 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1571864 CCGTTATACA
* *
1571874 AGGGGGGAATCGGTACCCCCT
1 AGGGAGGAATCGGTACACCCT
*
1571895 AGGGAGGAATCGGTATACCCT
1 AGGGAGGAATCGGTACACCCT
1571916 GGGCAATCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.17
Consensus pattern (21 bp):
AGGGAGGAATCGGTACACCCT
Found at i:1573669 original size:12 final size:12
Alignment explanation
Indices: 1573632--1573662 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1573622 TTGTTGGATA
1573632 GGAGGTGGATTT
1 GGAGGTGGATTT
1573644 GGAGGTGGATTT
1 GGAGGTGGATTT
1573656 GGAGGTG
1 GGAGGTG
1573663 AGTTTGGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.55, T:0.29
Consensus pattern (12 bp):
GGAGGTGGATTT
Found at i:1579631 original size:21 final size:21
Alignment explanation
Indices: 1579605--1579674 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
1579595 TGGAGCTTGG
*
1579605 GGGAATCGGTATCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
*
1579626 GGGAATCGATACCCCCTCATA
1 GGGAATCGGTACCCCCTCATA
*
1579647 GGGAATCGGTACCCCCTTATA
1 GGGAATCGGTACCCCCTCATA
1579668 GGGAATC
1 GGGAATC
1579675 TGTCCTGCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (21 bp):
GGGAATCGGTACCCCCTCATA
Found at i:1582549 original size:73 final size:73
Alignment explanation
Indices: 1582465--1582610 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
1582455 GGCAATCTGA
1582465 CTTCTTTTTATTGGGTTTACTACAATAGTAACAAATCATTTTGGATCGCGATTTAGATTACCCTC
1 CTTCTTTTTATTGGGTTTACTACAATAGTAACAAATCATTTTGGATCGCGATTTAGATTACCCTC
1582530 GAGACTTG
66 GAGACTTG
1582538 CTTCTTTTTATTGGGTTTACTACAATAGTAACAAATCATTTTGGATCGCGATTTAGATTACCCTC
1 CTTCTTTTTATTGGGTTTACTACAATAGTAACAAATCATTTTGGATCGCGATTTAGATTACCCTC
1582603 GAGACTTG
66 GAGACTTG
1582611 TTATAACCTC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (73 bp):
CTTCTTTTTATTGGGTTTACTACAATAGTAACAAATCATTTTGGATCGCGATTTAGATTACCCTC
GAGACTTG
Found at i:1584031 original size:20 final size:21
Alignment explanation
Indices: 1584006--1584044 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1583996 GTTGTGGCCG
1584006 TTTCTAGCC-ATTGGGGATAA
1 TTTCTAGCCGATTGGGGATAA
*
1584026 TTTCTAGCCGTTTGGGGAT
1 TTTCTAGCCGATTGGGGAT
1584045 GAAATCTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (21 bp):
TTTCTAGCCGATTGGGGATAA
Found at i:1587314 original size:6 final size:6
Alignment explanation
Indices: 1587305--1587329 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1587295 TATTACTATT
1587305 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
1587330 GACGGACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1587971 original size:6 final size:6
Alignment explanation
Indices: 1587955--1587985 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1587945 TCTCGTCTCG
*
1587955 GGTCGT AGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
1587986 ATAATACGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.16, G:0.48, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1588094 original size:42 final size:42
Alignment explanation
Indices: 1588035--1588155 Score: 197
Period size: 42 Copynumber: 2.9 Consensus size: 42
1588025 CAATACACCA
*
1588035 AAATCGCAACGAGAACTTCGACTATCGCAACGAACTTAGAAT
1 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAT
* *
1588077 AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAT
1 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAT
* *
1588119 AAATCACAATGCGAACTTCGACTATCGCAACGAACTT
1 AAATCGCAACGCGAACTTCGACTATCGCAACGAACTT
1588156 GGACTATTGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.21
Consensus pattern (42 bp):
AAATCGCAACGCGAACTTCGACTATCGCAACGAACTTAGAAT
Found at i:1588169 original size:61 final size:62
Alignment explanation
Indices: 1588079--1588209 Score: 201
Period size: 61 Copynumber: 2.1 Consensus size: 62
1588069 CTTAGAATAA
*
1588079 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAATGCGAACTTCGACT
1 ATCGCAAC-CGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
* * * *
1588142 ATCGCAA-CGAACTTGGACTATTGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
1588203 ATCGCAA
1 ATCGCAA
1588210 TGCGAATATG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 56 0.89
63 7 0.11
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (62 bp):
ATCGCAACCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTCGACT
Found at i:1588254 original size:21 final size:21
Alignment explanation
Indices: 1588230--1588273 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1588220 TAATTCACAA
*
1588230 TGCGATAGTCGAAGTTCACGT
1 TGCGATAGCCGAAGTTCACGT
* *
1588251 TGCGATAGCCGATGTTCGCGT
1 TGCGATAGCCGAAGTTCACGT
1588272 TG
1 TG
1588274 GGAATCTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.20, G:0.32, T:0.30
Consensus pattern (21 bp):
TGCGATAGCCGAAGTTCACGT
Found at i:1588637 original size:12 final size:12
Alignment explanation
Indices: 1588615--1588644 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
1588605 AATGGTTAAT
1588615 ATTTAATTAATTA
1 ATTT-ATTAATTA
1588628 ATTTATTAATTA
1 ATTTATTAATTA
1588640 ATTTA
1 ATTTA
1588645 AATATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
ATTTATTAATTA
Found at i:1591674 original size:17 final size:17
Alignment explanation
Indices: 1591649--1591685 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1591639 AGATGGCAGA
*
1591649 AAATGAAATCCAAAGAT
1 AAATGAAATCCAAAAAT
*
1591666 AAATTAAATCCAAAAAT
1 AAATGAAATCCAAAAAT
1591683 AAA
1 AAA
1591686 ACTACCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.19
Consensus pattern (17 bp):
AAATGAAATCCAAAAAT
Found at i:1597323 original size:17 final size:18
Alignment explanation
Indices: 1597287--1597323 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1597277 TGCAAGATAA
*
1597287 TTTTTAATTTCTGTGATT
1 TTTTTAATTTCTGAGATT
1597305 TTTTTAATTT-TGAG-TT
1 TTTTTAATTTCTGAGATT
1597321 TTT
1 TTT
1597324 ATATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 10 0.56
ACGTcount: A:0.16, C:0.03, G:0.11, T:0.70
Consensus pattern (18 bp):
TTTTTAATTTCTGAGATT
Found at i:1601706 original size:2 final size:2
Alignment explanation
Indices: 1601699--1601756 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1601689 TCGATACTCA
1601699 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
1601741 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
1601757 CTTTCTTACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1604107 original size:18 final size:18
Alignment explanation
Indices: 1604084--1604136 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
1604074 GCGTAGAATT
*
1604084 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1604102 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
1604120 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
1604137 GATAATCCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1605441 original size:10 final size:10
Alignment explanation
Indices: 1605426--1605501 Score: 77
Period size: 10 Copynumber: 7.3 Consensus size: 10
1605416 CTTGGTGTTT
1605426 TAAGCTTATA
1 TAAGCTTATA
1605436 TAAGCTT-TA
1 TAAGCTTATA
1605445 CTTAAGCTTATA
1 --TAAGCTTATA
1605457 TAAGCTT-TA
1 TAAGCTTATA
1605466 CTTAAGCTTATA
1 --TAAGCTTATA
1605478 TAAGCTT-TA
1 TAAGCTTATA
1605487 CTTAAGCTTATA
1 --TAAGCTTATA
1605499 TAA
1 TAA
1605502 CACCCAAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
9 6 0.11
10 24 0.42
11 21 0.37
12 6 0.11
ACGTcount: A:0.36, C:0.13, G:0.09, T:0.42
Consensus pattern (10 bp):
TAAGCTTATA
Found at i:1605451 original size:21 final size:21
Alignment explanation
Indices: 1605425--1605501 Score: 154
Period size: 21 Copynumber: 3.7 Consensus size: 21
1605415 TCTTGGTGTT
1605425 TTAAGCTTATATAAGCTTTAC
1 TTAAGCTTATATAAGCTTTAC
1605446 TTAAGCTTATATAAGCTTTAC
1 TTAAGCTTATATAAGCTTTAC
1605467 TTAAGCTTATATAAGCTTTAC
1 TTAAGCTTATATAAGCTTTAC
1605488 TTAAGCTTATATAA
1 TTAAGCTTATATAA
1605502 CACCCAAATA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (21 bp):
TTAAGCTTATATAAGCTTTAC
Found at i:1605452 original size:11 final size:11
Alignment explanation
Indices: 1605436--1605495 Score: 74
Period size: 11 Copynumber: 5.6 Consensus size: 11
1605426 TAAGCTTATA
1605436 TAAGCTTTACT
1 TAAGCTTTACT
1605447 TAAGC-TTA-T
1 TAAGCTTTACT
1605456 ATAAGCTTTACT
1 -TAAGCTTTACT
1605468 TAAGC-TTA-T
1 TAAGCTTTACT
1605477 ATAAGCTTTACT
1 -TAAGCTTTACT
1605489 TAAGCTT
1 TAAGCTT
1605496 ATATAACACC
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
9 2 0.05
10 16 0.37
11 23 0.53
12 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (11 bp):
TAAGCTTTACT
Found at i:1610572 original size:14 final size:14
Alignment explanation
Indices: 1610553--1610581 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1610543 GTTTTTGAAC
1610553 TTTATTAAAAAATA
1 TTTATTAAAAAATA
1610567 TTTATTAAAAAATA
1 TTTATTAAAAAATA
1610581 T
1 T
1610582 AACTGAGTTT
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTATTAAAAAATA
Found at i:1614859 original size:37 final size:36
Alignment explanation
Indices: 1614784--1614859 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1614774 TTTTTATATT
*
1614784 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1614820 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1614857 TTT
1 TTT
1614860 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1615041 original size:20 final size:20
Alignment explanation
Indices: 1615005--1615042 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1614995 ATCATATTCC
**
1615005 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1615025 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1615043 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1620076 original size:15 final size:15
Alignment explanation
Indices: 1620058--1620087 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1620048 CCACGGTGCT
1620058 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
1620073 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
1620088 GATTGTGATA
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:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:1622248 original size:19 final size:19
Alignment explanation
Indices: 1622224--1622260 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1622214 TTGAAGACAT
*
1622224 TTTAAAACAATTTAAAATA
1 TTTAAAACAATTCAAAATA
*
1622243 TTTAAATCAATTCAAAAT
1 TTTAAAACAATTCAAAAT
1622261 TATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTAAAACAATTCAAAATA
Found at i:1623304 original size:21 final size:21
Alignment explanation
Indices: 1623279--1623346 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 21
1623269 CCCCTATATA
*
1623279 TATTTTTTTAATTATATTTTT
1 TATTTATTTAATTATATTTTT
*
1623300 TATTTATTT-ACTATATTCCTTT
1 TATTTATTTAATTATATT--TTT
1623322 T-TTTATTTATATTATATTTTAT
1 TATTTATTTA-ATTATATTTT-T
1623344 TAT
1 TAT
1623347 ATATCTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
20 7 0.18
21 17 0.45
22 6 0.16
23 8 0.21
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (21 bp):
TATTTATTTAATTATATTTTT
Found at i:1623346 original size:19 final size:19
Alignment explanation
Indices: 1623319--1623400 Score: 65
Period size: 19 Copynumber: 4.1 Consensus size: 19
1623309 ACTATATTCC
* *
1623319 TTTTTTTATTTATATTATA
1 TTTTATTATATATATTATA
*
1623338 TTTTATTATATATCTTATA
1 TTTTATTATATATATTATA
**
1623357 TCATATATATATATATATATA
1 TTTTAT-TATATATAT-TATA
*
1623378 TATATATATATATATATATATA
1 T-TTTAT-TATATATAT-TATA
1623400 T
1 T
1623401 ATATGTATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 20 0.38
20 8 0.15
21 5 0.09
22 20 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATTATATATATTATA
Found at i:1623364 original size:2 final size:2
Alignment explanation
Indices: 1623344--1623404 Score: 97
Period size: 2 Copynumber: 30.5 Consensus size: 2
1623334 TATATTTTAT
*
1623344 TA TA TA TC T- TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
1623386 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1623405 GTATGTATAG
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
1 1 0.02
2 53 0.95
3 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1626938 original size:13 final size:14
Alignment explanation
Indices: 1626907--1626957 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 14
1626897 AAAAGAGAAA
*
1626907 AAAGAGAAAAAAAGC
1 AAAGAGAAAATAA-C
1626922 AAAGAGAAAATAA-
1 AAAGAGAAAATAAC
1626935 AAAGAGAAAA-AAC
1 AAAGAGAAAATAAC
1626948 AAAG-GAAAAT
1 AAAGAGAAAAT
1626958 TGAAGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
15 12 0.36
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (14 bp):
AAAGAGAAAATAAC
Found at i:1626951 original size:26 final size:27
Alignment explanation
Indices: 1626905--1626957 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1626895 CAAAAAGAGA
1626905 AAAAAGAGAAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAAGCAAAG-GAAAAT
1626933 AAAAAGAG-AAAAAA-CAAAGGAAAAT
1 AAAAAGAGAAAAAAAGCAAAGGAAAAT
1626958 TGAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 6 0.24
28 8 0.32
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAAGAGAAAAAAAGCAAAGGAAAAT
Found at i:1628667 original size:37 final size:38
Alignment explanation
Indices: 1628606--1628680 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
1628596 GAAGATTTTA
* * * *
1628606 TCTCGCTTGAGATAGTTTCCCTTGAAACA-AAATATTG
1 TCTCCCTTGAGACAATTTCCCTTGAAACATAAACATTG
*
1628643 TCTCCCTTGAGACAATTTCTCTTGAAACATAAACATTG
1 TCTCCCTTGAGACAATTTCCCTTGAAACATAAACATTG
1628681 AAAACATTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.35
Consensus pattern (38 bp):
TCTCCCTTGAGACAATTTCCCTTGAAACATAAACATTG
Done.