Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009572.1 Hibiscus syriacus cultivar Beakdansim tig00116937_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: 2529503
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 13
Found at i:1738463 original size:15 final size:16
Alignment explanation
Indices: 1738443--1738473 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1738433 AAAAAATACA
1738443 TTAAATTT-AATTATT
1 TTAAATTTAAATTATT
1738458 TTAAATTTAAATTATT
1 TTAAATTTAAATTATT
1738474 AGTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAAATTTAAATTATT
Found at i:1739012 original size:16 final size:15
Alignment explanation
Indices: 1738987--1739016 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1738977 ATTATGAACA
1738987 TGTAATGATTATGTC
1 TGTAATGATTATGTC
1739002 TGTATATGATTATGT
1 TGTA-ATGATTATGT
1739017 TTAGAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (15 bp):
TGTAATGATTATGTC
Found at i:1739253 original size:20 final size:21
Alignment explanation
Indices: 1739228--1739279 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1739218 TTTTCCCAAT
*
1739228 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1739248 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1739269 TCGCAATGCGA
1 TCGCAATGCGA
1739280 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1739362 original size:20 final size:20
Alignment explanation
Indices: 1739310--1739362 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1739300 TAATACAAAA
*
1739310 TCGCAACGAGATACTAACTT
1 TCGCAACGAGATTCTAACTT
* *
1739330 TCGCAACGTGATTCTGACTT
1 TCGCAACGAGATTCTAACTT
*
1739350 TCGCAACGCGATT
1 TCGCAACGAGATT
1739363 TACATAGCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.28
Consensus pattern (20 bp):
TCGCAACGAGATTCTAACTT
Found at i:1739917 original size:19 final size:19
Alignment explanation
Indices: 1739879--1739945 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
1739869 TTCGAGAATG
1739879 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1739899 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
* **
1739918 AAAAACGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1739937 AAAATCGCA
1 AAAATCGCA
1739946 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.49, C:0.25, G:0.16, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1739963 original size:19 final size:19
Alignment explanation
Indices: 1739941--1740085 Score: 130
Period size: 19 Copynumber: 8.1 Consensus size: 19
1739931 GAAACCAAAA
* *
1739941 TCGCATTGCGATTTTCTTT
1 TCGCGTTGCGATTTTCATT
1739960 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1739974 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1739993 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1740012 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* ** *
1740026 TCTCGTTGCGATAGTCACT
1 TCGCGTTGCGATTTTCATT
*
1740045 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1740064 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1740084 TC
1 TC
1740086 AACCAAAAGA
Statistics
Matches: 104, Mismatches: 11, Indels: 22
0.76 0.08 0.16
Matches are distributed among these distances:
14 20 0.19
16 5 0.05
17 6 0.06
19 56 0.54
20 17 0.16
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1740024 original size:52 final size:52
Alignment explanation
Indices: 1739941--1740077 Score: 202
Period size: 52 Copynumber: 2.6 Consensus size: 52
1739931 GAAACCAAAA
* * ** *
1739941 TCGCATTGCGATTTTCTTTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCACT
1739993 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCACT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCACT
* *
1740045 TCGCGTTGCGATTCTCATTATCTCGTTGCGATT
1 TCGCGTTGCGATTTTCATT-TCGCGTTGCGATT
1740078 TTCATTTCAA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 65 0.84
53 12 0.16
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCACT
Found at i:1740033 original size:33 final size:33
Alignment explanation
Indices: 1739996--1740060 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1739986 TTTCATTTCG
** *
1739996 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATAGTCACTTCGCGTTGCGATTCTCT
1740029 CGTTGCGATAGTCACTTCGCGTTGCGATTCTC
1 CGTTGCGATAGTCACTTCGCGTTGCGATTCTC
1740061 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.11, C:0.26, G:0.23, T:0.40
Consensus pattern (33 bp):
CGTTGCGATAGTCACTTCGCGTTGCGATTCTCT
Found at i:1742375 original size:20 final size:20
Alignment explanation
Indices: 1742352--1742405 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
1742342 GAAACTTAAA
1742352 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
1742372 ATCGCAA--CGTAGAAATGGCT
1 ATCGCAATGCG-A-AAATGACT
1742392 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
1742406 TGAAAATCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.07
19 1 0.03
20 23 0.79
21 1 0.03
22 2 0.07
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1742427 original size:14 final size:14
Alignment explanation
Indices: 1742408--1742465 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1742398 ATGCGAAATG
1742408 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1742422 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1742438 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1742454 AAAATCGCAACG
1 AAAATCGCAACG
1742466 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1742450 original size:32 final size:33
Alignment explanation
Indices: 1742392--1742470 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1742382 AGAAATGGCT
1742392 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1742425 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1742457 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1742471 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1742518 original size:14 final size:14
Alignment explanation
Indices: 1742499--1742556 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1742489 TTTCATTTCG
1742499 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1742513 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1742529 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1742545 CGTTGCGATTTT
1 CGTTGCGATTTT
1742557 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1742563 original size:33 final size:33
Alignment explanation
Indices: 1742482--1742572 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1742472 ACAAATCGCA
*
1742482 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1742515 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1742547 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1742573 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1742591 original size:20 final size:19
Alignment explanation
Indices: 1742557--1742611 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1742547 TTGCGATTTT
*
1742557 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1742576 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1742596 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1742612 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1743119 original size:18 final size:18
Alignment explanation
Indices: 1743093--1743137 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1743083 GTCGATCAGA
*
1743093 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1743111 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1743129 TGATGGCTC
1 TGATGGCTC
1743138 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1744505 original size:20 final size:20
Alignment explanation
Indices: 1744457--1744515 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1744447 AATAGTTTCT
** *
1744457 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
1744477 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
1744497 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
1744516 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:1744808 original size:22 final size:22
Alignment explanation
Indices: 1744778--1744821 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1744768 GATGGAGATA
*
1744778 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
1744800 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
1744822 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:1745024 original size:20 final size:20
Alignment explanation
Indices: 1745001--1745053 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1744991 CGATTATGTA
1745001 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1745021 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1745041 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1745054 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1745087 original size:20 final size:20
Alignment explanation
Indices: 1745062--1745135 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
1745052 GATTTTGTAT
1745062 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1745082 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
*
1745102 TATCGCATTGCGATAGTTAG
1 TATCGCATTGCGATAGTAAG
1745122 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1745136 TTTCCCAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1745115 original size:40 final size:40
Alignment explanation
Indices: 1745002--1745135 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
1744992 GATTATGTAA
* * * * * *
1745002 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTAAGT
* * * *
1745042 ATCTCGTTGCGATTTTGT-ATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGA--TAGTCAGTATCGCATTGCGATAGTAAGT
*
1745083 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTTAGT
1 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTAAGT
1745123 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1745136 TTTCCCAATT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
39 3 0.04
40 45 0.58
41 28 0.36
42 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (40 bp):
ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTAAGT
Found at i:1745154 original size:81 final size:81
Alignment explanation
Indices: 1745002--1745156 Score: 177
Period size: 81 Copynumber: 1.9 Consensus size: 81
1744992 GATTATGTAA
* * * * ** * *
1745002 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCG
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCA
1745067 CATTGCGATAGTAAGT
66 CATTGCGATAGTAAGT
* * * *
1745083 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTTAGTATCGCATTGCGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATC
*
1745147 ACGTTGCGAT
65 ACATTGCGAT
1745157 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
81 58 0.97
82 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (81 bp):
ATCGCATTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCA
CATTGCGATAGTAAGT
Found at i:1749114 original size:16 final size:16
Alignment explanation
Indices: 1749093--1749126 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1749083 TTTGTTTTGC
1749093 TTGATATGATACCCTT
1 TTGATATGATACCCTT
*
1749109 TTGATATGATATCCTT
1 TTGATATGATACCCTT
1749125 TT
1 TT
1749127 ATTTTAAGCA
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:0.24, C:0.15, G:0.12, T:0.50
Consensus pattern (16 bp):
TTGATATGATACCCTT
Found at i:1751340 original size:16 final size:16
Alignment explanation
Indices: 1751317--1751355 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1751307 CCTCTCTTGA
1751317 TTTTTTTCTAT-TTTT
1 TTTTTTTCTATGTTTT
*
1751332 TTCTTTTTCTCTGTTTT
1 TT-TTTTTCTATGTTTT
1751349 TTTTTTT
1 TTTTTTT
1751356 TTTTCGAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 13 0.62
17 6 0.29
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (16 bp):
TTTTTTTCTATGTTTT
Found at i:1751348 original size:18 final size:17
Alignment explanation
Indices: 1751317--1751356 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1751307 CCTCTCTTGA
1751317 TTTTTT-TCTATTTTTT
1 TTTTTTCTCTATTTTTT
*
1751333 TCTTTTTCTCTGTTTTTT
1 T-TTTTTCTCTATTTTTT
1751351 TTTTTT
1 TTTTTT
1751357 TTTCGAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.48
18 10 0.48
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTTTCTCTATTTTTT
Found at i:1751357 original size:18 final size:17
Alignment explanation
Indices: 1751317--1751358 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1751307 CCTCTCTTGA
1751317 TTTTTTTCTATTTTTTT
1 TTTTTTTCTATTTTTTT
* *
1751334 CTTTTTCTCTGTTTTTTT
1 -TTTTTTTCTATTTTTTT
1751352 TTTTTTT
1 TTTTTTT
1751359 TCGAATTCCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.02, C:0.10, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTCTATTTTTTT
Found at i:1751865 original size:15 final size:16
Alignment explanation
Indices: 1751845--1751874 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1751835 CTAAAAGAAA
1751845 ATAAAAATAA-AATAG
1 ATAAAAATAATAATAG
1751860 ATAAAAATAATAATA
1 ATAAAAATAATAATA
1751875 ATATTAGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
ATAAAAATAATAATAG
Found at i:1754694 original size:17 final size:17
Alignment explanation
Indices: 1754674--1754707 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1754664 CTGTTGTTCT
* *
1754674 CTCTTGTTGGTGTTGTC
1 CTCTTATTGGTGATGTC
1754691 CTCTTATTGGTGATGTC
1 CTCTTATTGGTGATGTC
1754708 ATTATGTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.18, G:0.26, T:0.50
Consensus pattern (17 bp):
CTCTTATTGGTGATGTC
Found at i:1755255 original size:19 final size:18
Alignment explanation
Indices: 1755224--1755311 Score: 99
Period size: 19 Copynumber: 4.8 Consensus size: 18
1755214 CCTAACAAAA
1755224 AATATGTAATAATAATAAT
1 AATAT-TAATAATAATAAT
1755243 AATATTAAGTAATAATAAT
1 AATATTAA-TAATAATAAT
* *
1755262 AGTAGTAATAATAATAAT
1 AATATTAATAATAATAAT
*
1755280 AATA--AATAATAATATT
1 AATATTAATAATAATAAT
*
1755296 ATTATTAAATAATAAT
1 AATATT-AATAATAAT
1755312 GTTAAATTTG
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
16 14 0.23
18 16 0.27
19 30 0.50
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.38
Consensus pattern (18 bp):
AATATTAATAATAATAAT
Found at i:1755311 original size:3 final size:3
Alignment explanation
Indices: 1755230--1755293 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
1755220 AAAAAATATG
* * *
1755230 TAA TAA TAA TAA TAA TAT TAA GTAA TAA TAA TAG TAG TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
1755276 TAA TAA TAAA TAA TAA TA
1 TAA TAA T-AA TAA TAA TA
1755294 TTATTATTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1755729 original size:134 final size:134
Alignment explanation
Indices: 1755478--1755830 Score: 519
Period size: 134 Copynumber: 2.6 Consensus size: 134
1755468 TCTGAGAAAC
* * *
1755478 GTTGACTCATTCCACTATTCTTTAGGGAAGATTGAATCGTGGTAGACTTGTTCCACTGTCACTCA
1 GTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATAGAGGTAGACTTGTTCCACTGTCACTCA
* * * *
1755543 GGGAATATCAAATCTTGAAAGAGATGGATCTATTCCACTTCTTCTTGAGGGAAAATCAGATCTGG
66 CGGAATATCAAATCTTGAAAGAGAGGGATATATTCCACTTCTTCTTGAGGGAAAATCAAATCTGG
1755608 GGACT
131 GGA-T
* * * * * *
1755613 -TTGATTCATTCCACTATTATTCAGGGAAGATTGAATTGAGGTAGACTTGTTCCATTATCACTTA
1 GTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATAGAGGTAGACTTGTTCCACTGTCACTCA
* * * *
1755677 TGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGCTTCTTCTTGTGGGAAAATCAAATCTGG
66 CGGAATATCAAATCTTGAAAGAGAGGGATATATTCCACTTCTTCTTGAGGGAAAATCAAATCTGG
1755742 GGAT
131 GGAT
*
1755746 GTTGATTCATTCCACTATTCTTTAAGGAAGATTGAATAGAGGTAGACTTGTTCCACTGTCACTCA
1 GTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATAGAGGTAGACTTGTTCCACTGTCACTCA
*
1755811 CAGAATATCAAATCTTGAAA
66 CGGAATATCAAATCTTGAAA
1755831 ATTAAACATT
Statistics
Matches: 193, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
133 1 0.01
134 192 0.99
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (134 bp):
GTTGATTCATTCCACTATTCTTTAGGGAAGATTGAATAGAGGTAGACTTGTTCCACTGTCACTCA
CGGAATATCAAATCTTGAAAGAGAGGGATATATTCCACTTCTTCTTGAGGGAAAATCAAATCTGG
GGAT
Found at i:1756971 original size:23 final size:23
Alignment explanation
Indices: 1756943--1756996 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1756933 GCCCTTTGCG
1756943 GTTTTCAACTTGAGACCTCCTTT
1 GTTTTCAACTTGAGACCTCCTTT
*
1756966 GTTTTCAACTTGAGACCTCTTTT
1 GTTTTCAACTTGAGACCTCCTTT
*
1756989 GGTTTCAA
1 GTTTTCAA
1756997 GATGCCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (23 bp):
GTTTTCAACTTGAGACCTCCTTT
Found at i:1757048 original size:7 final size:7
Alignment explanation
Indices: 1757040--1757193 Score: 132
Period size: 7 Copynumber: 20.7 Consensus size: 7
1757030 ATTTTGTTTA
1757040 TTCTTTAT
1 TTCTTT-T
1757048 TTCTTTT
1 TTCTTTT
*
1757055 TTTTTCATTT
1 TTCTT---TT
1757065 TTCTTTCT
1 TTCTTT-T
1757073 TTCTTTT
1 TTCTTTT
1757080 CTT-TTCTT
1 -TTCTT-TT
1757088 TTCTTTT
1 TTCTTTT
1757095 TTCTTTT
1 TTCTTTT
1757102 TTCTTTT
1 TTCTTTT
1757109 TTCTTTT
1 TTCTTTT
1757116 TTCTTTT
1 TTCTTTT
1757123 TTCTTTT
1 TTCTTTT
*
1757130 ATCTTTT
1 TTCTTTT
*
1757137 ATCTTTT
1 TTCTTTT
*
1757144 TTCCTTT
1 TTCTTTT
1757151 TTCATTTT
1 TTC-TTTT
*
1757159 CATT-TTCT
1 --TTCTTTT
1757167 TTCTTTT
1 TTCTTTT
*
1757174 ATCTTTT
1 TTCTTTT
*
1757181 ATCTTTCT
1 TTCTTT-T
1757189 TTCTT
1 TTCTT
1757194 CAGGCGAAAT
Statistics
Matches: 124, Mismatches: 10, Indels: 24
0.78 0.06 0.15
Matches are distributed among these distances:
6 2 0.02
7 84 0.68
8 30 0.24
10 8 0.06
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (7 bp):
TTCTTTT
Found at i:1758273 original size:17 final size:16
Alignment explanation
Indices: 1758251--1758284 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1758241 TAAAAATAGT
1758251 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1758268 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1758284 A
1 A
1758285 CCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1758796 original size:24 final size:24
Alignment explanation
Indices: 1758752--1758801 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1758742 ATAAAGAACC
*
1758752 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1758776 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
1758800 AA
1 AA
1758802 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1769897 original size:152 final size:157
Alignment explanation
Indices: 1769598--1769909 Score: 562
Period size: 152 Copynumber: 2.0 Consensus size: 157
1769588 ATGAAGCAAG
1769598 AGTGCAACATCACCGTACCGTTGGCTGAACTTCTATTTCCACCTCATTCTTCCAACTGTCCCAGA
1 AGTGCAACATCACCGTACCGTTGGCT--ACTTCTATTTCCACCTCATTCTTCCAACTGTCCCAGA
1769663 TGTCCCGGAGCTCTTGTACGTCATTCTGCTTTAGGCTGATCGAGGCGTAGCTACCAGCTCTGACA
64 TGTCCCGGAGCTCTTGTACGTCATTCTGCTTTAGGCTGATC-AGGCGTAGCTACCAGCTCTGACA
1769728 CATAGCTGTCTTGAAGACTGTCTCCCTTTT
128 CATAGCTGTCTTGAAGACTGTCTCCCTTTT
1769758 AGTGCAAC-TCACCGTACCGTTGGCT-CTTCTATTT-CACCTCATTCTTCCAACTGTCCCAGATG
1 AGTGCAACATCACCGTACCGTTGGCTACTTCTATTTCCACCTCATTCTTCCAACTGTCCCAGATG
1769820 TCCC-GAGCTCTTGTACGTCATTCTGCTTTAGGCTGATC-GGCGTAGCTACCAGCTCTGACACAT
66 TCCCGGAGCTCTTGTACGTCATTCTGCTTTAGGCTGATCAGGCGTAGCTACCAGCTCTGACACAT
1769883 AGCTGTCTTGAAGACTGTCTCCCTTTT
131 AGCTGTCTTGAAGACTGTCTCCCTTTT
1769910 CCTTCTGAGT
Statistics
Matches: 152, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
152 52 0.34
154 34 0.22
155 32 0.21
156 9 0.06
159 17 0.11
160 8 0.05
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (157 bp):
AGTGCAACATCACCGTACCGTTGGCTACTTCTATTTCCACCTCATTCTTCCAACTGTCCCAGATG
TCCCGGAGCTCTTGTACGTCATTCTGCTTTAGGCTGATCAGGCGTAGCTACCAGCTCTGACACAT
AGCTGTCTTGAAGACTGTCTCCCTTTT
Found at i:1772534 original size:81 final size:82
Alignment explanation
Indices: 1772399--1772562 Score: 321
Period size: 81 Copynumber: 2.0 Consensus size: 82
1772389 AAAAAAAAAT
1772399 AAATCGAATGGCCTCCCTTTCGTTCCTCGACCGTTCGGTTTTGGTTTAGTCCGAGCCAAATATCA
1 AAATCGAATGGCCTCCCTTTCGTTCCTCGACCGTTCGGTTTTGGTTTAGTCCGAGCCAAATATCA
1772464 CGC-AAATCAACATGCA
66 CGCAAAATCAACATGCA
1772480 AAATCGAATGGCCTCCCTTTCGTTCCTCGACCGTTCGGTTTTGGTTTAGTCCGAGCCAAATATCA
1 AAATCGAATGGCCTCCCTTTCGTTCCTCGACCGTTCGGTTTTGGTTTAGTCCGAGCCAAATATCA
1772545 CGCAAAATCAACATGCA
66 CGCAAAATCAACATGCA
1772562 A
1 A
1772563 GGGAAGCAAC
Statistics
Matches: 82, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 68 0.83
82 14 0.17
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (82 bp):
AAATCGAATGGCCTCCCTTTCGTTCCTCGACCGTTCGGTTTTGGTTTAGTCCGAGCCAAATATCA
CGCAAAATCAACATGCA
Found at i:1781212 original size:49 final size:50
Alignment explanation
Indices: 1781089--1781213 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 50
1781079 TGACCTTGAC
* * * * ** *
1781089 ATTTTAGCATAATCAGTACTAGACACTTAAGATAGTTCTTTGAACATAAT
1 ATTTTAGCATAATTAGTGCTAGGCACTCAAGATACCTCCTTGAACATAAT
* *
1781139 ATTTTAGCATAATTAGGGCTAGGCACTCAAGATACCTCCTTGAACATGAT
1 ATTTTAGCATAATTAGTGCTAGGCACTCAAGATACCTCCTTGAACATAAT
*
1781189 A-TTTAGCATAATTAGTGTTAGGCAC
1 ATTTTAGCATAATTAGTGCTAGGCAC
1781214 ACAAAGCACC
Statistics
Matches: 64, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
49 22 0.34
50 42 0.66
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (50 bp):
ATTTTAGCATAATTAGTGCTAGGCACTCAAGATACCTCCTTGAACATAAT
Found at i:1781225 original size:49 final size:50
Alignment explanation
Indices: 1781128--1781226 Score: 130
Period size: 49 Copynumber: 2.0 Consensus size: 50
1781118 AGATAGTTCT
* *
1781128 TTGAACATAATATTTTAGCATAATTAGGGCTAGGCACTCAAGATACCTCC
1 TTGAACATAATATTTTAGCATAATTAGGGCTAGGCACACAAGACACCTCC
* * *
1781178 TTGAACATGATA-TTTAGCATAATTAGTGTTAGGCACACAA-AGCACCTCC
1 TTGAACATAATATTTTAGCATAATTAGGGCTAGGCACACAAGA-CACCTCC
1781227 ATGGAGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
48 1 0.02
49 31 0.72
50 11 0.26
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (50 bp):
TTGAACATAATATTTTAGCATAATTAGGGCTAGGCACACAAGACACCTCC
Found at i:1785418 original size:15 final size:16
Alignment explanation
Indices: 1785400--1785429 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1785390 CTTAATTTAT
1785400 TAATTTATA-ATGTTA
1 TAATTTATATATGTTA
1785415 TAATTTATATATGTT
1 TAATTTATATATGTT
1785430 GATGTCGTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TAATTTATATATGTTA
Found at i:1792824 original size:15 final size:16
Alignment explanation
Indices: 1792804--1792846 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1792794 ATCATAAACC
1792804 TTACCCACATGTA-AT
1 TTACCCACATGTATAT
1792819 TTACCCAACATG-ATAT
1 TTACCC-ACATGTATAT
*
1792835 TTACCCTCATGT
1 TTACCCACATGT
1792847 TTTTATTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
TTACCCACATGTATAT
Found at i:1795033 original size:23 final size:25
Alignment explanation
Indices: 1794990--1795047 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
1794980 TTCATTTTTC
1794990 TTTTCTCTCTCTAAAAGAGAGAAAT
1 TTTTCTCTCTCTAAAAGAGAGAAAT
1795015 TTTTCTCTCTCTAAAAGAGAGAAAT
1 TTTTCTCTCTCTAAAAGAGAGAAAT
1795040 TTTTCTCT
1 TTTTCTCT
1795048 TTGACCTCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (25 bp):
TTTTCTCTCTCTAAAAGAGAGAAAT
Found at i:1795324 original size:17 final size:17
Alignment explanation
Indices: 1795304--1795337 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1795294 TTGTTGTTCT
*
1795304 CTCTTATTGGTGTTGTC
1 CTCTTATTGGTGATGTC
*
1795321 CTCTTGTTGGTGATGTC
1 CTCTTATTGGTGATGTC
1795338 AGTATGTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.18, G:0.26, T:0.50
Consensus pattern (17 bp):
CTCTTATTGGTGATGTC
Found at i:1795873 original size:3 final size:3
Alignment explanation
Indices: 1795865--1795917 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
1795855 AAATATGTAG
1795865 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
1795911 TAA TAA T
1 TAA TAA T
1795918 TTTAAATTTG
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1796615 original size:30 final size:30
Alignment explanation
Indices: 1796481--1796602 Score: 235
Period size: 30 Copynumber: 4.1 Consensus size: 30
1796471 GAAATATACA
1796481 TAGTCAATGTATTGAATATAAAGAATTACT
1 TAGTCAATGTATTGAATATAAAGAATTACT
*
1796511 TAGTCAATGTATTAAATATAAAGAATTACT
1 TAGTCAATGTATTGAATATAAAGAATTACT
1796541 TAGTCAATGTATTGAATATAAAGAATTACT
1 TAGTCAATGTATTGAATATAAAGAATTACT
1796571 TAGTCAATGTATTGAATATAAAGAATTACT
1 TAGTCAATGTATTGAATATAAAGAATTACT
1796601 TA
1 TA
1796603 TTAGACATAT
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (30 bp):
TAGTCAATGTATTGAATATAAAGAATTACT
Found at i:1796987 original size:16 final size:16
Alignment explanation
Indices: 1796966--1797011 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1796956 ATGTTAAATG
*
1796966 ATTAATTTATAAAAAA
1 ATTAATTAATAAAAAA
*
1796982 ATTAA-TAGACAAAAAA
1 ATTAATTA-ATAAAAAA
1796998 ATT-ATTAATAAAAA
1 ATTAATTAATAAAAA
1797012 TATATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
ATTAATTAATAAAAAA
Found at i:1801246 original size:14 final size:15
Alignment explanation
Indices: 1801216--1801252 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1801206 ATAAATTAGT
1801216 TAAAA-ATTCAAAGA
1 TAAAATATTCAAAGA
*
1801230 TAAAATATTTAAA-A
1 TAAAATATTCAAAGA
1801244 TAAAATATT
1 TAAAATATT
1801253 AATTACATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (15 bp):
TAAAATATTCAAAGA
Found at i:1802105 original size:20 final size:19
Alignment explanation
Indices: 1802057--1802145 Score: 81
Period size: 19 Copynumber: 4.5 Consensus size: 19
1802047 GAATTTGGTG
* *
1802057 AAATTGATTTTTAAAT-TT
1 AAATTTATTTTAAAATATT
*
1802075 AAAATTCATTTTAAAGATATT
1 -AAATTTATTTTAAA-ATATT
*
1802096 AAATTTATTTTTATACATATT
1 AAATTTA-TTTTA-AAATATT
*
1802117 GAATTTTATTTTAAAATATT
1 -AAATTTATTTTAAAATATT
1802137 AAATTTATT
1 AAATTTATT
1802146 ATTATTTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
19 20 0.34
20 14 0.24
21 17 0.29
22 7 0.12
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (19 bp):
AAATTTATTTTAAAATATT
Found at i:1802107 original size:21 final size:20
Alignment explanation
Indices: 1802057--1802145 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
1802047 GAATTTGGTG
*
1802057 AAATTGATTTTT-AAAT-TT
1 AAATTTATTTTTAAAATATT
*
1802075 AAAATTCA-TTTTAAAGATATT
1 -AAATTTATTTTTAAA-ATATT
*
1802096 AAATTTATTTTTATACATATT
1 AAATTTATTTTTA-AAATATT
*
1802117 GAATTT-TATTTTAAAATATT
1 AAATTTAT-TTTTAAAATATT
1802137 AAATTTATT
1 AAATTTATT
1802146 ATTATTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
18 4 0.07
19 8 0.14
20 21 0.37
21 23 0.40
22 1 0.02
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (20 bp):
AAATTTATTTTTAAAATATT
Found at i:1813684 original size:20 final size:22
Alignment explanation
Indices: 1813641--1813686 Score: 60
Period size: 24 Copynumber: 2.1 Consensus size: 22
1813631 TGTGCGCCGA
1813641 TATCTTTCTTTAGTGTGTCGTCGG
1 TATCTTTCTTTAG-GTGTC-TCGG
1813665 TATCTTTCTTTA-GTGT-TCGG
1 TATCTTTCTTTAGGTGTCTCGG
1813685 TA
1 TA
1813687 ACTCTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.27
22 4 0.18
24 12 0.55
ACGTcount: A:0.11, C:0.15, G:0.22, T:0.52
Consensus pattern (22 bp):
TATCTTTCTTTAGGTGTCTCGG
Found at i:1814489 original size:17 final size:17
Alignment explanation
Indices: 1814467--1814509 Score: 65
Period size: 14 Copynumber: 2.7 Consensus size: 17
1814457 AGAACACCTC
1814467 CGTCGACAAATTCGTAT
1 CGTCGACAAATTCGTAT
1814484 CGTCG---AATTCGTAT
1 CGTCGACAAATTCGTAT
1814498 CGTCGACAAATT
1 CGTCGACAAATT
1814510 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 14 0.61
17 9 0.39
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (17 bp):
CGTCGACAAATTCGTAT
Found at i:1815056 original size:28 final size:27
Alignment explanation
Indices: 1815014--1815073 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
1815004 TTTGAAAATC
* *
1815014 AACAATTCGACTGAATCAAGTTATTGA
1 AACAATTCAACTGAAACAAGTTATTGA
1815041 AACAATCTCAACTGAAACAAGTTATTGA
1 AACAAT-TCAACTGAAACAAGTTATTGA
1815069 AACAA
1 AACAA
1815074 CTGAAACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.25
Consensus pattern (27 bp):
AACAATTCAACTGAAACAAGTTATTGA
Found at i:1816305 original size:22 final size:22
Alignment explanation
Indices: 1816264--1816305 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1816254 AACATCGAAC
*
1816264 AATCACATAGCATCATCATTAA
1 AATCACATAGCATCACCATTAA
1816286 AATCACAT-GCATCGACCATT
1 AATCACATAGCATC-ACCATT
1816306 CCCACCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.40, C:0.26, G:0.07, T:0.26
Consensus pattern (22 bp):
AATCACATAGCATCACCATTAA
Found at i:1818440 original size:12 final size:12
Alignment explanation
Indices: 1818423--1818457 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1818413 TGAACCCTTT
*
1818423 CTTCCTTCTTCA
1 CTTCCTTCTCCA
1818435 CTTCCTTCTCCA
1 CTTCCTTCTCCA
1818447 CTTCCTTCTCC
1 CTTCCTTCTCC
1818458 GCTCCAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (12 bp):
CTTCCTTCTCCA
Found at i:1818710 original size:12 final size:12
Alignment explanation
Indices: 1818689--1818727 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1818679 TCTTGAACCT
1818689 TTCTTC-CTTCC
1 TTCTTCACTTCC
1818700 TTCTTCACTTCC
1 TTCTTCACTTCC
*
1818712 TTCTCCACTTCC
1 TTCTTCACTTCC
1818724 TTCT
1 TTCT
1818728 CCGCTCCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (12 bp):
TTCTTCACTTCC
Found at i:1819198 original size:15 final size:15
Alignment explanation
Indices: 1819178--1819207 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1819168 CGGTAAGGAT
1819178 GGGGAGATCCGAAAG
1 GGGGAGATCCGAAAG
1819193 GGGGAGATCCGAAAG
1 GGGGAGATCCGAAAG
1819208 AGATTTGGTG
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:0.33, C:0.13, G:0.47, T:0.07
Consensus pattern (15 bp):
GGGGAGATCCGAAAG
Found at i:1823728 original size:3 final size:3
Alignment explanation
Indices: 1823722--1823753 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1823712 ATCATCACCA
*
1823722 TCG TCG TCG TCG TCA TCG TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
1823754 CTGAGCAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.28, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:1823740 original size:15 final size:15
Alignment explanation
Indices: 1823720--1823750 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1823710 TCATCATCAC
1823720 CATCGTCGTCGTCGT
1 CATCGTCGTCGTCGT
1823735 CATCGTCGTCGTCGT
1 CATCGTCGTCGTCGT
1823750 C
1 C
1823751 GTCCTGAGCA
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:0.06, C:0.35, G:0.26, T:0.32
Consensus pattern (15 bp):
CATCGTCGTCGTCGT
Found at i:1825793 original size:17 final size:18
Alignment explanation
Indices: 1825768--1825803 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1825758 AAATTATATT
*
1825768 AGTATAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1825785 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
1825803 A
1 A
1825804 TTAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1826938 original size:31 final size:33
Alignment explanation
Indices: 1826900--1826971 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
1826890 ATTTCAAAAA
**
1826900 TAACAAATTAATCA-TT-AACATTGTCGATTTG
1 TAACAAATTAATCACTTCAACATTAACGATTTG
* *
1826931 TAACAAATTAGTCACTTCGACATTAACGATTTG
1 TAACAAATTAATCACTTCAACATTAACGATTTG
1826964 TAACAAAT
1 TAACAAAT
1826972 CCAACTACTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 13 0.37
32 2 0.06
33 20 0.57
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (33 bp):
TAACAAATTAATCACTTCAACATTAACGATTTG
Found at i:1832419 original size:21 final size:22
Alignment explanation
Indices: 1832395--1832440 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1832385 AAATGTGCGA
* *
1832395 AAAGATAGAGGAAA-ATGTCAT
1 AAAGATAAAGAAAATATGTCAT
*
1832416 AAAGATAAAGAAAATATGTTAT
1 AAAGATAAAGAAAATATGTCAT
1832438 AAA
1 AAA
1832441 AGTAGAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.59, C:0.02, G:0.17, T:0.22
Consensus pattern (22 bp):
AAAGATAAAGAAAATATGTCAT
Found at i:1832430 original size:20 final size:21
Alignment explanation
Indices: 1832373--1832430 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1832363 ACGACCGATA
1832373 AAAAGATAAA-ATAAATGTGCG
1 AAAAGATAAAGA-AAATGTGCG
*
1832394 AAAAGATAGAGGAAAATGT-C-
1 AAAAGATA-AAGAAAATGTGCG
1832414 ATAAAGATAAAGAAAAT
1 A-AAAGATAAAGAAAAT
1832431 ATGTTATAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 7 0.22
23 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.17
Consensus pattern (21 bp):
AAAAGATAAAGAAAATGTGCG
Found at i:1832439 original size:22 final size:21
Alignment explanation
Indices: 1832374--1832440 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
1832364 CGACCGATAA
*
1832374 AAAGATAAA-ATAAATGTGCGA-
1 AAAGATAAAGAAAAATGT-C-AT
* *
1832395 AAAGATAGAGGAAAATGTCAT
1 AAAGATAAAGAAAAATGTCAT
*
1832416 AAAGATAAAGAAAATATGTTAT
1 AAAGATAAAGAAAA-ATGTCAT
1832438 AAA
1 AAA
1832441 AGTAGAGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 21 0.57
22 15 0.41
ACGTcount: A:0.58, C:0.03, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAGATAAAGAAAAATGTCAT
Found at i:1833151 original size:85 final size:84
Alignment explanation
Indices: 1833022--1833179 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 84
1833012 TATGTTATAT
* * *
1833022 TATTTAACAAGAAATTTATTAAGTACAATAACTATTAGGTAACGCTTATATAA-GTAATAGGTGG
1 TATTTAACAAGAAATTTATCAAATACAATAACTATTAGATAACGCTTATATAATGTAATAGGT-G
1833086 CACTTATATAATAAAATAGG
65 CACTTATATAATAAAATAGG
** *
1833106 TATTTAACCGGAAATATTATCAAATACAATATATTA-TAGATAACGCTTATATAATGTAATAGGT
1 TATTTAACAAGAAAT-TTATCAAATACAATA-ACTATTAGATAACGCTTATATAATGTAATAGGT
*
1833170 GCGCTTATAT
64 GCACTTATAT
1833180 TGACATATTT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
84 13 0.20
85 39 0.61
86 12 0.19
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.35
Consensus pattern (84 bp):
TATTTAACAAGAAATTTATCAAATACAATAACTATTAGATAACGCTTATATAATGTAATAGGTGC
ACTTATATAATAAAATAGG
Found at i:1833682 original size:193 final size:194
Alignment explanation
Indices: 1833200--1833883 Score: 766
Period size: 193 Copynumber: 3.5 Consensus size: 194
1833190 TATAAGTAAG
*
1833200 CCGTATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
1 CCGTATATTTATACCGGTTACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * * *
1833265 TTTTGGATCGATACTTTTTATAAATGTATCGACACTATATGCGTTCACCCTTTTGGGCATTCATT
66 TTTGGGATCGATAC-TTTTAAAAATGTATCGACACTTTATGCGTACACCCGTTT-GGCATTCATT
* * * * * * *
1833330 CTGGA-AAAAAGTATCGACATAACA-TTAAAAAGTGTTGACACATTATGTA-GACATATTCTCAC
129 ATGGACAAAAA-TATCGACACAA-ATTTAAAAAGTGTCGATACATTATGTACCA-ATTTTCTCAT
1833392 ATAAA
191 A-AAA
** * * * *
1833397 CCGTATAAATATACCGGTTATATTACAAAATTACCT-TTACATTAT-ATTATGGGTTTCGATGTT
1 CCGTATATTTATACCGGTTACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* * * * * *
1833460 TTTTGGATCGATACTTTTTAAAATGTATCGATACTTTATGAGTGCACCCGTCTGGCATTCATTAT
66 TTTGGGATCGATACTTTTAAAAATGTATCGACACTTTATGCGTACACCCGTTTGGCATTCATTAT
* * *
1833525 GGACAAAATATATCGACACAAATTTAATAAGTATCGATACTTTATG-ACCAATTTTCTCATAAAA
131 GGACAAAA-ATATCGACACAAATTTAAAAAGTGTCGATACATTATGTACCAATTTTCTCATAAAA
* *
1833589 CCGTATATTTATACCGGTTACATTG-TAATTTACATATTACATTATAATTATCGGTTTCGAT-TT
1 CCGTATATTTATACCGGTTACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
*
1833652 TATTGGGATCGA-ACTTTTAATAATTGTATCGACACTTTATGCGTACACCCCGTTTGGCATTCAT
66 T-TTGGGATCGATACTTTTAA-AAATGTATCGACACTTTATGCGTACA-CCCGTTTGGCATTCAT
* * *
1833716 TTTGGACAATAATATCGACACAAA-TTAAACAAGTGTCGATACATTATGTTTACC--TGTTTCTA
128 TATGGACAAAAATATCGACACAAATTTAAA-AAGTGTCGATACATTATG--TACCAAT-TTTCTC
*
1833778 AT-TAA
189 ATAAAA
* ** *
1833783 CCGGTATATTTACACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTCGATGT
1 CC-GTATATTTATACCGGTTACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATG-
1833848 TTTTTGGG-TCGATACTTTTAGAAAATGTATCGACAC
64 TTTTTGGGATCGATACTTTTA-AAAATGTATCGACAC
1833884 ATATTAGGTA
Statistics
Matches: 416, Mismatches: 51, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
191 7 0.02
192 47 0.11
193 99 0.24
194 93 0.22
195 61 0.15
196 50 0.12
197 55 0.13
198 4 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (194 bp):
CCGTATATTTATACCGGTTACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
TTTGGGATCGATACTTTTAAAAATGTATCGACACTTTATGCGTACACCCGTTTGGCATTCATTAT
GGACAAAAATATCGACACAAATTTAAAAAGTGTCGATACATTATGTACCAATTTTCTCATAAAA
Found at i:1834380 original size:116 final size:117
Alignment explanation
Indices: 1834175--1834407 Score: 427
Period size: 116 Copynumber: 2.0 Consensus size: 117
1834165 TAATCGATGC
1834175 TTTTTAAACTATACTATGTTAATTGTGATGTGAAATAGTATAAACCTGCTAATCGCCAAAGGAAA
1 TTTTTAAACTATACTATGTTAATTGTGATGTGAAATAGTATAAACCTGCTAATCGCCAAAGGAAA
1834240 CTAAATGCAATTGGAAATTAAATATTTCACTATGAATTTATGTGATTAAATA
66 CTAAATGCAATTGGAAATTAAATATTTCACTATGAATTTATGTGATTAAATA
1834292 TTTTTAAACTATACTATGTTAATTGTGATGTGAAATAGTA-AAACCTGCCTAA-CGCCAAAGGAA
1 TTTTTAAACTATACTATGTTAATTGTGATGTGAAATAGTATAAACCTG-CTAATCGCCAAAGGAA
1834355 ACT-AATGCAAATTGGAAATTAAATATTTCACTATGAATTTATGTGATTAAATA
65 ACTAAATGC-AATTGGAAATTAAATATTTCACTATGAATTTATGTGATTAAATA
1834408 ATTTAATAAT
Statistics
Matches: 114, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
115 5 0.04
116 65 0.57
117 44 0.39
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (117 bp):
TTTTTAAACTATACTATGTTAATTGTGATGTGAAATAGTATAAACCTGCTAATCGCCAAAGGAAA
CTAAATGCAATTGGAAATTAAATATTTCACTATGAATTTATGTGATTAAATA
Found at i:1835491 original size:22 final size:24
Alignment explanation
Indices: 1835463--1835509 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1835453 ATAATATAGA
1835463 AAAATATAATGATA-ATAA-TAAT
1 AAAATATAATGATACATAATTAAT
* *
1835485 AAAATATCATTATACATAATTAAT
1 AAAATATAATGATACATAATTAAT
1835509 A
1 A
1835510 TTAAAAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 4 0.19
24 5 0.24
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (24 bp):
AAAATATAATGATACATAATTAAT
Found at i:1843805 original size:13 final size:13
Alignment explanation
Indices: 1843768--1843807 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1843758 TCGATACTGA
1843768 AAAATAAATA-TT
1 AAAATAAATATTT
*
1843780 AAAATAATTTATTT
1 AAAATAA-ATATTT
1843794 AAAATAAATATTT
1 AAAATAAATATTT
1843807 A
1 A
1843808 TTTATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:1845202 original size:3 final size:3
Alignment explanation
Indices: 1845194--1845239 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1845184 TTAATATATT
1845194 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1845240 TAATTAATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1845803 original size:112 final size:112
Alignment explanation
Indices: 1845572--1846292 Score: 1166
Period size: 112 Copynumber: 6.5 Consensus size: 112
1845562 CAAAAAGTTG
* *
1845572 TCTTCTTTCTTCTTCAGATGAGTTC-T-TCATTATGAACTTCTCT-GAAAATGTTGATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAA-GATGATCCATCAA
* * **
1845634 TTGATGAATTCATGTAAAAGGTTGAACAAGCTCTTCTCATTATGAACT
65 GTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
1845682 T-TCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTTTGGAAAAGATGATCCATCA
1 TCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGATGATCCATCA
*** **
1845746 AGTGATGAATTCAAACAAAAGGTTG-ATGAATTCTTCTCATTATGAACT
64 AGTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
1845794 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAG
*
1845859 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 TGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
1845906 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAG
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAG
*
1845971 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 TGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
*
1846018 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAG
*
1846083 TGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
66 TGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* *
1846130 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATCCATCAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGATGATCCATCAA
* **
1846195 GTAATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
65 GTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
1846243 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCT-GAAAA
1 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAA
1846293 TGTCAATCCA
Statistics
Matches: 575, Mismatches: 28, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
109 1 0.00
110 22 0.04
111 49 0.09
112 355 0.62
113 143 0.25
114 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (112 bp):
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGATGATCCATCAAG
TGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
Found at i:1847184 original size:83 final size:83
Alignment explanation
Indices: 1847038--1847511 Score: 857
Period size: 83 Copynumber: 5.7 Consensus size: 83
1847028 GTAGTTCCTA
*
1847038 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1847103 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
1847121 TCCAACT-AGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1 -CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1847185 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
1847204 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1 -CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTA
1847268 AATTCAATGATTGGTTCTG
65 AATTCAATGATTGGTTCTG
*
1847287 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1847352 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
*
1847370 CCAAATCAGATCAGATAACTCAAAG-A-ACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
1847433 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
1847451 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
1847512 TCATTTAATG
Statistics
Matches: 380, Mismatches: 6, Indels: 9
0.96 0.02 0.02
Matches are distributed among these distances:
81 80 0.21
82 5 0.01
83 291 0.77
84 4 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAA
ATTCAATGATTGGTTCTG
Found at i:1859853 original size:13 final size:13
Alignment explanation
Indices: 1859816--1859855 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
1859806 TTGATACTGA
1859816 AAAATAAATA-TT
1 AAAATAAATATTT
*
1859828 AAAATAATTTATTT
1 AAAATAA-ATATTT
1859842 AAAATAAATATTT
1 AAAATAAATATTT
1859855 A
1 A
1859856 TTATTATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:1861211 original size:3 final size:3
Alignment explanation
Indices: 1861203--1861250 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
1861193 TTAATATATT
*
1861203 TAA TAA TAA T-A TAA TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1861250 T
1 T
1861251 TAATTAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1865264 original size:3 final size:3
Alignment explanation
Indices: 1865258--1865349 Score: 77
Period size: 3 Copynumber: 31.7 Consensus size: 3
1865248 TTCATTTGAA
* * * *
1865258 TAT TAT T-T ATAT T-T TAT TAT AAT TAT AAT TAT AAT TAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
1865302 T-T ATAT T-T TAT TAT AAT TAT AAT TAT TA- TAT TAT TAT TAT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1865345 TAT TA
1 TAT TA
1865350 AATAATTTTA
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
2 8 0.11
3 60 0.86
4 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1865310 original size:38 final size:40
Alignment explanation
Indices: 1865259--1865342 Score: 145
Period size: 38 Copynumber: 2.1 Consensus size: 40
1865249 TCATTTGAAT
1865259 ATTATTTATATTTTATTATAATTATAATTA-TA-ATTATA
1 ATTATTTATATTTTATTATAATTATAATTATTATATTATA
*
1865297 ATTATTTATATTTTATTATAATTATAATTATTATATTATT
1 ATTATTTATATTTTATTATAATTATAATTATTATATTATA
1865337 ATTATT
1 ATTATT
1865343 ATTATTAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
38 30 0.70
39 2 0.05
40 11 0.26
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (40 bp):
ATTATTTATATTTTATTATAATTATAATTATTATATTATA
Found at i:1865314 original size:26 final size:26
Alignment explanation
Indices: 1865271--1865347 Score: 111
Period size: 26 Copynumber: 2.9 Consensus size: 26
1865261 TATTTATATT
*
1865271 TTATTATAATTATAATTATAATTATAA
1 TTATTAT-ATTATTATTATAATTATAA
1865298 TTATTTATATT-TTATTATAATTATAA
1 TTA-TTATATTATTATTATAATTATAA
*
1865324 TTATTATATTATTATTATTATTAT
1 TTATTATATTATTATTATAATTAT
1865348 TAAATAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
25 7 0.15
26 29 0.63
27 6 0.13
28 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATTATATTATTATTATAATTATAA
Found at i:1865365 original size:20 final size:20
Alignment explanation
Indices: 1865317--1865361 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1865307 TTTTATTATA
* * *
1865317 ATTATAATTATTATATTATT
1 ATTATTATTATTAAATAATT
1865337 ATTATTATTATTAAATAATT
1 ATTATTATTATTAAATAATT
1865357 -TTATT
1 ATTATT
1865362 TATTTACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATTATTATTAAATAATT
Found at i:1866962 original size:23 final size:25
Alignment explanation
Indices: 1866927--1866975 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
1866917 CATTTTCTGA
*
1866927 TATTTCTAAATAAA-TAA-ATATTT
1 TATTTATAAATAAATTAATATATTT
*
1866950 TATTTATATATAAATTAATATATTT
1 TATTTATAAATAAATTAATATATTT
1866975 T
1 T
1866976 TCATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 3 0.14
25 7 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTATAAATAAATTAATATATTT
Found at i:1867477 original size:28 final size:27
Alignment explanation
Indices: 1867446--1867499 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1867436 TAATTCTTTC
*
1867446 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATA-TTATTA
* *
1867474 TTTTCATAGTATTTATATATATTATT
1 TTTTCAAAATATTTATATATATTATT
1867500 TTATTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATATTATTA
Found at i:1867520 original size:24 final size:24
Alignment explanation
Indices: 1867463--1867520 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
1867453 AATTTTTATA
* *
1867463 TATACTTATTATTTTCATAGTATT
1 TATATTTATTATTTTCATAATATT
*
1867487 TATATATATTATTTT-ATTAATATT
1 TATATTTATTATTTTCA-TAATATT
1867511 TCAT-TTTATT
1 T-ATATTTATT
1867521 TGCAAGTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.04
24 25 0.89
25 2 0.07
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (24 bp):
TATATTTATTATTTTCATAATATT
Found at i:1870793 original size:15 final size:15
Alignment explanation
Indices: 1870773--1870804 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1870763 GATCAATACC
1870773 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1870788 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1870803 TT
1 TT
1870805 GCATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1874585 original size:9 final size:9
Alignment explanation
Indices: 1874571--1874602 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
1874561 AAATGGCAAT
1874571 CATTCTTTA
1 CATTCTTTA
1874580 CATTCTTTA
1 CATTCTTTA
1874589 CATTCTTTA
1 CATTCTTTA
1874598 CATTC
1 CATTC
1874603 ATTATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.22, C:0.25, G:0.00, T:0.53
Consensus pattern (9 bp):
CATTCTTTA
Found at i:1878120 original size:7 final size:7
Alignment explanation
Indices: 1878100--1878178 Score: 74
Period size: 7 Copynumber: 11.1 Consensus size: 7
1878090 ATTATGCTTG
1878100 AAGAAAA
1 AAGAAAA
*
1878107 AA-TAAA
1 AAGAAAA
*
1878113 ATGAAAA
1 AAGAAAA
1878120 AAGAAAAA
1 AAG-AAAA
1878128 AAGAAGAA
1 AAGAA-AA
1878136 GAAGAAGAA
1 -AAGAA-AA
1878145 AAGAAAA
1 AAGAAAA
*
1878152 AA-AAAG
1 AAGAAAA
1878158 AAGAAAA
1 AAGAAAA
1878165 AAG-AAA
1 AAGAAAA
1878171 AAGAAAA
1 AAGAAAA
1878178 A
1 A
1878179 GGAGGGTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
6 15 0.25
7 23 0.38
8 14 0.23
9 8 0.13
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:1878126 original size:6 final size:6
Alignment explanation
Indices: 1878125--1878179 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
1878115 GAAAAAAGAA
* * *
1878125 AAAAAG AAGAAG AAGAAG -AAAAG AAAAAA AAAGAAG AAAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAA-AAG -AAAAAG AAAAAG
1878174 AAAAAG
1 AAAAAG
1878180 GAGGGTCAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
5 4 0.10
6 30 0.71
7 5 0.12
8 3 0.07
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1878146 original size:27 final size:25
Alignment explanation
Indices: 1878110--1878178 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 25
1878100 AAGAAAAAAT
*
1878110 AAAATGAAAAAAGAAAAAAAGAAGA
1 AAAAAGAAAAAAGAAAAAAAGAAGA
1878135 AGAAGAAGAAAAGAA-AAAAAAAGAAGA
1 A-AA-AAGAAAA-AAGAAAAAAAGAAGA
1878162 AAAAAG-AAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
1878179 GGAGGGTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 2 0.05
24 8 0.21
25 4 0.10
26 4 0.10
27 19 0.49
28 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (25 bp):
AAAAAGAAAAAAGAAAAAAAGAAGA
Found at i:1878147 original size:25 final size:26
Alignment explanation
Indices: 1878117--1878178 Score: 92
Period size: 25 Copynumber: 2.4 Consensus size: 26
1878107 AATAAAATGA
*
1878117 AAAAAGAAAAAAAGAAGAAG-AAGAAG
1 AAAAAGAAAAAAA-AAGAAGAAAAAAG
1878143 -AAAAGAAAAAAAAAGAAGAAAAAAG
1 AAAAAGAAAAAAAAAGAAGAAAAAAG
1878168 AAAAAGAAAAA
1 AAAAAGAAAAA
1878179 GGAGGGTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
24 6 0.18
25 17 0.52
26 10 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAAGAAAAAAAAAGAAGAAAAAAG
Found at i:1879870 original size:113 final size:113
Alignment explanation
Indices: 1879672--1880804 Score: 1500
Period size: 113 Copynumber: 10.0 Consensus size: 113
1879662 TAGCAAAGAT
*
1879672 TCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1879737 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1879785 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATTAGAAGAACTTATCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1879850 AGAAGAAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * ** *
1879898 TTGAATTCATTATTCGATGGATCATCTTTTTTAGAGAAAGTTCATAATGAGAAGAACTCGTCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
*
1879963 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTTTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
1880011 TCAAATCCATCACTTGATGGATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1880076 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTAC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
*
1880124 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1880189 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
1880236 ---AATTCATCATTCGATAGATCAACTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1880298 AGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTACAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1880346 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1880411 AGAAGGAAGAAGAAGTTCATAATGACAAAAATTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* *
1880459 TCAAATCCATCAC-CTGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTC-GATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
* * *
1880523 AAGAAGGAAGAAGAAGTTTATAATAAGAAGAATTTGTTCAACCTTTTGT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * * * * **
1880572 TTGAATTCATCATTTGATGGATCAGCATTGCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * * *
1880636 AGAAGGAAGATGAATTTCATAATGAAAATAACTTGTTCAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * * *
1880684 AT-AACTCTATCAC-AGAAAGAGATATATCATCATCAACATTTCCAGA-AGGAGTTCATAATGAG
1 -TCAAATCCATCACTCG-ATG-G----------ATCAACTTTTCCAGAGA-AAGTTCATAATGAG
*
1880746 AAGAACTCATCT---GAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
52 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
1880804 T
1 T
1880805 AGATTACATC
Statistics
Matches: 901, Mismatches: 99, Indels: 34
0.87 0.10 0.03
Matches are distributed among these distances:
109 102 0.11
111 1 0.00
112 75 0.08
113 643 0.71
119 1 0.00
120 37 0.04
121 3 0.00
123 14 0.02
124 25 0.03
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
TCAAATCCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:1880448 original size:335 final size:336
Alignment explanation
Indices: 1879672--1880683 Score: 1602
Period size: 335 Copynumber: 3.0 Consensus size: 336
1879662 TAGCAAAGAT
* *
1879672 TCAAATCCATCACTCGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1879737 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTCGA
66 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTCGA
* * *
1879802 TGGATCAACTTTTCCAGAGAAAGTTCATAATTAGAAGAACTTATCTGAAGAAGAAAGAAGAAGTT
131 TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * **
1879867 CATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATTATTCGATGGATCATCTTTTTTAG
196 CATAATGAGAAGAATTTGTTCAACC--TTGTTTGAATTCATCATTCGATGGATCAACTTTTCCA-
*
1879932 AGAAAGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
258 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTT
*
1879997 TTTCAACCTTTTGC
323 GTTCAACCTTTTGC
1880011 TCAAATCCATCACTTGATGGATCAGCTTTTCCA-AAGAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAA-AAAGTTCATAATGAGAAGAACTCATCTG
1880075 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTCG
65 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTCG
*
1880140 ATGGATCAACTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
130 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
*
1880205 TCATAATGAGAAGAATTTGTTCAACC-T-TTTGAATTCATCATTCGATAGATCAACTTTTCCAAA
195 TCATAATGAGAAGAATTTGTTCAACCTTGTTTGAATTCATCATTCGATGGATCAACTTTTCC-AA
*
1880268 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTG
259 GAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
*
1880333 TACAACCTTTTGC
324 TTCAACCTTTTGC
*
1880346 TCAAATCCATCACTTGATGGATCAACTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
1880411 AGAAGGAAGAAGAAGTTCATAATGACAAAAATTTGTTCAACCTTTTGCTCAAATCCATCAC-CTG
66 AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTC-G
* *
1880475 ATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
130 ATGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGT
* * * * * *
1880540 TTATAATAAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATTGCC-
195 TCATAATGAGAAGAATTTGTTCAACC--TTGTTTGAATTCATCATTCGATGGATCAACTTTTCCA
* * * * * *
1880604 AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGATGAATTTCATAATGAAAATAACT
258 AGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATT
1880669 TGTTCAACCTTTTGC
322 TGTTCAACCTTTTGC
1880684 ATAACTCTAT
Statistics
Matches: 626, Mismatches: 38, Indels: 19
0.92 0.06 0.03
Matches are distributed among these distances:
334 1 0.00
335 308 0.49
336 4 0.01
337 4 0.01
338 69 0.11
339 240 0.38
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (336 bp):
TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTCGA
TGGATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAATTTGTTCAACCTTGTTTGAATTCATCATTCGATGGATCAACTTTTCCAAGA
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
CAACCTTTTGC
Found at i:1881027 original size:3 final size:3
Alignment explanation
Indices: 1881021--1881128 Score: 100
Period size: 3 Copynumber: 36.7 Consensus size: 3
1881011 TTCATTTGAA
* *
1881021 TAT TAT T-T ATAT T-T TAT TAT TAT TAT TAT TAT AAT TAT AAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
1881065 T-T ATAT T-T TAT TAT TAT AAT TAT AAT TAT AAT TAT AAT TATT TAT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
1881110 TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
1881129 AATAATTTTA
Statistics
Matches: 85, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
2 8 0.09
3 72 0.85
4 5 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1881073 original size:38 final size:39
Alignment explanation
Indices: 1881022--1881151 Score: 158
Period size: 38 Copynumber: 3.3 Consensus size: 39
1881012 TCATTTGAAT
1881022 ATTATTTA-TATTTTATTATTATTATTATTATAATTATA
1 ATTATTTACTATTTTATTATTATTATTATTATAATTATA
*
1881060 ATTATTTA-TATTTTATTATTATAATTATAATTATAATTATA
1 ATTATTTACTATTTTATTA-T-T-ATTATTATTATAATTATA
* * * *
1881101 ATTATTTATTATATTATTATTATTATTA-AATAATTTTA
1 ATTATTTACTATTTTATTATTATTATTATTATAATTATA
*
1881139 TTTATTTACTATT
1 ATTATTTACTATT
1881152 ACAGACCCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
38 36 0.45
39 7 0.09
40 2 0.03
41 26 0.32
42 9 0.11
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTATTTACTATTTTATTATTATTATTATTATAATTATA
Found at i:1881143 original size:17 final size:18
Alignment explanation
Indices: 1881101--1881144 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1881091 TATAATTATA
* *
1881101 ATTATTTATTATATTATT
1 ATTATTTATTAAATAATT
1881119 ATTA-TTATTAAATAATT
1 ATTATTTATTAAATAATT
1881136 -TTATTTATT
1 ATTATTTATT
1881145 TACTATTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTATTTATTAAATAATT
Found at i:1882655 original size:20 final size:19
Alignment explanation
Indices: 1882630--1882671 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1882620 CTATTTTATA
1882630 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
1882650 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
1882669 AAT
1 AAT
1882672 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:1882753 original size:23 final size:25
Alignment explanation
Indices: 1882718--1882766 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
1882708 CCTTTTCTGA
*
1882718 TATTTCTAAATAAA-TAA-ATATTT
1 TATTTATAAATAAATTAATATATTT
*
1882741 TATTTATATATAAATTAATATATTT
1 TATTTATAAATAAATTAATATATTT
1882766 T
1 T
1882767 TCATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 3 0.14
25 7 0.32
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTATAAATAAATTAATATATTT
Found at i:1884345 original size:56 final size:56
Alignment explanation
Indices: 1884248--1884452 Score: 185
Period size: 56 Copynumber: 3.8 Consensus size: 56
1884238 GGATGATTTG
* * * *
1884248 CTTTTGAAGATGACATTACT-CCTCATGTTGAGGAGAGCTAGTTTCCTTTTGATAA
1 CTTTTGAAGACGACGTTGCTCCCTCATGTTGAGGAGATCTAGTTTCCTTTTGATAA
* *
1884303 CTTTTGAAGACGATGTTGCTCCCTCATGTTGAGAAGATCTAGTTT-C-TTTG----
1 CTTTTGAAGACGACGTTGCTCCCTCATGTTGAGGAGATCTAGTTTCCTTTTGATAA
* * * * * * *
1884353 CTTTTAAAGTCGACATTGCT-TCTCCATGTAGAGGAGACCTA-TTTGCCTTTAGATAA
1 CTTTTGAAGACGACGTTGCTCCCT-CATGTTGAGGAGATCTAGTTT-CCTTTTGATAA
** *
1884409 CTTTTGAAGACGACGTTGCTCTTTCATGTTAAGGAGATCTAGTT
1 CTTTTGAAGACGACGTTGCTCCCTCATGTTGAGGAGATCTAGTT
1884453 GTCTTCGAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 20
0.74 0.14 0.13
Matches are distributed among these distances:
49 5 0.04
50 30 0.26
51 1 0.01
52 3 0.03
54 4 0.03
55 17 0.15
56 53 0.45
57 4 0.03
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.38
Consensus pattern (56 bp):
CTTTTGAAGACGACGTTGCTCCCTCATGTTGAGGAGATCTAGTTTCCTTTTGATAA
Found at i:1884428 original size:106 final size:106
Alignment explanation
Indices: 1884244--1884457 Score: 281
Period size: 106 Copynumber: 2.0 Consensus size: 106
1884234 CTTTGGATGA
* * * *
1884244 TTTGCTTTTGAAGATGACATTACTCCTCATGTTGAGGAGAGCTAGTTTCCTTTTGATAACTTTTG
1 TTTGCTTTTAAAGATGACATTACTCCTCATGTAGAGGAGACCTAGTTTCCTTTAGATAACTTTTG
* *
1884309 AAGACGATGTTGCTCCCTCATGTTGAGAAGATCTAGTT-TC
66 AAGACGACGTTGCTCCCTCATGTTAAGAAGATCTAGTTGTC
* *
1884349 TTTGCTTTTAAAG-TCGACATTGCTTCTCCATGTAGAGGAGACCTA-TTTGCCTTTAGATAACTT
1 TTTGCTTTTAAAGAT-GACATTACTCCT-CATGTAGAGGAGACCTAGTTT-CCTTTAGATAACTT
** *
1884412 TTGAAGACGACGTTGCTCTTTCATGTTAAGGAGATCTAGTTGTC
63 TTGAAGACGACGTTGCTCCCTCATGTTAAGAAGATCTAGTTGTC
1884456 TT
1 TT
1884458 CGAATGATTT
Statistics
Matches: 94, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
104 1 0.01
105 25 0.27
106 64 0.68
107 4 0.04
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (106 bp):
TTTGCTTTTAAAGATGACATTACTCCTCATGTAGAGGAGACCTAGTTTCCTTTAGATAACTTTTG
AAGACGACGTTGCTCCCTCATGTTAAGAAGATCTAGTTGTC
Found at i:1904195 original size:14 final size:14
Alignment explanation
Indices: 1904176--1904214 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1904166 TCTTTCCTAG
1904176 GCAAAACTTATCCA
1 GCAAAACTTATCCA
1904190 GCAAAACTTATCCA
1 GCAAAACTTATCCA
* *
1904204 CCACAACTTAT
1 GCAAAACTTAT
1904215 ATGTAACTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.31, G:0.05, T:0.23
Consensus pattern (14 bp):
GCAAAACTTATCCA
Found at i:1912117 original size:42 final size:42
Alignment explanation
Indices: 1912065--1912163 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 42
1912055 CTCCCACAAG
1912065 GCTATCAGAGTGTTAGTCAATATTGGAGTATCTGATCTCCAA
1 GCTATCAGAGTGTTAGTCAATATTGGAGTATCTGATCTCCAA
* * *
1912107 GCTATCAGAGTGTTAATCAATATTGGAGTATCTGGTTTCCAA
1 GCTATCAGAGTGTTAGTCAATATTGGAGTATCTGATCTCCAA
1912149 GCTATC--AGTGTTAGT
1 GCTATCAGAGTGTTAGT
1912164 ATGAAGTGGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 8 0.15
42 45 0.85
ACGTcount: A:0.27, C:0.15, G:0.22, T:0.35
Consensus pattern (42 bp):
GCTATCAGAGTGTTAGTCAATATTGGAGTATCTGATCTCCAA
Found at i:1924393 original size:3 final size:3
Alignment explanation
Indices: 1924385--1924424 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1924375 TTTTTCAACC
* *
1924385 ATT ATT ATT ATT ATT ATT ATT ATT ATAA AAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
1924425 TATTTATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 31 0.97
4 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1924435 original size:28 final size:25
Alignment explanation
Indices: 1924390--1924443 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 25
1924380 CAACCATTAT
*
1924390 TATTATTATTATTATTATTATAAAA
1 TATTATTATTATTATTATTACAAAA
1924415 TATTATTATTTATTTATTTATTACAAAA
1 TATTATTA-TTA-TTA-TTATTACAAAA
1924443 T
1 T
1924444 CCAAAACCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 3 0.12
27 3 0.12
28 11 0.44
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTATTATTATTATTATTACAAAA
Found at i:1944482 original size:14 final size:14
Alignment explanation
Indices: 1944443--1944510 Score: 66
Period size: 14 Copynumber: 4.8 Consensus size: 14
1944433 AAAAAATAAA
* *
1944443 AAAAATAAAATGATG
1 AAAAATAAAA-AAAG
* *
1944458 AAAAA-ATAAAATG
1 AAAAATAAAAAAAG
1944471 AAAAATAAAAAAAG
1 AAAAATAAAAAAAG
1944485 AAAAATTAAAAAAAG
1 AAAAA-TAAAAAAAG
*
1944500 AAAATTAAAAA
1 AAAAATAAAAA
1944511 GGGAAGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
13 8 0.17
14 20 0.43
15 18 0.39
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAATAAAAAAAG
Found at i:1944489 original size:15 final size:15
Alignment explanation
Indices: 1944442--1944503 Score: 58
Period size: 15 Copynumber: 4.3 Consensus size: 15
1944432 AAAAAAATAA
* *
1944442 AAAAAATAAAATGATG
1 AAAAAATAAAA-AAAG
*
1944458 AAAAAAT--AAAATG
1 AAAAAATAAAAAAAG
1944471 -AAAAATAAAAAAAG
1 AAAAAATAAAAAAAG
*
1944485 AAAAATTAAAAAAAG
1 AAAAAATAAAAAAAG
1944500 AAAA
1 AAAA
1944504 TTAAAAAGGG
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
12 6 0.15
13 3 0.08
14 7 0.17
15 17 0.43
16 7 0.17
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAAAG
Found at i:1944510 original size:15 final size:15
Alignment explanation
Indices: 1944465--1944510 Score: 69
Period size: 14 Copynumber: 3.2 Consensus size: 15
1944455 ATGAAAAAAT
*
1944465 AAAATGAAAAA-TAA
1 AAAAAGAAAAATTAA
1944479 AAAAAGAAAAATTAA
1 AAAAAGAAAAATTAA
1944494 AAAAAG-AAAATTAA
1 AAAAAGAAAAATTAA
1944508 AAA
1 AAA
1944511 GGGAAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 21 0.70
15 9 0.30
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AAAAAGAAAAATTAA
Found at i:1945165 original size:13 final size:13
Alignment explanation
Indices: 1945126--1945156 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1945116 TCTTTTATTT
1945126 TTTATAATTTTTA
1 TTTATAATTTTTA
1945139 TTTATAATTTTTA
1 TTTATAATTTTTA
1945152 TTTAT
1 TTTAT
1945157 CTATTTTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTATAATTTTTA
Found at i:1945751 original size:11 final size:11
Alignment explanation
Indices: 1945735--1945767 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1945725 AAAATCATAG
1945735 AAAAGAAAGAA
1 AAAAGAAAGAA
1945746 AAAAGAAAGAA
1 AAAAGAAAGAA
*
1945757 AGAA-AAAGAA
1 AAAAGAAAGAA
1945767 A
1 A
1945768 CAAAACAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAGAAAGAA
Found at i:1945756 original size:15 final size:15
Alignment explanation
Indices: 1945736--1945791 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
1945726 AAATCATAGA
1945736 AAAGAAAGAAAAAAG
1 AAAGAAAGAAAAAAG
1945751 AAAGAAAG-AAAAAG
1 AAAGAAAGAAAAAAG
* *
1945765 AAACAAAACAAAAAAG
1 AAA-GAAAGAAAAAAG
**
1945781 AGGGAAAGAAA
1 AAAGAAAGAAA
1945792 GAGATTTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
14 9 0.27
15 17 0.52
16 7 0.21
ACGTcount: A:0.77, C:0.04, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAAAAAG
Found at i:1947305 original size:28 final size:28
Alignment explanation
Indices: 1947271--1947332 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
1947261 ACTATTTTGG
1947271 TTTATTTATATC-TTTAGCCCTTATA-TT
1 TTTATTTA-ATCATTTAGCCCTTATACTT
*
1947298 TATTATTTAATCATTTTAGCCTTTATACTT
1 T-TTATTTAATCA-TTTAGCCCTTATACTT
1947328 TTTAT
1 TTTAT
1947333 AAATGTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
27 4 0.13
28 7 0.23
29 16 0.53
30 3 0.10
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTATTTAATCATTTAGCCCTTATACTT
Found at i:1947616 original size:11 final size:11
Alignment explanation
Indices: 1947582--1947635 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
1947572 CACCTATTTA
*
1947582 CAAACCAGACC
1 CAAACCATACC
*
1947593 CTAAACCAAACC
1 C-AAACCATACC
*
1947605 CGAACCATACCC
1 CAAACCATA-CC
1947617 CAAACCATACC
1 CAAACCATACC
1947628 TCAAACCA
1 -CAAACCA
1947636 AACCTAAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 9 0.25
12 27 0.75
ACGTcount: A:0.44, C:0.44, G:0.04, T:0.07
Consensus pattern (11 bp):
CAAACCATACC
Found at i:1948074 original size:39 final size:41
Alignment explanation
Indices: 1947989--1948089 Score: 102
Period size: 39 Copynumber: 2.5 Consensus size: 41
1947979 TTGTTTCTGA
* *
1947989 TTTTTACAATTTCGAATAACAACAAAACAAAGAAGGAAAAAAC
1 TTTTT-CAGTTTCGAAAAACAACAAAACAAAGAA-GAAAAAAC
*
1948032 TTTTT-AGTTTTCGAAAAACAAC-AAA-AAAGAA-AAAAACCC
1 TTTTTCAG-TTTCGAAAAACAACAAAACAAAGAAGAAAAA-AC
*
1948071 TTTTTCAGTTTGGAAAAAC
1 TTTTTCAGTTTCGAAAAAC
1948090 CAAACAACCA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
38 5 0.10
39 16 0.31
40 8 0.16
41 4 0.08
42 13 0.25
43 5 0.10
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (41 bp):
TTTTTCAGTTTCGAAAAACAACAAAACAAAGAAGAAAAAAC
Found at i:1950952 original size:153 final size:153
Alignment explanation
Indices: 1950651--1950929 Score: 382
Period size: 153 Copynumber: 1.8 Consensus size: 153
1950641 ATCATCATTT
* * * *
1950651 ATGTGTTTGAAATAATAATGAATTTTAGAAGGAAATAATAATATTTATCTATTTCGATTGGAGTA
1 ATGTGTTGGAAATAATAATGAACTTTAGAAGGAAATAATAATATTTATCTATTTCAATTGGAATA
*
1950716 AGAAATGATTGCTCTAAAGCATGAGAGGTATTTTCTTCTCAATAGGAAATAATTAAATATTGTCG
66 AGAAATGATTGCTCTAAAGCATGAGAGGTATATTCTTCTCAATAGGAAATAATTAAATATTGTCG
1950781 TTTTTCGAACTAAAATTCAAGGA
131 TTTTTCGAACTAAAATTCAAGGA
* * * * *
1950804 ATGTGTTGGAATTAATAATGAACTTTAGAATGGAATTCA-AATATTTCTTTATTTCAATTGGAAT
1 ATGTGTTGGAAATAATAATGAACTTTAGAA-GGAAATAATAATATTTATCTATTTCAATTGGAAT
* * * * **
1950868 AGGAATTGATTGCTTTAAGGCATGAGAGG-ATGATTCTTCTCGTTAGGAAATAATTAAATATT
65 AAGAAATGATTGCTCTAAAGCATGAGAGGTAT-ATTCTTCTCAATAGGAAATAATTAAATATT
1950930 TTTGTGTTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
152 2 0.02
153 100 0.93
154 6 0.06
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.38
Consensus pattern (153 bp):
ATGTGTTGGAAATAATAATGAACTTTAGAAGGAAATAATAATATTTATCTATTTCAATTGGAATA
AGAAATGATTGCTCTAAAGCATGAGAGGTATATTCTTCTCAATAGGAAATAATTAAATATTGTCG
TTTTTCGAACTAAAATTCAAGGA
Found at i:1954017 original size:94 final size:96
Alignment explanation
Indices: 1953856--1954053 Score: 310
Period size: 94 Copynumber: 2.1 Consensus size: 96
1953846 ATCACTAACC
* * * * *
1953856 ATGGTAACTTGAAATATATTCTCTGGTTACTTGTTTTCACTGTAAAATATGATCGTTCCTGATTT
1 ATGGTTACTTGAAATATATTCTCTGGTTACCTATTTTCACAGTAAAATATGATCATTCCTGATTT
1953921 ATGGATCATGGAA-CTACT-GTTTATGAACT
66 ATGGATCATGGAATCTACTAGTTTATGAACT
* *
1953950 ATGGTTACTTGAAATATGTTCTCTGGTTACCTATTTTCACAGTAAAATTTGATCATTCCTGATTT
1 ATGGTTACTTGAAATATATTCTCTGGTTACCTATTTTCACAGTAAAATATGATCATTCCTGATTT
*
1954015 ATGGATCATTGAATCTACTAGTTTATGAACT
66 ATGGATCATGGAATCTACTAGTTTATGAACT
1954046 ATGGTTAC
1 ATGGTTAC
1954054 CTTAAATGTG
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
94 70 0.74
95 5 0.05
96 19 0.20
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (96 bp):
ATGGTTACTTGAAATATATTCTCTGGTTACCTATTTTCACAGTAAAATATGATCATTCCTGATTT
ATGGATCATGGAATCTACTAGTTTATGAACT
Found at i:1954109 original size:96 final size:94
Alignment explanation
Indices: 1953856--1954120 Score: 300
Period size: 94 Copynumber: 2.8 Consensus size: 94
1953846 ATCACTAACC
* * * * * *
1953856 ATGGTAACTTGAAATATATTCTCTGGTTACTTGTTTTCACTGTAAAATATGATCGTTCCTGATTT
1 ATGGTTACTTGAAATATGTTATATGGTTACATGTTTTCAATGTAAAATATGATCGTTCCTGATTT
1953921 ATGGATCATGGAACTACTGTTTATGAACT
66 ATGGATCATGGAACTACTGTTTATGAACT
* * * * * *
1953950 ATGGTTACTTGAAATATGTTCTCTGGTTACCTATTTTCACA-GTAAAATTTGATCATTCCTGATT
1 ATGGTTACTTGAAATATGTTATATGGTTACATGTTTTCA-ATGTAAAATATGATCGTTCCTGATT
*
1954014 TATGGATCATTGAATCTACTAGTTTATGAACT
65 TATGGATCATGGAA-CTACT-GTTTATGAACT
* * * * **
1954046 ATGGTTACCTT-AAATGTGTTATATGGTTTCATGTTTTCAATGGAAAATATGATTGTTATTGATT
1 ATGGTTA-CTTGAAATATGTTATATGGTTACATGTTTTCAATGTAAAATATGATCGTTCCTGATT
*
1954110 TATGGACCATG
65 TATGGATCATG
1954121 AAATATATTG
Statistics
Matches: 144, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
94 69 0.48
95 6 0.04
96 66 0.46
97 3 0.02
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (94 bp):
ATGGTTACTTGAAATATGTTATATGGTTACATGTTTTCAATGTAAAATATGATCGTTCCTGATTT
ATGGATCATGGAACTACTGTTTATGAACT
Found at i:1958873 original size:96 final size:96
Alignment explanation
Indices: 1958766--1959052 Score: 403
Period size: 96 Copynumber: 3.0 Consensus size: 96
1958756 TTGATTTACC
* *
1958766 GTTTATAAACTATGGTTATTTGAAATATGTTCTCTGGTTACATGTTTTCACTATAAAATATGATC
1 GTTTATAAACTATGGTTACTTGAAATATGTTCTCTGGTTACATGTTTTCACTGTAAAATATGATC
* *
1958831 TTTAATGATTTATGGATCATGGAATCTACTA
66 GTTAATGATTTATGGATCATGAAATCTACTA
* *
1958862 GTTTATGAACTATGGTTACTTGAAATATGTTCTCTGGTTACCTGTTTTCACTGTAAAATATGATC
1 GTTTATAAACTATGGTTACTTGAAATATGTTCTCTGGTTACATGTTTTCACTGTAAAATATGATC
**
1958927 GTTCTTGATTTATGGATCATGAAATCTACTA
66 GTTAATGATTTATGGATCATGAAATCTACTA
* * * * * *
1958958 GTTTATAAACTATGGTTACTTGAAATGTGTTATCTAGTTTCATGTTTTCATTGGAAAATATGATC
1 GTTTATAAACTATGGTTACTTGAAATATGTTCTCTGGTTACATGTTTTCACTGTAAAATATGATC
** * * *
1959023 GTTCCTGATTTCTGGACCTTGAAATCTACT
66 GTTAATGATTTATGGATCATGAAATCTACT
1959053 GGTTACTACT
Statistics
Matches: 171, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 171 1.00
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (96 bp):
GTTTATAAACTATGGTTACTTGAAATATGTTCTCTGGTTACATGTTTTCACTGTAAAATATGATC
GTTAATGATTTATGGATCATGAAATCTACTA
Found at i:1962558 original size:115 final size:116
Alignment explanation
Indices: 1962356--1962593 Score: 365
Period size: 115 Copynumber: 2.1 Consensus size: 116
1962346 GATAAACCAG
*
1962356 TCAACATTTCCAATGGAAGGGTTCATAATAAGAGAACTCATCCGATGAGGGAGAAAAATTTCATA
1 TCAACATTTCCAATGGAAGGGTTCATAATAAGAGAACTCATCCGATGAGGGAGAAAAAGTTCATA
*
1962421 ATGAGAAGAACTTGTTCAACCTTAGCTTGATTCCATCAC-AAGGAGGTGGA
66 ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACAAAGGAGGTGGA
* *
1962471 TCAACATTTCCAGTGG-AGGGTTCATAATGAGA-ATTACTCATCCGATGAGGGAGAAAAAGTTCA
1 TCAACATTTCCAATGGAAGGGTTCATAATAAGAGA--ACTCATCCGATGAGGGAGAAAAAGTTCA
* *
1962534 TAATGAGAAGAACTTGTTCAACCTTAGCTCGTTTCCATCACATAAGGAGTTGGA
64 TAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACA-AAGGAGGTGGA
*
1962588 ACAACA
1 TCAACA
1962594 CCAATACTTG
Statistics
Matches: 112, Mismatches: 7, Indels: 6
0.90 0.06 0.05
Matches are distributed among these distances:
113 1 0.01
114 15 0.13
115 81 0.72
117 15 0.13
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (116 bp):
TCAACATTTCCAATGGAAGGGTTCATAATAAGAGAACTCATCCGATGAGGGAGAAAAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTAGCTCGATTCCATCACAAAGGAGGTGGA
Found at i:1963153 original size:3 final size:3
Alignment explanation
Indices: 1963145--1963222 Score: 84
Period size: 3 Copynumber: 24.7 Consensus size: 3
1963135 ATTTTCAACC
* *
1963145 ATT ATT ATT ACT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
1963193 ATAA AAT ATT ATT ATTT ATTT ATTT ATT AT
1 AT-T ATT ATT ATT A-TT A-TT A-TT ATT AT
1963223 AAAACCCAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
3 53 0.82
4 12 0.18
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1963219 original size:28 final size:25
Alignment explanation
Indices: 1963147--1963226 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 25
1963137 TTTCAACCAT
* *
1963147 TATTATTACTATTATTATTATTAATAT
1 TATTATTATTATTATTATTA-TAA-AA
1963174 TATTATTATTATTATTATTATAAAA
1 TATTATTATTATTATTATTATAAAA
1963199 TATTATTATTTATTTATTTATTATAAAA
1 TATTATTA-TTA-TTA-TTATTATAAAA
1963227 CCCAAAACCC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
25 9 0.19
26 6 0.12
27 22 0.46
28 11 0.23
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (25 bp):
TATTATTATTATTATTATTATAAAA
Found at i:1963251 original size:18 final size:18
Alignment explanation
Indices: 1963228--1963279 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
1963218 ATTATAAAAC
*
1963228 CCAAAACCCAGACCTAAA
1 CCAAAACCCAGACCCAAA
**
1963246 CCAAAACCTGGACCCAAA
1 CCAAAACCCAGACCCAAA
* *
1963264 TCAAAACCCAAACCCA
1 CCAAAACCCAGACCCA
1963280 GGCCCAAACC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.48, C:0.40, G:0.06, T:0.06
Consensus pattern (18 bp):
CCAAAACCCAGACCCAAA
Found at i:1963270 original size:24 final size:23
Alignment explanation
Indices: 1963234--1963294 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 23
1963224 AAACCCAAAA
* * *
1963234 CCCAGACCTAAACCAAAACCTGG
1 CCCAAACCAAAACCAAAACCAGG
* *
1963257 ACCCAAATCAAAACCCAAACCCAGG
1 -CCCAAACCAAAA-CCAAAACCAGG
1963282 CCCAAACCAAAAC
1 CCCAAACCAAAAC
1963295 ACTAACATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.03
24 20 0.67
25 9 0.30
ACGTcount: A:0.46, C:0.41, G:0.08, T:0.05
Consensus pattern (23 bp):
CCCAAACCAAAACCAAAACCAGG
Found at i:1966191 original size:2 final size:2
Alignment explanation
Indices: 1966184--1966226 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1966174 GTTAGGATTA
1966184 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
1966226 A
1 A
1966227 GTGAGATTAG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1966692 original size:23 final size:23
Alignment explanation
Indices: 1966662--1966754 Score: 141
Period size: 23 Copynumber: 4.0 Consensus size: 23
1966652 AGTCAATCTG
1966662 TATGGCACATTTTCCTCTGCCTT
1 TATGGCACATTTTCCTCTGCCTT
* *
1966685 TATGGCACGTTTTCCTCTGTCTT
1 TATGGCACATTTTCCTCTGCCTT
1966708 TATGGCACATTTTCCTCTGCCTT
1 TATGGCACATTTTCCTCTGCCTT
* * *
1966731 TATGGCACGTTTTCTTCTACCTT
1 TATGGCACATTTTCCTCTGCCTT
1966754 T
1 T
1966755 TGACATGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.12, C:0.28, G:0.14, T:0.46
Consensus pattern (23 bp):
TATGGCACATTTTCCTCTGCCTT
Found at i:1972087 original size:42 final size:42
Alignment explanation
Indices: 1971999--1972088 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 42
1971989 TTAAACCAGG
* **
1971999 TGAGATGCTCATTGGATGACTCCCCTTCACGAGAAAGTCATG
1 TGAGATGCTCATTGAATGACTCCCCTTCACGAGAAAGTCAAA
* * * ** *
1972041 TGAGATGTTCTTTGAATGACTCCTCTTCGTGATAAAGTCAAA
1 TGAGATGCTCATTGAATGACTCCCCTTCACGAGAAAGTCAAA
1972083 TGAGAT
1 TGAGAT
1972089 ATTTTTTCAT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (42 bp):
TGAGATGCTCATTGAATGACTCCCCTTCACGAGAAAGTCAAA
Found at i:1972484 original size:18 final size:18
Alignment explanation
Indices: 1972461--1972505 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1972451 TTTGTCTGTT
1972461 GATCTATTCCCTGGAGTC
1 GATCTATTCCCTGGAGTC
*
1972479 GATCTATTTCCTGGAGTC
1 GATCTATTCCCTGGAGTC
1972497 GATCT-TTCC
1 GATCTATTCC
1972506 ACAGCGCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.38
Consensus pattern (18 bp):
GATCTATTCCCTGGAGTC
Done.