Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008103.1 Hibiscus syriacus cultivar Beakdansim tig00110633_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: 1996589
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 11
Found at i:1889935 original size:37 final size:37
Alignment explanation
Indices: 1889873--1890228 Score: 269
Period size: 37 Copynumber: 9.5 Consensus size: 37
1889863 TCTTGCTCTA
*
1889873 AAGGCTTATAGA-TGAATTTGCTTCACTACTCTTTGGTG
1 AAGGCTTA-AGATTG-ATTTGCTTCACTACTCTCTGGTG
* * *
1889911 AAGGCTTAAGATTGATTTGTTTCACTATTCTCAGGTG
1 AAGGCTTAAGATTGATTTGCTTCACTACTCTCTGGTG
* * * *
1889948 AAGGCTTAAGATGGATTTGCTTCATTATTCTCAGGTG
1 AAGGCTTAAGATTGATTTGCTTCACTACTCTCTGGTG
* * * *
1889985 AAGGCTTAAGATGGATTTACTTCACTATTCTCAGGTG
1 AAGGCTTAAGATTGATTTGCTTCACTACTCTCTGGTG
* * *
1890022 AAGGCTTAAGA-TGAAATTGATTCACTCCT-TCTGGTG
1 AAGGCTTAAGATTG-ATTTGCTTCACTACTCTCTGGTG
* ** * * * *
1890058 GAGGCTTAAGATTGCCATGAGGACTT-AATCATTATGCTCG-G
1 AAGGCTTAAGATTG--AT-TTG-CTTCACT-ACTCT-CTGGTG
** *
1890099 AAGGCTTGCTGATGGATTTGCTTCACTACTCT-TCGGTG
1 AAGGCTT-AAGATTGATTTGCTTCACTACTCTCT-GGTG
* * **
1890137 AAGGCTTAAGA-CGGTTTGCTTCACTACTCTCCAGTG
1 AAGGCTTAAGATTGATTTGCTTCACTACTCTCTGGTG
* *
1890173 AAGGCTTCAGATTG-TTTGCTTCACTACTCTCTAGTG
1 AAGGCTTAAGATTGATTTGCTTCACTACTCTCTGGTG
*
1890209 AAGGCTTAAGATTGAATTGC
1 AAGGCTTAAGATTGATTTGC
1890229 CCCAATCTCA
Statistics
Matches: 255, Mismatches: 47, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
36 82 0.32
37 122 0.48
38 25 0.10
39 6 0.02
40 5 0.02
41 8 0.03
42 7 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (37 bp):
AAGGCTTAAGATTGATTTGCTTCACTACTCTCTGGTG
Found at i:1890162 original size:36 final size:36
Alignment explanation
Indices: 1890115--1890219 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
1890105 TGCTGATGGA
*
1890115 TTTGCTTCACTACTCTTCGGTGAAGGCTTAAGACGG
1 TTTGCTTCACTACTCTTCAGTGAAGGCTTAAGACGG
* * **
1890151 TTTGCTTCACTACTCTCCAGTGAAGGCTTCAGATTG
1 TTTGCTTCACTACTCTTCAGTGAAGGCTTAAGACGG
1890187 TTTGCTTCACTACTC-TCTAGTGAAGGCTTAAGA
1 TTTGCTTCACTACTCTTC-AGTGAAGGCTTAAGA
1890220 TTGAATTGCC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 1 0.02
36 60 0.98
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (36 bp):
TTTGCTTCACTACTCTTCAGTGAAGGCTTAAGACGG
Found at i:1890398 original size:18 final size:18
Alignment explanation
Indices: 1890375--1890410 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1890365 CAGGGTATGC
1890375 CTCTTTAAATGCAACTCT
1 CTCTTTAAATGCAACTCT
*
1890393 CTCTTTAAATGTAACTCT
1 CTCTTTAAATGCAACTCT
1890411 TTGCATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (18 bp):
CTCTTTAAATGCAACTCT
Found at i:1898659 original size:20 final size:20
Alignment explanation
Indices: 1898594--1898823 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
1898584 CGATTTTCCA
** *
1898594 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1898614 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
1898634 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1898654 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1898674 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1898694 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
1898714 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1898734 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1898754 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
*
1898774 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1898794 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1898814 AAATCACAAC
1 AAATCGCAAC
1898824 ACTGAAATTT
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:1899533 original size:23 final size:23
Alignment explanation
Indices: 1899504--1899548 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1899494 AATTTGGTCT
1899504 TGGTCAATATC-CGGACTTTGATA
1 TGGTCAATA-CACGGACTTTGATA
*
1899527 TGGTCAATACACGGATTTTGAT
1 TGGTCAATACACGGACTTTGAT
1899549 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (23 bp):
TGGTCAATACACGGACTTTGATA
Found at i:1902105 original size:19 final size:19
Alignment explanation
Indices: 1902065--1902215 Score: 196
Period size: 19 Copynumber: 8.4 Consensus size: 19
1902055 GATTCTCTCG
1902065 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1902085 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1902104 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1902118 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1902138 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1902157 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1902171 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1902190 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1902209 TTGCGAT
1 TTGCGAT
1902216 AGTCAATTTT
Statistics
Matches: 116, Mismatches: 4, Indels: 23
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.10
16 14 0.12
17 12 0.10
18 2 0.02
19 46 0.40
20 30 0.26
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1902113 original size:53 final size:53
Alignment explanation
Indices: 1902046--1902215 Score: 333
Period size: 53 Copynumber: 3.2 Consensus size: 53
1902036 CGAATGAAAA
1902046 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1902099 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1902152 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1902204 TCGCATTGCGAT
1 TCGCATTGCGAT
1902216 AGTCAATTTT
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 30 0.26
53 87 0.74
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1902180 original size:33 final size:34
Alignment explanation
Indices: 1902046--1902197 Score: 145
Period size: 33 Copynumber: 4.4 Consensus size: 34
1902036 CGAATGAAAA
1902046 TCGCATTGCGATTCTCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
* *
1902079 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 T-CGCATTGCGA--TTC-TCTCG-ATTGCGATT-T-TCATT
* *
1902120 GCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATT
1 TCGCA-TTGCGATTCTCTCG-ATTGCGATTTTCATT
1902152 TCGCATTGCGATTCTCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
1902185 TCGCATTGCGATT
1 TCGCATTGCGATT
1902198 TTCATTTCGC
Statistics
Matches: 98, Mismatches: 8, Indels: 26
0.74 0.06 0.20
Matches are distributed among these distances:
32 9 0.09
33 33 0.34
34 24 0.24
35 3 0.03
36 3 0.03
37 6 0.06
39 10 0.10
40 6 0.06
41 4 0.04
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
Found at i:1902326 original size:33 final size:33
Alignment explanation
Indices: 1902274--1902431 Score: 164
Period size: 33 Copynumber: 4.7 Consensus size: 33
1902264 CCATTACATT
1902274 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
*
1902308 TCGCAATGCGAAATGAAAATCGCAATGCGAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAA--CG-A-GAGAA
* * * *
1902345 TCGCAA--CGATATCG-CAATGCGAAATGA-A-AA
1 TCGCAATGCGAAAT-GAAAAT-CGCAACGAGAGAA
1902375 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
*
1902408 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
1902432 TTGCGATTCT
Statistics
Matches: 103, Mismatches: 10, Indels: 23
0.76 0.07 0.17
Matches are distributed among these distances:
30 8 0.08
31 8 0.08
32 9 0.09
33 42 0.41
34 10 0.10
35 10 0.10
36 6 0.06
37 10 0.10
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:1902330 original size:19 final size:19
Alignment explanation
Indices: 1902274--1902437 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1902264 CCATTACATT
1902274 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
1902294 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
1902308 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
1902327 TCGCAATGCG-AATGAAAA
1 TCGCAATGCGAAATGAAAA
1902345 TCGCAA--CG--AT----A
1 TCGCAATGCGAAATGAAAA
1902356 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
1902375 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
1902394 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
1902408 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
1902427 TCGCATTGCGA
1 TCGCAATGCGA
1902438 TTCTCCCATT
Statistics
Matches: 120, Mismatches: 6, Indels: 37
0.74 0.04 0.23
Matches are distributed among these distances:
11 7 0.06
13 2 0.02
14 20 0.17
15 6 0.05
16 6 0.05
17 3 0.03
18 17 0.14
19 53 0.44
20 6 0.05
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.16
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:1902485 original size:18 final size:18
Alignment explanation
Indices: 1902444--1902541 Score: 132
Period size: 18 Copynumber: 5.5 Consensus size: 18
1902434 GCGATTCTCC
1902444 CATTGCGATTTTCATTTCCG
1 CATTGCGA-TTTCATTT-CG
1902464 CATTGCGATTTCATTTCG
1 CATTGCGATTTCATTTCG
*
1902482 CATTGCGA-TTC-TCTCG
1 CATTGCGATTTCATTTCG
1902498 --TTGCGATTTTCATTTCG
1 CATTGCGA-TTTCATTTCG
1902515 CATTGCGATTTCATTTCG
1 CATTGCGATTTCATTTCG
1902533 CATTGCGAT
1 CATTGCGAT
1902542 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
18 29 0.41
19 14 0.20
20 8 0.11
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.44
Consensus pattern (18 bp):
CATTGCGATTTCATTTCG
Found at i:1902538 original size:51 final size:52
Alignment explanation
Indices: 1902427--1902541 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
1902417 GAAATTAAAA
1902427 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTCATT
* *
1902479 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTCATT
1902530 TCGCATTGCGAT
1 TCGCATTGCGAT
1902542 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
51 29 0.48
52 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTCATT
Found at i:1902667 original size:14 final size:14
Alignment explanation
Indices: 1902648--1902684 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1902638 CATCAATTAC
1902648 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1902662 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1902676 ACAAATCAA
1 ACAAATCAA
1902685 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1902767 original size:12 final size:12
Alignment explanation
Indices: 1902750--1902785 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1902740 AACTTTTACA
1902750 AATCAATTAAAC
1 AATCAATTAAAC
**
1902762 AATCAAAAAAAC
1 AATCAATTAAAC
1902774 AATCAATTAAAC
1 AATCAATTAAAC
1902786 TATTGAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:1904616 original size:20 final size:20
Alignment explanation
Indices: 1904591--1904657 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
1904581 TAGTTTACTT
* *
1904591 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
1904611 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
1904630 TCGCAAACGCGAAA-TGAAAA
1 TCGC-AACGCGAAACTCAAAA
1904650 TCGCAACG
1 TCGCAACG
1904658 ACAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.46, C:0.27, G:0.16, T:0.10
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:1904667 original size:14 final size:14
Alignment explanation
Indices: 1904648--1904704 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1904638 GCGAAATGAA
*
1904648 AATCGCAACGACAG
1 AATCGCAACGAAAG
1904662 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1904679 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1904695 AATCGCAACG
1 AATCGCAACG
1904705 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1904678 original size:33 final size:33
Alignment explanation
Indices: 1904628--1904721 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
1904618 GCGAAACCAA
*
1904628 AATCGCAAACGCGAAATGAAAATCGCAACGACAG
1 AATCGC-AACGCGAAATGAAAATCGCAACGAAAG
*
1904662 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1904695 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1904722 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 51 0.89
34 6 0.11
ACGTcount: A:0.48, C:0.21, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1904686 original size:19 final size:19
Alignment explanation
Indices: 1904591--1904726 Score: 121
Period size: 19 Copynumber: 7.6 Consensus size: 19
1904581 TAGTTTACTT
* *
1904591 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1904611 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1904630 TCGCAAACGCGAAATGAAAA
1 TCGC-AACGCGAAATGAAAA
*
1904650 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1904664 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1904683 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1904697 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1904716 TCGCAATGCGA
1 TCGCAACGCGA
1904727 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 30 0.31
20 29 0.30
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1904808 original size:20 final size:19
Alignment explanation
Indices: 1904722--1904816 Score: 112
Period size: 19 Copynumber: 5.3 Consensus size: 19
1904712 AAAATCGCAA
1904722 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1904741 TGCGA-TCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1904754 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1904773 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1904792 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1904812 TGCGA
1 TGCGA
1904817 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
13 8 0.12
14 2 0.03
15 2 0.03
17 2 0.03
18 2 0.03
19 36 0.55
20 13 0.20
ACGTcount: A:0.08, C:0.16, G:0.31, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1905150 original size:92 final size:93
Alignment explanation
Indices: 1904860--1905327 Score: 808
Period size: 92 Copynumber: 5.1 Consensus size: 93
1904850 TTGAATGGAT
* *
1904860 AAATTTACTTTCAACCAAAAGA-TAAACAAAGACAAATACTATTTCAAAGGGTGTTAAAGAATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACA--GTGTTAAAGAATAC
*
1904924 ACAGTTTAGCAGAATTGGCAGCAACGGAAC
64 ACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
1904954 AAATTTACTTTCAACCAAAAGACAAAACAAAGAC-AA-A-TATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1905016 AG-TTAGCAGAATTGGCAGCAACCG-AC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1905042 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1905107 AGTTTAGCAGAATTGGCAGCAACCG-AC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1905134 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1905199 AGTTTAGCAGAATTGGCAGCAA-CGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1905226 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1905291 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1905319 AAATTTACT
1 AAATTTACT
1905328 AAGCAATCTA
Statistics
Matches: 361, Mismatches: 6, Indels: 15
0.95 0.02 0.04
Matches are distributed among these distances:
88 36 0.10
89 23 0.06
90 18 0.05
91 29 0.08
92 207 0.57
93 14 0.04
94 24 0.07
95 10 0.03
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1909561 original size:20 final size:21
Alignment explanation
Indices: 1909528--1909566 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1909518 ATAAAACATA
1909528 AATAATATTAATATTATTAAC
1 AATAATATTAATATTATTAAC
1909549 AATAATA-TAATATTATTA
1 AATAATATTAATATTATTA
1909567 TAATAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAATATTAATATTATTAAC
Found at i:1909886 original size:20 final size:20
Alignment explanation
Indices: 1909863--1909902 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1909853 GGCTGAGACC
1909863 TCTTTTTTCTAAAAAAAAAA
1 TCTTTTTTCTAAAAAAAAAA
1909883 TCTTTTTTCTAAAAAAAAAA
1 TCTTTTTTCTAAAAAAAAAA
1909903 AGGTTGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (20 bp):
TCTTTTTTCTAAAAAAAAAA
Found at i:1920339 original size:3 final size:3
Alignment explanation
Indices: 1920331--1920357 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1920321 TTATAAACTC
1920331 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1920358 TTTCAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1921955 original size:35 final size:35
Alignment explanation
Indices: 1921909--1922035 Score: 98
Period size: 35 Copynumber: 3.6 Consensus size: 35
1921899 CCTTAGATTC
1921909 ATAAGGAATTACCAGTTGATAGGTACTGAACCTAT
1 ATAAGGAATTACCAGTTGATAGGTACTGAACCTAT
*** * * *
1921944 ATAAGGAATTACCAACCGATCGATGA-TGAACCTGT
1 ATAAGGAATTACCAGTTGATAGGT-ACTGAACCTAT
** * *
1921979 ATAAGGAATTATTATCTTGATCA-G-AGCTAAACCTAT
1 ATAAGGAATTACCA-GTTGAT-AGGTA-CTGAACCTAT
1922015 ATAAGGAATTACCAGCTTGAT
1 ATAAGGAATTACCAG-TTGAT
1922036 CAGAGCTGAA
Statistics
Matches: 68, Mismatches: 18, Indels: 11
0.70 0.19 0.11
Matches are distributed among these distances:
34 1 0.01
35 39 0.57
36 28 0.41
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (35 bp):
ATAAGGAATTACCAGTTGATAGGTACTGAACCTAT
Found at i:1922019 original size:36 final size:36
Alignment explanation
Indices: 1921909--1922049 Score: 130
Period size: 36 Copynumber: 4.0 Consensus size: 36
1921899 CCTTAGATTC
*
1921909 ATAAGGAATTACCAG-TTGAT-AG-GTACTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCAGAG--CTAAACCTAT
* * * * *
1921944 ATAAGGAATTACCAAC-CGATC-GATGATGAACCTGT
1 ATAAGGAATTACCAGCTTGATCAGA-GCTAAACCTAT
** *
1921979 ATAAGGAATTATTATCTTGATCAGAGCTAAACCTAT
1 ATAAGGAATTACCAGCTTGATCAGAGCTAAACCTAT
*
1922015 ATAAGGAATTACCAGCTTGATCAGAGCTGAACCTA
1 ATAAGGAATTACCAGCTTGATCAGAGCTAAACCTA
1922050 CAGAGACTTC
Statistics
Matches: 85, Mismatches: 15, Indels: 11
0.77 0.14 0.10
Matches are distributed among these distances:
35 39 0.46
36 43 0.51
37 3 0.04
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCAGAGCTAAACCTAT
Found at i:1923850 original size:21 final size:21
Alignment explanation
Indices: 1923776--1923844 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
1923766 ACCAAAGATC
1923776 AGTATCGATACTAATTGAATT
1 AGTATCGATACTAATTGAATT
1923797 AGTATCGATACTAATTGAATT
1 AGTATCGATACTAATTGAATT
*
1923818 AGTATCGATACTAATTAAATT
1 AGTATCGATACTAATTGAATT
1923839 AGTATC
1 AGTATC
1923845 AGTACTGATG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTAATTGAATT
Found at i:1924581 original size:15 final size:16
Alignment explanation
Indices: 1924563--1924614 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
1924553 ATGATGCGAA
1924563 GAAAAATGTTCTA-GT
1 GAAAAATGTTCTACGT
1924578 GAAAAATGTGATCTACGT
1 GAAAAATGT--TCTACGT
*
1924596 G-AAACTGTTCTACGT
1 GAAAAATGTTCTACGT
1924611 GAAA
1 GAAA
1924615 GTAAACTACG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 17 0.53
16 2 0.06
17 10 0.31
18 3 0.09
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (16 bp):
GAAAAATGTTCTACGT
Found at i:1924801 original size:23 final size:24
Alignment explanation
Indices: 1924775--1924830 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
1924765 ATAATCTATA
* *
1924775 TGGTCCTTTGGGAC-ATTTATACG
1 TGGTCCTTCGGGACAAATTATACG
*
1924798 TGGTCCTTCGGGACAAATTCTACG
1 TGGTCCTTCGGGACAAATTATACG
1924822 TGGTCCTTC
1 TGGTCCTTC
1924831 ATGACAAACC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 13 0.45
24 16 0.55
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (24 bp):
TGGTCCTTCGGGACAAATTATACG
Found at i:1928390 original size:32 final size:29
Alignment explanation
Indices: 1928349--1928437 Score: 97
Period size: 32 Copynumber: 2.9 Consensus size: 29
1928339 GAGTCGAGGG
*
1928349 TTACTTATGTCTTTCGGGACATATGGACAGGA
1 TTACATATGT-TTTCGGGACATATGGACA--A
* *
1928381 TTACCTATGTTCTTCGGGATATATGGACAA
1 TTACATATGTT-TTCGGGACATATGGACAA
*
1928411 TTACATATGTTTTTCGGAACATATGGA
1 TTACATATG-TTTTCGGGACATATGGA
1928438 TAGGTCTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
30 22 0.44
31 3 0.06
32 25 0.50
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (29 bp):
TTACATATGTTTTCGGGACATATGGACAA
Found at i:1928420 original size:30 final size:31
Alignment explanation
Indices: 1928361--1928437 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
1928351 ACTTATGTCT
*
1928361 TTCGGGACATATGGACAGGATTACCTATGTTC
1 TTCGGGACATATGGACA-GATTACATATGTTC
* *
1928393 TTCGGGATATATGGACA-ATTACATATGTTT
1 TTCGGGACATATGGACAGATTACATATGTTC
*
1928423 TTCGGAACATATGGA
1 TTCGGGACATATGGA
1928438 TAGGTCTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 24 0.60
32 16 0.40
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (31 bp):
TTCGGGACATATGGACAGATTACATATGTTC
Found at i:1931276 original size:17 final size:17
Alignment explanation
Indices: 1931251--1931291 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1931241 CTTGTCATTA
* *
1931251 GAAGGATTAATAAGATT
1 GAAGCATTAAGAAGATT
1931268 GAAGCATTAAGAAGATT
1 GAAGCATTAAGAAGATT
1931285 GAAGCAT
1 GAAGCAT
1931292 AGGAAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.24, T:0.24
Consensus pattern (17 bp):
GAAGCATTAAGAAGATT
Found at i:1932743 original size:32 final size:30
Alignment explanation
Indices: 1932696--1932784 Score: 97
Period size: 32 Copynumber: 2.9 Consensus size: 30
1932686 GAGTGTAGGG
* *
1932696 TTACCTATATTCTTCGGGACATATGGACATGA
1 TTACCTATGTCCTTCGGGACATATGGACA--A
* *
1932728 TTACCTTTGTCCTTCGGGACATATGAACAA
1 TTACCTATGTCCTTCGGGACATATGGACAA
* * *
1932758 TTACCTATGTTCTTCGGAATATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
1932785 TAGGTCCTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
30 23 0.48
32 25 0.52
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (30 bp):
TTACCTATGTCCTTCGGGACATATGGACAA
Found at i:1932782 original size:30 final size:31
Alignment explanation
Indices: 1932696--1932774 Score: 106
Period size: 32 Copynumber: 2.5 Consensus size: 31
1932686 GAGTGTAGGG
* *
1932696 TTACCTATATTCTTCGGGACATATGGACATGA
1 TTACCTATGTTCTTCGGGACATATGAACA-GA
* *
1932728 TTACCTTTGTCCTTCGGGACATATGAACA-A
1 TTACCTATGTTCTTCGGGACATATGAACAGA
1932758 TTACCTATGTTCTTCGG
1 TTACCTATGTTCTTCGG
1932775 AATATATGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
30 16 0.39
32 25 0.61
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGAACAGA
Found at i:1933125 original size:4 final size:4
Alignment explanation
Indices: 1933116--1933333 Score: 418
Period size: 4 Copynumber: 54.5 Consensus size: 4
1933106 AAATGATGAC
1933116 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1933164 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
1933212 ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
1933260 ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1933308 ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT AT
1933334 TTGTTACATG
Statistics
Matches: 210, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 210 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:1937770 original size:31 final size:31
Alignment explanation
Indices: 1937732--1937826 Score: 145
Period size: 31 Copynumber: 3.1 Consensus size: 31
1937722 GTAGGCAGAG
* * *
1937732 TATCGATAGTAGTTAGTATGAAATGTTACAT
1 TATCGATACTAGCTAGTCTGAAATGTTACAT
1937763 TATCGATACTAGCTAGTCTGAAATGTTACAT
1 TATCGATACTAGCTAGTCTGAAATGTTACAT
* *
1937794 TATCGATACTAACTAGTCTGAAATGTTAAAT
1 TATCGATACTAGCTAGTCTGAAATGTTACAT
1937825 TA
1 TA
1937827 AGTGTTTTAT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.37
Consensus pattern (31 bp):
TATCGATACTAGCTAGTCTGAAATGTTACAT
Found at i:1938655 original size:23 final size:24
Alignment explanation
Indices: 1938625--1938672 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
1938615 GGGACAAACC
1938625 TATGTGGCACTTCGGTGC-AATTA
1 TATGTGGCACTTCGGTGCAAATTA
1938648 TATGTGGCACTTCGGTGCAAATTA
1 TATGTGGCACTTCGGTGCAAATTA
1938672 T
1 T
1938673 GTGAGCTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (24 bp):
TATGTGGCACTTCGGTGCAAATTA
Found at i:1939774 original size:2 final size:2
Alignment explanation
Indices: 1939769--1939807 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1939759 CACAAGTAAC
1939769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1939808 CAACCATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1940810 original size:3 final size:3
Alignment explanation
Indices: 1940802--1940856 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
1940792 ACCCAAACCA
* *
1940802 TAT TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1940850 TAT TAT T
1 TAT TAT T
1940857 TGCCCCAGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1945932 original size:18 final size:17
Alignment explanation
Indices: 1945878--1945926 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1945868 TTGGACCCTT
* *
1945878 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1945896 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1945914 AGTGCATTCGATG
1 AGTGCA-TCGATG
1945927 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1946031 original size:65 final size:65
Alignment explanation
Indices: 1945898--1946057 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
1945888 TGCACTAAGA
* * * *
1945898 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATTGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
* ** * *
1945962 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAACATTCTCAGTGCATCGGTGCATGGTA-
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCAT-G-AC
1946026 T-
64 TG
*
1946027 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
1946058 CAATTTAATT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 28 0.34
65 52 0.63
66 2 0.02
67 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAACAGCCACAGTGCATCGATGCATGACTG
Found at i:1949062 original size:55 final size:55
Alignment explanation
Indices: 1948969--1949109 Score: 176
Period size: 55 Copynumber: 2.6 Consensus size: 55
1948959 GGAGCCAGGA
*** *
1948969 GTGTATCGATACATCGTCT-GTGTATCGGTACACTAATTACATTCGATGTAGGGG
1 GTGTATCGATACATCCAATAGTGTATCGGTACACAAATTACATTCGATGTAGGGG
* * *
1949023 GTGTATCGATACATCCAATAGTGTATTGGTACCCAAATTACATTCGATGTTGGGG
1 GTGTATCGATACATCCAATAGTGTATCGGTACACAAATTACATTCGATGTAGGGG
* * * *
1949078 GTGTATCCATACATTCAAGAGTGTATCAGTAC
1 GTGTATCGATACATCCAATAGTGTATCGGTAC
1949110 CACCCTTTGT
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
54 16 0.22
55 58 0.78
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (55 bp):
GTGTATCGATACATCCAATAGTGTATCGGTACACAAATTACATTCGATGTAGGGG
Found at i:1949701 original size:51 final size:51
Alignment explanation
Indices: 1949593--1949825 Score: 117
Period size: 49 Copynumber: 4.9 Consensus size: 51
1949583 ATTTTTATTT
* *
1949593 TATTAATT-TTTATTGGAAGTGTACTTCAAAATGTATAATTTAATAATTTA
1 TATTAATTATTTATTGGAAGTGTAATTCAAAATGTATAATTTAATAATTGA
* * * * * *
1949643 -ATGAATTATTTATTTGATTGTGTAATTGAAAATTTATAATTTAAT-GTTGA
1 TATTAATTATTTATTGGA-AGTGTAATTCAAAATGTATAATTTAATAATTGA
** * * * * *
1949693 TATTAATTAAATAAT-AAAATGT-A--C-AAA--T-T-ATTT-ATATTTTA
1 TATTAATTATTTATTGGAAGTGTAATTCAAAATGTATAATTTAATAATTGA
* * *
1949734 -ATTAATT-TTTATT-GAATTGTGTAGTTCAAAATTTATAATTTAATAATTTA
1 TATTAATTATTTATTGGAA--GTGTAATTCAAAATGTATAATTTAATAATTGA
* *
1949784 -ATT-ATT-TTTATTGGATTGTGTAATTGAAAATGTATAATTTAA
1 TATTAATTATTTATTGGA-AGTGTAATTCAAAATGTATAATTTAA
1949826 AGTTGTACAT
Statistics
Matches: 137, Mismatches: 29, Indels: 35
0.68 0.14 0.17
Matches are distributed among these distances:
39 5 0.04
40 9 0.07
41 10 0.07
42 1 0.01
43 1 0.01
44 1 0.01
45 6 0.04
47 1 0.01
48 2 0.01
49 44 0.32
50 24 0.18
51 33 0.24
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (51 bp):
TATTAATTATTTATTGGAAGTGTAATTCAAAATGTATAATTTAATAATTGA
Found at i:1949710 original size:139 final size:138
Alignment explanation
Indices: 1949560--1949830 Score: 420
Period size: 139 Copynumber: 1.9 Consensus size: 138
1949550 TAATTTACAT
*
1949560 TTAAATAATAAAATGTACAAATCATTTTTATTTT-ATTAATTTTTATTGGAA-GTGTACTTCAAA
1 TTAAATAATAAAATGTACAAATCATTTATATTTTAATTAATTTTTATT-GAATGTGTACTTCAAA
* * *
1949623 ATGTATAATTTAATAATTTAATGAATTATTTATTTGATTGTGTAATTGAAAATTTATAATTTAAT
65 ATGTATAATTTAATAATTTAAT-AATT-TTTATTGGATTGTGTAATTGAAAATGTATAATTTAAA
1949688 GTTGATATTAA
128 GTTGATATTAA
* *
1949699 TTAAATAATAAAATGTACAAATTATTTATATTTTAATTAATTTTTATTGAATTGTGTAGTTCAAA
1 TTAAATAATAAAATGTACAAATCATTTATATTTTAATTAATTTTTATTGAA-TGTGTACTTCAAA
* *
1949764 ATTTATAATTTAATAATTTAATTATTTTTATTGGATTGTGTAATTGAAAATGTATAATTTAAAGT
65 ATGTATAATTTAATAATTTAATAATTTTTATTGGATTGTGTAATTGAAAATGTATAATTTAAAGT
1949829 TG
130 TG
1949831 TACATTTTAT
Statistics
Matches: 121, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
139 73 0.60
140 16 0.13
141 32 0.26
ACGTcount: A:0.39, C:0.02, G:0.10, T:0.49
Consensus pattern (138 bp):
TTAAATAATAAAATGTACAAATCATTTATATTTTAATTAATTTTTATTGAATGTGTACTTCAAAA
TGTATAATTTAATAATTTAATAATTTTTATTGGATTGTGTAATTGAAAATGTATAATTTAAAGTT
GATATTAA
Found at i:1949791 original size:49 final size:50
Alignment explanation
Indices: 1949722--1949825 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 50
1949712 TGTACAAATT
* * *
1949722 ATTT-ATATTTTAATTAATTTTTATTGAATTGTGTAGTTCAAAATTTATA
1 ATTTAATAATTTAATTAATTTTTATTGAATTGTGTAATTCAAAATGTATA
* *
1949771 ATTTAATAATTTAATT-ATTTTTATTGGATTGTGTAATTGAAAATGTATA
1 ATTTAATAATTTAATTAATTTTTATTGAATTGTGTAATTCAAAATGTATA
1949820 ATTTAA
1 ATTTAA
1949826 AGTTGTACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 39 0.80
50 10 0.20
ACGTcount: A:0.37, C:0.01, G:0.10, T:0.53
Consensus pattern (50 bp):
ATTTAATAATTTAATTAATTTTTATTGAATTGTGTAATTCAAAATGTATA
Found at i:1955716 original size:31 final size:30
Alignment explanation
Indices: 1955681--1955760 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
1955671 ATTTAAGCAT
* *
1955681 TATTTTATAATAATTTGATA-AGTTTAATGA
1 TATTTTATAATAATTTGAGACA-CTTAATGA
* *
1955711 CTATTTTGTAACT-ATTTAAGACACTTAATGA
1 -TATTTTATAA-TAATTTGAGACACTTAATGA
1955742 TAGTTTTATAATAATTTGA
1 TA-TTTTATAATAATTTGA
1955761 AGTAATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
30 3 0.08
31 34 0.87
32 2 0.05
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (30 bp):
TATTTTATAATAATTTGAGACACTTAATGA
Found at i:1958649 original size:2 final size:2
Alignment explanation
Indices: 1958642--1958675 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1958632 ATGGTATGTG
1958642 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
1958676 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1959187 original size:21 final size:21
Alignment explanation
Indices: 1959152--1959227 Score: 86
Period size: 21 Copynumber: 3.8 Consensus size: 21
1959142 CAGGATATAA
* *
1959152 TGGTCATTCGGGACAATACAG
1 TGGTCCTTCGAGACAATACAG
*
1959173 TGCTCCTTCGAGACAATACAG
1 TGGTCCTTCGAGACAATACAG
* *
1959194 TGGTCATACGAGAC-AT--AG
1 TGGTCCTTCGAGACAATACAG
1959212 TGGTCCTTCGAGACAA
1 TGGTCCTTCGAGACAA
1959228 ATTTCAGTGC
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 14 0.30
19 1 0.02
20 2 0.04
21 29 0.63
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (21 bp):
TGGTCCTTCGAGACAATACAG
Found at i:1959215 original size:18 final size:18
Alignment explanation
Indices: 1959192--1959226 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1959182 GAGACAATAC
1959192 AGTGGTCATACGAGACAT
1 AGTGGTCATACGAGACAT
* *
1959210 AGTGGTCCTTCGAGACA
1 AGTGGTCATACGAGACA
1959227 AATTTCAGTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (18 bp):
AGTGGTCATACGAGACAT
Found at i:1972742 original size:12 final size:12
Alignment explanation
Indices: 1972701--1972733 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1972691 ACATATCATT
1972701 TCATTATTCTTA
1 TCATTATTCTTA
*
1972713 TTATTATTCTTA
1 TCATTATTCTTA
1972725 TCATTATTC
1 TCATTATTC
1972734 ATATGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.00, T:0.61
Consensus pattern (12 bp):
TCATTATTCTTA
Found at i:1974719 original size:15 final size:15
Alignment explanation
Indices: 1974699--1974728 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1974689 ATACCTCCCT
1974699 TATGGTATCGCTACC
1 TATGGTATCGCTACC
*
1974714 TATGGTATCGGTACC
1 TATGGTATCGCTACC
1974729 ACCTTCCCAG
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:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (15 bp):
TATGGTATCGCTACC
Found at i:1982617 original size:2 final size:2
Alignment explanation
Indices: 1982610--1982650 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1982600 GGTGGACGTG
1982610 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1982651 CGGGTCGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1983807 original size:229 final size:227
Alignment explanation
Indices: 1983400--1983848 Score: 765
Period size: 229 Copynumber: 2.0 Consensus size: 227
1983390 GTAAATTATC
* * * *
1983400 TATCCTTTTTATAAAAGTGTTCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
1983465 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
*
1983530 TGTATAAATGAAATTATTAAATTAATATTGTAGGTGGAAAATATGAAACACTATTAAAAAAATTG
131 TGTATAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
1983595 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
1983628 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1983693 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* * *
1983757 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTATAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
1983822 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
1983849 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
228 41 0.20
229 167 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTATAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1983937 original size:20 final size:19
Alignment explanation
Indices: 1983914--1983959 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
1983904 CGATATACCA
1983914 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1983934 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1983954 GGTAAA
1 GGTAAA
1983960 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1984109 original size:20 final size:20
Alignment explanation
Indices: 1984084--1984125 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1984074 TATAACAGGT
1984084 AAAAATGATAAAACCGGTAA
1 AAAAATGATAAAACCGGTAA
1984104 AAAAATGATAAAACCGGTAA
1 AAAAATGATAAAACCGGTAA
1984124 AA
1 AA
1984126 TGATACCGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAATGATAAAACCGGTAA
Found at i:1984127 original size:17 final size:18
Alignment explanation
Indices: 1984081--1984130 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 18
1984071 CGATATAACA
1984081 GGTAAAAATGATAAAACC
1 GGTAAAAATGATAAAACC
1984099 GGTAAAAAAATGATAAAACC
1 GGT--AAAAATGATAAAACC
1984119 GGT-AAAATGATA
1 GGTAAAAATGATA
1984131 CCGGATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.30
18 3 0.10
20 18 0.60
ACGTcount: A:0.56, C:0.08, G:0.18, T:0.18
Consensus pattern (18 bp):
GGTAAAAATGATAAAACC
Found at i:1986401 original size:21 final size:21
Alignment explanation
Indices: 1986354--1986418 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
1986344 AAGACAATCA
* *
1986354 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
1986376 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
1986396 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
1986417 AG
1 AG
1986419 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:1986513 original size:32 final size:33
Alignment explanation
Indices: 1986452--1986516 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1986442 AAATAGATGG
*
1986452 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
1986485 AGTGGTGAAAGAAGTTG-GGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1986517 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.47
33 16 0.53
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1988341 original size:18 final size:19
Alignment explanation
Indices: 1988297--1988344 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1988287 AATGTCGAGT
1988297 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1988316 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1988335 T-ATTTTGTAT
1 TAATTTTGTAT
1988345 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1989695 original size:196 final size:198
Alignment explanation
Indices: 1988463--1989823 Score: 2585
Period size: 197 Copynumber: 6.9 Consensus size: 198
1988453 CAATATGGCC
* *
1988463 AACAGGGTGCACCCATAAAGTGTCGATCCATATA-AAAAAGTGTCAATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1988527 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1988592 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
1988657 GGAA
196 GG-A
1988661 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1988726 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1988791 AATATGTCTAAATAATGTGTCGACACTAATATAGTTAGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
1988856 GGAA
196 GG-A
1988860 AACAAGGTGCACCCATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1988923 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1988988 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
1989053 GGA
196 GGA
1989056 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1989121 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAA-CGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1989185 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
1989250 GGA
196 GGA
*
1989253 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGACCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1989318 CAAAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
*
1989382 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCATAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
1989447 GGA
196 GGA
1989450 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1989515 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1989580 AATATGTCTAAATAATGTGTCGACACT-A-ATAGTTTGTGTCGATAC-TTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
1989642 GGAA
196 GG-A
*
1989646 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTTTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1989711 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
1989776 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACT
1989824 AATTTAAATA
Statistics
Matches: 1145, Mismatches: 9, Indels: 17
0.98 0.01 0.01
Matches are distributed among these distances:
195 18 0.02
196 216 0.19
197 532 0.46
198 188 0.16
199 191 0.17
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGA
Found at i:1991295 original size:3 final size:3
Alignment explanation
Indices: 1991287--1991361 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
1991277 TGAAGCTGAC
* * * ** * *
1991287 GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
1991335 GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1991362 CCAAACAAGT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1992904 original size:180 final size:181
Alignment explanation
Indices: 1992551--1993052 Score: 813
Period size: 180 Copynumber: 2.8 Consensus size: 181
1992541 CAAAGTTTTC
* * * *
1992551 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* * *
1992616 AAAAAAGTGTCG--ATTGAAAAAACA-TCGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATTGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
1992678 TATAACCGGTATAAATATACCGGTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAA-ATACCGGTTTATGAGCGAATAGGTCTACAACCTATATCG
1992733 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACC-TTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1992797 AAAAAAGTGTCGACATTTACACATTGGAACCCAGATTTATAATGT-ATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATTGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
1992861 AACCGGTATAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAATACCGG-TTTATGAGCGAATAGGTCTACAACCTATATCG
*
1992913 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAA--TGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
1992976 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATTGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
1993041 AACC-GTATAAAA
131 AACCGGTATAAAA
1993053 ATGTGTCGAT
Statistics
Matches: 304, Mismatches: 10, Indels: 15
0.92 0.03 0.05
Matches are distributed among these distances:
178 10 0.03
179 62 0.20
180 137 0.45
181 35 0.12
182 57 0.19
183 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (181 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATTGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAATACCGGTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1993086 original size:22 final size:23
Alignment explanation
Indices: 1993050--1993092 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1993040 TAACCGTATA
1993050 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
* *
1993073 AAAA-GTGTCTATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
1993093 CACTGTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:1996238 original size:23 final size:23
Alignment explanation
Indices: 1996196--1996240 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1996186 TAGCCCTTAT
*
1996196 ATGTAATAGGTATCGTTTATATA
1 ATGTAATAGGTATCGGTTATATA
1996219 ATGTAATAGGTAGT-GGTTATAT
1 ATGTAATAGGTA-TCGGTTATAT
1996241 TGTAAAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.42
Consensus pattern (23 bp):
ATGTAATAGGTATCGGTTATATA
Done.