Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 23
Found at i:4498853 original size:33 final size:33
Alignment explanation
Indices: 4498803--4498898 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
4498793 AAAACAGACT
* ** *
4498803 ATCGCAACGCAGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
4498837 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4498870 ATCGCAATGCGAAAATGAAAATTGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
4498899 CGAAACTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 31 0.55
34 25 0.45
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4498938 original size:20 final size:19
Alignment explanation
Indices: 4498909--4498975 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
4498899 CGAAACTAAA
*
4498909 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
4498929 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
4498945 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
4498962 TTCGCATTGCGATT
1 TTCGCATTGCGATT
4498976 ATCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 4 0.10
18 3 0.08
19 8 0.21
20 11 0.28
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:4498956 original size:34 final size:34
Alignment explanation
Indices: 4498913--4499008 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
4498903 ACTAAATTCG
*
4498913 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
4498947 CGTTGCGATTTTCA-TTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
** * *
4498980 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
4499009 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCT
Found at i:4499005 original size:20 final size:20
Alignment explanation
Indices: 4498980--4499068 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
4498970 GCGATTATCT
4498980 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
4499000 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
4499020 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
4499040 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
4499060 CGTTGCGAT
1 CGTTGCGAT
4499069 TTCCGCGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:4500561 original size:64 final size:65
Alignment explanation
Indices: 4500448--4500594 Score: 192
Period size: 64 Copynumber: 2.3 Consensus size: 65
4500438 CATTCATAAG
* * *
4500448 TGCATCGATGCATTCC-TTTAAAAGAAAGAACATCGAATGCCTTTGATGCATCGATGCA-TAGCT
1 TGCATCGATGCA-TCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-T
4500511 AA
64 AA
* * *
4500513 TGCATCGATGCATCCTTTTAAAATAAA-AACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
4500577 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
4500595 CATTGAAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
64 45 0.62
65 28 0.38
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:4501344 original size:31 final size:31
Alignment explanation
Indices: 4501250--4501357 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
4501240 AGTCGAGGGT
* *
4501250 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
4501281 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
4501312 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
4501343 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
4501358 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:4501364 original size:30 final size:30
Alignment explanation
Indices: 4501272--4501378 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
4501262 TTTCGAGACA
* * * *
4501272 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
4501303 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
4501334 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
4501364 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
4501379 GGGTCTGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:4502623 original size:20 final size:20
Alignment explanation
Indices: 4502598--4502671 Score: 130
Period size: 20 Copynumber: 3.7 Consensus size: 20
4502588 AAATTCAGTA
*
4502598 TTGCGATAGTCAGAATCACG
1 TTGCGATAGTCAGAATCTCG
*
4502618 TTGCGATAGTCAAAATCTCG
1 TTGCGATAGTCAGAATCTCG
4502638 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
4502658 TTGCGATAGTCAGA
1 TTGCGATAGTCAGA
4502672 TTCGCATTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:4502681 original size:20 final size:20
Alignment explanation
Indices: 4502597--4502684 Score: 104
Period size: 20 Copynumber: 4.4 Consensus size: 20
4502587 GAAATTCAGT
*
4502597 ATTGCGATAGTCAGAATCAC
1 ATTGCGATAGTCAGAATCGC
* * *
4502617 GTTGCGATAGTCAAAATCTC
1 ATTGCGATAGTCAGAATCGC
* *
4502637 GTTGCGATAGTCAGAATCTC
1 ATTGCGATAGTCAGAATCGC
* *
4502657 GTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCGC
4502677 ATTGCGAT
1 ATTGCGAT
4502685 TTACATATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 61 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (20 bp):
ATTGCGATAGTCAGAATCGC
Found at i:4502682 original size:40 final size:40
Alignment explanation
Indices: 4502597--4502684 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
4502587 GAAATTCAGT
*
4502597 ATTGCGATAGTCAGAATCACGTTGCGATAGTCAAAATCTC
1 ATTGCGATAGTCAGAATCACGTTGCGATAGTCAAAATCGC
* * * *
4502637 GTTGCGATAGTCAGAATCTCGTTGCGATAGTCAGATTCGC
1 ATTGCGATAGTCAGAATCACGTTGCGATAGTCAAAATCGC
4502677 ATTGCGAT
1 ATTGCGAT
4502685 TTACATATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (40 bp):
ATTGCGATAGTCAGAATCACGTTGCGATAGTCAAAATCGC
Found at i:4502694 original size:20 final size:20
Alignment explanation
Indices: 4502671--4502763 Score: 150
Period size: 20 Copynumber: 4.7 Consensus size: 20
4502661 CGATAGTCAG
*
4502671 ATTCGCATTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
4502691 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4502711 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
4502731 ATTCGTATTGCAATTTACGT
1 ATTCGCATTGCGATTTACGT
*
4502751 ATTCACATTGCGA
1 ATTCGCATTGCGA
4502764 ATTAGGAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:4502784 original size:21 final size:21
Alignment explanation
Indices: 4502760--4502805 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
4502750 TATTCACATT
4502760 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
4502781 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
4502802 GCGA
1 GCGA
4502806 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:4508985 original size:25 final size:28
Alignment explanation
Indices: 4508930--4508985 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 28
4508920 TTTTTATTAA
*
4508930 ATTTTTAATAAAATACATAGATGAGTGT
1 ATTTTTAATAAAATACATAGATGAATGT
* *
4508958 ATTTTTAA-ATAATATATA-ATGAAT-T
1 ATTTTTAATAAAATACATAGATGAATGT
4508983 ATT
1 ATT
4508986 AAATCGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.16
26 5 0.20
27 8 0.32
28 8 0.32
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (28 bp):
ATTTTTAATAAAATACATAGATGAATGT
Found at i:4511315 original size:54 final size:54
Alignment explanation
Indices: 4511251--4511467 Score: 256
Period size: 54 Copynumber: 4.0 Consensus size: 54
4511241 AGAAGCTCTT
*
4511251 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCGCTTGTTCCTTCTTCAAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
* * ** *
4511305 AGAGCTGAAACAATGGCTGCTGCTGGTGTTATTCCACTTGTTACTTCTTCGAAA-
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTC-AAAG
* ** * * * * **
4511359 AGAGCTGAAACAATGGTAGTTTCCAGTGTTGTTCCGCTTGTTCCTTCTTTGAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
* * *
4511413 AGGGCCGAAACAATGGTCGCTCCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
1 AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
4511467 A
1 A
4511468 ACAAATTACA
Statistics
Matches: 135, Mismatches: 26, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
53 2 0.01
54 130 0.96
55 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.32
Consensus pattern (54 bp):
AGAGCCGAAACAATGGCCGCTGCCAGTGTTATTCCACTTGTTCCTTCTTCAAAG
Found at i:4518490 original size:21 final size:21
Alignment explanation
Indices: 4518464--4518505 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4518454 TGTCAGCATA
4518464 ATGACTCAATCATTTATTTTT
1 ATGACTCAATCATTTATTTTT
4518485 ATGACTCAATCATTTATTTTT
1 ATGACTCAATCATTTATTTTT
4518506 CTGCCAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.05, T:0.52
Consensus pattern (21 bp):
ATGACTCAATCATTTATTTTT
Found at i:4520554 original size:16 final size:18
Alignment explanation
Indices: 4520522--4520561 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
4520512 AAATATAATA
4520522 TAAAAACTACTCAAATTC
1 TAAAAACTACTCAAATTC
*
4520540 -AAAAACTA-TCGAATTC
1 TAAAAACTACTCAAATTC
4520556 TAAAAA
1 TAAAAA
4520562 ATTTTAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (18 bp):
TAAAAACTACTCAAATTC
Found at i:4520594 original size:22 final size:22
Alignment explanation
Indices: 4520569--4520645 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
4520559 AAAATTTTAA
4520569 AAGCTCAATTGAAACTCGATCC
1 AAGCTCAATTGAAACTCGATCC
4520591 AAGCTCAATTGAAACTCGATCC
1 AAGCTCAATTGAAACTCGATCC
* * *
4520613 AAACTCAATTTTAAACTCAATCC
1 AAGCTCAA-TTGAAACTCGATCC
4520636 AAGCTCAATT
1 AAGCTCAATT
4520646 TTAAATTCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 31 0.62
23 19 0.38
ACGTcount: A:0.39, C:0.26, G:0.09, T:0.26
Consensus pattern (22 bp):
AAGCTCAATTGAAACTCGATCC
Found at i:4523084 original size:54 final size:54
Alignment explanation
Indices: 4522996--4523100 Score: 142
Period size: 54 Copynumber: 1.9 Consensus size: 54
4522986 GCACTTATTT
*
4522996 TAAATTTGTCCTTATACTTTTGAATATTTCAATTTAATCCTCAAACTATGATTC
1 TAAATTAGTCCTTATACTTTTGAATATTTCAATTTAATCCTCAAACTATGATTC
* * *
4523050 TAAATTAGTCCTTA-AGCTTTTGAATA-TTCTAATTTTATCCTTAATCTATGA
1 TAAATTAGTCCTTATA-CTTTTGAATATTTC-AATTTAATCCTCAAACTATGA
4523101 CCCTCTTTCT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.31, C:0.15, G:0.07, T:0.47
Consensus pattern (54 bp):
TAAATTAGTCCTTATACTTTTGAATATTTCAATTTAATCCTCAAACTATGATTC
Found at i:4526396 original size:36 final size:35
Alignment explanation
Indices: 4526337--4526444 Score: 162
Period size: 36 Copynumber: 3.0 Consensus size: 35
4526327 CACGAAATCT
*
4526337 CCTAAGAAGGAAAAAAGAACTGAAGATGAAGAGCTG
1 CCTAAGAAGG-AAAAGGAACTGAAGATGAAGAGCTG
*
4526373 CCTAAGAAGGAGAAAGGAGCTGAAGATGAAGAGCTG
1 CCTAAGAAGGA-AAAGGAACTGAAGATGAAGAGCTG
*
4526409 CTTAAGAAGGAAAGAGGAACTGAAGATGAAGAGCTG
1 CCTAAGAAGGAAA-AGGAACTGAAGATGAAGAGCTG
4526445 GGGTTAAGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
35 3 0.05
36 63 0.95
ACGTcount: A:0.45, C:0.10, G:0.32, T:0.12
Consensus pattern (35 bp):
CCTAAGAAGGAAAAGGAACTGAAGATGAAGAGCTG
Found at i:4530860 original size:18 final size:18
Alignment explanation
Indices: 4530837--4530871 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4530827 TTCCATCCGG
*
4530837 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
4530855 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4530872 GTCCTTTCGA
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:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:4532040 original size:19 final size:19
Alignment explanation
Indices: 4532018--4532067 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
4532008 CTAGGCGGCT
*
4532018 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
4532037 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
4532056 CGGCTCGGCTCA
1 CGGCTCGGCTCA
4532068 AACGGCTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.16, C:0.36, G:0.30, T:0.18
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:4532047 original size:14 final size:14
Alignment explanation
Indices: 4532042--4532075 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4532032 TCAAACGGCT
*
4532042 CGGCTCAGCTCAAG
1 CGGCTCAGCTCAAA
*
4532056 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
4532070 CGGCTC
1 CGGCTC
4532076 CTCAGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (14 bp):
CGGCTCAGCTCAAA
Found at i:4535840 original size:18 final size:18
Alignment explanation
Indices: 4535817--4535851 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4535807 TTCCATCCGG
*
4535817 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
4535835 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4535852 GTCCTTTCGA
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:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:4537024 original size:19 final size:19
Alignment explanation
Indices: 4537002--4537084 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
4536992 CTAGGCGGCT
*
4537002 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
4537021 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
4537040 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
4537054 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
4537073 CGGCTCGGCTCA
1 CGGCTCGGCTCA
4537085 AACGGCTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:4537031 original size:14 final size:14
Alignment explanation
Indices: 4537026--4537091 Score: 78
Period size: 14 Copynumber: 4.4 Consensus size: 14
4537016 TCAAACGGCT
*
4537026 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
4537040 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
4537054 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
4537072 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
4537087 CGGCT
1 CGGCT
4537092 TCTCAGGCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
14 30 0.65
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:4537051 original size:33 final size:33
Alignment explanation
Indices: 4537008--4537091 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
4536998 GGCTCGGCTT
*
4537008 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
4537041 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
4537074 GGCTCGGCTCAAACGGCT
1 GGCTCGGCTCAAACGGCT
4537092 TCTCAGGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:4540861 original size:17 final size:17
Alignment explanation
Indices: 4540839--4540872 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4540829 TTCCATCCGG
*
4540839 TCTTATTATTTAATTCA
1 TCTTATCATTTAATTCA
*
4540856 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
4540873 GTCCTTTCGA
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:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TCTTATCATTTAATTCA
Found at i:4542045 original size:19 final size:19
Alignment explanation
Indices: 4542023--4542105 Score: 113
Period size: 19 Copynumber: 4.6 Consensus size: 19
4542013 CTAGGCGGCT
*
4542023 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
4542042 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
4542061 CGGCTC-G----GCTCAAA
1 CGGCTCGGCTCAGCTCAAA
*
4542075 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
4542094 CGGCTCGGCTCA
1 CGGCTCGGCTCA
4542106 AACGGCTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.23
15 1 0.02
18 1 0.02
19 42 0.74
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:4542052 original size:14 final size:14
Alignment explanation
Indices: 4542047--4542112 Score: 78
Period size: 14 Copynumber: 4.4 Consensus size: 14
4542037 TCAAACGGCT
*
4542047 CGGCTCAGCTCAAA
1 CGGCTCGGCTCAAA
4542061 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
4542075 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
4542093 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
4542108 CGGCT
1 CGGCT
4542113 TCTCAGGCTT
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
14 30 0.65
15 2 0.04
18 2 0.04
19 12 0.26
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:4542072 original size:33 final size:33
Alignment explanation
Indices: 4542029--4542112 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
4542019 GGCTCGGCTT
*
4542029 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
*
4542062 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
4542095 GGCTCGGCTCAAACGGCT
1 GGCTCGGCTCAAACGGCT
4542113 TCTCAGGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.20, C:0.36, G:0.29, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:4546372 original size:21 final size:21
Alignment explanation
Indices: 4546348--4546388 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4546338 GAAGAAATAT
*
4546348 TAGGAGATAAGCCTCAAAAGA
1 TAGGAGAGAAGCCTCAAAAGA
*
4546369 TAGGAGAGAAGCCTCCAAAG
1 TAGGAGAGAAGCCTCAAAAG
4546389 GTTTATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.17, G:0.27, T:0.12
Consensus pattern (21 bp):
TAGGAGAGAAGCCTCAAAAGA
Found at i:4554465 original size:15 final size:15
Alignment explanation
Indices: 4554447--4554477 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4554437 AAATTCTAAA
4554447 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
4554462 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
4554477 T
1 T
4554478 CTATCCGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:4571798 original size:8 final size:7
Alignment explanation
Indices: 4571783--4571875 Score: 82
Period size: 7 Copynumber: 12.4 Consensus size: 7
4571773 ATTATGCTTG
4571783 AAGAAAA
1 AAGAAAA
4571790 AATGAAAA
1 AA-GAAAA
4571798 AAGAAAA
1 AAGAAAA
4571805 GAA-AAAGA
1 -AAGAAA-A
*
4571813 AAGAGAA
1 AAGAAAA
4571820 AAGAAAA
1 AAGAAAA
4571827 AAGAAAAGA
1 AAG-AAA-A
4571836 AAGAAAGA
1 AAGAAA-A
4571844 AAGAAAGAA
1 AAG-AA-AA
4571853 AAGAAAA
1 AAGAAAA
4571860 AA-AAAA
1 AAGAAAA
*
4571866 GAGAAAA
1 AAGAAAA
4571873 AAG
1 AAG
4571876 GGGGTCAAGA
Statistics
Matches: 73, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
6 5 0.07
7 32 0.44
8 25 0.34
9 10 0.14
10 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (7 bp):
AAGAAAA
Found at i:4571806 original size:5 final size:5
Alignment explanation
Indices: 4571796--4571872 Score: 67
Period size: 5 Copynumber: 15.8 Consensus size: 5
4571786 AAAAAATGAA
4571796 AAAAG AAAAG AAAAAG AAAGAG AAAAG AAAAAAG AAAAG -AAAG -AAAG
1 AAAAG AAAAG -AAAAG AAA-AG AAAAG --AAAAG AAAAG AAAAG AAAAG
*
4571843 -AAAG -AAAG AAAAG AAAA- AAAA- AAGAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
4571873 AAGGGGGTCA
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
4 23 0.36
5 26 0.41
6 10 0.16
7 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4571810 original size:12 final size:12
Alignment explanation
Indices: 4571788--4571875 Score: 83
Period size: 13 Copynumber: 7.0 Consensus size: 12
4571778 GCTTGAAGAA
4571788 AAAATGAAAAAAG
1 AAAA-GAAAAAAG
4571801 AAAAG-AAAAAG
1 AAAAGAAAAAAG
4571812 AAAGAGAAAAGAA-
1 AAA-AGAAAA-AAG
4571825 AAAAGAAAAGAA-
1 AAAAGAAAA-AAG
4571837 AGAAAGAAAGAAAG
1 A-AAAGAAA-AAAG
*
4571851 AAAAGAAAAAAA
1 AAAAGAAAAAAG
4571863 AAAGAGAAAAAAG
1 AAA-AGAAAAAAG
4571876 GGGGTCAAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
11 9 0.14
12 19 0.29
13 34 0.52
14 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:4571821 original size:17 final size:18
Alignment explanation
Indices: 4571783--4571872 Score: 100
Period size: 17 Copynumber: 5.1 Consensus size: 18
4571773 ATTATGCTTG
*
4571783 AAGAAAAAATGAAAAAAGAA
1 AAGAAAAAA-G-AAAGAGAA
4571803 AAG-AAAAAGAAAGAGAA
1 AAGAAAAAAGAAAGAGAA
4571820 AAGAAAAAAGAAA-AG-A
1 AAGAAAAAAGAAAGAGAA
4571836 AAGAAAGAAAG-AA-AGAA
1 AAGAAA-AAAGAAAGAGAA
*
4571853 AAGAAAAAAAAAAGAGAA
1 AAGAAAAAAGAAAGAGAA
4571871 AA
1 AA
4571873 AAGGGGGTCA
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
16 14 0.22
17 25 0.40
18 16 0.25
19 5 0.08
20 3 0.05
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (18 bp):
AAGAAAAAAGAAAGAGAA
Found at i:4571824 original size:37 final size:38
Alignment explanation
Indices: 4571783--4571875 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 38
4571773 ATTATGCTTG
4571783 AAGAAAAAATGAAAAAAGA-AAAG-AA-AAAGAAAGAGAA
1 AAGAAAAAA-GAAAAAAGAGAAAGAAAGAAAGAAA-AGAA
4571820 AAGAAAAAAGAAAAGAA-AGAAAGAAAGAAAGAAAAGAA
1 AAGAAAAAAGAAAA-AAGAGAAAGAAAGAAAGAAAAGAA
*
4571858 AAAAAAAAGAGAAAAAAG
1 AAGAAAAA-AGAAAAAAG
4571876 GGGGTCAAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
36 6 0.12
37 15 0.31
38 15 0.31
39 13 0.27
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (38 bp):
AAGAAAAAAGAAAAAAGAGAAAGAAAGAAAGAAAAGAA
Found at i:4571840 original size:4 final size:4
Alignment explanation
Indices: 4571783--4571867 Score: 67
Period size: 4 Copynumber: 22.0 Consensus size: 4
4571773 ATTATGCTTG
*
4571783 AAGA AA-A AATGA AA-A AAGA AA-A GAA-A AAGA AAGA GA-A AAGA AA-A
1 AAGA AAGA AA-GA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA AAGA AAGA
*
4571827 AAGAA AAGA AAGA AAGA AAGA AAGAA AAGA AA-A AAAA AAGA
1 AAG-A AAGA AAGA AAGA AAGA AAG-A AAGA AAGA AAGA AAGA
4571868 GAAAAAAGGG
Statistics
Matches: 68, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
3 17 0.25
4 40 0.59
5 11 0.16
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:4572269 original size:19 final size:17
Alignment explanation
Indices: 4572227--4572275 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
4572217 TATTTTCTCT
4572227 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
4572243 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
4572261 AAAATTCAACTTATT
1 -AAATTCAATTTATT
4572276 CTATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:4572793 original size:112 final size:114
Alignment explanation
Indices: 4572566--4572898 Score: 532
Period size: 113 Copynumber: 3.0 Consensus size: 114
4572556 TGCCACGTTA
* * *
4572566 TCATGGTAAAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
4572631 TTTGGTACAAACCCCAAAACCAATTATTAGATTT-AAAGATGAATTTGC
66 TTTGGTACAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
4572679 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTG-TCTTTGAGTTATCTGATC-GG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
4572742 TTTGGTATAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
66 TTTGGTACAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
4572791 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
** * * * *
4572856 TTCT-GTAGGAACCACAGAACCAA-CATTAGAATTGAAAGATGAA
66 TT-TGGTACAAACCCCAAAACCAATTATTAGATTTGAAAGATGAA
4572899 CTGCATGATG
Statistics
Matches: 206, Mismatches: 10, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
111 35 0.17
112 75 0.36
113 76 0.37
114 19 0.09
115 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTACAAACCCCAAAACCAATTATTAGATTTGAAAGATGAATTTGC
Found at i:4573813 original size:69 final size:70
Alignment explanation
Indices: 4573657--4573826 Score: 216
Period size: 69 Copynumber: 2.4 Consensus size: 70
4573647 TCTGAAGAAG
*
4573657 AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATC
1 AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG--T-AATTCATCACTCGATGGATC
4573722 AACAGTGC
63 AACAGTGC
* ** * * *
4573730 CAGTTAGAGTTCATAATGAGAAGAACTTGTTCAACTTTTTG-AATTCATCATTCGATGGATCATC
1 AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTAATTCATCACTCGATGGATCAAC
* *
4573794 ATTTC
66 AGTGC
*
4573799 AAGAGAAAGTTCATAATGAGAAGAACTT
1 AAGAAAAAGTTCATAATGAGAAGAACTT
4573827 ATCTAAAGAA
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
69 47 0.56
73 37 0.44
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (70 bp):
AAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTAATTCATCACTCGATGGATCAAC
AGTGC
Found at i:4573931 original size:182 final size:180
Alignment explanation
Indices: 4573595--4573936 Score: 515
Period size: 182 Copynumber: 1.9 Consensus size: 180
4573585 GATTTAAATC
* * *
4573595 CATCATTCAATGGAGCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAG
1 CATCATTCAATGGAGCAACATTTCAAGAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAG
*
4573660 AAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGGTGGATCAAC
66 AAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGATGGATCAAC
*
4573725 AGTGCCAGTTAGAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGAATT
131 AGTGCCAGGTAGAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGAATT
* * * *
4573775 CATCATTCGATGGATCATCATTTCAAGAGAAAGTTCATAATGAGAAGAACTTATCTAAAGAAGGA
1 CATCATTCAATGGAGCAACATTTCAAGA-AAAGTTCATAATGAGAAGAACTCATCTAAAGAA-GA
* * * * *
4573840 AGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTT-TTTAAATTCATCATTTGATGGATC
64 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTTGCTTAAATTCATCACTCGATGGATC
*
4573904 AACATTGCCAGGTAGAGTTCATAATGAGAAGAA
128 AACAGTGCCAGGTAGAGTTCATAATGAGAAGAA
4573937 TTCGTCATCT
Statistics
Matches: 144, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
180 24 0.17
181 30 0.21
182 84 0.58
183 6 0.04
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (180 bp):
CATCATTCAATGGAGCAACATTTCAAGAAAAGTTCATAATGAGAAGAACTCATCTAAAGAAGAAG
AAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTAAATTCATCACTCGATGGATCAAC
AGTGCCAGGTAGAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGAATT
Found at i:4573983 original size:20 final size:20
Alignment explanation
Indices: 4573919--4573983 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
4573909 TGCCAGGTAG
4573919 AGTTCATAATGAGAAGAATT
1 AGTTCATAATGAGAAGAATT
* * **
4573939 CG-TCAT-CTGAAGAAGAAGA
1 AGTTCATAATG-AGAAGAATT
*
4573958 AATTCATAATGAGAAGAATT
1 AGTTCATAATGAGAAGAATT
*
4573978 TGTTCA
1 AGTTCA
4573984 AATTTTTGTT
Statistics
Matches: 31, Mismatches: 11, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
18 2 0.06
19 11 0.35
20 16 0.52
21 2 0.06
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAATT
Found at i:4574001 original size:112 final size:109
Alignment explanation
Indices: 4573739--4574102 Score: 396
Period size: 112 Copynumber: 3.2 Consensus size: 109
4573729 CCAGTTAGAG
* * *
4573739 TTCATAATGAGAAGAACTTGTTC-AA--CTTTTTGAATTCATCATTCGATGGATCATCATTTCAA
1 TTCATAATGAGAAGAACTTGTTCAAATTTTTTTTGAATTCATCATTCGATGGATCAACATTTCCA
*
4573801 GAGAAAGTTCATAATGAGAAGAACTTATCTAAAGAAGGAAGAAGAAG
66 GAGAAAGTTCATAATGAGAAGAACTTATCT--AGAA-GAAGAAGAAA
* * * * *
4573848 TTCATAATGAGAAGAGCTTGTTCAACCTTTTTTTTAAATTCATCATTTGATGGATCAACATTGCC
1 TTCATAATGAGAAGAACTTGTTCAA-ATTTTTTTTGAATTCATCATTCGATGGATCAACATTTCC
* *
4573913 AG-GTAGAGTTCATAATGAGAAGAATTCGTCATCT-GAAGAAGAAGAAA
65 AGAG-AAAGTTCATAATGAGAAGAA--C-TTATCTAGAAGAAGAAGAAA
* *
4573960 TTCATAATGAGAAGAATTTGTTCAAATTTTTGTTTGAATTCATCATTCGATGGATCATCAACTTT
1 TTCATAATGAGAAGAACTTGTTCAAATTTTT-TTTGAATTCATCATTCGATGG---ATCAACATT
*
4574025 TCCAGAGAAAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAGAAGAA
62 TCCAGAGAAAGTTCATAATGAGAAGAACTTATCT--AGAAGAAGAAG-A-AA
**
4574077 GTTCATAATGAGAAGAGTTTGTTCAA
1 -TTCATAATGAGAAGAACTTGTTCAA
4574103 CCTTTTGCAT
Statistics
Matches: 214, Mismatches: 22, Indels: 29
0.81 0.08 0.11
Matches are distributed among these distances:
109 22 0.10
110 1 0.00
111 5 0.02
112 57 0.27
113 55 0.26
115 41 0.19
116 7 0.03
117 2 0.01
118 24 0.11
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (109 bp):
TTCATAATGAGAAGAACTTGTTCAAATTTTTTTTGAATTCATCATTCGATGGATCAACATTTCCA
GAGAAAGTTCATAATGAGAAGAACTTATCTAGAAGAAGAAGAAA
Found at i:4574213 original size:39 final size:39
Alignment explanation
Indices: 4574159--4574247 Score: 178
Period size: 39 Copynumber: 2.3 Consensus size: 39
4574149 TTTCCAGAGA
4574159 AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAG
1 AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAG
4574198 AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAG
1 AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAG
4574237 AAGTTCATAAT
1 AAGTTCATAAT
4574248 TTGTTCAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.51, C:0.08, G:0.19, T:0.22
Consensus pattern (39 bp):
AAGTTCATAATAAGAAGAACTTATCTGAAGAAGAAGAAG
Found at i:4574478 original size:3 final size:3
Alignment explanation
Indices: 4574472--4574533 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
4574462 CATTTGTTTT
4574472 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4574518 TTA TT- TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA
4574534 CAGGCCCAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:4589512 original size:21 final size:20
Alignment explanation
Indices: 4589466--4589513 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
4589456 GATTCTGACT
4589466 ATCGCATTGCGATTTCCCAA
1 ATCGCATTGCGATTTCCCAA
* *
4589486 ATTCGCGTTGCGATTTTCCTAA
1 A-TCGCATTGCGA-TTTCCCAA
4589508 ATCGCA
1 ATCGCA
4589514 ACGCGATTAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATTTCCCAA
Found at i:4589519 original size:21 final size:21
Alignment explanation
Indices: 4589495--4589541 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
4589485 AATTCGCGTT
*
4589495 GCGATTTTCCTAAATCGCAAC
1 GCGATTTACCTAAATCGCAAC
*
4589516 GCGA-TTACGTAAATCGCAAC
1 GCGATTTACCTAAATCGCAAC
*
4589536 GAGATT
1 GCGATT
4589542 CTGACTATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (21 bp):
GCGATTTACCTAAATCGCAAC
Found at i:4589582 original size:82 final size:80
Alignment explanation
Indices: 4589447--4589596 Score: 180
Period size: 82 Copynumber: 1.8 Consensus size: 80
4589437 GTTTCCAGAT
* * * **
4589447 TCGCAACGCGATTCTGACTATCGCATTGCGATTTCCCAAATTCGCGTTGCGATTTTCCTAAA-TC
1 TCGCAACGAGATTCTGACTATCGCAATACGATTT-CCAAATTCGCACTGCGA-TTT-CTAAATTC
4589511 GCAACGCGATTACGTAAA
63 GCAACGCGATTACGTAAA
4589529 TCGCAACGAGATTCTGACTATCGCAATACTGAATTT-CAAATTCGCAACT-CGATTTCTAAATTC
1 TCGCAACGAGATTCTGACTATCGCAATAC-G-ATTTCCAAATTCGC-ACTGCGATTTCTAAATTC
4589592 GCAAC
63 GCAAC
4589597 AGGTTTTAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
80 5 0.08
81 10 0.17
82 38 0.64
83 2 0.03
84 4 0.07
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (80 bp):
TCGCAACGAGATTCTGACTATCGCAATACGATTTCCAAATTCGCACTGCGATTTCTAAATTCGCA
ACGCGATTACGTAAA
Found at i:4590425 original size:24 final size:24
Alignment explanation
Indices: 4590398--4590451 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
4590388 GTATTCGAAA
4590398 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
4590422 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
4590446 TTTGAT
1 TTTGAT
4590452 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:4593031 original size:33 final size:33
Alignment explanation
Indices: 4592989--4593115 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
4592979 GGAAATAACT
*
4592989 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
*
4593022 ATCGCAATGCGAAATGAAAATCACAACAAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
*
4593055 ATCGCAATGCGAAATGAAAATCACAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
* *
4593088 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCACAACG
4593116 CGAATTTAGT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:4593168 original size:33 final size:33
Alignment explanation
Indices: 4593125--4593204 Score: 115
Period size: 33 Copynumber: 2.4 Consensus size: 33
4593115 GCGAATTTAG
* * *
4593125 TTTCGCGTTGCGATTTTGTCGTTGTGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
4593158 TTTCGTGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
*
4593191 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
4593205 AGTCATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.49
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:4593330 original size:14 final size:14
Alignment explanation
Indices: 4593311--4593347 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4593301 CAACAATTAA
4593311 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4593325 ACAAATCATCTTTT
1 ACAAATCAACTTTT
4593339 ACAAATCAA
1 ACAAATCAA
4593348 TTAAACAATA
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:4594762 original size:21 final size:21
Alignment explanation
Indices: 4594697--4594762 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
4594687 GTGAATCGAG
*
4594697 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
4594717 CTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA
4594738 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
4594759 CTCT
1 CTCT
4594763 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:4594781 original size:42 final size:41
Alignment explanation
Indices: 4594697--4594814 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 41
4594687 GTGAATCGAG
* * * *
4594697 CTCTTGAATGGTGGGA-GGGACTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGATGACAGGGGC
*
4594738 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
4594780 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGA
4594815 AAGGCGAGTC
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 19 0.30
42 43 0.67
43 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:4595261 original size:17 final size:18
Alignment explanation
Indices: 4595216--4595283 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 18
4595206 CTGGAACTTA
*
4595216 AAATCGCAACGTGAAAAATG
1 AAATCGCAACGCG--AAATG
*
4595236 ACTATCGCAACGCGAAATG
1 A-AATCGCAACGCGAAATG
4595255 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAAATG
4595272 AAAATCGCAACG
1 -AAATCGCAACG
4595284 AGAGAATTGC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
17 16 0.38
19 15 0.36
20 1 0.02
21 10 0.24
ACGTcount: A:0.44, C:0.22, G:0.21, T:0.13
Consensus pattern (18 bp):
AAATCGCAACGCGAAATG
Found at i:4595297 original size:14 final size:14
Alignment explanation
Indices: 4595274--4595309 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4595264 GCGAAATGAA
4595274 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4595288 AATTGCAACGAGAG
1 AATCGCAACGAGAG
4595302 AATCGCAA
1 AATCGCAA
4595310 TGCGAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4595364 original size:20 final size:19
Alignment explanation
Indices: 4595339--4595465 Score: 95
Period size: 19 Copynumber: 6.7 Consensus size: 19
4595329 CGCGATTATA
4595339 GTTTCGCGTTGCGATTTTTT
1 GTTTCGCGTTGCGA-TTTTT
4595359 GTTTCGCGTTGCGA-TTTT
1 GTTTCGCGTTGCGATTTTT
4595377 G--T--CGTTGCGATTTTT
1 GTTTCGCGTTGCGATTTTT
* * *
4595392 ATTTCGCGTTGCGACTTTC
1 GTTTCGCGTTGCGATTTTT
* *
4595411 ATTTCGCGTTGCGATAGTCATT
1 GTTTCGCGTTGCGAT--T-TTT
* *
4595433 -TTTCACGTTGCGATTTTAA
1 GTTTCGCGTTGCGATTTT-T
*
4595452 GTTTCGTGTTGCGA
1 GTTTCGCGTTGCGA
4595466 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
14 8 0.09
15 4 0.05
16 1 0.01
17 1 0.01
18 6 0.07
19 26 0.30
20 25 0.29
21 14 0.16
22 1 0.01
ACGTcount: A:0.11, C:0.17, G:0.24, T:0.47
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTT
Found at i:4595662 original size:94 final size:94
Alignment explanation
Indices: 4595516--4595894 Score: 611
Period size: 94 Copynumber: 4.1 Consensus size: 94
4595506 ATGGATTACA
* * * *
4595516 TTAC-TTCAACCAAAAGATAAAACAAAGGCAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
4595580 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
4595609 TTACTTTCAACCAAAACACAAAACAAAGACAAATGCTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
4595674 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
4595703 TTACTTTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
4595768 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
4595797 TTAC-TTCAACCAAAAGACAAAACAAAATACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* * *
4595861 TTTAGTAGTATT-GCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
4595890 TTACT
1 TTACT
4595895 AAGCAATCTA
Statistics
Matches: 268, Mismatches: 15, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
93 43 0.16
94 225 0.84
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4597611 original size:20 final size:20
Alignment explanation
Indices: 4597586--4597648 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
4597576 TTTTGGTTGA
4597586 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
4597606 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
4597625 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
4597646 AAT
1 AAT
4597649 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:4597628 original size:40 final size:34
Alignment explanation
Indices: 4597584--4597674 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 34
4597574 TCTTTTGGTT
4597584 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACG-GAG-A-G--AATCGCAACGC
**
4597623 GGAAATGACTATCGCAAC-GAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGGAGAGAATCGCAACGC
4597657 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
4597675 CGACGTTGCG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
33 15 0.33
34 11 0.24
36 1 0.02
37 1 0.02
38 3 0.07
40 15 0.33
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (34 bp):
GAAATGAAAATCGCAACGGAGAGAATCGCAACGC
Found at i:4597713 original size:21 final size:20
Alignment explanation
Indices: 4597689--4597764 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
4597679 GTTGCGATTA
*
4597689 TCTCGTTGCTATTTTCATTT
1 TCTCGTTGCGATTTTCATTT
**
4597709 CTCTCGTTGCGATAGTCATTT
1 -TCTCGTTGCGATTTTCATTT
4597730 TCGT-GTTGCGATTTTCATTT
1 TC-TCGTTGCGATTTTCATTT
4597750 TCAT-GTTGCGATTTT
1 TC-TCGTTGCGATTTT
4597765 AAGTTTAGAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.12, C:0.18, G:0.17, T:0.53
Consensus pattern (20 bp):
TCTCGTTGCGATTTTCATTT
Found at i:4598338 original size:21 final size:20
Alignment explanation
Indices: 4598294--4598339 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
4598284 ATAGTCAGAT
*
4598294 TCGCATTGCGATTTACGTAA
1 TCGCATTGCGATTTACGAAA
* *
4598314 TCGCGTTGCGATTTAGGAAAA
1 TCGCATTGCGATTTACG-AAA
4598335 TCGCA
1 TCGCA
4598340 ACGCGAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (20 bp):
TCGCATTGCGATTTACGAAA
Found at i:4599938 original size:31 final size:31
Alignment explanation
Indices: 4599900--4599964 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
4599890 GTTACGTCAA
*
4599900 GGACCATATT-ACAAACGGACTAAATGTTGAG
1 GGACCATATTGA-AAACGGACTAAATATTGAG
* *
4599931 GGACCATATTGAAAATGGACTAAATATTGGG
1 GGACCATATTGAAAACGGACTAAATATTGAG
4599962 GGA
1 GGA
4599965 TTATATTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.23
Consensus pattern (31 bp):
GGACCATATTGAAAACGGACTAAATATTGAG
Found at i:4602042 original size:31 final size:31
Alignment explanation
Indices: 4602007--4602065 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
4601997 AATCCCCCAC
4602007 CATTTAGTCCGTTTGCAATATGGTCCCTCAA
1 CATTTAGTCCGTTTGCAATATGGTCCCTCAA
4602038 CATTTAGTCCGTTTGCAATATGGTCCCT
1 CATTTAGTCCGTTTGCAATATGGTCCCT
4602066 GAAGTAACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.25, G:0.17, T:0.37
Consensus pattern (31 bp):
CATTTAGTCCGTTTGCAATATGGTCCCTCAA
Found at i:4602669 original size:13 final size:14
Alignment explanation
Indices: 4602646--4602678 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4602636 TAAAAATAAA
*
4602646 TTTTGTTTTATTTC
1 TTTTGTTTTATCTC
4602660 TTTT-TTTTATCTC
1 TTTTGTTTTATCTC
4602673 TTTTGT
1 TTTTGT
4602679 AAATTACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.06, C:0.09, G:0.06, T:0.79
Consensus pattern (14 bp):
TTTTGTTTTATCTC
Found at i:4602746 original size:18 final size:19
Alignment explanation
Indices: 4602715--4602751 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
4602705 TATCTATTAG
4602715 ATCCTTTGAAAATTTTATA
1 ATCCTTTGAAAATTTTATA
4602734 ATCCTTT-AAAATTTTATA
1 ATCCTTTGAAAATTTTATA
4602752 TTCTCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.49
Consensus pattern (19 bp):
ATCCTTTGAAAATTTTATA
Found at i:4608145 original size:72 final size:72
Alignment explanation
Indices: 4608028--4608171 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
4608018 GGTCCAACTA
* *
4608028 CCAGAGGTGGTCCTAACGTATCCTCGTCTTCTTCGAGGAATTACGATCTTGACTATATCTTGTTG
1 CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
4608093 AAGCTGC
66 AAGCTGC
*
4608100 CCAGAGGTGGTCCTAACGTATCCTTGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
1 CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
4608165 AAGCTGC
66 AAGCTGC
4608172 AGCTACAGCT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (72 bp):
CCAGAGGTGGTCCTAACGTATCCTCGTCGTCTTCGAGGAATTACGATATTGACTATATCTTGTTG
AAGCTGC
Found at i:4611627 original size:23 final size:23
Alignment explanation
Indices: 4611601--4611661 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
4611591 CTCATATAAA
*
4611601 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
4611624 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
4611647 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
4611662 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:4612701 original size:21 final size:21
Alignment explanation
Indices: 4612677--4612721 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4612667 TTTTGTTCGT
* *
4612677 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
4612698 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
4612719 TTG
1 TTG
4612722 CCCAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:4613716 original size:24 final size:22
Alignment explanation
Indices: 4613678--4613721 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
4613668 CATACTTAGC
*
4613678 ATTTTAAAAATAAAAATAAAAAA
1 ATTTTAAAAAGAAAAA-AAAAAA
4613701 ATTTTGAAAAAGAAAAAAAAA
1 ATTTT-AAAAAGAAAAAAAAA
4613722 CTTTCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
ATTTTAAAAAGAAAAAAAAAAA
Found at i:4615400 original size:18 final size:19
Alignment explanation
Indices: 4615365--4615402 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
4615355 AATTAAATAT
* *
4615365 AAAAAATTAATCATTTTAA
1 AAAAAATTAAACACTTTAA
4615384 AAAAAATTAAAC-CTTTAA
1 AAAAAATTAAACACTTTAA
4615402 A
1 A
4615403 CCACCAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAAATTAAACACTTTAA
Found at i:4618783 original size:31 final size:31
Alignment explanation
Indices: 4618748--4618813 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
4618738 AAAACATAAT
4618748 ATATGATCACTTTCGGTTTTATTTAATTAAG
1 ATATGATCACTTTCGGTTTTATTTAATTAAG
* *
4618779 ATATGATCACTTTTGTTTTTATTTAATTAAG
1 ATATGATCACTTTCGGTTTTATTTAATTAAG
4618810 ATAT
1 ATAT
4618814 AGTAACCACG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.52
Consensus pattern (31 bp):
ATATGATCACTTTCGGTTTTATTTAATTAAG
Found at i:4618976 original size:2 final size:2
Alignment explanation
Indices: 4618969--4619055 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
4618959 ACATGGCATA
4618969 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
4619011 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
4619053 AT A
1 AT A
4619056 ACTTTAAAAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4619129 original size:31 final size:30
Alignment explanation
Indices: 4619051--4619198 Score: 89
Period size: 31 Copynumber: 5.0 Consensus size: 30
4619041 ATATATATAT
*
4619051 ATATAACTTTAAAAATATT-TTTTA-TA-TA
1 ATATAA-TTTAAAAATATTAATTTATTATTA
* *
4619079 A-AT-ACTTAAAATTA-TAATTTATTATTA
1 ATATAATTTAAAAATATTAATTTATTATTA
4619106 ATATAATTTAAAAATATTTAATTTTATT-TTA
1 ATATAATTTAAAAATA-TTAA-TTTATTATTA
* * *
4619137 ATTTTAAATTAAAAAT-TATATTTTATTATTA
1 A-TATAATTTAAAAATAT-TAATTTATTATTA
* * *
4619168 TCTAAAATTTTAAAAATA-TATTTTATTATTA
1 -ATATAA-TTTAAAAATATTAATTTATTATTA
4619199 TGTCATGTGG
Statistics
Matches: 94, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
24 1 0.01
25 12 0.13
26 3 0.03
27 5 0.05
28 3 0.03
29 9 0.10
30 7 0.07
31 28 0.30
32 26 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATAATTTAAAAATATTAATTTATTATTA
Found at i:4619132 original size:32 final size:30
Alignment explanation
Indices: 4619051--4619198 Score: 107
Period size: 32 Copynumber: 5.0 Consensus size: 30
4619041 ATATATATAT
4619051 ATATAACTTTAAAAATATT-TTTTA-TA-TA
1 ATATAA-TTTAAAAATATTATTTTATTATTA
* * *
4619079 A-AT-ACTTAAAATTA-TAATTTATTATTA
1 ATATAATTTAAAAATATTATTTTATTATTA
4619106 ATATAATTTAAAAATATTTAATTTTATT-TTA
1 ATATAATTTAAAAATA-TT-ATTTTATTATTA
* *
4619137 ATTTTAAATTAAAAAT-TATATTTTATTATTA
1 A-TATAATTTAAAAATAT-TATTTTATTATTA
* *
4619168 TCTAAAATTTTAAAAATA-TATTTTATTATTA
1 -ATATAA-TTTAAAAATATTATTTTATTATTA
4619199 TGTCATGTGG
Statistics
Matches: 94, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
24 1 0.01
25 12 0.13
26 3 0.03
27 5 0.05
28 3 0.03
29 9 0.10
30 9 0.10
31 25 0.27
32 27 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATAATTTAAAAATATTATTTTATTATTA
Found at i:4628636 original size:19 final size:20
Alignment explanation
Indices: 4628612--4628652 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
4628602 TCATTCGAGC
4628612 ATTTAATA-CG-TTAGAAATA
1 ATTTAATATCGTTTA-AAATA
4628631 ATTTAATATCGTTTAAAATA
1 ATTTAATATCGTTTAAAATA
4628651 AT
1 AT
4628653 AATTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 9 0.45
21 3 0.15
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (20 bp):
ATTTAATATCGTTTAAAATA
Found at i:4631184 original size:30 final size:30
Alignment explanation
Indices: 4631136--4631230 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 30
4631126 GCACAAATTT
4631136 AAACATAAA-GGATTAAAATAATAAAAATAG
1 AAAC-TAAAGGGATTAAAATAATAAAAATAG
* * * * *
4631166 AAATTAAAGGGATCAAAATGGAT-GAAATAA
1 AAACTAAAGGGATTAAAAT-AATAAAAATAG
*
4631196 AAACTAAAGGGATTAAAATAGTAAAAATAG
1 AAACTAAAGGGATTAAAATAATAAAAATAG
4631226 AAACT
1 AAACT
4631231 TATGAGTCTA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
29 5 0.10
30 44 0.86
31 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.15, T:0.20
Consensus pattern (30 bp):
AAACTAAAGGGATTAAAATAATAAAAATAG
Found at i:4633228 original size:40 final size:40
Alignment explanation
Indices: 4633163--4633241 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
4633153 TTGGTTGTTG
* *
4633163 GGGACGACACTGCTCATACGTGATGAAGAAATCTGGTCAA
1 GGGACGACACGGCTCATACGCGATGAAGAAATCTGGTCAA
* **
4633203 GGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTCA
1 GGGACGACACGGCTCATACGCGATGAAGAAATCTGGTCA
4633242 TCTTTAAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.20
Consensus pattern (40 bp):
GGGACGACACGGCTCATACGCGATGAAGAAATCTGGTCAA
Found at i:4633340 original size:43 final size:44
Alignment explanation
Indices: 4633267--4633483 Score: 159
Period size: 43 Copynumber: 4.8 Consensus size: 44
4633257 ATAACTCGGT
* * * *
4633267 TCCTACGTGATGAGGACGGCTGATTATCTAAGGT-TGACACGGC
1 TCCTACGTGATGAGGAAGTCTGGTCATCTAAGGTATGACACGGC
* * *
4633310 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGT
1 TCCTACGTGATGAGGAAGTCTGGTCATCTAA-GGT--ATGACACGGC
* * * * * * * *
4633357 TCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGT
1 TCCTACGTGATGAGGAAGTCTGGTCATC--T---AA-GGT-ATGACACGGC
* * *
4633408 TCCTACGTGATGAGGACGGCTGGTTATCTAAGGT-TGACACGGC
1 TCCTACGTGATGAGGAAGTCTGGTCATCTAAGGTATGACACGGC
*
4633451 TCCTACGTGATGAGGAAGTCTGGTCGTCTAAGG
1 TCCTACGTGATGAGGAAGTCTGGTCATCTAAGG
4633484 GTAGATGACA
Statistics
Matches: 134, Mismatches: 31, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
43 61 0.46
44 3 0.02
45 3 0.02
46 2 0.01
47 29 0.22
49 2 0.01
51 28 0.21
52 6 0.04
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (44 bp):
TCCTACGTGATGAGGAAGTCTGGTCATCTAAGGTATGACACGGC
Found at i:4633368 original size:47 final size:46
Alignment explanation
Indices: 4633317--4633526 Score: 158
Period size: 47 Copynumber: 4.5 Consensus size: 46
4633307 GGCTCCTACG
*
4633317 TGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACA
1 TGATGAGGAAGTCTGGTCATCTAAGGGT-GATGACATGGTTCATACA
* * * * * *
4633364 TGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAAC-TCGGTTCCTACG
1 TGATGAGGAAGTCTGGTCATC--T---AAGGGTGATGACAT-GGTTCATACA
* * * * * * *
4633415 TGATGAGGACGGCTGGTTATCTAA-GGT--TGACACGGCTCCTACG
1 TGATGAGGAAGTCTGGTCATCTAAGGGTGATGACATGGTTCATACA
*
4633458 TGATGAGGAAGTCTGGTCGTCTAAGGGTAGATGACATGGTTCATACA
1 TGATGAGGAAGTCTGGTCATCTAAGGGT-GATGACATGGTTCATACA
* * *
4633505 TGATGAAGAACTCTGGCCATCT
1 TGATGAGGAAGTCTGGTCATCT
4633527 TTAGGAAGGG
Statistics
Matches: 124, Mismatches: 28, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
43 32 0.26
44 3 0.02
45 3 0.02
46 2 0.02
47 47 0.38
49 2 0.02
50 1 0.01
51 28 0.23
52 6 0.05
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (46 bp):
TGATGAGGAAGTCTGGTCATCTAAGGGTGATGACATGGTTCATACA
Found at i:4633415 original size:141 final size:141
Alignment explanation
Indices: 4633205--4633616 Score: 684
Period size: 141 Copynumber: 2.9 Consensus size: 141
4633195 CTGGTCAAGG
* * ** ** * *
4633205 GATGACACGGCTCATACGCGATGAAGAGTTCTGGTCATCTTTAAGAAGGGTGATAACTCGGTTCC
1 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
*
4633270 TACGTGATGAGGACGGCTGATTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTC
66 TACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTC
4633335 GTCTAAGGGTA
131 GTCTAAGGGTA
4633346 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
1 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
4633411 TACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTC
66 TACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTC
4633476 GTCTAAGGGTA
131 GTCTAAGGGTA
*
4633487 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAGCTCGGTTCC
1 GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
* *
4633552 TACGTGATGAGGACGGCTGGTTATCCTAATGTTGACAC-TCTCCTACGTGATGAGG-AGATCTGG
66 TACGTGATGAGGACGGCTGGTTAT-CTAAGGTTGACACGGCTCCTACGTGATGAGGAAG-TCTGG
4633615 TC
129 TC
4633617 AGTTGATGTT
Statistics
Matches: 257, Mismatches: 12, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
140 2 0.01
141 243 0.95
142 12 0.05
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (141 bp):
GATGACATGGTTCATACATGATGAAGAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCC
TACGTGATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAAGTCTGGTC
GTCTAAGGGTA
Found at i:4633419 original size:51 final size:46
Alignment explanation
Indices: 4633250--4633561 Score: 140
Period size: 47 Copynumber: 6.7 Consensus size: 46
4633240 CATCTTTAAG
* * ***
4633250 AAGGGTGATAACTCGGTTCCTACGTGATG-AGGACGGCTGATTATCT
1 AAGGGTGATAACTCGGTTCCTACGTGATGAAGAAC-TCTGGCCATCT
* * * * * * *
4633296 AA-GGT--TGACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCT
1 AAGGGTGATAACTCGGTTCCTACGTGATGAAGAACTCTGGCCATCT
* * *
4633339 AAGGGTAGATGACAT-GGTTCATACATGATGAAGAACTCTGGCCATCTTT
1 AAGGGT-GATAAC-TCGGTTCCTACGTGATGAAGAACTCTGGCCATC--T
* * **
4633388 AGGAAGGGTGATAACTCGGTTCCTACGTGATG-AGGACGGCTGGTTATCT
1 ---AAGGGTGATAACTCGGTTCCTACGTGATGAAGAAC-TCTGGCCATCT
* * * * * * *
4633437 AA-GGT--TGACACGGCTCCTACGTGATGAGGAAGTCTGGTCGTCT
1 AAGGGTGATAACTCGGTTCCTACGTGATGAAGAACTCTGGCCATCT
* * *
4633480 AAGGGTAGATGACAT-GGTTCATACATGATGAAGAACTCTGGCCATCTTT
1 AAGGGT-GATAAC-TCGGTTCCTACGTGATGAAGAACTCTGGCCATC--T
*
4633529 AGGAAGGGTGATAGCTCGGTTCCTACGTGATGA
1 ---AAGGGTGATAACTCGGTTCCTACGTGATGA
4633562 GGACGGCTGG
Statistics
Matches: 195, Mismatches: 46, Indels: 45
0.68 0.16 0.16
Matches are distributed among these distances:
43 55 0.28
44 10 0.05
45 6 0.03
46 4 0.02
47 56 0.29
49 3 0.02
50 6 0.03
51 43 0.22
52 12 0.06
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (46 bp):
AAGGGTGATAACTCGGTTCCTACGTGATGAAGAACTCTGGCCATCT
Found at i:4646425 original size:30 final size:30
Alignment explanation
Indices: 4646338--4646431 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
4646328 GCACAAATTT
*
4646338 AAACATAAA-GGATT-AAATAATAAAAATAG
1 AAAC-TAAAGGGATTAAAATAGTAAAAATAG
* * * * *
4646367 AAATTAAAGGGATCAAAAT-GGATGAAATAA
1 AAACTAAAGGGATTAAAATAGTA-AAAATAG
4646397 AAACTAAAGGGATTAAAATAGTAAAAATAG
1 AAACTAAAGGGATTAAAATAGTAAAAATAG
4646427 AAACT
1 AAACT
4646432 TATGAGTCTA
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
28 4 0.08
29 8 0.16
30 36 0.72
31 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.15, T:0.20
Consensus pattern (30 bp):
AAACTAAAGGGATTAAAATAGTAAAAATAG
Found at i:4648187 original size:3 final size:3
Alignment explanation
Indices: 4648179--4648221 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
4648169 TGTAATTAAT
**
4648179 TAA TAA TAA TAAA TAA CGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4648222 AAAACCCGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:4649449 original size:16 final size:16
Alignment explanation
Indices: 4649428--4649469 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
4649418 ATTTGTTTTA
* *
4649428 TTTATTATTATTTTGT
1 TTTATTATTATATTAT
4649444 TTTATTATTATATTAT
1 TTTATTATTATATTAT
*
4649460 ATTATTATTA
1 TTTATTATTA
4649470 AATAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTATTATTATATTAT
Found at i:4654098 original size:75 final size:75
Alignment explanation
Indices: 4653937--4654102 Score: 181
Period size: 75 Copynumber: 2.2 Consensus size: 75
4653927 ACAAGAAGCG
* * * *
4653937 AATGTTGTGGCATGCTGAAAACCCTTTTCAATCAGAATCAGGAATATTAAAGTATTCTGAATATT
1 AATGTTG-GGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGCATTCTGAACACT
4654002 TATATCAGCAA
65 TATATCAGCAA
* * * * * * *
4654013 AATGTTGGGCATGTTGAAAGCCCCTTTCAATCAGAATCAGGACTGTTGATGCATTTTGAACACTT
1 AATGTTGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGCATTCTGAACACTT
* * *
4654078 GTATTAGC-C
66 ATATCAGCAA
4654087 AATGTTAGGGCATGCT
1 AATGTT-GGGCATGCT
4654103 AAAGGCCCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
74 6 0.08
75 61 0.82
76 7 0.09
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (75 bp):
AATGTTGGGCATGCTGAAAACCCCTTTCAATCAGAATCAGGAATATTAAAGCATTCTGAACACTT
ATATCAGCAA
Found at i:4655459 original size:22 final size:22
Alignment explanation
Indices: 4655433--4655509 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
4655423 ATCTACACTC
4655433 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
4655455 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
4655477 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
4655499 TTCAAAGATGA
1 TTCAAAGATGA
4655510 AAGCTTTATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:4656306 original size:156 final size:162
Alignment explanation
Indices: 4656015--4656327 Score: 435
Period size: 156 Copynumber: 2.0 Consensus size: 162
4656005 AAGATGAACA
4656015 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCCAAAAATAATAATGAGAAAAT
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-C-AAAATAATAATGAGAAAAT
***
4656080 GATTCCATAGCTTCTCATTTTATCTTTTCTAAAATGAAATTGTTAAAAGTAAGAAAACGATTTCC
64 GATTCCATAGCTTCTCATACAATCTTTTCTAAAATGAAATTGTTAAAAGTAAGAAAACGATTTCC
* *
4656145 TTAGTTTTTTACTTAGTAAA-TATTTCCAACGCC
129 ATAGTTTCTTACTTAGTAAACTATTTCCAACGCC
**
4656178 TTATCTTGAGATTGGGGCATGTTACCC-ATCAACATGTTATTT-TGAA-AAT-A-GAG-AAATGA
1 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAATAATAATGAGAAAATGA
* * * *
4656237 TTTCATAGTTTCTCATACAATCTTTTCTAAAAATGAAATT-TTGAATAGTAAGAAAACGATTTTC
66 TTCCATAGCTTCTCATACAATCTTTTCT-AAAATGAAATTGTT-AAAAGTAAGAAAACGATTTCC
4656301 ATAGTTTCTTACTTAGTAAACTATTTC
129 ATAGTTTCTTACTTAGTAAACTATTTC
4656328 TCACATTTGT
Statistics
Matches: 136, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
155 31 0.23
156 51 0.38
157 7 0.05
158 3 0.02
159 2 0.01
162 15 0.11
163 27 0.20
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (162 bp):
TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAATAATAATGAGAAAATGA
TTCCATAGCTTCTCATACAATCTTTTCTAAAATGAAATTGTTAAAAGTAAGAAAACGATTTCCAT
AGTTTCTTACTTAGTAAACTATTTCCAACGCC
Found at i:4656739 original size:113 final size:112
Alignment explanation
Indices: 4656468--4656892 Score: 616
Period size: 108 Copynumber: 3.9 Consensus size: 112
4656458 TTTGAGGGTC
* *
4656468 ATCAGCATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAGCATTACCAGGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
4656532 AATGAGAAGAACTTGTTTAACCTTTGCTTGAATTCATCATTCGATGG
66 AATGAGAAGAACTTATTCAACCTTTGCTTGAATTCATCATTCGATGG
* * *
4656579 ATCAGCATTACCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCAT
1 ATCAGCATTACCAGGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
4656644 AATGAGAAGAACTTATTCAACCTTTCGCTTGAATTCATCATTCGATGG
66 AATGAGAAGAACTTATTCAACCTTT-GCTTGAATTCATCATTCGATGG
*
4656692 ATCAGCATTACCAGGTAGAGTTCATAATAAGAAGAACTCATCT---GAA-G-AGAAGAAGTTCAT
1 ATCAGCATTACCAGGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * *
4656752 AATGAGAAGAATTTATTCAACTTTTTGCTCGATTTCATCATTCGATGG
66 AATGAGAAGAACTTATTCAAC-CTTTGCTTGAATTCATCATTCGATGG
* *
4656800 ATCAGTATTGCCAGGAAGAGTTCATAATAAGAAGAACTCATCT---GAAGGAAGAAGAAGTTCAT
1 ATCAGCATTACCAGGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
4656862 AATGAGAAGAGCTTGTTCAACCTTTGTTTGA
66 AATGAGAAGAACTTATTCAACCTTTGCTTGA
4656893 TGCTATCATA
Statistics
Matches: 289, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
108 95 0.33
109 12 0.04
110 34 0.12
111 12 0.04
112 72 0.25
113 64 0.22
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (112 bp):
ATCAGCATTACCAGGAAGAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTATTCAACCTTTGCTTGAATTCATCATTCGATGG
Found at i:4657227 original size:16 final size:16
Alignment explanation
Indices: 4657195--4657240 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
4657185 AAGACACTAG
* *
4657195 TTTTTAT-TCATTTTT
1 TTTTTATATTATTATT
4657210 TTTTTATATTATTATT
1 TTTTTATATTATTATT
4657226 TTGTTT-TATTATTAT
1 TT-TTTATATTATTAT
4657241 ATATATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 17 0.63
17 3 0.11
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (16 bp):
TTTTTATATTATTATT
Done.