Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 104 of 208
Found at i:31579015 original size:14 final size:13
Alignment explanation
Indices: 31578995--31579059 Score: 57
Period size: 13 Copynumber: 5.2 Consensus size: 13
31578985 TTCTTTTTTA
31578995 TTATTA-TATTA-
1 TTATTATTATTAT
*
31579006 TTATTTTTATTAT
1 TTATTATTATTAT
** *
31579019 TCCTTATTTTTAT
1 TTATTATTATTAT
31579032 TTACTTATTATTAT
1 TTA-TTATTATTAT
31579046 TTATT-TTATT-T
1 TTATTATTATTAT
31579057 TTA
1 TTA
31579060 CTTTTATTCC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
11 9 0.21
12 10 0.23
13 12 0.28
14 12 0.28
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTATTAT
Found at i:31579039 original size:24 final size:25
Alignment explanation
Indices: 31579012--31579069 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
31579002 ATTATTATTT
31579012 TTATTATTCCTTATTTT-TATTTAC
1 TTATTATTCCTTATTTTATATTTAC
** *
31579036 TTATTATTATTTATTTTATTTTTAC
1 TTATTATTCCTTATTTTATATTTAC
31579061 TT-TTATTCC
1 TTATTATTCC
31579070 ATTTTCTTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (25 bp):
TTATTATTCCTTATTTTATATTTAC
Found at i:31579064 original size:12 final size:13
Alignment explanation
Indices: 31579001--31579067 Score: 61
Period size: 12 Copynumber: 5.3 Consensus size: 13
31578991 TTTATTATTA
*
31579001 TATTA-TTATTTT
1 TATTATTTACTTT
*
31579013 TATTA-TTCCTTAT
1 TATTATTTACTT-T
*
31579026 TTTTATTTACTTAT
1 TATTATTTACTT-T
31579040 TATTATTTA-TTT
1 TATTATTTACTTT
31579052 TATT-TTTACTTT
1 TATTATTTACTTT
31579064 TATT
1 TATT
31579068 CCATTTTCTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
11 4 0.09
12 21 0.45
13 7 0.15
14 15 0.32
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTATTTACTTT
Found at i:31579107 original size:14 final size:13
Alignment explanation
Indices: 31578982--31579131 Score: 72
Period size: 14 Copynumber: 10.8 Consensus size: 13
31578972 CAGTTTACCC
*
31578982 TTTTTCTTTTTTA
1 TTTTTATTTTTTA
* *
31578995 TTATTATATTATTA
1 TTTTTAT-TTTTTA
31579009 TTTTTATTATTCCTTA
1 TTTTTATT-TT--TTA
*
31579025 TTTTTATTTACTTA
1 TTTTTATTT-TTTA
*
31579039 TTATTATTTATTTTA
1 TTTTTA-TT-TTTTA
*
31579054 TTTTTA-CTTTTA
1 TTTTTATTTTTTA
**
31579066 -TTCCATTTTCTTA
1 TTTTTATTTT-TTA
* *
31579079 GTGTTATTCTTTTTA
1 TTTTTA-T-TTTTTA
31579094 TTTTTTATTTTTTA
1 -TTTTTATTTTTTA
31579108 -TTTTAGTTGTTTTA
1 TTTTTA-TT-TTTTA
31579122 TTTTTATTTT
1 TTTTTATTTT
31579132 CTTAGACATA
Statistics
Matches: 103, Mismatches: 18, Indels: 32
0.67 0.12 0.21
Matches are distributed among these distances:
11 3 0.03
12 12 0.12
13 13 0.13
14 35 0.34
15 21 0.20
16 19 0.18
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.73
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:31584071 original size:12 final size:12
Alignment explanation
Indices: 31584054--31584084 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
31584044 ACCTAGGGGG
*
31584054 TTTTTTTCCCCA
1 TTTTTTTCCACA
31584066 TTTTTTTCCACA
1 TTTTTTTCCACA
31584078 TTTTTTT
1 TTTTTTT
31584085 TTTTTTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTTCCACA
Found at i:31585582 original size:13 final size:13
Alignment explanation
Indices: 31585564--31585589 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31585554 CATTTCTAAG
31585564 TCATTTTCATTTT
1 TCATTTTCATTTT
31585577 TCATTTTCATTTT
1 TCATTTTCATTTT
31585590 CGTTTTGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:31585679 original size:57 final size:57
Alignment explanation
Indices: 31585541--31585689 Score: 174
Period size: 57 Copynumber: 2.6 Consensus size: 57
31585531 TATTTAATTC
* * * * * *
31585541 GAAAAACATAAATCATTTCTAAGTCATTTTCATTTTTCATTTTCATTTTCGTTTTGGA
1 GAAAACCAT-AATCATTTCCAAATGATTTTCATTTTCCATTTTCATTTTCATTTTGGA
* * *
31585599 GAAAACCACATTCATTTCCAAATGA-TTTCATTTCTCCATTTTCATTTTTATTTTGGA
1 GAAAACCATAATCATTTCCAAATGATTTTCATTT-TCCATTTTCATTTTCATTTTGGA
* *
31585656 GAAAACCATAATCATTTCCAAATGTTTTTTATTT
1 GAAAACCATAATCATTTCCAAATGATTTTCATTT
31585690 CTATATTTTC
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
56 8 0.11
57 54 0.71
58 14 0.18
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (57 bp):
GAAAACCATAATCATTTCCAAATGATTTTCATTTTCCATTTTCATTTTCATTTTGGA
Found at i:31599988 original size:14 final size:14
Alignment explanation
Indices: 31599952--31599985 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
31599942 TCATCATTTG
31599952 CCTATAACCAAAAC
1 CCTATAACCAAAAC
31599966 CCTATAACCAAAAC
1 CCTATAACCAAAAC
31599980 CC-ATAA
1 CCTATAA
31599986 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:31603399 original size:25 final size:25
Alignment explanation
Indices: 31603371--31603598 Score: 261
Period size: 25 Copynumber: 9.4 Consensus size: 25
31603361 GGAGTTTAGT
*
31603371 GTGCTATCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
31603396 GTGCTCTCTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
* *
31603421 GTGCTTTCTAATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
*
31603446 GTGCTCTCTGATTATTAGCACGTCA
1 GTGCTCTCTGATTATTAGCACATCA
* *
31603471 GTGCTCTCTGATTATTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACATCA
* * * *
31603496 GTGTTCTCTGATTACTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACATCA
* **
31603521 GTGCTCTCCGATTATTAGCACATTG
1 GTGCTCTCTGATTATTAGCACATCA
* *
31603546 GTGCTCTCCG--T-TTAGCACATCT
1 GTGCTCTCTGATTATTAGCACATCA
* *
31603568 GTGCTCTCTG--TA-TAGCACTTTA
1 GTGCTCTCTGATTATTAGCACATCA
31603590 GTGCTCTCT
1 GTGCTCTCT
31603599 ATTTAATAGT
Statistics
Matches: 182, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
22 35 0.19
23 1 0.01
25 146 0.80
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCA
Found at i:31603563 original size:22 final size:22
Alignment explanation
Indices: 31603511--31603597 Score: 86
Period size: 22 Copynumber: 3.8 Consensus size: 22
31603501 CTCTGATTAC
*
31603511 TAGCACGTTAGTGCTCTCCGATTAT
1 TAGCACATTAGTGCTCTCCG--T-T
*
31603536 TAGCACATTGGTGCTCTCCGTT
1 TAGCACATTAGTGCTCTCCGTT
* *
31603558 TAGCACATCT-GTGCTCTCTGTA
1 TAGCACAT-TAGTGCTCTCCGTT
*
31603580 TAGCACTTTAGTGCTCTC
1 TAGCACATTAGTGCTCTC
31603598 TATTTAATAG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
21 1 0.02
22 34 0.62
23 2 0.04
25 18 0.33
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.37
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCCGTT
Found at i:31603984 original size:45 final size:45
Alignment explanation
Indices: 31603935--31604099 Score: 222
Period size: 45 Copynumber: 3.6 Consensus size: 45
31603925 ATCCATGAAA
* *
31603935 ATAAAGGTGGTTGCTATGTGTTGATTCCACCGGATATTGTTAATT
1 ATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATATCGTTAATT
*
31603980 ATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATATCGTTATTT
1 ATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATATCGTTAATT
* * * *
31604025 ATAAAGGTGGTTGCTATGTGCTGATTTCACCAGATATCATTGATT
1 ATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATATCGTTAATT
* * * *
31604070 ACAAAGGGTGATTGCTGTGTGCTGAATCCA
1 ATAAA-GGTGGTTGCTATGTGCTGATTCCA
31604100 TCGTGTATCT
Statistics
Matches: 106, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 86 0.81
46 20 0.19
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (45 bp):
ATAAAGGTGGTTGCTATGTGCTGATTCCACCGGATATCGTTAATT
Found at i:31606634 original size:24 final size:24
Alignment explanation
Indices: 31606607--31606659 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
31606597 GAATACCACA
*
31606607 AAAGGACATATCAAAATATGCCAT
1 AAAGGACAGATCAAAATATGCCAT
* * * *
31606631 AAAGGCCAGATTAGAGTATGCCAT
1 AAAGGACAGATCAAAATATGCCAT
31606655 AAAGG
1 AAAGG
31606660 CTAGCAGAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.19
Consensus pattern (24 bp):
AAAGGACAGATCAAAATATGCCAT
Found at i:31608324 original size:15 final size:16
Alignment explanation
Indices: 31608292--31608325 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31608282 AGTTCATCTC
*
31608292 ATTTGCATTTAGGTTA
1 ATTTGCATCTAGGTTA
31608308 ATTTGCATCTA-GTTA
1 ATTTGCATCTAGGTTA
31608323 ATT
1 ATT
31608326 AATTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (16 bp):
ATTTGCATCTAGGTTA
Found at i:31612737 original size:39 final size:39
Alignment explanation
Indices: 31612677--31612849 Score: 213
Period size: 39 Copynumber: 4.4 Consensus size: 39
31612667 CAATTATACT
*
31612677 TGATCGCACATACGTGCCCCTGGTT-TACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCT-GTTGTACTTCGGTACCCC
* * * * *
31612716 TGATTGCACATAGGTGACCCTGTTGTACTTTGGAACCCT
1 TGATTGCACATACGTGCCCCTGTTGTACTTCGGTACCCC
* * *
31612755 TGATCGCACATACGTGCCCCTGTTGTATTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTGTACTTCGGTACCCC
* **
31612794 TGGTTGCACATACGTGCCCCTGTTGTACTTCGGTACCTT
1 TGATTGCACATACGTGCCCCTGTTGTACTTCGGTACCCC
*
31612833 TGATTGCACTTACGTGC
1 TGATTGCACATACGTGC
31612850 TTTGTTAACG
Statistics
Matches: 113, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
38 3 0.03
39 110 0.97
ACGTcount: A:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (39 bp):
TGATTGCACATACGTGCCCCTGTTGTACTTCGGTACCCC
Found at i:31612804 original size:78 final size:78
Alignment explanation
Indices: 31612675--31612849 Score: 244
Period size: 78 Copynumber: 2.2 Consensus size: 78
31612665 TGCAATTATA
*
31612675 CTTGATCGCACATACGTGCCCCTGGTTTACTTCGGTACCCCTGATTGCACATAGGTGACCCTGTT
1 CTTGATCGCACATACGTGCCCCTGGTTTACTTCGGTACCCCTGATTGCACATACGTGACCCTGTT
*
31612740 GTACTTTGGAACC
66 GTACTTCGGAACC
* * * *
31612753 CTTGATCGCACATACGTGCCCCT-GTTGTATTTTGGTACCCCTGGTTGCACATACGTGCCCCTGT
1 CTTGATCGCACATACGTGCCCCTGGTT-TACTTCGGTACCCCTGATTGCACATACGTGACCCTGT
*
31612817 TGTACTTCGGTACC
65 TGTACTTCGGAACC
* * *
31612831 TTTGATTGCACTTACGTGC
1 CTTGATCGCACATACGTGC
31612850 TTTGTTAACG
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 3 0.03
78 83 0.97
ACGTcount: A:0.16, C:0.29, G:0.22, T:0.33
Consensus pattern (78 bp):
CTTGATCGCACATACGTGCCCCTGGTTTACTTCGGTACCCCTGATTGCACATACGTGACCCTGTT
GTACTTCGGAACC
Found at i:31628561 original size:26 final size:26
Alignment explanation
Indices: 31628531--31628581 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
31628521 ACACCAATAT
31628531 CGCAGCAAAGCTGCCAATAACAGTAA
1 CGCAGCAAAGCTGCCAATAACAGTAA
* *
31628557 CGCAGCAAAGCTGCCAGTAATAGTA
1 CGCAGCAAAGCTGCCAATAACAGTA
31628582 TATGTGGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.22, T:0.14
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAATAACAGTAA
Found at i:31628790 original size:27 final size:27
Alignment explanation
Indices: 31628760--31629007 Score: 245
Period size: 27 Copynumber: 9.2 Consensus size: 27
31628750 GTATAACAGC
* *
31628760 CATTTTACCC-TATGGGGGTTTTTCGAT
1 CATTTTACCCAT-TGAGGGTATTTCGAT
* * *
31628787 CATTTTACCC-TTCGGGGGTATTTTGGT
1 CATTTTACCCATT-GAGGGTATTTCGAT
*
31628814 CATTTTACCCATCGAGGGTATTTCGAT
1 CATTTTACCCATTGAGGGTATTTCGAT
* * *
31628841 CATTTTACTCATTAAGGGTATTTCAAT
1 CATTTTACCCATTGAGGGTATTTCGAT
* * *
31628868 CATATTACCCATCGAAGGTATTTC-AGT
1 CATTTTACCCATTGAGGGTATTTCGA-T
* **
31628895 TATTTTACCCACCGAGGGTATTTCGAT
1 CATTTTACCCATTGAGGGTATTTCGAT
31628922 CATTTTACCCATTGAGGGTATTTC-AGT
1 CATTTTACCCATTGAGGGTATTTCGA-T
*
31628949 CATTTTACCCATTGAGGGTATTTCGGT
1 CATTTTACCCATTGAGGGTATTTCGAT
* * *
31628976 CATTTTACCCGTCGAGAGTATTTCCG-T
1 CATTTTACCCATTGAGGGTATTT-CGAT
31629003 CATTT
1 CATTT
31629008 GCCCACAAAT
Statistics
Matches: 187, Mismatches: 27, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.02
27 180 0.96
28 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (27 bp):
CATTTTACCCATTGAGGGTATTTCGAT
Found at i:31628876 original size:81 final size:81
Alignment explanation
Indices: 31628775--31629007 Score: 299
Period size: 81 Copynumber: 2.9 Consensus size: 81
31628765 TACCCTATGG
* * * *
31628775 GGGTTTTTCGATCATTTTACCCTTCGGGGGTATTTTGGTCATTTTACCCATCGAGGGTATTTCGA
1 GGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCGA
*
31628840 TCATTTTACTCATTAA
66 TCATTTTACCCATTAA
* * * * * *
31628856 GGGTATTTCAATCATATTACCCATCGAAGGTATTTCAGTTATTTTACCCACCGAGGGTATTTCGA
1 GGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCGA
*
31628921 TCATTTTACCCATTGA
66 TCATTTTACCCATTAA
* * *
31628937 GGGTATTTCAGTCATTTTACCCATT-GAGGGTATTTCGGTCATTTTACCCGTCGAGAGTATTTCC
1 GGGTATTTCAATCATTTTACCC-TTCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTT-C
31629001 G-TCATTT
64 GATCATTT
31629008 GCCCACAAAT
Statistics
Matches: 129, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
81 126 0.98
82 3 0.02
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (81 bp):
GGGTATTTCAATCATTTTACCCTTCGAGGGTATTTCGGTCATTTTACCCATCGAGGGTATTTCGA
TCATTTTACCCATTAA
Found at i:31638671 original size:3 final size:3
Alignment explanation
Indices: 31638663--31638694 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31638653 CTCTATGGGA
*
31638663 TCT TCT TCT TCT TCT TCT TCT TTT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
31638695 AGGATCCTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:31639781 original size:21 final size:20
Alignment explanation
Indices: 31639752--31639793 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
31639742 GTGTCTTGAT
31639752 GGTGTGGTGCGA-TAGGCAAG
1 GGTGTGGTGCGAGTA-GCAAG
31639772 GGTGTTGGTGCGAGTAGCAAG
1 GGTG-TGGTGCGAGTAGCAAG
31639793 G
1 G
31639794 AGGCAGCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.19, C:0.10, G:0.50, T:0.21
Consensus pattern (20 bp):
GGTGTGGTGCGAGTAGCAAG
Found at i:31640338 original size:15 final size:15
Alignment explanation
Indices: 31640318--31640350 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
31640308 TATAAAGTTG
31640318 ATAAT-AATATATATT
1 ATAATAAATATA-ATT
31640333 ATAATAAATATAATT
1 ATAATAAATATAATT
31640348 ATA
1 ATA
31640351 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:31649422 original size:55 final size:55
Alignment explanation
Indices: 31649356--31649485 Score: 251
Period size: 55 Copynumber: 2.4 Consensus size: 55
31649346 ACATTCATAG
*
31649356 TAGGGACACACGACCGTGTCGCAACCCATGTGTGCCTCCGTATGTGTATTGAAAA
1 TAGGGACACACGACCGTGTCGCAACCCATGTGTGCCCCCGTATGTGTATTGAAAA
31649411 TAGGGACACACGACCGTGTCGCAACCCATGTGTGCCCCCGTATGTGTATTGAAAA
1 TAGGGACACACGACCGTGTCGCAACCCATGTGTGCCCCCGTATGTGTATTGAAAA
31649466 TAGGGACACACGACCGTGTC
1 TAGGGACACACGACCGTGTC
31649486 ACAAGTCGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
55 74 1.00
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.22
Consensus pattern (55 bp):
TAGGGACACACGACCGTGTCGCAACCCATGTGTGCCCCCGTATGTGTATTGAAAA
Found at i:31658385 original size:29 final size:29
Alignment explanation
Indices: 31658333--31658611 Score: 135
Period size: 29 Copynumber: 9.6 Consensus size: 29
31658323 ATCGATGGTT
* *
31658333 GAAGCCATCCCTTTTCACATTCGATAGCC
1 GAAGCTATCCCTTTTCATATTCGATAGCC
* *
31658362 GAAGCTATCCCTTTTCATACTCGATGGTCATC
1 GAAGCTATCCCTTTTCATATTCGATAG-C--C
*
31658394 -AA-C-ATCCCTTTTCATAGTT-GAT-GATC
1 GAAGCTATCCCTTTTCATA-TTCGATAG-CC
* * *
31658420 GTCA-CCATCCCTTTTCATAATCGATAGCC
1 G-AAGCTATCCCTTTTCATATTCGATAGCC
* ***
31658449 GAAGCTATCCTTTTTCATAATTCGATAATT
1 GAAGCTATCCCTTTTCAT-ATTCGATAGCC
* * * *
31658479 GAAGCTATCCTTTTTCATAATTTGATGGTC
1 GAAGCTATCCCTTTTCAT-ATTCGATAGCC
* * * ** * *
31658509 GTCA-CCATCGCTTTTCATAGCCGATGGTC
1 G-AAGCTATCCCTTTTCATATTCGATAGCC
* * * *
31658538 GTCA-CCATCCC-TTACATAATCGATAGCC
1 G-AAGCTATCCCTTTTCATATTCGATAGCC
*
31658566 AAAGCTATCCCTTTTCATGATTCGATAGCC
1 GAAGCTATCCCTTTTCAT-ATTCGATAGCC
*
31658596 GAAGCTATCCCCTTTC
1 GAAGCTATCCCTTTTC
31658612 CTTGATCGAT
Statistics
Matches: 194, Mismatches: 41, Indels: 29
0.73 0.16 0.11
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 23 0.12
29 92 0.47
30 73 0.38
31 3 0.02
32 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (29 bp):
GAAGCTATCCCTTTTCATATTCGATAGCC
Found at i:31658483 original size:30 final size:30
Alignment explanation
Indices: 31658426--31658500 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
31658416 GATCGTCACC
* *
31658426 ATCCCTTTTCATAA-TCGATAGCCGAAGCT
1 ATCCTTTTTCATAATTCGATAACCGAAGCT
**
31658455 ATCCTTTTTCATAATTCGATAATTGAAGCT
1 ATCCTTTTTCATAATTCGATAACCGAAGCT
31658485 ATCCTTTTTCATAATT
1 ATCCTTTTTCATAATT
31658501 TGATGGTCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 13 0.32
30 28 0.68
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.41
Consensus pattern (30 bp):
ATCCTTTTTCATAATTCGATAACCGAAGCT
Found at i:31658557 original size:117 final size:117
Alignment explanation
Indices: 31658334--31658611 Score: 335
Period size: 117 Copynumber: 2.4 Consensus size: 117
31658324 TCGATGGTTG
* * ***
31658334 AAGCCATCCCTTTTCA-CATTCGATAGCCGAAGCTATCCCTTTTCATACTCGATGGTCATCAACA
1 AAGCTATCCCTTTTCATAATTCGATAATTGAAGCTATCCCTTTTCATACTCGATGGTCATCAACA
** * *
31658398 TCCCTTTTCATAGTTGATGATCGTCACCATCCCTTTTCATAATCGATAGCCG
66 TCCCTTTTCATAGCCGATGATCGTCACCATCCCTTTACATAATCGATAGCCA
* * * * * *
31658450 AAGCTATCCTTTTTCATAATTCGATAATTGAAGCTATCCTTTTTCATAATTTGATGGTCGTCACC
1 AAGCTATCCCTTTTCATAATTCGATAATTGAAGCTATCCCTTTTCAT-ACTCGATGGTCATCAAC
* *
31658515 ATCGCTTTTCATAGCCGATGGTCGTCACCATCCC-TTACATAATCGATAGCCA
65 ATCCCTTTTCATAGCCGATGATCGTCACCATCCCTTTACATAATCGATAGCCA
* *** *
31658567 AAGCTATCCCTTTTCATGATTCGATAGCCGAAGCTATCCCCTTTC
1 AAGCTATCCCTTTTCATAATTCGATAATTGAAGCTATCCCTTTTC
31658612 CTTGATCGAT
Statistics
Matches: 136, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
116 14 0.10
117 79 0.58
118 43 0.32
ACGTcount: A:0.24, C:0.28, G:0.13, T:0.34
Consensus pattern (117 bp):
AAGCTATCCCTTTTCATAATTCGATAATTGAAGCTATCCCTTTTCATACTCGATGGTCATCAACA
TCCCTTTTCATAGCCGATGATCGTCACCATCCCTTTACATAATCGATAGCCA
Found at i:31658575 original size:28 final size:30
Alignment explanation
Indices: 31658544--31658606 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
31658534 GGTCGTCACC
31658544 ATCCC-TTACAT-AATCGATAGCCAAAGCT
1 ATCCCTTTACATGAATCGATAGCCAAAGCT
* * *
31658572 ATCCCTTTTCATGATTCGATAGCCGAAGCT
1 ATCCCTTTACATGAATCGATAGCCAAAGCT
31658602 ATCCC
1 ATCCC
31658607 CTTTCCTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 5 0.17
29 5 0.17
30 20 0.67
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.29
Consensus pattern (30 bp):
ATCCCTTTACATGAATCGATAGCCAAAGCT
Found at i:31658621 original size:30 final size:29
Alignment explanation
Indices: 31658556--31658621 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
31658546 CCCTTACATA
*
31658556 ATCGATAGCCAAAGCTATCCCTTTTCATG
1 ATCGATAGCCAAAGCTATCCCTTTCCATG
* *
31658585 ATTCGATAGCCGAAGCTATCCCCTTTCCTTG
1 A-TCGATAGCCAAAGCTAT-CCCTTTCCATG
31658616 ATCGAT
1 ATCGAT
31658622 GATCATCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 21 0.66
31 10 0.31
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (29 bp):
ATCGATAGCCAAAGCTATCCCTTTCCATG
Found at i:31660885 original size:29 final size:29
Alignment explanation
Indices: 31660835--31661020 Score: 198
Period size: 29 Copynumber: 6.4 Consensus size: 29
31660825 AAAACATTTA
* * *
31660835 TTTAACTAAGATAACCATAAAGGCATCCT
1 TTTAACAAAGATAGCCACAAAGGCATCCT
*
31660864 TTTAACAAATATAGCCACAAAGGCATCCT
1 TTTAACAAAGATAGCCACAAAGGCATCCT
* *
31660893 TTTAATAGAGATAGACC-CAAAGGCATCCT
1 TTTAACAAAGATAG-CCACAAAGGCATCCT
* *
31660922 TTTAACAGAA-ATCGCCACAAAGGCTTCCT
1 TTTAACA-AAGATAGCCACAAAGGCATCCT
* * *
31660951 TTTAATAGAGATAGACACAAAGGCATCCT
1 TTTAACAAAGATAGCCACAAAGGCATCCT
* *
31660980 TTTAACAGAA-ATCGCCACAAAGGCTTCCT
1 TTTAACA-AAGATAGCCACAAAGGCATCCT
*
31661009 TTTAACAGAGAT
1 TTTAACAAAGAT
31661021 CACCGTAAAA
Statistics
Matches: 129, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
28 4 0.03
29 121 0.94
30 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (29 bp):
TTTAACAAAGATAGCCACAAAGGCATCCT
Found at i:31660897 original size:58 final size:59
Alignment explanation
Indices: 31660835--31661020 Score: 283
Period size: 58 Copynumber: 3.2 Consensus size: 59
31660825 AAAACATTTA
* * *
31660835 TTTAACTA-AGATA-ACCATAAAGGCATCCTTTTAACA-AATATAGCCACAAAGGCATCCT
1 TTTAA-TAGAGATAGACCACAAAGGCATCCTTTTAACAGAA-ATCGCCACAAAGGCTTCCT
31660893 TTTAATAGAGATAGACC-CAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
1 TTTAATAGAGATAGACCACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
31660951 TTTAATAGAGATAGA-CACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
1 TTTAATAGAGATAGACCACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
*
31661009 TTTAACAGAGAT
1 TTTAATAGAGAT
31661021 CACCGTAAAA
Statistics
Matches: 120, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
57 3 0.03
58 112 0.93
59 5 0.04
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (59 bp):
TTTAATAGAGATAGACCACAAAGGCATCCTTTTAACAGAAATCGCCACAAAGGCTTCCT
Found at i:31661035 original size:87 final size:87
Alignment explanation
Indices: 31660860--31661039 Score: 227
Period size: 87 Copynumber: 2.1 Consensus size: 87
31660850 CATAAAGGCA
* * * *
31660860 TCCTTTTAACAAATATAGCCACAAAGGCATCCTTTTAATAGAGATAGACCCAAAGGCATCCTTTT
1 TCCTTTTAACAAAGATAGACACAAAGGCATCCTTTTAACAGAAATAGACCCAAAGGCATCCTTTT
* *
31660925 AACAGAAATCGCCACAAAGGCT
66 AACAGAAATCACCACAAAAGCT
* * * *
31660947 TCCTTTTAATAGAGATAGACACAAAGGCATCCTTTTAACAGAAATCG-CCACAAAGGCTTCCTTT
1 TCCTTTTAACAAAGATAGACACAAAGGCATCCTTTTAACAGAAATAGACC-CAAAGGCATCCTTT
* **
31661011 TAACAGAGATCACCGTAAAAGCT
65 TAACAGAAATCACCACAAAAGCT
31661034 TCCTTT
1 TCCTTT
31661040 GTTAGAGATT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
86 2 0.03
87 77 0.97
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (87 bp):
TCCTTTTAACAAAGATAGACACAAAGGCATCCTTTTAACAGAAATAGACCCAAAGGCATCCTTTT
AACAGAAATCACCACAAAAGCT
Found at i:31665339 original size:42 final size:42
Alignment explanation
Indices: 31665292--31665433 Score: 158
Period size: 44 Copynumber: 3.3 Consensus size: 42
31665282 TTTTTCACAT
** * * *
31665292 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTAGCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTACCAC
* * *
31665334 AAACGCCACTAAAGAACATGATCTTTAGTGACGCTTTTTACCAT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGC--TTTACCAC
* **
31665378 AAACGTCGCTAAAGAACATGATCTTTAGCGACGCTTTGATTAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTT-ACCAC
31665421 AAACGCCGCTAAA
1 AAACGCCGCTAAA
31665434 AGTACCGTTC
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
42 31 0.38
43 14 0.17
44 37 0.45
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGACGCTTTACCAC
Found at i:31665521 original size:16 final size:16
Alignment explanation
Indices: 31665502--31665535 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31665492 AAACATTAAA
*
31665502 TATTAAAATCAAACAT
1 TATTAAAATCAAAAAT
*
31665518 TATTAATATCAAAAAT
1 TATTAAAATCAAAAAT
31665534 TA
1 TA
31665536 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATCAAAAAT
Found at i:31668076 original size:13 final size:13
Alignment explanation
Indices: 31668058--31668089 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
31668048 ATAAACGAAT
31668058 CCACTTCATGCAC
1 CCACTTCATGCAC
*
31668071 CCACTTCATGTAC
1 CCACTTCATGCAC
31668084 CCACTT
1 CCACTT
31668090 TTGTACAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.44, G:0.06, T:0.28
Consensus pattern (13 bp):
CCACTTCATGCAC
Found at i:31670037 original size:16 final size:16
Alignment explanation
Indices: 31670012--31670043 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31670002 ACACTTAACC
*
31670012 ATTTTTAAAATTTGGG
1 ATTTTGAAAATTTGGG
31670028 ATTTTGAAAATTTGGG
1 ATTTTGAAAATTTGGG
31670044 GATAATATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (16 bp):
ATTTTGAAAATTTGGG
Found at i:31670672 original size:7 final size:7
Alignment explanation
Indices: 31670658--31670820 Score: 80
Period size: 7 Copynumber: 23.0 Consensus size: 7
31670648 AATCCTCAAC
31670658 CCCT-AA
1 CCCTAAA
31670664 CCCTAAA
1 CCCTAAA
31670671 CCCTAAA
1 CCCTAAA
31670678 CCCTAAA
1 CCCTAAA
* *
31670685 -TCAAAA
1 CCCTAAA
* *
31670691 GACATAAA
1 -CCCTAAA
31670699 CCCTAAA
1 CCCTAAA
*
31670706 CTCCTAAC
1 C-CCTAAA
*
31670714 CCCTAAC
1 CCCTAAA
31670721 CCCTAAA
1 CCCTAAA
* *
31670728 CCTTGAA
1 CCCTAAA
*
31670735 CCC-CAA
1 CCCTAAA
31670741 CCCTTAAA
1 CCC-TAAA
* *
31670749 TCGTAAA
1 CCCTAAA
*
31670756 CCATAAA
1 CCCTAAA
*
31670763 CCATAAA
1 CCCTAAA
* *
31670770 TCATAAA
1 CCCTAAA
31670777 CCCTAAA
1 CCCTAAA
* *
31670784 CTCATAAT
1 C-CCTAAA
31670792 CCCTAAA
1 CCCTAAA
*
31670799 CCCCTAAT
1 -CCCTAAA
*
31670807 CCATAAA
1 CCCTAAA
*
31670814 CCTTAAA
1 CCCTAAA
31670821 ATAGTATCTT
Statistics
Matches: 120, Mismatches: 29, Indels: 15
0.73 0.18 0.09
Matches are distributed among these distances:
6 13 0.11
7 84 0.70
8 23 0.19
ACGTcount: A:0.43, C:0.36, G:0.02, T:0.19
Consensus pattern (7 bp):
CCCTAAA
Found at i:31670806 original size:15 final size:15
Alignment explanation
Indices: 31670771--31670815 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
31670761 AACCATAAAT
* *
31670771 CATAAACCCTAAACT
1 CATAATCCCTAAACC
31670786 CATAATCCCTAAACC
1 CATAATCCCTAAACC
* *
31670801 CCTAATCCATAAACC
1 CATAATCCCTAAACC
31670816 TTAAAATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (15 bp):
CATAATCCCTAAACC
Found at i:31670851 original size:14 final size:14
Alignment explanation
Indices: 31670832--31670877 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
31670822 TAGTATCTTT
*
31670832 TAAACCTTAAACCC
1 TAAACCATAAACCC
*
31670846 TAAACCATACACCC
1 TAAACCATAAACCC
*
31670860 CAAACCATAAACCC
1 TAAACCATAAACCC
31670874 TAAA
1 TAAA
31670878 TTATAATGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:31671032 original size:14 final size:14
Alignment explanation
Indices: 31671013--31671061 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
31671003 AACCCTAGAT
31671013 CCCTAACTCTTAAC
1 CCCTAACTCTTAAC
31671027 CCCTAACGTC-TAAC
1 CCCTAAC-TCTTAAC
*
31671041 CCCTAAACCCTTAA-
1 CCCT-AACTCTTAAC
31671055 CCCTAAC
1 CCCTAAC
31671062 CCCTAAACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.10
14 20 0.65
15 8 0.26
ACGTcount: A:0.31, C:0.45, G:0.02, T:0.22
Consensus pattern (14 bp):
CCCTAACTCTTAAC
Found at i:31671051 original size:21 final size:21
Alignment explanation
Indices: 31671036--31671074 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31671026 CCCCTAACGT
31671036 CTAACCCCTAAACCCTTAACC
1 CTAACCCCTAAACCCTTAACC
31671057 CTAACCCCTAAA-CCTTAA
1 CTAACCCCTAAACCCTTAA
31671075 ATCCCAGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAACCCCTAAACCCTTAACC
Found at i:31671511 original size:41 final size:41
Alignment explanation
Indices: 31671466--31671751 Score: 281
Period size: 41 Copynumber: 6.8 Consensus size: 41
31671456 TAAAATGTTT
* *
31671466 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAA-ACACAAAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGA-ACCAAGCA
* * *
31671507 TTAGCGGCACATTTTT-AAAAACGCCACTAAA-ACCCCAAGCA
1 TTAGCGGCGC-TTTTTCAAAAACGCCGCTAAAGA-ACCAAGCA
* *
31671548 TTAGCGGCACTTTCTCAAAAACGCCGCTAATGCGCTAAAGAACCAAGCA
1 TTAGCGGCGCTTTTTCAAAAA---CGC-----CGCTAAAGAACCAAGCA
* * ** *
31671597 TTAGCAGCGCTTTCTCAAAAACGCCATTAAAGAACCAACCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGAACCAAGCA
* *
31671638 TTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGAACCAACCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGAACCAAGCA
* *
31671679 TTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGAACCCAGCA
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGAACCAAGCA
* * *
31671720 TTAGTGACACTTTTTCAAAAACGCCGCTAAAG
1 TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAG
31671752 CCTCGGGCAT
Statistics
Matches: 210, Mismatches: 24, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.02
41 162 0.77
42 5 0.02
44 3 0.01
46 3 0.01
49 32 0.15
50 1 0.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (41 bp):
TTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGAACCAAGCA
Found at i:31671762 original size:41 final size:40
Alignment explanation
Indices: 31671580--31671796 Score: 166
Period size: 41 Copynumber: 5.3 Consensus size: 40
31671570 GCCGCTAATG
* * * *
31671580 CGCTAAAGAACCAAGCATTAGCAGCGCTTTCTCAAAAACGC
1 CGCTAAAG-ACCCAGCATTAGCAACACTTTTTCAAAAACGC
** * * ** * *
31671621 CATTAAAGAACCAACCATTAGCGGCGCTTTCTCAAAAACGC
1 CGCTAAAG-ACCCAGCATTAGCAACACTTTTTCAAAAACGC
* * ** * *
31671662 CGCTAAAGAACCAACCATTAGCGGCGCTTTTTCAAAAATGC
1 CGCTAAAG-ACCCAGCATTAGCAACACTTTTTCAAAAACGC
**
31671703 CGCTAAAGAACCCAGCATTAGTGACACTTTTTCAAAAACGC
1 CGCTAAAG-ACCCAGCATTAGCAACACTTTTTCAAAAACGC
* **
31671744 CGCTAAAG-CCTCGGGCATTAGCAACACTTTTTTGAAAACGC
1 CGCTAAAGACC-C-AGCATTAGCAACACTTTTTCAAAAACGC
31671785 CGCTAAAGACCC
1 CGCTAAAGACCC
31671797 GAAAGGTAAG
Statistics
Matches: 154, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
39 2 0.01
40 1 0.01
41 149 0.97
42 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.20
Consensus pattern (40 bp):
CGCTAAAGACCCAGCATTAGCAACACTTTTTCAAAAACGC
Found at i:31671763 original size:82 final size:82
Alignment explanation
Indices: 31671580--31671793 Score: 241
Period size: 82 Copynumber: 2.6 Consensus size: 82
31671570 GCCGCTAATG
* ** *
31671580 CGCTAAAGAACCAAGCATTAGCAGCGCTTTCTCAAAAACGCCATTAAAGAACCAACCATTAGCGG
1 CGCTAAAGAACCAAGCATTAGCAGCGCTTTTTCAAAAACGCCGCTAAAGAACCAACCATTAGCGA
*
31671645 CGCTTTCTCAAAAACGC
66 CACTTTCTCAAAAACGC
* * * * * *
31671662 CGCTAAAGAACCAACCATTAGCGGCGCTTTTTCAAAAATGCCGCTAAAGAACCCAGCATTAGTGA
1 CGCTAAAGAACCAAGCATTAGCAGCGCTTTTTCAAAAACGCCGCTAAAGAACCAACCATTAGCGA
*
31671727 CACTTTTTCAAAAACGC
66 CACTTTCTCAAAAACGC
* ** * * **
31671744 CGCTAAAG-CCTCGGGCATTAGCAACACTTTTTTGAAAACGCCGCTAAAGA
1 CGCTAAAGAAC-CAAGCATTAGCAGCGCTTTTTCAAAAACGCCGCTAAAGA
31671794 CCCGAAAGGT
Statistics
Matches: 109, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
81 1 0.01
82 108 0.99
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.21
Consensus pattern (82 bp):
CGCTAAAGAACCAAGCATTAGCAGCGCTTTTTCAAAAACGCCGCTAAAGAACCAACCATTAGCGA
CACTTTCTCAAAAACGC
Found at i:31676678 original size:28 final size:28
Alignment explanation
Indices: 31676647--31676709 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
31676637 CTATTCAGTA
* *
31676647 ACAGTAACAGTGTGGGCGTTAGCCCAAT
1 ACAGTAACAGTGTAGGCCTTAGCCCAAT
*
31676675 ACAGCAACAGTGTAGGCCTTAGCCCAAT
1 ACAGTAACAGTGTAGGCCTTAGCCCAAT
31676703 ACAGTAA
1 ACAGTAA
31676710 TAGTACAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (28 bp):
ACAGTAACAGTGTAGGCCTTAGCCCAAT
Found at i:31676843 original size:26 final size:26
Alignment explanation
Indices: 31676814--31676896 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 26
31676804 CCAACACACC
* * *
31676814 AATATCGCAGCAAAGCTACCAATAAT
1 AATATCACAGCAAAGCTGCCAGTAAT
31676840 AATATCACAGCAAAGCTGCCAGT-AT
1 AATATCACAGCAAAGCTGCCAGTAAT
* *
31676865 CAGTATCACAGCAAAGCTGCCAGTAAC
1 -AATATCACAGCAAAGCTGCCAGTAAT
31676892 AATAT
1 AATAT
31676897 ATGTGGCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.04
26 46 0.94
27 1 0.02
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.19
Consensus pattern (26 bp):
AATATCACAGCAAAGCTGCCAGTAAT
Found at i:31684587 original size:33 final size:34
Alignment explanation
Indices: 31684539--31684698 Score: 92
Period size: 28 Copynumber: 5.3 Consensus size: 34
31684529 ATACAACATG
* **
31684539 CAGTAACAGTCTGGG-CTTGAGCCCTATTCAGTAA
1 CAGTAACAGTCTGGGCCTT-AGCCCAACACAGTAA
*
31684573 CAGT-ACAGTGTGGGCCTTAGCCCAACACAGTAA
1 CAGTAACAGTCTGGGCCTTAGCCCAACACAGTAA
*
31684606 CAGT----G--TGGGTCTTAGCCCAACACAGTAA
1 CAGTAACAGTCTGGGCCTTAGCCCAACACAGTAA
31684634 CAGT----G--TGGGCCTTAGCCCAA-A-A-T--
1 CAGTAACAGTCTGGGCCTTAGCCCAACACAGTAA
* *
31684657 -AGTAACAGTGTGGGCCTTAGCCCAATACAGTAA
1 CAGTAACAGTCTGGGCCTTAGCCCAACACAGTAA
*
31684690 TAGT-ACAGT
1 CAGTAACAGT
31684699 GCAATAATGC
Statistics
Matches: 107, Mismatches: 6, Indels: 27
0.76 0.04 0.19
Matches are distributed among these distances:
22 3 0.03
25 1 0.01
26 2 0.02
27 1 0.01
28 56 0.52
29 1 0.01
30 2 0.02
31 1 0.01
33 30 0.28
34 10 0.09
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (34 bp):
CAGTAACAGTCTGGGCCTTAGCCCAACACAGTAA
Found at i:31684610 original size:28 final size:28
Alignment explanation
Indices: 31684572--31684689 Score: 193
Period size: 28 Copynumber: 4.2 Consensus size: 28
31684562 CTATTCAGTA
31684572 ACAGT-ACAGTGTGGGCCTTAGCCCAAC
1 ACAGTAACAGTGTGGGCCTTAGCCCAAC
*
31684599 ACAGTAACAGTGTGGGTCTTAGCCCAAC
1 ACAGTAACAGTGTGGGCCTTAGCCCAAC
*
31684627 ACAGTAACAGTGTGGGCCTTAGCCCAAA
1 ACAGTAACAGTGTGGGCCTTAGCCCAAC
* *
31684655 ATAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGTGGGCCTTAGCCCAAC
31684683 ACAGTAA
1 ACAGTAA
31684690 TAGTACAGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
27 5 0.06
28 79 0.94
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.20
Consensus pattern (28 bp):
ACAGTAACAGTGTGGGCCTTAGCCCAAC
Found at i:31686300 original size:26 final size:26
Alignment explanation
Indices: 31686271--31686321 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
31686261 CACCAATATC
* *
31686271 GCAGCAAATCTACCATTAATAGTATT
1 GCAGCAAAGCTACCAGTAATAGTATT
*
31686297 GCAGCAAAGCTGCCAGTAATAGTAT
1 GCAGCAAAGCTACCAGTAATAGTAT
31686322 ATGTGGCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (26 bp):
GCAGCAAAGCTACCAGTAATAGTATT
Found at i:31693090 original size:24 final size:24
Alignment explanation
Indices: 31693062--31693107 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31693052 TTAAAACTAC
31693062 TTCTAAAGAAAACTC-AAGAGAGAA
1 TTCT-AAGAAAACTCAAAGAGAGAA
* *
31693086 TTCTAGGAGAACTCAAAGAGAG
1 TTCTAAGAAAACTCAAAGAGAG
31693108 TTTTCACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (24 bp):
TTCTAAGAAAACTCAAAGAGAGAA
Found at i:31693335 original size:25 final size:25
Alignment explanation
Indices: 31693307--31693356 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
31693297 TAGAAATTTA
31693307 TTCATAAAGTCTAAAAATTAAAACT
1 TTCATAAAGTCTAAAAATTAAAACT
31693332 TTCATAAAGTCTAAAAATTAAAACT
1 TTCATAAAGTCTAAAAATTAAAACT
31693357 AAGTATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.32
Consensus pattern (25 bp):
TTCATAAAGTCTAAAAATTAAAACT
Found at i:31694390 original size:27 final size:27
Alignment explanation
Indices: 31694360--31694414 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
31694350 ACGGGCAATA
*
31694360 TATGTTAATTTAATATTTCTAAAATTG
1 TATGCTAATTTAATATTTCTAAAATTG
*
31694387 TATGCTAATTTAATATTTCTATAATTG
1 TATGCTAATTTAATATTTCTAAAATTG
31694414 T
1 T
31694415 TTCTTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.05, G:0.07, T:0.53
Consensus pattern (27 bp):
TATGCTAATTTAATATTTCTAAAATTG
Found at i:31706036 original size:25 final size:25
Alignment explanation
Indices: 31705999--31706083 Score: 109
Period size: 25 Copynumber: 3.4 Consensus size: 25
31705989 CTTACGAGCT
31705999 ATAATTGGTAAGCTCCTCTAAGCTGA
1 ATAA-TGGTAAGCTCCTCTAAGCTGA
31706025 ATAATGGTAAGCTCCTCTAAGCTGA
1 ATAATGGTAAGCTCCTCTAAGCTGA
* * * *
31706050 ATAACGGTAATCTCCTTTGAGCTGA
1 ATAATGGTAAGCTCCTCTAAGCTGA
*
31706075 A-ATTGGTAA
1 ATAATGGTAA
31706084 CCCTAATGAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 6 0.11
25 43 0.81
26 4 0.08
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Consensus pattern (25 bp):
ATAATGGTAAGCTCCTCTAAGCTGA
Found at i:31708238 original size:16 final size:16
Alignment explanation
Indices: 31708209--31708262 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
31708199 TTTGGTTCGC
* *
31708209 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
31708225 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31708241 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
31708257 TGTAAT
1 TGTAAT
31708263 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.33, C:0.02, G:0.35, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:31708346 original size:39 final size:43
Alignment explanation
Indices: 31708241--31708350 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
31708231 GGAATAGAGG
31708241 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
31708286 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
31708326 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
31708351 TAATAGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:31708512 original size:16 final size:16
Alignment explanation
Indices: 31708475--31708516 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31708465 TTAATCATAT
*
31708475 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
31708491 TT-AAATATATTATAA
1 TTAAAATATATTATAA
31708506 TTAAAATATAT
1 TTAAAATATAT
31708517 AATTTGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:31708591 original size:61 final size:60
Alignment explanation
Indices: 31708523--31708709 Score: 195
Period size: 61 Copynumber: 3.1 Consensus size: 60
31708513 ATATAATTTG
31708523 ATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 ATAAAATT-TTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
* * * * * * * * *
31708584 ATAAAATTTAAATTAA-C-ATAATTATTAT-TAAATATA-TTATAATTAAAATATATAAT-TT
1 ATAAAATTTTAA-TAATCAAT-ATTCTTATATGAATTTACTCA-AATCATAATATATGATACT
*
31708642 AATAAAATTGTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
1 -ATAAAATT-TTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
31708704 ATAAAA
1 ATAAAA
31708710 GATAATTTGA
Statistics
Matches: 97, Mismatches: 19, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
58 3 0.03
59 32 0.33
60 21 0.22
61 38 0.39
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (60 bp):
ATAAAATTTTAATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACT
Found at i:31708623 original size:120 final size:121
Alignment explanation
Indices: 31708478--31708770 Score: 491
Period size: 120 Copynumber: 2.4 Consensus size: 121
31708468 ATCATATTTA
*
31708478 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTGATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
**
31708543 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATTTAAATT-
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* *
31708598 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTGTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
31708663 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
* * *
31708719 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
31708771 TAAAATAATT
Statistics
Matches: 163, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 161 0.99
121 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:31708643 original size:14 final size:15
Alignment explanation
Indices: 31708594--31708645 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
31708584 ATAAAATTTA
31708594 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
31708609 TATTAAATATATTAT
1 AATTAAATATATTAT
31708624 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
31708637 AATTTAATA
1 AATTAAATA
31708646 AAATTGTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:31708648 original size:59 final size:57
Alignment explanation
Indices: 31708478--31708774 Score: 183
Period size: 59 Copynumber: 5.0 Consensus size: 57
31708468 ATCATATTTA
* *
31708478 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTGATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATTT-ATAAAATT-TAAAT
* * * * * * *
31708537 AATCA-ATATTCTTATATGAATTTACTCA-AATCATAATATATGATACTATAAAATTTAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATGAT-TTATAAAATTTAAA-T
* *
31708598 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTGTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATTT-ATAAAATT-TAAAT
* * * * * * ** *
31708657 AA-TTAA-TATTCTTATATGA-ATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
1 AACATAATTATTATTAAAT-ATA-TTA-T--AATTAAAATATATGAT-TTATAAAATTTAA-AT
* *
31708718 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATTT-ATAAAATTTAAA
31708775 ATAATTATAA
Statistics
Matches: 177, Mismatches: 40, Indels: 43
0.68 0.15 0.17
Matches are distributed among these distances:
57 10 0.06
58 11 0.06
59 57 0.32
60 26 0.15
61 52 0.29
62 12 0.07
63 9 0.05
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (57 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTATAAAATTTAAAT
Found at i:31708824 original size:101 final size:93
Alignment explanation
Indices: 31708711--31708993 Score: 315
Period size: 91 Copynumber: 3.0 Consensus size: 93
31708701 ACTATAAAAG
* * * *
31708711 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT---
* *
31708775 ATAATTATAACTAATAAATTTTCTTATATAAATTTGT
62 -T--CT-TAA-TAATAAATTTTCTTATATAAATTTAT
* *
31708812 ATAATTTAAAATAATTATTATTATATATAATTTAATAATAATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
* *
31708875 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTTTCTTATATAAATTTAT
* *
31708903 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
* *
31708966 AATAATAAAATGTTCTTATATGAATTTA
66 AATAAT-AAATTTTCTTATATAAATTTA
31708994 CTAAAATCAA
Statistics
Matches: 164, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
91 88 0.54
92 22 0.13
93 1 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 48 0.29
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
AATAATAAATTTTCTTATATAAATTTAT
Found at i:31708869 original size:47 final size:46
Alignment explanation
Indices: 31708818--31708961 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
31708808 TTGTATAATT
31708818 TAAAATAATTATTATTATATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
31708865 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
31708909 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
31708956 TAAAAT
1 TAAAAT
31708962 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:31708881 original size:91 final size:91
Alignment explanation
Indices: 31708786--31708993 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
31708776 TAATTATAAC
* * * * *
31708786 TAATAAATTTTCTTATATAAATTTGTATAATTTAAAATAATTATTATTATATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
31708851 AATATATAATTTCATAAAATTCTTGA
66 AATATATAATTTCATAAAATTCTTAA
31708877 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
31708942 GATATATAATTTCATAAAATTCTTAA
66 AATATATAATTTCATAAAATTCTTAA
*
31708968 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
31708994 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 88 0.81
92 20 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATATAATTTCATAAAATTCTTAA
Found at i:31708953 original size:44 final size:43
Alignment explanation
Indices: 31708811--31708953 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
31708801 TATAAATTTG
* *
31708811 TATAATTTAAAATAATTATTATTATATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
31708855 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
31708902 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
31708946 TATAATTT
1 TATAATTT
31708954 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:31708968 original size:47 final size:47
Alignment explanation
Indices: 31708836--31708974 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
31708826 TTATTATTAT
* *
31708836 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
31708883 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
31708927 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
31708974 A
1 A
31708975 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:31712607 original size:19 final size:19
Alignment explanation
Indices: 31712583--31712621 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
31712573 CTAGAAGGAA
31712583 GGAACAGAAGAGGCAAAGG
1 GGAACAGAAGAGGCAAAGG
*
31712602 GGAACAGAAGAGGCAGAGG
1 GGAACAGAAGAGGCAAAGG
31712621 G
1 G
31712622 TAAAACAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.10, G:0.46, T:0.00
Consensus pattern (19 bp):
GGAACAGAAGAGGCAAAGG
Found at i:31713459 original size:23 final size:22
Alignment explanation
Indices: 31713433--31713484 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 22
31713423 TTTTCATCTT
31713433 AGAAACAAAGAGAGCAGAAGAAA
1 AGAAA-AAAGAGAGCAGAAGAAA
*
31713456 AG---AAAGATAGCAGAAGAAA
1 AGAAAAAAGAGAGCAGAAGAAA
31713475 AGAAATAAAG
1 AGAAA-AAAG
31713485 GGGGCGACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
19 18 0.75
23 6 0.25
ACGTcount: A:0.65, C:0.06, G:0.25, T:0.04
Consensus pattern (22 bp):
AGAAAAAAGAGAGCAGAAGAAA
Found at i:31713467 original size:19 final size:19
Alignment explanation
Indices: 31713439--31713479 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
31713429 TCTTAGAAAC
31713439 AAAGAGAGCAGAAGAAAAG
1 AAAGAGAGCAGAAGAAAAG
*
31713458 AAAGATAGCAGAAGAAAAG
1 AAAGAGAGCAGAAGAAAAG
31713477 AAA
1 AAA
31713480 TAAAGGGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.27, T:0.02
Consensus pattern (19 bp):
AAAGAGAGCAGAAGAAAAG
Found at i:31717840 original size:20 final size:19
Alignment explanation
Indices: 31717799--31717839 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
31717789 CAAACACCCT
31717799 AAACCAAAAATTGGTATAA
1 AAACCAAAAATTGGTATAA
31717818 AAACCAAAAATTGGTATAA
1 AAACCAAAAATTGGTATAA
31717837 AAA
1 AAA
31717840 ATTGTGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.20
Consensus pattern (19 bp):
AAACCAAAAATTGGTATAA
Found at i:31718101 original size:13 final size:13
Alignment explanation
Indices: 31718083--31718110 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31718073 TATATAAAAG
31718083 AATATAACAGCAA
1 AATATAACAGCAA
31718096 AATATAACAGCAA
1 AATATAACAGCAA
31718109 AA
1 AA
31718111 AGAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (13 bp):
AATATAACAGCAA
Found at i:31718136 original size:18 final size:19
Alignment explanation
Indices: 31718094--31718133 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
31718084 ATATAACAGC
*
31718094 AAAATATAACAGCAAAAAG
1 AAAATATAAAAGCAAAAAG
31718113 AAAATA-AAAAGC-AAAAG
1 AAAATATAAAAGCAAAAAG
31718130 AAAA
1 AAAA
31718134 ATAGTTGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 5 0.25
19 6 0.30
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.07
Consensus pattern (19 bp):
AAAATATAAAAGCAAAAAG
Found at i:31720844 original size:56 final size:56
Alignment explanation
Indices: 31720772--31720890 Score: 229
Period size: 56 Copynumber: 2.1 Consensus size: 56
31720762 ACGACCGTGT
*
31720772 AAAGAAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
1 AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
31720828 AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
1 AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
31720884 AAAGCAA
1 AAAGCAA
31720891 ATCAAAGTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 62 1.00
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (56 bp):
AAAGCAATTCTAACTAAGATAGCATTGAAGCGTCCTTCAAATTGGATCAAGGCTTG
Found at i:31727600 original size:34 final size:34
Alignment explanation
Indices: 31727557--31727624 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
31727547 AAAGCACGAC
31727557 TTTCAAGTTAGATCCAATTCAATTTAAACCCTAA
1 TTTCAAGTTAGATCCAATTCAATTTAAACCCTAA
31727591 TTTCAAGTTAGATCCAATTCAATTTAAACCCTAA
1 TTTCAAGTTAGATCCAATTCAATTTAAACCCTAA
31727625 ACTTTCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (34 bp):
TTTCAAGTTAGATCCAATTCAATTTAAACCCTAA
Found at i:31727645 original size:36 final size:34
Alignment explanation
Indices: 31727557--31727647 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 34
31727547 AAAGCACGAC
* *
31727557 TTTCAAGTTAGATCCAATTCAATTTAAACCCTAA
1 TTTCAAGTTACAACCAATTCAATTTAAACCCTAA
* *
31727591 TTTCAAGTTAGATCCAATTCAATTTAAACCCTAAA
1 TTTCAAGTTACAACCAATTCAATTTAAACCCT-AA
*
31727626 CTTTCAA-TTCCAACTCAATTCA
1 -TTTCAAGTTACAAC-CAATTCA
31727648 TGAGAAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
34 32 0.63
35 6 0.12
36 13 0.25
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.35
Consensus pattern (34 bp):
TTTCAAGTTACAACCAATTCAATTTAAACCCTAA
Found at i:31728229 original size:22 final size:23
Alignment explanation
Indices: 31728176--31728231 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
31728166 TCCGTTTTTA
* * *
31728176 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
31728199 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
31728221 ATTAAAATTAA
1 ATTAAAATTAA
31728232 TTATTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:31728244 original size:16 final size:16
Alignment explanation
Indices: 31728207--31728246 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
31728197 TTAATAAAAT
* * *
31728207 TAAAACTAATTGTTAT
1 TAAAATTAATTATTAG
31728223 TAAAATTAATTATTAG
1 TAAAATTAATTATTAG
31728239 TAAAATTA
1 TAAAATTA
31728247 TCAAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTATTAG
Found at i:31728307 original size:24 final size:24
Alignment explanation
Indices: 31728280--31728354 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
31728270 ATTAATTGTT
31728280 GTAATAAAATCTAACATTTGATTA
1 GTAATAAAATCTAACATTTGATTA
** *
31728304 GTAA-ATTTATC-AA-ATTATTAATT-
1 GTAATA-AAATCTAACA-T-TTGATTA
31728327 GTAATAAAATCTAACATTTGATTA
1 GTAATAAAATCTAACATTTGATTA
31728351 GTAA
1 GTAA
31728355 ATTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
22 1 0.03
23 16 0.42
24 20 0.53
25 1 0.03
ACGTcount: A:0.45, C:0.07, G:0.08, T:0.40
Consensus pattern (24 bp):
GTAATAAAATCTAACATTTGATTA
Found at i:31728341 original size:47 final size:47
Alignment explanation
Indices: 31728278--31728376 Score: 198
Period size: 47 Copynumber: 2.1 Consensus size: 47
31728268 GTATTAATTG
31728278 TTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAA
1 TTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAA
31728325 TTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAA
1 TTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAA
31728372 TTGTA
1 TTGTA
31728377 TTAATTATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.43
Consensus pattern (47 bp):
TTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAA
Found at i:31728819 original size:21 final size:22
Alignment explanation
Indices: 31728768--31728819 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
31728758 TAAAAATAAG
*
31728768 AAATTAAAATAAAAACAATTTT
1 AAATTAAAATAAAAACAATTTC
* *
31728790 ACATT-AAATAAAATCAA-TTC
1 AAATTAAAATAAAAACAATTTC
31728810 AAATTAAAAT
1 AAATTAAAAT
31728820 TCATCTGGTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 6 0.24
21 15 0.60
22 4 0.16
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATTAAAATAAAAACAATTTC
Found at i:31732416 original size:26 final size:26
Alignment explanation
Indices: 31732339--31732421 Score: 98
Period size: 26 Copynumber: 3.2 Consensus size: 26
31732329 CGTACAAAGG
31732339 CTTTCATATTACGCCACAAACT-CTTT
1 CTTTCATATTACGCCACAAA-TGCTTT
* *
31732365 ATTTCTTATTACGCCACAAA-GACTTT
1 CTTTCATATTACGCCACAAATG-CTTT
* *
31732391 CTTTCATATTATGCCATAAATGCTTT
1 CTTTCATATTACGCCACAAATGCTTT
31732417 CTTTC
1 CTTTC
31732422 CTGACGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
26 47 0.98
27 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (26 bp):
CTTTCATATTACGCCACAAATGCTTT
Found at i:31739697 original size:3 final size:3
Alignment explanation
Indices: 31739675--31739780 Score: 140
Period size: 3 Copynumber: 35.3 Consensus size: 3
31739665 GATCTATCTC
* * * * *
31739675 ACA ACA CCA ACA AAA ACA ACA ACA ACA ACA ACA ACA AAA ATA GCA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
* * *
31739723 ACA ACA ACA AAA ACA ACA ACA ATA GCA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
31739771 ACA ACA ACA A
1 ACA ACA ACA A
31739781 AGCTTACTAC
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.67, C:0.29, G:0.02, T:0.02
Consensus pattern (3 bp):
ACA
Found at i:31741243 original size:32 final size:32
Alignment explanation
Indices: 31741202--31741264 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
31741192 ATAAGGTAAG
31741202 ATTTCTATCCTTAATTATAGGGATTCCAACAT
1 ATTTCTATCCTTAATTATAGGGATTCCAACAT
31741234 ATTTCTATCCTTAATTATAGGGATTCCAACA
1 ATTTCTATCCTTAATTATAGGGATTCCAACA
31741265 CTCCCCCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (32 bp):
ATTTCTATCCTTAATTATAGGGATTCCAACAT
Found at i:31745094 original size:32 final size:32
Alignment explanation
Indices: 31745053--31745117 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
31745043 TAATAAGGTA
31745053 AGATTTCTATCCTTAATTATAGGGATTCCAAC
1 AGATTTCTATCCTTAATTATAGGGATTCCAAC
31745085 AGATTTCTATCCTTAATTATAGGGATTCCAAC
1 AGATTTCTATCCTTAATTATAGGGATTCCAAC
31745117 A
1 A
31745118 ACAACTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (32 bp):
AGATTTCTATCCTTAATTATAGGGATTCCAAC
Found at i:31748669 original size:2 final size:2
Alignment explanation
Indices: 31748662--31748720 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
31748652 AAACAAGGAA
31748662 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
31748704 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
31748721 AACCTCTCAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31749084 original size:20 final size:21
Alignment explanation
Indices: 31749059--31749097 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
31749049 CATAAAATTA
31749059 ATTTTTCT-AAATA-TATTTTT
1 ATTTTT-TGAAATATTATTTTT
31749079 ATTTTTTGAAATATTATTT
1 ATTTTTTGAAATATTATTT
31749098 ACTGATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 11 0.65
21 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTTTTGAAATATTATTTTT
Found at i:31749562 original size:27 final size:27
Alignment explanation
Indices: 31749532--31749593 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
31749522 TTAAGAGTGC
* *
31749532 GCCACAAACGCGTTCTTTACGGAGTTT
1 GCCACAAACGCGTTCCTGACGGAGTTT
** *
31749559 GCCATGAAGGCGTTCCTGACGGAGTTT
1 GCCACAAACGCGTTCCTGACGGAGTTT
31749586 GCCACAAA
1 GCCACAAA
31749594 GACATTTCTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (27 bp):
GCCACAAACGCGTTCCTGACGGAGTTT
Found at i:31749632 original size:26 final size:26
Alignment explanation
Indices: 31749586--31749709 Score: 149
Period size: 26 Copynumber: 4.7 Consensus size: 26
31749576 GACGGAGTTT
* *
31749586 GCCACAAAGACATTTCTTTCATATTTC
1 GCCACAAAGGC-TTTCTTTCATATTAC
31749613 GCCACAAAGGCTTTCTTTCATATTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
** * *
31749639 TTCACAAAGGTTTTCTTTCATATTAT
1 GCCACAAAGGCTTTCTTTCATATTAC
* *
31749665 GCCTCAAAAGCTTTCTTTCATATTAC
1 GCCACAAAGGCTTTCTTTCATATTAC
* *
31749691 GCCATAAAGACTTTCTTTC
1 GCCACAAAGGCTTTCTTTC
31749710 CTAACGTGTT
Statistics
Matches: 81, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
26 71 0.88
27 10 0.12
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (26 bp):
GCCACAAAGGCTTTCTTTCATATTAC
Found at i:31753209 original size:36 final size:36
Alignment explanation
Indices: 31753162--31753233 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
31753152 TGATGCCCTA
**
31753162 CAAAAGTGAAACCTTTGGTAAATTCAAAGAGTTTTG
1 CAAAAGTGAAACCTTTGACAAATTCAAAGAGTTTTG
31753198 CAAAAGTGAAACCTTTGACAAATTCAAAGAGTTTTG
1 CAAAAGTGAAACCTTTGACAAATTCAAAGAGTTTTG
31753234 TGTGAAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (36 bp):
CAAAAGTGAAACCTTTGACAAATTCAAAGAGTTTTG
Found at i:31756993 original size:26 final size:26
Alignment explanation
Indices: 31756936--31756997 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 26
31756926 ACTTATTTTC
* * *
31756936 TCAAAATTTTACTTGGGGCAAAATCG
1 TCAAAATTTTACCTAGGGCAAAATCA
* * *
31756962 TTAAAATTTTACCTAGGGTAAAATTA
1 TCAAAATTTTACCTAGGGCAAAATCA
31756988 TCAAAATTTT
1 TCAAAATTTT
31756998 GTTGGAGGAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (26 bp):
TCAAAATTTTACCTAGGGCAAAATCA
Found at i:31757905 original size:498 final size:490
Alignment explanation
Indices: 31756969--31757950 Score: 1579
Period size: 498 Copynumber: 2.0 Consensus size: 490
31756959 TCGTTAAAAT
* *
31756969 TTTACCTAGGGTAAAATTATCAAAATTTTGTTGGAGGAAAATAGGGATGAGAAAATTGTTTTATA
1 TTTACCAAGGGTAAAATTATCAAAATTTTGTTGGAGGAAAATAGGGATGAGAAAATTATTTTATA
* * *
31757034 TATGAATAATAAAGGTTATTTTGGGAAAAAATGAATCGGGTTGGTTCACATTACAAAGTACTAGG
66 TATGAAGAATAAAGGTTATTTTGGGAAAAAATGAATCGAGTTGGATCACATTACAAAGTACTAGG
*
31757099 TAAAAAAGGCTCAAGTACTCATAATTGGACTCAATGTGAGAAAGGCCCAAAAACCCCTCATGGAC
131 TAAAAAAGGCTCAAGTACTCATAATTGGACTAAATGTGAGAAAGGCCCAAAAACCCCTCATGGAC
* * * *
31757164 ATGAAGGGGGTCGTAACCTTAGTAGGAATACTAGGTTGTGCCATCCACTCTAGTCCTATTCTAAG
196 ATGAAGGGGGCCGCAACCTTAGTAGGAATACTAGGTTGCGCCATCCACTCTAGTACTATTCTAAG
* *
31757229 TAAGATGTTGTTTTTCCATTTGAAATAAGCCACCGTTGCCACTGGTGGTTGAGTTTTCATCTTCT
261 TAAGATATTGTTTTTCCATTTGAAATAAGCCACCGTTGCCACTGGTGGTTGAGTTTTCATATTCT
*
31757294 TTTCTTTTAGATCTCTTCCATCTCCTCTAGTGATCAAACCTACTCCACTCTCCTACTTGAATTCC
326 TTTCTTTTAGATCTCTTCCATCTCCTCTAATGATCAAACCTACTCCACTCTCCTACTTGAATTCC
** * *
31757359 TTACTTTGTATTTTAGACTCACTGATCAAATGATTCTAGTAGATCACTAAACTTCTTCATTCCTT
391 TTACTTTGTATTTTAGACTCACCAATCAAATGATTCTAGTAGATCACTAAAATTCTCCATTCCTT
*
31757424 CACCAAGTCGAACCATCAATTTTGTCGTGGTAAAG
456 CACCAAGTCGAACCATCAATTTTGCCGTGGTAAAG
*
31757459 TTTACCAAGGGTAAAATTGTCAAAATTTTGTTGGAGGAAAATAGGGATGAGAAAATTATTTTATA
1 TTTACCAAGGGTAAAATTATCAAAATTTTGTTGGAGGAAAATAGGGATGAGAAAATTATTTTATA
* *
31757524 TATGAAGATTAAAGTTTATTTTTGGAAAAAGAAAAAAAATGAATCGAGTTGGATCACATTACAAA
66 TATGAAGAATAAAGGTTA-TTTTGG-----G--AAAAAATGAATCGAGTTGGATCACATTACAAA
* *
31757589 GTACTAGGTAAAAAAGGCTCAAGTACTCGTAATTGGACTAAATGTGAGAGAGGCCCAAAAACCCC
123 GTACTAGGTAAAAAAGGCTCAAGTACTCATAATTGGACTAAATGTGAGAAAGGCCCAAAAACCCC
31757654 TCATGGACATGAAGGGGGCCGCAACCTTAGTAGGAATACTAGCG-TGCGCCATCCACTCTAGTAC
188 TCATGGACATGAAGGGGGCCGCAACCTTAGTAGGAATACTAG-GTTGCGCCATCCACTCTAGTAC
* * *
31757718 TATTCTAAGTAGGATATTGTTTTTCCATTTGAAATAAGCCACCGTTGCCGCTTGTGGTTGAGTTT
252 TATTCTAAGTAAGATATTGTTTTTCCATTTGAAATAAGCCACCGTTGCCACTGGTGGTTGAGTTT
**
31757783 TCATATTCTTTTCTTTTAGATCTCTTCTGTCTCCTCTAATGATCAAACCTACTCCACTCTCCTAC
317 TCATATTCTTTTCTTTTAGATCTCTTCCATCTCCTCTAATGATCAAACCTACTCCACTCTCCTAC
* *
31757848 TTTAATTCCTTACTTTGTATTTTAGACTCACCAATCAAATGATTCTTGTAGATCACTAAAATTCT
382 TTGAATTCCTTACTTTGTATTTTAGACTCACCAATCAAATGATTCTAGTAGATCACTAAAATTCT
* * *
31757913 CCATTCCTTCACCAATTCGAATCATCGATTTTGCCGTG
447 CCATTCCTTCACCAAGTCGAACCATCAATTTTGCCGTG
31757951 TTAATTGAGT
Statistics
Matches: 450, Mismatches: 33, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
490 77 0.17
491 6 0.01
496 1 0.00
498 365 0.81
499 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (490 bp):
TTTACCAAGGGTAAAATTATCAAAATTTTGTTGGAGGAAAATAGGGATGAGAAAATTATTTTATA
TATGAAGAATAAAGGTTATTTTGGGAAAAAATGAATCGAGTTGGATCACATTACAAAGTACTAGG
TAAAAAAGGCTCAAGTACTCATAATTGGACTAAATGTGAGAAAGGCCCAAAAACCCCTCATGGAC
ATGAAGGGGGCCGCAACCTTAGTAGGAATACTAGGTTGCGCCATCCACTCTAGTACTATTCTAAG
TAAGATATTGTTTTTCCATTTGAAATAAGCCACCGTTGCCACTGGTGGTTGAGTTTTCATATTCT
TTTCTTTTAGATCTCTTCCATCTCCTCTAATGATCAAACCTACTCCACTCTCCTACTTGAATTCC
TTACTTTGTATTTTAGACTCACCAATCAAATGATTCTAGTAGATCACTAAAATTCTCCATTCCTT
CACCAAGTCGAACCATCAATTTTGCCGTGGTAAAG
Found at i:31758855 original size:49 final size:49
Alignment explanation
Indices: 31758802--31758949 Score: 206
Period size: 49 Copynumber: 3.0 Consensus size: 49
31758792 GTGGATGTAT
*
31758802 GTGGTAGTCTATTTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCA
1 GTGGTAGTTTATTTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCA
* * * * *
31758851 GTGGTTGTTTATTTGCAAATCAATGGTGGCTTGTCCTCAAAGTTTTTTA
1 GTGGTAGTTTATTTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCA
* *
31758900 GTGGCAGTTTATCTGCAAATCAGTGGTGGCTTGTCCACAAATGGTGTTTC
1 GTGGTAGTTTATTTGCAAATCAGTGGTGGCTTGTCCACAAA--GTGTTTC
31758950 GGATGGACGA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
49 79 0.94
51 5 0.06
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38
Consensus pattern (49 bp):
GTGGTAGTTTATTTGCAAATCAGTGGTGGCTTGTCCACAAAGTGTTTCA
Found at i:31764658 original size:22 final size:22
Alignment explanation
Indices: 31764620--31764664 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31764610 GGTGATGGGT
*
31764620 ATAATGTTTTATAAAAATTTGC
1 ATAATGTTTTATAAAAAATTGC
*
31764642 ATAATTGTTTTA-CAAAAATTGC
1 ATAA-TGTTTTATAAAAAATTGC
31764664 A
1 A
31764665 CTGTCATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (22 bp):
ATAATGTTTTATAAAAAATTGC
Found at i:31766332 original size:28 final size:28
Alignment explanation
Indices: 31766292--31766347 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
31766282 AGGTACTTTA
*
31766292 ACGATCCATTCTAATTGTACCTTGCATT
1 ACGATCCATTCTAATTATACCTTGCATT
31766320 ACGATCCATTCTAATTATACCTTGCATT
1 ACGATCCATTCTAATTATACCTTGCATT
31766348 GATTGGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (28 bp):
ACGATCCATTCTAATTATACCTTGCATT
Found at i:31777362 original size:15 final size:14
Alignment explanation
Indices: 31777342--31777369 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31777332 ATCTCCCCCA
31777342 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
31777356 TTTTTTTAGTTTTC
1 TTTTTTTAGTTTTC
31777370 AACACTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTAGTTTTC
Found at i:31781443 original size:26 final size:26
Alignment explanation
Indices: 31781387--31781455 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 26
31781377 ACAGAGTTTG
* * ***
31781387 CCACAAAGACTTACCTTTCATATTTTG
1 CCACAAAGGCTT-TCTTTCATATTACA
31781414 CCACAAAGGCTTTCTTTCATATTACA
1 CCACAAAGGCTTTCTTTCATATTACA
31781440 CCACAAAGGCTTTCTT
1 CCACAAAGGCTTTCTT
31781456 CCCCAACGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 26 0.70
27 11 0.30
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.35
Consensus pattern (26 bp):
CCACAAAGGCTTTCTTTCATATTACA
Found at i:31784510 original size:95 final size:95
Alignment explanation
Indices: 31784338--31784618 Score: 393
Period size: 95 Copynumber: 3.0 Consensus size: 95
31784328 ATGAGCTGTG
* * * * * * * *
31784338 AATC-AGACATTAACCATTACACAATGCTCCTCACACGAGCTTTGAAGAATCTGCAACAAATGCA
1 AATCGAGACATTAACCATTACACGATGTTACTCACACGAGCTGTGAAGAATCCGTAATATATGCA
* *
31784402 GAATCTTAACCATCAGTAAGGTATCCAGAA
66 GGATCTTAGCCATCAGTAAGGTATCCAGAA
* *
31784432 AATCGGGACATTAACCATTACACGATGTTGCTCACACGAGCTGTGAAGAATCCGTAATATATGCA
1 AATCGAGACATTAACCATTACACGATGTTACTCACACGAGCTGTGAAGAATCCGTAATATATGCA
*
31784497 GGATCTTAGCCATCAGTAAGGTATCCAGTA
66 GGATCTTAGCCATCAGTAAGGTATCCAGAA
* * *
31784527 AATCGAGACATTAACTATTACACGATGTTACCCACACGAGCTGTGAAGAATCCATAATATATGCA
1 AATCGAGACATTAACCATTACACGATGTTACTCACACGAGCTGTGAAGAATCCGTAATATATGCA
* *
31784592 GGATCTTAGCCATCGGTGAGGTATCCA
66 GGATCTTAGCCATCAGTAAGGTATCCA
31784619 CCACCATTAC
Statistics
Matches: 167, Mismatches: 19, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 4 0.02
95 163 0.98
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.24
Consensus pattern (95 bp):
AATCGAGACATTAACCATTACACGATGTTACTCACACGAGCTGTGAAGAATCCGTAATATATGCA
GGATCTTAGCCATCAGTAAGGTATCCAGAA
Found at i:31797281 original size:120 final size:120
Alignment explanation
Indices: 31797046--31797261 Score: 273
Period size: 120 Copynumber: 1.8 Consensus size: 120
31797036 ACGATTCTTT
*
31797046 TTAACTCTTTTCCCCATTATTAGTTCCTAAAAACAACAAATCCAAAAACCCATTAATACCTTAAA
1 TTAACTCTTTTCCCCATCATTAGTTCCTAAAAACAACAAATCCAAAAACCCATTAATACCTTAAA
* * * **
31797111 CCCAGAATCATAGAAGCAATCAAATAATAAAAAATGGAAAAAATTTCCAAACGTC
66 CCCAGAATCACAAAAGCAATCAAATAAGAAAAAATGGAAAAAAGATCCAAACGTC
* * *
31797166 TTAACTCTTTTCTCCATCATTAGTTCCT-AAAA-AACAACTCTAAATAA-CCATTAACTA-C-TA
1 TTAACTCTTTTCCCCATCATTAGTTCCTAAAAACAACAAATCCAAA-AACCCATTAA-TACCTTA
*
31797226 AACCC-TAATCACAAAAGCAATCAAATAAGGAAAAAA
64 AACCCAGAATCACAAAAGCAATCAAATAA-GAAAAAA
31797262 GTGAAGGAAA
Statistics
Matches: 85, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
116 20 0.24
117 13 0.15
118 18 0.21
119 8 0.09
120 26 0.31
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (120 bp):
TTAACTCTTTTCCCCATCATTAGTTCCTAAAAACAACAAATCCAAAAACCCATTAATACCTTAAA
CCCAGAATCACAAAAGCAATCAAATAAGAAAAAATGGAAAAAAGATCCAAACGTC
Found at i:31798770 original size:7 final size:7
Alignment explanation
Indices: 31798657--31798767 Score: 123
Period size: 7 Copynumber: 15.9 Consensus size: 7
31798647 TTCTTTTCAA
*
31798657 CTCAATA
1 CTCAATC
31798664 CTCAATC
1 CTCAATC
31798671 CTCAATC
1 CTCAATC
*
31798678 CTAAATC
1 CTCAATC
*
31798685 TTCAATC
1 CTCAATC
* *
31798692 TTCAATT
1 CTCAATC
* *
31798699 TTTAATC
1 CTCAATC
* *
31798706 ATCAATT
1 CTCAATC
*
31798713 CTCAATT
1 CTCAATC
31798720 CTCAATC
1 CTCAATC
31798727 CTCAATC
1 CTCAATC
31798734 CTCAATC
1 CTCAATC
31798741 CTCAATC
1 CTCAATC
31798748 CTCAATC
1 CTCAATC
*
31798755 CTCAATT
1 CTCAATC
31798762 CTCAAT
1 CTCAAT
31798768 TCTGAAATTT
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 91 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (7 bp):
CTCAATC
Found at i:31812382 original size:34 final size:34
Alignment explanation
Indices: 31812344--31812440 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 34
31812334 TAAAGTCATG
31812344 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
* *
31812378 CATTA---AAC--T-AAGTCATGTT-AGTTT--A-
1 CATTATGTAACTTTCATGTTA-GTTAAGTTTGCAT
31812403 -ATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
1 CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
31812436 CATTA
1 CATTA
31812441 AATTAAGTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 24
0.63 0.05 0.32
Matches are distributed among these distances:
24 4 0.09
26 1 0.02
27 3 0.06
28 9 0.19
29 8 0.17
30 9 0.19
31 3 0.06
32 1 0.02
34 9 0.19
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.45
Consensus pattern (34 bp):
CATTATGTAACTTTCATGTTAGTTAAGTTTGCAT
Found at i:31812394 original size:33 final size:33
Alignment explanation
Indices: 31812357--31812452 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 33
31812347 TATGTAACTT
31812357 TCATGTTAGTTAAGTTTGCATCATTAAACTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAACTAAG
* *
31812390 TCATGTTAGTTTAA--TT--AT--GT-AACT--T
1 TCATGTTAG-TTAAGTTTGCATCATTAAACTAAG
*
31812415 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAACTAAG
31812448 TCATG
1 TCATG
31812453 CATTAACTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
24 4 0.08
25 9 0.19
26 2 0.04
27 4 0.08
28 3 0.06
30 3 0.06
31 3 0.06
32 2 0.04
33 14 0.29
34 4 0.08
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (33 bp):
TCATGTTAGTTAAGTTTGCATCATTAAACTAAG
Found at i:31814185 original size:28 final size:28
Alignment explanation
Indices: 31814137--31814213 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
31814127 AGTAATAGGA
* *
31814137 AATTCCATTA-GTTATCTTAGACTAATT
1 AATTTCATTAGGTTATTTTAGACTAATT
*
31814164 AATTTCATTAGGTTATTTTAGATTAATT
1 AATTTCATTAGGTTATTTTAGACTAATT
* *
31814192 GATTTAATTAGGTTAATTTTAG
1 AATTTCATTAGGTT-ATTTTAG
31814214 GTTAAGTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 9 0.21
28 27 0.63
29 7 0.16
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.49
Consensus pattern (28 bp):
AATTTCATTAGGTTATTTTAGACTAATT
Found at i:31814227 original size:29 final size:29
Alignment explanation
Indices: 31814170--31814236 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
31814160 AATTAATTTC
* * *
31814170 ATTAGGTT-ATTTTAGATTAATTGATTTA
1 ATTAGGTTAATTTTAGATTAAGTAAATTA
*
31814198 ATTAGGTTAATTTTAGGTTAAGTAAATTA
1 ATTAGGTTAATTTTAGATTAAGTAAATTA
*
31814227 ATTAGTTTAA
1 ATTAGGTTAA
31814237 CTAATATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 8 0.24
29 25 0.76
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (29 bp):
ATTAGGTTAATTTTAGATTAAGTAAATTA
Found at i:31819721 original size:28 final size:29
Alignment explanation
Indices: 31819689--31819772 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
31819679 ATTAGTTACC
*
31819689 TTAGACTAATTAATTTCATTAGGTT-ATT
1 TTAGATTAATTAATTTCATTAGGTTAATT
31819717 TTAGATTAATTAA-TTCAATTAGGTTAATT
1 TTAGATTAATTAATTTC-ATTAGGTTAATT
* * * *
31819746 TTAGTTTAAGTAATTTAATTAGTTTAA
1 TTAGATTAATTAATTTCATTAGGTTAA
31819773 CTAATATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
27 3 0.06
28 20 0.42
29 23 0.48
30 2 0.04
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.50
Consensus pattern (29 bp):
TTAGATTAATTAATTTCATTAGGTTAATT
Found at i:31828989 original size:21 final size:22
Alignment explanation
Indices: 31828963--31829004 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
31828953 GTTCTTGCGT
31828963 TTTTTATTTT-CTTTATTTTTC
1 TTTTTATTTTACTTTATTTTTC
*
31828984 TTTTTATTTTATTTTATTTTT
1 TTTTTATTTTACTTTATTTTT
31829005 GTTCGTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTATTTTACTTTATTTTTC
Found at i:31834960 original size:54 final size:54
Alignment explanation
Indices: 31834902--31835358 Score: 335
Period size: 54 Copynumber: 8.4 Consensus size: 54
31834892 CAATTCGCTG
* * ** * *
31834902 CTTACAAGATTTTTCT-AGTCTTACGGCTGGCTAATTTAATATCTCAACCTTATA
1 CTTACAAGATTTTT-TGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
* ** * * *
31834956 CTTACAGGATTTTCCCG-ATCTTACAGTTTGCCGATTTAAGATCGCAACCTTATG
1 CTTACAAGATTTT-TTGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
* * * * ***
31835010 CTTATAAGATTTTTTAAATCTTGCGGCTGGCCGATTTAAGATCGTTGCCTTATA
1 CTTACAAGATTTTTTGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
* * ** ***
31835064 CTTACAGGATTTTTTGAATCTTGCGATTTTTTGATTTAAGATCGCAACCTTATA
1 CTTACAAGATTTTTTGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
* * * * * *
31835118 CTTACAAGATTTTCTGAATCTTACAGCTCGCTGATTTAAGATCGAAACATTATA
1 CTTACAAGATTTTTTGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
* * ** * *
31835172 CTTATAAGATTTTTTGAATATTGTGGGTTGCCGATTTAAGATCTCAACCTTATA
1 CTTACAAGATTTTTTGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
*** *** ** *
31835226 CTTACAAGATTTTCCAAATCTTGTTGCTCACCAATTTAAGATCGCAACCTGCCTTATA
1 CTTACAAGATTTTTTGAATCTTACGGCTTGCCGATTTAAGATCGCAA----CCTTATA
* * ** * * *
31835284 CTTGCAAGATTTTATGAATCTTGTGGCTCGCC-ATTTAAGATCCCAGCCTTATA
1 CTTACAAGATTTTTTGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
* *
31835337 CTTACAAGATTTCTAGAATCTT
1 CTTACAAGATTTTTTGAATCTT
31835359 GCAGTTTTCA
Statistics
Matches: 313, Mismatches: 83, Indels: 15
0.76 0.20 0.04
Matches are distributed among these distances:
53 25 0.08
54 243 0.78
57 12 0.04
58 33 0.11
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (54 bp):
CTTACAAGATTTTTTGAATCTTACGGCTTGCCGATTTAAGATCGCAACCTTATA
Found at i:31835178 original size:162 final size:162
Alignment explanation
Indices: 31834935--31835238 Score: 414
Period size: 162 Copynumber: 1.9 Consensus size: 162
31834925 CGGCTGGCTA
* * * * *
31834935 ATTTAATATCTCAACCTTATACTTACAGGATTTTCCCGATCTTACAGTTTGCCGATTTAAGATCG
1 ATTTAAGATCGCAACCTTATACTTACAAGATTTTCCCGATCTTACAGCTCGCCGATTTAAGATCG
* * * * **
31835000 CAACCTTATGCTTATAAGATTTTTTAAATCTTGCGGCTGGCCGATTTAAGATCGT-TGCCTTATA
66 AAACATTATACTTATAAGATTTTTTAAATATTGCGGCTGGCCGATTTAAGATC-TCAACCTTATA
*
31835064 CTTACAGGATTTTTTGAATCTTGCGATTTTTTG
130 CTTACAAGATTTTTTGAATCTTGCGATTTTTTG
* *
31835097 ATTTAAGATCGCAACCTTATACTTACAAGATTTT-CTGAATCTTACAGCTCGCTGATTTAAGATC
1 ATTTAAGATCGCAACCTTATACTTACAAGATTTTCCCG-ATCTTACAGCTCGCCGATTTAAGATC
* * * *
31835161 GAAACATTATACTTATAAGATTTTTTGAATATTGTGGGTTGCCGATTTAAGATCTCAACCTTATA
65 GAAACATTATACTTATAAGATTTTTTAAATATTGCGGCTGGCCGATTTAAGATCTCAACCTTATA
31835226 CTTACAAGATTTT
130 CTTACAAGATTTT
31835239 CCAAATCTTG
Statistics
Matches: 122, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
161 3 0.02
162 119 0.98
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.40
Consensus pattern (162 bp):
ATTTAAGATCGCAACCTTATACTTACAAGATTTTCCCGATCTTACAGCTCGCCGATTTAAGATCG
AAACATTATACTTATAAGATTTTTTAAATATTGCGGCTGGCCGATTTAAGATCTCAACCTTATAC
TTACAAGATTTTTTGAATCTTGCGATTTTTTG
Found at i:31835265 original size:162 final size:162
Alignment explanation
Indices: 31834934--31835348 Score: 397
Period size: 162 Copynumber: 2.5 Consensus size: 162
31834924 ACGGCTGGCT
* * * * * *
31834934 AATTTAATATCTCAACCTTATACTTACAGGATTTTCCCG-ATCTTACAGTTTGCCGATTTAAGAT
1 AATTTAAGATCGCAACCTTATACTTACAAGATTTT-CTGAATCTTACAGCTCGCCGATTTAAGAT
* * * * **
31834998 CGCAACCTTATGCTTATAAGATTTTTTAAATCTTGCGGCTGGCCGATTTAAGATCGTTGCCTTAT
65 CGAAACATTATACTTATAAGATTTTTTAAATATTGCGGCTGGCCGATTTAAGATCGTAACCTTAT
* *** * ****
31835063 ACTTACAGGATTTTTTGAATCTTGCGATTTTTT
130 ACTTACAAGATTTTCCAAATCTTGCGACTCACC
* *
31835096 GATTTAAGATCGCAACCTTATACTTACAAGATTTTCTGAATCTTACAGCTCGCTGATTTAAGATC
1 AATTTAAGATCGCAACCTTATACTTACAAGATTTTCTGAATCTTACAGCTCGCCGATTTAAGATC
* * * *
31835161 GAAACATTATACTTATAAGATTTTTTGAATATTGTGGGTTGCCGATTTAAGATC-TCAACCTTAT
66 GAAACATTATACTTATAAGATTTTTTAAATATTGCGGCTGGCCGATTTAAGATCGT-AACCTTAT
*
31835225 ACTTACAAGATTTTCCAAATCTTGTTG-CTCACC
130 ACTTACAAGATTTTCCAAATCTTG-CGACTCACC
* * ***
31835258 AATTTAAGATCGCAACCTGCCTTATACTTGCAAGATTTTATGAATCTTGTGGCTCGCC-ATTTAA
1 AATTTAAGATCGCAA----CCTTATACTTACAAGATTTTCTGAATCTTACAGCTCGCCGATTTAA
** * * *
31835322 GATCCCAGCCTTATACTTACAAGATTT
62 GATCGAAACATTATACTTATAAGATTT
31835349 CTAGAATCTT
Statistics
Matches: 206, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
161 3 0.01
162 141 0.68
163 1 0.00
165 28 0.14
166 33 0.16
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (162 bp):
AATTTAAGATCGCAACCTTATACTTACAAGATTTTCTGAATCTTACAGCTCGCCGATTTAAGATC
GAAACATTATACTTATAAGATTTTTTAAATATTGCGGCTGGCCGATTTAAGATCGTAACCTTATA
CTTACAAGATTTTCCAAATCTTGCGACTCACC
Found at i:31835500 original size:23 final size:23
Alignment explanation
Indices: 31835459--31835520 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
31835449 GTACAATTCG
* *
31835459 CAATATTTTCGCAACACTATTCT-
1 CAATATTTTCACAATACTATT-TA
* *
31835482 CATTATTTTTACAATACTATTTA
1 CAATATTTTCACAATACTATTTA
31835505 CAATATTTTCACAATA
1 CAATATTTTCACAATA
31835521 AAGCTAGCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (23 bp):
CAATATTTTCACAATACTATTTA
Found at i:31835605 original size:24 final size:24
Alignment explanation
Indices: 31835578--31835628 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
31835568 ACTCGTTGAA
*
31835578 TTTTTGCTGTACAGCTCG-CCAAT
1 TTTTTGCTATACAGCTCGTCCAAT
* *
31835601 TTTTTGTTATACAGCTCGTCTAAT
1 TTTTTGCTATACAGCTCGTCCAAT
31835625 TTTT
1 TTTT
31835629 CAATATACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.18, C:0.20, G:0.14, T:0.49
Consensus pattern (24 bp):
TTTTTGCTATACAGCTCGTCCAAT
Found at i:31836562 original size:27 final size:27
Alignment explanation
Indices: 31836484--31836562 Score: 81
Period size: 27 Copynumber: 3.0 Consensus size: 27
31836474 TCTAACCTAT
* * *
31836484 TAATTTATATTTCTAATTATCTTCACTA
1 TAATTTAAACTTCTAATTATCTT-AATA
* * *
31836512 -AATTAAAACTT-TAATTTTCATAATA
1 TAATTTAAACTTCTAATTATCTTAATA
31836537 TAATTTAAACTTCTAATTATCTTAAT
1 TAATTTAAACTTCTAATTATCTTAAT
31836563 TTACACAAAA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
25 3 0.08
26 18 0.45
27 19 0.47
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (27 bp):
TAATTTAAACTTCTAATTATCTTAATA
Found at i:31838484 original size:49 final size:49
Alignment explanation
Indices: 31838414--31838554 Score: 165
Period size: 49 Copynumber: 2.8 Consensus size: 49
31838404 CTGTACTGCA
* * * ** *
31838414 AATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCC
1 AATGCCATGTCC-AGACATGGTCTTACGTGGGACCTCTCATATCGGTGCC
* * *
31838464 CATGCCATGTCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCC
1 AATGCCATGTCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTGCC
* *
31838513 AACGCCATGTCCCAGACATGGTCTTACGTGGGACCTTTCATA
1 AATGCCATGT-CCAGACATGGTCTTACGTGGGACCTCTCATA
31838555 ACCTCAATAA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 38 0.50
50 38 0.50
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (49 bp):
AATGCCATGTCCAGACATGGTCTTACGTGGGACCTCTCATATCGGTGCC
Found at i:31843337 original size:18 final size:18
Alignment explanation
Indices: 31843309--31843352 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
31843299 GATGAAATTT
31843309 ATATGAAAATCCCAGAAGG
1 ATAT-AAAATCCCAGAAGG
*
31843328 ATTTAAAATCCCAGAAGG
1 ATATAAAATCCCAGAAGG
31843346 ATATAAA
1 ATATAAA
31843353 GTTTATCGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (18 bp):
ATATAAAATCCCAGAAGG
Found at i:31845926 original size:41 final size:41
Alignment explanation
Indices: 31845853--31846021 Score: 223
Period size: 41 Copynumber: 4.1 Consensus size: 41
31845843 ATTTCGGGGT
* * * * *
31845853 TTTAGCGACGTTTTTTGCAAACGCGCCGCTAATGATCAGGGC
1 TTTAGCGGCGTTTTTGGGAAA-GCGCCACTAATGCTCAGGGC
31845895 TTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGC
31845936 TTTAGCGGCGTTTTTGGGAAAGCG-CAGCTAATGCTCAGGGC
1 TTTAGCGGCGTTTTTGGGAAAGCGCCA-CTAATGCTCAGGGC
* ** * *
31845977 TTTAGCGGCGTTTTTTGTTAAGCGCCGCTAATGCTCAGGGA
1 TTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGC
31846018 TTTA
1 TTTA
31846022 AAATAATCTA
Statistics
Matches: 115, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
40 2 0.02
41 94 0.82
42 19 0.17
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCACTAATGCTCAGGGC
Found at i:31846596 original size:7 final size:7
Alignment explanation
Indices: 31846537--31846649 Score: 52
Period size: 7 Copynumber: 15.9 Consensus size: 7
31846527 TATGAATTAA
*
31846537 GGTTTAT
1 GGTTTAG
31846544 GGTTTAAG
1 GGTTT-AG
*
31846552 GG-TTGG
1 GGTTTAG
*
31846558 GGTTTAA
1 GGTTTAG
*
31846565 GGTGTAAG
1 GGT-TTAG
31846573 GG-TTAG
1 GGTTTAG
*
31846579 GGGTTAGG
1 GGTTTA-G
31846587 GGTTTAG
1 GGTTTAG
*
31846594 GGTTTAT
1 GGTTTAG
* *
31846601 GTTTTAT
1 GGTTTAG
**
31846608 AATTTAG
1 GGTTTAG
31846615 GGTTTAG
1 GGTTTAG
*
31846622 GAG-ATAG
1 G-GTTTAG
*
31846629 GGGTTAGG
1 GGTTTA-G
31846637 GGTTTAG
1 GGTTTAG
31846644 GGTTTA
1 GGTTTA
31846650 AATTAATTAG
Statistics
Matches: 80, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
6 9 0.11
7 51 0.64
8 20 0.25
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:31851721 original size:43 final size:41
Alignment explanation
Indices: 31851643--31851848 Score: 204
Period size: 43 Copynumber: 4.9 Consensus size: 41
31851633 GTTTATGAAA
*
31851643 AAAGTGCCGCTAAAGATCATGTT-TTTAGCGGCGTTTGTGGG
1 AAAGCGCCGCTAAAG-TCATGTTCTTTAGCGGCGTTTGTGGG
* *
31851684 TGAAGCGCTGCTAAATGTCATGTTCTTTAGCGGCGTTTGTGGG
1 -AAAGCGCCGCTAAA-GTCATGTTCTTTAGCGGCGTTTGTGGG
* * *
31851727 CAAAGCGCCGCTAAAAGT-ACGACTCTTTAG-GGCGTTCGTGGG
1 -AAAGCGCCGCT-AAAGTCATG-TTCTTTAGCGGCGTTTGTGGG
* *
31851769 AAAGTGCCGCTAAAGGTCA-GTGTCTTTAGCGGCGTTTGTAGGA
1 AAAGCGCCGCTAAA-GTCATGT-TCTTTAGCGGCGTTTGT-GGG
* *
31851812 AAAGCGCCGCTAAAGATTATGGTCTTTAGCGGCGTTT
1 AAAGCGCCGCTAAAG-TCATGTTCTTTAGCGGCGTTT
31851849 TTTAGAAAAG
Statistics
Matches: 137, Mismatches: 16, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
40 3 0.02
41 20 0.15
42 41 0.30
43 69 0.50
44 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.29
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGTCATGTTCTTTAGCGGCGTTTGTGGG
Found at i:31851806 original size:84 final size:86
Alignment explanation
Indices: 31851666--31851847 Score: 228
Period size: 84 Copynumber: 2.1 Consensus size: 86
31851656 AGATCATGTT
* * * * * *
31851666 TTTAGCGGCGTTTGTGGGTGAAGCGCTGCTAAATGTCATGTTCTTTAGCGGCGTTTGTGGGCAAA
1 TTTAGCGGCGTTCGTGGGTAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTAGGAAAA
31851731 GCGCCGCTAAAAGTACGACTC
66 GCGCCGCTAAAAGTACGACTC
*
31851752 TTTAG-GGCGTTCGTGGG-AAAGTGCCGCTAAAGGTCA-GTGTCTTTAGCGGCGTTTGTAGGAAA
1 TTTAGCGGCGTTCGTGGGTAAAGCGCCGCTAAAGGTCATGT-TCTTTAGCGGCGTTTGTAGGAAA
* * *
31851814 AGCGCCGCTAAAGATTATG-GTC
65 AGCGCCGCTAAA-AGTACGACTC
31851836 TTTAGCGGCGTT
1 TTTAGCGGCGTT
31851848 TTTTAGAAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
83 2 0.02
84 55 0.66
85 21 0.25
86 5 0.06
ACGTcount: A:0.20, C:0.18, G:0.32, T:0.29
Consensus pattern (86 bp):
TTTAGCGGCGTTCGTGGGTAAAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTAGGAAAA
GCGCCGCTAAAAGTACGACTC
Found at i:31851857 original size:43 final size:43
Alignment explanation
Indices: 31851624--31851866 Score: 187
Period size: 43 Copynumber: 5.7 Consensus size: 43
31851614 GAGTCGTACT
* * * * *
31851624 TTTAGTGGCGTTTATGAAAAAAGTGCCGCTAAAGATCAT-GTT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
* ** * *
31851666 TTTAGCGGCGTTTGTGGGTGAAGCGCTGCTAAATG-TCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAA-GATCATGGTC
* * * *
31851709 TTTAGCGGCGTTTGTGGGCAAAGCGCCGCTAAA-AGT-ACGACTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGA-TCATG-GTC
* * * *
31851752 TTTAG-GGCGTTCGTG-GGAAAGTGCCGCTAAAGGTCA-GTGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATG-GTC
*
31851793 TTTAGCGGCGTTTGT-AGGAAAAGCGCCGCTAAAGATTATGGTC
1 TTTAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGATCATGGTC
* * *
31851836 TTTAGCGGCGTTTTTTAGAAAAGCGCTGCTA
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTA
31851867 GAGTTAGCGA
Statistics
Matches: 161, Mismatches: 28, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
41 23 0.14
42 49 0.30
43 87 0.54
44 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
Found at i:31853442 original size:34 final size:34
Alignment explanation
Indices: 31853403--31853471 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
31853393 TAGATAATTT
31853403 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
1 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
*
31853437 TAAAGAGTTTTATTCGGGTTCAATTACTCTTGTA
1 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
31853471 T
1 T
31853472 TTTACCTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (34 bp):
TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
Found at i:31854006 original size:20 final size:20
Alignment explanation
Indices: 31853981--31854071 Score: 67
Period size: 20 Copynumber: 4.3 Consensus size: 20
31853971 ATTAGTTAAT
31853981 AAAAAAAGCAAAAAGCGCAA
1 AAAAAAAGCAAAAAGCGCAA
* * *
31854001 AAAAAAAGTTGAGAAAAATCGTAAA
1 AAAAAAA---G-CAAAAAGCG-CAA
*
31854026 AAAAAAAGCAAACTA-CGCAA
1 AAAAAAAGCAAA-AAGCGCAA
* *
31854046 AAAAAAGGCAAACAGCGCAA
1 AAAAAAAGCAAAAAGCGCAA
31854066 AAAAAA
1 AAAAAA
31854072 GAAAAAAAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.02
20 31 0.55
21 5 0.09
22 2 0.04
23 1 0.02
24 7 0.12
25 9 0.16
ACGTcount: A:0.67, C:0.13, G:0.14, T:0.05
Consensus pattern (20 bp):
AAAAAAAGCAAAAAGCGCAA
Found at i:31854072 original size:20 final size:20
Alignment explanation
Indices: 31854024--31854072 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
31854014 AAAAATCGTA
*
31854024 AAAAAAAAAGCAAACTACGC
1 AAAAAAAAGGCAAACTACGC
31854044 AAAAAAAAGGCAAAC-AGCGC
1 AAAAAAAAGGCAAACTA-CGC
31854064 AAAAAAAAG
1 AAAAAAAAG
31854073 AAAAAAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.67, C:0.16, G:0.14, T:0.02
Consensus pattern (20 bp):
AAAAAAAAGGCAAACTACGC
Found at i:31859656 original size:34 final size:34
Alignment explanation
Indices: 31859617--31859685 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
31859607 TAGATAATTT
31859617 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
1 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
*
31859651 TAAAGAGTTTTATTCGGGTTCAATTACTCTTGTA
1 TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
31859685 T
1 T
31859686 TTTGCCTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (34 bp):
TAAAGAGTTTTATTAGGGTTCAATTACTCTTGTA
Found at i:31863328 original size:11 final size:11
Alignment explanation
Indices: 31863312--31863336 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31863302 ATCTATTATT
31863312 ACATCAATTTC
1 ACATCAATTTC
31863323 ACATCAATTTC
1 ACATCAATTTC
31863334 ACA
1 ACA
31863337 ATTTATACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (11 bp):
ACATCAATTTC
Done.