Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 7 of 207
Found at i:2369174 original size:3 final size:3
Alignment explanation
Indices: 2369166--2369214 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
2369156 TGGTGTTTTA
*
2369166 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT TGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
2369214 G
1 G
2369215 TAATAGCCAC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GGT
Found at i:2372027 original size:27 final size:26
Alignment explanation
Indices: 2371997--2372054 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
2371987 TTATTTTTTA
2371997 TTTTTATTTTTAAATTTTAAAAATATT
1 TTTTTATTTTT-AATTTTAAAAATATT
* *
2372024 TTTTTATTTTTTATTTTTAAAATATT
1 TTTTTATTTTTAATTTTAAAAATATT
2372050 TTTTT
1 TTTTT
2372055 GTGTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 18 0.62
27 11 0.38
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (26 bp):
TTTTTATTTTTAATTTTAAAAATATT
Found at i:2372643 original size:7 final size:7
Alignment explanation
Indices: 2372631--2372655 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2372621 TATATATATT
2372631 TTTATAA
1 TTTATAA
2372638 TTTATAA
1 TTTATAA
2372645 TTTATAA
1 TTTATAA
2372652 TTTA
1 TTTA
2372656 ACAAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTATAA
Found at i:2393136 original size:19 final size:19
Alignment explanation
Indices: 2393114--2393150 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2393104 ATATTAACTT
2393114 TTTTTTAAAAAATAATTTA
1 TTTTTTAAAAAATAATTTA
* *
2393133 TTTTTTAAGAAATCATTT
1 TTTTTTAAAAAATAATTT
2393151 TTAGTAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (19 bp):
TTTTTTAAAAAATAATTTA
Found at i:2397954 original size:30 final size:31
Alignment explanation
Indices: 2397920--2397983 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
2397910 CCTTTGGGGC
2397920 AATATAATTAAAAAAT-ACGTAATTAATTTG
1 AATATAATTAAAAAATGACGTAATTAATTTG
2397950 AATATAATTAAAAAATGACGTAATTAATTTG
1 AATATAATTAAAAAATGACGTAATTAATTTG
2397981 AAT
1 AAT
2397984 TTAGTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (31 bp):
AATATAATTAAAAAATGACGTAATTAATTTG
Found at i:2397992 original size:30 final size:30
Alignment explanation
Indices: 2397920--2397992 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
2397910 CCTTTGGGGC
*
2397920 AATATAATTAAAAAATACGTAATTAATTTG
1 AATATAAGTAAAAAATACGTAATTAATTTG
*
2397950 AATATAATTAAAAAATGACGTAATTAATTTG
1 AATATAAGTAAAAAAT-ACGTAATTAATTTG
*
2397981 AAT-TTAGTAAAA
1 AATATAAGTAAAA
2397993 TAATTTTAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
30 23 0.57
31 17 0.43
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (30 bp):
AATATAAGTAAAAAATACGTAATTAATTTG
Found at i:2403302 original size:21 final size:21
Alignment explanation
Indices: 2403259--2403302 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2403249 ACCATGTTTA
*
2403259 AATAATTTTTTTTGTTGAAAT
1 AATAATTTTTTTAGTTGAAAT
2403280 AATAATTTTTTTAG-TGAATAT
1 AATAATTTTTTTAGTTGAA-AT
2403301 AA
1 AA
2403303 AACAAAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (21 bp):
AATAATTTTTTTAGTTGAAAT
Found at i:2412106 original size:15 final size:14
Alignment explanation
Indices: 2412086--2412115 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2412076 CCGTTCTCTT
2412086 TCCTTCTCCTTTCTC
1 TCCTTCTCC-TTCTC
2412101 TCCTTCTCCTTCTC
1 TCCTTCTCCTTCTC
2412115 T
1 T
2412116 TTCCGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
TCCTTCTCCTTCTC
Found at i:2420193 original size:127 final size:127
Alignment explanation
Indices: 2419967--2420221 Score: 465
Period size: 127 Copynumber: 2.0 Consensus size: 127
2419957 TGATCAGCAT
* * *
2419967 AACAAATCAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACATGGCATG
1 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
*
2420032 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCTAGGAATGAGGACTTACTGTATC
66 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
2420094 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
1 AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
*
2420159 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGGATGAGGACTTACTGTATC
66 ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
2420221 A
1 A
2420222 GCAGAAGAAG
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 123 1.00
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (127 bp):
AACAAATAAACACTGAAGAGAGTATATAACATTTGAATTAAACAACGAAAATTAGACAAGGCATA
ACCTCGTTATATTTCTGTTTAGCATACTATTTTATATCCCAGGAATGAGGACTTACTGTATC
Found at i:2421946 original size:31 final size:32
Alignment explanation
Indices: 2421911--2421971 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
2421901 ATTTTTTAAA
*
2421911 TTTTTTAT-TTTAATTTAGTTTAG-TTTTTAT
1 TTTTTTATATTTTATTTAGTTTAGCTTTTTAT
* *
2421941 TTTTTTATATTTTTTTTATTTTAGCTTTTTA
1 TTTTTTATATTTTATTTAGTTTAGCTTTTTA
2421972 GACTTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 8 0.31
31 12 0.46
32 6 0.23
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (32 bp):
TTTTTTATATTTTATTTAGTTTAGCTTTTTAT
Found at i:2421969 original size:16 final size:16
Alignment explanation
Indices: 2421913--2421971 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
2421903 TTTTTAAATT
*
2421913 TTTTA-TTTTAATTTA
1 TTTTAGTTTTTATTTA
*
2421928 GTTTAGTTTTTATTT-
1 TTTTAGTTTTTATTTA
*
2421943 TTTTA-TATTTTTTTTA
1 TTTTAGT-TTTTATTTA
2421959 TTTTAGCTTTTTA
1 TTTTAG-TTTTTA
2421972 GACTTGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
14 1 0.03
15 15 0.44
16 13 0.38
17 4 0.12
18 1 0.03
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.75
Consensus pattern (16 bp):
TTTTAGTTTTTATTTA
Found at i:2423795 original size:100 final size:99
Alignment explanation
Indices: 2423623--2423821 Score: 344
Period size: 100 Copynumber: 2.0 Consensus size: 99
2423613 TCTAATGACC
2423623 TTCATCGAGATTTACTTAGTGCTTACTCATCATGCTTAAAACATATGAATCATTTAAACGAGTAC
1 TTCATCGAGATTTACTTAGTGCTTACTCATCATGCTTAAAACATATGAATCATTTAAACGAGTAC
2423688 ATAACATGACATACACAATAAACCCAACAACAAA
66 ATAACATGACATACACAATAAACCCAACAACAAA
* *
2423722 TTCATCGAGATTTACTTAAGTGCTTAGTCATCATGCTTAAAACATATGAATTATTTAAACGAGTA
1 TTCATCGAGATTTACTT-AGTGCTTACTCATCATGCTTAAAACATATGAATCATTTAAACGAGTA
* * *
2423787 CATAACATGGCATACATAATAAACCCAATAACAAA
65 CATAACATGACATACACAATAAACCCAACAACAAA
2423822 AACATATGGA
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
99 17 0.18
100 77 0.82
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (99 bp):
TTCATCGAGATTTACTTAGTGCTTACTCATCATGCTTAAAACATATGAATCATTTAAACGAGTAC
ATAACATGACATACACAATAAACCCAACAACAAA
Found at i:2425539 original size:14 final size:14
Alignment explanation
Indices: 2425485--2425540 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
2425475 ACAAATAAAG
*
2425485 TAATTAAATTTTTA
1 TAATTAAAATTTTA
**
2425499 TAATTAAAATTAGA
1 TAATTAAAATTTTA
* *
2425513 AAATATTAAATTTTA
1 TAAT-TAAAATTTTA
2425528 TAATTAAAATTTT
1 TAATTAAAATTTT
2425541 CCCATTTTGA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 22 0.69
15 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
TAATTAAAATTTTA
Found at i:2426937 original size:78 final size:78
Alignment explanation
Indices: 2426808--2426964 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
2426798 GGGTTGTTAA
2426808 GTTTTTATTCTTTCTAAAGTTTAGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
1 GTTTTTATTCTTTCTAAAGTTTAGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
2426873 ATCAATATCTATC
66 ATCAATATCTATC
* *
2426886 GTTTTTATTCTTTTTAAAGTTTGGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
1 GTTTTTATTCTTTCTAAAGTTTAGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
2426951 ATCAATATCTATC
66 ATCAATATCTATC
2426964 G
1 G
2426965 ATGAGTAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (78 bp):
GTTTTTATTCTTTCTAAAGTTTAGTTAACGAGCTCCAAGTGATAATTTGACGATTGGTGCGATGA
ATCAATATCTATC
Found at i:2427551 original size:13 final size:12
Alignment explanation
Indices: 2427529--2427568 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
2427519 CAAACATGTT
*
2427529 TTTTAGTTTTTTA
1 TTTTA-TTTTTAA
2427542 TTTTATTTTTAA
1 TTTTATTTTTAA
2427554 TTTATATTTTTAA
1 TTT-TATTTTTAA
2427567 TT
1 TT
2427569 AATAACTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTATTTTTAA
Found at i:2427730 original size:22 final size:24
Alignment explanation
Indices: 2427705--2427754 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
2427695 ACTTTTCTTT
2427705 ATATATACTTTTT-A-TATGTTAA
1 ATATATACTTTTTCATTATGTTAA
* *
2427727 ATATTTATTTTTTCATTATGTTAA
1 ATATATACTTTTTCATTATGTTAA
2427751 ATAT
1 ATAT
2427755 CATATATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 1 0.04
24 12 0.50
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (24 bp):
ATATATACTTTTTCATTATGTTAA
Found at i:2431152 original size:7 final size:7
Alignment explanation
Indices: 2431132--2431167 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
2431122 TAACAATTGG
*
2431132 ATCTTAA
1 ATCTGAA
*
2431139 ATTTGAA
1 ATCTGAA
2431146 ATCTGAA
1 ATCTGAA
2431153 ATCTGAA
1 ATCTGAA
2431160 ATCTGAA
1 ATCTGAA
2431167 A
1 A
2431168 AGTATAGGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (7 bp):
ATCTGAA
Found at i:2437979 original size:139 final size:139
Alignment explanation
Indices: 2437720--2437993 Score: 401
Period size: 139 Copynumber: 2.0 Consensus size: 139
2437710 GTCCTATAAA
* * * *
2437720 GGAAATGGCTCCTATGACTAAGAAGGGAAAGAAAGCTAAATCTGTGAAGAAGGCTCGGAAAGTGA
1 GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
* * * *
2437785 TAAAGAGTATGTATCCTCTAGTCAAACGCACAAAGAAATTGAAATCTACTTCCTCTTAGCAGAGT
66 TAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACTCCCTCTTAGCAGAGT
2437850 CTGCTCAAG
131 CTGCTCAAG
*
2437859 GGAAATGCCTCCTATGTA-TAAGATGGTG-AAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
1 GGAAATGCCTCCTATG-ACTAAGAAGG-GAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGT
* *
2437922 GATAAAGAATGTGTATCCTCTAGTCAAACGAACGAAGAAATTGAAATCCA-TGCCCTCTTAGCAG
64 GATAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACT-CCCTCTTAGCAG
2437986 AGTCTGCT
128 AGTCTGCT
2437994 TTGTGAGTTT
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
138 1 0.01
139 118 0.98
140 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (139 bp):
GGAAATGCCTCCTATGACTAAGAAGGGAAAGAAAACTAAATCTGGGAAGAAGGCTCAGAAAGTGA
TAAAGAATATGTATCCTCTAGTCAAACGAACAAAGAAATTGAAATCCACTCCCTCTTAGCAGAGT
CTGCTCAAG
Found at i:2448535 original size:2 final size:2
Alignment explanation
Indices: 2448528--2448561 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2448518 AACATTCCTT
2448528 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
2448562 TGTATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:2450483 original size:30 final size:31
Alignment explanation
Indices: 2450442--2450500 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
2450432 AAAATTTTAA
*
2450442 AATTTAAAAAGTACAGG-AGTAAATTTGACT
1 AATTCAAAAAGTACAGGAAGTAAATTTGACT
* *
2450472 AATTCAAAAAGTACGGGAATTAAATTTGA
1 AATTCAAAAAGTACAGGAAGTAAATTTGA
2450501 TCAAATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (31 bp):
AATTCAAAAAGTACAGGAAGTAAATTTGACT
Found at i:2450807 original size:30 final size:30
Alignment explanation
Indices: 2450764--2450833 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
2450754 TTATGGGATC
* *
2450764 TGGATCAAATTAGTCCTTTTTATTATT-AAA
1 TGGATGAAATTAGT-CTTTATATTATTAAAA
*
2450794 TGGATGAATTTAGTCTTTATATTATTAAAA
1 TGGATGAAATTAGTCTTTATATTATTAAAA
*
2450824 AGGATGAAAT
1 TGGATGAAAT
2450834 AAGTTCAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (30 bp):
TGGATGAAATTAGTCTTTATATTATTAAAA
Found at i:2454618 original size:21 final size:21
Alignment explanation
Indices: 2454589--2454630 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2454579 TTCAAGTTTT
2454589 TGTTCTTGAGGTCTAGAGACA
1 TGTTCTTGAGGTCTAGAGACA
* * *
2454610 TGTTTTTGATGTCTCGAGACA
1 TGTTCTTGAGGTCTAGAGACA
2454631 CATGTCCGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.14, G:0.26, T:0.38
Consensus pattern (21 bp):
TGTTCTTGAGGTCTAGAGACA
Found at i:2459473 original size:7 final size:7
Alignment explanation
Indices: 2459465--2459498 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
2459455 TTGGGGGTTC
*
2459465 TTTGTTC
1 TTTGTTT
2459472 TTTGTTT
1 TTTGTTT
2459479 TTTGTTT
1 TTTGTTT
2459486 TTTGTTT
1 TTTGTTT
2459493 TTTGTT
1 TTTGTT
2459499 GGTTTGGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (7 bp):
TTTGTTT
Found at i:2465656 original size:87 final size:90
Alignment explanation
Indices: 2465473--2465675 Score: 304
Period size: 90 Copynumber: 2.3 Consensus size: 90
2465463 TGATTTTAGT
*
2465473 AAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATA
1 AAATTCATATAAGAA-A-TTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
* * *
2465538 TTTAATATTAATTATTTTAAATTGTAT
64 TGTAATATTAATTATTTTAAATTATAC
* *
2465565 AAATTCATATAAGAAAATTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATATG
1 AAATTCATATAAGAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATG
2465630 T-A-A-TAATTATTTTAAATTATAC
66 TAATATTAATTATTTTAAATTATAC
2465652 AAATTCATATAAGATAATTTATTA
1 AAATTCATATAAGA-AATTTATTA
2465676 GTTATAATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
87 31 0.30
88 9 0.09
89 1 0.01
90 46 0.45
91 1 0.01
92 15 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (90 bp):
AAATTCATATAAGAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATATG
TAATATTAATTATTTTAAATTATAC
Found at i:2465757 original size:59 final size:58
Alignment explanation
Indices: 2465687--2465890 Score: 159
Period size: 59 Copynumber: 3.4 Consensus size: 58
2465677 TTATAATTAT
*
2465687 TTTAAATTTTATTA-AATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAA
1 TTTATATTTTA-TAGAATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AA
* * * * **
2465746 TTTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTA-TT-A
1 TTTATATTTTATAGAATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTAA
* * * *
2465809 -TGA-ATTTTATTA-AATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAA
1 TTTATATTTTA-TAGAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAA
*
2465866 TTTATATTTTATAGTATCATATATT
1 TTTATATTTTATAGAATCATATATT
2465891 ATGATTTCAG
Statistics
Matches: 110, Mismatches: 20, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
54 10 0.09
55 4 0.04
56 3 0.03
57 3 0.03
58 6 0.05
59 35 0.32
60 8 0.07
61 15 0.14
62 4 0.04
63 4 0.04
64 1 0.01
65 6 0.05
66 11 0.10
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (58 bp):
TTTATATTTTATAGAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAA
Found at i:2465815 original size:120 final size:120
Alignment explanation
Indices: 2465680--2465984 Score: 504
Period size: 120 Copynumber: 2.5 Consensus size: 120
2465670 TTATTAGTTA
* * * * *
2465680 TAATTATTTTAAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTC
1 TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-
* *
2465744 AATTTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATAT
65 AATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
2465800 TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
1 TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
2465865 ATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
66 ATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
* *
2465920 TGATTATTAAGAATTTTATTATAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 TAATTATTATGAATTTTATTA-AATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
2465985 TAAATATGAT
Statistics
Matches: 174, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
120 129 0.74
121 45 0.26
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (120 bp):
TAATTATTATGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTA
ATTTATATTTTATAGTATCATATATTATGATTTCAGTAAATTCATATAAGAATAT
Found at i:2465851 original size:15 final size:15
Alignment explanation
Indices: 2465816--2465867 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2465806 TTATGAATTT
*
2465816 TATTAAATTAT-ATA
1 TATTTAATTATAATA
2465830 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2465844 TATTTAATAATAAT-
1 TATTTAATTATAATA
2465858 TATGTTAATT
1 TAT-TTAATT
2465868 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2465953 original size:18 final size:18
Alignment explanation
Indices: 2465932--2465967 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2465922 ATTATTAAGA
2465932 ATTTT-ATTATAATTATAT
1 ATTTTAATTATAA-TATAT
2465950 ATTTTAATTATAATATAT
1 ATTTTAATTATAATATAT
2465968 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTAATTATAATATAT
Found at i:2465957 original size:13 final size:14
Alignment explanation
Indices: 2465936--2465978 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2465926 TTAAGAATTT
*
2465936 TATTATAATTAT-A
1 TATTTTAATTATAA
2465949 TATTTTAATTATAA
1 TATTTTAATTATAA
*
2465963 TATATTTAATAATAA
1 TAT-TTTAATTATAA
2465978 T
1 T
2465979 TATGTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 4 0.15
15 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTTAATTATAA
Found at i:2465967 original size:16 final size:16
Alignment explanation
Indices: 2465940--2465987 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2465930 GAATTTTATT
*
2465940 ATAATTATATATTTTA
1 ATAATAATATATTTTA
*
2465956 ATTATAATATA-TTTA
1 ATAATAATATATTTTA
2465971 ATAATAAT-TATGTTTA
1 ATAATAATATAT-TTTA
2465987 A
1 A
2465988 ATATGATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 14 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATAATAATATATTTTA
Found at i:2465972 original size:15 final size:15
Alignment explanation
Indices: 2465936--2465978 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
2465926 TTAAGAATTT
2465936 TATTATAATTAT-ATA
1 TATT-TAATTATAATA
2465951 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
2465965 TATTTAATAATAAT
1 TATTTAATTATAAT
2465979 TATGTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 7 0.28
14 6 0.24
15 12 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:2466225 original size:16 final size:16
Alignment explanation
Indices: 2466201--2466246 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
2466191 TTGATTTGAT
2466201 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
*
2466217 ATTAAACCTCTATTCC
1 ATTACACCTCTATTCC
*
2466233 ATTACGCCTCTATT
1 ATTACACCTCTATT
2466247 ACAATACAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.26, C:0.33, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:2466865 original size:112 final size:111
Alignment explanation
Indices: 2466669--2466890 Score: 340
Period size: 112 Copynumber: 2.0 Consensus size: 111
2466659 TATTCTGTTA
* * *
2466669 AATTAGGGTTACATGTGACTGGATTTGGGGGAATTTTTTTAATTTCTGCTGGGTTTAAGGTTTCT
1 AATTAGGGTTACAGGTGACTGGATTTGGGGAAATTTTTTTAATTTCTGCTAGGTTTAAGGTTTCT
2466734 AAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
66 AAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
* * *
2466780 AATTAGGGTTACAGGTGACTGTCGATTT-GGGAAATTTTTTTACTTTCTGTTAGGTTTAGGGTTT
1 AATTAGGGTTACAGGTGACTG--GATTTGGGGAAATTTTTTTAATTTCTGCTAGGTTTAAGGTTT
*
2466844 CTAAG-CTTCTTTGTTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
64 CTAAGTC-TCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTT
2466891 TTAGAGCTGT
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
111 21 0.21
112 75 0.74
113 5 0.05
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.45
Consensus pattern (111 bp):
AATTAGGGTTACAGGTGACTGGATTTGGGGAAATTTTTTTAATTTCTGCTAGGTTTAAGGTTTCT
AAGTCTCTTTATTTTCAATTCCAGTGGTATAATATTTCTAGGGTTG
Found at i:2471937 original size:161 final size:161
Alignment explanation
Indices: 2471753--2472267 Score: 610
Period size: 160 Copynumber: 3.2 Consensus size: 161
2471743 TGTTCTTTGG
* * * * *
2471753 CTTGCTGCTCTAGTGATCCTCATATAATATTTTATCTTAGCCATGATTGTAAATCATAATCCTTC
1 CTTGCTGGTCTAGTGAACCTCATATAATATTTTATCATAGCCATGATTGTTAATCATACTCCTTC
* *** * * * * *
2471818 ATCAAATTATACCCAGTGAAGCTTCTTCTTTATCGTCTCCTTTCAAAGCTTTTTTTTATTGCCTT
66 ATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCTTTTCTTTATTGCCTT
* * *
2471883 AGAATTTTTATGTT-TGTCATGTTATTTATGA
131 AGAATTTATATGTTCTATCATATT-TTTATGA
* * *
2471914 CTTTCTGGTCTAGTGAACCTCATATAATTTTTTATAATAGCC-TGGATTGTTAATCATACTCCTT
1 CTTGCTGGTCTAGTGAACCTCATATAATATTTTATCATAGCCAT-GATTGTTAATCATACTCCTT
* * * *
2471978 CATTAAAGTATACTTTTTGAAGCTTTTTCTTTATTGCCTCCGTTT-GAAGCTTTTCTTTCTTGCC
65 CATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCC-TTTCGAAGCTTTTCTTTATTGCC
*
2472042 TTAGAATTTATATGTTCTATCATATTGTT-TGA
129 TTAGAATTTATATGTTCTATCATATTTTTATGA
* * * * * * *
2472074 CTTGCTGATCTAGTGTACCTCAGATAATTTTTTATCATAGCCAGGATTTTTAGTCATACT-CTGT
1 CTTGCTGGTCTAGTGAACCTCATATAATATTTTATCATAGCCATGATTGTTAATCATACTCCT-T
*
2472138 CATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCGTTTCTTTATTGCCT
65 CATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCTTTTCTTTATTGCCT
*
2472203 TAGAATTTATATTTTCTATCATATTGTTTATGA
130 TAGAATTTATATGTTCTATCATATT-TTTATGA
* *
2472236 CTTGCT-GTCTAGCGAACCACATATATATATTT
1 CTTGCTGGTCTAGTGAACCTCATATA-ATATTT
2472268 ATCTTAATTC
Statistics
Matches: 300, Mismatches: 45, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
159 5 0.02
160 136 0.45
161 135 0.45
162 24 0.08
ACGTcount: A:0.24, C:0.18, G:0.12, T:0.46
Consensus pattern (161 bp):
CTTGCTGGTCTAGTGAACCTCATATAATATTTTATCATAGCCATGATTGTTAATCATACTCCTTC
ATCAAAGTATACCTTTTGAAGCTTTTTCTTTATTGACTCCTTTCGAAGCTTTTCTTTATTGCCTT
AGAATTTATATGTTCTATCATATTTTTATGA
Found at i:2482034 original size:20 final size:20
Alignment explanation
Indices: 2481980--2482043 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
2481970 TTAGATAGAT
*
2481980 ATTTTTATTTAA--TTTTGAA
1 ATTTTTATATAATTTTTTG-A
*
2481999 ATTTTTTTATAATTTTTTGA
1 ATTTTTATATAATTTTTTGA
** *
2482019 ATTTTTATATGTTTTTTTTA
1 ATTTTTATATAATTTTTTGA
2482039 ATTTT
1 ATTTT
2482044 AAGAGCTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
19 10 0.27
20 22 0.59
21 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
ATTTTTATATAATTTTTTGA
Found at i:2482391 original size:23 final size:23
Alignment explanation
Indices: 2482361--2482406 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2482351 CTGTAGAATG
2482361 ACCAAAATGCAAT-TCGAAGTATA
1 ACCAAAATGCAATCT-GAAGTATA
2482384 ACCAAAATGCAATCTGAAGTATA
1 ACCAAAATGCAATCTGAAGTATA
2482407 GTTTAGGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 21 0.95
24 1 0.05
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (23 bp):
ACCAAAATGCAATCTGAAGTATA
Found at i:2506034 original size:32 final size:29
Alignment explanation
Indices: 2505956--2506034 Score: 72
Period size: 28 Copynumber: 2.6 Consensus size: 29
2505946 AACATATATA
* *
2505956 TTATAAAATTAAAATATATATATGAAAATAT
1 TTATAAAATT--AATAAATATATGAAAAAAT
2505987 TTAGTAAAATT--TAAATATATGAAATAAAT
1 TTA-TAAAATTAATAAATATATGAAA-AAAT
2506016 TCGTATAAAATTAATAAAT
1 T--TATAAAATTAATAAAT
2506035 TATAATTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
28 12 0.30
29 4 0.10
30 7 0.17
31 5 0.12
32 12 0.30
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (29 bp):
TTATAAAATTAATAAATATATGAAAAAAT
Found at i:2513430 original size:22 final size:24
Alignment explanation
Indices: 2513395--2513443 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2513385 ATGATGAAAT
2513395 AAATAATAATATAT-TAGATTTAA
1 AAATAATAATATATATAGATTTAA
2513418 AAATAA-AATATATAATAGATTTAA
1 AAATAATAATATAT-ATAGATTTAA
2513442 AA
1 AA
2513444 CATCAACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 11 0.46
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAATAATATATATAGATTTAA
Found at i:2521697 original size:88 final size:89
Alignment explanation
Indices: 2521545--2521707 Score: 195
Period size: 88 Copynumber: 1.8 Consensus size: 89
2521535 GTCTAGGGAC
* * * *
2521545 TAACTTGAAATAAAAAAAAGTCAAGCTTCAATGTGAGGACAATCGCCTAATTCAAGCCCCAATAT
1 TAACTTGAAACAAAAAAAAGTCAAGCCTCAACGTGAGGACAATCACCTAATTCAAGCCCCAATAT
* *
2521610 AGGAAGAATTACCCAGTTAGGTAT
66 AAGAACAATTACCCAGTTAGGTAT
* * * * * *
2521634 TAACTTGAAACAAAAAAGA-TCAAGCCTCAACGTG-GAGACAATTACCTAGTTCAGGTCCGAATA
1 TAACTTGAAACAAAAAAAAGTCAAGCCTCAACGTGAG-GACAATCACCTAATTCAAGCCCCAATA
2521697 TAAGAACAATT
65 TAAGAACAATT
2521708 GTCGACTTAC
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
87 1 0.02
88 43 0.70
89 17 0.28
ACGTcount: A:0.42, C:0.18, G:0.17, T:0.23
Consensus pattern (89 bp):
TAACTTGAAACAAAAAAAAGTCAAGCCTCAACGTGAGGACAATCACCTAATTCAAGCCCCAATAT
AAGAACAATTACCCAGTTAGGTAT
Found at i:2536024 original size:51 final size:51
Alignment explanation
Indices: 2535957--2536078 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
2535947 CATTGTTATC
* * * *
2535957 TGATCAGTGACGAGTGATAAGTGATTGTTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAG
* *
2536008 TGATAAGTGACAAGTGATGAGTGGTAGCTTTAGCTACACTTATCTGATCAG
1 TGATAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAG
* *
2536059 GGACAAGTGACAAGTGATAA
1 TGATAAGTGACAAGTGATAA
2536079 ATGTGATCCC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (51 bp):
TGATAAGTGACAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAG
Found at i:2537880 original size:21 final size:20
Alignment explanation
Indices: 2537840--2537907 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
2537830 AAGGTTAATC
2537840 TATATAGATAATAAAACGAA
1 TATATAGATAATAAAACGAA
*
2537860 TATATATGATAA-AAACCCGAAA
1 TATATA-GATAATAAA-ACG-AA
* * **
2537882 AATGTTCATAATAAAACGAA
1 TATATAGATAATAAAACGAA
2537902 TATATA
1 TATATA
2537908 AAAGACATTC
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
20 14 0.40
21 13 0.37
22 8 0.23
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (20 bp):
TATATAGATAATAAAACGAA
Found at i:2538713 original size:11 final size:11
Alignment explanation
Indices: 2538697--2538721 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2538687 TCTATCTTGG
2538697 TACCTCTATGT
1 TACCTCTATGT
2538708 TACCTCTATGT
1 TACCTCTATGT
2538719 TAC
1 TAC
2538722 GTTCACCATT
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:0.20, C:0.28, G:0.08, T:0.44
Consensus pattern (11 bp):
TACCTCTATGT
Found at i:2546141 original size:20 final size:22
Alignment explanation
Indices: 2546113--2546161 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2546103 TAAGAGTTTT
*
2546113 ACAATATCCAAAC-A-ATAATA
1 ACAAAATCCAAACAATATAATA
* *
2546133 ACAAAATCCTAGCAATATAATA
1 ACAAAATCCAAACAATATAATA
2546155 ACAAAAT
1 ACAAAAT
2546162 GATAGCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.42
21 1 0.04
22 13 0.54
ACGTcount: A:0.59, C:0.18, G:0.02, T:0.20
Consensus pattern (22 bp):
ACAAAATCCAAACAATATAATA
Found at i:2546167 original size:22 final size:22
Alignment explanation
Indices: 2546127--2546169 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2546117 TATCCAAACA
*
2546127 ATAATAACAAAATCCTAGCAAT
1 ATAATAACAAAATCATAGCAAT
*
2546149 ATAATAACAAAATGATAGCAA
1 ATAATAACAAAATCATAGCAA
2546170 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.07, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATCATAGCAAT
Found at i:2546829 original size:24 final size:24
Alignment explanation
Indices: 2546784--2546829 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
2546774 GAGTGATTTA
* *
2546784 TAAAAAAAATATAAATTCAAATAT
1 TAAAAAAAATAGAAAATCAAATAT
2546808 TAAAATAAAATAGAAAAT-AAAT
1 TAAAA-AAAATAGAAAATCAAAT
2546830 TAAATTGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (24 bp):
TAAAAAAAATAGAAAATCAAATAT
Found at i:2546883 original size:22 final size:20
Alignment explanation
Indices: 2546857--2546896 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
2546847 TGTTTTTTAT
2546857 AAAATTAAAAGAATAAATAATC
1 AAAATTAAAA-AA-AAATAATC
2546879 AAAATTAAAAAAAAATAA
1 AAAATTAAAAAAAAATAA
2546897 AAATTGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (20 bp):
AAAATTAAAAAAAAATAATC
Found at i:2547695 original size:21 final size:21
Alignment explanation
Indices: 2547669--2547712 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2547659 GAAATTTTGA
2547669 ATCGATTTAATATATTAT-TAT
1 ATCGATTTAA-ATATTATATAT
2547690 ATCGATTTAAATATTATATAT
1 ATCGATTTAAATATTATATAT
2547711 AT
1 AT
2547713 TAATATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (21 bp):
ATCGATTTAAATATTATATAT
Found at i:2548890 original size:23 final size:24
Alignment explanation
Indices: 2548822--2548897 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
2548812 CAGTCCATAT
*
2548822 TATTTTTTAAATAATAAAA-TTTAT-
1 TATTTTTT-AAT-TTAAAATTTTATA
*
2548846 TATTTTTTAATTTAATATTTTTATA
1 TATTTTTTAATTTAA-AATTTTATA
*
2548871 TATTTTTTTA-TTAAAATTTTATA
1 TATTTTTTAATTTAAAATTTTATA
2548894 TATT
1 TATT
2548898 ATCATCTTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
22 3 0.07
23 16 0.36
24 17 0.38
25 9 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TATTTTTTAATTTAAAATTTTATA
Found at i:2548956 original size:18 final size:18
Alignment explanation
Indices: 2548925--2548967 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2548915 TTACATTATA
* *
2548925 ATAATAT-TATAAATTAT
1 ATAATATATAAAAATAAT
*
2548942 GTAATATATAAAAATAAT
1 ATAATATATAAAAATAAT
2548960 ATAATATA
1 ATAATATA
2548968 AAATATTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATAATATATAAAAATAAT
Found at i:2563103 original size:30 final size:28
Alignment explanation
Indices: 2563036--2563105 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
2563026 TCTTCATAAA
*
2563036 TTGAAAATTTAGTCTCTATACTTTTATT
1 TTGAAAATTTAATCTCTATACTTTTATT
* *
2563064 TCT-AGAAATTTAATCTCTTTATTTTTTATAT
1 T-TGA-AAATTTAATCTCTATA-CTTTTAT-T
2563095 TTGAAAATTTA
1 TTGAAAATTTA
2563106 TGTCTAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
28 2 0.06
29 15 0.44
30 14 0.41
31 3 0.09
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (28 bp):
TTGAAAATTTAATCTCTATACTTTTATT
Found at i:2565572 original size:436 final size:436
Alignment explanation
Indices: 2564760--2565637 Score: 1702
Period size: 436 Copynumber: 2.0 Consensus size: 436
2564750 CCTTTTGTAC
2564760 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
1 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
2564825 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
66 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
* *
2564890 AATTTAAATGGGTTTGGGCTAGATTCTATTGAGCTCGCAAACTAAGCTCGCGGGGTACTCAGTAA
131 AATTTAAATGGGTTTGGGCTAAATTCTATTGAGCTCGCAAACTAAGCTCGCGGGGTACACAGTAA
2564955 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
196 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
2565020 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
261 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
2565085 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
326 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
2565150 AGACCATATAAACACGTGTTCAGTTTAGAGTAGGATACGTGTCTAT
391 AGACCATATAAACACGTGTTCAGTTTAGAGTAGGATACGTGTCTAT
2565196 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
1 ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
2565261 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
66 TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
*
2565326 ATTTTAAATGGGTTTGGGCTAAATTCTATTGAGCTCGCAAACTAAGCTCGCGGGGTACACAGTAA
131 AATTTAAATGGGTTTGGGCTAAATTCTATTGAGCTCGCAAACTAAGCTCGCGGGGTACACAGTAA
2565391 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
196 GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
*
2565456 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATTGATCCAAAAACCCAAATGG
261 CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
2565521 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
326 GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
**
2565586 AGACCATATAAACACGTGTTTGGTTTAGAGTAGGATACGTGTCTAT
391 AGACCATATAAACACGTGTTCAGTTTAGAGTAGGATACGTGTCTAT
2565632 ATACAT
1 ATACAT
2565638 GAAACCTACC
Statistics
Matches: 436, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
436 436 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (436 bp):
ATACATATTTTCTTGTTATACACACTTGCTAGTTTAATCTTGTATTTCTAACCACTTAAATAAAC
TTGTTTTGTACTACCTAAAAATAAAATTAAAGTTCTGTTAGGATAATTATCACCACCAGCCCAAA
AATTTAAATGGGTTTGGGCTAAATTCTATTGAGCTCGCAAACTAAGCTCGCGGGGTACACAGTAA
GTTTTACTTATGTCACTTCTATTCTAGTTGAATCAGATCCCAACTAGAGTCACTTTATGACTCTC
CTTCGAATCAAATGGGGGATAAATTGTTAAGATAATTACCATCATCGATCCAAAAACCCAAATGG
GTTTGGGTCGGATTCTATTGAGCTCGCAGATCGACCTTCGTCTATTGCGAAGTTACACATGCATG
AGACCATATAAACACGTGTTCAGTTTAGAGTAGGATACGTGTCTAT
Found at i:2568884 original size:8 final size:7
Alignment explanation
Indices: 2568851--2568875 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2568841 TTATAATTTG
2568851 TTTTGAA
1 TTTTGAA
2568858 TTTTGAA
1 TTTTGAA
2568865 TTTTGAA
1 TTTTGAA
2568872 TTTT
1 TTTT
2568876 TGTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (7 bp):
TTTTGAA
Found at i:2588809 original size:20 final size:20
Alignment explanation
Indices: 2588784--2588833 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2588774 TGGCTTAAAA
2588784 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2588804 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2588821 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2588834 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2593435 original size:20 final size:20
Alignment explanation
Indices: 2593410--2593459 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
2593400 TGGCTTAAAA
2593410 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
2593430 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
2593447 GTGGTAGTGGATT
1 TTGGTAGTGGATT
2593460 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:2603313 original size:23 final size:23
Alignment explanation
Indices: 2603287--2603330 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2603277 TTTTGGCCTT
2603287 AATTCTAAAAATTTA-ACAAATTC
1 AATT-TAAAAATTTACACAAATTC
* *
2603310 AATTTCAACATTTACACAAAT
1 AATTTAAAAATTTACACAAAT
2603331 GTTGTGGGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (23 bp):
AATTTAAAAATTTACACAAATTC
Found at i:2606268 original size:4 final size:4
Alignment explanation
Indices: 2606259--2606299 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
2606249 TTATTAGGAA
2606259 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
2606300 TACACTTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:2610745 original size:13 final size:13
Alignment explanation
Indices: 2610727--2610751 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2610717 GATTTCTAAA
2610727 TTATATTAAATTT
1 TTATATTAAATTT
2610740 TTATATTAAATT
1 TTATATTAAATT
2610752 ACTGAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTATATTAAATTT
Found at i:2617437 original size:13 final size:14
Alignment explanation
Indices: 2617416--2617454 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
2617406 TCTTTGATTT
2617416 ATTATTTTATTTTA
1 ATTATTTTATTTTA
*
2617430 GTTA-TTTATTTTA
1 ATTATTTTATTTTA
2617443 ATTATTTTATTT
1 ATTATTTTATTT
2617455 GACTTCGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
ATTATTTTATTTTA
Found at i:2620175 original size:14 final size:14
Alignment explanation
Indices: 2620156--2620182 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2620146 TCGAATGAAA
2620156 TCGAGTTAAATTAT
1 TCGAGTTAAATTAT
2620170 TCGAGTTAAATTA
1 TCGAGTTAAATTA
2620183 AAATTTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
TCGAGTTAAATTAT
Found at i:2625629 original size:47 final size:46
Alignment explanation
Indices: 2625576--2625742 Score: 170
Period size: 44 Copynumber: 3.7 Consensus size: 46
2625566 TCATATAAGA
*
2625576 ATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATT
1 ATATTTATTATTAATAATTTTATGAAATTATATAT-ATTATTAAATT
* *
2625623 ATATTTAATATTAATTA-TTT-T-AAATTATATATATTCATATAAGA--
1 ATATTTATTATTAATAATTTTATGAAATTATATATATT-AT-TAA-ATT
* *
2625667 ATATTTATTATCAATAATTTTATGAAATTATATATTATTACTAAATT
1 ATATTTATTATTAATAATTTTATGAAATTATATA-TATTATTAAATT
* *
2625714 ATATTTA--A-TAATAATTATATTAAATTATA
1 ATATTTATTATTAATAATTTTATGAAATTATA
2625743 CAAATTCATA
Statistics
Matches: 101, Mismatches: 10, Indels: 21
0.77 0.08 0.16
Matches are distributed among these distances:
43 3 0.03
44 45 0.45
45 9 0.09
46 8 0.08
47 32 0.32
48 4 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (46 bp):
ATATTTATTATTAATAATTTTATGAAATTATATATATTATTAAATT
Found at i:2625671 original size:44 final size:44
Alignment explanation
Indices: 2625564--2625786 Score: 159
Period size: 47 Copynumber: 4.9 Consensus size: 44
2625554 ATTTTAGTAA
* **
2625564 ATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATAT
1 ATTCATATAAGAATATTTAATATTAATTA-TTT-T-AAATTATATAT
2625611 CATT-AT-TAA-ATTATATTTAATATTAATTATTTTAAATTATATAT
1 -ATTCATATAAGA--ATATTTAATATTAATTATTTTAAATTATATAT
* * *
2625655 ATTCATATAAGAATATTTATTATCAATAATTTTATGAAATTATATATT
1 ATTCATATAAGAATATTTAATATTAATTA-TTT-T-AAATTATATA-T
** * * * *
2625703 ATT-ACTA-AATTATATTTAATAATAATTATATTAAATTATACAA
1 ATTCA-TATAAGAATATTTAATATTAATTATTTTAAATTATATAT
* *
2625746 ATTCATATAAGAAAATTTATTAGTAATAATTATTTTAAATT
1 ATTCATATAAGAATATTTA--A-TATTAATTATTTTAAATT
2625787 TTATTAAATC
Statistics
Matches: 141, Mismatches: 19, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
43 8 0.06
44 45 0.32
45 9 0.06
46 11 0.08
47 59 0.42
48 9 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (44 bp):
ATTCATATAAGAATATTTAATATTAATTATTTTAAATTATATAT
Found at i:2625671 original size:91 final size:91
Alignment explanation
Indices: 2625562--2625776 Score: 340
Period size: 91 Copynumber: 2.4 Consensus size: 91
2625552 TGATTTTAGT
* *
2625562 AAATTCATATAAGAATATTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATAT
1 AAATTCATATAAGAATATTTATTATTAATAATTTTATGAAATTATATATCATTACTAAATTATAT
* * *
2625627 TTAATATTAATTATTTTAAATTATAT
66 TTAATAATAATTATATTAAATTATAC
* * *
2625653 ATATTCATATAAGAATATTTATTATCAATAATTTTATGAAATTATATATTATTACTAAATTATAT
1 AAATTCATATAAGAATATTTATTATTAATAATTTTATGAAATTATATATCATTACTAAATTATAT
2625718 TTAATAATAATTATATTAAATTATAC
66 TTAATAATAATTATATTAAATTATAC
* *
2625744 AAATTCATATAAGAAAATTTATTAGTAATAATT
1 AAATTCATATAAGAATATTTATTATTAATAATT
2625777 ATTTTAAATT
Statistics
Matches: 112, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 112 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
AAATTCATATAAGAATATTTATTATTAATAATTTTATGAAATTATATATCATTACTAAATTATAT
TTAATAATAATTATATTAAATTATAC
Found at i:2626081 original size:120 final size:120
Alignment explanation
Indices: 2625783--2626192 Score: 745
Period size: 120 Copynumber: 3.4 Consensus size: 120
2625773 AATTATTTTA
*
2625783 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTAT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
*
2625848 ATAGTATCATATATTATGATTTTAAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGA-TTTGAGTAAATTCATATAAGAATATTGATTATTAAG
2625904 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
2625969 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
2626024 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTAT-TTCAAATTATATTT
2626088 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
2626144 AATTTTATTAAATTATATAATTTT-ATTAAAAT-TATTTAATAATAATTAT
1 AATTTTATTAAATCATAT-ATTTTAATTAAAATATATTTAATAATAATTAT
2626193 GTTAAAATAT
Statistics
Matches: 284, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
119 17 0.06
120 177 0.62
121 90 0.32
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATTTCAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:2626167 original size:18 final size:19
Alignment explanation
Indices: 2626144--2626183 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2626134 GATTATTAAG
2626144 AATTTTATT-AAATTATAT
1 AATTTTATTAAAATTATAT
*
2626162 AATTTTATTAAAATTATTT
1 AATTTTATTAAAATTATAT
2626181 AAT
1 AAT
2626184 AATAATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATTTTATTAAAATTATAT
Found at i:2626435 original size:16 final size:16
Alignment explanation
Indices: 2626414--2626449 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2626404 GATTTGCTAT
2626414 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2626430 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
2626446 TACA
1 TACA
2626450 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:2632748 original size:40 final size:41
Alignment explanation
Indices: 2632591--2632748 Score: 156
Period size: 41 Copynumber: 3.9 Consensus size: 41
2632581 GGCGCTAATG
* * * * * * *
2632591 GAAAAACGTCGCAATAGGTAAAGCAGTAGTGGGGTTTACGA
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* *
2632632 GAAAAATGCCACAAAAGGTCAAGCAGTAGCGGCATTTATGA
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* * ** * *
2632673 AAAAAACGCCTTAAAAAGTCAAGCAGTAGCAGCGTTTATGA
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
* *
2632714 GAAAAATACCGCAAAAGGT-AAGCAATAGCGGCGTT
1 GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTT
2632749 AAAAAACATC
Statistics
Matches: 93, Mismatches: 24, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
40 14 0.15
41 79 0.85
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (41 bp):
GAAAAATGCCGCAAAAGGTCAAGCAGTAGCGGCGTTTATGA
Found at i:2632866 original size:37 final size:36
Alignment explanation
Indices: 2632807--2632891 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 36
2632797 CTTAAACCAT
* * *
2632807 AATCCCAAAATCCATT-ATTTTTTCCCCTAAAAGTCAG
1 AATCCCCAAATCCATTAATTTTTTCCCCT-AAA-TAAA
* *
2632844 AATCCCCAAATCCCTTAATTTTTTTCCCTAAATAAA
1 AATCCCCAAATCCATTAATTTTTTCCCCTAAATAAA
2632880 AATCCCCAAATC
1 AATCCCCAAATC
2632892 GAAATCTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
36 14 0.33
37 17 0.40
38 11 0.26
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.32
Consensus pattern (36 bp):
AATCCCCAAATCCATTAATTTTTTCCCCTAAATAAA
Found at i:2634382 original size:92 final size:92
Alignment explanation
Indices: 2634224--2634419 Score: 338
Period size: 92 Copynumber: 2.1 Consensus size: 92
2634214 TGGTTGTTTG
* * *
2634224 AACCGATTGAATCGGTAGAGGTACCAATCTAGAGAGAGGCATCAAACTTATTGACTTGCAAACTG
1 AACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAACTG
*
2634289 GTACGAGCTGGTAGAACTAGACTAAAA
66 GTACGAGCTAGTAGAACTAGACTAAAA
*
2634316 AACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAGCTG
1 AACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAACTG
2634381 GTACGAGCTAGTAGAACTAGACTAAAA
66 GTACGAGCTAGTAGAACTAGACTAAAA
*
2634408 AATCGATTGAAC
1 AACCGATTGAAC
2634420 GCAATTTTTA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 98 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (92 bp):
AACCGATTGAACCGGTAGAGGTACCAATCCAGAGAGAGACATCAAACTTATTGACTTGCAAACTG
GTACGAGCTAGTAGAACTAGACTAAAA
Found at i:2640954 original size:85 final size:85
Alignment explanation
Indices: 2640811--2640978 Score: 300
Period size: 85 Copynumber: 2.0 Consensus size: 85
2640801 GTCACTTCAC
* *
2640811 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCTTTGGGCCTTCTTTAGACATGTTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2640876 AGCTTGAACAATGATAGACT
66 AGCTTGAACAATGATAGACT
* *
2640896 TTAATCGCTAAAACCTAGTACTTCTGTTTATGTCTGATCCCTTGGGCCTTCTTTAGACATGCTGC
1 TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
2640961 AGCTTGAACAATGATAGA
66 AGCTTGAACAATGATAGA
2640979 ATTGGGCTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (85 bp):
TTAATCACTAAAACCTAGTACTTCTGTTTATGTCTGAACCCTTGGGCCTTCTTTAGACATGCTGC
AGCTTGAACAATGATAGACT
Found at i:2651331 original size:29 final size:29
Alignment explanation
Indices: 2651287--2651343 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
2651277 GAATATAAAC
2651287 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
2651316 TATATTTTTTTATTTTTAAAATACACTA
1 TATA-TTTTTTATTTTTAAAATACACTA
2651344 ATACAGTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAATACACTACA
Found at i:2653902 original size:22 final size:22
Alignment explanation
Indices: 2653877--2653930 Score: 83
Period size: 21 Copynumber: 2.5 Consensus size: 22
2653867 AGCAAAAAAG
*
2653877 AGGGGAGAAACCATCAAGAACA
1 AGGGGAGAAACCAGCAAGAACA
*
2653899 A-GGGAGAAACCAGCAAGAACG
1 AGGGGAGAAACCAGCAAGAACA
2653920 AGGGGAGAAAC
1 AGGGGAGAAAC
2653931 TGCTGTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.48, C:0.17, G:0.33, T:0.02
Consensus pattern (22 bp):
AGGGGAGAAACCAGCAAGAACA
Found at i:2654452 original size:23 final size:23
Alignment explanation
Indices: 2654409--2654453 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2654399 GTATATGCAA
*
2654409 TTTAATATTTTTATTCTTTATAT
1 TTTAATATTTTTATTCATTATAT
2654432 TTTAATATTATTTATT-ATTATA
1 TTTAATATT-TTTATTCATTATA
2654454 AATTTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTAATATTTTTATTCATTATAT
Found at i:2654930 original size:22 final size:21
Alignment explanation
Indices: 2654886--2654930 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
2654876 CGTGTAATTC
*
2654886 ATAAAAATTTAAAATAAATAA
1 ATAAAAATTTAAAATAAACAA
*
2654907 ATAAAAATTTAAAAATCAACAA
1 ATAAAAATTT-AAAATAAACAA
2654929 AT
1 AT
2654931 TCCAAAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAAAAATTTAAAATAAACAA
Found at i:2661790 original size:83 final size:83
Alignment explanation
Indices: 2661659--2661844 Score: 259
Period size: 83 Copynumber: 2.2 Consensus size: 83
2661649 CTATATGCAT
* * * *
2661659 AGTACAAG-ACTAGTAATTTAGTTTAATCAAATGGATTTAAGCATTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTA-AAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACT
* *
2661723 AAAATTTCAAATTTTGAAA
65 AAAATTTAAAAATTTGAAA
* *
2661742 AGTAGAGGAACTAAAATTGAGTTTAATCAAACGGATTTAA-CTACTACTATTTTGGGTTAGGACT
1 AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGC-ACTACTATTTTGGGTTAGGACT
2661806 AAAATTTAAAAATTTGAAA
65 AAAATTTAAAAATTTGAAA
*
2661825 AGTACAATAACTAAAATTGA
1 AGTACAAGAACTAAAATTGA
2661845 CTAATTTGAA
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 85 0.94
84 4 0.04
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (83 bp):
AGTACAAGAACTAAAATTGAGTTTAATCAAACGGATTTAAGCACTACTATTTTGGGTTAGGACTA
AAATTTAAAAATTTGAAA
Found at i:2662534 original size:20 final size:18
Alignment explanation
Indices: 2662493--2662540 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
2662483 AATTATTTGG
*
2662493 AAAAAATATATAAAAATT
1 AAAAAAAATATAAAAATT
*
2662511 AAAAAAAATCTAAAAAGTT
1 AAAAAAAATATAAAAA-TT
*
2662530 CAAAAACAATA
1 -AAAAAAAATA
2662541 CCTAAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 14 0.58
19 2 0.08
20 8 0.33
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAAAAAATATAAAAATT
Found at i:2683647 original size:9 final size:9
Alignment explanation
Indices: 2683633--2683694 Score: 81
Period size: 9 Copynumber: 7.0 Consensus size: 9
2683623 TTGGGTAATT
2683633 TTCGGGTAA
1 TTCGGGTAA
2683642 TTCGGGTAA
1 TTCGGGTAA
*
2683651 TTCGGTTAA
1 TTCGGGTAA
*
2683660 TTCGGTTAA
1 TTCGGGTAA
**
2683669 TTCGATTAA
1 TTCGGGTAA
2683678 -TCGGGTAA
1 TTCGGGTAA
2683686 TTCGGGTAA
1 TTCGGGTAA
2683695 ATTTTAACCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
8 6 0.12
9 42 0.88
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.37
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:2683669 original size:27 final size:26
Alignment explanation
Indices: 2683633--2683694 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
2683623 TTGGGTAATT
* *
2683633 TTCGGGTAATTCGGGTAATTCGGTTAA
1 TTCGGGTAATTCGAGTAA-TCGGGTAA
* *
2683660 TTCGGTTAATTCGATTAATCGGGTAA
1 TTCGGGTAATTCGAGTAATCGGGTAA
2683686 TTCGGGTAA
1 TTCGGGTAA
2683695 ATTTTAACCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 15 0.50
27 15 0.50
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.37
Consensus pattern (26 bp):
TTCGGGTAATTCGAGTAATCGGGTAA
Found at i:2684171 original size:24 final size:25
Alignment explanation
Indices: 2684133--2684179 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2684123 CCCGAATAAT
* *
2684133 AAATATTTTTATTTTTTTATTTTTA
1 AAATACTTTTATTTTTTAATTTTTA
2684158 AAATACTTTT-TTTTTTAATTTT
1 AAATACTTTTATTTTTTAATTTT
2684180 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
AAATACTTTTATTTTTTAATTTTTA
Found at i:2684200 original size:16 final size:16
Alignment explanation
Indices: 2684152--2684201 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
2684142 TATTTTTTTA
*
2684152 TTTTTAAAATACTT-T
1 TTTTTTAAATACTTAT
* *
2684167 TTTTTTTAAT-TTTAAT
1 TTTTTTAAATACTT-AT
2684183 TTTTTTAAATACTTAT
1 TTTTTTAAATACTTAT
2684199 TTT
1 TTT
2684202 AATTTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
14 2 0.07
15 8 0.30
16 15 0.56
17 2 0.07
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTAAATACTTAT
Found at i:2695464 original size:30 final size:30
Alignment explanation
Indices: 2695414--2695486 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
2695404 TTAAATTAGT
* *
2695414 AAATT-TAAAAATATATTTTAATTTCTTTAA
1 AAATTATAAAAATATAGTTTAATAT-TTTAA
* *
2695444 AAA-TATGAAAATTTAGTTTAATATTTTAA
1 AAATTATAAAAATATAGTTTAATATTTTAA
2695473 AAATTATAAAAATA
1 AAATTATAAAAATA
2695487 GAATATGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 9 0.26
30 26 0.74
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTATAAAAATATAGTTTAATATTTTAA
Found at i:2695591 original size:29 final size:33
Alignment explanation
Indices: 2695559--2695622 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 33
2695549 TAATGTTAAA
* *
2695559 TATTTTATTTAGTT-AT-TAAA-TAATA-TATT
1 TATTTTATGTAATTAATATAAAGTAATATTATT
2695588 TATTTTATGTAATTAATATAAAGTAATATTATT
1 TATTTTATGTAATTAATATAAAGTAATATTATT
2695621 TA
1 TA
2695623 ATGTTGAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 12 0.41
30 2 0.07
31 4 0.14
32 5 0.17
33 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (33 bp):
TATTTTATGTAATTAATATAAAGTAATATTATT
Found at i:2695594 original size:25 final size:25
Alignment explanation
Indices: 2695557--2695608 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
2695547 TTTAATGTTA
*
2695557 AATATTTTATTTA-GTTATTAA-AT
1 AATATTTTATTTATGTAATTAATAT
2695580 AATATATTTATTTTATGTAATTAATAT
1 AATAT-TTTA-TTTATGTAATTAATAT
2695607 AA
1 AA
2695609 AGTAATATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 5 0.21
24 4 0.17
25 4 0.17
26 7 0.29
27 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (25 bp):
AATATTTTATTTATGTAATTAATAT
Found at i:2702556 original size:120 final size:120
Alignment explanation
Indices: 2702420--2702899 Score: 775
Period size: 120 Copynumber: 4.0 Consensus size: 120
2702410 ATTATTAATC
*
2702420 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
2702485 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * *
2702540 TATATTATATATTATTATATATTAGGATTTTATTAAATTCATATAAGAATATTTAATATTAA-AA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
2702604 TTTTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 -TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* *
2702659 TATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
2702724 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAA
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * * * * * *
2702779 TATATTTTATAGTATCATATATTATTATTTTAGTAAATTCAGATAAAAATATTGATTATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
2702844 TTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATG-TTAAAT
2702900 ATGATTAAAT
Statistics
Matches: 337, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
119 112 0.33
120 220 0.65
121 5 0.01
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
Found at i:2702676 original size:41 final size:41
Alignment explanation
Indices: 2702618--2702798 Score: 101
Period size: 41 Copynumber: 4.5 Consensus size: 41
2702608 TATTAAATTA
*
2702618 TATATTTTATTA-AATTATATTTAATAATAATTATGTTAAAT
1 TATATTTTA-TAGTATTATATTTAATAATAATTATGTTAAAT
* * *
2702659 TATATTTTATAGTATTATATATT-ATGAT-TTTA-G-AAAAT
1 TATATTTTATAGTATTATAT-TTAATAATAATTATGTTAAAT
* * * * * * * *
2702697 TCATA--TAAGAATATT-TA-ATATTAAGAATTTTATTAAAT
1 T-ATATTTTATAGTATTATATTTAATAATAATTATGTTAAAT
* * *
2702735 TATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAA
1 TATAT-TTTATAGT--ATTATATTTAATAATAATTATGTTAAAT
*
2702779 TATATTTTATAGTATCATAT
1 TATATTTTATAGTATTATAT
2702799 ATTATTATTT
Statistics
Matches: 98, Mismatches: 28, Indels: 28
0.64 0.18 0.18
Matches are distributed among these distances:
34 1 0.01
35 2 0.02
36 4 0.04
37 10 0.10
38 10 0.10
39 4 0.04
40 8 0.08
41 26 0.27
42 5 0.05
43 8 0.08
44 20 0.20
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (41 bp):
TATATTTTATAGTATTATATTTAATAATAATTATGTTAAAT
Found at i:2702850 original size:239 final size:241
Alignment explanation
Indices: 2702420--2702899 Score: 786
Period size: 239 Copynumber: 2.0 Consensus size: 241
2702410 ATTATTAATC
**
2702420 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
* *
2702485 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTATAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTATAT
* * * * * *
2702550 ATTATTATATATTAGGATTTTATTAAATTCATATAAGAATATTTAATATTAAAATTTTTATTAAA
131 AGTATCATATATTAGGATTTTAGTAAATTCAGATAAAAATATTGAATATTAAAATTTTTATTAAA
*
2702615 TTATATATTTT-ATTAAATTATATTTAATAATAATTATG-TTAAAT
196 TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
*
2702659 TATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
*
2702724 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTTTAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTATAT
** *
2702789 AGTATCATATATTATTATTTTAGTAAATTCAGATAAAAATATTGATTATTAAGAA-TTTTATTAA
131 AGTATCATATATTAGGATTTTAGTAAATTCAGATAAAAATATTGAATATTAA-AATTTTTATTAA
2702853 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
195 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
2702900 ATGATTAAAT
Statistics
Matches: 222, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
239 188 0.85
240 28 0.13
241 6 0.03
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (241 bp):
TATATTATATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATATTATAT
AGTATCATATATTAGGATTTTAGTAAATTCAGATAAAAATATTGAATATTAAAATTTTTATTAAA
TTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
Found at i:2702871 original size:18 final size:17
Alignment explanation
Indices: 2702843--2702877 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2702833 ATTATTAAGA
*
2702843 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2702860 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2702878 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2703150 original size:16 final size:16
Alignment explanation
Indices: 2703112--2703161 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2703102 GTTTTGCTAT
* * *
2703112 TACACCTCTATTTTAT
1 TACACCTCTAATTCAA
*
2703128 TATACCTCTAATTCAA
1 TACACCTCTAATTCAA
*
2703144 TACACCTCTAATCCAA
1 TACACCTCTAATTCAA
2703160 TA
1 TA
2703162 TAGCGAACCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (16 bp):
TACACCTCTAATTCAA
Found at i:2715836 original size:27 final size:30
Alignment explanation
Indices: 2715777--2715838 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
2715767 ATAATTTGAT
*
2715777 AATCAACTGAGTCCTTAATTGAAAATAAGC
1 AATCAACTGAGTCCCTAATTGAAAATAAGC
2715807 AATCAACTGAGTCCCT-A-T-AAAATAAGC
1 AATCAACTGAGTCCCTAATTGAAAATAAGC
2715834 AATCA
1 AATCA
2715839 GTTCAATTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
27 14 0.45
28 1 0.03
29 1 0.03
30 15 0.48
ACGTcount: A:0.45, C:0.19, G:0.11, T:0.24
Consensus pattern (30 bp):
AATCAACTGAGTCCCTAATTGAAAATAAGC
Found at i:2716632 original size:23 final size:23
Alignment explanation
Indices: 2716606--2716667 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
2716596 ATCGGATGAA
2716606 ATTTAAAAAAAAATCAA-ATCATT
1 ATTTAAAAAAAAAT-AATATCATT
*
2716629 ATTTAAAATAAAAATAATATTATT
1 ATTTAAAA-AAAAATAATATCATT
2716653 -TTTAATAAAAAAATA
1 ATTTAA-AAAAAAATA
2716668 TGATTAGCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
23 22 0.63
24 13 0.37
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (23 bp):
ATTTAAAAAAAAATAATATCATT
Found at i:2721519 original size:24 final size:24
Alignment explanation
Indices: 2721491--2721542 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
2721481 TTAGTAAGTC
* *
2721491 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* * *
2721515 AAATATATTATATTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2721539 AAAT
1 AAAT
2721543 TTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2725601 original size:13 final size:12
Alignment explanation
Indices: 2725581--2725614 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
2725571 TCGGTCTTGC
2725581 TTTTTTTTT-CT
1 TTTTTTTTTACT
2725592 TTTCTTTTTTACT
1 TTT-TTTTTTACT
2725605 TTTTTTTTTA
1 TTTTTTTTTA
2725615 AAAATTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 3 0.14
12 13 0.62
13 5 0.24
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTACT
Found at i:2727364 original size:24 final size:24
Alignment explanation
Indices: 2727336--2727385 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
2727326 TTAGTAAGTC
* *
2727336 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2727360 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2727384 AA
1 AA
2727386 TTTTTTTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2727941 original size:2 final size:2
Alignment explanation
Indices: 2727934--2727962 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2727924 CATTGTAAGC
2727934 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2727963 AAATCAGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2731836 original size:41 final size:37
Alignment explanation
Indices: 2731741--2731837 Score: 86
Period size: 37 Copynumber: 2.5 Consensus size: 37
2731731 CGCAATAAAG
*
2731741 TGACACCCAGTGTCTCATCGGCCAAGCCGAAGTAAGT
1 TGACACCCAGTGTCTCATCGACCAAGCCGAAGTAAGT
** ** * * *
2731778 TGGTACCCAGTACCTCATCGAATCTATCCGAAGTAACAGT
1 TGACACCCAGTGTCTCATCG-ACCAAGCCGAAGT-A-AGT
2731818 ATGACACCCAGTGTCTCATC
1 -TGACACCCAGTGTCTCATC
2731838 AACTCAAGGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
37 16 0.36
38 9 0.20
39 1 0.02
40 3 0.07
41 15 0.34
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.23
Consensus pattern (37 bp):
TGACACCCAGTGTCTCATCGACCAAGCCGAAGTAAGT
Found at i:2732142 original size:27 final size:27
Alignment explanation
Indices: 2732111--2732164 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2732101 CCACACATAA
*
2732111 TCATA-ATTTAATTCACTTTTATTCAAT
1 TCATATATTTAATTCA-TTTAATTCAAT
*
2732138 TCATATTTTTAATTCATTTAATTCAAT
1 TCATATATTTAATTCATTTAATTCAAT
2732165 ATCAACATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (27 bp):
TCATATATTTAATTCATTTAATTCAAT
Found at i:2733019 original size:8 final size:8
Alignment explanation
Indices: 2733006--2733038 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
2732996 TGTTTTATAG
2733006 ATATAATA
1 ATATAATA
2733014 ATATAATA
1 ATATAATA
2733022 ATATAATTA
1 ATATAA-TA
2733031 ATATAATA
1 ATATAATA
2733039 CTTATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:2736796 original size:3 final size:3
Alignment explanation
Indices: 2736788--2736821 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
2736778 AACATGTTTC
2736788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AACT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
2736822 TTTATGAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2737810 original size:27 final size:27
Alignment explanation
Indices: 2737779--2737832 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2737769 CCACAAATAA
*
2737779 TCATA-ATTTAATTCACTTTTATTCAAT
1 TCATATATTTAATTCA-TTTAATTCAAT
*
2737806 TCATATTTTTAATTCATTTAATTCAAT
1 TCATATATTTAATTCATTTAATTCAAT
2737833 ATCGACATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.62
28 9 0.38
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (27 bp):
TCATATATTTAATTCATTTAATTCAAT
Found at i:2738693 original size:8 final size:8
Alignment explanation
Indices: 2738680--2738712 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
2738670 TGTTTTTTAT
2738680 ATATAATA
1 ATATAATA
2738688 ATATAATA
1 ATATAATA
2738696 ATATAATTA
1 ATATAA-TA
2738705 ATATAATA
1 ATATAATA
2738713 CTTATTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAATA
Found at i:2739742 original size:13 final size:13
Alignment explanation
Indices: 2739724--2739750 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2739714 ACTGTCAAAC
2739724 GTTTCAGTTGTAA
1 GTTTCAGTTGTAA
2739737 GTTTCAGTTGTAA
1 GTTTCAGTTGTAA
2739750 G
1 G
2739751 CTGTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (13 bp):
GTTTCAGTTGTAA
Found at i:2739763 original size:20 final size:20
Alignment explanation
Indices: 2739738--2739778 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2739728 CAGTTGTAAG
2739738 TTTCAGTTGTAAGCTGTTAA
1 TTTCAGTTGTAAGCTGTTAA
2739758 TTTCAGTTGTAAGCTGTTAA
1 TTTCAGTTGTAAGCTGTTAA
2739778 T
1 T
2739779 AGGTTAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.46
Consensus pattern (20 bp):
TTTCAGTTGTAAGCTGTTAA
Found at i:2743799 original size:23 final size:22
Alignment explanation
Indices: 2743745--2743800 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2743735 ACTAAAAGTA
*
2743745 TATATTTAATACTAATTAATTT
1 TATATTTAATAATAATTAATTT
* **
2743767 TTTATATTAATAATGTTTAATTT
1 TATAT-TTAATAATAATTAATTT
2743790 TAATATTTAAT
1 T-ATATTTAAT
2743801 TTTTTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 4 0.15
23 20 0.74
24 3 0.11
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATATTTAATAATAATTAATTT
Found at i:2743951 original size:43 final size:43
Alignment explanation
Indices: 2743837--2744090 Score: 201
Period size: 43 Copynumber: 5.9 Consensus size: 43
2743827 CGTTTTTATG
2743837 TAAAA-CGCCGCTAAAGAACA-GTAGT-TTTAGCGGCGTTTGTGA
1 TAAAAGCGCCGCTAAAGAACATG-A-TCTTTAGCGGCGTTTGTGA
* ** ** * * *
2743879 TCAAAACCGTTGCTAAAGGTCATGTTCTTTAGCGACGTTTGTTA
1 T-AAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGA
* *
2743923 TAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTGG
1 TAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGA
** ** * *
2743966 TAAAAGCGATGCTAAAGGTCATGACCTTTAGCGGTGTTTGTGA
1 TAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGA
** * * *
2744009 GGAAAGCGCCGCTAAA-AGCCATGATCTATAGCGGCGTTTGTGG
1 TAAAAGCGCCGCTAAAGA-ACATGATCTTTAGCGGCGTTTGTGA
* * ** * *
2744052 GAGAAGCGCCGCTAAAGTTCATGACCTTTAGCAGCGTTT
1 TAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTT
2744091 ATTTCTAAAA
Statistics
Matches: 165, Mismatches: 41, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
42 1 0.01
43 136 0.82
44 27 0.16
45 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (43 bp):
TAAAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTGTGA
Found at i:2744005 original size:86 final size:86
Alignment explanation
Indices: 2743837--2744083 Score: 275
Period size: 86 Copynumber: 2.9 Consensus size: 86
2743827 CGTTTTTATG
* * * *
2743837 TAAAA-CGCCGCTAAAGAACAGTAGT-TTTAGCGGCGTTTGTGATCAAAACCGTTGCTAAAGGTC
1 TAAAAGCGCCGCTAAAGAACA-TGGTCTTTAGCGGCGTTTGTGGT-AAAAGCGATGCTAAAGGTC
** *
2743900 ATGTTCTTTAGCGACGTTTGTTA
64 ATGACCTTTAGCGACGTTTGTGA
2743923 TAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCAT
1 TAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCAT
**
2743988 GACCTTTAGCGGTGTTTGTGA
66 GACCTTTAGCGACGTTTGTGA
** * * * * * ** *
2744009 GGAAAGCGCCGCTAAA-AGCCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGTTCA
1 TAAAAGCGCCGCTAAAGA-ACATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCA
2744073 TGACCTTTAGC
65 TGACCTTTAGC
2744084 AGCGTTTATT
Statistics
Matches: 139, Mismatches: 19, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
85 1 0.01
86 106 0.76
87 32 0.23
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (86 bp):
TAAAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTGTGGTAAAAGCGATGCTAAAGGTCAT
GACCTTTAGCGACGTTTGTGA
Found at i:2746299 original size:17 final size:16
Alignment explanation
Indices: 2746279--2746318 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2746269 ATTTAAGTCT
2746279 ATAATTCAATTAATATC
1 ATAATTCAATTAATA-C
*
2746296 ATAAGTCAATTAATAC
1 ATAATTCAATTAATAC
2746312 -TAATTCA
1 ATAATTCA
2746319 GTTGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 6 0.29
16 1 0.05
17 14 0.67
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAATTCAATTAATAC
Found at i:2747377 original size:21 final size:21
Alignment explanation
Indices: 2747347--2747388 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2747337 CAGATAGCTG
* *
2747347 CATCTGTTTACATTATGCAAT
1 CATCTATTTACATTATACAAT
2747368 CATCTATTTACATTATACAAT
1 CATCTATTTACATTATACAAT
2747389 TATATGATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (21 bp):
CATCTATTTACATTATACAAT
Found at i:2747597 original size:93 final size:92
Alignment explanation
Indices: 2747439--2747627 Score: 360
Period size: 93 Copynumber: 2.0 Consensus size: 92
2747429 ATATGTTGAT
*
2747439 TTTAACATAGTTAATTGGGTTTAGAATTATCTATGATAACATCTTATTTATTCAGTCAAATAGGC
1 TTTAACATAGTTAATTGGATTTAGAATTATCTATGATAACATCTTATTTATTCAGTCAAATAGGC
2747504 ACACAATTATTATAACAGTTCAATCAA
66 ACACAATTATTATAACAGTTCAATCAA
2747531 TTTAACATAGTTAATTGGATTTAGAATTTATCTATGATAACATCTTATTTATTCAGTCAAATAGG
1 TTTAACATAGTTAATTGGATTTAGAA-TTATCTATGATAACATCTTATTTATTCAGTCAAATAGG
2747596 CACACAATTATTATAACAGTTCAATCAA
65 CACACAATTATTATAACAGTTCAATCAA
2747624 TTTA
1 TTTA
2747628 CATTATACTA
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 25 0.26
93 70 0.74
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (92 bp):
TTTAACATAGTTAATTGGATTTAGAATTATCTATGATAACATCTTATTTATTCAGTCAAATAGGC
ACACAATTATTATAACAGTTCAATCAA
Found at i:2756335 original size:44 final size:42
Alignment explanation
Indices: 2756241--2756397 Score: 120
Period size: 44 Copynumber: 3.6 Consensus size: 42
2756231 CATGACAAAC
* * *
2756241 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAGCCA-AT
1 CTTATCTCCCTGAAGTTGCAGTGGAGC-G-GATAA-AACCCAGAT
*
2756285 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGA-TAAAACC-CAGAT
** ** * ***
2756329 CTTATCTCTATGAAGTTAAAGTAGAGCAGGATCGCACCCAG-T
1 CTTATCTCCCTGAAGTTGCAGTGGAGC-GGATAAAACCCAGAT
* *
2756371 CTTATCTTCCTGAAGTTGTAGTGGAGC
1 CTTATCTCCCTGAAGTTGCAGTGGAGC
2756398 AAACTAAAGA
Statistics
Matches: 90, Mismatches: 19, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
42 26 0.29
43 8 0.09
44 53 0.59
45 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.24, T:0.25
Consensus pattern (42 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCGGATAAAACCCAGAT
Found at i:2758470 original size:11 final size:9
Alignment explanation
Indices: 2758432--2758472 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
2758422 ATATAAAGTA
2758432 AAATAAAAG
1 AAATAAAAG
*
2758441 AAACAAAAG
1 AAATAAAAG
2758450 AAATAAAAG
1 AAATAAAAG
2758459 AACATAAAAAG
1 AA-AT-AAAAG
2758470 AAA
1 AAA
2758473 CAGAGAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
9 18 0.64
10 3 0.11
11 7 0.25
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (9 bp):
AAATAAAAG
Found at i:2759581 original size:6 final size:6
Alignment explanation
Indices: 2759570--2759596 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2759560 GTGTGTCGAA
2759570 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
2759597 AGATTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:2759591 original size:51 final size:51
Alignment explanation
Indices: 2759531--2759649 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 51
2759521 ATGTGCCGAC
*** *
2759531 TACTGTTACTGTTACCGATTTGGCACTTTGTGTGTCGAATACTGTTACTGT
1 TACTGTTACTGTTACCGATTCAACACTTTGTGTGTCGAATACTGTCACTGT
* *
2759582 TACTGTTACTGTTACAGATTCAACACTTTGTGTGTTGAATACTGTCACTGT
1 TACTGTTACTGTTACCGATTCAACACTTTGTGTGTCGAATACTGTCACTGT
2759633 TACTGTTACTGTTACCG
1 TACTGTTACTGTTACCG
2759650 TTACTGATTA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 61 1.00
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (51 bp):
TACTGTTACTGTTACCGATTCAACACTTTGTGTGTCGAATACTGTCACTGT
Found at i:2759637 original size:6 final size:6
Alignment explanation
Indices: 2759621--2759668 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
2759611 GTGTGTTGAA
* *
2759621 TACTGT CACTGT TACTGT TACTGT TACCGT TACTGAT TACTGT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT TACTG
2759669 GTGTATTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
6 31 0.84
7 6 0.16
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.44
Consensus pattern (6 bp):
TACTGT
Found at i:2763504 original size:41 final size:41
Alignment explanation
Indices: 2763456--2763653 Score: 279
Period size: 41 Copynumber: 4.8 Consensus size: 41
2763446 TTGTATATAA
** * * *
2763456 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * * *
2763497 CATCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
2763538 CACCGGTATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
2763579 CACCGGCATAAAGCCTGCTAGACATAAAGCCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
**
2763620 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGA
2763654 ACTTACAAAA
Statistics
Matches: 138, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 138 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.20
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:2763593 original size:82 final size:82
Alignment explanation
Indices: 2763456--2763653 Score: 315
Period size: 82 Copynumber: 2.4 Consensus size: 82
2763446 TTGTATATAA
* * *
2763456 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTTCATCGGCACAAAGCCTGCTAGACA
1 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGATACAATTCACCGGCACAAAGCCTGCTAGACA
*
2763521 TAAAGTCTGATATAATT
66 TAAAGCCTGATATAATT
* ** * *
2763538 CACCGGTATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACCGGCATAAAGCCTGCTAGACA
1 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGATACAATTCACCGGCACAAAGCCTGCTAGACA
2763603 TAAAGCCTGATATAATT
66 TAAAGCCTGATATAATT
2763620 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGA
1 CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGA
2763654 ACTTACAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 104 1.00
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.20
Consensus pattern (82 bp):
CACCGGCATAAAGCCTGCTAGGCACCAAGCCTGATACAATTCACCGGCACAAAGCCTGCTAGACA
TAAAGCCTGATATAATT
Found at i:2764859 original size:41 final size:41
Alignment explanation
Indices: 2764765--2764919 Score: 127
Period size: 41 Copynumber: 3.7 Consensus size: 41
2764755 GGCTCGTACA
** *
2764765 ATGCCAATGTCCCAGAC-GTGGTCTTACATGTAATCACATAAG
1 ATGCCAATGTCCCAGACAG-GGTCTTACA-CAAATCAAATAAG
* *
2764807 ATGCCACTGTCCCAGACAGGGTCTTACACAAATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACAAATCAAATAAG
* * * ** *
2764848 ATGCTAATGTCCCGGACATGGTCTTACACGTATACACAAGTCA-
1 ATGCCAATGTCCCAGACAGGGTCTTACACAAAT-CA-AA-TAAG
*
2764891 ATGCCAACGTCCCAGAC-GTGGTCTTACAC
1 ATGCCAATGTCCCAGACAG-GGTCTTACAC
2764920 GAAAATACAT
Statistics
Matches: 91, Mismatches: 17, Indels: 9
0.78 0.15 0.08
Matches are distributed among these distances:
41 36 0.40
42 27 0.30
43 27 0.30
44 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACAAATCAAATAAG
Found at i:2765685 original size:24 final size:24
Alignment explanation
Indices: 2765653--2765703 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
2765643 TTGGTTTTAT
* *
2765653 TATTATTATAATAACTTTATAATA
1 TATTATTATAAAAACTATATAATA
2765677 TATTATTATAAAAACTATATAATA
1 TATTATTATAAAAACTATATAATA
2765701 TAT
1 TAT
2765704 ACATAGTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTATTATAAAAACTATATAATA
Found at i:2765900 original size:14 final size:15
Alignment explanation
Indices: 2765881--2765909 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2765871 TCACGAAACT
2765881 TTCACACAT-ATAAA
1 TTCACACATAATAAA
2765895 TTCACACATAATAAA
1 TTCACACATAATAAA
2765910 CACAGAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:2774123 original size:14 final size:14
Alignment explanation
Indices: 2774104--2774142 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
2774094 TGTTATTGTG
2774104 TTTTAGTTTTAGAC
1 TTTTAGTTTTAGAC
*
2774118 TTTTAGTTTTAGAT
1 TTTTAGTTTTAGAC
*
2774132 TTTTATTTTTA
1 TTTTAGTTTTA
2774143 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (14 bp):
TTTTAGTTTTAGAC
Found at i:2774185 original size:5 final size:5
Alignment explanation
Indices: 2774176--2774209 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
2774166 TATGATTGAG
* *
2774176 TTGGG TTGGG TTGGA TTGGA TTGGA TTGGA TTGG
1 TTGGA TTGGA TTGGA TTGGA TTGGA TTGGA TTGG
2774210 GTACTTGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.12, C:0.00, G:0.47, T:0.41
Consensus pattern (5 bp):
TTGGA
Found at i:2777646 original size:18 final size:18
Alignment explanation
Indices: 2777605--2777640 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2777595 AACAATTAAA
2777605 TAAA-TTGGAAATAAGAT
1 TAAATTTGGAAATAAGAT
2777622 TAAATTTGGAAATAA-AT
1 TAAATTTGGAAATAAGAT
2777639 TA
1 TA
2777641 GGATTTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (18 bp):
TAAATTTGGAAATAAGAT
Done.