Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 134 of 170
Found at i:40601999 original size:3 final size:3
Alignment explanation
Indices: 40601979--40602026 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
40601969 AATATAGTGG
* * *
40601979 TTA TAA TTA TTA TAA TTA TTA TTA TTA TTA TCA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40602026 T
1 T
40602027 ACCTACATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:40606933 original size:7 final size:7
Alignment explanation
Indices: 40606917--40606950 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
40606907 AAAAGGTGTG
*
40606917 AAAAAAT
1 AAAAATT
40606924 AAAAATT
1 AAAAATT
*
40606931 AAAAATG
1 AAAAATT
40606938 AAAAATT
1 AAAAATT
40606945 AAAAAT
1 AAAAAT
40606951 GGAGAAGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (7 bp):
AAAAATT
Found at i:40606950 original size:14 final size:14
Alignment explanation
Indices: 40606918--40606951 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40606908 AAAGGTGTGA
40606918 AAAAAT-AAAAATT
1 AAAAATGAAAAATT
40606931 AAAAATGAAAAATT
1 AAAAATGAAAAATT
40606945 AAAAATG
1 AAAAATG
40606952 GAGAAGCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (14 bp):
AAAAATGAAAAATT
Found at i:40608464 original size:100 final size:100
Alignment explanation
Indices: 40608336--40609198 Score: 1140
Period size: 100 Copynumber: 8.6 Consensus size: 100
40608326 CATTACTGTG
* * * *
40608336 AAAAAGATTGAAGTCACAACGGCAGATCTTATTTCCCTGACGGTGTAGTGGAATAGATTGAAGCT
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
* * *
40608401 ACGACCGCGGATCCGGTTTCCCCGACATTGTAATT
66 ACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
* * ** *
40608436 AAAAAGATTGAAGCCATAACGGTGGATCTTATTTCCCTGGTGGTGCAGTGGAACAAATTGAAGCT
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
* *
40608501 ACGACGGCGGATCTGGTTTCCCCAACATTGTAATT
66 ACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
* * * * *
40608536 AAAAAGATTGAAGCCACAACGGCGAATTTTATTTCCCTGGCGGTACAGTGGAGCAGATTGAAGCT
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
*
40608601 GCGACGGCGGATCTGGTTTCCCCGACATTGCAATT
66 ACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
* * * * *
40608636 AAAAAGATTGAAGCCACAACGGCAGATCTTATTTCCCTGGCGGTGCAGTGTAGCAAATTGAAGCT
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
*
40608701 ACGACGGAGGATCTGGTTTCCCCGACATTGCAATT
66 ACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
** * * *
40608736 AAAAAGATTGAAGCCACAACGATGGATCTTACTTCCCTGACGGTGTAGTGGAATAGATTGAAG-T
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
* * *
40608800 -CGTAACGGCGAATCTTGTTTCCCCGACATTGTAATT
66 ACG--ACGGCGGATCTGGTTTCCCCGACATTGCAATT
* * * * ** *
40608836 AAAAAGATTAAAGCCATAACAGTGGATCTTATTTCCCTGGTGGTGCAGTAGAACAGATTGAAGCT
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
*
40608901 ACGACGGCTGATCTGGTTTCCCCGACATTGCAATT
66 ACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
* *
40608936 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTTCAGTGGAGCAGATTGAAGCT
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
* * *
40609001 ACAACGGAGGATCTGGGTTCCCCGACATTGCAATT
66 ACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
* *
40609036 AAAAAGATTGAAGCCACAACGGTGGATCTTATTTCCCT-AGCGGTGCAGTGGAGCAGATTGAAGC
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGA-CGGTGCAGTGGAACAGATTGAAGC
* * *
40609100 TACAAAGGCGGATATGGTTTCCCCGACATTGCAATT
65 TACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
* * * * * *
40609136 CAAAAGATTGAAGCCACAATGACGGATCTTACTTCCCT-AGCGGTGTAGTGGAATAGATTGAAG
1 AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGA-CGGTGCAGTGGAACAGATTGAAG
40609199 TCGTAATGTC
Statistics
Matches: 672, Mismatches: 86, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
98 2 0.00
99 2 0.00
100 665 0.99
101 1 0.00
102 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (100 bp):
AAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCTGACGGTGCAGTGGAACAGATTGAAGCT
ACGACGGCGGATCTGGTTTCCCCGACATTGCAATT
Found at i:40610746 original size:3 final size:3
Alignment explanation
Indices: 40610733--40610771 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
40610723 AATATAGTGG
* *
40610733 TTA TAA TTA TTA TTA TTA TCA TTA TTA -TA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40610772 ACTTACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:40625431 original size:15 final size:16
Alignment explanation
Indices: 40625401--40625434 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40625391 ATATAATAAT
*
40625401 AATATAATAGCAAAAA
1 AATAAAATAGCAAAAA
40625417 AATAAAATA-CAAAAA
1 AATAAAATAGCAAAAA
40625432 AAT
1 AAT
40625435 TTTAGTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (16 bp):
AATAAAATAGCAAAAA
Found at i:40628330 original size:22 final size:20
Alignment explanation
Indices: 40628294--40628352 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
40628284 GGCCCGGCCC
40628294 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
40628316 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
**
40628337 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
40628353 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.06
21 16 0.48
22 7 0.21
23 8 0.24
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:40628373 original size:27 final size:28
Alignment explanation
Indices: 40628341--40628397 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
40628331 TAAAAAAAGT
40628341 ATTTTAAAAA-TATTTTAAAATTAAAAA
1 ATTTTAAAAAGTATTTTAAAATTAAAAA
40628368 ATTTTAAAAAGTATTTTAAAATTAAAAA
1 ATTTTAAAAAGTATTTTAAAATTAAAAA
40628396 AT
1 AT
40628398 AAAAAAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.34
28 19 0.66
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (28 bp):
ATTTTAAAAAGTATTTTAAAATTAAAAA
Found at i:40628377 original size:17 final size:17
Alignment explanation
Indices: 40628344--40628376 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
40628334 AAAAAGTATT
40628344 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
40628361 TTAAAAA-ATTTTAAAA
1 TTAAAAATATTTTAAAA
40628377 AGTATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:40628403 original size:27 final size:29
Alignment explanation
Indices: 40628346--40628437 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 29
40628336 AAAGTATTTT
**
40628346 AAAAA-TATTTTAAAATTAAAAAATT-TT
1 AAAAAGTATTTTAAAATTAAAAAATTAAA
40628373 AAAAAGTATTTTAAAATTAAAAAA-TAAA
1 AAAAAGTATTTTAAAATTAAAAAATTAAA
* **
40628401 AAAAAGTATTATACAAATATTTTAAAATTAAA
1 AAAAAGTATT-T-TAAA-ATTAAAAAATTAAA
40628433 AAAAA
1 AAAAA
40628438 AATAAAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
27 6 0.11
28 28 0.52
29 1 0.02
30 3 0.06
31 7 0.13
32 9 0.17
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAAGTATTTTAAAATTAAAAAATTAAA
Found at i:40628404 original size:28 final size:28
Alignment explanation
Indices: 40628346--40628410 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
40628336 AAAGTATTTT
***
40628346 AAAAA-TATTTTAAAATTAAAAAATTTT
1 AAAAAGTATTTTAAAATTAAAAAATAAA
40628373 AAAAAGTATTTTAAAATTAAAAAATAAA
1 AAAAAGTATTTTAAAATTAAAAAATAAA
40628401 AAAAAGTATT
1 AAAAAGTATT
40628411 ATACAAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAAGTATTTTAAAATTAAAAAATAAA
Found at i:40631460 original size:21 final size:21
Alignment explanation
Indices: 40631434--40631490 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
40631424 CTAACACCCA
40631434 CAACCACAACCCCCGCCAGAG
1 CAACCACAACCCCCGCCAGAG
** *
40631455 CAACCACAACCCTTGCTAGAG
1 CAACCACAACCCCCGCCAGAG
40631476 CAACCACAACCCCCG
1 CAACCACAACCCCCG
40631491 TCGAAAGCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.33, C:0.49, G:0.12, T:0.05
Consensus pattern (21 bp):
CAACCACAACCCCCGCCAGAG
Found at i:40631677 original size:22 final size:24
Alignment explanation
Indices: 40631615--40631676 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 24
40631605 TATATTATTT
*
40631615 TATTTAATAAAATAAGTTGTTTTTAA
1 TATTTAAT--AATAAATTGTTTTTAA
40631641 TATTTCAATAATAAATTGTTTTTATA
1 TATTT-AATAATAAATTGTTTTTA-A
*
40631667 TTTTTAATAA
1 TATTTAATAA
40631677 AATAGTTCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 19 0.59
26 10 0.31
27 3 0.09
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (24 bp):
TATTTAATAATAAATTGTTTTTAA
Found at i:40634955 original size:125 final size:125
Alignment explanation
Indices: 40634735--40634967 Score: 292
Period size: 125 Copynumber: 1.9 Consensus size: 125
40634725 CTACAGTAGG
*** * *
40634735 AAAAGAACGTCCACGTGGGAGTTTTTTTCATCAATTTTGCTAACAATGCATCCTGCTTGAAGTGT
1 AAAAGAACGTCCACGTGGGAAACTTTTTCATCAATTTTGCTAACAATGCATCCTACTTGAAGCGT
40634800 TTTTAACACCATTTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCATGAATTATTATGGA
66 TTTTAACACCATTTGTTCAGAACCGTCTTCTCAAAATT-TTTTTTCATGAATTATTATGGA
* * * *
40634861 AAAAGAGCGTCCACGT-GGAAACTTTTTCAGT-AATTTTGCTGATATTGCATCCTACTTGAAGCG
1 AAAAGAACGTCCACGTGGGAAACTTTTTCA-TCAATTTTGCTAACAATGCATCCTACTTGAAGCG
* * ** *
40634924 TTTTTTATATTATCTT-TTCAGAATCGTCTTCTCAAAATTTTTTT
65 TTTTTAACACCAT-TTGTTCAGAACCGTCTTCTCAAAATTTTTTT
40634968 AAGTACTGTA
Statistics
Matches: 91, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
124 5 0.05
125 68 0.75
126 18 0.20
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (125 bp):
AAAAGAACGTCCACGTGGGAAACTTTTTCATCAATTTTGCTAACAATGCATCCTACTTGAAGCGT
TTTTAACACCATTTGTTCAGAACCGTCTTCTCAAAATTTTTTTTCATGAATTATTATGGA
Found at i:40635101 original size:34 final size:34
Alignment explanation
Indices: 40635054--40635118 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
40635044 TTTTTAAAAA
*
40635054 CTAAACCATAATTTAATTAATTT-TCTTAAAAGCT
1 CTAAACCACAATTTAATTAATTTAT-TTAAAAGCT
*
40635088 CTAAACCCCAATTTAATTAATTTATTTAAAA
1 CTAAACCACAATTTAATTAATTTATTTAAAA
40635119 CCCCAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.40
Consensus pattern (34 bp):
CTAAACCACAATTTAATTAATTTATTTAAAAGCT
Found at i:40635233 original size:33 final size:33
Alignment explanation
Indices: 40635191--40635253 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
40635181 CCTTAAAACC
* *
40635191 TAACTCTAAATTATTTTAAGAAAACCCTAACTT
1 TAACCCTAAATTATTTTAACAAAACCCTAACTT
*
40635224 TAACCCTAAATTATTTTAACAAAACTCTAA
1 TAACCCTAAATTATTTTAACAAAACCCTAA
40635254 AATCATAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (33 bp):
TAACCCTAAATTATTTTAACAAAACCCTAACTT
Found at i:40642608 original size:12 final size:12
Alignment explanation
Indices: 40642591--40642615 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40642581 TTGGGAATTT
40642591 TTCCAAAAGAAA
1 TTCCAAAAGAAA
40642603 TTCCAAAAGAAA
1 TTCCAAAAGAAA
40642615 T
1 T
40642616 ATGTTGGCGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.16, G:0.08, T:0.20
Consensus pattern (12 bp):
TTCCAAAAGAAA
Found at i:40652127 original size:37 final size:36
Alignment explanation
Indices: 40652014--40652131 Score: 116
Period size: 37 Copynumber: 3.2 Consensus size: 36
40652004 CATTATTTTA
*
40652014 GCGTGTTATCGGGTGGATTAGCTCTAATGAGCATTTG
1 GCGTGTTATC-GGTGGATTAGCTCTTATGAGCATTTG
** * *
40652051 GTATGTT-TACGGTTGGACTAGCTCTTCA-GAGCAATTG
1 GCGTGTTAT-CGG-TGGATTAGCTCTT-ATGAGCATTTG
40652088 GCGTGTTATCGTGTGGATTAGCTCTTATGAGC-TTCTG
1 GCGTGTTATCG-GTGGATTAGCTCTTATGAGCATT-TG
40652125 GCGTGTT
1 GCGTGTT
40652132 TTTGGATGGA
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
36 5 0.08
37 57 0.88
38 3 0.05
ACGTcount: A:0.17, C:0.15, G:0.31, T:0.37
Consensus pattern (36 bp):
GCGTGTTATCGGTGGATTAGCTCTTATGAGCATTTG
Found at i:40655608 original size:46 final size:47
Alignment explanation
Indices: 40655540--40655638 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 47
40655530 AATCCTGTTT
* * *
40655540 TGGACAGCAATTATTCAACAAATTTGACAGCA-ATAATATGCTCAAAA
1 TGGACAGCAATTATACAACAAATTAGACAGCATA-AATATACTCAAAA
* *
40655587 TGGACAGC-ATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TGGACAGCAATTATACAACAAATTAGACAGCATAAATATACTCAAAA
*
40655633 TTGACA
1 TGGACA
40655639 TCAAATTTGG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
46 36 0.80
47 9 0.20
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.26
Consensus pattern (47 bp):
TGGACAGCAATTATACAACAAATTAGACAGCATAAATATACTCAAAA
Found at i:40656657 original size:28 final size:26
Alignment explanation
Indices: 40656625--40656722 Score: 124
Period size: 28 Copynumber: 3.6 Consensus size: 26
40656615 TTAATAAGTA
*
40656625 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT--TAATTAAACT
* *
40656653 CGCACACTTAGTGCTTTACCTTATACT
1 CGCACACTTAGTGCTTTA-ATTAAACT
40656680 CGCACACTTAGTGCATTTCAATTAAACT
1 CGCACACTTAGTGC-TTT-AATTAAACT
40656708 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40656723 AATCTCATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
26 2 0.03
27 20 0.32
28 39 0.63
29 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (26 bp):
CGCACACTTAGTGCTTTAATTAAACT
Found at i:40658992 original size:11 final size:11
Alignment explanation
Indices: 40658976--40659115 Score: 61
Period size: 11 Copynumber: 13.5 Consensus size: 11
40658966 TTATTTTTTA
40658976 AATTTTAAAAT
1 AATTTTAAAAT
40658987 AATTTTAAAAT
1 AATTTTAAAAT
* ***
40658998 ACTTTTTTTAT
1 AATTTTAAAAT
* *
40659009 TATTTT---TT
1 AATTTTAAAAT
40659017 AATTTT--AA-
1 AATTTTAAAAT
40659025 AATTTTAAAAT
1 AATTTTAAAAT
*
40659036 ATTTTTTAAAAT
1 A-ATTTTAAAAT
*
40659048 -TTTTTAAAAT
1 AATTTTAAAAT
* *
40659058 ACTTTT---TT
1 AATTTTAAAAT
40659066 AATTTTAAAAT
1 AATTTTAAAAT
*
40659077 ATTTTTAAAAT
1 AATTTTAAAAT
*
40659088 ACTTTTTAAAAT
1 A-ATTTTAAAAT
40659100 --TTTTAAAAT
1 AATTTTAAAAT
40659109 AAATTTT
1 -AATTTT
40659116 TAGTATTTAT
Statistics
Matches: 101, Mismatches: 15, Indels: 25
0.72 0.11 0.18
Matches are distributed among these distances:
8 18 0.18
9 9 0.09
10 12 0.12
11 39 0.39
12 23 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTAAAAT
Found at i:40659024 original size:48 final size:48
Alignment explanation
Indices: 40658971--40659109 Score: 142
Period size: 49 Copynumber: 2.8 Consensus size: 48
40658961 TATATTTATT
** *
40658971 TTTTAAATTTTAAAATA-ATTTTAAAATACTTTTTTTATTA-TTTTTTAA
1 TTTTAAATTTTAAAATATATTTTAAAAT--TTTTTAAAATACTTTTTTAA
*
40659019 TTTTAAAATTTTAAAATATTTTTTAAAATTTTTTAAAATACTTTTTTAA
1 TTTT-AAATTTTAAAATATATTTTAAAATTTTTTAAAATACTTTTTTAA
40659068 TTTTAAAATATTTTTAAAATACT-TTTTAAAA-TTTTTAAAATA
1 TTTT--AA-A-TTTTAAAATA-TATTTTAAAATTTTTTAAAATA
40659110 AATTTTTAGT
Statistics
Matches: 80, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
48 12 0.15
49 25 0.31
50 12 0.15
51 12 0.15
52 18 0.22
53 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (48 bp):
TTTTAAATTTTAAAATATATTTTAAAATTTTTTAAAATACTTTTTTAA
Found at i:40659032 original size:49 final size:49
Alignment explanation
Indices: 40658965--40659109 Score: 111
Period size: 50 Copynumber: 2.9 Consensus size: 49
40658955 AATAAATATA
* * * ** *
40658965 TTTATTTTTTAAATTTTAAAATA-ATTTTAAAATACTTTTTTTATTA-TTT
1 TTTAATTTTAAAATTTTAAAATACTTTTTAAAAT--TTTTTAAAATACTTT
* * *
40659014 TTTAATTTTAAAATTTTAAAATAT--TTTTTAAAATTTTTTAAAATACTTT
1 TTTAA-TTTTAAAATTTTAAA-ATACTTTTTAAAATTTTTTAAAATACTTT
40659063 TTTAATTTTAAAATATTTTTAAAATACTTTTTAAAA-TTTTTAAAATA
1 TTTAATTTT-AAA-A-TTTTAAAATACTTTTTAAAATTTTTTAAAATA
40659110 AATTTTTAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 14
0.75 0.12 0.14
Matches are distributed among these distances:
48 11 0.14
49 15 0.20
50 22 0.29
51 19 0.25
52 9 0.12
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (49 bp):
TTTAATTTTAAAATTTTAAAATACTTTTTAAAATTTTTTAAAATACTTT
Found at i:40659082 original size:30 final size:32
Alignment explanation
Indices: 40659038--40659109 Score: 114
Period size: 30 Copynumber: 2.3 Consensus size: 32
40659028 TTTAAAATAT
*
40659038 TTTTTAAAAT-TTTTTAAAATACTTTTT-TAA
1 TTTTTAAAATATTTTTAAAATACTTTTTAAAA
40659068 -TTTTAAAATATTTTTAAAATACTTTTTAAAA
1 TTTTTAAAATATTTTTAAAATACTTTTTAAAA
40659099 TTTTTAAAATA
1 TTTTTAAAATA
40659110 AATTTTTAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
29 9 0.24
30 17 0.45
31 2 0.05
32 10 0.26
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (32 bp):
TTTTTAAAATATTTTTAAAATACTTTTTAAAA
Found at i:40659109 original size:21 final size:22
Alignment explanation
Indices: 40659027--40659109 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 22
40659017 AATTTTAAAA
*
40659027 TTTTAAAATATTTTTTAAAAT-T
1 TTTTAAAATA-TTTTTAAAATAC
*
40659049 TTTTAAAATACTTTTT----TAA
1 TTTTAAAATA-TTTTTAAAATAC
40659068 TTTTAAAATATTTTTAAAATAC
1 TTTTAAAATATTTTTAAAATAC
*
40659090 TTTTTAAA-ATTTTTAAAATA
1 TTTTAAAATATTTTTAAAATA
40659110 AATTTTTAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
18 6 0.12
19 10 0.19
21 12 0.23
22 24 0.46
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAAAATATTTTTAAAATAC
Found at i:40659116 original size:52 final size:49
Alignment explanation
Indices: 40658965--40659117 Score: 109
Period size: 51 Copynumber: 3.1 Consensus size: 49
40658955 AATAAATATA
* * * ** *
40658965 TTTATTTTTTAAATTTTAAAATA-ATTTTAAAATACTTTTT-TTATTATTT
1 TTTAATTTTAAAATTTTAAAATACTTTTTAAAAT--TTTTTAAAATAATTT
* * * *
40659014 TTTAATTTTAAAATTTTAAAATAT--TTTTTAAAATTTTTTAAAATACTTT
1 TTTAA-TTTTAAAATTTTAAA-ATACTTTTTAAAATTTTTTAAAATAATTT
*
40659063 TTTAATTTTAAAATATTTTTAAAATACTTTTTAAAA-TTTTTAAAATAAATT
1 TTTAATTTT-AAA-A-TTTTAAAATACTTTTTAAAATTTTTTAAAATAATTT
40659114 TTTA
1 TTTA
40659118 GTATTTATTA
Statistics
Matches: 81, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
48 8 0.10
49 17 0.21
50 22 0.27
51 25 0.31
52 9 0.11
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (49 bp):
TTTAATTTTAAAATTTTAAAATACTTTTTAAAATTTTTTAAAATAATTT
Found at i:40659123 original size:22 final size:21
Alignment explanation
Indices: 40659065--40659130 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
40659055 AATACTTTTT
*
40659065 TAATTTTAAAATATTTTTAAAA
1 TAATTTT-TAATATTTTTAAAA
* *
40659087 TACTTTTTAAAATTTTTAAAA
1 TAATTTTTAATATTTTTAAAA
*
40659108 TAAATTTTTAGTATTTATTAAAA
1 T-AATTTTTAATATTT-TTAAAA
40659131 AACTGGGCCG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 13 0.36
22 17 0.47
23 6 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TAATTTTTAATATTTTTAAAA
Found at i:40660240 original size:29 final size:29
Alignment explanation
Indices: 40660199--40660256 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
40660189 CTGTCTTCTC
40660199 CCCCAAACGTTCTTTCCCCTCTGCCGGTT
1 CCCCAAACGTTCTTTCCCCTCTGCCGGTT
*
40660228 CCCCAAACGTTCTTTCCCCTCTGCTGGTT
1 CCCCAAACGTTCTTTCCCCTCTGCCGGTT
40660257 TTTGGGAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.10, C:0.43, G:0.14, T:0.33
Consensus pattern (29 bp):
CCCCAAACGTTCTTTCCCCTCTGCCGGTT
Found at i:40664530 original size:12 final size:13
Alignment explanation
Indices: 40664497--40664551 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
40664487 CAAATTTTTC
*
40664497 AAAAGCACTTCTC
1 AAAAGCACTTCTT
*
40664510 AAAATCAC-TCTT
1 AAAAGCACTTCTT
40664522 AAAAGCACTTCTT
1 AAAAGCACTTCTT
* *
40664535 AAAAGAACTTTTT
1 AAAAGCACTTCTT
40664548 AAAA
1 AAAA
40664552 ACAATGAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
12 10 0.28
13 26 0.72
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.29
Consensus pattern (13 bp):
AAAAGCACTTCTT
Found at i:40666504 original size:9 final size:9
Alignment explanation
Indices: 40666472--40666508 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40666462 TGAATTTTCG
40666472 AATTCGAAT
1 AATTCGAAT
*
40666481 AACTCGAAT
1 AATTCGAAT
40666490 AATTCGAAT
1 AATTCGAAT
*
40666499 AGTTCGAAT
1 AATTCGAAT
40666508 A
1 A
40666509 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40666881 original size:17 final size:16
Alignment explanation
Indices: 40666847--40666877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40666837 CCTATTTACT
*
40666847 TTCCCTCAAACTTTTA
1 TTCCCTAAAACTTTTA
40666863 TTCCCTAAAACTTTT
1 TTCCCTAAAACTTTT
40666878 TATTTTCTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (16 bp):
TTCCCTAAAACTTTTA
Found at i:40691344 original size:3 final size:3
Alignment explanation
Indices: 40691336--40691361 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40691326 ATAAAAGGAA
40691336 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
40691362 AGTTAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40692977 original size:44 final size:44
Alignment explanation
Indices: 40692909--40694161 Score: 304
Period size: 44 Copynumber: 28.7 Consensus size: 44
40692899 GATGTGATTT
* *
40692909 ACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * * * *
40692953 GCTCCACTGTAATCTCAGAGAGATAGGAT--TACTAGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTAATCC
* * * ** ** *
40692997 GCTCCGCTGTAATCTCAGGGAGATAAGATCATAAATTCTTCGGTCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATT-TT-AATCC
* * ***
40693043 ACTCCACTGTAACCTCAGGGAGATAAGA-CC-TGA-TGCGATCC
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
** *
40693084 ACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * *
40693128 ACTCCACTGTAATCTTAGGGAGATAGGAT--TACTATCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCT-TTAT-TTTAATCC
* * * * *
40693172 GCTCCGCTGTAACCTCAGGGAGATAAGAT-C-TGA--TGAGATCC
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTA-ATCC
** *
40693213 ACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * *
40693257 GCTCCACTGTAATCTCAGGGAGATAGGAT--TACTATCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCT-TTAT-TTTAATCC
* * ** * ** * *
40693301 ACTCCGCTGTAACCTCACAGAGATAAGAT-C-TGA-CGTGATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
** *
40693342 ACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * **
40693386 ACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGC
1 ACTCCACTGTAATCTCAGGGAGATAAGA-T-C---CTTTATTTTAAT-C-C
* * * *
40693437 TGTAACTCTACTGTAA-CTTCAGAGAGATAAGATCATTTATTTTAATTC
1 ----ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * * *
40693485 GCTCCACTGTAATCTCAGGGAGATAGGAT--TACTAGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTAATCC
* * ** ** *
40693529 GCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCT-TTATT-TT-AATCC
* * * **** *
40693575 ATTCCACTGTAATCTCAGGGAAATAAGA-CC-TGA-CGCGATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
** * * * **
40693616 ACTCTGCTGTAA-CTTTAGAGAGATAAGATCATTGGTTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * * *
40693660 GCTCCACTGTAAACTCAGGGAGATAGGATTACC---AGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGA-T-CCTTTA-TTTTAATCC
* ** * * *
40693704 ACTCCGCTGTAATCTCAGGGAGATAAGAT-CTGAAAATCTTCAGTCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCT--TTAT-TTTAATCC
** * * **** * *
40693750 GTTCCACTGTAATCTCAGGTAAATAAGA-CC--TGGCGTGATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
** * *
40693791 ACTCTGCTGTAA-CTTCAGAGAGATAAGATCCTTCATTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * ** ** * *
40693835 ACTCCATTGTAATCTCAAGGAGATAGGAT--AGTGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
* * * **** *
40693877 GCTCCGCTGTAATCTCAGGGAGATAAGAT-C-TGA-CACGATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
* * * *
40693918 ACTCTAC-GT-AGCTTCAGAGAGATAAGATCCTTCATTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* ** ** * *
40693961 ACTCCACTGTAATCTCAGGGAGATAGGAT--AGTGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * ** * *
40694003 GCTCCGCTGTAATCTCAGTGAGATAAGAT-C-TGA-CATGATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
* *
40694044 ACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATCC
1 ACTCCACTGTAATC-TCAGGGAGATAAGATCCTTTATTTTAATCC
* * * * *
40694088 GCTCCACTGTAATCTCAGGGAGATAAGAT--TACTAGCTTCAATCT
1 ACTCCACTGTAATCTCAGGGAGATAAGATCCT-TTA-TTTTAATCC
*
40694132 ACTCCGCTGTAATCTCAGGGAGATAAGATC
1 ACTCCACTGTAATCTCAGGGAGATAAGATC
40694162 TGAAATTCTT
Statistics
Matches: 863, Mismatches: 261, Indels: 169
0.67 0.20 0.13
Matches are distributed among these distances:
39 2 0.00
40 24 0.03
41 166 0.19
42 76 0.09
43 35 0.04
44 407 0.47
45 20 0.02
46 91 0.11
48 1 0.00
49 7 0.01
50 7 0.01
51 1 0.00
53 1 0.00
54 2 0.00
55 23 0.03
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
ACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCC
Found at i:40693205 original size:129 final size:129
Alignment explanation
Indices: 40692992--40693736 Score: 753
Period size: 129 Copynumber: 5.6 Consensus size: 129
40692982 TACTAGCTTC
* * * * ** *
40692992 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCATA-AATTCTTCGGTCTACTCCACTGTAAC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT--TACTA-TCTTCAATCTACTCCGCTGTAAC
*
40693056 CTCAGGGAGATAAGACCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATT
63 CTCAGGGAGATAAGATCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATT
40693121 TT
128 TT
* * *
40693123 AATCCACTCCACTGTAATCTTAGGGAGATAGGATTACTATCTTCAATCTGCTCCGCTGTAACCTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTACTCCGCTGTAACCTC
*
40693188 AGGGAGATAAGATCTGATGAGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTT
66 AGGGAGATAAGATCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTT
40693252 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTACTCCGCTGTAACCTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTACTCCGCTGTAACCTC
** * * *
40693317 ACAGAGATAAGATCTGACGTGATCTACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTT
66 AGGGAGATAAGATCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTT
* * *
40693381 AATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTGTAACTCT
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTACTCCGCTGT-A----
* * *** * * ** *
40693446 ACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCGCTCCACTGTAA-TCTCAGGGAGATA
61 AC-----C-TCAGGGAGATAAGATC--TGA-TGCGATCCACTCTGCTGTAACT-TCAGAGAGATA
* * * *
40693510 GGAT--TACTAGCTTC
116 AGATCCT-TTA-TTTT
* * * * ** * * *
40693524 AATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTCGGTCTATTCCACTGTAAT
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-T-ACTA-TCTTCAATCTACTCCGCTGTAAC
* * * * * * **
40693588 CTCAGGGAAATAAGACCTGACGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCATTGGTT
63 CTCAGGGAGATAAGATCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATT
40693653 TT
128 TT
* * * *
40693655 AATCCGCTCCACTGTAAACTCAGGGAGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTC
1 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTACTCCGCTGTAACCTC
40693720 AGGGAGATAAGATCTGA
66 AGGGAGATAAGATCTGA
40693737 AAATCTTCAG
Statistics
Matches: 506, Mismatches: 83, Indels: 52
0.79 0.13 0.08
Matches are distributed among these distances:
129 300 0.59
130 4 0.01
131 84 0.17
132 3 0.01
133 1 0.00
134 15 0.03
135 1 0.00
139 1 0.00
140 16 0.03
141 1 0.00
142 5 0.01
143 57 0.11
144 3 0.01
145 15 0.03
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (129 bp):
AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTCAATCTACTCCGCTGTAACCTC
AGGGAGATAAGATCTGATGCGATCCACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTT
Found at i:40693513 original size:99 final size:99
Alignment explanation
Indices: 40693342--40693540 Score: 353
Period size: 99 Copynumber: 2.0 Consensus size: 99
40693332 GACGTGATCT
* *
40693342 ACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTCAGGGA
1 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGA
40693407 GATAGGATTACTAACTTCAATCTGCTCCGCTGTA
66 GATAGGATTACTAACTTCAATCTGCTCCGCTGTA
* *
40693441 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCGCTCCACTGTAATCTCAGGGA
1 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGA
*
40693506 GATAGGATTACTAGCTTCAATCTGCTCCGCTGTA
66 GATAGGATTACTAACTTCAATCTGCTCCGCTGTA
40693540 A
1 A
40693541 TCTCAGGGAG
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (99 bp):
ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCACTCCACTGTAATCTCAGGGA
GATAGGATTACTAACTTCAATCTGCTCCGCTGTA
Found at i:40693738 original size:175 final size:175
Alignment explanation
Indices: 40692908--40693909 Score: 878
Period size: 175 Copynumber: 5.7 Consensus size: 175
40692898 TGATGTGATT
* * * *
40692908 TACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGAG
1 TACTCTGCTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCGCTCCACTGTAATCTCAGGG
* *
40692973 AGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCAT-AAATTCTT
66 AGATAGGATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATC-TGAAAATCTT
* * * * *
40693037 CGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATC
130 CAGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
* * * * *
40693083 CACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTTAGGG
1 TACTCTGCTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCGCTCCACTGTAATCTCAGGG
* * * *
40693148 AGATAGGATTACTATCTTCAATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCTGATGAGATC-
66 AGATAGGATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA--AAATCT
** * * * ****
40693212 -CA--C---TCTGCTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTAATC
129 TCAGTCTATTCCACTGTAATC-TCAGGGAAATAAGA-CC-TGA-CGCGATC
** ** * * * * * ** * * *
40693256 CGCTCCACTGTAA-TCTCAGGGAGATAGGATTACT-ATCTTCAATCTACTCCGCTGTAACCTCAC
1 TACTCTGCTGTAACT-TCAGAGAGATAAGATCATTCAT-TTTAATCCGCTCCACTGTAATCTCAG
* * * * * * **
40693319 AGAGATAAGATCTGA-C-G--T-GATCTACTCTGCTGTAA-CTTCAGAGAGATAAGATCCT--TT
64 GGAGATAGGAT-T-ACCAGCTTCAATCTGCTCCGCTGTAATC-TCAGGGAGATAAGAT-CTGAAA
* * * * * * * * *
40693376 AT-TTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCTCCGCTG
125 ATCTTCAGTCTATTCCACTGTAATCTCAGGGAAATA--A-GAC---C-T-GA-C-G---CGATC
* * *
40693439 TAACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCGCTCCACTGTAATCTCAGG
1 T-ACTCTGCTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCGCTCCACTGTAATCTCAGG
* *
40693504 GAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTT
65 GAGATAGGATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAATCTT
*
40693569 CGGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
130 CAGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
* ** *
40693615 TACTCTGCTGTAACTTTAGAGAGATAAGATCATTGGTTTTAATCCGCTCCACTGTAAACTCAGGG
1 TACTCTGCTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCGCTCCACTGTAATCTCAGGG
*
40693680 AGATAGGATTACCAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAATCTTC
66 AGATAGGATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAATCTTC
* * * *
40693745 AGTCTGTTCCACTGTAATCTCAGGTAAATAAGACCTGGCGTGATC
131 AGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
* * * *
40693790 TACTCTGCTGTAACTTCAGAGAGATAAGATCCTTCATTTTAATCCACTCCATTGTAATCTCAAGG
1 TACTCTGCTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCGCTCCACTGTAATCTCAGGG
**
40693855 AGATAGGA-TA-GTGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
66 AGATAGGATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
40693910 CACGATCTAC
Statistics
Matches: 671, Mismatches: 112, Indels: 90
0.77 0.13 0.10
Matches are distributed among these distances:
167 2 0.00
168 1 0.00
169 2 0.00
170 50 0.07
171 5 0.01
172 5 0.01
173 118 0.18
174 5 0.01
175 342 0.51
176 5 0.01
177 3 0.00
178 3 0.00
179 3 0.00
180 1 0.00
181 1 0.00
182 2 0.00
183 3 0.00
184 54 0.08
185 3 0.00
186 5 0.01
187 29 0.04
188 2 0.00
189 27 0.04
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (175 bp):
TACTCTGCTGTAACTTCAGAGAGATAAGATCATTCATTTTAATCCGCTCCACTGTAATCTCAGGG
AGATAGGATTACCAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAATCTTC
AGTCTATTCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATC
Found at i:40693962 original size:126 final size:127
Alignment explanation
Indices: 40693741--40694164 Score: 652
Period size: 126 Copynumber: 3.3 Consensus size: 127
40693731 ATCTGAAAAT
* * * * * * * * *
40693741 CTTCAGTCTGTTCCACTGTAATCTCAGGTAAATAAGACCTGGCGTGATCTACTCTGCTGTAACTT
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATGATCTACTCTACTGTAACTT
* *
40693806 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCATTGTAATCTCAAGGAGATAGGATAGTG
66 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATAGTG
* *
40693868 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACACGATCTACTCTAC-GTAGCTT
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATGATCTACTCTACTGTAACTT
40693932 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATAGTG
66 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATAGTG
*
40693994 CTTCAATCTGCTCCGCTGTAATCTCAGTGAGATAAGATCTGACATGATCTACTCTACTGTAACTT
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATGATCTACTCTACTGTAACTT
* * * *
40694059 CAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAAGATTACTAG
66 CAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGA-TAGT-G
*
40694123 CTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGA
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGA
40694165 AATTCTTCAG
Statistics
Matches: 272, Mismatches: 22, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
126 121 0.44
127 107 0.39
128 3 0.01
129 41 0.15
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (127 bp):
CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGACATGATCTACTCTACTGTAACTT
CAGAGAGATAAGATCCTTCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGATAGTG
Found at i:40696567 original size:9 final size:9
Alignment explanation
Indices: 40696555--40696656 Score: 75
Period size: 9 Copynumber: 11.0 Consensus size: 9
40696545 TTTTCTCTTT
40696555 TTTTTTTTA
1 TTTTTTTTA
40696564 TTTTTGACTTTGA
1 TTTTT---TTT-A
40696577 TTTTTTTTTGA
1 -TTTTTTTT-A
40696588 TTTTTTTTA
1 TTTTTTTTA
*
40696597 TTTTTTTAA
1 TTTTTTTTA
*
40696606 TTTTTTTGA
1 TTTTTTTTA
40696615 -TTTTTTTA
1 TTTTTTTTA
*
40696623 -TTTTATT-
1 TTTTTTTTA
* *
40696630 TTTGTTTTG
1 TTTTTTTTA
*
40696639 TTTTTTTTG
1 TTTTTTTTA
40696648 TTTTTTTTA
1 TTTTTTTTA
40696657 GTCTGAACTC
Statistics
Matches: 78, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
8 18 0.23
9 38 0.49
10 8 0.10
11 5 0.06
12 3 0.04
13 1 0.01
14 5 0.06
ACGTcount: A:0.11, C:0.01, G:0.07, T:0.81
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:40696581 original size:1 final size:1
Alignment explanation
Indices: 40696577--40696655 Score: 50
Period size: 1 Copynumber: 79.0 Consensus size: 1
40696567 TTGACTTTGA
** * ** ** * * * *
40696577 TTTTTTTTTGATTTTTTTTATTTTTTTAATTTTTTTGATTTTTTTATTTTATTTTTGTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
40696642 TTTTTGTTTTTTTT
1 TTTTTTTTTTTTTT
40696656 AGTCTGAACT
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (1 bp):
T
Found at i:40696593 original size:8 final size:9
Alignment explanation
Indices: 40696579--40696654 Score: 79
Period size: 9 Copynumber: 8.8 Consensus size: 9
40696569 GACTTTGATT
40696579 TTTTTTTGA
1 TTTTTTTGA
*
40696588 TTTTTTTTA
1 TTTTTTTGA
*
40696597 TTTTTTTAA
1 TTTTTTTGA
40696606 TTTTTTTGA
1 TTTTTTTGA
40696615 TTTTTTT-A
1 TTTTTTTGA
40696623 TTTTATTT--
1 TTTT-TTTGA
* *
40696631 TTGTTTTGT
1 TTTTTTTGA
40696640 TTTTTTTG-
1 TTTTTTTGA
40696648 TTTTTTT
1 TTTTTTT
40696655 TAGTCTGAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
7 3 0.05
8 15 0.25
9 41 0.69
ACGTcount: A:0.09, C:0.00, G:0.07, T:0.84
Consensus pattern (9 bp):
TTTTTTTGA
Found at i:40696594 original size:27 final size:24
Alignment explanation
Indices: 40696552--40696655 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 24
40696542 TCTTTTTCTC
* *
40696552 TTTTTTTTT-TTATTTTTGACTTTGA
1 TTTTTTTTTGTT-TTTTTTA-TTTTA
*
40696577 TTTTTTTTTGATTTTTTTTATTTTT
1 TTTTTTTTTG-TTTTTTTTATTTTA
*
40696602 TTAATTTTTTTGATTTTTTTATTTTA
1 TT--TTTTTTTGTTTTTTTTATTTTA
*
40696628 TTTTTGTTTTGTTTTTTTTGTTTT-
1 TTTTT-TTTTGTTTTTTTTATTTTA
40696652 TTTT
1 TTTT
40696656 AGTCTGAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
24 7 0.10
25 30 0.45
26 20 0.30
27 10 0.15
ACGTcount: A:0.10, C:0.01, G:0.07, T:0.83
Consensus pattern (24 bp):
TTTTTTTTTGTTTTTTTTATTTTA
Found at i:40696618 original size:51 final size:51
Alignment explanation
Indices: 40696555--40696654 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 51
40696545 TTTTCTCTTT
*
40696555 TTTTTTTTA-TTTTTGACTTTGATTTTT-TTTTGATTTTTTTTATTTTTTTAA
1 TTTTTTTGATTTTTTGA-TTTGATTTTTGTTTTG-TTTTTTTTATTTTTTTAA
* * *
40696606 TTTTTTTGATTTTTTTATTTTATTTTTGTTTTGTTTTTTTTGTTTTTTT
1 TTTTTTTGATTTTTTGATTTGATTTTTGTTTTGTTTTTTTTATTTTTTT
40696655 TAGTCTGAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 32 0.74
52 11 0.26
ACGTcount: A:0.10, C:0.01, G:0.07, T:0.82
Consensus pattern (51 bp):
TTTTTTTGATTTTTTGATTTGATTTTTGTTTTGTTTTTTTTATTTTTTTAA
Found at i:40696655 original size:18 final size:17
Alignment explanation
Indices: 40696553--40696654 Score: 91
Period size: 18 Copynumber: 5.9 Consensus size: 17
40696543 CTTTTTCTCT
40696553 TTTTTTTTTTATTTTTGA
1 TTTTTTTTTT-TTTTTGA
* **
40696571 CTTTGATTTTTTTTTGA
1 TTTTTTTTTTTTTTTGA
*
40696588 TTTTTTTTATTTTTTTAA
1 TTTTTTTT-TTTTTTTGA
*
40696606 TTTTTTTGATTTTTTT-A
1 TTTTTTT-TTTTTTTTGA
* *
40696623 TTTTATTTTTGTTTTG-
1 TTTTTTTTTTTTTTTGA
40696639 TTTTTTTTGTTTTTTT
1 TTTTTTTT-TTTTTTT
40696655 TAGTCTGAAC
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
16 13 0.19
17 25 0.37
18 29 0.43
ACGTcount: A:0.10, C:0.01, G:0.07, T:0.82
Consensus pattern (17 bp):
TTTTTTTTTTTTTTTGA
Found at i:40700646 original size:21 final size:22
Alignment explanation
Indices: 40700615--40700656 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40700605 AAAAATTGTT
*
40700615 ACTATTTTTTTACTGTTTTGCC
1 ACTATTTTTTTACTATTTTGCC
*
40700637 ACTA-TTTTTTATTATTTTGC
1 ACTATTTTTTTACTATTTTGC
40700657 TATCATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.17, C:0.14, G:0.07, T:0.62
Consensus pattern (22 bp):
ACTATTTTTTTACTATTTTGCC
Found at i:40706642 original size:22 final size:22
Alignment explanation
Indices: 40706614--40706672 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
40706604 ACAAAAAGAA
* * *
40706614 TTTTTTTCATAATTTTTGAATT
1 TTTTTTTCAAAATTTGTGAACT
*
40706636 TTTTTTTTAAAATTTGTGAACT
1 TTTTTTTCAAAATTTGTGAACT
**
40706658 TTTTTTAAAAAATTT
1 TTTTTTTCAAAATTT
40706673 TAAAAAATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (22 bp):
TTTTTTTCAAAATTTGTGAACT
Found at i:40707422 original size:21 final size:22
Alignment explanation
Indices: 40707371--40707433 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
40707361 GACATACTAA
*
40707371 CATTTAATTAATTTTTTAAAAT
1 CATTTAAATAATTTTTTAAAAT
* ***
40707393 TAAAAAAAT-ATTTTTTAAAAT
1 CATTTAAATAATTTTTTAAAAT
40707414 CATTTAAATAATTTTTTAAA
1 CATTTAAATAATTTTTTAAA
40707434 TTTTTTTAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.55
22 14 0.45
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (22 bp):
CATTTAAATAATTTTTTAAAAT
Found at i:40710537 original size:50 final size:50
Alignment explanation
Indices: 40710471--40710590 Score: 195
Period size: 50 Copynumber: 2.4 Consensus size: 50
40710461 AATGAAAAAG
* * *
40710471 ATATGATGGTAGCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATACAT
1 ATATGATAGTACCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATAAAT
*
40710521 ATATGATAGTACCTGTGCATTTCGACTTCTCTGATTTAGTTAGTATAAAT
1 ATATGATAGTACCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATAAAT
*
40710571 ATATGATAGTACCCGTGCAT
1 ATATGATAGTACCTGTGCAT
40710591 CATGTGGAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (50 bp):
ATATGATAGTACCTGTGCATTTCAACTTCTCTGATTTAGTTAGTATAAAT
Found at i:40714944 original size:22 final size:21
Alignment explanation
Indices: 40714919--40714959 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
40714909 TTCTTTATTT
*
40714919 TCTATTCTCTTCTGCTTCTCCC
1 TCTATTCTCCTCT-CTTCTCCC
*
40714941 TCTATTTTCCTCTCTTCTC
1 TCTATTCTCCTCTCTTCTC
40714960 AATCTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.05, C:0.39, G:0.02, T:0.54
Consensus pattern (21 bp):
TCTATTCTCCTCTCTTCTCCC
Found at i:40716596 original size:34 final size:34
Alignment explanation
Indices: 40716554--40716618 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
40716544 TTTTTAATTT
40716554 TAAAATTAAATT-AATTAATTATTTTAAGGAAGAA
1 TAAAATT-AATTAAATTAATTATTTTAAGGAAGAA
40716588 TAAAATTAATTAAATTAATTATTTTAAGGAA
1 TAAAATTAATTAAATTAATTATTTTAAGGAA
40716619 TAATTTCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 4 0.13
34 26 0.87
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (34 bp):
TAAAATTAATTAAATTAATTATTTTAAGGAAGAA
Found at i:40733865 original size:110 final size:110
Alignment explanation
Indices: 40733672--40733890 Score: 375
Period size: 110 Copynumber: 2.0 Consensus size: 110
40733662 TTAGCACATT
* * *
40733672 TTATGTGAGCTTTCCCGCGTATCTGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAATG
1 TTATGTAAGCTTTCCCGCGTATCCGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAAGG
* *
40733737 AACGGTAAGTGTTCTAATGGTTATGTTATAAACATATGGAAAGGA
66 AACAGTAAGTGTTCTAATGGTTATCTTATAAACATATGGAAAGGA
*
40733782 TTATGTAAGCTTTCCCGCGTATCCGATATTATTCTAAGTGATTCAACGGGCATGCATAGGGAAGG
1 TTATGTAAGCTTTCCCGCGTATCCGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAAGG
*
40733847 AACAGTAAGTGTTCTAATGGTTATCTTATAAACCTATGGAAAGG
66 AACAGTAAGTGTTCTAATGGTTATCTTATAAACATATGGAAAGG
40733891 TATGAAATGA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 102 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.32
Consensus pattern (110 bp):
TTATGTAAGCTTTCCCGCGTATCCGATATTATTCTAAGTGATTCAACGGGCATGCAAAGGGAAGG
AACAGTAAGTGTTCTAATGGTTATCTTATAAACATATGGAAAGGA
Found at i:40744852 original size:25 final size:24
Alignment explanation
Indices: 40744774--40744887 Score: 79
Period size: 25 Copynumber: 4.6 Consensus size: 24
40744764 GTACATGTAT
*
40744774 GCTCATACGAGCT-ATAAACGGTAA
1 GCTCATACGAGCTGA-AATCGGTAA
* * * *
40744798 GCTCCTCCAAGATGAAATAACGGTAA
1 GCTCATACGAGCTGAAAT--CGGTAA
40744824 GCTCATACGAGCTGAGAATCGGTAA
1 GCTCATACGAGCTGA-AATCGGTAA
* *
40744849 GCTC-TCATGAGCTGCAAATCAGTAA
1 GCTCAT-ACGAGCTG-AAATCGGTAA
* *
40744874 GCTTATATGAGCTG
1 GCTCATACGAGCTG
40744888 TGGTGTATCC
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
24 12 0.17
25 37 0.52
26 19 0.27
27 3 0.04
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (24 bp):
GCTCATACGAGCTGAAATCGGTAA
Found at i:40750635 original size:16 final size:17
Alignment explanation
Indices: 40750605--40750640 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40750595 AGTAAAAATG
*
40750605 ATAAAAATTATTTAAAA
1 ATAAAAATCATTTAAAA
*
40750622 ATAAAAATCATTAAAAA
1 ATAAAAATCATTTAAAA
40750639 AT
1 AT
40750641 GTAAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAAAATCATTTAAAA
Found at i:40755150 original size:21 final size:21
Alignment explanation
Indices: 40755126--40755176 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
40755116 ATAACTCTTC
*
40755126 TATTTTATATAA-ATAAATAT
1 TATTTTATATAATAAAAATAT
40755146 GTA--TTATATAATAAAAATAT
1 -TATTTTATATAATAAAAATAT
*
40755166 TATTTTTTATA
1 TATTTTATATA
40755177 TATTGTTATG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TATTTTATATAATAAAAATAT
Found at i:40755552 original size:13 final size:13
Alignment explanation
Indices: 40755522--40755546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40755512 CAATATATTT
40755522 ATTAATTAAAAAC
1 ATTAATTAAAAAC
40755535 ATTAATTAAAAA
1 ATTAATTAAAAA
40755547 ATTTAAAACA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:40755568 original size:22 final size:21
Alignment explanation
Indices: 40755525--40755569 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40755515 TATATTTATT
* *
40755525 AATTAAAAACATTAATTAAAA
1 AATTAAAAACATGAAATAAAA
*
40755546 AATTTAAAACATGAAATAGAAA
1 AATTAAAAACATGAAATA-AAA
40755568 AA
1 AA
40755570 GATTTGAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.24
Consensus pattern (21 bp):
AATTAAAAACATGAAATAAAA
Found at i:40755948 original size:28 final size:28
Alignment explanation
Indices: 40755915--40755968 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
40755905 TCTTTTCTTT
40755915 TCTGCCGATTTGC-TCCCTCTGTTTCTCA
1 TCTGCCGATTTGCGT-CCTCTGTTTCTCA
*
40755943 TCTGCCGATTTGCGTCTTCTGTTTCT
1 TCTGCCGATTTGCGTCCTCTGTTTCT
40755969 TTTCTTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 23 0.96
29 1 0.04
ACGTcount: A:0.06, C:0.31, G:0.17, T:0.46
Consensus pattern (28 bp):
TCTGCCGATTTGCGTCCTCTGTTTCTCA
Found at i:40757357 original size:23 final size:23
Alignment explanation
Indices: 40757327--40757375 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
40757317 GTGTTATTGA
*
40757327 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
40757350 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
40757373 TCA
1 TCA
40757376 ATGTTGCACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:40762153 original size:33 final size:33
Alignment explanation
Indices: 40762111--40762176 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
40762101 AATCTAACAA
40762111 ATACCAACAATTAATTTTACGTCAATTATACAT
1 ATACCAACAATTAATTTTACGTCAATTATACAT
*
40762144 ATACCAACAATTAATTTTAGGTCAATTATACAT
1 ATACCAACAATTAATTTTACGTCAATTATACAT
40762177 GCTTTATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.17, G:0.05, T:0.36
Consensus pattern (33 bp):
ATACCAACAATTAATTTTACGTCAATTATACAT
Found at i:40763865 original size:32 final size:29
Alignment explanation
Indices: 40763806--40763878 Score: 119
Period size: 32 Copynumber: 2.4 Consensus size: 29
40763796 ATTTCTTCTC
40763806 ATTTTAAATTTTAAATTTTTTGTGTTATA
1 ATTTTAAATTTTAAATTTTTTGTGTTATA
40763835 ATTTTAAATTTTAAATTATAGTTTGTGTTATA
1 ATTTTAAATTTTAAATT-T--TTTGTGTTATA
40763867 ATTTTAAATTTT
1 ATTTTAAATTTT
40763879 TTGTGGTATG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
29 17 0.41
30 1 0.02
32 23 0.56
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (29 bp):
ATTTTAAATTTTAAATTTTTTGTGTTATA
Found at i:40765353 original size:91 final size:91
Alignment explanation
Indices: 40765206--40765413 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
40765196 TTGATTTTAG
* * *
40765206 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAATTTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
40765271 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
40765298 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
40765363 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
*
40765389 AAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
40765414 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:40765382 original size:26 final size:28
Alignment explanation
Indices: 40765328--40765388 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
40765318 TATTATCAAG
* *
40765328 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
40765356 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
40765382 AATTATA
1 AATTATA
40765389 AAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:40765388 original size:44 final size:43
Alignment explanation
Indices: 40765246--40765388 Score: 112
Period size: 44 Copynumber: 3.2 Consensus size: 43
40765236 GAATTTTATG
* * *
40765246 AAATTATATATCATTATTAATTTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
40765290 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
40765337 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
40765381 AAATTATA
1 AAATTATA
40765389 AAAATTCATA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.15
47 13 0.17
48 3 0.04
49 5 0.07
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:40765557 original size:120 final size:120
Alignment explanation
Indices: 40765433--40765966 Score: 971
Period size: 120 Copynumber: 4.4 Consensus size: 120
40765423 ATTTTAAATG
* * *
40765433 TTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTTTATA
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AAATTATCTTTTATA
40765497 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
65 GTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
* *
40765553 TTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTTATAG
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTTATAG
40765618 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
66 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
40765673 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTTATAG
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTTATAG
40765738 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
66 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
*
40765793 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATATTTTATAG
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTTATAG
*
40765858 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATT
66 TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
*
40765913 TTATTAAATTATATATTTTAATTATAATACATTTAATAATAATTATGTTTAAAT
1 TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATG-TTAAAT
40765967 ATGATTAAAT
Statistics
Matches: 406, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
120 398 0.98
121 8 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (120 bp):
TTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAAATTATCTTTTATAG
TATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT
Found at i:40765704 original size:16 final size:16
Alignment explanation
Indices: 40765683--40765728 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
40765673 TTATTAAATT
40765683 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
40765699 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
40765714 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
40765729 CTTTTATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:40765824 original size:16 final size:16
Alignment explanation
Indices: 40765803--40765849 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
40765793 TTATTAAATT
40765803 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
40765819 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
40765834 AT-TATGTTAAATTATA
1 ATATAT-TTTAATTATA
40765850 TTTTATAGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.42
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:40768786 original size:22 final size:21
Alignment explanation
Indices: 40768761--40768804 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
40768751 CCTCTCCCAT
40768761 CCCA-CCCCCCTTCTACCCCAAA
1 CCCATCCCCCCTTC--CCCCAAA
40768783 CCCATTCCCCCCTTCCCCCAAA
1 CCCA-TCCCCCCTTCCCCCAAA
40768805 AAAATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.55
24 9 0.45
ACGTcount: A:0.20, C:0.64, G:0.00, T:0.16
Consensus pattern (21 bp):
CCCATCCCCCCTTCCCCCAAA
Found at i:40776153 original size:169 final size:169
Alignment explanation
Indices: 40775874--40776204 Score: 662
Period size: 169 Copynumber: 2.0 Consensus size: 169
40775864 TATTAATTGG
40775874 TATATAACATTTGGTTATTCTCATTAGGTCAGTAAATGCATCTAATAGTTAACTTGCAATAAAGT
1 TATATAACATTTGGTTATTCTCATTAGGTCAGTAAATGCATCTAATAGTTAACTTGCAATAAAGT
40775939 GAATTATTTTTTGAACTTCTAGTTCTAATTACTTTCTACGATGATCTAGAAAATAATAATTCATT
66 GAATTATTTTTTGAACTTCTAGTTCTAATTACTTTCTACGATGATCTAGAAAATAATAATTCATT
40776004 CCAAGCAATTCATCCAATTATTATGTTTCTCCAACGTTA
131 CCAAGCAATTCATCCAATTATTATGTTTCTCCAACGTTA
40776043 TATATAACATTTGGTTATTCTCATTAGGTCAGTAAATGCATCTAATAGTTAACTTGCAATAAAGT
1 TATATAACATTTGGTTATTCTCATTAGGTCAGTAAATGCATCTAATAGTTAACTTGCAATAAAGT
40776108 GAATTATTTTTTGAACTTCTAGTTCTAATTACTTTCTACGATGATCTAGAAAATAATAATTCATT
66 GAATTATTTTTTGAACTTCTAGTTCTAATTACTTTCTACGATGATCTAGAAAATAATAATTCATT
40776173 CCAAGCAATTCATCCAATTATTATGTTTCTCC
131 CCAAGCAATTCATCCAATTATTATGTTTCTCC
40776205 CCCTAACGTT
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 162 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (169 bp):
TATATAACATTTGGTTATTCTCATTAGGTCAGTAAATGCATCTAATAGTTAACTTGCAATAAAGT
GAATTATTTTTTGAACTTCTAGTTCTAATTACTTTCTACGATGATCTAGAAAATAATAATTCATT
CCAAGCAATTCATCCAATTATTATGTTTCTCCAACGTTA
Found at i:40778442 original size:22 final size:22
Alignment explanation
Indices: 40778417--40778459 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
40778407 TACACCAAAA
* *
40778417 TAGGCTTTTAGCGGCGCTTTTT
1 TAGGCCTTTAGCGACGCTTTTT
40778439 TAGGCCTTTAGCGACGCTTTT
1 TAGGCCTTTAGCGACGCTTTT
40778460 ATTACAAACG
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:0.12, C:0.21, G:0.26, T:0.42
Consensus pattern (22 bp):
TAGGCCTTTAGCGACGCTTTTT
Found at i:40778512 original size:43 final size:43
Alignment explanation
Indices: 40778443--40778728 Score: 230
Period size: 43 Copynumber: 6.7 Consensus size: 43
40778433 CTTTTTTAGG
* **
40778443 CCTTTAGCGACGCTTTTATTACAAACGCCGCTATAGACAATAA
1 CCTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGACAATAA
* * * * *
40778486 CCTTTAGCGGTG-TTTTGTTGGA-AAACGCCGCTAAAGACCATGA
1 CCTTTAGCGGCGCTTTTGCT--ACAAACGCCGCTATAGACAATAA
* *
40778529 CTTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGATC-ATGA
1 CCTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGA-CAATAA
* * * **
40778572 CCTTTAACGGCGCTTTTCCAACAAACGCCGCTATAGATC-AGGA
1 CCTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGA-CAATAA
* * * *
40778615 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAG-CTGAA-GA
1 CCTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGAC--AATAA
* *
40778658 CCTTTAGCGGCGCTTTTACCACAAACGCCGCTATAGA-ACA-AA
1 CCTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGACA-ATAA
* *
40778700 CCTTTAGCGACGCTTCTTGC-AAAAACGCC
1 CCTTTAGCGGCGCTT-TTGCTACAAACGCC
40778729 ACTTAAAACA
Statistics
Matches: 208, Mismatches: 24, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
41 2 0.01
42 31 0.15
43 166 0.80
44 9 0.04
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (43 bp):
CCTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGACAATAA
Found at i:40778598 original size:86 final size:85
Alignment explanation
Indices: 40778444--40778690 Score: 266
Period size: 86 Copynumber: 2.9 Consensus size: 85
40778434 TTTTTTAGGC
* * * * * **
40778444 CTTTAGCGACGCTTTTATTACAAACGCCGCTATAGA-CAATAACCTTTAGCGGTGTTTTGTTGGA
1 CTTTAGCGGCGCTTTTACTACAAACGCCGCTATAGATC-ATGACCTTTAGCGGCG-CTT-TTCCA
*
40778508 -AAACGCCGCTAAAGACCATGA-
63 CAAACGCCGCTAAAGACCAGGAT
* *
40778529 CTTTTAGCGGCGCTTTTGCTACAAACGCCGCTATAGATCATGACCTTTAACGGCGCTTTTCCAAC
1 C-TTTAGCGGCGCTTTTACTACAAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCC-AC
* *
40778594 AAACGCCGCTATAGATCAGGAT
64 AAACGCCGCTAAAGACCAGGAT
* * * * *
40778616 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGCTGAAGACCTTTAGCGGCGCTTTTACCACA
1 CTTTAGCGGCGCTTTTACTACAAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTT-CCACA
40778681 AACGCCGCTA
65 AACGCCGCTA
40778691 TAGAACAAAC
Statistics
Matches: 138, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
84 2 0.01
85 4 0.03
86 128 0.93
87 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (85 bp):
CTTTAGCGGCGCTTTTACTACAAACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTCCACAA
ACGCCGCTAAAGACCAGGAT
Found at i:40783675 original size:21 final size:20
Alignment explanation
Indices: 40783626--40783680 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
40783616 ACCCCAAATA
* *
40783626 TCTAAACCATAAATCTCTAAC
1 TCTAAACCCT-AATCTCAAAC
40783647 TCTAAACCTCTAATCTCAAAC
1 TCTAAACC-CTAATCTCAAAC
40783668 TC-ATAACCCTAAT
1 TCTA-AACCCTAAT
40783681 TACCCCAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 6 0.20
21 23 0.77
22 1 0.03
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (20 bp):
TCTAAACCCTAATCTCAAAC
Found at i:40783826 original size:7 final size:7
Alignment explanation
Indices: 40783798--40783840 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
40783788 TTAAATCCTA
*
40783798 AACCCAT
1 AACCCCT
40783805 AACCCC-
1 AACCCCT
*
40783811 AGCCCCT
1 AACCCCT
*
40783818 AACCTCT
1 AACCCCT
40783825 AACCCCT
1 AACCCCT
40783832 AACCCCT
1 AACCCCT
40783839 AA
1 AA
40783841 ACCTTATTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.33, C:0.51, G:0.02, T:0.14
Consensus pattern (7 bp):
AACCCCT
Found at i:40784886 original size:41 final size:41
Alignment explanation
Indices: 40784479--40784884 Score: 533
Period size: 41 Copynumber: 9.9 Consensus size: 41
40784469 TTTTATTATT
* * **
40784479 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACTGGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* **
40784520 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACTAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * **
40784561 ATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGACTGGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* **
40784602 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGACTAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
40784643 ATTAGCGGCGCTTTTTCAAAAACACCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
40784684 ATTAGCAGCGCTTCGTCAAAAACGCCGCTAAAGGCCCTAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
*
40784725 ATTAGCGGCGCTTCTTCACAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
40784766 ATTAGCGGCTCTTCGTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * * *
40784807 ATTAGTGGCGCTTCGTAAAAAACGCAGCTAAAGGCCCCAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
40784848 ATTAGCGGCGCTTTTTCTAAAACGCCGCTAAAGGCCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
40784885 CAAAAACTTA
Statistics
Matches: 329, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 329 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:40788146 original size:19 final size:19
Alignment explanation
Indices: 40788122--40788168 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
40788112 TAGAATATCT
40788122 ATAAGATTTATCTACCTAA
1 ATAAGATTTATCTACCTAA
*
40788141 ATAAGATTTATCTATCTAA
1 ATAAGATTTATCTACCTAA
40788160 ATAA-ATTTA
1 ATAAGATTTA
40788169 AAATATATCC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 5 0.19
19 22 0.81
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (19 bp):
ATAAGATTTATCTACCTAA
Found at i:40790340 original size:29 final size:30
Alignment explanation
Indices: 40790294--40790357 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
40790284 TGTAAGTTTG
**
40790294 AAATTTAGTTTTCATATTTTT-ACTTTTAA
1 AAATTTAGTTTTCATATTTTTCAAATTTAA
40790323 AAATTTAGTCTTTC-TATTTTTCAAATTTAA
1 AAATTTAGT-TTTCATATTTTTCAAATTTAA
40790353 AAATT
1 AAATT
40790358 CAGATCAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 16 0.52
30 15 0.48
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (30 bp):
AAATTTAGTTTTCATATTTTTCAAATTTAA
Found at i:40794050 original size:16 final size:15
Alignment explanation
Indices: 40794018--40794051 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40794008 AATAAATTAA
*
40794018 ATTTTATATTGAATT
1 ATTTTATATTAAATT
40794033 ATTTTATATTTAAATT
1 ATTTTATA-TTAAATT
40794049 ATT
1 ATT
40794052 ATGTTCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTATATTAAATT
Found at i:40794472 original size:3 final size:3
Alignment explanation
Indices: 40794466--40794508 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
40794456 ATTTGAAAAT
40794466 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40794509 ATAAAGTTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40846609 original size:26 final size:26
Alignment explanation
Indices: 40846562--40846611 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40846552 AAACTATTCA
* *
40846562 AGGTTTGGGTTTGGGTTCAGGGTTCG
1 AGGTTTGGGTTCGAGTTCAGGGTTCG
40846588 AGGTTTGAGGTTCGAGTT-AGGGTT
1 AGGTTTG-GGTTCGAGTTCAGGGTT
40846612 TAATGTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.12, C:0.06, G:0.44, T:0.38
Consensus pattern (26 bp):
AGGTTTGGGTTCGAGTTCAGGGTTCG
Found at i:40851114 original size:25 final size:29
Alignment explanation
Indices: 40851079--40851164 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
40851069 CATATTTATA
40851079 GAAAGTCAAAGATATGGGTATC-AA-A-T
1 GAAAGTCAAAGATATGGGTATCAAATATT
40851105 -AAAGTCAAAGATATGGGTATCAAATATT
1 GAAAGTCAAAGATATGGGTATCAAATATT
*
40851133 GGAAAGTCAAAGATATGGGTATCGAGATATT
1 -GAAAGTCAAAGATATGGGTATC-AAATATT
40851164 G
1 G
40851165 GCATAAGAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
25 21 0.40
26 2 0.04
27 1 0.02
28 1 0.02
30 22 0.42
31 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.24, T:0.26
Consensus pattern (29 bp):
GAAAGTCAAAGATATGGGTATCAAATATT
Found at i:40851141 original size:30 final size:30
Alignment explanation
Indices: 40851079--40851165 Score: 121
Period size: 25 Copynumber: 3.0 Consensus size: 30
40851069 CATATTTATA
40851079 GAAAGTCAAAGATATGGGTATC-AA-A-T-
1 GAAAGTCAAAGATATGGGTATCAAATATTG
40851105 -AAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATATTG
*
40851134 GAAAGTCAAAGATATGGGTATCGAGATATTG
1 GAAAGTCAAAGATATGGGTATC-AAATATTG
40851165 G
1 G
40851166 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
25 21 0.39
26 2 0.04
27 1 0.02
28 1 0.02
30 21 0.39
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.25
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATATTG
Found at i:40855680 original size:25 final size:25
Alignment explanation
Indices: 40855646--40855696 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
40855636 ATATTTATGG
40855646 AAAGTCAAAGATATAGGTATCAAAT
1 AAAGTCAAAGATATAGGTATCAAAT
*
40855671 AAAGTCAAAGATATGGGTATCAAAT
1 AAAGTCAAAGATATAGGTATCAAAT
40855696 A
1 A
40855697 TTGGAAAGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.24
Consensus pattern (25 bp):
AAAGTCAAAGATATAGGTATCAAAT
Found at i:40855707 original size:30 final size:30
Alignment explanation
Indices: 40855643--40855731 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
40855633 TCCATATTTA
*
40855643 TGGAAAGTCAAAGATATAGGTATC-AA-A-
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
40855670 T--AAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
40855698 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
40855729 TGG
1 TGG
40855732 CATAAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
25 20 0.37
26 2 0.04
27 2 0.04
28 1 0.02
30 21 0.39
31 8 0.15
ACGTcount: A:0.43, C:0.07, G:0.25, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:40859377 original size:25 final size:26
Alignment explanation
Indices: 40859337--40859386 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
40859327 TTGTAAATAA
40859337 AAATAATATCTCTAG-AAATTTTCTG
1 AAATAATATCTCTAGAAAATTTTCTG
* *
40859362 AAATAATTTCTTTAGAAAATTTTCT
1 AAATAATATCTCTAGAAAATTTTCT
40859387 TTTTACAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (26 bp):
AAATAATATCTCTAGAAAATTTTCTG
Found at i:40859530 original size:6 final size:6
Alignment explanation
Indices: 40859519--40859558 Score: 50
Period size: 5 Copynumber: 7.0 Consensus size: 6
40859509 AAATATTATC
40859519 AATATA AATATA AATATTA AAT-TA AAT-TA AAT-TA AATATA
1 AATATA AATATA AATA-TA AATATA AATATA AATATA AATATA
40859559 TCGTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 15 0.47
6 12 0.38
7 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
AATATA
Found at i:40859584 original size:29 final size:30
Alignment explanation
Indices: 40859533--40859590 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
40859523 TAAATATAAA
* *
40859533 TATTAAATTAAATTAAATTAAATA-TATCG
1 TATTAAATAAAATTAAATAAAATACTATCG
40859562 TATTAATATAAAATT-AATAAAATACTATC
1 TATTAA-ATAAAATTAAATAAAATACTATC
40859591 TAGATAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (30 bp):
TATTAAATAAAATTAAATAAAATACTATCG
Found at i:40862232 original size:43 final size:43
Alignment explanation
Indices: 40862184--40862276 Score: 168
Period size: 43 Copynumber: 2.2 Consensus size: 43
40862174 CTAATCACCT
*
40862184 AAACGCCGCTAAAGATCATGACCTTTAGTGACGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGACATTTAGTGACGCTTCTACCAC
*
40862227 AAACGCCGCTAAAGATTATGACATTTAGTGACGCTTCTACCAC
1 AAACGCCGCTAAAGATCATGACATTTAGTGACGCTTCTACCAC
40862270 AAACGCC
1 AAACGCC
40862277 ACTATAAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGATCATGACATTTAGTGACGCTTCTACCAC
Found at i:40862305 original size:43 final size:42
Alignment explanation
Indices: 40862184--40862338 Score: 116
Period size: 43 Copynumber: 3.6 Consensus size: 42
40862174 CTAATCACCT
* * **
40862184 AAACGCCGCTAAAGATCATGACCTTTAGTGACGCTTCTACCAC
1 AAACGCCACTAAAGAT-ATGACATTTAACGACGCTTCTACCAC
* **
40862227 AAACGCCGCTAAAGATTATGACATTTAGTGACGCTTCTACCAC
1 AAACGCCACTAAAGA-TATGACATTTAACGACGCTTCTACCAC
* * * **
40862270 AAACGCCACTATAAAGA-ATGGCTTTTAACGGCGCTT-TTTCAC
1 AAACGCCAC--TAAAGATATGACATTTAACGACGCTTCTACCAC
* * * *
40862312 AAACGCCGCTAAAAACATGACTTTTAA
1 AAACGCCACTAAAGATATGACATTTAA
40862339 AAAATATTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
40 5 0.05
41 10 0.10
42 12 0.12
43 62 0.65
44 1 0.01
45 6 0.06
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (42 bp):
AAACGCCACTAAAGATATGACATTTAACGACGCTTCTACCAC
Found at i:40862764 original size:19 final size:19
Alignment explanation
Indices: 40862740--40862790 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
40862730 AAATAAACAC
*
40862740 AAAAAAAATTTAGAAAATT
1 AAAAAAAATTTAGAAAAAT
**
40862759 AAAAAAAATATTTTAAAAAT
1 AAAAAAAAT-TTAGAAAAAT
40862779 AAAAAAATATTT
1 AAAAAAA-ATTT
40862791 TAAAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 9 0.33
20 16 0.59
21 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAAAATTTAGAAAAAT
Found at i:40862764 original size:21 final size:20
Alignment explanation
Indices: 40862740--40862795 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
40862730 AAATAAACAC
40862740 AAAAAA-AATTTAGAAAATTAA
1 AAAAAATAATTTA-AAAA-TAA
*
40862761 AAAAAATATTTTAAAAAT-A
1 AAAAAATAATTTAAAAATAA
*
40862780 AAAAAATATTTTAAAA
1 AAAAAATAATTTAAAA
40862796 TATTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 17 0.52
20 1 0.03
21 10 0.30
22 5 0.15
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAAATAATTTAAAAATAA
Found at i:40862785 original size:29 final size:30
Alignment explanation
Indices: 40862760--40862820 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
40862750 TAGAAAATTA
40862760 AAAAAAATA-TTTTAAAAATAAAAAAATAT
1 AAAAAAATATTTTTAAAAATAAAAAAATAT
***
40862789 TTTAAAATATTTTTAAAAATAAAAAATATAT
1 AAAAAAATATTTTTAAAAATAAAAAA-ATAT
40862820 A
1 A
40862821 TTTATTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 6 0.23
30 16 0.62
31 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (30 bp):
AAAAAAATATTTTTAAAAATAAAAAAATAT
Found at i:40862808 original size:12 final size:11
Alignment explanation
Indices: 40862762--40862809 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
40862752 GAAAATTAAA
40862762 AAAAATATTTT
1 AAAAATATTTT
*
40862773 AAAAATA---A
1 AAAAATATTTT
40862781 AAAAATATTTT
1 AAAAATATTTT
40862792 -AAAATATTTTT
1 AAAAATA-TTTT
40862803 AAAAATA
1 AAAAATA
40862810 AAAAATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
8 7 0.23
10 6 0.20
11 11 0.37
12 6 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:40864498 original size:13 final size:13
Alignment explanation
Indices: 40864477--40864510 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
40864467 GACCCTTTCT
*
40864477 GGAATGTCTGTCA
1 GGAAAGTCTGTCA
40864490 GGAAAGTCTGTCA
1 GGAAAGTCTGTCA
40864503 GGAAAGTC
1 GGAAAGTC
40864511 ATGCACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (13 bp):
GGAAAGTCTGTCA
Found at i:40866249 original size:14 final size:14
Alignment explanation
Indices: 40866230--40866260 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40866220 TACACCATAT
40866230 ACCTTAAACCCAAA
1 ACCTTAAACCCAAA
*
40866244 ACCTTAAACCCTAA
1 ACCTTAAACCCAAA
40866258 ACC
1 ACC
40866261 ATAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (14 bp):
ACCTTAAACCCAAA
Found at i:40871237 original size:14 final size:14
Alignment explanation
Indices: 40871220--40871277 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
40871210 ATAAATCATA
40871220 AACCCCTAACCCTT
1 AACCCCTAACCCTT
*
40871234 AACCCTTAACCCTT
1 AACCCCTAACCCTT
* *
40871248 AACCACTAAACCTT
1 AACCCCTAACCCTT
*
40871262 AAACTCC-AACCCTT
1 -AACCCCTAACCCTT
40871276 AA
1 AA
40871278 ACCATAAATC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
13 2 0.06
14 30 0.83
15 4 0.11
ACGTcount: A:0.36, C:0.41, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCCTAACCCTT
Found at i:40871261 original size:21 final size:21
Alignment explanation
Indices: 40871220--40871280 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
40871210 ATAAATCATA
*
40871220 AACCCCTAACCCTTAACCCTT
1 AACCCCTAACCCTTAAACCTT
*
40871241 AACCCTTAACCAC-TAAACCTT
1 AACCCCTAACC-CTTAAACCTT
*
40871262 AAACTCC-AACCCTTAAACC
1 -AACCCCTAACCCTTAAACC
40871281 ATAAATCATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.03
21 27 0.82
22 5 0.15
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (21 bp):
AACCCCTAACCCTTAAACCTT
Found at i:40871307 original size:15 final size:14
Alignment explanation
Indices: 40871279--40871320 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
40871269 AACCCTTAAA
*
40871279 CCATAAATCATAAT
1 CCATAAACCATAAT
*
40871293 CCCTAAACCCATAAT
1 CCATAAA-CCATAAT
40871308 CCATAAACCATAA
1 CCATAAACCATAA
40871321 GATAGTAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (14 bp):
CCATAAACCATAAT
Found at i:40871650 original size:20 final size:20
Alignment explanation
Indices: 40871612--40871650 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40871602 TTTAAATAAT
* *
40871612 ATAAATAAACCGATTAAATA
1 ATAAATAAACAGATAAAATA
*
40871632 ATAAATAGACAGATAAAAT
1 ATAAATAAACAGATAAAAT
40871651 GTTTTTTGCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (20 bp):
ATAAATAAACAGATAAAATA
Found at i:40872519 original size:8 final size:7
Alignment explanation
Indices: 40872502--40872551 Score: 59
Period size: 7 Copynumber: 7.0 Consensus size: 7
40872492 AAAGATGTGA
40872502 AAAAAT-
1 AAAAATG
40872508 AAAAATAG
1 AAAAAT-G
40872516 AAAAATG
1 AAAAATG
40872523 AAAAATG
1 AAAAATG
40872530 AAAAATGG
1 AAAAAT-G
40872538 AAAAA-G
1 AAAAATG
40872544 TAAAAATG
1 -AAAAATG
40872552 GAGAGGCTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 7 0.18
7 19 0.49
8 13 0.33
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:40872519 original size:14 final size:14
Alignment explanation
Indices: 40872502--40872551 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
40872492 AAAGATGTGA
40872502 AAAAAT-AAAAATAG
1 AAAAATGAAAAAT-G
40872516 AAAAATGAAAAATG
1 AAAAATGAAAAATG
40872530 AAAAATGGAAAAA-G
1 AAAAAT-GAAAAATG
40872544 TAAAAATG
1 -AAAAATG
40872552 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 15 0.45
15 18 0.55
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AAAAATGAAAAATG
Found at i:40872524 original size:22 final size:22
Alignment explanation
Indices: 40872502--40872551 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
40872492 AAAGATGTGA
40872502 AAAAAT-AAAAATAGAAAAATG
1 AAAAATGAAAAATAGAAAAATG
*
40872523 AAAAATGAAAAATGGAAAAA-G
1 AAAAATGAAAAATAGAAAAATG
40872544 TAAAAATG
1 -AAAAATG
40872552 GAGAGGCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (22 bp):
AAAAATGAAAAATAGAAAAATG
Found at i:40872552 original size:15 final size:15
Alignment explanation
Indices: 40872508--40872553 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
40872498 GTGAAAAAAT
40872508 AAAAATAGAAAAAT-G
1 AAAAAT-GAAAAATGG
40872523 AAAAATGAAAAATGG
1 AAAAATGAAAAATGG
40872538 AAAAA-GTAAAAATGG
1 AAAAATG-AAAAATGG
40872553 A
1 A
40872554 GAGGCTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAAATGG
Found at i:40874042 original size:101 final size:100
Alignment explanation
Indices: 40873890--40874901 Score: 1324
Period size: 101 Copynumber: 10.0 Consensus size: 100
40873880 ATCTCTTTGG
* * * * * * *
40873890 CATTACAATGAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTAGCGGTGTAGTGGAACA
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAGTGGAACA
*
40873955 GATTGAAGCTACGACGGCGGATCTGGTTTCCCCGA
66 GATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* * * *
40873990 CATTTGCAATTTAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCTTAGCGGTGCAGTGGAAC
1 CA-TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAGTGGAAC
* *
40874055 AGATTGAAGCTATGACGGTGGATCTGGTTTCCCAGA
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* * ** * ** * *
40874091 CATTGTAGTTAAAAAGATTGAAGCCACAACGATGGATCTTACTTCCCTAGTAGTCTAATTGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGT-AGTGGAAC
*
40874156 AGATTGAAGCTACGACGGCGGATCTTGTTTCCCAGA
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* * * * *
40874192 CATTGCAATTAAAAAGATTGAAGCCACAATGACGAATCTTACTTCCTTGGTGGTGTAGTTGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAG-TGGAAC
* * *
40874257 AGATTAAAGCCACGACGGCGGATCTGGTTTCCCAGT
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* * * * * * *
40874293 CATTGCAATGGAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
1 CATTGCAAT-TAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAGTGGAAC
*
40874358 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGA
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* * *
40874394 CATTTGCAATTTAAAAGATTGAAGCCACAATGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAAC
1 CA-TTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAGTGGAAC
* *
40874459 ATATTGAAGCTACGACGGCGGATCTGGTTTCCCAGT
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* * *
40874495 CATTGCAATTAAAAAGATTGAAGTCACAACGGCGAATCTTACTTCCTTGGCGGTGTAGTTGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAG-TGGAAC
** **
40874560 AGATTGAAGCTACGACGGTTGATCTTATTTCCCAGA
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* *
40874596 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCTTGGCGGTGTAGTTGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAG-TGGAAC
* * *
40874661 AGATTAAAGCCACGACGGCGGATCTGGTTTCCCAGT
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* *
40874697 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCTTAGTGGTGTAGTTGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAG-TGGAAC
* *
40874762 AGATTGAAGCCACGACGGCGGATCTGGTTTCCCAGT
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
* *
40874798 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCT-GATGGCGTAGTGGAAC
1 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAG-CGGTGTAGTGGAAC
* * * * *
40874862 AGATTGAAGCTACTACGGTGAATCTTGTTTCCCCGA
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
40874898 CATT
1 CATT
40874902 ACGGTTAAGC
Statistics
Matches: 802, Mismatches: 103, Indels: 14
0.87 0.11 0.02
Matches are distributed among these distances:
100 135 0.17
101 621 0.77
102 46 0.06
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (100 bp):
CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCTAGCGGTGTAGTGGAACA
GATTGAAGCTACGACGGCGGATCTGGTTTCCCAGA
Found at i:40874653 original size:404 final size:403
Alignment explanation
Indices: 40873890--40874901 Score: 1578
Period size: 404 Copynumber: 2.5 Consensus size: 403
40873880 ATCTCTTTGG
*
40873890 CATTACAATGAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTAGCGGTGTAGTGGAACA
1 CATTGCAATGAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTAGCGGTGTAGTGGAACA
40873955 GATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTTGCAATTTAAAAGATTGAAGCCACAA
66 GATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTTGCAATTTAAAAGATTGAAGCCACAA
* *
40874020 TGGCGAATCTTACTTCCTTAGCGGTGCAGTGGAACAGATTGAAGCTATGACGGTGGATCTGGTTT
131 TGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTGGATCTGGTTT
* * * * *
40874085 CCCAGACATTGTAGTTAAAAAGATTGAAGCCACAACGATGGATCTTACTTCCCTAGTAGTCTAAT
196 CCCAGACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGCAGTCTAAT
*
40874150 TGGAACAGATTGAAGCTACGACGGCGGATCTTGTTTCCCAGACATTGCAATTAAAAAGATTGAAG
261 TGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCAGACATTGCAATTAAAAAGATTGAAG
* *
40874215 CCACAATGACGAATCTTACTTCCTTGGTGGTGTAGTTGGAACAGATTAAAGCCACGACGGCGGAT
326 CCACAACGACGAATCTTACTTCCTTGGCGGTGTAGTTGGAACAGATTAAAGCCACGACGGCGGAT
40874280 CTGGTTTCCCAGT
391 CTGGTTTCCCAGT
*
40874293 CATTGCAATGGAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTGGCGGTGTAGTGGAAC
1 CATTGCAAT-GAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTAGCGGTGTAGTGGAAC
40874358 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTTGCAATTTAAAAGATTGAAGCCACA
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTTGCAATTTAAAAGATTGAAGCCACA
* *
40874423 ATGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACATATTGAAGCTACGACGGCGGATCTGGTT
130 ATGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTGGATCTGGTT
* * * * * * * *
40874488 TCCCAGTCATTGCAATTAAAAAGATTGAAGTCACAACGGCGAATCTTACTTCCTTGGCGGTGTAG
195 TCCCAGACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGCAGTCTAA
**
40874553 TTGGAACAGATTGAAGCTACGACGGTTGATCTTATTTCCCAGACATTGCAATTAAAAAGATTGAA
260 TTGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCAGACATTGCAATTAAAAAGATTGAA
*
40874618 GCCACAACGGCGAATCTTACTTCCTTGGCGGTGTAGTTGGAACAGATTAAAGCCACGACGGCGGA
325 GCCACAACGACGAATCTTACTTCCTTGGCGGTGTAGTTGGAACAGATTAAAGCCACGACGGCGGA
40874683 TCTGGTTTCCCAGT
390 TCTGGTTTCCCAGT
* * * * * * * *
40874697 CATTGCAATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCTTAGTGGTGTAGTTGGAAC
1 CATTGCAATGAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTAGCGGTGTAG-TGGAAC
* * * *
40874762 AGATTGAAGCCACGACGGCGGATCTGGTTTCCCAGTCA-TTGCAATTAAAAAGATTGAAGCCACA
65 AGATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTTGCAATTTAAAAGATTGAAGCCACA
* * * * * * *
40874826 ACGGCGAATCTTACTTCCCT-GATGGCGTAGTGGAACAGATTGAAGCTACTACGGTGAATCTTGT
130 ATGGCGAATCTTACTTCCCTAG-CGGTGCAGTGGAACAGATTGAAGCTACGACGGTGGATCTGGT
*
40874890 TTCCCCGACATT
194 TTCCCAGACATT
40874902 ACGGTTAAGC
Statistics
Matches: 557, Mismatches: 49, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
402 1 0.00
403 136 0.24
404 420 0.75
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (403 bp):
CATTGCAATGAAAAGGATTGAAACCACAACGGTGGATCTTATTTCCCTAGCGGTGTAGTGGAACA
GATTGAAGCTACGACGGCGGATCTGGTTTCCCCGACATTTGCAATTTAAAAGATTGAAGCCACAA
TGGCGAATCTTACTTCCCTAGCGGTGCAGTGGAACAGATTGAAGCTACGACGGTGGATCTGGTTT
CCCAGACATTGCAATTAAAAAGATTGAAGCCACAACGACGAATCTTACTTCCCTAGCAGTCTAAT
TGGAACAGATTGAAGCTACGACGGCGGATCTTATTTCCCAGACATTGCAATTAAAAAGATTGAAG
CCACAACGACGAATCTTACTTCCTTGGCGGTGTAGTTGGAACAGATTAAAGCCACGACGGCGGAT
CTGGTTTCCCAGT
Found at i:40876364 original size:24 final size:25
Alignment explanation
Indices: 40876328--40876378 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
40876318 TTTTTTTAGT
*
40876328 TTTTTTATATAT-ATTGTTTATATTA
1 TTTTTTATATATAATT-ATTATATTA
*
40876353 TTTTTTA-GTATAATTATTATATTA
1 TTTTTTATATATAATTATTATATTA
40876377 TT
1 TT
40876379 ATTGTATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTTTTATATATAATTATTATATTA
Found at i:40876479 original size:13 final size:12
Alignment explanation
Indices: 40876460--40876503 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
40876450 ATATAGTGCG
40876460 TATATATTTTAT
1 TATATATTTTAT
*
40876472 TATCATATTTTTT
1 TAT-ATATTTTAT
*
40876485 TATATAATTTA-
1 TATATATTTTAT
40876496 TATATATT
1 TATATATT
40876504 ATATACATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 7 0.26
12 9 0.33
13 11 0.41
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (12 bp):
TATATATTTTAT
Found at i:40876606 original size:75 final size:72
Alignment explanation
Indices: 40876514--40876650 Score: 170
Period size: 75 Copynumber: 1.9 Consensus size: 72
40876504 ATATACATTC
* *
40876514 ATATTTTTATAATTA-TTTATGTTTTCAT-GTTTTATAATTCATATGTTTATACATTTTTATAAT
1 ATATTTTTATAATTATTTTAT-TTTTCATAGCTTTAT-ATACATATG--TATACATTTTTATAAT
40876577 ATGTACAAATA
62 ATGTACAAATA
* * *
40876588 ATATATTTTATTATTATTTTATTTTTCTTAGCTTTATATACATATGTATATATTTTTATAATA
1 ATAT-TTTTATAATTATTTTATTTTTCATAGCTTTATATACATATGTATACATTTTTATAATA
40876651 GTTTTTATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
73 16 0.29
74 4 0.07
75 24 0.44
76 11 0.20
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (72 bp):
ATATTTTTATAATTATTTTATTTTTCATAGCTTTATATACATATGTATACATTTTTATAATATGT
ACAAATA
Found at i:40886125 original size:31 final size:30
Alignment explanation
Indices: 40886085--40886144 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 30
40886075 AAAATTTCAA
40886085 AATTCGAAAA-ACTTCAAGACTAAAATTGAGT
1 AATTCGAAAACAC-T-AAGACTAAAATTGAGT
*
40886116 AATTTGAAAAGCACTAAGACTAAAATTGA
1 AATTCGAAAA-CACTAAGACTAAAATTGA
40886145 TTAAATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
31 23 0.88
32 1 0.04
33 2 0.08
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.25
Consensus pattern (30 bp):
AATTCGAAAACACTAAGACTAAAATTGAGT
Found at i:40889346 original size:6 final size:6
Alignment explanation
Indices: 40889335--40889365 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
40889325 TCAAATGCCC
*
40889335 CAACCG CAACCG CAACCG CAACCG CGACCG C
1 CAACCG CAACCG CAACCG CAACCG CAACCG C
40889366 TAAACCTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.29, C:0.52, G:0.19, T:0.00
Consensus pattern (6 bp):
CAACCG
Found at i:40893407 original size:33 final size:33
Alignment explanation
Indices: 40893355--40893418 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
40893345 AAGGTCACTT
* * *
40893355 GGGGTTGGATTAGAAGACGAATACATTGGTAAA
1 GGGGTTAGATTAGAAGACGAAGACACTGGTAAA
* *
40893388 GGGGTTAGATTCGATGACGAAGACACTGGTA
1 GGGGTTAGATTAGAAGACGAAGACACTGGTA
40893419 TAGGACATGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.34, T:0.23
Consensus pattern (33 bp):
GGGGTTAGATTAGAAGACGAAGACACTGGTAAA
Found at i:40896874 original size:8 final size:9
Alignment explanation
Indices: 40896852--40896937 Score: 93
Period size: 9 Copynumber: 9.0 Consensus size: 9
40896842 TGTAGTATTT
40896852 TAAAAATTA
1 TAAAAATTA
40896861 TAAAAATTA
1 TAAAAATTA
40896870 TAAAAAAATTTA
1 T--AAAAA-TTA
40896882 TAAAAATTA
1 TAAAAATTA
*
40896891 TCAAAACTTA
1 T-AAAAATTA
40896901 TAATATAATT-
1 TAA-A-AATTA
40896911 TAAAAATTA
1 TAAAAATTA
*
40896920 TAAAAATCA
1 TAAAAATTA
40896929 TAAAAATTA
1 TAAAAATTA
40896938 CAACACAAAG
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
8 4 0.06
9 33 0.50
10 17 0.26
11 8 0.12
12 4 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:40896882 original size:12 final size:11
Alignment explanation
Indices: 40896853--40896925 Score: 52
Period size: 10 Copynumber: 7.3 Consensus size: 11
40896843 GTAGTATTTT
40896853 AAAAATTAT--
1 AAAAATTATAA
40896862 AAAAATTATAA
1 AAAAATTATAA
*
40896873 AAAAATT-TAT
1 AAAAATTATAA
*
40896883 AAAAATTAT-C
1 AAAAATTATAA
*
40896893 AAAACTTATAA
1 AAAAATTATAA
* *
40896904 TATAATT-T--
1 AAAAATTATAA
40896912 AAAAATTATAA
1 AAAAATTATAA
40896923 AAA
1 AAA
40896926 TCATAAAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
8 5 0.10
9 10 0.21
10 18 0.38
11 15 0.31
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (11 bp):
AAAAATTATAA
Found at i:40896901 original size:19 final size:18
Alignment explanation
Indices: 40896852--40896937 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 18
40896842 TGTAGTATTT
40896852 TAAAAATTATAAAAATTA
1 TAAAAATTATAAAAATTA
40896870 TAAAAAAATTTATAAAAATTA
1 T--AAAAA-TTATAAAAATTA
*
40896891 TCAAAACTTATAATATAATT-
1 T-AAAAATTATAA-A-AATTA
*
40896911 TAAAAATTATAAAAATCA
1 TAAAAATTATAAAAATTA
40896929 TAAAAATTA
1 TAAAAATTA
40896938 CAACACAAAG
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
17 3 0.05
18 11 0.19
19 16 0.28
20 11 0.19
21 17 0.29
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAATTATAAAAATTA
Found at i:40900575 original size:20 final size:20
Alignment explanation
Indices: 40900550--40900589 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40900540 AAACCATGTG
*
40900550 TAAGATAAGAGGAAGATACA
1 TAAGATAAGAGGAAAATACA
40900570 TAAGATAAGAGGAAAATACA
1 TAAGATAAGAGGAAAATACA
40900590 AAGGAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
TAAGATAAGAGGAAAATACA
Found at i:40908309 original size:19 final size:18
Alignment explanation
Indices: 40908259--40908305 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
40908249 GTAATACCTA
*
40908259 ATAAAAA-AAGTAAATTT
1 ATAAAAAGAAATAAATTT
* * *
40908276 TTAAAAATATATAAATTT
1 ATAAAAAGAAATAAATTT
40908294 ATAAAAAGAAAT
1 ATAAAAAGAAAT
40908306 TAAAATTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
ATAAAAAGAAATAAATTT
Found at i:40908785 original size:7 final size:7
Alignment explanation
Indices: 40908773--40908799 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40908763 GCTTTTTTTA
40908773 ATAATTT
1 ATAATTT
40908780 ATAATTT
1 ATAATTT
40908787 ATAATTT
1 ATAATTT
40908794 ATAATT
1 ATAATT
40908800 GATATAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATAATTT
Found at i:40912589 original size:12 final size:12
Alignment explanation
Indices: 40912572--40912613 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
40912562 ACTAATCCTA
40912572 TCTCAAATTTCT
1 TCTCAAATTTCT
*
40912584 TCTCAAATTCCT
1 TCTCAAATTTCT
40912596 TC-CAAATTTC-
1 TCTCAAATTTCT
40912606 TCTCAAAT
1 TCTCAAAT
40912614 CCATATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 2 0.07
11 12 0.44
12 13 0.48
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (12 bp):
TCTCAAATTTCT
Found at i:40912603 original size:11 final size:12
Alignment explanation
Indices: 40912567--40912613 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
40912557 CACAAACTAA
40912567 TCCTATCTCAAAT
1 TCCT-TCTCAAAT
*
40912580 TTCTTCTCAAAT
1 TCCTTCTCAAAT
40912592 TCCTTC-CAAAT
1 TCCTTCTCAAAT
*
40912603 TTC-TCTCAAAT
1 TCCTTCTCAAAT
40912614 CCATATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 2 0.07
11 12 0.40
12 13 0.43
13 3 0.10
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (12 bp):
TCCTTCTCAAAT
Found at i:40912699 original size:10 final size:10
Alignment explanation
Indices: 40912668--40912704 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
40912658 CTTAAATCCC
40912668 TTTTTTTAAA
1 TTTTTTTAAA
**
40912678 TAATTTTAAA
1 TTTTTTTAAA
40912688 TTTTTTTAAA
1 TTTTTTTAAA
40912698 TTTTTTT
1 TTTTTTT
40912705 TAAACCGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:40915783 original size:15 final size:15
Alignment explanation
Indices: 40915760--40915794 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40915750 TTTTTATGCC
*
40915760 ATTGATGTATTTATT
1 ATTGTTGTATTTATT
40915775 ATTGTTGTATTTATT
1 ATTGTTGTATTTATT
40915790 ATTGT
1 ATTGT
40915795 GGCATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (15 bp):
ATTGTTGTATTTATT
Found at i:40915801 original size:15 final size:15
Alignment explanation
Indices: 40915768--40915801 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40915758 CCATTGATGT
* *
40915768 ATTTATTATTGTTGT
1 ATTTATTATTGTGGC
40915783 ATTTATTATTGTGGC
1 ATTTATTATTGTGGC
40915798 ATTT
1 ATTT
40915802 GTACATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.15, T:0.62
Consensus pattern (15 bp):
ATTTATTATTGTGGC
Done.