Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 435 of 438
Found at i:134075435 original size:2 final size:2
Alignment explanation
Indices: 134075428--134075465 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
134075418 TCAAGCTTTT
134075428 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
134075466 AATTATTGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:134075649 original size:19 final size:18
Alignment explanation
Indices: 134075622--134075657 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
134075612 TTAATATATC
*
134075622 ATTTGATATTTATATTTAA
1 ATTTAATATTTA-ATTTAA
134075641 ATTTAATATTTAATTTA
1 ATTTAATATTTAATTTA
134075658 GTATTCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTAATATTTAATTTAA
Found at i:134076570 original size:18 final size:20
Alignment explanation
Indices: 134076532--134076570 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
134076522 TTTTAATTTG
*
134076532 AAATTTTCATTTTTCTTTAT
1 AAATTTTCATTTATCTTTAT
134076552 AAATTTTCA-TTAT-TTTAT
1 AAATTTTCATTTATCTTTAT
134076570 A
1 A
134076571 TTTTTTATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 9 0.50
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (20 bp):
AAATTTTCATTTATCTTTAT
Found at i:134078637 original size:3 final size:3
Alignment explanation
Indices: 134078629--134078679 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
134078619 TATAATTGCT
134078629 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
134078678 TT
1 TT
134078680 TCAAAATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:134081028 original size:18 final size:19
Alignment explanation
Indices: 134081005--134081049 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
134080995 TCCCTAAGAA
134081005 AGTATTCACT-CTTGAAAG
1 AGTATTCACTACTTGAAAG
*
134081023 AGTATTTA-TACTTGAAAG
1 AGTATTCACTACTTGAAAG
*
134081041 AGTGTTCAC
1 AGTATTCAC
134081050 ACTAAAAAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 21 0.95
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (19 bp):
AGTATTCACTACTTGAAAG
Found at i:134082030 original size:30 final size:29
Alignment explanation
Indices: 134081982--134082039 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
134081972 TAATCGAACT
*
134081982 TAAATTTTAAAATTTAAAAAGTAAAAAAAC
1 TAAATTTTAAAATATAAAAA-TAAAAAAAC
*
134082012 TAAATTTTTAAAA-ATAAAAATATAAAAA
1 TAAA-TTTTAAAATATAAAAATAAAAAAA
134082040 TTCAATGTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 7 0.28
30 10 0.40
31 8 0.32
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (29 bp):
TAAATTTTAAAATATAAAAATAAAAAAAC
Found at i:134088254 original size:93 final size:93
Alignment explanation
Indices: 134088095--134088281 Score: 356
Period size: 93 Copynumber: 2.0 Consensus size: 93
134088085 CGATGGGACA
* *
134088095 TAGTTGCTATCCTAAAGGGAAGGTAGTTATGGGCTGAGAATTTTTAGGACTTGACTAGCTGCTTC
1 TAGTTGCTATCCTAAAGGGAAGGTAGTTATGGGCTGAGAATTTTGAGGACTTGACTAACTGCTTC
134088160 TATCTTAAGGCACATCTGGTCTTATCTT
66 TATCTTAAGGCACATCTGGTCTTATCTT
134088188 TAGTTGCTATCCTAAAGGGAAGGTAGTTATGGGCTGAGAATTTTGAGGACTTGACTAACTGCTTC
1 TAGTTGCTATCCTAAAGGGAAGGTAGTTATGGGCTGAGAATTTTGAGGACTTGACTAACTGCTTC
134088253 TATCTTAAGGCACATCTGGTCTTATCTT
66 TATCTTAAGGCACATCTGGTCTTATCTT
134088281 T
1 T
134088282 TGGAGGTCAG
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (93 bp):
TAGTTGCTATCCTAAAGGGAAGGTAGTTATGGGCTGAGAATTTTGAGGACTTGACTAACTGCTTC
TATCTTAAGGCACATCTGGTCTTATCTT
Found at i:134092414 original size:16 final size:17
Alignment explanation
Indices: 134092384--134092424 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
134092374 GATAGCTGAC
134092384 TCAAGGCCAGTAGAAAT
1 TCAAGGCCAGTAGAAAT
134092401 TCAAGGCC-GTAGAAAT
1 TCAAGGCCAGTAGAAAT
134092417 TCAAGGCC
1 TCAAGGCC
134092425 TGGTACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (17 bp):
TCAAGGCCAGTAGAAAT
Found at i:134100357 original size:21 final size:21
Alignment explanation
Indices: 134100333--134100374 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
134100323 TGTTATTATA
134100333 CCAATCAAAATTATATACAAT
1 CCAATCAAAATTATATACAAT
134100354 CCAATCAAAATTATATACAAT
1 CCAATCAAAATTATATACAAT
134100375 TGATGGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (21 bp):
CCAATCAAAATTATATACAAT
Found at i:134107118 original size:2 final size:2
Alignment explanation
Indices: 134107111--134107137 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
134107101 ACACGCGCAC
134107111 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
134107138 AATGCAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134119227 original size:21 final size:21
Alignment explanation
Indices: 134119189--134119228 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
134119179 TATCATATCA
* *
134119189 TTACATAAAATTTTAAAATTT
1 TTACATAAAATATAAAAATTT
134119210 TTACATAAAATATAAAAAT
1 TTACATAAAATATAAAAAT
134119229 ATACATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTACATAAAATATAAAAATTT
Found at i:134120747 original size:29 final size:30
Alignment explanation
Indices: 134120684--134120739 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
134120674 GTTACAAAAT
134120684 AGTCACTGAATTATGTGAAAATTTTATTTA
1 AGTCACTGAATTATGTGAAAATTTTATTTA
* *
134120714 AGTCATTGAATTAT-TTAAAATTTTAT
1 AGTCACTGAATTATGTGAAAATTTTAT
134120740 ATTTGTCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.38, C:0.05, G:0.11, T:0.46
Consensus pattern (30 bp):
AGTCACTGAATTATGTGAAAATTTTATTTA
Found at i:134122010 original size:59 final size:59
Alignment explanation
Indices: 134121943--134122061 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
134121933 GAGCTCTTGA
134121943 TACTGTTGGTTTGTTCTTAATCTTCAACCTTCTATTTTTATTTGATGTGATTTTCCCAT
1 TACTGTTGGTTTGTTCTTAATCTTCAACCTTCTATTTTTATTTGATGTGATTTTCCCAT
134122002 TACTGTTGGTTTGTTCTTAATCTTCAACCTTCTATTTTTATTTGATGTGATTTTCCCAT
1 TACTGTTGGTTTGTTCTTAATCTTCAACCTTCTATTTTTATTTGATGTGATTTTCCCAT
134122061 T
1 T
134122062 TTGTATAAGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.55
Consensus pattern (59 bp):
TACTGTTGGTTTGTTCTTAATCTTCAACCTTCTATTTTTATTTGATGTGATTTTCCCAT
Found at i:134125421 original size:12 final size:12
Alignment explanation
Indices: 134125404--134125430 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
134125394 ATAGAAGAGC
134125404 TTTCATAGTACT
1 TTTCATAGTACT
134125416 TTTCATAGTACT
1 TTTCATAGTACT
134125428 TTT
1 TTT
134125431 ATCTAACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.15, G:0.07, T:0.56
Consensus pattern (12 bp):
TTTCATAGTACT
Found at i:134132537 original size:2 final size:2
Alignment explanation
Indices: 134132524--134132573 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
134132514 TCACAATTTG
*
134132524 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134132566 AT AT AT AT
1 AT AT AT AT
134132574 TAATATGGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134136086 original size:29 final size:31
Alignment explanation
Indices: 134136019--134136094 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 31
134136009 TTAATAACTC
*
134136019 AATTAAATTTTCGATTATAATAAAATATAAT
1 AATTAAATTTTCGATTATAATAAAATATAAA
*
134136050 AATCAAATTTT-GA-TA-AATTAAAATA-AAA
1 AATTAAATTTTCGATTATAA-TAAAATATAAA
134136078 AGATTAAATTTTCGATT
1 A-ATTAAATTTTCGATT
134136095 TTTAATTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
28 5 0.13
29 18 0.47
30 4 0.11
31 11 0.29
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.39
Consensus pattern (31 bp):
AATTAAATTTTCGATTATAATAAAATATAAA
Found at i:134136996 original size:20 final size:20
Alignment explanation
Indices: 134136971--134137018 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
134136961 AAATATAAAT
134136971 ATATATAATAATTATT-TAAC
1 ATATATAAT-ATTATTATAAC
*
134136991 ATATATAATATTTTTATAAC
1 ATATATAATATTATTATAAC
134137011 ATAATATA
1 AT-ATATA
134137019 TTCAACTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 15 0.60
21 5 0.20
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATAATATTATTATAAC
Found at i:134137846 original size:30 final size:29
Alignment explanation
Indices: 134137776--134137849 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 29
134137766 TTTTTGAGTC
*
134137776 TAATAAAAAATTTTAAAATTTTAAAGGGTT
1 TAATAAAAATTTTTAAAATTTTAAA-GGTT
*
134137806 TAATTAAAATTTTTAACAATTTTAAA-GTT
1 TAATAAAAATTTTTAA-AATTTTAAAGGTT
134137835 TAATAATAAATTTTT
1 TAATAA-AAATTTTT
134137850 TTAAATTGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 8 0.21
30 22 0.56
31 9 0.23
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (29 bp):
TAATAAAAATTTTTAAAATTTTAAAGGTT
Found at i:134137946 original size:32 final size:31
Alignment explanation
Indices: 134137911--134137972 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
134137901 AAAATTTAAA
134137911 AAAAAAATT-AAAGAATTTAATTAAAATTTTT
1 AAAAAAATTGAAAG-ATTTAATTAAAATTTTT
* * *
134137942 AAAAAATTTGAATGATTTAATTAAAAATTTT
1 AAAAAAATTGAAAGATTTAATTAAAATTTTT
134137973 GATTGCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (31 bp):
AAAAAAATTGAAAGATTTAATTAAAATTTTT
Found at i:134140536 original size:8 final size:8
Alignment explanation
Indices: 134140523--134140554 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
134140513 TTTTATTAAA
134140523 AATAAAAT
1 AATAAAAT
134140531 AATAAAAT
1 AATAAAAT
134140539 AATAAAAT
1 AATAAAAT
134140547 AATAAAAT
1 AATAAAAT
134140555 TTTAACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AATAAAAT
Found at i:134141147 original size:3 final size:3
Alignment explanation
Indices: 134141139--134141179 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
134141129 CCTACTTTCG
* * *
134141139 TTC TTC TTC TTC TTC TTC TTC TTC TTC ATA TTC TTC ATC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
134141180 TATCAGGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:134141973 original size:22 final size:22
Alignment explanation
Indices: 134141948--134142000 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
134141938 ATTTTTTAGA
*
134141948 TTTTTTTTGAAATTTCGTGTTT
1 TTTTTTTTGAAATTTCGTGATT
* *
134141970 TTTTTTTTTAAATTTGGTGATT
1 TTTTTTTTGAAATTTCGTGATT
*
134141992 CTTTTTTTG
1 TTTTTTTTG
134142001 GTGTTTAGGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.70
Consensus pattern (22 bp):
TTTTTTTTGAAATTTCGTGATT
Found at i:134145710 original size:25 final size:25
Alignment explanation
Indices: 134145688--134145739 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
134145678 TATCAAATTT
134145688 AAGCATAATACAGGGACTAAAATCA
1 AAGCATAATACAGGGACTAAAATCA
134145713 AAGCATAATACAGGGACTAAAATCA
1 AAGCATAATACAGGGACTAAAATCA
134145738 AA
1 AA
134145740 TTTGACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (25 bp):
AAGCATAATACAGGGACTAAAATCA
Found at i:134146877 original size:24 final size:24
Alignment explanation
Indices: 134146850--134146895 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
134146840 AACAGTAGAC
134146850 AATTTGTTTATAGAAAACTTAATG
1 AATTTGTTTATAGAAAACTTAATG
*
134146874 AATTTGTTTATAGAAAATTTAA
1 AATTTGTTTATAGAAAACTTAA
134146896 AGACCACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (24 bp):
AATTTGTTTATAGAAAACTTAATG
Found at i:134149979 original size:24 final size:24
Alignment explanation
Indices: 134149947--134149992 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
134149937 TACAAGAAAT
134149947 TATTCAAACCAGATTTCTCTCAAC
1 TATTCAAACCAGATTTCTCTCAAC
134149971 TATTCAAACCAGATTTCTCTCA
1 TATTCAAACCAGATTTCTCTCA
134149993 GTTTTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (24 bp):
TATTCAAACCAGATTTCTCTCAAC
Found at i:134153027 original size:19 final size:17
Alignment explanation
Indices: 134152996--134153043 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
134152986 TCCAGAAATT
134152996 AAAAAAAGAAAAATTCAG
1 AAAAAAAGAAAAATT-AG
*
134153014 AAAAATAAGTAAAATTAG
1 AAAAA-AAGAAAAATTAG
134153032 -AAAAAAGAAAAA
1 AAAAAAAGAAAAA
134153044 AACACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 4 0.15
18 7 0.26
19 9 0.33
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAAAGAAAAATTAG
Found at i:134156601 original size:22 final size:22
Alignment explanation
Indices: 134156576--134156629 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
134156566 ATAATAAAAT
*
134156576 AAATAATATATTAAATTAAGGA
1 AAATAATATATTAAATTAAAGA
* * *
134156598 AAATAA-CTCTTAATTTAAAGA
1 AAATAATATATTAAATTAAAGA
134156619 AAATAAATATA
1 AAAT-AATATA
134156630 ATTATCTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 15 0.62
22 8 0.33
23 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (22 bp):
AAATAATATATTAAATTAAAGA
Found at i:134157415 original size:6 final size:6
Alignment explanation
Indices: 134157404--134157434 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
134157394 TGATTTGGTT
134157404 CGGCTC CGGCTC CGGCTC CGGCTC CGGCTC C
1 CGGCTC CGGCTC CGGCTC CGGCTC CGGCTC C
134157435 TCCCCACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.32, T:0.16
Consensus pattern (6 bp):
CGGCTC
Found at i:134160463 original size:2 final size:2
Alignment explanation
Indices: 134160453--134160486 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
134160443 AAGTGTCCGC
*
134160453 GT GT AT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
134160487 AGGATAGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.03, C:0.00, G:0.47, T:0.50
Consensus pattern (2 bp):
GT
Found at i:134165805 original size:18 final size:18
Alignment explanation
Indices: 134165772--134165806 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
134165762 TCCTCCTCTA
* *
134165772 TCTCCTCTGTATCCTCCG
1 TCTCCTCTGCAGCCTCCG
134165790 TCTCCTCTGCAGCCTCC
1 TCTCCTCTGCAGCCTCC
134165807 ATTTCCAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.11, T:0.34
Consensus pattern (18 bp):
TCTCCTCTGCAGCCTCCG
Found at i:134175578 original size:22 final size:23
Alignment explanation
Indices: 134175544--134175600 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
134175534 TATATTTAAC
*
134175544 TTTTATTTATTTATAT-TGGGTT
1 TTTTTTTTATTTATATCTGGGTT
* *
134175566 TTTTTTTTTTTTATTTCTGGGTT
1 TTTTTTTTATTTATATCTGGGTT
*
134175589 TTATTTTATATT
1 TT-TTTTTTATT
134175601 ATGTTTTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
22 13 0.46
23 8 0.29
24 7 0.25
ACGTcount: A:0.14, C:0.02, G:0.11, T:0.74
Consensus pattern (23 bp):
TTTTTTTTATTTATATCTGGGTT
Found at i:134178815 original size:18 final size:20
Alignment explanation
Indices: 134178777--134178814 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
134178767 TTAGTTTTAG
134178777 TTTAAATATATTATTAAAAA
1 TTTAAATATATTATTAAAAA
*
134178797 TTTAAATATCTT-TTAAAA
1 TTTAAATATATTATTAAAA
134178815 TGTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATATATTATTAAAAA
Found at i:134184571 original size:257 final size:257
Alignment explanation
Indices: 134184115--134184633 Score: 885
Period size: 257 Copynumber: 2.0 Consensus size: 257
134184105 TTGTCACTTT
* *
134184115 TCAATTTTAAATTGAAGCAAAGAGTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
1 TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
*
134184180 GTGTTGAATTTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
66 GTGTTGAATCTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
* *
134184245 TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAGCGTCTTCAAGTACAGGATATTG
131 TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAACGTCTTCAAGTACAGAATATTG
* * *
134184310 ATGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCTACTATATTTGCTCAACTCA
196 ATGATGTAGAAAAAGACAATGTCTTGTTAAACTATTGTCACCCACTATAATTGCTCAACTCA
* *
134184372 TCAATTTTAAATTGAAACACAGACTGTGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
1 TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
* * *
134184437 GTGTTGAATCTTTCTCATTGACACTAATATTTGAATAACTATTTACTATATTCTTTAGGGATAAT
66 GTGTTGAATCTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
* * * *
134184502 TATTCATATCCAGTTGGATTTGTAGTAATTATTACTACAATAATGTGTTCAAGTACAGAATATTG
131 TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAACGTCTTCAAGTACAGAATATTG
134184567 ATGATGTAGAAAAAGACAATGTCTTGTTAAACTATTGTCACCCACTATAATTGCTCAACTCA
196 ATGATGTAGAAAAAGACAATGTCTTGTTAAACTATTGTCACCCACTATAATTGCTCAACTCA
134184629 TCAAT
1 TCAAT
134184634 GGTTTGCTAT
Statistics
Matches: 245, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
257 245 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (257 bp):
TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
GTGTTGAATCTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAACGTCTTCAAGTACAGAATATTG
ATGATGTAGAAAAAGACAATGTCTTGTTAAACTATTGTCACCCACTATAATTGCTCAACTCA
Found at i:134198908 original size:1 final size:1
Alignment explanation
Indices: 134198902--134198938 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
134198892 TAATATCCAT
134198902 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
134198939 CACCTCAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:134202772 original size:179 final size:179
Alignment explanation
Indices: 134202472--134202829 Score: 707
Period size: 179 Copynumber: 2.0 Consensus size: 179
134202462 AATTCTGCAC
134202472 CAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTAAT
1 CAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTAAT
134202537 CCTTGTGCTTATTTGACTTAAAAATTAAATTCCAATTGAGAAAAATTCTGCCAAGTTTAAATAGG
66 CCTTGTGCTTATTTGACTTAAAAATTAAATTCCAATTGAGAAAAATTCTGCCAAGTTTAAATAGG
*
134202602 TGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAATAATAT
131 TGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAATAT
134202651 CAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTAAT
1 CAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTAAT
134202716 CCTTGTGCTTATTTGACTTAAAAATTAAATTCCAATTGAGAAAAATTCTGCCAAGTTTAAATAGG
66 CCTTGTGCTTATTTGACTTAAAAATTAAATTCCAATTGAGAAAAATTCTGCCAAGTTTAAATAGG
134202781 TGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAATAT
131 TGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAATAT
134202830 TATAAGTCTA
Statistics
Matches: 178, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
179 178 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (179 bp):
CAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTAAT
CCTTGTGCTTATTTGACTTAAAAATTAAATTCCAATTGAGAAAAATTCTGCCAAGTTTAAATAGG
TGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAATAT
Found at i:134204536 original size:22 final size:24
Alignment explanation
Indices: 134204490--134204536 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
134204480 AGCTGGACTT
*
134204490 AAATTGTATATTTTTATGATATTA
1 AAATTGTATATTTTTATCATATTA
*
134204514 AAATTGTA-A-TTTTATCATTTTA
1 AAATTGTATATTTTTATCATATTA
134204536 A
1 A
134204537 CAGCCTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 1 0.05
24 8 0.38
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (24 bp):
AAATTGTATATTTTTATCATATTA
Found at i:134206721 original size:40 final size:40
Alignment explanation
Indices: 134206676--134206755 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
134206666 TAATATACAT
134206676 TTTGATCACTCAACTTTAAAAAATTATAAAATAACCACTA
1 TTTGATCACTCAACTTTAAAAAATTATAAAATAACCACTA
134206716 TTTGATCACTCAACTTTAAAAAATTATAAAATAACCACTA
1 TTTGATCACTCAACTTTAAAAAATTATAAAATAACCACTA
134206756 AACTATTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (40 bp):
TTTGATCACTCAACTTTAAAAAATTATAAAATAACCACTA
Found at i:134219220 original size:19 final size:19
Alignment explanation
Indices: 134219168--134219221 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
134219158 CCAAATATAT
*
134219168 ATATATATATATATAATAGA
1 ATATATAAATAT-TAATAGA
* *
134219188 ATTAAATTAA-ATTAATAGA
1 A-TATATAAATATTAATAGA
134219207 ATATATAAATATTAA
1 ATATATAAATATTAA
134219222 AGTATATCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
18 6 0.22
19 13 0.48
20 3 0.11
21 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (19 bp):
ATATATAAATATTAATAGA
Found at i:134225007 original size:30 final size:30
Alignment explanation
Indices: 134224971--134225027 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
134224961 TTTAAGCTTT
**
134224971 GGGGTTTGCTTAAAATTTTCAAAAATTTTG
1 GGGGTTTAATTAAAATTTTCAAAAATTTTG
* *
134225001 GGGGTTTAATTAGAATTTTTAAAAATT
1 GGGGTTTAATTAAAATTTTCAAAAATT
134225028 ATAAAATGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (30 bp):
GGGGTTTAATTAAAATTTTCAAAAATTTTG
Found at i:134229596 original size:24 final size:24
Alignment explanation
Indices: 134229564--134229609 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
134229554 AAATAAAAAT
134229564 GTAAGGATTAAATCTAAACAGAAC
1 GTAAGGATTAAATCTAAACAGAAC
134229588 GTAAGGATTAAATCTAAACAGA
1 GTAAGGATTAAATCTAAACAGA
134229610 CTTTCCCGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (24 bp):
GTAAGGATTAAATCTAAACAGAAC
Found at i:134230791 original size:24 final size:23
Alignment explanation
Indices: 134230754--134230800 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
134230744 AATTATAAAT
134230754 TTTTTAAAAAATATTATTT-TTCA
1 TTTTTAAAAAATATT-TTTATTCA
*
134230777 TTTTTATAAATATATTTTTATTCA
1 TTTTTA-AAAAATATTTTTATTCA
134230801 ATATCTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TTTTTAAAAAATATTTTTATTCA
Found at i:134241623 original size:18 final size:18
Alignment explanation
Indices: 134241586--134241620 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
134241576 AGGAAACAAT
*
134241586 TAATAGTATGATTAAAAA
1 TAATAGTATAATTAAAAA
134241604 TAATAGTA-AATTAAAAA
1 TAATAGTATAATTAAAAA
134241621 ATATTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (18 bp):
TAATAGTATAATTAAAAA
Found at i:134243405 original size:2 final size:2
Alignment explanation
Indices: 134243398--134243425 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
134243388 TGTATAAGAA
134243398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134243426 GCTTATGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:134245411 original size:3 final size:3
Alignment explanation
Indices: 134245403--134245455 Score: 97
Period size: 3 Copynumber: 17.3 Consensus size: 3
134245393 ATGTGTGGAT
134245403 ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
134245449 ATA ATA A
1 ATA ATA A
134245456 CGGTAAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:134253371 original size:7 final size:7
Alignment explanation
Indices: 134253359--134253384 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
134253349 ATATGATTGT
134253359 AGCAGCC
1 AGCAGCC
134253366 AGCAGCC
1 AGCAGCC
134253373 AGCAGCC
1 AGCAGCC
134253380 AGCAG
1 AGCAG
134253385 ACAGTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.38, G:0.31, T:0.00
Consensus pattern (7 bp):
AGCAGCC
Found at i:134255274 original size:28 final size:30
Alignment explanation
Indices: 134255237--134255301 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
134255227 TAGAGTTGTG
* *
134255237 ATCAAATTAGTCCTT-TATTATT-AAATGA
1 ATCAAATTAGTCATTATATTATTAAAAAGA
* *
134255265 ATCAATTTAGTCATTATATTGTTAAAAAGA
1 ATCAAATTAGTCATTATATTATTAAAAAGA
134255295 ATCAAAT
1 ATCAAAT
134255302 AATGCGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 13 0.43
29 6 0.20
30 11 0.37
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (30 bp):
ATCAAATTAGTCATTATATTATTAAAAAGA
Found at i:134264067 original size:31 final size:31
Alignment explanation
Indices: 134263970--134264079 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
134263960 GATGTCCTTT
* *
134263970 AAAATATTTGAAAATTTTAATTAGGTCCCTTCA
1 AAAAT-TTTAAAAATTTTAATTA-GACCCTTCA
* * * *
134264003 AAACTTTTAGAAATTCTAA-TAGAGCCTTTCA
1 AAAATTTTAAAAATTTTAATTAGA-CCCTTCA
*
134264034 AAAATTTTAAAAATTTTAATTAGACCCTCCA
1 AAAATTTTAAAAATTTTAATTAGACCCTTCA
134264065 AAAATTTTGAAAAAT
1 AAAATTTT-AAAAAT
134264080 CTTATTAATC
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
30 1 0.02
31 37 0.59
32 21 0.33
33 4 0.06
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (31 bp):
AAAATTTTAAAAATTTTAATTAGACCCTTCA
Found at i:134264673 original size:3 final size:3
Alignment explanation
Indices: 134264665--134264716 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
134264655 ACTGTAATGC
134264665 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
134264713 AAT A
1 AAT A
134264717 TTATAGGTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:134273724 original size:53 final size:53
Alignment explanation
Indices: 134273657--134273797 Score: 203
Period size: 53 Copynumber: 2.7 Consensus size: 53
134273647 ACAAGTGTGC
* *
134273657 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
* *
134273710 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
* * *
134273763 CCGTATAAGACAAT-GTCTGGGATATGGCTTCGGTA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTA
134273798 TGATATGTGA
Statistics
Matches: 80, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
52 1 0.01
53 79 0.99
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
Found at i:134279703 original size:26 final size:26
Alignment explanation
Indices: 134279666--134279749 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
134279656 TGATACAAAT
* *
134279666 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
134279692 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
134279718 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
134279744 TGATAA
1 TGATAA
134279750 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:134287615 original size:48 final size:48
Alignment explanation
Indices: 134287559--134287654 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
134287549 GCAGAACAAA
134287559 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
1 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
134287607 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
1 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
134287655 TAGAAGATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (48 bp):
CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
Found at i:134297276 original size:19 final size:19
Alignment explanation
Indices: 134297230--134297277 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
134297220 ATATATATTT
134297230 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
134297248 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
134297267 TAAGTTTTATT
1 TAAATTTTATT
134297278 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:134297353 original size:42 final size:42
Alignment explanation
Indices: 134297294--134297382 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
134297284 CTAGGAATAT
* * *
134297294 TTTTATTTTATGTTTTAGTAGTTTATTAGGACAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
*
134297336 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
134297378 TTTTC
1 TTTTC
134297383 CCAATTAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.51
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
Found at i:134298965 original size:18 final size:18
Alignment explanation
Indices: 134298934--134298968 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
134298924 TCTATTATTA
*
134298934 AGTGGGGAATGTGCAATG
1 AGTGGGGAAGGTGCAATG
*
134298952 AGTGGTGAAGGTGCAAT
1 AGTGGGGAAGGTGCAAT
134298969 TGCTGGGGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.43, T:0.23
Consensus pattern (18 bp):
AGTGGGGAAGGTGCAATG
Found at i:134305063 original size:2 final size:2
Alignment explanation
Indices: 134305056--134305087 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
134305046 ATGAACTGAA
*
134305056 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
134305088 GGGCTACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:134315496 original size:14 final size:14
Alignment explanation
Indices: 134315477--134315527 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
134315467 AATAAAATAA
134315477 ATAAATAAGTGAAT
1 ATAAATAAGTGAAT
*** *
134315491 ATAAATAAAACATT
1 ATAAATAAGTGAAT
134315505 AATAAATAAGTGAAT
1 -ATAAATAAGTGAAT
134315520 ATAAATAA
1 ATAAATAA
134315528 AACATTTGAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (14 bp):
ATAAATAAGTGAAT
Found at i:134315508 original size:29 final size:29
Alignment explanation
Indices: 134315476--134315533 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
134315466 AAATAAAATA
134315476 AATAAATAAGTGAATATAAATAAAACATT
1 AATAAATAAGTGAATATAAATAAAACATT
134315505 AATAAATAAGTGAATATAAATAAAACATT
1 AATAAATAAGTGAATATAAATAAAACATT
134315534 TGATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (29 bp):
AATAAATAAGTGAATATAAATAAAACATT
Found at i:134321348 original size:2 final size:2
Alignment explanation
Indices: 134321341--134321367 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
134321331 AATGTTTTCC
134321341 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
134321368 GCAGCACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134323056 original size:20 final size:20
Alignment explanation
Indices: 134323031--134323071 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
134323021 GATATGTCAA
134323031 GCAACAGCATCACATGAGCT
1 GCAACAGCATCACATGAGCT
134323051 GCAACAGCATCACATGAGCT
1 GCAACAGCATCACATGAGCT
134323071 G
1 G
134323072 ATCAACTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (20 bp):
GCAACAGCATCACATGAGCT
Found at i:134326507 original size:14 final size:14
Alignment explanation
Indices: 134326488--134326538 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
134326478 AATAAAATAA
134326488 ATAAATAAGTGAAT
1 ATAAATAAGTGAAT
*** *
134326502 ATAAATAAAACATT
1 ATAAATAAGTGAAT
134326516 AATAAATAAGTGAAT
1 -ATAAATAAGTGAAT
134326531 ATAAATAA
1 ATAAATAA
134326539 AACATTTGAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (14 bp):
ATAAATAAGTGAAT
Found at i:134326519 original size:29 final size:29
Alignment explanation
Indices: 134326487--134326544 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
134326477 AAATAAAATA
134326487 AATAAATAAGTGAATATAAATAAAACATT
1 AATAAATAAGTGAATATAAATAAAACATT
134326516 AATAAATAAGTGAATATAAATAAAACATT
1 AATAAATAAGTGAATATAAATAAAACATT
134326545 TGATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (29 bp):
AATAAATAAGTGAATATAAATAAAACATT
Found at i:134332357 original size:2 final size:2
Alignment explanation
Indices: 134332350--134332376 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
134332340 AATGTTTTCC
134332350 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
134332377 GCAGCACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:134334065 original size:20 final size:20
Alignment explanation
Indices: 134334040--134334080 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
134334030 GATATGTCAA
134334040 GCAACAGCATCACATGAGCT
1 GCAACAGCATCACATGAGCT
134334060 GCAACAGCATCACATGAGCT
1 GCAACAGCATCACATGAGCT
134334080 G
1 G
134334081 ATCAACTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.29, G:0.22, T:0.15
Consensus pattern (20 bp):
GCAACAGCATCACATGAGCT
Found at i:134339916 original size:19 final size:18
Alignment explanation
Indices: 134339894--134339933 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
134339884 TGAATAAAAC
*
134339894 TTATCTACCTAAATAAGAT
1 TTATATACCTAAATAA-AT
134339913 TTATATACCTAAATAAAT
1 TTATATACCTAAATAAAT
134339931 TTA
1 TTA
134339934 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATATACCTAAATAAAT
Found at i:134342209 original size:18 final size:18
Alignment explanation
Indices: 134342181--134342250 Score: 99
Period size: 18 Copynumber: 4.0 Consensus size: 18
134342171 GATCGTTTAT
134342181 GGTACT-TT-ACGTATAC
1 GGTACTATTCACGTATAC
*
134342197 GGTACTATTTACGTATAC
1 GGTACTATTCACGTATAC
*
134342215 GGCACTATTCACGTATAC
1 GGTACTATTCACGTATAC
*
134342233 GGTACTGTTCACGTATAC
1 GGTACTATTCACGTATAC
134342251 AGTAGTTGGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 6 0.12
17 2 0.04
18 40 0.83
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (18 bp):
GGTACTATTCACGTATAC
Found at i:134347630 original size:18 final size:18
Alignment explanation
Indices: 134347607--134347642 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
134347597 AGTAAGAGTA
134347607 AGTTCATTGGCAACACCT
1 AGTTCATTGGCAACACCT
134347625 AGTTCATTGGCAACACCT
1 AGTTCATTGGCAACACCT
134347643 CCCTTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
AGTTCATTGGCAACACCT
Found at i:134347838 original size:18 final size:18
Alignment explanation
Indices: 134347815--134347850 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
134347805 ACCAGAAGAG
134347815 GTTCGTGATACCAGTTTC
1 GTTCGTGATACCAGTTTC
134347833 GTTCGTGATACCAGTTTC
1 GTTCGTGATACCAGTTTC
134347851 ATTCTTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (18 bp):
GTTCGTGATACCAGTTTC
Found at i:134353226 original size:46 final size:46
Alignment explanation
Indices: 134353178--134353390 Score: 277
Period size: 46 Copynumber: 4.6 Consensus size: 46
134353168 GCTATCTGAT
** ** *
134353178 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAATGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
134353224 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
134353270 GA-GAAATGAATAAGACCATGGTTGAAAGATATCATGGCAGCGTAAC
1 -ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
134353316 ATGAAATGAATAAGACCATGGTTGAAAGATACTATGACAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
134353362 A-GAAAATGAGTAAGACCATAGTTGAAAGA
1 ATG-AAATGAATAAGACCATGGTTGAAAGA
134353391 CGCTATGGCA
Statistics
Matches: 147, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
45 2 0.01
46 144 0.98
47 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.21
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:134353337 original size:92 final size:92
Alignment explanation
Indices: 134353188--134353390 Score: 309
Period size: 92 Copynumber: 2.2 Consensus size: 92
134353178 ATGAAATGTG
* * *
134353188 TAAGACCATGGTTGAAAGATACCATGGCAATGTGATATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTAACATGAAATGAATAAGACCATGGTTGAAAGA
*
134353253 TACCATGGCAACATGAC-GAGAAATGAA
66 TACCATGACAACATGACAGA-AAATGAA
* *
134353280 TAAGACCATGGTTGAAAGATATCATGGCAGCGTAACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACGTAACATGAAATGAATAAGACCATGGTTGAAAGA
* *
134353345 TACTATGACAACATGACAGAAAATGAG
66 TACCATGACAACATGACAGAAAATGAA
*
134353372 TAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGA
134353391 CGCTATGGCA
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 99 0.98
93 2 0.02
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACGTAACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGACAACATGACAGAAAATGAA
Found at i:134353397 original size:46 final size:46
Alignment explanation
Indices: 134353188--134353427 Score: 247
Period size: 46 Copynumber: 5.2 Consensus size: 46
134353178 ATGAAATGTG
* ** *
134353188 TAAGACCATGGTTGAAAGATACCATGGCAATGTGATATG-AAATGAA
1 TAAGACCATGGTTGAAAGATACTATGGCAACATGACA-GAAAATGAA
*
134353234 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-GAGAAATGAA
1 TAAGACCATGGTTGAAAGATACTATGGCAACATGACAGA-AAATGAA
* * *
134353280 TAAGACCATGGTTGAAAGATA-TCATGGCAGCGTAACATG-AAATGAA
1 TAAGACCATGGTTGAAAGATACT-ATGGCAACATGACA-GAAAATGAA
* *
134353326 TAAGACCATGGTTGAAAGATACTATGACAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACTATGGCAACATGACAGAAAATGAA
* ** * * * *
134353372 TAAGACCATAGTTGAAAGACGCTATGGCATCATGTCA-AAGATAAA
1 TAAGACCATGGTTGAAAGATACTATGGCAACATGACAGAAAATGAA
*
134353417 TAAGGCCATGG
1 TAAGACCATGG
134353428 ATGGGAGACG
Statistics
Matches: 164, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
44 1 0.01
45 15 0.09
46 146 0.89
47 1 0.01
48 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACTATGGCAACATGACAGAAAATGAA
Found at i:134353707 original size:16 final size:17
Alignment explanation
Indices: 134353686--134353718 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
134353676 ATGATGGAGC
134353686 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
134353702 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
134353719 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:134356112 original size:42 final size:42
Alignment explanation
Indices: 134356054--134356139 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
134356044 TAGCATGTAC
134356054 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
1 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
134356096 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
1 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
134356138 AC
1 AC
134356140 TCACCAAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
Found at i:134359101 original size:18 final size:18
Alignment explanation
Indices: 134359078--134359166 Score: 115
Period size: 18 Copynumber: 4.9 Consensus size: 18
134359068 CGTTTACGGT
134359078 ACTATTCACGTATACAGC
1 ACTATTCACGTATACAGC
*
134359096 ACTATTCACGTATACAGT
1 ACTATTCACGTATACAGC
*
134359114 ACTATTCACGTATACGGC
1 ACTATTCACGTATACAGC
* * * *
134359132 ACTATTTACGAATACGGT
1 ACTATTCACGTATACAGC
*
134359150 ACTGTTCACGTATACAG
1 ACTATTCACGTATACAG
134359167 TAGTTGGGAT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 61 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (18 bp):
ACTATTCACGTATACAGC
Found at i:134359123 original size:36 final size:36
Alignment explanation
Indices: 134359076--134359166 Score: 137
Period size: 36 Copynumber: 2.5 Consensus size: 36
134359066 ACCGTTTACG
*
134359076 GTACTATTCACGTATACAGCACTATTCACGTATACA
1 GTACTATTCACGTATACAGCACTATTCACGAATACA
* * *
134359112 GTACTATTCACGTATACGGCACTATTTACGAATACG
1 GTACTATTCACGTATACAGCACTATTCACGAATACA
*
134359148 GTACTGTTCACGTATACAG
1 GTACTATTCACGTATACAG
134359167 TAGTTGGGAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (36 bp):
GTACTATTCACGTATACAGCACTATTCACGAATACA
Found at i:134366449 original size:19 final size:18
Alignment explanation
Indices: 134366414--134366452 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
134366404 CTATAGAGCT
* *
134366414 AATTTTTATATTCTTTTA
1 AATTTTTATAATATTTTA
134366432 AATTTTTATAAATATTTTA
1 AATTTTTAT-AATATTTTA
134366451 AA
1 AA
134366453 AAATTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTTATAATATTTTA
Found at i:134369106 original size:16 final size:17
Alignment explanation
Indices: 134369085--134369122 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
134369075 TAGTTGAACC
*
134369085 ATATTTT-ATATTTTTA
1 ATATTTTAATACTTTTA
134369101 ATATTTTAATACTTTTA
1 ATATTTTAATACTTTTA
134369118 A-ATTT
1 ATATTT
134369123 ATAGGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTTAATACTTTTA
Found at i:134377548 original size:19 final size:20
Alignment explanation
Indices: 134377525--134377568 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
134377515 AAAATTACAA
*
134377525 AAAAAATCAAAATAAATTTT
1 AAAAATTCAAAATAAATTTT
* *
134377545 AAAAATTTAAAATAATTTTT
1 AAAAATTCAAAATAAATTTT
134377565 AAAA
1 AAAA
134377569 CTAAAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTCAAAATAAATTTT
Found at i:134377575 original size:19 final size:19
Alignment explanation
Indices: 134377533--134377587 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
134377523 AAAAAAAATC
* *
134377533 AAAATAAATTTTAAAAATTT
1 AAAAT-AATTTTAAAAACTA
*
134377553 AAAATAATTTTTAAAACTA
1 AAAATAATTTTAAAAACTA
* *
134377572 AAAATAGTTATAAAAA
1 AAAATAATTTTAAAAA
134377588 TTCTAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATAATTTTAAAAACTA
Found at i:134380678 original size:13 final size:13
Alignment explanation
Indices: 134380660--134380687 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
134380650 GGATGCTTAT
134380660 CCTTAACCTTAGG
1 CCTTAACCTTAGG
134380673 CCTTAACCTTAGG
1 CCTTAACCTTAGG
134380686 CC
1 CC
134380688 CCAAGCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (13 bp):
CCTTAACCTTAGG
Found at i:134385431 original size:22 final size:22
Alignment explanation
Indices: 134385406--134385472 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
134385396 GTATGACTTA
134385406 AATAAGAACTTGTGAATGATCG
1 AATAAGAACTTGTGAATGATCG
* * *
134385428 AATATAG----TG-GATTAGCTCA
1 AATA-AGAACTTGTGAAT-GATCG
134385447 AATAAGAACTTGTGAATGATCG
1 AATAAGAACTTGTGAATGATCG
134385469 AATA
1 AATA
134385473 TAGTGGATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
22 13 0.41
23 5 0.16
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (22 bp):
AATAAGAACTTGTGAATGATCG
Found at i:134385450 original size:41 final size:41
Alignment explanation
Indices: 134385405--134385486 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
134385395 AGTATGACTT
134385405 AAATAAGAACTTGTGAATGATCGAATATAGTGGATTAGCTC
1 AAATAAGAACTTGTGAATGATCGAATATAGTGGATTAGCTC
134385446 AAATAAGAACTTGTGAATGATCGAATATAGTGGATTAGCTC
1 AAATAAGAACTTGTGAATGATCGAATATAGTGGATTAGCTC
134385487 TCTAAGTAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (41 bp):
AAATAAGAACTTGTGAATGATCGAATATAGTGGATTAGCTC
Found at i:134390451 original size:20 final size:20
Alignment explanation
Indices: 134390426--134390480 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
134390416 AAAAATATAA
134390426 ATTTTAAAATTTTTATAACT
1 ATTTTAAAATTTTTATAACT
* * *
134390446 ATTTT-AAATTTTAAAAATT
1 ATTTTAAAATTTTTATAACT
*
134390465 ATTTTATAATTTTTAT
1 ATTTTAAAATTTTTAT
134390481 TAAGAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTAAAATTTTTATAACT
Found at i:134390452 original size:45 final size:43
Alignment explanation
Indices: 134390364--134390462 Score: 112
Period size: 46 Copynumber: 2.2 Consensus size: 43
134390354 CAAAATTATT
**
134390364 ATTTTAAAAAAAATAAATTTTAACTTTCTTTATATATGCTTTAAA
1 ATTTTAAAAAAAATAAATTTTAAAATTCTTTATATAT-CTTT-AA
*
134390409 ATTTTTAAAAAATATAAATTTTAAAATT-TTTATAACTAT-TTTAA
1 A-TTTTAAAAAAAATAAATTTTAAAATTCTTTAT-A-TATCTTTAA
134390453 ATTTTAAAAA
1 ATTTTAAAAA
134390463 TTATTTTATA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
43 9 0.19
44 3 0.06
45 9 0.19
46 24 0.50
47 3 0.06
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (43 bp):
ATTTTAAAAAAAATAAATTTTAAAATTCTTTATATATCTTTAA
Found at i:134391516 original size:31 final size:32
Alignment explanation
Indices: 134391461--134391522 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
134391451 TCTTTTTTTA
* *
134391461 AATTAAATTTGGCATTCAATCTTTT-AAAAAG
1 AATTAAATTTGCCATTCAACCTTTTCAAAAAG
134391492 AATTAAATTTGACCATT-AACCTTTTCAAAAA
1 AATTAAATTTG-CCATTCAACCTTTTCAAAAA
134391523 TTGTTGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 18 0.67
32 9 0.33
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (32 bp):
AATTAAATTTGCCATTCAACCTTTTCAAAAAG
Found at i:134397280 original size:19 final size:16
Alignment explanation
Indices: 134397242--134397274 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
134397232 CAAAGATAGT
134397242 TCTTTTTTTACCTTTG
1 TCTTTTTTTACCTTTG
134397258 TCTTTTTTTACCTTTG
1 TCTTTTTTTACCTTTG
134397274 T
1 T
134397275 GGTCTTGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.70
Consensus pattern (16 bp):
TCTTTTTTTACCTTTG
Found at i:134417044 original size:27 final size:27
Alignment explanation
Indices: 134417014--134417072 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
134417004 AGTTCAGTTA
134417014 ATGTCCCGAAAGGCCATTTTGCTGTTT
1 ATGTCCCGAAAGGCCATTTTGCTGTTT
134417041 ATGTCCCGAAAGGCCATTTTGCTGTTT
1 ATGTCCCGAAAGGCCATTTTGCTGTTT
134417068 ATGTC
1 ATGTC
134417073 GGAGACGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (27 bp):
ATGTCCCGAAAGGCCATTTTGCTGTTT
Found at i:134427408 original size:29 final size:30
Alignment explanation
Indices: 134427376--134427469 Score: 69
Period size: 29 Copynumber: 3.3 Consensus size: 30
134427366 ATAAAAGGAG
134427376 TAATAATTTT-TAAAATTTTATAATTTATC
1 TAATAATTTTCTAAAATTTTATAATTTATC
*
134427405 TAAT--TTTTCCTATAATTTT-TATATTTCAT-
1 TAATAATTTT-CTAAAATTTTATA-ATTT-ATC
* *
134427434 TAA-AATTTTATAATATTTTAATAA-TT-TC
1 TAATAATTTTCTAAAATTTT-ATAATTTATC
134427462 TAATAATT
1 TAATAATT
134427470 GAAGATTCCG
Statistics
Matches: 51, Mismatches: 4, Indels: 20
0.68 0.05 0.27
Matches are distributed among these distances:
27 5 0.10
28 5 0.10
29 32 0.63
30 7 0.14
31 2 0.04
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (30 bp):
TAATAATTTTCTAAAATTTTATAATTTATC
Found at i:134431563 original size:16 final size:16
Alignment explanation
Indices: 134431529--134431579 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
134431519 AAATAAGATT
**
134431529 AATAATTAAAATTTGA
1 AATAATTAAAATTCAA
134431545 AATAATTAAAATTCAA
1 AATAATTAAAATTCAA
* * *
134431561 AATAACTCAAATTGAA
1 AATAATTAAAATTCAA
134431577 AAT
1 AAT
134431580 GACCCGAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (16 bp):
AATAATTAAAATTCAA
Found at i:134438046 original size:22 final size:22
Alignment explanation
Indices: 134438017--134438084 Score: 84
Period size: 22 Copynumber: 3.0 Consensus size: 22
134438007 TGCACAAATG
134438017 AACAGAGAGCACTAAAGTGCTA
1 AACAGAGAGCACTAAAGTGCTA
* *
134438039 TACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTA-AAGTGCTA
*
134438061 AACAGAGAGCACTTAACGTGCTA
1 AACAGAGAGCAC-TAAAGTGCTA
134438084 A
1 A
134438085 TAATAGTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.74
23 8 0.21
24 1 0.03
ACGTcount: A:0.41, C:0.19, G:0.24, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTAAAGTGCTA
Found at i:134439273 original size:7 final size:7
Alignment explanation
Indices: 134439263--134439350 Score: 51
Period size: 7 Copynumber: 12.0 Consensus size: 7
134439253 TATGTTTTAT
134439263 ATATATA
1 ATATATA
134439270 ATATA-A
1 ATATATA
134439276 TATAATATA
1 -AT-ATATA
134439285 ATATAATA
1 ATAT-ATA
134439293 ATATAT-
1 ATATATA
*
134439299 -TATATT
1 ATATATA
134439305 ATATATTA
1 ATATA-TA
134439313 ATACT-TA
1 ATA-TATA
134439320 A-ATATTA
1 ATATA-TA
134439327 AGTTAATATA
1 A--T-ATATA
134439337 ATATATA
1 ATATATA
134439344 ATATATA
1 ATATATA
134439351 TTTTTATATA
Statistics
Matches: 66, Mismatches: 1, Indels: 28
0.69 0.01 0.29
Matches are distributed among these distances:
5 6 0.09
6 2 0.03
7 33 0.50
8 17 0.26
9 2 0.03
10 3 0.05
11 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:134439285 original size:15 final size:16
Alignment explanation
Indices: 134439260--134439310 Score: 70
Period size: 15 Copynumber: 3.3 Consensus size: 16
134439250 TCTTATGTTT
134439260 TATATATATAATATAA
1 TATATATATAATATAA
134439276 TATA-ATATAATATAA
1 TATATATATAATATAA
* *
134439291 TA-ATATATTATATTA
1 TATATATATAATATAA
134439306 TATAT
1 TATAT
134439311 TAATACTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 1 0.03
15 24 0.77
16 6 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATATAATATAA
Found at i:134439298 original size:20 final size:20
Alignment explanation
Indices: 134439260--134439315 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
134439250 TCTTATGTTT
134439260 TATATATATAAT-ATAATATAA
1 TATA-ATATAATAAT-ATATAA
*
134439281 TATAATATAATAATATATTA
1 TATAATATAATAATATATAA
* *
134439301 TATTATATATTAATA
1 TATAATATAATAATA
134439316 CTTAAATATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 25 0.81
21 6 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAATATAATAATATATAA
Found at i:134439308 original size:5 final size:5
Alignment explanation
Indices: 134439260--134439292 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
134439250 TCTTATGTTT
134439260 TATATA TATAA TATAA TATAA TATAA TATAA TA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TA
134439293 ATATATTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:134440463 original size:103 final size:102
Alignment explanation
Indices: 134440282--134440476 Score: 261
Period size: 103 Copynumber: 1.9 Consensus size: 102
134440272 ATCACTTCAA
*
134440282 AAAGATATTACTTATTTAATTTCACTTGAATCCACAATTTCTAAGAATTTATGATAATATTAATG
1 AAAGATATTACTTATTTAATTTCACTTGAATCCACAATTTCTAAGAATTTATAATAATATTAATG
*
134440347 TCAATTGATAATTATTTAATCAACGATACATATATGAT
66 TCAATTGACAATTATTTAA-CAACGATACATATATGAT
* ****
134440385 AAAGATATTA-TTCATTTAATTTTACTTGAATTTGTAATTTC-ATA-AATTTATAATAATATTAA
1 AAAGATATTACTT-ATTTAATTTCACTTGAATCCACAATTTCTA-AGAATTTATAATAATATTAA
*
134440447 TTTCAATTGAACAATTATTTAACAACGATA
64 TGTCAATTG-ACAATTATTTAACAACGATA
134440477 AATTCAATAT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
102 36 0.44
103 45 0.56
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.43
Consensus pattern (102 bp):
AAAGATATTACTTATTTAATTTCACTTGAATCCACAATTTCTAAGAATTTATAATAATATTAATG
TCAATTGACAATTATTTAACAACGATACATATATGAT
Found at i:134442263 original size:25 final size:27
Alignment explanation
Indices: 134442225--134442274 Score: 70
Period size: 25 Copynumber: 1.9 Consensus size: 27
134442215 ATATGATTAA
134442225 TTATAATTTAAAAATAA-AATAAATATT
1 TTATAATTTAAAAATAACAA-AAATATT
134442252 TTAT-ATTT-AAAATAACAAAAATA
1 TTATAATTTAAAAATAACAAAAATA
134442275 ACTTAAAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 12 0.55
26 6 0.27
27 4 0.18
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (27 bp):
TTATAATTTAAAAATAACAAAAATATT
Found at i:134455947 original size:16 final size:16
Alignment explanation
Indices: 134455926--134455958 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
134455916 AAATGTCCCT
134455926 CTATTATTAAATGAAC
1 CTATTATTAAATGAAC
134455942 CTATTATTAAATGAAC
1 CTATTATTAAATGAAC
134455958 C
1 C
134455959 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (16 bp):
CTATTATTAAATGAAC
Found at i:134457986 original size:19 final size:19
Alignment explanation
Indices: 134457964--134458000 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
134457954 ATTGTTTGTT
134457964 GTATGTTAT-TTTTAAATAA
1 GTAT-TTATGTTTTAAATAA
134457983 GTATTTATGTTTTAAATA
1 GTATTTATGTTTTAAATA
134458001 TGTGATTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (19 bp):
GTATTTATGTTTTAAATAA
Found at i:134458157 original size:19 final size:19
Alignment explanation
Indices: 134458118--134458155 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
134458108 AAAGTGAATC
*
134458118 TTGGTCCTTAACTTTCAAA
1 TTGGTCCTTAACTATCAAA
134458137 TTGGTCCTTAAACTATCAA
1 TTGGTCCTT-AACTATCAA
134458156 TTAAGACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (19 bp):
TTGGTCCTTAACTATCAAA
Found at i:134459135 original size:15 final size:15
Alignment explanation
Indices: 134459090--134459136 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
134459080 AATGAGGTTT
*
134459090 TTTTATCTAACTTAA
1 TTTTATCTAATTTAA
134459105 TTATATAT-TAAATTTAA
1 TT-T-TATCT-AATTTAA
134459122 TTTTATCTAATTTAA
1 TTTTATCTAATTTAA
134459137 ATTAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTATCTAATTTAA
Found at i:134459394 original size:11 final size:12
Alignment explanation
Indices: 134459365--134459392 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
134459355 CTACTTATTA
134459365 TTTTTCAAGTAG
1 TTTTTCAAGTAG
134459377 TTTTTCAAGTAG
1 TTTTTCAAGTAG
134459389 TTTT
1 TTTT
134459393 CATTGTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (12 bp):
TTTTTCAAGTAG
Found at i:134464408 original size:30 final size:30
Alignment explanation
Indices: 134464374--134464435 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
134464364 TAGTAAAGGT
* *
134464374 AAATTTGTACTTTGACCCTTTAAAAA-TATA
1 AAATTT-TAATTTAACCCTTTAAAAATTATA
* *
134464404 AAATTTTAATTTAATCTTTTAAAAATTATA
1 AAATTTTAATTTAACCCTTTAAAAATTATA
134464434 AA
1 AA
134464436 GATATAGTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (30 bp):
AAATTTTAATTTAACCCTTTAAAAATTATA
Found at i:134470188 original size:23 final size:23
Alignment explanation
Indices: 134470139--134470200 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
134470129 ACATGTTGTG
* ** *
134470139 AACATTAAACAAACATATTTGCG
1 AACATTAAACAAACACATTCACA
134470162 AACATTAAACAAACACATTCACA
1 AACATTAAACAAACACATTCACA
*
134470185 AACAGTAAACCAAACA
1 AACATTAAA-CAAACA
134470201 AACAAACAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 27 0.82
24 6 0.18
ACGTcount: A:0.55, C:0.23, G:0.05, T:0.18
Consensus pattern (23 bp):
AACATTAAACAAACACATTCACA
Found at i:134470223 original size:24 final size:24
Alignment explanation
Indices: 134470196--134470246 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
134470186 ACAGTAAACC
134470196 AAACAAACAAACAAAATATTAAA-A
1 AAACAAACAAACAAAAT-TTAAATA
*
134470220 AAACAAACCAACAAAATTTAAATA
1 AAACAAACAAACAAAATTTAAATA
134470244 AAA
1 AAA
134470247 AAATAGATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.73, C:0.14, G:0.00, T:0.14
Consensus pattern (24 bp):
AAACAAACAAACAAAATTTAAATA
Found at i:134472869 original size:103 final size:103
Alignment explanation
Indices: 134472687--134472878 Score: 348
Period size: 103 Copynumber: 1.9 Consensus size: 103
134472677 TCTATACATT
134472687 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACATTATATAATATAAATATTACCA
1 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACATTATATAATATAAATATTACCA
* * *
134472752 CGTCCGTATGAAATACACGTAGACTAATATAGAAGTTG
66 CGTCAGTATAAAATACACATAGACTAATATAGAAGTTG
134472790 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACATTATATAATATAAATATTACCA
1 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACATTATATAATATAAATATTACCA
*
134472855 TGTCAGTATAAAATACACATAGAC
66 CGTCAGTATAAAATACACATAGAC
134472879 CAATGTAGGA
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 85 1.00
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (103 bp):
TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACATTATATAATATAAATATTACCA
CGTCAGTATAAAATACACATAGACTAATATAGAAGTTG
Found at i:134483399 original size:7 final size:7
Alignment explanation
Indices: 134483389--134483414 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
134483379 TTTATATTTT
134483389 TTTAAAA
1 TTTAAAA
134483396 TTTAAAA
1 TTTAAAA
134483403 TTTAAAA
1 TTTAAAA
134483410 TTTAA
1 TTTAA
134483415 TGCAAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTAAAA
Found at i:134483518 original size:16 final size:16
Alignment explanation
Indices: 134483497--134483530 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
134483487 ATAAATTATC
134483497 AAAAATAAAATAAATT
1 AAAAATAAAATAAATT
* *
134483513 AAAAATAACATAATTT
1 AAAAATAAAATAAATT
134483529 AA
1 AA
134483531 CCTTTGCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAATAAATT
Found at i:134488506 original size:18 final size:20
Alignment explanation
Indices: 134488466--134488507 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
134488456 TCTCTTATCA
*
134488466 AAAATTACAAAATAATTTTT
1 AAAATTACAAAATAATTTAT
134488486 AAAATT-CAAAAT-ATTTAT
1 AAAATTACAAAATAATTTAT
134488504 AAAA
1 AAAA
134488508 AATTCCAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTACAAAATAATTTAT
Found at i:134488508 original size:19 final size:21
Alignment explanation
Indices: 134488460--134488508 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
134488450 TTGGTCTCTC
134488460 TTATCAAAAATTACAAAATAAT
1 TTAT-AAAAATTACAAAATAAT
*
134488482 TT-TTAAAATT-CAAAAT-AT
1 TTATAAAAATTACAAAATAAT
134488500 TTATAAAAA
1 TTATAAAAA
134488509 ATTCCAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 6 0.25
21 1 0.04
22 2 0.08
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
TTATAAAAATTACAAAATAAT
Found at i:134491243 original size:98 final size:98
Alignment explanation
Indices: 134491074--134491268 Score: 266
Period size: 98 Copynumber: 2.0 Consensus size: 98
134491064 ACCCTAACGG
* * ** *
134491074 TTTGTTCGATTAGCTGAAATTTGGTTGCTCGGTTAATTCGAGAATATTGCTATATTCATTGTTTG
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGGTTG
* *
134491139 TTTAAGATTATCATAGAATGTGTAGGAGCATGT
66 TTTAAGATGATCATACAATGTGTAGGAGCATGT
* * *
134491172 TTTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCATTATATGT-ATTGGTT
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATAT-TCATTGGTT
* *
134491236 GTTTAAGATGATGATACATTGTGTAGGAGCATG
65 GTTTAAGATGATCATACAATGTGTAGGAGCATG
134491269 CTTTCTTCAG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 83 0.99
99 1 0.01
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (98 bp):
TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGGTTG
TTTAAGATGATCATACAATGTGTAGGAGCATGT
Found at i:134491487 original size:186 final size:185
Alignment explanation
Indices: 134491173--134491813 Score: 933
Period size: 186 Copynumber: 3.4 Consensus size: 185
134491163 GGAGCATGTT
* * * * * * *
134491173 TTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCATTATATGTATTGGTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
134491238 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
134491303 GAACTGTTTATATGCTGCTTCTGAGTCTGCTGAGGCTGCTAATCAACCCCAAAGGC
131 GAACTGTTTATATGCTGCTTCTGAGTCTG-TGAGGCTGCTAATCAACCCCAAAGGC
* ** ** *
134491359 TTGTTCGGTTAGCTGAAATTCAATTGCTCGGTTAATTTGAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
*
134491424 TTAAGACGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* *
134491489 GAGCTGTTTATATGCTGCTTCCGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
131 GAACTGTTTATATGCTGCTTCTGAGTCTG-TGAGGCTGCTAATCAACCCCAAAGGC
* *
134491545 TTGTTCCATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* * * *
134491610 CTAAGATGATGATACATAGTGTAGGAGCATACTTTCTTCAGTATGAATCTCATTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* * * *
134491675 GAACT-TTCTATATGCTGCTGCTGAGTCTGTGGAGGCTACTAATCAACCCTAAAGGT
131 GAACTGTT-TATATGCTGCTTCTGAGTCTGT-GAGGCTGCTAATCAACCCCAAAGGC
* ** * **
134491731 TTGTTCAATTAGCTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* *
134491796 TTTAGATGATAATACATT
66 TTAAGATGATGATACATT
134491814 TTTTAGTAGT
Statistics
Matches: 410, Mismatches: 43, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
185 3 0.01
186 407 0.99
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (185 bp):
TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
GAACTGTTTATATGCTGCTTCTGAGTCTGTGAGGCTGCTAATCAACCCCAAAGGC
Found at i:134491909 original size:98 final size:98
Alignment explanation
Indices: 134491734--134491911 Score: 227
Period size: 98 Copynumber: 1.8 Consensus size: 98
134491724 TAAAGGTTTG
* * *
134491734 TTCAATTAGCTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGTTTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
134491799 AGATGATAATACATTTTTTAGTAGTATGTTTTC
66 AGATGATAATACATTTTTTAGTAGTATGTTTTC
* ** * *
134491832 TTCATTTAGCTGAAATTAGATTGCTCGGTTAATTCGAGAATTC-TGGC-ATATTTATTGTTTGTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAA--CATGGCTATATGTATTGTTTGTT
*
134491895 TAA-AGTGATGATACATT
64 TAAGA-TGATAATACATT
134491912 GTGTAGGAGC
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
97 1 0.01
98 63 0.93
99 3 0.04
100 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.46
Consensus pattern (98 bp):
TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
AGATGATAATACATTTTTTAGTAGTATGTTTTC
Found at i:134491930 original size:98 final size:98
Alignment explanation
Indices: 134491734--134491933 Score: 217
Period size: 98 Copynumber: 2.0 Consensus size: 98
134491724 TAAAGGTTTG
* * *
134491734 TTCAATTAGCTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGTTTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
* * * * * *
134491799 AGATGATAATACATTTTTTAGTAGTATGTTTTC
66 AGATGATAATACATTGTGTAGGAGCACGCTTTC
* ** * *
134491832 TTCATTTAGCTGAAATTAGATTGCTCGGTTAATTCGAGAATTC-TGGC-ATATTTATTGTTTGTT
1 TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAA--CATGGCTATATGTATTGTTTGTT
*
134491895 TAA-AGTGATGATACATTGTGTAGGAGCACGCTTTC
64 TAAGA-TGATAATACATTGTGTAGGAGCACGCTTTC
134491930 TTCA
1 TTCA
134491934 GAATGAATCT
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
97 1 0.01
98 79 0.94
99 3 0.04
100 1 0.01
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (98 bp):
TTCAATTAGCTGAAATTAGATTGCTCAATTAATTCAAGAACATGGCTATATGTATTGTTTGTTTA
AGATGATAATACATTGTGTAGGAGCACGCTTTC
Found at i:134492345 original size:23 final size:23
Alignment explanation
Indices: 134492315--134492363 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
134492305 CTCCCCAATG
134492315 CTACTTTCTCTGCCCACAAGACT
1 CTACTTTCTCTGCCCACAAGACT
134492338 CTACTTTCTCTGCCCACAAGACT
1 CTACTTTCTCTGCCCACAAGACT
134492361 CTA
1 CTA
134492364 ACCCAAGCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.39, G:0.08, T:0.31
Consensus pattern (23 bp):
CTACTTTCTCTGCCCACAAGACT
Found at i:134496413 original size:31 final size:31
Alignment explanation
Indices: 134496375--134496436 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
134496365 AAAACTTGAT
134496375 TTAAATAAAAACTTTCAAATAGTTCAATGAC
1 TTAAATAAAAACTTTCAAATAGTTCAATGAC
* * *
134496406 TTAAATAAAAGCTTTCGAATAGTTCAGTGAC
1 TTAAATAAAAACTTTCAAATAGTTCAATGAC
134496437 CATACTGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAGTTCAATGAC
Found at i:134497411 original size:24 final size:23
Alignment explanation
Indices: 134497366--134497411 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
134497356 TAAACTAGTC
* *
134497366 TTTTTATTAAAAAATTTTATCTA
1 TTTTTATTAAAAAATCTAATCTA
*
134497389 TTTTTATTATTAAAATCTAATCT
1 TTTTTATTA-AAAAATCTAATCT
134497412 CTATATATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTATTAAAAAATCTAATCTA
Found at i:134501224 original size:56 final size:56
Alignment explanation
Indices: 134501163--134501274 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
134501153 TCGTTTTTCG
134501163 CCTGGTTTTCTCATCTTTAAACTGCTTTTTCATAAAAAACATTTCCCTATATTCTA
1 CCTGGTTTTCTCATCTTTAAACTGCTTTTTCATAAAAAACATTTCCCTATATTCTA
134501219 CCTGGTTTTCTCATCTTTAAACTGCTTTTTCATAAAAAACATTTCCCTATATTCTA
1 CCTGGTTTTCTCATCTTTAAACTGCTTTTTCATAAAAAACATTTCCCTATATTCTA
134501275 GCTCATCAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (56 bp):
CCTGGTTTTCTCATCTTTAAACTGCTTTTTCATAAAAAACATTTCCCTATATTCTA
Found at i:134506838 original size:31 final size:30
Alignment explanation
Indices: 134506796--134506873 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
134506786 AAAAAGCTCA
* * *
134506796 ATATTCGATTTGGTATTTGAGCTTGGTTTT
1 ATATTCAATTTGGTACTTGAGCTTGGCTTT
* *
134506826 GATATTCAATTTGTTACTTGAGTTTGGCTTT
1 -ATATTCAATTTGGTACTTGAGCTTGGCTTT
*
134506857 AGTATTCAATTTAGTAC
1 A-TATTCAATTTGGTAC
134506874 CTAACATTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.50
Consensus pattern (30 bp):
ATATTCAATTTGGTACTTGAGCTTGGCTTT
Found at i:134510678 original size:2 final size:2
Alignment explanation
Indices: 134510671--134510699 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
134510661 CCTAAAAAGT
134510671 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
134510700 GACACCCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:134515488 original size:19 final size:21
Alignment explanation
Indices: 134515464--134515502 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
134515454 GTGCTGGTAG
134515464 TTAATTA-TAA-GTATTTTTT
1 TTAATTATTAATGTATTTTTT
134515483 TTAATTATTAATGTATTTTT
1 TTAATTATTAATGTATTTTT
134515503 CATGTTCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 3 0.17
21 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TTAATTATTAATGTATTTTTT
Found at i:134516218 original size:20 final size:19
Alignment explanation
Indices: 134516181--134516221 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
134516171 TATATATATC
134516181 ATAAAAATGAAAATAAAAT
1 ATAAAAATGAAAATAAAAT
134516200 ATAAAAATCAGAAAA-AAAAT
1 ATAAAAAT--GAAAATAAAAT
134516220 AT
1 AT
134516222 TTCGAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAAAATGAAAATAAAAT
Done.