Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold54
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: 3629595
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8670 characters in sequence are not A, C, G, or T
File 14 of 20
Found at i:2267042 original size:2 final size:2
Alignment explanation
Indices: 2267005--2267031 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2266995 ACATATTAAC
2267005 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
2267032 ATTAGTATAT
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:2267539 original size:14 final size:14
Alignment explanation
Indices: 2267516--2267553 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
2267506 TAAATTTAAT
*
2267516 TATAAAAAATAATA
1 TATAAAAAATAAAA
*
2267530 TATTAAAAATAAAA
1 TATAAAAAATAAAA
2267544 TATAAAAAAT
1 TATAAAAAAT
2267554 TTATTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TATAAAAAATAAAA
Found at i:2269250 original size:21 final size:20
Alignment explanation
Indices: 2269226--2269264 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2269216 ATATTATTGT
2269226 ATATCTTATTTATTTTAAAAA
1 ATAT-TTATTTATTTTAAAAA
*
2269247 ATATTTTTTTATTTTAAA
1 ATATTTATTTATTTTAAA
2269265 TATGTCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATATTTATTTATTTTAAAAA
Found at i:2270015 original size:27 final size:26
Alignment explanation
Indices: 2269973--2270036 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
2269963 TATACGACAC
2269973 ATTTAAATA-ATAAAAATATAAAATAT
1 ATTTAAATATATAAAAATATAAAA-AT
*
2269999 GATTTAAATATAT-AAAATTTAAAAAT
1 -ATTTAAATATATAAAAATATAAAAAT
*
2270025 TTTTAAATATAT
1 ATTTAAATATAT
2270037 TTATTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 11 0.32
26 2 0.06
27 19 0.56
28 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
ATTTAAATATATAAAAATATAAAAAT
Found at i:2270042 original size:16 final size:17
Alignment explanation
Indices: 2270023--2270055 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2270013 AAATTTAAAA
2270023 ATTTTTAA-ATATATTT
1 ATTTTTAACATATATTT
2270039 ATTTTTAACATATATTT
1 ATTTTTAACATATATTT
2270056 TCATATCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTTAACATATATTT
Found at i:2270263 original size:2 final size:2
Alignment explanation
Indices: 2270247--2270286 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2270237 GAACACACAC
* * *
2270247 AT AT AA AT AT GT AT AT AT AT AA 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
2270287 CACTTAACGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2270266 original size:16 final size:16
Alignment explanation
Indices: 2270247--2270283 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2270237 GAACACACAC
*
2270247 ATATAAATATGTATAT
1 ATATAAATATATATAT
2270263 ATATAAATATATATAT
1 ATATAAATATATATAT
2270279 ATATA
1 ATATA
2270284 TATCACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
ATATAAATATATATAT
Found at i:2270860 original size:2 final size:2
Alignment explanation
Indices: 2270855--2270889 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2270845 AAAATCGTTA
2270855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2270890 AACAACTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2271735 original size:2 final size:2
Alignment explanation
Indices: 2271728--2271757 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2271718 ATTAAGGACA
2271728 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2271758 AAGAGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2277861 original size:36 final size:37
Alignment explanation
Indices: 2277821--2277896 Score: 91
Period size: 37 Copynumber: 2.1 Consensus size: 37
2277811 GATATGTCTT
* * *
2277821 TAAGAAATTGGAGATATG-AACTTTATGTATGTAAAA
1 TAAGAAATTGGAGACATGTAACTTTAGGTATCTAAAA
* * *
2277857 TAAGAATTTGGGGACATGTAACTTTAGGTATCTTAAA
1 TAAGAAATTGGAGACATGTAACTTTAGGTATCTAAAA
2277894 TAA
1 TAA
2277897 TCGAAGTATG
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
36 15 0.45
37 18 0.55
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (37 bp):
TAAGAAATTGGAGACATGTAACTTTAGGTATCTAAAA
Found at i:2279279 original size:18 final size:17
Alignment explanation
Indices: 2279253--2279286 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2279243 CAAATCAAAA
2279253 TGAAGACTTTCCACAGAG
1 TGAAGAC-TTCCACAGAG
*
2279271 TGAATACTTCCACAGA
1 TGAAGACTTCCACAGA
2279287 TATTTGCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (17 bp):
TGAAGACTTCCACAGAG
Found at i:2289025 original size:18 final size:18
Alignment explanation
Indices: 2288977--2289134 Score: 63
Period size: 18 Copynumber: 9.1 Consensus size: 18
2288967 TTATTTTTGG
2288977 ATAAT-AATACAAATTA-A
1 ATAATAAATA-AAATTATA
* *
2288994 AAAATAAA-ATAAATTTTA
1 ATAATAAATA-AAATTATA
2289012 ATAATAAATAAAATTATA
1 ATAATAAATAAAATTATA
* *
2289030 CTAATATAATATAA--A-A
1 ATAATA-AATAAAATTATA
*
2289046 ATAATAAAATAAAATTTAAA
1 ATAAT-AAATAAAA-TTATA
*
2289066 ATTTATATAATAAAATT-TA
1 A-TAATA-AATAAAATTATA
* * *
2289085 TTAATATATTATAATT-T-
1 ATAATA-AATAAAATTATA
*
2289102 AT-ATAAATATAATTATA
1 ATAATAAATAAAATTATA
2289119 AT-AT-AATAAAA-TATA
1 ATAATAAATAAAATTATA
2289134 A
1 A
2289135 AAAAATTTAC
Statistics
Matches: 110, Mismatches: 18, Indels: 28
0.71 0.12 0.18
Matches are distributed among these distances:
15 13 0.12
16 21 0.19
17 17 0.15
18 35 0.32
19 9 0.08
20 5 0.05
21 10 0.09
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATAAATAAAATTATA
Found at i:2289077 original size:21 final size:20
Alignment explanation
Indices: 2289020--2289084 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
2289010 TAATAATAAA
*
2289020 TAAAATTATACTAATATAATAT
1 TAAAATTATA-TAATAAAAT-T
* * *
2289042 AAAAATAATAAAATAAAATT
1 TAAAATTATATAATAAAATT
2289062 TAAAATTTATATAATAAAATT
1 TAAAA-TTATATAATAAAATT
2289083 TA
1 TA
2289085 TTAATATATT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
20 5 0.14
21 22 0.63
22 8 0.23
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATTATATAATAAAATT
Found at i:2289081 original size:14 final size:14
Alignment explanation
Indices: 2289062--2289130 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 14
2289052 AAATAAAATT
2289062 TAAAATTTATATAA
1 TAAAATTTATATAA
2289076 TAAAATTTATTAATATA
1 TAAAATTTA-T-ATA-A
*
2289093 TTATAATTTATATAAA
1 -TAAAATTTATAT-AA
*
2289109 TATAATTATAATATAA
1 TAAAATT-T-ATATAA
2289125 TAAAAT
1 TAAAAT
2289131 ATAAAAAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
14 9 0.20
15 8 0.17
16 14 0.30
17 7 0.15
18 8 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TAAAATTTATATAA
Found at i:2289125 original size:5 final size:5
Alignment explanation
Indices: 2289031--2289134 Score: 52
Period size: 5 Copynumber: 20.6 Consensus size: 5
2289021 AAAATTATAC
* * * * * * *
2289031 TAATA TAATA TAAAAA TAATA AAATA AAATT TAAAA TTTATA TAATA AAAT-
1 TAATA TAATA T-AATA TAATA TAATA TAATA TAATA -TAATA TAATA TAATA
* * * *
2289082 TTAT- TAATA TATTA TAAT- TTATA TAAATA TAATTA TAATA TAATA AAATA
1 TAATA TAATA TAATA TAATA TAATA T-AATA TAA-TA TAATA TAATA TAATA
2289132 TAA
1 TAA
2289135 AAAAATTTAC
Statistics
Matches: 73, Mismatches: 20, Indels: 12
0.70 0.19 0.11
Matches are distributed among these distances:
4 8 0.11
5 49 0.67
6 16 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:2289672 original size:13 final size:13
Alignment explanation
Indices: 2289632--2289672 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
2289622 TATTTAATAT
*
2289632 TTAAAAAAATTAA
1 TTAAAAATATTAA
*
2289645 ATAAAAATATTTAA
1 TTAAAAATA-TTAA
2289659 TTAAAAATATTAA
1 TTAAAAATATTAA
2289672 T
1 T
2289673 ATATGTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAAAAATATTAA
Found at i:2290640 original size:15 final size:16
Alignment explanation
Indices: 2290610--2290643 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2290600 TATTATTATT
2290610 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
*
2290626 TTAATTTTAAA-TAAA
1 TTAAATTTAAATTAAA
2290641 TTA
1 TTA
2290644 TTCAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:2290747 original size:16 final size:17
Alignment explanation
Indices: 2290714--2290754 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
2290704 ACTTGAATTT
2290714 AAATAATTTTATACTTA
1 AAATAATTTTATACTTA
2290731 AAAT-ATTTTAATA-TTA
1 AAATAATTTT-ATACTTA
*
2290747 AATTAATT
1 AAATAATT
2290755 AAACTTTAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATAATTTTATACTTA
Found at i:2291272 original size:22 final size:22
Alignment explanation
Indices: 2291185--2291266 Score: 75
Period size: 22 Copynumber: 3.7 Consensus size: 22
2291175 TATTTTGAAA
2291185 TATTTTTAA-ATAAAT-TAAAT
1 TATTTTTAATATAAATATAAAT
*
2291205 TATTGTTGACA-ATAAA-ATAAATTTT
1 TATT-TTTA-ATATAAATATAAA---T
2291230 TATTTTTAATATAAATATAAAT
1 TATTTTTAATATAAATATAAAT
2291252 TATTTTTAATA-AAAT
1 TATTTTTAATATAAAT
2291267 TTTAAAATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
20 4 0.08
21 7 0.13
22 22 0.42
23 1 0.02
24 8 0.15
25 10 0.19
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTTTAATATAAATATAAAT
Found at i:2291359 original size:52 final size:50
Alignment explanation
Indices: 2291250--2291359 Score: 114
Period size: 52 Copynumber: 2.1 Consensus size: 50
2291240 ATAAATATAA
* * ** * * *
2291250 ATTATTTTTAATAAAATTTTAAAATTTTATAAATTAATTAAAAAATTATT
1 ATTATTTGTAATAAAATTTAAAAAAATAATAAATTAATAAAAAAATTATG
2291300 ATATATTTGTAATATAAATTTAAAAAAATAATAAA-TAATAAATAAAATGTATG
1 AT-TATTTGTAATA-AAATTTAAAAAAATAATAAATTAATAAA-AAAAT-TATG
2291353 ATTATTT
1 ATTATTT
2291360 TTTAATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
50 2 0.04
51 16 0.33
52 26 0.53
53 5 0.10
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (50 bp):
ATTATTTGTAATAAAATTTAAAAAAATAATAAATTAATAAAAAAATTATG
Found at i:2292621 original size:17 final size:17
Alignment explanation
Indices: 2292607--2292662 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 17
2292597 TTTATATTGT
2292607 AATTATTATTTTATTTA
1 AATTATTATTTTATTTA
2292624 AATTA-TATTTT-TTTA
1 AATTATTATTTTATTTA
* *
2292639 TATAATT-TTTTATTCTTA
1 AATTATTATTTTA-T-TTA
2292657 AATTAT
1 AATTAT
2292663 AATCTCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 11 0.35
16 7 0.23
17 6 0.19
18 7 0.23
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
AATTATTATTTTATTTA
Found at i:2295483 original size:2 final size:2
Alignment explanation
Indices: 2295478--2295512 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2295468 TCCCCTCAAG
2295478 TA TA TA 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 TA TA TA T
2295513 TTTTGTTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2295988 original size:16 final size:15
Alignment explanation
Indices: 2295956--2296004 Score: 55
Period size: 16 Copynumber: 3.3 Consensus size: 15
2295946 CGAGTAATTT
*
2295956 ATTTGATTT-AATAA
1 ATTTAATTTAAATAA
*
2295970 ATTTAATTTATATTAA
1 ATTTAATTTA-AATAA
*
2295986 ATTAAATTTAAATAA
1 ATTTAATTTAAATAA
2296001 ATTT
1 ATTT
2296005 TTTAATAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTAATTTAAATAA
Found at i:2296069 original size:23 final size:23
Alignment explanation
Indices: 2296021--2296069 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
2296011 AATTCATATT
* * *
2296021 AATTTAATTTAAATTATTATTTA
1 AATTTAATTAAAATTAATATTAA
2296044 AATTTAATTAAAAATTAATA-TAA
1 AATTTAATT-AAAATTAATATTAA
2296067 AAT
1 AAT
2296070 ATATTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTTAATTAAAATTAATATTAA
Found at i:2296599 original size:2 final size:2
Alignment explanation
Indices: 2296592--2296617 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2296582 CCGTTTCTTT
2296592 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
2296618 AAATACTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2296744 original size:16 final size:14
Alignment explanation
Indices: 2296712--2296757 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
2296702 TTGATAATTT
2296712 ATTTAATTTAATAA
1 ATTTAATTTAATAA
2296726 ATTTAATTTATATTAA
1 ATTTAATTTA-A-TAA
*
2296742 ATTAAATTTAAATAA
1 ATTTAATTT-AATAA
2296757 A
1 A
2296758 AAATTTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.36
15 5 0.18
16 12 0.43
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAATTTAATAA
Found at i:2297206 original size:20 final size:21
Alignment explanation
Indices: 2297176--2297222 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
2297166 AGCTCGGCTC
*
2297176 TATTCATTTTATAATTATATA
1 TATTAATTTTATAATTATATA
*
2297197 -ATTAATTTTATATTTATATA
1 TATTAATTTTATAATTATATA
2297217 TATTAA
1 TATTAA
2297223 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTAATTTTATAATTATATA
Found at i:2297344 original size:15 final size:15
Alignment explanation
Indices: 2297326--2297356 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2297316 AAAGAAAATT
2297326 ATTAAATTATTAAAA
1 ATTAAATTATTAAAA
*
2297341 ATTAAATTTTTAAAA
1 ATTAAATTATTAAAA
2297356 A
1 A
2297357 GTATATCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAATTATTAAAA
Found at i:2298533 original size:21 final size:21
Alignment explanation
Indices: 2298499--2298548 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 21
2298489 TTTTATTATT
2298499 AATTATATAATTTTTTAAAAA-A
1 AATTAT-T-ATTTTTTAAAAATA
*
2298521 AATTATTATTTTTTAAAAATT
1 AATTATTATTTTTTAAAAATA
2298542 AATTATT
1 AATTATT
2298549 TTATATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 12 0.46
21 8 0.31
22 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTATTATTTTTTAAAAATA
Found at i:2298776 original size:6 final size:6
Alignment explanation
Indices: 2298765--2298790 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2298755 TATTTATAGC
2298765 CAAATG CAAATG CAAATG CAAATG CA
1 CAAATG CAAATG CAAATG CAAATG CA
2298791 TCCTTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.15
Consensus pattern (6 bp):
CAAATG
Found at i:2304665 original size:2 final size:2
Alignment explanation
Indices: 2304658--2304694 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2304648 TTATAGTTAA
* *
2304658 AT AT AT AT TT AT CT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2304695 CACACACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2316234 original size:19 final size:18
Alignment explanation
Indices: 2316212--2316279 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
2316202 ATTTTTTATA
2316212 TATTTATTTATTTGTATTG
1 TATTTATTTATTT-TATTG
* *
2316231 TATTAATATTATTTTTTTG
1 TATTTAT-TTATTTTATTG
*
2316250 TATTATATTATATTTTAAT-
1 TATT-TATT-TATTTTATTG
*
2316269 TATTTTTTTAT
1 TATTTATTTAT
2316280 ATATATTTTA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 3 0.08
18 3 0.08
19 19 0.47
20 15 0.38
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.69
Consensus pattern (18 bp):
TATTTATTTATTTTATTG
Found at i:2316249 original size:24 final size:23
Alignment explanation
Indices: 2316207--2316263 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
2316197 TATAAATTTT
2316207 TTATA-TAT-TTATTTATTTGTA
1 TTATATTATATTATTTATTTGTA
* *
2316228 TTGTATTAATATTATTTTTTTGTA
1 TTATATT-ATATTATTTATTTGTA
2316252 TTATATTATATT
1 TTATATTATATT
2316264 TTAATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 1 0.03
23 7 0.23
24 18 0.60
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTATATTATATTATTTATTTGTA
Found at i:2316263 original size:29 final size:30
Alignment explanation
Indices: 2316238--2316293 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
2316228 TTGTATTAAT
* *
2316238 ATTATTTTTTTGTAT-TATATTATATTTTA
1 ATTATTTTTTTATATATATATTATATTATA
*
2316267 ATTATTTTTTTATATATATTTTATATT
1 ATTATTTTTTTATATATATATTATATT
2316294 CAAATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (30 bp):
ATTATTTTTTTATATATATATTATATTATA
Found at i:2316290 original size:11 final size:12
Alignment explanation
Indices: 2316252--2316293 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 12
2316242 TTTTTTTGTA
2316252 TTATATTATATT
1 TTATATTATATT
2316264 TTA-ATTAT-TT
1 TTATATTATATT
*
2316274 TTTTATATATATT
1 TTATAT-TATATT
2316287 TTATATT
1 TTATATT
2316294 CAAATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 4 0.16
11 7 0.28
12 7 0.28
13 7 0.28
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATATTATATT
Found at i:2318767 original size:47 final size:47
Alignment explanation
Indices: 2318699--2318802 Score: 165
Period size: 47 Copynumber: 2.2 Consensus size: 47
2318689 ATTTGTTTGA
* * *
2318699 ATGGTAA-ATTGTCTGTCACTTTGCTTGTTTTGTTCATCTGATCTTC
1 ATGGTAATATTATCTATCACTTTGCTTCTTTTGTTCATCTGATCTTC
2318745 ATGGTAATATTATCTATCACTTTGCTTCTTTTGTTCATCTGATCTTC
1 ATGGTAATATTATCTATCACTTTGCTTCTTTTGTTCATCTGATCTTC
*
2318792 ATTGTAATATT
1 ATGGTAATATT
2318803 GTCTGTCAGT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 7 0.13
47 46 0.87
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.51
Consensus pattern (47 bp):
ATGGTAATATTATCTATCACTTTGCTTCTTTTGTTCATCTGATCTTC
Found at i:2325209 original size:16 final size:16
Alignment explanation
Indices: 2325188--2325220 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2325178 GAATTGCTTC
2325188 ATCATTTGTTAATACA
1 ATCATTTGTTAATACA
2325204 ATCATTTGTTAATACA
1 ATCATTTGTTAATACA
2325220 A
1 A
2325221 AGCTTCTGCT
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:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
ATCATTTGTTAATACA
Found at i:2326665 original size:2 final size:2
Alignment explanation
Indices: 2326660--2326702 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2326650 TGTGTGACAA
*
2326660 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2326702 A
1 A
2326703 CCTGTGACAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2331804 original size:15 final size:15
Alignment explanation
Indices: 2331784--2331815 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2331774 AAAAAAAGGT
*
2331784 AGAACTATTAATCTG
1 AGAACTATGAATCTG
2331799 AGAACTATGAATCTG
1 AGAACTATGAATCTG
2331814 AG
1 AG
2331816 TTATATACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (15 bp):
AGAACTATGAATCTG
Found at i:2332564 original size:21 final size:23
Alignment explanation
Indices: 2332530--2332571 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
2332520 CCTTTGACAG
*
2332530 AAAAAAATAGAAATT-AAAATTT
1 AAAAAAATACAAATTCAAAATTT
2332552 AAAAAAAT-CAAATTCAAAAT
1 AAAAAAATACAAATTCAAAAT
2332572 CCGATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (23 bp):
AAAAAAATACAAATTCAAAATTT
Found at i:2333619 original size:22 final size:23
Alignment explanation
Indices: 2333576--2333636 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
2333566 TACTTTATAC
*
2333576 ATAAAAAAATAAAA-ATATTTTA
1 ATAAAATAATAAAATATATTTTA
2333598 ATAAAATAATAAAATATA-TTTA
1 ATAAAATAATAAAATATATTTTA
* *
2333620 AAAATAATAATTAAATA
1 ATAA-AATAATAAAATA
2333637 AGATAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
ATAAAATAATAAAATATATTTTA
Found at i:2333628 original size:23 final size:21
Alignment explanation
Indices: 2333577--2333636 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
2333567 ACTTTATACA
2333577 TAAAAAAAT-A-AAAATATTT
1 TAAAAAAATAATAAAATATTT
*
2333596 TAATAAAATAATAAAATATATT
1 TAAAAAAATAATAAAATAT-TT
*
2333618 TAAAAATAATAATTAAATA
1 TAAAAA-AATAATAAAATA
2333637 AGATAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 8 0.24
20 1 0.03
21 7 0.21
22 7 0.21
23 11 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAAATAATAAAATATTT
Found at i:2334696 original size:5 final size:5
Alignment explanation
Indices: 2334687--2334733 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
2334677 CTTTTTTTTA
* *
2334687 ATAAT TTAAT ATAAT ATAAT ATAATT ATAAA AT-AT ATAAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAA-T ATAAT ATAAT AT-AAT ATAAT A
2334734 AAATTTAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 3 0.09
5 23 0.66
6 9 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:2334716 original size:26 final size:26
Alignment explanation
Indices: 2334695--2334830 Score: 72
Period size: 26 Copynumber: 5.3 Consensus size: 26
2334685 TAATAATTTA
*
2334695 ATAT-AATATAATATAATTATAAAAT
1 ATATAAATATAATAAAATTATAAAAT
* *
2334720 ATATAAATATAATAAAATTTAGTTAAGT
1 ATATAAATATAATAAAA-TTA-TAAAAT
* * *
2334748 CTATAATATTTAATTATAATTATGAAAA-
1 ATATAA-ATATAA-TAAAATTAT-AAAAT
*
2334776 A-AT-AATATAA-ATAATTATATAAAT
1 ATATAAATATAATAAAATTATA-AAAT
**
2334800 GCATAAATTATAAT-AAA-TATAAAA-
1 ATATAAA-TATAATAAAATTATAAAAT
2334824 ATATAAA
1 ATATAAA
2334831 ATGACGATTC
Statistics
Matches: 85, Mismatches: 14, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
22 1 0.01
23 11 0.13
24 5 0.06
25 14 0.16
26 18 0.21
27 12 0.14
28 10 0.12
29 10 0.12
30 4 0.05
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (26 bp):
ATATAAATATAATAAAATTATAAAAT
Found at i:2335499 original size:3 final size:3
Alignment explanation
Indices: 2335491--2335531 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2335481 TAACATTATC
2335491 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2335532 ATGGTTAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2336158 original size:9 final size:8
Alignment explanation
Indices: 2336133--2336161 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
2336123 TTTTTTGAAT
2336133 AAAAAT-A
1 AAAAATAA
2336140 AAAAATAA
1 AAAAATAA
2336148 AAAAATAA
1 AAAAATAA
2336156 AAAAAT
1 AAAAAT
2336162 TAGTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:2347704 original size:2 final size:2
Alignment explanation
Indices: 2347699--2347758 Score: 59
Period size: 2 Copynumber: 30.5 Consensus size: 2
2347689 CCCCCCCCTA
* * * * * *
2347699 TC TC TC TC TC TC TC TC TC TC TC TC -C CC CC CC CC CC TA TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2347740 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
2347759 ATATATATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.02, C:0.57, G:0.00, T:0.42
Consensus pattern (2 bp):
TC
Found at i:2347735 original size:37 final size:37
Alignment explanation
Indices: 2347685--2347758 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2347675 AAGTTCAATA
2347685 CCCCCCCCCCCCTATCTCTCTCTCTCTCTCTCTCTCT
1 CCCCCCCCCCCCTATCTCTCTCTCTCTCTCTCTCTCT
2347722 CCCCCCCCCCCCTATCTCTCTCTCTCTCTCTCTCTCT
1 CCCCCCCCCCCCTATCTCTCTCTCTCTCTCTCTCTCT
2347759 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.03, C:0.62, G:0.00, T:0.35
Consensus pattern (37 bp):
CCCCCCCCCCCCTATCTCTCTCTCTCTCTCTCTCTCT
Found at i:2347763 original size:2 final size:2
Alignment explanation
Indices: 2347758--2347790 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2347748 TCTCTCTCTC
2347758 TA TA 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 TA TA T
2347791 TTCTTCCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2348431 original size:3 final size:3
Alignment explanation
Indices: 2348423--2348448 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2348413 CATGCGTTAA
2348423 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2348449 CTGTAAGAGG
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:2348582 original size:26 final size:23
Alignment explanation
Indices: 2348546--2348594 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 23
2348536 GAAAACATTA
2348546 AAAAATATTTTATATTAATATTAAAT
1 AAAAATATTTTA-ATT-AT-TTAAAT
2348572 AAAAATATTTTAATTATTTAAAT
1 AAAAATATTTTAATTATTTAAAT
2348595 TGTAATTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.26
24 2 0.09
25 3 0.13
26 12 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAAATATTTTAATTATTTAAAT
Found at i:2352934 original size:19 final size:19
Alignment explanation
Indices: 2352912--2352952 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2352902 TATTTGATAT
* *
2352912 AAATATTTTTATTTTTTTA
1 AAATATTTTTATGTATTTA
*
2352931 AAATTTTTTTATGTATTTA
1 AAATATTTTTATGTATTTA
2352950 AAA
1 AAA
2352953 AAAAATATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
AAATATTTTTATGTATTTA
Found at i:2353995 original size:50 final size:50
Alignment explanation
Indices: 2353919--2354036 Score: 166
Period size: 50 Copynumber: 2.4 Consensus size: 50
2353909 AGATGCTTAG
* * *
2353919 AGTCAATAATTACGATCACCTTTCTCTATTATCAAAGGTTGGT-AATGAAT
1 AGTCAACAATTACGGTCACCTCTCTCTATTATCAAAGGTTGGTGAA-GAAT
* *
2353969 AGTCAACAATTACGGTTACCTCTCTCTATTATCAAATGTTGGTGAAGAAT
1 AGTCAACAATTACGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAAT
*
2354019 AATCAACAATTACGGTCA
1 AGTCAACAATTACGGTCA
2354037 GGTTGGTGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 58 0.97
51 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (50 bp):
AGTCAACAATTACGGTCACCTCTCTCTATTATCAAAGGTTGGTGAAGAAT
Found at i:2357299 original size:19 final size:19
Alignment explanation
Indices: 2357273--2357311 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2357263 ACGACTCAAC
*
2357273 TTTATTTTCT-CCACTCTT
1 TTTATTTTCTAACACTCTT
2357291 TTTATTTTTCTAACACTCTT
1 TTTA-TTTTCTAACACTCTT
2357311 T
1 T
2357312 CTTAATGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 6 0.33
20 8 0.44
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTTTCTAACACTCTT
Found at i:2360244 original size:13 final size:13
Alignment explanation
Indices: 2360228--2360261 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2360218 GATAAATTAG
2360228 TAATTAAAATAAA
1 TAATTAAAATAAA
*
2360241 TAATTAAAATAGA
1 TAATTAAAATAAA
2360254 TAATTAAA
1 TAATTAAA
2360262 TTATAGAATA
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:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (13 bp):
TAATTAAAATAAA
Found at i:2361252 original size:28 final size:27
Alignment explanation
Indices: 2361178--2361253 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
2361168 ACATAAACAT
* *
2361178 AAATTTTAAT-TTATATAATTATTTTTA
1 AAATTTTAATATTA-ATAATTAATATTA
*
2361205 AAA-ATTAATATTTAATTAATATAATATTA
1 AAATTTTAATA-TTAA-TAAT-TAATATTA
2361234 AAATTTTAATATTAATAATT
1 AAATTTTAATATTAATAATT
2361254 CATTACGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
26 5 0.12
27 5 0.12
28 11 0.28
29 13 0.32
30 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATTTTAATATTAATAATTAATATTA
Found at i:2364926 original size:3 final size:3
Alignment explanation
Indices: 2364918--2364963 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2364908 AATTCTTGTT
2364918 TTA 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 TTA T
2364964 CAAAGATGCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2367076 original size:2 final size:2
Alignment explanation
Indices: 2367069--2367100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2367059 AGGCTAAAGA
2367069 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
2367101 GTGTGTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2371934 original size:21 final size:19
Alignment explanation
Indices: 2371910--2371954 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
2371900 TGTCTCACAC
*
2371910 AAATATAATATAAAAAAATTA
1 AAATATAACAT-AAAAAA-TA
*
2371931 AAATATGACATAAAAAATA
1 AAATATAACATAAAAAATA
2371950 AAATA
1 AAATA
2371955 ACTATAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 6 0.27
21 9 0.41
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATATAACATAAAAAATA
Found at i:2372958 original size:28 final size:28
Alignment explanation
Indices: 2372917--2372983 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
2372907 GTTAAAATTT
* * *
2372917 ATATAAAAATAATATTTTAAATTTAATTATA
1 ATATAAAAATAATA---TAAATATAATAAAA
2372948 ATATAAAAATAATATAAATATAATAAAA
1 ATATAAAAATAATATAAATATAATAAAA
2372976 ATATAAAA
1 ATATAAAA
2372984 CAAAATTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 19 0.58
31 14 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
ATATAAAAATAATATAAATATAATAAAA
Found at i:2372978 original size:17 final size:17
Alignment explanation
Indices: 2372947--2372982 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2372937 ATTTAATTAT
2372947 AATATAAAAATAATATA
1 AATATAAAAATAATATA
2372964 AATATAATAAA-AATATA
1 AATATAA-AAATAATATA
2372981 AA
1 AA
2372983 ACAAAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
AATATAAAAATAATATA
Found at i:2372993 original size:28 final size:27
Alignment explanation
Indices: 2372933--2372993 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
2372923 AAATAATATT
* * * *
2372933 TTAAATTTAATTATAATATAAAAATAA
1 TTAAATATAATAAAAATATAAAAAAAA
2372960 TATAAATATAATAAAAATATAAAACAAAA
1 T-TAAATATAATAAAAATATAAAA-AAAA
2372989 TTAAA
1 TTAAA
2372994 AACTAAGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.04
28 23 0.82
29 4 0.14
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TTAAATATAATAAAAATATAAAAAAAA
Found at i:2373229 original size:15 final size:16
Alignment explanation
Indices: 2373193--2373236 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
2373183 TTGGTTGAAA
2373193 TAATAT-TTATTATTT
1 TAATATATTATTATTT
2373208 T-AT-TATTATT-TTT
1 TAATATATTATTATTT
2373221 TAATATATTAATTATT
1 TAATATATT-ATTATT
2373237 ATTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.21
14 9 0.38
15 5 0.21
16 3 0.12
17 2 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TAATATATTATTATTT
Found at i:2373229 original size:23 final size:24
Alignment explanation
Indices: 2373203--2373259 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
2373193 TAATATTTAT
2373203 TATTTTATTATTATTTTTTA-ATA
1 TATTTTATTATTATTTTTTATATA
*
2373226 TA-TTAATTATTATTTTTTATATA
1 TATTTTATTATTATTTTTTATATA
2373249 TAATATTTATT
1 T-AT-TTTATT
2373260 TATAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 16 0.57
23 6 0.21
24 1 0.04
26 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTTATTATTATTTTTTATATA
Found at i:2373234 original size:22 final size:23
Alignment explanation
Indices: 2373209--2373259 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 23
2373199 TTATTATTTT
*
2373209 ATTATTATTTTTTA-ATATATTA
1 ATTATTATTTTTTATATATAATA
2373231 ATTATTATTTTTTATATATAATA
1 ATTATTATTTTTTATATATAATA
*
2373254 TTTATT
1 ATTATT
2373260 TATAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTATTATTTTTTATATATAATA
Found at i:2374516 original size:17 final size:17
Alignment explanation
Indices: 2374476--2374518 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2374466 ATATTTATTT
*
2374476 TATTA-ATTTATTTAAA
1 TATTATATTTTTTTAAA
*
2374492 -AATATATTTTTTTAAA
1 TATTATATTTTTTTAAA
2374508 TATTATATTTT
1 TATTATATTTT
2374519 CATTAAGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 10 0.45
17 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATATTTTTTTAAA
Found at i:2375062 original size:2 final size:2
Alignment explanation
Indices: 2375055--2375082 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2375045 TTATATTGCC
2375055 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2375083 GGTTATAGAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2381578 original size:21 final size:21
Alignment explanation
Indices: 2381552--2381597 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2381542 ATATAATTAT
*
2381552 TTTTAAAAAATAATATTTAAA
1 TTTTAAAAAATAATATTAAAA
***
2381573 TTTTAAATTTTAATATTAAAA
1 TTTTAAAAAATAATATTAAAA
2381594 TTTT
1 TTTT
2381598 TTTAAATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTTAAAAAATAATATTAAAA
Found at i:2381606 original size:16 final size:18
Alignment explanation
Indices: 2381580--2381617 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2381570 AAATTTTAAA
2381580 TTTTAATATTA-AAATTT
1 TTTTAATATTATAAATTT
*
2381597 TTTTAA-ATTATAACTTT
1 TTTTAATATTATAAATTT
2381614 TTTT
1 TTTT
2381618 TTCGTAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAATATTATAAATTT
Found at i:2383144 original size:2 final size:2
Alignment explanation
Indices: 2383137--2383163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2383127 TTGGATCATT
2383137 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 T
2383164 GAATATTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2383293 original size:12 final size:12
Alignment explanation
Indices: 2383267--2383323 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
2383257 AAAATTATTT
* *
2383267 TATTTTTTAATA
1 TATTTTATAAAA
2383279 TATTTTATAAAA
1 TATTTTATAAAA
* *
2383291 TATATTATAAAT
1 TATTTTATAAAA
*
2383303 TTTATTTATAAAA
1 TAT-TTTATAAAA
*
2383316 TTTTTTAT
1 TATTTTAT
2383324 TTTATTATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
12 27 0.73
13 10 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTATAAAA
Found at i:2383313 original size:13 final size:13
Alignment explanation
Indices: 2383282--2383323 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
2383272 TTTAATATAT
*
2383282 TTTATAAAATATA
1 TTTATAAAATTTA
*
2383295 -TTATAAATTTTA
1 TTTATAAAATTTA
2383307 TTTATAAAATTT-
1 TTTATAAAATTTA
2383319 TTTAT
1 TTTAT
2383324 TTTATTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTATAAAATTTA
Found at i:2383325 original size:21 final size:20
Alignment explanation
Indices: 2383301--2383354 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
2383291 TATATTATAA
* **
2383301 ATTTTATTTATAAAATTTTTT
1 ATTTTA-TTATAAAAATAATT
2383322 ATTTTATTATTAAAAATAATT
1 ATTTTATTA-TAAAAATAATT
2383343 ATTTTATTATAA
1 ATTTTATTATAA
2383355 TTTTATTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTATTATAAAAATAATT
Found at i:2394316 original size:110 final size:110
Alignment explanation
Indices: 2394123--2394346 Score: 448
Period size: 110 Copynumber: 2.0 Consensus size: 110
2394113 GGCTGAAAGT
2394123 GTTTTGGATAGGCGATCAACTTTAGGGTATTGTACTTAAGTCTGGGGTAATCTTGTCACGTGGAG
1 GTTTTGGATAGGCGATCAACTTTAGGGTATTGTACTTAAGTCTGGGGTAATCTTGTCACGTGGAG
2394188 AAGTAAGAAACAACAAGTTGTAGCTCGCAGTAGTGCAGAAGCTGA
66 AAGTAAGAAACAACAAGTTGTAGCTCGCAGTAGTGCAGAAGCTGA
2394233 GTTTTGGATAGGCGATCAACTTTAGGGTATTGTACTTAAGTCTGGGGTAATCTTGTCACGTGGAG
1 GTTTTGGATAGGCGATCAACTTTAGGGTATTGTACTTAAGTCTGGGGTAATCTTGTCACGTGGAG
2394298 AAGTAAGAAACAACAAGTTGTAGCTCGCAGTAGTGCAGAAGCTGA
66 AAGTAAGAAACAACAAGTTGTAGCTCGCAGTAGTGCAGAAGCTGA
2394343 GTTT
1 GTTT
2394347 CGCGCCATGG
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 114 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (110 bp):
GTTTTGGATAGGCGATCAACTTTAGGGTATTGTACTTAAGTCTGGGGTAATCTTGTCACGTGGAG
AAGTAAGAAACAACAAGTTGTAGCTCGCAGTAGTGCAGAAGCTGA
Found at i:2405526 original size:134 final size:134
Alignment explanation
Indices: 2405296--2405567 Score: 535
Period size: 134 Copynumber: 2.0 Consensus size: 134
2405286 CAAACAAGTT
*
2405296 TGGTGCATCAAGATCACAGTCATAATTCACATAAATATCAACAAGCATCTGGGGTTCTCTGCAAA
1 TGGTACATCAAGATCACAGTCATAATTCACATAAATATCAACAAGCATCTGGGGTTCTCTGCAAA
2405361 CTTTCTCAAGCATCCTAAAAAAATAAAATTAAAAAGATTAGCTAATATAGAGCAAATAGCAAACT
66 CTTTCTCAAGCATCCTAAAAAAATAAAATTAAAAAGATTAGCTAATATAGAGCAAATAGCAAACT
2405426 AGCA
131 AGCA
2405430 TGGTACATCAAGATCACAGTCATAATTCACATAAATATCAACAAGCATCTGGGGTTCTCTGCAAA
1 TGGTACATCAAGATCACAGTCATAATTCACATAAATATCAACAAGCATCTGGGGTTCTCTGCAAA
2405495 CTTTCTCAAGCATCCTAAAAAAATAAAATTAAAAAGATTAGCTAATATAGAGCAAATAGCAAACT
66 CTTTCTCAAGCATCCTAAAAAAATAAAATTAAAAAGATTAGCTAATATAGAGCAAATAGCAAACT
2405560 AGCA
131 AGCA
2405564 TGGT
1 TGGT
2405568 GACGACAATA
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
134 137 1.00
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (134 bp):
TGGTACATCAAGATCACAGTCATAATTCACATAAATATCAACAAGCATCTGGGGTTCTCTGCAAA
CTTTCTCAAGCATCCTAAAAAAATAAAATTAAAAAGATTAGCTAATATAGAGCAAATAGCAAACT
AGCA
Found at i:2411520 original size:2 final size:2
Alignment explanation
Indices: 2411513--2411541 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2411503 TTTATGAACA
2411513 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2411542 AAGTGACAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2413823 original size:17 final size:16
Alignment explanation
Indices: 2413803--2413855 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 16
2413793 ATTTAAATTT
2413803 TTTTATATTTATATAAA
1 TTTTATA-TTATATAAA
2413820 TTTTATAAATTA-A-AAA
1 TTTTAT--ATTATATAAA
2413836 -TTTATATTATATAAA
1 TTTTATATTATATAAA
2413851 TTTTA
1 TTTTA
2413856 AAATATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
13 4 0.13
14 1 0.03
15 8 0.26
16 7 0.23
17 7 0.23
18 3 0.10
19 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTATATTATATAAA
Found at i:2413849 original size:22 final size:24
Alignment explanation
Indices: 2413823--2413872 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2413813 ATATAAATTT
2413823 TATAAA-TTAAAAAT-TTATATTA
1 TATAAATTTAAAAATATTATATTA
*
2413845 TATAAATTTTAAAATATTATATTA
1 TATAAATTTAAAAATATTATATTA
2413869 TATA
1 TATA
2413873 TTTTATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 6 0.24
23 7 0.28
24 12 0.48
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TATAAATTTAAAAATATTATATTA
Found at i:2414644 original size:22 final size:24
Alignment explanation
Indices: 2414596--2414654 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 24
2414586 TAAAAACTAT
*
2414596 TTTTATAATTAATTTAAATATATA
1 TTTTATAATTAATTCAAATATATA
2414620 TTTT-TAATT-ATTCAAATA-ATAA
1 TTTTATAATTAATTCAAATATAT-A
*
2414642 TTTTACAA-TAATT
1 TTTTATAATTAATT
2414655 TAACTTGACT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 14 0.47
23 10 0.33
24 4 0.13
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTATAATTAATTCAAATATATA
Found at i:2415149 original size:2 final size:2
Alignment explanation
Indices: 2415138--2415166 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2415128 TGACGAACAC
2415138 AT AT -T 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
2415167 TATCTTATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2416133 original size:15 final size:15
Alignment explanation
Indices: 2416088--2416134 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
2416078 AAAAAATAAA
2416088 AAATGTTGATA-TTT
1 AAATGTTGATATTTT
* * *
2416102 GAATTTTGATATGTT
1 AAATGTTGATATTTT
*
2416117 AAATGTTAATATTTT
1 AAATGTTGATATTTT
2416132 AAA
1 AAA
2416135 AATAATTATA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (15 bp):
AAATGTTGATATTTT
Found at i:2417333 original size:50 final size:50
Alignment explanation
Indices: 2417248--2417345 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 50
2417238 GAAATTGATG
* * * *
2417248 TGGTTCGAAGGAGTTAAAGCAAGACCATGAGACAAACGGATCAATACAGA
1 TGGTCCGAAAGAGTTAAAACAAGACCACGAGACAAACGGATCAATACAGA
* * *
2417298 TGGTCCGAAAGAGTTAAAACATGATCACGAGACAAACGGATTAATACA
1 TGGTCCGAAAGAGTTAAAACAAGACCACGAGACAAACGGATCAATACA
2417346 AATCAGGGCC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.43, C:0.16, G:0.23, T:0.17
Consensus pattern (50 bp):
TGGTCCGAAAGAGTTAAAACAAGACCACGAGACAAACGGATCAATACAGA
Found at i:2417872 original size:2 final size:2
Alignment explanation
Indices: 2417865--2417889 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2417855 ACTACACATC
2417865 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2417890 AAGCGGTACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2420066 original size:26 final size:26
Alignment explanation
Indices: 2420037--2420088 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
2420027 TCTATTTTTA
* *
2420037 ATTATAAAATATATATTAACAAATAT
1 ATTATAAAATAAATATTAAAAAATAT
**
2420063 ATTATAATGTAAATATTAAAAAATAT
1 ATTATAAAATAAATATTAAAAAATAT
2420089 GTTAAGTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
ATTATAAAATAAATATTAAAAAATAT
Found at i:2420570 original size:16 final size:15
Alignment explanation
Indices: 2420522--2420567 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
2420512 AATATTAATA
*
2420522 AATATT-TTTAATTT
1 AATATTATTAAATTT
2420536 -ATATTATATAAATTT
1 AATATTAT-TAAATTT
2420551 AATATTATTAAATTT
1 AATATTATTAAATTT
2420566 AA
1 AA
2420568 ATAATACTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.18
14 1 0.04
15 15 0.54
16 7 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
AATATTATTAAATTT
Found at i:2420883 original size:18 final size:16
Alignment explanation
Indices: 2420860--2420899 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
2420850 AATTTATGTG
2420860 ATTAAATTTATATTATAA
1 ATTAAATTT-TATT-TAA
2420878 ATTAAATTTTATTTAA
1 ATTAAATTTTATTTAA
2420894 A-TAAAT
1 ATTAAAT
2420900 AATAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.23
16 4 0.18
17 4 0.18
18 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTAAATTTTATTTAA
Found at i:2420899 original size:33 final size:33
Alignment explanation
Indices: 2420832--2420899 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 33
2420822 ATATCTATTT
* *
2420832 ATTTATATATAATATTATAATTTATGTGATTAA
1 ATTTATATATAATATTATAATTTATGTAAATAA
*
2420865 ATTTATATTATAA-ATTA-AATTTTATTTAAATAA
1 ATTTATA-TATAATATTATAA-TTTATGTAAATAA
2420898 AT
1 AT
2420900 AATAAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
32 2 0.07
33 23 0.77
34 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (33 bp):
ATTTATATATAATATTATAATTTATGTAAATAA
Found at i:2423353 original size:2 final size:2
Alignment explanation
Indices: 2423348--2423382 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2423338 TAGAAATCCT
2423348 TA TA TA 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 TA TA TA T
2423383 TTGATTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2423980 original size:12 final size:11
Alignment explanation
Indices: 2423961--2423993 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
2423951 TGAATGTTTG
2423961 AATTATATTAA
1 AATTATATTAA
2423972 AACTTATA-TAA
1 AA-TTATATTAA
2423983 AATTATATTAA
1 AATTATATTAA
2423994 TATATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 5 0.25
11 10 0.50
12 5 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
AATTATATTAA
Found at i:2423997 original size:8 final size:8
Alignment explanation
Indices: 2423976--2424021 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
2423966 TATTAAAACT
2423976 TATATAAAA
1 TATAT-AAA
*
2423985 TTATATTAA
1 -TATATAAA
2423994 TATATAAA
1 TATATAAA
2424002 -ATATAAA
1 TATATAAA
2424009 TATATAAA
1 TATATAAA
2424017 TATAT
1 TATAT
2424022 CTTATAATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 7 0.21
8 19 0.58
9 2 0.06
10 5 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TATATAAA
Found at i:2432518 original size:12 final size:12
Alignment explanation
Indices: 2432501--2432525 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2432491 TTTATTTACC
2432501 AGAAAAAAAAAA
1 AGAAAAAAAAAA
2432513 AGAAAAAAAAAA
1 AGAAAAAAAAAA
2432525 A
1 A
2432526 AGGAGAAGGG
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAA
Found at i:2432521 original size:13 final size:13
Alignment explanation
Indices: 2432503--2432527 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2432493 TATTTACCAG
2432503 AAAAAAAAAAAGA
1 AAAAAAAAAAAGA
2432516 AAAAAAAAAAAG
1 AAAAAAAAAAAG
2432528 GAGAAGGGTC
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAGA
Found at i:2438039 original size:22 final size:21
Alignment explanation
Indices: 2437995--2438039 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
2437985 GGATTTTTTA
* *
2437995 TTTATTATTTCATGAATTTTT
1 TTTATTATTTAATGAATTATT
*
2438016 TTTATATATTTAATGTATTATT
1 TTTAT-TATTTAATGAATTATT
2438038 TT
1 TT
2438040 ACATAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTATTATTTAATGAATTATT
Found at i:2440026 original size:32 final size:32
Alignment explanation
Indices: 2439985--2440048 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
2439975 TACTTGAAAT
2439985 TCTCTCAATTGGATTCAATTGAACTATGTAAA
1 TCTCTCAATTGGATTCAATTGAACTATGTAAA
2440017 TCTCTCAATTGGATTCAATTGAACTATGTAAA
1 TCTCTCAATTGGATTCAATTGAACTATGTAAA
2440049 CTTGTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (32 bp):
TCTCTCAATTGGATTCAATTGAACTATGTAAA
Found at i:2445459 original size:36 final size:36
Alignment explanation
Indices: 2445412--2445486 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
2445402 TTAAACATAA
2445412 TTTATAAGTCTGCTTACTTATGTATATATAAATGTT
1 TTTATAAGTCTGCTTACTTATGTATATATAAATGTT
*
2445448 TTTATAAGTCTGCTTACTTATGTATATATGAATGTT
1 TTTATAAGTCTGCTTACTTATGTATATATAAATGTT
2445484 TTT
1 TTT
2445487 CATCGTGGAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (36 bp):
TTTATAAGTCTGCTTACTTATGTATATATAAATGTT
Found at i:2447830 original size:8 final size:9
Alignment explanation
Indices: 2447806--2447835 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
2447796 TAAATTTAAT
2447806 TATAAAAAA
1 TATAAAAAA
2447815 TATAAAAAA
1 TATAAAAAA
2447824 TATAAAAAA
1 TATAAAAAA
2447833 TAT
1 TAT
2447836 TTTAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
TATAAAAAA
Found at i:2448258 original size:2 final size:2
Alignment explanation
Indices: 2448251--2448280 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2448241 CTGAAACCAA
2448251 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
2448281 CCATGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2460960 original size:17 final size:15
Alignment explanation
Indices: 2460942--2461009 Score: 52
Period size: 16 Copynumber: 4.3 Consensus size: 15
2460932 TATAATAATA
2460942 ATATTTATATAAATTT
1 ATATTTA-ATAAATTT
2460958 AATATATTAAT-AATTT
1 -ATAT-TTAATAAATTT
*
2460974 TTA-TTATATAAATTT
1 ATATTTA-ATAAATTT
2460989 -TATTTTAATTAAATTT
1 ATA-TTTAA-TAAATTT
2461005 ATATT
1 ATATT
2461010 ATTATTTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 3 0.07
14 4 0.09
15 8 0.19
16 17 0.40
17 8 0.19
18 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATTTAATAAATTT
Found at i:2460969 original size:31 final size:32
Alignment explanation
Indices: 2460927--2460988 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
2460917 ATATATATAT
2460927 ATATATATAATAATA-ATATTTATATAAATTTA
1 ATATATATAATAATATATA-TTATATAAATTTA
* *
2460959 ATATAT-TAATAATTTTTATTATATAAATTT
1 ATATATATAATAATATATATTATATAAATTT
2460989 TATTTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
ATATATATAATAATATATATTATATAAATTTA
Found at i:2461004 original size:31 final size:30
Alignment explanation
Indices: 2460946--2461039 Score: 90
Period size: 31 Copynumber: 3.1 Consensus size: 30
2460936 ATAATAATAT
*
2460946 TTATATAAATTTAATATATTAA-TAATTTTTA
1 TTATATAAATTT--TATATTAATTAATTTATA
*
2460977 TTATATAAATTTTATTTTAATTAAATTTATA
1 TTATATAAATTTTATATTAATT-AATTTATA
2461008 TTAT-T--ATTTTATATTAATTTATATTTA-A
1 TTATATAAATTTTATATTAA-TTA-ATTTATA
2461036 TTAT
1 TTAT
2461040 TTTATGTTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
28 17 0.30
29 14 0.25
30 2 0.04
31 23 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (30 bp):
TTATATAAATTTTATATTAATTAATTTATA
Found at i:2461018 original size:23 final size:25
Alignment explanation
Indices: 2460988--2461044 Score: 84
Period size: 23 Copynumber: 2.4 Consensus size: 25
2460978 TATATAAATT
2460988 TTATTTTA-ATTAAATTTATA-TT-A
1 TTATTTTATATT-AATTTATATTTAA
2461011 TTATTTTATATTAATTTATATTTAA
1 TTATTTTATATTAATTTATATTTAA
2461036 TTATTTTAT
1 TTATTTTAT
2461045 GTTATGATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
23 16 0.52
24 5 0.16
25 10 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTTTATATTAATTTATATTTAA
Found at i:2461514 original size:15 final size:15
Alignment explanation
Indices: 2461481--2461542 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
2461471 GATTATTGAA
*
2461481 AATTTATTT-TTTGTA
1 AATTTATTTATTT-TT
2461496 AATTTATTTATTTTT
1 AATTTATTTATTTTT
*
2461511 AATTTCTTTACTTATTT
1 AATTTATTTA-TT-TTT
* *
2461528 AATATATTAATTTTT
1 AATTTATTTATTTTT
2461543 TATGTGTTCG
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 22 0.56
16 7 0.18
17 10 0.26
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (15 bp):
AATTTATTTATTTTT
Found at i:2461716 original size:17 final size:16
Alignment explanation
Indices: 2461653--2461709 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
2461643 TTAATTATGT
2461653 AAATATAAATATAATA
1 AAATATAAATATAATA
* *
2461669 AATTATTAAATATATTA
1 AAATA-TAAATATAATA
* *
2461686 AAATTTAAAATAAAATA
1 AAATAT-AAATATAATA
*
2461703 TAATATA
1 AAATATA
2461710 TATTAAATAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 6 0.19
17 25 0.81
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATAAATATAATA
Found at i:2462764 original size:28 final size:29
Alignment explanation
Indices: 2462720--2462775 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
2462710 TTTGAATTTT
2462720 ATTTTATTTATTTAAATAT-TAAAAATTA
1 ATTTTATTTATTTAAATATATAAAAATTA
*
2462748 ATTTTA-TTATTTAAAATATATTAAAATT
1 ATTTTATTTATTT-AAATATATAAAAATT
2462776 TTTATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 6 0.24
28 12 0.48
29 7 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTTATTTATTTAAATATATAAAAATTA
Found at i:2462785 original size:28 final size:27
Alignment explanation
Indices: 2462721--2462794 Score: 66
Period size: 27 Copynumber: 2.8 Consensus size: 27
2462711 TTGAATTTTA
2462721 TTTTA-TTTATTT-AAATATTAAAAAT
1 TTTTATTTTATTTAAAATATTAAAAAT
* *
2462746 TAATTT-TATTATTTAAAATATATTAAAAT
1 T--TTTATTTTATTTAAAATAT-TAAAAAT
*
2462775 TTTTATTTTATAT-AAATATT
1 TTTTATTTTATTTAAAATATT
2462795 TATATAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 18 0.46
28 12 0.31
29 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTATTTTATTTAAAATATTAAAAAT
Found at i:2465551 original size:21 final size:23
Alignment explanation
Indices: 2465513--2465555 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2465503 AAAGTATGAT
*
2465513 TTAATTTTTTTGGATTTAAAAAA
1 TTAATTTTATTGGATTTAAAAAA
2465536 TTAATTTTATT-G-TTTAAAAA
1 TTAATTTTATTGGATTTAAAAA
2465556 CATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 1 0.05
23 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (23 bp):
TTAATTTTATTGGATTTAAAAAA
Found at i:2466340 original size:19 final size:21
Alignment explanation
Indices: 2466307--2466354 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2466297 AATGCATTTT
2466307 TTATTTATTTTTGAT-ATT-TAA
1 TTATTTA--TTTGATGATTATAA
*
2466328 TTATTTATTTGATGGTTATAA
1 TTATTTATTTGATGATTATAA
2466349 TTATTT
1 TTATTT
2466355 TAATTGTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (21 bp):
TTATTTATTTGATGATTATAA
Found at i:2466504 original size:2 final size:2
Alignment explanation
Indices: 2466497--2466548 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
2466487 TCTTTTTCAA
* * * *
2466497 AT AT AT AT AT AT AT GT AT AT GT AT AT AT AT AT AT AT AA AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2466539 AT AT AT AT AT
1 AT AT AT AT AT
2466549 GAAATAGCAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2466542 original size:16 final size:17
Alignment explanation
Indices: 2466523--2466554 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2466513 ATATGTATAT
2466523 ATATATATAT-AAATAC
1 ATATATATATGAAATAC
2466539 ATATATATATGAAATA
1 ATATATATATGAAATA
2466555 GCAAAAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
ATATATATATGAAATAC
Found at i:2472554 original size:2 final size:2
Alignment explanation
Indices: 2472549--2472587 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2472539 TTTTTATGTT
2472549 TA TA TA TA TA 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 TA TA TA TA TA T
2472588 GTGCGCGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2472903 original size:7 final size:7
Alignment explanation
Indices: 2472883--2472917 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
2472873 TTGAGATGAA
2472883 TTTAAAT
1 TTTAAAT
2472890 ATTTAAAT
1 -TTTAAAT
2472898 TTTAAAT
1 TTTAAAT
2472905 TTTAAA-
1 TTTAAAT
2472911 TTTAAAT
1 TTTAAAT
2472918 ATAAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTTAAAT
Found at i:2472908 original size:14 final size:14
Alignment explanation
Indices: 2472881--2472919 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
2472871 ATTTGAGATG
2472881 AATTTAAATATTTA
1 AATTTAAATATTTA
2472895 AATTTTAAAT-TTTA
1 AA-TTTAAATATTTA
2472909 AATTTAAATAT
1 AATTTAAATAT
2472920 AAATAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 9 0.39
15 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTAAATATTTA
Found at i:2472930 original size:20 final size:20
Alignment explanation
Indices: 2472907--2472951 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
2472897 TTTTAAATTT
2472907 TAAATTTA-AATATAAATAAA
1 TAAATTTATAAT-TAAATAAA
*
2472927 TAAATTTATAATTGAATAAA
1 TAAATTTATAATTAAATAAA
2472947 -AAATT
1 TAAATT
2472952 GAATTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 15 0.65
21 3 0.13
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAATTTATAATTAAATAAA
Found at i:2473052 original size:23 final size:23
Alignment explanation
Indices: 2472998--2473056 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
2472988 TAAGATCAAG
* * *
2472998 TAATTAAATTTTTTAATTCAAATT
1 TAATTAAA-TTTTAAAATAAAATT
*
2473022 AAACTTAAATTTTAAAATAAAATT
1 TAA-TTAAATTTTAAAATAAAATT
2473046 TAATTAAATTT
1 TAATTAAATTT
2473057 AAATTATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 8 0.28
24 16 0.55
25 5 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATTAAATTTTAAAATAAAATT
Found at i:2473220 original size:28 final size:27
Alignment explanation
Indices: 2473163--2473222 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 27
2473153 ATTTATATTA
*
2473163 TTATTTTTAAAAATAATATTTAATAAAT
1 TTATTTTTAAAAATAAAATTTAAT-AAT
2473191 TTATTTTTAAAAAATTAAAATTTAAT-AT
1 TTATTTTT-AAAAA-TAAAATTTAATAAT
2473219 TTAT
1 TTAT
2473223 AATTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 14 0.48
29 5 0.17
30 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTATTTTTAAAAATAAAATTTAATAAT
Found at i:2473250 original size:2 final size:2
Alignment explanation
Indices: 2473243--2473276 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2473233 TCATTAATAA
2473243 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
2473277 GGATATGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2473479 original size:17 final size:17
Alignment explanation
Indices: 2473457--2473517 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
2473447 CCATTTTATT
2473457 AAAATATTAATATATAG
1 AAAATATTAATATATAG
* * *
2473474 AAAATATTTATTTTTAG
1 AAAATATTAATATATAG
* *
2473491 AAGATA-TAATAATTATAT
1 AAAATATTAAT-A-TATAG
2473509 AAAATATTA
1 AAAATATTA
2473518 TTATTAAACA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
16 3 0.09
17 19 0.59
18 8 0.25
19 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (17 bp):
AAAATATTAATATATAG
Found at i:2473874 original size:18 final size:19
Alignment explanation
Indices: 2473821--2473876 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
2473811 AATTTTATTT
*
2473821 TATTTTTATAATTAAATAC
1 TATTTTTATAATAAAATAC
* *
2473840 TCAATTTT-CAATAAAAATA-
1 T-ATTTTTATAAT-AAAATAC
2473859 TATTTTTATAATAAAATA
1 TATTTTTATAATAAAATA
2473877 ACATTTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
18 11 0.38
19 8 0.28
20 10 0.34
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
TATTTTTATAATAAAATAC
Found at i:2481547 original size:2 final size:2
Alignment explanation
Indices: 2481538--2481583 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2481528 AAACTGTTAA
2481538 AT AT -T 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
2481579 AT AT A
1 AT AT A
2481584 ACTACAAACC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2484785 original size:23 final size:23
Alignment explanation
Indices: 2484755--2484809 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
2484745 CCCTAATTCC
2484755 AAATCAAATAAAATTTTCTTAGA
1 AAATCAAATAAAATTTTCTTAGA
2484778 AAATCAAATAAAATTTTCTTAGA
1 AAATCAAATAAAATTTTCTTAGA
2484801 AAATCAAAT
1 AAATCAAAT
2484810 CTATAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATCAAATAAAATTTTCTTAGA
Done.