Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold60
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: 3815296
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 18690 characters in sequence are not A, C, G, or T
File 15 of 21
Found at i:2266591 original size:16 final size:17
Alignment explanation
Indices: 2266546--2266592 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
2266536 ACGTCATATC
*
2266546 ATATTTAA-AATATTAT
1 ATATTTAATAATTTTAT
*
2266562 ATAATTATATAATTTTA-
1 ATATTTA-ATAATTTTAT
2266579 ATATTTAATAATTT
1 ATATTTAATAATTT
2266593 AAAATATTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 13 0.50
17 7 0.27
18 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTTAATAATTTTAT
Found at i:2269973 original size:14 final size:13
Alignment explanation
Indices: 2269949--2269978 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
2269939 CTCAAACTTT
2269949 TATTTTATTTAAA
1 TATTTTATTTAAA
2269962 TATTTATATTTAAA
1 TATTT-TATTTAAA
2269976 TAT
1 TAT
2269979 GATATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTTATTTAAA
Found at i:2273725 original size:22 final size:24
Alignment explanation
Indices: 2273675--2273730 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
2273665 TTATTTAAAA
2273675 TATATTAAAATATTAATAATATTTT
1 TATATT-AAATATTAATAATATTTT
2273700 TATATTAAAT-TT-AT-ATATATTT
1 TATATTAAATATTAATAATAT-TTT
*
2273722 TATAATAAA
1 TATATTAAA
2273731 AAATAATTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 4 0.14
22 13 0.45
23 2 0.07
24 4 0.14
25 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TATATTAAATATTAATAATATTTT
Found at i:2274237 original size:20 final size:20
Alignment explanation
Indices: 2274212--2274249 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2274202 TAAAAATAAT
2274212 TAAAAATTATTTTTAAAATA
1 TAAAAATTATTTTTAAAATA
*
2274232 TAAAAATTTTTTTTAAAA
1 TAAAAATTATTTTTAAAA
2274250 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAAATTATTTTTAAAATA
Found at i:2274350 original size:32 final size:34
Alignment explanation
Indices: 2274311--2274387 Score: 90
Period size: 32 Copynumber: 2.4 Consensus size: 34
2274301 TTATAAAATT
*
2274311 TTAAAAATAAAATTTATTTTTATAT-T-ATT-AAA
1 TTAAAAATAAAATTTATTTTCA-ATGTAATTAAAA
**
2274343 TTAAAAATAATGTTTATTTTCAATGTAATTAAAA
1 TTAAAAATAAAATTTATTTTCAATGTAATTAAAA
2274377 TT-AAAATAAAA
1 TTAAAAATAAAA
2274388 AATATATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
31 2 0.05
32 20 0.54
33 10 0.27
34 5 0.14
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (34 bp):
TTAAAAATAAAATTTATTTTCAATGTAATTAAAA
Found at i:2274350 original size:57 final size:57
Alignment explanation
Indices: 2274241--2274357 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 57
2274231 ATAAAAATTT
* * * *
2274241 TTTTTAAAAATTTTTAAAATAAAATATTATTCTTAATGATCATTTTTTAAAATCATG
1 TTTTTAAAAATTTTAAAAATAAAATATTATTCTTAATGATCATTATTAAAAATAATG
* *
2274298 TTTTTATAAAATTTTAAAAATAAAAT-TTATT-TTTAT-ATTATTAAATTAAAAATAATG
1 TTTTTA-AAAATTTTAAAAATAAAATATTATTCTTAATGATCATT--ATTAAAAATAATG
2274355 TTT
1 TTT
2274358 ATTTTCAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
55 5 0.10
56 4 0.08
57 24 0.47
58 18 0.35
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (57 bp):
TTTTTAAAAATTTTAAAAATAAAATATTATTCTTAATGATCATTATTAAAAATAATG
Found at i:2274461 original size:18 final size:18
Alignment explanation
Indices: 2274422--2274462 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
2274412 TCGTCTTTAA
*
2274422 AAATTATTTCTTTATAAT
1 AAATAATTTCTTTATAAT
2274440 -AATAATTT-TTTATATAT
1 AAATAATTTCTTTATA-AT
2274457 AAATAA
1 AAATAA
2274463 GTTCAGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 6 0.30
17 9 0.45
18 5 0.25
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATAATTTCTTTATAAT
Found at i:2276288 original size:19 final size:21
Alignment explanation
Indices: 2276250--2276289 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2276240 GCCCTAAATA
*
2276250 AAAGTAATATAAGAGGCCCTG
1 AAAGTAACATAAGAGGCCCTG
2276271 AAAGTAACAT-AG-GGCCCTG
1 AAAGTAACATAAGAGGCCCTG
2276290 GGTTGTGCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
21 9 0.50
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AAAGTAACATAAGAGGCCCTG
Found at i:2278410 original size:3 final size:3
Alignment explanation
Indices: 2278404--2278436 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2278394 TTAGGACATG
2278404 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2278437 ATTACTGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2279635 original size:14 final size:15
Alignment explanation
Indices: 2279612--2279653 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
2279602 AATATTATAA
2279612 AAAAATTAAATTTAT
1 AAAAATTAAATTTAT
* *
2279627 -AATATTAAATATAT
1 AAAAATTAAATTTAT
2279641 AAAAATTAAATTT
1 AAAAATTAAATTT
2279654 TTTTAATATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAAATTAAATTTAT
Found at i:2279865 original size:22 final size:21
Alignment explanation
Indices: 2279825--2279866 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2279815 TGATGGACAG
*
2279825 TAAATAAATAATTATGAAATA
1 TAAAAAAATAATTATGAAATA
2279846 TAAAAAAATAATATATGAAAT
1 TAAAAAAATAAT-TATGAAAT
2279867 CATATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
TAAAAAAATAATTATGAAATA
Found at i:2280510 original size:3 final size:3
Alignment explanation
Indices: 2280504--2280535 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2280494 ACCCAGAATT
2280504 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
2280536 TGAAGAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:2281046 original size:2 final size:2
Alignment explanation
Indices: 2281034--2281066 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2281024 AAATAAAAAT
*
2281034 TA TA AA 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
2281067 TAAAGCGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2284534 original size:32 final size:32
Alignment explanation
Indices: 2284498--2284560 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
2284488 AAATTTAATC
2284498 ATAAAAATATAAAAT-AATATTTT-AATAATATA
1 ATAAAAA-ATAAAATAAAT-TTTTAAATAATATA
*
2284530 ATAAATAATAAAATAAATTTTTAAATAATAT
1 ATAAAAAATAAAATAAATTTTTAAATAATAT
2284561 CTAAATTCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (32 bp):
ATAAAAAATAAAATAAATTTTTAAATAATATA
Found at i:2284566 original size:31 final size:30
Alignment explanation
Indices: 2284493--2284560 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 30
2284483 TATTTAAATT
2284493 TAATCATAA-AAATATAAAATAATATTTTAA
1 TAAT-ATAATAAATATAAAATAATATTTTAA
2284523 TAATATAATAAATAATAAAATAA-ATTTTTAAA
1 TAATATAATAAAT-ATAAAATAATA-TTTT-AA
2284555 TAATAT
1 TAATAT
2284561 CTAAATTCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 4 0.12
30 9 0.26
31 13 0.38
32 8 0.24
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (30 bp):
TAATATAATAAATATAAAATAATATTTTAA
Found at i:2287002 original size:2 final size:2
Alignment explanation
Indices: 2286990--2287038 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2286980 CAAAGGTACC
2286990 CT CT CT C- CT CT CT 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 CT CT CT CT CT CT CT
2287031 CT CT CT CT
1 CT CT CT CT
2287039 ATCTATCTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2289139 original size:8 final size:8
Alignment explanation
Indices: 2289128--2289168 Score: 68
Period size: 8 Copynumber: 5.4 Consensus size: 8
2289118 ATGATGTGAT
2289128 TATATATG
1 TATATATG
2289136 TATATATG
1 TATATATG
2289144 TATATA--
1 TATATATG
2289150 TATATATG
1 TATATATG
2289158 TATATATG
1 TATATATG
2289166 TAT
1 TAT
2289169 TTTGGTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
8 25 0.81
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (8 bp):
TATATATG
Found at i:2289147 original size:14 final size:14
Alignment explanation
Indices: 2289130--2289164 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2289120 GATGTGATTA
*
2289130 TATATGTATATATG
1 TATATATATATATG
2289144 TATATATATATATG
1 TATATATATATATG
2289158 TATATAT
1 TATATAT
2289165 GTATTTTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (14 bp):
TATATATATATATG
Found at i:2290753 original size:15 final size:15
Alignment explanation
Indices: 2290733--2290763 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2290723 GAAAAGAGAT
2290733 TGAGGAAGCAAGCAA
1 TGAGGAAGCAAGCAA
2290748 TGAGGAAGCAAGCAA
1 TGAGGAAGCAAGCAA
2290763 T
1 T
2290764 AAAACATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.32, T:0.10
Consensus pattern (15 bp):
TGAGGAAGCAAGCAA
Found at i:2293303 original size:2 final size:2
Alignment explanation
Indices: 2293298--2293354 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
2293288 TCTCTCTCTT
2293298 TA 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 TA TA
* *
2293339 TA TA TG TA TA TT TA TA
1 TA TA TA TA TA TA TA TA
2293355 AAATATTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2294984 original size:18 final size:16
Alignment explanation
Indices: 2294952--2294983 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2294942 TTTAAAATAA
2294952 ATATATTTAATTTTTT
1 ATATATTTAATTTTTT
2294968 ATATATTTAATTTTTT
1 ATATATTTAATTTTTT
2294984 TAAAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
ATATATTTAATTTTTT
Found at i:2301282 original size:19 final size:20
Alignment explanation
Indices: 2301246--2301283 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2301236 CTAAACAAAA
*
2301246 AAAAATATAAGAATAAATTT
1 AAAAATATAAGAAAAAATTT
*
2301266 AAAAATA-AATAAAAAATT
1 AAAAATATAAGAAAAAATT
2301284 ATCCTAGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAAAATATAAGAAAAAATTT
Found at i:2301817 original size:3 final size:3
Alignment explanation
Indices: 2301809--2301842 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2301799 TCCCCAGGGT
2301809 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2301843 CTCTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2304300 original size:28 final size:28
Alignment explanation
Indices: 2304246--2304301 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
2304236 CTCTAAGTGT
* *
2304246 TATTATATTATTATTCTATATTATATTA
1 TATTATATTAATATTCTATACTATATTA
*
2304274 TATTATATATAATATTC-ATACTGTATTA
1 TATTATAT-TAATATTCTATACTATATTA
2304302 AAATTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (28 bp):
TATTATATTAATATTCTATACTATATTA
Found at i:2304947 original size:2 final size:2
Alignment explanation
Indices: 2304940--2304992 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
2304930 ATGTGGCCTC
2304940 AT AT AT 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
2304982 AT AT AT AT AT A
1 AT AT AT AT AT A
2304993 AAGCGGGTAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2305099 original size:26 final size:24
Alignment explanation
Indices: 2305039--2305113 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 24
2305029 ATTTACATAT
* *
2305039 ATTTAATCAATTTTAATATAGT-A
1 ATTTAATTAATTTTAATATATTAA
2305062 ATTTAATTAA-TTTAATGATATATAA
1 ATTTAATTAATTTTAAT-ATAT-TAA
*
2305087 ATTTTATATAATTTTAATATATTAA
1 ATTTAAT-TAATTTTAATATATTAA
2305112 AT
1 AT
2305114 ATAAATATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
22 6 0.14
23 12 0.27
24 1 0.02
25 12 0.27
26 7 0.16
27 6 0.14
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (24 bp):
ATTTAATTAATTTTAATATATTAA
Found at i:2305121 original size:26 final size:25
Alignment explanation
Indices: 2305039--2305128 Score: 80
Period size: 26 Copynumber: 3.6 Consensus size: 25
2305029 ATTTACATAT
* *
2305039 ATTTAAT-CAATTTTAATATAGT-A
1 ATTTAATATAATTTTAATATATTAA
2305062 ATTTAAT-TAA-TTTAATGATATATAA
1 ATTTAATATAATTTTAAT-ATAT-TAA
*
2305087 ATTTTATATAATTTTAATATATTAA
1 ATTTAATATAATTTTAATATATTAA
*
2305112 ATATAAATATATATTTT
1 AT-TTAATATA-ATTTT
2305129 TTTGATGTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.11
23 12 0.22
24 1 0.02
25 12 0.22
26 13 0.24
27 11 0.20
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTTAATATAATTTTAATATATTAA
Found at i:2310099 original size:3 final size:3
Alignment explanation
Indices: 2310091--2310124 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2310081 AAAGGTTGTA
2310091 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2310125 GCCAATGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2314222 original size:18 final size:18
Alignment explanation
Indices: 2314199--2314240 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2314189 GTATAACGTG
2314199 ATATATATGA-TTAATATA
1 ATATAT-TGATTTAATATA
*
2314217 ATATATTTATTTAATATA
1 ATATATTGATTTAATATA
*
2314235 TTATAT
1 ATATAT
2314241 CATTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
ATATATTGATTTAATATA
Found at i:2314266 original size:17 final size:19
Alignment explanation
Indices: 2314246--2314289 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
2314236 TATATCATTT
2314246 TATATTTAA-AATTT-TAA
1 TATATTTAATAATTTATAA
*
2314263 TATATTTAATAATTTATAT
1 TATATTTAATAATTTATAA
2314282 TATATTTA
1 TATATTTA
2314290 TAAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 5 0.21
19 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTTAATAATTTATAA
Found at i:2314269 original size:24 final size:24
Alignment explanation
Indices: 2314224--2314278 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
2314214 ATAATATATT
* *
2314224 TATTTAATATATTATATCATTTTA
1 TATTTAAAATATTATATCATTTAA
*
2314248 TATTTAAAATTTTAATAT-ATTTAA
1 TATTTAAAATATT-ATATCATTTAA
2314272 TAATTTA
1 T-ATTTA
2314279 TATTATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTAAAATATTATATCATTTAA
Found at i:2314433 original size:2 final size:2
Alignment explanation
Indices: 2314426--2314456 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2314416 TAATTAATTC
2314426 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 A
2314457 AGAATTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2314617 original size:18 final size:17
Alignment explanation
Indices: 2314567--2314621 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
2314557 TTAAATAACT
2314567 TGATGACTTCAATTAAA
1 TGATGACTTCAATTAAA
*
2314584 TTCATAGA-TT-AATTAATA
1 -TGAT-GACTTCAATTAA-A
2314602 TGATGACTTCAATTAAA
1 TGATGACTTCAATTAAA
2314619 TGA
1 TGA
2314622 ACACAACTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 2 0.06
17 15 0.48
18 12 0.39
19 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (17 bp):
TGATGACTTCAATTAAA
Found at i:2316286 original size:16 final size:15
Alignment explanation
Indices: 2316213--2316283 Score: 54
Period size: 16 Copynumber: 4.5 Consensus size: 15
2316203 ATTCAAAATG
*
2316213 TTTTAAATGTTATAT
1 TTTTAAATATTATAT
*
2316228 TTTCAAAATACTTACGTA-
1 TTT-TAAATA-TTA--TAT
* *
2316246 TTTTAAATTTTAAAT
1 TTTTAAATATTATAT
2316261 TTATTAAATATTATAT
1 TT-TTAAATATTATAT
2316277 TTTTAAA
1 TTTTAAA
2316284 ATAATAACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 1 0.02
15 10 0.23
16 20 0.47
17 7 0.16
18 3 0.07
19 2 0.05
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.54
Consensus pattern (15 bp):
TTTTAAATATTATAT
Found at i:2324829 original size:20 final size:20
Alignment explanation
Indices: 2324804--2324846 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
2324794 TAAAGAAAAA
2324804 AAAAAGTCAATGAAATGAAG
1 AAAAAGTCAATGAAATGAAG
2324824 AAAAAGTCAATGAAATGAAG
1 AAAAAGTCAATGAAATGAAG
2324844 AAA
1 AAA
2324847 GTTTTTTGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.05, G:0.19, T:0.14
Consensus pattern (20 bp):
AAAAAGTCAATGAAATGAAG
Found at i:2333156 original size:14 final size:15
Alignment explanation
Indices: 2333122--2333160 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2333112 ACTGATAGAA
*
2333122 TTTAAATTTTATATT
1 TTTAAATATTATATT
2333137 TATTAAATATTAT-TT
1 T-TTAAATATTATATT
2333152 TTTAAATAT
1 TTTAAATAT
2333161 AATTATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTAAATATTATATT
Found at i:2334491 original size:2 final size:2
Alignment explanation
Indices: 2334486--2334517 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2334476 AAAAAAAAAA
2334486 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
2334518 TTAGAAGCTT
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:2341902 original size:2 final size:2
Alignment explanation
Indices: 2341895--2341922 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2341885 CCGAAGCTTC
2341895 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
2341923 GTACTATATC
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):
TA
Found at i:2348632 original size:6 final size:6
Alignment explanation
Indices: 2348621--2348662 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
2348611 AAACTCGAAA
2348621 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC
1 CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC CAAAAC
2348663 TGCTCTTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAAAC
Found at i:2359765 original size:2 final size:2
Alignment explanation
Indices: 2359758--2359790 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2359748 CATTATAACC
2359758 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
2359791 TCAAGTCGTT
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:2360382 original size:13 final size:13
Alignment explanation
Indices: 2360364--2360394 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2360354 ATTGACTAAC
2360364 GTTTTTTTTTCTT
1 GTTTTTTTTTCTT
*
2360377 GTTTTTTTTTTTT
1 GTTTTTTTTTCTT
2360390 GTTTT
1 GTTTT
2360395 CTTTCCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (13 bp):
GTTTTTTTTTCTT
Found at i:2366640 original size:22 final size:21
Alignment explanation
Indices: 2366608--2366674 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
2366598 TTTAAAATTT
*
2366608 ATATAAATATAAAATAACTTAA
1 ATATAAATATAAAATAA-TAAA
* *
2366630 ATATAATTATAATATAATAAAA
1 ATATAAATATAAAATAAT-AAA
*
2366652 TATATAAATATAATATAAATAAA
1 -ATATAAATATAAAAT-AATAAA
2366675 TAAATCAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
21 1 0.03
22 17 0.45
23 17 0.45
24 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (21 bp):
ATATAAATATAAAATAATAAA
Found at i:2366647 original size:5 final size:5
Alignment explanation
Indices: 2366629--2366677 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
2366619 AAATAACTTA
*
2366629 AATAT AATTAT AATAT AATAA AATAT -ATA- AATAT AATAT AA-AT AA-AT
1 AATAT AA-TAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
2366676 AA
1 AA
2366678 ATCAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
4 14 0.36
5 20 0.51
6 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:2367800 original size:21 final size:22
Alignment explanation
Indices: 2367775--2367817 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2367765 ATTAAAATAT
*
2367775 TTATAA-TTTTTTATTTTTAAA
1 TTATAATTTTTTTATATTTAAA
2367796 TTATAATTTTTTTATATTTAAA
1 TTATAATTTTTTTATATTTAAA
2367818 ATTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATAATTTTTTTATATTTAAA
Found at i:2367846 original size:21 final size:21
Alignment explanation
Indices: 2367817--2367861 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2367807 TTATATTTAA
* *
2367817 AATTTTTAAAATTTAAATATT
1 AATTATTAAAATTAAAATATT
*
2367838 AATTATTAAAATTAAAATTTT
1 AATTATTAAAATTAAAATATT
2367859 AAT
1 AAT
2367862 ATTTTAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AATTATTAAAATTAAAATATT
Found at i:2368403 original size:27 final size:25
Alignment explanation
Indices: 2368344--2368399 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
2368334 GATTAAGCTT
*
2368344 AATTTTTTTATAAAATAATATTAATTTA
1 AATTTTTTTA-AAAAT--TATAAATTTA
2368372 AATTTTTTTAAAAATTATAAATATTA
1 AATTTTTTTAAAAATTATAAAT-TTA
2368398 AA
1 AA
2368400 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 6 0.23
26 5 0.19
27 5 0.19
28 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTTTTTAAAAATTATAAATTTA
Found at i:2368414 original size:14 final size:14
Alignment explanation
Indices: 2368378--2368420 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
2368368 TTTAAATTTT
2368378 TTTAAAAATTATAAA
1 TTTAAAAATT-TAAA
2368393 TATT-AAAATTTAAA
1 T-TTAAAAATTTAAA
2368407 TTTAAAAATTTAAA
1 TTTAAAAATTTAAA
2368421 CTTATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.08
14 15 0.58
15 7 0.27
16 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTTAAAAATTTAAA
Found at i:2375820 original size:1 final size:1
Alignment explanation
Indices: 2375814--2375840 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
2375804 TATCAAAAGA
2375814 GGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGG
2375841 AGAAAGAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:2377783 original size:15 final size:15
Alignment explanation
Indices: 2377763--2377800 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
2377753 AAAAGTTTAA
2377763 ATAAAAATATTAAAT
1 ATAAAAATATTAAAT
*
2377778 ATAAAAAAATTAAAT
1 ATAAAAATATTAAAT
2377793 A-AAAAATA
1 ATAAAAATA
2377801 AGATTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAAAATATTAAAT
Found at i:2377798 original size:13 final size:13
Alignment explanation
Indices: 2377759--2377798 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
2377749 TTTAAAAAGT
*
2377759 TTAAATAAAAATA
1 TTAAATAAAAAAA
2377772 TTAAATATAAAAAAA
1 TT-AA-ATAAAAAAA
2377787 TTAAATAAAAAA
1 TTAAATAAAAAA
2377799 TAAGATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 10 0.42
14 4 0.17
15 10 0.42
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
TTAAATAAAAAAA
Found at i:2378299 original size:19 final size:19
Alignment explanation
Indices: 2378257--2378300 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
2378247 TTTAATTTAA
2378257 AATT-AATATATTAAATAT
1 AATTAAATATATTAAATAT
2378275 AA--AAATATA-TAAATAAT
1 AATTAAATATATTAAAT-AT
2378292 AATTAAATA
1 AATTAAATA
2378301 CTTACCGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.23
17 10 0.45
18 2 0.09
19 5 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTAAATATATTAAATAT
Found at i:2379322 original size:3 final size:3
Alignment explanation
Indices: 2379314--2379350 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2379304 CATATATGCA
2379314 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2379351 GCAATTATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2384986 original size:21 final size:22
Alignment explanation
Indices: 2384959--2385017 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
2384949 TATATAGTAG
*
2384959 TTTTTTAAAAATAAGTAGATAA
1 TTTTTTAAAAATAAGTAGAAAA
* *
2384981 -TTTTTAAGAATATA-TTGAAAA
1 TTTTTTAAAAATA-AGTAGAAAA
2385002 TTTTTTAAAAATAAGT
1 TTTTTTAAAAATAAGT
2385018 GAGCAGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 17 0.57
22 13 0.43
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.44
Consensus pattern (22 bp):
TTTTTTAAAAATAAGTAGAAAA
Found at i:2385070 original size:42 final size:43
Alignment explanation
Indices: 2384959--2385070 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
2384949 TATATAGTAG
* *
2384959 TTTTTTAAAAATAAGTAGATAATTTTTAAGAATATATTGAAAA
1 TTTTTTAAAAATAAGTAAATAATTTTTAAGAATATAATGAAAA
* ** * *
2385002 TTTTTTAAAAATAAGTGAGCAGTTTTTAAG-ATTTAATGAAAA
1 TTTTTTAAAAATAAGTAAATAATTTTTAAGAATATAATGAAAA
** *
2385044 TTTTTTTTAAATAAGTAAATACTTTTT
1 TTTTTTAAAAATAAGTAAATAATTTTT
2385071 CAAAATAAAA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
42 31 0.55
43 25 0.45
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.46
Consensus pattern (43 bp):
TTTTTTAAAAATAAGTAAATAATTTTTAAGAATATAATGAAAA
Found at i:2388969 original size:18 final size:19
Alignment explanation
Indices: 2388948--2388998 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
2388938 CTTATTAAAA
*
2388948 ATATTAAAATT-ATTTTTT
1 ATATTAAAATTAATATTTT
*
2388966 ATATTAATATTAATATTTT
1 ATATTAAAATTAATATTTT
*
2388985 ATAATTAAATTTAA
1 AT-ATTAAAATTAA
2388999 ATAAAAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 10 0.37
19 8 0.30
20 9 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTAAAATTAATATTTT
Found at i:2390063 original size:2 final size:2
Alignment explanation
Indices: 2390056--2390086 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2390046 CCCAAATACC
*
2390056 AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2390087 CTAATCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2390261 original size:2 final size:2
Alignment explanation
Indices: 2390254--2390286 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2390244 CTCCAACTAC
2390254 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 A
2390287 ACCTTAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2392713 original size:20 final size:20
Alignment explanation
Indices: 2392679--2392732 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
2392669 ATATTATATT
* * *
2392679 AAATTATTTTGAATTAATAGA
1 AAATTAATTT-AATTAACAAA
*
2392700 AAATTAATTTAATTGACAAA
1 AAATTAATTTAATTAACAAA
*
2392720 AAATAAATTTAAT
1 AAATTAATTTAAT
2392733 ATATATATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
AAATTAATTTAATTAACAAA
Found at i:2394856 original size:8 final size:8
Alignment explanation
Indices: 2394843--2394930 Score: 56
Period size: 8 Copynumber: 10.8 Consensus size: 8
2394833 AAAATATAAA
2394843 ATAAATAT
1 ATAAATAT
2394851 ATAAATAT
1 ATAAATAT
2394859 ATTAAAATTTAT
1 A-T-AAA--TAT
2394871 ATAAATAT
1 ATAAATAT
2394879 AT-AATAT
1 ATAAATAT
*
2394886 TTAAA-AT
1 ATAAATAT
*
2394893 ATTAATAT
1 ATAAATAT
* *
2394901 A-ATATTT
1 ATAAATAT
*
2394908 AAAAATAAT
1 ATAAAT-AT
*
2394917 ATAAATGT
1 ATAAATAT
2394925 ATAAAT
1 ATAAAT
2394931 TAATATTATG
Statistics
Matches: 62, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
7 15 0.24
8 29 0.47
9 7 0.11
10 6 0.10
11 1 0.02
12 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (8 bp):
ATAAATAT
Found at i:2394864 original size:22 final size:20
Alignment explanation
Indices: 2394822--2394880 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
2394812 TAATTACAGA
2394822 AAAATATA-ATTAAA-ATA-T
1 AAAATATATA-TAAATATATT
2394840 AAAATAAATATATAAATATATT
1 AAAAT--ATATATAAATATATT
*
2394862 AAAATTTATATAAATATAT
1 AAAATATATATAAATATAT
2394881 AATATTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 5 0.14
20 20 0.57
21 4 0.11
22 6 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATATATAAATATATT
Found at i:2394918 original size:18 final size:18
Alignment explanation
Indices: 2394873--2394920 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 18
2394863 AAATTTATAT
2394873 AAAT-ATATAATATTTAA
1 AAATAATATAATATTTAA
2394890 AATATTAATATAATATTTAA
1 AA-A-TAATATAATATTTAA
2394910 AAATAATATAA
1 AAATAATATAA
2394921 ATGTATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 2 0.07
18 9 0.32
19 2 0.07
20 15 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATAATATAATATTTAA
Found at i:2394934 original size:18 final size:18
Alignment explanation
Indices: 2394877--2394936 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
2394867 TTATATAAAT
*
2394877 ATATAATATTTAAAATATTA
1 ATATAATATGT-AAA-ATTA
* *
2394897 ATATAATATTTAAAAATA
1 ATATAATATGTAAAATTA
2394915 ATATAA-ATGTATAAATTA
1 ATATAATATGTA-AAATTA
2394933 ATAT
1 ATAT
2394937 TATGTGGTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 4 0.11
18 18 0.50
19 3 0.08
20 11 0.31
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATATAATATGTAAAATTA
Found at i:2400566 original size:42 final size:43
Alignment explanation
Indices: 2400473--2400582 Score: 127
Period size: 42 Copynumber: 2.6 Consensus size: 43
2400463 TTTATTATCC
*
2400473 TATGTAATGTATTAAAAGGTGATATTGGAGAAAGATACTCTCA
1 TATGTCATGTATTAAAAGGTGATATTGGAGAAAGATACTCTCA
* * *
2400516 TATGTCATGTATTAAAAGGTGATTTTCTG-G-AAGATATTCTCA
1 TATGTCATGTATTAAAAGGTGATATT-GGAGAAAGATACTCTCA
* *
2400558 TAAT-TCATGTACTAAAAAGTGATAT
1 T-ATGTCATGTATTAAAAGGTGATAT
2400583 CAGGGAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
42 30 0.52
43 27 0.47
44 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.36
Consensus pattern (43 bp):
TATGTCATGTATTAAAAGGTGATATTGGAGAAAGATACTCTCA
Found at i:2401945 original size:30 final size:30
Alignment explanation
Indices: 2401827--2401945 Score: 86
Period size: 30 Copynumber: 4.0 Consensus size: 30
2401817 TAAACTTATT
* *
2401827 ACTTG-ATCTATATAAGCCCCTATA-CTTTT
1 ACTTGTATCTAAATAAGCCCCTA-ACCTTTA
*
2401856 A-TTGCA-CTCAAATAAG-CCCTCAACCTTTA
1 ACTTGTATCT-AAATAAGCCCCT-AACCTTTA
* * * * **
2401885 ATTTGTACCCAAATGAGCCTTTAACCTTTA
1 ACTTGTATCTAAATAAGCCCCTAACCTTTA
*
2401915 ACTTGTATCTAAATAAGCCCCTAACATTTA
1 ACTTGTATCTAAATAAGCCCCTAACCTTTA
2401945 A
1 A
2401946 TATATACCTA
Statistics
Matches: 69, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
28 10 0.14
29 14 0.20
30 42 0.61
31 3 0.04
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (30 bp):
ACTTGTATCTAAATAAGCCCCTAACCTTTA
Found at i:2409180 original size:16 final size:16
Alignment explanation
Indices: 2409142--2409181 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
2409132 TATAATTTTT
2409142 TTATAAAT-A-TTAAA
1 TTATAAATAATTTAAA
2409156 TTA-AAATAATTTAAA
1 TTATAAATAATTTAAA
2409171 TTATAAATAAT
1 TTATAAATAAT
2409182 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 8 0.35
16 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTATAAATAATTTAAA
Found at i:2414175 original size:2 final size:2
Alignment explanation
Indices: 2414168--2414210 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2414158 TCAATTGTAG
2414168 AT AT AT 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
2414210 A
1 A
2414211 AACTAACTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2414898 original size:17 final size:17
Alignment explanation
Indices: 2414878--2414958 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 17
2414868 ATACGGCTTA
2414878 ATATTAATTTTTTATAT
1 ATATTAATTTTTTATAT
* *
2414895 ATATT--TTTATTA-AA
1 ATATTAATTTTTTATAT
2414909 ATATT-A-TTTTTA-AT
1 ATATTAATTTTTTATAT
* **
2414923 ATGTTAATAATTTATAT
1 ATATTAATTTTTTATAT
*
2414940 -TATATAATTTTTGATAT
1 ATAT-TAATTTTTTATAT
2414957 AT
1 AT
2414959 TTTTATATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 11
0.68 0.16 0.16
Matches are distributed among these distances:
14 16 0.34
15 7 0.15
16 6 0.13
17 17 0.36
18 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATATTAATTTTTTATAT
Found at i:2414991 original size:29 final size:28
Alignment explanation
Indices: 2414933--2414995 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
2414923 ATGTTAATAA
*
2414933 TTTATA-TTATATAATTTTTGATATATT
1 TTTATATTTATATAATTTTTGATATACT
* * *
2414960 TTTATATTTATGTTATTTTTTATTATACT
1 TTTATATTTATATAATTTTTGA-TATACT
2414989 TTTATAT
1 TTTATAT
2414996 CATATTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 6 0.20
28 12 0.40
29 12 0.40
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTATATTTATATAATTTTTGATATACT
Found at i:2415075 original size:2 final size:2
Alignment explanation
Indices: 2415068--2415104 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2415058 ACTCATAGAC
2415068 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 T
2415105 TCATCCTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2415195 original size:21 final size:19
Alignment explanation
Indices: 2415159--2415198 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
2415149 TGCTCTAAAT
*
2415159 TTTTTCCTCTTGGCTTCTA
1 TTTTTCCTCTTCGCTTCTA
2415178 TTTTTCTCTCTTTCGCTTCTA
1 TTTTTC-CTC-TTCGCTTCTA
2415199 ACCATAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 3 0.17
21 9 0.50
ACGTcount: A:0.05, C:0.28, G:0.07, T:0.60
Consensus pattern (19 bp):
TTTTTCCTCTTCGCTTCTA
Found at i:2416573 original size:32 final size:31
Alignment explanation
Indices: 2416537--2416600 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
2416527 TATAATATAC
* *
2416537 TATAATATAAAATATAAATATTTTAAAATTTA
1 TATAACATAAAATATAAATATATT-AAATTTA
* * *
2416569 TATAACATTAATTATTAATATATTAAATTTA
1 TATAACATAAAATATAAATATATTAAATTTA
2416600 T
1 T
2416601 GTTACAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 8 0.30
32 19 0.70
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (31 bp):
TATAACATAAAATATAAATATATTAAATTTA
Found at i:2430564 original size:16 final size:17
Alignment explanation
Indices: 2430526--2430565 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
2430516 TGAAATTAAG
2430526 AAACCAAACAGGTACCA
1 AAACCAAACAGGTACCA
2430543 AAACCAAACAGGTACC-
1 AAACCAAACAGGTACCA
2430559 AAACCAA
1 AAACCAA
2430566 GTTGAAGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.55, C:0.30, G:0.10, T:0.05
Consensus pattern (17 bp):
AAACCAAACAGGTACCA
Found at i:2435454 original size:287 final size:285
Alignment explanation
Indices: 2434618--2435462 Score: 1027
Period size: 287 Copynumber: 2.9 Consensus size: 285
2434608 TTTAAAATTT
* * *
2434618 TTAATTTTATTAACTGACGTATATTAATTTAAATTATTTGATAAGACATATATAATAATATATTT
1 TTAATTTTATTAACTGACATAT-TTGATTTAAATTATTTGATAAGACATATATAATAATGTATTT
* * * *
2434683 TAATTATTTATATTGAGGTTAGGA-TTTCTTTCTCATTGTTAGAGGTATGAAATTTTAACTGAAT
65 TAATTATTTATATTGAGGTTAGGACTTTC-TCCTCATCGTTGGAGGTATGAAATTTTAATTGAAT
* * *
2434747 TGATCTTCGATCCAATT-T--T-A-T-CAAGCAAGTATGTTTTTAAAATTAATAAAAGAAAAAGA
129 TGATCTTCCATCCTATTATCATCATTACAAGCAAGTATGTTTTTAAAGTTAATAAAAGAAAAAGA
* * *
2434806 AATTGACACATTGATTTGTGCTCGACTACGTGGCTAACAACATCCTCAATTAGTATTATTGCTTG
194 AATTCACACATTGATTTGTGCTCAACTACGTGGCTAACAACATCCTCAATTAGCATTATTGCTTG
* *
2434871 ATATGTCATTTGTCTCATATTTATAGATGTGC
259 ACATGTCA----T-TCATATTTATAGATGTAC
* * *
2434903 TCAACTTTATTAACTGACATATTGTGATTTGAATTATTTGATAAG--ATATATAATAATGTATTT
1 TTAATTTTATTAACTGACATATT-TGATTTAAATTATTTGATAAGACATATATAATAATGTATTT
* *
2434966 TAATTATTTACATTGAAGTTAGGAC-TTC-CCTCTATTCGTTCTTTGGAGGTATGAAATTTTAAT
65 TAATTATTTATATTGAGGTTAGGACTTTCTCCTC-A-TCG----TTGGAGGTATGAAATTTTAAT
* * * *
2435029 TGAATTGATTTTTCATCCAATATTATCATCATTAAAAGCAAGTATATTTTTAAAGTTAATAAAAG
124 TGAATTGATCTTCCATCC--TATTATCATCATTACAAGCAAGTATGTTTTTAAAGTTAATAAAAG
*
2435094 AAAAAGAAATTCACACATTGATTTGTGCTCAACTACGTGGCTAACAACATCCTTAATTAGCATTA
187 AAAAAGAAATTCACACATTGATTTGTGCTCAACTACGTGGCTAACAACATCCTCAATTAGCATTA
2435159 TTGCTTGACATGTCATT-ATATTTAT-GAATGTAC
252 TTGCTTGACATGTCATTCATATTTATAG-ATGTAC
* * * *
2435192 TTAATTTTATTAATTGACATATCTTGATTTAAATTATTTGATAAGACATGTCTAGTAATGTATTT
1 TTAATTTTATTAACTGACATAT-TTGATTTAAATTATTTGATAAGACATATATAATAATGTATTT
* * * *
2435257 TGACTTATTTATATTGAGGATAGGACTTTCTCCTCATCGTTGGAGATTTGAAATTTTAATTGAAT
65 T-AATTATTTATATTGAGGTTAGGACTTTCTCCTCATCGTTGGAGGTATGAAATTTTAATTGAAT
* *
2435322 TGATCTTCCATCCGGTATTATCATCATTACAAGTAAATATGTTTTTAAAGTTAATAAAA-AAAAA
129 TGATCTTCCATCC--TATTATCATCATTACAAGCAAGTATGTTTTTAAAGTTAATAAAAGAAAAA
* * * *
2435386 GAAATTCACACATTAATTTGTGCTCAACTACGTGGTTAACAATATTCTCAATT-GACATTATTGC
192 GAAATTCACACATTGATTTGTGCTCAACTACGTGGCTAACAACATCCTCAATTAG-CATTATTGC
*
2435450 TTGACTTGTCATT
256 TTGACATGTCATT
2435463 TGTCTCATAT
Statistics
Matches: 484, Mismatches: 52, Indels: 46
0.83 0.09 0.08
Matches are distributed among these distances:
281 3 0.01
282 1 0.00
283 44 0.09
284 1 0.00
285 38 0.08
286 1 0.00
287 108 0.22
288 76 0.16
289 55 0.11
290 3 0.01
291 17 0.04
292 24 0.05
293 5 0.01
294 5 0.01
295 103 0.21
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (285 bp):
TTAATTTTATTAACTGACATATTTGATTTAAATTATTTGATAAGACATATATAATAATGTATTTT
AATTATTTATATTGAGGTTAGGACTTTCTCCTCATCGTTGGAGGTATGAAATTTTAATTGAATTG
ATCTTCCATCCTATTATCATCATTACAAGCAAGTATGTTTTTAAAGTTAATAAAAGAAAAAGAAA
TTCACACATTGATTTGTGCTCAACTACGTGGCTAACAACATCCTCAATTAGCATTATTGCTTGAC
ATGTCATTCATATTTATAGATGTAC
Found at i:2438901 original size:30 final size:31
Alignment explanation
Indices: 2438860--2438917 Score: 109
Period size: 30 Copynumber: 1.9 Consensus size: 31
2438850 TGACCGACAA
2438860 ATCATGGAAAAAAAACTAGAGACAAATAAAG
1 ATCATGGAAAAAAAACTAGAGACAAATAAAG
2438891 ATCAT-GAAAAAAAACTAGAGACAAATA
1 ATCATGGAAAAAAAACTAGAGACAAATA
2438918 GGTATAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.62, C:0.10, G:0.14, T:0.14
Consensus pattern (31 bp):
ATCATGGAAAAAAAACTAGAGACAAATAAAG
Found at i:2444199 original size:26 final size:24
Alignment explanation
Indices: 2444170--2444218 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
2444160 TGTATAAAAT
2444170 TTATATGCT-ATTAATAAATTAATTTA
1 TTATAT-CTCATTAA-AAA-TAATTTA
2444196 TTATATCTCATTAAAAATAATTT
1 TTATATCTCATTAAAAATAATTT
2444219 TTTTATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 5 0.23
26 11 0.50
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (24 bp):
TTATATCTCATTAAAAATAATTTA
Found at i:2444224 original size:25 final size:26
Alignment explanation
Indices: 2444169--2444226 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
2444159 ATGTATAAAA
2444169 TTTATATGCTATTAATAAATTAATTT
1 TTTATATGCTATTAATAAATTAATTT
*
2444195 ATTATAT-CTCATTAA-AAA-TAATTTT
1 TTTATATGCT-ATTAATAAATTAA-TTT
2444220 TTTATAT
1 TTTATAT
2444227 TTATTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.11
25 14 0.50
26 11 0.39
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTATATGCTATTAATAAATTAATTT
Found at i:2445148 original size:19 final size:16
Alignment explanation
Indices: 2445115--2445154 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
2445105 TAAATTTGAG
2445115 TATAATATTTTAAATA
1 TATAATATTTTAAATA
*
2445131 TATAATAATTTTAAAAA
1 TATAAT-ATTTTAAATA
2445148 TA-AATAT
1 TATAATAT
2445155 ACTCTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 2 0.09
16 9 0.41
17 11 0.50
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATATTTTAAATA
Found at i:2445404 original size:17 final size:18
Alignment explanation
Indices: 2445382--2445419 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2445372 GAATTAAAAA
*
2445382 TTGATAGATTAT-TTAAT
1 TTGATAGAGTATATTAAT
*
2445399 TTGATATAGTATATTAAT
1 TTGATAGAGTATATTAAT
2445417 TTG
1 TTG
2445420 GTGAACCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (18 bp):
TTGATAGAGTATATTAAT
Found at i:2446092 original size:22 final size:24
Alignment explanation
Indices: 2446064--2446109 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
2446054 AATCTTTAAA
2446064 GAATCTTGTAAAGA-TCC-CCAAG
1 GAATCTTGTAAAGATTCCTCCAAG
2446086 GAATCTTGTAAAGATTCCTCCAAG
1 GAATCTTGTAAAGATTCCTCCAAG
2446110 TTAGGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.64
23 3 0.14
24 5 0.23
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (24 bp):
GAATCTTGTAAAGATTCCTCCAAG
Found at i:2448131 original size:2 final size:2
Alignment explanation
Indices: 2448124--2448153 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2448114 TCTGTGTTAA
2448124 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
2448154 GGATAACTGA
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:2449142 original size:34 final size:33
Alignment explanation
Indices: 2449104--2449182 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
2449094 TCTTTTTTTG
*
2449104 TTGATTAAATGAGAAATTTGATAGCTTACTATTA
1 TTGATTAAATG-GAAATTTGATAGCTTACCATTA
** * * *
2449138 TTGATTAAATGGTGATTTGGTAGTTTACCATTG
1 TTGATTAAATGGAAATTTGATAGCTTACCATTA
2449171 TTGATTAAATGG
1 TTGATTAAATGG
2449183 GTGATTTGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 28 0.72
34 11 0.28
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (33 bp):
TTGATTAAATGGAAATTTGATAGCTTACCATTA
Found at i:2449191 original size:34 final size:34
Alignment explanation
Indices: 2449101--2449214 Score: 131
Period size: 34 Copynumber: 3.4 Consensus size: 34
2449091 ACATCTTTTT
* ** * *
2449101 TTGTTGATTAAATGAGAAATTTGATAGCTTACTA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* *
2449135 TTATTGATTAAAT-GGTGATTTGGTAGTTTACCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
* **
2449168 TTGTTGATTAAATGGGTGATTTGGTAGGTTGTCA
1 TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
2449202 TTGTTGATTAAAT
1 TTGTTGATTAAAT
2449215 AGTGGTTTTT
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
33 26 0.38
34 42 0.62
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.45
Consensus pattern (34 bp):
TTGTTGATTAAATGGGTGATTTGGTAGCTTACCA
Found at i:2454601 original size:15 final size:16
Alignment explanation
Indices: 2454581--2454614 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2454571 AAATGATTTA
2454581 AAAAATAAT-AAAAAT
1 AAAAATAATAAAAAAT
*
2454596 AAAAATTATAAAAAAT
1 AAAAATAATAAAAAAT
2454612 AAA
1 AAA
2454615 TTTAAGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAATAATAAAAAAT
Found at i:2455931 original size:12 final size:12
Alignment explanation
Indices: 2455914--2456000 Score: 52
Period size: 12 Copynumber: 7.0 Consensus size: 12
2455904 TATAAATTTA
*
2455914 ATAATATTAAAT
1 ATAATATAAAAT
2455926 ATAATATAAAAT
1 ATAATATAAAAT
* *
2455938 AAAAAATAAAAT
1 ATAATATAAAAT
*
2455950 -TAAATTAAAAAAT
1 AT-AA-TATAAAAT
* *
2455963 AAAATTTACATAAT
1 ATAATATA-A-AAT
2455977 ATTAATATAAAA-
1 A-TAATATAAAAT
*
2455989 ATATTATAAAAT
1 ATAATATAAAAT
2456001 TTATATAATA
Statistics
Matches: 56, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
11 9 0.16
12 26 0.46
13 11 0.20
14 5 0.09
15 5 0.09
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:2455958 original size:18 final size:18
Alignment explanation
Indices: 2455896--2455968 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
2455886 AATCTCATAT
*
2455896 AATAAAAATATAAATTTAA
1 AATAAAAA-ATAAAATTAA
** *
2455915 TAATATTAAATATAATATAA
1 -AATAAAAAATAAAAT-TAA
2455935 AATAAAAAATAAAATTAA
1 AATAAAAAATAAAATTAA
*
2455953 ATTAAAAAATAAAATT
1 AATAAAAAATAAAATT
2455969 TACATAATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 18 0.41
19 17 0.39
20 9 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAAAAATAAAATTAA
Found at i:2455986 original size:11 final size:11
Alignment explanation
Indices: 2455915--2456008 Score: 52
Period size: 11 Copynumber: 8.7 Consensus size: 11
2455905 ATAAATTTAA
*
2455915 TAATATTAAAT
1 TAATATAAAAT
2455926 ATAATATAAAAT
1 -TAATATAAAAT
* *
2455938 AAAAAATAAAAT
1 -TAATATAAAAT
*
2455950 TAA-ATTAAA-
1 TAATATAAAAT
2455959 -AA-ATAAAAT
1 TAATATAAAAT
* * *
2455968 TTACATAATAT
1 TAATATAAAAT
*
2455979 TAATATAAAAA
1 TAATATAAAAT
*
2455990 TATTATAAAAT
1 TAATATAAAAT
*
2456001 TTATATAA
1 TAATATAA
2456009 TAAATTTATT
Statistics
Matches: 63, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
8 7 0.11
10 6 0.10
11 30 0.48
12 20 0.32
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATATAAAAT
Found at i:2455997 original size:22 final size:24
Alignment explanation
Indices: 2455972--2456028 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
2455962 TAAAATTTAC
2455972 ATAATATTAATATAA-AAA-TATT
1 ATAATATTAATATAATAAATTATT
* *
2455994 ATAAAATTTATATAATAAATTTATT
1 ATAATATTAATATAATAAA-TTATT
*
2456019 AAAATATTAA
1 ATAATATTAA
2456029 AATTATTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
22 13 0.48
23 3 0.11
25 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAATATTAATATAATAAATTATT
Found at i:2456023 original size:33 final size:32
Alignment explanation
Indices: 2455961--2456027 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 32
2455951 AAATTAAAAA
2455961 ATAAAATTTACATAATATTAATATAAAAATATT
1 ATAAAATTTACATAATATT-ATATAAAAATATT
* *
2455994 ATAAAATTTATATAATAAATT-TATTAAAATATT
1 ATAAAATTTACATAAT--ATTATATAAAAATATT
2456027 A
1 A
2456028 AAATTATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 27 0.90
35 3 0.10
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
ATAAAATTTACATAATATTATATAAAAATATT
Found at i:2456034 original size:17 final size:17
Alignment explanation
Indices: 2456009--2456042 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2455999 ATTTATATAA
*
2456009 TAAATTTATTAAAATAT
1 TAAAATTATTAAAATAT
*
2456026 TAAAATTATTTAAATAT
1 TAAAATTATTAAAATAT
2456043 AATAAAATAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATTATTAAAATAT
Found at i:2462763 original size:14 final size:14
Alignment explanation
Indices: 2462744--2462775 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2462734 AGGAGTAGTG
2462744 TCTTCTTTTAAGTT
1 TCTTCTTTTAAGTT
2462758 TCTTCTTTTAAGTT
1 TCTTCTTTTAAGTT
2462772 TCTT
1 TCTT
2462776 TGGTTCAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.16, G:0.06, T:0.66
Consensus pattern (14 bp):
TCTTCTTTTAAGTT
Found at i:2463022 original size:2 final size:2
Alignment explanation
Indices: 2463015--2463043 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2463005 TTCTTTTAAT
2463015 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
2463044 TGCCATTTTG
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:2464308 original size:21 final size:22
Alignment explanation
Indices: 2464278--2464320 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2464268 TTTAAAATTA
2464278 AAAAATTTTATA-TTTTTTAAAT
1 AAAAATTTTA-AGTTTTTTAAAT
2464300 AAAAA-TTTAAGTTTTTTAAAT
1 AAAAATTTTAAGTTTTTTAAAT
2464321 TTAAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 14 0.70
22 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
AAAAATTTTAAGTTTTTTAAAT
Found at i:2464766 original size:2 final size:2
Alignment explanation
Indices: 2464761--2464790 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2464751 CATATATATT
*
2464761 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2464791 CTCATATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2467831 original size:12 final size:12
Alignment explanation
Indices: 2467814--2467848 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2467804 GGTACTATAG
*
2467814 GAACAAGAAGAC
1 GAACAAGAAGAA
2467826 GAACAAGAAGAA
1 GAACAAGAAGAA
*
2467838 GAAGAAGAAGA
1 GAACAAGAAGA
2467849 TGATGATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.63, C:0.09, G:0.29, T:0.00
Consensus pattern (12 bp):
GAACAAGAAGAA
Found at i:2467853 original size:3 final size:3
Alignment explanation
Indices: 2467847--2467877 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
2467837 AGAAGAAGAA
2467847 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
2467878 TGAGGGCGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:2469145 original size:21 final size:21
Alignment explanation
Indices: 2469108--2469147 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2469098 TTTAAAAATA
*
2469108 AATATAAATAATTTTATTTTT
1 AATATAAAAAATTTTATTTTT
2469129 AATA-AAAAAATTATTATTT
1 AATATAAAAAATT-TTATTT
2469148 AATTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATAAAAAATTTTATTTTT
Found at i:2469426 original size:2 final size:2
Alignment explanation
Indices: 2469421--2469449 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2469411 ATATTTTTTA
2469421 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
2469450 AGTTCATATA
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:2489831 original size:7 final size:7
Alignment explanation
Indices: 2489819--2489848 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2489809 TTATAAATAA
2489819 TTTAAAT
1 TTTAAAT
2489826 TTTAAAT
1 TTTAAAT
2489833 TTTAAAT
1 TTTAAAT
2489840 TTTAAAT
1 TTTAAAT
2489847 TT
1 TT
2489849 ATTAATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
TTTAAAT
Found at i:2492180 original size:4 final size:4
Alignment explanation
Indices: 2492171--2492196 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2492161 TTTGGAGGAA
2492171 TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TT
2492197 TTTTATAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTCT
Found at i:2493071 original size:2 final size:2
Alignment explanation
Indices: 2493064--2493089 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2493054 ACACTGTTTG
2493064 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
2493090 GTTTGTTTTA
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):
AT
Found at i:2493843 original size:3 final size:3
Alignment explanation
Indices: 2493837--2493879 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2493827 ATAATAATAA
2493837 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2493880 TTGAAAAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:2497435 original size:39 final size:39
Alignment explanation
Indices: 2497392--2497469 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2497382 GTTGAGAGAA
2497392 CTCTTATTTATAGGATCTGAAAAAGGATTTACAGTCTTT
1 CTCTTATTTATAGGATCTGAAAAAGGATTTACAGTCTTT
2497431 CTCTTATTTATAGGATCTGAAAAAGGATTTACAGTCTTT
1 CTCTTATTTATAGGATCTGAAAAAGGATTTACAGTCTTT
2497470 GTAGTAATGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (39 bp):
CTCTTATTTATAGGATCTGAAAAAGGATTTACAGTCTTT
Found at i:2500464 original size:2 final size:2
Alignment explanation
Indices: 2500457--2500499 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2500447 CTACTAGTAT
*
2500457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2500499 T
1 T
2500500 TCAGGCTTAG
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:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2502454 original size:20 final size:20
Alignment explanation
Indices: 2502429--2502470 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2502419 CGGAGGCTCA
2502429 AATTGGTAGTGGCATAAACC
1 AATTGGTAGTGGCATAAACC
2502449 AATTGGTAGTGGCATAAACC
1 AATTGGTAGTGGCATAAACC
2502469 AA
1 AA
2502471 CCTACGTAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (20 bp):
AATTGGTAGTGGCATAAACC
Found at i:2504495 original size:3 final size:3
Alignment explanation
Indices: 2504487--2504523 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2504477 TTTCAAAAAG
2504487 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2504524 CAACAGAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2505315 original size:13 final size:13
Alignment explanation
Indices: 2505294--2505324 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2505284 AACTGAACTC
*
2505294 AAAATTAAAAAAT
1 AAAAATAAAAAAT
2505307 AAAAATAAAAAAT
1 AAAAATAAAAAAT
2505320 AAAAA
1 AAAAA
2505325 CTCTCCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:2505969 original size:23 final size:23
Alignment explanation
Indices: 2505891--2505957 Score: 57
Period size: 24 Copynumber: 2.9 Consensus size: 23
2505881 TTTAAAAATT
** *
2505891 ATTATATAT-AATAATTTTTTTA
1 ATTATATATGAATAAAATTATTA
*
2505913 TTTGATATATGAATAAAATTATTA
1 ATT-ATATATGAATAAAATTATTA
*
2505937 ATTATTATATTAA-AAAATTAT
1 ATTA-TATATGAATAAAATTAT
2505958 ATATATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
22 2 0.06
23 15 0.42
24 19 0.53
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (23 bp):
ATTATATATGAATAAAATTATTA
Found at i:2506549 original size:22 final size:22
Alignment explanation
Indices: 2506508--2506556 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
2506498 TAAAAATTAA
*
2506508 AAAATTATAAATGTTAAAATTT
1 AAAATTATAAATGTTAAAATAT
2506530 AAAATT-TAAAT-TTATTAAATAT
1 AAAATTATAAATGTTA--AAATAT
2506552 AAAAT
1 AAAAT
2506557 AATTATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 3 0.12
21 5 0.21
22 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (22 bp):
AAAATTATAAATGTTAAAATAT
Found at i:2507113 original size:32 final size:31
Alignment explanation
Indices: 2507057--2507128 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
2507047 AAATTTAAAT
2507057 TATATCTTTTATTAATTAAATTTAATAAT-TTA
1 TATAT-TTTTATTAATTAAATTTAA-AATATTA
* * *
2507089 TATATTTTTATTAATTTTATTTTAAAATATTT
1 TATATTTTTATTAA-TTAAATTTAAAATATTA
2507121 TATATTTT
1 TATATTTT
2507129 ATACAAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 12 0.34
32 23 0.66
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
TATATTTTTATTAATTAAATTTAAAATATTA
Found at i:2507128 original size:17 final size:17
Alignment explanation
Indices: 2507106--2507183 Score: 59
Period size: 17 Copynumber: 4.4 Consensus size: 17
2507096 TTATTAATTT
2507106 TATTTTAAAATATTTTA
1 TATTTTAAAATATTTTA
2507123 TATTTTATACAA-ATTTTAA
1 TATTTTA-A-AATATTTT-A
* * **
2507142 TATATTAATATAAATTA
1 TATTTTAAAATATTTTA
* *
2507159 TATTTTTATATATTATTA
1 TATTTTAAAATATT-TTA
2507177 TATTTTA
1 TATTTTA
2507184 TATTATATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
17 19 0.40
18 19 0.40
19 9 0.19
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (17 bp):
TATTTTAAAATATTTTA
Found at i:2507169 original size:25 final size:25
Alignment explanation
Indices: 2507135--2507187 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
2507125 TTTTATACAA
2507135 ATTTTAATATATTAATATAAATTAT
1 ATTTTAATATATTAATATAAATTAT
* * **
2507160 ATTTTTATATATTATTATATTTTAT
1 ATTTTAATATATTAATATAAATTAT
2507185 ATT
1 ATT
2507188 ATATTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTTTAATATATTAATATAAATTAT
Found at i:2507192 original size:20 final size:20
Alignment explanation
Indices: 2507155--2507212 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
2507145 ATTAATATAA
2507155 ATTATATTTT-TA-TATATT
1 ATTATATTTTATATTATATT
2507173 ATTATATTTTATATTATATT
1 ATTATATTTTATATTATATT
*
2507193 -TTAATTTTTTATATTATATT
1 ATT-ATATTTTATATTATATT
2507213 TGTACCTTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 10 0.28
19 4 0.11
20 22 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATATTTTATATTATATT
Found at i:2507467 original size:15 final size:15
Alignment explanation
Indices: 2507449--2507506 Score: 73
Period size: 15 Copynumber: 3.7 Consensus size: 15
2507439 TAATATAATT
2507449 ATATAATATAAAAAA
1 ATATAATATAAAAAA
2507464 ATATAATATAATAATAA
1 ATATAATATAA-AA-AA
*
2507481 ATATGATAT-AAAAA
1 ATATAATATAAAAAA
2507495 ATATAAATATAA
1 ATAT-AATATAA
2507507 TATAAATACA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 6 0.16
15 17 0.46
16 4 0.11
17 10 0.27
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (15 bp):
ATATAATATAAAAAA
Found at i:2507491 original size:11 final size:11
Alignment explanation
Indices: 2507433--2507514 Score: 82
Period size: 11 Copynumber: 7.5 Consensus size: 11
2507423 AATTTGATAT
*
2507433 TAAACATAATA
1 TAAATATAATA
2507444 TAATTATATAATA
1 TAA--ATATAATA
*
2507457 TAAA-AAAATA
1 TAAATATAATA
2507467 T-AATATAATAA
1 TAAATATAAT-A
*
2507478 TAAATATGATA
1 TAAATATAATA
2507489 TAAA-A-AATA
1 TAAATATAATA
2507498 TAAATATAATA
1 TAAATATAATA
2507509 TAAATA
1 TAAATA
2507515 CATAAATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
9 9 0.15
10 12 0.20
11 21 0.36
12 7 0.12
13 10 0.17
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (11 bp):
TAAATATAATA
Found at i:2507494 original size:31 final size:28
Alignment explanation
Indices: 2507438--2507520 Score: 96
Period size: 31 Copynumber: 2.8 Consensus size: 28
2507428 GATATTAAAC
*
2507438 ATAATATAAT-TATATAATATAAAAAAAT
1 ATAATATAATATAAAT-ATATAAAAAAAT
2507466 ATAATATAATAATAAATATGATATAAAAAAT
1 ATAATATAAT-ATAAATAT-ATA-AAAAAAT
*
2507497 ATAAATATAATATAAATACATAAA
1 AT-AATATAATATAAATATATAAA
2507521 TATTTTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
28 10 0.21
29 4 0.08
30 10 0.21
31 16 0.33
32 8 0.17
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (28 bp):
ATAATATAATATAAATATATAAAAAAAT
Found at i:2507495 original size:32 final size:31
Alignment explanation
Indices: 2507433--2507514 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 31
2507423 AATTTGATAT
*
2507433 TAAACATAATATAATTATATAATATAAAAAA-A
1 TAAATATAATATAA--ATATAATATAAAAAATA
*
2507465 TATAATATAATAATAAATATGATATAAAAAATA
1 TA-AATATAAT-ATAAATATAATATAAAAAATA
2507498 TAAATATAATATAAATA
1 TAAATATAATATAAATA
2507515 CATAAATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 7 0.16
32 24 0.53
33 10 0.22
34 4 0.09
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (31 bp):
TAAATATAATATAAATATAATATAAAAAATA
Found at i:2507687 original size:4 final size:4
Alignment explanation
Indices: 2507678--2507705 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
2507668 CATGAGACTA
2507678 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
2507706 TCCTTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:2508044 original size:18 final size:18
Alignment explanation
Indices: 2508012--2508051 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2508002 TCTTTTTTGA
*
2508012 TAAAATTCTCCAAAATTT
1 TAAAATTCTCCAAAATGT
**
2508030 TAAAATTCTTTAAAATGT
1 TAAAATTCTCCAAAATGT
2508048 TAAA
1 TAAA
2508052 CTTTAGTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (18 bp):
TAAAATTCTCCAAAATGT
Found at i:2508659 original size:19 final size:19
Alignment explanation
Indices: 2508604--2508661 Score: 57
Period size: 19 Copynumber: 3.2 Consensus size: 19
2508594 ATATAATGAC
***
2508604 ATAATATTAATATAATTTT
1 ATAATATTAATATAAAAAT
* *
2508623 AAAAAATTAAT-T-AAAAT
1 ATAATATTAATATAAAAAT
2508640 ATAATATTAATATAAAAAT
1 ATAATATTAATATAAAAAT
2508659 ATA
1 ATA
2508662 TTTAAATTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
19 17 0.57
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATATTAATATAAAAAT
Found at i:2508967 original size:21 final size:19
Alignment explanation
Indices: 2508942--2508984 Score: 63
Period size: 18 Copynumber: 2.3 Consensus size: 19
2508932 GACATAAATC
2508942 ATATAATAATTATTAAATTA
1 ATAT-ATAATTATTAAATTA
2508962 A-ATATAATTATTAAATTA
1 ATATATAATTATTAAATTA
2508980 A-ATAT
1 ATATAT
2508985 TTGAATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.87
19 2 0.09
20 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATAATTATTAAATTA
Done.