Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 9 of 33
Found at i:1185795 original size:11 final size:12
Alignment explanation
Indices: 1185760--1185811 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1185750 TTTTTTATAA
*
1185760 TATATCATATTT
1 TATATTATATTT
1185772 TATATTATATTT
1 TATATTATATTT
*
1185784 TA-ATTATTTTTT
1 TATATTA-TATTT
* *
1185796 TGTATTACATTT
1 TATATTATATTT
1185808 TATA
1 TATA
1185812 GTATTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
11 4 0.12
12 24 0.75
13 4 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (12 bp):
TATATTATATTT
Found at i:1186133 original size:27 final size:27
Alignment explanation
Indices: 1186078--1186134 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
1186068 AAAAAAAAGT
1186078 AATTATTACATTTTTTAAATTTATAAA
1 AATTATTACATTTTTTAAATTTATAAA
1186105 AATTATTA-ATTTGATTTAGAATTT-TAAA
1 AATTATTACATTT--TTTA-AATTTATAAA
1186133 AA
1 AA
1186135 GTTTAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.15
27 8 0.30
28 10 0.37
29 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.49
Consensus pattern (27 bp):
AATTATTACATTTTTTAAATTTATAAA
Found at i:1193876 original size:19 final size:20
Alignment explanation
Indices: 1193832--1193873 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1193822 TAATTAATAT
1193832 AAATATATTTGATATTTTAA
1 AAATATATTTGATATTTTAA
*
1193852 AAATAT-TTTTATATATTTAA
1 AAATATATTTGATAT-TTTAA
1193872 AA
1 AA
1193874 TATCACATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
AAATATATTTGATATTTTAA
Found at i:1195643 original size:2 final size:2
Alignment explanation
Indices: 1195636--1195662 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1195626 CTATTTTCAT
1195636 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
1195663 GGGGTGTGGC
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:1196377 original size:28 final size:27
Alignment explanation
Indices: 1196346--1196406 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
1196336 TTTTTTTTTA
* *
1196346 TAAATTATAATT-AATATTTAATACATAT
1 TAAATTAAAATTCAA-ACTTAATA-ATAT
1196374 TAAATTAAAATTCAAACTTAATAATAT
1 TAAATTAAAATTCAAACTTAATAATAT
*
1196401 CAAATT
1 TAAATT
1196407 GATTATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 9 0.31
28 18 0.62
29 2 0.07
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (27 bp):
TAAATTAAAATTCAAACTTAATAATAT
Found at i:1196635 original size:12 final size:12
Alignment explanation
Indices: 1196618--1196642 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1196608 AGCCCGTGCT
1196618 GCTGCTGCTGCC
1 GCTGCTGCTGCC
1196630 GCTGCTGCTGCC
1 GCTGCTGCTGCC
1196642 G
1 G
1196643 AAGGTCTTAT
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:0.00, C:0.40, G:0.36, T:0.24
Consensus pattern (12 bp):
GCTGCTGCTGCC
Found at i:1200387 original size:16 final size:19
Alignment explanation
Indices: 1200322--1200388 Score: 63
Period size: 19 Copynumber: 3.7 Consensus size: 19
1200312 TTATATGACA
1200322 TATTAA-AATTTTATTAATAT
1 TATTAATAA-TTT-TTAATAT
*
1200342 T-TAAATAATTTTTAATAT
1 TATTAATAATTTTTAATAT
*
1200360 TATTAATTATTTTT-AT-T
1 TATTAATAATTTTTAATAT
1200377 TATT-ATAATTTT
1 TATTAATAATTTT
1200389 AAAAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
16 7 0.17
17 5 0.12
18 10 0.24
19 16 0.39
20 3 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTAATAATTTTTAATAT
Found at i:1200404 original size:15 final size:15
Alignment explanation
Indices: 1200386--1200422 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1200376 TTATTATAAT
1200386 TTTAAAAATATAAAA
1 TTTAAAAATATAAAA
*
1200401 TTTAATAATATAAAA
1 TTTAAAAATATAAAA
*
1200416 ATTAAAA
1 TTTAAAA
1200423 TATTTTATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TTTAAAAATATAAAA
Found at i:1203940 original size:2 final size:2
Alignment explanation
Indices: 1203933--1203975 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1203923 AGATAAGAGA
1203933 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
1203975 A
1 A
1203976 AACAAATTCA
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:1204889 original size:18 final size:18
Alignment explanation
Indices: 1204863--1204898 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1204853 AAATAAAATA
*
1204863 TAAATTTATATAATAATT
1 TAAAATTATATAATAATT
*
1204881 TAAAATTATATTATAATT
1 TAAAATTATATAATAATT
1204899 AATATATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAAATTATATAATAATT
Found at i:1204944 original size:24 final size:24
Alignment explanation
Indices: 1204910--1204989 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 24
1204900 ATATATCAAC
1204910 ATAATAT--ATAATTTATTTTAT-
1 ATAATATAAATAATTTATTTTATA
* *
1204931 ATAATTTATAATAAATTT-TTGTATA
1 ATAATATA-AAT-AATTTATTTTATA
*
1204956 ATAATATAAATAATTTATTTTTAAA
1 ATAATATAAATAATTTA-TTTTATA
1204981 ATAAT-TAAA
1 ATAATATAAA
1204990 ATTAATTAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
21 6 0.13
23 5 0.11
24 14 0.30
25 22 0.47
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (24 bp):
ATAATATAAATAATTTATTTTATA
Found at i:1204948 original size:21 final size:21
Alignment explanation
Indices: 1204910--1204964 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
1204900 ATATATCAAC
**
1204910 ATAATATATAATTTATTTTAT
1 ATAATATATAATAAATTTTAT
* *
1204931 ATAATTTATAATAAATTTTTGT
1 ATAATATATAATAAA-TTTTAT
1204953 ATAATAATATAA
1 ATAAT-ATATAA
1204965 ATAATTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 12 0.44
22 10 0.37
23 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATAATATATAATAAATTTTAT
Found at i:1204959 original size:25 final size:25
Alignment explanation
Indices: 1204931--1205002 Score: 65
Period size: 25 Copynumber: 2.8 Consensus size: 25
1204921 TTTATTTTAT
*
1204931 ATAATTTATAATAAATT-TTTGTATA
1 ATAATTTA-AATAAATTATTTGTAAA
* * *
1204956 ATAATATAAATAATTTATTTTTAAA
1 ATAATTTAAATAAATTATTTGTAAA
* *
1204981 ATAATTAAAATTAATTAATTTG
1 ATAATTTAAATAAATT-ATTTG
1205003 ACCAAACAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
24 7 0.19
25 25 0.69
26 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
ATAATTTAAATAAATTATTTGTAAA
Found at i:1205205 original size:19 final size:18
Alignment explanation
Indices: 1205183--1205224 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
1205173 ATTTGTTATC
*
1205183 ATATTATAATTTATAATT
1 ATATTAAAATTTATAATT
*
1205201 GATATTAAAATTTATCATT
1 -ATATTAAAATTTATAATT
1205220 ATATT
1 ATATT
1205225 TATTTTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
ATATTAAAATTTATAATT
Found at i:1205490 original size:14 final size:15
Alignment explanation
Indices: 1205465--1205521 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
1205455 AATTATTATG
1205465 TATTTTATATTTAAT
1 TATTTTATATTTAAT
*
1205480 TATTTTA-ATTTGAT
1 TATTTTATATTTAAT
* * *
1205494 TAAATTTAATATTAAAA
1 T--ATTTTATATTTAAT
1205511 TATTTTATATT
1 TATTTTATATT
1205522 ATTGAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 7 0.21
15 16 0.48
16 5 0.15
17 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (15 bp):
TATTTTATATTTAAT
Found at i:1205571 original size:2 final size:2
Alignment explanation
Indices: 1205564--1205588 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1205554 ATTGATTTAT
1205564 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 T
1205589 GTAAACAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1206349 original size:19 final size:18
Alignment explanation
Indices: 1206320--1206356 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1206310 TTAATTTAAT
1206320 ATTAAAATATTTTATATA
1 ATTAAAATATTTTATATA
*
1206338 ATTAATAATATTTTTTATA
1 ATTAA-AATATTTTATATA
1206357 TTTTGAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTAAAATATTTTATATA
Found at i:1207014 original size:17 final size:19
Alignment explanation
Indices: 1206984--1207021 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1206974 TAGAGTCATT
*
1206984 TAAATTCAATTTTAAA-AA
1 TAAATTCAAATTTAAAGAA
1207002 TAAA-TCAAATTTAAAGAA
1 TAAATTCAAATTTAAAGAA
1207020 TA
1 TA
1207022 TTAAAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (19 bp):
TAAATTCAAATTTAAAGAA
Found at i:1208139 original size:3 final size:3
Alignment explanation
Indices: 1208131--1208186 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
1208121 AGTGATTTGG
*
1208131 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1208179 TTA TTA TT
1 TTA TTA TT
1208187 TTGAGCCAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1215429 original size:26 final size:25
Alignment explanation
Indices: 1215400--1215453 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1215390 GAAAAAAATG
*
1215400 TAAATATTTTTAATTT-TATATTTATT
1 TAAATAATTTT-ATTTATATA-TTATT
*
1215426 TAAATAATTTTATTTATTTATTATT
1 TAAATAATTTTATTTATATATTATT
1215451 TAA
1 TAA
1215454 TTAAATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TAAATAATTTTATTTATATATTATT
Found at i:1215670 original size:14 final size:14
Alignment explanation
Indices: 1215651--1215677 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1215641 TAAAATATTT
1215651 TAATTTTATTTTAC
1 TAATTTTATTTTAC
1215665 TAATTTTATTTTA
1 TAATTTTATTTTA
1215678 ATTTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (14 bp):
TAATTTTATTTTAC
Found at i:1221668 original size:2 final size:2
Alignment explanation
Indices: 1221661--1221706 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1221651 AAGGACAGCC
*
1221661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1221703 TA TA
1 TA TA
1221707 ATTGACCTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1223047 original size:13 final size:13
Alignment explanation
Indices: 1223016--1223040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1223006 ATTATTTTTA
1223016 AAATATTTATATG
1 AAATATTTATATG
1223029 AAATATTTATAT
1 AAATATTTATAT
1223041 TCAATATATT
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
AAATATTTATATG
Found at i:1223075 original size:28 final size:28
Alignment explanation
Indices: 1223044--1223102 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1223034 TTTATATTCA
*
1223044 ATATATTTTTAAATATAAATATAAAAAT
1 ATATATTTTTAAAAATAAATATAAAAAT
* ***
1223072 ATATTTTTTTAAAAATTTTTATAAAAAT
1 ATATATTTTTAAAAATAAATATAAAAAT
1223100 ATA
1 ATA
1223103 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATATTTTTAAAAATAAATATAAAAAT
Found at i:1223607 original size:2 final size:2
Alignment explanation
Indices: 1223600--1223627 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1223590 TTTAAGAGAA
1223600 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
1223628 GAAGATTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1224592 original size:2 final size:2
Alignment explanation
Indices: 1224578--1224615 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
1224568 ATTATGTATG
1224578 TA TA TA TGA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1224616 AATTCTTGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 32 0.94
3 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1224775 original size:15 final size:15
Alignment explanation
Indices: 1224752--1224787 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1224742 TTTTGGTTTT
* *
1224752 GTCGGCATCGTCGTC
1 GTCGTCATCATCGTC
1224767 GTCGTCATCATCGTC
1 GTCGTCATCATCGTC
1224782 GTCGTC
1 GTCGTC
1224788 GTGGTCTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.33, G:0.28, T:0.31
Consensus pattern (15 bp):
GTCGTCATCATCGTC
Found at i:1226207 original size:19 final size:18
Alignment explanation
Indices: 1226166--1226208 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1226156 ATAATTAAAT
*
1226166 TAAATAAATATAAATTATA
1 TAAA-AAATATAAAATATA
*
1226185 TAAAAAATATAAAAATATG
1 TAAAAAATAT-AAAATATA
1226204 TAAAA
1 TAAAA
1226209 TTAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
TAAAAAATATAAAATATA
Found at i:1228207 original size:26 final size:24
Alignment explanation
Indices: 1228168--1228216 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1228158 TTTCGAATCA
1228168 TTATTTATTTAA-TTAAATAATATT
1 TTATTTATTTAATTTAAA-AATATT
1228192 TTATTTAATTTTAATTTAAAAATAT
1 TTATTT-A-TTTAATTTAAAAATAT
1228217 ATAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.27
25 1 0.05
26 10 0.45
27 5 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTATTTAATTTAAAAATATT
Found at i:1229252 original size:21 final size:21
Alignment explanation
Indices: 1229218--1229258 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1229208 TTGTATAATA
*
1229218 TATTTAAATAAAAATGATTTT
1 TATTTAAATAAAAATAATTTT
1229239 TATTT-AATAAAAAATAATTT
1 TATTTAAAT-AAAAATAATTT
1229259 AAATCAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTTAAATAAAAATAATTTT
Found at i:1231364 original size:2 final size:2
Alignment explanation
Indices: 1231357--1231393 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1231347 ATTTAAGTTA
1231357 AT 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 AT A
1231394 AAACTATAAC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1232505 original size:17 final size:17
Alignment explanation
Indices: 1232478--1232528 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
1232468 TTTTAAAAAA
*
1232478 TATATGCTTATTAATTT
1 TATATTCTTATTAATTT
* *
1232495 TATATTTTTATTAAATT
1 TATATTCTTATTAATTT
*
1232512 TGTATTCTTATTAATTT
1 TATATTCTTATTAATTT
1232529 ATAATGCTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (17 bp):
TATATTCTTATTAATTT
Found at i:1232567 original size:25 final size:24
Alignment explanation
Indices: 1232514--1232564 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
1232504 ATTAAATTTG
1232514 TATTCTTATTAATTTATAATGCTAT
1 TATTCTTATTAATTTATAAT-CTAT
*
1232539 TATTCTTATTAATTTTTAAT-TAT
1 TATTCTTATTAATTTATAATCTAT
1232562 TAT
1 TAT
1232565 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.24
25 19 0.76
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (24 bp):
TATTCTTATTAATTTATAATCTAT
Found at i:1233184 original size:30 final size:29
Alignment explanation
Indices: 1233150--1233231 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
1233140 TTTGATTAAA
*
1233150 AAATTTATATAAAAATAATAATATTTTGAT
1 AAATTTAT-TAAAAATAATAATATTTAGAT
* *
1233180 AAATTGT-TTCAAAATAATATTATTTAGAT
1 AAATT-TATTAAAAATAATAATATTTAGAT
*
1233209 -AATTTATTTGTAAAATAATAATA
1 AAATTTA-TT-AAAAATAATAATA
1233232 GTCTAATACA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 1 0.02
28 4 0.09
29 20 0.47
30 17 0.40
31 1 0.02
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (29 bp):
AAATTTATTAAAAATAATAATATTTAGAT
Found at i:1233194 original size:29 final size:30
Alignment explanation
Indices: 1233161--1233231 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
1233151 AATTTATATA
* *
1233161 AAAATAATAATATTTTGATAAATTGTTT-C
1 AAAATAATAATATTTAGATAAATTATTTGC
* * *
1233190 AAAATAATATTATTTAGATAATTTATTTGT
1 AAAATAATAATATTTAGATAAATTATTTGC
1233220 AAAATAATAATA
1 AAAATAATAATA
1233232 GTCTAATACA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
29 24 0.69
30 11 0.31
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (30 bp):
AAAATAATAATATTTAGATAAATTATTTGC
Found at i:1234775 original size:37 final size:34
Alignment explanation
Indices: 1234733--1234806 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 34
1234723 TAAATTATTT
*
1234733 TTATATATTTTTATGTATT-ATAATTATATGTCAAATA
1 TTATATA-TTTTATATATTAATAATT-TATGT--AATA
1234770 TTATATATTTTATATATTAATAATTTATGTAATA
1 TTATATATTTTATATATTAATAATTTATGTAATA
1234804 TTA
1 TTA
1234807 ATTTTAATAC
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
34 7 0.20
36 15 0.43
37 13 0.37
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (34 bp):
TTATATATTTTATATATTAATAATTTATGTAATA
Found at i:1251722 original size:2 final size:2
Alignment explanation
Indices: 1251715--1251741 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1251705 ATACCAGAAC
1251715 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1251742 GGGATTTTGG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1252168 original size:17 final size:18
Alignment explanation
Indices: 1252146--1252183 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1252136 TTTTTAATTT
1252146 AATTAAAA-ATTAATTAA
1 AATTAAAATATTAATTAA
*
1252163 AATTAAAATATTACTTAA
1 AATTAAAATATTAATTAA
1252181 AAT
1 AAT
1252184 ATTCTATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTAAAATATTAATTAA
Found at i:1252383 original size:27 final size:25
Alignment explanation
Indices: 1252330--1252389 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 25
1252320 TTCAAATTAA
*
1252330 ATTTAATTTATAATAATTTTTAATTT
1 ATTTAAATTATAATAATTTTT-ATTT
1252356 ACTTTAAATTATAAATAATTTATT-TTT
1 A-TTTAAATTAT-AATAATTT-TTATTT
1252383 ATTTAAA
1 ATTTAAA
1252390 AATATAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 7 0.23
27 13 0.43
28 8 0.27
29 2 0.07
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTAAATTATAATAATTTTTATTT
Found at i:1252392 original size:21 final size:21
Alignment explanation
Indices: 1252350--1252393 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1252340 TAATAATTTT
*
1252350 TAATTTACTTTAAATTATAAA
1 TAATTTACTTTAAATTAAAAA
* * *
1252371 TAATTTATTTTTATTTAAAAA
1 TAATTTACTTTAAATTAAAAA
1252392 TA
1 TA
1252394 TAAAATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATTTACTTTAAATTAAAAA
Found at i:1253100 original size:15 final size:15
Alignment explanation
Indices: 1253080--1253110 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1253070 TTTGAATGGA
1253080 TTGTTAATTTGTAAT
1 TTGTTAATTTGTAAT
1253095 TTGTTAATTTGTAAT
1 TTGTTAATTTGTAAT
1253110 T
1 T
1253111 CTTTCCTAAT
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:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (15 bp):
TTGTTAATTTGTAAT
Found at i:1263908 original size:2 final size:2
Alignment explanation
Indices: 1263903--1263938 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1263893 CTTTTTTATT
1263903 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1263939 AATTTATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1265936 original size:25 final size:25
Alignment explanation
Indices: 1265889--1265937 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
1265879 TCTATCTATA
* *
1265889 ATAAAAATATATTTTATTTTTAATT
1 ATAAAAATATATTTTAATATTAATT
1265914 ATAAAAA-ATATTTATAATATTAAT
1 ATAAAAATATATTT-TAATATTAAT
1265938 AAATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
ATAAAAATATATTTTAATATTAATT
Found at i:1266086 original size:20 final size:19
Alignment explanation
Indices: 1266061--1266099 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1266051 AATTTATTTT
1266061 TAAAAGAAATTCACTCTTTA
1 TAAAAGAAA-TCACTCTTTA
**
1266081 TAAAAGCCATCACTCTTTA
1 TAAAAGAAATCACTCTTTA
1266100 ACCACTATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAAAGAAATCACTCTTTA
Found at i:1266902 original size:2 final size:2
Alignment explanation
Indices: 1266895--1266930 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1266885 TAGATGATGG
1266895 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
1266931 TTCATTTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1270130 original size:44 final size:44
Alignment explanation
Indices: 1270060--1270159 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
1270050 CTAATTAATG
* *
1270060 GCCTAAATTGTAGGATCTAATTATACAGCTATAGTTGACTTT-TA
1 GCCTAAATTGTAGAATCTAATCATACAGCTATAGTTGA-TTTCTA
* * * * *
1270104 GCTTAAATTGTAGAATCTGATCATACAGTTGTATTTGATTTCTA
1 GCCTAAATTGTAGAATCTAATCATACAGCTATAGTTGATTTCTA
1270148 GCCTAAATTGTA
1 GCCTAAATTGTA
1270160 AGATTTGATA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.06
44 44 0.94
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (44 bp):
GCCTAAATTGTAGAATCTAATCATACAGCTATAGTTGATTTCTA
Found at i:1274775 original size:47 final size:44
Alignment explanation
Indices: 1274707--1274838 Score: 151
Period size: 47 Copynumber: 3.0 Consensus size: 44
1274697 CGAGAAAGTA
*
1274707 GAGAAAAAAATTAT-AGTAATGAAGGCTGAATAAAACAGATTCTG
1 GAGAAAAAAATT-TCAGCAATGAAGGCTGAATAAAACAGATTCTG
* * *
1274751 GAAAGGAAAAAAATTTCAGCAATGAAGGCTGAATAACACAAATTTTG
1 G--A-GAAAAAAATTTCAGCAATGAAGGCTGAATAAAACAGATTCTG
* * *
1274798 GA-AAAAAAATTCCAGCAATAAAGGCTGAATAGAACAGATTC
1 GAGAAAAAAATTTCAGCAATGAAGGCTGAATAAAACAGATTC
1274839 GAGGAAGGTG
Statistics
Matches: 74, Mismatches: 10, Indels: 9
0.80 0.11 0.10
Matches are distributed among these distances:
43 33 0.45
44 1 0.01
45 1 0.01
46 2 0.03
47 37 0.50
ACGTcount: A:0.50, C:0.11, G:0.19, T:0.20
Consensus pattern (44 bp):
GAGAAAAAAATTTCAGCAATGAAGGCTGAATAAAACAGATTCTG
Found at i:1275006 original size:21 final size:21
Alignment explanation
Indices: 1274982--1275022 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1274972 CTATATTCTT
1274982 TTATATACACATTCTCTTAGC
1 TTATATACACATTCTCTTAGC
1275003 TTATATACACATTCTCTTAG
1 TTATATACACATTCTCTTAG
1275023 TATTAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (21 bp):
TTATATACACATTCTCTTAGC
Found at i:1275118 original size:44 final size:44
Alignment explanation
Indices: 1275055--1275157 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
1275045 TTGATAGTTT
* * * *
1275055 TTGTAGGATATGATTATACAGCTATAGTTGACTTTTAGCTTAAA
1 TTGTAGGATCTGATTATACAACTATAGTTGACTTCTAGCCTAAA
* * * *
1275099 TTGTAGGATCTGATTATACAATTGTATTTTACTTCTAGCCTAAA
1 TTGTAGGATCTGATTATACAACTATAGTTGACTTCTAGCCTAAA
1275143 TTGTAGGATCTGATT
1 TTGTAGGATCTGATT
1275158 TTTCAAAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.29, C:0.11, G:0.17, T:0.43
Consensus pattern (44 bp):
TTGTAGGATCTGATTATACAACTATAGTTGACTTCTAGCCTAAA
Found at i:1279134 original size:13 final size:13
Alignment explanation
Indices: 1279116--1279154 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
1279106 TATTTTTTTA
1279116 AATATTTATATTT
1 AATATTTATATTT
1279129 AATATTTATATTT
1 AATATTTATATTT
1279142 AATA--TATATTT
1 AATATTTATATTT
1279153 AA
1 AA
1279155 ATATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 9 0.35
13 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:1279151 original size:11 final size:11
Alignment explanation
Indices: 1279122--1279159 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
1279112 TTTAAATATT
1279122 TATATTTAATA
1 TATATTTAATA
1279133 TTTATATTTAATA
1 --TATATTTAATA
1279146 TATATTTAA-A
1 TATATTTAATA
1279156 TATA
1 TATA
1279160 AAAATAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 9 0.36
13 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTTAATA
Found at i:1279285 original size:14 final size:13
Alignment explanation
Indices: 1279244--1279286 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
1279234 AAATATATTC
*
1279244 ATATTTAATATTA
1 ATATTTAATATAA
*
1279257 ATATTTAAATTTAA
1 ATATTT-AATATAA
1279271 ATAATTTAATATAA
1 AT-ATTTAATATAA
1279285 AT
1 AT
1279287 TTTCAGATAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 6 0.24
14 15 0.60
15 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATATTTAATATAA
Found at i:1280168 original size:29 final size:29
Alignment explanation
Indices: 1280122--1280184 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
1280112 TATACATTAA
* *
1280122 ATATATTTTTATAAATATTATTAATTACATT
1 ATATACTTTTAT-AATATAATTAATTACA-T
1280153 ATATACTTTTAT-ATATAATTAATTACAT
1 ATATACTTTTATAATATAATTAATTACAT
1280181 ATAT
1 ATAT
1280185 GGATAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 14 0.47
31 11 0.37
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (29 bp):
ATATACTTTTATAATATAATTAATTACAT
Found at i:1280849 original size:8 final size:8
Alignment explanation
Indices: 1280836--1280972 Score: 52
Period size: 7 Copynumber: 16.4 Consensus size: 8
1280826 TTTATTTATA
1280836 ATATATTT
1 ATATATTT
1280844 ATATATTTT
1 ATATA-TTT
1280853 ATTATATTAT
1 A-TATATT-T
*
1280863 AATTATGTTT
1 -A-TATATTT
*
1280873 AAAATATTT
1 -ATATATTT
1280882 -TATATTT
1 ATATATTT
*
1280889 ATAAAAATTT
1 AT--ATATTT
1280899 A-ATATTT
1 ATATATTT
*
1280906 ATATTTTT
1 ATATATTT
1280914 ATTATGAATTT
1 A-TAT--ATTT
1280925 AGTAT-TTT
1 A-TATATTT
* *
1280933 ATACATGT
1 ATATATTT
1280941 -TATATTT
1 ATATATTT
*
1280948 ACATATTT
1 ATATATTT
*
1280956 -TATTTTT
1 ATATATTT
1280963 ATAT-TTT
1 ATATATTT
1280970 ATA
1 ATA
1280973 GAAAATATTA
Statistics
Matches: 99, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
7 30 0.30
8 27 0.27
9 14 0.14
10 14 0.14
11 14 0.14
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (8 bp):
ATATATTT
Found at i:1280889 original size:16 final size:17
Alignment explanation
Indices: 1280872--1280908 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1280862 TAATTATGTT
1280872 TAAAATATTTTATATTTA
1 TAAAA-ATTTTATATTTA
*
1280890 TAAAAATTTAATATTTA
1 TAAAAATTTTATATTTA
1280907 TA
1 TA
1280909 TTTTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TAAAAATTTTATATTTA
Found at i:1280903 original size:17 final size:18
Alignment explanation
Indices: 1280828--1280908 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 18
1280818 GTAATACGTT
*
1280828 TATTTATAATATATTTATA
1 TATTTATAAAATATTTA-A
**
1280847 TATTT-TATTATATTATAA
1 TATTTATAAAATATT-TAA
*
1280865 TTATGTT-TAAAATATTTTA
1 -TAT-TTATAAAATATTTAA
1280884 TATTTATAAAA-ATTTAA
1 TATTTATAAAATATTTAA
1280901 TATTTATA
1 TATTTATA
1280909 TTTTTATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
17 15 0.28
18 17 0.32
19 12 0.23
20 9 0.17
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
TATTTATAAAATATTTAA
Found at i:1283807 original size:18 final size:18
Alignment explanation
Indices: 1283784--1283830 Score: 67
Period size: 19 Copynumber: 2.6 Consensus size: 18
1283774 TTATCATATT
*
1283784 AAAATTATATTAAATTTA
1 AAAATTATATTAAATTAA
1283802 AAAATTATAATTAAATTAA
1 AAAATTAT-ATTAAATTAA
*
1283821 AAAAATATAT
1 AAAATTATAT
1283831 AATTTATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTATATTAAATTAA
Found at i:1283816 original size:19 final size:20
Alignment explanation
Indices: 1283784--1283834 Score: 70
Period size: 18 Copynumber: 2.6 Consensus size: 20
1283774 TTATCATATT
*
1283784 AAAATTAT-ATTAAATT-TA
1 AAAATTATAATTAAATTAAA
1283802 AAAATTATAATTAAATTAAA
1 AAAATTATAATTAAATTAAA
1283822 AAAATATATAATT
1 AAAAT-TATAATT
1283835 TATCCACACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 8 0.28
19 8 0.28
20 6 0.21
21 7 0.24
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATTATAATTAAATTAAA
Found at i:1284152 original size:2 final size:2
Alignment explanation
Indices: 1284145--1284169 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1284135 GTTAATAGCT
1284145 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 T
1284170 TTAGGTTGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1286314 original size:4 final size:4
Alignment explanation
Indices: 1286307--1286334 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1286297 TATGTATATA
1286307 TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG
1286335 GAAATAATAA
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:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1286943 original size:19 final size:19
Alignment explanation
Indices: 1286915--1286952 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1286905 TTCAGTTGGG
*
1286915 TTACAGTAATTATTATTGT
1 TTACAATAATTATTATTGT
1286934 TTACAATAATTATTATTGT
1 TTACAATAATTATTATTGT
1286953 ATTATTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (19 bp):
TTACAATAATTATTATTGT
Found at i:1288315 original size:4 final size:4
Alignment explanation
Indices: 1288306--1288339 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
1288296 TTAATATAGC
*
1288306 AATA AATA AATA AATA AATA AATA AACA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
1288340 AATTGCAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:1293020 original size:2 final size:2
Alignment explanation
Indices: 1293015--1293044 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1293005 AACTCCTCCT
1293015 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1293045 TGGTAGCAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1294032 original size:21 final size:23
Alignment explanation
Indices: 1293983--1294033 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
1293973 GAGTAGATTT
* * *
1293983 TTTTAAAATTTATCTCAATTTTT
1 TTTTAAAATTCATCTCAATATTA
1294006 TTTTAAAATTCAT-T-AATATTA
1 TTTTAAAATTCATCTCAATATTA
1294027 TTTTAAA
1 TTTTAAA
1294034 TTTTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
22 1 0.04
23 12 0.48
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTAAAATTCATCTCAATATTA
Found at i:1294225 original size:113 final size:116
Alignment explanation
Indices: 1294039--1294271 Score: 382
Period size: 113 Copynumber: 2.0 Consensus size: 116
1294029 TTAAATTTTT
*
1294039 AATAATTAAATATTCTTTTAATAAAGAGAAATATATTAAGAAATTACATGAAAAAATGAGGTAAA
1 AATAATTAAATATTCTTTAAATAAAGAGAAATATATTAAGAAATTACATGAAAAAATGAGGTAAA
*
1294104 AAGT-A-AAAAAA-AAAAATTGTCTTCTTTTGGTCTTAGTACTTATTAGAC
66 AAGTAATAAAAAATAAAAATTGTCTTCTTTTGGCCTTAGTACTTATTAGAC
*
1294152 AATAATTAAATGTTCTTTAAATAAAGAGAAATATATTAAGAAATTACATGAAAAAATGAGGTAAA
1 AATAATTAAATATTCTTTAAATAAAGAGAAATATATTAAGAAATTACATGAAAAAATGAGGTAAA
*
1294217 AAGTAAAAATAAAAAATAAAAATTGTCTTCTTTTGGCCTTATTACTTATTAGAC
66 AAGT---AATAAAAAATAAAAATTGTCTTCTTTTGGCCTTAGTACTTATTAGAC
1294271 A
1 A
1294272 TAGCCTTAAT
Statistics
Matches: 110, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
113 67 0.61
117 1 0.01
118 6 0.05
119 36 0.33
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.33
Consensus pattern (116 bp):
AATAATTAAATATTCTTTAAATAAAGAGAAATATATTAAGAAATTACATGAAAAAATGAGGTAAA
AAGTAATAAAAAATAAAAATTGTCTTCTTTTGGCCTTAGTACTTATTAGAC
Found at i:1296420 original size:2 final size:2
Alignment explanation
Indices: 1296413--1296437 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1296403 AATCATGTGA
1296413 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 A
1296438 ATAGATGTAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1296572 original size:13 final size:15
Alignment explanation
Indices: 1296554--1296590 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1296544 CTAATAAATC
1296554 CAAAATA-ATAT-AT
1 CAAAATATATATGAT
*
1296567 CAAAATATATTTGAT
1 CAAAATATATATGAT
1296582 CAAAATATA
1 CAAAATATA
1296591 CTAGATGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.33
14 3 0.14
15 11 0.52
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (15 bp):
CAAAATATATATGAT
Found at i:1297777 original size:2 final size:2
Alignment explanation
Indices: 1297765--1297794 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1297755 TTAATTAAGC
*
1297765 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1297795 AGTGGCCTTT
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:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1297897 original size:31 final size:31
Alignment explanation
Indices: 1297859--1297919 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
1297849 GATGGTTTTC
1297859 CATTTAAAAAGGGATTGAAAAATTATGTTAT
1 CATTTAAAAAGGGATTGAAAAATTATGTTAT
1297890 CATTTAAAAAGGGATTGAAAAATTATGTTA
1 CATTTAAAAAGGGATTGAAAAATTATGTTA
1297920 CCGGATTCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.03, G:0.16, T:0.34
Consensus pattern (31 bp):
CATTTAAAAAGGGATTGAAAAATTATGTTAT
Found at i:1297984 original size:21 final size:21
Alignment explanation
Indices: 1297960--1298011 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 21
1297950 TGTTCAATAT
*
1297960 AAATATTATATTATTTTTTAA
1 AAATATTATATTATATTTTAA
* *
1297981 AAATTTTTTA-TATATTTTAA
1 AAATATTATATTATATTTTAA
*
1298001 AAA-ATCATATT
1 AAATATTATATT
1298012 TTATATGTAG
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
19 3 0.12
20 13 0.54
21 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATTATATTATATTTTAA
Found at i:1299412 original size:2 final size:2
Alignment explanation
Indices: 1299407--1299435 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1299397 TATATATATA
1299407 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1299436 AATACAAATT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1300020 original size:30 final size:29
Alignment explanation
Indices: 1300008--1300079 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 29
1299998 AAAAAATTAT
1300008 TAAAATATATAAATATATAAAAAAAATTA
1 TAAAATATATAAATATATAAAAAAAATTA
* * *
1300037 TAAAATA-A-AAAT-TAT-TAATATATT-
1 TAAAATATATAAATATATAAAAAAAATTA
*
1300061 TAAAAAATATAAATATATA
1 TAAAATATATAAATATATA
1300080 TATATATAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
24 6 0.17
25 7 0.20
26 7 0.20
27 7 0.20
28 1 0.03
29 7 0.20
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (29 bp):
TAAAATATATAAATATATAAAAAAAATTA
Found at i:1300023 original size:8 final size:8
Alignment explanation
Indices: 1300010--1300101 Score: 54
Period size: 8 Copynumber: 11.9 Consensus size: 8
1300000 AAAATTATTA
1300010 AAATATAT
1 AAATATAT
1300018 AAATATAT
1 AAATATAT
1300026 AAA-A-A-
1 AAATATAT
1300031 AAAT-TAT
1 AAATATAT
*
1300038 AAA-ATAA
1 AAATATAT
1300045 AAAT-TATT
1 AAATATA-T
*
1300053 AATATATTT
1 AA-ATATAT
*
1300062 AAAAAATAT
1 -AAATATAT
1300071 AAATATAT
1 AAATATAT
*
1300079 ATATATAT
1 AAATATAT
*
1300087 -AATATTTT
1 AAATA-TAT
1300095 AAATATA
1 AAATATA
1300102 ATTATATATA
Statistics
Matches: 63, Mismatches: 10, Indels: 22
0.66 0.11 0.23
Matches are distributed among these distances:
5 3 0.05
6 2 0.03
7 14 0.22
8 30 0.48
9 11 0.17
10 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AAATATAT
Found at i:1300056 original size:13 final size:14
Alignment explanation
Indices: 1299981--1300051 Score: 60
Period size: 14 Copynumber: 5.0 Consensus size: 14
1299971 CAGATCCGTG
1299981 AAAATATAAAA-TAT
1 AAAATA-AAAATTAT
*
1299995 AATA-AAAAATTATT
1 AAAATAAAAATTA-T
1300009 AAAATATATAAA-TAT
1 AAAATA-A-AAATTAT
1300024 ATAAA-AAAAATTAT
1 A-AAATAAAAATTAT
1300038 AAAATAAAAATTAT
1 AAAATAAAAATTAT
1300052 TAATATATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
12 4 0.09
13 9 0.19
14 21 0.45
15 4 0.09
16 6 0.13
17 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAATAAAAATTAT
Found at i:1300066 original size:19 final size:19
Alignment explanation
Indices: 1300042--1300078 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1300032 AATTATAAAA
* *
1300042 TAAAAATTATTAATATATT
1 TAAAAAATATAAATATATT
1300061 TAAAAAATATAAATATAT
1 TAAAAAATATAAATATAT
1300079 ATATATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAAAATATAAATATATT
Found at i:1300090 original size:34 final size:34
Alignment explanation
Indices: 1300010--1300107 Score: 96
Period size: 34 Copynumber: 2.9 Consensus size: 34
1300000 AAAATTATTA
**
1300010 AAATATATA-AATATATAAAAAAAATTATAAAAT
1 AAATATATATAATATATTTAAAAAATTATAAAAT
*
1300043 AAAAAT-TATTAATATATTTAAAAAA-TATAAATAT
1 AAATATATA-TAATATATTTAAAAAATTATAAA-AT
*
1300077 ATATATATATAATAT-TTTAAATATAATTATA
1 AAATATATATAATATATTTAAA-A-AATTATA
1300108 TATAAAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
32 2 0.04
33 17 0.32
34 26 0.49
35 4 0.08
36 4 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
AAATATATATAATATATTTAAAAAATTATAAAAT
Found at i:1300918 original size:31 final size:32
Alignment explanation
Indices: 1300873--1300941 Score: 88
Period size: 31 Copynumber: 2.2 Consensus size: 32
1300863 TTTTAATTTA
* *
1300873 TTTAAATTATTTTTTAACT-TTTAAATA-TATT
1 TTTAAATTAATTTTTAA-TAATTAAATATTATT
*
1300904 TTTAATTTAATTTTTAATAATTAAATATTATT
1 TTTAAATTAATTTTTAATAATTAAATATTATT
1300936 TTTAAA
1 TTTAAA
1300942 AAATATATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 1 0.03
31 22 0.69
32 9 0.28
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTAAATTAATTTTTAATAATTAAATATTATT
Found at i:1300951 original size:20 final size:20
Alignment explanation
Indices: 1300913--1300951 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1300903 TTTTAATTTA
* *
1300913 ATTTTTAATAATTAAATATT
1 ATTTTTAAAAAATAAATATT
*
1300933 ATTTTTAAAAAATATATAT
1 ATTTTTAAAAAATAAATAT
1300952 ATTAAGAAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTTTAAAAAATAAATATT
Found at i:1301097 original size:2 final size:2
Alignment explanation
Indices: 1301090--1301114 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1301080 GTTCCTAGCC
1301090 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 T
1301115 TATTTCTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1301943 original size:17 final size:18
Alignment explanation
Indices: 1301899--1301952 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
1301889 AATAATTATG
*
1301899 ATTACAAAATTAAAAATT
1 ATTACAAAATAAAAAATT
*
1301917 -TTATATAAATAAAAAATT
1 ATTACA-AAATAAAAAATT
1301935 ATTA-AAAATAAAATAATT
1 ATTACAAAATAAAA-AATT
1301953 TAAAATATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 12 0.39
18 16 0.52
19 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTACAAAATAAAAAATT
Found at i:1302223 original size:25 final size:24
Alignment explanation
Indices: 1302167--1302232 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 24
1302157 ATAATTATTA
* *
1302167 AAAAATTAATTAAACTGTAATATAAT
1 AAAAATT-ATTAAAAT-TTATATAAT
*
1302193 ATAAATATATTAAAATTTATATAAT
1 AAAAAT-TATTAAAATTTATATAAT
1302218 AAAAATTATTAAAAT
1 AAAAATTATTAAAAT
1302233 ATTTAAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
24 9 0.26
25 13 0.37
26 12 0.34
27 1 0.03
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAATTATTAAAATTTATATAAT
Found at i:1302743 original size:18 final size:18
Alignment explanation
Indices: 1302720--1302755 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1302710 TTATTAAATA
1302720 AATTTATTTAAAAATTTT
1 AATTTATTTAAAAATTTT
*
1302738 AATTTATTTAAATATTTT
1 AATTTATTTAAAAATTTT
1302756 TTATACATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
AATTTATTTAAAAATTTT
Found at i:1303661 original size:32 final size:32
Alignment explanation
Indices: 1303620--1303683 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
1303610 GCTATCAAGA
1303620 GATAAATGATAATATATTAAAAAATTAAAAAT
1 GATAAATGATAATATATTAAAAAATTAAAAAT
*
1303652 GATAAATGATAATGTATTAAAAAATTAAAAAT
1 GATAAATGATAATATATTAAAAAATTAAAAAT
1303684 ATTTTGAAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (32 bp):
GATAAATGATAATATATTAAAAAATTAAAAAT
Found at i:1306968 original size:16 final size:16
Alignment explanation
Indices: 1306928--1306974 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1306918 TTAAATTTAT
*
1306928 TTAAATTATTTTTA-AA
1 TTAAATT-TTTTAATAA
*
1306944 TTTAA-TTTTTAATAA
1 TTAAATTTTTTAATAA
1306959 TTAAATTTTTTAATAA
1 TTAAATTTTTTAATAA
1306975 AAAGAAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 5 0.19
15 7 0.27
16 14 0.54
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAAATTTTTTAATAA
Found at i:1307129 original size:2 final size:2
Alignment explanation
Indices: 1307122--1307146 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1307112 GTTCATAGCC
1307122 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 T
1307147 TATTTTTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1308951 original size:23 final size:23
Alignment explanation
Indices: 1308908--1308955 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
1308898 ACTATTTATT
*
1308908 AAATTAAAAATAAATCTTAATATA
1 AAATTAAAAATAAATCATAAT-TA
1308932 AAATT-AAAA-AAATACATAATTA
1 AAATTAAAAATAAAT-CATAATTA
1308954 AA
1 AA
1308956 TATAAAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 8 0.36
23 9 0.41
24 5 0.23
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATTAAAAATAAATCATAATTA
Found at i:1312183 original size:10 final size:9
Alignment explanation
Indices: 1312163--1312211 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
1312153 TGAATCCGTG
1312163 AAAATATAA
1 AAAATATAA
*
1312172 AATATGATAA
1 AAAAT-ATAA
*
1312182 AAAATATTA
1 AAAATATAA
1312191 AAAATATAA
1 AAAATATAA
1312200 AAAATTATAA
1 AAAA-TATAA
1312210 AA
1 AA
1312212 TAAAAATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
9 19 0.56
10 15 0.44
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (9 bp):
AAAATATAA
Found at i:1312215 original size:33 final size:33
Alignment explanation
Indices: 1312178--1312243 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1312168 ATAAAATATG
1312178 ATAAAAAATATTAAAAATATAAAAAAT-TATAAA
1 ATAAAAAATATT-AAAATATAAAAAATATATAAA
* * *
1312211 ATAAAAATTATTAATATATTAAAAATATATAAA
1 ATAAAAAATATTAAAATATAAAAAATATATAAA
1312244 TATATAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (33 bp):
ATAAAAAATATTAAAATATAAAAAATATATAAA
Found at i:1312235 original size:24 final size:25
Alignment explanation
Indices: 1312164--1312274 Score: 84
Period size: 26 Copynumber: 4.4 Consensus size: 25
1312154 GAATCCGTGA
* * *
1312164 AAATATAAAATATGATAAAAAATATT
1 AAATATATAATAT-ATTAAAAATAAT
* * *
1312190 AAAAATATAAAAAATTATAAAATAA-
1 AAATATATAATATATTA-AAAATAAT
1312215 AAAT-TATTAATATATTAAAAATATAT
1 AAATATA-TAATATATTAAAAATA-AT
* *
1312241 AAATATATAATATTTTAAATATAAT
1 AAATATATAATATATTAAAAATAAT
*
1312266 -TATATATAA
1 AAATATATAA
1312275 AAAGTAGCAT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
24 16 0.24
25 17 0.25
26 33 0.49
27 2 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (25 bp):
AAATATATAATATATTAAAAATAAT
Found at i:1312245 original size:19 final size:19
Alignment explanation
Indices: 1312163--1312250 Score: 84
Period size: 19 Copynumber: 5.0 Consensus size: 19
1312153 TGAATCCGTG
1312163 AAAATATA-AAATATGATAA
1 AAAATATATAAATAT-ATAA
*
1312182 AAAATAT-TAAAAATATAA
1 AAAATATATAAATATATAA
1312200 AAAAT-TAT-AA-A-AT-A
1 AAAATATATAAATATATAA
* *
1312214 AAAAT-TATTAATATATTA
1 AAAATATATAAATATATAA
1312232 AAAATATATAAATATATAA
1 AAAATATATAAATATATAA
1312251 TATTTTAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
14 9 0.15
15 4 0.07
16 2 0.03
17 5 0.08
18 16 0.27
19 23 0.39
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAATATATAAATATATAA
Found at i:1312248 original size:10 final size:10
Alignment explanation
Indices: 1312166--1312249 Score: 52
Period size: 10 Copynumber: 8.3 Consensus size: 10
1312156 ATCCGTGAAA
1312166 ATAT-AAAAT
1 ATATAAAAAT
1312175 ATGATAAAAA-
1 AT-ATAAAAAT
1312185 ATATTAAAAAT
1 ATA-TAAAAAT
1312196 ATA-AAAAATT
1 ATATAAAAA-T
1312206 ATAAAATAAAAAT
1 AT---ATAAAAAT
* *
1312219 -TATTAATAT
1 ATATAAAAAT
1312228 AT-TAAAAAT
1 ATATAAAAAT
*
1312237 ATATAAATAT
1 ATATAAAAAT
1312247 ATA
1 ATA
1312250 ATATTTTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
9 21 0.36
10 23 0.39
11 7 0.12
12 1 0.02
13 2 0.03
14 5 0.08
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:1313325 original size:19 final size:21
Alignment explanation
Indices: 1313290--1313332 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
1313280 AAACCTTTTT
1313290 TAATTTTTTTAAGATTCAGGC
1 TAATTTTTTTAAGATTCAGGC
1313311 TAATTTTTTT-A-ATTCAGGC
1 TAATTTTTTTAAGATTCAGGC
1313330 TAA
1 TAA
1313333 AAGTCATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.50
20 1 0.05
21 10 0.45
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.49
Consensus pattern (21 bp):
TAATTTTTTTAAGATTCAGGC
Found at i:1314526 original size:22 final size:22
Alignment explanation
Indices: 1314488--1314544 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
1314478 AAATCAAATT
1314488 TTAATTTTATTA-AATT-ATATAA
1 TTAATTTT-TTATAATTAATA-AA
*
1314510 TTAATTTTTTATTATTAATAAA
1 TTAATTTTTTATAATTAATAAA
*
1314532 TTAAATTATTTAT
1 TT-AATTTTTTAT
1314545 GTTAATTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 12 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTTTTTATAATTAATAAA
Found at i:1315719 original size:14 final size:15
Alignment explanation
Indices: 1315697--1315730 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1315687 CATTTTTTAT
1315697 TTTTATAAAAAAATA
1 TTTTATAAAAAAATA
*
1315712 TTTT-TAAAAAATTA
1 TTTTATAAAAAAATA
1315726 TTTTA
1 TTTTA
1315731 ACTTCTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTATAAAAAAATA
Found at i:1317714 original size:19 final size:19
Alignment explanation
Indices: 1317671--1317722 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1317661 TTATAATTAA
* *
1317671 ATTTTAATAAAAATATCTT
1 ATTTTAATTAAAATATATT
* *
1317690 AATTTAATTAAAATTTATT
1 ATTTTAATTAAAATATATT
*
1317709 ATTTTAATTCAAAT
1 ATTTTAATTAAAAT
1317723 CAAATCAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTAATTAAAATATATT
Found at i:1320075 original size:2 final size:2
Alignment explanation
Indices: 1320068--1320104 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1320058 TTTCAAAAAC
1320068 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
1320105 TTCTAGTTAC
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:1320657 original size:3 final size:3
Alignment explanation
Indices: 1320649--1320682 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1320639 CACTTAAAGC
*
1320649 ATA ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1320683 ATACTCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1321155 original size:7 final size:7
Alignment explanation
Indices: 1321143--1321168 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1321133 CACTGCCACT
1321143 GCCATGA
1 GCCATGA
1321150 GCCATGA
1 GCCATGA
1321157 GCCATGA
1 GCCATGA
1321164 GCCAT
1 GCCAT
1321169 CTGCCATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (7 bp):
GCCATGA
Found at i:1321174 original size:14 final size:14
Alignment explanation
Indices: 1321137--1321175 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1321127 GTCTGGCACT
1321137 GCCA-CTGCCATGA
1 GCCATCTGCCATGA
**
1321150 GCCATGAGCCATGA
1 GCCATCTGCCATGA
1321164 GCCATCTGCCAT
1 GCCATCTGCCAT
1321176 TGCCAGCAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.23, C:0.36, G:0.23, T:0.18
Consensus pattern (14 bp):
GCCATCTGCCATGA
Found at i:1326286 original size:2 final size:2
Alignment explanation
Indices: 1326279--1326303 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1326269 AGTCAAATGT
1326279 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
1326304 GTGTATCAAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1326883 original size:2 final size:2
Alignment explanation
Indices: 1326876--1326904 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1326866 GGGAAATAGG
1326876 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
1326905 GGGTACTTAC
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:1328645 original size:21 final size:21
Alignment explanation
Indices: 1328620--1328662 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1328610 TTATGTACAA
*
1328620 AAAAGAAGCAGCAAAAAAACC
1 AAAAGAAGCAACAAAAAAACC
1328641 AAAAGAAGCAACAAAAAAACC
1 AAAAGAAGCAACAAAAAAACC
1328662 A
1 A
1328663 GAAGTTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.70, C:0.19, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAGAAGCAACAAAAAAACC
Found at i:1330052 original size:16 final size:17
Alignment explanation
Indices: 1330018--1330074 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 17
1330008 GTTAATTAAA
1330018 AAATAAT-TAAAAT-AT
1 AAATAATATAAAATAAT
*
1330033 --ATAATATAATATAA-
1 AAATAATATAAAATAAT
1330047 AAATAATATAAAATAAT
1 AAATAATATAAAATAAT
1330064 AAAT-ATATAAA
1 AAATAATATAAA
1330075 TATTTTAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 1 0.03
16 20 0.57
17 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAATAATATAAAATAAT
Found at i:1330055 original size:21 final size:20
Alignment explanation
Indices: 1330017--1330064 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
1330007 CGTTAATTAA
1330017 AAAATAAT-T-AAAATATAT
1 AAAATAATATAAAAATATAT
*
1330035 AATATAATATAAAAATAATAT
1 AAAATAATATAAAAAT-ATAT
1330056 AAAATAATA
1 AAAATAATA
1330065 AATATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 1 0.04
20 5 0.20
21 12 0.48
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAATAATATAAAAATATAT
Found at i:1330092 original size:27 final size:27
Alignment explanation
Indices: 1330062--1330142 Score: 74
Period size: 32 Copynumber: 2.9 Consensus size: 27
1330052 ATATAAAATA
*
1330062 ATAAATATATAAATATTTTAATTTTAT
1 ATAAATATATAAATATTTTAAATTTAT
* *
1330089 ATAATATAAATTATTAATATATTAAAATTTAT
1 ATAA-AT--A-TATAAATAT-TTTAAATTTAT
*
1330121 ATAAATATA-AAATATATTAAAT
1 ATAAATATATAAATATTTTAAAT
1330143 ACGAATATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
26 5 0.12
27 9 0.21
28 4 0.09
29 1 0.02
30 1 0.02
31 10 0.23
32 13 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATAAATATATAAATATTTTAAATTTAT
Found at i:1330143 original size:16 final size:15
Alignment explanation
Indices: 1330091--1330143 Score: 54
Period size: 17 Copynumber: 3.3 Consensus size: 15
1330081 AATTTTATAT
1330091 AATAT-AAATTATTA
1 AATATAAAATTATTA
1330105 ATATATTAAAATTTATATA
1 A-ATA-TAAAA-TTAT-TA
1330124 AATATAAAATATATTA
1 AATATAAAAT-TATTA
1330140 AATA
1 AATA
1330144 CGAATATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 1 0.03
15 3 0.09
16 8 0.24
17 11 0.33
18 7 0.21
19 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATAAAATTATTA
Found at i:1330166 original size:16 final size:16
Alignment explanation
Indices: 1330036--1330166 Score: 55
Period size: 16 Copynumber: 8.2 Consensus size: 16
1330026 AAAATATATA
1330036 ATATAATATAA-AAAT
1 ATATAATATAATAAAT
*
1330051 AATATAAAATAATAAAT
1 -ATATAATATAATAAAT
** *
1330068 ATATAAATATTTTAATT
1 ATAT-AATATAATAAAT
*
1330085 TTAT-ATA-ATATAAAT
1 ATATAATATA-ATAAAT
*
1330100 -TATTAATATATTAAA-
1 ATA-TAATATAATAAAT
1330115 AT-T--TAT-ATAAAT
1 ATATAATATAATAAAT
* *
1330127 ATAAAATATATTAAAT
1 ATATAATATAATAAAT
1330143 ACGAATATAATATAATAAAT
1 ----ATATAATATAATAAAT
1330163 ATAT
1 ATAT
1330167 TACTAAATTT
Statistics
Matches: 84, Mismatches: 15, Indels: 32
0.64 0.11 0.24
Matches are distributed among these distances:
11 4 0.05
12 5 0.06
14 3 0.04
15 11 0.13
16 31 0.37
17 16 0.19
20 14 0.17
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (16 bp):
ATATAATATAATAAAT
Found at i:1330884 original size:29 final size:30
Alignment explanation
Indices: 1330851--1330909 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1330841 ATCTAACACT
1330851 TTATTAAC-TTATCACATAACTATGAGCAA
1 TTATTAACTTTATCACATAACTATGAGCAA
* *
1330880 TTATTAACTTTTTCACATAACTATTAGCAA
1 TTATTAACTTTATCACATAACTATGAGCAA
1330910 GTTTGCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (30 bp):
TTATTAACTTTATCACATAACTATGAGCAA
Found at i:1340446 original size:3 final size:3
Alignment explanation
Indices: 1340438--1340463 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1340428 AGTAAATGAA
1340438 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1340464 AGGTAAAATG
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:1341126 original size:13 final size:13
Alignment explanation
Indices: 1341108--1341135 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1341098 ACTCTTTTCG
1341108 ATCGCATTTAGTT
1 ATCGCATTTAGTT
1341121 ATCGCATTTAGTT
1 ATCGCATTTAGTT
1341134 AT
1 AT
1341136 TGAATTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
ATCGCATTTAGTT
Found at i:1346316 original size:22 final size:20
Alignment explanation
Indices: 1346272--1346320 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
1346262 CATGTGCTTA
*
1346272 AATTAAAATAATTTAATAAT
1 AATTAAAATAATTTAAGAAT
*
1346292 AATTAAAGATAATTTTAAGATT
1 AATTAAA-ATAA-TTTAAGAAT
1346314 AATTAAA
1 AATTAAA
1346321 TTTTCATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 7 0.28
21 4 0.16
22 14 0.56
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
AATTAAAATAATTTAAGAAT
Found at i:1348367 original size:19 final size:19
Alignment explanation
Indices: 1348345--1348382 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1348335 TAAACGTATT
1348345 AAATTTT-ATATAAATATAA
1 AAATTTTAAT-TAAATATAA
1348364 AAATTTTAATTAAATATAA
1 AAATTTTAATTAAATATAA
1348383 TTATAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTTAATTAAATATAA
Found at i:1348424 original size:13 final size:11
Alignment explanation
Indices: 1348352--1348418 Score: 51
Period size: 10 Copynumber: 6.7 Consensus size: 11
1348342 ATTAAATTTT
1348352 ATATAAATATA
1 ATATAAATATA
* *
1348363 A-A-AATTTTA
1 ATATAAATATA
1348372 AT-TAAATATA
1 ATATAAATATA
1348382 AT-TATAATA-A
1 ATATA-AATATA
1348392 A-ATAAA-AT-
1 ATATAAATATA
1348400 ATATAAATATA
1 ATATAAATATA
1348411 ATATAAAT
1 ATATAAAT
1348419 TCATAAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
8 2 0.05
9 13 0.30
10 16 0.36
11 13 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATAAATATA
Found at i:1349612 original size:19 final size:19
Alignment explanation
Indices: 1349589--1349636 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1349579 AATTTTTTTT
* *
1349589 ATAAAAAATAATAAAAATG
1 ATAAAAAATAAGAAAAATA
*
1349608 GT-AAAAATAAAGAAAAATA
1 ATAAAAAAT-AAGAAAAATA
1349627 ATAAAAAATA
1 ATAAAAAATA
1349637 TTTACTGAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (19 bp):
ATAAAAAATAAGAAAAATA
Found at i:1350514 original size:20 final size:19
Alignment explanation
Indices: 1350475--1350514 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1350465 TTTGGTTTTT
* *
1350475 TTTTTAAAAAACAAATAAA
1 TTTTTAAAAAAAAAACAAA
1350494 TTTTTAAAAAATAAAACAAA
1 TTTTTAAAAAA-AAAACAAA
1350514 T
1 T
1350515 ATATCATACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
TTTTTAAAAAAAAAACAAA
Found at i:1351024 original size:20 final size:20
Alignment explanation
Indices: 1350985--1351024 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1350975 TATTTTTTAT
*
1350985 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
1351005 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
1351025 TTTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:1351034 original size:26 final size:26
Alignment explanation
Indices: 1350981--1351049 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
1350971 TATATATTTT
*
1350981 TTATATA-TTATAATTATATTTAAAATA
1 TTATATATTTAT-A-TAAATTTAAAATA
*
1351008 TTATATATTTATATAAATTTAATATA
1 TTATATATTTATATAAATTTAAAATA
* *
1351034 TTGTAAATTTAATATA
1 TTATATATTT-ATATA
1351050 TTTTAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 19 0.53
27 13 0.36
28 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
TTATATATTTATATAAATTTAAAATA
Found at i:1351034 original size:35 final size:33
Alignment explanation
Indices: 1350968--1351065 Score: 90
Period size: 35 Copynumber: 2.7 Consensus size: 33
1350958 AGGCTGTTTT
*
1350968 ATTTATATATTTTTTATATATTATAATTATATT-TAAA
1 ATTTATATA--TTTTATAAATT-TAA-TATATTGT-AA
1351005 ATATTATATATTTATATAAATTTAATATATTGTAA
1 AT-TTATATATTT-TATAAATTTAATATATTGTAA
*
1351040 ATTTAATATATTTTAATTAATTTAAT
1 ATTT-ATATATTTT-ATAAATTTAAT
1351066 TAATTTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
34 3 0.06
35 28 0.52
36 7 0.13
37 9 0.17
38 7 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
ATTTATATATTTTATAAATTTAATATATTGTAA
Found at i:1351060 original size:14 final size:16
Alignment explanation
Indices: 1351021--1351051 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1351011 TATATTTATA
1351021 TAAATTTAATATATTG
1 TAAATTTAATATATTG
1351037 TAAATTTAATATATT
1 TAAATTTAATATATT
1351052 TTAATTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
TAAATTTAATATATTG
Found at i:1351897 original size:20 final size:21
Alignment explanation
Indices: 1351858--1351897 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1351848 CAGAACCCAT
* *
1351858 GTTTCTTTTTCTTCATTTGTG
1 GTTTCTTCTTCTTCAATTGTG
1351879 GTTTCTTCTT-TTCAATTGT
1 GTTTCTTCTTCTTCAATTGT
1351898 TGAGGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.07, C:0.15, G:0.12, T:0.65
Consensus pattern (21 bp):
GTTTCTTCTTCTTCAATTGTG
Done.