Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold4
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: 5986281
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.33
Warning! 213817 characters in sequence are not A, C, G, or T
File 5 of 31
Found at i:1152808 original size:28 final size:28
Alignment explanation
Indices: 1152775--1152830 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1152765 TTAAATTTAA
1152775 TATATCCACCTTCAATCCAAAAAATGTT
1 TATATCCACCTTCAATCCAAAAAATGTT
* * *
1152803 TATATCCATCTTCAGTCCAAGAAATGTT
1 TATATCCACCTTCAATCCAAAAAATGTT
1152831 GATTTGTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (28 bp):
TATATCCACCTTCAATCCAAAAAATGTT
Found at i:1154996 original size:19 final size:19
Alignment explanation
Indices: 1154972--1155036 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
1154962 TTTATAAAAA
1154972 TAAATATAATATAAATTAT
1 TAAATATAATATAAATTAT
*
1154991 TAAATATATTA-AAATT-T
1 TAAATATAATATAAATTAT
1155008 TAAATATTAATATAATATTTAT
1 TAAATA-TAATATAA-A-TTAT
1155030 TAAATAT
1 TAAATAT
1155037 TTTTTTATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
17 7 0.18
18 9 0.23
19 12 0.31
20 1 0.03
21 3 0.08
22 7 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATATAATATAAATTAT
Found at i:1158928 original size:2 final size:2
Alignment explanation
Indices: 1158916--1158950 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1158906 CTTCCTGGAG
1158916 AT AT CAT 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
1158951 GTGTGTGTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1158955 original size:2 final size:2
Alignment explanation
Indices: 1158950--1158978 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1158940 TATATATATA
1158950 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
1158979 ATTTATATAT
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:1159339 original size:2 final size:2
Alignment explanation
Indices: 1159334--1159360 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1159324 ACACACACAC
1159334 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1159361 GACCCATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1159703 original size:81 final size:81
Alignment explanation
Indices: 1159568--1159731 Score: 301
Period size: 81 Copynumber: 2.0 Consensus size: 81
1159558 ATAGCAATTG
*
1159568 GGAAGGAAACACTCGGTCAATCAAGAACCAGAGCCAATACCCAAATCCATGTCTTAAAGCTGTAT
1 GGAAGGAAACACTCGGTCAATCAAGAACCAGAGCCAATACCCAAACCCATGTCTTAAAGCTGTAT
1159633 TGCCTAAATGGATAAT
66 TGCCTAAATGGATAAT
*
1159649 GGAAGGAAACAGTCGGTCAATCAAGAACCAGAGCCAATACCCAAACCCATGTCTTAAAGCTGTAT
1 GGAAGGAAACACTCGGTCAATCAAGAACCAGAGCCAATACCCAAACCCATGTCTTAAAGCTGTAT
*
1159714 TGTCTAAATGGATAAT
66 TGCCTAAATGGATAAT
1159730 GG
1 GG
1159732 TATAGAAGCA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (81 bp):
GGAAGGAAACACTCGGTCAATCAAGAACCAGAGCCAATACCCAAACCCATGTCTTAAAGCTGTAT
TGCCTAAATGGATAAT
Found at i:1165616 original size:17 final size:17
Alignment explanation
Indices: 1165594--1165629 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1165584 TATGTTAATA
1165594 TAATTAA-TAATTTTTAT
1 TAATTAATTAA-TTTTAT
1165611 TAATTAATTAATTTTAT
1 TAATTAATTAATTTTAT
1165628 TA
1 TA
1165630 TTATTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTAATTAATTTTAT
Found at i:1165632 original size:3 final size:3
Alignment explanation
Indices: 1165624--1165658 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1165614 TTAATTAATT
1165624 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1165659 GTTTTAATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1174932 original size:12 final size:12
Alignment explanation
Indices: 1174915--1174939 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1174905 CTATAATAGG
1174915 TCTATTCAAAGT
1 TCTATTCAAAGT
1174927 TCTATTCAAAGT
1 TCTATTCAAAGT
1174939 T
1 T
1174940 TGGAATATTT
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TCTATTCAAAGT
Found at i:1184627 original size:34 final size:34
Alignment explanation
Indices: 1184576--1184646 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
1184566 ATATATTTTT
*
1184576 TAAATATTATAATTTTAA-ATATAAAAATATAATA
1 TAAATATGATAATTTTAATATATAAAAA-ATAATA
1184610 TAAATATGAT-ATATTTAATATATAAAAAATAATA
1 TAAATATGATAAT-TTTAATATATAAAAAATAATA
1184644 TAA
1 TAA
1184647 TAAATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 2 0.06
34 23 0.68
35 9 0.26
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
TAAATATGATAATTTTAATATATAAAAAATAATA
Found at i:1188328 original size:13 final size:13
Alignment explanation
Indices: 1188310--1188334 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1188300 ATTTAGAGTC
1188310 GAAAATAAATATT
1 GAAAATAAATATT
1188323 GAAAATAAATAT
1 GAAAATAAATAT
1188335 GTATTTAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (13 bp):
GAAAATAAATATT
Found at i:1190740 original size:15 final size:16
Alignment explanation
Indices: 1190720--1190750 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1190710 CAATATAAAA
1190720 AAAAATTAAAA-AATT
1 AAAAATTAAAATAATT
1190735 AAAAATTAAAATAATT
1 AAAAATTAAAATAATT
1190751 TATTATGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTAAAATAATT
Found at i:1190896 original size:34 final size:34
Alignment explanation
Indices: 1190848--1190970 Score: 158
Period size: 34 Copynumber: 3.6 Consensus size: 34
1190838 TCATTTCTTA
*
1190848 CTTATCATTGTTGATTAAATGAGAAATTTGGTAG
1 CTTATCATTGTTGATTAAATGAGAGATTTGGTAG
* * * *
1190882 CTTACCATTATTGATTAAATGAGTGATTTGGTGG
1 CTTATCATTGTTGATTAAATGAGAGATTTGGTAG
*
1190916 CTTATCATTGTTGACTAAATG-GTAGATTTGGTAG
1 CTTATCATTGTTGATTAAATGAG-AGATTTGGTAG
* *
1190950 GTTGTCATTGTTGATTAAATG
1 CTTATCATTGTTGATTAAATG
1190971 GTGGTTTTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
33 1 0.01
34 74 0.99
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (34 bp):
CTTATCATTGTTGATTAAATGAGAGATTTGGTAG
Found at i:1193143 original size:56 final size:55
Alignment explanation
Indices: 1193028--1193143 Score: 128
Period size: 56 Copynumber: 2.1 Consensus size: 55
1193018 TAGTAAAATT
* * * *
1193028 TATATTTTATGTAATTTAAATTATTTAAATTTAAAAATAAATATCGAATATGGATA
1 TATATTGTATATAATTTAAATTATTTAAATTTAAAAATAAATATCAAATAT-GAAA
* *
1193084 TATATTGTATATAATTTAAAATT-TTTAAATTTTTTAAAATACATATCAAATAT-AAA
1 TATATTGTATATAATTT-AAATTATTTAAA--TTTAAAAATAAATATCAAATATGAAA
1193140 TATA
1 TATA
1193144 AATATAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
56 27 0.53
57 5 0.10
58 19 0.37
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (55 bp):
TATATTGTATATAATTTAAATTATTTAAATTTAAAAATAAATATCAAATATGAAA
Found at i:1193148 original size:12 final size:13
Alignment explanation
Indices: 1193126--1193154 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1193116 TTTAAAATAC
1193126 ATATCAAATATAA
1 ATATCAAATATAA
1193139 ATAT-AAATATAA
1 ATATCAAATATAA
1193151 ATAT
1 ATAT
1193155 TTAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (13 bp):
ATATCAAATATAA
Found at i:1199368 original size:24 final size:25
Alignment explanation
Indices: 1199327--1199374 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
1199317 ATTTTACTTT
*
1199327 AATATTTTTAATTAAATTTAATAAA
1 AATATTTTTAATTAAATTAAATAAA
1199352 AATATATTTT-ATT-AATTAAATAA
1 AATAT-TTTTAATTAAATTAAATAA
1199375 TAATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 8 0.38
26 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATTTTTAATTAAATTAAATAAA
Found at i:1209181 original size:2 final size:2
Alignment explanation
Indices: 1209174--1209208 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1209164 GAAACTCCAA
*
1209174 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1209209 AGGAAAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.03
Consensus pattern (2 bp):
AG
Found at i:1209586 original size:21 final size:22
Alignment explanation
Indices: 1209547--1209589 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1209537 TGATTTGTAA
*
1209547 AATAATAATAATTAAAATTATT
1 AATAATAAAAATTAAAATTATT
*
1209569 AATAA-AAAAATTATAATTATT
1 AATAATAAAAATTAAAATTATT
1209590 CAATTACTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATAAAAATTAAAATTATT
Found at i:1209860 original size:51 final size:49
Alignment explanation
Indices: 1209785--1209944 Score: 166
Period size: 52 Copynumber: 3.2 Consensus size: 49
1209775 TAAATTCTAT
*
1209785 ATTAAATTTTAAATTATTACTTAAAAAATAA-AAAATCAAAAAGTATTTTAC
1 ATTAAATTTTAAATTACTA-TTAAAAAATAATAAAAT-AAAAA-TATTTTAC
* * *
1209836 ATTAAATTTTGAATGACTATTTAAAAATAATAAAATTTTAAAAATATTTT-C
1 ATTAAATTTTAAATTACTATTAAAAAATAATAAAA---TAAAAATATTTTAC
* * *
1209887 TATTAAATCTTAAATTACTATTAAAAATTAATAAAATAAAAATA--TTAT
1 -ATTAAATTTTAAATTACTATTAAAAAATAATAAAATAAAAATATTTTAC
1209935 ATTAAATTTT
1 ATTAAATTTT
1209945 GAACTATAGT
Statistics
Matches: 92, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
47 11 0.12
49 8 0.09
50 10 0.11
51 21 0.23
52 36 0.39
53 5 0.05
54 1 0.01
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (49 bp):
ATTAAATTTTAAATTACTATTAAAAAATAATAAAATAAAAATATTTTAC
Found at i:1210118 original size:13 final size:14
Alignment explanation
Indices: 1210087--1210120 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1210077 TCAACTCTAA
*
1210087 ATATAAATATATTT
1 ATATAAATATATAT
1210101 ATATAAAT-TATAT
1 ATATAAATATATAT
1210114 ATATAAA
1 ATATAAA
1210121 AAATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAAATATATAT
Found at i:1210305 original size:21 final size:20
Alignment explanation
Indices: 1210279--1210355 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 20
1210269 ATAATATTAT
1210279 ATATTAAAATACTATTTAAAA
1 ATATTAAAATA-TATTTAAAA
*
1210300 ATATTAAAATAT-TTTATGTTAA
1 ATATTAAAATATATTTA---AAA
* *
1210322 ATTTTAAATTATTATTTAAAA
1 ATATTAAAATA-TATTTAAAA
*
1210343 ATAATAAAATATA
1 ATATTAAAATATA
1210356 AAAATATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
19 4 0.09
20 3 0.07
21 21 0.48
22 11 0.25
23 1 0.02
24 4 0.09
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (20 bp):
ATATTAAAATATATTTAAAA
Found at i:1210354 original size:51 final size:52
Alignment explanation
Indices: 1210295--1210526 Score: 233
Period size: 51 Copynumber: 4.5 Consensus size: 52
1210285 AAATACTATT
* * * *
1210295 TAAAAATATTAAAATATTTTATGTTAAATTTTAAATTATTATTTAAAAATAA
1 TAAAAATATTAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
* **
1210347 T-AAAATATAAAAATATTTTATATTAAATCTCAAAAAACT-TTT-AAAA-AA
1 TAAAAATATTAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
* * * * *
1210395 TAAAAGT-TTAAAAATATTTTAAATTAAAACCCAAATTATTATTTAAAAATAA
1 TAAAAATATT-AAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
* *
1210447 TGAAAAAT-TTAAAATATTTTATATTAAATCCTAAAATTACAATTTAAAAAATAA
1 T-AAAAATATTAAAATATTTTATATTAAAT-CTCAAATTACTATTT-AAAAATAA
*
1210501 TAAACAATTTTTAAAATATTTTATAT
1 TAAA-AA-TATTAAAATATTTTATAT
1210527 ATGTATTTAG
Statistics
Matches: 147, Mismatches: 22, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
48 4 0.03
49 32 0.22
50 6 0.04
51 35 0.24
52 21 0.14
53 21 0.14
54 11 0.07
55 1 0.01
56 16 0.11
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (52 bp):
TAAAAATATTAAAATATTTTATATTAAATCTCAAATTACTATTTAAAAATAA
Found at i:1210421 original size:49 final size:51
Alignment explanation
Indices: 1210334--1210526 Score: 187
Period size: 49 Copynumber: 3.7 Consensus size: 51
1210324 TTTAAATTAT
* *
1210334 TATTTAAAAATAATAAAATATAAAAATATTTTATATTAAATCTCAAAAAAC
1 TATTTAAAAATAATAAAATTTAAAAATATTTTATATTAAATCCCAAAAAAC
* * ** *
1210385 T-TTT-AAAA-AATAAAAGTTTAAAAATATTTTAAATTAAAACCCAAATTAT
1 TATTTAAAAATAATAAAA-TTTAAAAATATTTTATATTAAATCCCAAAAAAC
* *
1210434 TATTTAAAAATAATGAAAAATTT-AAAATATTTTATATTAAATCCTAAAATTAC
1 TATTTAAAAATAAT--AAAATTTAAAAATATTTTATATTAAATCCCAAAA-AAC
* *
1210487 AATTTAAAAAATAATAAACAATTTTTAAAATATTTTATAT
1 TATTT-AAAAATAAT-AA-AA-TTTAAAAATATTTTATAT
1210527 ATGTATTTAG
Statistics
Matches: 118, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
48 7 0.06
49 31 0.26
50 6 0.05
51 5 0.04
52 25 0.21
53 12 0.10
54 15 0.13
55 3 0.03
56 14 0.12
ACGTcount: A:0.55, C:0.05, G:0.01, T:0.38
Consensus pattern (51 bp):
TATTTAAAAATAATAAAATTTAAAAATATTTTATATTAAATCCCAAAAAAC
Found at i:1211008 original size:22 final size:21
Alignment explanation
Indices: 1210999--1211053 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 21
1210989 AGTTTAAATT
1210999 ATATGTACATATTATTATAATC
1 ATATGTACAT-TTATTATAATC
*
1211021 ATATGTATATTTAATTATAATC
1 ATATGTACATTT-ATTATAATC
1211043 ATATGTACATT
1 ATATGTACATT
1211054 CAATTTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.47
Consensus pattern (21 bp):
ATATGTACATTTATTATAATC
Found at i:1211245 original size:8 final size:9
Alignment explanation
Indices: 1211224--1211248 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1211214 TTATAATTTA
1211224 AAAAATAAT
1 AAAAATAAT
1211233 AAAAATAAT
1 AAAAATAAT
1211242 AAAAATA
1 AAAAATA
1211249 TTTTATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATAAT
Found at i:1211469 original size:21 final size:21
Alignment explanation
Indices: 1211428--1211470 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1211418 AAGAAGTCAA
*
1211428 TTTTTTCATAAAAGATCAATT
1 TTTTTTCATAAAAGATAAATT
*
1211449 TTTTTTCAGTAAAA-TTAAATT
1 TTTTTTCA-TAAAAGATAAATT
1211470 T
1 T
1211471 ACGTATGACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTTTTCATAAAAGATAAATT
Found at i:1211815 original size:16 final size:16
Alignment explanation
Indices: 1211783--1211812 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1211773 ATTTATTTGA
1211783 TATTTAAAATATTAAT
1 TATTTAAAATATTAAT
1211799 TATTTAAAAT-TTAA
1 TATTTAAAATATTAA
1211813 ATTTTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTAAAATATTAAT
Found at i:1212324 original size:34 final size:34
Alignment explanation
Indices: 1212254--1212470 Score: 249
Period size: 34 Copynumber: 6.4 Consensus size: 34
1212244 ATCATGAAAA
* * *
1212254 TGTTGATTAAAT-GATGATTTGGTAGTTTACCGT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * *
1212287 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
1212321 TGTTGATTAAATGGGAGATTTGGTAGCTTACTAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* ** *
1212355 TGTTGATTAAATGAGAAATTTGGTAACTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* *
1212389 TATTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
* * **
1212423 TGTTGACTAAAT-GGTAGATTTGGTAGGTTGTCAT
1 TGTTGATTAAATGGGT-GATTTGGTAGCTTACCAT
1212457 TGTTGATTAAATGG
1 TGTTGATTAAATGG
1212471 TAGTTTTTAC
Statistics
Matches: 155, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
33 15 0.10
34 139 0.90
35 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.42
Consensus pattern (34 bp):
TGTTGATTAAATGGGTGATTTGGTAGCTTACCAT
Found at i:1212434 original size:102 final size:101
Alignment explanation
Indices: 1212254--1212469 Score: 301
Period size: 102 Copynumber: 2.1 Consensus size: 101
1212244 ATCATGAAAA
** * * * *
1212254 TGTTGATTAAATGATGATTTGGTAGTTTACCGTTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGATGATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
*
1212319 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACT-AT
66 ATTGTTGACTAAATGGGAGATTTGGTAGCTT-CTCAT
1212355 TGTTGATTAAATGA-GAAATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
1 TGTTGATTAAATGATG--ATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTA
* * *
1212419 CCATTGTTGACTAAATGGTAGATTTGGTAGGTTGTCAT
64 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTCTCAT
1212457 TGTTGATTAAATG
1 TGTTGATTAAATG
1212470 GTAGTTTTTA
Statistics
Matches: 102, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
100 1 0.01
101 15 0.15
102 86 0.84
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.42
Consensus pattern (101 bp):
TGTTGATTAAATGATGATTTGGTAACTTACCATTATTGATTAAATGGGTGATTTGGTGGCTTACC
ATTGTTGACTAAATGGGAGATTTGGTAGCTTCTCAT
Found at i:1216935 original size:34 final size:34
Alignment explanation
Indices: 1216878--1217096 Score: 244
Period size: 34 Copynumber: 6.5 Consensus size: 34
1216868 AAGTGGGAGA
*
1216878 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * *
1216911 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* *
1216945 ATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* **
1216979 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* * * *
1217013 ATTATTGATTAAATGAGTGATTTAGTGGCTTACC
1 ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
* ** * *
1217047 ATTGTTGACTAAAT-AATAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGT-GATTTGGTAGCTTACC
*
1217081 ATTGTTGACTAAATGG
1 ATTGTTGATTAAATGG
1217097 TGGTTTTTAC
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
33 16 0.10
34 144 0.90
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGTGATTTGGTAGCTTACC
Found at i:1217021 original size:102 final size:101
Alignment explanation
Indices: 1216878--1217096 Score: 303
Period size: 102 Copynumber: 2.2 Consensus size: 101
1216868 AAGTGGGAGA
** * * * * * *
1216878 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTAGTGGCTTA
**
1216943 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATAAGAGATTTGGTAGCTTACC
1216979 ATTGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTAGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTAGTGGCTT
* * *
1217044 ACCATTGTTGACTAAATAATAGATTTGGTAGGTTGCC
65 ACCATTGTTGACTAAATAAGAGATTTGGTAGCTTACC
*
1217081 ATTGTTGACTAAATGG
1 ATTGTTGATTAAATGG
1217097 TGGTTTTTAC
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 16 0.16
102 87 0.84
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGGTAGCTTACCATTATTGATTAAATGAGTGATTTAGTGGCTTA
CCATTGTTGACTAAATAAGAGATTTGGTAGCTTACC
Found at i:1217324 original size:18 final size:18
Alignment explanation
Indices: 1217284--1217324 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1217274 CACATATTTC
1217284 TTTTATTTTTTATTTTAT
1 TTTTATTTTTTATTTTAT
* *
1217302 GTTTATTTTTTATTTTTT
1 TTTTATTTTTTATTTTAT
1217320 TTTTA
1 TTTTA
1217325 ATTTCTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTATTTTTTATTTTAT
Found at i:1217328 original size:12 final size:11
Alignment explanation
Indices: 1217284--1217324 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
1217274 CACATATTTC
1217284 TTTTATTTTTT
1 TTTTATTTTTT
1217295 ATTTTATGTTTATT
1 -TTTTAT-TTT-TT
1217309 TTTTATTTTTT
1 TTTTATTTTTT
1217320 TTTTA
1 TTTTA
1217325 ATTTCTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 7 0.26
12 9 0.33
13 9 0.33
14 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTATTTTTT
Found at i:1222719 original size:14 final size:14
Alignment explanation
Indices: 1222700--1222729 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1222690 TTGATGACCA
1222700 AACTATTTTGAAGT
1 AACTATTTTGAAGT
1222714 AACTATTTTGAAGT
1 AACTATTTTGAAGT
1222728 AA
1 AA
1222730 AGGCTAGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (14 bp):
AACTATTTTGAAGT
Found at i:1224876 original size:33 final size:34
Alignment explanation
Indices: 1224839--1224904 Score: 100
Period size: 33 Copynumber: 1.9 Consensus size: 34
1224829 ATAAAATTAT
1224839 AATAAAATAATTAT-TTT-ATGAAAATATAATAAA
1 AATAAAATAATTATATTTAAT-AAAATATAATAAA
1224872 AATAAAATAATTATAATTTAATAAAATATAATA
1 AATAAAATAATTAT-ATTTAATAAAATATAATA
1224905 TTATAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 14 0.47
35 14 0.47
36 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (34 bp):
AATAAAATAATTATATTTAATAAAATATAATAAA
Found at i:1224914 original size:25 final size:25
Alignment explanation
Indices: 1224829--1224917 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 25
1224819 AATAAATGAA
* *
1224829 ATAAAATTATAATAAAATAATTATTTT
1 ATAAAATT-TAATAAAAT-ATAATATT
* *
1224856 ATGAAAATATAATAAAAATAAAATAATT
1 AT-AAAATTTAAT-AAAATATAAT-ATT
1224884 AT--AATTTAATAAAATATAATATT
1 ATAAAATTTAATAAAATATAATATT
1224907 ATAAAATTTAA
1 ATAAAATTTAA
1224918 ATTTTTAGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
23 5 0.10
24 9 0.18
25 14 0.27
27 9 0.18
28 14 0.27
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (25 bp):
ATAAAATTTAATAAAATATAATATT
Found at i:1233440 original size:29 final size:33
Alignment explanation
Indices: 1233403--1233486 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 33
1233393 GATGTAAAGA
1233403 AAATATAAATATAATATAAAAATAT-TTA-TTT
1 AAATATAAATATAATATAAAAATATATTATTTT
* *
1233434 -AAT-TAAA-AT-TTATATAAATATATTATTTT
1 AAATATAAATATAATATAAAAATATATTATTTT
* *
1233463 AAATATAATTATAATAAAAAAATA
1 AAATATAAATATAATATAAAAATA
1233487 ATAAACATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
27 10 0.24
28 5 0.12
29 7 0.17
30 6 0.15
31 3 0.07
32 2 0.05
33 8 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
AAATATAAATATAATATAAAAATATATTATTTT
Found at i:1238395 original size:5 final size:5
Alignment explanation
Indices: 1238385--1238425 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
1238375 AGAAAAGCAC
*
1238385 ATATA ATATA ATGTA ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1238426 AAGAAGTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:1244080 original size:21 final size:21
Alignment explanation
Indices: 1244056--1244097 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1244046 AAATTATATT
1244056 TATATAAAT-TTAATTATAAAA
1 TATATAAATATTAA-TATAAAA
1244077 TATATAAATATTAATATAAAA
1 TATATAAATATTAATATAAAA
1244098 AAGTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATATAAATATTAATATAAAA
Found at i:1251004 original size:12 final size:12
Alignment explanation
Indices: 1250989--1251054 Score: 51
Period size: 12 Copynumber: 5.2 Consensus size: 12
1250979 TAAATTAAAT
1250989 TTTTATATTTAA
1 TTTTATATTTAA
*
1251001 TTTTAAATTTAA
1 TTTTATATTTAA
1251013 TTATTGATATTTAA
1 TT-TT-ATATTTAA
* * *
1251027 ATTTAAATTAAAA
1 TTTTATATT-TAA
*
1251040 TTTTTTATATTAA
1 TTTTATAT-TTAA
1251053 TT
1 TT
1251055 AAAAATAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
12 17 0.41
13 15 0.37
14 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:1251052 original size:26 final size:26
Alignment explanation
Indices: 1250979--1251050 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
1250969 TTGTAAAGAA
*
1250979 TAAATTAAA-TTTTTATATTTAATTT
1 TAAATTAAATTTTTTATATTTAAATT
* * *
1251004 TAAATTTAATTATTGATATTTAAATT
1 TAAATTAAATTTTTTATATTTAAATT
1251030 TAAATTAAAATTTTTTATATT
1 TAAATT-AAATTTTTTATATT
1251051 AATTAAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.21
26 19 0.50
27 11 0.29
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
TAAATTAAATTTTTTATATTTAAATT
Found at i:1265174 original size:37 final size:37
Alignment explanation
Indices: 1265125--1265196 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
1265115 GGCTGAAACC
*
1265125 TCATTTTGTAATCTACTTAACTTACATTATACTAGTT
1 TCATGTTGTAATCTACTTAACTTACATTATACTAGTT
* *
1265162 TCATGTTGTAATCTGCTTAACTTACATTGTACTAG
1 TCATGTTGTAATCTACTTAACTTACATTATACTAG
1265197 GTTTTTTGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.46
Consensus pattern (37 bp):
TCATGTTGTAATCTACTTAACTTACATTATACTAGTT
Found at i:1269867 original size:21 final size:22
Alignment explanation
Indices: 1269827--1269869 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1269817 AACCAATTTG
1269827 ATGAAACCAAGAAGGTTTCATC
1 ATGAAACCAAGAAGGTTTCATC
**
1269849 ATGAAACCTGGAA-GTTTCATC
1 ATGAAACCAAGAAGGTTTCATC
1269870 TTCATCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (22 bp):
ATGAAACCAAGAAGGTTTCATC
Found at i:1270162 original size:3 final size:3
Alignment explanation
Indices: 1270154--1270193 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
1270144 CTCTCGTTGC
*
1270154 TCT TCT TCT TCT TCT TGT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1270194 TTCGTTGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1271012 original size:21 final size:21
Alignment explanation
Indices: 1270987--1271026 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1270977 GTAAAAAGTC
1270987 CAAAACTAA-AAAAAGAAAAAA
1 CAAAAC-AACAAAAAGAAAAAA
*
1271008 CAAAACAACAAAAATAAAA
1 CAAAACAACAAAAAGAAAA
1271027 GTGGCTACGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.80, C:0.12, G:0.03, T:0.05
Consensus pattern (21 bp):
CAAAACAACAAAAAGAAAAAA
Found at i:1271668 original size:25 final size:25
Alignment explanation
Indices: 1271617--1271668 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1271607 ATCAATATTT
* *
1271617 TTTTTATATTTTTATATATAATTTA
1 TTTTTATATTTTTATATAAAATATA
*
1271642 TTTTTA-ATTTTTTTAGTAAAATATA
1 TTTTTATATTTTTATA-TAAAATATA
1271667 TT
1 TT
1271669 ACATTTACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTTTATATTTTTATATAAAATATA
Found at i:1274661 original size:2 final size:2
Alignment explanation
Indices: 1274654--1274685 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1274644 ATATGTAATA
1274654 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
1274686 TCACAGCACA
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:1277787 original size:8 final size:8
Alignment explanation
Indices: 1277774--1277802 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1277764 TTTTCATTAG
1277774 TAAAAAAA
1 TAAAAAAA
1277782 TAAAAAAA
1 TAAAAAAA
1277790 TAAAAAAA
1 TAAAAAAA
1277798 -AAAAA
1 TAAAAA
1277803 TACACAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1277984 original size:11 final size:11
Alignment explanation
Indices: 1277970--1278003 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1277960 GATATTTTTA
1277970 AATATATTAAT
1 AATATATTAAT
1277981 AATATA-TAAT
1 AATATATTAAT
1277991 AAATATATTAAT
1 -AATATATTAAT
1278003 A
1 A
1278004 TATGAACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 4 0.19
11 13 0.62
12 4 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AATATATTAAT
Found at i:1279244 original size:18 final size:17
Alignment explanation
Indices: 1279184--1279257 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 17
1279174 AAAAATATTT
*
1279184 TAAAATTCATATAATATGA
1 TAAAATTTATATAA-AT-A
*
1279203 TTAAATTTATAT-AATA
1 TAAAATTTATATAAATA
1279219 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
1279234 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
1279252 TAAAAT
1 TAAAAT
1279258 ATTTTAAACA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
13 1 0.02
14 5 0.11
15 7 0.15
16 2 0.04
17 10 0.21
18 9 0.19
19 13 0.28
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:1280875 original size:3 final size:3
Alignment explanation
Indices: 1280869--1280905 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1280859 AATATTTTTG
1280869 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1280906 GAGAATTGAT
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):
TTA
Found at i:1281460 original size:15 final size:15
Alignment explanation
Indices: 1281431--1281459 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1281421 TGGTGTAATA
1281431 ATTACCTTTTTTTTT
1 ATTACCTTTTTTTTT
1281446 ATTA-CTTTTTTTTT
1 ATTACCTTTTTTTTT
1281460 TCTTTTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTACCTTTTTTTTT
Found at i:1282254 original size:10 final size:10
Alignment explanation
Indices: 1282207--1282257 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 10
1282197 CAAATAAACC
1282207 AAATCAAATT
1 AAATCAAATT
1282217 -AATCAAATT
1 AAATCAAATT
*
1282226 TAATC-AATT
1 AAATCAAATT
**
1282235 TGAT-AAATT
1 AAATCAAATT
1282244 AAATCAAATT
1 AAATCAAATT
1282254 AAAT
1 AAAT
1282258 TTATTAATCC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
9 22 0.63
10 13 0.37
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (10 bp):
AAATCAAATT
Found at i:1287454 original size:3 final size:3
Alignment explanation
Indices: 1287446--1287486 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1287436 ATCATACTTG
1287446 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1287487 AATTTTCAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1292689 original size:2 final size:2
Alignment explanation
Indices: 1292668--1292707 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
1292658 GCAGCCTCAA
* * *
1292668 AT AT AT AA AA AT AT AA 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
1292708 TGGAGAGTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1311629 original size:22 final size:21
Alignment explanation
Indices: 1311581--1311631 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1311571 TATTTTATCT
*
1311581 AATTTATAAATAAAAATTTAA
1 AATTTATTAATAAAAATTTAA
*
1311602 ATTTTATTAA-AAAAATTTGATA
1 AATTTATTAATAAAAATTT-A-A
1311624 AATTTATT
1 AATTTATT
1311632 TGATAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (21 bp):
AATTTATTAATAAAAATTTAA
Found at i:1313346 original size:23 final size:24
Alignment explanation
Indices: 1313319--1313376 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
1313309 GTTGTTCAAC
*
1313319 TTATTATATTCATATAGATA-ATT
1 TTATTATATTAATATAGATATATT
**
1313342 TTATTATATTAATATTTATATATT
1 TTATTATATTAATATAGATATATT
1313366 TTA-TATATTAA
1 TTATTATATTAA
1313377 ATTTAAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 25 0.81
24 6 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATTATATTAATATAGATATATT
Found at i:1313561 original size:34 final size:34
Alignment explanation
Indices: 1313518--1313586 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
1313508 TATGCATATT
* *
1313518 TCAAAAGTTGCTTGTGCACCACTTATACCACTCC
1 TCAAAAGTTGCTTGTGAACCACTCATACCACTCC
1313552 TCAAAAGTTGCTTGTGAACCACTCATACCACTCC
1 TCAAAAGTTGCTTGTGAACCACTCATACCACTCC
1313586 T
1 T
1313587 TTTTTTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.29
Consensus pattern (34 bp):
TCAAAAGTTGCTTGTGAACCACTCATACCACTCC
Found at i:1313618 original size:8 final size:8
Alignment explanation
Indices: 1313605--1313630 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1313595 AGCTGGTTCA
1313605 GCTTTTGT
1 GCTTTTGT
1313613 GCTTTTGT
1 GCTTTTGT
1313621 GCTTTTGT
1 GCTTTTGT
1313629 GC
1 GC
1313631 ATGACTATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.15, G:0.27, T:0.58
Consensus pattern (8 bp):
GCTTTTGT
Found at i:1313961 original size:20 final size:20
Alignment explanation
Indices: 1313929--1313978 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1313919 TATATAAAAT
*
1313929 AAAAAAA-TCAATTTAATTA
1 AAAAAAATTTAATTTAATTA
* **
1313948 ATAAAAATTTAATTTTTTTA
1 AAAAAAATTTAATTTAATTA
1313968 AAAAAAATTTA
1 AAAAAAATTTA
1313979 TAATTGATGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAAAATTTAATTTAATTA
Found at i:1314462 original size:15 final size:17
Alignment explanation
Indices: 1314427--1314464 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
1314417 AAATTTAAAT
*
1314427 TTTAAAAATATTTATTA
1 TTTAAAAATATTTAATA
1314444 TTTAAAAA-A-TTAATA
1 TTTAAAAATATTTAATA
1314459 TTTAAA
1 TTTAAA
1314465 TTGAAATTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 1 0.05
17 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAAAAATATTTAATA
Found at i:1314581 original size:4 final size:4
Alignment explanation
Indices: 1314572--1314598 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1314562 GCTTGTCTGT
1314572 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1314599 GTTTTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:1315005 original size:24 final size:23
Alignment explanation
Indices: 1314935--1315006 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 23
1314925 ATTATTAAAC
* *
1314935 ATATTAAA-ATTTTAAATA-AAA
1 ATATTAAATATATTAAATATATA
* * *
1314956 ATA-AAAATATATTAAATATTTT
1 ATATTAAATATATTAAATATATA
1314978 ATATTAAATATATCTAAATATATA
1 ATATTAAATATAT-TAAATATATA
1315002 ATATT
1 ATATT
1315007 TTATTTATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
20 3 0.08
21 12 0.31
22 3 0.08
23 8 0.21
24 13 0.33
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTAAATATATTAAATATATA
Found at i:1315019 original size:21 final size:22
Alignment explanation
Indices: 1314995--1315042 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
1314985 ATATATCTAA
*
1314995 ATATATA-ATATTTTATTTATT
1 ATATATATATATTATATTTATT
*
1315016 ATAT-TATTTATTATATTTATT
1 ATATATATATATTATATTTATT
*
1315037 AAATAT
1 ATATAT
1315043 GTTATATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 2 0.09
21 19 0.86
22 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATATATATATTATATTTATT
Found at i:1315024 original size:12 final size:12
Alignment explanation
Indices: 1315007--1315032 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1314997 ATATAATATT
1315007 TTATTTATTATA
1 TTATTTATTATA
1315019 TTATTTATTATA
1 TTATTTATTATA
1315031 TT
1 TT
1315033 TATTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTATTATA
Found at i:1315047 original size:21 final size:21
Alignment explanation
Indices: 1315003--1315047 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1314993 AAATATATAA
* *
1315003 TATTTTATTTATTATATTATT
1 TATTATATTTATTATAATATT
1315024 TATTATATTTATTA-AATATGT
1 TATTATATTTATTATAATAT-T
1315045 TAT
1 TAT
1315048 ATACGTATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTATATTTATTATAATATT
Found at i:1315485 original size:16 final size:18
Alignment explanation
Indices: 1315464--1315502 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1315454 TCGTTTAATT
1315464 AAATAT-AAA-ATATATA
1 AAATATCAAATATATATA
*
1315480 AAATATCAAATATTTATA
1 AAATATCAAATATATATA
1315498 AAATA
1 AAATA
1315503 ATTATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 3 0.15
18 11 0.55
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATCAAATATATATA
Found at i:1315550 original size:14 final size:16
Alignment explanation
Indices: 1315524--1315557 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1315514 AATTTATTAA
1315524 AAATTTATTAAAT-AT
1 AAATTTATTAAATGAT
1315539 AAATTT-TTAAATGAT
1 AAATTTATTAAATGAT
1315554 AAAT
1 AAAT
1315558 ATATGTACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AAATTTATTAAATGAT
Found at i:1315654 original size:25 final size:24
Alignment explanation
Indices: 1315626--1315682 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
1315616 TACATATACA
* *
1315626 AAAATATAATTAATATAATATATTT
1 AAAATATAATAAAAATAATATA-TT
1315651 AAAACT-TAATAAAAATAATATATT
1 AAAA-TATAATAAAAATAATATATT
1315675 -AAATATAA
1 AAAATATAA
1315683 ATATTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 6 0.21
24 2 0.07
25 18 0.64
26 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
AAAATATAATAAAAATAATATATT
Found at i:1318983 original size:23 final size:21
Alignment explanation
Indices: 1318952--1319023 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 21
1318942 GAATCGTAAT
1318952 TTAAGAAAATAATGA-AAATATGA
1 TTAA-AAAATAAT-ATAAATAT-A
1318975 TATAAAAAATAATATAAATATA
1 T-TAAAAAATAATATAAATATA
1318997 TTAAAATTTAATAATATAAAT-TA
1 TTAAAA---AATAATATAAATATA
1319020 TTAA
1 TTAA
1319024 TATATTACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
21 5 0.11
22 3 0.07
23 21 0.48
24 15 0.34
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
TTAAAAAATAATATAAATATA
Found at i:1320271 original size:69 final size:69
Alignment explanation
Indices: 1320160--1320300 Score: 230
Period size: 69 Copynumber: 2.0 Consensus size: 69
1320150 CTTTCAGATA
1320160 AATAGCACGGAGAATAGGTCAGTTCTTCATGCAGCGACCCGAGCACCGAGGGATGCTGTTATATA
1 AATAGCACGGAGAATAGGTCAGTTCTTCATGCAGCGACCCGAGCACCGAGGGATGCTGTTATATA
1320225 CAGC
66 CAGC
* * * *
1320229 AATAGCACGGAGAATAGGTCAGTTCTTCATGTAGC-TCTCCGAGCACCGGGGGATGCTGTTCTAT
1 AATAGCACGGAGAATAGGTCAGTTCTTCATGCAGCGAC-CCGAGCACCGAGGGATGCTGTTATAT
1320293 ACAGC
65 ACAGC
1320298 AAT
1 AAT
1320301 GGAAAGAATG
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
68 1 0.01
69 66 0.99
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.23
Consensus pattern (69 bp):
AATAGCACGGAGAATAGGTCAGTTCTTCATGCAGCGACCCGAGCACCGAGGGATGCTGTTATATA
CAGC
Found at i:1328282 original size:12 final size:12
Alignment explanation
Indices: 1328265--1328331 Score: 61
Period size: 12 Copynumber: 5.7 Consensus size: 12
1328255 AAAAGTTAAA
*
1328265 TATTTATTTTAT
1 TATTTATATTAT
1328277 TATTTAT-TATAT
1 TATTTATAT-TAT
1328289 TATTATAATATTAT
1 TATT-T-ATATTAT
*
1328303 T-TTTATATTAA
1 TATTTATATTAT
1328314 TATTTATA-TAT
1 TATTTATATTAT
1328325 T-TTTATA
1 TATTTATA
1328332 ATTAAATTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
10 6 0.12
11 11 0.23
12 21 0.44
13 3 0.06
14 6 0.12
15 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTTATATTAT
Found at i:1328340 original size:22 final size:22
Alignment explanation
Indices: 1328264--1328341 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
1328254 TAAAAGTTAA
*
1328264 ATATTTAT-TTTAT-TATTTATT
1 ATATTAATATTTATATATTT-TT
* *
1328285 ATATTATTA-TAATATTATTTTT
1 ATATTAATATTTATA-TATTTTT
1328307 ATATTAATATTTATATATTTTT
1 ATATTAATATTTATATATTTTT
1328329 ATAATTAA-ATTTA
1 AT-ATTAATATTTA
1328342 ATTAAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
21 9 0.19
22 24 0.51
23 14 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTAATATTTATATATTTTT
Found at i:1331133 original size:19 final size:20
Alignment explanation
Indices: 1331109--1331147 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1331099 ATCAATTCGA
* *
1331109 CTGAAATAC-TAAAGTTAAT
1 CTGAAAGACATAAAGCTAAT
1331128 CTGAAAGACATAAAGCTAAT
1 CTGAAAGACATAAAGCTAAT
1331148 TGCCATTTCC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
CTGAAAGACATAAAGCTAAT
Found at i:1333305 original size:39 final size:38
Alignment explanation
Indices: 1333262--1333335 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
1333252 ATTATAATTA
1333262 TTAATATATTAATA-ATTTTATTATATAAATTTTAATATG
1 TTAATATATTAATATATTTT-TTATA-AAATTTTAATATG
* * * *
1333301 TTAATGTTTTTATATATTTTTTATAATATTTTAAT
1 TTAATATATTAATATATTTTTTATAAAATTTTAAT
1333336 TATTTTTAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
38 9 0.30
39 16 0.53
40 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (38 bp):
TTAATATATTAATATATTTTTTATAAAATTTTAATATG
Found at i:1333312 original size:31 final size:31
Alignment explanation
Indices: 1333248--1333317 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1333238 TTATATTATT
1333248 TTTTAT-TAT-AATTATTAATATATTAATAA
1 TTTTATATATAAATTATTAATATATTAATAA
* **
1333277 TTTTATTATATAAATT-TTAATATGTTAATGT
1 TTTTA-TATATAAATTATTAATATATTAATAA
1333308 TTTTATATAT
1 TTTTATATAT
1333318 TTTTTATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 5 0.14
30 6 0.17
31 20 0.57
32 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTATATATAAATTATTAATATATTAATAA
Found at i:1337153 original size:18 final size:17
Alignment explanation
Indices: 1337103--1337153 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
1337093 AAATACATAG
**
1337103 TAGATATATATAAAATT
1 TAGATATATATTTAATT
*
1337120 TA-AAATATATTT-ATT
1 TAGATATATATTTAATT
1337135 TAGATATATATTTTAATT
1 TAGATATATA-TTTAATT
1337153 T
1 T
1337154 GACATGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
15 5 0.19
16 13 0.48
17 5 0.19
18 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
TAGATATATATTTAATT
Found at i:1339856 original size:3 final size:3
Alignment explanation
Indices: 1339848--1339881 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1339838 ATGGTGTATC
1339848 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
1339882 AGAGTAAGAT
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:1340940 original size:18 final size:17
Alignment explanation
Indices: 1340908--1340956 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 17
1340898 GTTATCTATT
*
1340908 AAATAAAAATTAAAATTCA
1 AAAT-AAAA-TAAAAATCA
1340927 AAATAAAATAAAAATCA
1 AAATAAAATAAAAATCA
1340944 ATAATAATAATAA
1 A-AATAA-AATAA
1340957 TAATAAGAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 9 0.33
18 9 0.33
19 9 0.33
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAATAAAAATCA
Found at i:1343911 original size:14 final size:14
Alignment explanation
Indices: 1343892--1343989 Score: 123
Period size: 14 Copynumber: 7.2 Consensus size: 14
1343882 TATTAATATT
1343892 AAATATAATTATAA
1 AAATATAATTATAA
1343906 AAATATAATTA-AA
1 AAATATAATTATAA
* *
1343919 AGATATAATTATAT
1 AAATATAATTATAA
1343933 AAATATAA-TATAAA
1 AAATATAATTAT-AA
1343947 AAATATAATTAT-A
1 AAATATAATTATAA
*
1343960 AAATATAATTATAC
1 AAATATAATTATAA
*
1343974 GAATATAA-TATAA
1 AAATATAATTATAA
1343987 AAA
1 AAA
1343990 ATTTAATTAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
13 34 0.47
14 35 0.49
15 3 0.04
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (14 bp):
AAATATAATTATAA
Found at i:1343926 original size:27 final size:27
Alignment explanation
Indices: 1343894--1344001 Score: 130
Period size: 27 Copynumber: 4.0 Consensus size: 27
1343884 TTAATATTAA
1343894 ATATAATTATAAAAATATAATTAAAAG
1 ATATAATTATAAAAATATAATTAAAAG
* *
1343921 ATATAATTATATAAATATAATATAAAAA
1 ATATAATTATAAAAATATAAT-TAAAAG
* *
1343949 ATATAATTAT-AAAATATAATTATACG
1 ATATAATTATAAAAATATAATTAAAAG
*
1343975 AATATAA-TATAAAAAATTTAATTAAAA
1 -ATATAATTAT-AAAAATATAATTAAAA
1344002 TATAACGTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 6 0.09
27 35 0.51
28 27 0.40
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (27 bp):
ATATAATTATAAAAATATAATTAAAAG
Found at i:1343949 original size:41 final size:40
Alignment explanation
Indices: 1343891--1344021 Score: 176
Period size: 41 Copynumber: 3.2 Consensus size: 40
1343881 TTATTAATAT
1343891 TAAATATAAT-TATAAAAATATAATTAAAAGATATAATTATA
1 TAAATATAATATA-AAAAATATAATTAAAA-ATATAATTATA
1343932 TAAATATAATATAAAAAATATAATTATAAAATATAATTATA
1 TAAATATAATATAAAAAATATAATTA-AAAATATAATTATA
** *
1343973 CGAATATAATATAAAAAATTTAATT-AAAATATAACGTTATA
1 TAAATATAATATAAAAAATATAATTAAAAATATAA--TTATA
1344014 TAAATATA
1 TAAATATA
1344022 TAAATATTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
39 9 0.11
41 67 0.83
42 5 0.06
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (40 bp):
TAAATATAATATAAAAAATATAATTAAAAATATAATTATA
Found at i:1343996 original size:14 final size:13
Alignment explanation
Indices: 1343892--1344001 Score: 121
Period size: 14 Copynumber: 8.1 Consensus size: 13
1343882 TATTAATATT
1343892 AAATATAATTATAA
1 AAATATAATTA-AA
1343906 AAATATAATTAAA
1 AAATATAATTAAA
* *
1343919 AGATATAATTATAT
1 AAATATAATTA-AA
1343933 AAATATAATATAAA
1 AAATATAAT-TAAA
*
1343947 AAATATAATTATA
1 AAATATAATTAAA
*
1343960 AAATATAATTATAC
1 AAATATAATTA-AA
*
1343974 GAATATAATATAAA
1 AAATATAAT-TAAA
*
1343988 AAATTTAATTAAA
1 AAATATAATTAAA
1344001 A
1 A
1344002 TATAACGTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
13 31 0.38
14 46 0.57
15 4 0.05
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (13 bp):
AAATATAATTAAA
Found at i:1344095 original size:12 final size:13
Alignment explanation
Indices: 1344074--1344123 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
1344064 AAAATTTATG
1344074 TAATATAAAATAA
1 TAATATAAAATAA
*
1344087 TAA-ATAAAATTA
1 TAATATAAAATAA
*
1344099 TAATATAATA-AA
1 TAATATAAAATAA
1344111 T-ATATTAAAATAA
1 TAATA-TAAAATAA
1344124 GACAAATACA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
11 3 0.10
12 17 0.57
13 10 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
TAATATAAAATAA
Found at i:1347927 original size:15 final size:16
Alignment explanation
Indices: 1347904--1347936 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1347894 AATGTGAGAT
*
1347904 ATAAGGATT-TATTTA
1 ATAAAGATTATATTTA
1347919 ATAAAGATTATATTTA
1 ATAAAGATTATATTTA
1347935 AT
1 AT
1347937 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
ATAAAGATTATATTTA
Found at i:1347955 original size:22 final size:22
Alignment explanation
Indices: 1347920--1347978 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
1347910 ATTTATTTAA
*
1347920 TAAAGATTATATTTAAT-TATT
1 TAAAAATTATATTTAATATATT
* *
1347941 TTAAAATTTTAATTT-ATATATT
1 TAAAAATTAT-ATTTAATATATT
1347963 TAAAAATTATATTTAA
1 TAAAAATTATATTTAA
1347979 AAATTATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAAAATTATATTTAATATATT
Found at i:1347973 original size:13 final size:13
Alignment explanation
Indices: 1347957--1347992 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
1347947 TTTTAATTTA
1347957 TATATTTAAAAAT
1 TATATTTAAAAAT
1347970 TATATTTAAAAAT
1 TATATTTAAAAAT
1347983 TATATTTAAA
1 TATATTTAAA
1347993 TATACATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATTTAAAAAT
Found at i:1366076 original size:24 final size:23
Alignment explanation
Indices: 1366048--1366103 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
1366038 TTGTTACTTA
1366048 AAATAAAATTAAAAAATAATTTT
1 AAATAAAATTAAAAAATAATTTT
* * * *
1366071 ATAATAATATTTATAATTAATTTT
1 A-AATAAAATTAAAAAATAATTTT
1366095 AAATAAAAT
1 AAATAAAAT
1366104 AATAATTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AAATAAAATTAAAAAATAATTTT
Found at i:1366085 original size:12 final size:11
Alignment explanation
Indices: 1366062--1366100 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
1366052 AAAATTAAAA
1366062 AATAATTTTAT
1 AATAATTTTAT
1366073 AATAATATTTAT
1 AATAAT-TTTAT
1366085 AATTAATTTTA-
1 AA-TAATTTTAT
1366096 AATAA
1 AATAA
1366101 AATAATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.12
11 8 0.31
12 11 0.42
13 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AATAATTTTAT
Found at i:1367914 original size:2 final size:2
Alignment explanation
Indices: 1367907--1367932 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1367897 CCAAAATAGC
1367907 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
1367933 GCTAAATACA
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:1368086 original size:18 final size:20
Alignment explanation
Indices: 1368065--1368101 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1368055 AAAATAATAT
1368065 TATTT-AATATTTA-ATAAG
1 TATTTAAATATTTATATAAG
1368083 TATTTAAATATTTATATAA
1 TATTTAAATATTTATATAA
1368102 TTAATACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
TATTTAAATATTTATATAAG
Found at i:1370550 original size:25 final size:27
Alignment explanation
Indices: 1370522--1370591 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 27
1370512 ATTAAAAATA
*
1370522 AAAATAAATA-AATTTTATTTT-TAAT
1 AAAATAAATATAATTTAATTTTATAAT
*
1370547 AAAAT-AATATTATTTAATTTTATAAT
1 AAAATAAATATAATTTAATTTTATAAT
*
1370573 AAAATATAAT-TTATTTAAT
1 AAAATA-AATATAATTTAAT
1370592 GGATTCAACG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
24 4 0.10
25 14 0.36
26 9 0.23
27 9 0.23
28 3 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AAAATAAATATAATTTAATTTTATAAT
Found at i:1370578 original size:23 final size:24
Alignment explanation
Indices: 1370522--1370585 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 24
1370512 ATTAAAAATA
*
1370522 AAAATAA-ATAAATTTTATTTTTAAT
1 AAAATAATAT-AA-TTTAATTTTAAT
*
1370547 AAAATAATATTATTTAATTTT-AT
1 AAAATAATATAATTTAATTTTAAT
1370570 AATAA-AATATAATTTA
1 AA-AATAATATAATTTA
1370586 TTTAATGGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 14 0.41
24 10 0.29
25 8 0.24
26 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AAAATAATATAATTTAATTTTAAT
Found at i:1372858 original size:3 final size:3
Alignment explanation
Indices: 1372850--1372874 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1372840 GGAGAAAAAT
1372850 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
1372875 GAGAGAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1374327 original size:17 final size:16
Alignment explanation
Indices: 1374307--1374349 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1374297 TAATAATATA
1374307 AAATTATTAAATTTAAT
1 AAATTATTAAATTT-AT
1374324 AAA-TATATAAATTTAT
1 AAATTAT-TAAATTTAT
*
1374340 ATATTATTAA
1 AAATTATTAA
1374350 TATATCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATTATTAAATTTAT
Found at i:1376998 original size:12 final size:11
Alignment explanation
Indices: 1376941--1377007 Score: 55
Period size: 12 Copynumber: 5.8 Consensus size: 11
1376931 TAAATATTGT
*
1376941 AATTTAAATTTA
1 AATTT-AATTAA
1376953 AATTTAATT-A
1 AATTTAATTAA
* *
1376963 AATATATATATAT
1 AATTTA-AT-TAA
*
1376976 AATTGAATTAA
1 AATTTAATTAA
1376987 AATTTTAATTAA
1 AA-TTTAATTAA
1376999 AATTTAATT
1 AATTTAATT
1377008 TTTGAACTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
10 6 0.13
11 17 0.38
12 18 0.40
13 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (11 bp):
AATTTAATTAA
Found at i:1384003 original size:101 final size:101
Alignment explanation
Indices: 1383828--1384026 Score: 398
Period size: 101 Copynumber: 2.0 Consensus size: 101
1383818 TCTTCGAAAG
1383828 AAAAAAAAAAAAGAAGAAGAAACCTCTTAAATCCACTTGTGCTAATTGATACATGAGCATTGAAA
1 AAAAAAAAAAAAGAAGAAGAAACCTCTTAAATCCACTTGTGCTAATTGATACATGAGCATTGAAA
1383893 TTAGATGTCTAAATAATATTTGATATTTGTATTAAC
66 TTAGATGTCTAAATAATATTTGATATTTGTATTAAC
1383929 AAAAAAAAAAAAGAAGAAGAAACCTCTTAAATCCACTTGTGCTAATTGATACATGAGCATTGAAA
1 AAAAAAAAAAAAGAAGAAGAAACCTCTTAAATCCACTTGTGCTAATTGATACATGAGCATTGAAA
1383994 TTAGATGTCTAAATAATATTTGATATTTGTATT
66 TTAGATGTCTAAATAATATTTGATATTTGTATT
1384027 TGTTAATAAT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (101 bp):
AAAAAAAAAAAAGAAGAAGAAACCTCTTAAATCCACTTGTGCTAATTGATACATGAGCATTGAAA
TTAGATGTCTAAATAATATTTGATATTTGTATTAAC
Found at i:1408748 original size:2 final size:2
Alignment explanation
Indices: 1408741--1408772 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1408731 ATATGCTTAC
1408741 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
1408773 TCTAGAATGT
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:1411430 original size:21 final size:21
Alignment explanation
Indices: 1411405--1411460 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1411395 ACATTCAAAT
1411405 ATTTATTATTATCAAT-TTTAA
1 ATTTATTATTAT-AATATTTAA
*
1411426 TTTTATTATTATAATATTTAA
1 ATTTATTATTATAATATTTAA
**
1411447 ATTTACCATTATAA
1 ATTTATTATTATAA
1411461 AAACTAATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 3 0.10
21 27 0.90
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTATTATTATAATATTTAA
Found at i:1412108 original size:9 final size:9
Alignment explanation
Indices: 1412079--1412145 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 9
1412069 TATAATTATG
1412079 TAATATAAAT
1 TAATA-AAAT
1412089 ATAATTAAAAT
1 -TAA-TAAAAT
1412100 TAATAAAAT
1 TAATAAAAT
1412109 T-ATAAAA-
1 TAATAAAAT
1412116 TAATATAAA-
1 TAATA-AAAT
1412125 TATATAAACAT
1 TA-ATAAA-AT
1412136 T-ATAAAAT
1 TAATAAAAT
1412144 TA
1 TA
1412146 TATATAATAA
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
7 1 0.02
8 12 0.24
9 19 0.39
10 7 0.14
11 8 0.16
12 2 0.04
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (9 bp):
TAATAAAAT
Found at i:1412113 original size:27 final size:27
Alignment explanation
Indices: 1412102--1412154 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1412092 ATTAAAATTA
1412102 ATAAA-ATTATAAAATAATATAAATAT
1 ATAAACATTATAAAATAATATAAATAT
*
1412128 ATAAACATTATAAAATTATATATAATA
1 ATAAACATTATAAAATAATATA-AATA
1412155 AAAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 15 0.62
28 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
ATAAACATTATAAAATAATATAAATAT
Found at i:1412115 original size:8 final size:8
Alignment explanation
Indices: 1412094--1412147 Score: 63
Period size: 9 Copynumber: 6.2 Consensus size: 8
1412084 TAAATATAAT
1412094 TAAAATTAA
1 TAAAATT-A
1412103 TAAAATTA
1 TAAAATTA
*
1412111 TAAAATAA
1 TAAAATTA
1412119 TATAAATATA
1 TA-AAAT-TA
1412129 TAAACATTA
1 TAAA-ATTA
1412138 TAAAATTA
1 TAAAATTA
1412146 TA
1 TA
1412148 TATAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 16 0.40
9 19 0.47
10 5 0.12
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAAATTA
Found at i:1412116 original size:17 final size:17
Alignment explanation
Indices: 1412094--1412147 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
1412084 TAAATATAAT
1412094 TAAAATTAATAAAATTA
1 TAAAATTAATAAAATTA
1412111 TAAAA-TAATATAAATATA
1 TAAAATTAATA-AAAT-TA
1412129 TAAACATT-ATAAAATTA
1 TAAA-ATTAATAAAATTA
1412146 TA
1 TA
1412148 TATAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.15
17 13 0.39
18 10 0.30
19 4 0.12
20 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATTAATAAAATTA
Found at i:1412155 original size:37 final size:37
Alignment explanation
Indices: 1412079--1412147 Score: 108
Period size: 35 Copynumber: 1.9 Consensus size: 37
1412069 TATAATTATG
1412079 TAATATAAATATAATTAAAATTAATAAAATTATAAAA
1 TAATATAAATATAATTAAAATTAATAAAATTATAAAA
1412116 TAATATAAATAT-A-TAAACATT-ATAAAATTATA
1 TAATATAAATATAATTAAA-ATTAATAAAATTATA
1412148 TATAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
35 15 0.48
36 4 0.13
37 12 0.39
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (37 bp):
TAATATAAATATAATTAAAATTAATAAAATTATAAAA
Found at i:1418733 original size:24 final size:26
Alignment explanation
Indices: 1418687--1418734 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
1418677 TGATTATGAG
* *
1418687 AATTATATATTAATAATTTATATTAT
1 AATTAAATATTAATAATATATATTAT
1418713 AATTAAAT-TTAA-AATATATATT
1 AATTAAATATTAATAATATATATT
1418735 TATATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 4 0.20
26 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTAAATATTAATAATATATATTAT
Found at i:1418743 original size:35 final size:36
Alignment explanation
Indices: 1418690--1418757 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
1418680 TTATGAGAAT
1418690 TATATATTAATAATTTATATTATAATTAAATTTAAAA
1 TATATATTAATAATTTATATTATAA-TAAATTTAAAA
*
1418727 TATATATTTAT-A-TTATATTATAATAAATTTA
1 TATATATTAATAATTTATATTATAATAAATTTA
1418758 TATTTAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 8 0.27
35 11 0.37
36 1 0.03
37 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (36 bp):
TATATATTAATAATTTATATTATAATAAATTTAAAA
Found at i:1418758 original size:21 final size:20
Alignment explanation
Indices: 1418719--1418770 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1418709 TTATAATTAA
* *
1418719 ATTTAAAAT-ATATATTTAT
1 ATTTAATATAATAAATTTAT
*
1418738 ATTATATTATAATAAATTTAT
1 ATT-TAATATAATAAATTTAT
1418759 ATTTAATATAAT
1 ATTTAATATAAT
1418771 TATATAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 3 0.11
20 12 0.44
21 12 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAATATAATAAATTTAT
Found at i:1418767 original size:23 final size:24
Alignment explanation
Indices: 1418725--1418793 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 24
1418715 TTAAATTTAA
1418725 AATATATATTTATA-TT-ATATTAT
1 AATATA-ATTTATATTTAATATTAT
*
1418748 AATA-AATTTATATTTAATATAAT
1 AATATAATTTATATTTAATATTAT
* * *
1418771 TATATAATTT-TGTTTAAAATTAT
1 AATATAATTTATATTTAATATTAT
1418794 CACTGCAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 7 0.18
22 3 0.08
23 23 0.61
24 5 0.13
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
AATATAATTTATATTTAATATTAT
Found at i:1418773 original size:15 final size:15
Alignment explanation
Indices: 1418687--1418775 Score: 56
Period size: 15 Copynumber: 5.5 Consensus size: 15
1418677 TGATTATGAG
1418687 AATTATA-TATTAATA
1 AATTATATTA-TAATA
*
1418702 ATTTATATTATAATTA
1 AATTATATTATAA-TA
* *
1418718 AATTTAAAATATATATTTA
1 AA-TT-ATAT-TATA-ATA
*
1418737 TATTATATTATAATA
1 AATTATATTATAATA
1418752 AATTTATATT-TAATA
1 AA-TTATATTATAATA
1418767 TAATTATAT
1 -AATTATAT
1418776 AATTTTGTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
15 23 0.40
16 18 0.31
17 5 0.09
18 5 0.09
19 7 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTATATTATAATA
Found at i:1418776 original size:17 final size:16
Alignment explanation
Indices: 1418697--1418775 Score: 65
Period size: 17 Copynumber: 4.9 Consensus size: 16
1418687 AATTATATAT
1418697 TAAT-AATTTATATTA
1 TAATAAATTTATATTA
* *
1418712 TAATTAAATTTAAAATA
1 TAA-TAAATTTATATTA
**
1418729 TATATTTATATTATATTA
1 TA-ATAAAT-TTATATTA
1418747 TAATAAATTTATATT-
1 TAATAAATTTATATTA
1418762 TAATATAA-TTATAT
1 TAATA-AATTTATAT
1418776 AATTTTGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
15 14 0.27
16 10 0.20
17 18 0.35
18 9 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATAAATTTATATTA
Found at i:1419321 original size:11 final size:11
Alignment explanation
Indices: 1419305--1419415 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
1419295 ATAATTTTAA
*
1419305 AAATATTATAT
1 AAATATAATAT
1419316 AAATATAATAT
1 AAATATAATAT
*
1419327 --ATATAATAA
1 AAATATAATAT
1419336 AAATATAATA-
1 AAATATAATAT
* *
1419346 AAATATCATTAA
1 AAATAT-AATAT
*
1419358 AAATATATATTT
1 AAATATA-ATAT
* *
1419370 AAAAAAAATAT
1 AAATATAATAT
1419381 ATTAA-AT-ATAT
1 A--AATATAATAT
* *
1419392 TAA-AT-ATCT
1 AAATATAATAT
1419401 AAATATAATAT
1 AAATATAATAT
1419412 AAAT
1 AAAT
1419416 TATTAAATTA
Statistics
Matches: 77, Mismatches: 14, Indels: 18
0.71 0.13 0.17
Matches are distributed among these distances:
9 17 0.22
10 8 0.10
11 37 0.48
12 13 0.17
13 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATATAATAT
Found at i:1419362 original size:12 final size:11
Alignment explanation
Indices: 1419302--1419364 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
1419292 TTAATAATTT
*
1419302 TAAAAATATTA
1 TAAAAATATAA
*
1419313 TATAAATATAA
1 TAAAAATATAA
*
1419324 T--ATATATAA
1 TAAAAATATAA
1419333 TAAAAATATAA
1 TAAAAATATAA
*
1419344 T-AAAATATCAT
1 TAAAAATAT-AA
1419355 TAAAAATATA
1 TAAAAATATA
1419365 TATTTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
9 8 0.19
10 7 0.16
11 21 0.49
12 7 0.16
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAAAAATATAA
Found at i:1419363 original size:37 final size:36
Alignment explanation
Indices: 1419322--1419395 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
1419312 ATATAAATAT
*
1419322 AATATATA-TAATAAAAATATAATAAAATATCATTAAA
1 AATATATATTAAAAAAAATAT-ATAAAATAT-ATTAAA
*
1419359 AATATATATTTAAAAAAAATATATTAAATATATTAAA
1 AATATATA-TTAAAAAAAATATATAAAATATATTAAA
1419396 TATCTAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 14 0.42
38 8 0.24
39 11 0.33
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (36 bp):
AATATATATTAAAAAAAATATATAAAATATATTAAA
Found at i:1419385 original size:14 final size:14
Alignment explanation
Indices: 1419345--1419386 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1419335 AAAATATAAT
1419345 AAAATATCATT-AAA
1 AAAATAT-ATTAAAA
*
1419359 AATATATATTTAAAA
1 AAAATATA-TTAAAA
1419374 AAAATATATTAAA
1 AAAATATATTAAA
1419387 TATATTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 1 0.04
14 13 0.54
15 10 0.42
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATATTAAAA
Found at i:1419389 original size:9 final size:9
Alignment explanation
Indices: 1419375--1419431 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 9
1419365 TATTTAAAAA
1419375 AAATATATT
1 AAATATATT
1419384 AAATATATT
1 AAATATATT
*
1419393 AAATAT-CT
1 AAATATATT
1419401 AAATATAATAT
1 AAATAT-AT-T
1419412 AAAT-TATT
1 AAATATATT
1419420 AAAT-TATT
1 AAATATATT
1419428 AAAT
1 AAAT
1419432 TTAATTTTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
8 20 0.47
9 17 0.40
10 1 0.02
11 5 0.12
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (9 bp):
AAATATATT
Found at i:1419423 original size:27 final size:27
Alignment explanation
Indices: 1419375--1419437 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1419365 TATTTAAAAA
1419375 AAATAT-ATTAAATATATTAAA-TATCT
1 AAATATAATTAAATATATTAAATTAT-T
1419401 AAATATAATATAAAT-TATTAAATTATT
1 AAATATAAT-TAAATATATTAAATTATT
*
1419428 AAATTTAATT
1 AAATATAATT
1419438 TTAAATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.21
27 18 0.55
28 8 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (27 bp):
AAATATAATTAAATATATTAAATTATT
Found at i:1420828 original size:2 final size:2
Alignment explanation
Indices: 1420823--1420851 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1420813 TATATGTGTG
1420823 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
1420852 TGCATTTTCT
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:1423776 original size:28 final size:28
Alignment explanation
Indices: 1423736--1423799 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
1423726 ATCGGTGTAC
*
1423736 TTTTCATTCATATGTTATGTTCTTCAAA
1 TTTTCACTCATATGTTATGTTCTTCAAA
1423764 TTTTCACTCATATGTTATGTTCTTCAAA
1 TTTTCACTCATATGTTATGTTCTTCAAA
1423792 TTTTCACT
1 TTTTCACT
1423800 GGCAGAAACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.53
Consensus pattern (28 bp):
TTTTCACTCATATGTTATGTTCTTCAAA
Found at i:1431962 original size:3 final size:3
Alignment explanation
Indices: 1431954--1432006 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1431944 ACCAAAACAA
1431954 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1432002 AAG AA
1 AAG AA
1432007 AGGGCATGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1432563 original size:8 final size:8
Alignment explanation
Indices: 1432550--1432621 Score: 56
Period size: 10 Copynumber: 8.1 Consensus size: 8
1432540 AGACCTAATA
1432550 ATTTATAT
1 ATTTATAT
1432558 ATTTATTTAT
1 ATTTA--TAT
1432568 ATTTATAT
1 ATTTATAT
1432576 ATTTTATTAT
1 A-TTTA-TAT
1432586 ATTATAATTAT
1 ATT-T-A-TAT
*
1432597 ATTTAAAAT
1 ATTT-ATAT
1432606 ATTT-TAT
1 ATTTATAT
1432613 ATTTATAT
1 ATTTATAT
1432621 A
1 A
1432622 AATTTTAATA
Statistics
Matches: 55, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
7 6 0.11
8 13 0.24
9 12 0.22
10 16 0.29
11 8 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATTTATAT
Done.