Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold132
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: 2458301
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 25 characters in sequence are not A, C, G, or T
File 7 of 15
Found at i:1196778 original size:24 final size:24
Alignment explanation
Indices: 1196747--1196797 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
1196737 TATATTAAAA
1196747 TTTTAAATA-AA-TTATATATTATT
1 TTTTAAATATAATTTAT-TATTATT
*
1196770 TTTTAAAATATAATTTATTTTTATT
1 TTTT-AAATATAATTTATTATTATT
1196795 TTT
1 TTT
1196798 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 5 0.21
25 11 0.46
26 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTAAATATAATTTATTATTATT
Found at i:1200862 original size:34 final size:34
Alignment explanation
Indices: 1200824--1200891 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
1200814 TATAGTTAGT
1200824 ATTAAAATAA-TTTGAATTTGAATTTAAATTTAAG
1 ATTAAAA-AATTTTGAATTTGAATTTAAATTTAAG
*
1200858 ATTAAAAAATTTTTAATTTGAATTTAAATTTAAG
1 ATTAAAAAATTTTGAATTTGAATTTAAATTTAAG
1200892 TATAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.46
Consensus pattern (34 bp):
ATTAAAAAATTTTGAATTTGAATTTAAATTTAAG
Found at i:1202461 original size:42 final size:42
Alignment explanation
Indices: 1202414--1202529 Score: 169
Period size: 42 Copynumber: 2.8 Consensus size: 42
1202404 TTGACTGGTA
*
1202414 ACAGTGGAAGATCTAGAACTCTTTTACTGGTTGCATATTTAT
1 ACAGTGGAAGATCTAGAACTCTTTTAATGGTTGCATATTTAT
* ** *
1202456 ACAGTGGAAGATCTAGAACTATTTTAATGGCCGCTTATTTAT
1 ACAGTGGAAGATCTAGAACTCTTTTAATGGTTGCATATTTAT
* *
1202498 GCACTGGAAGATCTAGAACTCTTTTAATGGTT
1 ACAGTGGAAGATCTAGAACTCTTTTAATGGTT
1202530 ACTTATATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (42 bp):
ACAGTGGAAGATCTAGAACTCTTTTAATGGTTGCATATTTAT
Found at i:1203091 original size:43 final size:41
Alignment explanation
Indices: 1203025--1203109 Score: 143
Period size: 43 Copynumber: 2.0 Consensus size: 41
1203015 AAAACAACAA
1203025 TTCAAAAAGTCAAGCATAACTGCAGCTACTATAGATAAAAC
1 TTCAAAAAGTCAAGCATAACTGCAGCTACTATAGATAAAAC
*
1203066 TTCAAAAAGTCAAAAGCATAACTGCAGCTACTATGGATAAAAC
1 TTCAAAAAGTC--AAGCATAACTGCAGCTACTATAGATAAAAC
1203109 T
1 T
1203110 AGTTTTCTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 11 0.27
43 30 0.73
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (41 bp):
TTCAAAAAGTCAAGCATAACTGCAGCTACTATAGATAAAAC
Found at i:1206937 original size:21 final size:21
Alignment explanation
Indices: 1206913--1206952 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1206903 ATAAATTAAA
1206913 ATTTTAACT-TTTATTTTATTT
1 ATTTT-ACTATTTATTTTATTT
*
1206934 ATTTTATTATTTATTTTAT
1 ATTTTACTATTTATTTTAT
1206953 AAAATATATA
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:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
ATTTTACTATTTATTTTATTT
Found at i:1206943 original size:12 final size:12
Alignment explanation
Indices: 1206928--1206952 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1206918 AACTTTTATT
1206928 TTATTTATTTTA
1 TTATTTATTTTA
1206940 TTATTTATTTTA
1 TTATTTATTTTA
1206952 T
1 T
1206953 AAAATATATA
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTATTTTA
Found at i:1207744 original size:13 final size:14
Alignment explanation
Indices: 1207704--1207749 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
1207694 TAAAATGGTT
*
1207704 ATATAAATATAATAT
1 ATATAAATATAA-AA
*
1207719 ATATAATTATAAAA
1 ATATAAATATAAAA
1207733 AT-TAAATATAAAA
1 ATATAAATATAAAA
1207746 ATAT
1 ATAT
1207750 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.44
14 4 0.15
15 11 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATAAATATAAAA
Found at i:1207808 original size:20 final size:20
Alignment explanation
Indices: 1207761--1207843 Score: 68
Period size: 19 Copynumber: 4.3 Consensus size: 20
1207751 TTTAAATTTT
*
1207761 ATATAATTAAAATT--TATTA
1 ATAT-ATTAAAATTAATATAA
1207780 ATATATTAAAATTAATATAA
1 ATATATTAAAATTAATATAA
*
1207800 ATAT-TTTAAATATAATA-AA
1 ATATATTAAAAT-TAATATAA
* * *
1207819 ATATAATAATA-TAATATGA
1 ATATATTAAAATTAATATAA
1207838 ATATAT
1 ATATAT
1207844 AATATTTATT
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
18 14 0.27
19 22 0.42
20 16 0.31
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
ATATATTAAAATTAATATAA
Found at i:1207845 original size:18 final size:18
Alignment explanation
Indices: 1207808--1207848 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1207798 AAATATTTTA
1207808 AATATAATAAAATATAAT
1 AATATAATAAAATATAAT
*
1207826 AATATAATATGAATAT-AT
1 AATATAATA-AAATATAAT
1207844 AATAT
1 AATAT
1207849 TTATTCTGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATATAATAAAATATAAT
Found at i:1207846 original size:13 final size:13
Alignment explanation
Indices: 1207811--1207848 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1207801 TATTTTAAAT
*
1207811 ATAATAAAATATA
1 ATAATATAATATA
1207824 ATAATATAATATGA
1 ATAATATAATAT-A
1207838 AT-ATATAATAT
1 ATAATATAATAT
1207849 TTATTCTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (13 bp):
ATAATATAATATA
Found at i:1208373 original size:10 final size:10
Alignment explanation
Indices: 1208358--1208387 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1208348 TATCATTGTA
1208358 TTTTAATTTT
1 TTTTAATTTT
1208368 TTTTAATTTT
1 TTTTAATTTT
*
1208378 CTTTAATTTT
1 TTTTAATTTT
1208388 AATTTTTACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:1208926 original size:28 final size:29
Alignment explanation
Indices: 1208868--1208931 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
1208858 AAATAAATAT
1208868 AATT-AATTTAGTCAAAACATTAATTTTA
1 AATTAAATTTAGTCAAAACATTAATTTTA
1208896 AA-TAAATTTAGTCACAAA-ATT-ATTTTAA
1 AATTAAATTTAGTCA-AAACATTAATTTT-A
1208924 AATTAAAT
1 AATTAAAT
1208932 AAAAGTTAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 6 0.19
28 18 0.56
29 8 0.25
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (29 bp):
AATTAAATTTAGTCAAAACATTAATTTTA
Found at i:1209283 original size:22 final size:22
Alignment explanation
Indices: 1209258--1209299 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1209248 TTTCGTACAT
1209258 TATTT-AATTATCATAATAATAG
1 TATTTCAATTAT-ATAATAATAG
1209280 TATTTCAATTATATAATAAT
1 TATTTCAATTATATAATAAT
1209300 CTTTTAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
TATTTCAATTATATAATAATAG
Found at i:1210159 original size:22 final size:24
Alignment explanation
Indices: 1210132--1210178 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
1210122 AAAAAAATTT
1210132 AAATAAAAATAA-T-AATTTTAAA
1 AAATAAAAATAATTAAATTTTAAA
**
1210154 AAATAAATTTAATTAAATTTTAAA
1 AAATAAAAATAATTAAATTTTAAA
1210178 A
1 A
1210179 TTTATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 1 0.05
24 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATAAAAATAATTAAATTTTAAA
Found at i:1211012 original size:43 final size:43
Alignment explanation
Indices: 1210964--1211045 Score: 130
Period size: 43 Copynumber: 1.9 Consensus size: 43
1210954 ACCAAGTATG
*
1210964 AATAAGCATAACAATCATTAAGAT-ATTATCTTAATCCGACCCA
1 AATAAGCAGAACAATCATTAA-ATAATTATCTTAATCCGACCCA
*
1211007 AATAAGCAGAACAATCATTAATTAATTATCTTAATCCGA
1 AATAAGCAGAACAATCATTAAATAATTATCTTAATCCGA
1211046 TCTAAATCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 1 0.03
43 35 0.97
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.29
Consensus pattern (43 bp):
AATAAGCAGAACAATCATTAAATAATTATCTTAATCCGACCCA
Found at i:1213647 original size:3 final size:3
Alignment explanation
Indices: 1213639--1213684 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1213629 TAATTAAAAA
1213639 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1213685 TATTGATATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1214272 original size:20 final size:20
Alignment explanation
Indices: 1214222--1214260 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1214212 TCTTGTACAT
1214222 ATTATTTTT-AAATATTATA
1 ATTATTTTTAAAATATTATA
1214241 ATTATTTTTAAAATATTATA
1 ATTATTTTTAAAATATTATA
1214261 TATTTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTATTTTTAAAATATTATA
Found at i:1214522 original size:20 final size:19
Alignment explanation
Indices: 1214497--1214536 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1214487 CTTCTTTATA
1214497 TTTATATTAAATTTATATTT
1 TTTATATTAAA-TTATATTT
*
1214517 TTTATATTATATTATATTT
1 TTTATATTAAATTATATTT
1214536 T
1 T
1214537 ACTTTCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATATTAAATTATATTT
Found at i:1217307 original size:108 final size:108
Alignment explanation
Indices: 1217118--1217324 Score: 387
Period size: 108 Copynumber: 1.9 Consensus size: 108
1217108 TGAACTAAGA
*
1217118 GAGGACTAACCTTTGAGGAAACTTGAGAGGAATATATTCTTTAAGAAGAACTAAACCAAGTCACC
1 GAGGACTAACCCTTGAGGAAACTTGAGAGGAATATATTCTTTAAGAAGAACTAAACCAAGTCACC
* *
1217183 AGGGTATTCACTGAGAAAATGCTACTAAATTATGATAAAAAAT
66 AGAGTATTCAATGAGAAAATGCTACTAAATTATGATAAAAAAT
1217226 GAGGACTAACCCTTGAGGAAACTTGAGAGGAATATATTCTTTAAGAAGAACTAAACCAAGTCACC
1 GAGGACTAACCCTTGAGGAAACTTGAGAGGAATATATTCTTTAAGAAGAACTAAACCAAGTCACC
1217291 AGAGTATTCAATGAGAAAATGCTACTAAATTATG
66 AGAGTATTCAATGAGAAAATGCTACTAAATTATG
1217325 GTTATGGCAA
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 96 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (108 bp):
GAGGACTAACCCTTGAGGAAACTTGAGAGGAATATATTCTTTAAGAAGAACTAAACCAAGTCACC
AGAGTATTCAATGAGAAAATGCTACTAAATTATGATAAAAAAT
Found at i:1219838 original size:2 final size:2
Alignment explanation
Indices: 1219831--1219861 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1219821 ACTCAATAAA
1219831 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1219862 AAAAAACTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1223533 original size:19 final size:19
Alignment explanation
Indices: 1223501--1223562 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1223491 TATATTTATT
1223501 TAAAT-TTAATTATAAATTA
1 TAAATATTAA-TATAAATTA
*
1223520 TAAATATTAATATAAA-AA
1 TAAATATTAATATAAATTA
* *
1223538 TAATATTTTAATA-ATATTA
1 TAA-ATATTAATATAAATTA
1223557 TAAATA
1 TAAATA
1223563 AAAAATTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 8 0.23
19 23 0.66
20 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAATATTAATATAAATTA
Found at i:1225081 original size:3 final size:3
Alignment explanation
Indices: 1225073--1225098 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1225063 CGATGGGATC
1225073 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
1225099 TCTCGTGTTA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1226322 original size:52 final size:53
Alignment explanation
Indices: 1226244--1226346 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 53
1226234 CAGCAACAAA
** *
1226244 GTGAAAGATACACGGATATATGTTGCTGCAGGAAATTTTCAGAAT-CTGGAAG
1 GTGAAAGATACACCAATACATGTTGCTGCAGGAAATTTTCAGAATCCTGGAAG
* * *
1226296 GTGAAAGATATACCAATACATGTTGCTGCAGGCATTTTTCAGAATCCTGGA
1 GTGAAAGATACACCAATACATGTTGCTGCAGGAAATTTTCAGAATCCTGGA
1226347 TGTGCAAACT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
52 39 0.89
53 5 0.11
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (53 bp):
GTGAAAGATACACCAATACATGTTGCTGCAGGAAATTTTCAGAATCCTGGAAG
Found at i:1230615 original size:6 final size:6
Alignment explanation
Indices: 1230597--1230630 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1230587 AATAATTAAC
* *
1230597 ATTTTT ATTTAT ATCTAT ATTTAT ATTTAT ATTT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTT
1230631 TTTTAGTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:1230752 original size:14 final size:15
Alignment explanation
Indices: 1230718--1230760 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1230708 AAGTTTAATT
*
1230718 TAATTTTTTATATAA
1 TAATTTTTTATAAAA
*
1230733 TTATTTTTTA-AAAA
1 TAATTTTTTATAAAA
*
1230747 TAATTTTTAATAAA
1 TAATTTTTTATAAA
1230761 TTTAATATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATTTTTTATAAAA
Found at i:1230766 original size:16 final size:15
Alignment explanation
Indices: 1230717--1230762 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 15
1230707 TAAGTTTAAT
*
1230717 TTAATTTTTTATATAA
1 TTAATTTTTAATA-AA
*
1230733 TTATTTTTTAA-AAA
1 TTAATTTTTAATAAA
1230747 -TAATTTTTAATAAA
1 TTAATTTTTAATAAA
1230761 TT
1 TT
1230763 TAATATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
13 9 0.36
14 5 0.20
15 2 0.08
16 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTAATTTTTAATAAA
Found at i:1230928 original size:25 final size:24
Alignment explanation
Indices: 1230882--1230932 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
1230872 AAAATGTATT
1230882 TATTTATAATTAATAATATTAATAA
1 TATTTATAATTAATAATATTAA-AA
1230907 TATTTATAA-TAGAT-ATATTTAAAA
1 TATTTATAATTA-ATAATA-TTAAAA
1230931 TA
1 TA
1230933 ATAATTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TATTTATAATTAATAATATTAAAA
Found at i:1231328 original size:26 final size:25
Alignment explanation
Indices: 1231297--1231351 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
1231287 TTCATATGAT
* *
1231297 TTTAGATAATTTTTTAAATAGATAAA
1 TTTAGATAAATTTTTAAATAAAT-AA
1231323 TTTAGATAAATTTTTAAATAAATAA
1 TTTAGATAAATTTTTAAATAAATAA
1231348 TTTA
1 TTTA
1231352 AATATCTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (25 bp):
TTTAGATAAATTTTTAAATAAATAA
Found at i:1231343 original size:12 final size:13
Alignment explanation
Indices: 1231309--1231355 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
1231299 TAGATAATTT
*
1231309 TTTAAATAGATAAA
1 TTTAAATAAAT-AA
* *
1231323 TTTAGATAAAT-T
1 TTTAAATAAATAA
1231335 TTTAAATAAATAA
1 TTTAAATAAATAA
1231348 TTTAAATA
1 TTTAAATA
1231356 TCTTATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
12 10 0.37
13 8 0.30
14 9 0.33
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (13 bp):
TTTAAATAAATAA
Found at i:1231447 original size:14 final size:14
Alignment explanation
Indices: 1231428--1231454 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1231418 ATTTACCTCA
1231428 TTAAAATAATTATT
1 TTAAAATAATTATT
1231442 TTAAAATAATTAT
1 TTAAAATAATTAT
1231455 ATCTTTTAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAAATAATTATT
Found at i:1233624 original size:2 final size:2
Alignment explanation
Indices: 1233617--1233663 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1233607 CATATCTGTG
1233617 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1233659 TA TA T
1 TA TA T
1233664 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1233668 original size:2 final size:2
Alignment explanation
Indices: 1233663--1233687 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1233653 TATATATATA
1233663 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 T
1233688 ATCTATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1238932 original size:15 final size:16
Alignment explanation
Indices: 1238901--1238962 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 16
1238891 AATAATTTTT
*
1238901 AATTTATTGTTAAT-A
1 AATTTATTATTAATAA
*
1238916 AATTTATTATTAGTAA
1 AATTTATTATTAATAA
*
1238932 AAATTATTATTAA-AA
1 AATTTATTATTAATAA
*
1238947 ATATATATTTATTAAT
1 A-ATTTA-TTATTAAT
1238963 TTTTAAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
15 15 0.41
16 15 0.41
17 7 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AATTTATTATTAATAA
Found at i:1243587 original size:3 final size:3
Alignment explanation
Indices: 1243579--1243612 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1243569 TTCGTAAGTC
1243579 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1243613 CCAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1245449 original size:16 final size:17
Alignment explanation
Indices: 1245428--1245460 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1245418 AGTGAAATAA
1245428 GAATTT-AAGTTTAATT
1 GAATTTAAAGTTTAATT
1245444 GAATTTAAAGTTTAATT
1 GAATTTAAAGTTTAATT
1245461 TAAATTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
GAATTTAAAGTTTAATT
Found at i:1245468 original size:17 final size:17
Alignment explanation
Indices: 1245429--1245468 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1245419 GTGAAATAAG
*
1245429 AATTTAAGTTTAATTGA
1 AATTAAAGTTTAATTGA
* *
1245446 ATTTAAAGTTTAATTTA
1 AATTAAAGTTTAATTGA
1245463 AATTAA
1 AATTAA
1245469 TTTATAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (17 bp):
AATTAAAGTTTAATTGA
Found at i:1245807 original size:177 final size:174
Alignment explanation
Indices: 1245554--1245874 Score: 466
Period size: 176 Copynumber: 1.8 Consensus size: 174
1245544 CTTTTTTATA
* ** **
1245554 AAAAAATAATTTAAATTTATTTAAATGATTTATTCATTTCTTTTAAAAAGTAAATTCCAATTTAA
1 AAAAAATAATTTAAATTTATCTAAATGATTTATTCATTTCTTAAAAAAAGTAAATTCCAATAAAA
* * *
1245619 TCAAAATTCGATCTCAAAATTTATA-ATTTTTTTTCTTTAATTTCTCTTAAATTTTTGACCTTTT
66 TCAAAATTCGATCTCAAAATTTACACA--TTTTTTCTTTAATTTCTCTTAAA-TTTGGACCTCTT
* *
1245683 ACCTAAATGTTTAAATAACTTTGGTGTCGACACACTTGCTTTATACT
128 ACCCAAATGTTCAAATAACTTTGGTGTCGACACACTTGCTTTATACT
* * *
1245730 AAAAATTAATTTGAATTTATCTAAATGATTTATTTATTTCTTAAAAAAAAGTAAATTCTC-ATAA
1 AAAAAATAATTTAAATTTATCTAAATGATTTATTCATTTCTT-AAAAAAAGTAAATTC-CAATAA
1245794 AATCAAAATTCGATCTCAAAATTTACACATTTTTTCTTTAATTTCTCTTAAATTTGGACCTCTTA
64 AATCAAAATTCGATCTCAAAATTTACACATTTTTTCTTTAATTTCTCTTAAATTTGGACCTCTTA
1245859 CCCAAATGTTCAAATA
129 CCCAAATGTTCAAATA
1245875 TTCCTTGTGT
Statistics
Matches: 129, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
175 25 0.19
176 61 0.47
177 41 0.32
178 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.05, T:0.44
Consensus pattern (174 bp):
AAAAAATAATTTAAATTTATCTAAATGATTTATTCATTTCTTAAAAAAAGTAAATTCCAATAAAA
TCAAAATTCGATCTCAAAATTTACACATTTTTTCTTTAATTTCTCTTAAATTTGGACCTCTTACC
CAAATGTTCAAATAACTTTGGTGTCGACACACTTGCTTTATACT
Found at i:1248199 original size:19 final size:19
Alignment explanation
Indices: 1248154--1248204 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
1248144 TTATATTAAT
1248154 TTAATAT-AA-TTTATACA
1 TTAATATAAATTTTATACA
* *
1248171 -TAAAATAAATTTTATATA
1 TTAATATAAATTTTATACA
1248189 TTAATATAAATTTTAT
1 TTAATATAAATTTTAT
1248205 TAATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 5 0.18
17 2 0.07
18 7 0.25
19 14 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATATAAATTTTATACA
Found at i:1251164 original size:16 final size:15
Alignment explanation
Indices: 1251126--1251168 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
1251116 TCAATTAATT
1251126 AATTAAAT-TATTTA
1 AATTAAATATATTTA
*
1251140 ATTTAAAATATATTTAA
1 AATT-AAATATATTT-A
1251157 AATTAAATATAT
1 AATTAAATATAT
1251169 AATTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 3 0.12
15 4 0.17
16 13 0.54
17 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAATATATTTA
Found at i:1251181 original size:20 final size:18
Alignment explanation
Indices: 1251134--1251184 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
1251124 TTAATTAAAT
1251134 TATTTAAT-TTAAA-ATA
1 TATTTAATATTAAATATA
*
1251150 TATTTAAAATTAAATATA
1 TATTTAATATTAAATATA
1251168 TAATTTTAATATTAAAT
1 T-A-TTTAATATTAAAT
1251185 TAATATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 7 0.24
17 5 0.17
18 4 0.14
19 1 0.03
20 12 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTAATATTAAATATA
Found at i:1252064 original size:32 final size:33
Alignment explanation
Indices: 1251994--1252099 Score: 87
Period size: 32 Copynumber: 3.4 Consensus size: 33
1251984 AATCATTATT
* * * **
1251994 TATAA-ATATAATAAAAAATA-ATTAAAATAAA
1 TATAATATATAATTATAAATATATAAAAATTTA
* * * *
1252025 TAAAATATATATTTATAAAT-TTTTAAAATTTA
1 TATAATATATAATTATAAATATATAAAAATTTA
*
1252057 TATAATATA-AATTATTAATATATAAAAATTTA
1 TATAATATATAATTATAAATATATAAAAATTTA
1252089 TATAA-ATATAA
1 TATAATATATAA
1252100 ATATTTTAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
31 15 0.25
32 44 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
TATAATATATAATTATAAATATATAAAAATTTA
Found at i:1252065 original size:24 final size:23
Alignment explanation
Indices: 1252025--1252080 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 23
1252015 TTAAAATAAA
* *
1252025 TAAAATATATATTTATAAATTTT
1 TAAAATATATATATATAAATTAT
*
1252048 TAAAATTTATATAATATAAATTAT
1 TAAAATATATAT-ATATAAATTAT
*
1252072 TAATATATA
1 TAAAATATA
1252081 AAAATTTATA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TAAAATATATATATATAAATTAT
Found at i:1252089 original size:18 final size:18
Alignment explanation
Indices: 1252049--1252105 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1252039 ATAAATTTTT
1252049 AAAATTTA-T-ATA-ATA
1 AAAATTTATTAATATATA
*
1252064 TAAA-TTATTAATATATA
1 AAAATTTATTAATATATA
1252081 AAAATTTATATAA-ATATA
1 AAAATTTAT-TAATATATA
*
1252099 AATATTT
1 AAAATTT
1252106 TAAATATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 3 0.09
15 4 0.12
16 3 0.09
17 6 0.18
18 15 0.44
19 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATTTATTAATATATA
Found at i:1252113 original size:33 final size:32
Alignment explanation
Indices: 1252049--1252114 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
1252039 ATAAATTTTT
1252049 AAAATTTATATAATATAAATTATTAATATATA
1 AAAATTTATATAATATAAATTATTAATATATA
*
1252081 AAAATTTATATAAATATAAATATTTTAA-ATATA
1 AAAATTTATAT-AATATAAAT-TATTAATATATA
1252114 A
1 A
1252115 TAACATAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 11 0.35
33 15 0.48
34 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATTTATATAATATAAATTATTAATATATA
Found at i:1253469 original size:16 final size:17
Alignment explanation
Indices: 1253444--1253483 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1253434 TTATTTAATA
*
1253444 AAAATATAATTTTAAAT
1 AAAATATAATTATAAAT
1253461 AAAAT-TAATTATAAAT
1 AAAATATAATTATAAAT
1253477 ATAAATA
1 A-AAATA
1253484 AAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATATAATTATAAAT
Found at i:1253501 original size:18 final size:18
Alignment explanation
Indices: 1253437--1253501 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
1253427 ATATTATTTA
*
1253437 TTTAAT-AAAAATATAAT
1 TTTAATAAAAAATAAAAT
1253454 TTTAAATAAAATTAATTATAAAT
1 TTT-AATAAAA--AA-TA-AAAT
* *
1253477 ATAAATAAAAAATAAAAT
1 TTTAATAAAAAATAAAAT
1253495 TTTAATA
1 TTTAATA
1253502 TTATTTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
17 3 0.08
18 12 0.32
19 5 0.14
20 2 0.05
21 2 0.05
22 9 0.24
23 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTAATAAAAAATAAAAT
Found at i:1253796 original size:6 final size:6
Alignment explanation
Indices: 1253785--1253817 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1253775 TTTTTTTTCA
1253785 TAAATT TAAATT T-AATT T-AATT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAAT
1253818 AAAAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:1257465 original size:22 final size:22
Alignment explanation
Indices: 1257438--1257480 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1257428 CATGAAAATT
*
1257438 ATTTATAT-TATTTTAATTTTTA
1 ATTTATATATA-TATAATTTTTA
1257460 ATTTATATATATATAATTTTT
1 ATTTATATATATATAATTTTT
1257481 TAAAATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTATATATATATAATTTTTA
Found at i:1259927 original size:40 final size:39
Alignment explanation
Indices: 1259810--1259934 Score: 105
Period size: 40 Copynumber: 3.1 Consensus size: 39
1259800 GTTGGATGTT
** * *
1259810 CAAATCTGCTTTACTTATACGGATAACGGATTCGCATATC
1 CAAATCTGCTTTACTTATA-TTATAATGGATTCGGATATC
* *
1259850 CAGATCTGCTTTGGCTT-TAGTT-TGAATAGTG-TT-GGATATC
1 CAAATCTGCTTT-ACTTATA-TTAT-AAT-G-GATTCGGATATC
1259890 CAAATCTGCTTTACTTATATATATAATGGATTCGGATATC
1 CAAATCTGCTTTACTTATAT-TATAATGGATTCGGATATC
1259930 CAAAT
1 CAAAT
1259935 TCAATATTAT
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
38 1 0.01
39 8 0.12
40 50 0.75
41 7 0.10
42 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (39 bp):
CAAATCTGCTTTACTTATATTATAATGGATTCGGATATC
Found at i:1260643 original size:6 final size:6
Alignment explanation
Indices: 1260611--1260642 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1260601 AAAGATTGAA
*
1260611 AAAAAG AAAAAG AAAAAG AAAAAG AAGAAG AA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA
1260643 GCTAACCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1261051 original size:6 final size:6
Alignment explanation
Indices: 1261040--1261094 Score: 53
Period size: 6 Copynumber: 9.3 Consensus size: 6
1261030 AATTTTAAAA
* *
1261040 TATATT TATATT TATA-T TATA-T TATATT T-TAATT TTTATT ATATTTT
1 TATATT TATATT TATATT TATATT TATATT TAT-ATT TATATT -TATATT
1261087 TATATT TA
1 TATATT TA
1261095 AATTAACATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 11 0.26
6 26 0.62
7 5 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:1261060 original size:17 final size:17
Alignment explanation
Indices: 1261040--1261099 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
1261030 AATTTTAAAA
1261040 TATATTTATATTTATA-T
1 TATA-TTATATTTATATT
1261057 TATATTATATTT-TAATT
1 TATATTATATTTAT-ATT
*
1261074 TTTATTATATTTTTATATT
1 TATATTATA--TTTATATT
*
1261093 TAAATTA
1 TATATTA
1261100 ACATACCTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 1 0.03
16 9 0.26
17 13 0.37
19 11 0.31
20 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATTATATTTATATT
Found at i:1261562 original size:22 final size:21
Alignment explanation
Indices: 1261533--1261580 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
1261523 AATTTTTGCT
1261533 ATTT-ATTTTTATTAATAAAAA
1 ATTTAATTTTT-TTAATAAAAA
*
1261554 ATTTAA--TTTTTAATAAATA
1 ATTTAATTTTTTTAATAAAAA
1261573 ATTTAATT
1 ATTTAATT
1261581 AGCATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 15 0.65
20 3 0.13
21 4 0.17
22 1 0.04
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTAATTTTTTTAATAAAAA
Found at i:1261568 original size:19 final size:19
Alignment explanation
Indices: 1261544--1261580 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1261534 TTTATTTTTA
1261544 TTAATAAAAAATTTAATTT
1 TTAATAAAAAATTTAATTT
*
1261563 TTAATAAATAATTTAATT
1 TTAATAAAAAATTTAATT
1261581 AGCATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAAAAAATTTAATTT
Found at i:1262603 original size:2 final size:2
Alignment explanation
Indices: 1262596--1262625 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1262586 TCTTTAAGCA
1262596 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
1262626 TTGTTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1266996 original size:46 final size:47
Alignment explanation
Indices: 1266913--1267008 Score: 158
Period size: 46 Copynumber: 2.1 Consensus size: 47
1266903 ATATATATAT
* * *
1266913 ATATATATATTAATAAAATTAAAGCATATAGTAAAAACATTAATTAA
1 ATATATATATTAATAAAAATAAAGCAAATAGTAAAAACATTAATCAA
1266960 ATATATATATTAA-AAAAATAAAGCAAATAGTAAAAACATTAATCAA
1 ATATATATATTAATAAAAATAAAGCAAATAGTAAAAACATTAATCAA
1267006 ATA
1 ATA
1267009 AATTAATTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 33 0.72
47 13 0.28
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.30
Consensus pattern (47 bp):
ATATATATATTAATAAAAATAAAGCAAATAGTAAAAACATTAATCAA
Found at i:1267581 original size:42 final size:42
Alignment explanation
Indices: 1267522--1267607 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
1267512 TCCTTAACGT
1267522 ATTTGATGGAAGGATAAGTAAACTAATTCATGTTAAATTTGA
1 ATTTGATGGAAGGATAAGTAAACTAATTCATGTTAAATTTGA
1267564 ATTTGATGGAAGGATAAGTAAACTAATTCATGTTAAATTTGA
1 ATTTGATGGAAGGATAAGTAAACTAATTCATGTTAAATTTGA
1267606 AT
1 AT
1267608 ACCTTTTGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.36
Consensus pattern (42 bp):
ATTTGATGGAAGGATAAGTAAACTAATTCATGTTAAATTTGA
Found at i:1267781 original size:19 final size:19
Alignment explanation
Indices: 1267757--1267799 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1267747 CAGTTTGAAA
1267757 TAATAT-TTTAAAATTAAAT
1 TAATATATTT-AAATTAAAT
* *
1267776 TAATATATTTTATTTAAAT
1 TAATATATTTAAATTAAAT
1267795 TAATA
1 TAATA
1267800 ATAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATATTTAAATTAAAT
Found at i:1268855 original size:3 final size:3
Alignment explanation
Indices: 1268847--1268893 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1268837 CCCTTTCTTA
1268847 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1268894 ACTACAAAGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1272614 original size:19 final size:19
Alignment explanation
Indices: 1272576--1272613 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1272566 GTAATTAAAA
*
1272576 TAAATTATATTATAAATTT
1 TAAAATATATTATAAATTT
1272595 TAAAATATATT-TAAATTT
1 TAAAATATATTATAAATTT
1272613 T
1 T
1272614 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAAATATATTATAAATTT
Found at i:1272615 original size:97 final size:97
Alignment explanation
Indices: 1272512--1272689 Score: 250
Period size: 97 Copynumber: 1.8 Consensus size: 97
1272502 TATTTTGTGG
* * * * * * *
1272512 ATTTTTTTAAAATTTAGGTATGATCTTCATGAGTTTTTTTATAAGAAATGCA-CAGTAATTAAAA
1 ATTTTTTTAAAATTTAAGTATGATCATCATGAATTTTTTAATAA-AAATACATAAATAATTAAAA
*
1272576 TAAATTATATTATAAATTTTAAAATATATTTAA
65 TAAAATATATTATAAATTTTAAAATATATTTAA
* *
1272609 ATTTTTTTAAAATTTAAGTTTGATCATCATGAATTTTTTAATAAAAATATATAAATAATTAAAAT
1 ATTTTTTTAAAATTTAAGTATGATCATCATGAATTTTTTAATAAAAATACATAAATAATTAAAAT
1272674 AAAATATATTATAAAT
66 AAAATATATTATAAAT
1272690 ATAAGAGTAC
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
96 5 0.07
97 65 0.93
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (97 bp):
ATTTTTTTAAAATTTAAGTATGATCATCATGAATTTTTTAATAAAAATACATAAATAATTAAAAT
AAAATATATTATAAATTTTAAAATATATTTAA
Found at i:1273929 original size:17 final size:18
Alignment explanation
Indices: 1273903--1273955 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
1273893 TTATTCACTT
1273903 AATAACAATATTTATATAA
1 AATAA-AATATTTATATAA
*
1273922 AATAAATATATTTATATTA
1 AATAAA-ATATTTATATAA
*
1273941 AAT-ATATATTTATAT
1 AATAAAATATTTATAT
1273956 TTACTATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 10 0.32
18 2 0.06
19 19 0.61
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATAAAATATTTATATAA
Found at i:1273956 original size:17 final size:18
Alignment explanation
Indices: 1273910--1273956 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
1273900 CTTAATAACA
*
1273910 ATATTTATATAAAATAAAT
1 ATATTTATATTAAAT-AAT
1273929 ATATTTATATTAAAT-AT
1 ATATTTATATTAAATAAT
1273946 ATATTTATATT
1 ATATTTATATT
1273957 TACTATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 13 0.48
19 14 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTTATATTAAATAAT
Found at i:1274268 original size:2 final size:2
Alignment explanation
Indices: 1274263--1274299 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1274253 ATATATGGGA
*
1274263 AG AG AG CG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1274300 CGGAGAAGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1274794 original size:23 final size:24
Alignment explanation
Indices: 1274762--1274824 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
1274752 TTCATAAATA
1274762 TATTTATTTATGTTATAT-TTATAT
1 TATTTATTTAT-TTATATATTATAT
*
1274786 TATTT-TTTATTTTTATATTATATTT
1 TATTTATTTATTTATATATTATA--T
*
1274811 TAATTATTTATTTA
1 TATTTATTTATTTA
1274825 ACTCATGTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
22 5 0.16
23 10 0.31
24 5 0.16
25 5 0.16
26 7 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TATTTATTTATTTATATATTATAT
Found at i:1274800 original size:18 final size:18
Alignment explanation
Indices: 1274760--1274823 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
1274750 AATTCATAAA
1274760 TATATTTATTTATGTTATATT
1 TATA-TTATTT-T-TTATATT
*
1274781 TATATTATTTTTTATTTT
1 TATATTATTTTTTATATT
*
1274799 TATATTATATTTTA-A-T
1 TATATTATTTTTTATATT
1274815 TAT-TTATTT
1 TATATTATTT
1274824 AACTCATGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 5 0.13
16 4 0.10
18 19 0.49
19 1 0.03
20 6 0.15
21 4 0.10
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (18 bp):
TATATTATTTTTTATATT
Found at i:1274806 original size:29 final size:30
Alignment explanation
Indices: 1274732--1274824 Score: 82
Period size: 29 Copynumber: 3.0 Consensus size: 30
1274722 AAAATTTAAA
* * ** *
1274732 ATTTTTAAATTATAATTTAATTCATAAATAT
1 ATTTTTATATTATATTTTAATT-ATTTATTT
*
1274763 ATTTATTTATGTTATA-TTTATATTATTT-TTT
1 A-TT-TTTATATTATATTTTA-ATTATTTATTT
1274794 ATTTTTATATTATATTTTAATTATTTATTT
1 ATTTTTATATTATATTTTAATTATTTATTT
1274824 A
1 A
1274825 ACTCATGTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
29 17 0.33
30 10 0.20
31 4 0.08
32 8 0.16
33 12 0.24
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (30 bp):
ATTTTTATATTATATTTTAATTATTTATTT
Found at i:1275366 original size:7 final size:7
Alignment explanation
Indices: 1275351--1275475 Score: 61
Period size: 6 Copynumber: 18.1 Consensus size: 7
1275341 AAAAAATTAA
1275351 AATATTAT
1 AATA-TAT
*
1275359 ATTATAT
1 AATATAT
1275366 AATATA-
1 AATATAT
*
1275372 AAAATAT
1 AATATAT
*
1275379 AAAAATATT
1 -AATATA-T
1275388 AAT-T-T
1 AATATAT
*
1275393 TATATA-
1 AATATAT
*
1275399 AATATAA
1 AATATAT
*
1275406 AATATTTT
1 AATA-TAT
1275414 AA-ATAT
1 AATATAT
1275420 AAT-TAT
1 AATATAT
1275426 AATATA-
1 AATATAT
1275432 AATATAT
1 AATATAT
1275439 -ATATAT
1 AATATAT
1275445 -ATATAT
1 AATATAT
*
1275451 ATGTATAT
1 A-ATATAT
1275459 ATATATAT
1 A-ATATAT
1275467 ATATATAT
1 A-ATATAT
1275475 A
1 A
1275476 CACACACGAA
Statistics
Matches: 94, Mismatches: 11, Indels: 24
0.73 0.09 0.19
Matches are distributed among these distances:
5 3 0.03
6 39 0.41
7 16 0.17
8 35 0.37
9 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (7 bp):
AATATAT
Found at i:1275403 original size:33 final size:33
Alignment explanation
Indices: 1275340--1275437 Score: 105
Period size: 33 Copynumber: 3.0 Consensus size: 33
1275330 GATTATTTAA
* *
1275340 AAAAAAATTAAAATATT-ATATTATAT-AATAT
1 AAAAATATTAAAATATTAATTTTATATAAATAT
*
1275371 AAAAATATAAAAATATTAATTTTATATAAATAT
1 AAAAATATTAAAATATTAATTTTATATAAATAT
* *
1275404 -AAAATATTTTAAATA-TAATTATAATATAAATAT
1 AAAAATA-TTAAAATATTAATT-TTATATAAATAT
1275437 A
1 A
1275438 TATATATATA
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
31 15 0.27
32 19 0.34
33 22 0.39
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (33 bp):
AAAAATATTAAAATATTAATTTTATATAAATAT
Found at i:1275404 original size:8 final size:8
Alignment explanation
Indices: 1275361--1275471 Score: 59
Period size: 8 Copynumber: 13.8 Consensus size: 8
1275351 AATATTATAT
1275361 TATAT-AA
1 TATATAAA
*
1275368 TATAAAAA
1 TATATAAA
*
1275376 TATAAAAA
1 TATATAAA
*
1275384 TAT-TAATTT
1 TATATAA--A
1275393 TATATAAA
1 TATATAAA
1275401 TATA-AAA
1 TATATAAA
*
1275408 TATTTTAAA
1 TA-TATAAA
*
1275417 TATA-ATTA
1 TATATA-AA
1275425 TAATATAAA
1 T-ATATAAA
*
1275434 TATATATA
1 TATATAAA
*
1275442 TATATATA
1 TATATAAA
* *
1275450 TATGTATA
1 TATATAAA
*
1275458 TATATATA
1 TATATAAA
1275466 TATATA
1 TATATA
1275472 TATACACACA
Statistics
Matches: 84, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
7 12 0.14
8 55 0.65
9 13 0.15
10 4 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (8 bp):
TATATAAA
Found at i:1275440 original size:2 final size:2
Alignment explanation
Indices: 1275423--1275475 Score: 81
Period size: 2 Copynumber: 27.0 Consensus size: 2
1275413 TAAATATAAT
* *
1275423 TA TA -A TA TA AA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1275464 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1275476 CACACACGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1275796 original size:21 final size:21
Alignment explanation
Indices: 1275771--1275856 Score: 70
Period size: 21 Copynumber: 4.0 Consensus size: 21
1275761 TTTTTTAAAT
1275771 ATTTAAATTTAAATTTATTTA
1 ATTTAAATTTAAATTTATTTA
*
1275792 ATTT--ATTTAAAATTTATATTT
1 ATTTAAATTT-AAATTTAT-TTA
* * *
1275813 ATTTATTATTTAAATATAATT-
1 ATTTA-AATTTAAATTTATTTA
*
1275834 ATTTAAATTTACATTTAATTTA
1 ATTTAAATTTAAATTT-ATTTA
1275856 A
1 A
1275857 ATAGTAATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
19 4 0.08
20 16 0.31
21 18 0.35
22 3 0.06
23 6 0.12
24 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAAATTTAAATTTATTTA
Found at i:1275812 original size:26 final size:24
Alignment explanation
Indices: 1275770--1275826 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 24
1275760 ATTTTTTAAA
1275770 TATTT-AAATTTAAATTTATTTAATT
1 TATTTAAAATTTAAATTTATTT-A-T
*
1275795 TATTTAAAATTTATATTTATTTAT
1 TATTTAAAATTTAAATTTATTTAT
1275819 TATTTAAA
1 TATTTAAA
1275827 TATAATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 9 0.30
25 6 0.20
26 15 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTTAAAATTTAAATTTATTTAT
Found at i:1275814 original size:17 final size:17
Alignment explanation
Indices: 1275787--1275871 Score: 57
Period size: 17 Copynumber: 4.8 Consensus size: 17
1275777 ATTTAAATTT
1275787 ATTTA-ATTTATTTAAA
1 ATTTATATTTATTTAAA
**
1275803 ATTTATATTTATTTATT
1 ATTTATATTTATTTAAA
1275820 ATTTAAATATAATTATTT-AA
1 ATTT--ATAT--TTATTTAAA
*
1275840 ATTTACATTTAATTTAAA
1 ATTTATATTT-ATTTAAA
* *
1275858 TAGTAATATTTATT
1 -ATTTATATTTATT
1275872 GAATATTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
16 7 0.13
17 17 0.32
18 8 0.15
19 11 0.21
20 4 0.08
21 6 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (17 bp):
ATTTATATTTATTTAAA
Found at i:1275844 original size:31 final size:30
Alignment explanation
Indices: 1275768--1275869 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 30
1275758 TAATTTTTTA
* *
1275768 AATATTTAAATTTAAATTT-ATTTAATTTATTT
1 AATATTTAAATTT-AATTTAATTTAA-ATA-GT
* *
1275800 AAAATTTATATTT-ATTTATTATTTAAATA-T
1 AATATTTAAATTTAATTTA--ATTTAAATAGT
1275830 AATTATTTAAATTTACATTTAATTTAAATAGT
1 AA-TATTTAAATTTA-ATTTAATTTAAATAGT
1275862 AATATTTA
1 AATATTTA
1275870 TTGAATATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
30 7 0.12
31 24 0.41
32 16 0.28
33 11 0.19
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (30 bp):
AATATTTAAATTTAATTTAATTTAAATAGT
Found at i:1283400 original size:14 final size:12
Alignment explanation
Indices: 1283379--1283452 Score: 50
Period size: 14 Copynumber: 6.2 Consensus size: 12
1283369 ATTTTTTTGA
1283379 TTTTAAATATCTT
1 TTTTAAATAT-TT
*
1283392 TTGTTAAATA-TA
1 TT-TTAAATATTT
1283404 TTTTAAATATGTT
1 TTTTAAATAT-TT
1283417 TTATTAAATA--T
1 TT-TTAAATATTT
*
1283428 ATTT--ATATTT
1 TTTTAAATATTT
*
1283438 TATTAAATATTT
1 TTTTAAATATTT
1283450 TTT
1 TTT
1283453 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 17
0.67 0.09 0.24
Matches are distributed among these distances:
8 3 0.06
10 5 0.11
11 9 0.19
12 11 0.23
13 5 0.11
14 14 0.30
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (12 bp):
TTTTAAATATTT
Found at i:1283412 original size:25 final size:25
Alignment explanation
Indices: 1283378--1283453 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
1283368 GATTTTTTTG
*
1283378 ATTTTAAATATCTTTTGTTAAATAT
1 ATTTTAAATATCTTTTATTAAATAT
*
1283403 ATTTTAAATATGTTTTATTAAATAT
1 ATTTTAAATATCTTTTATTAAATAT
1283428 A-TTT--ATA--TTTTATTAAATAT
1 ATTTTAAATATCTTTTATTAAATAT
*
1283448 TTTTTA
1 ATTTTA
1283454 TTTTATTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
20 13 0.28
21 3 0.07
22 3 0.07
24 3 0.07
25 24 0.52
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTTTAAATATCTTTTATTAAATAT
Found at i:1283457 original size:19 final size:20
Alignment explanation
Indices: 1283415--1283471 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 20
1283405 TTTAAATATG
1283415 TTTTATTAAATATATTTATA
1 TTTTATTAAATATATTTATA
*
1283435 TTTTATTAAATAT-TTTTTA
1 TTTTATTAAATATATTTATA
*
1283454 TTTTATTATATATATTTA
1 TTTTATTAAATATATTTA
1283472 AAATATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTATTAAATATATTTATA
Found at i:1283652 original size:28 final size:27
Alignment explanation
Indices: 1283602--1283655 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
1283592 TTAATTGAAC
1283602 TGATTAAATTGAATTAATCGATTTTTT
1 TGATTAAATTGAATTAATCGATTTTTT
1283629 TGATTAAATT-AATTTTAATCGATTTTT
1 TGATTAAATTGAA--TTAATCGATTTTT
1283656 ACTCACCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 2 0.08
27 10 0.40
28 13 0.52
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (27 bp):
TGATTAAATTGAATTAATCGATTTTTT
Found at i:1283707 original size:29 final size:29
Alignment explanation
Indices: 1283675--1283751 Score: 95
Period size: 27 Copynumber: 2.7 Consensus size: 29
1283665 AAATTAAGCT
*
1283675 TTTATTTAAAATAAAATAAAAAATAAATA
1 TTTATTTAAAATAAAATAAAAAATAAACA
* *
1283704 TTTATTT-AAATATAAT-AAAAATATACA
1 TTTATTTAAAATAAAATAAAAAATAAACA
1283731 TTTATTTTAAAAATAAAATAA
1 TTTA-TTT-AAAATAAAATAA
1283752 TTTACAAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 13 0.32
28 11 0.28
29 7 0.17
30 8 0.20
31 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (29 bp):
TTTATTTAAAATAAAATAAAAAATAAACA
Found at i:1283757 original size:27 final size:27
Alignment explanation
Indices: 1283675--1283746 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
1283665 AAATTAAGCT
* * *
1283675 TTTATTTAAAATAAAATAAAAAATAAATA
1 TTTATTTAAAA-ATAAT-AAAAATATACA
*
1283704 TTTATTTAAATATAATAAAAATATACA
1 TTTATTTAAAAATAATAAAAATATACA
1283731 TTTATTTTAAAAATAA
1 TTTA-TTTAAAAATAA
1283747 AATAATTTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 13 0.35
28 14 0.38
29 10 0.27
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
TTTATTTAAAAATAATAAAAATATACA
Found at i:1284375 original size:33 final size:32
Alignment explanation
Indices: 1284336--1284410 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1284326 CTAAAAAATT
1284336 TTAAAAATAATATTCATCCTTGATATAATTAAA
1 TTAAAAATAATATTCAT-CTTGATATAATTAAA
* * * *
1284369 TTAAAAACAATATTTATTTTTATATAATTAAA
1 TTAAAAATAATATTCATCTTGATATAATTAAA
* *
1284401 ATCAAAATAA
1 TTAAAAATAA
1284411 AAAATATTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
32 20 0.57
33 15 0.43
ACGTcount: A:0.52, C:0.07, G:0.01, T:0.40
Consensus pattern (32 bp):
TTAAAAATAATATTCATCTTGATATAATTAAA
Found at i:1284636 original size:11 final size:11
Alignment explanation
Indices: 1284620--1284656 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1284610 GGATAACCTA
1284620 TATATTTATAT
1 TATATTTATAT
1284631 TATATTTATAT
1 TATATTTATAT
* *
1284642 AATTTTTATAT
1 TATATTTATAT
1284653 TATA
1 TATA
1284657 ATTAATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTTATAT
Found at i:1284726 original size:14 final size:16
Alignment explanation
Indices: 1284699--1284745 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
1284689 GTTAATAATT
1284699 TATAAT-TTATATTTTA
1 TATAATATTA-ATTTTA
1284715 -A-AATATTAATTTTA
1 TATAATATTAATTTTA
*
1284729 TATTATATTAATTTTA
1 TATAATATTAATTTTA
1284745 T
1 T
1284746 TTTTTGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.33
15 5 0.19
16 13 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATAATATTAATTTTA
Found at i:1285455 original size:5 final size:5
Alignment explanation
Indices: 1285410--1285474 Score: 51
Period size: 5 Copynumber: 12.2 Consensus size: 5
1285400 ATAATTTTAA
* * *
1285410 TATAT TGATAAT TAATAT TATA- TAAAT TATAA TATATT TATAT TATTTT
1 TATAT T-AT-AT T-ATAT TATAT TATAT TATAT TATA-T TATAT TA-TAT
1285459 TATAT TATAT TATAT T
1 TATAT TATAT TATAT T
1285475 TTTATTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 3 0.06
5 27 0.56
6 13 0.27
7 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:1285471 original size:32 final size:31
Alignment explanation
Indices: 1285391--1285472 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 31
1285381 TTATAAGTAA
*
1285391 ATTTATTATATAATTTTAATATATTGATAATT
1 ATTT-TTATATAATTATAATATATTGATAATT
* * *
1285423 AATATTATATAAATTATAATATATTTAT-ATT
1 ATTTTTATAT-AATTATAATATATTGATAATT
1285454 ATTTTTATATTATATTATA
1 ATTTTTATA-TA-ATTATA
1285473 TTTTTATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
31 17 0.41
32 24 0.59
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (31 bp):
ATTTTTATATAATTATAATATATTGATAATT
Found at i:1289653 original size:21 final size:21
Alignment explanation
Indices: 1289627--1289671 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1289617 CTCGATCAGT
*
1289627 ACTCAAATCAAGTGTTACTAA
1 ACTCAAATCAAGTGCTACTAA
1289648 ACTCAAATCAAGTGCTACTAA
1 ACTCAAATCAAGTGCTACTAA
1289669 ACT
1 ACT
1289672 GTGGGTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (21 bp):
ACTCAAATCAAGTGCTACTAA
Found at i:1292203 original size:5 final size:5
Alignment explanation
Indices: 1292193--1292217 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1292183 GCTGATTTAA
1292193 CATTC CATTC CATTC CATTC CATTC
1 CATTC CATTC CATTC CATTC CATTC
1292218 ATCCACAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (5 bp):
CATTC
Found at i:1292495 original size:23 final size:23
Alignment explanation
Indices: 1292469--1292513 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1292459 GTTATAGTCA
1292469 TATACTTTATTATATCATAATCG
1 TATACTTTATTATATCATAATCG
*
1292492 TATACTTTATTATGTCATAATC
1 TATACTTTATTATATCATAATC
1292514 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.49
Consensus pattern (23 bp):
TATACTTTATTATATCATAATCG
Found at i:1293626 original size:17 final size:17
Alignment explanation
Indices: 1293601--1293638 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1293591 AAAATAAGCT
*
1293601 TATTGGGGTCCATGTCA
1 TATTAGGGTCCATGTCA
*
1293618 TATTAGGGTTCATGTCA
1 TATTAGGGTCCATGTCA
1293635 TATT
1 TATT
1293639 TGGCCAGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.24, T:0.42
Consensus pattern (17 bp):
TATTAGGGTCCATGTCA
Found at i:1294503 original size:31 final size:26
Alignment explanation
Indices: 1294467--1294549 Score: 82
Period size: 31 Copynumber: 3.1 Consensus size: 26
1294457 ACTCAAAAAC
1294467 TTATTTTATTATTTAAATTAATATTAAAATT
1 TTATTTTATTATTTAAATTAA-A-T--AA-T
* *
1294498 TTATTTTATAATTAAAATTAAATAAT
1 TTATTTTATTATTTAAATTAAATAAT
1294524 TT-TTTTATTATTTAAATT--ATAAT
1 TTATTTTATTATTTAAATTAAATAAT
1294547 TTA
1 TTA
1294550 AATTAAATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
23 7 0.15
25 14 0.30
26 3 0.06
27 2 0.04
29 1 0.02
30 1 0.02
31 19 0.40
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TTATTTTATTATTTAAATTAAATAAT
Found at i:1294517 original size:25 final size:25
Alignment explanation
Indices: 1294469--1294548 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
1294459 TCAAAAACTT
*
1294469 ATTTTATTATT-TAAATTAATATTAAA
1 ATTTTATT-TTAT-AATTAAAATTAAA
1294495 ATTTTATTTTATAATTAAAATTAAA
1 ATTTTATTTTATAATTAAAATTAAA
* * * *
1294520 TAATTT-TTTTATTATTTAAATTATA
1 -ATTTTATTTTATAATTAAAATTAAA
1294545 ATTT
1 ATTT
1294549 AAATTAAATC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
24 3 0.07
25 30 0.65
26 13 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTTATTTTATAATTAAAATTAAA
Found at i:1300298 original size:13 final size:13
Alignment explanation
Indices: 1300273--1300314 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
1300263 TATTTATTTT
1300273 TATTTATTTAAAA
1 TATTTATTTAAAA
1300286 TATTT-TTTAAAAA
1 TATTTATTT-AAAA
1300299 TATTCATATTTAAAA
1 TATT--TATTTAAAA
1300314 T
1 T
1300315 TAAATTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 13 0.52
15 6 0.24
16 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTTATTTAAAA
Found at i:1301000 original size:14 final size:15
Alignment explanation
Indices: 1300943--1301018 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
1300933 ATCAAGAATT
1300943 TAATTTAATTATTTATA
1 TAATTTAA-TATTT-TA
1300960 TAA-TT-AT-TTTTA
1 TAATTTAATATTTTA
* **
1300972 AAAAATAATATTTTA
1 TAATTTAATATTTTA
1300987 TAATTTAA-ATTTTA
1 TAATTTAATATTTTA
1301001 -AATTTTAATATTTT-
1 TAA-TTTAATATTTTA
1301015 TAAT
1 TAAT
1301019 ATTTTTTCGT
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
12 4 0.08
13 6 0.12
14 15 0.31
15 18 0.38
16 2 0.04
17 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATTTAATATTTTA
Found at i:1301023 original size:8 final size:8
Alignment explanation
Indices: 1300977--1301023 Score: 55
Period size: 7 Copynumber: 6.1 Consensus size: 8
1300967 TTTTAAAAAA
1300977 TAATATTT
1 TAATATTT
*
1300985 T-ATAATT
1 TAATATTT
1300992 TAA-ATTT
1 TAATATTT
1300999 TAA-ATTT
1 TAATATTT
1301006 TAATATTTT
1 TAATA-TTT
1301015 TAATATTT
1 TAATATTT
1301023 T
1 T
1301024 TTCGTTCCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 19 0.56
8 7 0.21
9 8 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TAATATTT
Found at i:1301693 original size:6 final size:6
Alignment explanation
Indices: 1301665--1301717 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
1301655 TTAATAATTT
* * *
1301665 TAAATA T-AATA TAATTA TAAAATA TAAATA TAACATA AAAAAA TAAATA
1 TAAATA TAAATA TAAATA T-AAATA TAAATA TAA-ATA TAAATA TAAATA
1301714 TAAA
1 TAAA
1301718 AAATACTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 5 0.13
6 23 0.61
7 10 0.26
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (6 bp):
TAAATA
Found at i:1301696 original size:19 final size:19
Alignment explanation
Indices: 1301666--1301716 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1301656 TAATAATTTT
*
1301666 AAATAT-AATATAA-TTATA
1 AAATATAAATATAACATA-A
1301684 AAATATAAATATAACATAA
1 AAATATAAATATAACATAA
*
1301703 AAAAATAAATATAA
1 AAATATAAATATAA
1301717 AAAATACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 6 0.21
19 21 0.72
20 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAATATAAATATAACATAA
Found at i:1305924 original size:32 final size:33
Alignment explanation
Indices: 1305864--1305925 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
1305854 CGATGTAGAA
1305864 TTTAAAATAATAATTTATATTAATATTTAATAT
1 TTTAAAATAATAATTTATATTAATATTTAATAT
*
1305897 TTTAAAAT-ATATTTTATAATTAA-ATTTAA
1 TTTAAAATAATAATTTAT-ATTAATATTTAA
1305926 ATAAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 14 0.52
33 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (33 bp):
TTTAAAATAATAATTTATATTAATATTTAATAT
Found at i:1307335 original size:3 final size:3
Alignment explanation
Indices: 1307327--1307355 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1307317 TTGTAACATC
1307327 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1307356 TTTAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1311341 original size:24 final size:21
Alignment explanation
Indices: 1311310--1311355 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 21
1311300 AGTATAAATG
1311310 AAAAAATTTAAAATATTATTTTT
1 AAAAAA-TTAAAA-ATTATTTTT
*
1311333 AAAAGAATTCAAAATTATTTTT
1 AAAA-AATTAAAAATTATTTTT
1311355 A
1 A
1311356 TAAATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 10 0.48
23 9 0.43
24 2 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
AAAAAATTAAAAATTATTTTT
Found at i:1311359 original size:24 final size:23
Alignment explanation
Indices: 1311310--1311364 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1311300 AGTATAAATG
* *
1311310 AAAAAATTTAAAATATTATTTTT
1 AAAAAATTCAAAATATTATTTAT
1311333 AAAAGAATTCAAAATTATT-TTTAT
1 AAAA-AATTCAAAA-TATTATTTAT
1311357 AAATAAAT
1 AAA-AAAT
1311365 AGATTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 4 0.15
24 18 0.67
25 5 0.19
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAAAATTCAAAATATTATTTAT
Found at i:1315003 original size:14 final size:14
Alignment explanation
Indices: 1314986--1315039 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
1314976 AATTTATATA
*
1314986 ATTATTTTTAAAAT
1 ATTATATTTAAAAT
*
1315000 ATTATATTTAATAT
1 ATTATATTTAAAAT
*
1315014 ATTTAAAATTTAAAAT
1 A-TT-ATATTTAAAAT
*
1315030 TTTATATTTA
1 ATTATATTTA
1315040 TAATTAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
14 19 0.59
15 4 0.12
16 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTATATTTAAAAT
Found at i:1315037 original size:21 final size:20
Alignment explanation
Indices: 1315011--1315057 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1315001 TTATATTTAA
1315011 TATATTTAAAATTTAAAATTT
1 TATATTTAAAA-TTAAAATTT
* *
1315032 TATATTTATAATTAAATTTT
1 TATATTTAAAATTAAAATTT
1315052 TA-ATTT
1 TATATTT
1315058 GAGTTATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATATTTAAAATTAAAATTT
Found at i:1315934 original size:14 final size:14
Alignment explanation
Indices: 1315917--1315967 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1315907 TAATTAAAAA
*
1315917 ATAAATAAAAATTT
1 ATAAATATAAATTT
1315931 ATAAATACTAAATTT
1 ATAAATA-TAAATTT
*
1315946 -TAAATTTAAATTT
1 ATAAATATAAATTT
1315959 ATTAAATAT
1 A-TAAATAT
1315968 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 7 0.23
14 12 0.39
15 12 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATAAATATAAATTT
Found at i:1315943 original size:15 final size:15
Alignment explanation
Indices: 1315925--1315966 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1315915 AAATAAATAA
1315925 AAATTTATAAATACT
1 AAATTTATAAATACT
*
1315940 AAATTT-TAAAT-TT
1 AAATTTATAAATACT
1315953 AAATTTATTAAATA
1 AAATTTA-TAAATA
1315967 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 7 0.30
14 5 0.22
15 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTTATAAATACT
Found at i:1317153 original size:18 final size:18
Alignment explanation
Indices: 1317130--1317187 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
1317120 AATTTAACTT
*
1317130 AAATTTTATCGTTATTTA
1 AAATTTTATCATTATTTA
*
1317148 AAATTTTAT-AATATTTTA
1 AAATTTTATCATTA-TTTA
*
1317166 AAATTTTTTCATTGATTTA
1 AAATTTTATCATT-ATTTA
1317185 AAA
1 AAA
1317188 AAATATTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 2 0.06
18 21 0.64
19 9 0.27
20 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (18 bp):
AAATTTTATCATTATTTA
Found at i:1330040 original size:12 final size:12
Alignment explanation
Indices: 1330023--1330052 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1330013 CTGAAAAGGG
*
1330023 GAAAAAAAGAAA
1 GAAAAAAAAAAA
1330035 GAAAAAAAAAAA
1 GAAAAAAAAAAA
1330047 GAAAAA
1 GAAAAA
1330053 GAAAGAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAA
Found at i:1334239 original size:19 final size:18
Alignment explanation
Indices: 1334192--1334239 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
1334182 TTTATTTAAA
1334192 TTTAAATTAAATTTGATC
1 TTTAAATTAAATTTGATC
* * *
1334210 TTAAAATTTAAATTATTATT
1 TTTAAA-TTAAATT-TGATC
1334230 TTTAAATTAA
1 TTTAAATTAA
1334240 TATAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.21
19 11 0.46
20 8 0.33
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTTAAATTAAATTTGATC
Found at i:1335550 original size:22 final size:21
Alignment explanation
Indices: 1335517--1335576 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
1335507 ATTATTTATA
*
1335517 TTATATTAATTTAATTTATATAT
1 TTATATT-ATTTAATTT-TAAAT
* *
1335540 TTTTATTATTTTTATTTTAAAT
1 TTATATTA-TTTAATTTTAAAT
1335562 TTATATTATTATAAT
1 TTATATTATT-TAAT
1335577 AATTTAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 2 0.07
22 15 0.50
23 13 0.43
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATTATTTAATTTTAAAT
Found at i:1335590 original size:2 final size:2
Alignment explanation
Indices: 1335583--1335609 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1335573 TAATAATTTA
1335583 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
1335610 ATGTCCAATG
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:1335870 original size:8 final size:8
Alignment explanation
Indices: 1335859--1335917 Score: 65
Period size: 8 Copynumber: 7.8 Consensus size: 8
1335849 TAAAATATAT
1335859 TAATATGA
1 TAATATGA
1335867 TAATATGA
1 TAATATGA
1335875 TAATAT-A
1 TAATATGA
1335882 TTTAATATGA
1 --TAATATGA
1335892 TAATAT--
1 TAATATGA
1335898 TAATAT--
1 TAATATGA
1335904 TAATATGA
1 TAATATGA
1335912 TAATAT
1 TAATAT
1335918 AATTAATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
6 12 0.26
7 1 0.02
8 26 0.57
9 6 0.13
10 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (8 bp):
TAATATGA
Found at i:1335889 original size:17 final size:17
Alignment explanation
Indices: 1335867--1335924 Score: 80
Period size: 17 Copynumber: 3.2 Consensus size: 17
1335857 ATTAATATGA
1335867 TAATATGATAATATATT
1 TAATATGATAATATATT
1335884 TAATATGATAATATTAATAT
1 TAATATGATAATA-T-AT-T
*
1335904 TAATATGATAATATAAT
1 TAATATGATAATATATT
1335921 TAAT
1 TAAT
1335925 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 18 0.49
18 2 0.05
19 3 0.08
20 14 0.38
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
TAATATGATAATATATT
Found at i:1335908 original size:20 final size:20
Alignment explanation
Indices: 1335855--1335917 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
1335845 TATTTAAAAT
1335855 ATATTAATATGATAATATGATA
1 ATATTAATAT--TAATATGATA
1335877 ATA-T-AT-TTAATATGATA
1 ATATTAATATTAATATGATA
1335894 ATATTAATATTAATATGATA
1 ATATTAATATTAATATGATA
1335914 ATAT
1 ATAT
1335918 AATTAATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
17 13 0.34
18 1 0.03
19 3 0.08
20 17 0.45
21 1 0.03
22 3 0.08
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
ATATTAATATTAATATGATA
Found at i:1335920 original size:25 final size:25
Alignment explanation
Indices: 1335848--1335902 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
1335838 AAATTTATAT
1335848 TTAA-AATATATTAATATGATAATA
1 TTAATAATATATTAATATGATAATA
*
1335872 -TGATAATATATTTAATATGATAATA
1 TTAATAATATA-TTAATATGATAATA
1335897 TTAATA
1 TTAATA
1335903 TTAATATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 2 0.08
24 6 0.23
25 14 0.54
26 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (25 bp):
TTAATAATATATTAATATGATAATA
Found at i:1337176 original size:2 final size:2
Alignment explanation
Indices: 1337171--1337205 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1337161 AATATTAAAG
*
1337171 AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1337206 ACTTAAACAA
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:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1337746 original size:24 final size:25
Alignment explanation
Indices: 1337719--1337766 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1337709 AGATTTGATA
*
1337719 ATTTTAAATACGATAT-GATTAAAC
1 ATTTTAAAAACGATATCGATTAAAC
*
1337743 ATTTTAAAAATGATATCGATTAAA
1 ATTTTAAAAACGATATCGATTAAA
1337767 ATATAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (25 bp):
ATTTTAAAAACGATATCGATTAAAC
Found at i:1337797 original size:19 final size:19
Alignment explanation
Indices: 1337764--1337822 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
1337754 GATATCGATT
*
1337764 AAAATATAATA-TAATACA
1 AAAAAATAATATTAATACA
*
1337782 AAAAAATAATATTAATATA
1 AAAAAATAATATTAATACA
* *
1337801 ATATAAAT-ATATAAATACA
1 A-AAAAATAATATTAATACA
1337820 AAA
1 AAA
1337823 TTTAAAACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 11 0.33
19 17 0.52
20 5 0.15
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATAATATTAATACA
Found at i:1339240 original size:2 final size:2
Alignment explanation
Indices: 1339233--1339274 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1339223 TTATTTCTTT
1339233 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1339275 ATTTGTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1340426 original size:22 final size:21
Alignment explanation
Indices: 1340400--1340443 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
1340390 AAATAATAAA
1340400 ATATATTTT-TATATTAATATTT
1 ATATATTTTAT-TATTAA-ATTT
1340422 ATATATTTTATTATTAAATTT
1 ATATATTTTATTATTAAATTT
1340443 A
1 A
1340444 AAAATTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 15 0.71
23 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTATTATTAAATTT
Found at i:1341080 original size:21 final size:20
Alignment explanation
Indices: 1341063--1341110 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
1341053 AAAATAATTT
*
1341063 TTTAATATTTTTAAATAATAA
1 TTTAA-ATTATTAAATAATAA
1341084 TTTAAATTATTAAAT--TAA
1 TTTAAATTATTAAATAATAA
*
1341102 ATTAAATTA
1 TTTAAATTA
1341111 AAATTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
20 9 0.36
21 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAAATTATTAAATAATAA
Done.