Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167826.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_1, whole genome shotgun sequence
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: 36299135
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Warning! 357000 characters in sequence are not A, C, G, or T
File 9 of 402
Found at i:1578263 original size:14 final size:15
Alignment explanation
Indices: 1578244--1578273 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1578234 AAAATTTTAA
1578244 ATTATATTAT-TTTT
1 ATTATATTATATTTT
1578258 ATTATATTATATTTT
1 ATTATATTATATTTT
1578273 A
1 A
1578274 AATTATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTATATTATATTTT
Found at i:1581664 original size:24 final size:23
Alignment explanation
Indices: 1581636--1581690 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
1581626 ACCACTGCCC
1581636 TTTGAGAGTTGAAAC-TTTTTCTTT
1 TTTGAGAG-T-AAACATTTTTCTTT
*
1581660 TTTGAAAGTAAACATTTTTTCTTT
1 TTTGAGAGTAAACA-TTTTTCTTT
*
1581684 ATTGAGA
1 TTTGAGA
1581691 TACTTAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 4 0.15
23 1 0.04
24 21 0.81
ACGTcount: A:0.27, C:0.07, G:0.15, T:0.51
Consensus pattern (23 bp):
TTTGAGAGTAAACATTTTTCTTT
Found at i:1591767 original size:16 final size:17
Alignment explanation
Indices: 1591713--1591778 Score: 55
Period size: 16 Copynumber: 3.8 Consensus size: 17
1591703 TAATAAAATA
1591713 TTTAAATGATTAATTTATT
1 TTTAAATGA-TAATTTA-T
* *
1591732 AATTTATATGAT-ACTTAT
1 --TTTAAATGATAATTTAT
*
1591750 TTTTAAT-ATAATTTAT
1 TTTAAATGATAATTTAT
1591766 TTTAAATGATAAT
1 TTTAAATGATAAT
1591779 ATATAATAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
15 2 0.05
16 16 0.43
17 5 0.14
18 1 0.03
19 4 0.11
20 1 0.03
21 8 0.22
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATGATAATTTAT
Found at i:1600331 original size:201 final size:201
Alignment explanation
Indices: 1599986--1600591 Score: 1059
Period size: 201 Copynumber: 3.0 Consensus size: 201
1599976 TCGGCAGTCA
* * *
1599986 TTTCACTGCTGTCTTCATTAATTGAGGGTTCAAGAATTTCACCTAGGTTGTTGATTTCATTGTCA
1 TTTCACTGCTGTCTTCATTAATTGAGGGTTCCAGAGTTTCACATAGGTTGTTGATTTCATTGTCA
* *
1600051 TCGTATTCATCATTAGCTGCTTCATGATCTTCCTGACAGCATTCTATAACATCTTCTCTTGCTTC
66 TCGTATTCATCATTAGCTGCTTCAAGATCTTCCTGACAGCATTCTATAGCATCTTCTCTTGCTTC
1600116 TGTCATCTCATCTGCTTTTTGATCAGTCTGTTTTTGCATCTCTTCAGTTCCCAGCCTCTCAGGAG
131 TGTCATCTCATCTGCTTTTTGATCAGTCTGTTTTTGCATCTCTTCAGTTCCCAGCCTCTCAGGAG
1600181 CCTCTT
196 CCTCTT
* *
1600187 TTTCACTGCTGTCTTCATTAATTGAGGGTTCCAGAGTTTCACATAGGTTGTTGCTTTCATTGTGA
1 TTTCACTGCTGTCTTCATTAATTGAGGGTTCCAGAGTTTCACATAGGTTGTTGATTTCATTGTCA
* * * *
1600252 TCGAATTCATCATTAGCTGCTTCAAGATCTTCGTGACAGCATTCTATAGCCTCTTCTATTGCTTC
66 TCGTATTCATCATTAGCTGCTTCAAGATCTTCCTGACAGCATTCTATAGCATCTTCTCTTGCTTC
1600317 TGTCATCTCATCTGCTTTTTGATCAGTCTGTTTTTGCATCTCTTCAGTTCCCAGCCTCTCAGGAG
131 TGTCATCTCATCTGCTTTTTGATCAGTCTGTTTTTGCATCTCTTCAGTTCCCAGCCTCTCAGGAG
1600382 CCTCTT
196 CCTCTT
*
1600388 TTTCACTGCCGTCTTCATTAATTGAGGGTTCCAGAGTTTCACATAGGTTGTTGATTTCATTGTCA
1 TTTCACTGCTGTCTTCATTAATTGAGGGTTCCAGAGTTTCACATAGGTTGTTGATTTCATTGTCA
* *
1600453 TTGTGTTCATCATTAGCTGCTTCAAGATCTTCCTGACAGCATTCTATAGCATCTTCTCTTGCTTC
66 TCGTATTCATCATTAGCTGCTTCAAGATCTTCCTGACAGCATTCTATAGCATCTTCTCTTGCTTC
* * *
1600518 TGTCATCTCATCTGCTTTTTTATCACTCTGTTTTTGCATCTCTTCAGTTCCCAGCCTCTCAAGAG
131 TGTCATCTCATCTGCTTTTTGATCAGTCTGTTTTTGCATCTCTTCAGTTCCCAGCCTCTCAGGAG
1600583 CCTCTT
196 CCTCTT
1600589 TTT
1 TTT
1600592 GTCCCTCCTC
Statistics
Matches: 382, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
201 382 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (201 bp):
TTTCACTGCTGTCTTCATTAATTGAGGGTTCCAGAGTTTCACATAGGTTGTTGATTTCATTGTCA
TCGTATTCATCATTAGCTGCTTCAAGATCTTCCTGACAGCATTCTATAGCATCTTCTCTTGCTTC
TGTCATCTCATCTGCTTTTTGATCAGTCTGTTTTTGCATCTCTTCAGTTCCCAGCCTCTCAGGAG
CCTCTT
Found at i:1600684 original size:63 final size:63
Alignment explanation
Indices: 1600612--1600738 Score: 218
Period size: 63 Copynumber: 2.0 Consensus size: 63
1600602 CACCGCTTCT
*
1600612 ATCTGATAAGCATCTTTAAACAAATCTGCATTCTCTTCAGCCTCCATAAATTCCTCATTCCCC
1 ATCTGATAAGCATCTTTAAACAAATCTGCATTCTCTTCAGCCTCCATAAATACCTCATTCCCC
* * *
1600675 ATCTGATAAGCATCTTTAAACAATTCTTCATTCTCTTCCGCCTCCATAAATACCTCATTCCCC
1 ATCTGATAAGCATCTTTAAACAAATCTGCATTCTCTTCAGCCTCCATAAATACCTCATTCCCC
1600738 A
1 A
1600739 ATGAATCACT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.28, C:0.32, G:0.06, T:0.34
Consensus pattern (63 bp):
ATCTGATAAGCATCTTTAAACAAATCTGCATTCTCTTCAGCCTCCATAAATACCTCATTCCCC
Found at i:1603296 original size:13 final size:13
Alignment explanation
Indices: 1603278--1603302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1603268 AAGACTGAGG
1603278 ACGAGAAAATGAA
1 ACGAGAAAATGAA
1603291 ACGAGAAAATGA
1 ACGAGAAAATGA
1603303 GGAGAAGAAG
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:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (13 bp):
ACGAGAAAATGAA
Found at i:1603921 original size:23 final size:24
Alignment explanation
Indices: 1603885--1603929 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1603875 TATGTATTTT
*
1603885 ATATAAAAATTATAAATTATATTG
1 ATATAAAAATTATAAAATATATTG
1603909 ATATAAAAA-TATAAAATATAT
1 ATATAAAAATTATAAAATATAT
1603930 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATAAAAATTATAAAATATATTG
Found at i:1606152 original size:19 final size:19
Alignment explanation
Indices: 1606103--1606152 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1606093 AAATTAAAAA
*
1606103 AATAAAATTTAATTTTATC
1 AATAAAAATTAATTTTATC
* *
1606122 AATTAAACTTAATTTATAT-
1 AATAAAAATTAATTT-TATC
1606141 AATAAAAATTAA
1 AATAAAAATTAA
1606153 AAAATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
AATAAAAATTAATTTTATC
Found at i:1606198 original size:58 final size:55
Alignment explanation
Indices: 1606093--1606215 Score: 153
Period size: 58 Copynumber: 2.2 Consensus size: 55
1606083 AATCTGACTT
*
1606093 AAATTAAAAAA-ATAAAATTTAATTTTATCAATTAAACTTAATTTATATA-ATAA
1 AAATTAAAAAATATAAAAATTAATTTTATCAATTAAACTTAATTTATATACATAA
* * *
1606146 AAATTAAAAAATATAATTAAATTAATTTTAATGAGATTATATTTAATTTATATACATAA
1 AAATTAAAAAATATAA--AAATTAATTTT-ATCA-ATTAAACTTAATTTATATACATAA
1606205 AAA-TAAAAAAT
1 AAATTAAAAAAT
1606216 TTATATATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
53 11 0.18
54 4 0.07
56 10 0.17
57 3 0.05
58 25 0.42
59 7 0.12
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (55 bp):
AAATTAAAAAATATAAAAATTAATTTTATCAATTAAACTTAATTTATATACATAA
Found at i:1627320 original size:14 final size:14
Alignment explanation
Indices: 1627300--1627336 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1627290 TAAATATTAA
1627300 TTTTAA-TAAAATT
1 TTTTAATTAAAATT
1627313 TATTTAATTAAAATT
1 T-TTTAATTAAAATT
1627328 TTTT-ATTAA
1 TTTTAATTAA
1627337 TTTGTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTTAATTAAAATT
Found at i:1627324 original size:15 final size:15
Alignment explanation
Indices: 1627287--1627336 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1627277 TATTAATTAA
*
1627287 AATTAAATATTAATTTT
1 AATTAAA-ATTTA-TTT
1627304 AA-TAAAATTTATTT
1 AATTAAAATTTATTT
1627318 AATTAAAATTT-TTT
1 AATTAAAATTTATTT
1627332 -ATTAA
1 AATTAA
1627337 TTTGTTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 5 0.16
14 8 0.26
15 12 0.39
16 4 0.13
17 2 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATTAAAATTTATTT
Found at i:1634934 original size:2 final size:2
Alignment explanation
Indices: 1634929--1634965 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1634919 TAAAACTTCT
*
1634929 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1634966 CACCAACTTG
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:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1642002 original size:25 final size:24
Alignment explanation
Indices: 1641993--1642089 Score: 77
Period size: 29 Copynumber: 3.7 Consensus size: 24
1641983 ATTATTAAAC
1641993 ATAAATATTTTTAATATTTTAATA
1 ATAAATATTTTTAATATTTTAATA
* *
1642017 ATAAATAGAATTATATCATTATTTTAATA
1 ATAAAT---ATT-T-TTAATATTTTAATA
* *
1642046 ATAAATAATTTTTTATTATTTCAATA
1 ATAAAT-A-TTTTTAATATTTTAATA
*
1642072 ATTAATATTGTTTAATAT
1 ATAAATATT-TTTAATAT
1642090 AATAATTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 13
0.76 0.08 0.16
Matches are distributed among these distances:
24 8 0.13
25 8 0.13
26 17 0.28
27 6 0.10
28 3 0.05
29 18 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
ATAAATATTTTTAATATTTTAATA
Found at i:1642063 original size:26 final size:26
Alignment explanation
Indices: 1641993--1642078 Score: 86
Period size: 26 Copynumber: 3.3 Consensus size: 26
1641983 ATTATTAAAC
*
1641993 ATAAAT-A-TTTTTAATATTTTAATA
1 ATAAATAATTTTTTATTATTTTAATA
* *
1642017 ATAAATAGAATTATATCATTATTTTAATA
1 ATAAAT--AATT-TTTTATTATTTTAATA
*
1642046 ATAAATAATTTTTTATTATTTCAATA
1 ATAAATAATTTTTTATTATTTTAATA
*
1642072 ATTAATA
1 ATAAATA
1642079 TTGTTTAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
24 6 0.12
26 19 0.38
27 5 0.10
28 1 0.02
29 19 0.38
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (26 bp):
ATAAATAATTTTTTATTATTTTAATA
Found at i:1645612 original size:26 final size:26
Alignment explanation
Indices: 1645554--1645612 Score: 57
Period size: 26 Copynumber: 2.1 Consensus size: 26
1645544 AATTAAATTA
1645554 TAAATTTATTAATTAATATAATATAAATCTT
1 TAAATTT-TTAA-T-ATATAAT-TAAAT-TT
1645585 TAAATTTTTAATATA-AATTAATATTT
1 TAAATTTTTAATATATAATTAA-ATTT
1645611 TA
1 TA
1645613 TTTGGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
26 7 0.26
27 5 0.19
28 3 0.11
29 1 0.04
30 4 0.15
31 7 0.26
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TAAATTTTTAATATATAATTAAATTT
Found at i:1658205 original size:135 final size:136
Alignment explanation
Indices: 1657951--1658222 Score: 456
Period size: 135 Copynumber: 2.0 Consensus size: 136
1657941 GAGGGTATGA
* * * *
1657951 AATAGGTAGATTACCCATATACGTGTAGTACTTGGCACAGGAATTTCATGTTATCCCTTTTGCCA
1 AATAGCTAGATTACCCATATACGTGGACTACTTGGCACAGGAATTTCATGTCATCCCTTTTGCCA
* *
1658016 AAATCAAACCATTTAGGAGTCCTTGCTAGAAGGGGAGAGGTAGGAGGTTTGATCAATTCAACATG
66 AAATCAAACCATTTAGGAGTCCTTGCTAGAAAGGGAGAGGTAGGAGGTTGGATCAATTCAACATG
1658081 AAAGAG
131 AAAGAG
*
1658087 AATAGCTAGATTACCCATATACGTGGACTACTTGGCAGAGGAATTTCATGTCATCCC-TTTGCCA
1 AATAGCTAGATTACCCATATACGTGGACTACTTGGCACAGGAATTTCATGTCATCCCTTTTGCCA
* *
1658151 AAATCAAACCATTTAGGAGTCCTTGCTAGAAAGGGAGGGGTAGGAGGTTGGATCAATTCAATATG
66 AAATCAAACCATTTAGGAGTCCTTGCTAGAAAGGGAGAGGTAGGAGGTTGGATCAATTCAACATG
1658216 AAAGAG
131 AAAGAG
1658222 A
1 A
1658223 GATAATACTA
Statistics
Matches: 127, Mismatches: 9, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
135 75 0.59
136 52 0.41
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (136 bp):
AATAGCTAGATTACCCATATACGTGGACTACTTGGCACAGGAATTTCATGTCATCCCTTTTGCCA
AAATCAAACCATTTAGGAGTCCTTGCTAGAAAGGGAGAGGTAGGAGGTTGGATCAATTCAACATG
AAAGAG
Found at i:1660960 original size:6 final size:6
Alignment explanation
Indices: 1660951--1660993 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
1660941 TATATAATTA
*
1660951 TATATT TATATT TATATT TATATT TA-ATT TTTATT TATATT TA
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TA
1660994 AAAAATAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 4 0.12
6 30 0.88
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TATATT
Found at i:1660985 original size:17 final size:17
Alignment explanation
Indices: 1660951--1660994 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
1660941 TATATAATTA
1660951 TATATTTATATTTATATT
1 TATATTTA-ATTTATATT
*
1660969 TATATTTAATTTTTATT
1 TATATTTAATTTATATT
1660986 TATATTTAA
1 TATATTTAA
1660995 AAAATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATTTAATTTATATT
Found at i:1664844 original size:6 final size:6
Alignment explanation
Indices: 1664833--1664862 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1664823 CTCTGCAGTT
1664833 TGCTTA TGCTTA TGCTTA TGCTTA TGCTTA
1 TGCTTA TGCTTA TGCTTA TGCTTA TGCTTA
1664863 AATTTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TGCTTA
Found at i:1666356 original size:2 final size:2
Alignment explanation
Indices: 1666349--1666383 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1666339 GTGGAGGTAC
1666349 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1666384 ACACACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1675284 original size:63 final size:63
Alignment explanation
Indices: 1675185--1675312 Score: 186
Period size: 63 Copynumber: 2.0 Consensus size: 63
1675175 TTATTTTTTT
* *
1675185 TTATCTTTAGATTATTGCTTGTTTAATATAAAATATATATTTATTATACTTGCAAACGTAAAA
1 TTATCTTTAGATTACTGCTTGTTTAATATAAAATATATATTTATTATACATGCAAACGTAAAA
* * * *
1675248 TTATCTTTAGATTACTGTCTT-TTTTATATAAAATATATATTTATTGTACATGCAGACGTAGAA
1 TTATCTTTAGATTACTG-CTTGTTTAATATAAAATATATATTTATTATACATGCAAACGTAAAA
1675311 TT
1 TT
1675313 CTACGTGTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
63 55 0.95
64 3 0.05
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (63 bp):
TTATCTTTAGATTACTGCTTGTTTAATATAAAATATATATTTATTATACATGCAAACGTAAAA
Found at i:1680018 original size:12 final size:12
Alignment explanation
Indices: 1680002--1680046 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
1679992 AACTAAGTAA
1680002 AAAAAAAAAGGAG
1 AAAAAAAAA-GAG
*
1680015 AAAAAAAAAAAG
1 AAAAAAAAAGAG
1680027 CAAAAAAAATAGAG
1 -AAAAAAAA-AGAG
1680041 AAAAAA
1 AAAAAA
1680047 TAGAAAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 2 0.07
13 23 0.82
14 3 0.11
ACGTcount: A:0.82, C:0.02, G:0.13, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:1680018 original size:15 final size:14
Alignment explanation
Indices: 1680000--1680035 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
1679990 AAAACTAAGT
*
1680000 AAAAAAAAAAAGGA
1 AAAAAAAAAAAGCA
1680014 GAAAAAAAAAAAGCA
1 -AAAAAAAAAAAGCA
1680029 AAAAAAA
1 AAAAAAA
1680036 TAGAGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGCA
Found at i:1688757 original size:26 final size:24
Alignment explanation
Indices: 1688728--1688780 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
1688718 ATTTTTAAAA
* *
1688728 TAATCATTTAATTATTAATTTTTATT
1 TAATCATTTAAAT-TTAAATTTT-TT
*
1688754 TAATTATTTAAATTTAAATTTTTT
1 TAATCATTTAAATTTAAATTTTTT
1688778 TAA
1 TAA
1688781 CTCAATCGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.21
25 8 0.33
26 11 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATCATTTAAATTTAAATTTTTT
Found at i:1689932 original size:23 final size:23
Alignment explanation
Indices: 1689900--1689955 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
1689890 TATAGTAAAG
*
1689900 TCGAG-TCGACACAGTTAGAAGC
1 TCGAGCTCGACACAGTGAGAAGC
* *
1689922 TCGAGCTCGACTCTGTGAGAAGC
1 TCGAGCTCGACACAGTGAGAAGC
1689945 TCGAGCTCGAC
1 TCGAGCTCGAC
1689956 TCTCAACTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 5 0.17
23 25 0.83
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.20
Consensus pattern (23 bp):
TCGAGCTCGACACAGTGAGAAGC
Found at i:1691204 original size:2 final size:2
Alignment explanation
Indices: 1691197--1691231 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1691187 TAATTTATTA
1691197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1691232 GACAATTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1727677 original size:2 final size:2
Alignment explanation
Indices: 1727670--1727701 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1727660 CACATTTTAA
1727670 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
1727702 CATACAAAGA
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:1729493 original size:13 final size:13
Alignment explanation
Indices: 1729469--1729501 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1729459 GATACGATTT
1729469 AAAAATAATATAA
1 AAAAATAATATAA
1729482 ATAAAA-AATATAA
1 A-AAAATAATATAA
1729495 AAAAATA
1 AAAAATA
1729502 TGATTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.22
13 10 0.56
14 4 0.22
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAATAATATAA
Found at i:1741768 original size:39 final size:39
Alignment explanation
Indices: 1741716--1741794 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
1741706 TTTTCATTTG
* *
1741716 TTTTCTTCGTAAAAGGCAAATCCAACCCAAACTTTTTCT
1 TTTTCATCATAAAAGGCAAATCCAACCCAAACTTTTTCT
*
1741755 TTTTCATCATAAAAGGCAAATCCGACCCAAACTTTTTCT
1 TTTTCATCATAAAAGGCAAATCCAACCCAAACTTTTTCT
1741794 T
1 T
1741795 AAAAACCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (39 bp):
TTTTCATCATAAAAGGCAAATCCAACCCAAACTTTTTCT
Found at i:1752139 original size:2 final size:2
Alignment explanation
Indices: 1752134--1752160 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1752124 AAAAAAGATA
1752134 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 A
1752161 TCAGAGATTG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1757086 original size:18 final size:18
Alignment explanation
Indices: 1757029--1757117 Score: 81
Period size: 18 Copynumber: 4.8 Consensus size: 18
1757019 TTTTGAGGAT
*
1757029 GATACATTTGTGGTGGAG
1 GATACATTTGAGGTGGAG
* * * *
1757047 GGTACATTTGTGGT-AACT
1 GATACATTTGAGGTGGA-G
1757065 GATACATTTGAGGTGGAG
1 GATACATTTGAGGTGGAG
*
1757083 GATATATTTAAAGAGGTGGAG
1 GATACATTT---GAGGTGGAG
1757104 GATACATTTGAGGT
1 GATACATTTGAGGT
1757118 AGATAATAAC
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
17 1 0.02
18 38 0.67
19 1 0.02
21 17 0.30
ACGTcount: A:0.28, C:0.06, G:0.34, T:0.33
Consensus pattern (18 bp):
GATACATTTGAGGTGGAG
Found at i:1757504 original size:6 final size:6
Alignment explanation
Indices: 1757460--1757500 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1757450 AAATTCGCAT
* *
1757460 CATCAC CATCAC CATCAC CATCTC CATCAC CATCAT CATCA
1 CATCAC CATCAC CATCAC CATCAC CATCAC CATCAC CATCA
1757501 TCATATGGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.46, G:0.00, T:0.22
Consensus pattern (6 bp):
CATCAC
Found at i:1760638 original size:27 final size:28
Alignment explanation
Indices: 1760580--1760638 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
1760570 TTTTATCACA
* *
1760580 AATAACTTCAAATAATTATATAATAAAT
1 AATAACTTCAAATAATTACACAATAAAT
1760608 -ATAATCTT-AAATAATTACACAA-AAAT
1 AATAA-CTTCAAATAATTACACAATAAAT
1760634 AATAA
1 AATAA
1760639 GAATTAATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
26 4 0.15
27 20 0.74
28 3 0.11
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (28 bp):
AATAACTTCAAATAATTACACAATAAAT
Found at i:1760969 original size:26 final size:26
Alignment explanation
Indices: 1760920--1760968 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
1760910 TTTTAAAAAT
*
1760920 TAAAAGTTTTCAAACTTATATTTTAA
1 TAAAAGTTTTCAAACCTATATTTTAA
1760946 TAAAA-TTTTCAAACCTATATTTT
1 TAAAAGTTTTCAAACCTATATTTT
1760969 TTATTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.41, C:0.10, G:0.02, T:0.47
Consensus pattern (26 bp):
TAAAAGTTTTCAAACCTATATTTTAA
Found at i:1761517 original size:20 final size:20
Alignment explanation
Indices: 1761436--1761517 Score: 57
Period size: 20 Copynumber: 4.2 Consensus size: 20
1761426 CAAACACCCT
1761436 ACCACACCCAATCCCTCCCC
1 ACCACACCCAATCCCTCCCC
*
1761456 ACC-C-CCATCAATCCCTCTCC
1 ACCACACC--CAATCCCTCCCC
* * *
1761476 ACCTTCCCCCCAA--CAT-CCC
1 ACC--ACACCCAATCCCTCCCC
1761495 ACCACACCCAATCCCTCCCC
1 ACCACACCCAATCCCTCCCC
1761515 ACC
1 ACC
1761518 TTCCCCCCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 18
0.66 0.08 0.25
Matches are distributed among these distances:
17 6 0.13
18 2 0.04
19 8 0.17
20 25 0.53
22 3 0.06
23 1 0.02
24 2 0.04
ACGTcount: A:0.23, C:0.63, G:0.00, T:0.13
Consensus pattern (20 bp):
ACCACACCCAATCCCTCCCC
Found at i:1761550 original size:38 final size:39
Alignment explanation
Indices: 1761464--1761555 Score: 141
Period size: 39 Copynumber: 2.4 Consensus size: 39
1761454 CCACCCCCAT
* *
1761464 CAATCCCTCTCCACCTTCCCCCCAACATCCCACCACACC
1 CAATCCCTCCCCACCTTCCCCCCAACAGCCCACCACACC
* *
1761503 CAATCCCTCCCCACCTTCCCCCCAACGGCCCATCACACC
1 CAATCCCTCCCCACCTTCCCCCCAACAGCCCACCACACC
1761542 CAAT-CCTCCCCACC
1 CAATCCCTCCCCACC
1761556 CCATCCAATC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 10 0.20
39 39 0.80
ACGTcount: A:0.22, C:0.62, G:0.02, T:0.14
Consensus pattern (39 bp):
CAATCCCTCCCCACCTTCCCCCCAACAGCCCACCACACC
Found at i:1763245 original size:24 final size:24
Alignment explanation
Indices: 1763218--1763269 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1763208 ACTTATTTAT
*
1763218 AATATATATAATTTATATACTAAC
1 AATATATAAAATTTATATACTAAC
*
1763242 AATATATAAAATTTATATACTTAC
1 AATATATAAAATTTATATACTAAC
1763266 AATA
1 AATA
1763270 CATCAAATGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (24 bp):
AATATATAAAATTTATATACTAAC
Found at i:1763277 original size:24 final size:24
Alignment explanation
Indices: 1763218--1763277 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1763208 ACTTATTTAT
* *
1763218 AATATATATAATTTATATACTAAC
1 AATACATAAAATTTATATACTAAC
* *
1763242 AATATATAAAATTTATATACTTAC
1 AATACATAAAATTTATATACTAAC
*
1763266 AATACATCAAAT
1 AATACATAAAAT
1763278 GCAAACTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (24 bp):
AATACATAAAATTTATATACTAAC
Found at i:1771982 original size:27 final size:27
Alignment explanation
Indices: 1771934--1771987 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1771924 TCATGCCGAA
* *
1771934 TTCTGCTGATCCCAGCTCTAGACCTGC
1 TTCTGCTGATCCCAACTATAGACCTGC
* * *
1771961 TTCTGTTGATCCCAATTATAGAGCTGC
1 TTCTGCTGATCCCAACTATAGACCTGC
1771988 CCCAGAGCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (27 bp):
TTCTGCTGATCCCAACTATAGACCTGC
Found at i:1774167 original size:2 final size:2
Alignment explanation
Indices: 1774160--1774188 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1774150 GATGCATGAT
1774160 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 A
1774189 AAATACCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1780452 original size:6 final size:6
Alignment explanation
Indices: 1780441--1780500 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
1780431 AATTTGAGTC
* * * *
1780441 AAATTT AAATTT AAATTT AAATTT -TATTT -TATTT AAATCT AATTTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
1780487 ATCAATTT AAATTT
1 A--AATTT AAATTT
1780501 GTTTGATTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
5 9 0.20
6 31 0.69
8 5 0.11
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (6 bp):
AAATTT
Found at i:1780476 original size:16 final size:16
Alignment explanation
Indices: 1780455--1780488 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1780445 TTAAATTTAA
* *
1780455 ATTTAAATTTTATTTT
1 ATTTAAATCTAATTTT
1780471 ATTTAAATCTAATTTT
1 ATTTAAATCTAATTTT
1780487 AT
1 AT
1780489 CAATTTAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTAAATCTAATTTT
Found at i:1780528 original size:19 final size:19
Alignment explanation
Indices: 1780491--1780544 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1780481 AATTTTATCA
* *
1780491 ATTTAAATTTGTTTGATTTT
1 ATTT-AATTTTTTTAATTTT
*
1780511 TTTTAATTTTTTTAATTTT
1 ATTTAATTTTTTTAATTTT
*
1780530 ATTT-ATTATTTTAAT
1 ATTTAATTTTTTTAAT
1780545 ATATTTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 10 0.34
19 16 0.55
20 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (19 bp):
ATTTAATTTTTTTAATTTT
Found at i:1780541 original size:18 final size:19
Alignment explanation
Indices: 1780506--1780544 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1780496 AATTTGTTTG
* *
1780506 ATTTTTTTTAATTTTTTTA
1 ATTTTATTTAATTATTTTA
1780525 ATTTTATTT-ATTATTTTA
1 ATTTTATTTAATTATTTTA
1780543 AT
1 AT
1780545 ATATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTATTTAATTATTTTA
Found at i:1780684 original size:11 final size:11
Alignment explanation
Indices: 1780641--1780689 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
1780631 AATTTTAATT
1780641 TTTAATTTAAAA
1 TTTAATTT-AAA
**
1780653 TTTAATCCAAA
1 TTTAATTTAAA
1780664 TTTAATATTTAAA
1 TTT-A-ATTTAAA
1780677 TTTAATTTAAA
1 TTTAATTTAAA
1780688 TT
1 TT
1780690 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 15 0.48
12 8 0.26
13 8 0.26
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:1780694 original size:24 final size:25
Alignment explanation
Indices: 1780645--1780694 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1780635 TTAATTTTTA
*
1780645 ATTTAAAATTTAATCCAAATTTAAT
1 ATTTAAAATTTAATCCAAATTAAAT
**
1780670 ATTT-AAATTTAATTTAAATTAAAT
1 ATTTAAAATTTAATCCAAATTAAAT
1780694 A
1 A
1780695 AAAATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (25 bp):
ATTTAAAATTTAATCCAAATTAAAT
Found at i:1780710 original size:22 final size:22
Alignment explanation
Indices: 1780674--1780725 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
1780664 TTTAATATTT
* * *
1780674 AAATTTAATTTAAATTAAATAA
1 AAATTTTATTCAAATCAAATAA
*
1780696 AAATTTTATTCAAATCAAATTA
1 AAATTTTATTCAAATCAAATAA
*
1780718 ATATTTTA
1 AAATTTTA
1780726 ATTTTAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATTTTATTCAAATCAAATAA
Found at i:1781482 original size:35 final size:34
Alignment explanation
Indices: 1781441--1781511 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 34
1781431 TATATCAATA
1781441 TAAAAATATAAAAT-ATAATT-TTATTTATGATTTTT
1 TAAAAATATAAAATCAT-ATTATT-TTTAT-ATTTTT
* *
1781476 TAAAAATTTTAAATCATATTATTTTTATATTTTT
1 TAAAAATATAAAATCATATTATTTTTATATTTTT
1781510 TA
1 TA
1781512 TTTATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 8 0.25
35 20 0.62
36 4 0.12
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
TAAAAATATAAAATCATATTATTTTTATATTTTT
Found at i:1781509 original size:24 final size:24
Alignment explanation
Indices: 1781482--1781530 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1781472 TTTTTAAAAA
*
1781482 TTTTAAATCATATTATTTTTATAT
1 TTTTAAATCATATAATTTTTATAT
* * *
1781506 TTTTTATTTATATAATTTTTATAT
1 TTTTAAATCATATAATTTTTATAT
1781530 T
1 T
1781531 ATATCATCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTTAAATCATATAATTTTTATAT
Found at i:1781512 original size:15 final size:15
Alignment explanation
Indices: 1781494--1781534 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1781484 TTAAATCATA
* *
1781494 TTATTTTTATATTTT
1 TTATTTATATAATTT
1781509 TTATTTATATAATTT
1 TTATTTATATAATTT
1781524 TTATATTATAT
1 TTAT-TTATAT
1781535 CATCATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTATTTATATAATTT
Found at i:1781542 original size:24 final size:23
Alignment explanation
Indices: 1781488--1781542 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
1781478 AAAATTTTAA
* * *
1781488 ATCATATTATTTTTATATTTTTT
1 ATCATATAATTTTTATATTTATC
*
1781511 ATTTATATAATTTTTATATTATATC
1 A-TCATATAATTTTTATATT-TATC
1781536 ATCATAT
1 ATCATAT
1781543 CATGTACCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 21 0.84
25 3 0.12
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
ATCATATAATTTTTATATTTATC
Found at i:1781719 original size:11 final size:11
Alignment explanation
Indices: 1781637--1781723 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 11
1781627 AGATACGTGT
1781637 TATTATAATTTA
1 TATTAT-ATTTA
* *
1781649 TTTTTTATTT-
1 TATTATATTTA
*
1781659 TATTAAATTTA
1 TATTATATTTA
*
1781670 TA-TATAATTA
1 TATTATATTTA
*
1781680 TTATTAAAATTTTA
1 -TATT-ATA-TTTA
*
1781694 AATTAT-TTTA
1 TATTATATTTA
1781704 TTATTATATTTA
1 -TATTATATTTA
1781716 TATTATAT
1 TATTATAT
1781724 CATCATCTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 15
0.67 0.14 0.18
Matches are distributed among these distances:
10 17 0.30
11 21 0.38
12 10 0.18
13 5 0.09
14 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATATTTA
Found at i:1781720 original size:22 final size:22
Alignment explanation
Indices: 1781636--1781721 Score: 70
Period size: 22 Copynumber: 3.8 Consensus size: 22
1781626 GAGATACGTG
*
1781636 TTATTATAATTTAT-TT-TTTATT
1 TTATTA-AATTTATATTATTT-TA
*
1781658 TTATTAAATTTATA-TATAATTA
1 TTATTAAATTTATATTAT-TTTA
*
1781680 TTATTAAAATTTTAAATTATTTTA
1 TTATT-AAA-TTTATATTATTTTA
*
1781704 TTATTATATTTATATTAT
1 TTATTAAATTTATATTAT
1781722 ATCATCATCT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
21 8 0.15
22 22 0.42
23 6 0.12
24 13 0.25
25 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATTAAATTTATATTATTTTA
Found at i:1782627 original size:14 final size:13
Alignment explanation
Indices: 1782610--1782639 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1782600 TTTTATATTA
1782610 ATATAATTTATGAT
1 ATATAATTTAT-AT
1782624 ATATAATTTATAT
1 ATATAATTTATAT
1782637 ATA
1 ATA
1782640 AAATATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
ATATAATTTATAT
Found at i:1782645 original size:20 final size:20
Alignment explanation
Indices: 1782622--1782691 Score: 52
Period size: 20 Copynumber: 3.3 Consensus size: 20
1782612 ATAATTTATG
1782622 ATATATAATTTATATATAAA
1 ATATATAATTTATATATAAA
**
1782642 ATATA-ATATAAATATATAAA
1 ATATATA-ATTTATATATAAA
* *
1782662 TTATTAATATTTTATATGATATAA
1 ATA-T-ATAATTTATAT-ATA-AA
1782686 ATATAT
1 ATATAT
1782692 GAATAGACGA
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
19 1 0.03
20 18 0.49
21 1 0.03
22 8 0.22
23 5 0.14
24 4 0.11
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
ATATATAATTTATATATAAA
Found at i:1782647 original size:18 final size:19
Alignment explanation
Indices: 1782624--1782662 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1782614 AATTTATGAT
* *
1782624 ATATAATTTATATATA-AA
1 ATATAATATAAATATATAA
1782642 ATATAATATAAATATATAA
1 ATATAATATAAATATATAA
1782661 AT
1 AT
1782663 TATTAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAATATAAATATATAA
Found at i:1783685 original size:12 final size:11
Alignment explanation
Indices: 1783658--1783698 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
1783648 TGATAATACG
*
1783658 ATATAAAAATA
1 ATATAAAAAAA
1783669 ATATAATAAAAA
1 ATATAA-AAAAA
1783681 ATATAAAAAATA
1 ATATAAAAAA-A
1783693 ATATAA
1 ATATAA
1783699 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATATAAAAAAA
Found at i:1783762 original size:29 final size:29
Alignment explanation
Indices: 1783730--1783799 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 29
1783720 ATAAATAAAT
*
1783730 TTAATAAAATATAAAATATATATTTTTTA
1 TTAATAAAATATAAAATATATAATTTTTA
* *
1783759 TTAA-AACAA-ACTATAATATTTAATTTTTA
1 TTAATAA-AATA-TAAAATATATAATTTTTA
1783788 -T-ATAAAATATAA
1 TTAATAAAATATAA
1783800 TATTTTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
27 5 0.15
28 7 0.21
29 21 0.64
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAATAAAATATAAAATATATAATTTTTA
Found at i:1783798 original size:25 final size:24
Alignment explanation
Indices: 1783738--1783817 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 24
1783728 ATTTAATAAA
1783738 ATATAAAATAT-ATATTTTTTATT
1 ATATAAAATATAATATTTTTTATT
*
1783761 A-AAACAAACTATAATATTTAATTT-TT
1 ATATA-AAA-TATAATATTT--TTTATT
* *
1783787 ATATAAAATATAATATTTTATATA
1 ATATAAAATATAATATTTTTTATT
1783811 ATATAAA
1 ATATAAA
1783818 TACATAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
22 2 0.04
23 6 0.13
24 11 0.24
25 16 0.35
26 6 0.13
27 5 0.11
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATAAAATATAATATTTTTTATT
Found at i:1783819 original size:18 final size:18
Alignment explanation
Indices: 1783770--1783819 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
1783760 TAAAACAAAC
*
1783770 TATAATATTTAAT-TTTTA
1 TATAATA-TAAATATTTTA
*
1783788 TATAAAATATAATATTTTA
1 TATAATATA-AATATTTTA
1783807 TATAATATAAATA
1 TATAATATAAATA
1783820 CATAAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 1 0.04
18 13 0.48
19 13 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAATATAAATATTTTA
Found at i:1784394 original size:25 final size:24
Alignment explanation
Indices: 1784351--1784403 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
1784341 TAAAATATTT
*
1784351 AAATTTATATTATATTTTATATAA
1 AAATTTATATTATAATTTATATAA
* *
1784375 AAATTATATGTTATAATTTATATTA
1 AAATT-TATATTATAATTTATATAA
1784400 AAAT
1 AAAT
1784404 AAAAATATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
AAATTTATATTATAATTTATATAA
Found at i:1790826 original size:21 final size:19
Alignment explanation
Indices: 1790800--1790847 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 19
1790790 CCACCACTTA
1790800 ATTTCTTTCTACAGCCAAGAC
1 ATTTCTTTCT--AGCCAAGAC
1790821 ATTTC-TT-TAGCCAAGAC
1 ATTTCTTTCTAGCCAAGAC
1790838 ATTTCTTTCT
1 ATTTCTTTCT
1790848 GCTTCTATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 2 0.08
20 2 0.08
21 5 0.20
ACGTcount: A:0.25, C:0.25, G:0.08, T:0.42
Consensus pattern (19 bp):
ATTTCTTTCTAGCCAAGAC
Found at i:1790832 original size:17 final size:17
Alignment explanation
Indices: 1790812--1790845 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1790802 TTCTTTCTAC
1790812 AGCCAAGACATTTCTTT
1 AGCCAAGACATTTCTTT
1790829 AGCCAAGACATTTCTTT
1 AGCCAAGACATTTCTTT
1790846 CTGCTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (17 bp):
AGCCAAGACATTTCTTT
Found at i:1793412 original size:42 final size:44
Alignment explanation
Indices: 1793330--1793413 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 44
1793320 AATTTTTTTA
*
1793330 AAAATTATATATTTAATTTATATAATAAAAACTTTCAATTTATT
1 AAAATTATATATTTAATTTATACAATAAAAACTTTCAATTTATT
*
1793374 AAAATT-TAT-TTTAATTTA-ACAA-AATAACTTTACGAATTTA
1 AAAATTATATATTTAATTTATACAATAAAAACTTT-C-AATTTA
1793414 CCTACCAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
40 8 0.22
41 4 0.11
42 15 0.42
43 3 0.08
44 6 0.17
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (44 bp):
AAAATTATATATTTAATTTATACAATAAAAACTTTCAATTTATT
Found at i:1798317 original size:3 final size:3
Alignment explanation
Indices: 1798309--1798355 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
1798299 AGCCTTTTCA
* * *
1798309 CTT CTT CTT CTT CTT CGT CTT CTT CTT CGT CTT CTT CTT CTT GTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1798356 CTCTCTCTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.06, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:1802875 original size:13 final size:13
Alignment explanation
Indices: 1802857--1802883 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1802847 GTTCTTAGTG
1802857 ACAATAGAAGTAA
1 ACAATAGAAGTAA
1802870 ACAATAGAAGTAA
1 ACAATAGAAGTAA
1802883 A
1 A
1802884 AATTACCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.15, T:0.15
Consensus pattern (13 bp):
ACAATAGAAGTAA
Found at i:1803530 original size:2 final size:2
Alignment explanation
Indices: 1803523--1803549 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1803513 TGTAATTAAG
1803523 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1803550 CAGTTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1804907 original size:2 final size:2
Alignment explanation
Indices: 1804902--1804939 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1804892 AAAGAGATTA
1804902 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1804940 TATGGCTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1815810 original size:17 final size:17
Alignment explanation
Indices: 1815790--1815829 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1815780 AAATATTATA
1815790 CTTAAAAATAG-AAACTT
1 CTTAAAAATAGTAAA-TT
1815807 CTTAAAAATAGTAAATT
1 CTTAAAAATAGTAAATT
1815824 -TTAAAA
1 CTTAAAA
1815830 TTCATGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.27
17 13 0.59
18 3 0.14
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (17 bp):
CTTAAAAATAGTAAATT
Found at i:1819626 original size:18 final size:18
Alignment explanation
Indices: 1819603--1819639 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1819593 CGTTAATAAA
*
1819603 TTTAATTTTTATTTAATT
1 TTTAATTTTTATTAAATT
1819621 TTTAATTTTTATTAAATT
1 TTTAATTTTTATTAAATT
1819639 T
1 T
1819640 AATAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTAATTTTTATTAAATT
Found at i:1819720 original size:61 final size:60
Alignment explanation
Indices: 1819634--1819770 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 60
1819624 AATTTTTATT
* ** *
1819634 AAATTTAATAAAAAGTTATTAATAATATTTTAAAAATTATTAATT-AAATAAATATATCAT
1 AAATATAATAAAATTTTATTAATAATATTTTAAAAATTATTAATTAAAATAAATA-ATCAC
* ** * *
1819694 TAATATAATAAAATTTTATTTAATAATATTTTAAATTTTATTAATTAAAATAATTAATTAC
1 AAATATAATAAAATTTTA-TTAATAATATTTTAAAAATTATTAATTAAAATAAATAATCAC
1819755 AAATATAATAAAATTT
1 AAATATAATAAAATTT
1819771 ATTCATATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
60 14 0.22
61 43 0.66
62 8 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (60 bp):
AAATATAATAAAATTTTATTAATAATATTTTAAAAATTATTAATTAAAATAAATAATCAC
Found at i:1819750 original size:23 final size:24
Alignment explanation
Indices: 1819692--1819750 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 24
1819682 TAAATATATC
*
1819692 ATTAATATAATAAAATTTTATTTA
1 ATTAATATAATTAAATTTTATTTA
*
1819716 A-TAATAT-TTTAAATTTTA-TTA
1 ATTAATATAATTAAATTTTATTTA
*
1819737 ATTAAAATAATTAA
1 ATTAATATAATTAA
1819751 TTACAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.14
22 14 0.48
23 10 0.34
24 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAATATAATTAAATTTTATTTA
Found at i:1820636 original size:12 final size:12
Alignment explanation
Indices: 1820607--1820681 Score: 50
Period size: 13 Copynumber: 6.2 Consensus size: 12
1820597 TTAAAAAATG
1820607 ATTTAAT-AAAA
1 ATTTAATAAAAA
1820618 ATATTAATAAAAA
1 AT-TTAATAAAAA
*
1820631 ATTTAAATTAATAA
1 ATTT-AA-TAAAAA
*
1820645 A-TTGAT--AAA
1 ATTTAATAAAAA
1820654 ATTTAATATAAAA
1 ATTTAATA-AAAA
* *
1820667 AATTATTAAAAA
1 ATTTAATAAAAA
1820679 ATT
1 ATT
1820682 ATTTATAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
9 3 0.06
10 4 0.08
11 3 0.06
12 14 0.29
13 19 0.39
14 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (12 bp):
ATTTAATAAAAA
Found at i:1823558 original size:23 final size:23
Alignment explanation
Indices: 1823537--1823601 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
1823527 TTAAATTTAT
1823537 TTATGATT-TTTTTAATATTTTAAG
1 TTAT-ATTATTTTT-ATATTTTAAG
*
1823561 TTATATTATTTTTATATTTTTA-
1 TTATATTATTTTTATATTTTAAG
*
1823583 TTCGTATTATTTTTATATT
1 TT-ATATTATTTTTATATT
1823602 ATATTATCGT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
22 2 0.05
23 26 0.70
24 9 0.24
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.68
Consensus pattern (23 bp):
TTATATTATTTTTATATTTTAAG
Found at i:1823575 original size:11 final size:11
Alignment explanation
Indices: 1823561--1823603 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
1823551 ATATTTTAAG
1823561 TTATATTATTT
1 TTATATTATTT
1823572 TTATATT-TTT
1 TTATATTATTT
*
1823582 ATTCGTATTATTT
1 -TT-ATATTATTT
1823595 TTATATTAT
1 TTATATTAT
1823604 ATTATCGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.11
11 15 0.56
12 6 0.22
13 3 0.11
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (11 bp):
TTATATTATTT
Found at i:1824541 original size:22 final size:22
Alignment explanation
Indices: 1824516--1824558 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1824506 CAATGGGTCC
1824516 ACTATCTGAAAGTTGAAAGATT
1 ACTATCTGAAAGTTGAAAGATT
1824538 ACTATCTGAAAGTTGAAAGAT
1 ACTATCTGAAAGTTGAAAGAT
1824559 ATTAGATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (22 bp):
ACTATCTGAAAGTTGAAAGATT
Found at i:1835220 original size:30 final size:31
Alignment explanation
Indices: 1835186--1835251 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
1835176 ATTATTTTAT
* *
1835186 ATTTTTATATCACATCAATTA-AAACATA-AA
1 ATTTTTATATAAAAT-AATTATAAACATATAA
*
1835216 ATTTTTATATAAAATAATTATAAATATATAA
1 ATTTTTATATAAAATAATTATAAACATATAA
1835247 ATTTT
1 ATTTT
1835252 AATGTTTCAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 19 0.61
31 7 0.23
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (31 bp):
ATTTTTATATAAAATAATTATAAACATATAA
Found at i:1839886 original size:14 final size:15
Alignment explanation
Indices: 1839867--1839908 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
1839857 TTCATTTAGG
*
1839867 ATTTATTTGTTTA-A
1 ATTTATTTGATTATA
1839881 ATTTATTTGATTATA
1 ATTTATTTGATTATA
1839896 ATTTATTT-ATTAT
1 ATTTATTTGATTAT
1839909 TTATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 17 0.65
15 9 0.35
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTTATTTGATTATA
Found at i:1840240 original size:29 final size:31
Alignment explanation
Indices: 1840172--1840228 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1840162 AACTCTTTTA
* *
1840172 ATTTAATTAAATCAAATACGAATAATTTATT
1 ATTTAAATAAATCAAATACAAATAATTTATT
1840203 ATTTAAATAAAT-AAATA-AAATAATTT
1 ATTTAAATAAATCAAATACAAATAATTT
1840229 TTTTATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 5 0.21
31 11 0.46
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (31 bp):
ATTTAAATAAATCAAATACAAATAATTTATT
Found at i:1841371 original size:18 final size:16
Alignment explanation
Indices: 1841350--1841398 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
1841340 ATATTTTTTC
1841350 ATTATATCATATAAAAA
1 ATTATAT-ATATAAAAA
*
1841367 TATTATATTTTATATAAAA
1 -ATTATA-TATATA-AAAA
1841386 ATTATATATATAA
1 ATTATATATATAA
1841399 TTTATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 16 0.59
19 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTATATATATAAAAA
Found at i:1841404 original size:49 final size:45
Alignment explanation
Indices: 1841351--1841446 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 45
1841341 TATTTTTTCA
1841351 TTATATC-ATATAAAAATATTATATTTTATATAAAAATTATATATATAAT
1 TTATATCAATA-AAAAATA-TAT-TTTTATATAAAAA-TA-ATATATAAT
* * *
1841400 TTATATTAATAAAAAATATATTTTTTTATAAAAATAATTTATAAT
1 TTATATCAATAAAAAATATATTTTTATATAAAAATAATATATAAT
1841445 TT
1 TT
1841447 TTATTAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
45 10 0.23
46 2 0.05
47 12 0.28
48 3 0.07
49 13 0.30
50 3 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (45 bp):
TTATATCAATAAAAAATATATTTTTATATAAAAATAATATATAAT
Found at i:1841450 original size:22 final size:21
Alignment explanation
Indices: 1841359--1841450 Score: 71
Period size: 24 Copynumber: 4.1 Consensus size: 21
1841349 CATTATATCA
1841359 TATAAAAAT-AT-TATATTTT
1 TATAAAAATAATATATATTTT
*
1841378 ATATAAAAATTATATATATAATTTA
1 -TATAAAAA-TA-ATATAT-ATTTT
* *
1841403 TATTAATAAAAAATATATTTTTT
1 TA-TAA-AAATAATATATATTTT
*
1841426 TATAAAAATAATTTATAATTTT
1 TATAAAAATAATATAT-ATTTT
1841448 TAT
1 TAT
1841451 TAAATTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
20 8 0.14
21 10 0.18
22 10 0.18
23 7 0.12
24 11 0.19
25 8 0.14
26 3 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATAAAAATAATATATATTTT
Found at i:1841480 original size:16 final size:15
Alignment explanation
Indices: 1841454--1841483 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1841444 TTTTTATTAA
1841454 ATTTTTAATTATATT
1 ATTTTTAATTATATT
1841469 ATTTTTATATTATAT
1 ATTTTTA-ATTATAT
1841484 CATCGTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTAATTATATT
Found at i:1842319 original size:9 final size:9
Alignment explanation
Indices: 1842305--1842334 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1842295 TATATTTTAT
1842305 TAATTAAAA
1 TAATTAAAA
1842314 TAATTAAAA
1 TAATTAAAA
1842323 TATATTAAAA
1 TA-ATTAAAA
1842333 TA
1 TA
1842335 TAAAAACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:1842331 original size:10 final size:10
Alignment explanation
Indices: 1842307--1842336 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1842297 TATTTTATTA
1842307 ATTAAAATA-
1 ATTAAAATAT
1842316 ATTAAAATAT
1 ATTAAAATAT
1842326 ATTAAAATAT
1 ATTAAAATAT
1842336 A
1 A
1842337 AAAACTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1851230 original size:99 final size:99
Alignment explanation
Indices: 1851059--1851246 Score: 349
Period size: 99 Copynumber: 1.9 Consensus size: 99
1851049 TTCTTGTATT
* *
1851059 AATATTAGGTTCCATTTCCACATAAATTTTGCTTGCAAATATAAAAAAATTTGTCCCAACTTTTC
1 AATATTAGGGTCCATTTCCACATAAAATTTGCTTGCAAATATAAAAAAATTTGTCCCAACTTTTC
1851124 GTGAACAAAATTAGATTTTTTTTTAAATGAACAA
66 GTGAACAAAATTAGATTTTTTTTTAAATGAACAA
1851158 AATATTAGGGTCCATTTCCACATAAAATTTGCTTGCAAATATAAAAAAATTTGTCCCAACTTTTC
1 AATATTAGGGTCCATTTCCACATAAAATTTGCTTGCAAATATAAAAAAATTTGTCCCAACTTTTC
*
1851223 GTGAACAAGATTAGATTTTTTTTT
66 GTGAACAAAATTAGATTTTTTTTT
1851247 TTTATAAAAT
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
99 86 1.00
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.39
Consensus pattern (99 bp):
AATATTAGGGTCCATTTCCACATAAAATTTGCTTGCAAATATAAAAAAATTTGTCCCAACTTTTC
GTGAACAAAATTAGATTTTTTTTTAAATGAACAA
Found at i:1858972 original size:13 final size:13
Alignment explanation
Indices: 1858954--1858980 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1858944 TAGTTTTAAT
1858954 TAATTATTTAAAA
1 TAATTATTTAAAA
1858967 TAATTATTTAAAA
1 TAATTATTTAAAA
1858980 T
1 T
1858981 TTTTTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTATTTAAAA
Found at i:1858986 original size:10 final size:11
Alignment explanation
Indices: 1858923--1858992 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 11
1858913 ATTAATTCGA
1858923 TTAATTAATTAT
1 TTAA-TAATTAT
*
1858935 TTATTGAATTAGTT
1 TTAAT-AATTA--T
1858949 TTAATTAATTAT
1 TTAA-TAATTAT
1858961 TTAAAATAATTAT
1 TT--AATAATTAT
*
1858974 TTAA-AATTTT
1 TTAATAATTAT
1858984 TTAATAATT
1 TTAATAATT
1858993 CAATTTAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
10 9 0.19
11 7 0.15
12 11 0.23
13 9 0.19
14 11 0.23
15 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (11 bp):
TTAATAATTAT
Found at i:1859031 original size:22 final size:22
Alignment explanation
Indices: 1859006--1859048 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1858996 TTTAAAAAAT
1859006 AAATTAATCAAAATTTTAATTA
1 AAATTAATCAAAATTTTAATTA
* **
1859028 AAATTATTCAAGTTTTTAATT
1 AAATTAATCAAAATTTTAATT
1859049 TAATAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATTAATCAAAATTTTAATTA
Found at i:1859126 original size:16 final size:16
Alignment explanation
Indices: 1859083--1859138 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
1859073 TGATTTTATT
1859083 TAATTTATTTTAAATA
1 TAATTTATTTTAAATA
**
1859099 TAAAATATTTTAAATA
1 TAATTTATTTTAAATA
*
1859115 TAATTTAATTT-AATA
1 TAATTTATTTTAAATA
*
1859130 TATTTTATT
1 TAATTTATT
1859139 GTTAGAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
15 11 0.33
16 22 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATTTATTTTAAATA
Found at i:1859130 original size:31 final size:30
Alignment explanation
Indices: 1859047--1859131 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
1859037 AAGTTTTTAA
**
1859047 TTTA-ATAATTTAATATTTTTATAAAATGAT
1 TTTATATAATTTAAT-TTAATATAAAATGAT
* *
1859077 TTTATTTAATTTATTTTAAATATAAAAT-AT
1 TTTATATAATTTAATTT-AATATAAAATGAT
1859107 TTTAAATATAATTTAATTTAATATA
1 TTT--ATATAATTTAATTTAATATA
1859132 TTTTATTGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 11 0.24
31 22 0.49
32 12 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
TTTATATAATTTAATTTAATATAAAATGAT
Found at i:1859268 original size:16 final size:16
Alignment explanation
Indices: 1859247--1859283 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1859237 ATAATTTGAT
1859247 TAATTTAATTTAAAAA
1 TAATTTAATTTAAAAA
* *
1859263 TAATTTATTTTAAAAT
1 TAATTTAATTTAAAAA
1859279 TAATT
1 TAATT
1859284 AAATCAATCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTTAATTTAAAAA
Found at i:1859984 original size:131 final size:129
Alignment explanation
Indices: 1859828--1860066 Score: 363
Period size: 131 Copynumber: 1.8 Consensus size: 129
1859818 GTGAACAAAT
* *
1859828 AAAATTAACATAAGATATATGGATTTAGGTAACTTAATTAAAAATTAAATAGAATTACATTAACA
1 AAAATTAACATAAAATATATGGATTTAGGTAACTTAATTAAAAATTAAATAGAATTACATCAACA
* *
1859893 CATCTAGAATGTCGTGCTAAAATAAAATAAATATTAC-TCATCTAACAAGCAATACATGAATAAA
66 CATCTAGAATATCGTACTAAAAT-AAA-AAATATTACGT-ATCTAACAAGCAATACATGAATAAA
1859957 CA
128 CA
* * *
1859959 AAAATTAGCATAAAATATATTGATTTAGGTAACTTAATTAAAAATTAAATAGTATTACATCAACA
1 AAAATTAACATAAAATATATGGATTTAGGTAACTTAATTAAAAATTAAATAGAATTACATCAACA
* *
1860024 CATCTAGAATATCTTACTTAAATAAAAAATATTACGTATCTAA
66 CATCTAGAATATCGTACTAAAATAAAAAATATTACGTATCTAA
1860067 ATTTTTTTAA
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
129 15 0.15
130 4 0.04
131 79 0.81
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.31
Consensus pattern (129 bp):
AAAATTAACATAAAATATATGGATTTAGGTAACTTAATTAAAAATTAAATAGAATTACATCAACA
CATCTAGAATATCGTACTAAAATAAAAAATATTACGTATCTAACAAGCAATACATGAATAAACA
Found at i:1866113 original size:14 final size:14
Alignment explanation
Indices: 1866094--1866122 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1866084 ATTTACATTC
1866094 AAATATATATATTT
1 AAATATATATATTT
1866108 AAATATATATATTT
1 AAATATATATATTT
1866122 A
1 A
1866123 TCATTGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATATATTT
Found at i:1884263 original size:19 final size:19
Alignment explanation
Indices: 1884239--1884278 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1884229 TTAGTAAGAT
*
1884239 TAATTCTTTCATGTCGTGA
1 TAATTCTTTCATGTCATGA
1884258 TAATTCTTTCATGTCATGA
1 TAATTCTTTCATGTCATGA
1884277 TA
1 TA
1884279 TCAAATCATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (19 bp):
TAATTCTTTCATGTCATGA
Found at i:1890577 original size:65 final size:65
Alignment explanation
Indices: 1890473--1890602 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
1890463 GTGTTTTTCA
* *
1890473 TGAGTTAGCTTTATACCTAGTCCATTAGGGCTTCTCTGTTATCAACTGAAAGTAGAAAATAGACC
1 TGAGTTAGCTTTATACCTAGTCCATTAGGGCTTCTCTGTTATCAACCGAAAGTACAAAATAGACC
1890538 TGAGTTAGCTTTATACCTAGTCCATTAGGGCTTCTCTGTTATCAACCGAAAGTACAAAATAGACC
1 TGAGTTAGCTTTATACCTAGTCCATTAGGGCTTCTCTGTTATCAACCGAAAGTACAAAATAGACC
1890603 AGAAGTCAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (65 bp):
TGAGTTAGCTTTATACCTAGTCCATTAGGGCTTCTCTGTTATCAACCGAAAGTACAAAATAGACC
Found at i:1897026 original size:20 final size:20
Alignment explanation
Indices: 1897001--1897042 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1896991 AAACGTAAAC
1897001 AATGTTCATATTTAACATAT
1 AATGTTCATATTTAACATAT
1897021 AATGTTCATATTTAACATAT
1 AATGTTCATATTTAACATAT
1897041 AA
1 AA
1897043 AATTATTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.43
Consensus pattern (20 bp):
AATGTTCATATTTAACATAT
Found at i:1897225 original size:33 final size:34
Alignment explanation
Indices: 1897183--1897248 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
1897173 TAAATTTTAA
*
1897183 TTTATAAAATTAAAATT-ATATATTATATTATATT
1 TTTATAAAATT-AAATTAATATATTAAATTATATT
*
1897217 TTTA-AAAATTAAATTAATATTTTAAATTATAT
1 TTTATAAAATTAAATTAATATATTAAATTATAT
1897249 AAATTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 5 0.17
33 20 0.69
34 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (34 bp):
TTTATAAAATTAAATTAATATATTAAATTATATT
Found at i:1898081 original size:23 final size:20
Alignment explanation
Indices: 1898044--1898106 Score: 56
Period size: 19 Copynumber: 3.0 Consensus size: 20
1898034 TGTTTTGATT
*
1898044 TTATAAATTTAATATTTAAA
1 TTATTAATTTAATATTTAAA
*
1898064 TGTAATTTAATTTGATA-TTAAA
1 T-T-A-TTAATTTAATATTTAAA
* *
1898086 TTATTATTTTTATATTTAAA
1 TTATTAATTTAATATTTAAA
1898106 T
1 T
1898107 CTGACTCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 9 0.26
20 8 0.23
21 2 0.06
22 7 0.20
23 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTATTAATTTAATATTTAAA
Found at i:1898191 original size:20 final size:20
Alignment explanation
Indices: 1898160--1898209 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1898150 TGGTTAAAAA
1898160 TTAATA-AAAATATTAATTT
1 TTAATATAAAATATTAATTT
1898179 TTAATATAAAATATTAATTT
1 TTAATATAAAATATTAATTT
1898199 TTAAATATAAA
1 TT-AATATAAA
1898210 TATAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.21
20 15 0.52
21 8 0.28
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATATAAAATATTAATTT
Found at i:1898218 original size:21 final size:20
Alignment explanation
Indices: 1898160--1898215 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
1898150 TGGTTAAAAA
*
1898160 TTAATA-AAAATATTAATTT
1 TTAATATAAAATATAAATTT
*
1898179 TTAATATAAAATATTAATTT
1 TTAATATAAAATATAAATTT
1898199 TTAA-ATATAAATATAAA
1 TTAATATA-AAATATAAA
1898216 ATTAAATAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 9 0.26
20 25 0.74
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAATATAAAATATAAATTT
Found at i:1899522 original size:23 final size:22
Alignment explanation
Indices: 1899475--1899537 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 22
1899465 TCTGATTTGA
*
1899475 TTTTAAATTAATAAAATATTATT
1 TTTTAAAAT-ATAAAATATTATT
1899498 TTTTAAAATATAAAATATTATT
1 TTTTAAAATATAAAATATTATT
1899520 TTTT-AAATATAAATATAT
1 TTTTAAAATATAAA-ATAT
1899538 AAATAAAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
21 9 0.24
22 21 0.55
23 8 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAATATAAAATATTATT
Found at i:1900575 original size:6 final size:6
Alignment explanation
Indices: 1900564--1900618 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
1900554 GAATATAATA
* * *
1900564 TTAAAT TTAAAT TTAACT GTAAAT TTAAAAT TT-AAT TTAAA- TTCAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT
1900611 TTAAAT TT
1 TTAAAT TT
1900619 TATTTTTAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 9 0.22
6 25 0.62
7 6 0.15
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:1900604 original size:18 final size:17
Alignment explanation
Indices: 1900559--1900606 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 17
1900549 CAAATGAATA
1900559 TAATATTAAATTTAAATT
1 TAAT-TTAAATTTAAATT
*
1900577 TAACTGTAAATTTAAAATT
1 TAA-TTTAAATTT-AAATT
1900596 TAATTTAAATT
1 TAATTTAAATT
1900607 CAATTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
TAATTTAAATTTAAATT
Found at i:1900623 original size:11 final size:11
Alignment explanation
Indices: 1900559--1900623 Score: 58
Period size: 11 Copynumber: 5.5 Consensus size: 11
1900549 CAAATGAATA
1900559 TAATATTAAATT
1 TAAT-TTAAATT
*
1900571 TAAATTTAACTGT
1 T-AATTTAAAT-T
*
1900584 AAATTTAAAATT
1 TAATTT-AAATT
1900596 TAATTTAAATT
1 TAATTTAAATT
*
1900607 CAATTTAAATT
1 TAATTTAAATT
*
1900618 TTATTT
1 TAATTT
1900624 TTAAGTTTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
11 19 0.44
12 17 0.40
13 7 0.16
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.51
Consensus pattern (11 bp):
TAATTTAAATT
Found at i:1900657 original size:42 final size:42
Alignment explanation
Indices: 1900602--1900703 Score: 104
Period size: 43 Copynumber: 2.4 Consensus size: 42
1900592 AATTTAATTT
* * *
1900602 AAATTCAATTTAAATT-TTATTTTTAAGTTTAATT-TGATATAA
1 AAATTAAATTTAAATTATT-TTATTAAATTTAATTAT-ATATAA
*
1900644 AAATTAAAATTAAAATTATTTTATTAAATTTAATTAATATATAA
1 AAATT-AAATTTAAATTATTTTATTAAATTTAATT-ATATATAA
1900688 AAA-TAAATTT-AATTAT
1 AAATTAAATTTAAATTAT
1900704 AATAATTAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
41 6 0.12
42 10 0.20
43 23 0.45
44 11 0.22
45 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (42 bp):
AAATTAAATTTAAATTATTTTATTAAATTTAATTATATATAA
Found at i:1900717 original size:23 final size:23
Alignment explanation
Indices: 1900666--1900720 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
1900656 AAATTATTTT
1900666 ATTAAATTTAATTAATATATAAA
1 ATTAAATTTAATTAATATATAAA
*
1900689 AATAAATTTAATT-ATA-ATAATTA
1 ATTAAATTTAATTAATATATAA--A
1900712 ATTAAATTT
1 ATTAAATTT
1900721 TGATTATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 4 0.14
22 3 0.11
23 21 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
ATTAAATTTAATTAATATATAAA
Found at i:1900719 original size:18 final size:17
Alignment explanation
Indices: 1900673--1900716 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1900663 TTTATTAAAT
1900673 TTAATTAATATATAAAAA
1 TTAATTAAT-TATAAAAA
* *
1900691 TAAATTTAATTATAATAA
1 TTAA-TTAATTATAAAAA
1900709 TTAATTAA
1 TTAATTAA
1900717 ATTTTGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 4 0.18
18 13 0.59
19 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAATTATAAAAA
Found at i:1917716 original size:27 final size:27
Alignment explanation
Indices: 1917678--1917730 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1917668 TGACTCCAAA
*
1917678 TGCTATTATTTGGGTTTAGGTTGCAAT
1 TGCTATTATTTGGGTTTAGATTGCAAT
*
1917705 TGCTGTTATTTGGGTTTAGATTGCAA
1 TGCTATTATTTGGGTTTAGATTGCAA
1917731 ATGTTGTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.19, C:0.08, G:0.26, T:0.47
Consensus pattern (27 bp):
TGCTATTATTTGGGTTTAGATTGCAAT
Found at i:1917742 original size:27 final size:27
Alignment explanation
Indices: 1917674--1917743 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
1917664 GATTTGACTC
* * *
1917674 CAAATGCTATTATTTGGGTTTAGGTTG
1 CAAATGCTGTCATTTGGGTTTAGATTG
* *
1917701 CAATTGCTGTTATTTGGGTTTAGATTG
1 CAAATGCTGTCATTTGGGTTTAGATTG
*
1917728 CAAATGTTGTCATTTG
1 CAAATGCTGTCATTTG
1917744 ACTTCAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.46
Consensus pattern (27 bp):
CAAATGCTGTCATTTGGGTTTAGATTG
Found at i:1918044 original size:26 final size:22
Alignment explanation
Indices: 1918015--1918070 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 22
1918005 ATCTTACATG
1918015 AGTTTTTGGAGAAACTTCTTGCTTC
1 AGTTTTTGGAGAAA-TT-TT-CTTC
1918040 AAGTTTTTGGAGAAATTTTCTTC
1 -AGTTTTTGGAGAAATTTTCTTC
1918063 AGTTTTTG
1 AGTTTTTG
1918071 TAACCCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.27
23 4 0.13
24 2 0.07
25 2 0.07
26 14 0.47
ACGTcount: A:0.21, C:0.11, G:0.20, T:0.48
Consensus pattern (22 bp):
AGTTTTTGGAGAAATTTTCTTC
Found at i:1922831 original size:2 final size:2
Alignment explanation
Indices: 1922818--1922851 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1922808 ACTAAATCTA
*
1922818 AT AT AT AA 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
1922852 TACAACAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1923023 original size:28 final size:28
Alignment explanation
Indices: 1922953--1923033 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
1922943 AATAGTTTTT
*
1922953 TTTAATTACAAATTAAAATCATTTTAAA
1 TTTAATTAAAAATTAAAATCATTTTAAA
* *
1922981 TTT-ATTCAAATATTAAAATTA-TTTAAA
1 TTTAATT-AAAAATTAAAATCATTTTAAA
*
1923008 TTATAATTAAAAATT-AAATCAATTTA
1 TT-TAATTAAAAATTAAAATCATTTTA
1923034 TAGATATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
27 16 0.36
28 25 0.57
29 3 0.07
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (28 bp):
TTTAATTAAAAATTAAAATCATTTTAAA
Found at i:1923266 original size:29 final size:29
Alignment explanation
Indices: 1923230--1923302 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 29
1923220 TTATCTTTTT
1923230 AAAAAATTTACATAAGACATTAAAAATTC
1 AAAAAATTTACATAAGACATTAAAAATTC
* * **
1923259 AAATAATTTTATATAAGATTTTAAAAATTC
1 AAA-AAATTTACATAAGACATTAAAAATTC
*
1923289 AAAAAATTTTCATA
1 AAAAAATTTACATA
1923303 TTAAATTTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 11 0.31
30 25 0.69
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAAAATTTACATAAGACATTAAAAATTC
Found at i:1923283 original size:30 final size:31
Alignment explanation
Indices: 1923249--1923311 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
1923239 ACATAAGACA
*
1923249 TTAAAAATTCAAATAATTTT-ATA-TAAGATT
1 TTAAAAATTCAAAAAATTTTCATATTAA-ATT
1923279 TTAAAAATTCAAAAAATTTTCATATTAAATT
1 TTAAAAATTCAAAAAATTTTCATATTAAATT
1923310 TT
1 TT
1923312 TAAATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 19 0.63
31 8 0.27
32 3 0.10
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (31 bp):
TTAAAAATTCAAAAAATTTTCATATTAAATT
Found at i:1923986 original size:22 final size:21
Alignment explanation
Indices: 1923942--1923994 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
1923932 TTATGTATAC
*
1923942 TATAAATTTAAAAAATTTAAA
1 TATAAATTTAAAAAAATTAAA
1923963 TATAAATTTAAAAAGAGATT-AA
1 TATAAATTTAAAAA-A-ATTAAA
*
1923985 TATATATTTA
1 TATAAATTTA
1923995 TATTAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 14 0.50
22 12 0.43
23 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (21 bp):
TATAAATTTAAAAAAATTAAA
Found at i:1924331 original size:21 final size:21
Alignment explanation
Indices: 1924307--1924348 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1924297 ATTCAAGTAA
1924307 TTTTATATAAAATTTTAAAAT
1 TTTTATATAAAATTTTAAAAT
* *
1924328 TTTTATTTAAAATTTTTAAAT
1 TTTTATATAAAATTTTAAAAT
1924349 AATAAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATATAAAATTTTAAAAT
Found at i:1924338 original size:13 final size:13
Alignment explanation
Indices: 1924320--1924345 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1924310 TATATAAAAT
1924320 TTTAAAATTTTTA
1 TTTAAAATTTTTA
1924333 TTTAAAATTTTTA
1 TTTAAAATTTTTA
1924346 AATAATAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTAAAATTTTTA
Found at i:1936284 original size:2 final size:2
Alignment explanation
Indices: 1936277--1936315 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1936267 TTTCATTATC
*
1936277 AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1936316 AATTGAACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1951525 original size:81 final size:81
Alignment explanation
Indices: 1951417--1951623 Score: 299
Period size: 81 Copynumber: 2.6 Consensus size: 81
1951407 AGCCTTTGCC
* * **
1951417 ACCATCACCAAAACCAGAA-CCCCCAAAAGAACAACAGCCTGAACCAAAACCATCTCCAAAGCTT
1 ACCAACACCAAAACCA-AAGCCCCCAAAAGAACAACCGCCTGAACCAAAACCATCTCCAAAGCCA
*
1951481 CAGCCGCCTAAAACAGA
65 CAGCCACCTAAAACAGA
* * *
1951498 AGCAACGCCAAAACCAAAGCCCCCAAAAGAACAACCGCCTGAACCAAAACTATCTCCAAAGCCAC
1 ACCAACACCAAAACCAAAGCCCCCAAAAGAACAACCGCCTGAACCAAAACCATCTCCAAAGCCAC
1951563 AGCCACCTAAAACAGA
66 AGCCACCTAAAACAGA
* * *
1951579 ACCAACACAAAAACCAGAGCCCCCAAAAGAACAACCGTCTGAACC
1 ACCAACACCAAAACCAAAGCCCCCAAAAGAACAACCGCCTGAACC
1951624 TCCAAAGCTG
Statistics
Matches: 112, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 2 0.02
81 110 0.98
ACGTcount: A:0.45, C:0.37, G:0.11, T:0.07
Consensus pattern (81 bp):
ACCAACACCAAAACCAAAGCCCCCAAAAGAACAACCGCCTGAACCAAAACCATCTCCAAAGCCAC
AGCCACCTAAAACAGA
Done.