Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168380.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_599, 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: 21853
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.45
Found at i:69 original size:31 final size:29
Alignment explanation
Indices: 32--127 Score: 86
Period size: 31 Copynumber: 3.2 Consensus size: 29
22 TATATAATAA
32 ATTAATAAATTATTATATTATATCTATATTT
1 ATTAATAAATTATTATATTATAT-TATA-TT
* * * *
63 TTTAATATATAATAATA-TATATTATATT
1 ATTAATAAATTATTATATTATATTATATT
* *
91 ATTAATAAATCATAATATATTATATTAATAAT
1 ATTAATAAAT--TATTATATTATATT-ATATT
123 ATTAA
1 ATTAA
128 ATAATAATAT
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
28 10 0.20
29 4 0.08
30 9 0.18
31 19 0.37
32 9 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
ATTAATAAATTATTATATTATATTATATT
Found at i:78 original size:10 final size:10
Alignment explanation
Indices: 65--147 Score: 55
Period size: 10 Copynumber: 8.5 Consensus size: 10
55 CTATATTTTT
65 TAATATATAA
1 TAATATATAA
75 TAATATAT-A
1 TAATATATAA
* *
84 TTATAT-TAT
1 TAATATATAA
* *
93 TAATAAATCA
1 TAATATATAA
*
103 TAATATATTA
1 TAATATATAA
*
113 TATTA-ATAA
1 TAATATATAA
* *
122 TATTAAATAA
1 TAATATATAA
*
132 TAATATCATAT
1 TAATAT-ATAA
143 TAATA
1 TAATA
148 ATTGTCTACA
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
8 1 0.02
9 18 0.32
10 29 0.52
11 8 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (10 bp):
TAATATATAA
Found at i:81 original size:28 final size:27
Alignment explanation
Indices: 32--137 Score: 79
Period size: 28 Copynumber: 3.7 Consensus size: 27
22 TATATAATAA
*
32 ATTAATAAATTATTATATTATATCTATATTT
1 ATTAATAAA-TA--ATAATATAT-TATATTT
* *
63 TTTAATATATAATAATATA-TATTATATT
1 ATTAATAAATAATAATATATTA-TAT-TT
*
91 ATTAATAAATCATAATATATTATATTAAT
1 ATTAATAAATAATAATATATTATATT--T
* *
120 AATATTAAATAATAATAT
1 ATTAATAAATAATAATAT
138 CATATTAATA
Statistics
Matches: 61, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
26 2 0.03
27 4 0.07
28 28 0.46
29 18 0.30
30 2 0.03
31 7 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTAATAAATAATAATATATTATATTT
Found at i:131 original size:26 final size:25
Alignment explanation
Indices: 79--149 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 25
69 ATATAATAAT
*
79 ATATATTATATTATTAATAAATCATA
1 ATATATTATATTAATAATAAA-CATA
105 ATATATTATATTAATAATATTAA-ATA
1 ATATATTATATTAATAATA--AACATA
*
131 ATAATATCATATTAATAAT
1 AT-ATATTATATTAATAAT
150 TGTCTACATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 23 0.57
27 15 0.38
28 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTATATTAATAATAAACATA
Found at i:132 original size:13 final size:14
Alignment explanation
Indices: 65--149 Score: 70
Period size: 13 Copynumber: 6.3 Consensus size: 14
55 CTATATTTTT
65 TAATA-TATAATAA
1 TAATATTATAATAA
* *
78 TATATATTATATTAT
1 TA-ATATTATAATAA
* *
93 TAATA-AATCATAA
1 TAATATTATAATAA
*
106 T-ATATTATATTAA
1 TAATATTATAATAA
119 TAATATTA-AATAA
1 TAATATTATAATAA
* *
132 TAATATCATATTAA
1 TAATATTATAATAA
146 TAAT
1 TAAT
150 TGTCTACATT
Statistics
Matches: 55, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
12 3 0.05
13 24 0.44
14 20 0.36
15 8 0.15
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATATTATAATAA
Found at i:586 original size:21 final size:20
Alignment explanation
Indices: 556--609 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 20
546 TTATTATTTA
556 ATAA-AGATTAAAATATTAATT
1 ATAATAGATTAAAATA--AATT
*
577 ATAAT-TATT-AAATAAATT
1 ATAATAGATTAAAATAAATT
595 ATAATAGATTAAAAT
1 ATAATAGATTAAAAT
610 TAGTATTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 9 0.32
19 3 0.11
20 9 0.32
21 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (20 bp):
ATAATAGATTAAAATAAATT
Found at i:797 original size:23 final size:23
Alignment explanation
Indices: 726--805 Score: 63
Period size: 23 Copynumber: 3.4 Consensus size: 23
716 ATTAAGATAA
*
726 TAATATAATTATTTAGTTTTATATT
1 TAAT-TAATTATTTATTTTTA-ATT
* * *
751 TAATTAATTAATGATTATCT-ATT
1 TAATTAATTATTTATT-TTTAATT
**
774 TCCTTAATTATTTATTTTTAATT
1 TAATTAATTATTTATTTTTAATT
*
797 TAAATAATT
1 TAATTAATT
806 GCAATAGTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 6
0.69 0.20 0.10
Matches are distributed among these distances:
22 2 0.05
23 24 0.59
24 9 0.22
25 6 0.15
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (23 bp):
TAATTAATTATTTATTTTTAATT
Found at i:1037 original size:19 final size:19
Alignment explanation
Indices: 1015--1061 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1005 TAATTCTTTA
1015 TATTATA-AATTAAATATAT
1 TATTATATAATTAAATA-AT
*
1034 TATTA-ATAATTATATAAT
1 TATTATATAATTAAATAAT
1052 TATATATATA
1 TAT-TATATA
1062 TTTAGTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.25
19 15 0.62
20 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATATAATTAAATAAT
Found at i:1136 original size:15 final size:15
Alignment explanation
Indices: 1111--1153 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
1101 ATCTTATTTA
1111 CTATAATATATATAAT
1 CTAT-ATATATATAAT
1127 CTATATATATATAAT
1 CTATATATATATAAT
1142 -TATATAT-TATAA
1 CTATATATATATAA
1154 ATAAATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.19
14 7 0.26
15 11 0.41
16 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (15 bp):
CTATATATATATAAT
Found at i:1145 original size:8 final size:8
Alignment explanation
Indices: 1112--1216 Score: 52
Period size: 7 Copynumber: 13.8 Consensus size: 8
1102 TCTTATTTAC
1112 TATAATATA
1 TATAAT-TA
1121 TATAATCTA
1 TATAAT-TA
1130 TAT-A-TA
1 TATAATTA
1136 TATAATTA
1 TATAATTA
1144 TAT-ATTA
1 TATAATTA
1151 TA-AA-TA
1 TATAATTA
*
1157 AATAAATTA
1 TAT-AATTA
1166 TA-AA-TA
1 TATAATTA
*
1172 TAT-TTTA
1 TATAATTA
*
1179 AATAA-TA
1 TATAATTA
1186 TAATAACATTA
1 T-AT-A-ATTA
1197 TATAA-T-
1 TATAATTA
1203 TATAATTA
1 TATAATTA
1211 TATAAT
1 TATAAT
1217 ACTTAGAATA
Statistics
Matches: 74, Mismatches: 7, Indels: 31
0.66 0.06 0.28
Matches are distributed among these distances:
6 17 0.23
7 18 0.24
8 17 0.23
9 16 0.22
10 3 0.04
11 3 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (8 bp):
TATAATTA
Found at i:1315 original size:34 final size:34
Alignment explanation
Indices: 1269--1334 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
1259 GTTTTATAAC
* *
1269 TAATATATAATTATATTATTAT-ATATCAAATTAT
1 TAATATAGAATTA-ATTAATATAATATCAAATTAT
*
1303 TAATATAGAATTAATTAATATAATATTAAATT
1 TAATATAGAATTAATTAATATAATATCAAATT
1335 CAGATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (34 bp):
TAATATAGAATTAATTAATATAATATCAAATTAT
Found at i:1331 original size:15 final size:13
Alignment explanation
Indices: 1283--1330 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 13
1273 ATATAATTAT
1283 ATTATTATATATCAA
1 ATTATTA-ATAT-AA
1298 ATTATTAATATAGA
1 ATTATTAATATA-A
1312 ATTAATTAATATAA
1 ATT-ATTAATATAA
1326 TATTA
1 -ATTA
1331 AATTCAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
15 19 0.63
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (13 bp):
ATTATTAATATAA
Found at i:3069 original size:18 final size:20
Alignment explanation
Indices: 3029--3073 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
3019 TTTAATTGCT
*
3029 AATTAT-ATATATATATATT
1 AATTATAATATATATATATA
3048 AATTATAATATA-ATA-ATA
1 AATTATAATATATATATATA
3066 AATTATAA
1 AATTATAA
3074 ATAGAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 9 0.38
20 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTATAATATATATATATA
Found at i:3405 original size:20 final size:19
Alignment explanation
Indices: 3374--3412 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
3364 AATAACAACA
3374 ATTTATTAATTAAACAAAT
1 ATTTATTAATTAAACAAAT
3393 ATTTATATAATTAAACAAAT
1 ATTTAT-TAATTAAACAAAT
3413 TAAAATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTATTAATTAAACAAAT
Found at i:3665 original size:21 final size:20
Alignment explanation
Indices: 3606--3665 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
3596 TATCTATATT
* *
3606 ATAATAAAATAATATTATAA
1 ATAATAATATAATATTACAA
* *
3626 CTAATTAATATACAGATTACAA
1 ATAA-TAATATA-ATATTACAA
3648 ATAATAATATCAATATTA
1 ATAATAATAT-AATATTA
3666 GGTATAATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 3 0.10
21 17 0.55
22 11 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.35
Consensus pattern (20 bp):
ATAATAATATAATATTACAA
Found at i:4201 original size:16 final size:15
Alignment explanation
Indices: 4165--4207 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
4155 TAAATAATAA
4165 TATAATTATAA-TAT
1 TATAATTATAATTAT
4179 TAT-ATTATAATTAT
1 TATAATTATAATTAT
4193 TATAAATTATAATTA
1 TAT-AATTATAATTA
4208 ACTTATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.27
14 9 0.35
16 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATAATTATAATTAT
Found at i:4608 original size:17 final size:17
Alignment explanation
Indices: 4573--4611 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4563 TATAGCTTAT
*
4573 TTAAATTATTATTTAAA
1 TTAAATTATAATTTAAA
*
4590 TTAAATTATAATATTAAT
1 TTAAATTATAAT-TTAAA
4608 TTAA
1 TTAA
4612 CATGACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTAAATTATAATTTAAA
Found at i:4833 original size:180 final size:181
Alignment explanation
Indices: 4631--5163 Score: 467
Period size: 180 Copynumber: 3.0 Consensus size: 181
4621 TTGAACTTGT
*
4631 TCAGTAAACATATTTATTTTTTAAATCTCCTACCTATTAA-T-TTGCAAAATATTAATAAAGTAA
1 TCAGTAAACAGATTTATTTTTTAAATCTCCTACCTATTAATTGTTG--AAATATTAATAAAGTAA
* * * * * *
4694 TATTATTTTATTTTGAATAAACTTGTA-TGAATAGGAACAATT-ATTTTATGACAAAACAAAA-A
64 TATTATTTTATTTTGAATAAACTTATACAG-ACAGAAACAATTGA-TTCATCACAAAACAAAAGA
* *
4756 TTATAACTATTAGAAATAAAAAATTGTTCAAACAGTTATAA-CTATTTAACCTTAC
127 TCATAACTATTAGAAATAAAAAATTGTTCAAACAGTCA-AATCTATTTAACCTTAC
* ** * * * *
4811 TCAGTAAATAGATTTATTTTTTAAATCTTTTACTTATTAATTGTTGGAATATTATTAAATTAATA
1 TCAGTAAACAGATTTATTTTTTAAATCTCCTACCTATTAATTGTTGAAATATTAATAAAGTAATA
* *
4876 TTATTTTATTTTGAATAAGCTTATACAGACAGAAACAATTGATTCATCACAAAACAAAAGGTCAT
66 TTATTTTATTTTGAATAAACTTATACAGACAGAAACAATTGATTCATCACAAAACAAAAGATCAT
* * * * * * **
4941 AACTATTTGAAATAGATAATTGTTCAAATAGTCAAATCTATTTAAACATGT
131 AACTATTAGAAATAAAAAATTGTTCAAACAGTCAAATCTATTTAACCTTAC
** * ** * * * *
4992 TCAAAAAACAAATTTATTTTTTAAAT-TTTTACTTATTAAATT-TTGGAATATTAATAAATTTA-
1 TCAGTAAACAGATTTATTTTTTAAATCTCCTACCTATT-AATTGTTGAAATATTAATAAAGTAAT
** * * * ** * * *
5054 ATTATTTTATTCGGTATAAGCTTGTATGGACAGAAACAATTGGTTTATCACAAAACAAAAAAGGT
65 ATTATTTTATTTTGAATAAACTTATACAGACAGAAACAATTGATTCATCACAAAAC--AAAAGAT
* * *
5119 CATAACTATTTA-AAATAAATAATTTTTCAAATAGTCAGAA-CTATT
128 CATAACTA-TTAGAAATAAAAAATTGTTCAAACAGTCA-AATCTATT
5164 CCAACATGTT
Statistics
Matches: 299, Mismatches: 43, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
179 48 0.16
180 130 0.43
181 114 0.38
182 7 0.02
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (181 bp):
TCAGTAAACAGATTTATTTTTTAAATCTCCTACCTATTAATTGTTGAAATATTAATAAAGTAATA
TTATTTTATTTTGAATAAACTTATACAGACAGAAACAATTGATTCATCACAAAACAAAAGATCAT
AACTATTAGAAATAAAAAATTGTTCAAACAGTCAAATCTATTTAACCTTAC
Found at i:5118 original size:181 final size:181
Alignment explanation
Indices: 4616--5241 Score: 687
Period size: 181 Copynumber: 3.5 Consensus size: 181
4606 ATTTAACATG
* * ** * ** * *
4616 ACTATTTGAACTTGTTCAGTAAACATATTTATTTTTTAAATCTCCTACCTATTAA-TTTGCAAAA
1 ACTATTTAAACATGTTCAAAAAACAAATTTATTTTTTAAATCTTTTACTTATTAATTTTG--GAA
* * * * * *
4680 TATTAATAAAGTAATATTATTTTATTTTGAATAAACTTGTATGAATAGGAACAATT-ATTTTATG
64 TATTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGGACAGAAACAATTGA-TTTATC
* * * * * *
4744 ACAAAACAAAAA--TTATAACTATTAGAAATAAAAAATTGTTCAAACAGTTATA
128 ACAAAACAAAAAGGTCATAACTATTTGAAATAAATAATTGTTCAAATAGTCAGA
* * ** ** * *
4796 ACTATTTAACCTTACTCAGTAAATAGATTTATTTTTTAAATCTTTTACTTATTAATTGTTGGAAT
1 ACTATTTAAACATGTTCAAAAAACAAATTTATTTTTTAAATCTTTTACTTATTAATT-TTGGAAT
* * ** *
4861 ATTATTAAATTAATATTATTTTATTTTGAATAAGCTTATACAGACAGAAACAATTGATTCATCAC
65 ATTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGGACAGAAACAATTGATTTATCAC
*
4926 AAAAC-AAAAGGTCATAACTATTTGAAATAGATAATTGTTCAAATAGTCA-A
130 AAAACAAAAAGGTCATAACTATTTGAAATAAATAATTGTTCAAATAGTCAGA
4976 ATCTATTTAAACATGTTCAAAAAACAAATTTATTTTTTAAAT-TTTTACTTATTAAATTTTGGAA
1 A-CTATTTAAACATGTTCAAAAAACAAATTTATTTTTTAAATCTTTTACTTATT-AATTTTGGAA
* ** * *
5040 TATTAATAAATTTA-ATTATTTTATTCGGTATAAGCTTGTATGGACAGAAACAATTGGTTTATCA
64 TATTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGGACAGAAACAATTGATTTATCA
* *
5104 CAAAACAAAAAAGGTCATAACTATTTAAAATAAATAATTTTTCAAATAGTCAGA
129 CAAAAC-AAAAAGGTCATAACTATTTGAAATAAATAATTGTTCAAATAGTCAGA
** *
5158 ACTATTCCAACATGTTCAAAAAACAAATTTATTTTTTAAAT-TTTCACTTATTAAATTTTGGAAT
1 ACTATTTAAACATGTTCAAAAAACAAATTTATTTTTTAAATCTTTTACTTATT-AATTTTGGAAT
* *
5222 ATTAATTAATTTA-ATTATTT
65 ATTAATAAATTAATATTATTT
5242 CAAATAATTA
Statistics
Matches: 384, Mismatches: 52, Indels: 19
0.84 0.11 0.04
Matches are distributed among these distances:
179 52 0.14
180 137 0.36
181 190 0.49
182 5 0.01
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.41
Consensus pattern (181 bp):
ACTATTTAAACATGTTCAAAAAACAAATTTATTTTTTAAATCTTTTACTTATTAATTTTGGAATA
TTAATAAATTAATATTATTTTATTTTGAATAAGCTTGTATGGACAGAAACAATTGATTTATCACA
AAACAAAAAGGTCATAACTATTTGAAATAAATAATTGTTCAAATAGTCAGA
Found at i:5375 original size:15 final size:17
Alignment explanation
Indices: 5341--5379 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
5331 TATAACTAAG
*
5341 TAAAAATTAAATATTAT
1 TAAAAATGAAATATTAT
5358 TAAAAATGAAA-A-TAT
1 TAAAAATGAAATATTAT
5373 TAAAAAT
1 TAAAAAT
5380 TTAATATACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 1 0.05
17 10 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAAATGAAATATTAT
Found at i:5562 original size:17 final size:16
Alignment explanation
Indices: 5530--5589 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 16
5520 ATTTATCATT
5530 ATTTTATAT-TTA-TA
1 ATTTTATATATTATTA
5544 ATTTTATGATATTATTA
1 ATTTTAT-ATATTATTA
*
5561 ATGATTATATATTATT-
1 AT-TTTATATATTATTA
*
5577 ATATTA-ATATTAT
1 ATTTTATATATTAT
5590 AATAATAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 14 0.34
15 6 0.15
16 5 0.12
17 12 0.29
18 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
ATTTTATATATTATTA
Found at i:5604 original size:11 final size:11
Alignment explanation
Indices: 5559--5615 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
5549 ATGATATTAT
5559 TAATGATTAT-A
1 TAAT-ATTATAA
* *
5570 TATTATTATAT
1 TAATATTATAA
5581 TAATATTATAA
1 TAATATTATAA
5592 TAATAATTA-AA
1 TAAT-ATTATAA
5603 TAATTATTATAA
1 TAA-TATTATAA
5615 T
1 T
5616 TATTTTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 5 0.13
11 25 0.66
12 8 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
TAATATTATAA
Found at i:5687 original size:17 final size:17
Alignment explanation
Indices: 5527--5687 Score: 60
Period size: 17 Copynumber: 9.7 Consensus size: 17
5517 ATAATTTATC
*
5527 ATTATTTTATATT-TATA
1 ATTATTATATATTAT-TA
5544 ATT-TTATGATATTATTA
1 ATTATTAT-ATATTATTA
*
5561 ATGATTATATATTATT-
1 ATTATTATATATTATTA
5577 A-TATTA-ATATTATAATA
1 ATTATTATATATTAT--TA
* *
5594 ATAATTAAATAATTATTATA
1 ATTATTATAT-ATTA-T-TA
*
5614 ATTATT-T-TAATATTA
1 ATTATTATATATTATTA
* *
5629 ACTATT-TCT-TT-TT-
1 ATTATTATATATTATTA
* **
5642 ACTATTGGA-ATTATTA
1 ATTATTATATATTATTA
5658 TATTAATTA-ATATTATTA
1 -ATT-ATTATATATTATTA
5676 ATTATTATATAT
1 ATTATTATATAT
5688 ATAATAAAAT
Statistics
Matches: 112, Mismatches: 13, Indels: 38
0.69 0.08 0.23
Matches are distributed among these distances:
13 6 0.05
14 11 0.10
15 15 0.13
16 11 0.10
17 34 0.30
18 20 0.18
19 2 0.02
20 12 0.11
21 1 0.01
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTATTATATATTATTA
Found at i:6208 original size:3 final size:3
Alignment explanation
Indices: 6202--6227 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6192 ATAATAATAA
6202 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
6228 GGAATAAAGT
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6678 original size:20 final size:20
Alignment explanation
Indices: 6623--6682 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
6613 TAGTATAAAT
*
6623 ATTAA-TTTATTAATTTATTA
1 ATTAATTTTAATAA-TTATTA
* *
6643 ACTAATCGTTAA-AATTATTA
1 ATTAAT-TTTAATAATTATTA
6663 ATTAATTTTAATAATT-TTA
1 ATTAATTTTAATAATTATTA
6682 A
1 A
6683 ACAATAGTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
19 8 0.25
20 19 0.59
21 2 0.06
22 3 0.09
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTAATTTTAATAATTATTA
Found at i:6759 original size:22 final size:22
Alignment explanation
Indices: 6726--6768 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6716 CTTTTAGTTA
*
6726 TATTCAAATAATACTATAATAT
1 TATTCAAATAATACAATAATAT
6748 TATT-AAATTAATACAATAATA
1 TATTCAAA-TAATACAATAATA
6769 ATTGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TATTCAAATAATACAATAATAT
Found at i:6873 original size:22 final size:21
Alignment explanation
Indices: 6834--6887 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
6824 GTTTATCATT
6834 ATTAATAGTTAATAATTATAA
1 ATTAATAGTTAATAATTATAA
* * *
6855 ATTAATATTATAATTATTATAT
1 ATTAATAGT-TAATAATTATAA
6877 ATTAAATAGTT
1 ATT-AATAGTT
6888 TTGTTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 8 0.30
22 14 0.52
23 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
ATTAATAGTTAATAATTATAA
Found at i:8216 original size:182 final size:179
Alignment explanation
Indices: 7875--8222 Score: 477
Period size: 182 Copynumber: 1.9 Consensus size: 179
7865 TTTTAAATAA
*
7875 ATTTATTTTTGAAATTTTTACTTATTAATTTTGGAACATTAATAAATTTATATTATTTTATTTGA
1 ATTTATTTTTGAAATTTTTACTTATTAATTTTGGAACATTAATAAATTTATATTATTTTATTTCA
* * ** *
7940 AATAAGCTTGAATGAATAGAACCAATTGTTTTATGACAAAACAAAAGGTTGTAATGTTTTGAAAT
66 AATAAGCTTAAATGAATAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAAT
8005 AGATAATTATTAAGATAGTCATAACTATTTGAACTTCTTCGATAAAAAT
131 AGATAATTATTAAGATAGTCATAACTATTTGAACTTCTTCGATAAAAAT
** * *
8054 ATTTATTTTTTTAATTCTCTTACTTTTTAATTTTTGGAATATTAATAAA-TTAGTATTATTTTAT
1 ATTTATTTTTGAAATT-T-TTACTTATTAA-TTTTGGAACATTAATAAATTTA-TATTATTTTAT
* * * *
8118 TTCAAATAAGC-TAACATGATTTGAAACAATTGTTTTATTACAAAACAAAATGTTACAATGATTT
62 TTCAAATAAGCTTAA-ATGAATAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATGATTT
* *
8182 GAAGTAGATAATTATTCAA-ATAGTCATGACTATTTGAACTT
126 GAAATAGATAATTATT-AAGATAGTCATAACTATTTGAACTT
8223 GATTGGTAAA
Statistics
Matches: 147, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
179 14 0.10
180 1 0.01
181 15 0.10
182 115 0.78
183 2 0.01
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (179 bp):
ATTTATTTTTGAAATTTTTACTTATTAATTTTGGAACATTAATAAATTTATATTATTTTATTTCA
AATAAGCTTAAATGAATAGAAACAATTGTTTTATGACAAAACAAAAGGTTACAATGATTTGAAAT
AGATAATTATTAAGATAGTCATAACTATTTGAACTTCTTCGATAAAAAT
Found at i:8408 original size:11 final size:11
Alignment explanation
Indices: 8392--8433 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
8382 TTGATATTAT
8392 ATTATCAAATA
1 ATTATCAAATA
8403 ATTATCAAATA
1 ATTATCAAATA
* *
8414 A-TAT-TACTA
1 ATTATCAAATA
8423 ATTATCAAATA
1 ATTATCAAATA
8434 TTACAAGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
9 4 0.16
10 6 0.24
11 15 0.60
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (11 bp):
ATTATCAAATA
Found at i:8435 original size:17 final size:17
Alignment explanation
Indices: 8413--8487 Score: 78
Period size: 17 Copynumber: 4.9 Consensus size: 17
8403 ATTATCAAAT
8413 AATATTACTAATTATCA
1 AATATTACTAATTATCA
8430 AATATTAC-AAGTT-T--
1 AATATTACTAA-TTATCA
8444 -A-A-TA-TAATTATCA
1 AATATTACTAATTATCA
8457 AATATTACTAATTATCA
1 AATATTACTAATTATCA
8474 AATATTA-TAATTAT
1 AATATTACTAATTAT
8488 TGTGTATTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 19
0.72 0.00 0.28
Matches are distributed among these distances:
10 2 0.04
11 5 0.10
12 1 0.02
13 1 0.02
14 1 0.02
15 1 0.02
16 12 0.24
17 26 0.53
ACGTcount: A:0.48, C:0.08, G:0.01, T:0.43
Consensus pattern (17 bp):
AATATTACTAATTATCA
Found at i:8941 original size:19 final size:19
Alignment explanation
Indices: 8917--8956 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
8907 ATAAATGAAG
*
8917 ATTAAA-TATTATTAATTAA
1 ATTAAATTAATATT-ATTAA
8936 ATTAAATTAATATTATTAA
1 ATTAAATTAATATTATTAA
8955 AT
1 AT
8957 ATTATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAAATTAATATTATTAA
Found at i:8988 original size:19 final size:19
Alignment explanation
Indices: 8945--8991 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
8935 AATTAAATTA
8945 ATATTATT-AAATATTATT
1 ATATTATTGAAATATTATT
*
8963 ATAATTATTGTAATATTGA-T
1 AT-ATTATTGAAATATT-ATT
8983 ATATTATTG
1 ATATTATTG
8992 CTCTGATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 13 0.52
20 9 0.36
21 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
ATATTATTGAAATATTATT
Found at i:9368 original size:34 final size:34
Alignment explanation
Indices: 9273--9368 Score: 78
Period size: 34 Copynumber: 2.8 Consensus size: 34
9263 TTTGAATTTA
9273 TATAATTAATTAA-ATTAATTAATTAAT-AAATATT
1 TATAA-TAATTAATATTAATTAA-TAATAAAATATT
* *
9307 AATAAATATATT--TATTCATTACA-AATAAAATATT
1 TAT-AATA-ATTAATATTAATTA-ATAATAAAATATT
9341 TATAATAATTAATATT-ATTATATAATAA
1 TATAATAATTAATATTAATTA-ATAATAA
9369 GTATATACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
32 3 0.06
33 12 0.24
34 29 0.58
35 6 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (34 bp):
TATAATAATTAATATTAATTAATAATAAAATATT
Found at i:9595 original size:23 final size:23
Alignment explanation
Indices: 9551--9595 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
9541 TATATACAAT
* * *
9551 ATATTATTTATACAATTGTTTTA
1 ATATTATTCAAACAATTCTTTTA
*
9574 ATATTATTCAAACTATTCTTTT
1 ATATTATTCAAACAATTCTTTT
9596 TATTTTAAGT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATTATTCAAACAATTCTTTTA
Found at i:10588 original size:25 final size:25
Alignment explanation
Indices: 10540--10624 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 25
10530 TTATAAATTT
*
10540 TATTTTATATGAATT-TA-T-TCAAA
1 TATTTTATAT-AATTATAGTATTAAA
10563 TATTTTATATAATTATAGTATTAAA
1 TATTTTATATAATTATAGTATTAAA
** *
10588 TATTATTA-ATAAAAATAGTAAT-AA
1 TATT-TTATATAATTATAGTATTAAA
10612 TATTTT-T-TAATTA
1 TATTTTATATAATTA
10625 ATATAATATA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
22 8 0.16
23 14 0.27
24 7 0.14
25 19 0.37
26 3 0.06
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.51
Consensus pattern (25 bp):
TATTTTATATAATTATAGTATTAAA
Found at i:10862 original size:22 final size:22
Alignment explanation
Indices: 10815--10864 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
10805 TATAGTTAAT
* * *
10815 TAATAATTGATTAATTTTATTA
1 TAATATTTGATTAAATTAATTA
10837 TAATATTTG-TTAAATTAATTA
1 TAATATTTGATTAAATTAATTA
10858 GTAATAT
1 -TAATAT
10865 AATTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (22 bp):
TAATATTTGATTAAATTAATTA
Found at i:10996 original size:19 final size:20
Alignment explanation
Indices: 10973--11019 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
10963 TGTTTATCTA
*
10973 AATATATTATAATTATTTAT
1 AATATATTATAATTATTAAT
* *
10993 -ATATAATATTATTATTAAT
1 AATATATTATAATTATTAAT
11012 AATATATT
1 AATATATT
11020 GATATTATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
AATATATTATAATTATTAAT
Found at i:11004 original size:22 final size:23
Alignment explanation
Indices: 10976--11028 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
10966 TTATCTAAAT
* *
10976 ATATTATAATTATTTATATA-TA
1 ATATTATAATTAATAATATATTA
* *
10998 ATATTATTATTAATAATATATTG
1 ATATTATAATTAATAATATATTA
11021 ATATTATA
1 ATATTATA
11029 GAAATATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATATTATAATTAATAATATATTA
Found at i:11833 original size:20 final size:20
Alignment explanation
Indices: 11805--11854 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
11795 TAAGAAAATT
* *
11805 TAATGTTATAATATATAAAA
1 TAATTTTATAATAAATAAAA
* *
11825 TAATTTTATATTAAATAAAT
1 TAATTTTATAATAAATAAAA
*
11845 TTATTTTATA
1 TAATTTTATA
11855 TATTTTTAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAATTTTATAATAAATAAAA
Found at i:11840 original size:15 final size:15
Alignment explanation
Indices: 11816--11929 Score: 56
Period size: 15 Copynumber: 7.4 Consensus size: 15
11806 AATGTTATAA
*
11816 TATATAAAATAATTT
1 TATATTAAATAATTT
*
11831 TATATTAAATAAATT
1 TATATTAAATAATTT
* * *
11846 TATTTTATATATTTT
1 TATATTAAATAATTT
*
11861 TAATTATTATAAATATATAT
1 T-A-TA-T-TAAATA-ATTT
* * *
11881 AATAATATAATTATTT
1 TATATTA-AATAATTT
11897 TATATGTAAATAA-TT
1 TATAT-TAAATAATTT
11912 TATA-T-AATAA-TT
1 TATATTAAATAATTT
11924 TATATT
1 TATATT
11930 GTTATTTAAG
Statistics
Matches: 74, Mismatches: 17, Indels: 18
0.68 0.16 0.17
Matches are distributed among these distances:
12 11 0.15
13 2 0.03
15 31 0.42
16 13 0.18
17 6 0.08
18 3 0.04
19 6 0.08
20 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
TATATTAAATAATTT
Found at i:11909 original size:27 final size:28
Alignment explanation
Indices: 11861--11928 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 28
11851 TATATATTTT
* * *
11861 TAATTATTATAAATATATATAA-TAATA
1 TAATTATTTTATATATAAATAATTAATA
* *
11888 TAATTATTTTATATGTAAATAATTTATA
1 TAATTATTTTATATATAAATAATTAATA
*
11916 TAA-TAATTTATAT
1 TAATTATTTTATAT
11929 TGTTATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 27 0.79
28 7 0.21
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (28 bp):
TAATTATTTTATATATAAATAATTAATA
Found at i:12123 original size:23 final size:23
Alignment explanation
Indices: 12097--12144 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
12087 TTATTTGATA
*
12097 ATTTATATATATTATAAGT-ATAT
1 ATTTATATA-ATTATAAATAATAT
12120 ATTTATATAATTATAAATAATAT
1 ATTTATATAATTATAAATAATAT
12143 AT
1 AT
12145 AATTTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTATATAATTATAAATAATAT
Found at i:12592 original size:18 final size:18
Alignment explanation
Indices: 12546--12597 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
12536 TATAATTTAT
*
12546 TATAGTAATTAATAATTAA
1 TATACTAATTAA-AATTAA
*
12565 T-TATTAAATTAAAATTAA
1 TATACT-AATTAAAATTAA
*
12583 TATACTAATTTAAAT
1 TATACTAATTAAAAT
12598 AACTAATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TATACTAATTAAAATTAA
Found at i:12595 original size:19 final size:18
Alignment explanation
Indices: 12552--12596 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
12542 TTATTATAGT
*
12552 AATTAATAATTAATTATTA
1 AATTAA-AATTAATTACTA
12571 AATTAAAATTAATATACTA
1 AATTAAAATTAAT-TACTA
*
12590 ATTTAAA
1 AATTAAA
12597 TAACTAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTAAAATTAATTACTA
Found at i:12970 original size:23 final size:22
Alignment explanation
Indices: 12944--12992 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
12934 TTTATAATTA
* *
12944 ATTAATTGTAATTAATATATAAT
1 ATTAATTATAATTAAT-TAAAAT
*
12967 ATTAATTATTATTAATTAAAAT
1 ATTAATTATAATTAATTAAAAT
12989 ATTA
1 ATTA
12993 TTTTAATGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
ATTAATTATAATTAATTAAAAT
Found at i:12982 original size:27 final size:27
Alignment explanation
Indices: 12952--13006 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
12942 TAATTAATTG
* *
12952 TAATTAATATATAATATTAATTATTAT
1 TAATTAAAATATAATATTAATGATTAT
* *
12979 TAATTAAAATATTATTTTAATGATTAT
1 TAATTAAAATATAATATTAATGATTAT
13006 T
1 T
13007 TAATAAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TAATTAAAATATAATATTAATGATTAT
Found at i:13434 original size:21 final size:20
Alignment explanation
Indices: 13387--13448 Score: 65
Period size: 21 Copynumber: 3.1 Consensus size: 20
13377 AATGATTTGA
*
13387 AACTTAATTAT-TTATATAT
1 AACTTAATAATATTATATAT
*
13406 AACTTAATGATATTATATA-
1 AACTTAATAATATTATATAT
*
13425 ATACTATAATAATATTAAATAT
1 A-ACT-TAATAATATTATATAT
13447 AA
1 AA
13449 GAGATTATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.31
20 10 0.28
21 14 0.39
22 1 0.03
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (20 bp):
AACTTAATAATATTATATAT
Found at i:13490 original size:34 final size:32
Alignment explanation
Indices: 13452--13527 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 32
13442 AATATAAGAG
*
13452 ATTATAAAATAATTACTTAATAACAT-TATAAATA
1 ATTATAAAATAATTAATTAA-AA-ATATA-AAATA
13486 ATTATAAAAAATAATTAATTAAAAATATAAAATA
1 ATTAT--AAAATAATTAATTAAAAATATAAAATA
*
13520 TTTATAAA
1 ATTATAAA
13528 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
32 3 0.08
34 16 0.43
35 4 0.11
36 14 0.38
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (32 bp):
ATTATAAAATAATTAATTAAAAATATAAAATA
Found at i:13941 original size:12 final size:13
Alignment explanation
Indices: 13913--13962 Score: 52
Period size: 12 Copynumber: 4.0 Consensus size: 13
13903 AAATAGTATT
13913 ATTCATATAATATA
1 ATTCAT-TAATATA
13927 ATTCATTAA-ATA
1 ATTCATTAATATA
*
13939 ATT-ATTAATATT
1 ATTCATTAATATA
*
13951 ATT-AATAATATA
1 ATTCATTAATATA
13963 TAACTATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 5 0.16
12 18 0.56
13 3 0.09
14 6 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTCATTAATATA
Found at i:13970 original size:20 final size:19
Alignment explanation
Indices: 13935--13995 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
13925 TAATTCATTA
*
13935 AATAATTATTAATATTATT
1 AATAATTATTAATATTAGT
13954 AATAA-TATATAACTATTAGT
1 AATAATTAT-TAA-TATTAGT
*
13974 AATAAATTATGAATATTA-T
1 AAT-AATTATTAATATTAGT
13993 AAT
1 AAT
13996 TCTTTAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
18 3 0.08
19 12 0.33
20 14 0.39
21 4 0.11
22 3 0.08
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (19 bp):
AATAATTATTAATATTAGT
Found at i:14116 original size:10 final size:10
Alignment explanation
Indices: 14089--14160 Score: 60
Period size: 10 Copynumber: 7.3 Consensus size: 10
14079 TATACTATAG
14089 TATTATTAA-
1 TATTATTAAT
*
14098 -ATAATTAAT
1 TATTATTAAT
14107 TATTATTAAT
1 TATTATTAAT
* *
14117 TAATATTATT
1 TATTATTAAT
14127 TATTATT-AT
1 TATTATTAAT
*
14136 AATTATTTAAT
1 TATTA-TTAAT
*
14147 TATTTTATAAT
1 TATTAT-TAAT
14158 TAT
1 TAT
14161 AAATAATAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
8 7 0.14
9 5 0.10
10 25 0.51
11 12 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATTATTAAT
Found at i:14134 original size:16 final size:16
Alignment explanation
Indices: 14103--14160 Score: 57
Period size: 16 Copynumber: 3.4 Consensus size: 16
14093 ATTAAATAAT
14103 TAATTA-TTATTAATTA
1 TAATTATTTATT-ATTA
14119 -ATATTATTTATTATTA
1 TA-ATTATTTATTATTA
14135 TAATTATTTAATTATTTTA
1 TAATTATTT-ATTA--TTA
14154 TAATTAT
1 TAATTAT
14161 AAATAATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 1 0.03
16 15 0.42
17 10 0.28
19 10 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTATTTATTATTA
Found at i:14930 original size:17 final size:17
Alignment explanation
Indices: 14908--14964 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
14898 TAATTATAAT
*
14908 ATAATTATTTAATGTTA
1 ATAATTATTTAATATTA
*
14925 ATAATTAATTAATATTA
1 ATAATTATTTAATATTA
* *
14942 ATAAATTATATATTATT-
1 AT-AATTATTTAATATTA
14959 ATAATT
1 ATAATT
14965 TATAATAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
16 4 0.12
17 19 0.56
18 11 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATAATTATTTAATATTA
Found at i:14998 original size:26 final size:25
Alignment explanation
Indices: 14938--15000 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
14928 ATTAATTAAT
14938 ATTAATA-AATTATATATTATTATA
1 ATTAATATAATTATATATTATTATA
*
14962 ATTTATAATAATTATATACTATATTATA
1 ATTAAT-ATAATTATATA-T-TATTATA
14990 A-TAATATAATT
1 ATTAATATAATT
15001 CTCCTTAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 5 0.15
25 1 0.03
26 15 0.45
27 4 0.12
28 8 0.24
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
ATTAATATAATTATATATTATTATA
Found at i:15366 original size:21 final size:21
Alignment explanation
Indices: 15319--15373 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
15309 ATTTATAATA
15319 AACAATAATTTATTATATTCAT
1 AACAAT-ATTTATTATATTCAT
*
15341 -GCAATATTTATTATACTT-AT
1 AACAATATTTATTATA-TTCAT
15361 AACAATAGTTTAT
1 AACAATA-TTTAT
15374 ATAATAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 12 0.43
21 11 0.39
22 5 0.18
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (21 bp):
AACAATATTTATTATATTCAT
Found at i:15417 original size:13 final size:13
Alignment explanation
Indices: 15399--15424 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15389 ATACTTTATT
15399 AATAATTAGATTA
1 AATAATTAGATTA
15412 AATAATTAGATTA
1 AATAATTAGATTA
15425 TTTGTATAAT
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:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (13 bp):
AATAATTAGATTA
Found at i:16290 original size:28 final size:28
Alignment explanation
Indices: 16259--16343 Score: 66
Period size: 28 Copynumber: 2.9 Consensus size: 28
16249 ACAATAATCG
16259 TTATTAAAACTATTTAATTATTTATTAA
1 TTATTAAAACTATTTAATTATTTATTAA
* * *
16287 TTATAATAAACT-TTTTATAATTTATATAA
1 TTATTA-AAACTATTTAATTATTTAT-TAA
* *
16316 CTATATAAAA-TATTATAAATTATCTATT
1 TTAT-TAAAACTATT-T-AATTATTTATT
16344 TTAGTTATAA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
28 17 0.40
29 16 0.37
30 3 0.07
31 7 0.16
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.51
Consensus pattern (28 bp):
TTATTAAAACTATTTAATTATTTATTAA
Found at i:16922 original size:14 final size:13
Alignment explanation
Indices: 16905--16946 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
16895 TTTATTATGA
16905 TTATATTAATTTAT
1 TTATATT-ATTTAT
16919 TTATATTATTTA-
1 TTATATTATTTAT
**
16931 GAATATTATTTAT
1 TTATATTATTTAT
16944 TTA
1 TTA
16947 AATAATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATTATTTAT
Found at i:17468 original size:18 final size:18
Alignment explanation
Indices: 17428--17488 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
17418 TTTTATTTAT
* *
17428 ATTAATTAACATTTAATA
1 ATTAATTAATATTGAATA
* *
17446 TTTAATTAATATTGATTA
1 ATTAATTAATATTGAATA
**
17464 ATTAATTAAT-TAAAATA
1 ATTAATTAATATTGAATA
17481 ATTAATTA
1 ATTAATTA
17489 TAATAATAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
17 12 0.34
18 23 0.66
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
ATTAATTAATATTGAATA
Found at i:17484 original size:13 final size:13
Alignment explanation
Indices: 17466--17495 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17456 ATTGATTAAT
17466 TAATTAATTAAAA
1 TAATTAATTAAAA
*
17479 TAATTAATTATAA
1 TAATTAATTAAAA
17492 TAAT
1 TAAT
17496 AAAATAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATTAATTAAAA
Found at i:17484 original size:21 final size:21
Alignment explanation
Indices: 17448--17516 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
17438 ATTTAATATT
* *
17448 TAATTAATATTGATTAATTAA
1 TAATTAAAATAGATTAATTAA
17469 TTAATTAAAATA-ATTAATT-A
1 -TAATTAAAATAGATTAATTAA
17489 TAATAATAAAATAGA--AATTAA
1 TAAT--TAAAATAGATTAATTAA
17510 TAATTAA
1 TAATTAA
17517 TATTTTTAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 7 0.17
20 5 0.12
21 19 0.46
22 10 0.24
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (21 bp):
TAATTAAAATAGATTAATTAA
Found at i:17973 original size:30 final size:33
Alignment explanation
Indices: 17934--18021 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 33
17924 ACAATTAAGT
17934 TAATAATTATTTTAATAAT-TTATAA-TACTAA
1 TAATAATTATTTTAATAATATTATAATTACTAA
* *
17965 TAAT-ATTA---TAATTATCTTAATAATTACTAA
1 TAATAATTATTTTAATAATATT-ATAATTACTAA
*
17995 TAATGATTATCTTTAATTAATATTATA
1 TAATAATTAT-TTTAA-TAATATTATA
18022 TAATGGAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
27 6 0.13
28 2 0.04
29 4 0.09
30 14 0.31
31 8 0.18
35 6 0.13
36 5 0.11
ACGTcount: A:0.45, C:0.05, G:0.01, T:0.49
Consensus pattern (33 bp):
TAATAATTATTTTAATAATATTATAATTACTAA
Found at i:17989 original size:12 final size:12
Alignment explanation
Indices: 17933--18025 Score: 57
Period size: 12 Copynumber: 7.7 Consensus size: 12
17923 AACAATTAAG
*
17933 TTAATAATTATT
1 TTAATAATTATA
17945 TTAATAATTTATA
1 TTAATAA-TTATA
* * *
17958 ATACTAATAATA
1 TTAATAATTATA
*
17970 TT-ATAATTATC
1 TTAATAATTATA
17981 TTAATAATTACTA
1 TTAATAATTA-TA
* * *
17994 ATAATGATTATC
1 TTAATAATTATA
18006 TT--TAATTAATA
1 TTAATAATT-ATA
18017 TTATATAAT
1 TTA-ATAAT
18026 GGAATTTAAT
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
10 4 0.07
11 12 0.20
12 21 0.36
13 18 0.31
14 4 0.07
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (12 bp):
TTAATAATTATA
Found at i:18234 original size:21 final size:22
Alignment explanation
Indices: 18196--18239 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
18186 ATATGAGTGG
**
18196 AATATAGATTATCTATATTTAT
1 AATATAGATTATAAATATTTAT
18218 AATATAG-TTATAAATATTTAT
1 AATATAGATTATAAATATTTAT
18239 A
1 A
18240 TTGTAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (22 bp):
AATATAGATTATAAATATTTAT
Found at i:19241 original size:12 final size:12
Alignment explanation
Indices: 19199--19242 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
19189 ATTTATAATC
19199 TTAATTAT-AAA
1 TTAATTATAAAA
*
19210 TTAATTACAAAA
1 TTAATTATAAAA
19222 TTAA-TATAAAA
1 TTAATTATAAAA
*
19233 ATAATTATAA
1 TTAATTATAA
19243 TTATTTGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 16 0.57
12 12 0.43
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (12 bp):
TTAATTATAAAA
Found at i:19296 original size:17 final size:19
Alignment explanation
Indices: 19250--19297 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
19240 TAATTATTTG
19250 TTTAATAATTTAATTAATA
1 TTTAATAATTTAATTAATA
19269 TTATATGATAATTT-ATTAA-A
1 TT-TA--ATAATTTAATTAATA
19289 TTTAATAAT
1 TTTAATAAT
19298 AAGCTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 5 0.19
19 4 0.15
20 5 0.19
21 5 0.19
22 7 0.27
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATAATTTAATTAATA
Found at i:19775 original size:30 final size:29
Alignment explanation
Indices: 19715--19771 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
19705 TTAACATTTG
*
19715 AAAAATTAAAAATAACTGTTAATTGTATT
1 AAAAATTAAAAATAACTGTTAATAGTATT
19744 AAAAATTAATAAAT-A-TGTTAATAG-ATT
1 AAAAATTAA-AAATAACTGTTAATAGTATT
19771 A
1 A
19772 TTAATTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 8 0.31
29 10 0.38
30 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (29 bp):
AAAAATTAAAAATAACTGTTAATAGTATT
Found at i:20493 original size:27 final size:28
Alignment explanation
Indices: 20440--20497 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
20430 TAATATGTTA
**
20440 TTAAATATTAATAAAATTATATTTAATT
1 TTAAATATTAATAAAATTATAAATAATT
20468 TTAAATA-TAATAAAATT-TAAAATAATT
1 TTAAATATTAATAAAATTAT-AAATAATT
20495 TTA
1 TTA
20498 TACTAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 1 0.04
27 19 0.70
28 7 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTAAATATTAATAAAATTATAAATAATT
Found at i:20663 original size:24 final size:24
Alignment explanation
Indices: 20614--20673 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
20604 AATAAGACCA
*
20614 TATAATTAATATAATAAATTGTAT
1 TATAATTAATATAATAAATTGAAT
20638 TATAATTAATATAATAAATCT-AAT
1 TATAATTAATATAATAAAT-TGAAT
*
20662 TATTAACTAATA
1 TA-TAATTAATA
20674 ATATTAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (24 bp):
TATAATTAATATAATAAATTGAAT
Found at i:20724 original size:22 final size:22
Alignment explanation
Indices: 20681--20732 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
20671 ATAATATTAA
* *
20681 TAATATTATAATTAATTTAATT
1 TAATATAATAATTAATTCAATT
20703 TAATATAATAATT-ATATCAATT
1 TAATATAATAATTAAT-TCAATT
*
20725 TATTATAA
1 TAATATAA
20733 AAACATATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATATAATAATTAATTCAATT
Found at i:21616 original size:14 final size:14
Alignment explanation
Indices: 21582--21620 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
21572 ATAATCATCA
21582 AATAAT-ATTAATT
1 AATAATAATTAATT
21595 AATAAATAATTAATT
1 AAT-AATAATTAATT
*
21610 AGTAATAATTA
1 AATAATAATTA
21621 GTATAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (14 bp):
AATAATAATTAATT
Found at i:21631 original size:35 final size:35
Alignment explanation
Indices: 21591--21679 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 35
21581 AAATAATATT
21591 AATTAATAAATAATTAATTAGTAATAATTAGTATA
1 AATTAATAAATAATTAATTAGTAATAATTAGTATA
* * * *
21626 AATTAAAAAATAATT-ATTAGT-TTAATTATTCTA
1 AATTAATAAATAATTAATTAGTAATAATTAGTATA
*
21659 AA-TAATAAACAATTAA-TAGTA
1 AATTAATAAATAATTAATTAGTA
21680 TTAGTTTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
32 14 0.30
33 12 0.26
34 6 0.13
35 14 0.30
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.39
Consensus pattern (35 bp):
AATTAATAAATAATTAATTAGTAATAATTAGTATA
Done.