Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 4 of 193
Found at i:1411920 original size:56 final size:56
Alignment explanation
Indices: 1411836--1411952 Score: 130
Period size: 56 Copynumber: 2.1 Consensus size: 56
1411826 CTTTGGTTAC
** * * *
1411836 TGTTTTTATGTTGTTTTTGTTGTAATTTTT-CTTTCTGTTTTTGTTGCTATTTTTAT
1 TGTTTTTATGTTGTTTTTCCTGTAATTTTTAC-TGCTATTTTGGTTGCTATTTTTAT
* * *
1411892 TGTTTTTAATGTTG-TTTTCCTGTTATTTTTACTGCTATTTTGGTTGTTATTTTTGT
1 TGTTTTT-ATGTTGTTTTTCCTGTAATTTTTACTGCTATTTTGGTTGCTATTTTTAT
1411948 TGTTT
1 TGTTT
1411953 AGATGTTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
56 44 0.86
57 7 0.14
ACGTcount: A:0.09, C:0.06, G:0.15, T:0.69
Consensus pattern (56 bp):
TGTTTTTATGTTGTTTTTCCTGTAATTTTTACTGCTATTTTGGTTGCTATTTTTAT
Found at i:1412162 original size:38 final size:38
Alignment explanation
Indices: 1412079--1412163 Score: 93
Period size: 38 Copynumber: 2.2 Consensus size: 38
1412069 TAATATAAAT
* * * *
1412079 TTTTTTAATGTATTTTAAATTTATTTATTTTTTAATGT
1 TTTTTTAATGTATTTTAAATGTATTTATATATTAATGA
1412117 TTGTTTTAATGT-TTTTAAATGTATTTGATATATTATAT-A
1 TT-TTTTAATGTATTTTAAATGTATTT-ATATATTA-ATGA
1412156 TTTTTTAA
1 TTTTTTAA
1412164 ATTTGTTGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
38 21 0.52
39 17 0.43
40 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (38 bp):
TTTTTTAATGTATTTTAAATGTATTTATATATTAATGA
Found at i:1415859 original size:15 final size:15
Alignment explanation
Indices: 1415839--1415891 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
1415829 TCATGTTTCT
1415839 GAATTTTTTATGGGA
1 GAATTTTTTATGGGA
**
1415854 GAATTTTGCAT-GGA
1 GAATTTTTTATGGGA
1415868 -AATTTTTTTATGGGA
1 GAA-TTTTTTATGGGA
*
1415883 AAATTTTTT
1 GAATTTTTT
1415892 CTCCAGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 2 0.06
14 9 0.29
15 18 0.58
16 2 0.06
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (15 bp):
GAATTTTTTATGGGA
Found at i:1416566 original size:22 final size:23
Alignment explanation
Indices: 1416541--1416586 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
1416531 AATGAAAGAA
1416541 AAAAGAG-ACTCGAAACAAAAGT
1 AAAAGAGAACTCGAAACAAAAGT
*
1416563 AAAAGAGAAATTCGAAACAAAAGT
1 AAAAGAG-AACTCGAAACAAAAGT
1416587 GACTAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
24 14 0.67
ACGTcount: A:0.61, C:0.11, G:0.17, T:0.11
Consensus pattern (23 bp):
AAAAGAGAACTCGAAACAAAAGT
Found at i:1420510 original size:177 final size:175
Alignment explanation
Indices: 1420201--1420580 Score: 512
Period size: 177 Copynumber: 2.2 Consensus size: 175
1420191 TTGATGTTTT
* * ** * *
1420201 AGTATGCAATCCCTAATCAACCTCAAAACAGTCTTTTGTATGGTATTGATGCAATGTATAGTTTA
1 AGTATCCAATCCCTAATAAACCTCAAAACAGTCTTTTGTATGGTATTGACACAATGCAGAGTTTA
* * * * *
1420266 CAGTTCTTTGACTCAAACATACGATGAGGCCATCTAACTTCACCGAGAATATTGTAAAAGTAACC
66 AAGTTCTTTGACTCAAACAAACAATGAGGCCATCCAACTTCACCGAGAATATTGTAAAAGAAACC
* **
1420331 ACCTTGGACGACAG-AAGTTGTATCGAAAAAGTTTAACTCGACTGCC
131 ACCTTGGACGACAGAAAGTCGTATCGAAAAAGTTTAA--AAACTGCC
* *
1420377 AGTATCCAAATCCCTAATAAACCTCAAGACAGTCTTTTGTATGGTATTGACACAATGCAGGGTTT
1 AGTATCC-AATCCCTAATAAACCTCAAAACAGTCTTTTGTATGGTATTGACACAATGCAGAGTTT
* * *
1420442 AAAGTTCTTTGACTCAAAGAAACAATGAGGCTATCCAACTTCACCGTGAATATTGTAAAAGAAAC
65 AAAGTTCTTTGACTCAAACAAACAATGAGGCCATCCAACTTCACCGAGAATATTGTAAAAGAAAC
* *
1420507 CACCTTGGATGACAGAAAGTCGTATTGAAAAAGTTTAAAAACTGCC
130 CACCTTGGACGACAGAAAGTCGTATCGAAAAAGTTTAAAAACTGCC
* *
1420553 AGTATGCAAT-CCTAATAAACCTCGAAAC
1 AGTATCCAATCCCTAATAAACCTCAAAAC
1420581 GGTTTTCTGC
Statistics
Matches: 178, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
174 16 0.09
175 3 0.02
176 18 0.10
177 121 0.68
178 20 0.11
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (175 bp):
AGTATCCAATCCCTAATAAACCTCAAAACAGTCTTTTGTATGGTATTGACACAATGCAGAGTTTA
AAGTTCTTTGACTCAAACAAACAATGAGGCCATCCAACTTCACCGAGAATATTGTAAAAGAAACC
ACCTTGGACGACAGAAAGTCGTATCGAAAAAGTTTAAAAACTGCC
Found at i:1421825 original size:19 final size:19
Alignment explanation
Indices: 1421801--1421839 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1421791 TTCGTTTTAA
* *
1421801 GTATTTTTCGTCAAAATTC
1 GTATTTTCCATCAAAATTC
1421820 GTATTTTCCATCAAAATTC
1 GTATTTTCCATCAAAATTC
1421839 G
1 G
1421840 CCATTACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (19 bp):
GTATTTTCCATCAAAATTC
Found at i:1422580 original size:30 final size:31
Alignment explanation
Indices: 1422535--1422638 Score: 105
Period size: 30 Copynumber: 3.5 Consensus size: 31
1422525 AATTTTATAA
*
1422535 TTAGTCTCTGTATTTTACTCAACTTATAAAT
1 TTAGTCCCTGTATTTTACTCAACTTATAAAT
*
1422566 TTAGTCCCT-TATTTTA---AA-TTTTATAA-
1 TTAGTCCCTGTATTTTACTCAACTTATA-AAT
* *
1422592 TTAATCCCTGTATTTTACTCAACTTGTAAAT
1 TTAGTCCCTGTATTTTACTCAACTTATAAAT
*
1422623 TTAGT-CCTTTATTTTA
1 TTAGTCCCTGTATTTTA
1422639 TTAGTTTACC
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
26 12 0.20
27 11 0.18
30 21 0.35
31 16 0.27
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (31 bp):
TTAGTCCCTGTATTTTACTCAACTTATAAAT
Found at i:1422593 original size:57 final size:57
Alignment explanation
Indices: 1422524--1422638 Score: 194
Period size: 57 Copynumber: 2.0 Consensus size: 57
1422514 ATTACTGGTC
* *
1422524 AAATTTTATAATTAGTCTCTGTATTTTACTCAACTTATAAATTTAGTCCCTTATTTT
1 AAATTTTATAATTAATCCCTGTATTTTACTCAACTTATAAATTTAGTCCCTTATTTT
* *
1422581 AAATTTTATAATTAATCCCTGTATTTTACTCAACTTGTAAATTTAGTCCTTTATTTT
1 AAATTTTATAATTAATCCCTGTATTTTACTCAACTTATAAATTTAGTCCCTTATTTT
1422638 A
1 A
1422639 TTAGTTTACC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.50
Consensus pattern (57 bp):
AAATTTTATAATTAATCCCTGTATTTTACTCAACTTATAAATTTAGTCCCTTATTTT
Found at i:1428022 original size:16 final size:16
Alignment explanation
Indices: 1427987--1428031 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1427977 ATCTTTATTT
*
1427987 GAATAAATGTAGAGCGAA
1 GAATAAA-G-AGAACGAA
1428005 GAATAAAGAGAACGAA
1 GAATAAAGAGAACGAA
*
1428021 GAACAAAGAGA
1 GAATAAAGAGA
1428032 GCAATAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.68
17 1 0.04
18 7 0.28
ACGTcount: A:0.58, C:0.07, G:0.27, T:0.09
Consensus pattern (16 bp):
GAATAAAGAGAACGAA
Found at i:1428181 original size:20 final size:22
Alignment explanation
Indices: 1428148--1428191 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1428138 CCCACCATAT
1428148 CCCTTTCTCCTTTTT-ATTTTC
1 CCCTTTCTCCTTTTTAATTTTC
*
1428169 CCCTTTCT-GTTTTTAATTTTC
1 CCCTTTCTCCTTTTTAATTTTC
1428190 CC
1 CC
1428192 ACCTCCCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.07, C:0.32, G:0.02, T:0.59
Consensus pattern (22 bp):
CCCTTTCTCCTTTTTAATTTTC
Found at i:1429738 original size:22 final size:20
Alignment explanation
Indices: 1429708--1429750 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
1429698 TTAGGAATGA
1429708 TAGGGAGTTAGATTGTTAGGTT
1 TAGGGAGTT-GATT-TTAGGTT
* *
1429730 TAGGTAGTTTATTTTAGGTT
1 TAGGGAGTTGATTTTAGGTT
1429750 T
1 T
1429751 TGTTTTTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (20 bp):
TAGGGAGTTGATTTTAGGTT
Found at i:1431276 original size:29 final size:30
Alignment explanation
Indices: 1431222--1431286 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1431212 TTTAATGCGA
* *
1431222 AATTGTATACATAAATTTTGATTTTG-TCT
1 AATTTTATACATAAATTTCGATTTTGATCT
*
1431251 AATTTTATACATGAAATTTCGA-TTTGATTT
1 AATTTTATACAT-AAATTTCGATTTTGATCT
1431281 AATTTT
1 AATTTT
1431287 CACAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.52
Consensus pattern (30 bp):
AATTTTATACATAAATTTCGATTTTGATCT
Found at i:1433890 original size:20 final size:22
Alignment explanation
Indices: 1433857--1433900 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
1433847 AGCTTCTTTA
* *
1433857 TTTTTTTCTTTAAT-TTTA-AT
1 TTTTTTTATATAATATTTATAT
1433877 TTTTTTTATATAATATTTATAT
1 TTTTTTTATATAATATTTATAT
1433899 TT
1 TT
1433901 ATCTATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 12 0.60
21 4 0.20
22 4 0.20
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTTTATATAATATTTATAT
Found at i:1434519 original size:21 final size:22
Alignment explanation
Indices: 1434484--1434524 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1434474 TTCAAAATTT
*
1434484 ATTTTGATATTTGAGCTTTTCA
1 ATTTTGATACTTGAGCTTTTCA
*
1434506 ATTTT-ATACTTGAGTTTTT
1 ATTTTGATACTTGAGCTTTT
1434525 TTTTCCTTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.22, C:0.07, G:0.12, T:0.59
Consensus pattern (22 bp):
ATTTTGATACTTGAGCTTTTCA
Found at i:1435570 original size:31 final size:31
Alignment explanation
Indices: 1435475--1435591 Score: 84
Period size: 31 Copynumber: 3.9 Consensus size: 31
1435465 TAATTATAAC
* * * *
1435475 ATTTGGTATCTAAACTTGATAATTTTTCCTA
1 ATTTGGTACCTAAACTTAACACTTTTTCCTA
* **
1435506 ATTTGGTACCTAAA-TT----TTTTTTGGTGCA
1 ATTTGGTACCTAAACTTAACACTTTTTCCT--A
1435534 ATTTGGTA-CTCAAACTTAACACTTTTTCCTA
1 ATTTGGTACCT-AAACTTAACACTTTTTCCTA
* *
1435565 ATTTGGTACCTAACCTTGACACTTTTT
1 ATTTGGTACCTAAACTTAACACTTTTT
1435592 TAGAAGTTGG
Statistics
Matches: 68, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
26 6 0.09
27 2 0.03
28 12 0.18
29 2 0.03
30 2 0.03
31 36 0.53
32 2 0.03
33 6 0.09
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTAACACTTTTTCCTA
Found at i:1435925 original size:59 final size:59
Alignment explanation
Indices: 1435837--1436007 Score: 225
Period size: 59 Copynumber: 2.9 Consensus size: 59
1435827 TTGAATCTAA
** * * * *
1435837 AAAAAAAACTTAGGTACCAAAATAGGAAAAAATATCAAGTTCAAGTACCAAATTGGGTT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTC
* * * * *
1435896 AAAAAAAGTTTAGGTACCGAATTAAGAAAAAGCGTCAAGTTCAAGTACTAAATTTGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTC
* *
1435955 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGCCAAGTTCAGGTACCAAAT
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACCAAAT
1436008 ATTATATTAA
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 95 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.23
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTGTCAAGTTCAAGTACCAAATTGGGTC
Found at i:1436570 original size:159 final size:159
Alignment explanation
Indices: 1436281--1436596 Score: 598
Period size: 159 Copynumber: 2.0 Consensus size: 159
1436271 TTCACGTTTC
*
1436281 ATGTTCAGGTTTTGTAACTGTTCCTCTCAACAATGTTGTTTTCAAAGTTCAAACCTATATCTCCC
1 ATGTTCAGGGTTTGTAACTGTTCCTCTCAACAATGTTGTTTTCAAAGTTCAAACCTATATCTCCC
*
1436346 CTTGGAAGTGCATTGTGCCTTATCACTAGATCCAACTCTTGTTGGTGACGATTCACACAATTGAG
66 CTTGGAAGTGCATTGTGCCTTATCACTAGATCCAACCCTTGTTGGTGACGATTCACACAATTGAG
1436411 TAGTAATATTGAGAACCACTAGTGATTTT
131 TAGTAATATTGAGAACCACTAGTGATTTT
1436440 ATGTTCAGGGTTTGTAACTGTTCCTCTCAACAATGTTGTTTTCAAAGTTCAAACCTATATCTCCC
1 ATGTTCAGGGTTTGTAACTGTTCCTCTCAACAATGTTGTTTTCAAAGTTCAAACCTATATCTCCC
1436505 CTT-GAGAGTGCATTGTGCCTTATCACTAGATCCAACCCTTGTTGGTGACGATTCACACAATTGA
66 CTTGGA-AGTGCATTGTGCCTTATCACTAGATCCAACCCTTGTTGGTGACGATTCACACAATTGA
1436569 GTAGTAATATTGAGAACCACTAGTGATT
130 GTAGTAATATTGAGAACCACTAGTGATT
1436597 CTAACTTTAC
Statistics
Matches: 154, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
158 2 0.01
159 152 0.99
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (159 bp):
ATGTTCAGGGTTTGTAACTGTTCCTCTCAACAATGTTGTTTTCAAAGTTCAAACCTATATCTCCC
CTTGGAAGTGCATTGTGCCTTATCACTAGATCCAACCCTTGTTGGTGACGATTCACACAATTGAG
TAGTAATATTGAGAACCACTAGTGATTTT
Found at i:1440170 original size:32 final size:32
Alignment explanation
Indices: 1440129--1440192 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1440119 ATTAGAGGAC
1440129 CCCTTTGTAGACCTTACTAATTTTAGCTGTAA
1 CCCTTTGTAGACCTTACTAATTTTAGCTGTAA
1440161 CCCTTTGTAGACCTTACTAATTTTAGCTGTAA
1 CCCTTTGTAGACCTTACTAATTTTAGCTGTAA
1440193 AAATTGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (32 bp):
CCCTTTGTAGACCTTACTAATTTTAGCTGTAA
Found at i:1447147 original size:292 final size:286
Alignment explanation
Indices: 1446589--1447219 Score: 640
Period size: 292 Copynumber: 2.1 Consensus size: 286
1446579 CTTCAATGAT
*
1446589 ATTGTTTCCTTGTCAAGATGGAACTTGTTGAAAACCAACCTCTATGTGTGAATATTAAATAAAAG
1 ATTGTTTCCTTGTCAAGATGGAACATGTTGAAAACCAACCTCTATGTGTGAATATTAAATAAAAG
* *
1446654 CTCGAATAGTAGATTGATAAGAAATTTGATTCTTTTTAATCTATAATTTTAGATTTCAAATTTTG
66 CTCGAATAGTAGATTGATAAGAAATTTGATGCTTTTTAATCTATAATTTTAAATTTCAAATTTTG
* * **
1446719 GGTTTTGAAAAGTTTTAACTTTTGTATAAAAATTGGATTAATTTAATTTAAATTTAATCGAAATT
131 GATTTAGAAAAGTTTTAACTTTCATATAAAAATTGGATTAATTTAATTTAAATTTAATCGAAATT
* * *
1446784 TAATATAATTAATTGAAAGATTTCTTTTTAAGAAAAAAAACCCAACTTTCTCTTAACTTTCAATG
196 TAATATAATTAATTAAAAAAATTCTTTTTAAG--AAAAAACCCAAC-TTCTCTT-AC--TCAATG
1446849 AAAAAAAAGATTAGGGACCTTCTTTTAATGGC
255 AAAAAAAAGATTAGGGACCTTCTTTTAATGGC
* * * * * *
1446881 ATTGTTTTCTTGTCAAGATGGGACATGTTGAAAAGCAACCTCTTTTTGTGTATATTAAATAAAAG
1 ATTGTTTCCTTGTCAAGATGGAACATGTTGAAAACCAACCTCTATGTGTGAATATTAAATAAAAG
* * * * * *
1446946 CTCGAATAGTAG-TTTAGTAAGGAGTTTGATGCTTTTTAATTTGTAATTTTAAATTTTTAAATTT
66 CTCGAATAGTAGATTGA-TAAGAAATTTGATGCTTTTTAATCTATAATTTTAAA-TTTCAAATTT
* * * * * * * *
1447010 TGGATTTAGGAGAGTTTTATCTTTCATTTAAAGATTTGATTCAATTCTATTTTGAATTTAATCGA
129 TGGATTTAGAAAAGTTTTAACTTTCATATAAAAATTGGATT-AATT-TAATTTAAATTTAATCGA
* * *
1447075 AATTTAATGTAATTATTGAATATTAAAAAAAAATTC-TTTTAAG-AAAAACTCAACTTCTTCCTA
192 AATTTAA--T-ATAATT--A-ATT--AAAAAAATTCTTTTTAAGAAAAAACCCAACTTC-TCTTA
* ** * * *
1447138 -TGAAAAAAAAAAAAAGTGATTAGGGGCCTTTTCTTTCAATGAC
248 CT-CAATGAAAAAAAA--GATTAGGGACC--TTCTTTTAATGGC
* * *
1447181 ATTGTTTCCTTGTCAAGATTGAACATATTGAAAAACAAC
1 ATTGTTTCCTTGTCAAGATGGAACATGTTGAAAACCAAC
1447220 TTTTTTTTTT
Statistics
Matches: 277, Mismatches: 44, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
291 3 0.01
292 100 0.36
293 40 0.14
294 4 0.01
295 24 0.09
296 10 0.04
297 1 0.00
298 19 0.07
299 13 0.05
300 46 0.17
301 3 0.01
302 7 0.03
303 7 0.03
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (286 bp):
ATTGTTTCCTTGTCAAGATGGAACATGTTGAAAACCAACCTCTATGTGTGAATATTAAATAAAAG
CTCGAATAGTAGATTGATAAGAAATTTGATGCTTTTTAATCTATAATTTTAAATTTCAAATTTTG
GATTTAGAAAAGTTTTAACTTTCATATAAAAATTGGATTAATTTAATTTAAATTTAATCGAAATT
TAATATAATTAATTAAAAAAATTCTTTTTAAGAAAAAACCCAACTTCTCTTACTCAATGAAAAAA
AAGATTAGGGACCTTCTTTTAATGGC
Found at i:1447869 original size:20 final size:21
Alignment explanation
Indices: 1447832--1447876 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1447822 CTATCAAATA
*
1447832 AAAAAAATTAAAATTCATACT
1 AAAAAAATTAAAATTCATAAT
*
1447853 AAAAAGATTAAAA-TCATAAT
1 AAAAAAATTAAAATTCATAAT
1447873 AAAA
1 AAAA
1447877 TCAACAAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAAATTAAAATTCATAAT
Found at i:1452796 original size:31 final size:31
Alignment explanation
Indices: 1452761--1452824 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
1452751 TTACGTAATG
* * *
1452761 GTTATTAAAATATTTGATAATTTTTATTTAA
1 GTTATTAAAATATTTAAAAATTTCTATTTAA
* *
1452792 GTTATTTAATTATTTAAAAATTTCTATTTAA
1 GTTATTAAAATATTTAAAAATTTCTATTTAA
1452823 GT
1 GT
1452825 CAATTGGTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.55
Consensus pattern (31 bp):
GTTATTAAAATATTTAAAAATTTCTATTTAA
Found at i:1458062 original size:15 final size:16
Alignment explanation
Indices: 1458037--1458070 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1458027 AAAAAGTAAT
1458037 TTTATTATTTTAATAA
1 TTTATTATTTTAATAA
*
1458053 TTTA-TATTTTCATAA
1 TTTATTATTTTAATAA
1458068 TTT
1 TTT
1458071 TTAAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATTATTTTAATAA
Found at i:1470038 original size:31 final size:32
Alignment explanation
Indices: 1469981--1470043 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
1469971 ATTATGCTTA
1469981 AATTTAAGATTTAGTCTCCGTGTTTTTTTTTT
1 AATTTAAGATTTAGTCTCCGTGTTTTTTTTTT
* **
1470013 AATTTAAGATTTA-TTTTTGTGTTTTTTTTTT
1 AATTTAAGATTTAGTCTCCGTGTTTTTTTTTT
1470044 CTGATTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 15 0.54
32 13 0.46
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (32 bp):
AATTTAAGATTTAGTCTCCGTGTTTTTTTTTT
Found at i:1475258 original size:117 final size:118
Alignment explanation
Indices: 1475124--1475360 Score: 424
Period size: 118 Copynumber: 2.0 Consensus size: 118
1475114 TATCAATAAG
1475124 TAAATTACAATTAATTATATCATCTAAAAAAAA-AGAAAATATTCAATGTATTTATCGGAGCGAG
1 TAAATTACAATTAATTATATCATCTAAAAAAAAGAGAAAATATTCAATGTATTTATCGGAGCGAG
*
1475188 TCCAAAAATTAATTTTCTGCATTCTATAGATCTATT-AAAGAGTAGATGCTGAC
66 TCCAAAAATTAATCTTCTGCATTCTATAGATCTATTAAAAG-GTAGATGCTGAC
*
1475241 TAAATTACAATTAATTATATCATCTAAAAAAAAGAGAAAATTTTCAATGTATTTATCGGAGCGAG
1 TAAATTACAATTAATTATATCATCTAAAAAAAAGAGAAAATATTCAATGTATTTATCGGAGCGAG
*
1475306 TCCAGAAATTAATCTTCTGCATTCTATAGATCTATTAAAAGGTAGATGCTGAC
66 TCCAAAAATTAATCTTCTGCATTCTATAGATCTATTAAAAGGTAGATGCTGAC
1475359 TA
1 TA
1475361 CGAGTTTTAA
Statistics
Matches: 115, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
117 33 0.29
118 78 0.68
119 4 0.03
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (118 bp):
TAAATTACAATTAATTATATCATCTAAAAAAAAGAGAAAATATTCAATGTATTTATCGGAGCGAG
TCCAAAAATTAATCTTCTGCATTCTATAGATCTATTAAAAGGTAGATGCTGAC
Found at i:1477092 original size:2 final size:2
Alignment explanation
Indices: 1477085--1477141 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1477075 CAAGAAGCAA
1477085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1477127 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1477142 GCTAATTCCC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1478530 original size:2 final size:2
Alignment explanation
Indices: 1478523--1478588 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
1478513 ACTTATTAGG
1478523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1478565 AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
1478589 TTGGGTAGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1481097 original size:59 final size:59
Alignment explanation
Indices: 1480895--1481243 Score: 510
Period size: 58 Copynumber: 5.9 Consensus size: 59
1480885 GAAGAAACGA
* * * * * *
1480895 TGAAATCGGGGTTGAAAACGAGACTTTTGGATA-TCCGGGGGCAAAATGGTAA-TTTTGG
1 TGAAATCGGGGTTAAAAATG-GAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
*
1480953 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGG-AAATTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* *
1481011 TAAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
1481070 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* *
1481129 TGAAATTGGGGTT-AAAATGGAATTTTAGG-AAGTTTGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTT-GGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
* * *
1481187 TGAAATCGGTGTTAAAAATGGAATTTTGGAAAGTTTGAGGCGTAAAATGGTAATTTT
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCG-GGGGTAAAATGGTAATTTT
1481244 CGGACAGTCT
Statistics
Matches: 268, Mismatches: 16, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
57 12 0.04
58 139 0.52
59 99 0.37
60 18 0.07
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (59 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
Found at i:1481102 original size:117 final size:117
Alignment explanation
Indices: 1480897--1481243 Score: 495
Period size: 117 Copynumber: 3.0 Consensus size: 117
1480887 AGAAACGATG
** * * * *
1480897 AAATCGGGGTTGAAAACGAGACTTTTGGATA-TCCGGGGGCAAAATGGTAA-TTTTGGTGAAATC
1 AAATCGGGGTT-AAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATC
1480960 GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGAAATTTTGGTA
65 GGGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGAAATTTTGGTA
1481013 AAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCG
1 AAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCG
* *
1481078 GGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTG
66 GGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGG-AAATTTTGGTA
* * *
1481131 AAATTGGGGTT-AAAATGGAATTTTAGG-AAGTTTGGGGGTAAAATGGTAATTTTTGGTGAAATC
1 AAATCGGGGTTAAAAATAGAATTTT-GGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATC
* * * *
1481194 GGTGTTAAAAATGGAATTTTGGAAAGTTTGAGGCGTAAAATGGTAATTTT
65 GGGGTTAAAAATGGAATTTTGGAAAGTTCG-GGGGTAAAATGGAAATTTT
1481244 CGGACAGTCT
Statistics
Matches: 210, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
115 15 0.07
116 28 0.13
117 135 0.64
118 32 0.15
ACGTcount: A:0.33, C:0.04, G:0.31, T:0.32
Consensus pattern (117 bp):
AAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGGTGAAATCG
GGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGAAATTTTGGTA
Found at i:1481935 original size:21 final size:19
Alignment explanation
Indices: 1481905--1481951 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1481895 TAAGGCCCTT
*
1481905 TTTTCTTCTTTTTCATTTCA
1 TTTTCTTCTTGTT-ATTTCA
*
1481925 TTTTCTCTCTTGTTATTTCG
1 TTTTCT-TCTTGTTATTTCA
1481945 TTTTCTT
1 TTTTCTT
1481952 TTTCTTTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 17 0.71
21 6 0.25
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.70
Consensus pattern (19 bp):
TTTTCTTCTTGTTATTTCA
Found at i:1481996 original size:24 final size:24
Alignment explanation
Indices: 1481965--1482010 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1481955 CTTTTTCTTT
1481965 TAAATCCTTTTTTAT-TTTAAAAC
1 TAAATCCTTTTTTATCTTTAAAAC
*
1481988 TAAACTCCTTTTTTTTCTTTAAA
1 TAAA-TCCTTTTTTATCTTTAAA
1482011 GACCAAACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.54
Consensus pattern (24 bp):
TAAATCCTTTTTTATCTTTAAAAC
Found at i:1482018 original size:26 final size:24
Alignment explanation
Indices: 1481969--1482018 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1481959 TTCTTTTAAA
*
1481969 TCCTTTTTTATTTTAAAACTAAAC
1 TCCTTTTTTATTTTAAAACCAAAC
*
1481993 TCCTTTTTTTTCTTTAAAGACCAAAC
1 TCCTTTTTTAT-TTTAAA-ACCAAAC
1482019 CCAGATCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 6 0.27
26 6 0.27
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (24 bp):
TCCTTTTTTATTTTAAAACCAAAC
Found at i:1482313 original size:3 final size:3
Alignment explanation
Indices: 1482307--1482390 Score: 51
Period size: 3 Copynumber: 26.7 Consensus size: 3
1482297 TAATGGTTGA
* * * * *
1482307 TAT TAT TAAT TAT TAA TAT TAAT TAT AAT TAT AAA TATT TAT TAC TAT
1 TAT TAT T-AT TAT TAT TAT T-AT TAT TAT TAT TAT TA-T TAT TAT TAT
* * * *
1482355 TAT TAAT TAT TAT GAT TAT TAA TAA TAT TTT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1482391 ATGATATTTA
Statistics
Matches: 61, Mismatches: 16, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
3 50 0.82
4 11 0.18
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:1482335 original size:6 final size:7
Alignment explanation
Indices: 1482308--1482377 Score: 67
Period size: 7 Copynumber: 10.3 Consensus size: 7
1482298 AATGGTTGAT
1482308 ATTATTA
1 ATTATTA
1482315 ATTATTA
1 ATTATTA
1482322 A-TATTA
1 ATTATTA
1482328 ATTA-TA
1 ATTATTA
1482334 ATTA-TA
1 ATTATTA
* *
1482340 AATATTT
1 ATTATTA
*
1482347 ATTACT-
1 ATTATTA
1482353 ATTATTA
1 ATTATTA
1482360 ATTATTA
1 ATTATTA
1482367 TGATTATTA
1 --ATTATTA
1482376 AT
1 AT
1482378 AATATTTTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
6 22 0.42
7 24 0.45
9 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (7 bp):
ATTATTA
Found at i:1482337 original size:19 final size:19
Alignment explanation
Indices: 1482307--1482383 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
1482297 TAATGGTTGA
*
1482307 TATTATTAATTATTAATAT
1 TATTACTAATTATTAATAT
*
1482326 TAATTA-TAATTATAAATATT
1 T-ATTACTAATTATTAATA-T
1482346 TATTACT-ATTATT-A-AT
1 TATTACTAATTATTAATAT
* *
1482362 TATTA-TGATTATTAATAA
1 TATTACTAATTATTAATAT
1482380 TATT
1 TATT
1482384 TTTATTAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 1 0.02
16 12 0.24
17 2 0.04
18 6 0.12
19 21 0.43
20 7 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (19 bp):
TATTACTAATTATTAATAT
Found at i:1482390 original size:15 final size:15
Alignment explanation
Indices: 1482370--1482399 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1482360 ATTATTATGA
1482370 TTATTAATAATATTT
1 TTATTAATAATATTT
*
1482385 TTATTAATGATATTT
1 TTATTAATAATATTT
1482400 ATGAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (15 bp):
TTATTAATAATATTT
Found at i:1483101 original size:11 final size:11
Alignment explanation
Indices: 1483086--1483167 Score: 89
Period size: 11 Copynumber: 7.4 Consensus size: 11
1483076 ACAAATAATA
1483086 TTAAATTTAAA-
1 TTAAA-TTAAAT
*
1483097 TTAAATTCAAAC
1 TTAAATT-AAAT
1483109 TTAAATTAAAT
1 TTAAATTAAAT
1483120 TTAAA-TAAAT
1 TTAAATTAAAT
1483130 TTAAATTTAAA-
1 TTAAA-TTAAAT
1483141 TTAAATTAAAAT
1 TTAAATT-AAAT
*
1483153 TTAAAATAAAT
1 TTAAATTAAAT
1483164 TTAA
1 TTAA
1483168 TTTCAAAGTA
Statistics
Matches: 63, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
10 14 0.22
11 32 0.51
12 17 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:1483114 original size:17 final size:16
Alignment explanation
Indices: 1483086--1483181 Score: 104
Period size: 17 Copynumber: 5.8 Consensus size: 16
1483076 ACAAATAATA
1483086 TTAAATTTAAATTAAAT
1 TTAAA-TTAAATTAAAT
*
1483103 TCAAACTTAAATTAAAT
1 TTAAA-TTAAATTAAAT
1483120 TTAAA-TAAATTTAAAT
1 TTAAATTAAA-TTAAAT
1483136 TTAAATTAAATTAAAAT
1 TTAAATTAAATT-AAAT
* *
1483153 TTAAAATAAATTTAAT
1 TTAAATTAAATTAAAT
*
1483169 TTCAAAGTAAATT
1 TT-AAATTAAATT
1483182 CTAAAACGGT
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.06
16 18 0.26
17 47 0.68
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (16 bp):
TTAAATTAAATTAAAT
Found at i:1483134 original size:44 final size:45
Alignment explanation
Indices: 1483068--1483167 Score: 141
Period size: 44 Copynumber: 2.2 Consensus size: 45
1483058 ATTGGACATT
*
1483068 TTAAATTTACAAATAATATTAAATTTAAATTAAATTCAAACTTAAA
1 TTAAATTTA-AAATAATATTAAATTTAAATTAAATTAAAACTTAAA
*
1483114 TTAAATTT-AAATAA-ATTTAAATTTAAATTAAATTAAAATTTAAA
1 TTAAATTTAAAATAATA-TTAAATTTAAATTAAATTAAAACTTAAA
*
1483158 ATAAATTTAA
1 TTAAATTTAA
1483168 TTTCAAAGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
43 1 0.02
44 39 0.80
45 1 0.02
46 8 0.16
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (45 bp):
TTAAATTTAAAATAATATTAAATTTAAATTAAATTAAAACTTAAA
Found at i:1483180 original size:28 final size:29
Alignment explanation
Indices: 1483131--1483187 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
1483121 TAAATAAATT
*
1483131 TAAATTTAAATTAAATTAAAATT-TAAAA
1 TAAATTTAAATTAAAGTAAAATTCTAAAA
*
1483159 TAAATTTAATTTCAAAGT-AAATTCTAAAA
1 TAAATTTAAATT-AAAGTAAAATTCTAAAA
1483188 CGGTTTGGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAATTTAAATTAAAGTAAAATTCTAAAA
Found at i:1485709 original size:23 final size:22
Alignment explanation
Indices: 1485660--1485716 Score: 105
Period size: 22 Copynumber: 2.5 Consensus size: 22
1485650 TATTTAAAGG
1485660 GATAAAGATCATACCTAAAAAA
1 GATAAAGATCATACCTAAAAAA
1485682 GATAAAGATCATACCTAAAAAA
1 GATAAAGATCATACCTAAAAAA
1485704 GAATAAAGATCAT
1 G-ATAAAGATCAT
1485717 TTAATAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.58, C:0.12, G:0.11, T:0.19
Consensus pattern (22 bp):
GATAAAGATCATACCTAAAAAA
Found at i:1489914 original size:28 final size:29
Alignment explanation
Indices: 1489860--1489914 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1489850 AATTATTATT
* * *
1489860 AAATGATTAAATTATACTTTGACCTCTTA
1 AAATGATTAAATTACACTTTAAACTCTTA
1489889 AAATGATTAAATTACA-TTTAAACTCT
1 AAATGATTAAATTACACTTTAAACTCT
1489915 CATAAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (29 bp):
AAATGATTAAATTACACTTTAAACTCTTA
Found at i:1491284 original size:2 final size:2
Alignment explanation
Indices: 1491277--1491306 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1491267 TTATTCTGGC
1491277 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
1491307 TTATGCATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1491505 original size:17 final size:17
Alignment explanation
Indices: 1491480--1491524 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
1491470 CCAACAGAAT
1491480 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* *
1491497 TTAAGTTTATTTTAAAT
1 TTAAATTTATTTTAAAA
1491514 TTAAATTTATT
1 TTAAATTTATT
1491525 AAATTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:1492245 original size:19 final size:19
Alignment explanation
Indices: 1492221--1492268 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1492211 ATAGTGATAG
*
1492221 TAATAAATTTTTTTAATAA
1 TAATAAATATTTTTAATAA
*
1492240 TAATAAATATTTTTGATAA
1 TAATAAATATTTTTAATAA
1492259 TAAT-AATATT
1 TAATAAATATT
1492269 AATAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TAATAAATATTTTTAATAA
Found at i:1493400 original size:60 final size:59
Alignment explanation
Indices: 1493336--1493524 Score: 215
Period size: 60 Copynumber: 3.2 Consensus size: 59
1493326 CTAAAAATTA
* * *
1493336 CATTTTAACCCCCAAAACTTTCCAAAAATTACCATTTTACTCTCGAATATCCAAAAAATC
1 CATTTTGACCCCC-AAACTTTCTAAAAATTACCATTTTACCCTCGAATATCCAAAAAATC
** * *
1493396 CATTTTTGA--CCCGTACTTTCTAAAAATTACCATTTTACCCTC-AAAATTCAAAAAAATTC
1 CA-TTTTGACCCCCAAACTTTCTAAAAATTACCATTTTACCCTCGAATA-TCCAAAAAA-TC
* *
1493455 CATTTTGACCCCCAAACTTTCTAAAAATTACCATTTTACCCTCGAACT-TCCAAAGATTC
1 CATTTTGACCCCCAAACTTTCTAAAAATTACCATTTTACCCTCGAA-TATCCAAAAAATC
1493514 CATTTTTGACC
1 CA-TTTTGACC
1493525 TCAAAATGTC
Statistics
Matches: 108, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
57 3 0.03
58 40 0.37
59 11 0.10
60 47 0.44
61 7 0.06
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (59 bp):
CATTTTGACCCCCAAACTTTCTAAAAATTACCATTTTACCCTCGAATATCCAAAAAATC
Found at i:1493451 original size:30 final size:30
Alignment explanation
Indices: 1493319--1493519 Score: 116
Period size: 30 Copynumber: 6.8 Consensus size: 30
1493309 AAAGGTCCTT
* * *
1493319 AAACTTTCTAAAAATTA-CATTTTAACCCCC
1 AAACATTCAAAAAATTACCATTTT-ACCCTC
* * *
1493349 AAAACTTTCCAAAAATTACCATTTTACTCTC
1 -AAACATTCAAAAAATTACCATTTTACCCTC
* * *
1493380 GAATATCCAAAAAA-T-CCATTTTTGACCCGT-
1 AAACATTCAAAAAATTACCA-TTTT-ACCC-TC
* *
1493410 --ACTTTCTAAAAATTACCATTTTACCCTC
1 AAACATTCAAAAAATTACCATTTTACCCTC
*
1493438 AAA-ATTCAAAAAAATT-CCATTTTGACCCCC
1 AAACATTC-AAAAAATTACCATTTT-ACCCTC
* *
1493468 AAACTTTCTAAAAATTACCATTTTACCCTC
1 AAACATTCAAAAAATTACCATTTTACCCTC
* * *
1493498 GAAC-TTCCAAAGATT-CCATTTT
1 AAACATTCAAAAAATTACCATTTT
1493520 TGACCTCAAA
Statistics
Matches: 135, Mismatches: 22, Indels: 29
0.73 0.12 0.16
Matches are distributed among these distances:
27 1 0.01
28 22 0.16
29 29 0.21
30 46 0.34
31 31 0.23
32 6 0.04
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (30 bp):
AAACATTCAAAAAATTACCATTTTACCCTC
Found at i:1493545 original size:118 final size:119
Alignment explanation
Indices: 1493328--1493547 Score: 293
Period size: 118 Copynumber: 1.9 Consensus size: 119
1493318 TAAACTTTCT
*
1493328 AAAAATTACATTTTAACCCCCAAAACTTTCCAAAAATTACCATTTTACTCTCGAATATCCAAAAA
1 AAAAATTACATTTTAACCCCCAAAACTTTCCAAAAATTACCATTTTACCCTCGAATATCCAAAAA
** * * *
1493393 ATCCATTTTTGACCCGTACTTTCTAAAAATTACCATTTTACCCTCAAAATTCAA
66 ATCCATTTTTGACCCAAAATGTCTAAAAAGTACCATTTTACCCTCAAAATTCAA
* * * *
1493447 AAAAATTCCATTTTGACCCCC-AAACTTTCTAAAAATTACCATTTTACCCTCGAACT-TCCAAAG
1 AAAAATTACATTTTAACCCCCAAAACTTTCCAAAAATTACCATTTTACCCTCGAA-TATCCAAAA
* *
1493510 ATTCCATTTTTGACCTCAAAATGTC-CAAAAGTACCATT
65 AATCCATTTTTGACC-CAAAATGTCTAAAAAGTACCATT
1493548 CCCCCCCCTG
Statistics
Matches: 87, Mismatches: 12, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
118 62 0.71
119 25 0.29
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (119 bp):
AAAAATTACATTTTAACCCCCAAAACTTTCCAAAAATTACCATTTTACCCTCGAATATCCAAAAA
ATCCATTTTTGACCCAAAATGTCTAAAAAGTACCATTTTACCCTCAAAATTCAA
Found at i:1495548 original size:22 final size:22
Alignment explanation
Indices: 1495523--1495565 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1495513 ACAATGATTG
1495523 AAAAATAAAAAAGAATT-GAACC
1 AAAAATAAAAAA-AATTCGAACC
*
1495545 AAAATTAAAAAAAATTCGAAC
1 AAAAATAAAAAAAATTCGAAC
1495566 TGAACGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.67, C:0.09, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAAAAATTCGAACC
Found at i:1497855 original size:5 final size:6
Alignment explanation
Indices: 1497812--1497855 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
1497802 TTTTTTTTTA
* *
1497812 AAATTT AAACTT -AATAT AAATTT AAATTT AAATTT AAA-TT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
1497856 GTCCAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 8 0.25
6 24 0.75
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (6 bp):
AAATTT
Found at i:1499870 original size:58 final size:58
Alignment explanation
Indices: 1499679--1499996 Score: 412
Period size: 59 Copynumber: 5.4 Consensus size: 58
1499669 CTTGAACTGT
1499679 CCAAAAATTA-CATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCC-GATTTCA
* * * *
1499737 CCAAAAATTACCATTTTATCCCTGAACTTTTCAAAATTCCATTTTTAACCCCGATTTCC
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAA-CCCGATTTCA
* * * *
1499796 CCAAAACTTACTATTTTACCCTCGAACTTTCCAAAATCCCA-TTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACC-CGATTTCA
* *
1499854 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAA-CCTCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTC-CATTTTTAA-CCCGATTTCA
* ** *
1499913 CCAAAAATTACCGTTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCTAATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCC-GATTTCA
1499971 CCAAAAATTA-CATTTTTACCCCCGAA
1 CCAAAAATTACCA-TTTTACCCCCGAA
1499997 AGTCAAAAAT
Statistics
Matches: 228, Mismatches: 23, Indels: 18
0.85 0.09 0.07
Matches are distributed among these distances:
57 8 0.04
58 90 0.39
59 124 0.54
60 6 0.03
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCGATTTCA
Found at i:1499889 original size:117 final size:115
Alignment explanation
Indices: 1499679--1499993 Score: 429
Period size: 117 Copynumber: 2.7 Consensus size: 115
1499669 CTTGAACTGT
1499679 CCAAAAATTACATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCTGATTTCACCAAAAA
1 CCAAAAATTACATTTTA-CCCCGAACTTTCCAAAATTCCA-TTTTAACCCTGATTTCACCAAAAA
* ** * * *
1499744 TTACCATTTTATCCCTGAACTTTTCAAAA-TTCCATTTTTAACCCCGATTTCC
64 TTACCATTTTACCCCCAAACTTTCCAAAACCT-CATTTTTAACCCCGATTTCA
* *
1499796 CCAAAACTTACTATTTTACCCTCGAACTTTCCAAAATCCCATTTTAA-CCTCGATTTCACCAAAA
1 CCAAAAATTAC-ATTTTACCC-CGAACTTTCCAAAATTCCATTTTAACCCT-GATTTCACCAAAA
1499860 ATTACCATTTTACCCCCAAACTTTCCAAAACCTCATTTTTAACCCCGATTTCA
63 ATTACCATTTTACCCCCAAACTTTCCAAAACCTCATTTTTAACCCCGATTTCA
* * *
1499913 CCAAAAATTACCGTTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCTAATTTCACCAAAAA
1 CCAAAAATTA-CATTTTACCCC-GAACTTTCCAAAATTCCATTTTAACCCTGATTTCACCAAAAA
1499978 TTA-CATTTTTACCCCC
64 TTACCA-TTTTACCCCC
1499994 GAAAGTCAAA
Statistics
Matches: 177, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
116 6 0.03
117 142 0.80
118 29 0.16
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (115 bp):
CCAAAAATTACATTTTACCCCGAACTTTCCAAAATTCCATTTTAACCCTGATTTCACCAAAAATT
ACCATTTTACCCCCAAACTTTCCAAAACCTCATTTTTAACCCCGATTTCA
Found at i:1504091 original size:48 final size:48
Alignment explanation
Indices: 1504020--1504118 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
1504010 AACTAGGGAC
1504020 AAAGGCAAGGGAGGCAGTCTCTAACCTTAGTGCCCCCTCTCAAGTGTG
1 AAAGGCAAGGGAGGCAGTCTCTAACCTTAGTGCCCCCTCTCAAGTGTG
1504068 AAAGGCAAGGGAGGCAGTCTCTAACCTTAGTGCCCCCTCTCAAGTGTG
1 AAAGGCAAGGGAGGCAGTCTCTAACCTTAGTGCCCCCTCTCAAGTGTG
1504116 AAA
1 AAA
1504119 TTATATGTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.20
Consensus pattern (48 bp):
AAAGGCAAGGGAGGCAGTCTCTAACCTTAGTGCCCCCTCTCAAGTGTG
Found at i:1508766 original size:2 final size:2
Alignment explanation
Indices: 1508761--1508787 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1508751 AAAAAACCGG
1508761 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
1508788 GACTAATTCA
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:1513968 original size:16 final size:18
Alignment explanation
Indices: 1513929--1513962 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1513919 AAAGTTTATA
1513929 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
1513946 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
1513963 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:1518858 original size:30 final size:31
Alignment explanation
Indices: 1518796--1518858 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
1518786 ATGAAGTATT
* *
1518796 AATTGAAAAGTTGCACTATTATATGGATTTA
1 AATTGAAAAGTTGCACTATGATATGAATTTA
*
1518827 AATTGAAAAGTTTCA-TATGATACT-AATTTA
1 AATTGAAAAGTTGCACTATGATA-TGAATTTA
1518857 AA
1 AA
1518859 AATATTGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.38
Consensus pattern (31 bp):
AATTGAAAAGTTGCACTATGATATGAATTTA
Found at i:1529614 original size:29 final size:28
Alignment explanation
Indices: 1529537--1529616 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 28
1529527 ACAATCTTTC
*
1529537 TATTTTTTAAAATTTTAAAATTTAATTTT
1 TATTTTTT-AAATTTAAAAATTTAATTTT
* *
1529566 TA-TATTTATATTTGTAAAAATTTAATTTTT
1 TATTTTTTA-AATT-TAAAAATTTAA-TTTT
*
1529596 TATTTTTTAAATTTCAAAATT
1 TATTTTTTAAATTTAAAAATT
1529617 CAAGTTAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
27 1 0.02
28 7 0.17
29 19 0.46
30 9 0.22
31 5 0.12
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (28 bp):
TATTTTTTAAATTTAAAAATTTAATTTT
Found at i:1529765 original size:29 final size:27
Alignment explanation
Indices: 1529714--1529767 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
1529704 ATAATAGCGG
* *
1529714 TAAAAATTAGATTAGATTTTTAAAATC
1 TAAAAATTAGATTAAATTCTTAAAATC
1529741 TAAAAATTAAAGATTAAATTCTTAAAA
1 TAAAAATT--AGATTAAATTCTTAAAA
1529768 ATATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
29 15 0.65
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (27 bp):
TAAAAATTAGATTAAATTCTTAAAATC
Found at i:1529781 original size:36 final size:36
Alignment explanation
Indices: 1529736--1529809 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 36
1529726 TAGATTTTTA
*
1529736 AAATCTAAAAATTAAAGATTA-AATTCTT-AAAAATAT
1 AAATATAAAAA-TAAA-ATTATAATTCTTAAAAAATAT
*
1529772 AAATATAAAAATAAAATTATTAATTTTTAAAAAATAT
1 AAATATAAAAATAAAATTA-TAATTCTTAAAAAATAT
1529809 A
1 A
1529810 GGGATTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 4 0.12
35 4 0.12
36 16 0.48
37 9 0.27
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (36 bp):
AAATATAAAAATAAAATTATAATTCTTAAAAAATAT
Found at i:1529887 original size:25 final size:24
Alignment explanation
Indices: 1529833--1529887 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1529823 GTTTTAACTT
*
1529833 TTTTTATTTAAATTTTCTTAAACC
1 TTTTTATTTAAATTTTCATAAACC
*
1529857 TTTTTTATTTAAATTGTTGATATAACC
1 -TTTTTATTTAAATT-TTCATA-AACC
1529884 TTTT
1 TTTT
1529888 GAAATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 14 0.54
26 8 0.31
27 4 0.15
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTTATTTAAATTTTCATAAACC
Found at i:1529957 original size:13 final size:13
Alignment explanation
Indices: 1529936--1529965 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1529926 AACATTATCA
*
1529936 TAAATTTGAATTT
1 TAAACTTGAATTT
1529949 TAAACTTGAATTT
1 TAAACTTGAATTT
1529962 TAAA
1 TAAA
1529966 ATTTAAAAAA
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:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (13 bp):
TAAACTTGAATTT
Found at i:1529996 original size:22 final size:22
Alignment explanation
Indices: 1529961--1530002 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1529951 AACTTGAATT
1529961 TTAAAATTTAAAAAATAAAAAA
1 TTAAAATTTAAAAAATAAAAAA
* *
1529983 TTAAATTTTTAAAAATAAAA
1 TTAAAATTTAAAAAATAAAA
1530003 TACAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAAAATTTAAAAAATAAAAAA
Found at i:1530551 original size:22 final size:22
Alignment explanation
Indices: 1530523--1530564 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1530513 CCATATCAAC
1530523 CGATAACTTAAATAAAAATTTT
1 CGATAACTTAAATAAAAATTTT
*
1530545 CGATAACTTCAATAAAAATT
1 CGATAACTTAAATAAAAATT
1530565 ATTACACTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (22 bp):
CGATAACTTAAATAAAAATTTT
Found at i:1533620 original size:3 final size:3
Alignment explanation
Indices: 1533612--1533651 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
1533602 GAAGGTAAGA
1533612 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT -AT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1533652 AGGGACAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1534337 original size:24 final size:28
Alignment explanation
Indices: 1534278--1534337 Score: 65
Period size: 27 Copynumber: 2.2 Consensus size: 28
1534268 CTTTTTTTTT
1534278 ATTAATTAATTTTAATTTAATATTATAAA
1 ATTAATTAATTTTAATTTAATATTAT-AA
*
1534307 AGATAATTAA-TTT-A-TTAATATTAT-A
1 A-TTAATTAATTTTAATTTAATATTATAA
1534332 ATTAAT
1 ATTAAT
1534338 ATTTTGCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 4 0.14
25 2 0.07
27 10 0.36
28 1 0.04
29 4 0.14
30 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTAATTAATTTTAATTTAATATTATAA
Found at i:1534390 original size:21 final size:21
Alignment explanation
Indices: 1534366--1534407 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1534356 TATATTTCTT
1534366 GAAGGGTCATTAGATTTTTTG
1 GAAGGGTCATTAGATTTTTTG
1534387 GAAGGGTCATTAGATTTTTTG
1 GAAGGGTCATTAGATTTTTTG
1534408 TGTACTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.29, T:0.43
Consensus pattern (21 bp):
GAAGGGTCATTAGATTTTTTG
Found at i:1540310 original size:20 final size:20
Alignment explanation
Indices: 1540281--1540319 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1540271 ATGTTTACAA
1540281 TTTTTATTAAA-TTGATTCC
1 TTTTTATTAAATTTGATTCC
1540300 TTTTTAGTTAAATTTGATTC
1 TTTTTA-TTAAATTTGATTC
1540320 TTAACGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 5 0.28
21 7 0.39
ACGTcount: A:0.26, C:0.08, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTTTATTAAATTTGATTCC
Found at i:1540419 original size:7 final size:7
Alignment explanation
Indices: 1540409--1540435 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1540399 AATAAATAAT
1540409 AATTTAA
1 AATTTAA
1540416 AATTTAA
1 AATTTAA
1540423 AATTTAA
1 AATTTAA
1540430 AATTTA
1 AATTTA
1540436 TAAAAATTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTAA
Found at i:1540636 original size:21 final size:23
Alignment explanation
Indices: 1540593--1540638 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1540583 TTTAAAAAGT
*
1540593 TAAGAGTCAAATTTAACTAAAAA
1 TAAGAGCCAAATTTAACTAAAAA
1540616 TAAGAGCCAAA-TTAA-TAAAAA
1 TAAGAGCCAAATTTAACTAAAAA
1540637 TA
1 TA
1540639 TAAACATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 4 0.18
23 10 0.45
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.24
Consensus pattern (23 bp):
TAAGAGCCAAATTTAACTAAAAA
Found at i:1540641 original size:23 final size:25
Alignment explanation
Indices: 1540585--1540641 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
1540575 TGATTCTTTT
*
1540585 TAAAAAGT-TAAGAGTCAAATTTAAC
1 TAAAAA-TATAAGAGCCAAATTTAAC
1540610 T-AAAA-ATAAGAGCCAAA-TTAA-
1 TAAAAATATAAGAGCCAAATTTAAC
1540631 TAAAAATATAA
1 TAAAAATATAA
1540642 ACATTAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 1 0.04
22 8 0.29
23 14 0.50
24 4 0.14
25 1 0.04
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.25
Consensus pattern (25 bp):
TAAAAATATAAGAGCCAAATTTAAC
Found at i:1541515 original size:22 final size:22
Alignment explanation
Indices: 1541489--1541532 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1541479 TAATAACTTT
*
1541489 AATATG-ATAAATTAGTTTTAAA
1 AATATGAAT-AATTAGATTTAAA
*
1541511 AATATTAATAATTAGATTTAAA
1 AATATGAATAATTAGATTTAAA
1541533 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
AATATGAATAATTAGATTTAAA
Found at i:1541550 original size:15 final size:15
Alignment explanation
Indices: 1541530--1541575 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1541520 AATTAGATTT
1541530 AAATTTTAAAATATA
1 AAATTTTAAAATATA
*
1541545 AAATTTGAAAAT-T-
1 AAATTTTAAAATATA
1541558 AAATTTTCAAAA-ATA
1 AAATTTT-AAAATATA
1541573 AAA
1 AAA
1541576 GTACAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 6 0.23
14 6 0.23
15 14 0.54
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (15 bp):
AAATTTTAAAATATA
Found at i:1541583 original size:28 final size:29
Alignment explanation
Indices: 1541528--1541596 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1541518 ATAATTAGAT
***
1541528 TTAAATTTTAAAATATAAAA-TTTGAAAA
1 TTAAATTTTAAAATATAAAAGTACAAAAA
1541556 TTAAATTTTCAAAA-ATAAAAGTACAAAAA
1 TTAAATTTT-AAAATATAAAAGTACAAAAA
1541585 TTAAATTCTTAA
1 TTAAATT-TTAA
1541597 TTTGAGAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
28 15 0.43
29 18 0.51
30 2 0.06
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (29 bp):
TTAAATTTTAAAATATAAAAGTACAAAAA
Found at i:1550989 original size:197 final size:197
Alignment explanation
Indices: 1550677--1551349 Score: 996
Period size: 197 Copynumber: 3.4 Consensus size: 197
1550667 TGCAATAGGC
*
1550677 CAATAGCAATGCTTGAATAATTTGAAATTTGGGTTATTGG-TTTGCTGTGTAAACATTAGAGGAA
1 CAATAGCAATGCTTGAATAATTTGAAA-TTGGGTTATTGGTTTTGCCGTGT-AACATTAGAGGAA
* * *
1550741 CCTT-TTTCTGAAGTAGAACTATGGTCGGTACTTCTGTTTTGACAATTTTCTAAACTACCCGTAA
64 CCTTATTT-TGAAGTAGAACGATGGTCGGTACTTCTTTTTTGACAATTTTCTAAACTACCTGTAA
** * *
1550805 ACCCAAACTAATTAAATGCGACGATACTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGT
128 ACCCAAACTAATTAAATTTGATGATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGT
1550870 TGCTG
193 TGCTG
* ** *
1550875 CAACAGTTATGCTTGAATAATTTGAAATTGGGTTTTTGGTTTTGCCGTGTAACATTAGAGGAACC
1 CAATAGCAATGCTTGAATAATTTGAAATTGGGTTATTGGTTTTGCCGTGTAACATTAGAGGAACC
* *
1550940 TTATTTTGAAGTAGAACGATGGTCGGTACTTCTTTTTTGGCAATTTTCTAAACTACTTGTAAACC
66 TTATTTTGAAGTAGAACGATGGTCGGTACTTCTTTTTTGACAATTTTCTAAACTACCTGTAAACC
* * * *
1551005 CCAACTAATTAAATTTGATGATATTACGCACTTAAGTGTGTTTGAATCCACAACCTCCAAGTTGT
131 CAAACTAATTAAATTTGATGATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGC
1551070 TG
196 TG
* * *
1551072 CAATAGCAATGCTTGAATAAATTTGAAATTGGGTTATTGGTTTTGCTGTGTAACATTAGGGGAAT
1 CAATAGCAATGCTTGAAT-AATTTGAAATTGGGTTATTGGTTTTGCCGTGTAACATTAGAGGAAC
*
1551137 TTTATTTTGAAGTAGAACGATGGTCGGTACTTCTTTTTTTGACAA--TTCTAAACTACCTGTAAA
65 CTTATTTTGAAGTAGAACGATGGTCGGTACTTC-TTTTTTGACAATTTTCTAAACTACCTGTAAA
* * * **
1551200 CCCAAACTAATTAAATTTGATGATATTACGCAGTTAAGCGTGCTCGAATCCACAATCTCTGAGTT
129 CCCAAACTAATTAAATTTGATGATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGTT
*
1551265 GCCG
194 GCTG
*
1551269 CGATAGCAATGCTTGAATAATTTGAAATTGGGTTATTGGTTTTGCTC-TGTAACATTAGAGGAAC
1 CAATAGCAATGCTTGAATAATTTGAAATTGGGTTATTGGTTTTGC-CGTGTAACATTAGAGGAAC
1551333 CTTATTTTGAAGTAGAA
65 CTTATTTTGAAGTAGAA
1551350 TGACGGTTGA
Statistics
Matches: 427, Mismatches: 43, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
196 58 0.14
197 249 0.58
198 110 0.26
199 10 0.02
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (197 bp):
CAATAGCAATGCTTGAATAATTTGAAATTGGGTTATTGGTTTTGCCGTGTAACATTAGAGGAACC
TTATTTTGAAGTAGAACGATGGTCGGTACTTCTTTTTTGACAATTTTCTAAACTACCTGTAAACC
CAAACTAATTAAATTTGATGATATTACGCACTTAAGTGTGCTCGAATCCACAACCTCCAAGTTGC
TG
Found at i:1555887 original size:19 final size:19
Alignment explanation
Indices: 1555859--1555897 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1555849 TTTGATTGTT
1555859 AAAATATT-AACTGTATAA
1 AAAATATTAAACTGTATAA
*
1555877 AAAATTATTAAAGTGTATAA
1 AAAA-TATTAAACTGTATAA
1555897 A
1 A
1555898 TTTCACCTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.56, C:0.03, G:0.08, T:0.33
Consensus pattern (19 bp):
AAAATATTAAACTGTATAA
Found at i:1557117 original size:31 final size:31
Alignment explanation
Indices: 1557082--1557143 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1557072 AACATCCTAT
* *
1557082 TGACTTAAATAAAAACTTTCAGATAGTTCAA
1 TGACTTAAATAAAAAATTTCAAATAGTTCAA
1557113 TGACTTAAATAAAAAATTTCAAATAGTTCAA
1 TGACTTAAATAAAAAATTTCAAATAGTTCAA
1557144 AGATCATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTCAAATAGTTCAA
Found at i:1558954 original size:19 final size:20
Alignment explanation
Indices: 1558925--1558965 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1558915 AAATATCTAA
* *
1558925 AAATATATAAATTCAAAAAT
1 AAATATATAAAATAAAAAAT
1558945 AAAT-TATAAAATAAAAAAT
1 AAATATATAAAATAAAAAAT
1558964 AA
1 AA
1558966 TTAAACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATATATAAAATAAAAAAT
Found at i:1559121 original size:2 final size:2
Alignment explanation
Indices: 1559116--1559158 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1559106 TTTTAGGGTT
1559116 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1559158 T
1 T
1559159 TAATTCTTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1566159 original size:18 final size:18
Alignment explanation
Indices: 1566116--1566160 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1566106 TTGAATGCGC
*
1566116 ATGCATGCATGTATATAT
1 ATGCATGTATGTATATAT
** *
1566134 ATATATGTATGTATATGT
1 ATGCATGTATGTATATAT
1566152 ATGCATGTA
1 ATGCATGTA
1566161 ATCAACCTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (18 bp):
ATGCATGTATGTATATAT
Found at i:1570686 original size:3 final size:3
Alignment explanation
Indices: 1570678--1570724 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
1570668 TAAATTAATC
**
1570678 TTA TTA TTA TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA TTAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
1570724 T
1 T
1570725 AATTGTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1571273 original size:22 final size:22
Alignment explanation
Indices: 1571247--1571289 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1571237 TAGTCCTTTT
*
1571247 ATTTTT-ACTTTTAAAAATATA
1 ATTTTTAACTTATAAAAATATA
*
1571268 ATTTTTAACTTATATAAATATA
1 ATTTTTAACTTATAAAAATATA
1571290 TTTATATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTTTAACTTATAAAAATATA
Found at i:1572580 original size:29 final size:29
Alignment explanation
Indices: 1572539--1572599 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
1572529 ATTAACCTAT
* * *
1572539 CAAAAAATGTAAAATCACTATTTTTTTTAA
1 CAAAAAATCTAAAA-CACTAATTTTCTTAA
*
1572569 CAAAAAA-CTAAAACATTAATTTTCTTAA
1 CAAAAAATCTAAAACACTAATTTTCTTAA
1572597 CAA
1 CAA
1572600 TGTTGGACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 15 0.56
29 5 0.19
30 7 0.26
ACGTcount: A:0.51, C:0.13, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAAAAATCTAAAACACTAATTTTCTTAA
Found at i:1574504 original size:16 final size:17
Alignment explanation
Indices: 1574485--1574525 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1574475 TAATTTTTTA
1574485 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATGAT
**
1574501 AAAA-TATTCAAATGAT
1 AAAATTATAAAAATGAT
1574517 AAAATTATA
1 AAAATTATA
1574526 TTTTTACTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
15 7 0.35
16 10 0.50
17 3 0.15
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
AAAATTATAAAAATGAT
Found at i:1580245 original size:18 final size:17
Alignment explanation
Indices: 1580213--1580246 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1580203 GATTTCTCTC
*
1580213 TATATTAATTATCAATT
1 TATATTAAATATCAATT
1580230 TATATATAAATATCAAT
1 TATAT-TAAATATCAAT
1580247 CCAACATAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATTAAATATCAATT
Found at i:1592751 original size:33 final size:33
Alignment explanation
Indices: 1592677--1592751 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
1592667 CCATTCAGTG
*
1592677 ATTTTTTTTTCACTTTCACTACTATCAAGTTAA
1 ATTTTTTTTTCACTATCACTACTATCAAGTTAA
* * * *
1592710 AATGTTTTTTCACTATCACTA-TAATTAAGTTGA
1 ATTTTTTTTTCACTATCACTACT-ATCAAGTTAA
1592743 ATTTTTTTT
1 ATTTTTTTT
1592752 ACTAGGTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
32 1 0.03
33 33 0.97
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.53
Consensus pattern (33 bp):
ATTTTTTTTTCACTATCACTACTATCAAGTTAA
Found at i:1593746 original size:22 final size:23
Alignment explanation
Indices: 1593721--1593766 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
1593711 ATTCAGTGGC
*
1593721 GGCACAAAAAAA-AGTCATTTTT
1 GGCACAAAAAAATAATCATTTTT
1593743 GGCACAAAAAAATAATCATTTTT
1 GGCACAAAAAAATAATCATTTTT
1593766 G
1 G
1593767 CTTAAATCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (23 bp):
GGCACAAAAAAATAATCATTTTT
Found at i:1595718 original size:6 final size:6
Alignment explanation
Indices: 1595710--1595762 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
1595700 GCTTTTTTCT
* * *
1595710 CTCTCT CTCTCT CTCTCT CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1595758 CTCTC
1 CTCTC
1595763 TCCTGTATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
CTCTCC
Found at i:1595730 original size:18 final size:18
Alignment explanation
Indices: 1595707--1595764 Score: 89
Period size: 18 Copynumber: 3.2 Consensus size: 18
1595697 TCAGCTTTTT
* *
1595707 TCTCTCTCTCTCTCTCTC
1 TCTCTCTCCCTCTCCCTC
1595725 TCTCTCTCCCTCTCCCTC
1 TCTCTCTCCCTCTCCCTC
*
1595743 TCCCTCTCCCTCTCCCTC
1 TCTCTCTCCCTCTCCCTC
1595761 TCTC
1 TCTC
1595765 CTGTATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (18 bp):
TCTCTCTCCCTCTCCCTC
Found at i:1598466 original size:2 final size:2
Alignment explanation
Indices: 1598459--1598548 Score: 121
Period size: 2 Copynumber: 46.0 Consensus size: 2
1598449 CACTTCTTTA
* * *
1598459 AT AT AT AT A- AT A- AT GT TT AT AT GT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1598499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1598541 GT AT AT AT
1 AT AT AT AT
1598549 GAAAAAAAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
1 2 0.03
2 75 0.97
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1606270 original size:31 final size:30
Alignment explanation
Indices: 1606203--1606270 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 30
1606193 CTTAATACCA
*
1606203 TAATGACTTAAATAAAAACTTTCAAATAGT
1 TAATGAATTAAATAAAAACTTTCAAATAGT
* ** *
1606233 TCAATGAATTAAATGAAAGTTTTCGAATAAGT
1 T-AATGAATTAAATAAAAACTTTCAAAT-AGT
1606265 TAATGA
1 TAATGA
1606271 TCATTTTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 1 0.03
31 26 0.84
32 4 0.13
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.34
Consensus pattern (30 bp):
TAATGAATTAAATAAAAACTTTCAAATAGT
Found at i:1608210 original size:13 final size:13
Alignment explanation
Indices: 1608192--1608216 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1608182 ATTAAAAGCT
1608192 ATATATATATATG
1 ATATATATATATG
1608205 ATATATATATAT
1 ATATATATATAT
1608217 ATGCCATTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
ATATATATATATG
Found at i:1608211 original size:15 final size:15
Alignment explanation
Indices: 1608191--1608219 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1608181 AATTAAAAGC
1608191 TATATATATATATGA
1 TATATATATATATGA
1608206 TATATATATATATG
1 TATATATATATATG
1608220 CCATTACCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
TATATATATATATGA
Found at i:1609447 original size:6 final size:6
Alignment explanation
Indices: 1609436--1609468 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
1609426 CTTTCTTTCC
1609436 CTTCAT CTTCAT CTTCAT CTTCAT CTTC-T CTTC
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT CTTC
1609469 TTTTTATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTCAT
Found at i:1610913 original size:2 final size:2
Alignment explanation
Indices: 1610908--1610941 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1610898 AAAAAAATGC
1610908 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1610942 AATTTAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1615747 original size:13 final size:13
Alignment explanation
Indices: 1615729--1615753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1615719 TTTATAGGTT
1615729 AAAACTTATAATC
1 AAAACTTATAATC
1615742 AAAACTTATAAT
1 AAAACTTATAAT
1615754 AAGATTGTTA
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:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAACTTATAATC
Found at i:1619787 original size:31 final size:31
Alignment explanation
Indices: 1619752--1619810 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1619742 GAAAAGAATG
1619752 TAGGTTTAATATATAATTTGGTACTTGACAT
1 TAGGTTTAATATATAATTTGGTACTTGACAT
* *
1619783 TAGGTTTAATATTTAATTTGGTATTTGA
1 TAGGTTTAATATATAATTTGGTACTTGA
1619811 GTATTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (31 bp):
TAGGTTTAATATATAATTTGGTACTTGACAT
Found at i:1620665 original size:24 final size:24
Alignment explanation
Indices: 1620633--1620681 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1620623 GTGAGTTGAA
1620633 TGACATTACATATATGATCATATT
1 TGACATTACATATATGATCATATT
*
1620657 TGACATTACATATATTATCATATT
1 TGACATTACATATATGATCATATT
1620681 T
1 T
1620682 TTGGTACATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (24 bp):
TGACATTACATATATGATCATATT
Found at i:1623083 original size:145 final size:144
Alignment explanation
Indices: 1622820--1623107 Score: 357
Period size: 145 Copynumber: 2.0 Consensus size: 144
1622810 CTACATTCCA
* * *
1622820 AAGGTTGAACTGATTCACTCGAATCCAATCCAATCGTCAAAAGCTTATAATTGGTTTTTATAGAT
1 AAGGTTGAACTGATTCACTCAAATCCAATCCAATCGTCAAAAGCTAATAATTGGTTTCTATAGAT
* * *
1622885 GTACAATAGTATCTTCAATATAACAACACATCAATAGATCAAAAAGATTTTTTTCATTAAATTGT
66 GTACAATAATATCTTCAATATAACAACACATCAATAAATCAAAAAGA-TTTTTTCATTAAATTAT
1622950 CAATCCAAATATTTC
130 CAATCCAAATATTTC
* * * *
1622965 AAGGTTGAATTGATTCACTCAAATCTAATCCAATCTTCAAAAG-TCAATGATTGGTTTCTATAGA
1 AAGGTTGAACTGATTCACTCAAATCCAATCCAATCGTCAAAAGCT-AATAATTGGTTTCTATAGA
* * **
1623029 TGATGA-ATCATAATATCTTTAATATAACAACACATTAATAAAT-TTAAAGATTTTTTTCATTAA
65 TG-T-ACA--ATAATATCTTCAATATAACAACACATCAATAAATCAAAAAGA-TTTTTTCATTAA
*
1623092 ATTATCAATCTAAATA
125 ATTATCAATCCAAATA
1623108 ATGCAAGTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
144 1 0.01
145 57 0.46
146 2 0.02
147 33 0.27
148 30 0.24
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (144 bp):
AAGGTTGAACTGATTCACTCAAATCCAATCCAATCGTCAAAAGCTAATAATTGGTTTCTATAGAT
GTACAATAATATCTTCAATATAACAACACATCAATAAATCAAAAAGATTTTTTCATTAAATTATC
AATCCAAATATTTC
Found at i:1623846 original size:15 final size:15
Alignment explanation
Indices: 1623826--1623857 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1623816 TGTAATATAA
1623826 TTAATTAATTTTAAT
1 TTAATTAATTTTAAT
*
1623841 TTAATTACTTTTAAT
1 TTAATTAATTTTAAT
1623856 TT
1 TT
1623858 TCATATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTAATTTTAAT
Found at i:1627872 original size:31 final size:29
Alignment explanation
Indices: 1627829--1627908 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 29
1627819 AAATTTAAAA
1627829 TTAAAAAA-ATAAAATTATATTTTAACCCTT
1 TTAAAAAATATAAAATTATA-TTTAA-CCTT
*
1627859 TTAAAAAATATAAAAATT-TGATTTAATCTT
1 TTAAAAAATAT-AAAATTAT-ATTTAACCTT
* *
1627889 TTAAAAATTATAAAAATATA
1 TTAAAAAATATAAAATTATA
1627909 AACTATTAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
29 6 0.14
30 22 0.51
31 8 0.19
32 7 0.16
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (29 bp):
TTAAAAAATATAAAATTATATTTAACCTT
Found at i:1634855 original size:15 final size:16
Alignment explanation
Indices: 1634826--1634858 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1634816 GTGATTTAAT
1634826 AAAAAAATTAAAAATTA
1 AAAAAAATT-AAAATTA
1634843 AAAAAAATT-AAATTA
1 AAAAAAATTAAAATTA
1634858 A
1 A
1634859 TGATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAAAATTAAAATTA
Found at i:1645372 original size:15 final size:13
Alignment explanation
Indices: 1645339--1645364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1645329 TGATAAACAA
1645339 AAATATACTCTTT
1 AAATATACTCTTT
1645352 AAATATACTCTTT
1 AAATATACTCTTT
1645365 TTAAATATTG
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:0.15, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATATACTCTTT
Found at i:1657229 original size:16 final size:16
Alignment explanation
Indices: 1657208--1657263 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 16
1657198 AATAAATAAA
1657208 AAATATATAAATTATT
1 AAATATATAAATTATT
* *
1657224 AAATAT-TAAAATAAT
1 AAATATATAAATTATT
* *
1657239 ATAATATATATATTTTT
1 A-AATATATAAATTATT
*
1657256 AAAAATAT
1 AAATATAT
1657264 TAAAAATAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
15 8 0.26
16 17 0.55
17 6 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATATATAAATTATT
Found at i:1657246 original size:32 final size:34
Alignment explanation
Indices: 1657201--1657275 Score: 93
Period size: 32 Copynumber: 2.3 Consensus size: 34
1657191 TGATTTCAAT
*
1657201 AAATAA-AAAATATATAAATTATT-AAATATT-A
1 AAATAATATAATATATAAATTATTAAAATATTAA
* *
1657232 AAATAATATAATATATATATTTTTAAAAATATTAA
1 AAATAATATAATATATAAATTATT-AAAATATTAA
1657267 AAATAATAT
1 AAATAATAT
1657276 GAGTGAACTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 6 0.16
32 14 0.38
34 7 0.19
35 10 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
AAATAATATAATATATAAATTATTAAAATATTAA
Found at i:1665757 original size:17 final size:17
Alignment explanation
Indices: 1665719--1665779 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 17
1665709 AACTTGGATC
* *
1665719 TTAAA-TTAAGTTTGAA
1 TTAAATTTAAATTTGAT
*
1665735 TTAATTTTAAATTT-AT
1 TTAAATTTAAATTTGAT
*
1665751 TTAAATTTAAATTTGTT
1 TTAAATTTAAATTTGAT
1665768 TTAAATTTAAAT
1 TTAAATTTAAAT
1665780 ACATTTAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (17 bp):
TTAAATTTAAATTTGAT
Found at i:1665763 original size:27 final size:27
Alignment explanation
Indices: 1665722--1665804 Score: 76
Period size: 27 Copynumber: 3.1 Consensus size: 27
1665712 TTGGATCTTA
* *
1665722 AATTAAGTTTGAATTAATTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* **
1665749 ATTTAAATTTAAATTTGTTTTAAATTT
1 AATTAAATTTAAATTAATTTTAAATTT
* * * * *
1665776 AAATACATTTAAAATAATTTGAAACTT
1 AATTAAATTTAAATTAATTTTAAATTT
1665803 AA
1 AA
1665805 ACTTAAAATT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (27 bp):
AATTAAATTTAAATTAATTTTAAATTT
Found at i:1665788 original size:16 final size:16
Alignment explanation
Indices: 1665735--1665788 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
1665725 TAAGTTTGAA
* *
1665735 TTAATTTTAAATTTAT
1 TTAAATTTAAATTCAT
**
1665751 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTCAT
*
1665768 TTAAATTTAAATACAT
1 TTAAATTTAAATTCAT
1665784 TTAAA
1 TTAAA
1665789 ATAATTTGAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (16 bp):
TTAAATTTAAATTCAT
Found at i:1666675 original size:16 final size:13
Alignment explanation
Indices: 1666643--1666681 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1666633 ATTAAACTGT
1666643 TTAGTAATTAATA
1 TTAGTAATTAATA
1666656 TTAGTAATTAATA
1 TTAGTAATTAATA
* *
1666669 TTATTAGTTAATA
1 TTAGTAATTAATA
1666682 ATTAATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (13 bp):
TTAGTAATTAATA
Found at i:1668021 original size:29 final size:29
Alignment explanation
Indices: 1667930--1668029 Score: 84
Period size: 29 Copynumber: 3.4 Consensus size: 29
1667920 AAAATTACCA
* *
1667930 TTTTACCCTCGAACTTTCCAAATTCCCAT
1 TTTTACCCTCGAACTTTCCAAAATCTCAT
1667959 TTTTAACCC-CG-A-TTTCACCAAAAAT-TACCA-
1 TTTT-ACCCTCGAACTTT--CC-AAAATCT--CAT
1667989 TTTTACCCTCGAACTTTCCAAAATCTCAT
1 TTTTACCCTCGAACTTTCCAAAATCTCAT
*
1668018 TTTTAACCTCGA
1 TTTTACCCTCGA
1668030 TTTCACTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 22
0.70 0.04 0.27
Matches are distributed among these distances:
27 3 0.05
28 3 0.05
29 28 0.49
30 17 0.30
31 3 0.05
32 3 0.05
ACGTcount: A:0.29, C:0.31, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTTACCCTCGAACTTTCCAAAATCTCAT
Found at i:1668040 original size:29 final size:28
Alignment explanation
Indices: 1667885--1668040 Score: 83
Period size: 29 Copynumber: 5.4 Consensus size: 28
1667875 ACCCCTAAAC
* *
1667885 TTTC-CAAAATCCCATTTTTAACCCCGA
1 TTTCACAAAATCTCATTTTTAACCTCGA
*
1667912 TTTCACCAAAAAT-TACCA-TTTTACCCTCGAA
1 TTTCA-C-AAAATCT--CATTTTTAACCTCG-A
* * *
1667943 CTTTC-CAAATTCCCATTTTTAACCCCGA
1 -TTTCACAAAATCTCATTTTTAACCTCGA
*
1667971 TTTCACCAAAAAT-TACCA-TTTTACCCTCGAA
1 TTTCA-C-AAAATCT--CATTTTTAACCTCG-A
1668002 CTTTC-CAAAATCTCATTTTTAACCTCGA
1 -TTTCACAAAATCTCATTTTTAACCTCGA
1668030 TTTCACTAAAA
1 TTTCAC-AAAA
1668041 ATTACCATTT
Statistics
Matches: 97, Mismatches: 12, Indels: 38
0.66 0.08 0.26
Matches are distributed among these distances:
27 12 0.12
28 7 0.07
29 34 0.35
30 30 0.31
31 6 0.06
32 8 0.08
ACGTcount: A:0.32, C:0.30, G:0.03, T:0.35
Consensus pattern (28 bp):
TTTCACAAAATCTCATTTTTAACCTCGA
Found at i:1668069 original size:59 final size:60
Alignment explanation
Indices: 1667645--1668058 Score: 599
Period size: 59 Copynumber: 7.0 Consensus size: 60
1667635 CTCTAGTCCC
* ** *
1667645 CAAACTTTCTAAAATTTCA-TTTTAACCCCGATTTCACCTAAAATTACCATTTTACCCCT
1 CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
* * * * *
1667704 -AAGCTTTCCAAAATTCCATTTTTGACCCCTATTTCACCAAAAATCACCATTTTACCCCT
1 CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
* *
1667763 -AAACTTTCCAAAATCCCATTTTTAACCCTGATTTCACCAAAAATTACTATTTTA-CCCT
1 CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
* *
1667821 CAAACTTTCCAATATCCCATTTTTAACCCCGATTTCACCAAAGATTACCATTTTACCCCT
1 CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
1667881 -AAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCT
1 CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
* *
1667939 CGAACTTTCCAAATTCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTA-CCCT
1 CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
* * * * *
1667998 CGAACTTTCCAAAATCTCATTTTTAACCTCGATTTCACTAAAAATTACCATTTCACCCCT
1 CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
1668058 C
1 C
1668059 GAGCATCCAA
Statistics
Matches: 323, Mismatches: 27, Indels: 9
0.90 0.08 0.03
Matches are distributed among these distances:
58 23 0.07
59 291 0.90
60 9 0.03
ACGTcount: A:0.32, C:0.31, G:0.03, T:0.35
Consensus pattern (60 bp):
CAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCT
Found at i:1670106 original size:25 final size:24
Alignment explanation
Indices: 1670032--1670113 Score: 69
Period size: 25 Copynumber: 3.3 Consensus size: 24
1670022 ATTAAAATAA
*
1670032 ATAAAATATCATATTT-TACAAAAAT
1 ATAAAA-AT-ATATTTATATAAAAAT
* * *
1670057 AT-AAAATATATTTGTCTAAATAT
1 ATAAAAATATATTTATATAAAAAT
*
1670080 ATAAAAATATGTTTTATATAAAAAT
1 ATAAAAATAT-ATTTATATAAAAAT
1670105 ATATAAAAT
1 ATA-AAAAT
1670114 CTAAAAATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
22 6 0.13
23 10 0.22
24 10 0.22
25 15 0.33
26 5 0.11
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
ATAAAAATATATTTATATAAAAAT
Found at i:1674169 original size:87 final size:87
Alignment explanation
Indices: 1674023--1674196 Score: 330
Period size: 87 Copynumber: 2.0 Consensus size: 87
1674013 AGGAAAGTTA
*
1674023 TTAAAGGAGGAAAAAAGAAAAGAAAAGAGGCTTTTTCAATATAAAAAAGAAAGTGAAGAACAATA
1 TTAAAGGAGGAAAAAAGAAAAGAAAAGAGGATTTTTCAATATAAAAAAGAAAGTGAAGAACAATA
*
1674088 CTCCGTTAAATTTTGAATGGTG
66 CTCCATTAAATTTTGAATGGTG
1674110 TTAAAGGAGGAAAAAAGAAAAGAAAAGAGGATTTTTCAATATAAAAAAGAAAGTGAAGAACAATA
1 TTAAAGGAGGAAAAAAGAAAAGAAAAGAGGATTTTTCAATATAAAAAAGAAAGTGAAGAACAATA
1674175 CTCCATTAAATTTTGAATGGTG
66 CTCCATTAAATTTTGAATGGTG
1674197 GGTCAGTGGT
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (87 bp):
TTAAAGGAGGAAAAAAGAAAAGAAAAGAGGATTTTTCAATATAAAAAAGAAAGTGAAGAACAATA
CTCCATTAAATTTTGAATGGTG
Found at i:1678592 original size:18 final size:18
Alignment explanation
Indices: 1678550--1678598 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1678540 AGTTTAAGTT
1678550 AATTCTAAATTTATTTATA
1 AATT-TAAATTTATTTATA
*
1678569 AATTTAGATTTATTT-TA
1 AATTTAAATTTATTTATA
1678586 AATTTTAAATTTA
1 AA-TTTAAATTTA
1678599 AATTAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 19 0.70
19 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
AATTTAAATTTATTTATA
Found at i:1678594 original size:24 final size:25
Alignment explanation
Indices: 1678562--1678621 Score: 79
Period size: 24 Copynumber: 2.4 Consensus size: 25
1678552 TTCTAAATTT
* *
1678562 ATTTATAAATTTAGATTTA-TTTTAA
1 ATTT-TAAATTTAAATTAATTTTTAA
1678587 ATTTTAAATTTAAATTAATTTTTAA
1 ATTTTAAATTTAAATTAATTTTTAA
1678612 A-TTTAAATTT
1 ATTTTAAATTT
1678622 GTGTTAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATTTTAAATTTAAATTAATTTTTAA
Found at i:1678604 original size:5 final size:6
Alignment explanation
Indices: 1678567--1678638 Score: 53
Period size: 6 Copynumber: 12.2 Consensus size: 6
1678557 AATTTATTTA
* * *
1678567 TAAATT TAGATT T-ATTT TAAATTT TAAATT TAAA-T TAATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAA-ATT TAAATT
*
1678615 TAAATT T--GTGT TAAATT TAAATT T
1 TAAATT TAAAT-T TAAATT TAAATT T
1678639 GGCAAATTTG
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
4 1 0.02
5 9 0.18
6 30 0.59
7 11 0.22
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
TAAATT
Found at i:1678604 original size:18 final size:18
Alignment explanation
Indices: 1678583--1678620 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1678573 TAGATTTATT
1678583 TTAAATTTTAAATTTAAA
1 TTAAATTTTAAATTTAAA
*
1678601 TTAATTTTTAAATTTAAA
1 TTAAATTTTAAATTTAAA
1678619 TT
1 TT
1678621 TGTGTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATTTTAAATTTAAA
Found at i:1678606 original size:17 final size:17
Alignment explanation
Indices: 1678586--1678637 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
1678576 ATTTATTTTA
1678586 AATTTTAAATTTAAATT
1 AATTTTAAATTTAAATT
1678603 AATTTTTAAATTTAAATT
1 AA-TTTTAAATTTAAATT
** *
1678621 TGTGTTAAATTTAAATT
1 AATTTTAAATTTAAATT
1678638 TGGCAAATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTTAAATTTAAATT
Found at i:1678613 original size:42 final size:41
Alignment explanation
Indices: 1678550--1678638 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
1678540 AGTTTAAGTT
* * *
1678550 AATTCTAAATTTATTTATAAATTTAGATTTATTTTAAATTTTA
1 AATT-TAAATTAATTTATAAATTTAAATTTATGTTAAA-TTTA
* *
1678593 AATTTAAATTAATTTTTAAATTTAAATTTGTGTTAAATTTA
1 AATTTAAATTAATTTATAAATTTAAATTTATGTTAAATTTA
1678634 AATTT
1 AATTT
1678639 GGCAAATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 9 0.22
42 28 0.68
43 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (41 bp):
AATTTAAATTAATTTATAAATTTAAATTTATGTTAAATTTA
Found at i:1679714 original size:14 final size:14
Alignment explanation
Indices: 1679691--1679729 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1679681 TTAAAAGGGG
*
1679691 AAAAAT-AAGAAGA
1 AAAAATAAAGAACA
1679704 AAAAATAAAGAACA
1 AAAAATAAAGAACA
*
1679718 AAAAAAAAAGAA
1 AAAAATAAAGAA
1679730 ACTAAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (14 bp):
AAAAATAAAGAACA
Found at i:1680374 original size:161 final size:162
Alignment explanation
Indices: 1680194--1680558 Score: 477
Period size: 162 Copynumber: 2.3 Consensus size: 162
1680184 TTTCAATTTA
1680194 GTCCTTTGACTGCTTGACTGCACCT-GAGGCTGCCACGTGTCA-TTTTTGGCTTATTTATGCATT
1 GTCCTTTGACTGCTTGACTGCA-CTAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATT
**
1680257 TAGTCCCTAACATTTTTAATTCGTTTTAATTTAATCCCTAAACCAACTTTTGTTTAATTACAAAA
65 TAGTCCCTAACATTTTTAATTCGTTTTAATTTAATCCCTAAACCAACTTTTACTTAATTACAAAA
*
1680322 TTGGCCCAAGAATTTTTCAAGGTTTATAAATTC
130 TTGGCCCAAGAATTTTTCAAGATTTATAAATTC
* * **
1680355 GTCCTTTGACTGTTTGACTGCACTAGGGGCTGCCTTGTGTCACTTTTTGGCTTATTTATGCATTT
1 GTCCTTTGACTGCTTGACTGCACTAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATTT
* * ** * *
1680420 AGTCCTTGACATTTTTAATTTTTTTTAATTTAATCCCTAAATCAACTTTTACTTAATTACGAAAT
66 AGTCCCTAACATTTTTAATTCGTTTTAATTTAATCCCTAAACCAACTTTTACTTAATTACAAAAT
* * * * *
1680485 TGGCTCAATAATTTTTCAAGATTTACAATTTA
131 TGGCCCAAGAATTTTTCAAGATTTATAAATTC
* * * * *
1680517 ATCCCTTGACTGCTGGA-TGC-CTGTGGGGCTGCCACGTGTCAC
1 GTCCTTTGACTGCTTGACTGCACT-AGAGGCTGCCACGTGTCAC
1680559 CCAGTCTTTG
Statistics
Matches: 176, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
160 4 0.02
161 54 0.31
162 118 0.67
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (162 bp):
GTCCTTTGACTGCTTGACTGCACTAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGCATTT
AGTCCCTAACATTTTTAATTCGTTTTAATTTAATCCCTAAACCAACTTTTACTTAATTACAAAAT
TGGCCCAAGAATTTTTCAAGATTTATAAATTC
Done.