Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 5 of 135
Found at i:1442086 original size:33 final size:34
Alignment explanation
Indices: 1442022--1442091 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 34
1442012 CAGCAATAAG
* * * *
1442022 TGAGCTCAACTCTAGTTGGATTAACCAACGAT-T
1 TGAGCCCAACGCTAGTCGGATAAACCAACGATCT
**
1442055 TGAGCCCAACGCTAGTCGGATAAACTGACGATCT
1 TGAGCCCAACGCTAGTCGGATAAACCAACGATCT
1442089 TGA
1 TGA
1442092 CACCCAGTAC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (34 bp):
TGAGCCCAACGCTAGTCGGATAAACCAACGATCT
Found at i:1445635 original size:14 final size:14
Alignment explanation
Indices: 1445618--1445648 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1445608 CGTCTACTGA
1445618 ACCACAGTATCCTC
1 ACCACAGTATCCTC
1445632 ACCACAGTATCCTC
1 ACCACAGTATCCTC
1445646 ACC
1 ACC
1445649 GGAAAAGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.45, G:0.06, T:0.19
Consensus pattern (14 bp):
ACCACAGTATCCTC
Found at i:1451091 original size:24 final size:24
Alignment explanation
Indices: 1451043--1451092 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
1451033 TTCTTCACCC
* * *
1451043 TCTTCATCATCACCTTCATCTTCT
1 TCTTCATCATCACCCTCAACCTCT
*
1451067 TCTTCATCTTCACCCTCAACCTCT
1 TCTTCATCATCACCCTCAACCTCT
1451091 TC
1 TC
1451093 ATCACCCTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (24 bp):
TCTTCATCATCACCCTCAACCTCT
Found at i:1466079 original size:21 final size:22
Alignment explanation
Indices: 1466042--1466098 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
1466032 ATATAATAAT
1466042 CGAATAATAAACT-AGTTT-TAAA
1 CGAAT-ATAAA-TGAGTTTGTAAA
**
1466064 CGAATATAAATGAGTTTGTTCA
1 CGAATATAAATGAGTTTGTAAA
*
1466086 TGAATATAAATGA
1 CGAATATAAATGA
1466099 ACTAAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 1 0.03
21 10 0.33
22 19 0.63
ACGTcount: A:0.46, C:0.07, G:0.14, T:0.33
Consensus pattern (22 bp):
CGAATATAAATGAGTTTGTAAA
Found at i:1468195 original size:15 final size:16
Alignment explanation
Indices: 1468165--1468203 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1468155 TAATAAAAAT
1468165 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
1468182 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
1468197 ATAATTT
1 ATAATTT
1468204 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1468203 original size:9 final size:9
Alignment explanation
Indices: 1468164--1468234 Score: 51
Period size: 9 Copynumber: 8.2 Consensus size: 9
1468154 ATAATAAAAA
1468164 TATAA-TTT
1 TATAATTTT
*
1468172 TATTATTTT
1 TATAATTTT
*
1468181 AATAA--TT
1 TATAATTTT
1468188 TAT-ATTTT
1 TATAATTTT
1468196 TATAATTTT
1 TATAATTTT
* **
1468205 TAAAAAATT
1 TATAATTTT
*
1468214 AATTAATTTT
1 TA-TAATTTT
1468224 TATAATTTT
1 TATAATTTT
1468233 TA
1 TA
1468235 AGAGGTTAAA
Statistics
Matches: 46, Mismatches: 12, Indels: 9
0.69 0.18 0.13
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
8 9 0.20
9 27 0.59
10 5 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TATAATTTT
Found at i:1469314 original size:21 final size:21
Alignment explanation
Indices: 1469258--1469301 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1469248 ATATACAATA
1469258 CCCAAACCCAGAATAAAAAAC
1 CCCAAACCCAGAATAAAAAAC
1469279 CCCAAACCCAGAATAAAAAAC
1 CCCAAACCCAGAATAAAAAAC
1469300 CC
1 CC
1469302 TAACTCAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.55, C:0.36, G:0.05, T:0.05
Consensus pattern (21 bp):
CCCAAACCCAGAATAAAAAAC
Found at i:1480255 original size:18 final size:18
Alignment explanation
Indices: 1480232--1480274 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1480222 GAATAGATTT
1480232 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
1480250 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
1480268 TTAATTA
1 TTAATTA
1480275 CACATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:1489887 original size:3 final size:3
Alignment explanation
Indices: 1489867--1489902 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
1489857 TGAGACCCTC
* *
1489867 ATT ATT AAT ATT AAT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1489903 TGGGTTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1490727 original size:19 final size:17
Alignment explanation
Indices: 1490703--1490740 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 17
1490693 TCAATCACTC
1490703 AATATTATTAATTTATTAT
1 AATATTATT-A-TTATTAT
1490722 AATATTATTATTATTAT
1 AATATTATTATTATTAT
1490739 AA
1 AA
1490741 ATAAATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTATTATTATTAT
Found at i:1490943 original size:16 final size:17
Alignment explanation
Indices: 1490922--1490954 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1490912 GTAGGTTAAA
1490922 AAGTGA-TTTTTTTTAT
1 AAGTGAGTTTTTTTTAT
1490938 AAGTGAGTTTTTTTTAT
1 AAGTGAGTTTTTTTTAT
1490955 TTTATAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.61
Consensus pattern (17 bp):
AAGTGAGTTTTTTTTAT
Found at i:1490959 original size:22 final size:20
Alignment explanation
Indices: 1490928--1490969 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1490918 TAAAAAGTGA
*
1490928 TTTTTTTTATAAGTGAGTTTT
1 TTTTTTTTATAAAT-AGTTTT
1490949 TTTTATTTTATAAATAGTTTT
1 TTTT-TTTTATAAATAGTTTT
1490970 AAAAAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTTTTTTATAAATAGTTTT
Found at i:1492390 original size:17 final size:17
Alignment explanation
Indices: 1492368--1492403 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1492358 TAGTAAAAAT
1492368 ATAATTT-TATTATTTTA
1 ATAATTTATATT-TTTTA
1492385 ATAATTTATATTTTTTA
1 ATAATTTATATTTTTTA
1492402 AT
1 AT
1492404 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATAATTTATATTTTTTA
Found at i:1492436 original size:29 final size:29
Alignment explanation
Indices: 1492372--1492464 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 29
1492362 AAAAATATAA
1492372 TTTTATTATTTTAATAAT-TT--A-T-ATT
1 TTTTATTATTTTAA-AATATTAAATTAATT
*
1492397 TTTTAAT-TTTTAAAATATTAAATTAATT
1 TTTTATTATTTTAAAATATTAAATTAATT
1492425 TTTTATTATTTTTAAAA-ATTAAAGTATAATT
1 TTTTATTA-TTTTAAAATATTAAA-T-TAATT
1492456 TTATTATTA
1 TT-TTATTA
1492465 ATAATTTAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.05
24 8 0.14
25 6 0.11
26 1 0.02
27 1 0.02
28 9 0.16
29 6 0.11
30 9 0.16
31 7 0.12
32 6 0.11
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (29 bp):
TTTTATTATTTTAAAATATTAAATTAATT
Found at i:1492455 original size:31 final size:30
Alignment explanation
Indices: 1492394--1492464 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
1492384 AATAATTTAT
1492394 ATTTTTTA--ATTTTTAAAATATTAAATTA
1 ATTTTTTATTATTTTTAAAATATTAAATTA
1492422 ATTTTTTATTATTTTTAAAA-ATTAAAGTATA
1 ATTTTTTATTATTTTTAAAATATTAAA-T-TA
1492453 ATTTTATTATTA
1 ATTTT-TTATTA
1492465 ATAATTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
28 8 0.21
29 6 0.16
30 11 0.29
31 7 0.18
32 6 0.16
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
ATTTTTTATTATTTTTAAAATATTAAATTA
Found at i:1494909 original size:48 final size:48
Alignment explanation
Indices: 1494853--1494958 Score: 194
Period size: 48 Copynumber: 2.2 Consensus size: 48
1494843 CACGCAATTC
*
1494853 AACGGTGACAGTGGTGAAATTGTTGATAAGGATCAGGGACATTAAAAA
1 AACGGTGACAGTGGTGAAACTGTTGATAAGGATCAGGGACATTAAAAA
1494901 AACGGTGACAGTGGTGAAACTGTTGATAAGGATCAGGGACATTAAAAA
1 AACGGTGACAGTGGTGAAACTGTTGATAAGGATCAGGGACATTAAAAA
*
1494949 AACAGTGACA
1 AACGGTGACA
1494959 TCTAAAGTAC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (48 bp):
AACGGTGACAGTGGTGAAACTGTTGATAAGGATCAGGGACATTAAAAA
Found at i:1496745 original size:24 final size:24
Alignment explanation
Indices: 1496717--1496773 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1496707 ATAAAGTTTA
1496717 ATATTATTATATTTATAATAA-ATTT
1 ATATTATTAT-TTTATAA-AATATTT
*
1496742 -TATTATTATTTTTTAAAATATTT
1 ATATTATTATTTTATAAAATATTT
1496765 ATATTATTA
1 ATATTATTA
1496774 AAATATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 2 0.07
23 10 0.34
24 17 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATTATTATTTTATAAAATATTT
Found at i:1496760 original size:21 final size:24
Alignment explanation
Indices: 1496718--1496772 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 24
1496708 TAAAGTTTAA
1496718 TATTATTATATTTATAATAAAT-TT
1 TATTATTAT-TTTATAATAAATATT
*
1496742 TATTATTATTTT-TTA-AAATATT
1 TATTATTATTTTATAATAAATATT
1496764 TA-TATTATT
1 TATTATTATT
1496773 AAAATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.38
22 6 0.21
23 3 0.10
24 9 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATTATTATTTTATAATAAATATT
Found at i:1496763 original size:18 final size:19
Alignment explanation
Indices: 1496716--1496786 Score: 56
Period size: 21 Copynumber: 3.6 Consensus size: 19
1496706 AATAAAGTTT
*
1496716 AATATTATTATATTTATAATA
1 AATATTATTATA-TTATTA-A
* *
1496737 AATTTTATTATTATTTTTTAA
1 AATATTATTA-TA-TTATTAA
1496758 AATA-T-TTATATTATTAA
1 AATATTATTATATTATTAA
*
1496775 AATATTAATATA
1 AATATTATTATA
1496787 AAATGTTACA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
17 10 0.24
18 3 0.07
19 7 0.17
20 1 0.02
21 13 0.32
22 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATATTATTATATTATTAA
Found at i:1496857 original size:26 final size:26
Alignment explanation
Indices: 1496826--1496895 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 26
1496816 ATACATATTT
1496826 AATTATTTATATTTAGTCA-TACAATA
1 AATTATTTATATTTA-TCATTACAATA
**
1496852 AATTATTAATATAATTTATCATTTTAATA
1 AATTATT--TAT-ATTTATCATTACAATA
1496881 AATTATTTAATATTT
1 AATTATTT-ATATTT
1496896 CAATAATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
26 7 0.19
27 5 0.14
28 8 0.22
29 17 0.46
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (26 bp):
AATTATTTATATTTATCATTACAATA
Found at i:1496869 original size:29 final size:30
Alignment explanation
Indices: 1496836--1496893 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
1496826 AATTATTTAT
1496836 ATTTAGTCA-TACAATAAATTA-TTAATATA
1 ATTTA-TCATTACAATAAATTATTTAATATA
**
1496865 ATTTATCATTTTAATAAATTATTTAATAT
1 ATTTATCATTACAATAAATTATTTAATAT
1496894 TTCAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.60
30 7 0.28
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (30 bp):
ATTTATCATTACAATAAATTATTTAATATA
Found at i:1496966 original size:15 final size:15
Alignment explanation
Indices: 1496948--1497004 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1496938 ATTCAATATT
1496948 AATATTTTAATAATA
1 AATATTTTAATAATA
*
1496963 AATATTTATTATAATTATA
1 AATA--T-TT-TAATAATA
* *
1496982 AATATATCAATAATA
1 AATATTTTAATAATA
1496997 AATATTTT
1 AATATTTT
1497005 GTAGTATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.50
16 1 0.03
17 2 0.06
18 2 0.06
19 11 0.34
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:1496977 original size:19 final size:19
Alignment explanation
Indices: 1496950--1496986 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1496940 TCAATATTAA
*
1496950 TATTTTAATAATAAATATT
1 TATTATAATAATAAATATT
*
1496969 TATTATAATTATAAATAT
1 TATTATAATAATAAATAT
1496987 ATCAATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATAATAATAAATATT
Found at i:1497489 original size:14 final size:13
Alignment explanation
Indices: 1497467--1497498 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1497457 AGTAAGTTAT
1497467 TTTTCAAAAATCA
1 TTTTCAAAAATCA
1497480 TTTTCAAAAATCA
1 TTTTCAAAAATCA
1497493 TTTTCA
1 TTTTCA
1497499 GTGAAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTTCAAAAATCA
Found at i:1504086 original size:53 final size:54
Alignment explanation
Indices: 1503994--1504106 Score: 183
Period size: 53 Copynumber: 2.1 Consensus size: 54
1503984 TTTCAAATTT
*
1503994 TAAATCAAGTAATCTAATTCGTTAAGAATTGTATTAACTCTTTGTTTATTTGTACAA
1 TAAATCAAGTAATCTAA-T--TTAAGAATTGTATTAACTCTTAGTTTATTTGTACAA
1504051 TAAATCAAGTAATCTAA-TTAAGAATTGTATTAACTCTTAGTTTATTTGTACAA
1 TAAATCAAGTAATCTAATTTAAGAATTGTATTAACTCTTAGTTTATTTGTACAA
1504104 TAA
1 TAA
1504107 TTACTTGATA
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
53 38 0.69
57 17 0.31
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.42
Consensus pattern (54 bp):
TAAATCAAGTAATCTAATTTAAGAATTGTATTAACTCTTAGTTTATTTGTACAA
Found at i:1506200 original size:18 final size:18
Alignment explanation
Indices: 1506157--1506202 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1506147 AATAAAAATC
*
1506157 AAAATTTAAAATTACAAA
1 AAAAATTAAAATTACAAA
**
1506175 AAAAATTAAAATTATGAA
1 AAAAATTAAAATTACAAA
1506193 AAAAATTAAA
1 AAAAATTAAA
1506203 GTAAAAGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAAAATTAAAATTACAAA
Found at i:1506200 original size:30 final size:29
Alignment explanation
Indices: 1506164--1506225 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 29
1506154 ATCAAAATTT
*
1506164 AAAATTACAA-AAAAAATTAAAATTATGAAA
1 AAAATTA-AAGAAAAAATAAAAATTAT-AAA
*
1506194 AAAATTAAAGTAAAAGATAAAAATTATAAA
1 AAAATTAAAG-AAAAAATAAAAATTATAAA
1506224 AA
1 AA
1506226 GTGAATAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 2 0.07
30 12 0.43
31 14 0.50
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.23
Consensus pattern (29 bp):
AAAATTAAAGAAAAAATAAAAATTATAAA
Found at i:1506260 original size:18 final size:18
Alignment explanation
Indices: 1506239--1506345 Score: 67
Period size: 18 Copynumber: 5.9 Consensus size: 18
1506229 AATAAGAATT
1506239 AAAAATATTAAAAAATAA
1 AAAAATATTAAAAAATAA
* *
1506257 AAAACGT-TTAAAAACTAA
1 AAAA-ATATTAAAAAATAA
* * *
1506275 AAAATTGTAAAAAAAATAA
1 AAAAATAT-TAAAAAATAA
* * *
1506294 AAAAATATTAGAAATTTA
1 AAAAATATTAAAAAATAA
*
1506312 AAAAGTA-TAAAAAATCAA
1 AAAAATATTAAAAAAT-AA
*
1506330 AACAAA-ATTTAAAAAT
1 AA-AAATATTAAAAAAT
1506346 TATTAAAAGT
Statistics
Matches: 66, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
17 7 0.11
18 35 0.53
19 24 0.36
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAAATATTAAAAAATAA
Found at i:1506346 original size:37 final size:35
Alignment explanation
Indices: 1506237--1506364 Score: 98
Period size: 37 Copynumber: 3.5 Consensus size: 35
1506227 TGAATAAGAA
** *
1506237 TTAAAAA-TATTAAAAAATAAAAAACGTTTAAAAAC
1 TTAAAAAGTA-TAAAAAATAAAAAAAATTTAAAAAT
* * *
1506272 TAAAAAATTGTAAAAAAAAT-AAAAAAATATTAGAAAT
1 TTAAAAA--GTATAAAAAATAAAAAAAAT-TTAAAAAT
1506309 TTAAAAAGTATAAAAAATCAAAACAAAATTTAAAAAT
1 TTAAAAAGTATAAAAAAT-AAAA-AAAATTTAAAAAT
* *
1506346 TATTAAAAGTTCTAAAAAA
1 T-TAAAAAG-TATAAAAAA
1506365 AACACTTACA
Statistics
Matches: 73, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
35 16 0.22
36 6 0.08
37 30 0.41
38 13 0.18
39 8 0.11
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (35 bp):
TTAAAAAGTATAAAAAATAAAAAAAATTTAAAAAT
Found at i:1507292 original size:29 final size:29
Alignment explanation
Indices: 1507259--1507314 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1507249 AAAATATAAT
* *
1507259 TTTTAAAAGATTAAATTAAAATTTTATCA
1 TTTTAAAAGATCAAAATAAAATTTTATCA
* *
1507288 TTTTAAGAGATCAAAATATAATTTTAT
1 TTTTAAAAGATCAAAATAAAATTTTAT
1507315 TTTCAATAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTAAAAGATCAAAATAAAATTTTATCA
Found at i:1530848 original size:23 final size:22
Alignment explanation
Indices: 1530822--1530904 Score: 84
Period size: 22 Copynumber: 3.8 Consensus size: 22
1530812 ATTATATTGT
*
1530822 TGTTTTGGTGCTCTTTTTTTTAC
1 TGTTTTGGTG-TCTATTTTTTAC
1530845 TGTTTTGGT-TGCTATTTTTTAC
1 TGTTTTGGTGT-CTATTTTTTAC
**
1530867 T-TTTTTATGT-TATTTTTTAC
1 TGTTTTGGTGTCTATTTTTTAC
1530887 TGTTTTGGTTGT-TATTTT
1 TGTTTTGG-TGTCTATTTT
1530905 AGTGTTGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
20 11 0.22
21 10 0.20
22 21 0.41
23 9 0.18
ACGTcount: A:0.08, C:0.07, G:0.16, T:0.69
Consensus pattern (22 bp):
TGTTTTGGTGTCTATTTTTTAC
Found at i:1530865 original size:22 final size:22
Alignment explanation
Indices: 1530837--1530904 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
1530827 TGGTGCTCTT
*
1530837 TTTTTTACTGTTTTGGTTGCTA
1 TTTTTTACTGTTTTGGTTGTTA
1530859 TTTTTTACT-TTTT--TATGTTA
1 TTTTTTACTGTTTTGGT-TGTTA
1530879 TTTTTTACTGTTTTGGTTGTTA
1 TTTTTTACTGTTTTGGTTGTTA
1530901 TTTT
1 TTTT
1530905 AGTGTTGTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
19 1 0.02
20 13 0.32
21 8 0.20
22 18 0.44
23 1 0.02
ACGTcount: A:0.10, C:0.06, G:0.13, T:0.71
Consensus pattern (22 bp):
TTTTTTACTGTTTTGGTTGTTA
Found at i:1530904 original size:12 final size:12
Alignment explanation
Indices: 1530889--1531002 Score: 69
Period size: 12 Copynumber: 9.9 Consensus size: 12
1530879 TTTTTTACTG
*
1530889 TTTTGGTTGTTA
1 TTTTTGTTGTTA
* *
1530901 TTTTAG-TGTTG
1 TTTTTGTTGTTA
*
1530912 TTTTTGCTGTTA
1 TTTTTGTTGTTA
*
1530924 TTTTTGTTGCTA
1 TTTTTGTTGTTA
*
1530936 TTTTTATTG---
1 TTTTTGTTGTTA
**
1530945 TTTTTAATGTTA
1 TTTTTGTTGTTA
*
1530957 -TTTTGCTGTTA
1 TTTTTGTTGTTA
* *
1530968 TTTTTGCTT-CTG
1 TTTTTG-TTGTTA
*
1530980 TTTTGGTTGTTA
1 TTTTTGTTGTTA
1530992 TTTTTGTTGTT
1 TTTTTGTTGTT
1531003 TGGATGTTAT
Statistics
Matches: 78, Mismatches: 17, Indels: 14
0.72 0.16 0.13
Matches are distributed among these distances:
9 8 0.10
11 20 0.26
12 49 0.63
13 1 0.01
ACGTcount: A:0.09, C:0.04, G:0.18, T:0.68
Consensus pattern (12 bp):
TTTTTGTTGTTA
Found at i:1530905 original size:20 final size:19
Alignment explanation
Indices: 1530837--1530910 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
1530827 TGGTGCTCTT
1530837 TTTTTTACTGTTTTGGTTG
1 TTTTTTACTGTTTTGGTTG
* * *
1530856 CTATTTTTTACTTTTTTATGTTA
1 ---TTTTTTACTGTTTT-GGTTG
1530879 TTTTTTACTGTTTTGGTTG
1 TTTTTTACTGTTTTGGTTG
*
1530898 TTATTTTAGTGTT
1 TT-TTTTACTGTT
1530911 GTTTTTGCTG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
19 5 0.12
20 22 0.51
22 13 0.30
23 3 0.07
ACGTcount: A:0.11, C:0.05, G:0.15, T:0.69
Consensus pattern (19 bp):
TTTTTTACTGTTTTGGTTG
Found at i:1530947 original size:56 final size:56
Alignment explanation
Indices: 1530880--1531015 Score: 152
Period size: 56 Copynumber: 2.4 Consensus size: 56
1530870 TTTATGTTAT
* * * *
1530880 TTTTTACTGTTTTGGTTGTTATTTTAG-TGTTGTTTTTGCTGT-TATTTTTGTTGCTA
1 TTTTTATTGTTTTGGATGTTATTTT-GCTGTTATTTTTGCT-TCTATTTTGGTTGCTA
** * *
1530936 TTTTTATTGTTTTTAATGTTATTTTGCTGTTATTTTTGCTTCTGTTTTGGTTGTTA
1 TTTTTATTGTTTTGGATGTTATTTTGCTGTTATTTTTGCTTCTATTTTGGTTGCTA
*
1530992 TTTTTGTTG-TTTGGATGTTATTTT
1 TTTTTATTGTTTTGGATGTTATTTT
1531016 TTATGCGTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
55 15 0.22
56 52 0.78
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.68
Consensus pattern (56 bp):
TTTTTATTGTTTTGGATGTTATTTTGCTGTTATTTTTGCTTCTATTTTGGTTGCTA
Found at i:1530990 original size:44 final size:43
Alignment explanation
Indices: 1530874--1531016 Score: 128
Period size: 44 Copynumber: 3.2 Consensus size: 43
1530864 TACTTTTTTA
* * *
1530874 TGTTATTTTT-TACTGTTTTGGTTGTTATTTTAGTGTTGTTTTTGC
1 TGTTATTTTTGTTCTGTTTTGGTTG-T-TTTTAATGTT-ATTTTGC
* **
1530919 TGTTATTTTTGTTGCTATTTTTATTGTTTTTAATGTTATTTTGC
1 TGTTATTTTTGTT-CTGTTTTGGTTGTTTTTAATGTTATTTTGC
* * * *
1530963 TGTTATTTTTGCTTCTGTTTTGGTTGTTATTT-TTGTTGTTTGGA
1 TGTTATTTTTG-TTCTGTTTTGGTTGTT-TTTAATGTTATTTTGC
1531007 TGTTATTTTT
1 TGTTATTTTT
1531017 TATGCGTTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
44 46 0.57
45 24 0.30
46 2 0.02
47 9 0.11
ACGTcount: A:0.10, C:0.04, G:0.18, T:0.68
Consensus pattern (43 bp):
TGTTATTTTTGTTCTGTTTTGGTTGTTTTTAATGTTATTTTGC
Found at i:1537270 original size:29 final size:28
Alignment explanation
Indices: 1537227--1537282 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
1537217 TTTTGAGATT
* *
1537227 AAATTTTGAAGTTTAATTAAATTTTTTA
1 AAATTTTAAAGTTTAAATAAATTTTTTA
*
1537255 AAATTTTAAAAGTTTAAATAGATTTTTT
1 AAATTTT-AAAGTTTAAATAAATTTTTT
1537283 TTCTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (28 bp):
AAATTTTAAAGTTTAAATAAATTTTTTA
Found at i:1549418 original size:6 final size:6
Alignment explanation
Indices: 1549407--1549435 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1549397 CACACCCGTT
1549407 CTGGTG CTGGTG CTGGTG CTGGTG CTGGT
1 CTGGTG CTGGTG CTGGTG CTGGTG CTGGT
1549436 TTAATATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.48, T:0.34
Consensus pattern (6 bp):
CTGGTG
Found at i:1555650 original size:28 final size:28
Alignment explanation
Indices: 1555598--1555651 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
1555588 GTGTGCTCTA
*
1555598 ATAAAAAAAAACATAGGTACTTAATTGG
1 ATAAAAAAAAACATAAGTACTTAATTGG
1555626 ATAAAAGAAAAAC-TCAAGTAC-TAATT
1 ATAAAA-AAAAACAT-AAGTACTTAATT
1555652 TGAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.56, C:0.09, G:0.11, T:0.24
Consensus pattern (28 bp):
ATAAAAAAAAACATAAGTACTTAATTGG
Found at i:1555697 original size:60 final size:60
Alignment explanation
Indices: 1555606--1555762 Score: 181
Period size: 60 Copynumber: 2.6 Consensus size: 60
1555596 TAATAAAAAA
* * ** * *
1555606 AAACATAGGTACTTAATTGGATAAAAGAAAAACTCAAGTACTAATTTGAATATTAAAATC
1 AAACTTAGGTACTTAATGGGATAAAAGAAAAACTCAAGTACTAAACTAAATATTAAAACC
* * *
1555666 AAACTTAGGTACTTATATGGGGT-AAATAAAAACTCAAGTATTAAACTAAATATTAAAACC
1 AAACTTAGGTACTTA-ATGGGATAAAAGAAAAACTCAAGTACTAAACTAAATATTAAAACC
* * * *
1555726 AAACTTAAGTACTTAATTGGAAAAAAAAAAAACTCAA
1 AAACTTAGGTACTTAATGGGATAAAAGAAAAACTCAA
1555763 CTATCAATTT
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
59 4 0.05
60 72 0.89
61 5 0.06
ACGTcount: A:0.52, C:0.11, G:0.11, T:0.27
Consensus pattern (60 bp):
AAACTTAGGTACTTAATGGGATAAAAGAAAAACTCAAGTACTAAACTAAATATTAAAACC
Found at i:1556370 original size:30 final size:30
Alignment explanation
Indices: 1556310--1556374 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
1556300 TATCTATATC
**
1556310 TTTAT-AATTTTAGAGGATTAAATCAAAAT
1 TTTATCAATTTTAGAGGACAAAATCAAAAT
*
1556339 TTTATCAATTTTAGAGGACCAAAAT-ATAAT
1 TTTATCAATTTTAGAGGA-CAAAATCAAAAT
1556369 TTTATC
1 TTTATC
1556375 TTTACTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 22 0.71
31 4 0.13
ACGTcount: A:0.42, C:0.08, G:0.09, T:0.42
Consensus pattern (30 bp):
TTTATCAATTTTAGAGGACAAAATCAAAAT
Found at i:1556855 original size:11 final size:12
Alignment explanation
Indices: 1556827--1556856 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1556817 CAAATAAATT
1556827 TAAAAATTAATA
1 TAAAAATTAATA
1556839 TAAAAATTAATA
1 TAAAAATTAATA
1556851 TAAAAA
1 TAAAAA
1556857 ATCAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
TAAAAATTAATA
Found at i:1559914 original size:23 final size:23
Alignment explanation
Indices: 1559884--1559940 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1559874 TGTAATACTA
*
1559884 AATT-TAATTTTAATTGATAT-AT
1 AATTATAATTTTAATT-AAATGAT
*
1559906 AATTATAATATTAATTAAATGAT
1 AATTATAATTTTAATTAAATGAT
1559929 AATTAATAATTT
1 AATT-ATAATTT
1559941 AAAATAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 16 0.55
24 6 0.21
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AATTATAATTTTAATTAAATGAT
Found at i:1560310 original size:19 final size:20
Alignment explanation
Indices: 1560286--1560341 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
1560276 TATGATTACG
1560286 ATTTAATTTAAAATATTAT-
1 ATTTAATTTAAAATATTATA
* *
1560305 ATTTAAATT-AATTATTATA
1 ATTTAATTTAAAATATTATA
*
1560324 ATTT-ATTTAAAACATTAT
1 ATTTAATTTAAAATATTAT
1560342 TTTTTCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAATTTAAAATATTATA
Found at i:1560637 original size:18 final size:16
Alignment explanation
Indices: 1560614--1560647 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
1560604 ATTTAAATAT
1560614 ATATTATAAATATATAAA
1 ATATTA-AAAT-TATAAA
1560632 ATATTAAAATTATAAA
1 ATATTAAAATTATAAA
1560648 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 4 0.25
18 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATTAAAATTATAAA
Found at i:1561310 original size:24 final size:26
Alignment explanation
Indices: 1561274--1561324 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 26
1561264 AATGTTGCCA
*
1561274 ATAATTTATAATG-TTA-AAATATTT
1 ATAATTTATAATGCATACAAATATTT
1561298 ATAATTT-TAAATGCATACAAATATTT
1 ATAATTTAT-AATGCATACAAATATTT
1561324 A
1 A
1561325 ATTTATTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 1 0.04
24 11 0.48
25 2 0.09
26 9 0.39
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (26 bp):
ATAATTTATAATGCATACAAATATTT
Found at i:1572005 original size:58 final size:57
Alignment explanation
Indices: 1571904--1572021 Score: 130
Period size: 58 Copynumber: 2.1 Consensus size: 57
1571894 TTATATTAAT
* ***** *
1571904 AGTCATTCAATTATGAAAAATTATAAAATAATTATTTGTTTATTAGTAATTTT-TCTGC
1 AGTCATTCAATTATGAAAAATTATAAAATAATCACCACATTATT--TAATTTTGTCTAC
* *
1571962 AGTCATTCAATTATGAAAAGTTATAAAATAGTCACCACATTATTTAATTTTGTCTAC
1 AGTCATTCAATTATGAAAAATTATAAAATAATCACCACATTATTTAATTTTGTCTAC
1572019 AGT
1 AGT
1572022 GATAGCTTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
56 7 0.14
57 7 0.14
58 36 0.72
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.42
Consensus pattern (57 bp):
AGTCATTCAATTATGAAAAATTATAAAATAATCACCACATTATTTAATTTTGTCTAC
Found at i:1580335 original size:22 final size:22
Alignment explanation
Indices: 1580310--1580351 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1580300 GGGTTTAATT
1580310 TATTAAAAATTAAAATAGAAAA
1 TATTAAAAATTAAAATAGAAAA
** *
1580332 TATTTTAAATTAAATTAGAA
1 TATTAAAAATTAAAATAGAA
1580352 TGTAACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
TATTAAAAATTAAAATAGAAAA
Found at i:1581238 original size:20 final size:21
Alignment explanation
Indices: 1581213--1581257 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1581203 ACTCTATTTA
*
1581213 AATTTTA-AAATACTTTCATT
1 AATTTTACAAATAATTTCATT
*
1581233 AATTTTACAAATAATTTTATT
1 AATTTTACAAATAATTTCATT
1581254 AATT
1 AATT
1581258 ACTAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTACAAATAATTTCATT
Found at i:1584758 original size:28 final size:28
Alignment explanation
Indices: 1584718--1584775 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1584708 ATATGGTTAC
1584718 GAGGATATAACATCGTAAGTGTATCATG
1 GAGGATATAACATCGTAAGTGTATCATG
1584746 GAGGATATAACATCGTAAGTGTATCATG
1 GAGGATATAACATCGTAAGTGTATCATG
1584774 GA
1 GA
1584776 AGTTCCTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (28 bp):
GAGGATATAACATCGTAAGTGTATCATG
Found at i:1588586 original size:129 final size:129
Alignment explanation
Indices: 1588351--1588604 Score: 436
Period size: 129 Copynumber: 2.0 Consensus size: 129
1588341 ATAACGATAA
* * *
1588351 TACAAAGTCAAAAACTATTAACGTATGATTAAATTGTGGCAAAAGTTGTGGTTTGACATGTAATC
1 TACAAAATCAAAAACTACTAACGTATGATTAAATTGTGGCAAAAGTTATGGTTTGACATGTAATC
* * * *
1588416 ACAATCGTTAACACAACTTATTATATAATTTGATCCTTGACATAAAGATTAAACCCACAACTTG
66 ACAATCGTTAACACAACTTACTATATAATATGATCCCTGACATAAAGACTAAACCCACAACTTG
*
1588480 TACAAAATCAAAAACTGCTAACGTATGATTAAATTGTGGCAAAAGTTATGGTTTGACATGTAATC
1 TACAAAATCAAAAACTACTAACGTATGATTAAATTGTGGCAAAAGTTATGGTTTGACATGTAATC
1588545 ACAATCGTTAACACAACTTACTATATAATATGATCCCTGACATAAAGACTAAACCCACAA
66 ACAATCGTTAACACAACTTACTATATAATATGATCCCTGACATAAAGACTAAACCCACAA
1588605 TTTACACATA
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
129 117 1.00
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (129 bp):
TACAAAATCAAAAACTACTAACGTATGATTAAATTGTGGCAAAAGTTATGGTTTGACATGTAATC
ACAATCGTTAACACAACTTACTATATAATATGATCCCTGACATAAAGACTAAACCCACAACTTG
Found at i:1589111 original size:18 final size:18
Alignment explanation
Indices: 1589088--1589122 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1589078 AGCTTAAGCA
*
1589088 CAAAGAGCCATTTTCCCT
1 CAAAGAACCATTTTCCCT
1589106 CAAAGAACCATTTTCCC
1 CAAAGAACCATTTTCCC
1589123 CTTGAAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.09, T:0.26
Consensus pattern (18 bp):
CAAAGAACCATTTTCCCT
Found at i:1589962 original size:18 final size:18
Alignment explanation
Indices: 1589939--1589980 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1589929 TTTTCAATTT
1589939 AATTAATTTAAAATT-TTC
1 AATTAA-TTAAAATTATTC
*
1589957 AATTAATTAAAATTATTT
1 AATTAATTAAAATTATTC
1589975 AATTAA
1 AATTAA
1589981 AAATTTATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTAATTAAAATTATTC
Found at i:1595786 original size:41 final size:41
Alignment explanation
Indices: 1595741--1595823 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1595731 TCAATCAACG
* *
1595741 ACATTTTTTTATTAAAATCGTTGAATGATATGTCAAATATT
1 ACATTTCTTTATTAAAATCATTGAATGATATGTCAAATATT
*
1595782 ACATTTCTTTATTAAAATCATTGAATGATGTGTCAAATATT
1 ACATTTCTTTATTAAAATCATTGAATGATATGTCAAATATT
1595823 A
1 A
1595824 TGTAATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (41 bp):
ACATTTCTTTATTAAAATCATTGAATGATATGTCAAATATT
Found at i:1595934 original size:25 final size:25
Alignment explanation
Indices: 1595904--1595953 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1595894 TTTAAGGATC
1595904 AATTTAAAATGAGGATCATAGTTTG
1 AATTTAAAATGAGGATCATAGTTTG
1595929 AATTTAAAATGAGGATCATAGTTTG
1 AATTTAAAATGAGGATCATAGTTTG
1595954 GGATGTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (25 bp):
AATTTAAAATGAGGATCATAGTTTG
Found at i:1607332 original size:3 final size:3
Alignment explanation
Indices: 1607324--1607369 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1607314 TACATAAAAA
1607324 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1607370 TGCTTAGCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1615261 original size:9 final size:9
Alignment explanation
Indices: 1615243--1615290 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
1615233 TGAATTTTAC
*
1615243 AATTCAAAT
1 AATTCGAAT
*
1615252 AATTTGAAT
1 AATTCGAAT
*
1615261 AACTCGAAT
1 AATTCGAAT
1615270 AATTCGAAT
1 AATTCGAAT
1615279 AATTCGAAT
1 AATTCGAAT
1615288 AAT
1 AAT
1615291 AGATTAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.33
Consensus pattern (9 bp):
AATTCGAAT
Found at i:1619538 original size:20 final size:20
Alignment explanation
Indices: 1619513--1619592 Score: 108
Period size: 20 Copynumber: 4.0 Consensus size: 20
1619503 TAAATAATCT
*
1619513 TTAATTATTATTGGCATACA
1 TTAATTATTGTTGGCATACA
**
1619533 TTAATTATTGTTGTTATACA
1 TTAATTATTGTTGGCATACA
*
1619553 TTAATT-TTTTTGGCATACA
1 TTAATTATTGTTGGCATACA
*
1619572 TTAATTAATGTTGGCATACA
1 TTAATTATTGTTGGCATACA
1619592 T
1 T
1619593 CAATGACAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.31
20 35 0.69
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (20 bp):
TTAATTATTGTTGGCATACA
Found at i:1619591 original size:39 final size:40
Alignment explanation
Indices: 1619513--1619592 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
1619503 TAAATAATCT
* **
1619513 TTAATTATTATTGGCATACATTAATTATTGTTGTTATACA
1 TTAATTATTATTGGCATACATTAATTAATGTTGGCATACA
*
1619553 TTAATT-TTTTTGGCATACATTAATTAATGTTGGCATACA
1 TTAATTATTATTGGCATACATTAATTAATGTTGGCATACA
1619592 T
1 T
1619593 CAATGACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 30 0.83
40 6 0.17
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (40 bp):
TTAATTATTATTGGCATACATTAATTAATGTTGGCATACA
Found at i:1620370 original size:6 final size:6
Alignment explanation
Indices: 1620359--1620391 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1620349 TTTAAGCGAC
1620359 CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCT
1 CCTGTG CCTGTG CCTGTG CCTGTG CCTGTG CCT
1620392 CACTCTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.36, G:0.30, T:0.33
Consensus pattern (6 bp):
CCTGTG
Found at i:1627581 original size:21 final size:21
Alignment explanation
Indices: 1627528--1627582 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1627518 GAAAAATGAC
*
1627528 AAATTAAATAAATAATATATT
1 AAATTAAAAAAATAATATATT
*
1627549 AAATTAAAAAAATAAT-TCTT
1 AAATTAAAAAAATAATATATT
*
1627569 AATTTAAAGAAAAT
1 AAATTAAA-AAAAT
1627583 TAACGTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 10 0.33
21 20 0.67
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATTAAAAAAATAATATATT
Found at i:1633206 original size:31 final size:32
Alignment explanation
Indices: 1633171--1633238 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
1633161 TCTAGGGATT
1633171 TTTAAT-TTT-TGCACATGATTTTAGGAGTAAA
1 TTTAATGTTTGTG-ACATGATTTTAGGAGTAAA
* *
1633202 TTTAATGTTTGTGGCATGATTTTAGGAGTAAG
1 TTTAATGTTTGTGACATGATTTTAGGAGTAAA
1633234 TTTAA
1 TTTAA
1633239 CAGATTTATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 6 0.18
32 25 0.76
33 2 0.06
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (32 bp):
TTTAATGTTTGTGACATGATTTTAGGAGTAAA
Found at i:1638263 original size:21 final size:21
Alignment explanation
Indices: 1638218--1638271 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
1638208 TTGGTTGTTC
* * *
1638218 TTGGATTGCATCGGTTCCATC
1 TTGGATTGTATCGGATCCATA
*
1638239 TTGGATTGTATCGGATCTATA
1 TTGGATTGTATCGGATCCATA
*
1638260 TTGGGTTGTATC
1 TTGGATTGTATC
1638272 CTCTTTCGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.43
Consensus pattern (21 bp):
TTGGATTGTATCGGATCCATA
Found at i:1638336 original size:204 final size:203
Alignment explanation
Indices: 1637979--1638387 Score: 764
Period size: 204 Copynumber: 2.0 Consensus size: 203
1637969 CAGTTAGCTA
*
1637979 TTTATATCTTTTTTTTCTTCCCTTATTGGTTGTTCTTGGATTGCATCGGTTCCACCTTGGATTGG
1 TTTATATCTTTTTTTTCTTCCCCTATTGGTTGTTCTTGGATTGCATCGGTTCCACCTTGGATTGG
*
1638044 ATCGGATCTATATAGGGTTGTATCGTCTTTCGAGGTCCAAAAGTAATCATTCCAGGCACTAGTGC
66 ATCGGATCTATATAGGGTTGTATCCTCTTTCGAGGTCCAAAAGTAATCATTCCAGGCACTAGTGC
1638109 CTAGATTGTATCCAACACAATATTATATTTAGAGACGTGGCTACTAGTGATTGTATCCATCACAA
131 CTAGATTGTATCCAACACAATATTATATTTAGAGACGTGGCTACTAGTGATTGTATCCATCACAA
1638174 TATGATAT
196 TATGATAT
*
1638182 TTTATATCCTTTTTTTTCTTCCCCTATTGGTTGTTCTTGGATTGCATCGGTTCCATCTTGGATTG
1 TTTATAT-CTTTTTTTTCTTCCCCTATTGGTTGTTCTTGGATTGCATCGGTTCCACCTTGGATTG
* *
1638247 TATCGGATCTATATTGGGTTGTATCCTCTTTCGAGGTCCAAAAGTAATCATTCCAGGCACTAGTG
65 GATCGGATCTATATAGGGTTGTATCCTCTTTCGAGGTCCAAAAGTAATCATTCCAGGCACTAGTG
1638312 CCTAGATTGTATCCAACACAATATTATATTTAGAGACGTGGCTACTAGTGATTGTATCCATCACA
130 CCTAGATTGTATCCAACACAATATTATATTTAGAGACGTGGCTACTAGTGATTGTATCCATCACA
1638377 ATATGATAT
195 ATATGATAT
1638386 TT
1 TT
1638388 AGAGATGTGG
Statistics
Matches: 200, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
203 7 0.04
204 193 0.96
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (203 bp):
TTTATATCTTTTTTTTCTTCCCCTATTGGTTGTTCTTGGATTGCATCGGTTCCACCTTGGATTGG
ATCGGATCTATATAGGGTTGTATCCTCTTTCGAGGTCCAAAAGTAATCATTCCAGGCACTAGTGC
CTAGATTGTATCCAACACAATATTATATTTAGAGACGTGGCTACTAGTGATTGTATCCATCACAA
TATGATAT
Found at i:1638380 original size:45 final size:45
Alignment explanation
Indices: 1638316--1638406 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
1638306 CTAGTGCCTA
*
1638316 GATTGTATCCAACACAATATTATATTTAGAGACGTGGCTACTAGT
1 GATTGTATCCAACACAATATGATATTTAGAGACGTGGCTACTAGT
* *
1638361 GATTGTATCCATCACAATATGATATTTAGAGATGTGGCTACTAGT
1 GATTGTATCCAACACAATATGATATTTAGAGACGTGGCTACTAGT
1638406 G
1 G
1638407 CCTGGAATGG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (45 bp):
GATTGTATCCAACACAATATGATATTTAGAGACGTGGCTACTAGT
Found at i:1638494 original size:21 final size:21
Alignment explanation
Indices: 1638438--1638494 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
1638428 CCTCGAAATA
* * *
1638438 CGATTCAACCCAAGCTAGAAC
1 CGATGCAAACCAAGATAGAAC
*
1638459 CGATGCAAACTAAGATAGAAC
1 CGATGCAAACCAAGATAGAAC
* *
1638480 GGATGCAATCCAAGA
1 CGATGCAAACCAAGA
1638495 ACAACCAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.42, C:0.25, G:0.19, T:0.14
Consensus pattern (21 bp):
CGATGCAAACCAAGATAGAAC
Found at i:1640479 original size:40 final size:40
Alignment explanation
Indices: 1640407--1640485 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
1640397 TTTAAGTTGC
* *
1640407 CTTGTTGTTAGACTTTGTCCTCCTCTTGTAATTCACCAAT
1 CTTGTTGTTAGACTTTATCCTCCTCTTATAATTCACCAAT
* * *
1640447 CTTGTTGTTAGATTTTATCTTCCTTTTATAATTCACCAA
1 CTTGTTGTTAGACTTTATCCTCCTCTTATAATTCACCAA
1640486 AAAATAAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.48
Consensus pattern (40 bp):
CTTGTTGTTAGACTTTATCCTCCTCTTATAATTCACCAAT
Found at i:1659908 original size:16 final size:16
Alignment explanation
Indices: 1659887--1659918 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1659877 TCCCTTGAAA
1659887 TGGCATGACATGTGTC
1 TGGCATGACATGTGTC
*
1659903 TGGCATGGCATGTGTC
1 TGGCATGACATGTGTC
1659919 ATTATCTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.34, T:0.31
Consensus pattern (16 bp):
TGGCATGACATGTGTC
Found at i:1660102 original size:16 final size:16
Alignment explanation
Indices: 1660081--1660113 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1660071 ATACAAAATC
1660081 TTCTATAACACTTTTA
1 TTCTATAACACTTTTA
1660097 TTCTATAACACTTTTA
1 TTCTATAACACTTTTA
1660113 T
1 T
1660114 GTAATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (16 bp):
TTCTATAACACTTTTA
Found at i:1665857 original size:19 final size:19
Alignment explanation
Indices: 1665808--1665863 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
1665798 CACTCTCAAC
*
1665808 AAAAATTAC-AAAATAATTT
1 AAAAATTTCTAAAAT-ATTT
*
1665827 TAAAATTT-TAAAATATTT
1 AAAAATTTCTAAAATATTT
1665845 AAAAATTTCTAAAAT-TTT
1 AAAAATTTCTAAAATATTT
1665863 A
1 A
1665864 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATTTCTAAAATATTT
Found at i:1665858 original size:9 final size:8
Alignment explanation
Indices: 1665822--1665863 Score: 57
Period size: 8 Copynumber: 4.9 Consensus size: 8
1665812 ATTACAAAAT
1665822 AATTTTAA
1 AATTTTAA
1665830 AATTTTAA
1 AATTTTAA
1665838 AATATTTAAA
1 AAT-TTT-AA
1665848 AATTTCTAA
1 AATTT-TAA
1665857 AATTTTA
1 AATTTTA
1665864 TTTTCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 13 0.42
9 12 0.39
10 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:1665968 original size:25 final size:25
Alignment explanation
Indices: 1665940--1665991 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1665930 TCCATATACA
*
1665940 TATACATATTTGTTTCTTGATAAAT
1 TATACACATTTGTTTCTTGATAAAT
*
1665965 TATATACATTTGTTTCTTGATAAAT
1 TATACACATTTGTTTCTTGATAAAT
1665990 TA
1 TA
1665992 CTTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.52
Consensus pattern (25 bp):
TATACACATTTGTTTCTTGATAAAT
Found at i:1670882 original size:3 final size:3
Alignment explanation
Indices: 1670874--1670941 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
1670864 TGTATCTTTT
1670874 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1670922 ATA ATA AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
1670942 TTTTAAGTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1676857 original size:39 final size:41
Alignment explanation
Indices: 1676814--1676901 Score: 108
Period size: 44 Copynumber: 2.1 Consensus size: 41
1676804 GTAGTAAATA
*
1676814 CAATT-ATATA-TATATAGTTTTGTACACCTTACCTCTTGT
1 CAATTCATATACTATATAGTTTTGTACACCTCACCTCTTGT
* *
1676853 CAATTTCGTTATACGTATGTAGTTTTGTACACCTCACCTCTTGT
1 CAA-TTC-ATATAC-TATATAGTTTTGTACACCTCACCTCTTGT
1676897 CAATT
1 CAATT
1676902 TCGTGGATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
39 3 0.07
40 2 0.05
42 4 0.10
43 2 0.05
44 30 0.73
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.44
Consensus pattern (41 bp):
CAATTCATATACTATATAGTTTTGTACACCTCACCTCTTGT
Found at i:1679732 original size:16 final size:16
Alignment explanation
Indices: 1679713--1679753 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1679703 TTCTAAAGTT
1679713 TTTGGATCATTTTATA
1 TTTGGATCATTTTATA
*
1679729 TTTGGATTATTTTATA
1 TTTGGATCATTTTATA
*
1679745 TTTGTATCA
1 TTTGGATCA
1679754 CTCGAGTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.24, C:0.05, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTGGATCATTTTATA
Found at i:1681543 original size:6 final size:6
Alignment explanation
Indices: 1681518--1681619 Score: 66
Period size: 6 Copynumber: 17.0 Consensus size: 6
1681508 GGAACCTAAT
* * *
1681518 TTTAAA CTTTAAA TTTTAAA TTTAAAA TTTAAA TTTAAA TTT-AT TTTGAG
1 TTTAAA -TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * * *
1681568 TTTGAA TTT-AT TTTAAA TTCAAA TTT-AT TTTAAA TTAAAA ATTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1681614 TTTAAA
1 TTTAAA
1681620 ATGTCCAAAT
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
5 12 0.16
6 45 0.60
7 18 0.24
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:1681543 original size:13 final size:13
Alignment explanation
Indices: 1681515--1681559 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
1681505 AATGGAACCT
1681515 AATTTTAAACTTTA
1 AATTTTAAA-TTTA
1681529 AATTTTAAATTTA
1 AATTTTAAATTTA
*
1681542 AAATTTAAATTTA
1 AATTTTAAATTTA
1681555 AATTT
1 AATTT
1681560 ATTTTGAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:1681592 original size:17 final size:17
Alignment explanation
Indices: 1681525--1681603 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
1681515 AATTTTAAAC
*
1681525 TTTAAATTTTAAATTTAAAA
1 TTTAAA-TTTAAATTT--AT
1681545 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
* * *
1681562 TTTGAGTTTGAATTTAT
1 TTTAAATTTAAATTTAT
*
1681579 TTTAAATTCAAATTTAT
1 TTTAAATTTAAATTTAT
1681596 TTTAAATT
1 TTTAAATT
1681604 AAAAATTAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
17 36 0.71
19 9 0.18
20 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:1682941 original size:40 final size:41
Alignment explanation
Indices: 1682885--1682962 Score: 140
Period size: 40 Copynumber: 1.9 Consensus size: 41
1682875 GAGAGAATAA
1682885 AAGGTTTTTTTTTGGTGAAAATGAGAGAAACGAAATTTTTG
1 AAGGTTTTTTTTTGGTGAAAATGAGAGAAACGAAATTTTTG
*
1682926 AAGG-TTTTTTTTGGTGAAAATGAGAGAAATGAAATTT
1 AAGGTTTTTTTTTGGTGAAAATGAGAGAAACGAAATTT
1682963 CGTCATACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.38
Consensus pattern (41 bp):
AAGGTTTTTTTTTGGTGAAAATGAGAGAAACGAAATTTTTG
Found at i:1683379 original size:59 final size:58
Alignment explanation
Indices: 1683295--1683548 Score: 200
Period size: 59 Copynumber: 4.4 Consensus size: 58
1683285 AATTCACATT
* * *
1683295 TTTA-CCCCAAACTTT-CAAAATTACCATTTTGGCCTTGGACTTTTCAAAAATTACCA
1 TTTAGCCCCAAACTTTCCAAAATTACCATTTTGACCCTGAACTTTTCAAAAATTACCA
* * * *
1683351 TTTAGCCCTAAACTTTTCCAAAATTACCATTTTAACCCTAAACTTTTCCAAAATTA-CA
1 TTTAGCCCCAAAC-TTTCCAAAATTACCATTTTGACCCTGAACTTTTCAAAAATTACCA
* * * * * * *
1683409 TTTTTGTCCTCAAAC-ATCCAAAAATTACCATTTTTACCCCGAAC-ATCCAAAAATTACCA
1 -TTTAG-CCCCAAACTTTCC-AAAATTACCATTTTGACCCTGAACTTTTCAAAAATTACCA
* ** * * *
1683468 TTTTGACCCCAAACTTTTCCAAAATTACCATTTTG-CCCCCAAATATCCAAAAATTACCA
1 TTTAG-CCCCAAAC-TTTCCAAAATTACCATTTTGACCCTGAACTTTTCAAAAATTACCA
1683527 TTTTA-CCCTCAAA-TTTCCAAAA
1 -TTTAGCCC-CAAACTTTCCAAAA
1683549 ATCACATTTT
Statistics
Matches: 162, Mismatches: 24, Indels: 23
0.78 0.11 0.11
Matches are distributed among these distances:
56 4 0.02
57 16 0.10
58 38 0.23
59 92 0.57
60 12 0.07
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (58 bp):
TTTAGCCCCAAACTTTCCAAAATTACCATTTTGACCCTGAACTTTTCAAAAATTACCA
Found at i:1683439 original size:88 final size:86
Alignment explanation
Indices: 1683283--1683578 Score: 255
Period size: 88 Copynumber: 3.4 Consensus size: 86
1683273 TGTTTTGTTT
* * **** * *
1683283 AAAATT-CACATTTTTACCCCAAAC-TTT-CAAAATTACCATTTTGGCCTTGGACTTTTCAAAAA
1 AAAATTAC-CATTTTAACCCCAAACTTTTCCAAAATTACCATTTTGCCCCCAAAC-ATCCAAAAA
* *
1683345 TTACCATTTAGCCCTAAACTTTTCC-
64 TTACCATTTA-CCCCAAAC--ATCCA
* * *
1683370 AAAATTACCATTTTAACCCTAAACTTTTCCAAAATTA-CATTTTTGTCCTCAAACATCCAAAAAT
1 AAAATTACCATTTTAACCCCAAACTTTTCCAAAATTACCA-TTTTGCCCCCAAACATCCAAAAAT
*
1683434 TACCATTTTTACCCCGAACATCCA
65 TACCA--TTTACCCCAAACATCCA
* *
1683458 AAAATTACCATTTTGACCCCAAACTTTTCCAAAATTACCATTTTGCCCCCAAATATCCAAAAATT
1 AAAATTACCATTTTAACCCCAAACTTTTCCAAAATTACCATTTTGCCCCCAAACATCCAAAAATT
**
1683523 ACCATTTTACCCTCAAATTTCCA
66 ACCA-TTTACCC-CAAACATCCA
* * *
1683546 AAAATCA-CATTTTCGACCTCAAA-TTTTCCAAAA
1 AAAATTACCATTTT-AACCCCAAACTTTTCCAAAA
1683579 GTTTGATTTT
Statistics
Matches: 178, Mismatches: 21, Indels: 20
0.81 0.10 0.09
Matches are distributed among these distances:
87 47 0.26
88 101 0.57
89 26 0.15
90 4 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.33
Consensus pattern (86 bp):
AAAATTACCATTTTAACCCCAAACTTTTCCAAAATTACCATTTTGCCCCCAAACATCCAAAAATT
ACCATTTACCCCAAACATCCA
Found at i:1683565 original size:29 final size:30
Alignment explanation
Indices: 1683283--1683610 Score: 220
Period size: 29 Copynumber: 11.2 Consensus size: 30
1683273 TGTTTTGTTT
* *
1683283 AAAATT-CACATTTTTACCCCAAACTTT-C-
1 AAAATTAC-CATTTTGACCCCAAATTTTCCA
* *** *
1683311 AAAATTACCATTTTGGCCTTGGACTTTT-CA
1 AAAATTACCATTTTGACC-CCAAATTTTCCA
* *
1683341 AAAATTACCATTTAG-CCCTAAACTTTTCC-
1 AAAATTACCATTTTGACCCCAAA-TTTTCCA
* *
1683370 AAAATTACCATTTTAACCCTAAACTTTTCC-
1 AAAATTACCATTTTGACCCCAAA-TTTTCCA
* * **
1683400 AAAATTA-CATTTTTGTCCTCAAA-CATCCA
1 AAAATTACCA-TTTTGACCCCAAATTTTCCA
* * **
1683429 AAAATTACCATTTTTACCCCGAA-CATCCA
1 AAAATTACCATTTTGACCCCAAATTTTCCA
1683458 AAAATTACCATTTTGACCCCAAACTTTTCC-
1 AAAATTACCATTTTGACCCCAAA-TTTTCCA
* *
1683488 AAAATTACCATTTTGCCCCCAAA-TATCCA
1 AAAATTACCATTTTGACCCCAAATTTTCCA
1683517 AAAATTACCATTTT-ACCCTCAAA-TTTCCA
1 AAAATTACCATTTTGACCC-CAAATTTTCCA
* *
1683546 AAAATCA-CATTTTCGACCTCAAATTTTCCA
1 AAAATTACCATTTT-GACCCCAAATTTTCCA
* ** * *
1683576 AAAGTT-TGATTTTAATCCCAAATTTTCCA
1 AAAATTACCATTTTGACCCCAAATTTTCCA
1683605 AAAATT
1 AAAATT
1683611 TTAATTTTGA
Statistics
Matches: 242, Mismatches: 41, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
28 31 0.13
29 121 0.50
30 87 0.36
31 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTGACCCCAAATTTTCCA
Found at i:1683576 original size:59 final size:58
Alignment explanation
Indices: 1683339--1683578 Score: 188
Period size: 59 Copynumber: 4.1 Consensus size: 58
1683329 TTGGACTTTT
* * * * * *
1683339 CAAAAATTACCATTTAG-CCCTAAACTTTTCCAAAATTACCATTTTAACCCTAAACTTTTC
1 CAAAAATTACCATTTTGACCCCAAAC-TTTCCAAAATCACCATTTTGACCCCAAA--TATC
* * * * * * *
1683399 C-AAAATTA-CATTTTTGTCCTCAAAC-ATCCAAAAATTACCATTTTTACCCCGAACATC
1 CAAAAATTACCA-TTTTGACCCCAAACTTTCC-AAAATCACCATTTTGACCCCAAATATC
* *
1683456 CAAAAATTACCATTTTGACCCCAAACTTTTCCAAAATTACCATTTTGCCCCCAAATATC
1 CAAAAATTACCATTTTGACCCCAAAC-TTTCCAAAATCACCATTTTGACCCCAAATATC
* *
1683515 CAAAAATTACCATTTT-ACCCTCAAA-TTTCCAAAAATCA-CATTTTCGACCTCAAATTTTC
1 CAAAAATTACCATTTTGACCC-CAAACTTTCC-AAAATCACCATTTT-GACCCCAAA-TATC
1683574 CAAAA
1 CAAAA
1683579 GTTTGATTTT
Statistics
Matches: 149, Mismatches: 20, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
57 14 0.09
58 41 0.28
59 84 0.56
60 10 0.07
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.32
Consensus pattern (58 bp):
CAAAAATTACCATTTTGACCCCAAACTTTCCAAAATCACCATTTTGACCCCAAATATC
Found at i:1683605 original size:88 final size:88
Alignment explanation
Indices: 1683370--1683610 Score: 240
Period size: 88 Copynumber: 2.7 Consensus size: 88
1683360 AAACTTTTCC
* * * ** * *
1683370 AAAATTACCATTTTAACCCTAAACTTTTCCAAAATTA-CATTTTTGTCCTCAAACATCCAAAAAT
1 AAAATCACCATTTTGACCCCAAACTTTTCCAAAATTACCA-TTTTAACCCCAAATATCCAAAAAT
*
1683434 TACCATTTTTACCCCGAACATCCA
65 TACCATTTTTACCCCAAACATCCA
* **
1683458 AAAATTACCATTTTGACCCCAAACTTTTCCAAAATTACCATTTTGCCCCCAAATATCCAAAAATT
1 AAAATCACCATTTTGACCCCAAACTTTTCCAAAATTACCATTTTAACCCCAAATATCCAAAAATT
**
1683523 ACCA-TTTTACCCTCAAATTTCCA
66 ACCATTTTTACCC-CAAACATCCA
* ** * *
1683546 AAAATCA-CATTTTCGACCTCAAA-TTTTCCAAAAGTT-TGATTTTAATCCCAAATTTTCCAAAA
1 AAAATCACCATTTT-GACCCCAAACTTTTCCAAAA-TTACCATTTTAACCCCAAA-TATCCAAAA
1683608 ATT
63 ATT
1683611 TTAATTTTGA
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
87 35 0.27
88 95 0.72
89 2 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (88 bp):
AAAATCACCATTTTGACCCCAAACTTTTCCAAAATTACCATTTTAACCCCAAATATCCAAAAATT
ACCATTTTTACCCCAAACATCCA
Found at i:1686385 original size:22 final size:22
Alignment explanation
Indices: 1686347--1686401 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1686337 GATAAATAAG
*
1686347 AAAATAAATA-AATAAAA-TAGA
1 AAAATAAAAATAATAAAATTA-A
1686368 AAAATAAAAATAATAAAATTAA
1 AAAATAAAAATAATAAAATTAA
*
1686390 AAATTAAAAATA
1 AAAATAAAAATA
1686402 GGGTTGCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 9 0.30
22 19 0.63
23 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATAAAAATAATAAAATTAA
Found at i:1688803 original size:6 final size:6
Alignment explanation
Indices: 1688792--1688819 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1688782 TGATCAAAAT
1688792 TGAAAG TGAAAG TGAAAG TGAAAG TGAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAA
1688820 GTTGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
TGAAAG
Found at i:1688825 original size:18 final size:17
Alignment explanation
Indices: 1688792--1688836 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1688782 TGATCAAAAT
1688792 TGAAAGTGAAAGTGAAAG
1 TGAAAGTG-AAGTGAAAG
*
1688810 TGAAAGTGAAGTTGAAAT
1 TGAAAGTGAAG-TGAAAG
*
1688828 TAAAAGTGA
1 TGAAAGTGA
1688837 TATGAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (17 bp):
TGAAAGTGAAGTGAAAG
Found at i:1688986 original size:41 final size:40
Alignment explanation
Indices: 1688938--1689038 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
1688928 TCGACCTCGA
** *
1688938 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
1688978 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
1689016 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
1689039 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:1694282 original size:6 final size:6
Alignment explanation
Indices: 1694271--1694298 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1694261 TGATCAAAAT
1694271 TGAAAG TGAAAG TGAAAG TGAAAG TGAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAA
1694299 GTTGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
TGAAAG
Found at i:1694304 original size:18 final size:17
Alignment explanation
Indices: 1694271--1694315 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
1694261 TGATCAAAAT
1694271 TGAAAGTGAAAGTGAAAG
1 TGAAAGTG-AAGTGAAAG
*
1694289 TGAAAGTGAAGTTGAAAT
1 TGAAAGTGAAG-TGAAAG
*
1694307 TAAAAGTGA
1 TGAAAGTGA
1694316 TATGAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (17 bp):
TGAAAGTGAAGTGAAAG
Found at i:1698112 original size:8 final size:9
Alignment explanation
Indices: 1698101--1698149 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
1698091 ATTATAAAAT
1698101 AATTTT-AA
1 AATTTTCAA
1698109 AATTTT-AA
1 AATTTTCAA
*
1698117 AATATTTAAA
1 AAT-TTTCAA
1698127 AATTTTCAA
1 AATTTTCAA
1698136 AATTTTCAA
1 AATTTTCAA
1698145 AATTT
1 AATTT
1698150 ATATTTTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
8 11 0.29
9 22 0.58
10 5 0.13
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTTTCAA
Found at i:1698112 original size:19 final size:18
Alignment explanation
Indices: 1698087--1698171 Score: 68
Period size: 18 Copynumber: 4.7 Consensus size: 18
1698077 CTCTCTCAAC
1698087 AAAAATTATAAAATAATTT
1 AAAAATTATAAAAT-ATTT
* *
1698106 TAAAATTTTAAAATATTT
1 AAAAATTATAAAATATTT
*
1698124 AAAAATTTTCAAAAT-TTT
1 AAAAATTAT-AAAATATTT
* * *
1698142 CAAAATT-T-ATATTTTT
1 AAAAATTATAAAATATTT
1698158 AAAAATATATAAAA
1 AAAAAT-TATAAAA
1698172 ATTAGAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
15 3 0.06
16 8 0.15
17 2 0.04
18 22 0.41
19 19 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAATTATAAAATATTT
Found at i:1698428 original size:27 final size:25
Alignment explanation
Indices: 1698398--1698447 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
1698388 TAAATTATAT
1698398 ATTATATTAACATACAAATATATCTCA
1 ATTATATT--CATACAAATATATCTCA
*
1698425 ATTATATTCATATAAATATATCT
1 ATTATATTCATACAAATATATCT
1698448 ATTTATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 14 0.64
27 8 0.36
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATATTCATACAAATATATCTCA
Found at i:1704519 original size:40 final size:40
Alignment explanation
Indices: 1704474--1704554 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
1704464 AAAGCCTCAT
1704474 AATTATAATAGAGCAATGAGATTCCCAAAAGACCTCATTC
1 AATTATAATAGAGCAATGAGATTCCCAAAAGACCTCATTC
* *
1704514 AATTATAATAGAGCAATGGGATTCCCAAAAGACCTCCTTC
1 AATTATAATAGAGCAATGAGATTCCCAAAAGACCTCATTC
1704554 A
1 A
1704555 TAGCTATGCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.25
Consensus pattern (40 bp):
AATTATAATAGAGCAATGAGATTCCCAAAAGACCTCATTC
Found at i:1706966 original size:14 final size:14
Alignment explanation
Indices: 1706944--1707005 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 14
1706934 ATTTAGATAT
1706944 TAAATTAAAAAATA
1 TAAATTAAAAAATA
* *
1706958 TATATTAAATTTAAGTA
1 TAAATTAAA---AAATA
1706975 TCAAATTAAAAAAT-
1 T-AAATTAAAAAATA
1706989 TAAATATAAAAAATA
1 TAAAT-TAAAAAATA
1707004 TA
1 TA
1707006 TTTTAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
13 4 0.11
14 17 0.45
15 5 0.13
17 5 0.13
18 7 0.18
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
TAAATTAAAAAATA
Found at i:1707132 original size:19 final size:20
Alignment explanation
Indices: 1707097--1707134 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1707087 TGAATTAAGG
1707097 GTGTTTTATTTTATCATTTA
1 GTGTTTTATTTTATCATTTA
*
1707117 GTGTTTT-TTTTTTCATTT
1 GTGTTTTATTTTATCATTT
1707135 TTATAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.13, C:0.05, G:0.11, T:0.71
Consensus pattern (20 bp):
GTGTTTTATTTTATCATTTA
Found at i:1721695 original size:3 final size:3
Alignment explanation
Indices: 1721687--1721725 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1721677 GCACCAACTT
1721687 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1721726 AATTATGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1723152 original size:7 final size:8
Alignment explanation
Indices: 1723121--1723150 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
1723111 AAAATTCATA
1723121 AAAAAAAT
1 AAAAAAAT
1723129 AAAAAAAT
1 AAAAAAAT
1723137 AAAAAAAT
1 AAAAAAAT
1723145 AAAAAA
1 AAAAAA
1723151 TATTAAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1734600 original size:21 final size:21
Alignment explanation
Indices: 1734574--1734687 Score: 77
Period size: 21 Copynumber: 5.2 Consensus size: 21
1734564 AAATAACAGT
1734574 AAAATAACATTAAAAACAACA
1 AAAATAACATTAAAAACAACA
* *
1734595 AAAATAGCAATAAAAACAGTAACA
1 AAAATAACATTAAAAAC---AACA
* *
1734619 AAAATAACATCAAAAATAACA
1 AAAATAACATTAAAAACAACA
* * * *
1734640 TGAAAATAGCAATCAAAACAATAA
1 --AAAATAACATTAAAAACAA-CA
* *
1734664 AAAATAAC-TCAAAAACAATA
1 AAAATAACATTAAAAACAACA
1734684 AAAA
1 AAAA
1734688 AAAACATAAT
Statistics
Matches: 70, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
20 5 0.07
21 26 0.37
22 7 0.10
23 14 0.20
24 18 0.26
ACGTcount: A:0.69, C:0.13, G:0.04, T:0.14
Consensus pattern (21 bp):
AAAATAACATTAAAAACAACA
Found at i:1734662 original size:56 final size:53
Alignment explanation
Indices: 1734543--1734666 Score: 126
Period size: 56 Copynumber: 2.2 Consensus size: 53
1734533 AGTAACATCC
* * *
1734543 AAACAACAAAAACAGCAGCAAAAATAACAGTAAAATAACATTAAAAACAACAAA
1 AAACAATAAAAACAGCAACAAAAATAACAGTAAAATAACATGAAAAACAAC-AA
*
1734597 AATAGCAATAAAAACAGTAACAAAAATAACA-TCAAAAATAACATGAAAATAGCAATC-A
1 AA-A-CAATAAAAACAGCAACAAAAATAACAGT--AAAATAACATGAAAA-A-CAA-CAA
1734655 AAACAATAAAAA
1 AAACAATAAAAA
1734667 ATAACTCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
54 2 0.03
55 2 0.03
56 32 0.54
57 15 0.25
58 4 0.07
59 3 0.05
60 1 0.02
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.12
Consensus pattern (53 bp):
AAACAATAAAAACAGCAACAAAAATAACAGTAAAATAACATGAAAAACAACAA
Found at i:1734667 original size:45 final size:45
Alignment explanation
Indices: 1734565--1734687 Score: 144
Period size: 45 Copynumber: 2.7 Consensus size: 45
1734555 CAGCAGCAAA
*
1734565 AATAACAGTAAAATAACATTAAAAACAACAAAAATAGCAATAAAAAC
1 AATAACA--AAAATAACATCAAAAACAACAAAAATAGCAATAAAAAC
* * *
1734612 AGTAACAAAAATAACATCAAAAATAACATGAAAATAGCAATCAAAAC
1 AATAACAAAAATAACATCAAAAACAACA--AAAATAGCAATAAAAAC
*
1734659 AAT-A-AAAAATAAC-TCAAAAACAATAAAAA
1 AATAACAAAAATAACATCAAAAACAACAAAAA
1734688 AAAACATAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
42 4 0.06
44 10 0.15
45 28 0.42
46 1 0.01
47 24 0.36
ACGTcount: A:0.68, C:0.13, G:0.04, T:0.15
Consensus pattern (45 bp):
AATAACAAAAATAACATCAAAAACAACAAAAATAGCAATAAAAAC
Found at i:1734703 original size:25 final size:25
Alignment explanation
Indices: 1734662--1734714 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1734652 TCAAAACAAT
1734662 AAAAAATAACTCAAAAACAA-TAAAA
1 AAAAAATAACTCAAAAA-AAGTAAAA
*
1734687 AAAAACATAA-TCCAAAAAAGTAAAA
1 AAAAA-ATAACTCAAAAAAAGTAAAA
1734712 AAA
1 AAA
1734715 GCACCAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 19 0.76
26 4 0.16
ACGTcount: A:0.75, C:0.11, G:0.02, T:0.11
Consensus pattern (25 bp):
AAAAAATAACTCAAAAAAAGTAAAA
Found at i:1748736 original size:31 final size:31
Alignment explanation
Indices: 1748692--1748826 Score: 86
Period size: 31 Copynumber: 4.5 Consensus size: 31
1748682 AATAAAAAAA
1748692 TTAGGTA-CTAAATTAGAAAAAAGAATCAAGT
1 TTAGGTATC-AAATTAGAAAAAAGAATCAAGT
*****
1748723 TTAGGTATCAAATTAG-ACTCTTAA--AA-T
1 TTAGGTATCAAATTAGAAAAAAGAATCAAGT
* * *
1748750 TTAAGTATTAACTTAAGAAAAAA-AAGTCAAGT
1 TTAGGTATCAAATT-AGAAAAAAGAA-TCAAGT
* **
1748782 TTAGGTATCAAATTAGGAAAAAGTGTCAAGT
1 TTAGGTATCAAATTAGAAAAAAGAATCAAGT
1748813 TT-GAGTATCAAATT
1 TTAG-GTATCAAATT
1748827 GGACCAAAAC
Statistics
Matches: 77, Mismatches: 18, Indels: 18
0.68 0.16 0.16
Matches are distributed among these distances:
27 12 0.16
28 6 0.08
29 1 0.01
30 4 0.05
31 41 0.53
32 13 0.17
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (31 bp):
TTAGGTATCAAATTAGAAAAAAGAATCAAGT
Found at i:1756268 original size:21 final size:21
Alignment explanation
Indices: 1756242--1756292 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1756232 ATTAATTTTA
1756242 AAAATGATAAAAAAT-TAAAAT
1 AAAATGA-AAAAAATATAAAAT
1756263 AAAATGAAAAAAATATAAAAT
1 AAAATGAAAAAAATATAAAAT
*
1756284 ATAAT-AAAA
1 AAAATGAAAA
1756293 TTAACCTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (21 bp):
AAAATGAAAAAAATATAAAAT
Found at i:1764678 original size:18 final size:18
Alignment explanation
Indices: 1764655--1764697 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1764645 TTTTTAGTTG
1764655 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
1764673 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
1764691 TAATTAA
1 TAATTAA
1764698 AAAGTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:1765220 original size:17 final size:17
Alignment explanation
Indices: 1765195--1765231 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1765185 AAAATTTTAA
*
1765195 AATATTTTTAAATTTTT
1 AATAATTTTAAATTTTT
*
1765212 AATAATTTTAATTTTTT
1 AATAATTTTAAATTTTT
1765229 AAT
1 AAT
1765232 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATAATTTTAAATTTTT
Found at i:1765221 original size:9 final size:9
Alignment explanation
Indices: 1765195--1765231 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
1765185 AAAATTTTAA
1765195 AATATTTTT
1 AATATTTTT
1765204 AA-ATTTTT
1 AATATTTTT
*
1765212 AATAATTTT
1 AATATTTTT
1765221 AAT-TTTTT
1 AATATTTTT
1765229 AAT
1 AAT
1765232 TCTTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 15 0.60
9 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
AATATTTTT
Found at i:1765232 original size:24 final size:23
Alignment explanation
Indices: 1765175--1765269 Score: 100
Period size: 24 Copynumber: 3.8 Consensus size: 23
1765165 AAACATTTAA
1765175 TTAATTTTTCAAAATTTTAAAATATTT
1 TTAATTTTT-AAAATTTT--AAT-TTT
1765202 TTAAATTTTTAATAATTTTAATTTT
1 TT-AATTTTTAA-AATTTTAATTTT
* * *
1765227 TTAATTCTTAAAAATATATATTTT
1 TTAATTTTTAAAATTTTA-ATTTT
1765251 TTAATTTTTAAAATTTTAA
1 TTAATTTTTAAAATTTTAA
1765270 AAATTAATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
23 6 0.10
24 28 0.47
25 5 0.08
26 3 0.05
27 4 0.07
28 13 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TTAATTTTTAAAATTTTAATTTT
Found at i:1767631 original size:18 final size:18
Alignment explanation
Indices: 1767608--1767656 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 18
1767598 TTTTCAGTTG
1767608 TAATTAATTAAAAATTCT
1 TAATTAATTAAAAATTCT
1767626 TAATTAATT--AAA-T-T
1 TAATTAATTAAAAATTCT
*
1767640 TATTTAATTAAAAATTC
1 TAATTAATTAAAAATTC
1767657 ATTCTCATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 9 0.35
15 1 0.04
16 6 0.23
17 1 0.04
18 9 0.35
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATTAATTAAAAATTCT
Found at i:1768191 original size:9 final size:9
Alignment explanation
Indices: 1768179--1768235 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
1768169 ATTAAAAACT
1768179 TTTTTATAA
1 TTTTTATAA
*
1768188 TTTTTATAC
1 TTTTTATAA
*
1768197 TTTTTTTAA
1 TTTTTATAA
*
1768206 TAATTT-TAA
1 T-TTTTATAA
1768215 TTTTT-TAA
1 TTTTTATAA
*
1768223 TTTTTAAAA
1 TTTTTATAA
1768232 TTTT
1 TTTT
1768236 AAAAAATTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 11 0.28
9 26 0.65
10 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1776325 original size:15 final size:15
Alignment explanation
Indices: 1776305--1776355 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1776295 ACAAAATAAT
1776305 AATATAAGCGATTAA
1 AATATAAGCGATTAA
*
1776320 AATATAA-C-ATTTCA
1 AATATAAGCGA-TTAA
*
1776334 AATATAAGTGATTAA
1 AATATAAGCGATTAA
1776349 AATATAA
1 AATATAA
1776356 TCTAAGGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.37
15 17 0.57
16 1 0.03
ACGTcount: A:0.55, C:0.06, G:0.08, T:0.31
Consensus pattern (15 bp):
AATATAAGCGATTAA
Found at i:1778818 original size:2 final size:2
Alignment explanation
Indices: 1778811--1778840 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1778801 GGTGTGAATT
*
1778811 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1778841 ATAGGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1783174 original size:29 final size:30
Alignment explanation
Indices: 1783110--1783182 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
1783100 AATTCTAAAA
1783110 TTATACATGAATTATGATTTAATGTGCAATT
1 TTATACATGAATTATGATTT-ATGTGCAATT
* *
1783141 GTATACATGAACTT-TGATTT-TGTGTAATT
1 TTATACATGAA-TTATGATTTATGTGCAATT
*
1783170 TTATACATAAATT
1 TTATACATGAATT
1783183 TTTTATTTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 2 0.05
29 17 0.46
31 16 0.43
32 2 0.05
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.47
Consensus pattern (30 bp):
TTATACATGAATTATGATTTATGTGCAATT
Found at i:1783399 original size:30 final size:29
Alignment explanation
Indices: 1783313--1783402 Score: 81
Period size: 31 Copynumber: 2.9 Consensus size: 29
1783303 ATTTCTTTAA
* *
1783313 ATGTGTATGATTAAATCAAAATTAAAGTTTC
1 ATGTGTATAATT-AA-CCAAATTAAAGTTTC
* * * *
1783344 AAGTATACATTTGAACCACAATTAAAGTTTC
1 ATGTGTATAATT-AACCA-AATTAAAGTTTC
1783375 ATGTGTATAATTACACCAAATTAAAGTT
1 ATGTGTATAATTA-ACCAAATTAAAGTT
1783403 CATATGTGCA
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
30 13 0.28
31 33 0.72
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (29 bp):
ATGTGTATAATTAACCAAATTAAAGTTTC
Found at i:1783415 original size:29 final size:30
Alignment explanation
Indices: 1783358--1783436 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
1783348 ATACATTTGA
* *
1783358 ACCACAATTAAAGTTTCATGTGTATAATT-AC
1 ACCA-AATTAAAG-TTCATATGTACAATTCAC
*
1783389 ACCAAATTAAAGTTCATATGTGCAATTGCAC
1 ACCAAATTAAAGTTCATATGTACAATT-CAC
**
1783420 ATTAAATTAAAGTTCAT
1 ACCAAATTAAAGTTCAT
1783437 TTATAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 12 0.29
30 8 0.20
31 21 0.51
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.34
Consensus pattern (30 bp):
ACCAAATTAAAGTTCATATGTACAATTCAC
Found at i:1783544 original size:18 final size:19
Alignment explanation
Indices: 1783509--1783546 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1783499 TTTACCCCCA
*
1783509 TTTTCAAAAGTTGTAATTT
1 TTTTCAAAAGTTGAAATTT
*
1783528 TTTTCAATA-TTGAAATTT
1 TTTTCAAAAGTTGAAATTT
1783546 T
1 T
1783547 AAAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.32, C:0.05, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTTCAAAAGTTGAAATTT
Found at i:1784972 original size:26 final size:26
Alignment explanation
Indices: 1784935--1785009 Score: 105
Period size: 28 Copynumber: 2.8 Consensus size: 26
1784925 CGAAGTACTT
*
1784935 AACAGTAAGCACACAAGTGCTGGGGA
1 AACAGTAGGCACACAAGTGCTGGGGA
*
1784961 AACAGTAGGCACACACAAGTGTTGGGGA
1 AACAGTAGG--CACACAAGTGCTGGGGA
1784989 AACAGTAGGCACACACAGTGC
1 AACAGTAGGCACACA-AGTGC
1785010 AATCCAGTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 14 0.33
27 4 0.09
28 25 0.58
ACGTcount: A:0.37, C:0.21, G:0.29, T:0.12
Consensus pattern (26 bp):
AACAGTAGGCACACAAGTGCTGGGGA
Found at i:1784986 original size:28 final size:28
Alignment explanation
Indices: 1784944--1785009 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
1784934 TAACAGTAAG
1784944 CACACAAGTGCTGGGGAAACAGTAGGCA
1 CACACAAGTGCTGGGGAAACAGTAGGCA
*
1784972 CACACAAGTGTTGGGGAAACAGTAGGCA
1 CACACAAGTGCTGGGGAAACAGTAGGCA
1785000 CACAC-AGTGC
1 CACACAAGTGC
1785010 AATCCAGTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 4 0.11
28 32 0.89
ACGTcount: A:0.35, C:0.23, G:0.30, T:0.12
Consensus pattern (28 bp):
CACACAAGTGCTGGGGAAACAGTAGGCA
Found at i:1785017 original size:23 final size:22
Alignment explanation
Indices: 1784991--1785071 Score: 117
Period size: 23 Copynumber: 3.6 Consensus size: 22
1784981 GTTGGGGAAA
1784991 CAGTAGGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
1785013 CCAGTAGGCACACACAGTGCAAT
1 -CAGTAGGCACACACAGTGCAAT
* * *
1785036 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
1785059 CAGTAGGCACACA
1 CAGTAGGCACACA
1785072 AGGTGCGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.36, C:0.28, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:1785085 original size:23 final size:22
Alignment explanation
Indices: 1784987--1785109 Score: 108
Period size: 23 Copynumber: 5.4 Consensus size: 22
1784977 AAGTGTTGGG
1784987 GAAACAGTAGGCACACACAGTGC
1 GAAACAGTAGGCACACA-AGTGC
*
1785010 -AATCCAGTAGGCACACACAGTGC
1 GAA-ACAGTAGGCACACA-AGTGC
* * *
1785033 -AATCAGTAGGCGCACATAGCGC
1 GAAACAGTAGGCACACA-AGTGC
1785055 -AAATCAGTAGGCACACAAGGTGC
1 GAAA-CAGTAGGCACACAA-GTGC
**
1785078 GAAACAGTAAACACACAAAGTGC
1 GAAACAGTAGGCACAC-AAGTGC
1785101 GAAACAGTA
1 GAAACAGTA
1785110 AGCGCGCTAA
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
22 21 0.25
23 59 0.69
24 5 0.06
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (22 bp):
GAAACAGTAGGCACACAAGTGC
Done.