Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009604.1 Hibiscus syriacus cultivar Beakdansim tig00116984_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3548142
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 17
Found at i:2124712 original size:33 final size:33
Alignment explanation
Indices: 2124667--2124750 Score: 118
Period size: 31 Copynumber: 2.6 Consensus size: 33
2124657 ATTTTTAGTG
* *
2124667 TATACTAGATAGTTTATATATACTAATTAACTA
1 TATACTATATAGTTTATATATACTAATAAACTA
2124700 TATACTATATAG-TT-TATATACTAATAAACTA
1 TATACTATATAGTTTATATATACTAATAAACTA
* *
2124731 TGTAATATATAGTTTATATA
1 TATACTATATAGTTTATATA
2124751 CCATATAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
31 26 0.58
32 4 0.09
33 15 0.33
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (33 bp):
TATACTATATAGTTTATATATACTAATAAACTA
Found at i:2124719 original size:16 final size:16
Alignment explanation
Indices: 2124698--2124766 Score: 77
Period size: 16 Copynumber: 4.4 Consensus size: 16
2124688 ACTAATTAAC
2124698 TATATACTATATAGTT
1 TATATACTATATAGTT
***
2124714 TATATACTA-ATAAAC
1 TATATACTATATAGTT
* *
2124729 TATGTAATATATAGTT
1 TATATACTATATAGTT
*
2124745 TATATACCATATAGTT
1 TATATACTATATAGTT
2124761 TATATA
1 TATATA
2124767 TACTAATGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
15 10 0.24
16 31 0.76
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (16 bp):
TATATACTATATAGTT
Found at i:2124769 original size:49 final size:47
Alignment explanation
Indices: 2124698--2124799 Score: 159
Period size: 49 Copynumber: 2.1 Consensus size: 47
2124688 ACTAATTAAC
* *
2124698 TATATACTATATAGTTTATATACTAATAAACTATGTAATATATAGTT
1 TATATACCATATAGTTTATATACTAATAAACTATATAATATATAGTT
*
2124745 TATATACCATATAGTTTATATATACTAATGAACTATATAATATATAGTT
1 TATATACCATATAG-TT-TATATACTAATAAACTATATAATATATAGTT
2124794 TATATA
1 TATATA
2124800 TACCATATTC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
47 13 0.26
48 2 0.04
49 35 0.70
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (47 bp):
TATATACCATATAGTTTATATACTAATAAACTATATAATATATAGTT
Found at i:2124799 original size:16 final size:16
Alignment explanation
Indices: 2124698--2124799 Score: 66
Period size: 16 Copynumber: 6.4 Consensus size: 16
2124688 ACTAATTAAC
*
2124698 TATATACTATATAGTT
1 TATATAATATATAGTT
* ***
2124714 TATATACTA-ATAAAC
1 TATATAATATATAGTT
*
2124729 TATGTAATATATAGTT
1 TATATAATATATAGTT
**
2124745 TATATACCATATAGTT
1 TATATAATATATAGTT
**
2124761 TATAT-ATACTA-ATGAAC
1 TATATAATA-TATA-G-TT
2124778 TATATAATATATAGTT
1 TATATAATATATAGTT
2124794 TATATA
1 TATATA
2124800 TACCATATTC
Statistics
Matches: 63, Mismatches: 17, Indels: 12
0.68 0.18 0.13
Matches are distributed among these distances:
15 12 0.19
16 39 0.62
17 8 0.13
18 4 0.06
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (16 bp):
TATATAATATATAGTT
Found at i:2124922 original size:2 final size:2
Alignment explanation
Indices: 2124915--2125052 Score: 78
Period size: 2 Copynumber: 70.0 Consensus size: 2
2124905 CCATTTACTT
* *
2124915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA CTA TA TGG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA T-A
* * * *
2124959 TT TA T- TA -A TA TA TA TA TT TA GT- TCA TA TA TA CA CTA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA -TA TA TA
* *
2124999 GTT TA TA TA TA T- TA TA T- TA -A TA TA TA CTT 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
2125040 T- TA -A TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
2125053 ATTGATTTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 32
0.69 0.10 0.21
Matches are distributed among these distances:
1 9 0.09
2 89 0.85
3 7 0.07
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2125003 original size:41 final size:38
Alignment explanation
Indices: 2124923--2125024 Score: 107
Period size: 40 Copynumber: 2.6 Consensus size: 38
2124913 TTTATATATA
* * *
2124923 TATATATATATATATATATATATATAAACTATATGGTT
1 TATATATATATATTTATATATATATAAACTACATAGTT
*
2124961 TATTAATATATATATTTAGT-TCATATATACACTACATAGTT
1 TA-T-ATATATATATTTA-TAT-ATATATAAACTACATAGTT
*
2125002 TATATATATTATATTAATATATA
1 TATATATA-TATATTTATATATA
2125025 CTTTATATAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
38 2 0.04
39 10 0.19
40 22 0.42
41 19 0.36
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (38 bp):
TATATATATATATTTATATATATATAAACTACATAGTT
Found at i:2125023 original size:13 final size:13
Alignment explanation
Indices: 2125005--2125052 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
2124995 CATAGTTTAT
2125005 ATATATTATATTA
1 ATATATTATATTA
2125018 ATATA-TACT-TT-
1 ATATATTA-TATTA
2125029 ATATATATATATTA
1 ATATAT-TATATTA
2125043 ATATATTATA
1 ATATATTATA
2125053 ATTGATTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
11 5 0.17
12 5 0.17
13 14 0.47
14 6 0.20
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATATTATATTA
Found at i:2125023 original size:15 final size:15
Alignment explanation
Indices: 2125002--2125052 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
2124992 CTACATAGTT
2125002 TATATATATTATAT-
1 TATATATATTATATA
2125016 TAATATATACTT-TATA
1 T-ATATATA-TTATATA
2125032 TATATATATTA-ATA
1 TATATATATTATATA
2125046 TAT-TATA
1 TATATATA
2125053 ATTGATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 4 0.12
14 9 0.27
15 17 0.52
16 3 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATTATATA
Found at i:2125045 original size:25 final size:26
Alignment explanation
Indices: 2125000--2125048 Score: 91
Period size: 25 Copynumber: 1.9 Consensus size: 26
2124990 CACTACATAG
2125000 TTTATATATATTATATTAATATATAC
1 TTTATATATATTATATTAATATATAC
2125026 TTTATATATA-TATATTAATATAT
1 TTTATATATATTATATTAATATAT
2125049 TATAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (26 bp):
TTTATATATATTATATTAATATATAC
Found at i:2127465 original size:15 final size:15
Alignment explanation
Indices: 2127447--2127476 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2127437 ACATGTCAGT
2127447 TTGTTATATGTTAGA
1 TTGTTATATGTTAGA
2127462 TTGTTATATGTTAGA
1 TTGTTATATGTTAGA
2127477 GGGTTTCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (15 bp):
TTGTTATATGTTAGA
Found at i:2133489 original size:3 final size:3
Alignment explanation
Indices: 2133481--2133512 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2133471 TGAGAAAGCT
2133481 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
2133513 TGATGATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2135608 original size:20 final size:21
Alignment explanation
Indices: 2135583--2135662 Score: 69
Period size: 20 Copynumber: 3.9 Consensus size: 21
2135573 ATCTTAAAAA
2135583 TGGTATCGATACCATCCC-C-T
1 TGGTATCGATACCA-CCCTCAT
*
2135603 TGGTATCGATACTACCCTCAT
1 TGGTATCGATACCACCCTCAT
* *
2135624 T-GTATCGATACC-CTCTTCAAC
1 TGGTATCGATACCAC-CCTC-AT
*
2135645 TGGTATCGATACTACCCT
1 TGGTATCGATACCACCCT
2135663 TAAGAAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.08
20 27 0.56
21 4 0.08
22 12 0.25
23 1 0.02
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.33
Consensus pattern (21 bp):
TGGTATCGATACCACCCTCAT
Found at i:2140744 original size:13 final size:12
Alignment explanation
Indices: 2140725--2140784 Score: 50
Period size: 13 Copynumber: 4.8 Consensus size: 12
2140715 TTAAAATAAA
*
2140725 TAAAATATAATT
1 TAAAAAATAATT
2140737 T-AAAAATATATT
1 TAAAAAATA-ATT
* *
2140749 AAAAAAATTAGTT
1 TAAAAAA-TAATT
*
2140762 TAAAAAATAAAGT
1 TAAAAAAT-AATT
2140775 TAAAAAATAA
1 TAAAAAATAA
2140785 CCTTGTAGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
11 6 0.16
12 7 0.18
13 23 0.61
14 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
TAAAAAATAATT
Found at i:2140755 original size:26 final size:27
Alignment explanation
Indices: 2140721--2140781 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
2140711 ATGGTTAAAA
*
2140721 TAAATAAAATATAATTT-AAAAATATA-T
1 TAAA-AAAAT-TAATTTAAAAAATAAAGT
*
2140748 TAAAAAAATTAGTTTAAAAAATAAAGT
1 TAAAAAAATTAATTTAAAAAATAAAGT
2140775 TAAAAAA
1 TAAAAAA
2140782 TAACCTTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 13 0.43
27 12 0.40
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (27 bp):
TAAAAAAATTAATTTAAAAAATAAAGT
Found at i:2150503 original size:29 final size:32
Alignment explanation
Indices: 2150458--2150529 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 32
2150448 GTTACAAGTC
* * *
2150458 TTAGAAAATTTTGGGGAC-CATTTGA-AATTT
1 TTAGAAAAGTTTGGGGACTAATTCGATAATTT
2150488 TT-GAAAAGTTTGGGGACTAATTCGATAATTT
1 TTAGAAAAGTTTGGGGACTAATTCGATAATTT
2150519 TTAGAAAAGTT
1 TTAGAAAAGTT
2150530 GTGAATGGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 14 0.39
30 7 0.19
31 7 0.19
32 8 0.22
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (32 bp):
TTAGAAAAGTTTGGGGACTAATTCGATAATTT
Found at i:2155195 original size:67 final size:67
Alignment explanation
Indices: 2155086--2155219 Score: 187
Period size: 67 Copynumber: 2.0 Consensus size: 67
2155076 CGAAGTGTTT
* * * *
2155086 ACACATAAGATCGTGCTCACCATATGCACTAAGTGTCTTTACACACTATAGCGCTATCCCAAATA
1 ACACACAAGATCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
2155151 TG
66 TG
* * * * *
2155153 ACACACAAGGTCGTGCCCACCACCTGCACTAAGTGTCCTTACACACTATAGTGCTATCTCGAATA
1 ACACACAAGATCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
2155218 TG
66 TG
2155220 CAGTGTACTG
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (67 bp):
ACACACAAGATCGTGCCCACCACATGCACTAAGTGTCCTTACACACTATAGCGCTATCCCAAATA
TG
Found at i:2156655 original size:19 final size:20
Alignment explanation
Indices: 2156631--2156674 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2156621 AAACAATCCG
*
2156631 ATTTC-ACATTCTAACATCA
1 ATTTCAACACTCTAACATCA
*
2156650 ATTTCAACACTCTAACATTA
1 ATTTCAACACTCTAACATCA
2156670 ATTTC
1 ATTTC
2156675 TAGAATAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTTCAACACTCTAACATCA
Found at i:2160411 original size:19 final size:20
Alignment explanation
Indices: 2160364--2160414 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
2160354 TTAGTCTTTC
**
2160364 AGTATCGATACTGACCCTTG
1 AGTATCGATACCCACCCTTG
* *
2160384 AGTACCGATACCCACCTTTG
1 AGTATCGATACCCACCCTTG
2160404 -GTATCGATACC
1 AGTATCGATACC
2160415 GAAAATGGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTATCGATACCCACCCTTG
Found at i:2165078 original size:22 final size:23
Alignment explanation
Indices: 2165020--2165116 Score: 119
Period size: 23 Copynumber: 4.3 Consensus size: 23
2165010 TATCGAAGTG
* *
2165020 CCACATA-TTTT-TCCTGAAGCA
1 CCACATAGTTTTGTCCCGAAGGA
* **
2165041 CCACATAGGTTTGTCCTAAAGGA
1 CCACATAGTTTTGTCCCGAAGGA
*
2165064 CCAC-TAGTTTTGTCCCGAATGA
1 CCACATAGTTTTGTCCCGAAGGA
2165086 CCACATAGTTTTGTCCCGAAGGA
1 CCACATAGTTTTGTCCCGAAGGA
2165109 CCACATAG
1 CCACATAG
2165117 AACACTCGAC
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
21 7 0.11
22 21 0.32
23 37 0.57
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (23 bp):
CCACATAGTTTTGTCCCGAAGGA
Found at i:2165849 original size:18 final size:19
Alignment explanation
Indices: 2165770--2165859 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
2165760 TTTGATTATT
* * *
2165770 GTATAGATACCTTCCTCTTG
1 GTATCGATACCTACC-CTTC
*
2165790 GTATCGATACCTACCCTTG
1 GTATCGATACCTACCCTTC
2165809 GTATCGATACCTACCCTTC
1 GTATCGATACCTACCCTTC
2165828 GTATCGATACCTACCC-TC
1 GTATCGATACCTACCCTTC
2165846 GTATCGATACCTAC
1 GTATCGATACCTAC
2165860 ACCTCAGTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
18 16 0.24
19 38 0.57
20 13 0.19
ACGTcount: A:0.22, C:0.32, G:0.13, T:0.32
Consensus pattern (19 bp):
GTATCGATACCTACCCTTC
Found at i:2167134 original size:71 final size:69
Alignment explanation
Indices: 2167059--2167251 Score: 187
Period size: 69 Copynumber: 2.7 Consensus size: 69
2167049 TAAGAACTAT
* *
2167059 TTATTTCATTAATAAAAATTAAAAATATGTAAAAACT-TCTGTAAATTATTGTTAATAAATAAAA
1 TTATTTCATTAATAAAAATTAAAAATATATAAAAACTAT-TGTAAATTATAGTTAAT-AA-AAAA
2167123 ATAAAAA
63 ATAAAAA
* * *
2167130 TTATTTCTTCCATTAACAAAAATAAAAAATATAT-AAAACTATTGTAATTTATAGTTAATAAAAA
1 TTA--T-TT-CATTAATAAAAATTAAAAATATATAAAAACTATTGTAAATTATAGTTAATAAAAA
*
2167194 ATTAAAAA
62 AATAAAAA
** * *
2167202 TTATTTC-TTCCTTAAAAAATTTAAAATATATAAAAA-TGTTGTAAATTATA
1 TTATTTCATT-AAT-AAAAATTAAAAATATATAAAAACTATTGTAAATTATA
2167252 TTCAAATATG
Statistics
Matches: 101, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
67 2 0.02
68 1 0.01
69 29 0.29
70 5 0.05
71 3 0.03
72 13 0.13
73 3 0.03
74 23 0.23
75 22 0.22
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (69 bp):
TTATTTCATTAATAAAAATTAAAAATATATAAAAACTATTGTAAATTATAGTTAATAAAAAAATA
AAAA
Found at i:2167244 original size:69 final size:73
Alignment explanation
Indices: 2167056--2167251 Score: 231
Period size: 75 Copynumber: 2.7 Consensus size: 73
2167046 AATTAAGAAC
* * * * *
2167056 TATTTATTTCATTAATAAAAATTAAAAATATGTAAAAACTTCTGTAAATTATTGTTAATAAATAA
1 TATTTCTTCCATTAACAAAAATTAAAAATATATAAAAA-TT-TGTAAATTATAGTTAATAAATAA
2167121 AAATAAAAAT
64 AAATAAAAAT
* * *
2167131 TATTTCTTCCATTAACAAAAATAAAAAATATATAAAACTATTGTAATTTATAGTTAAT-AA-AAA
1 TATTTCTTCCATTAACAAAAATTAAAAATATATAAAAAT-TTGTAAATTATAGTTAATAAATAAA
*
2167194 ATTAAAAAT
65 AATAAAAAT
*
2167203 TATTTCTTCC-TT-A-AAAAATTTAAAATATATAAAAATGTTGTAAATTATA
1 TATTTCTTCCATTAACAAAAATTAAAAATATATAAAAAT-TTGTAAATTATA
2167252 TTCAAATATG
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
69 31 0.29
70 1 0.01
71 2 0.02
72 21 0.20
73 2 0.02
74 16 0.15
75 33 0.31
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.39
Consensus pattern (73 bp):
TATTTCTTCCATTAACAAAAATTAAAAATATATAAAAATTTGTAAATTATAGTTAATAAATAAAA
ATAAAAAT
Found at i:2168398 original size:30 final size:30
Alignment explanation
Indices: 2168339--2168417 Score: 117
Period size: 30 Copynumber: 2.7 Consensus size: 30
2168329 AAATGATGCG
* *
2168339 CTCTCAACCCGTAAACAT--TACATCAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
*
2168367 CTCTCAACCCGAAAACATCACACAACAATC
1 CTCTCAACCCGTAAACATCACACAACAATC
2168397 CTCTCAACCCGTAAACATCAC
1 CTCTCAACCCGTAAACATCAC
2168418 CCGATAATCT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 17 0.38
30 28 0.62
ACGTcount: A:0.38, C:0.39, G:0.04, T:0.19
Consensus pattern (30 bp):
CTCTCAACCCGTAAACATCACACAACAATC
Found at i:2174283 original size:27 final size:28
Alignment explanation
Indices: 2174229--2174287 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
2174219 TTCTAAAAAT
*
2174229 ATTAATAATTACAAAAATTAATATATAA
1 ATTAATAATTACAAAAATTAATAAATAA
2174257 ATTAATAA-TA-AAAAATTAAATAAATAA
1 ATTAATAATTACAAAAATT-AATAAATAA
2174284 ATTA
1 ATTA
2174288 TTACTAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 7 0.24
27 14 0.48
28 8 0.28
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (28 bp):
ATTAATAATTACAAAAATTAATAAATAA
Found at i:2174451 original size:29 final size:28
Alignment explanation
Indices: 2174402--2174456 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
2174392 ATAACAGCGA
*
2174402 AAAAAATAAAATAATTAAATAAAATACT
1 AAAAAATAAAATAAATAAATAAAATACT
* *
2174430 AAAAAATAAATTAAATAGAATAGAATA
1 AAAAAATAAAATAAATA-AATAAAATA
2174457 TAATATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (28 bp):
AAAAAATAAAATAAATAAATAAAATACT
Found at i:2174592 original size:21 final size:22
Alignment explanation
Indices: 2174568--2174609 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2174558 TTTATAGAAT
2174568 AGGATAGAGG-GTGTGAACGGG
1 AGGATAGAGGAGTGTGAACGGG
* *
2174589 AGGATGGGGGAGTGTGAACGG
1 AGGATAGAGGAGTGTGAACGG
2174610 TCCGGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.26, C:0.05, G:0.55, T:0.14
Consensus pattern (22 bp):
AGGATAGAGGAGTGTGAACGGG
Found at i:2177182 original size:2 final size:2
Alignment explanation
Indices: 2177175--2177214 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2177165 TAAAATAGTC
2177175 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
2177215 TTATGGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2179729 original size:54 final size:57
Alignment explanation
Indices: 2179634--2179752 Score: 149
Period size: 55 Copynumber: 2.2 Consensus size: 57
2179624 TTGGATAAAT
* ** * *
2179634 TTAGCTT-TTTCGAAAAGATTCATTTACAATTATCAATAAACCCCT-AAACTTAGGC
1 TTAGCTTCTTTCGAAAAGATTCATTTAAAAACATCAATAAACCCCTAAAAATCAGGC
2179689 TTAGCTTCTTTC-AAAA-ATTCATTTAAAAACATC-ATGAAACCCCTAAAAATCAGGC
1 TTAGCTTCTTTCGAAAAGATTCATTTAAAAACATCAAT-AAACCCCTAAAAATCAGGC
2179744 TTAGCTTCT
1 TTAGCTTCT
2179753 AAAAATCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
53 2 0.04
54 22 0.39
55 28 0.50
56 4 0.07
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (57 bp):
TTAGCTTCTTTCGAAAAGATTCATTTAAAAACATCAATAAACCCCTAAAAATCAGGC
Found at i:2179985 original size:42 final size:42
Alignment explanation
Indices: 2179926--2180049 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 42
2179916 AAGTTCTTAT
* * *
2179926 CATCTTGCTCGAAAGACTTATAGATAACCCGAAGGATTTAAG
1 CATCATGCTCGAAAGACTTATAGATAGCCCGAAGGACTTAAG
* * **
2179968 CATCATGCTCGAAAGACTTACT-GATGGCCCAAAGGACTTACT
1 CATCATGCTCGAAAGACTTA-TAGATAGCCCGAAGGACTTAAG
*
2180010 CATCATGCTCAAAAGACTTA-ATGATAGCCCGAAGGACTTA
1 CATCATGCTCGAAAGACTTATA-GATAGCCCGAAGGACTTA
2180050 TGCTAATTCG
Statistics
Matches: 69, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
42 68 0.99
43 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (42 bp):
CATCATGCTCGAAAGACTTATAGATAGCCCGAAGGACTTAAG
Found at i:2180027 original size:22 final size:22
Alignment explanation
Indices: 2179968--2180029 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 22
2179958 AGGATTTAAG
*
2179968 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCAAAAGACTTACT
* * * *
2179990 GAT--GGCCCAAAGGACTTACT
1 CATCATGCTCAAAAGACTTACT
2180010 CATCATGCTCAAAAGACTTA
1 CATCATGCTCAAAAGACTTA
2180030 ATGATAGCCC
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
20 15 0.52
22 14 0.48
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (22 bp):
CATCATGCTCAAAAGACTTACT
Found at i:2180255 original size:85 final size:85
Alignment explanation
Indices: 2180111--2180279 Score: 259
Period size: 85 Copynumber: 2.0 Consensus size: 85
2180101 GTGAGGCATT
* * * *
2180111 GCTGATTCGAAGTATTGTGAATCGAGCAAAGGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
1 GCTGATTCGAAGTAGTGTGAATCGAGAAAAGGAAACGTTGAAAACATCATGCCCAAAGGTCTTAT
*
2180176 GGATGGCCCGAAGGACTTAA
66 GGATGGCACGAAGGACTTAA
* *
2180196 GCTGATTCGAAGT-GTGTGAATCGAGAAAAAGGAAACGTTGAAAACATCTTGCCTAAAGGTCTTA
1 GCTGATTCGAAGTAGTGTGAATCGAG-AAAAGGAAACGTTGAAAACATCATGCCCAAAGGTCTTA
2180260 TGGATGGCACGAAGGACTTA
65 TGGATGGCACGAAGGACTTA
2180280 TCATCTTGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
84 11 0.14
85 65 0.86
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (85 bp):
GCTGATTCGAAGTAGTGTGAATCGAGAAAAGGAAACGTTGAAAACATCATGCCCAAAGGTCTTAT
GGATGGCACGAAGGACTTAA
Found at i:2180577 original size:53 final size:53
Alignment explanation
Indices: 2180406--2180655 Score: 252
Period size: 52 Copynumber: 4.6 Consensus size: 53
2180396 TTCTTAGTTG
* * * *
2180406 TCAAGAAACCCCTAAAAATTACGCTTAAATTCTTTTTAAAAACTCTTTTGAAAATCATCA
1 TCAAGAAACCCCTAAAAATTAGGCTT-AGTT-TCTTT-AAAACTCATTT-AAAA--A-CA
* * *
2180466 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTC-TAAAAACTCATTTAAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTAAAAACA
* * * * *
2180518 TCAAGAAATCCTTAAAAATTAGGCTTAATTTCTTTAAAATTCATTTGAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTAAAAACA
* * * * *
2180571 TTAAGAAACCCCT-AAAATTAGGTTTAGCTTCTTTCAAATTCATTTAAAAACA
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTAAAAACA
* *
2180623 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCT
2180656 AAAAATCTTT
Statistics
Matches: 161, Mismatches: 27, Indels: 11
0.81 0.14 0.06
Matches are distributed among these distances:
52 75 0.47
53 44 0.27
55 4 0.02
56 10 0.06
57 1 0.01
58 1 0.01
59 3 0.02
60 23 0.14
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (53 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAGTTTCTTTAAAACTCATTTAAAAACA
Found at i:2180627 original size:105 final size:109
Alignment explanation
Indices: 2180406--2180655 Score: 294
Period size: 105 Copynumber: 2.3 Consensus size: 109
2180396 TTCTTAGTTG
* * *
2180406 TCAAGAAACCCCTAAAAATTACGCTTAAATTCTTTTTAAAAACTCTTTTGAAAATCATCATCAAG
1 TCAAGAAACCCCTAAAAATTAGGCTT-AATT-TCTTTAAAAACTCATTTGAAAATCAT-ATCAAG
*
2180471 AAACCCCTGAAAATCAGGCTTAGTTTCTAAAAACTCATTTAAAAACA
63 AAACCCCTGAAAATCAGGCTTAGCTTCTAAAAACTCATTTAAAAACA
* * *
2180518 TCAAGAAATCCTTAAAAATTAGGCTTAATTTCTTT-AAAATTCATTTGAAAA-CAT-T-AAGAAA
1 TCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTAAAAACTCATTTGAAAATCATATCAAGAAA
* * ** *
2180579 CCCCT-AAAATTAGGTTTAGCTTCTTTCAAATTCATTTAAAAACA
66 CCCCTGAAAATCAGGCTTAGCTTC-TAAAAACTCATTTAAAAACA
* * *
2180623 TCAAGAAACCCCTGAAAATCAGGCTTAGTTTCT
1 TCAAGAAACCCCTAAAAATTAGGCTTAATTTCT
2180656 AAAAATCTTT
Statistics
Matches: 120, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
104 15 0.12
105 56 0.47
106 1 0.01
108 3 0.03
109 14 0.12
110 4 0.03
111 4 0.03
112 23 0.19
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (109 bp):
TCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTAAAAACTCATTTGAAAATCATATCAAGAAA
CCCCTGAAAATCAGGCTTAGCTTCTAAAAACTCATTTAAAAACA
Found at i:2180711 original size:39 final size:39
Alignment explanation
Indices: 2180657--2180848 Score: 103
Period size: 36 Copynumber: 5.1 Consensus size: 39
2180647 TTAGTTTCTA
* * * * *
2180657 AAAATCTTTTGTTTCGAGCGAAACTATCTTAAGTGAGAT
1 AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
* *
2180696 AAAATCTTCTATTTCGAGTGAAACTGTCTAAAGGGAGAC
1 AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
* * ** * * *
2180735 AAAA--TT-TGTTTCAAGAAAAACTGTCTCAAGAGAGAC
1 AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
* ** * * *
2180771 AAAAT-TTGT-TTTTAAGGGAAACTGTCTAAAGAGAGAC
1 AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
* * * * *
2180808 AAAAT-TTGT-TTT-AAGGGAAACTGTCTAAAGAGAGAC
1 AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
2180844 AAAAT
1 AAAAT
2180849 TCGTTTCAAG
Statistics
Matches: 134, Mismatches: 17, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
36 57 0.43
37 40 0.30
38 1 0.01
39 36 0.27
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (39 bp):
AAAATCTTCTATTTCGAGCGAAACTATCTAAAGGGAGAC
Found at i:2180803 original size:37 final size:36
Alignment explanation
Indices: 2180715--2180864 Score: 228
Period size: 36 Copynumber: 4.1 Consensus size: 36
2180705 TATTTCGAGT
* *
2180715 GAAACTGTCTAAAGGGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
* * *
2180751 AAAACTGTCTCAAGAGAGACAAAATTTGTTTTTAAGG
1 GAAACTGTCTAAAGAGAGACAAAATTTG-TTTCAAGG
*
2180788 GAAACTGTCTAAAGAGAGACAAAATTTGTTTTAAGG
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
*
2180824 GAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGG
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
2180860 GAAAC
1 GAAAC
2180865 GTTCTCAAAG
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
36 72 0.69
37 32 0.31
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.25
Consensus pattern (36 bp):
GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGG
Found at i:2180807 original size:73 final size:72
Alignment explanation
Indices: 2180715--2180864 Score: 228
Period size: 73 Copynumber: 2.1 Consensus size: 72
2180705 TATTTCGAGT
* * *
2180715 GAAACTGTCTAAAGGGAGACAAAATTTGTTTCAAGAAAAACTGTCTCAAGAGAGACAAAATTTGT
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAATTCG-
*
2180780 TTTTAAGG
65 TTTCAAGG
* **
2180788 GAAACTGTCTAAAGAGAGACAAAATTTGTTTTAAGGGAAACTGTCTAAAGAGAGACAAAATTCGT
1 GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAATTCGT
2180853 TTCAAGG
66 TTCAAGG
2180860 GAAAC
1 GAAAC
2180865 GTTCTCAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 12 0.17
73 58 0.83
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.25
Consensus pattern (72 bp):
GAAACTGTCTAAAGAGAGACAAAATTTGTTTCAAGAAAAACTGTCTAAAGAGAGACAAAATTCGT
TTCAAGG
Found at i:2180928 original size:65 final size:65
Alignment explanation
Indices: 2180824--2180993 Score: 252
Period size: 65 Copynumber: 2.6 Consensus size: 65
2180814 TGTTTTAAGG
* * * * *
2180824 GAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGGAAACGT-TCTCAAAGTTTATTTTTCAAT
1 GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAACGTAT-TCAAAGTTTATATTTCAAG
2180888 A
65 A
* *
2180889 GAAACTGTCTCAAGGGAGACAAAATTTGTTTAAAGGGAAACGTATTCAAAGTTTATATTTCAAGA
1 GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAACGTATTCAAAGTTTATATTTCAAGA
*
2180954 GAAACTGTCTCAAGGGAGACAAAAGTAGTTTCAAGGGAAA
1 GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAA
2180994 ATGTCTTAAG
Statistics
Matches: 95, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
65 94 0.99
66 1 0.01
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (65 bp):
GAAACTGTCTCAAGGGAGACAAAATTAGTTTCAAGGGAAACGTATTCAAAGTTTATATTTCAAGA
Found at i:2181381 original size:73 final size:72
Alignment explanation
Indices: 2181261--2181395 Score: 200
Period size: 73 Copynumber: 1.9 Consensus size: 72
2181251 TGTCTCAATC
*
2181261 GAGACAAAATTTGGTTCAAGTAAAACAACATTGAAATTTGATCTCCGAAGGAAAATATCTCATGT
1 GAGACAAAATTTGGTTCAAGAAAAACAACATTGAAATTTGATCTCCGAAGGAAAATATCTCATGT
2181326 ATCAAGT
66 ATCAAGT
* * * *
2181333 GAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTAT-TCCGAAGGAAAATGTCTCA
1 GAGACAAAATTTG-GTTCAAGAAAAACAACATTGAAATTTG-ATCTCCGAAGGAAAATATCTCA
2181396 AGTGAGACGA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
72 13 0.23
73 41 0.73
74 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (72 bp):
GAGACAAAATTTGGTTCAAGAAAAACAACATTGAAATTTGATCTCCGAAGGAAAATATCTCATGT
ATCAAGT
Found at i:2181424 original size:36 final size:37
Alignment explanation
Indices: 2181384--2181580 Score: 121
Period size: 37 Copynumber: 5.5 Consensus size: 37
2181374 TATTCCGAAG
*
2181384 GAAAATGTCTCAAGTGAGACGAAATATG-ATTTAAGA
1 GAAAATGTCTCAAGTGAGACAAAATATGTATTTAAGA
* *
2181420 GAAAATGTCTCAAGTGAGACAAAATTTGTTTTTAAGA
1 GAAAATGTCTCAAGTGAGACAAAATATGTATTTAAGA
* ** * * *
2181457 -AAAA----T-AACTTTG---AAATTTGTGTTCCGAAG-
1 GAAAATGTCTCAAGTGAGACAAAATATGTATT--TAAGA
* *
2181486 GAAAATGTCTCAAGTGAGACGAAATTTGT-TTTAAGA
1 GAAAATGTCTCAAGTGAGACAAAATATGTATTTAAGA
* * *
2181522 GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTTATGA
1 G-AAAATGTCTCAAGTGAGACAAAATATGTATTTAAGA
* * *
2181560 AAACAATGTCTCTAGCGAGAC
1 GAA-AATGTCTCAAGTGAGAC
2181581 GACATTTTGT
Statistics
Matches: 128, Mismatches: 17, Indels: 30
0.73 0.10 0.17
Matches are distributed among these distances:
28 10 0.08
30 7 0.05
31 4 0.03
32 1 0.01
34 1 0.01
35 7 0.05
36 31 0.24
37 38 0.30
38 29 0.23
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (37 bp):
GAAAATGTCTCAAGTGAGACAAAATATGTATTTAAGA
Found at i:2181447 original size:102 final size:103
Alignment explanation
Indices: 2181322--2181562 Score: 421
Period size: 102 Copynumber: 2.3 Consensus size: 103
2181312 AAAATATCTC
*
2181322 ATGTATCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTATTCCGAAGGAA
1 ATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTATTCCGAAGGAA
2181387 AATGTCTCAAGTGAGACGAAATATGATTTAAGAG-AAA
66 AATGTCTCAAGTGAGACGAAATATGATTTAAGAGAAAA
* *
2181424 ATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAATAACTTTGAAATTTGTGTTCCGAAGGAA
1 ATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTATTCCGAAGGAA
* *
2181489 AATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGAAAA
66 AATGTCTCAAGTGAGACGAAATATGATTTAAGAGAAAA
*
2181527 ATGTCTCAAGTGAGACAAAATTTGTTTTTATGAAAA
1 ATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAA
2181563 CAATGTCTCT
Statistics
Matches: 132, Mismatches: 6, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
102 94 0.71
103 38 0.29
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.32
Consensus pattern (103 bp):
ATGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAAACAACTTTGAAATTTGTATTCCGAAGGAA
AATGTCTCAAGTGAGACGAAATATGATTTAAGAGAAAA
Found at i:2181532 original size:37 final size:37
Alignment explanation
Indices: 2181487--2181601 Score: 133
Period size: 37 Copynumber: 3.1 Consensus size: 37
2181477 GTTCCGAAGG
2181487 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA
1 AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA
* *
2181524 AAAATGTCTCAAGTGAGACAAAATTTGTTTTTATGA-A
1 AAAATGTCTCAAGTGAGACGAAATTTG-TTTTAAGAGA
* * * **
2181561 AACAATGTCTCTAGCGAGACGACATTTTGTTTCGAGAGA
1 AA-AATGTCTCAAGTGAGACGA-AATTTGTTTTAAGAGA
2181600 AA
1 AA
2181602 TAACACCCAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
37 29 0.45
38 28 0.43
39 8 0.12
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (37 bp):
AAAATGTCTCAAGTGAGACGAAATTTGTTTTAAGAGA
Found at i:2183958 original size:20 final size:21
Alignment explanation
Indices: 2183924--2183971 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
2183914 TGCTCATGCA
2183924 AATGCAAAGATGCAAAATGGG
1 AATGCAAAGATGCAAAATGGG
**
2183945 AATGCAAA-ATGCAAAATGTA
1 AATGCAAAGATGCAAAATGGG
2183965 AATGCAA
1 AATGCAA
2183972 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (21 bp):
AATGCAAAGATGCAAAATGGG
Found at i:2192449 original size:2 final size:2
Alignment explanation
Indices: 2192442--2192470 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2192432 GATCGGAGTT
2192442 TA 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 TA T
2192471 GTGTTCAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2192523 original size:14 final size:14
Alignment explanation
Indices: 2192504--2192530 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2192494 ATATATTATA
2192504 GTTTTTTGAAAACG
1 GTTTTTTGAAAACG
2192518 GTTTTTTGAAAAC
1 GTTTTTTGAAAAC
2192531 ATATAATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.19, T:0.44
Consensus pattern (14 bp):
GTTTTTTGAAAACG
Found at i:2192594 original size:33 final size:33
Alignment explanation
Indices: 2192557--2192681 Score: 105
Period size: 33 Copynumber: 3.7 Consensus size: 33
2192547 TATTTAAAAA
2192557 AAAATCGGTTTTCAAAATA-ATATTATAATTTTG
1 AAAATC-GTTTTCAAAATATATATTATAATTTTG
* * *
2192590 AAAAT-ATTTTGTAAAATATATATTATAGTTTTG
1 AAAATCGTTTT-CAAAATATATATTATAATTTTG
*
2192623 AAAA-CGTTTTGAAAATATATACAATATATAATTTTTG
1 AAAATCGTTTTCAAAATATAT---AT-TATAA-TTTTG
* *
2192660 AAAA-CATTTTGAAAATATATAT
1 AAAATCGTTTTCAAAATATATAT
2192682 AATATAGTTT
Statistics
Matches: 77, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
31 4 0.05
32 15 0.19
33 26 0.34
34 2 0.03
35 2 0.03
36 4 0.05
37 24 0.31
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (33 bp):
AAAATCGTTTTCAAAATATATATTATAATTTTG
Found at i:2192662 original size:37 final size:36
Alignment explanation
Indices: 2192585--2192738 Score: 192
Period size: 37 Copynumber: 4.3 Consensus size: 36
2192575 AATATTATAA
*
2192585 TTTTGAAAATATTTTGTAAAATATAT--AT-TATAG-
1 TTTTGAAAACATTTTG-AAAATATATAAATATATAGT
* *
2192618 TTTTGAAAACGTTTTGAAAATATATACAATATATAAT
1 TTTTGAAAACATTTTGAAAATATATA-AATATATAGT
*
2192655 TTTTGAAAACATTTTGAAAATATATATA-ATATAGT
1 TTTTGAAAACATTTTGAAAATATATAAATATATAGT
* *
2192690 TTTTGTAAACATTTTGAAAACATATATAATATATAGT
1 TTTTGAAAACATTTTGAAAATATATA-AATATATAGT
2192727 TTTTGAAAACAT
1 TTTTGAAAACAT
2192739 ATATATTATA
Statistics
Matches: 104, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
32 9 0.09
33 14 0.13
35 32 0.31
36 6 0.06
37 43 0.41
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (36 bp):
TTTTGAAAACATTTTGAAAATATATAAATATATAGT
Found at i:2192687 original size:35 final size:35
Alignment explanation
Indices: 2192565--2192738 Score: 182
Period size: 37 Copynumber: 5.0 Consensus size: 35
2192555 AAAAAATCGG
* *
2192565 TTTTCAAAATA-ATAT--TATAA-TTTTGAAAATA
1 TTTTGAAAATATATATAATATAATTTTTGAAAACA
* *
2192596 TTTTGTAAAATATATAT--TAT-AGTTTTGAAAACG
1 TTTTG-AAAATATATATAATATAATTTTTGAAAACA
*
2192629 TTTTGAAAATATATACAATATATAATTTTTGAAAACA
1 TTTTGAAAATATATA-TA-ATATAATTTTTGAAAACA
* *
2192666 TTTTGAAAATATATATAATATAGTTTTTGTAAACA
1 TTTTGAAAATATATATAATATAATTTTTGAAAACA
*
2192701 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
1 TTTTGAAAATATATATAATATA-A-TTTTTGAAAACA
2192738 T
1 T
2192739 ATATATTATA
Statistics
Matches: 121, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
31 4 0.03
32 17 0.14
33 21 0.17
35 37 0.31
36 4 0.03
37 38 0.31
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTTGAAAATATATATAATATAATTTTTGAAAACA
Found at i:2192721 original size:72 final size:70
Alignment explanation
Indices: 2192573--2192738 Score: 228
Period size: 72 Copynumber: 2.3 Consensus size: 70
2192563 GGTTTTCAAA
* *
2192573 ATAATATTATAA-TTTTGAAAATATTTTGTAAAATATATATTATAGTTTTGAAAACGTTTTGAAA
1 ATAATA-TATAATTTTTGAAAACATTTTGTAAAATATATATTATAGTTTTGAAAACATTTTGAAA
*
2192637 ATATAT
65 ACATAT
* *
2192643 ACAATATATAATTTTTGAAAACATTTTG-AAAATATATATAATATAGTTTTTGTAAACATTTTGA
1 ATAATATATAATTTTTGAAAACATTTTGTAAAATATATAT--TATAG-TTTTGAAAACATTTTGA
2192707 AAACATAT
63 AAACATAT
*
2192715 ATAATATATAGTTTTTGAAAACAT
1 ATAATATATAATTTTTGAAAACAT
2192739 ATATATTATA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
69 16 0.19
70 20 0.24
71 5 0.06
72 44 0.52
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (70 bp):
ATAATATATAATTTTTGAAAACATTTTGTAAAATATATATTATAGTTTTGAAAACATTTTGAAAA
CATAT
Found at i:2192731 original size:26 final size:25
Alignment explanation
Indices: 2192701--2192795 Score: 110
Period size: 26 Copynumber: 3.9 Consensus size: 25
2192691 TTTGTAAACA
2192701 TTTTGAAAACATATATAATATATAGT
1 TTTTGAAAACATATAT-ATATATAGT
2192727 TTTTGAAAACATATATATTATATAGT
1 TTTTGAAAACATATATA-TATATAGT
2192753 TTTTG--AA-ATATAT-TATATAG-
1 TTTTGAAAACATATATATATATAGT
* * *
2192773 TTTTGAAAATATTTATATGTATA
1 TTTTGAAAACATATATATATATA
2192796 TGTATATTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
20 5 0.08
21 7 0.11
22 2 0.03
23 11 0.18
24 7 0.11
25 1 0.02
26 29 0.47
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTGAAAACATATATATATATAGT
Found at i:2192750 original size:35 final size:34
Alignment explanation
Indices: 2192636--2192750 Score: 97
Period size: 35 Copynumber: 3.2 Consensus size: 34
2192626 ACGTTTTGAA
* * *
2192636 AATATATACAATATATAATTTTTGAAAACATTTT
1 AATATATATAATATATAGTTTTTGAAAACATTAT
* * *
2192670 GAAAATATAT-ATAATATAGTTTTTGTAAACATTTTGAA
1 -AATATATATAAT-ATATAGTTTTTGAAAACA--TT-AT
*
2192708 AACATATATAATATATAGTTTTTGAAAACATATAT
1 AATATATATAATATATAGTTTTTGAAAACAT-TAT
*
2192743 ATTATATA
1 AATATATA
2192751 GTTTTTGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
34 2 0.03
35 31 0.49
36 1 0.02
37 27 0.43
38 2 0.03
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (34 bp):
AATATATATAATATATAGTTTTTGAAAACATTAT
Found at i:2192763 original size:21 final size:20
Alignment explanation
Indices: 2192739--2192789 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
2192729 TTGAAAACAT
2192739 ATATATTATATAGTTTTTGAA
1 ATATATTATATAG-TTTTGAA
2192760 ATATATTATATAGTTTTGAA
1 ATATATTATATAGTTTTGAA
2192780 A-ATATT-TATA
1 ATATATTATATA
2192790 TGTATATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 4 0.13
19 5 0.17
20 8 0.27
21 13 0.43
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATATATTATATAGTTTTGAA
Found at i:2192784 original size:19 final size:21
Alignment explanation
Indices: 2192739--2192790 Score: 81
Period size: 20 Copynumber: 2.5 Consensus size: 21
2192729 TTGAAAACAT
2192739 ATATATTATATAGTTTTTGAA
1 ATATATTATATAGTTTTTGAA
2192760 ATATATTATATAG-TTTTGAA
1 ATATATTATATAGTTTTTGAA
2192780 A-ATATTTATAT
1 ATATA-TTATAT
2192791 GTATATGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.10
20 14 0.47
21 13 0.43
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (21 bp):
ATATATTATATAGTTTTTGAA
Found at i:2192852 original size:29 final size:29
Alignment explanation
Indices: 2192785--2192869 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
2192775 TTGAAAATAT
* *
2192785 TTATATGTATATGTATATTAT-ATATTATA
1 TTATATATATAT-TATATTATGGTATTATA
* *
2192814 TTGTACATATATTATATTATGGTATTATA
1 TTATATATATATTATATTATGGTATTATA
2192843 TTATATATATTATT-TATTATGGT-TTAT
1 TTATATATA-TATTATATTATGGTATTAT
2192870 TATTTATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
28 12 0.25
29 32 0.67
30 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.08, T:0.56
Consensus pattern (29 bp):
TTATATATATATTATATTATGGTATTATA
Found at i:2192859 original size:18 final size:17
Alignment explanation
Indices: 2192782--2192859 Score: 54
Period size: 18 Copynumber: 4.4 Consensus size: 17
2192772 GTTTTGAAAA
2192782 TATTTATATGTATATGTA-
1 TATTTATAT-TATAT-TAT
*
2192800 TATTATATATTATATT-G
1 TATT-TATATTATATTAT
**
2192817 TACATATATTATATTAT
1 TATTTATATTATATTAT
2192834 GGTA-TTATATTATATATAT
1 --TATTTATATTATAT-TAT
2192853 TATTTAT
1 TATTTAT
2192860 TATGGTTTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
16 11 0.22
17 5 0.10
18 23 0.47
19 10 0.20
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.56
Consensus pattern (17 bp):
TATTTATATTATATTAT
Found at i:2192975 original size:18 final size:18
Alignment explanation
Indices: 2192952--2192990 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2192942 AGTCCAACCG
2192952 AGCCTGCAAGCCTGACCC
1 AGCCTGCAAGCCTGACCC
2192970 AGCCTGCAAGCCTGACCC
1 AGCCTGCAAGCCTGACCC
2192988 AGC
1 AGC
2192991 AAACAGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.44, G:0.23, T:0.10
Consensus pattern (18 bp):
AGCCTGCAAGCCTGACCC
Found at i:2194043 original size:15 final size:16
Alignment explanation
Indices: 2194016--2194047 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2194006 ACTTTTTTTC
2194016 TCTTTCTTTTATTTAA
1 TCTTTCTTTTATTTAA
2194032 TCTTTC-TTTATTTAA
1 TCTTTCTTTTATTTAA
2194047 T
1 T
2194048 TCACGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.69
Consensus pattern (16 bp):
TCTTTCTTTTATTTAA
Found at i:2194083 original size:22 final size:22
Alignment explanation
Indices: 2194053--2194105 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2194043 TTAATTCACG
*
2194053 TTTTAATTTAATTGT-TTTTATT
1 TTTTCATTTAATTGTATTTTA-T
* *
2194075 TTTTCATTTTATTTTATTTTAT
1 TTTTCATTTAATTGTATTTTAT
2194097 TTTTCATTT
1 TTTTCATTT
2194106 CTTTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTCATTTAATTGTATTTTAT
Found at i:2194094 original size:23 final size:23
Alignment explanation
Indices: 2194068--2194117 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
2194058 ATTTAATTGT
2194068 TTTTATTTTTTCATTT-TATTTTA
1 TTTTA-TTTTTCATTTCTATTTTA
*
2194091 TTTTATTTTTCATTTCTTTTTTA
1 TTTTATTTTTCATTTCTATTTTA
2194114 TTTT
1 TTTT
2194118 TAATTTAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTATTTTTCATTTCTATTTTA
Found at i:2194431 original size:127 final size:131
Alignment explanation
Indices: 2194289--2194546 Score: 488
Period size: 129 Copynumber: 2.0 Consensus size: 131
2194279 ATTTTTCAGT
2194289 AATTGTTTATATTTAATTTCACAATTAACATTTTTTC-TTACCGTTA-TTCATTTTGATTCAGCA
1 AATTGTTTATATTTAATTTCACAATTAACATTTTTTCTTTACCGTTATTTCATTTTGATTCAGCA
2194352 TTTTACTTTACCAATCTAACATCTTTTTGACC-TTTTAAGGGTA-TCTTTTAAATCGATCAGGGT
66 TTTTACTTTACCAATCTAACATCTTTTTGACCTTTTTAAGGGTATTCTTTTAAATCGATCAGGGT
2194415 A
131 A
2194416 AATTGTTTATATTTAATTTCACAATTAACATTTTTTCTTTACCGTTATTTCATTTTGATTCAGCA
1 AATTGTTTATATTTAATTTCACAATTAACATTTTTTCTTTACCGTTATTTCATTTTGATTCAGCA
2194481 TTTTACTTTACCAATCTAACATCTTTTTGACCTTTTTAAGGGTATTCTTTTAAATCGATCAGGGT
66 TTTTACTTTACCAATCTAACATCTTTTTGACCTTTTTAAGGGTATTCTTTTAAATCGATCAGGGT
2194546 A
131 A
2194547 TTCTTTTGAC
Statistics
Matches: 127, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
127 37 0.29
128 9 0.07
129 49 0.39
130 11 0.09
131 21 0.17
ACGTcount: A:0.27, C:0.16, G:0.09, T:0.48
Consensus pattern (131 bp):
AATTGTTTATATTTAATTTCACAATTAACATTTTTTCTTTACCGTTATTTCATTTTGATTCAGCA
TTTTACTTTACCAATCTAACATCTTTTTGACCTTTTTAAGGGTATTCTTTTAAATCGATCAGGGT
A
Found at i:2200347 original size:85 final size:85
Alignment explanation
Indices: 2200086--2200411 Score: 472
Period size: 85 Copynumber: 3.8 Consensus size: 85
2200076 TCCCAGCCTA
* * * ** *
2200086 TTACAGTATAGTTCAAGGCGAGAATGGCTATCTGTCAACAGCAACCTTCGAGTTCGATTCCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
2200151 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGGCATATCAAAT
* * *
2200171 TTACAACATAGCTCAAGGCGAGAAGGGTTATGTGTCAACAAAAAACCTTCGAGTTCGATTACATT
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAAACCTTCGAGTTCGATTACATT
* *
2200236 TAGTTCAAGGGCATATCAAAT
65 CAGCTCAAGGGCATATCAAAT
* * *
2200257 TTACAGCATAGCTCAAGGTGAAAAGGGCTATCTGTCAACAAAAACCTTTGAGTTCGATTACATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
2200322 AGCTCAAGGGCATATCAAAT
66 AGCTCAAGGGCATATCAAAT
** * * *
2200342 TTACAGCATAATTCAAGGCGAGAAGAGTTATCTGTCAACAAAAACCTTCGAGTTCGATTTCATTC
1 TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
2200407 AGCTC
66 AGCTC
2200412 GATGACAGCG
Statistics
Matches: 213, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
85 138 0.65
86 75 0.35
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (85 bp):
TTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
AGCTCAAGGGCATATCAAAT
Found at i:2200972 original size:2 final size:2
Alignment explanation
Indices: 2200965--2201029 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
2200955 GTCCAGAGTT
2200965 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
2201007 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2201030 GTGTGTGTGT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2201077 original size:13 final size:13
Alignment explanation
Indices: 2201059--2201084 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2201049 TATAGTATAA
2201059 TTTTTGAAAATAT
1 TTTTTGAAAATAT
2201072 TTTTTGAAAATAT
1 TTTTTGAAAATAT
2201085 ATATTATATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (13 bp):
TTTTTGAAAATAT
Found at i:2201257 original size:37 final size:36
Alignment explanation
Indices: 2201159--2201329 Score: 199
Period size: 37 Copynumber: 4.8 Consensus size: 36
2201149 CGGTTTTCGA
* * * *
2201159 ATATATATTATATAATTTTAAAAACATTTTG-GAA-
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAAT
*
2201193 A-ATAT-AT-TATAGTTTTGAAAACGTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACATTTTGAAAAT
*
2201226 ACATATAATATATAGTTTTGGAAAACATTTTGAAAAT
1 ATATATAATATATAGTTTT-GAAAACATTTTGAAAAT
*
2201263 ATATATAATATATAGTTTTTGAAAACATTTTGAAAAC
1 ATATATAATATATAG-TTTTGAAAACATTTTGAAAAT
* *
2201300 ATATATATTATATAGTTTTTGAAAATATTT
1 ATATATAATATATAG-TTTTGAAAACATTT
2201330 ATATTTATAT
Statistics
Matches: 120, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
31 18 0.15
32 3 0.03
33 5 0.04
34 5 0.04
35 2 0.02
36 9 0.08
37 74 0.62
38 4 0.03
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (36 bp):
ATATATAATATATAGTTTTGAAAACATTTTGAAAAT
Found at i:2201365 original size:2 final size:2
Alignment explanation
Indices: 2201324--2201383 Score: 54
Period size: 2 Copynumber: 31.0 Consensus size: 2
2201314 GTTTTTGAAA
* * * *
2201324 AT AT TT AT AT TT AT AT GT AT AT -T AT AT AT -T AT AT -T GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2201363 AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT -AT AT
2201384 TATGGTATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
1 3 0.06
2 42 0.89
3 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (2 bp):
AT
Found at i:2201370 original size:31 final size:30
Alignment explanation
Indices: 2201324--2201386 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 30
2201314 GTTTTTGAAA
* *
2201324 ATATTTATATTTATATGTATATTAT-ATATT
1 ATATTTATATATATATATATA-TATGATATT
2201354 ATATTGTATATATATATATATATATGATATT
1 ATATT-TATATATATATATATATATGATATT
2201385 AT
1 AT
2201387 GGTATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (30 bp):
ATATTTATATATATATATATATATGATATT
Found at i:2201379 original size:39 final size:39
Alignment explanation
Indices: 2201303--2201397 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 39
2201293 TGAAAACATA
* *
2201303 TATATTATATAGTT-T-TTGAAAATATTTATATTTATATG
1 TATATTATATA-TTATATTGAAAATATATATATATATATG
* *
2201341 TATATTATATATTATATTGTATATATATATATATATATG
1 TATATTATATATTATATTGAAAATATATATATATATATG
*
2201380 -ATATTATGGTATTATATT
1 TATATTAT-ATATTATATT
2201398 ATATGTATTA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
37 2 0.04
38 19 0.39
39 28 0.57
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (39 bp):
TATATTATATATTATATTGAAAATATATATATATATATG
Found at i:2201391 original size:29 final size:26
Alignment explanation
Indices: 2201335--2201408 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 26
2201325 TATTTATATT
* *
2201335 TATATGTATAT-TATATATTATATTG
1 TATATATATATATATATATTATATGG
2201360 TATATATATATATATATATGATATTATGG
1 TATATATATATATATATAT--TA-TATGG
*
2201389 TAT-TATAT-TATATGTATTAT
1 TATATATATATATATATATTAT
2201409 TTATTATGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
24 1 0.02
25 12 0.29
26 7 0.17
27 8 0.19
28 7 0.17
29 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (26 bp):
TATATATATATATATATATTATATGG
Found at i:2201422 original size:14 final size:15
Alignment explanation
Indices: 2201381--2201423 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
2201371 ATATATATGA
2201381 TATTATGGTATTATAT
1 TATTATGGTATTAT-T
2201397 TA-TAT-GTATTATT
1 TATTATGGTATTATT
2201410 TATTATGGT-TTATT
1 TATTATGGTATTATT
2201424 ATTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.12
14 15 0.60
15 5 0.20
16 2 0.08
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (15 bp):
TATTATGGTATTATT
Found at i:2201445 original size:12 final size:13
Alignment explanation
Indices: 2201424--2201463 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
2201414 ATGGTTTATT
2201424 ATTTTCTTTTTTC
1 ATTTTCTTTTTTC
*
2201437 -TTTT-TTTTTTT
1 ATTTTCTTTTTTC
2201448 ATTTTCTTTTTT-
1 ATTTTCTTTTTTC
2201460 ATTT
1 ATTT
2201464 GGTCCAAGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 6 0.25
12 12 0.50
13 6 0.25
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (13 bp):
ATTTTCTTTTTTC
Found at i:2201802 original size:7 final size:7
Alignment explanation
Indices: 2201790--2201820 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2201780 TAGGACTAAT
2201790 CAACAAA
1 CAACAAA
2201797 CAACAAA
1 CAACAAA
*
2201804 CAACCAA
1 CAACAAA
2201811 CAACAAA
1 CAACAAA
2201818 CAA
1 CAA
2201821 ATAGCATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (7 bp):
CAACAAA
Found at i:2203516 original size:206 final size:205
Alignment explanation
Indices: 2203164--2203574 Score: 797
Period size: 206 Copynumber: 2.0 Consensus size: 205
2203154 ACTTAAGTCG
2203164 AAGCCCACCAGAAAGACGGTTGCGATAAAAAGATTATGTATGGTTTCATGGACATCCAAGTTATC
1 AAGCCCACCAGAAAGACGGTTGCGATAAAAAGATTATGTATGGTTTCATGGACATCCAAGTTATC
2203229 TAAGTTGGTAAGGCAAGGCCAGCCAGAGGAAGCCATTTGCTTGTTCAAGAGAATGCTATTGCTGA
66 TAAGTTGGTAAGGCAAGGCCAGCCAGAGGAAGCCATTTGCTTGTTCAAGAGAATGCTATTGCTGA
2203294 TGAGTAATCAAAGGACAAACTATGTTACAATTTTAAGCTTAAT-AAAGCCTTCGATGCTCTGAAT
131 TGAGTAATCAAAGGACAAACTATGTTACAATTTTAAGCTTAATAAAAGCCTTCGATGCTCTGAAT
2203358 TGGGATGCTC
196 TGGGATGCTC
2203368 AAGCCCACCAGAAAGACGGTTGCGATAAAAATGATTATGTATTGGTTTCATGGACATCCAAGTTA
1 AAGCCCACCAGAAAGACGGTTGCGATAAAAA-GATTATGTA-TGGTTTCATGGACATCCAAGTTA
2203433 TCTAAGTTGGTAAGGCAAGGCCAGCCAGAGGAAGCCATTTGCTTGTTCAAGAGAATGCTATTGCT
64 TCTAAGTTGGTAAGGCAAGGCCAGCCAGAGGAAGCCATTTGCTTGTTCAAGAGAATGCTATTGCT
2203498 GATGAGTAATCAAAGGACAAACTATGTTACAATTTTAAGCTTAATAAAAGCCTTCGATGCTCTGA
129 GATGAGTAATCAAAGGACAAACTATGTTACAATTTTAAGCTTAATAAAAGCCTTCGATGCTCTGA
2203563 ATTGGGATGCTC
194 ATTGGGATGCTC
2203575 CAGTAATGAT
Statistics
Matches: 204, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
204 31 0.15
205 9 0.04
206 133 0.65
207 31 0.15
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (205 bp):
AAGCCCACCAGAAAGACGGTTGCGATAAAAAGATTATGTATGGTTTCATGGACATCCAAGTTATC
TAAGTTGGTAAGGCAAGGCCAGCCAGAGGAAGCCATTTGCTTGTTCAAGAGAATGCTATTGCTGA
TGAGTAATCAAAGGACAAACTATGTTACAATTTTAAGCTTAATAAAAGCCTTCGATGCTCTGAAT
TGGGATGCTC
Found at i:2208408 original size:31 final size:31
Alignment explanation
Indices: 2208367--2208440 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
2208357 CAAAATACAT
2208367 AAGATATGGTCACTTACGTTTTTATTTAAAC
1 AAGATATGGTCACTTACGTTTTTATTTAAAC
* * **
2208398 AAGATCTGGTCACTTTCGTTTTTATTTAATT
1 AAGATATGGTCACTTACGTTTTTATTTAAAC
*
2208429 AAGATGTGGTCA
1 AAGATATGGTCA
2208441 TAACTGCCGC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (31 bp):
AAGATATGGTCACTTACGTTTTTATTTAAAC
Found at i:2208793 original size:16 final size:17
Alignment explanation
Indices: 2208772--2208805 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2208762 ACTCGATTTA
2208772 TTATATT-TTTTTTATT
1 TTATATTATTTTTTATT
2208788 TTATATTAATTTTTTATT
1 TTATATT-ATTTTTTATT
2208806 CATAATCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATATTATTTTTTATT
Found at i:2208917 original size:39 final size:39
Alignment explanation
Indices: 2208816--2208921 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 39
2208806 CATAATCCTC
* * *
2208816 AAATTATTGCACACTAACATTCTAAAATCTTAATTTATT
1 AAATTATTTCACATTAACATTCTAAATTCTTAATTTATT
* * *
2208855 AAA-T-TTTGACACTATAACGTTCTAAATTCTTAATTTTTT
1 AAATTATTTCACA-T-TAACATTCTAAATTCTTAATTTATT
2208894 AAATTATTTCACATTAACATTCTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
2208922 ATTTTTTAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
37 5 0.09
38 1 0.02
39 41 0.75
40 2 0.04
41 6 0.11
ACGTcount: A:0.39, C:0.14, G:0.03, T:0.44
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTCTAAATTCTTAATTTATT
Found at i:2209226 original size:25 final size:26
Alignment explanation
Indices: 2209191--2209256 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 26
2209181 ATATATATTA
2209191 AATTAAAATATTTTTA-TATT-ACTT
1 AATTAAAATATTTTTACTATTAACTT
*
2209215 TATT-AAATATATTTTACTATTAACTT
1 AATTAAAATAT-TTTTACTATTAACTT
2209241 AATTTAAAAATATTTT
1 AA-TT-AAAATATTTT
2209257 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
23 6 0.18
24 8 0.24
25 4 0.12
26 5 0.15
27 2 0.06
28 3 0.09
29 6 0.18
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (26 bp):
AATTAAAATATTTTTACTATTAACTT
Found at i:2209254 original size:27 final size:24
Alignment explanation
Indices: 2209191--2209258 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 24
2209181 ATATATATTA
2209191 AATT-AAAATATTTTTATATTACTT
1 AATTAAAAATA-TTTTATATTACTT
* *
2209215 TATTAAATATATTTTACTATTAACTT
1 AATTAAAAATATTTTA-TATT-ACTT
2209241 AATTTAAAAATATTTTAT
1 AA-TTAAAAATATTTTAT
2209259 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 8 0.22
25 9 0.25
26 6 0.17
27 13 0.36
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAAAAATATTTTATATTACTT
Found at i:2210721 original size:24 final size:23
Alignment explanation
Indices: 2210677--2210735 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 23
2210667 CATTATATAT
2210677 ATATATGAATATAATAATTTT-AA
1 ATATAT-AATATAATAATTTTGAA
2210700 ATATATAATATATATAAGTTTTGAA
1 ATATATAATATA-ATAA-TTTTGAA
*
2210725 A-ATATAGTATA
1 ATATATAATATA
2210736 GTTTTTGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 6 0.19
23 10 0.31
24 13 0.41
25 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (23 bp):
ATATATAATATAATAATTTTGAA
Found at i:2210727 original size:26 final size:23
Alignment explanation
Indices: 2210677--2210730 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 23
2210667 CATTATATAT
2210677 ATATATGAATATAATAATTTTAA
1 ATATATGAATATAATAATTTTAA
2210700 ATATAT-AATATATATAAGTTTTGAAA
1 ATATATGAATATA-ATAA-TTTT--AA
2210726 ATATA
1 ATATA
2210731 GTATAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.22
23 10 0.37
24 4 0.15
26 7 0.26
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
ATATATGAATATAATAATTTTAA
Found at i:2210741 original size:20 final size:20
Alignment explanation
Indices: 2210706--2210766 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
2210696 TTAAATATAT
2210706 AATATA-TATAAG-TTTTGAA
1 AATATAGTAT-AGTTTTTGAA
2210725 AATATAGTATAGTTTTTGAA
1 AATATAGTATAGTTTTTGAA
*
2210745 AACATAGTATAGTTTTTGAA
1 AATATAGTATAGTTTTTGAA
2210765 AA
1 AA
2210767 CATGTTTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
19 8 0.21
20 31 0.79
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.41
Consensus pattern (20 bp):
AATATAGTATAGTTTTTGAA
Found at i:2210767 original size:20 final size:20
Alignment explanation
Indices: 2210718--2210769 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2210708 TATATATAAG
*
2210718 TTTTGAAAATATAGTATAGT
1 TTTTGAAAACATAGTATAGT
2210738 TTTTGAAAACATAGTATAGT
1 TTTTGAAAACATAGTATAGT
2210758 TTTTGAAAACAT
1 TTTTGAAAACAT
2210770 GTTTTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.13, T:0.42
Consensus pattern (20 bp):
TTTTGAAAACATAGTATAGT
Found at i:2210823 original size:39 final size:38
Alignment explanation
Indices: 2210752--2210839 Score: 117
Period size: 37 Copynumber: 2.3 Consensus size: 38
2210742 GAAAACATAG
* * *
2210752 TATAGTTTTTGAAAACATGTTTTTGAAAATATATAATA
1 TATAGTTTTTGAAAAAACGGTTTTGAAAATATATAATA
*
2210790 TATAGTTTTT-AAAAAACGGTTTTGAAAACATAT-ATAA
1 TATAGTTTTTGAAAAAACGGTTTTGAAAATATATAAT-A
2210827 TATAGTTTTTGAA
1 TATAGTTTTTGAA
2210840 TATATATATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
36 2 0.05
37 30 0.68
38 12 0.27
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.43
Consensus pattern (38 bp):
TATAGTTTTTGAAAAAACGGTTTTGAAAATATATAATA
Found at i:2210844 original size:2 final size:2
Alignment explanation
Indices: 2210839--2210876 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2210829 TAGTTTTTGA
2210839 AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2210877 ATTTTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2210936 original size:22 final size:21
Alignment explanation
Indices: 2210911--2210958 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2210901 ACGTAGAAAA
2210911 TATATGACGTTTGAAAATATAT
1 TATATGACGTTTG-AAATATAT
* **
2210933 TATATTATTTTTGAAATATAT
1 TATATGACGTTTGAAATATAT
2210954 TATAT
1 TATAT
2210959 AGTTTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (21 bp):
TATATGACGTTTGAAATATAT
Found at i:2210993 original size:13 final size:13
Alignment explanation
Indices: 2210975--2211038 Score: 60
Period size: 13 Copynumber: 4.9 Consensus size: 13
2210965 AATACATATA
2210975 TTTTATTTTTCAT
1 TTTTATTTTTCAT
* *
2210988 TTTTATCTTTCTT
1 TTTTATTTTTCAT
*
2211001 TTTTATTATT-AT
1 TTTTATTTTTCAT
*
2211013 TTTT-TATTTCAT
1 TTTTATTTTTCAT
2211025 TTAATTATTTTTCA
1 TT--TTATTTTTCA
2211039 GGTCCAAGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
11 3 0.08
12 9 0.23
13 19 0.49
14 2 0.05
15 6 0.15
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATTTTTCAT
Found at i:2211002 original size:19 final size:17
Alignment explanation
Indices: 2210973--2211036 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 17
2210963 TTAATACATA
2210973 TATTTTATTTTTCATTTT
1 TATTTT-TTTTTCATTTT
* *
2210991 TATCTTTCTTTTTTATTAT
1 TAT-TTT-TTTTTCATTTT
2211010 TATTTTTTATTTCATTTAAT
1 TATTTTTT-TTTCATTT--T
2211030 TATTTTT
1 TATTTTT
2211037 CAGGTCCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 2 0.05
18 12 0.32
19 15 0.41
20 8 0.22
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (17 bp):
TATTTTTTTTTCATTTT
Found at i:2211004 original size:26 final size:26
Alignment explanation
Indices: 2210975--2211038 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
2210965 AATACATATA
*
2210975 TTTTATTTTTCATTTTTATCTTTC-TT
1 TTTTATTTTTCATTTTT-TATTTCATT
*
2211001 TTTTATTATT-ATTTTTTATTTCATT
1 TTTTATTTTTCATTTTTTATTTCATT
*
2211026 TAATTATTTTTCA
1 T-TTTATTTTTCA
2211039 GGTCCAAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 5 0.16
25 9 0.29
26 16 0.52
27 1 0.03
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATTTTTCATTTTTTATTTCATT
Found at i:2215228 original size:45 final size:45
Alignment explanation
Indices: 2215164--2215253 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
2215154 AAGGTAACCG
2215164 ATCTGGAGAGGTCTCTTCAAAAAGAGCAGGAGCATGATAACAAAA
1 ATCTGGAGAGGTCTCTTCAAAAAGAGCAGGAGCATGATAACAAAA
2215209 ATCTGGAGAGGTCTCTTCAAAAAGAGCAGGAGCATGATAACAAAA
1 ATCTGGAGAGGTCTCTTCAAAAAGAGCAGGAGCATGATAACAAAA
2215254 CTATAGCAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (45 bp):
ATCTGGAGAGGTCTCTTCAAAAAGAGCAGGAGCATGATAACAAAA
Found at i:2219715 original size:20 final size:20
Alignment explanation
Indices: 2219678--2219716 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2219668 AGATTGAGTG
* * *
2219678 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
2219698 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
2219717 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:2219899 original size:23 final size:23
Alignment explanation
Indices: 2219869--2219931 Score: 126
Period size: 23 Copynumber: 2.7 Consensus size: 23
2219859 CCAGAACCCC
2219869 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
2219892 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
2219915 AGGGGGAATCGGTTCCC
1 AGGGGGAATCGGTTCCC
2219932 TCATCGGGGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.25, G:0.33, T:0.21
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:2227794 original size:15 final size:16
Alignment explanation
Indices: 2227769--2227798 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2227759 GTGGAATGCA
2227769 TCAGTTGAATTGATAT
1 TCAGTTGAATTGATAT
2227785 TCAG-TGAATTGATA
1 TCAGTTGAATTGATA
2227799 CTTTGCTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (16 bp):
TCAGTTGAATTGATAT
Found at i:2229877 original size:195 final size:196
Alignment explanation
Indices: 2229573--2230063 Score: 563
Period size: 195 Copynumber: 2.5 Consensus size: 196
2229563 TCCATTCGGC
* * * *
2229573 TCGAGGGCATATCAACTTCATGGTAACAACGAGGAACTACTTTCTAGTTGAATTTTTAAACCGAG
1 TCGAGGGCATATCAACTACATGGTAGCAGCGAGGAACTACTTTCTGGTTGAA-TTTT-AACCGAG
* * * * ** **
2229638 GTCTTTAATCCAAGAAGAAGACCTAGGTTGGCTGTGATTTAGCAATAAGGAACTATCTCTTAGTC
64 GTCTTTAAGCCAAGAAGAAGACCTAGGTTGGATGTGATTTAGCAACAAGAAACTATCTCCCAACC
** * * * *
2229703 TGATTTACAGCATAGCTTAAGTCGAGAAAA-TCTATTTATCAACAAAAACTTTCGAATTCG-ATT
129 AAAGTTACAACATAGCTTAAGTCAAGAAAAGT-TATATATCAACAAAAACTTTCGAATTCGTATT
2229766 CAGA
193 CAGA
* * * * *
2229770 TCGAGGGCATATCAACTGCCTGATAGCAGCGAGGAACTACTTTCCGGTTGAATTTTAACCGATGT
1 TCGAGGGCATATCAACTACATGGTAGCAGCGAGGAACTACTTTCTGGTTGAATTTTAACCGAGGT
*
2229835 CTTTAAGCCAAGAAGAATACCTAGGTTGGATGTGATTTAGCAACAAGAAACTATCTCCCAACCAA
66 CTTTAAGCCAAGAAGAAGACCTAGGTTGGATGTGATTTAGCAACAAGAAACTATCTCCCAACCAA
* * *
2229900 AGTTACAACATAGCTTAAGTCAAGAAAAGTTGTATGTCAACAAAAACTTTCGAGTTCGATTTCAT
131 AGTTACAACATAGCTTAAGTCAAGAAAAGTTATATATCAACAAAAACTTTCGAATTCG---T-AT
*
2229965 TCAGT
192 TCAGA
* * * ** * *
2229970 TTGAGGGCGTATCAACCATTTGGTAGCAGCGAGGAACTACTTTTTGGTTGAATTTCAAACCGAGG
1 TCGAGGGCATATCAACTACATGGTAGCAGCGAGGAACTACTTTCTGGTTGAATTT-TAACCGAGG
* *
2230035 TCTTTAAGCCAATAAGAAGACCAAGGTTG
65 TCTTTAAGCCAAGAAGAAGACCTAGGTTG
2230064 ACTACGATTT
Statistics
Matches: 246, Mismatches: 41, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
195 111 0.45
196 5 0.02
197 45 0.18
200 52 0.21
201 33 0.13
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (196 bp):
TCGAGGGCATATCAACTACATGGTAGCAGCGAGGAACTACTTTCTGGTTGAATTTTAACCGAGGT
CTTTAAGCCAAGAAGAAGACCTAGGTTGGATGTGATTTAGCAACAAGAAACTATCTCCCAACCAA
AGTTACAACATAGCTTAAGTCAAGAAAAGTTATATATCAACAAAAACTTTCGAATTCGTATTCAG
A
Found at i:2230631 original size:20 final size:20
Alignment explanation
Indices: 2230600--2230646 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
2230590 TCAAATATAT
2230600 AATATATATAG-TTTTTGAA
1 AATATATATAGTTTTTTGAA
2230619 AATATAGTATAGTTTTTTGAA
1 AATATA-TATAGTTTTTTGAA
*
2230640 AACATAT
1 AATATAT
2230647 TTTTGAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 6 0.24
21 13 0.52
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (20 bp):
AATATATATAGTTTTTTGAA
Found at i:2230651 original size:14 final size:14
Alignment explanation
Indices: 2230632--2230660 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
2230622 ATAGTATAGT
2230632 TTTTTGAAAACATA
1 TTTTTGAAAACATA
2230646 TTTTTGAAAACATA
1 TTTTTGAAAACATA
2230660 T
1 T
2230661 AGTATATAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTGAAAACATA
Found at i:2230681 original size:39 final size:37
Alignment explanation
Indices: 2230620--2230744 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 37
2230610 GTTTTTGAAA
**
2230620 ATATAGTATAGTTTTTTGAAAACATATTTTTGAAAACAT
1 ATATA-TATAG-TTTTAAAAAACATATTTTTGAAAACAT
**
2230659 ATAGTATATAGCTTTTAAAAAAC--GGTTTTGAAAACAT
1 ATA-TATATAG-TTTTAAAAAACATATTTTTGAAAACAT
** *
2230696 ATATAATATAGTTTTTCAAAACATATTATTTTGAAAATAT
1 ATAT-ATATAGTTTTAAAAAACATA-T-TTTTGAAAACAT
2230736 ATATATATA
1 ATATATATA
2230745 TATGTTTTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
36 10 0.14
37 21 0.30
39 22 0.31
40 17 0.24
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.42
Consensus pattern (37 bp):
ATATATATAGTTTTAAAAAACATATTTTTGAAAACAT
Found at i:2230811 original size:22 final size:20
Alignment explanation
Indices: 2230786--2230833 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
2230776 ACGTATAAAA
2230786 TATATGATGTTTGAAAATATAT
1 TATATG-TGTTTG-AAATATAT
*
2230808 TATATTGTTTTTGAAATATAT
1 TATA-TGTGTTTGAAATATAT
2230829 TATAT
1 TATAT
2230834 TATATAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 9 0.38
23 2 0.08
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (20 bp):
TATATGTGTTTGAAATATAT
Found at i:2230904 original size:17 final size:18
Alignment explanation
Indices: 2230869--2230906 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
2230859 ATTTTCGATT
**
2230869 TTTATCTTTATTTTTTTA
1 TTTATCTTTATTTAATTA
2230887 TTTAT-TTTATTTAATTA
1 TTTATCTTTATTTAATTA
2230904 TTT
1 TTT
2230907 TTTAGGTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATCTTTATTTAATTA
Found at i:2236566 original size:16 final size:17
Alignment explanation
Indices: 2236542--2236583 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
2236532 GGGAGTACGA
*
2236542 TTTAGTTTTATAT-TAAT
1 TTTA-TTTTATATCAAAT
2236559 TTTATTTT-TATCAAAT
1 TTTATTTTATATCAAAT
2236575 TTTATTTTA
1 TTTATTTTA
2236584 CGCTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 15 0.68
17 4 0.18
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (17 bp):
TTTATTTTATATCAAAT
Found at i:2236848 original size:33 final size:33
Alignment explanation
Indices: 2236806--2236878 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
2236796 TTGTGATGAG
2236806 CCAATGACAGAGTTACTACAGTAAAAAGTGACT
1 CCAATGACAGAGTTACTACAGTAAAAAGTGACT
2236839 CCAATGACAGAGTTACTACAGTAAAAAGTGACT
1 CCAATGACAGAGTTACTACAGTAAAAAGTGACT
2236872 CCTAATG
1 CC-AATG
2236879 TTATGTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 35 0.90
34 4 0.10
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (33 bp):
CCAATGACAGAGTTACTACAGTAAAAAGTGACT
Found at i:2239012 original size:18 final size:17
Alignment explanation
Indices: 2238991--2239046 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
2238981 AATAATAAAT
2238991 TAATTTAAATAAAATTAA
1 TAATTTAAATAAAA-TAA
* *
2239009 TAATTT-ATTAAAAATAT
1 TAATTTAAAT-AAAATAA
2239026 TAGATTTATAATAAAATAA
1 TA-ATTTA-AATAAAATAA
2239045 TA
1 TA
2239047 GAAAGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.20
18 14 0.47
19 8 0.27
20 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
TAATTTAAATAAAATAA
Found at i:2239832 original size:17 final size:17
Alignment explanation
Indices: 2239790--2239832 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2239780 AACCGATCCA
2239790 ATAATC-ACCTAACTCG
1 ATAATCGACCTAACTCG
* * *
2239806 AAAATTGACCTGACTCG
1 ATAATCGACCTAACTCG
2239823 ATAATCGACC
1 ATAATCGACC
2239833 CGATACGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.23
Consensus pattern (17 bp):
ATAATCGACCTAACTCG
Found at i:2240370 original size:34 final size:32
Alignment explanation
Indices: 2240308--2240377 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2240298 ACCTTACAAC
* *
2240308 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
2240340 TCCCTAGCTTTTACGCGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
2240374 TCCC
1 TCCC
2240378 CATTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:2240790 original size:20 final size:20
Alignment explanation
Indices: 2240750--2240793 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2240740 TTGGTGCATT
**
2240750 GATGCACAACAGGATGTATC
1 GATGCACAACAGGATACATC
*
2240770 GATGCACAGCAGGATACATC
1 GATGCACAACAGGATACATC
2240790 GATG
1 GATG
2240794 TACTACTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.27, T:0.18
Consensus pattern (20 bp):
GATGCACAACAGGATACATC
Found at i:2240861 original size:21 final size:21
Alignment explanation
Indices: 2240816--2240892 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
2240806 TCGAAAAGGA
* *
2240816 GTGCATGGATGCACTACA-TG
1 GTGCATGGATGCACTGCAGGG
*
2240836 GTGCATCGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
**
2240857 GTGCATGGATGCACTGTTGGG
1 GTGCATGGATGCACTGCAGGG
2240878 GTGCATGGATGCACT
1 GTGCATGGATGCACT
2240893 TTGACACCCT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
20 16 0.32
21 34 0.68
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.25
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:2241139 original size:21 final size:21
Alignment explanation
Indices: 2241115--2241158 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
2241105 ATGTTTAATG
2241115 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
2241136 AAAATGATATCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
2241157 AA
1 AA
2241159 TTGTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:2244297 original size:20 final size:20
Alignment explanation
Indices: 2244274--2244338 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
2244264 TGGTGCATGA
2244274 ATGCACAACAGGATGCATCG
1 ATGCACAACAGGATGCATCG
*
2244294 ATGCACAACAGGATGCATTG
1 ATGCACAACAGGATGCATCG
*
2244314 ATACACAACAGGATGCATCG
1 ATGCACAACAGGATGCATCG
2244334 ATGCA
1 ATGCA
2244339 TTAATTGCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (20 bp):
ATGCACAACAGGATGCATCG
Found at i:2246646 original size:20 final size:20
Alignment explanation
Indices: 2246609--2246647 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2246599 ATTTTACCAC
**
2246609 ATGCAACTATATTCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2246629 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
2246648 TATGAGCTCT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2251941 original size:20 final size:20
Alignment explanation
Indices: 2251912--2251950 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2251902 ATTTCACCAC
*
2251912 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
2251932 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
2251951 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:2252315 original size:53 final size:53
Alignment explanation
Indices: 2252235--2252498 Score: 386
Period size: 53 Copynumber: 5.0 Consensus size: 53
2252225 TACTAAGGTA
*
2252235 ACGAAATGGTAATTCACAAACTCATTATGAAAACCATAGG-TGCACACATAGTG
1 ACGAAATGGTAATTCACAAACTCATTATGAATACCAT-GGATGCACACATAGTG
*
2252288 ACGAAATGGTAATTCACAAACTCATTATGAATACCATAGATGCACACATAGTG
1 ACGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTG
* * * * *
2252341 CCAAAATAGTAATTCACAAACTAATTATGAATACCATGGATGCACAAATAGTG
1 ACGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTG
** *
2252394 TTGAAATGGTCATTCACAAACTCATTATGAATACCATGGATGCACACATAGTG
1 ACGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTG
* * * *
2252447 TCGAAATGGTAATTTACAAACTAATTATGAATACCATGGATGCACAGATAGT
1 ACGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGT
2252499 ACTGATACGA
Statistics
Matches: 190, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
52 1 0.01
53 189 0.99
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (53 bp):
ACGAAATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTG
Found at i:2252387 original size:28 final size:28
Alignment explanation
Indices: 2252355--2252439 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
2252345 AATAGTAATT
2252355 CACAAACTAATTATGAATACCATGGATG
1 CACAAACTAATTATGAATACCATGGATG
* *
2252383 CACAAA-TAGTGT-TG-A-A--ATGGTCATT
1 CACAAACTAAT-TATGAATACCATGG--ATG
*
2252408 CACAAACTCATTATGAATACCATGGATG
1 CACAAACTAATTATGAATACCATGGATG
2252436 CACA
1 CACA
2252440 CATAGTGTCG
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 4 0.09
25 10 0.23
26 5 0.12
27 6 0.14
28 14 0.33
30 4 0.09
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (28 bp):
CACAAACTAATTATGAATACCATGGATG
Found at i:2253994 original size:241 final size:242
Alignment explanation
Indices: 2253570--2254007 Score: 869
Period size: 241 Copynumber: 1.8 Consensus size: 242
2253560 TCTTAAGATT
2253570 ATCTTGGATAACTTTCACTTTATCTTCCATTTCTTTCATTAAGTCAAGGCCAGATAGATCTCAAT
1 ATCTTGGATAACTTTCACTTTATCTTCCATTTCTTTCATTAAGTCAAGGCCAGATAGATCTCAAT
2253635 CTTTTAGCTCAAACCAATTTAATAGTGCTCGACACTTTCTCCCATATAAGACTTCTGTTGAAAAC
66 CTTTTAGCTCAAACCAATTTAATAGTGCTCGACACTTTCTCCCATATAAGACTTCTGTTGAAAAC
2253700 ATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATGATTTTCTA
131 ATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATGATTTTCTA
2253765 AATATCGATTTATTATAATATACTAATATCAACAATTAAAATTTTAA
196 AATATCGATTTATTATAATATACTAATATCAACAATTAAAATTTTAA
2253812 ATCTTGGATAACTTTCACTTTATCTTCCATTTCTTTCATTAAGTCAAGGCCAGATAGATCTCAAT
1 ATCTTGGATAACTTTCACTTTATCTTCCATTTCTTTCATTAAGTCAAGGCCAGATAGATCTCAAT
2253877 CTTTTAGCTC-AACCAATTTAATAGTGCTCGACACTTTCTCCCATATAAGACTTCTGTTGAAAAC
66 CTTTTAGCTCAAACCAATTTAATAGTGCTCGACACTTTCTCCCATATAAGACTTCTGTTGAAAAC
2253941 ATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATGATTTTCTA
131 ATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATGATTTTCTA
2254006 AA
196 AA
2254008 AGTATATTCG
Statistics
Matches: 196, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
241 121 0.62
242 75 0.38
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.39
Consensus pattern (242 bp):
ATCTTGGATAACTTTCACTTTATCTTCCATTTCTTTCATTAAGTCAAGGCCAGATAGATCTCAAT
CTTTTAGCTCAAACCAATTTAATAGTGCTCGACACTTTCTCCCATATAAGACTTCTGTTGAAAAC
ATTTTGATGTTTCGATATAACAAATTAAGTTAAATGAATTTTAAGATTTTACAAATGATTTTCTA
AATATCGATTTATTATAATATACTAATATCAACAATTAAAATTTTAA
Found at i:2254204 original size:20 final size:20
Alignment explanation
Indices: 2254179--2254217 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2254169 TTTTCAAGTG
2254179 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
2254199 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
2254218 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:2260062 original size:22 final size:22
Alignment explanation
Indices: 2260034--2260090 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
2260024 ACACCTAACA
2260034 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
2260056 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCATCCTTGAAT
2260078 GTGCATCGATGCA
1 GTGCATCGATGCA
2260091 CAAGGCCATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
GTGCATCGATGCATCCTTGAAT
Found at i:2264650 original size:240 final size:239
Alignment explanation
Indices: 2264179--2264659 Score: 953
Period size: 240 Copynumber: 2.0 Consensus size: 239
2264169 CGGTCAATAT
2264179 GGCGACTGGGAACTTCCATCGATTTTTTCTGGGCGATCATCAATTTCATTGGAGTGTTCTTCTCA
1 GGCGACTGGGAACTTCCATCGATTTTTTCTGGGCGATCATCAATTTCATTGGAGTGTTCTTCTCA
2264244 ACCATATTTTCAGGTTTTTATTTTTATTTTGGTCATTGGCAATTAGAGTTTTCTTCTCATTTTCA
66 ACCATATTTTCAGGTTTTTATTTTTATTTTGGTCATTGGCAATTAGAGTTTTCTTCTCATTTTCA
2264309 TTCTTTTGTTAATCTGTATCAATCAACTAGAAACTTGAATGCTGGATGTGCATCAGATGGAAAAG
131 TTCTTTTGTTAATCTGTATCAATCAACTAGAAACTTGAATGCTGGATGTGCATCAGATGGAAAAG
2264374 TCGGAAGAGAAAAAGCTGAGGGAAGAGGAGGAGGAAGAAGAGGA
196 TCGGAAGAGAAAAAGCTGAGGGAAGAGGAGGAGGAAGAAGAGGA
2264418 GGCGACTGGGAACTTCCATCGATTTTTTCTGGGCGATCATCAATTTCATTGGAGTGTTCTTCTCA
1 GGCGACTGGGAACTTCCATCGATTTTTTCTGGGCGATCATCAATTTCATTGGAGTGTTCTTCTCA
2264483 ACCATATTTTCAGGTTTTTATTTTTATTTTGGTCATTGGCAATTAGAGTTTCTCTTCTCATTTTC
66 ACCATATTTTCAGGTTTTTATTTTTATTTTGGTCATTGGCAATTAGAGTTT-TCTTCTCATTTTC
2264548 ATTCTTTTGTTAATCTGTATCAATCAACTAGAAACTTGAATGCTGGATGTGCATCAGATGGAAAA
130 ATTCTTTTGTTAATCTGTATCAATCAACTAGAAACTTGAATGCTGGATGTGCATCAGATGGAAAA
2264613 GTCGGAAGAGAAAAAGCTGAGGGAAGAGGAGGAGGAAGAAGAGGA
195 GTCGGAAGAGAAAAAGCTGAGGGAAGAGGAGGAGGAAGAAGAGGA
2264658 GG
1 GG
2264660 AGGAGAAGAA
Statistics
Matches: 241, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
239 116 0.48
240 125 0.52
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (239 bp):
GGCGACTGGGAACTTCCATCGATTTTTTCTGGGCGATCATCAATTTCATTGGAGTGTTCTTCTCA
ACCATATTTTCAGGTTTTTATTTTTATTTTGGTCATTGGCAATTAGAGTTTTCTTCTCATTTTCA
TTCTTTTGTTAATCTGTATCAATCAACTAGAAACTTGAATGCTGGATGTGCATCAGATGGAAAAG
TCGGAAGAGAAAAAGCTGAGGGAAGAGGAGGAGGAAGAAGAGGA
Found at i:2264655 original size:15 final size:14
Alignment explanation
Indices: 2264631--2264668 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
2264621 AGAAAAAGCT
2264631 GAGG-GAAGAGGAG
1 GAGGAGAAGAGGAG
2264644 GAGGAAGAAGAGGAG
1 GAGG-AGAAGAGGAG
2264659 GAGGAGAAGA
1 GAGGAGAAGA
2264669 AGAAGGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (14 bp):
GAGGAGAAGAGGAG
Found at i:2284342 original size:20 final size:20
Alignment explanation
Indices: 2284314--2284362 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
2284304 GTAATTGTTA
* **
2284314 TATCAATACTAAGAAGGGGG
1 TATCGATACTAAGAAGAAGG
*
2284334 TATCGATACTATGAAGAAGG
1 TATCGATACTAAGAAGAAGG
2284354 TATCGATAC
1 TATCGATAC
2284363 CATTGGTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (20 bp):
TATCGATACTAAGAAGAAGG
Found at i:2284872 original size:53 final size:54
Alignment explanation
Indices: 2284784--2284933 Score: 230
Period size: 53 Copynumber: 2.8 Consensus size: 54
2284774 AATGGCAATA
* *
2284784 TGTGTGCAAAAACTAAGAAATTCATACTAAGTTTATGAATTTCTGTATGAGCAC-
1 TGTGTGC-AAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGAGCACG
* * *
2284838 TGTGTGCAAAACTATGAAATTCATAATAAATTTATGAATTTCAGTATGTGCACTG
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGAGCAC-G
2284893 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT
1 TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTT
2284934 TCGTATTGGT
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 41 0.47
54 7 0.08
55 39 0.45
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (54 bp):
TGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCAGTATGAGCACG
Found at i:2285158 original size:45 final size:45
Alignment explanation
Indices: 2285107--2285412 Score: 345
Period size: 45 Copynumber: 6.8 Consensus size: 45
2285097 AGGCCTAATG
* *
2285107 TTGCATTAAAGGCATGAAATGATGCTATAAATTAAATGCATAACA
1 TTGCATTAAAGGCATGAAAGGATGCTATAAATGAAATGCATAACA
*
2285152 TTGCATTAAAGGCATGAAAGGATGCCATAAATGAAATGCATAACGA
1 TTGCATTAAAGGCATGAAAGGATGCTATAAATGAAATGCATAAC-A
* *
2285198 -TGCATTAAAGGCATGAAAGGGTGCCATAAATGAAATGCATAACGA
1 TTGCATTAAAGGCATGAAAGGATGCTATAAATGAAATGCATAAC-A
*
2285243 -TGCATTAAAGGCATGAAAGGATG-TCATAAATAAAATGCATAACA
1 TTGCATTAAAGGCATGAAAGGATGCT-ATAAATGAAATGCATAACA
* * * *
2285287 GTGCATTGAAGGCATGAAAGGATG-TCATAAATTAAATGCATAACG
1 TTGCATTAAAGGCATGAAAGGATGCT-ATAAATGAAATGCATAACA
* ** * * *
2285332 TTGCTTTAAATACATGAAAGGATGCCATAAATGAAATACTTAACA
1 TTGCATTAAAGGCATGAAAGGATGCTATAAATGAAATGCATAACA
* * *
2285377 GTATG--TTAAAAGCATGAAATGATGCTCTAAATGAAA
1 -T-TGCATTAAAGGCATGAAAGGATGCTATAAATGAAA
2285413 ATAATGAATA
Statistics
Matches: 230, Mismatches: 25, Indels: 12
0.86 0.09 0.04
Matches are distributed among these distances:
44 1 0.00
45 225 0.98
46 2 0.01
47 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.25
Consensus pattern (45 bp):
TTGCATTAAAGGCATGAAAGGATGCTATAAATGAAATGCATAACA
Found at i:2285261 original size:90 final size:90
Alignment explanation
Indices: 2285108--2285401 Score: 385
Period size: 90 Copynumber: 3.3 Consensus size: 90
2285098 GGCCTAATGT
* *
2285108 TGCATTAAAGGCATGAAATGATGCTATAAATTAAATGCATAAC-ATTGCATTAAAGGCATGAAAG
1 TGCATTAAAGGCATGAAAGGATGCCATAAATTAAATGCATAACGA-TGCATTAAAGGCATGAAAG
2285172 GATGCCATAAATGAAATGCATAAC-G
65 GATGCCATAAATGAAATGCATAACAG
* *
2285197 ATGCATTAAAGGCATGAAAGGGTGCCATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAG
1 -TGCATTAAAGGCATGAAAGGATGCCATAAATTAAATGCATAACGATGCATTAAAGGCATGAAAG
* *
2285262 GATGTCATAAATAAAATGCATAACAG
65 GATGCCATAAATGAAATGCATAACAG
* * * * **
2285288 TGCATTGAAGGCATGAAAGGATGTCATAAATTAAATGCATAACGTTGCTTTAAATACATGAAAGG
1 TGCATTAAAGGCATGAAAGGATGCCATAAATTAAATGCATAACGATGCATTAAAGGCATGAAAGG
* *
2285353 ATGCCATAAATGAAATACTTAACAG
66 ATGCCATAAATGAAATGCATAACAG
*** * *
2285378 TATGTTAAAAGCATGAAATGATGC
1 TGCATTAAAGGCATGAAAGGATGC
2285402 TCTAAATGAA
Statistics
Matches: 177, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
90 175 0.99
91 2 0.01
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.24
Consensus pattern (90 bp):
TGCATTAAAGGCATGAAAGGATGCCATAAATTAAATGCATAACGATGCATTAAAGGCATGAAAGG
ATGCCATAAATGAAATGCATAACAG
Found at i:2285280 original size:135 final size:135
Alignment explanation
Indices: 2285108--2285414 Score: 413
Period size: 135 Copynumber: 2.3 Consensus size: 135
2285098 GGCCTAATGT
* * *
2285108 TGCATTAAAGGCATGAAATGATGCTATAAATTAAATGCATAACATTGCATTAAAGGCATGAAAGG
1 TGCATTAAAGGCATGAAAGGATGCTATAAATAAAATGCATAACAGTGCATTAAAGGCATGAAAGG
* *
2285173 ATGCCATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGGTGCCATAAATGAAATGCAT
66 ATGCCATAAATGAAATGCATAACGATGCATTAAAGACATGAAAGGATGCCATAAATGAAATGCAT
2285238 AACGA
131 AACGA
*
2285243 TGCATTAAAGGCATGAAAGGATG-TCATAAATAAAATGCATAACAGTGCATTGAAGGCATGAAAG
1 TGCATTAAAGGCATGAAAGGATGCT-ATAAATAAAATGCATAACAGTGCATTAAAGGCATGAAAG
* * * * * * *
2285307 GATGTCATAAATTAAATGCATAACGTTGCTTTAAATACATGAAAGGATGCCATAAATGAAATACT
65 GATGCCATAAATGAAATGCATAACGATGCATTAAAGACATGAAAGGATGCCATAAATGAAATGCA
2285372 TAACAGTA
130 TAAC-G-A
* * *
2285380 TG--TTAAAAGCATGAAATGATGCTCTAAATGAAAAT
1 TGCATTAAAGGCATGAAAGGATGCTATAAAT-AAAAT
2285415 AATGAATAAT
Statistics
Matches: 151, Mismatches: 16, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
134 1 0.01
135 140 0.93
136 7 0.05
137 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.25
Consensus pattern (135 bp):
TGCATTAAAGGCATGAAAGGATGCTATAAATAAAATGCATAACAGTGCATTAAAGGCATGAAAGG
ATGCCATAAATGAAATGCATAACGATGCATTAAAGACATGAAAGGATGCCATAAATGAAATGCAT
AACGA
Found at i:2289701 original size:19 final size:19
Alignment explanation
Indices: 2289677--2289724 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
2289667 TGCAAAAATG
*
2289677 GTATCGATACTGTAAAGGA
1 GTATCGATACTGTAAAGAA
2289696 GTATCGATACTGTAAAGAA
1 GTATCGATACTGTAAAGAA
2289715 GTATCGATAC
1 GTATCGATAC
2289725 CACAATAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (19 bp):
GTATCGATACTGTAAAGAA
Done.