Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008092.1 Hibiscus syriacus cultivar Beakdansim tig00110607_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: 2324158
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1206935 original size:19 final size:19
Alignment explanation
Indices: 1206911--1206961 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1206901 GAAAAAATTC
1206911 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
1206930 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
1206949 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
1206962 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:1207003 original size:65 final size:64
Alignment explanation
Indices: 1206805--1207012 Score: 210
Period size: 65 Copynumber: 3.2 Consensus size: 64
1206795 GCACCAAGTG
* * * ** *
1206805 TGCATCGATGCATGAAATGCATTCGATGTTTGAGAAATAGCCTGATGCATCGATGCATGG-CTTG
1 TGCATCGGTGCATGAAATGCATTCGATGTTTCA-AAAAATTCAGATGCATCGATGCATGGAC-TG
1206869 -
64 A
* * *
1206869 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAAAATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATGAAATGCATTCGATG-TTTCAAAAAATTCAGA-TGCATCGATGCATGGACTG
1206932 A
64 A
* **
1206933 GTGCATCGGTGCATGGAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCA--GATGCATCGATGCATGGACT
1206997 GA
63 GA
1206999 TGCATCGGTGCATG
1 TGCATCGGTGCATG
1207013 CCTTTGAATA
Statistics
Matches: 124, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
63 11 0.09
64 50 0.40
65 61 0.49
66 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (64 bp):
TGCATCGGTGCATGAAATGCATTCGATGTTTCAAAAAATTCAGATGCATCGATGCATGGACTGA
Found at i:1209116 original size:68 final size:68
Alignment explanation
Indices: 1209032--1209167 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
1209022 TTCAGATTCT
1209032 CTCATTTCACAGCCTTTTTGAACGTAGACCATGAGACACCACCAAATTCAACCAAGTTAGATTTA
1 CTCATTTCACAGCCTTTTTGAACGTAGACCATGAGACACCACCAAATTCAACCAAGTTAGATTTA
1209097 AAA
66 AAA
1209100 CTCATTTCACAGCCTTTTTGAACGTAGACCATGAGACACCACCAAATTCAACCAAGTTAGATTTA
1 CTCATTTCACAGCCTTTTTGAACGTAGACCATGAGACACCACCAAATTCAACCAAGTTAGATTTA
1209165 AAA
66 AAA
1209168 GATATATTTC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (68 bp):
CTCATTTCACAGCCTTTTTGAACGTAGACCATGAGACACCACCAAATTCAACCAAGTTAGATTTA
AAA
Found at i:1209606 original size:21 final size:21
Alignment explanation
Indices: 1209582--1209624 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1209572 TGAAACAGAT
1209582 GTGGTGGCATCTGAAAGTGGG
1 GTGGTGGCATCTGAAAGTGGG
*
1209603 GTGGTGTCATCTGAAAGTGGG
1 GTGGTGGCATCTGAAAGTGGG
1209624 G
1 G
1209625 CAGTGGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.09, G:0.47, T:0.26
Consensus pattern (21 bp):
GTGGTGGCATCTGAAAGTGGG
Found at i:1210334 original size:2 final size:2
Alignment explanation
Indices: 1210327--1210398 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
1210317 ATCCTATTTA
1210327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1210368 AT AT AT AT -T 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
1210399 GCCATTCTAT
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1212983 original size:5 final size:5
Alignment explanation
Indices: 1212973--1213027 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
1212963 TAGTTTAATT
* *
1212973 TTTTA TTTTA TTTTA TTTTA -TTTA TTTCA TTTTG TTATT- TTATTA GTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT-TTA TT-TTA -TTTTA
1213024 TTTT
1 TTTT
1213028 TCTTCTCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
4 4 0.09
5 32 0.74
6 5 0.12
7 2 0.05
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:1212995 original size:22 final size:21
Alignment explanation
Indices: 1212970--1213028 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 21
1212960 GATTAGTTTA
*
1212970 ATTTTTTATTTTATTTTATTTT
1 ATTTTTTATTTT-TGTTATTTT
1212992 ATTTATTTCA-TTTTGTTATTTT
1 ATTT-TTT-ATTTTTGTTATTTT
1213014 ATTAGTTTTATTTTT
1 ATT--TTTTATTTTT
1213029 CTTCTCATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
22 16 0.52
23 13 0.42
24 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (21 bp):
ATTTTTTATTTTTGTTATTTT
Found at i:1212998 original size:14 final size:14
Alignment explanation
Indices: 1212973--1213016 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1212963 TAGTTTAATT
1212973 TTTTATTTTATTTTA
1 TTTTA-TTTATTTTA
*
1212988 TTTTATTTATTTCA
1 TTTTATTTATTTTA
*
1213002 TTTT-GTTATTTTA
1 TTTTATTTATTTTA
1213015 TT
1 TT
1213017 AGTTTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 9 0.35
14 12 0.46
15 5 0.19
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTTATTTATTTTA
Found at i:1213733 original size:15 final size:14
Alignment explanation
Indices: 1213710--1213744 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1213700 GCAATCATAT
*
1213710 AAAAAAAAGAGAGA
1 AAAAAAAAGAAAGA
1213724 AAAAACAAAGAAAGA
1 AAAAA-AAAGAAAGA
1213739 AAAAAA
1 AAAAAA
1213745 GTATATATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAGA
Found at i:1213828 original size:33 final size:34
Alignment explanation
Indices: 1213788--1213867 Score: 92
Period size: 38 Copynumber: 2.3 Consensus size: 34
1213778 GGTTCCAACA
1213788 TTTTAGGA-AATAAGTTGGAATGCTCCAACA-TAG
1 TTTTAGGATAATAAGTTGGAAT-CTCCAACATTAG
1213821 TTTTAGGAAATTGAATAAGTTGGAATCTCCAACATTAG
1 TTTTAGG--A-T-AATAAGTTGGAATCTCCAACATTAG
*
1213859 CTTTAGGAT
1 TTTTAGGAT
1213868 GATTGCTACA
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
33 7 0.17
35 2 0.05
36 1 0.03
37 8 0.20
38 22 0.55
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (34 bp):
TTTTAGGATAATAAGTTGGAATCTCCAACATTAG
Found at i:1219266 original size:2 final size:2
Alignment explanation
Indices: 1219259--1219302 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1219249 AATTTCTAAC
*
1219259 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1219301 AT
1 AT
1219303 TCTAACATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1220457 original size:23 final size:23
Alignment explanation
Indices: 1220427--1220470 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1220417 ACACCATAAG
*
1220427 TTCACCAATCTACAACCCAACCC
1 TTCACCAATCCACAACCCAACCC
1220450 TTCACCAATCCACAACCCAAC
1 TTCACCAATCCACAACCCAAC
1220471 TGATATTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (23 bp):
TTCACCAATCCACAACCCAACCC
Found at i:1226044 original size:35 final size:35
Alignment explanation
Indices: 1225998--1226073 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
1225988 AAAACAGTCC
* *
1225998 TCAATTTCATTCTAAATCCC-AATTTCCAAAGTAAT
1 TCAATTTCATTCTAAA-CCCTAAATTCCAAAATAAT
*
1226033 TCAATTTCATTCTAAACCCTAAATTCTAAAATAAT
1 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1226068 TCAATT
1 TCAATT
1226074 AAATTCAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 3 0.08
35 34 0.92
ACGTcount: A:0.39, C:0.21, G:0.01, T:0.38
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
Found at i:1226619 original size:130 final size:130
Alignment explanation
Indices: 1226473--1226720 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1226463 TATTTATATA
* **
1226473 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
1226538 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
1226603 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
1226668 TTAACACATTATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
1226721 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1226751 original size:130 final size:129
Alignment explanation
Indices: 1226487--1226751 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
1226477 ATTTGGTCCT
* ** *
1226487 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
1226552 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
*
1226617 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATTATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
1226682 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1226746 -A
128 CA
1226747 AAATT
1 AAATT
1226752 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1227081 original size:28 final size:27
Alignment explanation
Indices: 1227050--1227112 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1227040 AGTTGATACA
*
1227050 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1227078 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1227106 ATATTTT
1 ATATTTT
1227113 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1227213 original size:16 final size:18
Alignment explanation
Indices: 1227192--1227225 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1227182 ATTTCTTATT
1227192 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
1227208 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
1227226 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:1235956 original size:51 final size:52
Alignment explanation
Indices: 1235887--1235997 Score: 197
Period size: 51 Copynumber: 2.1 Consensus size: 52
1235877 TTAAATTTTA
*
1235887 TTTTTTATTTACTATATATATATATATAAACATAAAAACTTGCTTTATACATG
1 TTTTTAATTTAC-ATATATATATATATAAACATAAAAACTTGCTTTATACATG
1235940 TTTTTAATTTAC-TATATATATATATAAACATAAAAACTTGCTTTATACATG
1 TTTTTAATTTACATATATATATATATAAACATAAAAACTTGCTTTATACATG
1235991 TTTTTAA
1 TTTTTAA
1235998 ATCTAAATAC
Statistics
Matches: 57, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
51 46 0.81
53 11 0.19
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.48
Consensus pattern (52 bp):
TTTTTAATTTACATATATATATATATAAACATAAAAACTTGCTTTATACATG
Found at i:1237904 original size:12 final size:12
Alignment explanation
Indices: 1237887--1237916 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1237877 CATTAATGCA
1237887 TATTAATCACAT
1 TATTAATCACAT
1237899 TATTAATCACAT
1 TATTAATCACAT
1237911 TATTAA
1 TATTAA
1237917 ACACTCGCAG
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:0.43, C:0.13, G:0.00, T:0.43
Consensus pattern (12 bp):
TATTAATCACAT
Found at i:1238143 original size:21 final size:21
Alignment explanation
Indices: 1238127--1238180 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1238117 GCGTTGCATT
1238127 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
1238148 TCGCGTTGCGATAGTTGGAAA
1 TCGCGTTGCGATAGTTGGAAA
1238169 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1238181 GATATACAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGGAAA
Found at i:1238236 original size:20 final size:21
Alignment explanation
Indices: 1238211--1238262 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1238201 TTTTCCCAAT
*
1238211 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1238231 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1238252 TCGCAATGCGA
1 TCGCAATGCGA
1238263 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1238341 original size:20 final size:20
Alignment explanation
Indices: 1238293--1238345 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1238283 TAATACAAAA
* *
1238293 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
1238313 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
1238333 TCGCAACGCGATT
1 TCGCAACGCGATT
1238346 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:1238901 original size:19 final size:19
Alignment explanation
Indices: 1238863--1238917 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1238853 TTCGAGAATG
*
1238863 AAAATCACAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1238883 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
1238902 AAAATCGCAACGCGAA
1 AAAATCGCAACGCGAA
1238918 CCAAAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.49, C:0.24, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1238925 original size:18 final size:19
Alignment explanation
Indices: 1238863--1238928 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 19
1238853 TTCGAGAATG
* *
1238863 AAAATCACAACGCGGAAATA
1 AAAATCGCAACGC-GAAACA
** *
1238883 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAACA
*
1238902 AAAATCGCAACGCG-AACC
1 AAAATCGCAACGCGAAACA
1238920 AAAATCGCA
1 AAAATCGCA
1238929 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.28
19 18 0.46
20 10 0.26
ACGTcount: A:0.48, C:0.26, G:0.15, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:1238951 original size:19 final size:19
Alignment explanation
Indices: 1238924--1239108 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
1238914 CGAACCAAAA
*
1238924 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1238943 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1238962 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1238981 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1239001 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1239017 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1239034 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1239048 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1239067 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1239087 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1239107 TC
1 TC
1239109 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1239001 original size:39 final size:38
Alignment explanation
Indices: 1238924--1239108 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
1238914 CGAACCAAAA
*
1238924 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
1238962 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
1239001 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
1239034 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
1239067 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
1239107 TC
1 TC
1239109 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:1239085 original size:20 final size:20
Alignment explanation
Indices: 1239051--1239108 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1239041 GCGATTCTCT
**
1239051 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1239071 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1239091 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1239109 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1241169 original size:42 final size:42
Alignment explanation
Indices: 1241108--1241230 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
1241098 GCCCGACTCG
* * *
1241108 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * *
1241150 CCTATTATTCCTCGAGAGTCCTCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1241192 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1241231 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.35, G:0.18, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1242596 original size:14 final size:14
Alignment explanation
Indices: 1242577--1242612 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1242567 ATTGTTTAAT
1242577 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1242591 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1242605 TGATTTGT
1 TGATTTGT
1242613 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1242822 original size:19 final size:19
Alignment explanation
Indices: 1242791--1242889 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
1242781 CGAAATTAAA
1242791 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
1242810 TTCGCGTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1242825 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
1242843 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
1242857 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1242876 TTCGCATTGCGATT
1 TTCGCGTTGCGATT
1242890 CTCTCATTGC
Statistics
Matches: 59, Mismatches: 11, Indels: 20
0.66 0.12 0.22
Matches are distributed among these distances:
14 20 0.34
16 3 0.05
17 3 0.05
19 33 0.56
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1242837 original size:33 final size:32
Alignment explanation
Indices: 1242795--1242902 Score: 137
Period size: 33 Copynumber: 3.3 Consensus size: 32
1242785 ATTAAATTCG
*
1242795 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
1242828 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
1242861 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
1242894 CATTGCGAT
1 CGTTGCGAT
1242903 AGTAATTTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 3 0.05
33 59 0.91
35 3 0.05
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:1242911 original size:66 final size:67
Alignment explanation
Indices: 1242788--1242921 Score: 189
Period size: 66 Copynumber: 2.0 Consensus size: 67
1242778 ACGCGAAATT
* * * ** *
1242788 AAATTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTT-CGCATTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATAGTAATTTCCGCATTG
1242852 CG
66 CG
* *
1242854 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATAGTAATTTCCGCGTTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATAGTAATTTCCGCATTG
1242919 CG
66 CG
1242921 A
1 A
1242922 TGGACATTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
66 50 0.85
67 9 0.15
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (67 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATAGTAATTTCCGCATTG
CG
Found at i:1245200 original size:12 final size:12
Alignment explanation
Indices: 1245183--1245207 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1245173 TCTTCGGGGA
1245183 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1245195 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1245207 C
1 C
1245208 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1245403 original size:21 final size:22
Alignment explanation
Indices: 1245377--1245420 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1245367 CTGAAACATC
*
1245377 ATCAAA-TCCGTGTATTGACCA
1 ATCAAAGTCCGGGTATTGACCA
1245398 ATCAAAGTCCGGGTATTGACCA
1 ATCAAAGTCCGGGTATTGACCA
1245420 A
1 A
1245421 GATCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (22 bp):
ATCAAAGTCCGGGTATTGACCA
Found at i:1246507 original size:20 final size:20
Alignment explanation
Indices: 1246462--1246518 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
1246452 CATTCATTGA
*
1246462 CTATCGCAACGCGAAAA-GG
1 CTATCGCAACGAGAAAATGG
*
1246481 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
1246501 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
1246519 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:1246601 original size:18 final size:18
Alignment explanation
Indices: 1246537--1246602 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
1246527 GAAATGAAAA
1246537 TCGCATTGCGATTTTC--
1 TCGCATTGCGATTTTCAT
1246553 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCA-T
1246569 TCGCATTGCGATTTTCAT
1 TCGCATTGCGATTTTCAT
1246587 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1246603 GTTGCGATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
13 4 0.09
14 6 0.14
16 6 0.14
18 23 0.52
19 5 0.11
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTTCAT
Found at i:1248244 original size:176 final size:171
Alignment explanation
Indices: 1247955--1248302 Score: 651
Period size: 176 Copynumber: 2.0 Consensus size: 171
1247945 TTCCGGTAGT
1247955 TGTCTCCTCTCCACTTCAGATACCGGAAGGGTACTAGCGGTAACATGAGAGCCAACTCTCATCCA
1 TGTCTCCTCTCCACTTCAGATACCGGAAGGGTACTAGCGGTAACATGAGAGCCAACTCTCATCCA
1248020 TCATGTCCGGAATCGGTGGGGGTTTCTCAATACTTTGATATATTACCCCATGTGAATCGGGCTCT
66 TCATGTCCGGAATCGGTGGGGGTTTCTCAATACTTTGATATATTACCCCATGTGAATCGGGCTCT
1248085 GGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGCCTC
131 GGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGCCTC
1248126 TGTCTCCTCTCCACTTCAGATACCGGAAGGGTACTAGCCGGTAACTCATATGAGAGCCAACTCTC
1 TGTCTCCTCTCCACTTCAGATACCGGAAGGGTACTAG-CGGTAA--C--ATGAGAGCCAACTCTC
1248191 ATCCATCATGTCCGGAATCGGTGGGGGTTTCTCAATACTTTGATATATTACCCCATGTGAATCGG
61 ATCCATCATGTCCGGAATCGGTGGGGGTTTCTCAATACTTTGATATATTACCCCATGTGAATCGG
1248256 GCTCTGGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGCCTC
126 GCTCTGGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGCCTC
1248302 T
1 T
1248303 TGAACGGTGG
Statistics
Matches: 172, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
171 37 0.22
172 6 0.03
174 1 0.01
176 128 0.74
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (171 bp):
TGTCTCCTCTCCACTTCAGATACCGGAAGGGTACTAGCGGTAACATGAGAGCCAACTCTCATCCA
TCATGTCCGGAATCGGTGGGGGTTTCTCAATACTTTGATATATTACCCCATGTGAATCGGGCTCT
GGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGCCTC
Found at i:1248776 original size:20 final size:19
Alignment explanation
Indices: 1248741--1248807 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1248731 GAAACTTAAA
1248741 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1248760 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1248780 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1248799 ATCGCAACG
1 ATCGCAACG
1248808 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1248815 original size:14 final size:14
Alignment explanation
Indices: 1248796--1248853 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1248786 ATGCGAAATG
1248796 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1248810 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1248826 ATCAAATCGCAACGAC
1 A--AAATCGCAACGAC
1248842 AAAATCGCAACG
1 AAAATCGCAACG
1248854 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1248838 original size:32 final size:32
Alignment explanation
Indices: 1248780--1248869 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
1248770 GGAAATGGCT
*
1248780 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-CAAATCGCAACGACAAA
1248813 ATCGCAATGCGAAATCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATCAAATCGCAACGACAAA
* *
1248845 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAA-TCAAATCGCA
1248870 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 2
0.91 0.05 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (32 bp):
ATCGCAATGCGAAATCAAATCGCAACGACAAA
Found at i:1248865 original size:19 final size:18
Alignment explanation
Indices: 1248811--1248869 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
1248801 CGCAACGACA
*
1248811 AAATCGCAATGCGAAA-TC
1 AAATCGCAA-GCGAAACAC
1248829 AAATCGCAA-CG--ACA-
1 AAATCGCAAGCGAAACAC
1248843 AAATCGCAACGCGAAACAC
1 AAATCGCAA-GCGAAACAC
1248862 AAATCGCA
1 AAATCGCA
1248870 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
14 10 0.29
16 4 0.12
18 12 0.35
19 8 0.24
ACGTcount: A:0.47, C:0.27, G:0.15, T:0.10
Consensus pattern (18 bp):
AAATCGCAAGCGAAACAC
Found at i:1248906 original size:14 final size:14
Alignment explanation
Indices: 1248887--1248944 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1248877 TTTTATTTCG
1248887 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1248901 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1248917 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1248933 CGTTGCGATTTT
1 CGTTGCGATTTT
1248945 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1248951 original size:33 final size:33
Alignment explanation
Indices: 1248870--1248960 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1248860 ACAAATCGCA
* *
1248870 TTGCGATTTTTATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1248903 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1248935 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1248961 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1248979 original size:20 final size:19
Alignment explanation
Indices: 1248945--1248999 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1248935 TTGCGATTTT
*
1248945 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1248964 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1248984 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
1249000 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1249507 original size:18 final size:18
Alignment explanation
Indices: 1249481--1249525 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1249471 GTCGATCAGA
*
1249481 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1249499 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1249517 TGATGGCTC
1 TGATGGCTC
1249526 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1250858 original size:20 final size:20
Alignment explanation
Indices: 1250833--1250870 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1250823 AATAGTTTCT
1250833 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
1250853 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
1250871 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:1251158 original size:22 final size:22
Alignment explanation
Indices: 1251133--1251176 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1251123 GATTTAGATA
*
1251133 GACGGATTTCGCCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
*
1251155 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGCCGGAGATGGG
1251177 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGAATTTCGCCGGAGATGGG
Found at i:1251433 original size:21 final size:21
Alignment explanation
Indices: 1251402--1251502 Score: 68
Period size: 20 Copynumber: 4.9 Consensus size: 21
1251392 TGCGAAAGTA
* *
1251402 AGTATCTCATTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
1251423 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
1251443 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
1251465 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
1251486 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
1251503 CCCAATTCGC
Statistics
Matches: 63, Mismatches: 13, Indels: 11
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 28 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:1251458 original size:20 final size:20
Alignment explanation
Indices: 1251344--1251458 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1251334 CGCTTTGAAA
*
1251344 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
1251365 ATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1251385 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* ** * *
1251405 ATCTCATTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1251426 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1251446 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1251459 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 48 0.65
21 24 0.32
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1251477 original size:41 final size:41
Alignment explanation
Indices: 1251386--1251520 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1251376 AAAGTCAGTA
* * ** *
1251386 TCGCGTTGCGAAAGTAAGTATCTCATTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
1251426 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1251468 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1251509 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1251521 TTACTTATTC
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 3 0.04
41 75 0.94
42 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1251512 original size:21 final size:20
Alignment explanation
Indices: 1251447--1251539 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
1251437 ATAGTCAGTA
*
1251447 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
1251468 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
1251488 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
1251509 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
1251529 TCGCATTGCGA
1 TCGCATTGCGA
1251540 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:1251521 original size:41 final size:41
Alignment explanation
Indices: 1251447--1251539 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1251437 ATAGTCAGTA
1251447 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1251488 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1251529 TCGCATTGCGA
1 TCGCATTGCGA
1251540 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1254258 original size:20 final size:21
Alignment explanation
Indices: 1254213--1254258 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1254203 TAGGCGTGAG
*
1254213 TTTAGTTCTAATTATTTAATA
1 TTTAGTTCGAATTATTTAATA
* *
1254234 TTTAGTTCGATTTATTTTA-A
1 TTTAGTTCGAATTATTTAATA
1254254 TTTAG
1 TTTAG
1254259 GATAAAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (21 bp):
TTTAGTTCGAATTATTTAATA
Found at i:1257637 original size:17 final size:18
Alignment explanation
Indices: 1257607--1257642 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1257597 TGATCTTGTC
*
1257607 AAACTTATTGACTTGTGA
1 AAACTTATTAACTTGTGA
1257625 AAACTTA-TAACTTGTGA
1 AAACTTATTAACTTGTGA
1257642 A
1 A
1257643 TAATCTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (18 bp):
AAACTTATTAACTTGTGA
Found at i:1259376 original size:57 final size:57
Alignment explanation
Indices: 1259288--1259400 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
1259278 TTTTGCTATC
* *
1259288 ATCAATGGAGATAATAAAGTATTTATTCTCCATCGCCTATGCCATTATTACGAATTA
1 ATCAATAGAGATAATAAAGTATTTATTCTCCATCGCCTATGCCACTATTACGAATTA
* *
1259345 ATCAATAGAGATAATAATGTATTTATTCTCCATCGCCTGTGCCACTATTACGAATT
1 ATCAATAGAGATAATAAAGTATTTATTCTCCATCGCCTATGCCACTATTACGAATT
1259401 TTAAGAACTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (57 bp):
ATCAATAGAGATAATAAAGTATTTATTCTCCATCGCCTATGCCACTATTACGAATTA
Found at i:1260495 original size:20 final size:20
Alignment explanation
Indices: 1260470--1260509 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1260460 AAAACTTGCC
*
1260470 AAAGGTTTTAAAACCCCCTT
1 AAAGGTTTCAAAACCCCCTT
*
1260490 AAAGGTTTCGAAACCCCCTT
1 AAAGGTTTCAAAACCCCCTT
1260510 GGCCAACGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (20 bp):
AAAGGTTTCAAAACCCCCTT
Found at i:1262630 original size:17 final size:18
Alignment explanation
Indices: 1262600--1262635 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1262590 TGAACTTGTC
*
1262600 AAACTTATTGACTTGTGA
1 AAACTTATTAACTTGTGA
1262618 AAACTTA-TAACTTGTGA
1 AAACTTATTAACTTGTGA
1262635 A
1 A
1262636 TAACCTAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (18 bp):
AAACTTATTAACTTGTGA
Found at i:1268793 original size:15 final size:15
Alignment explanation
Indices: 1268773--1268864 Score: 78
Period size: 15 Copynumber: 6.2 Consensus size: 15
1268763 TACTATGAGT
*
1268773 ATATGTTATAGGTGA
1 ATATGTTATATGTGA
1268788 ATATGTTATATGTGA
1 ATATGTTATATGTGA
* * * *
1268803 AAATATTCTACGTGA
1 ATATGTTATATGTGA
*
1268818 AAATG-TATATGTGA
1 ATATGTTATATGTGA
** *
1268832 ATATGTGCTAAGTGA
1 ATATGTTATATGTGA
* *
1268847 ATGTGTTCTATGTGA
1 ATATGTTATATGTGA
1268862 ATA
1 ATA
1268865 AAAAATACTT
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
14 11 0.18
15 49 0.82
ACGTcount: A:0.35, C:0.04, G:0.22, T:0.39
Consensus pattern (15 bp):
ATATGTTATATGTGA
Found at i:1268846 original size:29 final size:30
Alignment explanation
Indices: 1268784--1268862 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 30
1268774 TATGTTATAG
* * *
1268784 GTGAATATGTTATATGTGAAAATATTCTAC
1 GTGAAAATGTTATATGTGAAAATATGCTAA
* *
1268814 GTGAAAATG-TATATGTGAATATGTGCTAA
1 GTGAAAATGTTATATGTGAAAATATGCTAA
** *
1268843 GTGAATGTGTTCTATGTGAA
1 GTGAAAATGTTATATGTGAA
1268863 TAAAAAATAC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (30 bp):
GTGAAAATGTTATATGTGAAAATATGCTAA
Found at i:1269005 original size:23 final size:23
Alignment explanation
Indices: 1268979--1269070 Score: 60
Period size: 24 Copynumber: 3.9 Consensus size: 23
1268969 CTACGCGGTT
1268979 CTTCAGGATAATTCTATGTGGTC
1 CTTCAGGATAATTCTATGTGGTC
* * * *
1269002 CTTCGGGAAAAATTCTACGCGGTC
1 CTTCAGG-ATAATTCTATGTGGTC
* * * *
1269026 CTTCGGGACAAATCTATGTTG-C
1 CTTCAGGATAATTCTATGTGGTC
* *
1269048 ACTTCAGTGCTTATTCTATGTGG
1 -CTTCAG-GATAATTCTATGTGG
1269071 CAGTTCGGTG
Statistics
Matches: 51, Mismatches: 15, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
22 1 0.02
23 20 0.39
24 30 0.59
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (23 bp):
CTTCAGGATAATTCTATGTGGTC
Found at i:1269017 original size:24 final size:24
Alignment explanation
Indices: 1268988--1269044 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
1268978 TCTTCAGGAT
1268988 AATTCTATGTGGTCCTTCGGGAAA
1 AATTCTATGTGGTCCTTCGGGAAA
* * *
1269012 AATTCTACGCGGTCCTTCGGGACA
1 AATTCTATGTGGTCCTTCGGGAAA
1269036 AA-TCTATGT
1 AATTCTATGT
1269045 TGCACTTCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (24 bp):
AATTCTATGTGGTCCTTCGGGAAA
Found at i:1269087 original size:24 final size:24
Alignment explanation
Indices: 1269034--1269094 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 24
1269024 TCCTTCGGGA
*
1269034 CAAA-TCTATGTTGCACTTCAGTG
1 CAAATTCTATGTGGCACTTCAGTG
** * *
1269057 CTTATTCTATGTGGCAGTTCGGTG
1 CAAATTCTATGTGGCACTTCAGTG
*
1269081 CAAATTCTACGTGG
1 CAAATTCTATGTGG
1269095 TAGTGGTGAC
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
23 2 0.07
24 27 0.93
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (24 bp):
CAAATTCTATGTGGCACTTCAGTG
Found at i:1273142 original size:17 final size:18
Alignment explanation
Indices: 1273120--1273163 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1273110 AAGAAAAGAT
*
1273120 ATAAATAAAATT-TTAAA
1 ATAAATAAAATTCATAAA
*
1273137 ATAAATATAATTCATAAA
1 ATAAATAAAATTCATAAA
*
1273155 ATACATAAA
1 ATAAATAAA
1273164 TAATTGAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAAAATTCATAAA
Found at i:1277345 original size:157 final size:157
Alignment explanation
Indices: 1277059--1277372 Score: 628
Period size: 157 Copynumber: 2.0 Consensus size: 157
1277049 ATTTATGTTC
1277059 CATGCATTGAAAATCAATCAATAACCCAATGAATCCCAGATGTCTCTCCTTATGAAGCAAATGGA
1 CATGCATTGAAAATCAATCAATAACCCAATGAATCCCAGATGTCTCTCCTTATGAAGCAAATGGA
1277124 GTCACAATTCTTCCTAAGCTAAAAGGAAACATCTACGAAAACAAGATGCAATAATGCAGTCACAA
66 GTCACAATTCTTCCTAAGCTAAAAGGAAACATCTACGAAAACAAGATGCAATAATGCAGTCACAA
1277189 TTATGGAACTTATTCAAAATAAATTGT
131 TTATGGAACTTATTCAAAATAAATTGT
1277216 CATGCATTGAAAATCAATCAATAACCCAATGAATCCCAGATGTCTCTCCTTATGAAGCAAATGGA
1 CATGCATTGAAAATCAATCAATAACCCAATGAATCCCAGATGTCTCTCCTTATGAAGCAAATGGA
1277281 GTCACAATTCTTCCTAAGCTAAAAGGAAACATCTACGAAAACAAGATGCAATAATGCAGTCACAA
66 GTCACAATTCTTCCTAAGCTAAAAGGAAACATCTACGAAAACAAGATGCAATAATGCAGTCACAA
1277346 TTATGGAACTTATTCAAAATAAATTGT
131 TTATGGAACTTATTCAAAATAAATTGT
1277373 TGTCATACTT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.25
Consensus pattern (157 bp):
CATGCATTGAAAATCAATCAATAACCCAATGAATCCCAGATGTCTCTCCTTATGAAGCAAATGGA
GTCACAATTCTTCCTAAGCTAAAAGGAAACATCTACGAAAACAAGATGCAATAATGCAGTCACAA
TTATGGAACTTATTCAAAATAAATTGT
Found at i:1283986 original size:16 final size:15
Alignment explanation
Indices: 1283931--1284017 Score: 94
Period size: 15 Copynumber: 6.1 Consensus size: 15
1283921 GTGAAATTAT
*
1283931 AATTA-TTAAATAAA
1 AATTATTTATATAAA
1283945 AATTATTTATATAAA
1 AATTATTTATATAAA
1283960 AATTATTTATATAAA
1 AATTATTTATATAAA
*
1283975 AATTCA--TCTAT-AA
1 AATT-ATTTATATAAA
* *
1283988 TA-TATTTAAATAAA
1 AATTATTTATATAAA
1284002 AATTATTTATATAAA
1 AATTATTTATATAAA
1284017 A
1 A
1284018 TTCATCGATA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 6 0.10
14 12 0.20
15 39 0.65
16 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
AATTATTTATATAAA
Found at i:1284030 original size:41 final size:42
Alignment explanation
Indices: 1283948--1284035 Score: 144
Period size: 42 Copynumber: 2.1 Consensus size: 42
1283938 AAATAAAAAT
* *
1283948 TATTTATATAAAAATTATTTATATAAAAATTCATCTATAATA
1 TATTTAAATAAAAATTATTTATATAAAAATTCATCGATAATA
1283990 TATTTAAATAAAAATTATTTATAT-AAAATTCATCGATAATA
1 TATTTAAATAAAAATTATTTATATAAAAATTCATCGATAATA
1284031 T-TTTA
1 TATTTA
1284036 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 4 0.09
41 17 0.39
42 23 0.52
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (42 bp):
TATTTAAATAAAAATTATTTATATAAAAATTCATCGATAATA
Found at i:1286741 original size:21 final size:21
Alignment explanation
Indices: 1286699--1286742 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1286689 CAAACCCATT
* * * *
1286699 AACAACTGCATTTGACGGAAA
1 AACAAATGCATTTCAAGAAAA
1286720 AACAAATGCATTTCAAGAAAA
1 AACAAATGCATTTCAAGAAAA
1286741 AA
1 AA
1286743 AAACATTCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.14, T:0.18
Consensus pattern (21 bp):
AACAAATGCATTTCAAGAAAA
Found at i:1287918 original size:15 final size:16
Alignment explanation
Indices: 1287880--1287927 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
1287870 ATAAAATAAC
*
1287880 CATAGTTAATAGTAAAT
1 CATAGTTAATA-TTAAT
*
1287897 TATAGTTAA-ATTAAT
1 CATAGTTAATATTAAT
1287912 CATAGTTAATATTAAT
1 CATAGTTAATATTAAT
1287928 AAAAATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 12 0.44
16 7 0.26
17 8 0.30
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (16 bp):
CATAGTTAATATTAAT
Found at i:1287939 original size:32 final size:32
Alignment explanation
Indices: 1287854--1287939 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 32
1287844 TTTAATAAGA
*
1287854 TAATATTAATAAAAATATAAAATAACCATAGT
1 TAATATTAATAAAAATATAAATTAACCATAGT
* * * * *
1287886 TAATAGTAAATTATAGT-TAAATTAATCATAGT
1 TAATA-TTAATAAAAATATAAATTAACCATAGT
1287918 TAATATTAATAAAAATATAAAT
1 TAATATTAATAAAAATATAAAT
1287940 CAATTTGTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
31 7 0.17
32 28 0.67
33 7 0.17
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (32 bp):
TAATATTAATAAAAATATAAATTAACCATAGT
Found at i:1289138 original size:22 final size:22
Alignment explanation
Indices: 1289110--1289160 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1289100 GGAAGTTATG
1289110 AAAAAATGATGGACTAAATTGA
1 AAAAAATGATGGACTAAATTGA
1289132 AAAAAATGATGGACTAAATTGA
1 AAAAAATGATGGACTAAATTGA
1289154 AAAAAAT
1 AAAAAAT
1289161 TATCAGAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.59, C:0.04, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAAAATGATGGACTAAATTGA
Found at i:1298501 original size:28 final size:28
Alignment explanation
Indices: 1298443--1298506 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1298433 TAGAGATTGA
* * *
1298443 AATCCCTAATTCCTCTCTCTTTTCTCTC
1 AATCCCTAATTCCTCTCTCATTTCCCCC
1298471 AATCCCTAATTCCTCGTC-CATTTCCCCC
1 AATCCCTAATTCCTC-TCTCATTTCCCCC
1298499 AATTCCCT
1 AA-TCCCT
1298507 CGCTTCCATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 24 0.77
29 7 0.23
ACGTcount: A:0.17, C:0.42, G:0.02, T:0.39
Consensus pattern (28 bp):
AATCCCTAATTCCTCTCTCATTTCCCCC
Found at i:1309914 original size:31 final size:31
Alignment explanation
Indices: 1309793--1309920 Score: 118
Period size: 31 Copynumber: 4.1 Consensus size: 31
1309783 AGAGTCGAGG
1309793 GTTTACCTATGTTC-TACGGAACATATGGACAA
1 GTTTACCTATGTTCTTA-GGAACATATGGAC-A
** * * *
1309825 AATTACCTATG-TCTTTCGGGACATATGAACA
1 GTTTACCTATGTTC-TTAGGAACATATGGACA
* * *
1309856 GTATACCTATGTTCTAAGGAATATATGGACA
1 GTTTACCTATGTTCTTAGGAACATATGGACA
*
1309887 GTTTACCTATGTTCTTTAGG-ACCTATGGACA
1 GTTTACCTATGTTC-TTAGGAACATATGGACA
1309918 GTT
1 GTT
1309921 GCCGAGGTTC
Statistics
Matches: 75, Mismatches: 17, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
31 48 0.64
32 26 0.35
33 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTTAGGAACATATGGACA
Found at i:1309933 original size:30 final size:31
Alignment explanation
Indices: 1309879--1309945 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
1309869 CTAAGGAATA
* *
1309879 TATGGACAGTTTACCTATGTTCTTTAGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
* *
1309910 TATGGACAG-TTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
*
1309940 TCTGGA
1 TATGGA
1309946 TACGTCCTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
30 22 0.71
31 9 0.29
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:1312249 original size:21 final size:21
Alignment explanation
Indices: 1312223--1312267 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1312213 GATTTCTGGG
* *
1312223 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1312244 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1312265 CAA
1 CAA
1312268 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1312637 original size:16 final size:16
Alignment explanation
Indices: 1312616--1312649 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1312606 AGTCATGGAC
* *
1312616 ATAATTATGTGTGGTT
1 ATAATTATATGTGATT
1312632 ATAATTATATGTGATT
1 ATAATTATATGTGATT
1312648 AT
1 AT
1312650 CTGTATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (16 bp):
ATAATTATATGTGATT
Found at i:1313741 original size:32 final size:31
Alignment explanation
Indices: 1313699--1313826 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
1313689 AGAGTCGAGG
1313699 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
1313730 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* * *
1313762 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
1313793 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1313824 GTT
1 GTT
1313827 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 52 0.65
32 28 0.35
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1316827 original size:21 final size:21
Alignment explanation
Indices: 1316801--1316845 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1316791 GATTTCTGGG
*
1316801 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
1316822 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1316843 CAA
1 CAA
1316846 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1318333 original size:31 final size:31
Alignment explanation
Indices: 1318260--1318387 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
1318250 AGAGTCGAGG
*
1318260 GTTTACCTATGTTCTACGAAACATATGGACA
1 GTTTACCTATGTTCTACGAGACATATGGACA
*
1318291 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTC-TACGAGACATATGGACA
* *
1318323 GTATACCTATGTTCTAAG-GAACATATGGACA
1 GTTTACCTATGTTCTACGAG-ACATATGGACA
* * * *
1318354 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGAGACATATGGACA
1318385 GTT
1 GTT
1318388 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.01
31 52 0.63
32 29 0.35
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGAGACATATGGACA
Found at i:1326338 original size:31 final size:31
Alignment explanation
Indices: 1326300--1326366 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1326290 GAAAATTTTC
1326300 GAGTCGAGTTGAATTCAACTTTAAACTCTTT
1 GAGTCGAGTTGAATTCAACTTTAAACTCTTT
1326331 GAGTCGAGTTGAATTCAACTTTAAACTCTTT
1 GAGTCGAGTTGAATTCAACTTTAAACTCTTT
*
1326362 AAGTC
1 GAGTC
1326367 AAGATTAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.37
Consensus pattern (31 bp):
GAGTCGAGTTGAATTCAACTTTAAACTCTTT
Found at i:1326903 original size:2 final size:2
Alignment explanation
Indices: 1326898--1327069 Score: 172
Period size: 2 Copynumber: 91.0 Consensus size: 2
1326888 TAGTTTTTTA
1326898 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1326939 AT TT AT AT AT AGT AT AT AT -T AT AT -T AT AT -T AT AT -T AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1326978 -T TT A- AT AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1327016 AT AT AT AGT AT AA AT -T AT AT -T AT AT -T TT A- AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1327055 AT AT AGT AT AC AT AT
1 AT AT A-T AT AT AT AT
1327070 TGTATAGGGT
Statistics
Matches: 144, Mismatches: 10, Indels: 32
0.77 0.05 0.17
Matches are distributed among these distances:
1 13 0.09
2 125 0.87
3 6 0.04
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1326905 original size:21 final size:20
Alignment explanation
Indices: 1326871--1326910 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1326861 AGATATTTTA
*
1326871 TTTTTTAAAAATATGTATAG
1 TTTTTTAAAAATATATATAG
*
1326891 TTTTTTAATATATATATATA
1 TTTTTTAA-AAATATATATA
1326911 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TTTTTTAAAAATATATATAG
Found at i:1326944 original size:73 final size:72
Alignment explanation
Indices: 1326821--1327069 Score: 203
Period size: 72 Copynumber: 3.4 Consensus size: 72
1326811 TACATGTGAT
** * * *
1326821 TTTTTTAA-ATATATATATAGTATGCAT-TATATAT-TATAGTAGA-TAT-TTTATTTTTTAAAA
1 TTTTTTAATATATATATATA-TATATATATATATATATATAGTATATTATATTTATTTTATATAA
1326881 ATATGTATA
65 ATAT-TATA
*
1326890 GTTTTTTAATATATATATATATATATATATATATATATATA-TATATTATATTTA-TATATAGTA
1 -TTTTTTAATATATATATATATATATATATATATATATATAGTATATTATATTTATTTTATA-TA
*
1326953 TATATTATA
64 AATATTATA
* * * *
1326962 TTATATT-ATAT-TATATTTTAATATATATATATATATATATATTATATTATATTTATATATAGT
1 TT-TTTTAATATATATA-TAT-ATATATATATATATATATATAGTATATTATATTTAT-TTTA-T
1327025 ATAAAT-TATATTA
61 ATAAATAT-TA-TA
* *
1327038 TATTTTAATATATATATATATAGTATACATAT
1 TTTTTTAATATATATATATATA-TATATATAT
1327070 TGTATAGGGT
Statistics
Matches: 147, Mismatches: 14, Indels: 30
0.77 0.07 0.16
Matches are distributed among these distances:
70 17 0.12
71 29 0.20
72 39 0.27
73 22 0.15
74 1 0.01
75 16 0.11
76 19 0.13
77 4 0.03
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (72 bp):
TTTTTTAATATATATATATATATATATATATATATATATAGTATATTATATTTATTTTATATAAA
TATTATA
Found at i:1327004 original size:68 final size:63
Alignment explanation
Indices: 1326919--1327064 Score: 220
Period size: 63 Copynumber: 2.2 Consensus size: 63
1326909 TATATATATA
*
1326919 TATATATATATATATATTATATTTATATATAGTATATATTATATTATATTATATTATATTTTAAT
1 TATATATATATATATATTATA-TTATATATA-TATATAGTATA--A-ATTATATTATATTTTAAT
1326984 ATA
61 ATA
*
1326987 TATATATATATATATATTATATTATATTTATATATAGTATAAATTATATTATATTTTAATATA
1 TATATATATATATATATTATATTATATATATATATAGTATAAATTATATTATATTTTAATATA
1327050 TATATATATAGTATA
1 TATATATATA-TATA
1327065 CATATTGTAT
Statistics
Matches: 75, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
63 31 0.41
64 5 0.07
66 10 0.13
67 8 0.11
68 21 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (63 bp):
TATATATATATATATATTATATTATATATATATATAGTATAAATTATATTATATTTTAATATA
Found at i:1329151 original size:18 final size:18
Alignment explanation
Indices: 1329122--1329217 Score: 106
Period size: 18 Copynumber: 5.3 Consensus size: 18
1329112 ATTTGTGCAG
1329122 TCGATCCACAGTCGTTGGA
1 TCGAT-CACAGTCGTTGGA
1329141 TCGATCACAGTCGTTGGA
1 TCGATCACAGTCGTTGGA
** * * **
1329159 TCGATC-CCCTTGAT-CC
1 TCGATCACAGTCGTTGGA
1329175 TCGATCCACAGTCGTTGGA
1 TCGAT-CACAGTCGTTGGA
1329194 TCGATCACAGTCGTTGGA
1 TCGATCACAGTCGTTGGA
1329212 TCGATC
1 TCGATC
1329218 CCCTTGATCC
Statistics
Matches: 62, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
16 5 0.08
17 5 0.08
18 42 0.68
19 10 0.16
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (18 bp):
TCGATCACAGTCGTTGGA
Found at i:1329202 original size:53 final size:53
Alignment explanation
Indices: 1329122--1329227 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
1329112 ATTTGTGCAG
1329122 TCGATCCACAGTCGTTGGATCGATCACAGTCGTTGGATCGATCCCCTTGATCC
1 TCGATCCACAGTCGTTGGATCGATCACAGTCGTTGGATCGATCCCCTTGATCC
1329175 TCGATCCACAGTCGTTGGATCGATCACAGTCGTTGGATCGATCCCCTTGATCC
1 TCGATCCACAGTCGTTGGATCGATCACAGTCGTTGGATCGATCCCCTTGATCC
1329228 AACAGTCCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.28
Consensus pattern (53 bp):
TCGATCCACAGTCGTTGGATCGATCACAGTCGTTGGATCGATCCCCTTGATCC
Found at i:1330656 original size:23 final size:25
Alignment explanation
Indices: 1330603--1330656 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1330593 TAACCAATTG
* *
1330603 CACATATATATATCATGTCATGTAAA
1 CACATATATATAT-ATATCATGAAAA
1330629 C-CATATATATAT-TATCAT-AAAA
1 CACATATATATATATATCATGAAAA
1330651 CACATA
1 CACATA
1330657 CACCCAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 4 0.16
23 9 0.36
25 11 0.44
26 1 0.04
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (25 bp):
CACATATATATATATATCATGAAAA
Found at i:1330939 original size:23 final size:23
Alignment explanation
Indices: 1330913--1330996 Score: 150
Period size: 23 Copynumber: 3.7 Consensus size: 23
1330903 CTCGTATAAA
1330913 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
1330936 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1330959 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
1330982 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
1330997 TATAATAAGA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.27, C:0.27, G:0.26, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1332385 original size:49 final size:50
Alignment explanation
Indices: 1332328--1332427 Score: 193
Period size: 49 Copynumber: 2.0 Consensus size: 50
1332318 GATACTTAAG
1332328 CTTTCCTTAAGCTTAAGTAACACCTAAGAATCATAACCCAAC-TTTAATT
1 CTTTCCTTAAGCTTAAGTAACACCTAAGAATCATAACCCAACTTTTAATT
1332377 CTTTCCTTAAGCTTAAGTAACACCTAAGAATCATAACCCAACTTTTAATT
1 CTTTCCTTAAGCTTAAGTAACACCTAAGAATCATAACCCAACTTTTAATT
1332427 C
1 C
1332428 AACAAATAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 42 0.84
50 8 0.16
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (50 bp):
CTTTCCTTAAGCTTAAGTAACACCTAAGAATCATAACCCAACTTTTAATT
Found at i:1335664 original size:50 final size:45
Alignment explanation
Indices: 1335620--1335706 Score: 165
Period size: 45 Copynumber: 1.9 Consensus size: 45
1335610 AATACTAAAA
1335620 ACATTATTCACTCTTTTCTGATCTGACCTTTAGTAAGGAGAATAC
1 ACATTATTCACTCTTTTCTGATCTGACCTTTAGTAAGGAGAATAC
*
1335665 ATATTATTCACTCTTTTCTGATCTGACCTTTAGTAAGGAGAA
1 ACATTATTCACTCTTTTCTGATCTGACCTTTAGTAAGGAGAA
1335707 CTGACCTGTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (45 bp):
ACATTATTCACTCTTTTCTGATCTGACCTTTAGTAAGGAGAATAC
Found at i:1336253 original size:23 final size:23
Alignment explanation
Indices: 1336227--1336310 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
1336217 CTCGTATAAA
*
1336227 TGCACTGAAGTGTCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
1336250 TGCACTGAAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
* *
1336273 TGCACCGTAGTGCCACGTAGAAT
1 TGCACTGAAGTGCCACGTAGAAT
* * *
1336296 TACACCGTAGTGCCA
1 TGCACTGAAGTGCCA
1336311 TATAATAATG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (23 bp):
TGCACTGAAGTGCCACGTAGAAT
Found at i:1338121 original size:4 final size:4
Alignment explanation
Indices: 1338112--1338168 Score: 60
Period size: 4 Copynumber: 13.0 Consensus size: 4
1338102 TTTTACAGTG
*
1338112 TTTA TTTA TTTA TCTTA TTTT TTTA TTTA TCTTTA TTTA TTATA TTTAA
1 TTTA TTTA TTTA T-TTA TTTA TTTA TTTA --TTTA TTTA TT-TA TTT-A
1338161 TTTA TTTA
1 TTTA TTTA
1338169 AATTGATATG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
4 30 0.65
5 12 0.26
6 4 0.09
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:1338129 original size:13 final size:12
Alignment explanation
Indices: 1338112--1338168 Score: 60
Period size: 13 Copynumber: 4.3 Consensus size: 12
1338102 TTTTACAGTG
1338112 TTTATTTATTTA
1 TTTATTTATTTA
*
1338124 TCTTATTTTTTTA
1 T-TTATTTATTTA
1338137 TTTATCTTTATTTA
1 TTTA--TTTATTTA
1338151 TTATATTTAATTTA
1 TT-TATTT-ATTTA
1338165 TTTA
1 TTTA
1338169 AATTGATATG
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 4 0.11
13 16 0.42
14 16 0.42
15 2 0.05
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTATTTATTTA
Found at i:1338136 original size:17 final size:19
Alignment explanation
Indices: 1338112--1338168 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
1338102 TTTTACAGTG
1338112 TTTA-TTTATTTATC-TTA
1 TTTATTTTATTTATCTTTA
1338129 TTT-TTTTATTTATCTTTA
1 TTTATTTTATTTATCTTTA
* *
1338147 TTTATTATATTTA-ATTTA
1 TTTATTTTATTTATCTTTA
1338165 TTTA
1 TTTA
1338169 AATTGATATG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 13 0.37
18 14 0.40
19 8 0.23
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTTATTTATCTTTA
Found at i:1338146 original size:27 final size:28
Alignment explanation
Indices: 1338116--1338168 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1338106 ACAGTGTTTA
*
1338116 TTTATTTATCT-TATTT-TTTTATTTATC
1 TTTATTTAT-TATATTTAATTTATTTATC
1338143 TTTATTTATTATATTTAATTTATTTA
1 TTTATTTATTATATTTAATTTATTTA
1338169 AATTGATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 14 0.61
28 8 0.35
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.72
Consensus pattern (28 bp):
TTTATTTATTATATTTAATTTATTTATC
Found at i:1339706 original size:30 final size:30
Alignment explanation
Indices: 1339649--1339706 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
1339639 ATAATATTAG
* *
1339649 AAGAGAGTGAAAGTGTGCAAAGCGAAGTGA
1 AAGAGAATGAAAGTGTGCAAAACGAAGTGA
* * *
1339679 AAGAGAATTAAAGTGTGTAAAATGAAGT
1 AAGAGAATGAAAGTGTGCAAAACGAAGT
1339707 ATTTGATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.47, C:0.03, G:0.31, T:0.19
Consensus pattern (30 bp):
AAGAGAATGAAAGTGTGCAAAACGAAGTGA
Found at i:1343369 original size:46 final size:46
Alignment explanation
Indices: 1343317--1343410 Score: 188
Period size: 46 Copynumber: 2.0 Consensus size: 46
1343307 GTAAGAGAGG
1343317 ATCATATTAGATCTTTAAACATGCTAAAAACATCAATTACTAGAAA
1 ATCATATTAGATCTTTAAACATGCTAAAAACATCAATTACTAGAAA
1343363 ATCATATTAGATCTTTAAACATGCTAAAAACATCAATTACTAGAAA
1 ATCATATTAGATCTTTAAACATGCTAAAAACATCAATTACTAGAAA
1343409 AT
1 AT
1343411 ACCATGAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.31
Consensus pattern (46 bp):
ATCATATTAGATCTTTAAACATGCTAAAAACATCAATTACTAGAAA
Found at i:1344282 original size:15 final size:14
Alignment explanation
Indices: 1344248--1344290 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
1344238 ACTATAACAA
*
1344248 AATATAAAAAATAC
1 AATATAAAAAATAT
1344262 AA-ATAAAAAATAT
1 AATATAAAAAATAT
1344275 AATTATAATAAAATAT
1 AA-TATAA-AAAATAT
1344291 GTTTTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 12 0.48
14 2 0.08
15 4 0.16
16 7 0.28
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AATATAAAAAATAT
Found at i:1344368 original size:13 final size:13
Alignment explanation
Indices: 1344346--1344378 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1344336 TTTTATTTTT
1344346 TAAATAATTAAAA
1 TAAATAATTAAAA
*
1344359 TAAATTATTAAAA
1 TAAATAATTAAAA
1344372 TAAATAA
1 TAAATAA
1344379 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAATAATTAAAA
Found at i:1351173 original size:22 final size:22
Alignment explanation
Indices: 1351138--1351179 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1351128 ATAATTATTT
1351138 AAAAAAATTAAATAAAAAATTC
1 AAAAAAATTAAATAAAAAATTC
* *
1351160 AAAAATATTTAATAAAAAAT
1 AAAAAAATTAAATAAAAAAT
1351180 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAAATTAAATAAAAAATTC
Found at i:1355376 original size:28 final size:25
Alignment explanation
Indices: 1355319--1355415 Score: 81
Period size: 26 Copynumber: 3.6 Consensus size: 25
1355309 TCAAGAACGC
1355319 TAAACAAATCACAAAT-A-ATTATAAAA
1 TAAACAAAT-A-AAATAATATTA-AAAA
*
1355345 TAAATAAATAAACATAATATTAAAAGTA
1 TAAACAAATAAA-ATAATATTAAAA--A
* *
1355373 TAAACAAATATAAATATTTTTAAAAA
1 TAAACAAATA-AAATAATATTAAAAA
1355399 TAAACAAATAAATATAA
1 TAAACAAATAAA-ATAA
1355416 CTTTTATTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
24 2 0.03
25 5 0.08
26 26 0.44
27 4 0.07
28 20 0.34
29 2 0.03
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (25 bp):
TAAACAAATAAAATAATATTAAAAA
Found at i:1355497 original size:46 final size:46
Alignment explanation
Indices: 1355447--1355537 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
1355437 TTTAAACTTG
1355447 TAATAAAAATACATTATGTCCCGACTGTTGACAAGGAATTCACACC
1 TAATAAAAATACATTATGTCCCGACTGTTGACAAGGAATTCACACC
* * *
1355493 TAATAAGAATACATTATGTCTCGACTGTTGACGAGGAATTCACAC
1 TAATAAAAATACATTATGTCCCGACTGTTGACAAGGAATTCACAC
1355538 ATTTTAATTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (46 bp):
TAATAAAAATACATTATGTCCCGACTGTTGACAAGGAATTCACACC
Found at i:1357351 original size:6 final size:6
Alignment explanation
Indices: 1357340--1357364 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1357330 GTTGCTTCAA
1357340 CGGTTT CGGTTT CGGTTT CGGTTT C
1 CGGTTT CGGTTT CGGTTT CGGTTT C
1357365 CTGGAAGGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.32, T:0.48
Consensus pattern (6 bp):
CGGTTT
Found at i:1358858 original size:19 final size:19
Alignment explanation
Indices: 1358834--1358879 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1358824 AAATCTAATT
*
1358834 ATAAAAAAATATTACAAAA
1 ATAAAAAAATAATACAAAA
* *
1358853 ATAAAAATATAATACAATA
1 ATAAAAAAATAATACAAAA
1358872 ATAAAAAA
1 ATAAAAAA
1358880 TCATATTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAAAAAATAATACAAAA
Found at i:1360207 original size:13 final size:13
Alignment explanation
Indices: 1360189--1360219 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1360179 AACAAGAAAA
*
1360189 GTAAGGATGTGAG
1 GTAAGGATGCGAG
1360202 GTAAGGATGCGAG
1 GTAAGGATGCGAG
1360215 GTAAG
1 GTAAG
1360220 AAAATAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.45, T:0.19
Consensus pattern (13 bp):
GTAAGGATGCGAG
Found at i:1361096 original size:28 final size:28
Alignment explanation
Indices: 1361045--1361111 Score: 127
Period size: 28 Copynumber: 2.4 Consensus size: 28
1361035 CTTTATTTTG
1361045 TTCGGGTCGGG-TTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1361072 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTTAAGTGTGATA
1361100 TTCGGGTCGGGT
1 TTCGGGTCGGGT
1361112 CGGATTCGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
27 11 0.28
28 28 0.72
ACGTcount: A:0.12, C:0.09, G:0.36, T:0.43
Consensus pattern (28 bp):
TTCGGGTCGGGTTTTTTTAAGTGTGATA
Found at i:1361273 original size:250 final size:240
Alignment explanation
Indices: 1360840--1361436 Score: 762
Period size: 250 Copynumber: 2.4 Consensus size: 240
1360830 TTTTGGTCGG
* * *
1360840 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTC--G-GGTTCGAGTTTATGGTGAAAAAAAT
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGCGGTTCGGGTTTAGGGTGAAAAAAAT
1360902 CGGACCGACCCGAAAATATATATAA--TTCGGGTCGGGTCGGATTAAGTCACTGTTTTATTAAAT
66 CGGACCGACCCGAAAATATATATAATTTTCGGGTCGGGTCGGATTAAGTCACTGTTTTATTAAAT
*
1360965 AAAAATATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTTGGGTCGGGTCGGA
131 AAAAATATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGA
*
1361030 TGAAACTTTATTTTGTTC-GGGTCGGGTTTTTTAAGTGTGATA-T
196 TGAAACTTTATTTTGTTCGGGGTCGGGTTTTTTAAGTGTAATATT
1361073 -TCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGATTCGGGTTTAGGGTGAAAAAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG-CGG-TTCGGGTTTAGGGTGAAAAAA
*
1361137 ATCGGACCGGCCCGAAAATATATATAATTCGGGTTCGGGTCGGGTCGGATTAAGTCACTGTTTTT
64 ATCGGACCGACCCGAAAATATATATAATT----TTCGGGTCGGGTCGGATTAAGTCACTG-TTTT
*
1361202 ATTAAATAAAAATAATTTTTTATTATTTTGGGTCGGGTCGGGTCGGATTTCTAATTTATATATTC
124 ATTAAATAAAAAT-ATTTTTTATTA--TT---TCGGGTCGGGTCGGATTTCTAATTCATATATTC
1361267 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGATTGGGTCGGGTTTTTTAAGTGTAATATT
183 GGGTCGGGTCGGATGAAACTTTATTTTGTTC-G---GGGTCGGGTTTTTTAAGTGTAATATT
1361329 CGGGTCGAGTAGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGGCCGGGTTCGGGTT
1 ---GTC-----GGGTCGGGTTTTTTTAAGTGTGATATTC--G---GGTCGGG-C-GGTTCGGGTT
*
1361394 TAGGGTG-AAAAAATAGGACCGACCCGAAAAATATATATAATTT
51 TAGGGTGAAAAAAATCGGACCGACCCG-AAAATATATATAATTT
1361437 ACCTTATATA
Statistics
Matches: 314, Mismatches: 10, Indels: 47
0.85 0.03 0.13
Matches are distributed among these distances:
232 34 0.11
234 1 0.00
236 2 0.01
237 45 0.14
243 27 0.09
244 17 0.05
245 11 0.04
247 2 0.01
250 62 0.20
255 23 0.07
256 1 0.00
260 2 0.01
265 28 0.09
266 1 0.00
267 1 0.00
269 17 0.05
270 38 0.12
271 2 0.01
ACGTcount: A:0.23, C:0.11, G:0.28, T:0.37
Consensus pattern (240 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGCGGTTCGGGTTTAGGGTGAAAAAAAT
CGGACCGACCCGAAAATATATATAATTTTCGGGTCGGGTCGGATTAAGTCACTGTTTTATTAAAT
AAAAATATTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGA
TGAAACTTTATTTTGTTCGGGGTCGGGTTTTTTAAGTGTAATATT
Found at i:1361386 original size:38 final size:38
Alignment explanation
Indices: 1361307--1361387 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
1361297 CGGATTGGGT
*
1361307 CGGG-TTTTTTAAGTGTAATATTCGGGTCGAGTAGGGT
1 CGGGTTTTTTTAAGTGTAATATTCGGGTCGAGTAGGGC
* *
1361344 CGGGTTTTTTTAAGTGTGATATTCGGGTC-AGGTCGGGC
1 CGGGTTTTTTTAAGTGTAATATTCGGGTCGA-GTAGGGC
1361382 CGGGTT
1 CGGGTT
1361388 CGGGTTTAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 5 0.13
38 34 0.87
ACGTcount: A:0.15, C:0.11, G:0.37, T:0.37
Consensus pattern (38 bp):
CGGGTTTTTTTAAGTGTAATATTCGGGTCGAGTAGGGC
Found at i:1362012 original size:18 final size:16
Alignment explanation
Indices: 1361970--1362015 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 16
1361960 TATGGAATTG
*
1361970 GATTCCAATTCCTATA
1 GATTCCAATTCCTACA
*
1361986 GATTTCAATTCCTTCACA
1 GATTCCAATTCC-T-ACA
1362004 GATTCCAATTCC
1 GATTCCAATTCC
1362016 CTCATAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.28, C:0.28, G:0.07, T:0.37
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:1362395 original size:20 final size:20
Alignment explanation
Indices: 1362370--1362407 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1362360 TTTGGTTCAC
1362370 GGAATGGAAGATTACCAGTG
1 GGAATGGAAGATTACCAGTG
* *
1362390 GGAATGTAATATTACCAG
1 GGAATGGAAGATTACCAG
1362408 GAAATAGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGGAAGATTACCAGTG
Found at i:1379663 original size:21 final size:20
Alignment explanation
Indices: 1379605--1379659 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
1379595 ACCCGAATCA
1379605 GACGGATTTTGATTTAATTC
1 GACGGATTTTGATTTAATTC
*
1379625 GATGGATTTTGATTTAATTC
1 GACGGATTTTGATTTAATTC
1379645 GACGGATTTTGATTT
1 GACGGATTTTGATTT
1379660 TAATCCGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (20 bp):
GACGGATTTTGATTTAATTC
Found at i:1379668 original size:21 final size:20
Alignment explanation
Indices: 1379600--1379668 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
1379590 CATGGACCCG
*
1379600 AATCAGACGGATTTTGATTT
1 AATCCGACGGATTTTGATTT
* *
1379620 AATTCGATGGATTTTGATTT
1 AATCCGACGGATTTTGATTT
*
1379640 AATTCGACGGATTTTGATTTT
1 AATCCGACGGATTTTGA-TTT
1379661 AATCCGAC
1 AATCCGAC
1379669 TCGATCGGGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 33 0.77
21 10 0.23
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.42
Consensus pattern (20 bp):
AATCCGACGGATTTTGATTT
Found at i:1382034 original size:60 final size:60
Alignment explanation
Indices: 1381935--1382049 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
1381925 TCAAGGTCTG
* * *
1381935 ACTCTCATTTTAAATTGATCCCTGAACTATAGAACATTTCAATTTCATTCACAAAGTAAA
1 ACTCTCATTCTAAATTGATCCCTCAACTATAGAACATTTCAAATTCATTCACAAAGTAAA
* * * * *
1381995 ACTCTCATTCTAAATTGATTCCTCAACTCTTGAATATTTCAAATTCATTCCCAAA
1 ACTCTCATTCTAAATTGATCCCTCAACTATAGAACATTTCAAATTCATTCACAAA
1382050 ATATGACCCT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.37
Consensus pattern (60 bp):
ACTCTCATTCTAAATTGATCCCTCAACTATAGAACATTTCAAATTCATTCACAAAGTAAA
Found at i:1382062 original size:60 final size:60
Alignment explanation
Indices: 1381933--1382073 Score: 156
Period size: 60 Copynumber: 2.4 Consensus size: 60
1381923 CCTCAAGGTC
* * * *
1381933 TGACTCTCATTTTAAATTGATCCCTGAACTATAGAACATTTCAATTTCATTCACAAAGTA
1 TGACTCTCATTATAAATTGATCCCTCAACTATAGAACATTTCAAATTCATTCACAAAATA
** * * * * * *
1381993 AAACTCTCATTCTAAATTGATTCCTCAACTCTTGAATATTTCAAATTCATTCCCAAAATA
1 TGACTCTCATTATAAATTGATCCCTCAACTATAGAACATTTCAAATTCATTCACAAAATA
* *
1382053 TGACCCTCATTATAAAATGAT
1 TGACTCTCATTATAAATTGAT
1382074 GCCCAAACTT
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 65 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (60 bp):
TGACTCTCATTATAAATTGATCCCTCAACTATAGAACATTTCAAATTCATTCACAAAATA
Found at i:1382088 original size:60 final size:60
Alignment explanation
Indices: 1381938--1382089 Score: 135
Period size: 60 Copynumber: 2.5 Consensus size: 60
1381928 AGGTCTGACT
* * * * * * * * * *
1381938 CTCATTTTAAATTGATCCCTGAACTATAGAACATTTCAATTTCATTCACAAAGTAAAACT
1 CTCATTATAAAATGATGCCTCAACTCTTGAATATTTCAAATTCATTCACAAAATAAAACC
* * * * **
1381998 CTCATTCTAAATTGATTCCTCAACTCTTGAATATTTCAAATTCATTCCCAAAATATGACC
1 CTCATTATAAAATGATGCCTCAACTCTTGAATATTTCAAATTCATTCACAAAATAAAACC
*
1382058 CTCATTATAAAATGATGCC-CAAACTTTTGAAT
1 CTCATTATAAAATGATGCCTC-AACTCTTGAAT
1382090 GCTCCAACAA
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
59 1 0.01
60 74 0.99
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (60 bp):
CTCATTATAAAATGATGCCTCAACTCTTGAATATTTCAAATTCATTCACAAAATAAAACC
Found at i:1387194 original size:22 final size:22
Alignment explanation
Indices: 1387168--1387209 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1387158 CAGATAGAAT
* *
1387168 TATGGTGGTATCGGTACCATAG
1 TATGGTAGTATCGATACCATAG
1387190 TATGGTAGTATCGATACCAT
1 TATGGTAGTATCGATACCAT
1387210 GATAAGGGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (22 bp):
TATGGTAGTATCGATACCATAG
Found at i:1387718 original size:55 final size:55
Alignment explanation
Indices: 1387648--1388237 Score: 841
Period size: 55 Copynumber: 10.8 Consensus size: 55
1387638 CCAAATAGGA
* * *
1387648 ACTATGTGTGTAGATCCACAGAATTCATCATGAGTTGATGAATAAACATACATGC
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
*
1387703 ACTATGTGTGCAGATCCAC-GAAATTCATCATGAGTTGATGAATAACCGTACATAC
1 ACTATGTGTGCAGATCCACAG-AATTCATCATGAGTTGATGAATAACCGTACATGC
* * *
1387758 ACTATGTGTGCAGATCCA-AGGAATTTATCATGAGTTGATGAATAACCGTATAGGC
1 ACTATGTGTGCAGATCCACA-GAATTCATCATGAGTTGATGAATAACCGTACATGC
* * * * *
1387813 ATTCTGTGTGCAAATCCACGGAATTCATCATGAGTTTATGAATAACCGTACATGC
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
* *
1387868 ACTATATGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGC
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
* *
1387923 ACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCGTACATGC
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
* *
1387978 ACTATGTGTGCAGATCCACGGAATTCATCATGAGTTGATGAATAATCGTACA-GAC
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATG-C
* * *
1388033 ACTATGTGTGCAAATCCACAAAATTCATCATGAGTTGATGAATAACCGTACATGT
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
* *
1388088 ATTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACAAGC
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
* * * *
1388143 ACTATATGTACAGATCCACAGAATTCATCATGAGTTGATGAATAA-CATA-AGGC
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
* * *
1388196 ACGATGTGTGCA-ATCCACATAATTCATCATGAGTTAATGAAT
1 ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAAT
1388238 TATTGTATAG
Statistics
Matches: 480, Mismatches: 49, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
52 28 0.06
53 12 0.03
54 5 0.01
55 433 0.90
56 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (55 bp):
ACTATGTGTGCAGATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATGC
Found at i:1388506 original size:81 final size:81
Alignment explanation
Indices: 1388400--1388649 Score: 365
Period size: 81 Copynumber: 3.1 Consensus size: 81
1388390 TAGTCCAAAA
* *
1388400 TAAAAGAATAATGGCATAACTGTGCAATTGGCAGAAAAGTTTCAATTATGCCAGTTATATGAACA
1 TAAAAGAATAATGGCATAACTGTGCAATTGGCAGAAAAGTGTCAATTATGCCAGTTATATGAACG
*
1388465 GTTAAATACCGTTGAG
66 GATAAATACCGTTGAG
* * *
1388481 TAAAAGAATAATGACATAATTGTGCAATTGGCAGAAAAGTGTCAATTATGCTAGTTATATGAACG
1 TAAAAGAATAATGGCATAACTGTGCAATTGGCAGAAAAGTGTCAATTATGCCAGTTATATGAACG
* *
1388546 GATAAGTATCGTTGAG
66 GATAAATACCGTTGAG
* * * * *
1388562 TAAAAGAATAATGGCCTAACTGTGCAATTGGCAGAAATGTGTCAATTATGTCAATTAGATGAACG
1 TAAAAGAATAATGGCATAACTGTGCAATTGGCAGAAAAGTGTCAATTATGCCAGTTATATGAACG
* *
1388627 GCTAAATACTGTTGAG
66 GATAAATACCGTTGAG
1388643 TAAAAGA
1 TAAAAGA
1388650 TGAAAGGTCA
Statistics
Matches: 149, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 149 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (81 bp):
TAAAAGAATAATGGCATAACTGTGCAATTGGCAGAAAAGTGTCAATTATGCCAGTTATATGAACG
GATAAATACCGTTGAG
Found at i:1395363 original size:23 final size:23
Alignment explanation
Indices: 1395333--1395378 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1395323 GGTCTGAGTC
1395333 AAAGTACATATATAGATAAAGTG
1 AAAGTACATATATAGATAAAGTG
1395356 AAAGTACATATATAGATAAAGTG
1 AAAGTACATATATAGATAAAGTG
1395379 CTGAAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.26
Consensus pattern (23 bp):
AAAGTACATATATAGATAAAGTG
Found at i:1402846 original size:19 final size:20
Alignment explanation
Indices: 1402818--1402859 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1402808 AATATTTAAA
1402818 ATATTATTA-TCATAAAAAT
1 ATATTATTATTCATAAAAAT
* *
1402837 ATATTTTTATTTATAAAAAT
1 ATATTATTATTCATAAAAAT
1402857 ATA
1 ATA
1402860 ATCTAAAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATTATTATTCATAAAAAT
Found at i:1415974 original size:76 final size:76
Alignment explanation
Indices: 1415866--1416033 Score: 282
Period size: 76 Copynumber: 2.2 Consensus size: 76
1415856 TTTATTTAGT
* * *
1415866 ATGGTATCGATACCCCCATATAGGGTATCGATACCCCTATGAACATTTTGGTTCTGAGAAATAAC
1 ATGGTATCGATACCCCCATATAGGGTACCGATACCCCTATGAACATTTTGATTCCGAGAAATAAC
1415931 AGAATACTCGG
66 AGAATACTCGG
* *
1415942 ATGGTACCGATACCCCCCTATAGGGTACCGATACCCCTATGAACATTTTGATTCCGAGAAATAAC
1 ATGGTATCGATACCCCCATATAGGGTACCGATACCCCTATGAACATTTTGATTCCGAGAAATAAC
*
1416007 AGAATGCTCGG
66 AGAATACTCGG
1416018 ATGGTATCGATACCCC
1 ATGGTATCGATACCCC
1416034 TTAGTAGGTA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
76 85 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (76 bp):
ATGGTATCGATACCCCCATATAGGGTACCGATACCCCTATGAACATTTTGATTCCGAGAAATAAC
AGAATACTCGG
Done.