Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007770.1 Hibiscus syriacus cultivar Beakdansim tig00110050_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: 1450453
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1052075 original size:30 final size:30
Alignment explanation
Indices: 1052035--1052095 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
1052025 GTCCCAAAGG
1052035 ACCTATCCATATGTTCCGAAGAACATAGGT
1 ACCTATCCATATGTTCCGAAGAACATAGGT
* *
1052065 ACCTGTCCATATGTTCCGAAGGACATAGGT
1 ACCTATCCATATGTTCCGAAGAACATAGGT
1052095 A
1 A
1052096 ACCCTCGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (30 bp):
ACCTATCCATATGTTCCGAAGAACATAGGT
Found at i:1073254 original size:145 final size:147
Alignment explanation
Indices: 1073024--1073315 Score: 493
Period size: 146 Copynumber: 2.0 Consensus size: 147
1073014 TTTTTAATTT
*
1073024 ACAACATAATATTCAAAATGAATATTTTATCTCTTCAAATCACTTTTTAACAATAATCTCAATCA
1 ACAACATAATATTCAAAACGAATATTTTATCTCTTCAAATCACTTTTTAACAATAATCTCAATCA
*
1073089 ATTAAATTTTGAACTCTACTTTTAATAAAACAAAATT-AAAAATTATTTTCTACGTCACTTTTAA
66 ATTAAATTTTAAACTCTACTTTTAATAAAACAAAATTAAAAAATTATTTTCTACGTCACTTTTAA
1073153 GAATCACTTTTCGAAAG
131 GAATCACTTTTCGAAAG
1073170 ACAACATAATA-TCTAAAACGAATATTTTATCTCTTCAAATCA-TTTTTAACAATAATCTCAAAT
1 ACAACATAATATTC-AAAACGAATATTTTATCTCTTCAAATCACTTTTTAACAATAATCTC-AAT
* * *
1073233 -AATTAAATTTTAAACTTTACTTTTAATAAAACAAATTTAAAAAATTATTTTCTACTTCACTTTT
64 CAATTAAATTTTAAACTCTACTTTTAATAAAACAAAATTAAAAAATTATTTTCTACGTCACTTTT
1073297 AAGAATCACTTTTCGAAAG
129 AAGAATCACTTTTCGAAAG
1073316 TAATTTCAAA
Statistics
Matches: 138, Mismatches: 5, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
145 54 0.39
146 84 0.61
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (147 bp):
ACAACATAATATTCAAAACGAATATTTTATCTCTTCAAATCACTTTTTAACAATAATCTCAATCA
ATTAAATTTTAAACTCTACTTTTAATAAAACAAAATTAAAAAATTATTTTCTACGTCACTTTTAA
GAATCACTTTTCGAAAG
Found at i:1075292 original size:21 final size:21
Alignment explanation
Indices: 1075266--1075318 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1075256 ATTCTGACTA
1075266 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
1075287 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1075308 TTGCAATGCGA
1 TCGCATTGCGA
1075319 ATACGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1075332 original size:41 final size:40
Alignment explanation
Indices: 1075287--1075419 Score: 149
Period size: 41 Copynumber: 3.3 Consensus size: 40
1075277 TTTTCCAAAT
* * * *
1075287 TCGCATTGCGATTTTCCTAATTTGCAATGCGAATACGTAAA
1 TCGCAATGCGA-TTTCGTAAATCGCAATGCGAATACGTAAA
* * *
1075328 TCGCAACGCGAATTTGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCG-ATTTCGTAAATCGCAATGCGAATACGTAAA
* * *
1075369 TTGCAATGCGAATACGTAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAAA
*
1075409 TCGCAACGCGA
1 TCGCAATGCGA
1075420 ATCTGACTAT
Statistics
Matches: 76, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
40 35 0.46
41 40 0.53
42 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (40 bp):
TCGCAATGCGATTTCGTAAATCGCAATGCGAATACGTAAA
Found at i:1075338 original size:20 final size:20
Alignment explanation
Indices: 1075310--1075421 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
1075300 TTCCTAATTT
1075310 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
* ** *
1075330 GCAACGCGAATTTGGAAAATC
1 GCAATGCGAA-TACGTAAATC
*
1075351 GCAATGCGAATACGTAAATT
1 GCAATGCGAATACGTAAATC
1075371 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
1075391 GCAATGCGAATACGTAAATC
1 GCAATGCGAATACGTAAATC
*
1075411 GCAACGCGAAT
1 GCAATGCGAAT
1075422 CTGACTATCG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 64 0.80
21 16 0.20
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (20 bp):
GCAATGCGAATACGTAAATC
Found at i:1075431 original size:20 final size:20
Alignment explanation
Indices: 1075408--1075454 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1075398 GAATACGTAA
*
1075408 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGAATCTGACT
*
1075428 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGAATCTGACT
1075448 ATCGCAA
1 ATCGCAA
1075455 TACTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGAATCTGACT
Found at i:1075432 original size:40 final size:39
Alignment explanation
Indices: 1075310--1075434 Score: 162
Period size: 40 Copynumber: 3.1 Consensus size: 39
1075300 TTCCTAATTT
*
1075310 GCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAATC
1 GCAATGCGAATACGTAAATCGCAACGCGAATCT-G-AAATC
* *
1075351 GCAATGCGAATACGTAAATTGCAATGCGAATAC-GTAAATC
1 GCAATGCGAATACGTAAATCGCAACGCGAAT-CTG-AAATC
*
1075391 GCAATGCGAATACGTAAATCGCAACGCGAATCTGACTATC
1 GCAATGCGAATACGTAAATCGCAACGCGAATCTGA-AATC
1075431 GCAA
1 GCAA
1075435 CGAGATTCTG
Statistics
Matches: 74, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
39 2 0.03
40 43 0.58
41 29 0.39
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (39 bp):
GCAATGCGAATACGTAAATCGCAACGCGAATCTGAAATC
Found at i:1076323 original size:24 final size:24
Alignment explanation
Indices: 1076296--1076349 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1076286 GTATTCAAAA
1076296 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1076320 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1076344 TTTGAT
1 TTTGAT
1076350 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1078786 original size:20 final size:20
Alignment explanation
Indices: 1078713--1078785 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
1078703 GACATTCATT
1078713 TGACTATCGCAACAC-GAATA
1 TGACTATCGCAACACGGAA-A
1078733 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACACGGAAA
*
1078753 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACACGGAAA
1078773 TGACTATCGCAAC
1 TGACTATCGCAAC
1078786 GAGAGAATCG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
20 48 0.94
21 3 0.06
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (20 bp):
TGACTATCGCAACACGGAAA
Found at i:1078846 original size:34 final size:33
Alignment explanation
Indices: 1078758--1078853 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
1078748 GGAAATGACT
* **
1078758 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
1078792 ATCGCAATGCGAAATGAAAATCGCAAGGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1078825 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
1078854 CGAAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1078849 original size:20 final size:19
Alignment explanation
Indices: 1078791--1078859 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 19
1078781 GCAACGAGAG
1078791 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1078810 AATCGCAA-G-G-AGTG--
1 AATCGCAATGCGAAATGAA
1078824 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
1078844 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
1078860 TAGTTTCCGT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 8 0.20
15 1 0.02
16 4 0.10
17 1 0.02
18 4 0.10
19 12 0.29
20 11 0.27
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1078925 original size:33 final size:33
Alignment explanation
Indices: 1078869--1078951 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
1078859 TTAGTTTCCG
1078869 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
1 TTGCGATTTTCA-TTTCGCATTGCGATTCACTCA
* * *
1078903 TTGCGATTTTCATTTCGTATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCACTCA
**
1078936 TTGCGATAGTCATTTC
1 TTGCGATTTTCATTTC
1078952 CGTGTTACGA
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.16, C:0.22, G:0.17, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCACTCA
Found at i:1079087 original size:14 final size:14
Alignment explanation
Indices: 1079068--1079104 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1079058 CATCAATTAA
1079068 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1079082 ACAAATCATCTTTT
1 ACAAATCAACATTT
1079096 ACAAATCAA
1 ACAAATCAA
1079105 TTAAATAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1081099 original size:20 final size:20
Alignment explanation
Indices: 1081074--1081120 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1081064 GAAACTTAAA
1081074 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
* **
1081094 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCAAAAATGACT
1081114 ATCGCAA
1 ATCGCAA
1081121 TACGAATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:1081126 original size:20 final size:20
Alignment explanation
Indices: 1081089--1081141 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1081079 AACGCAAAAA
**
1081089 TGACTATCGCAACGCGAATT
1 TGACTATCGCAATACGAATT
1081109 TGACTATCGCAATACGAATT
1 TGACTATCGCAATACGAATT
1081129 TGACTATCGCAAT
1 TGACTATCGCAAT
1081142 GAGAGAATCG
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:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (20 bp):
TGACTATCGCAATACGAATT
Found at i:1081209 original size:34 final size:34
Alignment explanation
Indices: 1081165--1081320 Score: 154
Period size: 34 Copynumber: 4.4 Consensus size: 34
1081155 TGCGATTTTC
*
1081165 ATTTTGCATTGCGATTCTTTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
1081199 AATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCA
1 ATTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCA
* * * **
1081239 TTTTCGCGTTGCGATT-TTGTTGTTGCGATTTTC-
1 ATTTCGCATTGCGATTCTT-TCGTTGCGATAGTCA
*
1081272 ATTTCGCATTGCGATTCTCTCGTTGCGATAGTCA
1 ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
*
1081306 TTTTCGCATTGCGAT
1 ATTTCGCATTGCGAT
1081321 AGTAAACTAT
Statistics
Matches: 98, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
33 25 0.26
34 37 0.38
35 2 0.02
36 4 0.04
38 6 0.06
40 24 0.24
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (34 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATAGTCA
Found at i:1081212 original size:20 final size:20
Alignment explanation
Indices: 1081187--1081323 Score: 113
Period size: 20 Copynumber: 7.5 Consensus size: 20
1081177 GATTCTTTCG
**
1081187 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
1081207 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1081227 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1081247 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
**
1081261 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1081280 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
1081294 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1081314 TTGCGATAGT
1 TTGCGATAGT
1081324 AAACTATTCT
Statistics
Matches: 98, Mismatches: 5, Indels: 28
0.75 0.04 0.21
Matches are distributed among these distances:
14 14 0.14
16 12 0.12
17 6 0.06
18 5 0.05
19 7 0.07
20 54 0.55
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1081318 original size:53 final size:53
Alignment explanation
Indices: 1081149--1081320 Score: 154
Period size: 53 Copynumber: 3.2 Consensus size: 53
1081139 AATGAGAGAA
* * * **
1081149 TCGCAATGCGATTTTCATTTTGCATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
** ** * *
1081202 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCAT-TTTCGCG-TTG-CGATTT
1 TCGCATTGCGATTTTCA-TTTCGCATTGCGATTCTC-TCGTT-GCGATAGTC-ATTT
**
1081256 T-GTTGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCG-CATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1081309 TCGCATTGCGAT
1 TCGCATTGCGAT
1081321 AGTAAACTAT
Statistics
Matches: 89, Mismatches: 21, Indels: 18
0.70 0.16 0.14
Matches are distributed among these distances:
52 4 0.04
53 48 0.54
54 33 0.37
55 4 0.04
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
Found at i:1083222 original size:20 final size:20
Alignment explanation
Indices: 1083199--1083288 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
1083189 TCTGAAACTT
1083199 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
1083219 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
1083239 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
1083259 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
1083278 AAAATCGCAAC
1 AAAATCGCAAC
1083289 GACAGAATCG
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 12 0.20
20 49 0.80
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1083687 original size:22 final size:22
Alignment explanation
Indices: 1083625--1083690 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
1083615 TGACCGTGAA
* *
1083625 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
1083647 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1083669 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
1083691 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:1083909 original size:20 final size:20
Alignment explanation
Indices: 1083868--1083979 Score: 102
Period size: 20 Copynumber: 5.5 Consensus size: 20
1083858 GCTATGTAAA
1083868 TCGCATTGCGATAGTTA-G-AT
1 TCGCATTGCGAT--TTACGTAT
*
1083888 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
* *
1083908 TCGCATTGTGATTTACGTAA
1 TCGCATTGCGATTTACGTAT
* * **
1083928 TCGCATTTCGATTTTCCAAAT
1 TCGCATTGCGA-TTTACGTAT
* *
1083949 TTGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
1083969 TCGCATTGCGA
1 TCGCATTGCGA
1083980 ATTAGAAAAA
Statistics
Matches: 71, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
18 3 0.04
19 1 0.01
20 54 0.76
21 13 0.18
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:1084000 original size:21 final size:21
Alignment explanation
Indices: 1083976--1084021 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1083966 TATTCGCATT
1083976 GCGAATTAGAAAAATCGCAAC
1 GCGAATTAGAAAAATCGCAAC
* * *
1083997 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGAAAAATCGCAAC
1084018 GCGA
1 GCGA
1084022 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGAAAAATCGCAAC
Found at i:1091737 original size:17 final size:18
Alignment explanation
Indices: 1091715--1091752 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1091705 GGGATTTTAG
*
1091715 AAAATAACAA-AAATAAT
1 AAAATAAAAAGAAATAAT
*
1091732 AAAATAAAAAGAAATAGT
1 AAAATAAAAAGAAATAAT
1091750 AAA
1 AAA
1091753 CGAAATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (18 bp):
AAAATAAAAAGAAATAAT
Found at i:1096638 original size:18 final size:18
Alignment explanation
Indices: 1096615--1096655 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1096605 TATAATGATA
1096615 TATAA-TTAAATATTTTTT
1 TATAATTTAAAT-TTTTTT
*
1096633 TATAATTTTAATTTTTTT
1 TATAATTTAAATTTTTTT
1096651 TATAA
1 TATAA
1096656 ATTCTAACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATAATTTAAATTTTTTT
Found at i:1098974 original size:12 final size:12
Alignment explanation
Indices: 1098957--1098982 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1098947 GTTTCTTTCT
1098957 TTCTTTTTCCTC
1 TTCTTTTTCCTC
1098969 TTCTTTTTCCTC
1 TTCTTTTTCCTC
1098981 TT
1 TT
1098983 TTTATGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TTCTTTTTCCTC
Found at i:1100688 original size:15 final size:15
Alignment explanation
Indices: 1100668--1100697 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1100658 ACGAGGCTGG
1100668 AATTACAACAACAAC
1 AATTACAACAACAAC
1100683 AATTACAACAACAAC
1 AATTACAACAACAAC
1100698 TATGAGAAAG
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:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:1106629 original size:58 final size:58
Alignment explanation
Indices: 1106560--1106676 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
1106550 GACCGCGATT
1106560 TTAAACCTAGTTACGAGGATTCTACTTTTTTTTGTCCAATTCTCTACTAGGGCTATGA
1 TTAAACCTAGTTACGAGGATTCTACTTTTTTTTGTCCAATTCTCTACTAGGGCTATGA
1106618 TTAAACCTAGTTACGAGGATTCTACTTTTTTTTGTCCAATTCTCTACTAGGGCTATGA
1 TTAAACCTAGTTACGAGGATTCTACTTTTTTTTGTCCAATTCTCTACTAGGGCTATGA
1106676 T
1 T
1106677 GGAATGGGTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.24, C:0.19, G:0.15, T:0.42
Consensus pattern (58 bp):
TTAAACCTAGTTACGAGGATTCTACTTTTTTTTGTCCAATTCTCTACTAGGGCTATGA
Found at i:1108361 original size:11 final size:11
Alignment explanation
Indices: 1108347--1108371 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1108337 GAAGAAGAAG
1108347 AGAAAAAAAAA
1 AGAAAAAAAAA
1108358 AGAAAAAAAAA
1 AGAAAAAAAAA
1108369 AGA
1 AGA
1108372 TCGAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:1108693 original size:12 final size:12
Alignment explanation
Indices: 1108678--1108711 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1108668 ATTTATTCAC
1108678 AAATAATTAATA
1 AAATAATTAATA
1108690 AAATAATTAATA
1 AAATAATTAATA
1108702 AAATAATTAA
1 AAATAATTAA
1108712 AATTTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAATTAATA
Found at i:1109615 original size:74 final size:74
Alignment explanation
Indices: 1109512--1109775 Score: 189
Period size: 74 Copynumber: 3.5 Consensus size: 74
1109502 TTAAGTCATG
* * *
1109512 TTTTTTGGATGGCTCTCCTTTGTGAGTTTAAGTCAAGTGAAATGACCCCTC-TTCGTGGTTTAAG
1 TTTTTTGGATGGCTCTCCTTCGTGAGTTTAAGTCAAATGAAACGA--CCTCATTCGTGGTTTAAG
* **
1109576 CCAGTCTTTA-
64 CCAATCTCGAT
* * * *
1109586 TTTTTTGGATGTCTCAT-CTTCGTGGGTTTAAGTCAAATGAGACGACTTCATTCGTGGTTTAAGC
1 TTTTTTGGATGGCTC-TCCTTCGTGAGTTTAAGTCAAATGAAACGACCTCATTCGTGGTTTAAGC
1109650 CAATCTCGAT
65 CAATCTCGAT
* * * * * * * * *
1109660 TTTTTTGGATGACTCCCCTTC-TCAAGTTTAAGTTAATTGAGACGACTTCCCTTCGCAT-GTCTA
1 TTTTTTGGATGGCTCTCCTTCGT-GAGTTTAAGTCAAATGAAACGACCT-CATTCG--TGGTTTA
* * *
1109723 AGCTAGTCTTGAT
62 AGCCAATCTCGAT
* * *
1109736 TTTTTTGGATGACTC-CTCTTCGCGGGTTTAAGTCAAATGA
1 TTTTTTGGATGGCTCTC-CTTCGTGAGTTTAAGTCAAATGA
1109776 GATAACTCAC
Statistics
Matches: 154, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
72 3 0.02
73 21 0.14
74 76 0.49
75 7 0.05
76 46 0.30
77 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (74 bp):
TTTTTTGGATGGCTCTCCTTCGTGAGTTTAAGTCAAATGAAACGACCTCATTCGTGGTTTAAGCC
AATCTCGAT
Found at i:1109765 original size:76 final size:74
Alignment explanation
Indices: 1109563--1109777 Score: 245
Period size: 76 Copynumber: 2.9 Consensus size: 74
1109553 ATGACCCCTC
* * * * *
1109563 TTCGTGGTTTAAGCCAGTCTTTA-TTTTTTGGATGTCTCATCTTCGTGGGTTTAAGTCAAATGAG
1 TTCGTGGTCTAAGCCAGTCTTGATTTTTTTGGATGACTCCTCTTCGCGGGTTTAAGTCAAATGAG
1109627 ACGACTTCA
66 ACGACTTCA
* * * * * ** * *
1109636 TTCGTGGTTTAAGCCAATCTCGATTTTTTTGGATGACTCCCCTTCTCAAGTTTAAGTTAATTGAG
1 TTCGTGGTCTAAGCCAGTCTTGATTTTTTTGGATGACTCCTCTTCGCGGGTTTAAGTCAAATGAG
*
1109701 ACGACTTCCC
66 ACGACTT-CA
*
1109711 TTCGCAT-GTCTAAGCTAGTCTTGATTTTTTTGGATGACTCCTCTTCGCGGGTTTAAGTCAAATG
1 TTCG--TGGTCTAAGCCAGTCTTGATTTTTTTGGATGACTCCTCTTCGCGGGTTTAAGTCAAATG
1109775 AGA
64 AGA
1109778 TAACTCACTT
Statistics
Matches: 115, Mismatches: 23, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
73 20 0.17
74 39 0.34
75 5 0.04
76 50 0.43
77 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (74 bp):
TTCGTGGTCTAAGCCAGTCTTGATTTTTTTGGATGACTCCTCTTCGCGGGTTTAAGTCAAATGAG
ACGACTTCA
Found at i:1111479 original size:36 final size:36
Alignment explanation
Indices: 1111438--1111510 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1111428 AACTCAGTAT
1111438 TGTATTATTTTGAATACTTTGGGAGTCCCCCCGTAC
1 TGTATTATTTTGAATACTTTGGGAGTCCCCCCGTAC
1111474 TGTATTATTTTGAATACTTTGGGAGTCCCCCCGTAC
1 TGTATTATTTTGAATACTTTGGGAGTCCCCCCGTAC
1111510 T
1 T
1111511 TGTAAACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (36 bp):
TGTATTATTTTGAATACTTTGGGAGTCCCCCCGTAC
Found at i:1115168 original size:20 final size:20
Alignment explanation
Indices: 1115143--1115181 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1115133 AGTGATGGTG
1115143 TCTATAGTGTCTTTGTGATA
1 TCTATAGTGTCTTTGTGATA
1115163 TCTATAGTGTCTTTGTGAT
1 TCTATAGTGTCTTTGTGAT
1115182 TTTGGCTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.21, T:0.51
Consensus pattern (20 bp):
TCTATAGTGTCTTTGTGATA
Found at i:1122461 original size:27 final size:26
Alignment explanation
Indices: 1122427--1122481 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
1122417 GGTTTATTAA
*
1122427 ATATTATTAAA-ATATATTATATATAT
1 ATATTATTAAATAT-TATTATAGATAT
*
1122453 ATATATATTAAATATTATTTTAGATAT
1 ATAT-TATTAAATATTATTATAGATAT
1122480 AT
1 AT
1122482 GTACATATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.16
27 19 0.76
28 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATTATTAAATATTATTATAGATAT
Found at i:1122497 original size:23 final size:21
Alignment explanation
Indices: 1122455--1122497 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1122445 ATATATATAT
*
1122455 ATATATTAAATATTATTTTAG
1 ATATATTAAATATTAATTTAG
*
1122476 ATATATGTACATATGTAATTTA
1 ATATAT-TAAATAT-TAATTTA
1122498 TCAAAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 6 0.33
23 6 0.33
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
ATATATTAAATATTAATTTAG
Found at i:1124877 original size:25 final size:25
Alignment explanation
Indices: 1124835--1124891 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
1124825 TTCCCGATGG
*
1124835 TTGTTCATACAAAATAGTA-TCTTTT
1 TTGTTCGTACAAAATAGTATTC-TTT
1124860 TTGTTCGTA-AAAAGTAGTATTCTTT
1 TTGTTCGTACAAAA-TAGTATTCTTT
1124885 TTGTTCG
1 TTGTTCG
1124892 AGTGATTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 4 0.14
25 23 0.79
26 2 0.07
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (25 bp):
TTGTTCGTACAAAATAGTATTCTTT
Found at i:1125755 original size:15 final size:15
Alignment explanation
Indices: 1125735--1125785 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
1125725 TGAGACATTA
1125735 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
*
1125750 CCCGCCCCGTATCCG
1 CCCGCCCCGCATCCG
*
1125765 CCCG-CCCACATCCG
1 CCCGCCCCGCATCCG
*
1125779 CCTGCCC
1 CCCGCCC
1125786 AGCTAATATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.08, C:0.65, G:0.18, T:0.10
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:1125779 original size:14 final size:14
Alignment explanation
Indices: 1125744--1125786 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1125734 ACCCGCCCCG
1125744 CATCCGCCCGCCC-
1 CATCCGCCCGCCCA
1125757 CGTATCCGCCCGCCCA
1 C--ATCCGCCCGCCCA
*
1125773 CATCCGCCTGCCCA
1 CATCCGCCCGCCCA
1125787 GCTAATATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 12 0.46
15 12 0.46
16 1 0.04
ACGTcount: A:0.12, C:0.60, G:0.16, T:0.12
Consensus pattern (14 bp):
CATCCGCCCGCCCA
Found at i:1126730 original size:219 final size:221
Alignment explanation
Indices: 1126316--1126755 Score: 809
Period size: 219 Copynumber: 2.0 Consensus size: 221
1126306 CCTTTATTAT
1126316 GGTGTTTTATGTATTTTAAGATCTATATTACACTTAACTTAGATAATCCTTGGATTATTTTATTA
1 GGTGTTTTATGTATTTTAAGATCTATATTACACTTAACTTAGATAATCCTTGGATTATTTTATTA
1126381 TGTTTCTTAATGGACATGTTTTTTATGTTTTTGCTTATGTATAACTTAAGTTTGCTGTCAGGCGG
66 TGTTTCTTAATGGACATGTTTTTTATGTTTTTGCTTATGTATAACTTAAGTTTGCTGTCAGGCGG
1126446 GTATAGACGGTACGTCGCTAGTGGGTAGTGGGTGTGGGGATGGATTTGAGAATGTACCCCGTGGG
131 GTATAGACGGTACGTCGCTAGTGGGTAGTGGGTGTGGGGATGGATTTGAGAATGTACCCCGTGGG
1126511 CGGGTGTGGATTTGAAAATTTGTATC
196 CGGGTGTGGATTTGAAAATTTGTATC
1126537 GGTG-TTT-TGTATTTTAAGATCTATATTACACTTAACTTAGATAATCCTTGGATTATTTTATTA
1 GGTGTTTTATGTATTTTAAGATCTATATTACACTTAACTTAGATAATCCTTGGATTATTTTATTA
1126600 TGTTTCTTAATGGACATG-TTTTT-TGTTTGTTGCTTATGTATAACTTAAGTTTGCTGTCAGGCG
66 TGTTTCTTAATGGACATGTTTTTTATGTTT-TTGCTTATGTATAACTTAAGTTTGCTGTCAGGCG
*
1126663 GGTCTAGACGGGTACGTCG-TAGTGGGTAGTGGGTGTGGGGATGGATTTGAGAATGTACCCGCGT
130 GGTATAGAC-GGTACGTCGCTAGTGGGTAGTGGGTGTGGGGATGGATTTGAGAATGTACCC-CGT
1126727 GGGCGGGTGTGGATTTGAAAATTTGTATC
193 GGGCGGGTGTGGATTTGAAAATTTGTATC
1126756 CATCATGGGT
Statistics
Matches: 215, Mismatches: 1, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
217 5 0.02
218 88 0.41
219 115 0.53
220 3 0.01
221 4 0.02
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (221 bp):
GGTGTTTTATGTATTTTAAGATCTATATTACACTTAACTTAGATAATCCTTGGATTATTTTATTA
TGTTTCTTAATGGACATGTTTTTTATGTTTTTGCTTATGTATAACTTAAGTTTGCTGTCAGGCGG
GTATAGACGGTACGTCGCTAGTGGGTAGTGGGTGTGGGGATGGATTTGAGAATGTACCCCGTGGG
CGGGTGTGGATTTGAAAATTTGTATC
Found at i:1130977 original size:43 final size:43
Alignment explanation
Indices: 1130916--1131000 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
1130906 ACAGTATACC
1130916 AAAACATAAAAAGATTAGCAATAATCGATTAGATAAGAGAAAA
1 AAAACATAAAAAGATTAGCAATAATCGATTAGATAAGAGAAAA
*
1130959 AAAACATAAAAAGATTAGCAATAATCGATTATATAAGAGAAA
1 AAAACATAAAAAGATTAGCAATAATCGATTAGATAAGAGAAA
1131001 TCGCCTCAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (43 bp):
AAAACATAAAAAGATTAGCAATAATCGATTAGATAAGAGAAAA
Found at i:1131156 original size:21 final size:20
Alignment explanation
Indices: 1131072--1131229 Score: 88
Period size: 21 Copynumber: 7.8 Consensus size: 20
1131062 AAATGACCAA
**
1131072 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
***
1131091 -AAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* **
1131110 CAGAATCGCAAATC-AGTTTT
1 CAAAATCGCAACGCGA-TTTT
1131130 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGATT-TT
* * * *
1131152 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1131173 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1131193 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1131214 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1131230 ACACATAAAT
Statistics
Matches: 104, Mismatches: 27, Indels: 15
0.71 0.18 0.10
Matches are distributed among these distances:
18 15 0.14
19 1 0.01
20 27 0.26
21 58 0.56
22 3 0.03
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1131182 original size:42 final size:42
Alignment explanation
Indices: 1131133--1131229 Score: 103
Period size: 42 Copynumber: 2.3 Consensus size: 42
1131123 CAGTTTTCCA
* *
1131133 AAATCGCAACGCGATTCTT-GAAAATCGCAATGCG-ATA-GTAC
1 AAATCGCAACGCGATT-TTCCAAAATCGCAACGCGAATATG-AC
**
1131174 AAATTCGCATTGCGATTTTCCAAAATCGCAACGCGAATATGA-
1 AAA-TCGCAACGCGATTTTCCAAAATCGCAACGCGAATATGAC
1131216 AAATCGCAACGCGA
1 AAATCGCAACGCGA
1131230 ACACATAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
41 14 0.30
42 27 0.59
43 4 0.09
44 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
AAATCGCAACGCGATTTTCCAAAATCGCAACGCGAATATGAC
Found at i:1131220 original size:20 final size:19
Alignment explanation
Indices: 1131194--1131248 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1131184 TGCGATTTTC
*
1131194 CAAAATCGCAACGCGAATA
1 CAAAATCGCAACGCGAACA
*
1131213 TGAAAATCGCAACGCGAACA
1 -CAAAATCGCAACGCGAACA
1131233 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
1131249 TATCCGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.44, C:0.27, G:0.18, T:0.11
Consensus pattern (19 bp):
CAAAATCGCAACGCGAACA
Found at i:1131281 original size:59 final size:58
Alignment explanation
Indices: 1131217--1131347 Score: 158
Period size: 59 Copynumber: 2.2 Consensus size: 58
1131207 CGAATATGAA
* * * *
1131217 AATCGCAACGCGAACACATAAATCGCAACGCGT-ATCCGT-AATCGCAACGTGTATCCGT
1 AATCGCAACGCGAAC-CATAAATCGCAACG-ATAATACATAAATCGCAACGCGTATCCGT
*
1131275 ATATCGCAACGCGTATCCATAAATCGCAACGATAATACATAAATCGCAACGCGTATCCGT
1 A-ATCGCAACGCG-AACCATAAATCGCAACGATAATACATAAATCGCAACGCGTATCCGT
*
1131335 AATCGCTACGCGA
1 AATCGCAACGCGA
1131348 TATTTAAAGC
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
58 3 0.05
59 39 0.62
60 21 0.33
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (58 bp):
AATCGCAACGCGAACCATAAATCGCAACGATAATACATAAATCGCAACGCGTATCCGT
Found at i:1131282 original size:20 final size:19
Alignment explanation
Indices: 1131237--1131346 Score: 123
Period size: 20 Copynumber: 5.6 Consensus size: 19
1131227 CGAACACATA
1131237 AATCGCAACGCGTATCCGT
1 AATCGCAACGCGTATCCGT
*
1131256 AATCGCAACGTGTATCCGT
1 AATCGCAACGCGTATCCGT
*
1131275 ATATCGCAACGCGTATCCAT
1 A-ATCGCAACGCGTATCCGT
* * *
1131295 AAATCGCAACG-ATAATACAT
1 -AATCGCAACGCGT-ATCCGT
1131315 AAATCGCAACGCGTATCCGT
1 -AATCGCAACGCGTATCCGT
*
1131335 AATCGCTACGCG
1 AATCGCAACGCG
1131347 ATATTTAAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
19 31 0.40
20 45 0.58
21 2 0.03
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (19 bp):
AATCGCAACGCGTATCCGT
Found at i:1131518 original size:21 final size:21
Alignment explanation
Indices: 1131492--1131544 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1131482 CTCTCTACGG
1131492 CGAAGAAATCCGTCCCATCTC
1 CGAAGAAATCCGTCCCATCTC
**
1131513 CGAAGATTTCCGTCCCATCTC
1 CGAAGAAATCCGTCCCATCTC
**
1131534 CGGCGAAATCC
1 CGAAGAAATCC
1131545 CTCACAACCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.21
Consensus pattern (21 bp):
CGAAGAAATCCGTCCCATCTC
Found at i:1131761 original size:33 final size:33
Alignment explanation
Indices: 1131722--1131792 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1131712 TTCACTTAGA
*
1131722 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1131755 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1131788 TTTCA
1 TTTCA
1131793 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1131898 original size:21 final size:20
Alignment explanation
Indices: 1131872--1131979 Score: 95
Period size: 21 Copynumber: 5.7 Consensus size: 20
1131862 TGCAGAAGAG
1131872 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1131893 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1131913 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
1131934 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
1131948 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
*
1131967 TCGCAACGCGAAA
1 TCGCAACGAGAAA
1131980 CCAAAATCGC
Statistics
Matches: 71, Mismatches: 9, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
14 11 0.15
16 2 0.03
17 2 0.03
19 12 0.17
20 18 0.25
21 26 0.37
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1131916 original size:20 final size:20
Alignment explanation
Indices: 1131872--1131948 Score: 100
Period size: 21 Copynumber: 3.8 Consensus size: 20
1131862 TGCAGAAGAG
*
1131872 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
1131893 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
1131913 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
1131934 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
1131949 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 20 0.42
21 28 0.58
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:1131929 original size:41 final size:41
Alignment explanation
Indices: 1131871--1131948 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1131861 TTGCAGAAGA
*
1131871 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1131912 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1131949 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1131970 original size:19 final size:19
Alignment explanation
Indices: 1131884--1131990 Score: 80
Period size: 19 Copynumber: 5.7 Consensus size: 19
1131874 GCAACGAGAT
*
1131884 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*** *
1131903 AGAATGACTGTCGCAACGAGAG
1 A-AATGAAAATCGCAAC--GCG
1131925 AAATGAAAATCGCAA--CG
1 AAATGAAAATCGCAACGCG
*
1131942 --A-GAGAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
1131958 AAATGAAAATCGCAACGCG
1 AAATGAAAATCGCAACGCG
**
1131977 AAACCAAAATCGCA
1 AAATGAAAATCGCA
1131991 TTGCGATTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 27 0.39
20 12 0.17
21 11 0.16
22 4 0.06
ACGTcount: A:0.47, C:0.21, G:0.22, T:0.10
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:1132026 original size:14 final size:14
Alignment explanation
Indices: 1132007--1132096 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
1131997 TTTCATTTCG
1132007 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1132021 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
1132040 CGTTGCGATTATCT
1 CGTTGCGATTCTCT
* *
1132054 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1132073 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1132087 CGTTGCGATT
1 CGTTGCGATT
1132097 TTCATTTCAA
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
14 29 0.50
16 5 0.09
17 5 0.09
19 19 0.33
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1132038 original size:33 final size:33
Alignment explanation
Indices: 1131991--1132104 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1131981 CAAAATCGCA
1131991 TTGCGA-TTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
1132023 TTGCGATTTTCATTTCGCGTTGCGATTATCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1132056 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1132089 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1132105 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 6 0.08
33 71 0.92
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1132045 original size:19 final size:18
Alignment explanation
Indices: 1131986--1132082 Score: 84
Period size: 14 Copynumber: 5.7 Consensus size: 18
1131976 GAAACCAAAA
*
1131986 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
1132004 TCGCGTTGCGA-TTC---
1 TCGCGTTGCGATTTCATT
*
1132018 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
1132037 TCGCGTTGCGA-TT-A--
1 TCGCGTTGCGATTTCATT
**
1132051 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
1132070 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1132083 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
16 6 0.10
17 6 0.10
18 12 0.19
19 19 0.31
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:1139362 original size:30 final size:32
Alignment explanation
Indices: 1139299--1139371 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
1139289 GCTCGACTCG
*
1139299 TGCTCGTTAAGAAAATTTATTGTTCAACTTGT
1 TGCTCGTTAAGAAAATTTATTGCTCAACTTGT
* **
1139331 TGCTCGTTAAG-AAATTTGTT-CTCGTCTTGT
1 TGCTCGTTAAGAAAATTTATTGCTCAACTTGT
*
1139361 TGCTTGTTAAG
1 TGCTCGTTAAG
1139372 CTCACGGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 17 0.47
31 8 0.22
32 11 0.31
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (32 bp):
TGCTCGTTAAGAAAATTTATTGCTCAACTTGT
Found at i:1141687 original size:2 final size:2
Alignment explanation
Indices: 1141680--1141715 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1141670 AAAATACTGA
1141680 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
1141716 GGGGGAGCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1142081 original size:33 final size:33
Alignment explanation
Indices: 1142044--1142110 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1142034 ATTACCTCAT
*
1142044 TAAGATCTTATGTTATCAAATAAATTATTAAGA
1 TAAGATCTTATGTTATCAAACAAATTATTAAGA
**
1142077 TAAGATCTTATGTTATCGCACAAATTATTAAGA
1 TAAGATCTTATGTTATCAAACAAATTATTAAGA
1142110 T
1 T
1142111 TCTCACTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (33 bp):
TAAGATCTTATGTTATCAAACAAATTATTAAGA
Found at i:1142580 original size:21 final size:21
Alignment explanation
Indices: 1142556--1142595 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1142546 TAACAAAGGT
*
1142556 AGTACCGATACTCC-CTGTAGG
1 AGTACCAATAC-CCTCTGTAGG
1142577 AGTACCAATACCCTCTGTA
1 AGTACCAATACCCTCTGTA
1142596 CTGGGCAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.25
Consensus pattern (21 bp):
AGTACCAATACCCTCTGTAGG
Found at i:1143007 original size:17 final size:17
Alignment explanation
Indices: 1142985--1143023 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1142975 TAAAGTAGTG
1142985 GAAGTAGACTTGGTTGA
1 GAAGTAGACTTGGTTGA
1143002 GAAGTAGACTTGGTTGA
1 GAAGTAGACTTGGTTGA
1143019 GAAGT
1 GAAGT
1143024 CGAACCACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.36, T:0.28
Consensus pattern (17 bp):
GAAGTAGACTTGGTTGA
Found at i:1151467 original size:72 final size:72
Alignment explanation
Indices: 1151303--1151447 Score: 197
Period size: 72 Copynumber: 2.0 Consensus size: 72
1151293 CGCTCAATAC
**
1151303 TTAATTGATGAGGTATAGAAAGAGCAG-A--GATTATTACACATCATCTCAAGAAGATAAAGCTA
1 TTAATTGAACAGGTATAGAAAGAGCAGCATTGATTATTACACATCATCTCAAGAAGATAAAGCTA
* *
1151365 GCATTAC
66 GCATAAA
**
1151372 TTAATTGATGAGGTATAGAAAGAGCAGCATTGATTATTACACATCATCTCAAGAAGATACAAGCT
1 TTAATTGAACAGGTATAGAAAGAGCAGCATTGATTATTACACATCATCTCAAGAAGATA-AAGCT
1151437 AGCATGAAA
65 AGCAT-AAA
1151446 TT
1 TT
1151448 TCTTAACAGG
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
69 27 0.39
70 1 0.01
72 28 0.41
73 10 0.14
74 3 0.04
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.27
Consensus pattern (72 bp):
TTAATTGAACAGGTATAGAAAGAGCAGCATTGATTATTACACATCATCTCAAGAAGATAAAGCTA
GCATAAA
Found at i:1153185 original size:2 final size:2
Alignment explanation
Indices: 1153173--1153217 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1153163 GGATTTCTCA
1153173 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1153214 AT AT
1 AT AT
1153218 TCACGGGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1159092 original size:225 final size:224
Alignment explanation
Indices: 1158637--1159094 Score: 629
Period size: 225 Copynumber: 2.0 Consensus size: 224
1158627 AAAACCATAC
* * * * *
1158637 AACTGATTACGGGTTGTTACAAAAATCTCAACATTTTTAGGTGAGAGTTTAGCTCTTAATTTTTG
1 AACTGATTACGAGTTGGTACAAAAATATAAACATTTTTAGGTGAGAGTTTAGCTCTTAATTTTTC
* * ** *
1158702 AAAATTCGGTCCCCATACTAATGATGATTGATGCAACTGAAGTAATTGGAATAGCCAATATATTT
66 AAAATTCGGACCCCATACTAATGACGATTGATAAAACTAAAGTAATTGGAATAGCCAATATATTT
*
1158767 CTCGCCATACGAGAAAGTACCAGATATGAAATACTTTGATTTCCAATACTCTAAAATATCAAAGT
131 CTCGCCATA-GAGAAAGTACCAGATATGAAATACTTTGATTTCCAATACTCCAAAATATCAAAGT
*
1158832 CAGATTCTCCAGCACGAGGGACAAAGGGCA
195 CAGATTCTCAAGCACGAGGGACAAAGGGCA
*
1158862 AACTGATTGCGAGTTGGTACAAAAATATAAACATTTTTAGGTGAGAGTTTAGCTCTTAATTTGTT
1 AACTGATTACGAGTTGGTACAAAAATATAAACATTTTTAGGTGAGAGTTTAGCTCTTAATTT-TT
1158927 CAAAATTCGGACCCCATACTAAATGACGATTTAGATAAAACTAAAGTAATTGGAAT-GCCAATAT
65 CAAAATTCGGACCCCATACT-AATGACGA-TT-GATAAAACTAAAGTAATTGGAATAGCCAATAT
* * * * *
1158991 ATTTCTTGTCAT-GA-AAAGTACTAGATATG-AATACTTTGATTTTTTCAATACTCCAAATTATC
127 ATTTCTCGCCATAGAGAAAGTACCAGATATGAAATACTTTGA--TTTCCAATACTCCAAAATATC
* * *
1159053 AAAGTCGGGTTCTCAAGTACGAGGGACAAAGGG-A
190 AAAGTCAGATTCTCAAGCACGAGGGACAAAGGGCA
1159087 AACTGATT
1 AACTGATT
1159095 TAAGAGTTAA
Statistics
Matches: 206, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
224 10 0.05
225 80 0.39
226 69 0.33
227 7 0.03
228 20 0.10
229 20 0.10
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (224 bp):
AACTGATTACGAGTTGGTACAAAAATATAAACATTTTTAGGTGAGAGTTTAGCTCTTAATTTTTC
AAAATTCGGACCCCATACTAATGACGATTGATAAAACTAAAGTAATTGGAATAGCCAATATATTT
CTCGCCATAGAGAAAGTACCAGATATGAAATACTTTGATTTCCAATACTCCAAAATATCAAAGTC
AGATTCTCAAGCACGAGGGACAAAGGGCA
Found at i:1160842 original size:2 final size:2
Alignment explanation
Indices: 1160837--1160886 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1160827 TATACAAAAA
1160837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1160879 AT AT AT AT
1 AT AT AT AT
1160887 GCATATAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1162974 original size:2 final size:2
Alignment explanation
Indices: 1162967--1162992 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1162957 CTACACGATG
1162967 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
1162993 TAGGGGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1166723 original size:13 final size:13
Alignment explanation
Indices: 1166699--1166740 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1166689 AAATTATTAA
1166699 TAAAAATATAAAAAT
1 TAAAAAT-T-AAAAT
1166714 T-AAAATTAAAAT
1 TAAAAATTAAAAT
*
1166726 GAAAAATTAAAAT
1 TAAAAATTAAAAT
1166739 TA
1 TA
1166741 TCAACAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 5 0.21
13 13 0.54
14 5 0.21
15 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:1167069 original size:28 final size:28
Alignment explanation
Indices: 1167010--1167069 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1167000 GTTATTTGAG
* *
1167010 TTGATGAGTTATATTTTACAACTCGGAG
1 TTGATGAGTTATATTTTACAACTCGAAA
**
1167038 TTGATGAGTTATATTTTGTAACTCGAAA
1 TTGATGAGTTATATTTTACAACTCGAAA
1167066 TTGA
1 TTGA
1167070 CTTAATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (28 bp):
TTGATGAGTTATATTTTACAACTCGAAA
Found at i:1172095 original size:21 final size:22
Alignment explanation
Indices: 1172070--1172129 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1172060 CTATAAGGGG
*
1172070 AGTATCGATACTCTAGGG-AG-A
1 AGTATCGATACT-GAGGGTAGCA
1172091 AGTATCGATACTGAGGGTAGCA
1 AGTATCGATACTGAGGGTAGCA
1172113 A-TATCGATACT-AGGGTA
1 AGTATCGATACTGAGGGTA
1172130 AATTTTGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 10 0.28
21 24 0.67
22 2 0.06
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.25
Consensus pattern (22 bp):
AGTATCGATACTGAGGGTAGCA
Found at i:1177927 original size:20 final size:20
Alignment explanation
Indices: 1177902--1177939 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1177892 TGGGTTCGAG
1177902 TATCGATACTAGATGAACAA
1 TATCGATACTAGATGAACAA
* *
1177922 TATCGATTCTGGATGAAC
1 TATCGATACTAGATGAAC
1177940 TGGGTCGATT
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:0.16, G:0.18, T:0.29
Consensus pattern (20 bp):
TATCGATACTAGATGAACAA
Found at i:1178259 original size:21 final size:20
Alignment explanation
Indices: 1178235--1178274 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1178225 GATACCAAAG
1178235 TTAAGAGAAGTATCAATACTC
1 TTAAG-GAAGTATCAATACTC
* *
1178256 TTAAGGTAGTATCGATACT
1 TTAAGGAAGTATCAATACT
1178275 ACCAACTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (20 bp):
TTAAGGAAGTATCAATACTC
Found at i:1181497 original size:20 final size:20
Alignment explanation
Indices: 1181472--1181521 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
1181462 TTGAGTTAGA
1181472 AGATACCATTGAATCTTCTT
1 AGATACCATTGAATCTTCTT
1181492 AGATACCATTGAATCTTCTT
1 AGATACCATTGAATCTTCTT
*
1181512 TGATGACCAT
1 AGAT-ACCAT
1181522 GAGGCATAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (20 bp):
AGATACCATTGAATCTTCTT
Found at i:1186227 original size:20 final size:21
Alignment explanation
Indices: 1186184--1186229 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1186174 TATTTTACAG
*
1186184 AGAAAACATCCCCAAACGGCT
1 AGAAAACATCCCCAAACAGCT
*
1186205 AGAAATCATCCCC-AACAGCT
1 AGAAAACATCCCCAAACAGCT
1186225 AGAAA
1 AGAAA
1186230 CAACCACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.46, C:0.30, G:0.13, T:0.11
Consensus pattern (21 bp):
AGAAAACATCCCCAAACAGCT
Found at i:1186846 original size:20 final size:20
Alignment explanation
Indices: 1186801--1186863 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
1186791 ATACTTAAAG
* *
1186801 GGGTATCGATATTGACCT-AA
1 GGGTATCGATACTG-CATGAA
*
1186821 GAGTATCGATACTGCATGAA
1 GGGTATCGATACTGCATGAA
1186841 GGGTATCGATACTGCATGAA
1 GGGTATCGATACTGCATGAA
1186861 GGG
1 GGG
1186864 ATACTACGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.05
20 36 0.95
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACTGCATGAA
Found at i:1187208 original size:22 final size:22
Alignment explanation
Indices: 1187181--1187227 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
1187171 GAACGAATGA
1187181 AATAATATACCAAGTGGGTAGT
1 AATAATATACCAAGTGGGTAGT
1187203 AATAATATACCAAGTGGGTAGT
1 AATAATATACCAAGTGGGTAGT
1187225 AAT
1 AAT
1187228 GGTTACAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.28
Consensus pattern (22 bp):
AATAATATACCAAGTGGGTAGT
Found at i:1187670 original size:43 final size:44
Alignment explanation
Indices: 1187613--1187719 Score: 144
Period size: 43 Copynumber: 2.4 Consensus size: 44
1187603 GACTCGACCC
1187613 AATTATATTAATATTTTAAAATAATTAAAATAATATATTTT-TAAT
1 AATT-TATT-ATATTTTAAAATAATTAAAATAATATATTTTATAAT
** *
1187658 AATTTATTATATTTTTTAATTATTAAAATAATATATTTTATAAT
1 AATTTATTATATTTTAAAATAATTAAAATAATATATTTTATAAT
*
1187702 AATATATTATAATTTTAA
1 AATTTATTAT-ATTTTAA
1187720 TGGTTAAATA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
43 28 0.52
44 17 0.31
45 9 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (44 bp):
AATTTATTATATTTTAAAATAATTAAAATAATATATTTTATAAT
Found at i:1187693 original size:24 final size:24
Alignment explanation
Indices: 1187623--1187704 Score: 84
Period size: 24 Copynumber: 3.6 Consensus size: 24
1187613 AATTATATTA
**
1187623 ATATTTTAAAATAATTAAAATAAT
1 ATATTTTTTAATAATTAAAATAAT
*
1187647 ATA-TTTTTAATAATT----TATT
1 ATATTTTTTAATAATTAAAATAAT
*
1187666 ATATTTTTTAATTATTAAAATAAT
1 ATATTTTTTAATAATTAAAATAAT
*
1187690 ATATTTTATAATAAT
1 ATATTTTTTAATAAT
1187705 ATATTATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
19 6 0.13
20 11 0.24
23 10 0.22
24 19 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTTTTTAATAATTAAAATAAT
Found at i:1187727 original size:43 final size:43
Alignment explanation
Indices: 1187616--1187731 Score: 139
Period size: 43 Copynumber: 2.7 Consensus size: 43
1187606 TCGACCCAAT
*
1187616 TATATTA-ATATTTTAAAATAATTAAAATAATATATTTTTAATAA
1 TATATTATATATTTT--AATGATTAAAATAATATATTTTTAATAA
* * *
1187660 TTTATTATATTTTTTAATTATTAAAATAATATATTTTATAATAA
1 TATATTATATATTTTAATGATTAAAATAATATATTTT-TAATAA
*
1187704 TATATTATA-ATTTTAATGGTT-AAATAAT
1 TATATTATATATTTTAATGATTAAAATAAT
1187732 GCTTTTTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
42 7 0.11
43 30 0.48
44 20 0.32
45 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (43 bp):
TATATTATATATTTTAATGATTAAAATAATATATTTTTAATAA
Found at i:1191630 original size:19 final size:19
Alignment explanation
Indices: 1191594--1191630 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1191584 TGAAAATGAT
*
1191594 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
1191613 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
1191631 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:1192547 original size:16 final size:16
Alignment explanation
Indices: 1192526--1192564 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1192516 GCCTTTGATT
1192526 TTTCAAATAATTTTAA
1 TTTCAAATAATTTTAA
1192542 TTTCAAATAATTTTAA
1 TTTCAAATAATTTTAA
*
1192558 TGTCAAA
1 TTTCAAA
1192565 ATTACCACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (16 bp):
TTTCAAATAATTTTAA
Found at i:1193547 original size:20 final size:22
Alignment explanation
Indices: 1193522--1193561 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1193512 TGTTGTATAT
1193522 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
1193542 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
1193562 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:1193611 original size:21 final size:22
Alignment explanation
Indices: 1193577--1193618 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1193567 TCAAAAAGGC
1193577 TGCACATAACATGGTGCATCGG
1 TGCACATAACATGGTGCATCGG
*
1193599 TGCAC-TATCATGGTGCATCG
1 TGCACATAACATGGTGCATCG
1193619 ATACCCCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (22 bp):
TGCACATAACATGGTGCATCGG
Found at i:1193703 original size:20 final size:20
Alignment explanation
Indices: 1193674--1193726 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1193664 GCAGCCTTCG
*
1193674 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
1193694 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACAGCAGGA
1193714 TGCATCGATGCAC
1 TGCATCGATGCAC
1193727 TAAGTGCATT
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:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:1195254 original size:19 final size:20
Alignment explanation
Indices: 1195211--1195255 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
1195201 TCTAAATCCT
1195211 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTTCATTTTGG
* *
1195231 CTTTCAAAATTT-ATTTTTG
1 TTTTCAAAATTTCATTTTGG
1195250 TTTTCA
1 TTTTCA
1195256 GAAGAAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.58
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGG
Found at i:1196568 original size:20 final size:20
Alignment explanation
Indices: 1196539--1196593 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1196529 GTAGCCTTCG
*
1196539 TGCATGGATGCACAACAGGA
1 TGCATCGATGCACAACAGGA
*
1196559 TGCATCGATGCACATCAGGA
1 TGCATCGATGCACAACAGGA
1196579 TGCATCGATGCACAA
1 TGCATCGATGCACAA
1196594 AGTGCATTCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.25, T:0.18
Consensus pattern (20 bp):
TGCATCGATGCACAACAGGA
Found at i:1196678 original size:21 final size:21
Alignment explanation
Indices: 1196611--1196709 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
1196601 TCGAAATGGA
*
1196611 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
* * * **
1196631 ATGCATCGATGCACTAGTACAG
1 GTGCATGGATGCACT-GCAGGG
**
1196653 GTGCATAAATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
1196674 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
1196695 GTGCATGGATGCACT
1 GTGCATGGATGCACT
1196710 TTGACACCCT
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 13 0.20
21 39 0.60
22 13 0.20
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:1202188 original size:27 final size:30
Alignment explanation
Indices: 1202158--1202216 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 30
1202148 TGTGTAATTT
*
1202158 TTTAGAATAAACAT-A-ATAATATTTT-AG
1 TTTAAAATAAACATAATATAATATTTTCAG
**
1202185 TTTAAAATTTACATAATATAATATTTTCAG
1 TTTAAAATAAACATAATATAATATTTTCAG
1202215 TT
1 TT
1202217 ATAATTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 1 0.04
29 10 0.38
30 4 0.15
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (30 bp):
TTTAAAATAAACATAATATAATATTTTCAG
Found at i:1203531 original size:21 final size:21
Alignment explanation
Indices: 1203505--1203547 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1203495 ATACTACGCA
1203505 TTTAGTACTTAAACTATCAAT
1 TTTAGTACTTAAACTATCAAT
* *
1203526 TTTAGTATTTAAACTTTCAAT
1 TTTAGTACTTAAACTATCAAT
1203547 T
1 T
1203548 CTTTTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (21 bp):
TTTAGTACTTAAACTATCAAT
Found at i:1207209 original size:45 final size:45
Alignment explanation
Indices: 1207154--1207259 Score: 194
Period size: 45 Copynumber: 2.4 Consensus size: 45
1207144 AAATTTGATT
*
1207154 AAAAACTGACTTTGCATACTTGGTTTCGATGAATATACAAAGATA
1 AAAAACTGACTTTGCATACTTGGTTTCGAAGAATATACAAAGATA
*
1207199 AAAAACTGACTTTGCATATTTGGTTTCGAAGAATATACAAAGATA
1 AAAAACTGACTTTGCATACTTGGTTTCGAAGAATATACAAAGATA
1207244 AAAAACTGACTTTGCA
1 AAAAACTGACTTTGCA
1207260 CGAGCTTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (45 bp):
AAAAACTGACTTTGCATACTTGGTTTCGAAGAATATACAAAGATA
Found at i:1208958 original size:35 final size:35
Alignment explanation
Indices: 1208897--1208983 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
1208887 GGATGACATC
* * *
1208897 TCTATAACCATCTTTAGCAATAAACAATAATAATG
1 TCTATGACCATCTTTAACAATAAACAATAATAATA
*
1208932 TCTATGACCATACTTTAACAAT-AACAATAGTAATA
1 TCTATGACCAT-CTTTAACAATAAACAATAATAATA
* *
1208967 TCAATGATCATGCTTTA
1 TCTATGACCAT-CTTTA
1208984 GTGTTAAACA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 35 0.80
36 9 0.20
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (35 bp):
TCTATGACCATCTTTAACAATAAACAATAATAATA
Found at i:1209679 original size:15 final size:15
Alignment explanation
Indices: 1209659--1209689 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1209649 ATTTATATAA
1209659 TTTAATTACCTAGAC
1 TTTAATTACCTAGAC
*
1209674 TTTAATTTCCTAGAC
1 TTTAATTACCTAGAC
1209689 T
1 T
1209690 AACAAAACCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.19, G:0.06, T:0.45
Consensus pattern (15 bp):
TTTAATTACCTAGAC
Found at i:1209731 original size:16 final size:14
Alignment explanation
Indices: 1209699--1209743 Score: 51
Period size: 11 Copynumber: 3.3 Consensus size: 14
1209689 TAACAAAACC
1209699 TAATCCAATT--A-
1 TAATCCAATTAAAT
1209710 TAATCCAATTTCAAAT
1 TAATCCAA-TT-AAAT
1209726 TAATCCAATTAAAT
1 TAATCCAATTAAAT
1209740 TAAT
1 TAAT
1209744 ATCATATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 8 0.28
12 2 0.07
14 8 0.28
15 3 0.10
16 8 0.28
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.38
Consensus pattern (14 bp):
TAATCCAATTAAAT
Found at i:1209837 original size:2 final size:2
Alignment explanation
Indices: 1209825--1209861 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1209815 GTAATTGGAT
1209825 TA TA T- 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
1209862 AACTAACCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1210364 original size:34 final size:34
Alignment explanation
Indices: 1210321--1210418 Score: 187
Period size: 34 Copynumber: 2.9 Consensus size: 34
1210311 TTGTATTTCA
1210321 TATTTATAACTCTAAGTTAGTACTATTTTGGTTT
1 TATTTATAACTCTAAGTTAGTACTATTTTGGTTT
1210355 TATTTATAACTCTAAGTTAGTACTATTTTGGTTT
1 TATTTATAACTCTAAGTTAGTACTATTTTGGTTT
*
1210389 TATTTATAACTCTAAGTTCGTACTATTTTG
1 TATTTATAACTCTAAGTTAGTACTATTTTG
1210419 AACACATATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (34 bp):
TATTTATAACTCTAAGTTAGTACTATTTTGGTTT
Found at i:1215172 original size:13 final size:13
Alignment explanation
Indices: 1215154--1215178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1215144 TTGTGTAAAA
1215154 TTTATATTTTAAT
1 TTTATATTTTAAT
1215167 TTTATATTTTAA
1 TTTATATTTTAA
1215179 ATTTGTAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTATATTTTAAT
Found at i:1215913 original size:55 final size:55
Alignment explanation
Indices: 1215825--1215930 Score: 185
Period size: 55 Copynumber: 1.9 Consensus size: 55
1215815 TTCCTTTCTC
*
1215825 CCTTTCTTTTCCCCTTTTTTAGTTCCAACAATCAACACACATGTTCTTGTTATTT
1 CCTTTCTTTTCCCCTTTTTTAGTTCCAAAAATCAACACACATGTTCTTGTTATTT
* *
1215880 CCTTTCTTTTCCCCTTTTTTAGTTTCAAAAATCAACACCCATGTTCTTGTT
1 CCTTTCTTTTCCCCTTTTTTAGTTCCAAAAATCAACACACATGTTCTTGTT
1215931 CTTCTCCTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.20, C:0.27, G:0.06, T:0.47
Consensus pattern (55 bp):
CCTTTCTTTTCCCCTTTTTTAGTTCCAAAAATCAACACACATGTTCTTGTTATTT
Found at i:1216546 original size:16 final size:15
Alignment explanation
Indices: 1216510--1216547 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
1216500 TCTCTAATTG
1216510 ATCATAAATAATTAA
1 ATCATAAATAATTAA
*
1216525 AT-ATAAATAATATTA
1 ATCATAAATAAT-TAA
1216540 ATCATAAA
1 ATCATAAA
1216548 ATTATTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 6 0.30
16 5 0.25
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (15 bp):
ATCATAAATAATTAA
Found at i:1218725 original size:6 final size:5
Alignment explanation
Indices: 1218703--1218739 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
1218693 ATTGCATCCA
1218703 TTGAT TTGAT TTGAT TCTGAT TCTGAT TTGAT TTGAT
1 TTGAT TTGAT TTGAT T-TGAT T-TGAT TTGAT TTGAT
1218740 CTTATTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 20 0.65
6 11 0.35
ACGTcount: A:0.19, C:0.05, G:0.19, T:0.57
Consensus pattern (5 bp):
TTGAT
Found at i:1224484 original size:2 final size:2
Alignment explanation
Indices: 1224477--1224506 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1224467 TAAGTTGAAG
1224477 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
1224507 TAATAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1227807 original size:20 final size:20
Alignment explanation
Indices: 1227778--1227817 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1227768 ACCTCGGTTT
*
1227778 TACCGATTTTCAGCCGATTC
1 TACCGATTTTCAACCGATTC
*
1227798 TACCGGTTTTCAACCGATTC
1 TACCGATTTTCAACCGATTC
1227818 ATTGCTAGAC
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:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (20 bp):
TACCGATTTTCAACCGATTC
Found at i:1228147 original size:40 final size:40
Alignment explanation
Indices: 1228077--1228173 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 40
1228067 CGCAACTCGA
*
1228077 TTTCTGAATTCGCAACACAAGTTTCCTTTTCACAACAAGAT
1 TTTCT-AATTCGCAACACAAGTTTACTTTTCACAACAAGAT
* * * **
1228118 TTTCTAAATCGCAACACGAA-TTTAGTTTTCGCAACTCGAT
1 TTTCTAATTCGCAACAC-AAGTTTACTTTTCACAACAAGAT
*
1228158 TTTCGAATTCGCAACA
1 TTTCTAATTCGCAACA
1228174 GCTTTTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 40 0.85
41 7 0.15
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.34
Consensus pattern (40 bp):
TTTCTAATTCGCAACACAAGTTTACTTTTCACAACAAGAT
Found at i:1228149 original size:20 final size:20
Alignment explanation
Indices: 1228126--1228192 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
1228116 ATTTTCTAAA
*
1228126 TCGCAACACGAATTTAGTTT
1 TCGCAACACGATTTTAGTTT
* * **
1228146 TCGCAACTCGATTTTCGAAT
1 TCGCAACACGATTTTAGTTT
*
1228166 TCGCAACA-GCTTTTA-TTT
1 TCGCAACACGATTTTAGTTT
1228184 TCGCAACAC
1 TCGCAACAC
1228193 AAATGTTTGG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
18 9 0.25
19 5 0.14
20 22 0.61
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
TCGCAACACGATTTTAGTTT
Found at i:1229158 original size:24 final size:24
Alignment explanation
Indices: 1229107--1229160 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1229097 GTATTCGAAA
*
1229107 TTTGATCTTGGTCAATACCCGGGC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1229131 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1229155 TTTGAT
1 TTTGAT
1229161 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1231790 original size:20 final size:20
Alignment explanation
Indices: 1231708--1231783 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1231698 GATTGTTGCA
*
1231708 AAAGTCAAATTCGCAACGCG
1 AAAGTCAAATTCGCAACACG
*** *
1231728 AAAGTCAAATTCGCGTTATG
1 AAAGTCAAATTCGCAACACG
* * *
1231748 AAAGTCAAATTTGAAACATG
1 AAAGTCAAATTCGCAACACG
*
1231768 AAAGTAAAATTCGCAA
1 AAAGTCAAATTCGCAA
1231784 TGCGAAAATT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (20 bp):
AAAGTCAAATTCGCAACACG
Found at i:1231936 original size:16 final size:15
Alignment explanation
Indices: 1231915--1231949 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1231905 TGCAGATTGA
*
1231915 AATTAAACAACAAATC
1 AATTAAACAA-AAAAC
1231931 AATTAAACAAAAAAC
1 AATTAAACAAAAAAC
1231946 AATT
1 AATT
1231950 CTTATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (15 bp):
AATTAAACAAAAAAC
Found at i:1233370 original size:21 final size:21
Alignment explanation
Indices: 1233346--1233439 Score: 122
Period size: 21 Copynumber: 4.6 Consensus size: 21
1233336 GCGAATCGGG
*
1233346 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
1233367 CTCTTGAACGAT--GAGAGG-
1 CTCTTGAACGATGGGAGGGGC
1233385 CTCTTGAACGATGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* * *
1233406 CTTTTGAATGATAGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
1233427 CTCTTGAACGATG
1 CTCTTGAACGATG
1233440 ACAGGTGAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
18 12 0.20
19 5 0.08
20 5 0.08
21 39 0.64
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:1233390 original size:18 final size:18
Alignment explanation
Indices: 1233344--1233402 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
1233334 ATGCGAATCG
* *
1233344 GGCTCTTGAACGGTGGGAGG
1 GGCTCTTGAACGAT--GAGA
1233364 GGCCTCTTGAACGATGAGA
1 GG-CTCTTGAACGATGAGA
*
1233383 GGCTCTTGAACGATGGGA
1 GGCTCTTGAACGATGAGA
1233401 GG
1 GG
1233403 GGCCTTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 17 0.49
19 5 0.14
20 2 0.06
21 11 0.31
ACGTcount: A:0.20, C:0.17, G:0.42, T:0.20
Consensus pattern (18 bp):
GGCTCTTGAACGATGAGA
Found at i:1233400 original size:39 final size:40
Alignment explanation
Indices: 1233344--1233439 Score: 131
Period size: 39 Copynumber: 2.4 Consensus size: 40
1233334 ATGCGAATCG
*
1233344 GGCTCTTGAACGGTGGGAGGGGCCTCTTGAACGAT-GAGA
1 GGCTCTTGAACGATGGGAGGGGCCTCTTGAACGATAGAGA
* * *
1233383 GGCTCTTGAACGATGGGAGGGGCCTTTTGAATGATAGGAGG
1 GGCTCTTGAACGATGGGAGGGGCCTCTTGAACGATA-GAGA
1233424 GGCCTCTTGAACGATG
1 GG-CTCTTGAACGATG
1233440 ACAGGTGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 32 0.64
41 5 0.10
42 13 0.26
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.23
Consensus pattern (40 bp):
GGCTCTTGAACGATGGGAGGGGCCTCTTGAACGATAGAGA
Found at i:1233599 original size:4 final size:4
Alignment explanation
Indices: 1233583--1233620 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
1233573 GGGCCGCTAA
* *
1233583 AAAT AAAT TAAT AAAT AAAT CAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1233621 TGCCAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1233757 original size:21 final size:21
Alignment explanation
Indices: 1233730--1233788 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
1233720 GTAGAGCGGC
*
1233730 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
*
1233751 TATCTCACCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
1233772 TACCTCACCACGTAAAG
1 TACCTCACCACGTAAAG
1233789 CACCATTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:1233893 original size:21 final size:21
Alignment explanation
Indices: 1233869--1233909 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1233859 GTTGTCATGT
*
1233869 AAAGTACCGACCTCATCACGC
1 AAAGCACCGACCTCATCACGC
*
1233890 AAAGCACTGACCTCATCACG
1 AAAGCACCGACCTCATCACG
1233910 TAACTCCCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.34, C:0.37, G:0.15, T:0.15
Consensus pattern (21 bp):
AAAGCACCGACCTCATCACGC
Found at i:1234086 original size:42 final size:42
Alignment explanation
Indices: 1234027--1234125 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
1234017 GTGATGGAAT
* *
1234027 AGGTGATGGCTCTCGGTGTGGAGGTGTATAATCGGCTCAATC
1 AGGTGATGGCTCTCGGTGTGGAGCTGTAGAATCGGCTCAATC
* * * *
1234069 AGGTGATGGCTCTCGGTGTTGAGCTGTAGAATTGGCTCGATT
1 AGGTGATGGCTCTCGGTGTGGAGCTGTAGAATCGGCTCAATC
1234111 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
1234126 AAGTAGGGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.17, C:0.16, G:0.36, T:0.30
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTGGAGCTGTAGAATCGGCTCAATC
Found at i:1235087 original size:20 final size:19
Alignment explanation
Indices: 1235064--1235106 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1235054 AAACTTAAAT
*
1235064 TCGCAGCACGAAAATGAAAA
1 TCGCAACACGAAAATG-AAA
*
1235084 TCGCAACGCGAAAATGAAA
1 TCGCAACACGAAAATGAAA
1235103 TCGC
1 TCGC
1235107 GTTACGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
TCGCAACACGAAAATGAAA
Found at i:1235495 original size:22 final size:22
Alignment explanation
Indices: 1235467--1235517 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1235457 ATAGAGGGAG
*
1235467 GTCGCCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
*
1235489 GTCGCCGGAGATGGGGATGGAT
1 GTCGCCGGAGATGGGGACGGAT
*
1235511 ATCGCCG
1 GTCGCCG
1235518 TAGAGGGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.45, T:0.18
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Found at i:1235749 original size:20 final size:20
Alignment explanation
Indices: 1235684--1235749 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
1235674 TGACTTATGT
* *
1235684 GTTGCGATTTACATTTTCGC
1 GTTGCGATTTACATATTCAC
* * *
1235704 GTTGCGAATT-CGGAAAATCAC
1 GTTGCGATTTAC--ATATTCAC
*
1235725 GTTGCGATTTACATATTCTC
1 GTTGCGATTTACATATTCAC
1235745 GTTGC
1 GTTGC
1235750 AGAAAAGAAA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
19 1 0.03
20 19 0.56
21 13 0.38
22 1 0.03
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACATATTCAC
Found at i:1236351 original size:20 final size:20
Alignment explanation
Indices: 1236326--1236392 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1236316 TTTTCCCAAT
1236326 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1236346 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
1236367 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
1236387 TCGCAA
1 TCGCAA
1236393 CACGAATTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1236369 original size:21 final size:21
Alignment explanation
Indices: 1236343--1236418 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1236333 GCGAATAAGT
1236343 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1236364 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
1236384 AAATCGCAACACGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
1236405 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1236419 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1236432 original size:20 final size:20
Alignment explanation
Indices: 1236407--1236501 Score: 93
Period size: 20 Copynumber: 4.7 Consensus size: 20
1236397 AATTGGGAAA
*
1236407 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1236427 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1236448 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1236468 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1236488 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1236502 ATACATAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 46 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1236433 original size:41 final size:41
Alignment explanation
Indices: 1236326--1236418 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1236316 TTTTCCCAAT
*
1236326 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1236367 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
1236408 TCGCAATGCGA
1 TCGCAATGCGA
1236419 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACACGAATTGGGAAAA
Found at i:1236449 original size:41 final size:41
Alignment explanation
Indices: 1236404--1236481 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
1236394 ACGAATTGGG
* * *
1236404 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
* *
1236445 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
1236482 CTGACTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:1236717 original size:22 final size:22
Alignment explanation
Indices: 1236689--1236732 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1236679 CACTCTCTCA
1236689 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1236711 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1236733 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1237021 original size:20 final size:20
Alignment explanation
Indices: 1236996--1237033 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1236986 CGATTCTCTC
1236996 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1237016 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1237034 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Done.