Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007918.1 Hibiscus syriacus cultivar Beakdansim tig00110321_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: 2302251
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:1212094 original size:37 final size:37
Alignment explanation
Indices: 1212011--1212102 Score: 100
Period size: 37 Copynumber: 2.5 Consensus size: 37
1212001 AAAGAAAATA
* *
1212011 ATAAAGAAT-AAAAAAATAAATGAATAAAAAAATAAAG
1 ATAAA-AATGAAAAAAATAAATGAAAAAAAAAAGAAAG
*
1212048 ATAAAAATGAATAAAATAAATGAAAAATAAAGAAGAAA-
1 ATAAAAATGAAAAAAATAAATGAAAAA-AAA-AAGAAAG
*
1212086 A-AATAATGAAAAAAATA
1 ATAAAAATGAAAAAAATA
1212103 TAACAACTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
36 3 0.06
37 35 0.74
38 4 0.09
39 5 0.11
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (37 bp):
ATAAAAATGAAAAAAATAAATGAAAAAAAAAAGAAAG
Found at i:1212203 original size:25 final size:24
Alignment explanation
Indices: 1212170--1212240 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 24
1212160 TATAAGGGAG
*
1212170 ATAAGAAAATAAAAGTAAAGAATAA
1 ATAAAAAAATAAAAGTAAA-AATAA
*
1212195 ATAAAAAAA-CAAA-TAAAAATAA
1 ATAAAAAAATAAAAGTAAAAATAA
*
1212217 ATAAATAAATAAAATGTAAAAATA
1 ATAAAAAAATAAAA-GTAAAAATA
1212241 GTAGAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 13 0.33
23 7 0.18
24 3 0.08
25 16 0.41
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (24 bp):
ATAAAAAAATAAAAGTAAAAATAA
Found at i:1212214 original size:18 final size:18
Alignment explanation
Indices: 1212193--1212230 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1212183 AGTAAAGAAT
1212193 AAATAAAAAAACAAATAA
1 AAATAAAAAAACAAATAA
* *
1212211 AAATAAATAAATAAATAA
1 AAATAAAAAAACAAATAA
1212229 AA
1 AA
1212231 TGTAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (18 bp):
AAATAAAAAAACAAATAA
Found at i:1212280 original size:3 final size:3
Alignment explanation
Indices: 1212272--1212330 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
1212262 GTAACCATAG
1212272 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1212320 AAT AAC AAT AA
1 AAT AAT AAT AA
1212331 ACAAAGTAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1212398 original size:2 final size:2
Alignment explanation
Indices: 1212391--1212436 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1212381 ATAGAAAATA
*
1212391 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1212433 AT AT
1 AT AT
1212437 GTAATAATGA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1214222 original size:68 final size:66
Alignment explanation
Indices: 1214145--1214310 Score: 217
Period size: 65 Copynumber: 2.5 Consensus size: 66
1214135 GGTTTTTTTC
* * * *
1214145 TCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCATGTGAAAACATATTCAAAGATTGGT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTAAAG-GAAAACAGATTCAAAGATT-GT
1214210 GTT
64 GTT
* * * * *
1214213 TCAAAAGAAACTATCTCGAGAGAGACGAAA-TTTGTTTAAAGGAAAACAGATTCAAAGATTTTGT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTAAAGGAAAACAGATTCAAAGATTGTGT
1214277 T
66 T
*
1214278 TCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 TCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
1214311 GATTCAAGGG
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
65 29 0.35
66 20 0.24
67 9 0.11
68 25 0.30
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (66 bp):
TCAAGAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTAAAGGAAAACAGATTCAAAGATTGTGT
T
Found at i:1214300 original size:65 final size:66
Alignment explanation
Indices: 1214129--1214311 Score: 224
Period size: 68 Copynumber: 2.7 Consensus size: 66
1214119 AGAGAAACAT
* * * * *
1214129 TTCAAAGGTTTTTTTCTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCATGTGAAAAC
1 TTCAAAGATTTTGTT-TCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTAAAGTGAAAAC
*
1214194 ATA
64 AGA
* * * * *
1214197 TTCAAAGATTGGTGTTTCAAAAGAAACTATCTCGAGAGAGACGAAATTTGTTTAAAG-GAAAACA
1 TTCAAAGATT-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGTGAAAACA
1214261 GA
65 GA
*
1214263 TTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
1214312 ATTCAAGGGA
Statistics
Matches: 97, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
65 33 0.34
66 18 0.19
67 9 0.09
68 34 0.35
69 3 0.03
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (66 bp):
TTCAAAGATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAGTGAAAACAG
A
Found at i:1214329 original size:36 final size:36
Alignment explanation
Indices: 1214272--1214593 Score: 288
Period size: 36 Copynumber: 9.2 Consensus size: 36
1214262 ATTCAAAGAT
1214272 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
1214308 TTTGATTCAAGGGAAATTGTCTCAAGAGATACAAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
1214344 TTT-ATT-AAGAGAAACTGTCTAAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * ***
1214378 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACGGTA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** *
1214415 TTTGTTTCAAGGAAAACAGAGTC-A-A-AG----AT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1214444 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
1214480 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1214516 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGAC-AAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1214551 TTT-TTTTAAGAGAAATTGTCTTAAGAGAGACCAAAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-CAAAA
1214587 TTTGTTT
1 TTTGTTT
1214594 TGAGTAAATT
Statistics
Matches: 230, Mismatches: 43, Indels: 25
0.77 0.14 0.08
Matches are distributed among these distances:
29 19 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 2 0.01
34 47 0.20
35 13 0.06
36 120 0.52
37 25 0.11
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:1214503 original size:172 final size:174
Alignment explanation
Indices: 1214214--1214550 Score: 516
Period size: 172 Copynumber: 1.9 Consensus size: 174
1214204 ATTGGTGTTT
* *
1214214 CAAAAGAAACTATCTCGAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTT
1 CAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGAGTCAAAGATTTTGTTT
* * * *
1214279 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGGGAAATTGTCTCAAGAGATACAAGA
66 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGAGAAAATGTCTCAAGAGAGACAAAA
1214344 -TT-TATTAAGAGAAACTGTCTAAAGAGAGACAAAACTTAGTTC
131 TTTGTATTAAGAGAAACTGTCTAAAGAGAGACAAAACTTAGTTC
* * ** *
1214386 CAAAAGAAACTGTCTCAAGGGAGACGGTATTTGTTTCAAGGAAAACAGAGTCAAAGATTTTGTTT
1 CAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGAGTCAAAGATTTTGTTT
* *
1214451 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
66 CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGAGAAAATGTCTCAAGAGAGACAAAA
* * *
1214516 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAA
131 TTTGTATTAAGAGAAACTGTCTAAAGAGAGACAAA
1214551 TTTTTTTAAG
Statistics
Matches: 147, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
172 117 0.80
173 2 0.01
174 28 0.19
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (174 bp):
CAAAAGAAACTATCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGAGTCAAAGATTTTGTTT
CAAGGGAAACTGTCTCAAGAGAGACAAAATTTGATTCAAGAGAAAATGTCTCAAGAGAGACAAAA
TTTGTATTAAGAGAAACTGTCTAAAGAGAGACAAAACTTAGTTC
Found at i:1220155 original size:13 final size:12
Alignment explanation
Indices: 1220120--1220171 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 12
1220110 GATAAAAAAT
*
1220120 GAAAATAATAAA
1 GAAAGTAATAAA
1220132 GAAAGTAATAAA
1 GAAAGTAATAAA
1220144 CGAAAG-ACATAAA
1 -GAAAGTA-ATAAA
1220157 GGAAA-TAATAAA
1 -GAAAGTAATAAA
1220169 GAA
1 GAA
1220172 TAAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 3 0.09
12 17 0.49
13 15 0.43
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.13
Consensus pattern (12 bp):
GAAAGTAATAAA
Found at i:1220216 original size:16 final size:15
Alignment explanation
Indices: 1220163--1220208 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
1220153 TAAAGGAAAT
1220163 AATAAAGAATAAAAA
1 AATAAAGAATAAAAA
1220178 AATAAATGAATAAAAA
1 AATAAA-GAATAAAAA
1220194 AAGTAAAG-ATAAAAA
1 AA-TAAAGAATAAAAA
1220209 TGAATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.45
16 12 0.41
17 4 0.14
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (15 bp):
AATAAAGAATAAAAA
Found at i:1220229 original size:20 final size:19
Alignment explanation
Indices: 1220204--1220241 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1220194 AAGTAAAGAT
*
1220204 AAAAATGAATAAAATAAATG
1 AAAAATGAAGAAAA-AAATG
1220224 AAAAATGAAGAAAAAAAT
1 AAAAATGAAGAAAAAAAT
1220242 AATGAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (19 bp):
AAAAATGAAGAAAAAAATG
Found at i:1220272 original size:44 final size:44
Alignment explanation
Indices: 1220159--1220272 Score: 110
Period size: 44 Copynumber: 2.5 Consensus size: 44
1220149 GACATAAAGG
* *
1220159 AAATAATA-AAGAATAAAAAAATAAATGAATAAAAAAAGTAAAGAT
1 AAATAATATAA-AATAAATAAA-AAATGAAGAAAAAAAGTAAAGAT
* *
1220204 AAA-AATGAATAAAATAAATGAAAAATGAAGAAAAAAA-TAATGA-
1 AAATAAT--ATAAAATAAATAAAAAATGAAGAAAAAAAGTAAAGAT
1220247 AAATAATATAACAACTAAATAAAAAA
1 AAATAATATAA-AA-TAAATAAAAAA
1220273 AATAAGAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 13
0.76 0.07 0.17
Matches are distributed among these distances:
42 4 0.07
43 5 0.09
44 21 0.36
45 17 0.29
46 9 0.16
47 2 0.03
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (44 bp):
AAATAATATAAAATAAATAAAAAATGAAGAAAAAAAGTAAAGAT
Found at i:1220392 original size:25 final size:23
Alignment explanation
Indices: 1220321--1220396 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 23
1220311 TATATAAGGA
1220321 AAATAAGAAAATAAAAGTAAAGAAT
1 AAATAA-AAAATAAAAGTAAA-AAT
* *
1220346 AAATAAAAAGAAAACAAATAAAAAT
1 AAATAAAAA-ATAA-AAGTAAAAAT
1220371 AAATAAATAAATAAAATGTAAAAAT
1 AAATAAA-AAATAAAA-GTAAAAAT
1220396 A
1 A
1220397 GTAGAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 5 0.12
25 30 0.70
26 8 0.19
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (23 bp):
AAATAAAAAATAAAAGTAAAAAT
Found at i:1220627 original size:20 final size:20
Alignment explanation
Indices: 1220591--1220628 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1220581 CGTGATATGC
1220591 ATAAAAAATAATAAAAATAA
1 ATAAAAAATAATAAAAATAA
*
1220611 ATAAATAAA-AATTAAAAT
1 ATAAA-AAATAATAAAAAT
1220629 TTAAAACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.81
21 3 0.19
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAAAAATAATAAAAATAA
Found at i:1226710 original size:24 final size:26
Alignment explanation
Indices: 1226659--1226713 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1226649 TCATGGACAC
*
1226659 TCTCTCCTCTTCAAACTCCATCGCCT
1 TCTCTCCTCTACAAACTCCATCGCCT
* *
1226685 TCTCTCCTCTAC-CACTGCATCG-CT
1 TCTCTCCTCTACAAACTCCATCGCCT
1226709 TCTCT
1 TCTCT
1226714 TCATCGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 7 0.27
25 8 0.31
26 11 0.42
ACGTcount: A:0.13, C:0.45, G:0.05, T:0.36
Consensus pattern (26 bp):
TCTCTCCTCTACAAACTCCATCGCCT
Found at i:1237311 original size:206 final size:207
Alignment explanation
Indices: 1236957--1237370 Score: 812
Period size: 206 Copynumber: 2.0 Consensus size: 207
1236947 ATCAATATCT
1236957 TAAGTAAATTCTGCAAAAAGTTCGGGATTTTATTCATACAACGCTATCATACTGAGGAGTTTCAT
1 TAAGTAAATTCTGCAAAAAGTTCGGGATTTTATTCATACAACGCTATCATACTGAGGAGTTTCAT
1237022 AGATGGTAATATCCATGGTTTCTCCCAACAGAGGAATGGGGGAATTCCTGTTACTAAGTTAAGTT
66 AGATGGTAATATCCATGGTTTCTCCCAACAGAGGAATGGGGGAATTCCTGTTACTAAGTTAAGTT
1237087 TACGGTGCAGCTGATTTGCAGCCCCCATGTTTGCATTTACATGAAGGTTCTTG-TTTTATTCTTC
131 TACGGTGCAGCTGATTTGCAGCCCCCATGTTTGCATTTACATGAAGGTTCTTGTTTTTATTCTTC
1237151 AACTCATCTCCA
196 AACTCATCTCCA
1237163 TAAGTAAATTCTGCAAAAAGTTCGGGATTTTATTCATACAACGCTATCATACTGAGGAGTTTCAT
1 TAAGTAAATTCTGCAAAAAGTTCGGGATTTTATTCATACAACGCTATCATACTGAGGAGTTTCAT
1237228 AGATGGTAATATCCATGGTTTCTCCCAACAGAGGAATGGGGGAATTCCTGTTACTAAGTTAAGTT
66 AGATGGTAATATCCATGGTTTCTCCCAACAGAGGAATGGGGGAATTCCTGTTACTAAGTTAAGTT
1237293 TACGGTGCAGCTGATTTGCAGCCCCCATGTTTGCATTTACATGAAGGTTCTTGTTTTTTATTCTT
131 TACGGTGCAGCTGATTTGCAGCCCCCATGTTTGCATTTACATGAAGGTTCTTG-TTTTTATTCTT
1237358 CAACTCATCTCCA
195 CAACTCATCTCCA
1237371 GCCACAAGAA
Statistics
Matches: 206, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
206 183 0.89
208 23 0.11
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (207 bp):
TAAGTAAATTCTGCAAAAAGTTCGGGATTTTATTCATACAACGCTATCATACTGAGGAGTTTCAT
AGATGGTAATATCCATGGTTTCTCCCAACAGAGGAATGGGGGAATTCCTGTTACTAAGTTAAGTT
TACGGTGCAGCTGATTTGCAGCCCCCATGTTTGCATTTACATGAAGGTTCTTGTTTTTATTCTTC
AACTCATCTCCA
Found at i:1239458 original size:19 final size:20
Alignment explanation
Indices: 1239421--1239459 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1239411 TTGATGATGA
**
1239421 TTTTATTATGTAATTATAAT
1 TTTTATTATGTAAAAATAAT
1239441 TTTTATTAT-TAAAAATAAT
1 TTTTATTATGTAAAAATAAT
1239460 ATATAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTATTATGTAAAAATAAT
Found at i:1240790 original size:32 final size:31
Alignment explanation
Indices: 1240744--1240809 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
1240734 TATCAAATTA
*
1240744 TATCTTTTAATTTTTAATGGTAAATTATACTT
1 TATCTTTTAATTTTTAATGATAAATTATA-TT
* *
1240776 TATCATTTT-ATTTTTTATGATTAATTATATT
1 TATC-TTTTAATTTTTAATGATAAATTATATT
1240807 TAT
1 TAT
1240810 TTGAACTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 5 0.17
32 21 0.70
33 4 0.13
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (31 bp):
TATCTTTTAATTTTTAATGATAAATTATATT
Found at i:1243474 original size:13 final size:13
Alignment explanation
Indices: 1243456--1243480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1243446 TTGGTATATT
1243456 TTTTTAAAAGTGA
1 TTTTTAAAAGTGA
1243469 TTTTTAAAAGTG
1 TTTTTAAAAGTG
1243481 CTATAGTAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTTAAAAGTGA
Found at i:1243713 original size:20 final size:21
Alignment explanation
Indices: 1243667--1243713 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 21
1243657 ATTTTATTGC
*
1243667 TTTTAATTAATTAAAATAAAT
1 TTTTAAATAATTAAAATAAAT
* * *
1243688 TATTAAATAA-TAAATTAGAT
1 TTTTAAATAATTAAAATAAAT
1243708 TTTTAA
1 TTTTAA
1243714 GGATGTTAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTTTAAATAATTAAAATAAAT
Found at i:1245798 original size:10 final size:10
Alignment explanation
Indices: 1245778--1245832 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
1245768 ATAAAAAATC
1245778 AATAA-ATTT
1 AATAATATTT
1245787 AATAATATTT
1 AATAATATTT
*
1245797 AATGATATTT
1 AATAATATTT
* *
1245807 TATAATCGTTT
1 AATAAT-ATTT
*
1245818 GATAAT-TTT
1 AATAATATTT
1245827 AATAAT
1 AATAAT
1245833 TATTCTATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
9 13 0.34
10 17 0.45
11 8 0.21
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (10 bp):
AATAATATTT
Found at i:1255372 original size:11 final size:11
Alignment explanation
Indices: 1255356--1255383 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1255346 TAAAGTCATA
1255356 TGCTCCAAGAT
1 TGCTCCAAGAT
1255367 TGCTCCAAGAT
1 TGCTCCAAGAT
1255378 TGCTCC
1 TGCTCC
1255384 CTCTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.32, G:0.18, T:0.29
Consensus pattern (11 bp):
TGCTCCAAGAT
Found at i:1256755 original size:16 final size:16
Alignment explanation
Indices: 1256734--1256766 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1256724 TTCAATTATC
1256734 CTTTTACAGGTTATAG
1 CTTTTACAGGTTATAG
1256750 CTTTTACAGGTTATAG
1 CTTTTACAGGTTATAG
1256766 C
1 C
1256767 AAGTCATGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.42
Consensus pattern (16 bp):
CTTTTACAGGTTATAG
Found at i:1260162 original size:122 final size:122
Alignment explanation
Indices: 1259913--1260140 Score: 395
Period size: 122 Copynumber: 1.9 Consensus size: 122
1259903 AGTTTTCTGC
1259913 AAAATTTAAAAACCCAATATTAAGTATATATATTTTTTGTTTTTTTTTTTGGGGGGGGGGGTTGG
1 AAAATTTAAAAACCCAATATTAAGTATATATATTTTTTG-TTTTTTTTTTGGGGGGGGGGGTTGG
*** *
1259978 CAGAGGGCTTCATAATCATAAAGAATTATGAATTTGAGTGTCACCAAAAGTTTTCTGC
65 CAGAGGGCTTCATAATCATAAAGAATTATGAATTTGAGTGTCACCAAAAGTACGCTGA
1260036 AAAATTTAAAAACCCAATATTAAGTATATATATTTTTTG-TTTTTTTTTGGGGGGGTGGGGTTGG
1 AAAATTTAAAAACCCAATATTAAGTATATATATTTTTTGTTTTTTTTTTGGGGGGG-GGGGTTGG
1260100 CAGAGGGCTTCATAATCATAAAGAATTATGAATTTGAGTGT
65 CAGAGGGCTTCATAATCATAAAGAATTATGAATTTGAGTGT
1260141 GATGCACTGA
Statistics
Matches: 104, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
121 16 0.15
122 49 0.47
123 39 0.38
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (122 bp):
AAAATTTAAAAACCCAATATTAAGTATATATATTTTTTGTTTTTTTTTTGGGGGGGGGGGTTGGC
AGAGGGCTTCATAATCATAAAGAATTATGAATTTGAGTGTCACCAAAAGTACGCTGA
Found at i:1264448 original size:16 final size:16
Alignment explanation
Indices: 1264427--1264461 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1264417 ATATTAATTT
*
1264427 ATATCTAACGTAAATA
1 ATATCTAACATAAATA
1264443 ATATCTAACATAAATA
1 ATATCTAACATAAATA
1264459 ATA
1 ATA
1264462 AATAATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.11, G:0.03, T:0.31
Consensus pattern (16 bp):
ATATCTAACATAAATA
Found at i:1266207 original size:43 final size:43
Alignment explanation
Indices: 1266159--1266245 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
1266149 CCCACGTAAA
1266159 TATATCAAAACAAATGCAATCATGTTAAGAGTGACAAACCTAT
1 TATATCAAAACAAATGCAATCATGTTAAGAGTGACAAACCTAT
*
1266202 TATATCGAAACAAATGCAATCATGTTAAGAGTGACAAACCTAT
1 TATATCAAAACAAATGCAATCATGTTAAGAGTGACAAACCTAT
1266245 T
1 T
1266246 GGCTATGTTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.26
Consensus pattern (43 bp):
TATATCAAAACAAATGCAATCATGTTAAGAGTGACAAACCTAT
Found at i:1267392 original size:25 final size:24
Alignment explanation
Indices: 1267359--1267405 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1267349 TCTATTTATT
*
1267359 TATAATTAATTTTAATCATAATTG
1 TATAATTAATTATAATCATAATTG
*
1267383 TATATATTAATTATAATTATAAT
1 TATA-ATTAATTATAATCATAAT
1267406 CAAATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 4 0.20
25 16 0.80
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATAATTAATTATAATCATAATTG
Found at i:1292598 original size:14 final size:14
Alignment explanation
Indices: 1292577--1292615 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1292567 CGCTGGGCAT
1292577 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1292591 CTGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
1292605 CCGAGGTCATC
1 CCGAGGCCATC
1292616 TGAGAGCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.21, C:0.38, G:0.28, T:0.13
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:1292644 original size:14 final size:14
Alignment explanation
Indices: 1292625--1292657 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1292615 CTGAGAGCAT
1292625 CCGAGGTCATCCGA
1 CCGAGGTCATCCGA
1292639 CCGAGGTCATCCGA
1 CCGAGGTCATCCGA
*
1292653 ACGAG
1 CCGAG
1292658 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.33, G:0.30, T:0.12
Consensus pattern (14 bp):
CCGAGGTCATCCGA
Found at i:1292686 original size:33 final size:33
Alignment explanation
Indices: 1292638--1292711 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
1292628 AGGTCATCCG
* * *
1292638 ACCGAGGTCATCCGAACGAGCTATGCGAGGGCA
1 ACCGAGGGCAACCGAACGAGCTATGCGAGGGAA
*
1292671 TCCGAGGGCAACCGAACGAGCTATGCGAGGGAA
1 ACCGAGGGCAACCGAACGAGCTATGCGAGGGAA
1292704 ACCGAGGG
1 ACCGAGGG
1292712 AAGCCGAGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.26, G:0.36, T:0.09
Consensus pattern (33 bp):
ACCGAGGGCAACCGAACGAGCTATGCGAGGGAA
Found at i:1292828 original size:12 final size:12
Alignment explanation
Indices: 1292811--1292835 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1292801 TGCCATGCAA
1292811 CACGTTCATTCT
1 CACGTTCATTCT
1292823 CACGTTCATTCT
1 CACGTTCATTCT
1292835 C
1 C
1292836 TCTGTTTGAA
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (12 bp):
CACGTTCATTCT
Found at i:1292895 original size:29 final size:29
Alignment explanation
Indices: 1292853--1292909 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
1292843 GAATAATGGT
*
1292853 AGGTCGTCCGGAGTGCATGGCGACCTACA
1 AGGTCGTCCGGAGTGCATAGCGACCTACA
1292882 AGGTCG-CCTGGAGTGCATAGCGACCTAC
1 AGGTCGTCC-GGAGTGCATAGCGACCTAC
1292910 GGCCAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.18
Consensus pattern (29 bp):
AGGTCGTCCGGAGTGCATAGCGACCTACA
Found at i:1309685 original size:21 final size:21
Alignment explanation
Indices: 1309632--1309688 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1309622 CATATGAAAT
* *
1309632 TTGTCCCGAAGAACCACTGTA
1 TTGTCCCGAAGGACCACTATA
*
1309653 TTGTCCTGAAGGACCACTATA
1 TTGTCCCGAAGGACCACTATA
1309674 TTGTCCCGAAGGACC
1 TTGTCCCGAAGGACC
1309689 TATGAAACCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (21 bp):
TTGTCCCGAAGGACCACTATA
Found at i:1318809 original size:83 final size:83
Alignment explanation
Indices: 1318670--1318836 Score: 334
Period size: 83 Copynumber: 2.0 Consensus size: 83
1318660 GACTTTTTGG
1318670 CAGCCCACATTTAATGTCTTTCCTCTCTAAGGAAAGTCTTGATAGTTGTATATTATCACCAACTC
1 CAGCCCACATTTAATGTCTTTCCTCTCTAAGGAAAGTCTTGATAGTTGTATATTATCACCAACTC
1318735 CTCCAGAACCATAAAAAA
66 CTCCAGAACCATAAAAAA
1318753 CAGCCCACATTTAATGTCTTTCCTCTCTAAGGAAAGTCTTGATAGTTGTATATTATCACCAACTC
1 CAGCCCACATTTAATGTCTTTCCTCTCTAAGGAAAGTCTTGATAGTTGTATATTATCACCAACTC
1318818 CTCCAGAACCATAAAAAA
66 CTCCAGAACCATAAAAAA
1318836 C
1 C
1318837 TCCCTGGTCA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 84 1.00
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.30
Consensus pattern (83 bp):
CAGCCCACATTTAATGTCTTTCCTCTCTAAGGAAAGTCTTGATAGTTGTATATTATCACCAACTC
CTCCAGAACCATAAAAAA
Found at i:1319618 original size:21 final size:21
Alignment explanation
Indices: 1319594--1319646 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
1319584 TTTCCCCCAT
1319594 TGCATCTCTATGTGACATCAA
1 TGCATCTCTATGTGACATCAA
1319615 TGCATCTCTATGTGACATCAA
1 TGCATCTCTATGTGACATCAA
1319636 TGCATCTCTAT
1 TGCATCTCTAT
1319647 AAGTTCTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (21 bp):
TGCATCTCTATGTGACATCAA
Found at i:1325184 original size:42 final size:42
Alignment explanation
Indices: 1325125--1325248 Score: 191
Period size: 42 Copynumber: 3.0 Consensus size: 42
1325115 AAAAGGAGCA
*
1325125 GGGGGTGCAGATGATGAACCAGTTGTGGGTGGTGGTGGTGGT
1 GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGTGGTGGT
1325167 GGGGGTGCTGATGATGAACCAGTTGT--G-GGTGGTGGTGGT
1 GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGTGGTGGT
* * *
1325206 GGGGGTGTTGTTGATGAACCAGTTGTGGGTGGTGGTGGGGGT
1 GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGTGGTGGT
1325248 G
1 G
1325249 CAGATGATGG
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
39 36 0.48
40 1 0.01
41 1 0.01
42 37 0.49
ACGTcount: A:0.12, C:0.06, G:0.53, T:0.28
Consensus pattern (42 bp):
GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGTGGTGGT
Found at i:1325237 original size:36 final size:36
Alignment explanation
Indices: 1325125--1325353 Score: 228
Period size: 36 Copynumber: 6.1 Consensus size: 36
1325115 AAAAGGAGCA
*
1325125 GGGGGTGCAGATGATGAACCAGTTGTGGGTGGTGGTGGTGGT
1 GGGGGTGCTGATGATGAACCAG-T-T--GT-G-GGTGGTGGT
1325167 GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGTGGT
1 GGGGGTGCTGATGATGAACCAGTTGT--G-GGTGGTGGT
* *
1325206 GGGGGTGTTGTTGATGAACCAGTTGTGGGTGGTGGT
1 GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGT
* *
1325242 GGGGGTGCAGATGATGGACCAGTTAGT-GGTGGTGGT
1 GGGGGTGCTGATGATGAACCAGTT-GTGGGTGGTGGT
* * * * * *
1325278 GAGGATGCAGATGATGAAACAATTGAGGGTGGTGGT
1 GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGT
* *
1325314 GGGGGTGCTGATGATGAAACAATTG-GGGTTGGTGGT
1 GGGGGTGCTGATGATGAACCAGTTGTGGG-TGGTGGT
1325350 GGGG
1 GGGG
1325354 ATGGTGCGGG
Statistics
Matches: 167, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
35 4 0.02
36 99 0.59
37 3 0.02
38 2 0.01
39 36 0.22
40 1 0.01
41 1 0.01
42 21 0.13
ACGTcount: A:0.17, C:0.07, G:0.50, T:0.27
Consensus pattern (36 bp):
GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGT
Found at i:1325351 original size:42 final size:39
Alignment explanation
Indices: 1325125--1325383 Score: 194
Period size: 36 Copynumber: 6.6 Consensus size: 39
1325115 AAAAGGAGCA
*
1325125 GGGGGTGCAGATGATGAACCAGTTGTGGGTGGTGGTGGTGGT
1 GGGGGTGCAGATGATGAAACAGTTGT---TGGTGGTGGTGGT
* * *
1325167 GGGGGTGCTGATGATGAACCAGTTGTGGGTGGTGGTGGT
1 GGGGGTGCAGATGATGAAACAGTTGTTGGTGGTGGTGGT
** * *
1325206 GGGGGTGTTGTTGATGAACCAGTTG-T-G-GGTGGTGGT
1 GGGGGTGCAGATGATGAAACAGTTGTTGGTGGTGGTGGT
* * *
1325242 GGGGGTGCAGATGATGGACCA---GTTAGTGGTGGTGGT
1 GGGGGTGCAGATGATGAAACAGTTGTTGGTGGTGGTGGT
* * * *
1325278 GAGGATGCAGATGATGAAACAATTG--AG-GGTGGTGGT
1 GGGGGTGCAGATGATGAAACAGTTGTTGGTGGTGGTGGT
* *
1325314 GGGGGTGCTGATGATGAAACAATTGGGGTTGGTGGTGGGGATGGT
1 GGGGGTGCAGATGATGAAACAGTT---GTTGGTGGT--GG-TGGT
* * *
1325359 GCGGGTGGAGACGATGAAACAGTTG
1 GGGGGTGCAGATGATGAAACAGTTG
1325384 GGTGAGGTTG
Statistics
Matches: 180, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
33 1 0.01
34 1 0.01
35 1 0.01
36 82 0.46
37 3 0.02
39 37 0.21
41 1 0.01
42 29 0.16
44 2 0.01
45 23 0.13
ACGTcount: A:0.18, C:0.07, G:0.49, T:0.26
Consensus pattern (39 bp):
GGGGGTGCAGATGATGAAACAGTTGTTGGTGGTGGTGGT
Found at i:1325534 original size:45 final size:45
Alignment explanation
Indices: 1325479--1325593 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
1325469 TGGTAGTGAG
1325479 GGTGCTGATGATGAAACAATTGGGGCTTGT-AGTGGCGGTGGTACA
1 GGTGCTGATGATGAAACAATTGGGGCTTGTGA-TGGCGGTGGTACA
* * * *
1325524 GGTGCTGATGATGGAACAATTAGGGCTTGTGATGGGGGTGGTGCA
1 GGTGCTGATGATGAAACAATTGGGGCTTGTGATGGCGGTGGTACA
* * *
1325569 GGTGTTGATAATGAAACAGTTGGGG
1 GGTGCTGATGATGAAACAATTGGGG
1325594 GTGATAGTGG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
45 59 0.98
46 1 0.02
ACGTcount: A:0.23, C:0.09, G:0.42, T:0.27
Consensus pattern (45 bp):
GGTGCTGATGATGAAACAATTGGGGCTTGTGATGGCGGTGGTACA
Found at i:1328908 original size:21 final size:21
Alignment explanation
Indices: 1328884--1328933 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1328874 ATATATAATA
* *
1328884 TTAATATGTATAGATGTGATT
1 TTAATATGCATAGATGTGATG
* *
1328905 TTAACATGCATAGCTGTGATG
1 TTAATATGCATAGATGTGATG
1328926 TTAATATG
1 TTAATATG
1328934 AAGAGACATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (21 bp):
TTAATATGCATAGATGTGATG
Found at i:1328968 original size:21 final size:21
Alignment explanation
Indices: 1328919--1329011 Score: 73
Period size: 21 Copynumber: 4.4 Consensus size: 21
1328909 CATGCATAGC
* *
1328919 TGTGATGTTAATATGAAGAGA
1 TGTGATATTAATATAAAGAGA
** *
1328940 CATAATATTAATATAAAGAGA
1 TGTGATATTAATATAAAGAGA
*
1328961 TGTGATATTAACATGAAA-A-A
1 TGTGATATTAATAT-AAAGAGA
* *
1328981 TTGTGATATTAATATGAAGGGA
1 -TGTGATATTAATATAAAGAGA
*
1329003 TATGATATT
1 TGTGATATT
1329012 TGCACGAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
20 3 0.05
21 48 0.87
22 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.19, T:0.34
Consensus pattern (21 bp):
TGTGATATTAATATAAAGAGA
Found at i:1329011 original size:63 final size:63
Alignment explanation
Indices: 1328876--1329011 Score: 164
Period size: 63 Copynumber: 2.2 Consensus size: 63
1328866 ATATAAATAT
** * * * * * *
1328876 ATATAATATTAATATGTATAGATGTGATTTTAACATGCATAGCTGTGATGTTAATATGAAGAG
1 ATATAATATTAATATAAAGAGATGTGATATTAACATGAAAAACTGTGATATTAATATGAAGAG
* * *
1328939 ACATAATATTAATATAAAGAGATGTGATATTAACATGAAAAATTGTGATATTAATATGAAGGG
1 ATATAATATTAATATAAAGAGATGTGATATTAACATGAAAAACTGTGATATTAATATGAAGAG
*
1329002 ATATGATATT
1 ATATAATATT
1329012 TGCACGAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.43, C:0.04, G:0.18, T:0.36
Consensus pattern (63 bp):
ATATAATATTAATATAAAGAGATGTGATATTAACATGAAAAACTGTGATATTAATATGAAGAG
Found at i:1329021 original size:42 final size:42
Alignment explanation
Indices: 1328944--1329038 Score: 102
Period size: 42 Copynumber: 2.3 Consensus size: 42
1328934 AAGAGACATA
* * * *
1328944 ATATTAATATAAAGAGATGTGATATTAACATGAAAAATTGTG
1 ATATTAATATGAAGAGATATGATATTAACACGAAAAATTATG
* ** *
1328986 ATATTAATATGAAGGGATATGATATTTGCACGAAAAGTTATG
1 ATATTAATATGAAGAGATATGATATTAACACGAAAAATTATG
*
1329028 ATGTT-ATATGA
1 ATATTAATATGA
1329039 TTTCAACATG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
41 6 0.14
42 38 0.86
ACGTcount: A:0.43, C:0.03, G:0.19, T:0.35
Consensus pattern (42 bp):
ATATTAATATGAAGAGATATGATATTAACACGAAAAATTATG
Found at i:1329113 original size:21 final size:21
Alignment explanation
Indices: 1329099--1329198 Score: 69
Period size: 21 Copynumber: 4.8 Consensus size: 21
1329089 TGAAGAATTG
1329099 TGATATTAACATGAAGAGATA
1 TGATATTAACATGAAGAGATA
* ** *
1329120 TGATGTTAACATGATTAGATT
1 TGATATTAACATGAAGAGATA
* * * *
1329141 TGATATTTATATAAAGAGATG
1 TGATATTAACATGAAGAGATA
* * *
1329162 T-ATATTAATACGAAGAGACAA
1 TGATATTAACATGAAGAGA-TA
*
1329183 T-ATATTAACACGAAGA
1 TGATATTAACATGAAGA
1329199 ATTATAACAT
Statistics
Matches: 61, Mismatches: 17, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 14 0.23
21 47 0.77
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (21 bp):
TGATATTAACATGAAGAGATA
Found at i:1331415 original size:21 final size:22
Alignment explanation
Indices: 1331367--1331425 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
1331357 TTTTATTAGA
1331367 TTATATAAAATTAATTTAAATG
1 TTATATAAAATTAATTTAAATG
* * *
1331389 TT-TATAAATTTAATTT-ATTT
1 TTATATAAAATTAATTTAAATG
1331409 TTATATAATAATTAATT
1 TTATATAA-AATTAATT
1331426 AATAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 18 0.58
22 9 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
TTATATAAAATTAATTTAAATG
Found at i:1331443 original size:40 final size:42
Alignment explanation
Indices: 1331367--1331451 Score: 104
Period size: 40 Copynumber: 2.1 Consensus size: 42
1331357 TTTTATTAGA
** * *
1331367 TTATATAAAATTAATTTAAATGTTTATAAATTTAATTTATTT
1 TTATATAAAATTAATTTAAATAATTATAAATATAATTTAGTT
1331409 TTATATAATAATTAA-TT-AATAATT-TAAATATAATTTAGTT
1 TTATATAA-AATTAATTTAAATAATTATAAATATAATTTAGTT
1331449 TTA
1 TTA
1331452 GAATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 17 0.45
41 5 0.13
42 10 0.26
43 6 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (42 bp):
TTATATAAAATTAATTTAAATAATTATAAATATAATTTAGTT
Found at i:1331544 original size:2 final size:2
Alignment explanation
Indices: 1331532--1331582 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1331522 AAATAAATCG
*
1331532 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1331574 TA TA TA TA T
1 TA TA TA TA T
1331583 TCACATGAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1331639 original size:12 final size:13
Alignment explanation
Indices: 1331612--1331637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1331602 ATTTTTTATA
1331612 GAAAAAATGGTGG
1 GAAAAAATGGTGG
1331625 GAAAAAATGGTGG
1 GAAAAAATGGTGG
1331638 AAGACTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (13 bp):
GAAAAAATGGTGG
Found at i:1331968 original size:17 final size:18
Alignment explanation
Indices: 1331946--1331983 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
1331936 TGTGCATAAT
*
1331946 TACTTTTTA-TATATATA
1 TACTTTATACTATATATA
1331963 TACTTTATACTTATATATA
1 TACTTTATAC-TATATATA
1331982 TA
1 TA
1331984 TATAAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.55
Consensus pattern (18 bp):
TACTTTATACTATATATA
Found at i:1332086 original size:2 final size:2
Alignment explanation
Indices: 1332075--1332298 Score: 123
Period size: 2 Copynumber: 113.0 Consensus size: 2
1332065 TTCATCATAC
*
1332075 AT AT -T AT AT AT AT AT AT AT -T AT A- AGT AT A- AT GT AT ACT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT
* * * *
1332114 AT AT -T AT AT ACT -T AT AT A- AGT AT AT AC GT AT A- AT GT AT AC
1 AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
1332154 AT A- AGT AT A- AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1332195 AT AT AT AT AT AT AT AT AT TT AT AGT TT AT AGT TT AT AT ACT TT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT
* * * *
1332238 AT AC AT AT ACT AT AT A- AT TT AT AT -T GT AT AT GT AT ACT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
1332280 ACT TT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT
1332299 TGTCGCAACC
Statistics
Matches: 169, Mismatches: 29, Indels: 48
0.69 0.12 0.20
Matches are distributed among these distances:
1 13 0.08
2 143 0.85
3 13 0.08
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1332878 original size:26 final size:25
Alignment explanation
Indices: 1332849--1332970 Score: 76
Period size: 26 Copynumber: 4.7 Consensus size: 25
1332839 AACTAAAAAT
1332849 ATAATGAAAATAAATAAATAGTATAA
1 ATAAT-AAAATAAATAAATAGTATAA
*
1332875 ATAA-AATAATAAA-AATATA-TATAT
1 ATAATAA-AATAAATAA-ATAGTATAA
*
1332899 ATATATAAATATAAA-AATGTATGTATAA
1 ATA-ATAAA-ATAAATAA-ATA-GTATAA
*
1332927 TATAATAAAAT-ACTAAATAGTA-ATA
1 -ATAATAAAATAAATAAATAGTATA-A
1332952 ATAATAATAAATAAATAAA
1 ATAAT-A-AAATAAATAAA
1332971 AAATAAATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
24 17 0.22
25 16 0.21
26 23 0.30
27 9 0.12
28 9 0.12
29 3 0.04
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (25 bp):
ATAATAAAATAAATAAATAGTATAA
Found at i:1332890 original size:31 final size:32
Alignment explanation
Indices: 1332849--1333228 Score: 95
Period size: 30 Copynumber: 12.2 Consensus size: 32
1332839 AACTAAAAAT
*
1332849 ATAATGAAAATA-A-ATAAATAGTATAAATAAA
1 ATAATAAAAATATATATAAATA-TATAAATAAA
1332880 ATAATAAAAATATATAT--ATATAT--AT-AA
1 ATAATAAAAATATATATAAATATATAAATAAA
* * *
1332907 AT-ATAAAAATGTATGTATA-ATAT-AATAAA
1 ATAATAAAAATATATATAAATATATAAATAAA
* * *
1332936 ATACTAAATAGTA-ATAATAATAATAAATAAATAAA
1 ATAATAAA-AATATAT-AT-A-AATATATAAATAAA
* *
1332971 A-AATAAATATACT-TAT-AATAT-TAACTAAA
1 ATAATAAAAATA-TATATAAATATATAAATAAA
* ** *
1333000 AAAATAGTAAT-CATATAAATATA-AAATAAA
1 ATAATAAAAATATATATAAATATATAAATAAA
* *
1333030 ATAAAGTAAGAATATATATATATAACGT-TAGAAA-AAT
1 AT-AA-TAA-AA-ATATATATA-AA--TATATAAATAAA
* * * *
1333067 ATAATAAAAACATA-GTAAATA-AGTAAACATAG
1 ATAATAAAAATATATATAAATATA-TAAATA-AA
* * *
1333099 ATAA-AAAAATA-ATATATATATATATATATA
1 ATAATAAAAATATATATAAATATATAAATAAA
*
1333129 ATAATAGGAAAATA-ATAT-AATATAACGTAAAGAAA
1 ATAATA--AAAATATATATAAATAT-A--TAAATAAA
* * *
1333164 A-AATAAAAAAATTTAT-AATAAATAAAT-AA
1 ATAATAAAAATATATATAAATATATAAATAAA
* *
1333193 AT-A-AAATATA-AT-TAAATATATACATATAA
1 ATAATAAAAATATATATAAATATATAAATA-AA
1333222 ATAATAA
1 ATAATAA
1333229 GGGTTCAATT
Statistics
Matches: 254, Mismatches: 48, Indels: 94
0.64 0.12 0.24
Matches are distributed among these distances:
26 13 0.05
27 18 0.07
28 10 0.04
29 25 0.10
30 44 0.17
31 40 0.16
32 22 0.09
33 30 0.12
34 17 0.07
35 21 0.08
36 4 0.02
37 6 0.02
38 4 0.02
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (32 bp):
ATAATAAAAATATATATAAATATATAAATAAA
Found at i:1333184 original size:96 final size:100
Alignment explanation
Indices: 1333043--1333228 Score: 217
Period size: 96 Copynumber: 1.9 Consensus size: 100
1333033 AAGTAAGAAT
* * *
1333043 ATATATATATAACGTTAGAAAAATATAATAAAAACATAGTAAATAAGTAAACATAGATAAAA-A-
1 ATATATATATAACGTAAGAAAAATATAATAAAAACATAGTAAATAAAT-AA-ATAAATAAAATAT
* *
1333106 AA-TAATATATATATATATATATAATAATAGGAAAATA
64 AATTAA-ATATATACATATAAATAATAATAGGAAAATA
**
1333143 ATATA-ATATAACGTAAAGAAAAA-ATAA-AAAAATTTA-T-AATAAATAAATAAATAAAATATA
1 ATATATATATAACGT-AAGAAAAATATAATAAAAACATAGTAAATAAATAAATAAATAAAATATA
1333203 ATTAAATATATACATATAAATAATAA
65 ATTAAATATATACATATAAATAATAA
1333229 GGGTTCAATT
Statistics
Matches: 75, Mismatches: 7, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
94 9 0.12
95 3 0.04
96 27 0.36
97 4 0.05
98 7 0.09
99 13 0.17
100 12 0.16
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (100 bp):
ATATATATATAACGTAAGAAAAATATAATAAAAACATAGTAAATAAATAAATAAATAAAATATAA
TTAAATATATACATATAAATAATAATAGGAAAATA
Found at i:1333203 original size:19 final size:18
Alignment explanation
Indices: 1333181--1333225 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1333171 AAAATTTATA
1333181 ATAAATAAATAAATAAAAT
1 ATAAATAAATAAAT-AAAT
* * *
1333200 ATAATTAAATATATACAT
1 ATAAATAAATAAATAAAT
1333218 ATAAATAA
1 ATAAATAA
1333226 TAAGGGTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAATAAATAAATAAAT
Found at i:1333442 original size:20 final size:21
Alignment explanation
Indices: 1333417--1333463 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1333407 TCGCATTGCG
*
1333417 ATGCGAA-TAAGTAAATCGCA
1 ATGCGAATTAAGAAAATCGCA
**
1333437 ATGCGAATTTGGAAAATCGCA
1 ATGCGAATTAAGAAAATCGCA
1333458 ATGCGA
1 ATGCGA
1333464 TACTGACTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (21 bp):
ATGCGAATTAAGAAAATCGCA
Found at i:1333463 original size:41 final size:41
Alignment explanation
Indices: 1333417--1333625 Score: 128
Period size: 41 Copynumber: 5.1 Consensus size: 41
1333407 TCGCATTGCG
* **
1333417 ATGCGAATAAGTAAATCGCAATGCGAATTTGGAAAATCGCA
1 ATGCGAATACGTAAATCGCAATGCGAATTTACAAAATCGCA
* * * * *
1333458 ATGCG-ATAC-TGACTATCGTAATGC-AATTTTCCTAATTCGCA
1 ATGCGAATACGT-A-AATCGCAATGCGAA-TTTACAAAATCGCA
* * * ** * *
1333499 TTGCGATTTACGT-ATTCGCGTTGCG-ATTTTCATAATTCGCA
1 ATGCGA-ATACGTAAATCGCAATGCGAATTTACA-AAATCGCA
* * **
1333540 ATGCGAATACGTAAATCGCAACGCG-ATTAAGTAAATCGCA
1 ATGCGAATACGTAAATCGCAATGCGAATTTACAAAATCGCA
*
1333580 ATGCGAATACGTAAATCGCAATGCGAATCTTAC--TATCGCA
1 ATGCGAATACGTAAATCGCAATGCGAAT-TTACAAAATCGCA
1333620 ATGCGA
1 ATGCGA
1333626 TTTACATAGC
Statistics
Matches: 126, Mismatches: 31, Indels: 23
0.70 0.17 0.13
Matches are distributed among these distances:
39 1 0.01
40 58 0.46
41 61 0.48
42 2 0.02
43 3 0.02
44 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (41 bp):
ATGCGAATACGTAAATCGCAATGCGAATTTACAAAATCGCA
Found at i:1333538 original size:21 final size:21
Alignment explanation
Indices: 1333483--1333545 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 21
1333473 TCGTAATGCA
*
1333483 ATTTTCCTAATTCGCATTGCG
1 ATTTTCATAATTCGCATTGCG
* * *
1333504 ATTTACGT-ATTCGCGTTGCG
1 ATTTTCATAATTCGCATTGCG
*
1333524 ATTTTCATAATTCGCAATGCG
1 ATTTTCATAATTCGCATTGCG
1333545 A
1 A
1333546 ATACGTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 17 0.50
21 17 0.50
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTTTCATAATTCGCATTGCG
Found at i:1333560 original size:20 final size:20
Alignment explanation
Indices: 1333535--1333625 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
1333525 TTTTCATAAT
1333535 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1333555 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
1333575 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1333595 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
1333615 TCGCAATGCGA
1 TCGCAATGCGA
1333626 TTTACATAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
19 3 0.05
20 59 0.95
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1334310 original size:20 final size:19
Alignment explanation
Indices: 1334202--1334333 Score: 139
Period size: 19 Copynumber: 7.1 Consensus size: 19
1334192 GAAACCAAAA
*
1334202 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1334221 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1334240 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1334259 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1334273 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1334292 TCCGCGTTTCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
1334312 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1334332 TC
1 TC
1334334 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
14 10 0.11
16 2 0.02
17 2 0.02
19 49 0.52
20 30 0.32
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1337902 original size:14 final size:14
Alignment explanation
Indices: 1337883--1337918 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1337873 ATTGTTTAAT
1337883 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1337897 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1337911 TGATTTGT
1 TGATTTGT
1337919 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:1338047 original size:19 final size:19
Alignment explanation
Indices: 1338025--1338116 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
1338015 AAAAATTACT
1338025 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1338044 ATCGCAA--CG--AT-ATA
1 ATCGCAATGCGAAATGAAA
1338058 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1338077 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1338091 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
1338110 ATCGCAA
1 ATCGCAA
1338117 CGACAAAATC
Statistics
Matches: 58, Mismatches: 5, Indels: 20
0.70 0.06 0.24
Matches are distributed among these distances:
14 19 0.33
15 3 0.05
16 4 0.07
17 4 0.07
18 3 0.05
19 25 0.43
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1338067 original size:33 final size:33
Alignment explanation
Indices: 1338025--1338150 Score: 182
Period size: 33 Copynumber: 3.8 Consensus size: 33
1338015 AAAAATTACT
* *
1338025 ATCGCAATGCGAAATGAAAATCGCAACGATATA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
1338058 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1338091 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1338124 ATCGCAACGCGAAACT-AAAATCGCAAC
1 ATCGCAATGCGAAA-TGAAAATCGCAAC
1338151 ACGAAACTAA
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1338145 original size:19 final size:19
Alignment explanation
Indices: 1338090--1338166 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
1338080 GCAACGAGAG
*
1338090 AATCGCAATGCGAAA-TAAA
1 AATCGCAACGCGAAACT-AA
1338109 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
1338123 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
1338142 AATCGCAACACGAAACTAA
1 AATCGCAACGCGAAACTAA
*
1338161 ATTCGC
1 AATCGC
1338167 GTTGCGATTT
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 33 0.66
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:1338208 original size:33 final size:33
Alignment explanation
Indices: 1338166--1338292 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
1338156 ACTAAATTCG
* * *
1338166 CGTTGCGATTTTCATTCCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1338199 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
1338232 CGTTACGATTTTCATTTCGCATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1338265 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1338293 AGTAATTTCT
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1338225 original size:19 final size:19
Alignment explanation
Indices: 1338201--1338292 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
1338191 GATTCCCTCG
1338201 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1338220 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1338234 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1338253 TTGCGA--TT-ATCTCG--
1 TTGCGATTTTCATTTCGCA
1338267 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1338286 TTGCGAT
1 TTGCGAT
1338293 AGTAATTTCT
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 11 0.19
16 14 0.25
17 14 0.25
19 18 0.32
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1338358 original size:20 final size:20
Alignment explanation
Indices: 1338286--1338358 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 20
1338276 TCATTTCGCA
* * *
1338286 TTGCGATAGTAATTTCTGCG
1 TTGCGATAGTCATTTCAGTG
* *
1338306 TTGCGATAGACA-TTAAGATG
1 TTGCGATAGTCATTTCAG-TG
*
1338326 ATTGCGA-ATGTCATTTCCGTG
1 -TTGCGATA-GTCATTTCAGTG
1338347 TTGCGATAGTCA
1 TTGCGATAGTCA
1338359 AATGATTGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
19 3 0.08
20 22 0.55
21 12 0.30
22 3 0.08
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCATTTCAGTG
Found at i:1340638 original size:12 final size:12
Alignment explanation
Indices: 1340621--1340657 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1340611 TCTTCGGGGA
1340621 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1340633 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1340645 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1340657 C
1 C
1340658 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1340866 original size:24 final size:24
Alignment explanation
Indices: 1340832--1340885 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1340822 CTGAAACATC
*
1340832 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1340856 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1340880 ATCAAA
1 ATCAAA
1340886 TTTCAAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1341713 original size:21 final size:20
Alignment explanation
Indices: 1341670--1341723 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1341660 TTTTCCTAAT
*
1341670 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
**
1341690 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
1341711 TCGCAATGC-AATA
1 TCGCAATGCGAATA
1341724 CTGACTATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 14 0.48
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1342016 original size:20 final size:20
Alignment explanation
Indices: 1341991--1342058 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1341981 CAACGGGTAA
1341991 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* ***
1342011 ATCGCAATGC-AAAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
1342031 AGCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
1342051 ATCGCAAC
1 ATCGCAAC
1342059 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 6 0.17
20 24 0.67
21 6 0.17
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:1342071 original size:34 final size:34
Alignment explanation
Indices: 1341975--1342078 Score: 100
Period size: 40 Copynumber: 2.9 Consensus size: 34
1341965 ATTCATTTGA
** *
1341975 CTATCGCAACGGGTAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
*
1342009 CTATCGCAATGCAAAATGAAAAAGCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
1342049 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
1342079 TGAAAATCGC
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
34 24 0.42
35 1 0.02
36 2 0.04
38 1 0.02
39 1 0.02
40 28 0.49
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.14
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:1342126 original size:19 final size:19
Alignment explanation
Indices: 1342085--1342152 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
1342075 GAAATGAAAA
1342085 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1342101 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1342118 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1342137 TCGCATTGTGATTTTC
1 TCGCATTGCGATTTTC
1342153 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.49
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1343790 original size:41 final size:42
Alignment explanation
Indices: 1343736--1343827 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
1343726 CCTCTTCAAC
*
1343736 GATGACAGTGGCCTCTTGAACG-GTGG-GTGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAG-GGGACTCTTGAGG
* *
1343777 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
1343819 GATGACAGG
1 GATGACAGG
1343828 TGAGTCGGGC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 20 0.44
42 24 0.53
43 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.41, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:1343794 original size:21 final size:21
Alignment explanation
Indices: 1343764--1343823 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1343754 AACGGTGGGT
*
1343764 GGGACTCTTGAGGGATGATAG
1 GGGACTCTTGAGGGATGAGAG
* **
1343785 GGGCCTCTTGAACGATTG-GAG
1 GGGACTCTTGAGGGA-TGAGAG
1343806 GGGACTCTTGAGGGATGA
1 GGGACTCTTGAGGGATGA
1343824 CAGGTGAGTC
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.22, C:0.13, G:0.42, T:0.23
Consensus pattern (21 bp):
GGGACTCTTGAGGGATGAGAG
Found at i:1344245 original size:20 final size:20
Alignment explanation
Indices: 1344170--1344281 Score: 136
Period size: 20 Copynumber: 5.7 Consensus size: 20
1344160 TAGTTTACTT
* * * *
1344170 TCGCAACACGAAACTTACTT
1 TCGCAACGCGAAAATGACTA
1344190 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
1344210 TCGCAACGCGGAAATGACTA
1 TCGCAACGCGAAAATGACTA
*
1344230 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGAAAATGACTA
* **
1344250 TCGCAATGCG-AAATGAAAA
1 TCGCAACGCGAAAATGACTA
1344269 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1344282 TAAAAATCGC
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
19 15 0.19
20 64 0.81
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:1344298 original size:19 final size:19
Alignment explanation
Indices: 1344249--1344298 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
1344239 GAAAATGGCT
*
1344249 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATAAAA
*
1344268 ATCGCAACGCGAAATAAAA
1 ATCGCAATGCGAAATAAAA
*
1344287 ATCGCATTGCGA
1 ATCGCAATGCGA
1344299 TTTGTGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATAAAA
Found at i:1344329 original size:14 final size:14
Alignment explanation
Indices: 1344310--1344368 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
1344300 TTGTGTTTCG
1344310 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1344324 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
*
1344341 CGCATTGCAATTTTGT
1 CG--TTGCGATTTTGT
1344357 CGTTGCGATTTT
1 CGTTGCGATTTT
1344369 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 5 0.14
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1344342 original size:33 final size:33
Alignment explanation
Indices: 1344305--1344384 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
1344295 GCGATTTGTG
*
1344305 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
*
1344338 TTTCGCATTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1344371 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1344385 AGTCATTTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1344353 original size:19 final size:19
Alignment explanation
Indices: 1344326--1344404 Score: 69
Period size: 19 Copynumber: 4.4 Consensus size: 19
1344316 GATTTTGTCG
1344326 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1344345 TTGC-AATTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
1344359 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
1344378 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
1344398 TTGCGAT
1 TTGCGAT
1344405 AGTCATTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.09
15 4 0.09
16 4 0.09
17 4 0.09
18 4 0.09
19 17 0.36
20 10 0.21
ACGTcount: A:0.15, C:0.20, G:0.20, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1344421 original size:20 final size:20
Alignment explanation
Indices: 1344357--1344412 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
1344347 GCAATTTTGT
**
1344357 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
1344376 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
1344396 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
1344413 TCGTGTTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1346649 original size:22 final size:22
Alignment explanation
Indices: 1346622--1346665 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1346612 GATGGAGATA
*
1346622 GACGGATTTTGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1346644 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1346666 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:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1346886 original size:20 final size:21
Alignment explanation
Indices: 1346858--1346924 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
1346848 GTATTATCTC
*
1346858 GTTGCGAAAGTCAA-TATTGA
1 GTTGCGAAAGTCAAGTATCGA
* *
1346878 GTTGTGAAA-TTAAGTATCGA
1 GTTGCGAAAGTCAAGTATCGA
*
1346898 GTTGCGAAAGTC-AGTATCGC
1 GTTGCGAAAGTCAAGTATCGA
1346918 GTTGCGA
1 GTTGCGA
1346925 TTTTGTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.08
20 35 0.90
21 1 0.03
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (21 bp):
GTTGCGAAAGTCAAGTATCGA
Found at i:1346951 original size:41 final size:41
Alignment explanation
Indices: 1346832--1346969 Score: 152
Period size: 41 Copynumber: 3.4 Consensus size: 41
1346822 CGCTTTGAAA
* * * *
1346832 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAAT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * * ** * * *
1346873 ATTGAGTTGTGAAATT-AAGTATCGAGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
1346913 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1346954 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
1346970 CCAAATTCGC
Statistics
Matches: 75, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
40 30 0.40
41 45 0.60
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1346958 original size:20 final size:20
Alignment explanation
Indices: 1346890--1346966 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
1346880 TGTGAAATTA
* *
1346890 AGTATCGAGTTGCGAAAGTC
1 AGTATCGCGTTGCGATAGTC
*
1346910 AGTATCGCGTTGCGATTTTGT-
1 AGTATCGCGTTGCGA--TAGTC
*
1346931 ATTATCGCGTTGCGATAGTC
1 AGTATCGCGTTGCGATAGTC
1346951 AGTATCGCGTTGCGAT
1 AGTATCGCGTTGCGAT
1346967 TTTCCAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.06
20 29 0.60
21 14 0.29
22 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.29, T:0.34
Consensus pattern (20 bp):
AGTATCGCGTTGCGATAGTC
Found at i:1346987 original size:21 final size:21
Alignment explanation
Indices: 1346963--1347010 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
1346953 TATCGCGTTG
1346963 CGATTTTCCAAATTCGCATTA
1 CGATTTTCCAAATTCGCATTA
*
1346984 CGATTTTCCAAATTCGCATTG
1 CGATTTTCCAAATTCGCATTA
1347005 CGATTT
1 CGATTT
1347011 ACTTTTTCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (21 bp):
CGATTTTCCAAATTCGCATTA
Found at i:1347069 original size:21 final size:22
Alignment explanation
Indices: 1347017--1347069 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1347007 ATTTACTTTT
1347017 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1347038 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1347059 TCGCATTGCGA
1 TCGCATTGCGA
1347070 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1347651 original size:37 final size:37
Alignment explanation
Indices: 1347610--1347702 Score: 114
Period size: 37 Copynumber: 2.5 Consensus size: 37
1347600 ATGCTTGTGG
* * *
1347610 ATCATATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTAAATAATAGCAAAACTCT
* ** *
1347647 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCATATTTTTAGGAGTTTAAATAATAGCAAAACTCT
*
1347684 ATCATATTTTTAGAAGTTT
1 ATCATATTTTTAGGAGTTT
1347703 TGAATCATAG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTAAATAATAGCAAAACTCT
Found at i:1356778 original size:31 final size:30
Alignment explanation
Indices: 1356732--1356810 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 30
1356722 TTCGATAATA
*
1356732 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
1356763 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
1356794 TAATAAGTATTTTATAA
1 TAATAA-TATTTTATAA
1356811 CTTTTTTAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 35 0.85
32 5 0.12
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:1357571 original size:19 final size:19
Alignment explanation
Indices: 1357549--1357636 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 19
1357539 AAAGTTTAAA
1357549 AAATTATAAAATATTTATT
1 AAATTATAAAATATTTATT
* *
1357568 AAATTTATTAAAAGA-TTATA
1 AAA-TTA-TAAAATATTTATT
1357588 AAATTATTAATAA-ATTTATCT
1 AAATTA-TAA-AATATTTAT-T
*
1357609 AAATACTATAAAATAATTATT
1 AAAT--TATAAAATATTTATT
*
1357630 ATATTAT
1 AAATTAT
1357637 CGAACTTTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
19 14 0.25
20 16 0.29
21 16 0.29
22 8 0.14
23 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (19 bp):
AAATTATAAAATATTTATT
Found at i:1357579 original size:31 final size:31
Alignment explanation
Indices: 1357544--1357630 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
1357534 TCAATAAAGT
1357544 TTAAAAAATTATAAAATATTTATTAAATTTA
1 TTAAAAAATTATAAAATATTTATTAAATTTA
* *
1357575 TTAAAAGATTATAAAAT-TATTAATAAATTTA
1 TTAAAAAATTATAAAATAT-TTATTAAATTTA
* * *
1357606 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAATATTTATTA
1357631 TATTATCGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
30 1 0.02
31 45 0.96
32 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (31 bp):
TTAAAAAATTATAAAATATTTATTAAATTTA
Found at i:1357606 original size:20 final size:20
Alignment explanation
Indices: 1357539--1357606 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
1357529 TTTCGTCAAT
*
1357539 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* *
1357557 AAATATTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
1357578 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
1357597 ATAA-ATTTAT
1 A-AAGATTTAT
1357607 CTAAATACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
18 3 0.08
19 16 0.40
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:1361536 original size:13 final size:12
Alignment explanation
Indices: 1361518--1361578 Score: 56
Period size: 11 Copynumber: 5.1 Consensus size: 12
1361508 ATTCGAGATA
1361518 AATTAAAATTTAT
1 AATTAAAA-TTAT
*
1361531 AATT-AAATTAA
1 AATTAAAATTAT
*
1361542 AATTTATAATTA-
1 AA-TTAAAATTAT
1361554 AATTAAAATTTAT
1 AATTAAAA-TTAT
1361567 AATT-AAATTAT
1 AATTAAAATTAT
1361578 A
1 A
1361579 TCACAAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
11 15 0.37
12 13 0.32
13 13 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATTAAAATTAT
Found at i:1361539 original size:18 final size:18
Alignment explanation
Indices: 1361516--1361576 Score: 122
Period size: 18 Copynumber: 3.4 Consensus size: 18
1361506 TGATTCGAGA
1361516 TAAATTAAAATTTATAAT
1 TAAATTAAAATTTATAAT
1361534 TAAATTAAAATTTATAAT
1 TAAATTAAAATTTATAAT
1361552 TAAATTAAAATTTATAAT
1 TAAATTAAAATTTATAAT
1361570 TAAATTA
1 TAAATTA
1361577 TATCACAAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTAAAATTTATAAT
Found at i:1367365 original size:46 final size:45
Alignment explanation
Indices: 1367281--1367379 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 45
1367271 TTACGTTTCA
* * *
1367281 TAAATCATGCTCCTGATGATCTTAATTTATGCAGTTTTCATCAAAT
1 TAAA-CATGCTCCTGATGATCCTAATTGATGCAATTTTCATCAAAT
*
1367327 TAAACATGCTCCTGGA-GATCCTAACTTGATGCAATTTTCATTAAAT
1 TAAACATGCTCCT-GATGATCCTAA-TTGATGCAATTTTCATCAAAT
*
1367373 AAAACAT
1 TAAACAT
1367380 CAGTCTGTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 16 0.35
46 30 0.65
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (45 bp):
TAAACATGCTCCTGATGATCCTAATTGATGCAATTTTCATCAAAT
Found at i:1370843 original size:15 final size:15
Alignment explanation
Indices: 1370817--1370861 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
1370807 TAATTTTTCA
1370817 AAATATTATATATTTT
1 AAATA-TATATATTTT
1370833 AAATATATATATTTT
1 AAATATATATATTTT
*
1370848 TAATA-ATATATTTT
1 AAATATATATATTTT
1370862 TATCTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
14 9 0.32
15 14 0.50
16 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATATATATATTTT
Found at i:1370855 original size:18 final size:17
Alignment explanation
Indices: 1370809--1370858 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
1370799 TCTTTTTTTA
1370809 ATTTTTCAAAATAT-TAT
1 ATTTTT-AAAATATATAT
1370826 ATATTTT-AAATATATAT
1 AT-TTTTAAAATATATAT
1370843 ATTTTTAATAATATAT
1 ATTTTTAA-AATATAT
1370859 TTTTATCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.34
17 8 0.28
18 11 0.38
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTAAAATATATAT
Found at i:1377348 original size:31 final size:31
Alignment explanation
Indices: 1377307--1377400 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
1377297 AGGGTCTAGG
*
1377307 GTTTATCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1377338 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1377369 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1377400 G
1 G
1377401 GTCCTTCGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1379166 original size:22 final size:23
Alignment explanation
Indices: 1379141--1379189 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
1379131 TTTTCCAAAT
1379141 TGCTAACAGGGAACCGATT-CCC
1 TGCTAACAGGGAACCGATTCCCC
*
1379163 TGCT-ACAGGGTACCGATTCCCC
1 TGCTAACAGGGAACCGATTCCCC
1379185 TGCTA
1 TGCTA
1379190 CAGTACTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (23 bp):
TGCTAACAGGGAACCGATTCCCC
Found at i:1379171 original size:21 final size:22
Alignment explanation
Indices: 1379141--1379192 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
1379131 TTTTCCAAAT
1379141 TGCTAACAGGGAACCGATT-CCC
1 TGCT-ACAGGGAACCGATTCCCC
*
1379163 TGCTACAGGGTACCGATTCCCC
1 TGCTACAGGGAACCGATTCCCC
1379185 TGCTACAG
1 TGCTACAG
1379193 TACTTCCGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.21
Consensus pattern (22 bp):
TGCTACAGGGAACCGATTCCCC
Found at i:1379778 original size:21 final size:21
Alignment explanation
Indices: 1379729--1379792 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
1379719 ATATGAAATT
* *
1379729 TTGTCCCAAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
1379750 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
1379772 TTGTCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
1379793 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:1380333 original size:18 final size:18
Alignment explanation
Indices: 1380303--1380345 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1380293 CCCCAGGGGT
*
1380303 ATCTGTACTCTCTGCATA
1 ATCTGTACCCTCTGCATA
*
1380321 ATTTGTACCCTCTGCATA
1 ATCTGTACCCTCTGCATA
1380339 ATCTGTA
1 ATCTGTA
1380346 ATTTTACCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.40
Consensus pattern (18 bp):
ATCTGTACCCTCTGCATA
Found at i:1394397 original size:17 final size:17
Alignment explanation
Indices: 1394370--1394418 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
1394360 ATTCACTAAC
1394370 AAGTT-GAAAACGGAAT
1 AAGTTAGAAAACGGAAT
1394386 AAGTTAGAAAACGGAAT
1 AAGTTAGAAAACGGAAT
1394403 AAGTTAGAAAACGGAA
1 AAGTTAGAAAACGGAA
1394419 AGAGAGGTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.16
Consensus pattern (17 bp):
AAGTTAGAAAACGGAAT
Found at i:1405296 original size:19 final size:20
Alignment explanation
Indices: 1405261--1405301 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
1405251 CTCTCGCACA
1405261 CTATCTTATAATTTTTTTTGT
1 CTATCTTAT-ATTTTTTTTGT
1405282 CTATCTTAT-TTTTTTTTGT
1 CTATCTTATATTTTTTTTGT
1405301 C
1 C
1405302 CATCACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
21 9 0.45
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (20 bp):
CTATCTTATATTTTTTTTGT
Found at i:1405494 original size:29 final size:29
Alignment explanation
Indices: 1405441--1405499 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 29
1405431 ATTGTCGAGA
1405441 TAAATATTAAAATTATATATGAATTTTAAT
1 TAAATATTAAAATTATATA-GAATTTTAAT
*
1405471 TAAATATATAATATTATATA-AATTTTAAT
1 TAAATAT-TAAAATTATATAGAATTTTAAT
1405500 ATTCTATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 9 0.33
30 7 0.26
31 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TAAATATTAAAATTATATAGAATTTTAAT
Found at i:1411274 original size:16 final size:17
Alignment explanation
Indices: 1411253--1411307 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
1411243 AAGAGCCCCA
1411253 GGGTGACACTT-TTGAG
1 GGGTGACACTTATTGAG
1411269 GGGTGACACTTGTATT-AG
1 GGGTGACAC-T-TATTGAG
* *
1411287 AGGTGATACTTATTGAG
1 GGGTGACACTTATTGAG
1411304 GGGT
1 GGGT
1411308 TGCTTGGGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
16 13 0.41
17 7 0.22
18 10 0.31
19 2 0.06
ACGTcount: A:0.22, C:0.09, G:0.36, T:0.33
Consensus pattern (17 bp):
GGGTGACACTTATTGAG
Found at i:1411357 original size:49 final size:49
Alignment explanation
Indices: 1411300--1411394 Score: 163
Period size: 49 Copynumber: 1.9 Consensus size: 49
1411290 TGATACTTAT
** *
1411300 TGAGGGGTTGCTTGGGATACCCGGGGCACCATGGAGGTCCGCCCCTAGA
1 TGAGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCGCCCCTAGA
1411349 TGAGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCGCCCCT
1 TGAGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCGCCCCT
1411395 GCTTAAGAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.15, C:0.31, G:0.38, T:0.17
Consensus pattern (49 bp):
TGAGGGGTTGCCCGGGATACCCCGGGCACCATGGAGGTCCGCCCCTAGA
Found at i:1411555 original size:25 final size:24
Alignment explanation
Indices: 1411527--1411581 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
1411517 GTTGTTTTTG
1411527 TTATCTGTCTTTATCTC-TAACTTAA
1 TTATCTGT-TTTATCTCATAA-TTAA
* * *
1411552 TTATATGTTTTATTTCATAATTTA
1 TTATCTGTTTTATCTCATAATTAA
1411576 TTATCT
1 TTATCT
1411582 TTTCCAGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.25, C:0.13, G:0.04, T:0.58
Consensus pattern (24 bp):
TTATCTGTTTTATCTCATAATTAA
Found at i:1414376 original size:2 final size:2
Alignment explanation
Indices: 1414369--1414406 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1414359 TTAATTTTAA
1414369 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
1414407 TAATATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1416253 original size:3 final size:3
Alignment explanation
Indices: 1416240--1416315 Score: 86
Period size: 3 Copynumber: 25.3 Consensus size: 3
1416230 GTCCGGGTCT
*
1416240 TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTT TTA
1 TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
*
1416287 -TA TT- TATA TTA TTA TT- TTA TTA ATA TTA T
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T
1416316 ATTTTTACAT
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.08
3 51 0.81
4 7 0.11
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1416296 original size:14 final size:13
Alignment explanation
Indices: 1416240--1416306 Score: 59
Period size: 13 Copynumber: 4.9 Consensus size: 13
1416230 GTCCGGGTCT
1416240 TTATTA-TTTATTA
1 TTATTATTTTA-TA
1416253 TTATTATTATTATTA
1 TTATTATT-TTA-TA
1416268 TTTATTATTATTAT-
1 -TTATTATT-TTATA
1416282 TT-TTATATTTATA
1 TTATTAT-TTTATA
1416295 TTATTATTTTAT
1 TTATTATTTTAT
1416307 TAATATTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
12 8 0.17
13 16 0.33
14 5 0.10
15 7 0.15
16 12 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTATTTTATA
Found at i:1416318 original size:22 final size:22
Alignment explanation
Indices: 1416244--1416318 Score: 91
Period size: 22 Copynumber: 3.4 Consensus size: 22
1416234 GGGTCTTTAT
*
1416244 TATTTATTATTATTATTATTAT
1 TATTTATTATTATTATTATTAA
*
1416266 TATTTATTATTATTATT-TTTA
1 TATTTATTATTATTATTATTAA
1416287 TATTTA-TATTATTATTTTATTAA
1 TATTTATTATTATTA--TTATTAA
1416310 TATTATATT
1 TATT-TATT
1416319 TTTACATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
20 8 0.18
21 8 0.18
22 19 0.42
23 7 0.16
24 2 0.04
25 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTATTATTATTATTATTAA
Found at i:1418421 original size:22 final size:22
Alignment explanation
Indices: 1418396--1418439 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1418386 TCAAACGATG
*
1418396 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
1418418 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
1418440 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:1422859 original size:11 final size:11
Alignment explanation
Indices: 1422840--1422947 Score: 78
Period size: 11 Copynumber: 9.5 Consensus size: 11
1422830 AGATCCAATC
1422840 AAAAA-CAAAG
1 AAAAATCAAAG
1422850 AAAAATCAAAG
1 AAAAATCAAAG
*
1422861 AGAAAA-GAGCAAG
1 A-AAAATCA--AAG
*
1422874 AAAAAACAAAG
1 AAAAATCAAAG
* * *
1422885 AGAGAGCAGAAG
1 AAAAATCA-AAG
1422897 AAAAAATCAAAG
1 -AAAAATCAAAG
1422909 CAAAAA-CAAAG
1 -AAAAATCAAAG
1422920 AAAAATCAAAG
1 AAAAATCAAAG
*
1422931 CAAAAGTCAAAG
1 -AAAAATCAAAG
1422943 AAAAA
1 AAAAA
1422948 AAAGCAAAGA
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
10 10 0.13
11 29 0.37
12 29 0.37
13 10 0.13
ACGTcount: A:0.70, C:0.10, G:0.16, T:0.04
Consensus pattern (11 bp):
AAAAATCAAAG
Found at i:1422866 original size:23 final size:23
Alignment explanation
Indices: 1422840--1422947 Score: 89
Period size: 24 Copynumber: 4.7 Consensus size: 23
1422830 AGATCCAATC
1422840 AAAAACAAAGAAAAATCAAAGAG
1 AAAAACAAAGAAAAATCAAAGAG
*
1422863 AAAAGAGC-AAGAAAAAACAAAGAG
1 AAAA-A-CAAAGAAAAATCAAAGAG
* * *
1422887 -AGAGCAGAAGAAAAAATCAAAG-C
1 AAAAACA-AAG-AAAAATCAAAGAG
1422910 AAAAACAAAGAAAAATCAAAGCA-
1 AAAAACAAAGAAAAATCAAAG-AG
**
1422933 AAAGTCAAAGAAAAA
1 AAAAACAAAGAAAAA
1422948 AAAGCAAAGA
Statistics
Matches: 68, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
21 1 0.01
22 11 0.16
23 25 0.37
24 30 0.44
25 1 0.01
ACGTcount: A:0.70, C:0.10, G:0.16, T:0.04
Consensus pattern (23 bp):
AAAAACAAAGAAAAATCAAAGAG
Found at i:1422947 original size:24 final size:23
Alignment explanation
Indices: 1422839--1422948 Score: 95
Period size: 23 Copynumber: 4.7 Consensus size: 23
1422829 AAGATCCAAT
*
1422839 CAAAAACAAAG-AAAAATCAAAG
1 CAAAAGCAAAGAAAAAATCAAAG
*
1422861 AGAAAAG-AGCAAGAAAAAA-CAAAG
1 -CAAAAGCA--AAGAAAAAATCAAAG
*
1422885 -AGAGAGCAGAAGAAAAAATCAAAG
1 CA-AAAGCA-AAGAAAAAATCAAAG
*
1422909 CAAAAACAAAG-AAAAATCAAAG
1 CAAAAGCAAAGAAAAAATCAAAG
1422931 CAAAAGTCAAAGAAAAAA
1 CAAAAG-CAAAGAAAAAA
1422949 AAGCAAAGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
22 18 0.25
23 24 0.34
24 23 0.32
25 6 0.08
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.04
Consensus pattern (23 bp):
CAAAAGCAAAGAAAAAATCAAAG
Found at i:1422949 original size:35 final size:34
Alignment explanation
Indices: 1422840--1422948 Score: 121
Period size: 35 Copynumber: 3.1 Consensus size: 34
1422830 AGATCCAATC
*
1422840 AAAAACAAAGAAAAATCAAAGAGAAAAGAGC-AAGA
1 AAAAACAAAGAAAAATCAAAGA-AAAAG-TCAAAGA
* * * * *
1422875 AAAAACAAAGAGAGAGCAGAAGAAAAAATCAAAGC
1 AAAAACAAAGAAAAATCA-AAGAAAAAGTCAAAGA
*
1422910 AAAAACAAAGAAAAATCAAAGCAAAAGTCAAAGA
1 AAAAACAAAGAAAAATCAAAGAAAAAGTCAAAGA
1422944 AAAAA
1 AAAAA
1422949 AAGCAAAGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
34 19 0.32
35 37 0.62
36 4 0.07
ACGTcount: A:0.71, C:0.10, G:0.16, T:0.04
Consensus pattern (34 bp):
AAAAACAAAGAAAAATCAAAGAAAAAGTCAAAGA
Found at i:1422955 original size:14 final size:15
Alignment explanation
Indices: 1422932--1422965 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1422922 AAATCAAAGC
1422932 AAAAGTCAAAGAAAA
1 AAAAGTCAAAGAAAA
*
1422947 AAAAG-CAAAGAACA
1 AAAAGTCAAAGAAAA
1422961 AAAAG
1 AAAAG
1422966 AGGACAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAGTCAAAGAAAA
Found at i:1422962 original size:21 final size:21
Alignment explanation
Indices: 1422839--1422962 Score: 83
Period size: 22 Copynumber: 5.5 Consensus size: 21
1422829 AAGATCCAAT
1422839 CAAAAACAAAGAAAAATCAAAG
1 CAAAAACAAAGAAAAA-CAAAG
*
1422861 -AGAAAAGAGCAAGAAAAAACAAAG
1 CA-AAAACA--AAG-AAAAACAAAG
* *
1422885 -AGAGAGCAGAAGAAAAAATCAAAG
1 CA-AAAACA-AAG-AAAAA-CAAAG
1422909 CAAAAACAAAGAAAAATCAAAG
1 CAAAAACAAAGAAAAA-CAAAG
*
1422931 CAAAAGTCAAAGAAAAA-AAAG
1 CAAAA-ACAAAGAAAAACAAAG
1422952 CAAAGAACAAA
1 CAAA-AACAAA
1422963 AAGAGGACAA
Statistics
Matches: 85, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
21 13 0.15
22 22 0.26
23 22 0.26
24 22 0.26
25 6 0.07
ACGTcount: A:0.70, C:0.11, G:0.15, T:0.03
Consensus pattern (21 bp):
CAAAAACAAAGAAAAACAAAG
Found at i:1424164 original size:18 final size:16
Alignment explanation
Indices: 1424141--1424175 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
1424131 GATCGAGAGT
1424141 ACATACATACATATATAC
1 ACATACATA-ATA-ATAC
1424159 ACATACATAATAATAC
1 ACATACATAATAATAC
1424175 A
1 A
1424176 TAAAATTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (16 bp):
ACATACATAATAATAC
Done.