Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008798.1 Hibiscus syriacus cultivar Beakdansim tig00111947_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: 1825372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:1066117 original size:22 final size:21
Alignment explanation
Indices: 1066063--1066126 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
1066053 AGTCGAGGGT
*
1066063 TTCATAGGTCCTTCGAGACAA
1 TTCATAGGTCCTTCGGGACAA
*
1066084 CTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
* *
1066106 TTCACAGGTCCTTTGGGACAA
1 TTCATAGGTCCTTCGGGACAA
1066127 ATTTCATATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:1066674 original size:21 final size:21
Alignment explanation
Indices: 1066650--1066715 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
1066640 TTTACGAAAT
1066650 CACTGTAGTAGTGTATCGATG
1 CACTGTAGTAGTGTATCGATG
1066671 CACTGTAGTAGTGTATCGATG
1 CACTGTAGTAGTGTATCGATG
* * *
1066692 CACTGTAGCAGTGCATCCATG
1 CACTGTAGTAGTGTATCGATG
1066713 CAC
1 CAC
1066716 AATTTGTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (21 bp):
CACTGTAGTAGTGTATCGATG
Found at i:1066761 original size:20 final size:20
Alignment explanation
Indices: 1066736--1066776 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1066726 CGAAGTTTTT
*
1066736 ATGCATCGATGGACTCTAGC
1 ATGCATCGATGCACTCTAGC
*
1066756 ATGCATCGATGCACTGTAGC
1 ATGCATCGATGCACTCTAGC
1066776 A
1 A
1066777 AGTTACTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (20 bp):
ATGCATCGATGCACTCTAGC
Found at i:1071766 original size:27 final size:26
Alignment explanation
Indices: 1071729--1071779 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
1071719 CTAGAAGGTA
1071729 CTGACTAGATCTTCTAGAAAACTACTG
1 CTGACTAGATCTTCTAG-AAACTACTG
*
1071756 CTGACTGGATCTTCTAGAAACTAC
1 CTGACTAGATCTTCTAGAAACTAC
1071780 CACATCAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (26 bp):
CTGACTAGATCTTCTAGAAACTACTG
Found at i:1072929 original size:17 final size:17
Alignment explanation
Indices: 1072908--1072959 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1072898 TTTTTTAAAA
*
1072908 AAAAATATACAAACTATT
1 AAAATTATA-AAACTATT
*
1072926 AAAATTATAAAACTTTT
1 AAAATTATAAAACTATT
**
1072943 AAAAAGATAAAA-TATT
1 AAAATTATAAAACTATT
1072959 A
1 A
1072960 TTTAAAAGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 4 0.14
17 17 0.59
18 8 0.28
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAATTATAAAACTATT
Found at i:1073231 original size:20 final size:20
Alignment explanation
Indices: 1073208--1073252 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1073198 TTCCAATTTT
*
1073208 GCAACGCGAATCTGTAAATC
1 GCAACGCAAATCTGTAAATC
* *
1073228 GCAATGCAAATTTGTAAATC
1 GCAACGCAAATCTGTAAATC
1073248 GCAAC
1 GCAAC
1073253 ACAGAAGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
GCAACGCAAATCTGTAAATC
Found at i:1073269 original size:20 final size:20
Alignment explanation
Indices: 1073246--1073333 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
1073236 AATTTGTAAA
1073246 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
1073266 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* * *
1073286 TCACAACACTGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
* *
1073307 TTGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
1073327 TCGCAAC
1 TCGCAAC
1073334 GCGAAACACA
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
19 2 0.04
20 36 0.65
21 17 0.31
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.20
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:1073905 original size:19 final size:18
Alignment explanation
Indices: 1073862--1073908 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1073852 CAAAACATTT
1073862 GTGTTGCGAAACTAAAAC
1 GTGTTGCGAAACTAAAAC
* * *
1073880 ATGTTGCGAAATTAAATTC
1 GTGTTGCGAAACTAAA-AC
1073899 GTGTTGCGAA
1 GTGTTGCGAA
1073909 TTCGAAAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (18 bp):
GTGTTGCGAAACTAAAAC
Found at i:1073944 original size:19 final size:20
Alignment explanation
Indices: 1073902--1073952 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
1073892 TAAATTCGTG
* *
1073902 TTGCGAATTCGAAAATCTAG
1 TTGCGAATTTGAAAATCTAA
*
1073922 TTGCGAATTTGAAATTC-AA
1 TTGCGAATTTGAAAATCTAA
1073941 TTGCGAATTTGA
1 TTGCGAATTTGA
1073953 CTATCGCGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGCGAATTTGAAAATCTAA
Found at i:1074003 original size:20 final size:20
Alignment explanation
Indices: 1073980--1074026 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1073970 TGACTTCTGT
*
1073980 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCAC
* *
1074000 GTTGCGATTTATAGATTCAC
1 GTTGCGATTTACAAATTCAC
1074020 GTTGCGA
1 GTTGCGA
1074027 ATTTGGAAAA
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:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCAC
Found at i:1074931 original size:12 final size:12
Alignment explanation
Indices: 1074914--1074939 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1074904 TACCGGATCT
1074914 ACTAACATACCC
1 ACTAACATACCC
1074926 ACTAACATACCC
1 ACTAACATACCC
1074938 AC
1 AC
1074940 AGAAACAATC
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:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (12 bp):
ACTAACATACCC
Found at i:1078610 original size:101 final size:102
Alignment explanation
Indices: 1078453--1078661 Score: 330
Period size: 101 Copynumber: 2.0 Consensus size: 102
1078443 ACTATTTTTC
* * *
1078453 ATACTTTTGACAGCTTTTTCACCTTAAGCTAATATGTTAGTTAGTAAGTAAGTAAG-TAAATAAA
1 ATACTTTTGACAACTTTTTCACCTTAAGCTAATACGTTAGTTAGTAAGTAAATAAGATAAATAAA
*
1078517 TAAATAAGGCTTTATTAAAAAAATAAGTGTTTAAATT
66 TAAATAAGGCTTTATTAAAAAAATAAATGTTTAAATT
*
1078554 ATACTTTTGACAACTTTTTCACCTTACGCTAATACGTTAGTTAGTAAGTAAATAAGTAAATAAAT
1 ATACTTTTGACAACTTTTTCACCTTAAGCTAATACGTTAGTTAGTAAGTAAATAAG---ATAAAT
*
1078619 AAATAAATAAGGCTTTATTAGAAAAATAAATGTTTAAATT
63 AAATAAATAAGGCTTTATTAAAAAAATAAATGTTTAAATT
1078659 ATA
1 ATA
1078662 TCGTTTTTAT
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
101 52 0.53
105 46 0.47
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (102 bp):
ATACTTTTGACAACTTTTTCACCTTAAGCTAATACGTTAGTTAGTAAGTAAATAAGATAAATAAA
TAAATAAGGCTTTATTAAAAAAATAAATGTTTAAATT
Found at i:1078631 original size:105 final size:101
Alignment explanation
Indices: 1078453--1078661 Score: 328
Period size: 105 Copynumber: 2.0 Consensus size: 101
1078443 ACTATTTTTC
* * *
1078453 ATACTTTTGACAGCTTTTTCACCTTAAGCTAATATGTTAGTTAGTAAGTAAGTAAGTAAATAAAT
1 ATACTTTTGACAACTTTTTCACCTTAAGCTAATACGTTAGTTAGTAAGTAAGTAAATAAATAAAT
*
1078518 AAATAAGGCTTTATTAAAAAAATAAGTGTTTAAATT
66 AAATAAGGCTTTATTAAAAAAATAAATGTTTAAATT
*
1078554 ATACTTTTGACAACTTTTTCACCTTACGCTAATACGTTAGTTAGTAAGTAAATAAGTAAATAAAT
1 ATACTTTTGACAACTTTTTCACCTTAAGCTAATACGTTAGTTAGTAAG----TAAGTAAATAAAT
*
1078619 AAATAAATAAGGCTTTATTAGAAAAATAAATGTTTAAATT
62 AAATAAATAAGGCTTTATTAAAAAAATAAATGTTTAAATT
1078659 ATA
1 ATA
1078662 TCGTTTTTAT
Statistics
Matches: 98, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
101 45 0.46
105 53 0.54
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (101 bp):
ATACTTTTGACAACTTTTTCACCTTAAGCTAATACGTTAGTTAGTAAGTAAGTAAATAAATAAAT
AAATAAGGCTTTATTAAAAAAATAAATGTTTAAATT
Found at i:1080243 original size:25 final size:25
Alignment explanation
Indices: 1080213--1080262 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1080203 TTATTGTAAT
1080213 TTTGGATAATTCTTATTTTGAATAA
1 TTTGGATAATTCTTATTTTGAATAA
1080238 TTTGGATAATTCTTATTTTGAATAA
1 TTTGGATAATTCTTATTTTGAATAA
1080263 AATTAGTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.52
Consensus pattern (25 bp):
TTTGGATAATTCTTATTTTGAATAA
Found at i:1081287 original size:3 final size:3
Alignment explanation
Indices: 1081279--1081321 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1081269 TACCCAAAAA
1081279 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1081322 GAAATGAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1084022 original size:16 final size:16
Alignment explanation
Indices: 1084001--1084034 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1083991 TATTTGATTT
1084001 TTTTAAAACAAAAATA
1 TTTTAAAACAAAAATA
**
1084017 TTTTAAATTAAAAATA
1 TTTTAAAACAAAAATA
1084033 TT
1 TT
1084035 CAAAAAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTAAAACAAAAATA
Found at i:1084047 original size:23 final size:23
Alignment explanation
Indices: 1084019--1084087 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
1084009 CAAAAATATT
1084019 TTAAATTAAAAATATTCAAAAAA
1 TTAAATTAAAAATATTCAAAAAA
* *
1084042 TTAAATATAATAATA-T-GAAAAA
1 TTAAAT-TAAAAATATTCAAAAAA
* *
1084064 TAAAAATT-AAATTATTCAAAAAA
1 T-TAAATTAAAAATATTCAAAAAA
1084087 T
1 T
1084088 AAAAATATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 4 0.11
22 8 0.22
23 17 0.47
24 7 0.19
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (23 bp):
TTAAATTAAAAATATTCAAAAAA
Found at i:1084063 original size:24 final size:23
Alignment explanation
Indices: 1084019--1084063 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
1084009 CAAAAATATT
**
1084019 TTAAATTAAAAATATTCAAAAAA
1 TTAAATTAAAAATATGAAAAAAA
*
1084042 TTAAATATAATAATATGAAAAA
1 TTAAAT-TAAAAATATGAAAAA
1084064 TAAAAATTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 6 0.33
24 12 0.67
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (23 bp):
TTAAATTAAAAATATGAAAAAAA
Found at i:1084088 original size:23 final size:24
Alignment explanation
Indices: 1084059--1084103 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1084049 TAATAATATG
1084059 AAAAATAAAAAT-TAAATTATTCA
1 AAAAATAAAAATATAAATTATTCA
*
1084082 AAAAATAAAAATATATATTATT
1 AAAAATAAAAATATAAATTATT
1084104 ACTTTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
AAAAATAAAAATATAAATTATTCA
Found at i:1085634 original size:20 final size:20
Alignment explanation
Indices: 1085609--1085663 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
1085599 CCAAGGTCCC
1085609 AGTATCGATACTCCCATATG
1 AGTATCGATACTCCCATATG
1085629 AGTATCGATACTCCCATATG
1 AGTATCGATACTCCCATATG
1085649 AGTATCGATACTCCC
1 AGTATCGATACTCCC
1085664 CTCTTCTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTCCCATATG
Found at i:1091068 original size:13 final size:13
Alignment explanation
Indices: 1091050--1091074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1091040 ATAGTTGAAC
1091050 AGTCTTCATATGA
1 AGTCTTCATATGA
1091063 AGTCTTCATATG
1 AGTCTTCATATG
1091075 CAAATCTGTA
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:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (13 bp):
AGTCTTCATATGA
Found at i:1097619 original size:3 final size:3
Alignment explanation
Indices: 1097611--1097643 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1097601 CGTCTTTTAA
1097611 TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
1097644 ATATAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1099422 original size:2 final size:2
Alignment explanation
Indices: 1099417--1099445 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1099407 TTTAAAAAGG
1099417 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1099446 TAAGAAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1102274 original size:21 final size:21
Alignment explanation
Indices: 1102222--1102267 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
1102212 AAATGATTGA
1102222 TGAAGCAAGGAAGTTCCAAGT
1 TGAAGCAAGGAAGTTCCAAGT
1102243 TGAAGCAAGGAAGTTCCAAGT
1 TGAAGCAAGGAAGTTCCAAGT
1102264 TGAA
1 TGAA
1102268 TCTAGGAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (21 bp):
TGAAGCAAGGAAGTTCCAAGT
Found at i:1102466 original size:72 final size:72
Alignment explanation
Indices: 1102349--1102499 Score: 257
Period size: 72 Copynumber: 2.1 Consensus size: 72
1102339 CCCTATTACA
* * *
1102349 CAAGAAAATATGAAGACTTCGGGTGAGAATCTGAATGTTAGTGGTGCAACCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGGGTGAGAATCTGAATGTTAATGGTGCAACCAATGTGATGATAGC
1102414 AAATGAT
66 AAATGAT
*
1102421 CAAGAACAGATGAAGACTTCGGGTGAGAATCTGAATGTTAATGGTGCAGCCAATGTGATGATAGC
1 CAAGAACAGATGAAGACTTCGGGTGAGAATCTGAATGTTAATGGTGCAACCAATGTGATGATAGC
*
1102486 AACTGAT
66 AAATGAT
1102493 CAAGAAC
1 CAAGAAC
1102500 CTGTTAGGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.23
Consensus pattern (72 bp):
CAAGAACAGATGAAGACTTCGGGTGAGAATCTGAATGTTAATGGTGCAACCAATGTGATGATAGC
AAATGAT
Found at i:1107304 original size:42 final size:42
Alignment explanation
Indices: 1107257--1107606 Score: 551
Period size: 42 Copynumber: 8.3 Consensus size: 42
1107247 CCAAAATTTA
*
1107257 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGTT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1107299 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1107341 TAAATCC-TCTGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTC-GGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1107383 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
* *
1107425 TAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
*
1107467 TAAATCCTTCGGGTCATCTA-TAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCATC-AGTAAGTCTTCCGAGCATGATGCT
* *
1107509 TAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
* * * * *
1107551 TAAATCCTTTGGGTCATCTGTAAGCCTTTCGAGCATGATGAT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
* *
1107593 TAAGTCCTCCGGGT
1 TAAATCCTTCGGGT
1107607 AATCTAAAGC
Statistics
Matches: 293, Mismatches: 11, Indels: 8
0.94 0.04 0.03
Matches are distributed among these distances:
41 2 0.01
42 288 0.98
43 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
Found at i:1107656 original size:37 final size:37
Alignment explanation
Indices: 1107613--1107732 Score: 186
Period size: 37 Copynumber: 3.2 Consensus size: 37
1107603 GGGTAATCTA
* *
1107613 AAGCCTTCACCGAAGAGTGGTGAAGCAGATCCATCAT
1 AAGCCTTCACGGAAGAGTAGTGAAGCAGATCCATCAT
* *
1107650 AAGCCTTCATGGAAGAGTAGTGAAGCAAATCCATCAT
1 AAGCCTTCACGGAAGAGTAGTGAAGCAGATCCATCAT
*
1107687 AAGCCTTCACGGAAGAGTAGTGAAGAAGATCCATCAGT
1 AAGCCTTCACGGAAGAGTAGTGAAGCAGATCCATCA-T
1107725 AAGCCTTC
1 AAGCCTTC
1107733 CGAGCATGAC
Statistics
Matches: 75, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
37 66 0.88
38 9 0.12
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (37 bp):
AAGCCTTCACGGAAGAGTAGTGAAGCAGATCCATCAT
Found at i:1107810 original size:37 final size:37
Alignment explanation
Indices: 1107759--1107869 Score: 177
Period size: 37 Copynumber: 3.0 Consensus size: 37
1107749 GTCCTCCGGG
* *
1107759 CAATCTAAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CAATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
* *
1107796 CAATTTTAAGCCTTCACCAAAGAGTAGTGAAACAAAT
1 CAATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
*
1107833 CAATCTTAAGCCTTCACAAAAGAGTAGTGAAGCAAAT
1 CAATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
1107870 TCAGATCTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (37 bp):
CAATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
Found at i:1107848 original size:153 final size:153
Alignment explanation
Indices: 1107565--1107864 Score: 447
Period size: 153 Copynumber: 2.0 Consensus size: 153
1107555 TCCTTTGGGT
* * * *
1107565 CATCTGTAAGCCTTTCGAGCATGATGATTAAGTCCTCCGGGTAATCTAAAGCCTTCACCGAAGAG
1 CATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTCCGGGCAATCTAAAGCCTTCACCGAAGAG
* * * *** * *
1107630 TGGTGAAGCAGATCCATCATAAGCCTTCATGGAAGAGTAGTGAAGCAAATCCATCATAAGCCTTC
66 TAGTGAAGCAAATCAATCATAAGCCTTCACCAAAGAGTAGTGAAACAAATCAATCATAAGCCTTC
**
1107695 ACGGAAGAGTAGTGAAGAAGATC
131 ACAAAAGAGTAGTGAAGAAGATC
1107718 CATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTCCGGGCAATCTAAAGCCTTCACCGAAGAG
1 CATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTCCGGGCAATCTAAAGCCTTCACCGAAGAG
** *
1107783 TAGTGAAGCAAATCAATTTTAAGCCTTCACCAAAGAGTAGTGAAACAAATCAATCTTAAGCCTTC
66 TAGTGAAGCAAATCAATCATAAGCCTTCACCAAAGAGTAGTGAAACAAATCAATCATAAGCCTTC
1107848 ACAAAAGAGTAGTGAAG
131 ACAAAAGAGTAGTGAAG
1107865 CAAATTCAGA
Statistics
Matches: 130, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
153 130 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (153 bp):
CATCAGTAAGCCTTCCGAGCATGACGATTAAGTCCTCCGGGCAATCTAAAGCCTTCACCGAAGAG
TAGTGAAGCAAATCAATCATAAGCCTTCACCAAAGAGTAGTGAAACAAATCAATCATAAGCCTTC
ACAAAAGAGTAGTGAAGAAGATC
Found at i:1108074 original size:109 final size:109
Alignment explanation
Indices: 1107871--1108436 Score: 848
Period size: 109 Copynumber: 5.2 Consensus size: 109
1107861 GAAGCAAATT
* * * *
1107871 CAGATCTGATATTCCCTCAGAGGAAGCGAAACATATCCCTCTTTTTCAAGATTTGATATTCCTTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGAT--CTCTCTTTCAAGATTTGATATTCCCTG
* * * *
1107936 AGTGACAGCGGAACAAATCTGC-CTCGATTCAATAAATCAACTTTCT
64 AGTGACAGCGGAACAAGTCTACTCT-GATTCAATGAATCAACTTTCC
*
1107982 CAGATATGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAG
* *
1108047 TGACAGCGGAACAAGTCTACTCTGATTCATTGAATCAGCTTTCC
66 TGACAGCGGAACAAGTCTACTCTGATTCAATGAATCAACTTTCC
* *
1108091 CAGATCTGATATTCCCTCAGAGGAAGCAGAATAGATCTCTCTTTCAAGATTTGATATTCCCTGAG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAG
* *
1108156 TGACAGTGGAACAAGTCTACTCTGATTCAATGAATCAACTTTTC
66 TGACAGCGGAACAAGTCTACTCTGATTCAATGAATCAACTTTCC
*
1108200 CAGATATGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAG
*
1108265 TGACAACGGAACAAGTCTACTCTGATTCAATGAATCAACTTTCC
66 TGACAGCGGAACAAGTCTACTCTGATTCAATGAATCAACTTTCC
* * *
1108309 CAGATCTGATATTCCCTCAGAGGAAGCGGAACATATCCATCTTTTTCAAGATTTGATATTTCCTG
1 CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGAT-C-TCTCTTTCAAGATTTGATATTCCCTG
* * * *
1108374 AGTAACAGCGGAACAAGTCTAC-CTTGATTTAATGAATCAACATCCC
64 AGTGACAGCGGAACAAGTCTACTC-TGATTCAATGAATCAACTTTCC
1108420 CAGATCTGATATTCCCT
1 CAGATCTGATATTCCCT
1108437 GAGTGATAGG
Statistics
Matches: 418, Mismatches: 33, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
109 301 0.72
110 4 0.01
111 113 0.27
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (109 bp):
CAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAG
TGACAGCGGAACAAGTCTACTCTGATTCAATGAATCAACTTTCC
Found at i:1108600 original size:3 final size:3
Alignment explanation
Indices: 1108592--1108624 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1108582 CGTCTTTTAA
1108592 TAT TAT TAT ATAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA
1108625 ATATAACTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1110154 original size:2 final size:2
Alignment explanation
Indices: 1110147--1110171 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1110137 TTGTCTCATT
1110147 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1110172 GTGCATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1111760 original size:20 final size:21
Alignment explanation
Indices: 1111735--1111773 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1111725 TATTAAAAGG
1111735 ATAAATTA-CACATTTTGTGC
1 ATAAATTATCACATTTTGTGC
*
1111755 ATAAATTATCACTTTTTGT
1 ATAAATTATCACATTTTGT
1111774 TTTGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
ATAAATTATCACATTTTGTGC
Found at i:1112161 original size:8 final size:8
Alignment explanation
Indices: 1112150--1112174 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1112140 TAATGAAATA
1112150 ATTTATAT
1 ATTTATAT
1112158 ATTTATAT
1 ATTTATAT
1112166 ATTTATAT
1 ATTTATAT
1112174 A
1 A
1112175 AAATTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTATAT
Found at i:1112409 original size:15 final size:15
Alignment explanation
Indices: 1112359--1112412 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
1112349 TTGGTTCCAT
1112359 ATAATATCATTTAAA
1 ATAATATCATTTAAA
*
1112374 ATTAAATAGATAATTTAAAA
1 A-T-AAT--ATCATTT-AAA
1112394 ATAATATCATTTAAA
1 ATAATATCATTTAAA
1112409 ATAA
1 ATAA
1112413 ATAAATATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
15 8 0.25
16 7 0.22
17 3 0.09
18 3 0.09
19 7 0.22
20 4 0.12
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (15 bp):
ATAATATCATTTAAA
Found at i:1112415 original size:16 final size:16
Alignment explanation
Indices: 1112361--1112415 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 16
1112351 GGTTCCATAT
1112361 AATATCATTTAAAATTA
1 AATATCATTTAAAA-TA
*
1112378 AATAGATAATTTAAAA-A
1 AAT--ATCATTTAAAATA
1112395 TAATATCATTTAAAATA
1 -AATATCATTTAAAATA
1112412 AATA
1 AATA
1112416 AATATTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 14 0.44
17 5 0.16
18 3 0.09
19 10 0.31
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
AATATCATTTAAAATA
Found at i:1112425 original size:20 final size:20
Alignment explanation
Indices: 1112361--1112439 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
1112351 GGTTCCATAT
1112361 AATATCATTTAAAATTAAATA
1 AATATCATTTAAAA-TAAATA
*
1112382 GATA--ATTT--AA-AAAT-
1 AATATCATTTAAAATAAATA
1112396 AATATCATTTAAAATAAATA
1 AATATCATTTAAAATAAATA
*
1112416 AATATTATTTAAAATAAATA
1 AATATCATTTAAAATAAATA
1112436 AATA
1 AATA
1112440 AATAATATGA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.06
15 4 0.08
16 4 0.08
17 2 0.04
18 2 0.04
19 8 0.16
20 23 0.47
21 3 0.06
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (20 bp):
AATATCATTTAAAATAAATA
Found at i:1112432 original size:35 final size:35
Alignment explanation
Indices: 1112359--1112429 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
1112349 TTGGTTCCAT
*
1112359 ATAATATCATTTAAAATTAAATAGATAATTTAAAA
1 ATAATATCATTTAAAATTAAATAAATAATTTAAAA
1112394 ATAATATCATTTAAAA-TAAATAAATATTATTTAAAA
1 ATAATATCATTTAAAATTAAATAAATA--ATTTAAAA
1112430 TAAATAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 9 0.27
35 16 0.48
36 8 0.24
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (35 bp):
ATAATATCATTTAAAATTAAATAAATAATTTAAAA
Found at i:1112517 original size:23 final size:22
Alignment explanation
Indices: 1112470--1112531 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
1112460 TAATTTAATG
*
1112470 TTTTTATAATATTATAAATATA
1 TTTTTATAATATTATAAATAAA
*
1112492 TTTTTATAATTATT-TCATATAAA
1 TTTTTATAA-TATTAT-AAATAAA
1112515 -TTTTATAA-ATATATAAA
1 TTTTTATAATAT-TATAAA
1112532 AATTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.06
21 3 0.09
22 19 0.58
23 9 0.27
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTTATAATATTATAAATAAA
Found at i:1114540 original size:27 final size:27
Alignment explanation
Indices: 1114510--1114564 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1114500 ATATGATGTC
1114510 TTAGATATGATTAGTAGAACATGTGAT
1 TTAGATATGATTAGTAGAACATGTGAT
1114537 TTAGATATGATTAGTAGAACATGTGAT
1 TTAGATATGATTAGTAGAACATGTGAT
1114564 T
1 T
1114565 GATCGATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (27 bp):
TTAGATATGATTAGTAGAACATGTGAT
Found at i:1124927 original size:20 final size:21
Alignment explanation
Indices: 1124904--1124983 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
1124894 TTGGTGCAGA
*
1124904 GGGAATCGATACCCCCATGA-
1 GGGAACCGATACCCCCATGAG
* *
1124924 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCCC-ATG-AG
*
1124947 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGA-TACCCCCATGAG
*
1124968 GGGAATCGATACCCCC
1 GGGAACCGATACCCCC
1124984 CTAGGGTTCT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
20 20 0.41
21 12 0.24
22 1 0.02
23 10 0.20
24 6 0.12
ACGTcount: A:0.25, C:0.34, G:0.25, T:0.16
Consensus pattern (21 bp):
GGGAACCGATACCCCCATGAG
Found at i:1124971 original size:21 final size:21
Alignment explanation
Indices: 1124915--1124989 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
1124905 GGAATCGATA
1124915 CCCCCAT-GAGGGAACCGATTC
1 CCCCCATAG-GGGAACCGATTC
**
1124936 CCCCTTTGAAGGGGAACCGATTC
1 CCCCCAT--AGGGGAACCGATTC
* *
1124959 CCCCCATAGGGGAATCGATAC
1 CCCCCATAGGGGAACCGATTC
1124980 CCCCC-TAGGG
1 CCCCCATAGGG
1124990 TTCTGGATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
20 5 0.11
21 22 0.49
23 17 0.38
24 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
CCCCCATAGGGGAACCGATTC
Found at i:1142274 original size:36 final size:36
Alignment explanation
Indices: 1142188--1142274 Score: 84
Period size: 36 Copynumber: 2.4 Consensus size: 36
1142178 AAGAATAATG
* *
1142188 CCAAAAAAATAAGTCCCAATCTCATTCAAACAAACAA
1 CCAAAAAAA-AAATCCCAATCTCATTAAAACAAACAA
** * ** **
1142225 CCAACCAACAAATCCCAATCTTGTTAAAACAAGTAA
1 CCAAAAAAAAAATCCCAATCTCATTAAAACAAACAA
1142261 CCAAAAAAAAAATC
1 CCAAAAAAAAAATC
1142275 AAATCACCCA
Statistics
Matches: 38, Mismatches: 12, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
36 32 0.84
37 6 0.16
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.16
Consensus pattern (36 bp):
CCAAAAAAAAAATCCCAATCTCATTAAAACAAACAA
Found at i:1145337 original size:19 final size:20
Alignment explanation
Indices: 1145313--1145354 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1145303 AAGAATAAAG
*
1145313 GAAAAATGAA-AAAAAAAAT
1 GAAAAACGAACAAAAAAAAT
*
1145332 GAAAAACGAACAAAATAAAT
1 GAAAAACGAACAAAAAAAAT
1145352 GAA
1 GAA
1145355 GAACAATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.10
Consensus pattern (20 bp):
GAAAAACGAACAAAAAAAAT
Found at i:1145400 original size:20 final size:20
Alignment explanation
Indices: 1145375--1145412 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1145365 ATAATAAAGA
*
1145375 AGAAGAACGAAGAAGAAATG
1 AGAAGAACAAAGAAGAAATG
1145395 AGAAGAACAAAGAAGAAA
1 AGAAGAACAAAGAAGAAA
1145413 AGAGTGACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.66, C:0.05, G:0.26, T:0.03
Consensus pattern (20 bp):
AGAAGAACAAAGAAGAAATG
Found at i:1146633 original size:18 final size:17
Alignment explanation
Indices: 1146579--1146627 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
1146569 TTGGACCCTT
* *
1146579 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
1146597 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
1146615 AGTGCATTCGATG
1 AGTGCA-TCGATG
1146628 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:1163091 original size:25 final size:23
Alignment explanation
Indices: 1163063--1163109 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
1163053 AGATAAAATA
*
1163063 TAATAATTTTATTACTGATTTGATC
1 TAATAAATTTATT--TGATTTGATC
*
1163088 TAATAAATTTGTTTGATTTGAT
1 TAATAAATTTATTTGATTTGAT
1163110 AGTATTGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (23 bp):
TAATAAATTTATTTGATTTGATC
Found at i:1173256 original size:3 final size:3
Alignment explanation
Indices: 1173248--1173279 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1173238 TTTAAAATTA
1173248 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1173280 ATGTCGCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1174551 original size:20 final size:21
Alignment explanation
Indices: 1174521--1174573 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1174511 TCAAGTTTTA
1174521 TATTT-TTATTATT-ATAATT
1 TATTTATTATTATTAATAATT
1174540 TATTTATTATTATTAATAATT
1 TATTTATTATTATTAATAATT
*
1174561 TCTTTATT-TTATT
1 TATTTATTATTATT
1174574 TTTTGTAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 5 0.16
20 13 0.42
21 13 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATTATTATTAATAATT
Found at i:1179712 original size:105 final size:105
Alignment explanation
Indices: 1179432--1180661 Score: 2120
Period size: 105 Copynumber: 11.7 Consensus size: 105
1179422 GGCGACTGAC
* * *
1179432 TGTCAACAAACAACTTCTCAATTTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
1179497 AGACAACGCAAGTTCAACTTCAAGACGAAGGGACCGCTGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1179538 TGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGTATATTGGACTCC
1 TGTCAA-CAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
1179603 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1179644 TGTCAACAACAACTTCCCAAATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
*
1179709 GACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1179749 TGTCAACAACAACTTCCTAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
1179814 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
1179854 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
1179919 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
1179959 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
*
1180024 GACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1180064 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
1180129 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1180169 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
* *
1180234 GACAATGCAAGTTTAACTTCACGACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1180274 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
*
1180339 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1180379 TGTCAACAACAACTTCCCAATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAA
1 TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
*
1180444 GACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGT
66 GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1180484 TGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCG
1 TGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
1180549 AGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGT
65 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGT
* * * *
1180590 TGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCG
1 TGTCAAC-AACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
1180655 AGACAAC
65 AGACAAC
1180662 ACAACTTTCA
Statistics
Matches: 1076, Mismatches: 45, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
105 814 0.76
106 262 0.24
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
TGTCAACAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA
GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:1180911 original size:124 final size:124
Alignment explanation
Indices: 1180671--1180915 Score: 355
Period size: 124 Copynumber: 2.0 Consensus size: 124
1180661 CACAACTTTC
* * * *
1180671 ATTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGCTCAACTCCACGACGGAGGGGCCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTCCACAACGAAGGGACCA
* * ** *
1180736 TCCACGGTTTCAACTTCACGATGAAGGTAAGCATACACACAAGCAGCATTCATCTTTAG
66 TCCACAGTTTCAACTTCACGACGAAGACAAGCATACACACAAGCAACATTCATCTTTAG
*
1180795 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGACCA
1 ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTCCACAACGAAGGGACCA
* * * * *
1180860 TCCACAGTTTCAACTTCACGACGAAGACAATCGTACCCACCAGCAATATTCATCTT
66 TCCACAGTTTCAACTTCACGACGAAGACAAGCATACACACAAGCAACATTCATCTT
1180916 CAGGAACAAG
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 106 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.23
Consensus pattern (124 bp):
ATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTCCACAACGAAGGGACCA
TCCACAGTTTCAACTTCACGACGAAGACAAGCATACACACAAGCAACATTCATCTTTAG
Found at i:1181046 original size:36 final size:36
Alignment explanation
Indices: 1181006--1181111 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
1180996 CAAAACTAAG
* *
1181006 TTTTGTCTCTCTTGAGACGGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
1181042 TTTTGTCCCTCTTGAGACAGTTTCCCTTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1181078 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1181112 CCAATCTTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:1181567 original size:20 final size:21
Alignment explanation
Indices: 1181537--1181589 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1181527 CCGGGTTTTA
1181537 TATTT-TTATTATT-ATAATT
1 TATTTATTATTATTAATAATT
1181556 TATTTATTATTATTAATAATT
1 TATTTATTATTATTAATAATT
*
1181577 TCTTTATT-TTATT
1 TATTTATTATTATT
1181590 TTTTGTAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 5 0.16
20 13 0.42
21 13 0.42
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTATTATTATTAATAATT
Found at i:1184149 original size:13 final size:13
Alignment explanation
Indices: 1184131--1184155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184121 GTTTACAATC
1184131 AGAAATAGAGAAG
1 AGAAATAGAGAAG
1184144 AGAAATAGAGAA
1 AGAAATAGAGAA
1184156 AATGGCGACA
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:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (13 bp):
AGAAATAGAGAAG
Found at i:1184791 original size:20 final size:20
Alignment explanation
Indices: 1184768--1184814 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1184758 GTTTTCAAAT
1184768 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
1184788 TCGCAACGCGAATCTGTAAT
1 TCGCAACGCGAATCTGTAAA
1184808 TCGCAAC
1 TCGCAAC
1184815 ACAAGTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:1184828 original size:18 final size:19
Alignment explanation
Indices: 1184805--1184851 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
1184795 GCGAATCTGT
1184805 AATTCGCAACAC-AAGTCA
1 AATTCGCAACACAAAGTCA
*
1184823 AATTCGAAACACATAAGTCA
1 AATTCGCAACACA-AAGTCA
1184843 AATTCGCAA
1 AATTCGCAA
1184852 AGCGCGTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.44
20 14 0.56
ACGTcount: A:0.47, C:0.23, G:0.11, T:0.19
Consensus pattern (19 bp):
AATTCGCAACACAAAGTCA
Found at i:1185027 original size:22 final size:22
Alignment explanation
Indices: 1185002--1185056 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1184992 CTCTCTACGG
1185002 CGAAATCCGTCCCCATCTCCGA
1 CGAAATCCGTCCCCATCTCCGA
*
1185024 CGAAATCCGTCCCCATCTCCGG
1 CGAAATCCGTCCCCATCTCCGA
1185046 CGAAATCCGTC
1 CGAAATCCGTC
1185057 TATCTCCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.22, C:0.44, G:0.16, T:0.18
Consensus pattern (22 bp):
CGAAATCCGTCCCCATCTCCGA
Found at i:1185277 original size:65 final size:65
Alignment explanation
Indices: 1185185--1185320 Score: 263
Period size: 65 Copynumber: 2.1 Consensus size: 65
1185175 TTTTCATATT
1185185 TAAATTGATAATAAATTTACTGGTAATTTCAGTAATAGATTAACCATTTCACGTAGATTGCTTAG
1 TAAATTGATAATAAATTTACTGGTAATTTCAGTAATAGATTAACCATTTCACGTAGATTGCTTAG
*
1185250 TAAATTGATGATAAATTTACTGGTAATTTCAGTAATAGATTAACCATTTCACGTAGATTGCTTAG
1 TAAATTGATAATAAATTTACTGGTAATTTCAGTAATAGATTAACCATTTCACGTAGATTGCTTAG
1185315 TAAATT
1 TAAATT
1185321 CATTCGGTTA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 70 1.00
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (65 bp):
TAAATTGATAATAAATTTACTGGTAATTTCAGTAATAGATTAACCATTTCACGTAGATTGCTTAG
Found at i:1185509 original size:19 final size:20
Alignment explanation
Indices: 1185487--1185559 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 20
1185477 AAATCGCAAC
1185487 GCGATTTT-AGTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
*
1185506 GCGATTTTCA-TTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
* *
1185525 GCGATTTTTATTTTCGCGTT
1 GCGATTTTAAGTTTCGCGTT
1185545 GCGATTTTAAGTTTC
1 GCGATTTTAAGTTTC
1185560 AGAAACTATT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
19 26 0.53
20 23 0.47
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (20 bp):
GCGATTTTAAGTTTCGCGTT
Found at i:1187730 original size:42 final size:42
Alignment explanation
Indices: 1187684--1187802 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
1187674 GAAGCACCTG
* * *
1187684 TCATCATTCAAGAGGCCTCTCCTATCATTCAAGAGGCCCCTA
1 TCATCATTCAAGAGGCCACTCCCACCATTCAAGAGGCCCCTA
* * * *
1187726 TCATCCTTCAAGATGCCACTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCACTCCCACCATTCAAGAGGCCCCTA
* * * *
1187768 CCATCGTTCAAGAGGTCC-CTCCCACCGTTCGAGAG
1 TCATCATTCAAGAGG-CCACTCCCACCATTCAAGAG
1187803 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 63 0.97
43 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATCATTCAAGAGGCCACTCCCACCATTCAAGAGGCCCCTA
Found at i:1187796 original size:21 final size:21
Alignment explanation
Indices: 1187690--1187802 Score: 102
Period size: 21 Copynumber: 5.4 Consensus size: 21
1187680 CCTGTCATCA
* * * *
1187690 TTCAAGAGGCCTCTCCTATCA
1 TTCAAGAGGCCCCTCCCACCG
**
1187711 TTCAAGAGGCCCCTATCATCC-
1 TTCAAGAGGCCCCTCCCA-CCG
* *
1187732 TTCAAGATGCCACTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
* *
1187753 TTCAAGAGGCCCCTGCCATCG
1 TTCAAGAGGCCCCTCCCACCG
*
1187774 TTCAAGAGGTCCCTCCCACCG
1 TTCAAGAGGCCCCTCCCACCG
*
1187795 TTCGAGAG
1 TTCAAGAG
1187803 CCCGATTCAC
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
20 2 0.03
21 70 0.96
22 1 0.01
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCCACCG
Found at i:1189233 original size:64 final size:64
Alignment explanation
Indices: 1189152--1189300 Score: 244
Period size: 64 Copynumber: 2.3 Consensus size: 64
1189142 AAATTGATGT
1189152 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTA
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTA
* * * ***
1189216 ATTTTTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTA
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTA
1189280 ATTTGTAAAAGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
1189301 GTTTTAAATT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 78 1.00
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTA
Found at i:1189400 original size:20 final size:20
Alignment explanation
Indices: 1189368--1189476 Score: 70
Period size: 20 Copynumber: 5.8 Consensus size: 20
1189358 TTTCACAACA
1189368 CGAAAGT-AAATTCGCAATG
1 CGAAAGTCAAATTCGCAATG
* *
1189387 CGAAAGTCAAATTCACATTG
1 CGAAAGTCAAATTCGCAATG
* ** *
1189407 CG--A-T---TTTCGCGTTA
1 CGAAAGTCAAATTCGCAATG
* **
1189421 CGATAGTCAAATTCGCAACA
1 CGAAAGTCAAATTCGCAATG
*
1189441 CGAAAGTCAAATTCACAATG
1 CGAAAGTCAAATTCGCAATG
*
1189461 TGAAAGTCAAATTCGC
1 CGAAAGTCAAATTCGC
1189477 GTTGCGATTT
Statistics
Matches: 67, Mismatches: 16, Indels: 13
0.70 0.17 0.14
Matches are distributed among these distances:
14 8 0.12
16 1 0.01
17 2 0.03
18 1 0.01
19 7 0.10
20 48 0.72
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (20 bp):
CGAAAGTCAAATTCGCAATG
Found at i:1189559 original size:20 final size:20
Alignment explanation
Indices: 1189536--1189573 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1189526 CAATCGCAAC
1189536 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTCGCATT
1189556 GCGAATTTGACTTTCGCA
1 GCGAATTTGACTTTCGCA
1189574 ACAATTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
GCGAATTTGACTTTCGCATT
Found at i:1189766 original size:18 final size:18
Alignment explanation
Indices: 1189743--1189778 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1189733 AAGCTGGTTG
*
1189743 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1189761 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1189779 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1190020 original size:14 final size:15
Alignment explanation
Indices: 1189986--1190021 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
1189976 GAAATCATTG
1189986 AAAAATTATATAGAA
1 AAAAATTATATAGAA
1190001 ATAAAATTATATA-AA
1 A-AAAATTATATAGAA
1190016 AAAAAT
1 AAAAAT
1190022 GTCTTCCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 4 0.20
16 11 0.55
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1190965 original size:18 final size:18
Alignment explanation
Indices: 1190942--1190978 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1190932 CAAAATTTAT
1190942 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1190960 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1190978 A
1 A
1190979 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1191392 original size:25 final size:25
Alignment explanation
Indices: 1191364--1191413 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1191354 CATTATTTTC
*
1191364 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1191389 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1191414 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1191825 original size:18 final size:18
Alignment explanation
Indices: 1191802--1191837 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1191792 AAGCCGGTTG
1191802 TGATTGAGATTTTGATTT
1 TGATTGAGATTTTGATTT
**
1191820 TGATTGCTATTTTGATTT
1 TGATTGAGATTTTGATTT
1191838 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.19, T:0.58
Consensus pattern (18 bp):
TGATTGAGATTTTGATTT
Found at i:1194118 original size:24 final size:24
Alignment explanation
Indices: 1194091--1194144 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1194081 TTGAAACATC
1194091 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1194115 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1194139 ATCAAA
1 ATCAAA
1194145 TTTCAAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1194618 original size:19 final size:19
Alignment explanation
Indices: 1194574--1194620 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1194564 ATAAGATAGC
*
1194574 CTAAATCCACTTAGAGGCT
1 CTAAATTCACTTAGAGGCT
1194593 CTAAATTCACTTAGAGGCT
1 CTAAATTCACTTAGAGGCT
1194612 CTAAATTCA
1 CTAAATTCA
1194621 ATTACTTTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.30
Consensus pattern (19 bp):
CTAAATTCACTTAGAGGCT
Found at i:1194946 original size:14 final size:15
Alignment explanation
Indices: 1194910--1194947 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1194900 GAAATCATTG
1194910 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1194925 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1194940 AAAAATTA
1 AAAAATTA
1194948 GAGATGAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1195335 original size:60 final size:60
Alignment explanation
Indices: 1195123--1195336 Score: 243
Period size: 60 Copynumber: 3.5 Consensus size: 60
1195113 TTAAAATTCT
* * * ** **
1195123 TGTTGCGAATTCGAAAATCGAGTTGCGAATTCAGAAATCG-AGTTGCGAATTCAGAAATCG
1 TGTTGCGAATTTGGAAATCGTGTTGCGAATTTGGAAATCGCA-TTGCGAATTTGGAAATCG
* * * * * *
1195183 AGTTGCGAATTT-GAAATTCAGTGTTGTGAATTTGTAAATCGCATGGCGAATTTGTAAATCA
1 TGTTGCGAATTTGGAAA-TC-GTGTTGCGAATTTGGAAATCGCATTGCGAATTTGGAAATCG
* **
1195244 CGTTGCGAATTTGGAAATCGCATTGCGAATTTGGAAATCGCATTGCGAATTTGGAAATCG
1 TGTTGCGAATTTGGAAATCGTGTTGCGAATTTGGAAATCGCATTGCGAATTTGGAAATCG
1195304 TGTTGCGAATTTGGAAATCGTGTTGCGAATTTG
1 TGTTGCGAATTTGGAAATCGTGTTGCGAATTTG
1195337 ACTTTTGTGT
Statistics
Matches: 126, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
59 3 0.02
60 76 0.60
61 42 0.33
62 5 0.04
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (60 bp):
TGTTGCGAATTTGGAAATCGTGTTGCGAATTTGGAAATCGCATTGCGAATTTGGAAATCG
Found at i:1195404 original size:20 final size:20
Alignment explanation
Indices: 1195124--1195404 Score: 196
Period size: 20 Copynumber: 14.0 Consensus size: 20
1195114 TAAAATTCTT
* *
1195124 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTTGAAAATCGC
* *
1195144 GTTGCGAA-TTCAGAAATCGA
1 GTTGCGAATTTGA-AAATCGC
* *
1195164 GTTGCGAA-TTCAGAAATCGA
1 GTTGCGAATTTGA-AAATCGC
* *
1195184 GTTGCGAATTTGAAATTCAGT
1 GTTGCGAATTTGAAAATC-GC
* *
1195205 GTTGTGAATTTGTAAATCGC
1 GTTGCGAATTTGAAAATCGC
* * * *
1195225 ATGGCGAATTTGTAAATCAC
1 GTTGCGAATTTGAAAATCGC
*
1195245 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGAAAATCGC
* *
1195265 ATTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGAAAATCGC
* * *
1195285 ATTGCGAATTTGGAAATCGT
1 GTTGCGAATTTGAAAATCGC
* *
1195305 GTTGCGAATTTGGAAATCGT
1 GTTGCGAATTTGAAAATCGC
*** * *
1195325 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAAATCGC
*
1195345 GTTGCG-ATTT-ATAGATTCGC
1 GTTGCGAATTTGA-A-AATCGC
*
1195365 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGA-A-AATCGC
1195385 GTTGCGAATTTGAAAATCGC
1 GTTGCGAATTTGAAAATCGC
1195405 AACGCGAATT
Statistics
Matches: 223, Mismatches: 31, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
18 1 0.00
19 6 0.03
20 191 0.86
21 24 0.11
22 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATCGC
Found at i:1202724 original size:282 final size:281
Alignment explanation
Indices: 1201956--1202798 Score: 1341
Period size: 282 Copynumber: 3.0 Consensus size: 281
1201946 ATGTTTTCAA
* * * * **
1201956 ATGA-GTTTTTAGAAACTAAACCTGGTTTTCAGGGGTTTCTTGATGATTATCTCTAAAGAATTTT
1 ATGATGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAAAAAATT
* *
1202020 TAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTGAAAACGAAAGATTTTAAGA
66 TAAGGGAAGTTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTGAAAACGAAAGATTTTAAGA
* *
1202085 AACTAAGCTTGATTTT-AAGGGTTTCTTGATGAGTAAGTCCTTCGGTCTATCAGTAAGTCTTTCG
131 AACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGTCCATGAGTAAGTCTTTCG
* * * **
1202149 AGCATGATGCTTAAATCCTTTGGGTCATCTATAAGTCTTTCAAACAATATGATAAGTTCTTTGGG
196 AGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAATATGATAAGTTCTTCAGG
1202214 CCATCCATAAGACCTTCGGGC
261 CCATCCATAAGACCTTCGGGC
* *
1202235 ATGATGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTAATGATTATCTCCAAAAAAACTT
1 ATGATGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAAAAAATT
* *
1202300 TAAGGGAAGTTAAGCCTAATTTTTAGGGGTTCCTTGATGATAACTGAAAACAAAAGATTTTAAGA
66 TAAGGGAAGTTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTGAAAACGAAAGATTTTAAGA
* *
1202365 AACTAAGTTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCAGG-CCACGAGTAAGTCTTTC
131 AACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTC-GGTCCATGAGTAAGTCTTTC
*
1202429 GAGCATTATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAATATGATAAGTTCTTCAG
195 GAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAATATGATAAGTTCTTCAG
1202494 GCCATCCATAAGACCTTCGGGC
260 GCCATCCATAAGACCTTCGGGC
* *
1202516 ATGATGTTTTTAGAAGCTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAAAAAAAA
1 ATGATGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC-AAAAAAAAT
* * *
1202581 TTAAGGGAAATTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTGAAAATGAAAGATTTTAGG
65 TTAAGGGAAGTTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTGAAAACGAAAGATTTTAAG
*
1202646 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATTAGTAAGTCCTTCGGTCCATGAGTAAGTCTTTC
130 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGTCCATGAGTAAGTCTTTC
* * * * *
1202711 GAGCATGATGCTTAAATCATTCGAGTCATCTATAAGTCTTTCGAGCAAGACGATAAGTCCTTCAG
195 GAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAATATGATAAGTTCTTCAG
*
1202776 TCCATCCATAAGACCTTCGGGC
260 GCCATCCATAAGACCTTCGGGC
1202798 A
1 A
1202799 GGGTTTTTCA
Statistics
Matches: 519, Mismatches: 40, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
279 4 0.01
280 129 0.25
281 177 0.34
282 209 0.40
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (281 bp):
ATGATGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAAAAAATT
TAAGGGAAGTTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTGAAAACGAAAGATTTTAAGA
AACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGTCCATGAGTAAGTCTTTCG
AGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAATATGATAAGTTCTTCAGG
CCATCCATAAGACCTTCGGGC
Found at i:1202897 original size:43 final size:43
Alignment explanation
Indices: 1202836--1202920 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
1202826 TTCACAACAT
** *
1202836 TTCGAATCAGTGACGCCCCATCAGAGGGGTTAACATTTCTTTG
1 TTCGAATCAGAAACGCCCCACCAGAGGGGTTAACATTTCTTTG
* * *
1202879 TTCGAATCAGAAATGCCCCACCAGAGGGGTTCACTTTTCTTT
1 TTCGAATCAGAAACGCCCCACCAGAGGGGTTAACATTTCTTT
1202921 TTTTCGATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (43 bp):
TTCGAATCAGAAACGCCCCACCAGAGGGGTTAACATTTCTTTG
Found at i:1204925 original size:30 final size:31
Alignment explanation
Indices: 1204889--1204977 Score: 121
Period size: 32 Copynumber: 2.9 Consensus size: 31
1204879 ATGACCACTA
1204889 TCCATATGT-TCCGAAGAACATAGGTAAT-TG
1 TCCATATGTCT-CGAAGAACATAGGTAATCTG
*
1204919 TCCATATGTCTTGAAGAACATAGGTAATCCTG
1 TCCATATGTCTCGAAGAACATAGGTAAT-CTG
1204951 TCCATATGTCTCGAA-AGACATAGGTAA
1 TCCATATGTCTCGAAGA-ACATAGGTAA
1204978 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
30 25 0.47
31 2 0.04
32 26 0.49
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (31 bp):
TCCATATGTCTCGAAGAACATAGGTAATCTG
Found at i:1208631 original size:21 final size:21
Alignment explanation
Indices: 1208569--1208624 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1208559 TTTTGGGTTG
1208569 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
1208590 TGTGCATCGATGCATCTTCAA
1 TGTGCATCGATGCATCTTCAA
1208611 TGTGCATCGATGCA
1 TGTGCATCGATGCA
1208625 CTCTCAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTGCATCGATGCATCTTCAA
Found at i:1212266 original size:32 final size:31
Alignment explanation
Indices: 1212194--1212311 Score: 123
Period size: 30 Copynumber: 3.8 Consensus size: 31
1212184 CGAAGAACCA
* *
1212194 CTATCCATATGTTCCGAAGAACATAGGTAA-
1 CTATCCATATGTCCCGAAGGACATAGGTAAT
1212224 CTATCCATATGTCCCGAAGGACATAGGTAAT
1 CTATCCATATGTCCCGAAGGACATAGGTAAT
* * * *
1212255 CCTATCTATATGTCTCGAAAGACATATGTAAT
1 -CTATCCATATGTCCCGAAGGACATAGGTAAT
* * *
1212287 ATGTCCATATG-CCTCGAAAGACATA
1 CTATCCATATGTCC-CGAAGGACATA
1212312 TGCAACCCTC
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
30 29 0.39
31 19 0.25
32 27 0.36
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (31 bp):
CTATCCATATGTCCCGAAGGACATAGGTAAT
Found at i:1212303 original size:31 final size:32
Alignment explanation
Indices: 1212225--1212313 Score: 101
Period size: 31 Copynumber: 2.8 Consensus size: 32
1212215 CATAGGTAAC
* * *
1212225 TATCCATATGTCC-CGAAGGACATAGGTAATCC
1 TATCCATATG-CCTCGAAAGACATATGTAATCA
* *
1212257 TATCTATATGTCTCGAAAGACATATGTAAT-A
1 TATCCATATGCCTCGAAAGACATATGTAATCA
*
1212288 TGTCCATATGCCTCGAAAGACATATG
1 TATCCATATGCCTCGAAAGACATATG
1212314 CAACCCTCGA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 24 0.50
32 24 0.50
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (32 bp):
TATCCATATGCCTCGAAAGACATATGTAATCA
Found at i:1214928 original size:17 final size:17
Alignment explanation
Indices: 1214889--1214931 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1214879 TTCGATTGCA
*
1214889 TGTTTAATTTTGCATTT
1 TGTTTAATTTAGCATTT
*
1214906 TTTTTAATTTAGTCA-TT
1 TGTTTAATTTAG-CATTT
1214923 TGTTTAATT
1 TGTTTAATT
1214932 CACATAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (17 bp):
TGTTTAATTTAGCATTT
Found at i:1215163 original size:13 final size:13
Alignment explanation
Indices: 1215147--1215171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1215137 TTTCTCAGTC
1215147 TTATTTATTTTAT
1 TTATTTATTTTAT
1215160 TTATTTATTTTA
1 TTATTTATTTTA
1215172 ATTGTTTAAT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTATTTTAT
Found at i:1216557 original size:35 final size:35
Alignment explanation
Indices: 1216501--1216574 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1216491 AGGCGCTTAT
*
1216501 ATTTAAGGTTTAAGATATAATTGAAGTATTTTGGA
1 ATTTAAGGTTTAAGATATAATTGAAGTATTTTAGA
* * *
1216536 ATTTGAGGTTT-AGAATGTAATTGAAGTGTTTTAGA
1 ATTTAAGGTTTAAG-ATATAATTGAAGTATTTTAGA
1216571 ATTT
1 ATTT
1216575 TGAACATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.45
Consensus pattern (35 bp):
ATTTAAGGTTTAAGATATAATTGAAGTATTTTAGA
Found at i:1221943 original size:15 final size:16
Alignment explanation
Indices: 1221923--1221963 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1221913 GTTTATTTCA
*
1221923 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
1221938 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
1221954 GAATGATTCA
1 GAATGATTCA
1221964 GAGGCTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:1224007 original size:24 final size:24
Alignment explanation
Indices: 1223957--1224020 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
1223947 ATTTTGGAAT
* *
1223957 AAAAAT-AATTAAATATATGTTTT
1 AAAAATAAATTAAAAATATGTTTA
1223980 AAAAATAAATATAAAAATAT-TTTA
1 AAAAATAAAT-TAAAAATATGTTTA
* *
1224004 AAAATTAAATTTAAAAT
1 AAAAATAAATTAAAAAT
1224021 TTTTATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 12 0.34
24 15 0.43
25 8 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAATAAATTAAAAATATGTTTA
Found at i:1224020 original size:23 final size:22
Alignment explanation
Indices: 1223976--1224025 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
1223966 TAAATATATG
1223976 TTTTAAAAATAAATATAAAAAT
1 TTTTAAAAATAAATATAAAAAT
*
1223998 ATTTTAAAAATTAAAT-TTAAAAT
1 -TTTTAAAAA-TAAATATAAAAAT
1224021 TTTTA
1 TTTTA
1224026 TTTATGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 5 0.20
23 15 0.60
24 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TTTTAAAAATAAATATAAAAAT
Found at i:1224021 original size:12 final size:12
Alignment explanation
Indices: 1223977--1224019 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1223967 AAATATATGT
1223977 TTTAAAAATAAA
1 TTTAAAAATAAA
* *
1223989 TATAAAAAT-AT
1 TTTAAAAATAAA
1224000 TTTAAAAATTAAA
1 TTTAAAAA-TAAA
1224013 TTTAAAA
1 TTTAAAA
1224020 TTTTTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
11 8 0.32
12 9 0.36
13 8 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TTTAAAAATAAA
Found at i:1227219 original size:3 final size:3
Alignment explanation
Indices: 1227204--1227252 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
1227194 GGTTAAAGAA
* *
1227204 TAT TAT TA- AAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1227251 TA
1 TA
1227253 AGTGTGCAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 1 0.02
3 40 0.98
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1230727 original size:55 final size:55
Alignment explanation
Indices: 1230643--1231226 Score: 865
Period size: 55 Copynumber: 10.7 Consensus size: 55
1230633 CTCCATAGTC
1230643 CTTCAGAGAGTATAAGACTCGAACAATCTTTC-ACAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATC-TTCAACAATCGCGTCTGCCCCCTATTT
* ** * *
1230698 CTTCAGAGAGTATAAGACTCGAATAATCTTCAATGATCACGTCTGCCCCCCATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
1230753 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCGTCTGCCCCTTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
1230806 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1230861 CTTCAGAGAGTATAAGAC-C-CACAATATTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1230914 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
1230969 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1231024 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
1231079 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCT-CCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
1231133 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCATCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
1231188 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
1231227 TGGGGAACCT
Statistics
Matches: 477, Mismatches: 46, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
53 93 0.19
54 54 0.11
55 330 0.69
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:1230834 original size:108 final size:109
Alignment explanation
Indices: 1230643--1231226 Score: 861
Period size: 108 Copynumber: 5.3 Consensus size: 109
1230633 CTCCATAGTC
1230643 CTTCAGAGAGTATAAGACTCGAACAATCTTTC-ACAATCGCGTCTGCCCCCTATTTCTTCAGAGA
1 CTTCAGAGAGTATAAGACTC-AACAATC-TTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGA
* * * * *
1230707 GTATAAGACTCGAATAATCTTCAATGATCACGTCTGCCCCCCATTT
64 GTATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* * *
1230753 CTTCAGAGAGTATAAGACTC-ACAATCTTCATCAATCGCGTCTGCCCCTTATTTCGTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
*
1230817 ATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* * *
1230861 CTTCAGAGAGTATAAGAC-CCACAATATTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
* * *
1230925 ATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
1230969 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
1231034 TATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
1231079 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCT-CCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* *
1231143 TATAAGACTTGAACAATCTTCAACGATCGCATCCGCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
* *
1231188 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCG
1 CTTCAGAGAGTATAAGAC-TCAACAATCTTCAACAATCG
1231227 TGGGGAACCT
Statistics
Matches: 439, Mismatches: 30, Indels: 11
0.91 0.06 0.02
Matches are distributed among these distances:
107 4 0.01
108 194 0.44
109 94 0.21
110 147 0.33
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (109 bp):
CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
ATAAGACTCGAACAATCTTCAACGATCGCGTCCGCCCCCTATTT
Found at i:1230847 original size:163 final size:164
Alignment explanation
Indices: 1230643--1231226 Score: 872
Period size: 163 Copynumber: 3.6 Consensus size: 164
1230633 CTCCATAGTC
*
1230643 CTTCAGAGAGTATAAGACTCGAACAATCTTTC-ACAATCGCGTCTGCCCCCTATTTCTTCAGAGA
1 CTTCAGAGAGTATAAGACTCGAACAATC-TTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGA
* ** * *
1230707 GTATAAGACTCGAATAATCTTCAATGATCACGTCTGCCCCCCATTTCTTCAGAGAGTATAAGACT
65 GTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACT
* *
1230772 C-ACAATCTTCATCAATCGCGTCTGCCCCTTATTT
130 CAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
1230806 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * *
1230871 TATAAGAC-C-CACAATATTCATCAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACCC
66 TATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
* *
1230934 GAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
131 -AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
1230969 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCTCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * * *
1231034 TATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCCTCAGAGAGTATAAGACTC
66 TATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
*
1231099 GAACAATCTTCAACTATCGCGTCT-CCCCCTATTT
131 -AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1231133 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCATCCGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* *
1231198 TATAAGACTTGAACAATCTTCAACGATCG
66 TATAAGACTCGAACAATCTTCAACAATCG
1231227 TGGGGAACCT
Statistics
Matches: 382, Mismatches: 34, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
161 45 0.12
162 4 0.01
163 167 0.44
164 98 0.26
165 68 0.18
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (164 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAG
TATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTC
AACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:1231717 original size:13 final size:13
Alignment explanation
Indices: 1231699--1231732 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
1231689 ATGCTTGTAA
1231699 AAGGGAAATTGAG
1 AAGGGAAATTGAG
1231712 AAGGGAAATTGAG
1 AAGGGAAATTGAG
1231725 AAGGGAAA
1 AAGGGAAA
1231733 ATGTCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (13 bp):
AAGGGAAATTGAG
Found at i:1232276 original size:13 final size:12
Alignment explanation
Indices: 1232256--1232309 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 12
1232246 TTGTTTATTT
*
1232256 TTCATTTTTTCA
1 TTCATTTTTTTA
1232268 TTCA-TTTTTTA
1 TTCATTTTTTTA
1232279 TT--TTTATTTT-
1 TTCATTT-TTTTA
1232289 TTCATTTTTTTTA
1 TTCA-TTTTTTTA
1232302 TTCATTTT
1 TTCATTTT
1232310 CCCTTCTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
10 4 0.11
11 12 0.34
12 12 0.34
13 7 0.20
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCATTTTTTTA
Found at i:1232288 original size:25 final size:24
Alignment explanation
Indices: 1232243--1232303 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
1232233 TGTTTCTTTT
1232243 TTTTTGTTTATTTTTCATTTTTTCA
1 TTTTT-TTTATTTTTCATTTTTTCA
1232268 TTCATTTTTTATTTTT-ATTTTTTCA
1 TT--TTTTTTATTTTTCATTTTTTCA
1232293 TTTTTTTTATT
1 TTTTTTTTATT
1232304 CATTTTCCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 9 0.26
25 13 0.38
26 9 0.26
27 3 0.09
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.79
Consensus pattern (24 bp):
TTTTTTTTATTTTTCATTTTTTCA
Found at i:1232290 original size:33 final size:34
Alignment explanation
Indices: 1232239--1232309 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
1232229 TTTTTGTTTC
*
1232239 TTTTTTTTTGTTTATTTTTCA-TTTTTTCATTCA
1 TTTTTTATTGTTTATTTTTCATTTTTTTCATTCA
*
1232272 TTTTTTATT-TTTATTTTTTCATTTTTTTTATTCA
1 TTTTTTATTGTTTA-TTTTTCATTTTTTTCATTCA
1232306 TTTT
1 TTTT
1232310 CCCTTCTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 4 0.12
33 15 0.44
34 15 0.44
ACGTcount: A:0.13, C:0.07, G:0.01, T:0.79
Consensus pattern (34 bp):
TTTTTTATTGTTTATTTTTCATTTTTTTCATTCA
Found at i:1232323 original size:34 final size:33
Alignment explanation
Indices: 1232253--1232325 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 33
1232243 TTTTTGTTTA
** *
1232253 TTTTTCATTTTTTCATTCATTTTTTATTTTTAT
1 TTTTTCATTTTTTCATTCATTTTCCATTCTTAT
* * *
1232286 TTTTTCATTTTTTTTATTCATTTTCCCTTCTTCT
1 TTTTTCA-TTTTTTCATTCATTTTCCATTCTTAT
1232320 TTTTTC
1 TTTTTC
1232326 TTCAAGCAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTTCATTTTTTCATTCATTTTCCATTCTTAT
Found at i:1244231 original size:15 final size:15
Alignment explanation
Indices: 1244204--1244237 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1244194 TTTGTCTTAA
1244204 AAAATTGATTTTTCTT
1 AAAATTGATTTTT-TT
1244220 AAAATT-ATTTTTTT
1 AAAATTGATTTTTTT
1244234 AAAA
1 AAAA
1244238 GACGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 6 0.33
16 6 0.33
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
AAAATTGATTTTTTT
Found at i:1246566 original size:40 final size:39
Alignment explanation
Indices: 1246501--1246576 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
1246491 CTATAAACAA
*
1246501 AAGTGTTTGAGCATGTTTTTGGTCAAAATCTTGTAGACAT
1 AAGTGTTTGAGCATGTTATTGGTCAAAATCTT-TAGACAT
*
1246541 AAGTGTTTGAGCGTGTTCATT-GTCAAAATCTTTAGA
1 AAGTGTTTGAGCATGTT-ATTGGTCAAAATCTTTAGA
1246577 ACAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.82
41 2 0.06
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (39 bp):
AAGTGTTTGAGCATGTTATTGGTCAAAATCTTTAGACAT
Found at i:1250740 original size:20 final size:20
Alignment explanation
Indices: 1250712--1250789 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
1250702 AGGCTCATGA
* *
1250712 TATCTAGTCTACTGCTTTTC
1 TATCAAGTCTACTACTTTTC
1250732 TATCAAGTCTACTACTTTTC
1 TATCAAGTCTACTACTTTTC
*
1250752 TATCAAGTCTACTATTTTTC
1 TATCAAGTCTACTACTTTTC
*
1250772 TATCAAGTCTACTGCTTT
1 TATCAAGTCTACTACTTT
1250790 GTTCTGCTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.22, C:0.23, G:0.08, T:0.47
Consensus pattern (20 bp):
TATCAAGTCTACTACTTTTC
Found at i:1251462 original size:21 final size:22
Alignment explanation
Indices: 1251438--1251482 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1251428 AATCTAGTAG
*
1251438 GGTTTTA-AAAGCTACTATAGA
1 GGTTTTAGAAACCTACTATAGA
*
1251459 GG-TTTAGAAACCTACTGTAGA
1 GGTTTTAGAAACCTACTATAGA
1251480 GGT
1 GGT
1251483 CTAGGTAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.31
Consensus pattern (22 bp):
GGTTTTAGAAACCTACTATAGA
Found at i:1252343 original size:16 final size:16
Alignment explanation
Indices: 1252313--1252346 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1252303 CTTACTCTTG
**
1252313 GAGAGGAAAGGAAGAA
1 GAGAGGAAAAAAAGAA
1252329 GAGAGGAAAAAAAGAA
1 GAGAGGAAAAAAAGAA
1252345 GA
1 GA
1252347 AGATGAAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
GAGAGGAAAAAAAGAA
Found at i:1253600 original size:10 final size:10
Alignment explanation
Indices: 1253571--1253658 Score: 85
Period size: 10 Copynumber: 9.1 Consensus size: 10
1253561 GCTGCTGGAA
1253571 AACCGGTTTG
1 AACCGGTTTG
*
1253581 -ACCAGTTTTG
1 AACC-GGTTTG
1253591 AACCGGTTTG
1 AACCGGTTTG
*
1253601 -ACCGGTTCG
1 AACCGGTTTG
1253610 AACCGGTTTG
1 AACCGGTTTG
* *
1253620 -ACCGGTCTA
1 AACCGGTTTG
1253629 AACCGGTTTG
1 AACCGGTTTG
*
1253639 -ACCGGTCTG
1 AACCGGTTTG
*
1253648 AACCGGGTTG
1 AACCGGTTTG
1253658 A
1 A
1253659 CCCGACCCGA
Statistics
Matches: 62, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
9 26 0.42
10 33 0.53
11 3 0.05
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:1253614 original size:19 final size:19
Alignment explanation
Indices: 1253571--1253660 Score: 119
Period size: 19 Copynumber: 4.7 Consensus size: 19
1253561 GCTGCTGGAA
* *
1253571 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
1253591 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
*
1253610 AACCGGTTTGACCGGTCTA
1 AACCGGTTTGACCGGTCTG
1253629 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
1253648 AACCGGGTTGACC
1 AACCGGTTTGACC
1253661 CGACCCGACT
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
18 1 0.02
19 49 0.77
20 14 0.22
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1253676 original size:17 final size:17
Alignment explanation
Indices: 1253654--1253728 Score: 141
Period size: 17 Copynumber: 4.4 Consensus size: 17
1253644 TCTGAACCGG
*
1253654 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
1253671 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
1253688 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
1253705 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
1253722 GTTGACC
1 GTTGACC
1253729 GTGACCGTTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.17, C:0.44, G:0.24, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:1253728 original size:7 final size:7
Alignment explanation
Indices: 1253718--1253756 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1253708 GACCCGACCC
1253718 GACCGTT
1 GACCGTT
1253725 GACCG-T
1 GACCGTT
1253731 GACCGTT
1 GACCGTT
1253738 GACCG-T
1 GACCGTT
*
1253744 GACAGTT
1 GACCGTT
1253751 GACCGT
1 GACCGT
1253757 CGACTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:1253736 original size:13 final size:13
Alignment explanation
Indices: 1253718--1253756 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1253708 GACCCGACCC
1253718 GACCGTTGACCGT
1 GACCGTTGACCGT
1253731 GACCGTTGACCGT
1 GACCGTTGACCGT
*
1253744 GACAGTTGACCGT
1 GACCGTTGACCGT
1253757 CGACTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:1260965 original size:10 final size:10
Alignment explanation
Indices: 1260936--1261023 Score: 76
Period size: 10 Copynumber: 9.1 Consensus size: 10
1260926 GCTGCTGGAA
1260936 AACCGGTTTG
1 AACCGGTTTG
*
1260946 -ACCAGTTTTG
1 AACC-GGTTTG
1260956 AACCGGTTTG
1 AACCGGTTTG
*
1260966 -ACCGGTTCG
1 AACCGGTTTG
1260975 AACCGGTTTG
1 AACCGGTTTG
*
1260985 -ACCGGTCTG
1 AACCGGTTTG
* *
1260994 AACTGATTTG
1 AACCGGTTTG
*
1261004 -ACCGGTCTG
1 AACCGGTTTG
*
1261013 AACCGGGTTG
1 AACCGGTTTG
1261023 A
1 A
1261024 CCCGACCCGA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 25 0.42
10 32 0.53
11 3 0.05
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:1260979 original size:19 final size:19
Alignment explanation
Indices: 1260936--1261025 Score: 110
Period size: 19 Copynumber: 4.7 Consensus size: 19
1260926 GCTGCTGGAA
* *
1260936 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
1260956 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
1260975 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
* *
1260994 AACTGATTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
1261013 AACCGGGTTGACC
1 AACCGGTTTGACC
1261026 CGACCCGACT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
18 1 0.02
19 47 0.76
20 14 0.23
ACGTcount: A:0.19, C:0.24, G:0.29, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1261041 original size:17 final size:17
Alignment explanation
Indices: 1261019--1261051 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1261009 TCTGAACCGG
1261019 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
1261036 GTTGACCCGACCCGAC
1 GTTGACCCGACCCGAC
1261052 CATTGACCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.42, G:0.24, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:1261057 original size:17 final size:17
Alignment explanation
Indices: 1261020--1261059 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1261010 CTGAACCGGG
**
1261020 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACCA
1261037 TTGACCCGACCCGACCA
1 TTGACCCGACCCGACCA
1261054 TTGACC
1 TTGACC
1261060 GTGACCGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.17
Consensus pattern (17 bp):
TTGACCCGACCCGACCA
Found at i:1261070 original size:13 final size:13
Alignment explanation
Indices: 1261049--1261087 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1261039 GACCCGACCC
*
1261049 GACCATTGACCGT
1 GACCGTTGACCGT
1261062 GACCGTTGACCGT
1 GACCGTTGACCGT
1261075 GACCGTTGACCGT
1 GACCGTTGACCGT
1261088 TGACTTTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.31, G:0.28, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:1261071 original size:7 final size:7
Alignment explanation
Indices: 1261049--1261091 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
1261039 GACCCGACCC
*
1261049 GACCATT
1 GACCGTT
1261056 GACCG-T
1 GACCGTT
1261062 GACCGTT
1 GACCGTT
1261069 GACCG-T
1 GACCGTT
1261075 GACCGTT
1 GACCGTT
1261082 GACCGTT
1 GACCGTT
1261089 GAC
1 GAC
1261092 TTTCTTTAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
6 12 0.36
7 21 0.64
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:1263124 original size:2 final size:2
Alignment explanation
Indices: 1263117--1263151 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1263107 ACCATGATTA
1263117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1263152 ATAATTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1263175 original size:3 final size:3
Alignment explanation
Indices: 1263163--1263209 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
1263153 TAATTATTTG
* * *
1263163 TTA TTAA TTA TTA TTA TTA TTA -TA TTA TTA ATA CTA TTA ATA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1263208 TT
1 TT
1263210 TTTGCAGGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1263175 original size:17 final size:16
Alignment explanation
Indices: 1263163--1263209 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
1263153 TAATTATTTG
1263163 TTATTAATTATTATTA
1 TTATTAATTATTATTA
*
1263179 TTATTATATTATTAATA
1 TTATTA-ATTATTATTA
*
1263196 CTATTAA-TATTATT
1 TTATTAATTATTATT
1263210 TTTGCAGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.22
16 7 0.26
17 14 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTAATTATTATTA
Found at i:1263183 original size:9 final size:9
Alignment explanation
Indices: 1263169--1263209 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
1263159 TTTGTTATTA
*
1263169 ATTATTATT
1 ATTATTAAT
1263178 ATTATT-AT
1 ATTATTAAT
1263186 ATTATTAAT
1 ATTATTAAT
*
1263195 ACTATTAAT
1 ATTATTAAT
1263204 ATTATT
1 ATTATT
1263210 TTTGCAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (9 bp):
ATTATTAAT
Found at i:1264576 original size:8 final size:8
Alignment explanation
Indices: 1264563--1264593 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1264553 CATTATATTC
1264563 TATTATAT
1 TATTATAT
1264571 TATTATAT
1 TATTATAT
1264579 TATTACTAT
1 TATTA-TAT
1264588 TATTAT
1 TATTAT
1264594 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (8 bp):
TATTATAT
Found at i:1267643 original size:23 final size:22
Alignment explanation
Indices: 1267617--1267685 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
1267607 CACCACAGCT
*
1267617 CGTATAAATGCACTGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
* * *
1267640 CGTAGAATAGCACCGTAGTGCCG
1 CGTAAAAT-GCACCGAAGTGCCA
1267663 CGTAGAAATGCACCGAAGTGCCA
1 CGTA-AAATGCACCGAAGTGCCA
1267686 TATAAGGTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 3 0.08
23 31 0.84
24 3 0.08
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.17
Consensus pattern (22 bp):
CGTAAAATGCACCGAAGTGCCA
Found at i:1267806 original size:20 final size:20
Alignment explanation
Indices: 1267778--1267824 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1267768 GACCTCACAC
*
1267778 ATGTTCCAAAGAATACATAT
1 ATGTCCCAAAGAATACATAT
*
1267798 GTGTCCCAAAGAATACATAT
1 ATGTCCCAAAGAATACATAT
1267818 ATGTCCC
1 ATGTCCC
1267825 GAAAAACCGC
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:0.21, G:0.13, T:0.28
Consensus pattern (20 bp):
ATGTCCCAAAGAATACATAT
Found at i:1268174 original size:2 final size:2
Alignment explanation
Indices: 1268167--1268194 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1268157 ATCTTCCTAC
1268167 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
1268195 CATCTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.