Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008003.1 Hibiscus syriacus cultivar Beakdansim tig00110462_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: 3297763
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 14
Found at i:1091907 original size:14 final size:14
Alignment explanation
Indices: 1091888--1091915 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1091878 GTTTGGGAAA
1091888 TTTGACCCGACCCG
1 TTTGACCCGACCCG
1091902 TTTGACCCGACCCG
1 TTTGACCCGACCCG
1091916 ACTCGTTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.43, G:0.21, T:0.21
Consensus pattern (14 bp):
TTTGACCCGACCCG
Found at i:1091915 original size:19 final size:18
Alignment explanation
Indices: 1091891--1091927 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
1091881 TGGGAAATTT
1091891 GACCCGACCCGTTTGACCC
1 GACCCGACCCG-TTGACCC
*
1091910 GACCCGACTCGTTGACCC
1 GACCCGACCCGTTGACCC
1091928 AACTCGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.16, C:0.46, G:0.22, T:0.16
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:1091932 original size:13 final size:13
Alignment explanation
Indices: 1091910--1091939 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1091900 CGTTTGACCC
*
1091910 GACCCGACTCGTT
1 GACCCAACTCGTT
1091923 GACCCAACTCGTT
1 GACCCAACTCGTT
1091936 GACC
1 GACC
1091940 GTTGACTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (13 bp):
GACCCAACTCGTT
Found at i:1092160 original size:125 final size:125
Alignment explanation
Indices: 1091938--1092166 Score: 307
Period size: 125 Copynumber: 1.8 Consensus size: 125
1091928 AACTCGTTGA
** * *
1091938 CCGTTGACTTTGACCAAAAAGTCAATTTTTTCAAAAAGTCATATATTATGTTTTTTAACGTCCTG
1 CCGTTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGTCATATATTATATTTTTTAACGTCATG
* * * **
1092003 AGTTCGATTCCGAAGTCATTTTTTCAAAATTCGAACCCGAAAGCCTCGAAATTGTCAAAC
66 AATCCGAATCCGAAGTCATTTCGTCAAAATTCGAACCCGAAAGCCTCGAAATTGTCAAAC
* * *
1092063 CCGTTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGTCATATTTTATATTTTTTGATGTCATG
1 CCGTTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGTCATATATTATATTTTTTAACGTCATG
* * *
1092128 AATCCGAATCTGATGTCCGTTTCGTC-AAATTCGAACCCG
66 AATCCGAATCCGAAGT-CATTTCGTCAAAATTCGAACCCG
1092167 GTAAGCTATT
Statistics
Matches: 88, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
125 82 0.93
126 6 0.07
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (125 bp):
CCGTTGACTTTGACCAAAAAGTCAAAATTTTCAAAAAGTCATATATTATATTTTTTAACGTCATG
AATCCGAATCCGAAGTCATTTCGTCAAAATTCGAACCCGAAAGCCTCGAAATTGTCAAAC
Found at i:1094110 original size:24 final size:24
Alignment explanation
Indices: 1094077--1094162 Score: 136
Period size: 24 Copynumber: 3.6 Consensus size: 24
1094067 AATTATGTTA
1094077 TGATACTTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
1094101 TGATATTTGACCTGGATTTTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
1094125 TGTTACTTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
1094149 TGATACTTGACCTG
1 TGATACTTGACCTG
1094163 AATTATGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:1094176 original size:24 final size:24
Alignment explanation
Indices: 1094068--1094169 Score: 123
Period size: 24 Copynumber: 4.2 Consensus size: 24
1094058 TTCGATTTGA
* *
1094068 ATTATGTTATGATACTTGACCTGG
1 ATTATGATCTGATACTTGACCTGG
* *
1094092 ATTCTGATCTGATATTTGACCTGG
1 ATTATGATCTGATACTTGACCTGG
* * *
1094116 ATTTTGATCTGTTACTTGACATGG
1 ATTATGATCTGATACTTGACCTGG
* *
1094140 ATTCTGATCTGATACTTGACCTGA
1 ATTATGATCTGATACTTGACCTGG
1094164 ATTATG
1 ATTATG
1094170 TTTTGATTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (24 bp):
ATTATGATCTGATACTTGACCTGG
Found at i:1099590 original size:2 final size:2
Alignment explanation
Indices: 1099585--1099612 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1099575 TTTACTTCAA
1099585 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
1099613 CACCAATAAC
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
Found at i:1100369 original size:18 final size:18
Alignment explanation
Indices: 1100345--1100391 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1100335 CTCGGGCGGA
1100345 GAAGAGGAAGAGGAGAAG
1 GAAGAGGAAGAGGAGAAG
* * *
1100363 TAAGAGGAGGAGGAGGAG
1 GAAGAGGAAGAGGAGAAG
*
1100381 GAAGAAGAAGA
1 GAAGAGGAAGA
1100392 TGCAGAGAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (18 bp):
GAAGAGGAAGAGGAGAAG
Found at i:1101349 original size:12 final size:12
Alignment explanation
Indices: 1101310--1101350 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
1101300 CGTTTTCGTT
*
1101310 TCCGTTCCCGTA
1 TCCGTCCCCGTA
*
1101322 TCCATCCCCGTA
1 TCCGTCCCCGTA
1101334 TCCGTCCCCGTA
1 TCCGTCCCCGTA
1101346 TCCGT
1 TCCGT
1101351 ATCAGTGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.10, C:0.46, G:0.15, T:0.29
Consensus pattern (12 bp):
TCCGTCCCCGTA
Found at i:1101482 original size:59 final size:59
Alignment explanation
Indices: 1101390--1101507 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
1101380 AAGCGATAAT
1101390 CCATATCAGAAACTCACCTCTCTGTTTTGATGTTTTTACAACCCAACATTTCCAAATAG
1 CCATATCAGAAACTCACCTCTCTGTTTTGATGTTTTTACAACCCAACATTTCCAAATAG
1101449 CCATATCAGAAACTCACCTCTCTGTTTTGATGTTTTTACAACCCAACATTTCCAAATAG
1 CCATATCAGAAACTCACCTCTCTGTTTTGATGTTTTTACAACCCAACATTTCCAAATAG
1101508 GTGCACACTG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.31, C:0.27, G:0.08, T:0.34
Consensus pattern (59 bp):
CCATATCAGAAACTCACCTCTCTGTTTTGATGTTTTTACAACCCAACATTTCCAAATAG
Found at i:1104076 original size:2 final size:2
Alignment explanation
Indices: 1104069--1104100 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1104059 TTAAACCCAA
1104069 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1104101 AATTGTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1105731 original size:17 final size:17
Alignment explanation
Indices: 1105701--1105743 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
1105691 ATACAAAGAA
1105701 TAAATTTTAGAATTATG
1 TAAATTTTAGAATTATG
1105718 TAAACTTTTA-AATTATTTG
1 TAAA-TTTTAGAATTA--TG
1105737 TAAATTT
1 TAAATTT
1105744 GGTTTACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 9 0.39
18 8 0.35
19 6 0.26
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (17 bp):
TAAATTTTAGAATTATG
Found at i:1105902 original size:24 final size:20
Alignment explanation
Indices: 1105850--1105891 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1105840 TTTCTTAATC
*
1105850 ATTAACAACATACACATTCA
1 ATTAACAACATACACATGCA
1105870 ATTAACAACATACACATGCA
1 ATTAACAACATACACATGCA
1105890 AT
1 AT
1105892 GATACGACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (20 bp):
ATTAACAACATACACATGCA
Found at i:1110295 original size:16 final size:16
Alignment explanation
Indices: 1110274--1110306 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1110264 TAAAAAATAA
1110274 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1110290 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1110306 A
1 A
1110307 AAATTTTTTT
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:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1110397 original size:16 final size:16
Alignment explanation
Indices: 1110376--1110436 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
1110366 TAATAAATAA
1110376 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1110392 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1110408 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
1110424 ACGAACATAAACG
1 ACGAACATAAACG
1110437 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1111197 original size:14 final size:14
Alignment explanation
Indices: 1111180--1111235 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1111170 AATGAACATA
*
1111180 AACGAACATAATCG
1 AACGAACATAACCG
1111194 AACGAACAT-A---
1 AACGAACATAACCG
*
1111204 AACGAACATAACCA
1 AACGAACATAACCG
1111218 AACGAACATAACCG
1 AACGAACATAACCG
1111232 AACG
1 AACG
1111236 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1111200 original size:24 final size:24
Alignment explanation
Indices: 1111160--1111234 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
1111150 GATTGTGTTA
*
1111160 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
1111184 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
1111208 AACATAACCAAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
1111232 AAC
1 AAC
1111235 GTTCACGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 3 0.07
24 43 0.93
ACGTcount: A:0.56, C:0.21, G:0.11, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:1113729 original size:2 final size:2
Alignment explanation
Indices: 1113722--1113752 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1113712 TGAAAAATAT
1113722 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1113753 ATATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1123754 original size:85 final size:85
Alignment explanation
Indices: 1123624--1123800 Score: 284
Period size: 85 Copynumber: 2.1 Consensus size: 85
1123614 TCTTTAAATA
* *
1123624 GAATAACATTCTCTTAGACTAATATATTCATTCAATATGTT-AAAAAAAGATATTAAAATAAAAT
1 GAATAACATTCTCTTAGACTAATAAAATCATTCAATATGTTAAAAAAAAGATATTAAAATAAAA-
1123688 AAATAAATAATTAGGGCAATT
65 AAATAAATAATTAGGGCAATT
* *
1123709 GAATAACATTTTCTTAGACTAATAAAATCATTCAATATGTTAAAAAAAATATATTAAAATAAAAA
1 GAATAACATTCTCTTAGACTAATAAAATCATTCAATATGTTAAAAAAAAGATATTAAAATAAAAA
* *
1123774 TATAAATAATTAGTGCAATT
66 AATAAATAATTAGGGCAATT
1123794 GAATAAC
1 GAATAAC
1123801 CTATATTTTA
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
85 64 0.75
86 21 0.25
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (85 bp):
GAATAACATTCTCTTAGACTAATAAAATCATTCAATATGTTAAAAAAAAGATATTAAAATAAAAA
AATAAATAATTAGGGCAATT
Found at i:1125447 original size:2 final size:2
Alignment explanation
Indices: 1125440--1125466 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1125430 TTAAACAAGT
1125440 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 T
1125467 GTTTTGATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1126471 original size:193 final size:191
Alignment explanation
Indices: 1126144--1126503 Score: 571
Period size: 193 Copynumber: 1.9 Consensus size: 191
1126134 ATTAATCTGA
* *
1126144 AAAATGATCGTCCCTTTTTCCCATATGTATGGGGTAAGGGGAGGTAAGATAGTAGGCTACTCCCA
1 AAAATGATCGTCCCTTGTTCCCATATGTATGGGGTAAGGGGAGATAAGATAGTAGGCTACTCCCA
* * *
1126209 ACACCAGGTTGAGAGTAGCTTCCGTAAGAGACCTCTGAATTATGAAATGCCCTCCGTGGGACTCG
66 ACACCAGGTTGAGAGCAGCTTCCGTAAGAGACCTCCGAATTATGAAATGCCCTCAGTGGGACTCG
*
1126274 ATCCCACGACCTCAAGGTTAAGAACATTGTGCTCTACCAATTGAGCTGGATGGTCATTTTT
131 ATCCCACGACCTCAAGATTAAGAACATTGTGCTCTACCAATTGAGCTGGATGGTCATTTTT
* * *
1126335 AAAATGATTGTCCCTTGTTCTCATATGTAATGGGGTAAGGGGGAGATAAGATAGTAGGCTGC-CT
1 AAAATGATCGTCCCTTGTTCCCATATGT-ATGGGGTAA-GGGGAGATAAGATAGTAGGCTACTC-
*
1126399 CCAACACCAGGTTGAGAGCATCTTCCGT-AGAAGACCTCCGAATTATGAAATGCCCTCAGTGGGA
63 CCAACACCAGGTTGAGAGCAGCTTCCGTAAG-AGACCTCCGAATTATGAAATGCCCTCAGTGGGA
*
1126463 CTCGATCCCACGACCTCAAGATTAAGAACCTTGTGCTCTAC
127 CTCGATCCCACGACCTCAAGATTAAGAACATTGTGCTCTAC
1126504 ACATATATAA
Statistics
Matches: 154, Mismatches: 11, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
191 25 0.16
192 12 0.08
193 117 0.76
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (191 bp):
AAAATGATCGTCCCTTGTTCCCATATGTATGGGGTAAGGGGAGATAAGATAGTAGGCTACTCCCA
ACACCAGGTTGAGAGCAGCTTCCGTAAGAGACCTCCGAATTATGAAATGCCCTCAGTGGGACTCG
ATCCCACGACCTCAAGATTAAGAACATTGTGCTCTACCAATTGAGCTGGATGGTCATTTTT
Found at i:1126980 original size:25 final size:22
Alignment explanation
Indices: 1126950--1127002 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 22
1126940 TTATTAATAA
*
1126950 TTTAATTTTATATCTATTGAAATT
1 TTTAATTTTACATCT-TT-AAATT
1126974 TTATAATTTTACATCTTTAAATT
1 TT-TAATTTTACATCTTTAAATT
1126997 TTTAAT
1 TTTAAT
1127003 ATAACTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 4 0.15
25 12 0.44
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTAATTTTACATCTTTAAATT
Found at i:1128514 original size:30 final size:30
Alignment explanation
Indices: 1128480--1128540 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1128470 GATAATGTCT
1128480 TTTCATTCTTCTCCTTTTCCTCCTTAACAG
1 TTTCATTCTTCTCCTTTTCCTCCTTAACAG
1128510 TTTCATTCTTCTCCTTTTCCTCCTTAACAG
1 TTTCATTCTTCTCCTTTTCCTCCTTAACAG
1128540 T
1 T
1128541 CAGCAATGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.13, C:0.33, G:0.03, T:0.51
Consensus pattern (30 bp):
TTTCATTCTTCTCCTTTTCCTCCTTAACAG
Found at i:1134831 original size:20 final size:20
Alignment explanation
Indices: 1134808--1134858 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1134798 CACGGAATGT
1134808 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
1134828 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
1134848 AAGATTACCAG
1 AAGATTACCAG
1134859 GAAATAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:1135066 original size:20 final size:21
Alignment explanation
Indices: 1135041--1135092 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
1135031 GACCAACAAA
1135041 TTCGCAACGCGA-ATTCCAAT
1 TTCGCAACGCGAGATTCCAAT
* *
1135061 TTCGCAACTC-AGTTTCCAAT
1 TTCGCAACGCGAGATTCCAAT
1135081 TTCGCAACGCGA
1 TTCGCAACGCGA
1135093 TAGTCAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (21 bp):
TTCGCAACGCGAGATTCCAAT
Found at i:1135283 original size:22 final size:22
Alignment explanation
Indices: 1135257--1135307 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1135247 CTACAACGAC
1135257 ATCCGTCCCCATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
*
1135279 ATCCGTCCCTATCTCCGACAAA
1 ATCCGTCCCCATCTCCGACAAA
1135301 ATCCGTC
1 ATCCGTC
1135308 TATCTCCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.43, G:0.10, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACAAA
Found at i:1135312 original size:20 final size:21
Alignment explanation
Indices: 1135257--1135314 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 21
1135247 CTACAACGAC
*
1135257 ATCCGTCCCCATCTCCGACAAA
1 ATCCGT-CCTATCTCCGACAAA
1135279 ATCCGTCCCTATCTCCGACAAA
1 ATCCGT-CCTATCTCCGACAAA
1135301 ATCCGT-CTATCTCC
1 ATCCGTCCTATCTCC
1135315 ATCTCTCAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 8 0.23
22 27 0.77
ACGTcount: A:0.24, C:0.43, G:0.09, T:0.24
Consensus pattern (21 bp):
ATCCGTCCTATCTCCGACAAA
Found at i:1135628 original size:20 final size:20
Alignment explanation
Indices: 1135587--1135628 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1135577 GAAACTAAAA
* * *
1135587 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGAATTTAAGTT
1135607 TCGCGTTGCGAATTTAAGTT
1 TCGCGTTGCGAATTTAAGTT
1135627 TC
1 TC
1135629 AGAAACTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGAATTTAAGTT
Found at i:1137824 original size:42 final size:42
Alignment explanation
Indices: 1137777--1137875 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
1137767 CCTGATGCAC
* ***
1137777 CTATCATCATTCAAGAGGTGTCTCCTATC-GTTCAAGAGGCCA
1 CTATCATCATTCAAGAAGCCCCTCCTA-CAGTTCAAGAGGCCA
1137819 CTATCATCA-TCGAAGAAGCCCCTCCTACAGTTCAAGAGGCCA
1 CTATCATCATTC-AAGAAGCCCCTCCTACAGTTCAAGAGGCCA
* *
1137861 CTGTCATCGTTCAAG
1 CTATCATCATTCAAG
1137876 TGGTCCCGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.06
42 43 0.90
43 2 0.04
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.25
Consensus pattern (42 bp):
CTATCATCATTCAAGAAGCCCCTCCTACAGTTCAAGAGGCCA
Found at i:1139737 original size:39 final size:39
Alignment explanation
Indices: 1139683--1139769 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
1139673 TCAAGTTGTA
1139683 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
1139722 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1139761 GATTTTGAT
1 GATTTTGAT
1139770 GAGCATCAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1140061 original size:18 final size:18
Alignment explanation
Indices: 1140038--1140074 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1140028 CGAAATTTAT
1140038 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1140056 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1140074 A
1 A
1140075 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:1140498 original size:25 final size:25
Alignment explanation
Indices: 1140461--1140510 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
1140451 ATTATTTTTC
*
1140461 CAAATAATATACCCATAACAATGTT
1 CAAATAATATACCCACAACAATGTT
*
1140486 CAAATAATGTACCCACAACAATGTT
1 CAAATAATATACCCACAACAATGTT
1140511 TAATTGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (25 bp):
CAAATAATATACCCACAACAATGTT
Found at i:1140594 original size:20 final size:20
Alignment explanation
Indices: 1140571--1140608 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1140561 AGACCTGTTG
1140571 AAGGTAAATTCGCAACGCGA
1 AAGGTAAATTCGCAACGCGA
1140591 AAGGTAAATTCGCAACGC
1 AAGGTAAATTCGCAACGC
1140609 AAAATAAGCA
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:0.39, C:0.21, G:0.24, T:0.16
Consensus pattern (20 bp):
AAGGTAAATTCGCAACGCGA
Found at i:1140643 original size:20 final size:20
Alignment explanation
Indices: 1140620--1140690 Score: 55
Period size: 20 Copynumber: 3.9 Consensus size: 20
1140610 AAATAAGCAT
1140620 TGCGATAGTCAAATTCGTAA
1 TGCGATAGTCAAATTCGTAA
* *
1140640 TGCGA-AAT--AA-GCGT--
1 TGCGATAGTCAAATTCGTAA
*
1140654 TGCGATAGTCAAATTCGCAA
1 TGCGATAGTCAAATTCGTAA
* *
1140674 CGCGAAAGTCAAATTCG
1 TGCGATAGTCAAATTCG
1140691 CAACGCTTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 3 0.08
17 4 0.11
18 2 0.05
19 2 0.05
20 20 0.53
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (20 bp):
TGCGATAGTCAAATTCGTAA
Found at i:1140648 original size:34 final size:34
Alignment explanation
Indices: 1140596--1140680 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
1140586 CGCGAAAGGT
*
1140596 AAATTCGCAACGCAAAATAAGCATTGCGATAGTC
1 AAATTCGCAACGCGAAATAAGCATTGCGATAGTC
* * *
1140630 AAATTCGTAATGCGAAATAAGCGTTGCGATAGTC
1 AAATTCGCAACGCGAAATAAGCATTGCGATAGTC
1140664 AAATTCGCAACGCGAAA
1 AAATTCGCAACGCGAAA
1140681 GTCAAATTCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (34 bp):
AAATTCGCAACGCGAAATAAGCATTGCGATAGTC
Found at i:1140691 original size:20 final size:20
Alignment explanation
Indices: 1140655--1140696 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1140645 AATAAGCGTT
*
1140655 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
1140675 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
1140695 GC
1 GC
1140697 TTATTTCGCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1143337 original size:24 final size:24
Alignment explanation
Indices: 1143310--1143363 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1143300 CCATCACATC
*
1143310 ATCAAAATCCGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1143334 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1143358 ATCAAA
1 ATCAAA
1143364 TTTAGAATAC
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:0.19, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1143510 original size:12 final size:12
Alignment explanation
Indices: 1143489--1143522 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1143479 GGTTGTGGGT
*
1143489 TTTGAGATTGTG
1 TTTGATATTGTG
1143501 TTTGATATTGTG
1 TTTGATATTGTG
*
1143513 TTTGGTATTG
1 TTTGATATTG
1143523 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1144306 original size:20 final size:20
Alignment explanation
Indices: 1144281--1144337 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1144271 CGAAATTAAA
1144281 TTCGCGTTGCGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
*
1144301 TTCGCGTTGAGAATTTGACT
1 TTCGCGTTGCGAATTTGACT
*
1144321 ATCGCGTTGCGAATTTG
1 TTCGCGTTGCGAATTTG
1144338 GAAAATCGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.39
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTGACT
Found at i:1144390 original size:20 final size:20
Alignment explanation
Indices: 1144267--1144414 Score: 90
Period size: 20 Copynumber: 7.4 Consensus size: 20
1144257 ACTAAAACCT
*
1144267 GTTGCGAAATT-AAATTCGC
1 GTTGCGAAATTGGAATTCGC
* *
1144286 GTTGCG-AATTTGACTTTCGC
1 GTTGCGAAATTGGA-ATTCGC
* * *
1144306 GTTGAG-AATTTGACTATCGC
1 GTTGCGAAATTGGAAT-TCGC
* *
1144326 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAAATTGG-AATTCGC
** * **
1144347 AATGCG-ATTTACATATTCGC
1 GTTGCGAAATTGGA-ATTCGC
*
1144367 GTTGCGAAATTGGAAATT-GG
1 GTTGCGAAATTGG-AATTCGC
1144387 GTTGCGAAATTGGAATTCGC
1 GTTGCGAAATTGGAATTCGC
1144407 GTTGCGAA
1 GTTGCGAA
1144415 TTTGTTGGTG
Statistics
Matches: 99, Mismatches: 21, Indels: 17
0.72 0.15 0.12
Matches are distributed among these distances:
18 4 0.04
19 13 0.13
20 62 0.63
21 18 0.18
22 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGAAATTGGAATTCGC
Found at i:1144983 original size:16 final size:16
Alignment explanation
Indices: 1144958--1144989 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1144948 TGGATTCCAT
*
1144958 TCCCGGGGAATCCCAA
1 TCCCGAGGAATCCCAA
1144974 TCCCGAGGAATCCCAA
1 TCCCGAGGAATCCCAA
1144990 ATTCCCCCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.38, G:0.22, T:0.12
Consensus pattern (16 bp):
TCCCGAGGAATCCCAA
Found at i:1147711 original size:18 final size:17
Alignment explanation
Indices: 1147688--1147721 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1147678 CAGTCTGTTT
1147688 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
1147706 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
1147722 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1152104 original size:21 final size:21
Alignment explanation
Indices: 1152078--1152122 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1152068 GATTTCTGGG
* *
1152078 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1152099 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1152120 CAA
1 CAA
1152123 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1152731 original size:18 final size:18
Alignment explanation
Indices: 1152708--1152742 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1152698 CTAGGAGATT
1152708 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1152726 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1152743 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1152876 original size:2 final size:2
Alignment explanation
Indices: 1152869--1152902 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1152859 CAGATTAGAT
1152869 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
1152903 GAAATAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1153833 original size:149 final size:149
Alignment explanation
Indices: 1153655--1153958 Score: 554
Period size: 149 Copynumber: 2.0 Consensus size: 149
1153645 GAGTCGAGGG
* *
1153655 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1153720 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTTCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
1153785 TATGGCACTACGGTGCAAT
131 TATGGCACTACGATGCAAT
*
1153804 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1153869 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
1153934 TATGGCATTACGATGCAAT
131 TATGGCACTACGATGCAAT
1153953 TCTACG
1 TCTACG
1153959 ATGCACTTCG
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGATGCAAT
Found at i:1159102 original size:18 final size:17
Alignment explanation
Indices: 1159079--1159112 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1159069 CAGTCTGTTT
1159079 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
1159097 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
1159113 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:1160230 original size:20 final size:20
Alignment explanation
Indices: 1160194--1160231 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1160184 ATCTTATTCT
**
1160194 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
1160214 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
1160232 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:1160920 original size:8 final size:8
Alignment explanation
Indices: 1160899--1160929 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
1160889 TATATGCTCC
1160899 TATTATATG
1 TATTATA-G
1160908 TATTATAG
1 TATTATAG
1160916 TATTATAG
1 TATTATAG
1160924 TATTAT
1 TATTAT
1160930 TGATTGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 15 0.68
9 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (8 bp):
TATTATAG
Found at i:1161500 original size:28 final size:28
Alignment explanation
Indices: 1161446--1161500 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1161436 TTTTACTCAC
**
1161446 ATTAGAGTACAAAGACTAAAATTACAAA
1 ATTAGAGTACAAAGACTAAAACCACAAA
* *
1161474 ATTAGAGTACAAGGACTAAAGCCACAA
1 ATTAGAGTACAAAGACTAAAACCACAA
1161501 TATACATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.18
Consensus pattern (28 bp):
ATTAGAGTACAAAGACTAAAACCACAAA
Found at i:1164408 original size:20 final size:22
Alignment explanation
Indices: 1164365--1164409 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
1164355 CCGAAAATAT
*
1164365 TAAAAAATATTAATGTTTTAAG
1 TAAAAAATATTAATGTTTCAAG
*
1164387 TAAAAAA-A-TAATGTTTCCAG
1 TAAAAAATATTAATGTTTCAAG
1164407 TAA
1 TAA
1164410 TTTTTTATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 1 0.05
22 7 0.33
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (22 bp):
TAAAAAATATTAATGTTTCAAG
Found at i:1165560 original size:9 final size:9
Alignment explanation
Indices: 1165548--1165581 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1165538 GCTTCTTCCA
*
1165548 CTTCATCTC
1 CTTCACCTC
1165557 CTTCACCTC
1 CTTCACCTC
*
1165566 CTTCACCAC
1 CTTCACCTC
1165575 CTTCACC
1 CTTCACC
1165582 ATCATCTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.15, C:0.53, G:0.00, T:0.32
Consensus pattern (9 bp):
CTTCACCTC
Found at i:1176433 original size:69 final size:69
Alignment explanation
Indices: 1176066--1176394 Score: 586
Period size: 69 Copynumber: 4.8 Consensus size: 69
1176056 CTTATCTATT
* * * * *
1176066 TTTGCAGACTCTGTTCCAAGCACCCCTGCTTATGCAGATAACATGCTCAAGGGTCAGAGTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1176131 CTTG
66 CTTG
1176135 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1176200 CTTG
66 CTTG
*
1176204 TTTGCAGATTCCGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1176269 CTTG
66 CTTG
*
1176273 TTTACAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
1176338 CTTG
66 CTTG
*
1176342 TTTGCAGATTCTGTTCCGAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGG
1176395 GAAGGGCTCT
Statistics
Matches: 250, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 250 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.31
Consensus pattern (69 bp):
TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCGGATAACATGTTCAAGGGTCAGAGTTCATC
CTTG
Found at i:1178691 original size:15 final size:15
Alignment explanation
Indices: 1178673--1178717 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
1178663 GATTTACTGT
1178673 ATATTTTTTTATATG
1 ATATTTTTTTATATG
*
1178688 ATATTTGTTTAT-TG
1 ATATTTTTTTATATG
*
1178702 -TATTTTTGTATATG
1 ATATTTTTTTATATG
1178716 AT
1 AT
1178718 TTCTGAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
13 9 0.36
14 4 0.16
15 12 0.48
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.64
Consensus pattern (15 bp):
ATATTTTTTTATATG
Found at i:1191733 original size:3 final size:3
Alignment explanation
Indices: 1191727--1191772 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
1191717 AACAACAGAT
*
1191727 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG AGGG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A-AG AAG AAG AAG
1191772 A
1 A
1191773 GATTGAATTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1200149 original size:2 final size:2
Alignment explanation
Indices: 1200142--1200172 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1200132 ACCTTTCTGC
1200142 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 A
1200173 ATGTGTAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1208920 original size:18 final size:19
Alignment explanation
Indices: 1208891--1208935 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
1208881 TTTTAGACCA
* *
1208891 TTTAATTT-AATTTTAACT
1 TTTAATTTAAATTATAAAT
1208909 TTT-ATTTAAATTATAAAT
1 TTTAATTTAAATTATAAAT
1208927 TTTAATTTA
1 TTTAATTTA
1208936 GTCAAATTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 14 0.61
19 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATTTAAATTATAAAT
Found at i:1208935 original size:23 final size:24
Alignment explanation
Indices: 1208899--1208944 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
1208889 CATTTAATTT
* *
1208899 AATTTTAACTTTTATTTAAATTATA
1 AATTTTAAC-TTTAGTCAAATTATA
1208924 AATTTTAA-TTTAGTCAAATTA
1 AATTTTAACTTTAGTCAAATTA
1208945 CATCATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (24 bp):
AATTTTAACTTTAGTCAAATTATA
Found at i:1208998 original size:23 final size:26
Alignment explanation
Indices: 1208972--1209041 Score: 92
Period size: 26 Copynumber: 2.8 Consensus size: 26
1208962 TATTGATAGA
*
1208972 TTAAATCATT-T-AT-ACTAACATGG
1 TTAAATCATTATAATAAATAACATGG
*
1208995 TTAAATGATTATAATAAATAACATGG
1 TTAAATCATTATAATAAATAACATGG
*
1209021 TTAAATGATTATAATAAATAA
1 TTAAATCATTATAATAAATAA
1209042 ATTAAAATTG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
23 9 0.21
24 1 0.02
25 2 0.05
26 30 0.71
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (26 bp):
TTAAATCATTATAATAAATAACATGG
Found at i:1209018 original size:26 final size:26
Alignment explanation
Indices: 1208987--1209041 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1208977 TCATTTATAC
1208987 TAACATGGTTAAATGATTATAATAAA
1 TAACATGGTTAAATGATTATAATAAA
1209013 TAACATGGTTAAATGATTATAATAAA
1 TAACATGGTTAAATGATTATAATAAA
1209039 TAA
1 TAA
1209042 ATTAAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (26 bp):
TAACATGGTTAAATGATTATAATAAA
Found at i:1210594 original size:23 final size:23
Alignment explanation
Indices: 1210524--1210731 Score: 202
Period size: 23 Copynumber: 9.1 Consensus size: 23
1210514 GAATACGAAT
*
1210524 AAATGGGTTTATGGAAGAATAAG
1 AAATGGGTTTATGGAAGAAGAAG
**** **
1210547 AAACACATTTATGGGGGAA-AAG
1 AAATGGGTTTATGGAAGAAGAAG
*
1210569 AAATGGGTTTATGGAAGAAAAAG
1 AAATGGGTTTATGGAAGAAGAAG
*
1210592 AAAGGGGTTTATGGAAGAAGAAG
1 AAATGGGTTTATGGAAGAAGAAG
* *
1210615 AAAGGGGTTTATGGGAGAAGAAG
1 AAATGGGTTTATGGAAGAAGAAG
**** *
1210638 AAGCAAGTTTATGGAAGAATAAG
1 AAATGGGTTTATGGAAGAAGAAG
* *
1210661 CAATGAGTTTATGGAAGAAGAAG
1 AAATGGGTTTATGGAAGAAGAAG
* * *
1210684 CAATGAGTTTGTGGAAGAAGAAG
1 AAATGGGTTTATGGAAGAAGAAG
* *
1210707 AAACGTGTTTATGGAAGAAGAAG
1 AAATGGGTTTATGGAAGAAGAAG
1210730 AA
1 AA
1210732 TGATTTAAAT
Statistics
Matches: 153, Mismatches: 31, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
22 16 0.10
23 137 0.90
ACGTcount: A:0.44, C:0.03, G:0.32, T:0.21
Consensus pattern (23 bp):
AAATGGGTTTATGGAAGAAGAAG
Found at i:1210768 original size:4 final size:4
Alignment explanation
Indices: 1210759--1210796 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1210749 TGATTCCCCC
*
1210759 TTAA TTAA TTAA TTAA TTAG TTAA TTAA TT-A TTAA TTA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTA
1210797 CATATTAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (4 bp):
TTAA
Found at i:1211945 original size:34 final size:32
Alignment explanation
Indices: 1211906--1211975 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1211896 TTTTGTAAAG
*
1211906 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1211940 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1211972 GGGA
1 GGGA
1211976 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1213861 original size:21 final size:21
Alignment explanation
Indices: 1213836--1213876 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1213826 TATGGGCAAA
* *
1213836 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
1213857 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
1213877 ACGAACAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:1215612 original size:149 final size:149
Alignment explanation
Indices: 1215340--1215654 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
1215330 GAGTCGAGGG
* * *
1215340 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1215405 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTA
1215470 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
1215489 TTTACGCGGTCCTTCGGGATATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
1215554 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTA
1215619 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
1215638 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1215655 TGCAATTATA
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTATGTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATATGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAAT
Found at i:1215655 original size:23 final size:23
Alignment explanation
Indices: 1215622--1215666 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1215612 ATTATTATAT
*
1215622 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1215645 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1215667 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1217543 original size:17 final size:18
Alignment explanation
Indices: 1217523--1217556 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1217513 AGAATGTCCA
1217523 GGGGTACAGA-TCCCCCC
1 GGGGTACAGATTCCCCCC
*
1217540 GGGGTACCGATTCCCCC
1 GGGGTACAGATTCCCCC
1217557 TGTCTAACGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.41, G:0.29, T:0.15
Consensus pattern (18 bp):
GGGGTACAGATTCCCCCC
Found at i:1218461 original size:12 final size:12
Alignment explanation
Indices: 1218424--1218449 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1218414 ATTATCAAGT
1218424 AAAAATATCTAA
1 AAAAATATCTAA
1218436 AAAAATATCTAA
1 AAAAATATCTAA
1218448 AA
1 AA
1218450 TATATAAAAA
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:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATATCTAA
Found at i:1224843 original size:6 final size:7
Alignment explanation
Indices: 1224827--1224854 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1224817 ATAACATTGT
1224827 AAAAAGA
1 AAAAAGA
1224834 AAAAAGA
1 AAAAAGA
1224841 AAAAAGA
1 AAAAAGA
1224848 AAAAAGA
1 AAAAAGA
1224855 GAGGATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:1226912 original size:19 final size:19
Alignment explanation
Indices: 1226866--1226914 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
1226856 TTCTCATCTC
*
1226866 AGAAAATAAAAAATTTCCCA
1 AGAAAA-AAAAAAGTTCCCA
*
1226886 AG-AAAAAAATAGTTCCCA
1 AGAAAAAAAAAAGTTCCCA
1226904 AGAAAAAAAAA
1 AGAAAAAAAAA
1226915 CTATGTCTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 13 0.52
19 10 0.40
20 2 0.08
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.14
Consensus pattern (19 bp):
AGAAAAAAAAAAGTTCCCA
Found at i:1238301 original size:20 final size:20
Alignment explanation
Indices: 1238276--1238325 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1238266 GGTTGAAGAA
1238276 GTATCGATACTTATATGAAG
1 GTATCGATACTTATATGAAG
1238296 GTATCGATACTTATATGAAG
1 GTATCGATACTTATATGAAG
1238316 GTATCGATAC
1 GTATCGATAC
1238326 CAAGGATAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.34
Consensus pattern (20 bp):
GTATCGATACTTATATGAAG
Found at i:1238968 original size:27 final size:27
Alignment explanation
Indices: 1238938--1239017 Score: 103
Period size: 27 Copynumber: 3.0 Consensus size: 27
1238928 TGTGATATAC
1238938 TATGT-AAAAGTTTCTACATGAAGATGA
1 TATGTGAAAAGTTT-TACATGAAGATGA
1238965 TATGTGAAAA-TGTTTACATGAAGATGA
1 TATGTGAAAAGT-TTTACATGAAGATGA
*
1238992 TATGTGAAAA-TGTTTATATGAAGATG
1 TATGTGAAAAGT-TTTACATGAAGATG
1239018 TTCTATATGA
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
27 44 0.88
28 6 0.12
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (27 bp):
TATGTGAAAAGTTTTACATGAAGATGA
Found at i:1239018 original size:14 final size:14
Alignment explanation
Indices: 1238955--1239028 Score: 62
Period size: 14 Copynumber: 5.4 Consensus size: 14
1238945 AAGTTTCTAC
*
1238955 ATGAAGATG-ATAT
1 ATGAAGATGTTTAT
* * *
1238968 GTGAAAATGTTTAC
1 ATGAAGATGTTTAT
*
1238982 ATGAAGATG-ATAT
1 ATGAAGATGTTTAT
* *
1238995 GTGAAAATGTTTAT
1 ATGAAGATGTTTAT
1239009 ATGAAGATGTTCTAT
1 ATGAAGATGTT-TAT
1239024 ATGAA
1 ATGAA
1239029 AATAATCTAT
Statistics
Matches: 45, Mismatches: 13, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
13 16 0.36
14 21 0.47
15 8 0.18
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.35
Consensus pattern (14 bp):
ATGAAGATGTTTAT
Found at i:1239026 original size:15 final size:14
Alignment explanation
Indices: 1238969--1239031 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
1238959 AGATGATATG
*
1238969 TGAAAATGTTTACA
1 TGAAAATGTTTATA
* * *
1238983 TGAAGATG-ATATG
1 TGAAAATGTTTATA
1238996 TGAAAATGTTTATA
1 TGAAAATGTTTATA
*
1239010 TGAAGATGTTCTATA
1 TGAAAATGTT-TATA
1239025 TGAAAAT
1 TGAAAAT
1239032 AATCTATGTG
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
13 9 0.24
14 19 0.50
15 10 0.26
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.37
Consensus pattern (14 bp):
TGAAAATGTTTATA
Found at i:1239262 original size:22 final size:23
Alignment explanation
Indices: 1239226--1239277 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
1239216 TTGTACAAGT
1239226 CTATGTGCCACTTCGGTACAAAC
1 CTATGTGCCACTTCGGTACAAAC
*
1239249 CTATGTG-CACTTCGGTGCAAAC
1 CTATGTGCCACTTCGGTACAAAC
1239271 CTATGTG
1 CTATGTG
1239278 GTTCTTCGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 21 0.75
23 7 0.25
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (23 bp):
CTATGTGCCACTTCGGTACAAAC
Found at i:1239275 original size:45 final size:44
Alignment explanation
Indices: 1239226--1239313 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 44
1239216 TTGTACAAGT
*
1239226 CTATGTGCCACTTCGGTACAAACCTATGT-GCACTTCGGTGCAAAC
1 CTATGTGCCACTTCGGGACAAA--TATGTGGCACTTCGGTGCAAAC
*** *
1239271 CTATGTGGTTCTTCGGGATAAATATGTGGCACTTCGGTGCAAA
1 CTATGTGCCACTTCGGGACAAATATGTGGCACTTCGGTGCAAA
1239314 TTATGTGAGC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
43 5 0.14
44 15 0.41
45 17 0.46
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.30
Consensus pattern (44 bp):
CTATGTGCCACTTCGGGACAAATATGTGGCACTTCGGTGCAAAC
Found at i:1241240 original size:6 final size:6
Alignment explanation
Indices: 1241229--1241258 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1241219 CTAGTTCTTT
1241229 CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG
1 CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG
1241259 TCTCTTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
CCCTTG
Found at i:1241897 original size:3 final size:3
Alignment explanation
Indices: 1241884--1241913 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1241874 GGAAGATGGT
*
1241884 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1241914 GAGGAGGAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:1246004 original size:77 final size:77
Alignment explanation
Indices: 1245919--1246071 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 77
1245909 GCATTACAAT
*
1245919 AAGAAACCAAAAAAAATCAAATTCTTGCCCGATAATAATAATAATAGCAATAATCCCCTCGATTA
1 AAGAAACCAAAAAAAATCAAATTCTTGCCCGATAATAATAATAATAGAAATAATCCCCTCGATTA
1245984 CTGCTGATGAAC
66 CTGCTGATGAAC
*
1245996 AAGAAACCAAACAAAATCAAATTCTTGCCCGATAATAATAATAATAGAAATAATCCCCTCGATTA
1 AAGAAACCAAAAAAAATCAAATTCTTGCCCGATAATAATAATAATAGAAATAATCCCCTCGATTA
1246061 CTGCTGATGAA
66 CTGCTGATGAA
1246072 TGTATAAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (77 bp):
AAGAAACCAAAAAAAATCAAATTCTTGCCCGATAATAATAATAATAGAAATAATCCCCTCGATTA
CTGCTGATGAAC
Found at i:1246278 original size:21 final size:20
Alignment explanation
Indices: 1246248--1246295 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
1246238 CTTCGTCCTA
* *
1246248 AATCAAAGAAGACAAACATTC
1 AATCACAGAACAC-AACATTC
*
1246269 AATCACAGAACACCACATTC
1 AATCACAGAACACAACATTC
*
1246289 AAGCACA
1 AATCACA
1246296 TGCAAATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.52, C:0.27, G:0.08, T:0.12
Consensus pattern (20 bp):
AATCACAGAACACAACATTC
Found at i:1249692 original size:36 final size:36
Alignment explanation
Indices: 1249620--1249692 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1249610 TACTATAATT
*
1249620 AATTTATATATATTCTTTAAAAAATTAAATTCATAA
1 AATTTATATATATTCTTTAAAAAATTAAAATCATAA
* * *
1249656 AATTTATATA-ATTTTTTTACAAAATTAAAATGATAA
1 AATTTATATATA-TTCTTTAAAAAATTAAAATCATAA
1249692 A
1 A
1249693 TAGGTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.03
36 31 0.97
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (36 bp):
AATTTATATATATTCTTTAAAAAATTAAAATCATAA
Found at i:1251798 original size:20 final size:21
Alignment explanation
Indices: 1251775--1251815 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1251765 ACAAACCCCA
1251775 AAAAAAACAAG-GAAAAAAAG
1 AAAAAAACAAGAGAAAAAAAG
*
1251795 AAAAGAACAAGAAGAAAAAAA
1 AAAAAAACAAG-AGAAAAAAA
1251816 AGGAAGGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAAACAAGAGAAAAAAAG
Found at i:1256093 original size:12 final size:12
Alignment explanation
Indices: 1256078--1256131 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
1256068 TTTCTCTAGT
1256078 TCTTTCCCTTGC
1 TCTTTCCCTTGC
*
1256090 TCTTGCCCTTGC
1 TCTTTCCCTTGC
1256102 -CTTTGCCCTTGC
1 TCTTT-CCCTTGC
* *
1256114 CCTTGCCCTTGAC
1 TCTTTCCCTTG-C
1256127 TCTTT
1 TCTTT
1256132 AAGAGGGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
11 3 0.09
12 24 0.71
13 7 0.21
ACGTcount: A:0.02, C:0.41, G:0.13, T:0.44
Consensus pattern (12 bp):
TCTTTCCCTTGC
Found at i:1256100 original size:6 final size:6
Alignment explanation
Indices: 1256083--1256124 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
1256073 CTAGTTCTTT
* *
1256083 CCCTTG CTCTTG CCCTTG CCTTTG CCCTTG CCCTTG CCCTTG
1 CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG CCCTTG
1256125 ACTCTTTAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.45, G:0.17, T:0.38
Consensus pattern (6 bp):
CCCTTG
Found at i:1256107 original size:18 final size:18
Alignment explanation
Indices: 1256083--1256130 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
1256073 CTAGTTCTTT
1256083 CCCTTGCTCTTGCCCTTG
1 CCCTTGCTCTTGCCCTTG
* *
1256101 CCTTTGCCCTTGCCCTTG
1 CCCTTGCTCTTGCCCTTG
1256119 CCCTTGACTCTT
1 CCCTTG-CTCTT
1256131 TAAGAGGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.02, C:0.44, G:0.15, T:0.40
Consensus pattern (18 bp):
CCCTTGCTCTTGCCCTTG
Found at i:1257409 original size:29 final size:29
Alignment explanation
Indices: 1257355--1257426 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
1257345 GATAGTGCCC
1257355 TCGCCATGCACG-CCAGCGACCTACCAGG
1 TCGCCATGCACGCCCAGCGACCTACCAGG
1257383 TCGCCATGCACGCCCAGCGACCTACCAGG
1 TCGCCATGCACGCCCAGCGACCTACCAGG
1257412 TCGCCATGCACGCCC
1 TCGCCATGCACGCCC
1257427 CAACACGCTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 12 0.28
29 31 0.72
ACGTcount: A:0.19, C:0.46, G:0.24, T:0.11
Consensus pattern (29 bp):
TCGCCATGCACGCCCAGCGACCTACCAGG
Found at i:1257495 original size:10 final size:10
Alignment explanation
Indices: 1257480--1257569 Score: 63
Period size: 10 Copynumber: 8.4 Consensus size: 10
1257470 ACGAGCTATG
1257480 CGAGGGCATC
1 CGAGGGCATC
*
1257490 CGAGGGCAAC
1 CGAGGGCATC
*
1257500 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
1257513 CGAGGGAATC
1 CGAGGGCATC
*
1257523 CGAGGGCAAC
1 CGAGGGCATC
*
1257533 CGAGCGAGCTATG
1 CGAG-G-GC-ATC
*
1257546 CGAGGGAATC
1 CGAGGGCATC
*
1257556 CGAGGGCAAC
1 CGAGGGCATC
1257566 CGAG
1 CGAG
1257570 CGAGCCATGT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
10 41 0.67
11 4 0.07
12 6 0.10
13 10 0.16
ACGTcount: A:0.27, C:0.26, G:0.40, T:0.08
Consensus pattern (10 bp):
CGAGGGCATC
Found at i:1257508 original size:33 final size:33
Alignment explanation
Indices: 1257456--1257574 Score: 202
Period size: 33 Copynumber: 3.6 Consensus size: 33
1257446 GACCATCCGA
* * * *
1257456 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1257489 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1257522 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1257555 CCGAGGGCAACCGAGCGAGC
1 CCGAGGGCAACCGAGCGAGC
1257575 CATGTACTCC
Statistics
Matches: 82, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 82 1.00
ACGTcount: A:0.26, C:0.28, G:0.38, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:1257645 original size:10 final size:10
Alignment explanation
Indices: 1257632--1257762 Score: 55
Period size: 10 Copynumber: 12.1 Consensus size: 10
1257622 GCATAGCTCG
*
1257632 CTCGGTTGCC
1 CTCGGATGCC
1257642 CTCGGATGCC
1 CTCGGATGCC
*
1257652 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
1257664 GTTCGGATGCC
1 -CTCGGATGCC
**
1257675 CTCACATAGCTC
1 CTCGGAT-GC-C
* *
1257687 GTTCGGATGGC
1 -CTCGGATGCC
*
1257698 CTCGGATGCT
1 CTCGGATGCC
*
1257708 CTCGGATGGC
1 CTCGGATGCC
* *
1257718 ATCGGATGCT
1 CTCGGATGCC
*
1257728 TTCGGATGGCC
1 CTCGGAT-GCC
*
1257739 TCGGTCGGATGGC
1 -C--TCGGATGCC
1257752 CTCGGATGCC
1 CTCGGATGCC
1257762 C
1 C
1257763 AGCGTGTTGG
Statistics
Matches: 87, Mismatches: 24, Indels: 20
0.66 0.18 0.15
Matches are distributed among these distances:
10 56 0.64
11 8 0.09
12 6 0.07
13 11 0.13
14 6 0.07
ACGTcount: A:0.11, C:0.32, G:0.31, T:0.25
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:1257659 original size:33 final size:31
Alignment explanation
Indices: 1257597--1257678 Score: 119
Period size: 33 Copynumber: 2.6 Consensus size: 31
1257587 GCGACCTACC
1257597 CTCGCTCGGTTGCCCTCATACCCTCGCATAG
1 CTCGCTCGGTTGCCCTCATACCCTCGCATAG
*
1257628 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTC--ATACCCTCGCATAG
* *
1257661 CTCGTTCGGATGCCCTCA
1 CTCGCTCGGTTGCCCTCA
1257679 CATAGCTCGT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 18 0.39
33 28 0.61
ACGTcount: A:0.11, C:0.40, G:0.23, T:0.26
Consensus pattern (31 bp):
CTCGCTCGGTTGCCCTCATACCCTCGCATAG
Found at i:1257670 original size:23 final size:23
Alignment explanation
Indices: 1257643--1257701 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
1257633 TCGGTTGCCC
1257643 TCGGATGCCCTCGCATAGCTCGT
1 TCGGATGCCCTCGCATAGCTCGT
*
1257666 TCGGATGCCCTCACATAGCTCGT
1 TCGGATGCCCTCGCATAGCTCGT
*
1257689 TCGGATGGCCTCG
1 TCGGATGCCCTCG
1257702 GATGCTCTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.34, G:0.27, T:0.25
Consensus pattern (23 bp):
TCGGATGCCCTCGCATAGCTCGT
Found at i:1257714 original size:20 final size:20
Alignment explanation
Indices: 1257689--1257742 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1257679 CATAGCTCGT
1257689 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
* *
1257709 TCGGATGGCATCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
1257729 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1257743 TCGGATGGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:1257748 original size:14 final size:14
Alignment explanation
Indices: 1257729--1257756 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1257719 TCGGATGCTT
1257729 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1257743 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
1257757 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:1258101 original size:29 final size:29
Alignment explanation
Indices: 1258059--1258168 Score: 155
Period size: 29 Copynumber: 4.1 Consensus size: 29
1258049 AACACCCCAC
1258059 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
*
1258088 AGGTCGCCCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
1258117 A--------GGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
1258138 AGGTCGCTCGGATGCCATGGCGACCTCCA
1 AGGTCGCTCGGATGCCATGGCGACCTCCA
1258167 AG
1 AG
1258169 CTCACTGTAG
Statistics
Matches: 72, Mismatches: 1, Indels: 16
0.81 0.01 0.18
Matches are distributed among these distances:
21 21 0.29
29 51 0.71
ACGTcount: A:0.19, C:0.35, G:0.31, T:0.15
Consensus pattern (29 bp):
AGGTCGCTCGGATGCCATGGCGACCTCCA
Found at i:1258123 original size:21 final size:21
Alignment explanation
Indices: 1258097--1258140 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1258087 AAGGTCGCCC
1258097 GGATGCCATGGCGACCTCCAA
1 GGATGCCATGGCGACCTCCAA
1258118 GGATGCCATGGCGACCTCCAA
1 GGATGCCATGGCGACCTCCAA
1258139 GG
1 GG
1258141 TCGCTCGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.32, G:0.32, T:0.14
Consensus pattern (21 bp):
GGATGCCATGGCGACCTCCAA
Found at i:1258128 original size:50 final size:50
Alignment explanation
Indices: 1258068--1258168 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
1258058 CAGGTCGCTC
1258068 GGATGCCATGGCGACCTCCAAGGTCGCCCGGATGCCATGGCGACCTCCAA
1 GGATGCCATGGCGACCTCCAAGGTCGCCCGGATGCCATGGCGACCTCCAA
*
1258118 GGATGCCATGGCGACCTCCAAGGTCGCTCGGATGCCATGGCGACCTCCAA
1 GGATGCCATGGCGACCTCCAAGGTCGCCCGGATGCCATGGCGACCTCCAA
1258168 G
1 G
1258169 CTCACTGTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.20, C:0.35, G:0.31, T:0.15
Consensus pattern (50 bp):
GGATGCCATGGCGACCTCCAAGGTCGCCCGGATGCCATGGCGACCTCCAA
Found at i:1259979 original size:2 final size:2
Alignment explanation
Indices: 1259972--1260032 Score: 60
Period size: 2 Copynumber: 33.0 Consensus size: 2
1259962 ATGTTTTGTT
* * *
1259972 TA TA TA TA TA TA -A T- TA -A TA TA AA AA TA TA TA -A AA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1260009 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
1260033 ATCGGGGCAG
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
1 5 0.10
2 46 0.90
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1261705 original size:30 final size:29
Alignment explanation
Indices: 1261654--1261732 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
1261644 CATTATTTTT
*
1261654 TAATATTTTCGGTCATTTTTAGCGTCTAA
1 TAATATTTTCGGTCATTTTTAGCGCCTAA
*
1261683 TAATATTTTCGGTTATTTTTTAGCGCCTAA
1 TAATATTTTCGGTCA-TTTTTAGCGCCTAA
*
1261713 TAAT-TTTTCCGATCATTTTT
1 TAATATTTT-CGGTCATTTTT
1261733 TTTCAAAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (29 bp):
TAATATTTTCGGTCATTTTTAGCGCCTAA
Found at i:1261733 original size:30 final size:30
Alignment explanation
Indices: 1261654--1261733 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
1261644 CATTATTTTT
* *
1261654 TAATATTTTCGGTCA-TTTTTAGCGTCTAA
1 TAATATTTTCGATCATTTTTTAGCGCCTAA
* *
1261683 TAATATTTTCGGTTATTTTTTAGCGCCTAA
1 TAATATTTTCGATCATTTTTTAGCGCCTAA
1261713 TAAT-TTTTCCGATCATTTTTT
1 TAATATTTT-CGATCATTTTTT
1261734 TTCAAAAATC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
29 18 0.40
30 27 0.60
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.53
Consensus pattern (30 bp):
TAATATTTTCGATCATTTTTTAGCGCCTAA
Found at i:1272963 original size:14 final size:14
Alignment explanation
Indices: 1272917--1272956 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1272907 CCTCGCATAG
*
1272917 CTCGCTCGGATGCC
1 CTCGGTCGGATGCC
*
1272931 CTCGGTCGAATGCC
1 CTCGGTCGGATGCC
1272945 CTCGGTCGGATG
1 CTCGGTCGGATG
1272957 GCTTCGGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.10, C:0.35, G:0.33, T:0.23
Consensus pattern (14 bp):
CTCGGTCGGATGCC
Found at i:1275066 original size:21 final size:21
Alignment explanation
Indices: 1275002--1275066 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1274992 ATTATTACTA
*
1275002 TCGCAATGCGATTTT-CCAATT
1 TCGCATTGCGATTTTCCCAA-T
*
1275023 TCTCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
1275044 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
1275065 TC
1 TC
1275067 ACAATGTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
21 36 0.90
22 4 0.10
ACGTcount: A:0.20, C:0.28, G:0.12, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1275097 original size:20 final size:21
Alignment explanation
Indices: 1275068--1275116 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1275058 TCCCAATTCA
* *
1275068 CAATGTGAATAAG-TAAATCG
1 CAATGCGAATAAGAAAAATCG
**
1275088 CAATGCGAATTTGAAAAATCG
1 CAATGCGAATAAGAAAAATCG
1275109 CAATGCGA
1 CAATGCGA
1275117 TACTGACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.22
Consensus pattern (21 bp):
CAATGCGAATAAGAAAAATCG
Found at i:1275692 original size:20 final size:20
Alignment explanation
Indices: 1275667--1275757 Score: 121
Period size: 20 Copynumber: 4.6 Consensus size: 20
1275657 GAAGAATACT
1275667 ATCGCAACGAGAGAATGAAA
1 ATCGCAACGAGAGAATGAAA
* * **
1275687 ATCGCAACGCGAAAATGACT
1 ATCGCAACGAGAGAATGAAA
1275707 ATCGCAACGAGAGAATGAAA
1 ATCGCAACGAGAGAATGAAA
*
1275727 ATCGCAACGCGA-AATGAAA
1 ATCGCAACGAGAGAATGAAA
*
1275746 ATCGCAATGAGA
1 ATCGCAACGAGA
1275758 TAATCACAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 17 0.28
20 43 0.72
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGAAA
Found at i:1275719 original size:40 final size:39
Alignment explanation
Indices: 1275664--1275757 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 39
1275654 GAAGAAGAAT
1275664 ACTATCGCAACGAGAGAATGAAAATCGCAACGCGAAAATG
1 ACTATCGCAACGAGAGAATGAAAATCGCAACGCG-AAATG
1275704 ACTATCGCAACGAGAGAATGAAAATCGCAACGCGAAATG
1 ACTATCGCAACGAGAGAATGAAAATCGCAACGCGAAATG
** *
1275743 AAAATCGCAATGAGA
1 ACTATCGCAACGAGA
1275758 TAATCACAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 17 0.33
40 34 0.67
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (39 bp):
ACTATCGCAACGAGAGAATGAAAATCGCAACGCGAAATG
Found at i:1275827 original size:20 final size:19
Alignment explanation
Indices: 1275788--1275839 Score: 86
Period size: 20 Copynumber: 2.7 Consensus size: 19
1275778 AATCGCATTA
1275788 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
1275807 CGATTTTCATTCTCTCGTTG
1 CGATTTTCATT-TCGCGTTG
1275827 CGATTTTCATTTC
1 CGATTTTCATTTC
1275840 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.42
20 18 0.58
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:1277686 original size:94 final size:94
Alignment explanation
Indices: 1277525--1277739 Score: 394
Period size: 94 Copynumber: 2.3 Consensus size: 94
1277515 TAGATTGCTT
* *
1277525 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTGTTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1277590 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1277619 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1277684 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1277713 AATAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTGTTCGGTTGCTGCCAATT
1277740 GAAACTATTC
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 117 1.00
ACGTcount: A:0.21, C:0.13, G:0.20, T:0.47
Consensus pattern (94 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1278101 original size:21 final size:21
Alignment explanation
Indices: 1278077--1278143 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1278067 TCATTCCTCG
1278077 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1278098 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1278119 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1278140 AGAG
1 AGAG
1278144 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1278101 original size:42 final size:42
Alignment explanation
Indices: 1278025--1278143 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
1278015 GACTCGCCTG
* * * * * * *
1278025 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
1278067 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
1278109 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
1278144 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:1279515 original size:14 final size:14
Alignment explanation
Indices: 1279496--1279531 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1279486 ATTGTTTAAT
1279496 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1279510 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1279524 TGATTTGT
1 TGATTTGT
1279532 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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1279654 original size:19 final size:19
Alignment explanation
Indices: 1279638--1279701 Score: 110
Period size: 19 Copynumber: 3.4 Consensus size: 19
1279628 AAAAATGACT
1279638 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1279657 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1279676 ATCGCAACGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1279695 ATCGCAA
1 ATCGCAA
1279702 CGACAAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1279702 original size:19 final size:19
Alignment explanation
Indices: 1279638--1279750 Score: 107
Period size: 19 Copynumber: 6.3 Consensus size: 19
1279628 AAAAATGACT
*
1279638 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1279657 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1279676 ATCGCAACGTGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1279695 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
*
1279709 ATCGCAACGTGAAACT--AA
1 ATCGCAACGCGAAA-TGAAA
1279727 ATCGCAACGCGAAACT-AAA
1 ATCGCAACGCGAAA-TGAAA
1279746 ATCGC
1 ATCGC
1279751 GTTGCGATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 1 0.01
17 1 0.01
18 18 0.22
19 50 0.62
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1279710 original size:33 final size:32
Alignment explanation
Indices: 1279673--1279735 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 32
1279663 ATGCGAAATG
1279673 AAAATCGCAACGTGAAA-TGAAAATCGCAACGAC
1 AAAATCGCAACGTGAAACT--AAATCGCAACGAC
1279706 AAAATCGCAACGTGAAACTAAATCGCAACG
1 AAAATCGCAACGTGAAACTAAATCGCAACG
1279736 CGAAACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 11 0.38
33 17 0.59
34 1 0.03
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (32 bp):
AAAATCGCAACGTGAAACTAAATCGCAACGAC
Found at i:1279769 original size:19 final size:19
Alignment explanation
Indices: 1279747--1279873 Score: 86
Period size: 19 Copynumber: 7.5 Consensus size: 19
1279737 GAAACTAAAA
1279747 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1279766 TCGCTTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1279780 CCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1279799 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1279813 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1279832 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1279846 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1279865 TCGCATTGC
1 TCGCGTTGC
1279874 ATTGGTCAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 27 0.34
16 9 0.11
17 9 0.11
19 35 0.44
ACGTcount: A:0.10, C:0.25, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1279792 original size:33 final size:33
Alignment explanation
Indices: 1279750--1279873 Score: 221
Period size: 33 Copynumber: 3.8 Consensus size: 33
1279740 ACTAAAATCG
* *
1279750 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
1279783 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1279816 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1279849 CGTTGCGATTTTCATTTCGCATTGC
1 CGTTGCGATTTTCATTTCGCATTGC
1279874 ATTGGTCAAA
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 88 1.00
ACGTcount: A:0.10, C:0.25, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:1279821 original size:14 final size:14
Alignment explanation
Indices: 1279802--1279858 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1279792 TTTCATTTCG
1279802 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1279816 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
1279833 CGCATTGCGATTCTCT
1 CG--TTGCGATTCTCT
1279849 CGTTGCGATT
1 CGTTGCGATT
1279859 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1282372 original size:24 final size:24
Alignment explanation
Indices: 1282338--1282391 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1282328 CTGAAACATC
* *
1282338 ATCAAAATCCGAGTATTGACTAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1282362 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1282386 ATCAAA
1 ATCAAA
1282392 TTTTGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1283406 original size:19 final size:19
Alignment explanation
Indices: 1283382--1283445 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
1283372 TCATTTGACC
1283382 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1283401 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
1283415 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1283434 ATCGCAACGCGA
1 ATCGCAATGCGA
1283446 TTTTAGTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 21 0.62
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1283464 original size:19 final size:19
Alignment explanation
Indices: 1283442--1283498 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
1283432 AAATCGCAAC
1283442 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1283461 GCGATTTT-G--T--CGTT
1 GCGATTTTAGTTTCGCGTT
1283475 G-GATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
1283493 GCGATT
1 GCGATT
1283499 CTCGCATTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
13 6 0.19
14 5 0.16
16 2 0.06
18 6 0.19
19 12 0.39
ACGTcount: A:0.11, C:0.16, G:0.26, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1283518 original size:33 final size:34
Alignment explanation
Indices: 1283442--1283534 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 34
1283432 AAATCGCAAC
* *
1283442 GCGATTTT-AGTTTCGCGTTGCGATT-TTGTCGTT
1 GCGATTTTCA-TTTCGCGTTGCGATTCTCGTCATT
1283475 G-GATTTTCATTTCGCGTTGCGATTCTCG-CATT
1 GCGATTTTCATTTCGCGTTGCGATTCTCGTCATT
*
1283507 GCGATTTTCATTTCGCATTGCGATTCTC
1 GCGATTTTCATTTCGCGTTGCGATTCTC
1283535 TCGTTGCAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
32 25 0.46
33 29 0.54
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (34 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCGTCATT
Found at i:1283524 original size:19 final size:19
Alignment explanation
Indices: 1283476--1283531 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
1283466 TTTGTCGTTG
*
1283476 GATTTTCATTTCGCGTTGC
1 GATTTTCATTTCGCATTGC
1283495 GA--TTC---TCGCATTGC
1 GATTTTCATTTCGCATTGC
1283509 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
1283528 GATT
1 GATT
1283532 CTCTCGTTGC
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
14 10 0.32
16 3 0.10
17 3 0.10
19 15 0.48
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Done.