Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001497.1 Hibiscus syriacus cultivar Beakdansim tig00002919_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: 1780709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:423170 original size:21 final size:20
Alignment explanation
Indices: 423110--423196 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
423100 GAAATTCAGT
*
423110 ATTGCGA-TTACGTAAATCGC
1 ATTGCGATTTACCT-AATCGC
* * *
423130 AATGCGA-ATACGTAATCGC
1 ATTGCGATTTACCTAATCGC
*
423149 ATTGCGATTTTCCTAATTCGC
1 ATTGCGATTTACCTAA-TCGC
*
423170 ATTGCGATTTACGTAATCGC
1 ATTGCGATTTACCTAATCGC
423190 ATTGCGA
1 ATTGCGA
423197 ATTAGGAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
19 12 0.21
20 27 0.47
21 18 0.32
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (20 bp):
ATTGCGATTTACCTAATCGC
Found at i:423211 original size:41 final size:41
Alignment explanation
Indices: 423110--423240 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
423100 GAAATTCAGT
*
423110 ATTGCG-ATTACGTAAATCGCAATGCGA-ATACGTAATCGC
1 ATTGCGAATTACGTAAATCGCAATGCGATTTACGTAATCGC
* * * * *
423149 ATTGCGATTTTCCTAATTCGCATTGCGATTTACGTAATCGC
1 ATTGCGAATTACGTAAATCGCAATGCGATTTACGTAATCGC
* * * * *
423190 ATTGCGAATTAGGAAAATCGCAACGCGAATTTAGGAAATCGC
1 ATTGCGAATTACGTAAATCGCAATGCG-ATTTACGTAATCGC
423232 ATTGCGAAT
1 ATTGCGAAT
423241 CTGGAAACTG
Statistics
Matches: 73, Mismatches: 16, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
39 6 0.08
40 16 0.22
41 30 0.41
42 21 0.29
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (41 bp):
ATTGCGAATTACGTAAATCGCAATGCGATTTACGTAATCGC
Found at i:424065 original size:216 final size:215
Alignment explanation
Indices: 423715--424156 Score: 681
Period size: 216 Copynumber: 2.1 Consensus size: 215
423705 TTTACCCTAA
* *
423715 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCCGAACAAAATAAAGTTTCATCCGA
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCAGAACAAAATAAAGTTTCATACGA
* * *
423780 CCCGACCCGAATATATGAATTAGAAATATGACCCGACCCGAAATAATAAAAAATATTTTTATTTA
66 CCCGACCCAAATATATGAATTAGAAATACGACCCAACCCGAAATAATAAAAAATATTTTTATTTA
**
423845 ATAAAAACAGTGACTTAATCCGACCCGACCCAAATTATATATATTTTCGGGTCGGCCCGGTTTTT
131 ATAAAAACAGTGACTTAATCCGACCCGACCCAAATTATATATATTTTCGGGTCGGCCCAATTTTT
423910 TTCACCCTAAACCCAAACCCG
196 TTCACCCTAAACCC-AACCCG
* * * *
423931 ACCCAACCCGACCCGAATATCACACTT-AAAAAATCCGACCATAACAAAATAAAGTTTCATATGA
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCAGAACAAAATAAAGTTTCATACGA
* *
423995 CCCGACCCAAATATATGAATTAGAAATCCG-GCCAACCCGAAATAATAAAAAATATATTTTTATT
66 CCCGACCCAAATATATGAATTAGAAATACGACCCAACCCGAAATAAT-AAAAA-ATATTTTTATT
* * *
424059 TAATAAAAACAGTGACTTAATCCGACCCGATCCGAATTATATATATTTTCGGGTCGGTCCAATTT
129 TAATAAAAACAGTGACTTAATCCGACCCGACCCAAATTATATATATTTTCGGGTCGGCCCAATTT
*
424124 TTTTCACCCTAAACCCGACCCG
194 TTTTCACCCTAAACCCAACCCG
*
424146 TCCCGACCCGA
1 ACCCGACCCGA
424157 ATATATGAAT
Statistics
Matches: 205, Mismatches: 19, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
214 14 0.07
215 78 0.38
216 113 0.55
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.24
Consensus pattern (215 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGACCAGAACAAAATAAAGTTTCATACGA
CCCGACCCAAATATATGAATTAGAAATACGACCCAACCCGAAATAATAAAAAATATTTTTATTTA
ATAAAAACAGTGACTTAATCCGACCCGACCCAAATTATATATATTTTCGGGTCGGCCCAATTTTT
TTCACCCTAAACCCAACCCG
Found at i:429665 original size:16 final size:16
Alignment explanation
Indices: 429644--429703 Score: 106
Period size: 16 Copynumber: 3.9 Consensus size: 16
429634 TCATTATTTT
429644 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
429660 TGTAGAAAACAGACTG
1 TGTAGAAAACAGACTG
429676 TGTAGAAAACAGAC--
1 TGTAGAAAACAGACTG
429690 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
429704 AAGTCTGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.32
16 30 0.68
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (16 bp):
TGTAGAAAACAGACTG
Found at i:429685 original size:32 final size:30
Alignment explanation
Indices: 429644--429703 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 30
429634 TCATTATTTT
429644 TGTAGAAAACAGACTGTGTAGAAAACAGACTG
1 TGTAGAAAACAGAC--TGTAGAAAACAGACTG
429676 TGTAGAAAACAGACTGTAGAAAACAGAC
1 TGTAGAAAACAGACTGTAGAAAACAGAC
429704 AAGTCTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 14 0.50
32 14 0.50
ACGTcount: A:0.47, C:0.13, G:0.23, T:0.17
Consensus pattern (30 bp):
TGTAGAAAACAGACTGTAGAAAACAGACTG
Found at i:432010 original size:51 final size:51
Alignment explanation
Indices: 431929--432027 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
431919 TAAGGAAAAG
*
431929 ATAGACTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAATTA
1 ATAGACTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAATTA
*
431980 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAA
1 ATAGACTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAA
432028 CTCTCCCCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (51 bp):
ATAGACTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAATTA
Found at i:433594 original size:370 final size:369
Alignment explanation
Indices: 433114--433849 Score: 1436
Period size: 370 Copynumber: 2.0 Consensus size: 369
433104 ACCAAAATCT
*
433114 TTAATTAATTTGCTGACTGGCAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
1 TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
433179 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
66 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
*
433244 TTTTGATAGAAGCTGGTAGACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
131 TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
433309 TGATTTGATGCACCCGAGTCTATTATCCATTGTACCGAGGAAGCATATGGATTATTTCCATCAGT
196 TGATTTGATGCA-CCGAGTCTATTATCCATTGTACCGAGGAAGCATATGGATTATTTCCATCAGT
433374 AGTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTA
260 AGTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTA
433439 TCTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGGACA
325 TCTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGGACA
433484 TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
1 TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
433549 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
66 TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
433614 TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
131 TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
433679 TGATTTGATGCACCGAGTCTATTATCCATTGTACCGAGGAAGCATATGGATTATTTCCATCAGTA
196 TGATTTGATGCACCGAGTCTATTATCCATTGTACCGAGGAAGCATATGGATTATTTCCATCAGTA
*
433744 GTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTTCTCTAT
261 GTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTAT
433809 CTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGG
326 CTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGG
433850 CAATATGAGG
Statistics
Matches: 363, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
369 158 0.44
370 205 0.56
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (369 bp):
TTAATTAATTTGCTGACTGACAACAGATTGCATGCAAGTCTAGGAACATAGAGGACATTATGAAG
TAGTAGATTTTTGTTTAATGTAACAGAACCACTCCCTTTGACTGTAGTGAGAGAGCCATCTGTTA
TTTTGATAGAAGCTGGTAAACTGCTTTCACTATATTCCTCCAAGAGATCAATATTTCCTGTCATA
TGATTTGATGCACCGAGTCTATTATCCATTGTACCGAGGAAGCATATGGATTATTTCCATCAGTA
GTAGTATAAGTCACATTTGTAGGCTTGGCTGTTATACTGCTCAAAATCTGCTGCAGTTCCTCTAT
CTGTTTCTTGCTAAAACTGCTTGAGGAATCATCTTGAGAGGACA
Found at i:444935 original size:19 final size:18
Alignment explanation
Indices: 444913--444956 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
444903 AAAATAAAAA
444913 TAATATAGTTAAATAAT-AT
1 TAATATAG-T-AATAATAAT
444932 TAATAATAGTAATAATAAT
1 TAAT-ATAGTAATAATAAT
444951 TAATAT
1 TAATAT
444957 TAAAAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
TAATATAGTAATAATAAT
Found at i:447968 original size:7 final size:7
Alignment explanation
Indices: 447956--447987 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
447946 TCCCAAGCCA
447956 TGCATTT
1 TGCATTT
447963 TGCATTT
1 TGCATTT
447970 TGCATTT
1 TGCATTT
447977 TGCATTT
1 TGCATTT
447984 TGCA
1 TGCA
447988 GATATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.53
Consensus pattern (7 bp):
TGCATTT
Found at i:451059 original size:17 final size:18
Alignment explanation
Indices: 451027--451060 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
451017 GTTTGATCAA
451027 CACAAAGTCCAAACCAAT
1 CACAAAGTCCAAACCAAT
*
451045 CACAAA-TCTAAACCAA
1 CACAAAGTCCAAACCAA
451061 ATACAAACTT
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:0.53, C:0.32, G:0.03, T:0.12
Consensus pattern (18 bp):
CACAAAGTCCAAACCAAT
Found at i:452085 original size:16 final size:16
Alignment explanation
Indices: 452066--452117 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
452056 ACATTGCATT
452066 TTGATCACTTGTATTA
1 TTGATCACTTGTATTA
* **
452082 TTGATTTA-TTAAATT-
1 TTGA-TCACTTGTATTA
452097 TTGATCACTTGTATTA
1 TTGATCACTTGTATTA
452113 TTGAT
1 TTGAT
452118 TTATTAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 2 0.07
15 9 0.33
16 14 0.52
17 2 0.07
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (16 bp):
TTGATCACTTGTATTA
Found at i:452101 original size:31 final size:31
Alignment explanation
Indices: 452063--452164 Score: 152
Period size: 31 Copynumber: 3.3 Consensus size: 31
452053 AAAACATTGC
452063 ATTTTGATCACTTGTATTATTGATTTATTAA
1 ATTTTGATCACTTGTATTATTGATTTATTAA
452094 ATTTTGATCACTTGTATTATTGATTTATTAA
1 ATTTTGATCACTTGTATTATTGATTTATTAA
** * * *
452125 ATTTTGATCACTTACATTA-TCAATTATTAT
1 ATTTTGATCACTTGTATTATTGATTTATTAA
452155 ATTTTGATCA
1 ATTTTGATCA
452165 GTGAGTCGTT
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 18 0.27
31 48 0.73
ACGTcount: A:0.30, C:0.09, G:0.08, T:0.53
Consensus pattern (31 bp):
ATTTTGATCACTTGTATTATTGATTTATTAA
Found at i:452266 original size:31 final size:30
Alignment explanation
Indices: 452226--452292 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
452216 TTAATTTTTA
* * *
452226 ATTTTACCTCTAAATTTTAGATAAAATATC
1 ATTTTACCTCTAAACTTTAAACAAAATATC
452256 ATTTTGACCTCTAAACTTTAAACAAAATATC
1 ATTTT-ACCTCTAAACTTTAAACAAAATATC
452287 ATTTTA
1 ATTTTA
452293 GGTTTGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 6 0.18
31 27 0.82
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTTTACCTCTAAACTTTAAACAAAATATC
Found at i:459641 original size:37 final size:37
Alignment explanation
Indices: 459587--459659 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
459577 TTACCTAAAA
*
459587 TTTTTACTTTTCGTTTTTCTATAATTGTGGGGTATGT
1 TTTTTACTTTTCGTTTTTCTATAATTGCGGGGTATGT
* *
459624 TTTTTACTTTTCTTTTTTCTATAGTTGCGGGGTATG
1 TTTTTACTTTTCGTTTTTCTATAATTGCGGGGTATG
459660 GTTAAGGCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.12, C:0.10, G:0.19, T:0.59
Consensus pattern (37 bp):
TTTTTACTTTTCGTTTTTCTATAATTGCGGGGTATGT
Found at i:463095 original size:10 final size:10
Alignment explanation
Indices: 463067--463101 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
463057 TATATATATA
463067 TATATTTTAT
1 TATATTTTAT
463077 GTATATTTTAT
1 -TATATTTTAT
*
463088 TTTATTTTAT
1 TATATTTTAT
463098 TATA
1 TATA
463102 CATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (10 bp):
TATATTTTAT
Found at i:463121 original size:51 final size:52
Alignment explanation
Indices: 463015--463121 Score: 130
Period size: 51 Copynumber: 2.1 Consensus size: 52
463005 TATTATATAC
* * *
463015 TATATTTTCATTATTATTATATTTTATTCCTTTATTCATATATATATATATA
1 TATATTTTCATTATTATTATATTTTATTCCTTTATACATATATATATACACA
* *
463067 TATATTTT-ATGTA-TATTTTATTTTATT-TTATTATACATATATATATACACA
1 TATATTTTCAT-TATTATTATATTTTATTCCT-TTATACATATATATATACACA
463118 TATA
1 TATA
463122 ATCATCGTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
50 1 0.02
51 37 0.77
52 10 0.21
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.58
Consensus pattern (52 bp):
TATATTTTCATTATTATTATATTTTATTCCTTTATACATATATATATACACA
Found at i:474288 original size:1 final size:1
Alignment explanation
Indices: 474282--474348 Score: 62
Period size: 1 Copynumber: 67.0 Consensus size: 1
474272 TCTTAAGTTG
* * * * * * * *
474282 AAAAAAAAAAAAACAAAAACAAAAACAAAAACAAAAACAAAAAACAAAAAAACAAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
474347 AA
1 AA
474349 CGCTTAGGGT
Statistics
Matches: 50, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:474349 original size:7 final size:7
Alignment explanation
Indices: 474282--474349 Score: 81
Period size: 6 Copynumber: 10.0 Consensus size: 7
474272 TCTTAAGTTG
*
474282 AAAAAAA
1 AAAAAAC
474289 AAAAAAC
1 AAAAAAC
474296 -AAAAAC
1 AAAAAAC
474302 -AAAAAC
1 AAAAAAC
474308 -AAAAAC
1 AAAAAAC
474314 -AAAAAC
1 AAAAAAC
474320 AAAAAAC
1 AAAAAAC
474327 AAAAAAAC
1 -AAAAAAC
474335 AAAAAAAC
1 -AAAAAAC
474343 AAAAAAC
1 AAAAAAC
474350 GCTTAGGGTG
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
6 24 0.41
7 19 0.33
8 15 0.26
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:476223 original size:105 final size:105
Alignment explanation
Indices: 475126--476215 Score: 1910
Period size: 105 Copynumber: 10.4 Consensus size: 105
475116 AGGTTTTACC
*
475126 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
475191 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
475231 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
475296 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
475336 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
475401 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
475441 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACCTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
475506 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
475546 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
475611 ACGAAGGAACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
475651 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
475716 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
475756 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTACAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
475821 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
475861 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
475926 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
475966 CAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
476031 ACGAAGGAACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
** *
476071 CAGAGCCAATTTCTGCTTCACAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
476136 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
476176 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
476216 GAAACAACAC
Statistics
Matches: 940, Mismatches: 45, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 940 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:477783 original size:49 final size:50
Alignment explanation
Indices: 477729--477833 Score: 128
Period size: 49 Copynumber: 2.1 Consensus size: 50
477719 CTACTATTAT
*
477729 TATATACTATAT-TTTCAT-TATTATTATATTTTATTCCT-TTATTCATATA
1 TATATACTATATATTTCATGTA-TATTATATTTTATT-CTATTATACATATA
* * *
477778 TATATA-TATATATTTTATGTATATTTTATTTTATTTTATTATACATATA
1 TATATACTATATATTTCATGTATATTATATTTTATTCTATTATACATATA
477827 TATATAC
1 TATATAC
477834 ACATATAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
48 6 0.12
49 40 0.83
50 2 0.04
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (50 bp):
TATATACTATATATTTCATGTATATTATATTTTATTCTATTATACATATA
Found at i:477814 original size:10 final size:10
Alignment explanation
Indices: 477786--477820 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
477776 TATATATATA
477786 TATATTTTAT
1 TATATTTTAT
477796 GTATATTTTAT
1 -TATATTTTAT
*
477807 TTTATTTTAT
1 TATATTTTAT
477817 TATA
1 TATA
477821 CATATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (10 bp):
TATATTTTAT
Found at i:484349 original size:14 final size:14
Alignment explanation
Indices: 484330--484360 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
484320 TCGAATTGCT
484330 CAAAAGTTGAATAA
1 CAAAAGTTGAATAA
484344 CAAAAGTTGAATAA
1 CAAAAGTTGAATAA
484358 CAA
1 CAA
484361 GTGGCTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (14 bp):
CAAAAGTTGAATAA
Found at i:484453 original size:27 final size:26
Alignment explanation
Indices: 484423--484478 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
484413 ACTTTGATCG
484423 AGTCAATCTCGTATCACTTATAACCCT
1 AGTCAATCTCGTATCACTTATAA-CCT
*
484450 AGTCAATCTCGTCTCACTTATAACCT
1 AGTCAATCTCGTATCACTTATAACCT
484476 AGT
1 AGT
484479 TACCGCATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.34
Consensus pattern (26 bp):
AGTCAATCTCGTATCACTTATAACCT
Found at i:485233 original size:15 final size:15
Alignment explanation
Indices: 485213--485246 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
485203 GGAGTCTCCT
485213 TCACTGGCTCCTCAG
1 TCACTGGCTCCTCAG
485228 TCACTGGCTCCTCAG
1 TCACTGGCTCCTCAG
485243 TCAC
1 TCAC
485247 AACCTTGGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.15, C:0.41, G:0.18, T:0.26
Consensus pattern (15 bp):
TCACTGGCTCCTCAG
Found at i:486660 original size:29 final size:31
Alignment explanation
Indices: 486628--486699 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 31
486618 TTAAAAAAAA
* *
486628 TATAATATTTTAATTATTTA-GTTA-TAATT
1 TATAATATTTTAATCATTTATATTATTAATT
* *
486657 TATAACATTTTGATCATTTATATTATTAATT
1 TATAATATTTTAATCATTTATATTATTAATT
486688 TATAATATTTTA
1 TATAATATTTTA
486700 GTCACTGAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.49
30 3 0.09
31 15 0.43
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (31 bp):
TATAATATTTTAATCATTTATATTATTAATT
Found at i:489346 original size:17 final size:17
Alignment explanation
Indices: 489308--489351 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
489298 GGGCTTCGCC
489308 CTTTTCTTTCTCTCTTA
1 CTTTTCTTTCTCTCTTA
* * *
489325 GTTTTCTTTCTTTCTTT
1 CTTTTCTTTCTCTCTTA
*
489342 CTTTTTTTTC
1 CTTTTCTTTC
489352 CCAATGGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (17 bp):
CTTTTCTTTCTCTCTTA
Found at i:489990 original size:14 final size:14
Alignment explanation
Indices: 489982--490017 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
489972 AATATGTAAT
489982 TAATAATATAATAA
1 TAATAATATAATAA
489996 TAATAATAATAATAA
1 TAATAAT-ATAATAA
490011 TAA-AATA
1 TAATAATA
490018 ACGATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 10 0.48
15 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAATATAATAA
Found at i:489995 original size:3 final size:3
Alignment explanation
Indices: 489982--490018 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
489972 AATATGTAAT
489982 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
490019 CGATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 28 0.88
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:490366 original size:40 final size:40
Alignment explanation
Indices: 490310--490550 Score: 234
Period size: 40 Copynumber: 5.8 Consensus size: 40
490300 TATCTATGGT
* *
490310 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
490350 TGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-A
* *
490390 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGA
* * * * * ** *
490436 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG---TCTGGGGA
* *
490479 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
*
490519 TGACACGGCTCATACGTGATGAAGAGTTCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
490551 CCATCTAAAG
Statistics
Matches: 167, Mismatches: 24, Indels: 20
0.79 0.11 0.09
Matches are distributed among these distances:
39 4 0.02
40 98 0.59
42 1 0.01
43 30 0.18
46 30 0.18
47 4 0.02
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGA
Found at i:490467 original size:169 final size:171
Alignment explanation
Indices: 490171--490550 Score: 622
Period size: 169 Copynumber: 2.2 Consensus size: 171
490161 TATTGGTTGT
* * * * *
490171 TGGGGACGACACTGCTCATACGTGATGAAGAGTTTGGGTCGTCTAAAGGTGACACGGCTCCTACG
1 TGGGGATGACACGGCTCATACGTGATGAAGAGTCT-GGTCGTCGAAA-GTGACACGGCTCATACG
* *
490236 TGATGAAGAGTTCTTGGCTATTTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
64 TGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTT
490301 ATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
129 ATCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
* *
490344 TGGGGATGACACGGCTCATACGTGATGAAGAGATCTGGTCG-GGGAA-TGACACGGCTCATACGT
1 TGGGGATGACACGGCTCATACGTGATGAAGAG-TCTGGTCGTCGAAAGTGACACGGCTCATACGT
490407 GATGAAGAGTTC-TGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTA
65 GATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTA
490471 TCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
130 TCTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
490513 TGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGG
1 TGGGGATGACACGGCTCATACGTGATGAAGAG-TCTGG
490551 CCATCTAAAG
Statistics
Matches: 196, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
169 129 0.66
170 28 0.14
172 2 0.01
173 35 0.18
174 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (171 bp):
TGGGGATGACACGGCTCATACGTGATGAAGAGTCTGGTCGTCGAAAGTGACACGGCTCATACGTG
ATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAT
CTATGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC
Found at i:490507 original size:129 final size:129
Alignment explanation
Indices: 490350--490602 Score: 463
Period size: 129 Copynumber: 2.0 Consensus size: 129
490340 GGTCTGGGGA
490350 TGACACGGCTCATACGTGATGAAGAGATCTGGTC-GGGGAATGACACGGCTCATACGTGATGAAG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAG
490414 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
65 AGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* *
490479 TGACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
*
490544 GTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTATCT
66 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCT
490603 CTAGGATAAT
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
129 116 0.97
130 4 0.03
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (129 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGA
GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:491003 original size:35 final size:36
Alignment explanation
Indices: 490956--491038 Score: 100
Period size: 35 Copynumber: 2.3 Consensus size: 36
490946 ACAAAATTCA
**
490956 TTTCAAGAGAAA-CGATCTCAAAGAT-GTTTATTTTG
1 TTTCAAGAGAAACCGAT-TCAAAGATGGTGAATTTTG
*
490991 TTTCAAGGGAAACCGATTCAAAGATGGTGAATTTTG
1 TTTCAAGAGAAACCGATTCAAAGATGGTGAATTTTG
491027 TTTCCAA-AGAAA
1 TTT-CAAGAGAAA
491039 TAAATCAAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 19 0.46
36 19 0.46
37 3 0.07
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TTTCAAGAGAAACCGATTCAAAGATGGTGAATTTTG
Found at i:491567 original size:63 final size:62
Alignment explanation
Indices: 491495--491618 Score: 169
Period size: 64 Copynumber: 2.0 Consensus size: 62
491485 AATATGGGTA
* * *
491495 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAA-AAACTCAAAGATT
* * *
491557 TTTTCCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAAAGACTCAAAGAT
1 TTTT-CAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAAAAACTCAAAGAT
491619 GGATCCCATC
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
62 4 0.07
63 24 0.44
64 26 0.48
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (62 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAAAAACTCAAAGATT
Found at i:491907 original size:37 final size:36
Alignment explanation
Indices: 491858--491979 Score: 117
Period size: 37 Copynumber: 3.4 Consensus size: 36
491848 ATTCAAAGAT
* *
491858 TTTTGTCTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAA
* * * ***
491895 TTTTGTTTCAAAAGAAACAAAC-TCA-A-AG-ATTT
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
491927 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAGAA
1 TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAA-AA
*
491964 TTTTGTTTCCAAAGAA
1 TTTTGTTTCAAAAGAA
491980 CAAACTCAAA
Statistics
Matches: 65, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
32 21 0.32
33 2 0.03
34 3 0.05
35 3 0.05
36 3 0.05
37 33 0.51
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (36 bp):
TTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAA
Found at i:491995 original size:68 final size:69
Alignment explanation
Indices: 491840--491998 Score: 236
Period size: 69 Copynumber: 2.3 Consensus size: 69
491830 TCAATTTAAG
* * *
491840 AGAAACAGATTCAAAGA--TTTTTGTCTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTT
1 AGAAACAAACTCAAAGATTTTTTTGTCTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT
491903 CAAA
66 CAAA
*
491907 AGAAACAAACTCAAAGATTTTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAGAATTTTGTT
1 AGAAACAAACTCAAAGATTTTTTTGTCTCAAAAGAAACTATCTTAAGAGAGACAA-AATTTTGTT
*
491971 TCCAA
65 TCAAA
491976 AG-AACAAACTCAAAGATTTTTTT
1 AGAAACAAACTCAAAGATTTTTTT
491999 CGCAAAATTG
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
67 15 0.18
68 23 0.27
69 46 0.55
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (69 bp):
AGAAACAAACTCAAAGATTTTTTTGTCTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT
CAAA
Found at i:492082 original size:51 final size:53
Alignment explanation
Indices: 491983--492086 Score: 158
Period size: 51 Copynumber: 2.0 Consensus size: 53
491973 CAAAGAACAA
* *
491983 ACTCAAAGATTTTTTTCGCAAAATTGTCTCAAGAGATACAAAACTTTGTTTCAG
1 ACTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
*
492037 ACTCAAAGA-TTTTTCACGAAATTGTCTC-AGAGAGACAAAACTTTGTTTCA
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
492087 AAATAAATAG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
51 21 0.45
52 17 0.36
54 9 0.19
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:492111 original size:26 final size:27
Alignment explanation
Indices: 492082--492203 Score: 92
Period size: 29 Copynumber: 4.4 Consensus size: 27
492072 CAAAACTTTG
*
492082 TTTCAAAATAAATAGACTCAAAG-T-TT
1 TTTCAAAAGAAA-AGACTCAAAGATATT
*
492108 TTTCAAAAGAAACGACTCAAAGATATT
1 TTTCAAAAGAAAAGACTCAAAGATATT
* * *
492135 TATTCAAAAGGAACCA-ACTCCAAGATTTT
1 T-TTCAAAA-GAA-AAGACTCAAAGATATT
492164 TATTCAAAAGGAACAA-ACTCAAAGAT-TT
1 T-TTCAAAA-GAA-AAGACTCAAAGATATT
*
492192 TTTCAAGAGAAA
1 TTTCAAAAGAAA
492204 CTGTCTCAAG
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
25 10 0.12
26 15 0.18
27 9 0.11
28 10 0.12
29 38 0.46
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.28
Consensus pattern (27 bp):
TTTCAAAAGAAAAGACTCAAAGATATT
Found at i:492159 original size:29 final size:28
Alignment explanation
Indices: 492097--492197 Score: 120
Period size: 29 Copynumber: 3.7 Consensus size: 28
492087 AAATAAATAG
* *
492097 ACTCAAAG-TTTT-TTCAAAA-GAAACG
1 ACTCAAAGATTTTATTCAAAAGGAACCA
492122 ACTCAAAGATATTTATTCAAAAGGAACCA
1 ACTCAAAGAT-TTTATTCAAAAGGAACCA
* *
492151 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGA-TTTTATTCAAAAGGAACCA
492180 ACTCAAAGATTTT-TTCAA
1 ACTCAAAGATTTTATTCAA
492198 GAGAAACTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.12
26 1 0.02
27 8 0.12
28 11 0.17
29 37 0.56
30 1 0.02
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTATTCAAAAGGAACCA
Found at i:492514 original size:35 final size:34
Alignment explanation
Indices: 492473--492538 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
492463 TTAAGATATA
*
492473 GTCTCAAATGAGACAAA-TTTGTTTTTAGAGAAGTT
1 GTCTCAAACG-GACAAAGTTTGTTTTT-GAGAAGTT
*
492508 GTCTCAAGCGGACAAAGTTTGTTTTTGAGAA
1 GTCTCAAACGGACAAAGTTTGTTTTTGAGAA
492539 AACGATCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 11 0.39
35 17 0.61
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.35
Consensus pattern (34 bp):
GTCTCAAACGGACAAAGTTTGTTTTTGAGAAGTT
Found at i:492548 original size:35 final size:34
Alignment explanation
Indices: 492484--492550 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
492474 TCTCAAATGA
***
492484 GACAAATTTGTTTTTAGAGAAGTTGTCTCAAGCG
1 GACAAATTTGTTTTTAGAGAAAACGTCTCAAGCG
492518 GACAAAGTTTGTTTTT-GAGAAAACGATCTCAAG
1 GACAAA-TTTGTTTTTAGAGAAAACG-TCTCAAG
492551 TGAGATCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 12 0.43
35 16 0.57
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (34 bp):
GACAAATTTGTTTTTAGAGAAAACGTCTCAAGCG
Found at i:492680 original size:105 final size:100
Alignment explanation
Indices: 492508--492738 Score: 252
Period size: 104 Copynumber: 2.3 Consensus size: 100
492498 TAGAGAAGTT
* *
492508 GTCTCAAGCG-GACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* *
492572 TGAAATAAATCCGAAATTTGGATCTCAAAGGGAAAAG
65 TG-AATAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
492609 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTGTTT
* * * * *
492673 -TTAGTGAATCAATTCAAAATTTGTATCTCAAAGGAAAAAT
61 AAT-GTGAATAAATCCAAAATTTGGATCTCAAAGGAAAAAG
* *
492713 GTCTCAAGCGAAACACAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
492739 AAAATTCTCA
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
101 15 0.14
102 10 0.09
103 2 0.02
104 57 0.52
105 26 0.24
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (100 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAATAAATCCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:493210 original size:4 final size:4
Alignment explanation
Indices: 493201--493240 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
493191 TGTATCATGG
493201 ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
493241 ATACTTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 32 0.94
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:494462 original size:13 final size:12
Alignment explanation
Indices: 494430--494463 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
494420 TTCTCTTTGC
494430 TTTTCTTTGATT
1 TTTTCTTTGATT
*
494442 TTTGCTTTGATT
1 TTTTCTTTGATT
494454 TTTCTCTTTG
1 TTT-TCTTTG
494464 CTCTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.06, C:0.12, G:0.12, T:0.71
Consensus pattern (12 bp):
TTTTCTTTGATT
Found at i:494481 original size:35 final size:35
Alignment explanation
Indices: 494400--494483 Score: 100
Period size: 35 Copynumber: 2.4 Consensus size: 35
494390 TTTCTCTTCT
* *
494400 TTTTTCTTTGTTTTGTTTCTTTCTCTTTGCTTTTC
1 TTTTTCTTTGCTTTGATTCTTTCTCTTTGCTTTTC
*
494435 TTTGATT-TTTGCTTTGATT-TTTCTCTTTGCTCTTTG
1 TTT--TTCTTTGCTTTGATTCTTTCTCTTTGCT-TTTC
494471 TTTTTCTTTGCTT
1 TTTTTCTTTGCTT
494484 ATTTCTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
34 2 0.05
35 22 0.52
36 16 0.38
37 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.11, T:0.71
Consensus pattern (35 bp):
TTTTTCTTTGCTTTGATTCTTTCTCTTTGCTTTTC
Found at i:494490 original size:12 final size:10
Alignment explanation
Indices: 494400--494495 Score: 63
Period size: 10 Copynumber: 9.4 Consensus size: 10
494390 TTTCTCTTCT
494400 TTTTTCTTTG
1 TTTTTCTTTG
* *
494410 -TTTTGTTTC
1 TTTTTCTTTG
*
494419 TTTCTCTTTG
1 TTTTTCTTTG
*
494429 CTTTTCTTTG
1 TTTTTCTTTG
494439 ATTTTTGCTTTG
1 -TTTTT-CTTTG
*
494451 ATTTTTCTCT-
1 -TTTTTCTTTG
**
494461 TTGCTCTTTG
1 TTTTTCTTTG
494471 TTTTTCTTTG
1 TTTTTCTTTG
494481 CTTATTTCTTT-
1 -TT-TTTCTTTG
494492 TTTT
1 TTTT
494496 ATTGGATCTT
Statistics
Matches: 66, Mismatches: 14, Indels: 13
0.71 0.15 0.14
Matches are distributed among these distances:
9 15 0.23
10 24 0.36
11 9 0.14
12 18 0.27
ACGTcount: A:0.03, C:0.15, G:0.09, T:0.73
Consensus pattern (10 bp):
TTTTTCTTTG
Found at i:495147 original size:20 final size:20
Alignment explanation
Indices: 495119--495160 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
495109 CAAAGAGAGG
*
495119 GAATGTTTCAAGGTCTAAAA
1 GAATATTTCAAGGTCTAAAA
*
495139 GAATATTTCAAGGTCTCAAA
1 GAATATTTCAAGGTCTAAAA
495159 GA
1 GA
495161 GATAGAATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (20 bp):
GAATATTTCAAGGTCTAAAA
Found at i:495167 original size:26 final size:25
Alignment explanation
Indices: 495091--495170 Score: 89
Period size: 26 Copynumber: 3.3 Consensus size: 25
495081 TCAAGGTGGA
495091 AAGAATGTTTCAAGGTCTCAAAGAG
1 AAGAATGTTTCAAGGTCTCAAAGAG
*
495116 AGGGAATGTTTCAAGGTCT---A-A-
1 A-AGAATGTTTCAAGGTCTCAAAGAG
*
495137 AAGAATATTTCAAGGTCTCAAAGAG
1 AAGAATGTTTCAAGGTCTCAAAGAG
495162 ATAGAATGT
1 A-AGAATGT
495171 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 13
0.72 0.07 0.21
Matches are distributed among these distances:
20 15 0.34
21 1 0.02
22 1 0.02
23 2 0.05
24 1 0.02
25 2 0.05
26 22 0.50
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (25 bp):
AAGAATGTTTCAAGGTCTCAAAGAG
Found at i:495169 original size:46 final size:45
Alignment explanation
Indices: 495077--495170 Score: 134
Period size: 46 Copynumber: 2.1 Consensus size: 45
495067 AAAAATGCAG
* * *
495077 TGTTTCAAGGTGGAAAGAATGTTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* *
495122 TGTTTCAAGGTCTAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
495168 TGT
1 TGT
495171 CAAAAATTGG
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
45 11 0.26
46 32 0.74
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.28
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:497643 original size:30 final size:32
Alignment explanation
Indices: 497589--497649 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
497579 TGACAAAATG
497589 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
497621 ACACAAACAAAAGAG-A-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
497650 CATGTAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 13 0.45
31 1 0.03
32 15 0.52
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:501125 original size:17 final size:17
Alignment explanation
Indices: 501087--501130 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
501077 GGGCTTCGCC
501087 CTTTTCTTTCTCTCTTA
1 CTTTTCTTTCTCTCTTA
* * *
501104 GTTTTCTTTCTTTCTTT
1 CTTTTCTTTCTCTCTTA
*
501121 CTTTTTTTTC
1 CTTTTCTTTC
501131 CCAATGGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (17 bp):
CTTTTCTTTCTCTCTTA
Found at i:501771 original size:3 final size:3
Alignment explanation
Indices: 501763--501799 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
501753 ATTAATAAAC
501763 ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
501800 CGATAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:504911 original size:22 final size:23
Alignment explanation
Indices: 504863--504912 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
504853 AAAATATATT
* *
504863 TTATATTGAAATTTAGTATACAA
1 TTATATTGAAATTTAATATAAAA
*
504886 -TATATTGATA-TTAATATAAAA
1 TTATATTGAAATTTAATATAAAA
504907 TTATAT
1 TTATAT
504913 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 9 0.39
22 14 0.61
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (23 bp):
TTATATTGAAATTTAATATAAAA
Found at i:509421 original size:21 final size:19
Alignment explanation
Indices: 509397--509435 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
509387 GGAAACCACC
509397 CTTCTATCTTAGTTTCTCTTT
1 CTTCTATC-T-GTTTCTCTTT
*
509418 CTTCTCTCTGTTTCTCTT
1 CTTCTATCTGTTTCTCTT
509436 AAGGTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.05, C:0.28, G:0.05, T:0.62
Consensus pattern (19 bp):
CTTCTATCTGTTTCTCTTT
Found at i:513212 original size:23 final size:23
Alignment explanation
Indices: 513186--513229 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
513176 TTAATTTCTG
513186 TTTGGGTGTTA-TTTGTGTAAAAC
1 TTTGGGTGTTAGTTT-TGTAAAAC
513209 TTTGGGTGTTAGTTTTGTAAA
1 TTTGGGTGTTAGTTTTGTAAA
513230 TATTTTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.20, C:0.02, G:0.27, T:0.50
Consensus pattern (23 bp):
TTTGGGTGTTAGTTTTGTAAAAC
Found at i:515686 original size:24 final size:24
Alignment explanation
Indices: 515659--515707 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
515649 TGGTGATGGT
515659 TTATAGACTATGACTGATATATGA
1 TTATAGACTATGACTGATATATGA
* ** *
515683 TTATTGGTTTTGACTGATATATGA
1 TTATAGACTATGACTGATATATGA
515707 T
1 T
515708 AACGATGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (24 bp):
TTATAGACTATGACTGATATATGA
Found at i:516012 original size:82 final size:82
Alignment explanation
Indices: 515872--516083 Score: 291
Period size: 82 Copynumber: 2.6 Consensus size: 82
515862 AGATGCTCCA
* * * *
515872 TTAGGTTGGCTCCCTTTGCTGTGTGCTTAGGTTAAGCCCTATTGACTTACGAATTTAAGGATACA
1 TTAGGTTGGCTCCCTTTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGAACTTAAGGATACA
*
515937 TA-CCTCAAAGCCTATCC
66 -AGACTCAAAGCCTATCC
* *
515954 TTAGGTTGGCTCCCATTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGGACTTAAGGATACA
1 TTAGGTTGGCTCCCTTTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGAACTTAAGGATACA
516019 AGACTCAAAGCCTATCC
66 AGACTCAAAGCCTATCC
* * * *
516036 TTAGGTTGGCCTCCTTTTTGTCGTGTGTTTAAGGTAAGCCCTATGGAC
1 TTAGGTTGG-CTCC-CTTTGCCGTGTGCTTAGGGTAAGCCCTATGGAC
516084 GCAGTTATGG
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
81 1 0.01
82 82 0.71
83 4 0.03
84 28 0.24
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (82 bp):
TTAGGTTGGCTCCCTTTGCCGTGTGCTTAGGGTAAGCCCTATGGACTTACGAACTTAAGGATACA
AGACTCAAAGCCTATCC
Found at i:517001 original size:10 final size:10
Alignment explanation
Indices: 516972--517059 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
516962 GCTGCTGGAA
516972 AACCGGTTTG
1 AACCGGTTTG
*
516982 -ACCAGTTTTG
1 AACC-GGTTTG
516992 AACCGGTTTG
1 AACCGGTTTG
*
517002 -ACCGGTTCG
1 AACCGGTTTG
517011 AACCGGTTTG
1 AACCGGTTTG
*
517021 -ACCGGTCTG
1 AACCGGTTTG
517030 AACCGGTTTG
1 AACCGGTTTG
*
517040 -ACCGGTCTG
1 AACCGGTTTG
*
517049 AACCGGGTTG
1 AACCGGTTTG
517059 A
1 A
517060 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:517015 original size:19 final size:19
Alignment explanation
Indices: 516972--517061 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
516962 GCTGCTGGAA
* *
516972 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
516992 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
517011 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
517030 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
517049 AACCGGGTTGACC
1 AACCGGTTTGACC
517062 CGACCCGACC
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:517077 original size:17 final size:17
Alignment explanation
Indices: 517055--517095 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
517045 TCTGAACCGG
517055 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
517072 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
517089 GTTGACC
1 GTTGACC
517096 GTGACCGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.17, C:0.44, G:0.24, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:517102 original size:6 final size:7
Alignment explanation
Indices: 517085--517127 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
517075 GACCCGACCC
517085 GACCGTT
1 GACCGTT
517092 GACCG-T
1 GACCGTT
517098 GACCGTT
1 GACCGTT
517105 GACCG-T
1 GACCGTT
517111 GACCGTT
1 GACCGTT
*
517118 GACCATT
1 GACCGTT
517125 GAC
1 GAC
517128 TTTCTTTGAC
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:517103 original size:13 final size:13
Alignment explanation
Indices: 517085--517121 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
517075 GACCCGACCC
517085 GACCGTTGACCGT
1 GACCGTTGACCGT
517098 GACCGTTGACCGT
1 GACCGTTGACCGT
517111 GACCGTTGACC
1 GACCGTTGACC
517122 ATTGACTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.32, G:0.30, T:0.22
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:517110 original size:20 final size:20
Alignment explanation
Indices: 517085--517127 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
517075 GACCCGACCC
*
517085 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCATT
517105 GACCG-TGACCGTTGACCATT
1 GACCGTTGACCG-TGACCATT
517125 GAC
1 GAC
517128 TTTCTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCATT
Found at i:518099 original size:63 final size:63
Alignment explanation
Indices: 517997--518120 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
517987 CTAATGTGAC
* ** * * *
517997 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGACCCT-CAGGCCCTAAGATGTGT
* *
518060 TCTTAGGTAGGCCCCACGGCCCCGAAATC-TATCTTGGGTAGACTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCAT-TCTCGGGTAGACCCTCAGGCCCTAAGATGT
518121 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCATTCTCGGGTAGACCCTCAGGCCCTAAGATGTGT
Found at i:524354 original size:10 final size:10
Alignment explanation
Indices: 524325--524393 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
524315 GCTGCTGGAA
524325 AACCGGTTTG
1 AACCGGTTTG
*
524335 -ACCAGTTTTG
1 AACC-GGTTTG
*
524345 AACTGGTTTG
1 AACCGGTTTG
*
524355 -ACCGGTTCG
1 AACCGGTTTG
524364 AACCGGTTTG
1 AACCGGTTTG
*
524374 -ACCGGTCTG
1 AACCGGTTTG
*
524383 AACCGGGTTG
1 AACCGGTTTG
524393 A
1 A
524394 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 26 0.57
11 2 0.04
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:524371 original size:19 final size:19
Alignment explanation
Indices: 524325--524395 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 19
524315 GCTGCTGGAA
* *
524325 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
*
524345 AACTGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
524364 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
524383 AACCGGGTTGACC
1 AACCGGTTTGACC
524396 CGACCCGATC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.04
19 31 0.69
20 12 0.27
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:524411 original size:17 final size:17
Alignment explanation
Indices: 524389--524429 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
524379 TCTGAACCGG
*
524389 GTTGACCCGACCCGATC
1 GTTGACCCGACCCGACC
524406 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
524423 GTTGACC
1 GTTGACC
524430 GTGACCGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:524431 original size:7 final size:7
Alignment explanation
Indices: 524419--524461 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
524409 GACCCGACCC
524419 GACCGTT
1 GACCGTT
524426 GACCG-T
1 GACCGTT
524432 GACCGTT
1 GACCGTT
524439 GACCG-T
1 GACCGTT
524445 GACCGTT
1 GACCGTT
524452 GACCGTT
1 GACCGTT
524459 GAC
1 GAC
524462 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:524437 original size:13 final size:13
Alignment explanation
Indices: 524419--524457 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
524409 GACCCGACCC
524419 GACCGTTGACCGT
1 GACCGTTGACCGT
524432 GACCGTTGACCGT
1 GACCGTTGACCGT
524445 GACCGTTGACCGT
1 GACCGTTGACCGT
524458 TGACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:524444 original size:20 final size:20
Alignment explanation
Indices: 524419--524461 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
524409 GACCCGACCC
524419 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
524439 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
524459 GAC
1 GAC
524462 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:525399 original size:63 final size:63
Alignment explanation
Indices: 525331--525454 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
525321 CTAATGTGAC
* ** * *
525331 TCTTAGGTAGGCTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
525394 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
525455 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:536408 original size:32 final size:31
Alignment explanation
Indices: 536366--536431 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
536356 AGAATTTTTT
*
536366 TTATTAAAAATATTAATATTTT-TGATAAAATA
1 TTATTAAAAATATTAAT-TTTTATCA-AAAATA
*
536398 TTATTTAAAATATTAATTTTTATCAAAAATA
1 TTATTAAAAATATTAATTTTTATCAAAAATA
536429 TTA
1 TTA
536432 ATTTTGTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (31 bp):
TTATTAAAAATATTAATTTTTATCAAAAATA
Found at i:536639 original size:61 final size:62
Alignment explanation
Indices: 536574--536693 Score: 188
Period size: 61 Copynumber: 2.0 Consensus size: 62
536564 AACATTTTCA
* *
536574 GTAAATAATAATATTTTAAATATCATTTTACCAGAAATATT-AAAAAATATTAATATTTCTT
1 GTAAAAAATAATATTTTAAATATCATTTTACCAAAAATATTAAAAAAATATTAATATTTCTT
* **
536635 GTAAAAAATAATATTTTAGATATCATTTTATTAAAAATATTAAAAAAATATTAATATTT
1 GTAAAAAATAATATTTTAAATATCATTTTACCAAAAATATTAAAAAAATATTAATATTT
536694 ACTATTGTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
61 36 0.68
62 17 0.32
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (62 bp):
GTAAAAAATAATATTTTAAATATCATTTTACCAAAAATATTAAAAAAATATTAATATTTCTT
Found at i:537199 original size:33 final size:33
Alignment explanation
Indices: 537161--537238 Score: 79
Period size: 34 Copynumber: 2.3 Consensus size: 33
537151 AATTCATTTT
* *
537161 TTATTTATAATATC-AATATTTAAACCTATAACA
1 TTATTTATAATATCTAACATTCAAACCTATAA-A
* *
537194 TTATTTGATAA-ATCTAACATTCCATCCTATAAA
1 TTATTT-ATAATATCTAACATTCAAACCTATAAA
537227 TTAATTTATAAT
1 TT-ATTTATAAT
537239 TAATTGTCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
33 16 0.43
34 21 0.57
ACGTcount: A:0.42, C:0.13, G:0.01, T:0.44
Consensus pattern (33 bp):
TTATTTATAATATCTAACATTCAAACCTATAAA
Found at i:538424 original size:21 final size:21
Alignment explanation
Indices: 538400--538499 Score: 100
Period size: 21 Copynumber: 4.9 Consensus size: 21
538390 GTCTCCACCT
*
538400 CCGTAACCTCCACT-TCCACTG
1 CCGTATCCTCCA-TGTCCACTG
* *
538421 CCGTATCCACCATGTCCGCTG
1 CCGTATCCTCCATGTCCACTG
**
538442 CCGTATCCTCCATGTCCACCA
1 CCGTATCCTCCATGTCCACTG
*
538463 CCGTATCCACCATGT-C-C-G
1 CCGTATCCTCCATGTCCACTG
*
538481 CCATATCCTCCATGTCCAC
1 CCGTATCCTCCATGTCCAC
538500 CACTGCATCC
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
18 13 0.20
19 2 0.03
20 3 0.05
21 47 0.72
ACGTcount: A:0.18, C:0.46, G:0.12, T:0.24
Consensus pattern (21 bp):
CCGTATCCTCCATGTCCACTG
Found at i:538460 original size:42 final size:39
Alignment explanation
Indices: 538421--538560 Score: 138
Period size: 42 Copynumber: 3.4 Consensus size: 39
538411 ACTTCCACTG
538421 CCGTATCCACCATGTCCGCTGCCGTATCCTCCATGTCCACCA
1 CCGTATCCACCATGT-C-C-GCCGTATCCTCCATGTCCACCA
*
538463 CCGTATCCACCATGTCCGCCATATCCTCCATGTCCACCA
1 CCGTATCCACCATGTCCGCCGTATCCTCCATGTCCACCA
* * * ** *
538502 CTGCATCCACCATATCTTTTACC-TTTCCCTCCATGTCCACCA
1 CCGTATCCACCATGTC---CGCCGTAT-CCTCCATGTCCACCA
*
538544 CCGTATCCACTATGTCC
1 CCGTATCCACCATGTCC
538561 ACTGCCGTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
39 34 0.41
40 1 0.01
41 3 0.04
42 44 0.54
ACGTcount: A:0.19, C:0.44, G:0.10, T:0.27
Consensus pattern (39 bp):
CCGTATCCACCATGTCCGCCGTATCCTCCATGTCCACCA
Found at i:538509 original size:21 final size:20
Alignment explanation
Indices: 538446--538514 Score: 70
Period size: 21 Copynumber: 3.5 Consensus size: 20
538436 CCGCTGCCGT
* *
538446 ATCCTCCATGTCCACCACCG
1 ATCCACCATGTCCACCACTG
*
538466 TATCCACCATGTCCGCCA-T-
1 -ATCCACCATGTCCACCACTG
*
538485 ATCCTCCATGTCCACCACTG
1 ATCCACCATGTCCACCACTG
538505 CATCCACCAT
1 -ATCCACCAT
538515 ATCTTTTACC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
21 23 0.59
ACGTcount: A:0.22, C:0.46, G:0.09, T:0.23
Consensus pattern (20 bp):
ATCCACCATGTCCACCACTG
Found at i:538801 original size:10 final size:10
Alignment explanation
Indices: 538786--538814 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
538776 AGCTGCCACT
538786 TGAGAAGAAA
1 TGAGAAGAAA
538796 TGAGAAGAAA
1 TGAGAAGAAA
538806 TGAGAAGAA
1 TGAGAAGAA
538815 CAAGAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.31, T:0.10
Consensus pattern (10 bp):
TGAGAAGAAA
Found at i:538833 original size:23 final size:20
Alignment explanation
Indices: 538787--538834 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 20
538777 GCTGCCACTT
* *
538787 GAGAAGAAATGAGAAGAAAT
1 GAGAAGAAAAGAGAAGAAAA
538807 GAGAAGAACAAGAGAAGTTAAAA
1 GAGAAGAA-AAGAGAAG--AAAA
538830 GAGAA
1 GAGAA
538835 AGGAGAAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 7 0.30
23 8 0.35
ACGTcount: A:0.60, C:0.02, G:0.29, T:0.08
Consensus pattern (20 bp):
GAGAAGAAAAGAGAAGAAAA
Found at i:539202 original size:14 final size:15
Alignment explanation
Indices: 539183--539211 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
539173 AAATATAAAA
539183 AGTGTT-ATTGTAAT
1 AGTGTTAATTGTAAT
539197 AGTGTTAATTGTAAT
1 AGTGTTAATTGTAAT
539212 TTAAAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
AGTGTTAATTGTAAT
Found at i:550161 original size:22 final size:22
Alignment explanation
Indices: 550124--550197 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
550114 GAAAATACTA
550124 AATTATAAAGTT-AATTTTATTT
1 AATTATAAA-TTAAATTTTATTT
*
550146 AATTATAAATTAAATTTGTA-TC
1 AATTATAAATTAAATTT-TATTT
* *
550168 AATTATATTATTAAATATTAGTTTT
1 AATTATA-AATTAAATTTTA--TTT
550193 AATTA
1 AATTA
550198 ATTTATCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 2 0.05
22 24 0.57
23 10 0.24
25 6 0.14
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (22 bp):
AATTATAAATTAAATTTTATTT
Found at i:550602 original size:41 final size:41
Alignment explanation
Indices: 550555--550636 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
550545 AGATTAAATA
550555 TATCAAATTAGTTTATTTAAGACCATATTGATTACATGTGT
1 TATCAAATTAGTTTATTTAAGACCATATTGATTACATGTGT
550596 TATCAAATTAGTTTATTTAAGACCATATTGATTACATGTGT
1 TATCAAATTAGTTTATTTAAGACCATATTGATTACATGTGT
550637 ATTAATGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (41 bp):
TATCAAATTAGTTTATTTAAGACCATATTGATTACATGTGT
Found at i:563506 original size:15 final size:15
Alignment explanation
Indices: 563486--563536 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
563476 ATATTTAGCT
*
563486 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
563501 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
563516 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
563531 GGGCGG
1 GGGCGG
563537 ATAATGTCTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.06, C:0.18, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:573320 original size:26 final size:27
Alignment explanation
Indices: 573280--573331 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
573270 AGTTGAAGTC
573280 AAATTTAATT-TTTTTTATCTTATTTA
1 AAATTTAATTATTTTTTATCTTATTTA
* *
573306 AAATTTTATTATTTTTTATGTTATTT
1 AAATTTAATTATTTTTTATCTTATTT
573332 TTCTTGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
AAATTTAATTATTTTTTATCTTATTTA
Found at i:575320 original size:2 final size:2
Alignment explanation
Indices: 575313--575344 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
575303 CATAAAAACC
575313 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
575345 TTTTAGCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:578981 original size:2 final size:2
Alignment explanation
Indices: 578974--578998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
578964 TACGTGTATG
578974 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
578999 CAAAATGTAT
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:581038 original size:25 final size:23
Alignment explanation
Indices: 581005--581050 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
580995 TTTTGTTTCA
*
581005 TTTTTAATAATAAATCAAACCCCT
1 TTTTTAAT-AGAAATCAAACCCCT
581029 TTTTTAAATAGAAATCAAACCC
1 TTTTT-AATAGAAATCAAACCC
581051 TCTTAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (23 bp):
TTTTTAATAGAAATCAAACCCCT
Found at i:582962 original size:16 final size:16
Alignment explanation
Indices: 582941--582994 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
582931 TGTATAGTTT
582941 ATCTAATAATTATTAA
1 ATCTAATAATTATTAA
*
582957 ATCTAATAA-GA-TAA
1 ATCTAATAATTATTAA
* *
582971 A-ATATTAATTATTAA
1 ATCTAATAATTATTAA
582986 ATCTAATAA
1 ATCTAATAA
582995 GATAAAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
13 5 0.17
14 5 0.17
15 5 0.17
16 14 0.48
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.39
Consensus pattern (16 bp):
ATCTAATAATTATTAA
Found at i:582980 original size:29 final size:29
Alignment explanation
Indices: 582947--583006 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
582937 GTTTATCTAA
582947 TAATTATTAAATCTAATAAGATAAAATAT
1 TAATTATTAAATCTAATAAGATAAAATAT
582976 TAATTATTAAATCTAATAAGATAAAATAT
1 TAATTATTAAATCTAATAAGATAAAATAT
583005 TA
1 TA
583007 GGCTTTTACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (29 bp):
TAATTATTAAATCTAATAAGATAAAATAT
Found at i:596124 original size:210 final size:210
Alignment explanation
Indices: 595762--596391 Score: 1242
Period size: 210 Copynumber: 3.0 Consensus size: 210
595752 AATTTATTTT
595762 CAGTCAGTGTTAACATTATATTTTGCAGCAGTACTATTTCCAACCCTATGATTATGTTTAGTATA
1 CAGTCAGTGTTAACATTATATTTTGCAGCAGTACTATTTCCAACCCTATGATTATGTTTAGTATA
595827 GCAAATGGTTTGTTACTCTCTTGAATCCACCCCTTAAAATGATTTATAGTTGTTTTGTTTGTATA
66 GCAAATGGTTTGTTACTCTCTTGAATCCACCCCTTAAAATGATTTATAGTTGTTTTGTTTGTATA
595892 GAAGGGGAAAAATGTTATGTGGGTGAACAATACGTGATCAAATATGGAGTTTGAAAAAAGAAAAT
131 GAAGGGGAAAAATGTTATGTGGGTGAACAATACGTGATCAAATATGGAGTTTGAAAAAAGAAAAT
595957 TGGTCGATATTGCAG
196 TGGTCGATATTGCAG
595972 CAGTCAGTGTTAACATTATATTTTGCAGCAGTACTATTTCCAACCCTATGATTATGTTTAGTATA
1 CAGTCAGTGTTAACATTATATTTTGCAGCAGTACTATTTCCAACCCTATGATTATGTTTAGTATA
596037 GCAAATGGTTTGTTACTCTCTTGAATCCACCCCTTAAAATGATTTATAGTTGTTTTGTTTGTATA
66 GCAAATGGTTTGTTACTCTCTTGAATCCACCCCTTAAAATGATTTATAGTTGTTTTGTTTGTATA
596102 GAAGGGGAAAAATGTTATGTGGGTGAACAATACGTGATCAAATATGGAGTTTGAAAAAAGAAAAT
131 GAAGGGGAAAAATGTTATGTGGGTGAACAATACGTGATCAAATATGGAGTTTGAAAAAAGAAAAT
596167 TGGTCGATATTGCAG
196 TGGTCGATATTGCAG
596182 CAGTCAGTGTTAACATTATATTTTGCAGCAGTACTATTTCCAACCCTATGATTATGTTTAGTATA
1 CAGTCAGTGTTAACATTATATTTTGCAGCAGTACTATTTCCAACCCTATGATTATGTTTAGTATA
*
596247 GCAAATGGTTTGTTACTCTCTTGAATCCACCCCTTAAAACGATTTATAGTTGTTTTGTTTGTATA
66 GCAAATGGTTTGTTACTCTCTTGAATCCACCCCTTAAAATGATTTATAGTTGTTTTGTTTGTATA
*
596312 GAAGGGGAAAAATGTTATGTGGGTGAACAATACGTGATCAAATATTGAGTTTGAAAAAAGAAAAT
131 GAAGGGGAAAAATGTTATGTGGGTGAACAATACGTGATCAAATATGGAGTTTGAAAAAAGAAAAT
596377 TGGTCGATATTGCAG
196 TGGTCGATATTGCAG
596392 AGGATAATGG
Statistics
Matches: 418, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 418 1.00
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (210 bp):
CAGTCAGTGTTAACATTATATTTTGCAGCAGTACTATTTCCAACCCTATGATTATGTTTAGTATA
GCAAATGGTTTGTTACTCTCTTGAATCCACCCCTTAAAATGATTTATAGTTGTTTTGTTTGTATA
GAAGGGGAAAAATGTTATGTGGGTGAACAATACGTGATCAAATATGGAGTTTGAAAAAAGAAAAT
TGGTCGATATTGCAG
Found at i:613904 original size:22 final size:21
Alignment explanation
Indices: 613873--613913 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
613863 TTTCTTGGAG
613873 AATAACATTGGTCTAGTAGACA
1 AATAACATTGGTCTA-TAGACA
* *
613895 AATAATATTGTTCTATAGA
1 AATAACATTGGTCTATAGA
613914 TGCATGAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (21 bp):
AATAACATTGGTCTATAGACA
Found at i:619792 original size:27 final size:27
Alignment explanation
Indices: 619757--619809 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
619747 AGTTTTAAAA
619757 TTTATATTT-A-TTTAATCTAAGTATATC
1 TTTATATTTAATTTTAAT-TAA-TATATC
619784 TTTATATTTAATTTTAATTAATATAT
1 TTTATATTTAATTTTAATTAATATAT
619810 AAAACAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 14 0.58
28 4 0.17
29 6 0.25
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTATATTTAATTTTAATTAATATATC
Found at i:621758 original size:17 final size:17
Alignment explanation
Indices: 621736--621769 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
621726 ATAATTTATA
621736 ATATTATAAATTATAAT
1 ATATTATAAATTATAAT
*
621753 ATATTATAATTTATAAT
1 ATATTATAAATTATAAT
621770 GTAAACAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTATAAATTATAAT
Found at i:624666 original size:15 final size:14
Alignment explanation
Indices: 624646--624679 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
624636 ACCTAATTAA
*
624646 TAATACTTATTATAT
1 TAATACTTAATAT-T
624661 TAATACTTAATATT
1 TAATACTTAATATT
624675 TAATA
1 TAATA
624680 GACAATTCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATACTTAATATT
Found at i:631980 original size:20 final size:20
Alignment explanation
Indices: 631952--631989 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
631942 ATAGATTTTT
631952 AATAAAAAATATATAATATA
1 AATAAAAAATATATAATATA
*
631972 AATATAAAATATATAATA
1 AATAAAAAATATATAATA
631990 ATTTTATATT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAAAAATATATAATATA
Found at i:638756 original size:9 final size:9
Alignment explanation
Indices: 638741--638778 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
638731 ATTCATCTCG
638741 AATTAATTT
1 AATTAATTT
*
638750 TATTAA-TT
1 AATTAATTT
638758 AATTAATTT
1 AATTAATTT
*
638767 AATTAATAT
1 AATTAATTT
638776 AAT
1 AAT
638779 CAGATCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTAATTT
Found at i:640255 original size:68 final size:68
Alignment explanation
Indices: 640174--640577 Score: 566
Period size: 68 Copynumber: 6.1 Consensus size: 68
640164 TGCATGATAC
640174 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
640239 TAT
66 TAT
* * *
640242 TTCAACTGTATCAGAAA-TTGTAGTTGAG----CTA--TTAATTTTTGGGACCAATTTACATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
640300 TAT
66 TAT
* *
640303 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATTTAATTTTTGGGATCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
640368 TAT
66 TAT
* ** * *
640371 TTCAACTATATCA-AAAATTGTAGTTGAG----CTA--TTAATTTTTGAGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
640429 TAT
66 TAT
* * *
640432 TTCAATTGCCTCAGAAATTTGTAGTTGAACTATCTATTTTAATTTATGGGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
640497 TAT
66 TAT
* * *
640500 TTCAATTGCATCAGAAATTTGTAGTTGAGTTATCTATTTTAATTTTTGAGACCGATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
640565 TAT
66 TAT
640568 TTCAATTGCA
1 TTCAATTGCA
640578 ATCTCCTTCC
Statistics
Matches: 295, Mismatches: 27, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
61 81 0.27
62 24 0.08
63 6 0.02
66 6 0.02
67 25 0.08
68 153 0.52
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.45
Consensus pattern (68 bp):
TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
TAT
Found at i:640404 original size:129 final size:129
Alignment explanation
Indices: 640174--640577 Score: 628
Period size: 129 Copynumber: 3.1 Consensus size: 129
640164 TGCATGATAC
640174 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
* * *
640239 TATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAATTTTTGGGACCAATTTACATTTATAT
66 TATTTCAACTGTATCAAAAATTGTAGTTGAGCTATTAATTTTTGAGACCAATTTGCATTTATAT
* *
640303 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATTTAATTTTTGGGATCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
*
640368 TATTTCAACTATATCAAAAATTGTAGTTGAGCTATTAATTTTTGAGACCAATTTGCATTTATAT
66 TATTTCAACTGTATCAAAAATTGTAGTTGAGCTATTAATTTTTGAGACCAATTTGCATTTATAT
* * *
640432 TTCAATTGCCTCAGAAATTTGTAGTTGAACTATCTATTTTAATTTATGGGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
* * * *
640497 TATTTCAATTGCATCAGAAATTTGTAGTTGAGTTATCTATTTTAATTTTTGAGACCGATTTGCAT
66 TATTTCAACTGTATCA-AAAATTGTAGTTGAG----CTA--TTAATTTTTGAGACCAATTTGCAT
640562 TTATAT
124 TTATAT
640568 TTCAATTGCA
1 TTCAATTGCA
640578 ATCTCCTTCC
Statistics
Matches: 251, Mismatches: 17, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
129 196 0.78
130 14 0.06
134 3 0.01
136 38 0.15
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.45
Consensus pattern (129 bp):
TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
TATTTCAACTGTATCAAAAATTGTAGTTGAGCTATTAATTTTTGAGACCAATTTGCATTTATAT
Found at i:640543 original size:197 final size:190
Alignment explanation
Indices: 640212--640572 Score: 551
Period size: 197 Copynumber: 1.9 Consensus size: 190
640202 GCTATCTATT
* *
640212 TTAATTTTTGGGACCAATTTGCATTTATATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAA
1 TTAATTTTTGAGACCAATTTGCATTTATATTTCAACTGCATCAGAAATTGTAGTTGAGCTATTAA
*
640277 TTTTTGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATT
66 TTTATGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATT
* *
640342 TAATTTTTGGGATCAATTTGCATTTATATTTCAACTATATCAAAAATTGTAGTTGAGCTA
131 TAATTTTTGAGACCAATTTGCATTTATATTTCAACTATATCAAAAATTGTAGTTGAGCTA
* * *
640402 TTAATTTTTGAGACCAATTTGCATTTATATTTCAATTGCCTCAGAAATTTGTAGTTGAACTATCT
1 TTAATTTTTGAGACCAATTTGCATTTATATTTCAACTGCATCAGAAA-TTGTAGTTG----AGCT
* *
640467 ATTTTAATTTATGGGACCAATTTGCATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGTTA
61 A--TTAATTTATGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTA
* *
640532 TCTATTTTAATTTTTGAGACCGATTTGCATTTATATTTCAA
124 TCTAATTTAATTTTTGAGACCAATTTGCATTTATATTTCAA
640573 TTGCAATCTC
Statistics
Matches: 152, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
190 43 0.28
191 9 0.06
195 4 0.03
197 96 0.63
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (190 bp):
TTAATTTTTGAGACCAATTTGCATTTATATTTCAACTGCATCAGAAATTGTAGTTGAGCTATTAA
TTTATGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATT
TAATTTTTGAGACCAATTTGCATTTATATTTCAACTATATCAAAAATTGTAGTTGAGCTA
Found at i:641067 original size:68 final size:67
Alignment explanation
Indices: 640859--641126 Score: 371
Period size: 68 Copynumber: 4.1 Consensus size: 67
640849 GGAAGGAGAT
* *
640859 TGCAATTGAAATATAAATGTAAATTGGTCCCAAAAATTAAGATAGATAGCTCAACTTCAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAA-ATAGATAGCTCAACTACAAATTTC
640924 TGA
65 TGA
*
640927 TGCAATTGAAATATAAATGCAAATTTGTCCCAAAAA-T---TA-ATAGCTCAACTAC-AATTTCT
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAATAGATAGCTCAACTACAAATTTCT
640986 GA
66 GA
* * *
640988 TACAGTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGTTCAACTACAAATTTC
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATT-AAATAGATAGCTCAACTACAAATTTC
641053 TGA
65 TGA
*
641056 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAA-T---TA-ATAGCTCGACTAC-AATTTCT
1 TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAATAGATAGCTCAACTACAAATTTCT
641115 GA
66 GA
641117 TGCAATTGAA
1 TGCAATTGAA
641127 TTCACCGGTC
Statistics
Matches: 182, Mismatches: 11, Indels: 21
0.85 0.05 0.10
Matches are distributed among these distances:
61 61 0.34
62 24 0.13
63 4 0.02
66 2 0.01
67 14 0.08
68 77 0.42
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (67 bp):
TGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAATAGATAGCTCAACTACAAATTTCT
GA
Found at i:641094 original size:129 final size:129
Alignment explanation
Indices: 640861--641126 Score: 460
Period size: 129 Copynumber: 2.1 Consensus size: 129
640851 AAGGAGATTG
* * *
640861 CAATTGAAATATAAATGTAAATTGGTCCCAAAAATTAAGATAGATAGCTCAACTTCAAATTTCTG
1 CAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTCTG
*
640926 ATGCAATTGAAATATAAATGCAAATTTGTCCCAAAAATTAATAGCTCAACTACAATTTCTGATA
66 ATGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAATAGCTCAACTACAATTTCTGATA
* *
640990 CAGTTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGTTCAACTACAAATTTCTG
1 CAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTCTG
* *
641055 ATGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAATAGCTCGACTACAATTTCTGATG
66 ATGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAATAGCTCAACTACAATTTCTGATA
641119 CAATTGAA
1 CAATTGAA
641127 TTCACCGGTC
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (129 bp):
CAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAAAATAGATAGCTCAACTACAAATTTCTG
ATGCAATTGAAATATAAATGCAAATTGGTCCCAAAAATTAATAGCTCAACTACAATTTCTGATA
Found at i:643338 original size:68 final size:68
Alignment explanation
Indices: 643252--643655 Score: 557
Period size: 68 Copynumber: 6.1 Consensus size: 68
643242 TGCATGATAC
*
643252 TTCAATTGCATCATAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
643317 TAT
66 TAT
* * *
643320 TTCAACTGTATCAGAAA-TTGTAGTTGAG----CTA--TTAATTTTTGGGACCAATTTACATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
643378 TAT
66 TAT
* * *
643381 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATTTAATTTTTGGGATCGATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
643446 TAT
66 TAT
* * **
643449 TTCAACTGTATCAGAAA-TTGTAGTTGAG----CTA--TTAATTTTTTAGACCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
643507 TAT
66 TAT
* * * * *
643510 TTCAATTGCCTCATAAATTTGTAGTTGAACTATCTATTTTAATTTATGGGATCAATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
643575 TAT
66 TAT
*
643578 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCGATTTGCATTTA
1 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
643643 TAT
66 TAT
643646 TTCAATTGCA
1 TTCAATTGCA
643656 ATCTCCTTCC
Statistics
Matches: 292, Mismatches: 30, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
61 83 0.28
62 21 0.07
63 6 0.02
66 6 0.02
67 22 0.08
68 154 0.53
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (68 bp):
TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
TAT
Found at i:643482 original size:129 final size:129
Alignment explanation
Indices: 643252--643655 Score: 628
Period size: 129 Copynumber: 3.1 Consensus size: 129
643242 TGCATGATAC
*
643252 TTCAATTGCATCATAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCAATTTGCATTTA
1 TTCAATTGCATCATAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGATCAATTTGCATTTA
*
643317 TATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAATTTTTGGGACCAATTTACATTTATAT
66 TATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAATTTTTGGGACCAATTTGCATTTATAT
* * *
643381 TTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATTTAATTTTTGGGATCGATTTGCATTTA
1 TTCAATTGCATCATAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGATCAATTTGCATTTA
**
643446 TATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAATTTTTTAGACCAATTTGCATTTATAT
66 TATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAATTTTTGGGACCAATTTGCATTTATAT
* * *
643510 TTCAATTGCCTCATAAATTTGTAGTTGAACTATCTATTTTAATTTATGGGATCAATTTGCATTTA
1 TTCAATTGCATCATAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGATCAATTTGCATTTA
* * *
643575 TATTTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGACCGATTTGCAT
66 TATTTCAACTGTATCAGAAA-TTGTAGTTGAG----CTA--TTAATTTTTGGGACCAATTTGCAT
643640 TTATAT
124 TTATAT
643646 TTCAATTGCA
1 TTCAATTGCA
643656 ATCTCCTTCC
Statistics
Matches: 249, Mismatches: 19, Indels: 7
0.91 0.07 0.03
Matches are distributed among these distances:
129 199 0.80
130 11 0.04
134 3 0.01
136 36 0.14
ACGTcount: A:0.29, C:0.12, G:0.14, T:0.45
Consensus pattern (129 bp):
TTCAATTGCATCATAAATTTGTAGTTGAGCTATCTATTTTAATTTTTGGGATCAATTTGCATTTA
TATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAATTTTTGGGACCAATTTGCATTTATAT
Found at i:643604 original size:197 final size:190
Alignment explanation
Indices: 643290--643650 Score: 551
Period size: 197 Copynumber: 1.9 Consensus size: 190
643280 GCTATCTATT
* *
643290 TTAATTTTTGGGACCAATTTGCATTTATATTTCAACTGTATCAGAAATTGTAGTTGAGCTATTAA
1 TTAATTTTTGAGACCAATTTGCATTTATATTTCAACTGCATCAGAAATTGTAGTTGAGCTATTAA
*
643355 TTTTTGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATT
66 TTTATGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATT
*
643420 TAATTTTTGGGATCGATTTGCATTTATATTTCAACTGTATCAGAAATTGTAGTTGAGCTA
131 TAATTTTTGGGACCGATTTGCATTTATATTTCAACTGTATCAGAAATTGTAGTTGAGCTA
* * * * *
643480 TTAATTTTTTAGACCAATTTGCATTTATATTTCAATTGCCTCATAAATTTGTAGTTGAACTATCT
1 TTAATTTTTGAGACCAATTTGCATTTATATTTCAACTGCATCAGAAA-TTGTAGTTG----AGCT
* *
643545 ATTTTAATTTATGGGATCAATTTGCATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTA
61 A--TTAATTTATGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTA
*
643610 TCTATTTTAATTTTTGGGACCGATTTGCATTTATATTTCAA
124 TCTAATTTAATTTTTGGGACCGATTTGCATTTATATTTCAA
643651 TTGCAATCTC
Statistics
Matches: 152, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
190 41 0.27
191 9 0.06
195 4 0.03
197 98 0.64
ACGTcount: A:0.29, C:0.11, G:0.14, T:0.45
Consensus pattern (190 bp):
TTAATTTTTGAGACCAATTTGCATTTATATTTCAACTGCATCAGAAATTGTAGTTGAGCTATTAA
TTTATGGGACCAATTTACATTTATATTTCAATTGCATCAGAAATTTGTAGTTGAGCTATCTAATT
TAATTTTTGGGACCGATTTGCATTTATATTTCAACTGTATCAGAAATTGTAGTTGAGCTA
Found at i:651203 original size:18 final size:19
Alignment explanation
Indices: 651180--651217 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
651170 GGCACAACTG
651180 CCTATT-TATAGCATCTAT
1 CCTATTATATAGCATCTAT
*
651198 CCTATTCATATGGCATCTAT
1 CCTATT-ATATAGCATCTAT
651218 GAAGCTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (19 bp):
CCTATTATATAGCATCTAT
Found at i:655027 original size:23 final size:22
Alignment explanation
Indices: 655001--655055 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
654991 TATCTTGATT
*
655001 TTTTAAAATTATTTCTTTAATA
1 TTTTAAAATTATTTCTATAATA
** *
655023 CTTTTAATTTTATTTGTATAATA
1 -TTTTAAAATTATTTCTATAATA
655046 TATTTAAAAT
1 T-TTTAAAAT
655056 GTTATTAATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTAAAATTATTTCTATAATA
Found at i:663283 original size:31 final size:33
Alignment explanation
Indices: 663225--663288 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
663215 AACATCATTT
* *
663225 AGATTGTTATAGTTTGTTGTTATAAAATTTAAA
1 AGATTGTTATAGTTTGTTGTTAAAAAATATAAA
*
663258 AGATTG-TATA-TTTGTTTTTAAAAAATATAAA
1 AGATTGTTATAGTTTGTTGTTAAAAAATATAAA
663289 TTATAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 18 0.64
32 4 0.14
33 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (33 bp):
AGATTGTTATAGTTTGTTGTTAAAAAATATAAA
Found at i:663302 original size:24 final size:23
Alignment explanation
Indices: 663275--663329 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
663265 ATATTTGTTT
663275 TTAAAAAA-TATAAATTATAAATAA
1 TTAAAAAATTAT-AATT-TAAATAA
* *
663299 TTAAAACATTATACTTTAAATAA
1 TTAAAAAATTATAATTTAAATAA
*
663322 ATAAAAAA
1 TTAAAAAA
663330 CTCAAAATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 13 0.50
24 10 0.38
25 3 0.12
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAAAAAATTATAATTTAAATAA
Found at i:663481 original size:12 final size:12
Alignment explanation
Indices: 663464--663494 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
663454 GTATTATTTA
663464 TGTGGAACTATG
1 TGTGGAACTATG
663476 TGTGGAACTATG
1 TGTGGAACTATG
*
663488 CGTGGAA
1 TGTGGAA
663495 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.10, G:0.35, T:0.29
Consensus pattern (12 bp):
TGTGGAACTATG
Found at i:664500 original size:10 final size:10
Alignment explanation
Indices: 664485--664538 Score: 54
Period size: 10 Copynumber: 5.0 Consensus size: 10
664475 CGTTCGGTAA
664485 TATGTTCGTT
1 TATGTTCGTT
*
664495 TATGTTGGTTCATT
1 TATGTTCG-T---T
664509 TATGTTCGTT
1 TATGTTCGTT
664519 TATGTTCGTT
1 TATGTTCGTT
*
664529 TATGTGCGTT
1 TATGTTCGTT
664539 CATTTATGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 27 0.73
11 1 0.03
13 1 0.03
14 8 0.22
ACGTcount: A:0.11, C:0.09, G:0.22, T:0.57
Consensus pattern (10 bp):
TATGTTCGTT
Found at i:664528 original size:34 final size:36
Alignment explanation
Indices: 664467--664548 Score: 116
Period size: 34 Copynumber: 2.3 Consensus size: 36
664457 GGCTCATTCA
*
664467 TTCATTTACGTTCGGTAATATGTTCGTTTATGTTG-G
1 TTCATTTATGTTCGGTAATATGTTCGTTTATG-TGCG
*
664503 TTCATTTATGTTC-GT-TTATGTTCGTTTATGTGCG
1 TTCATTTATGTTCGGTAATATGTTCGTTTATGTGCG
664537 TTCATTTATGTT
1 TTCATTTATGTT
664549 TAGCTCAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
33 2 0.05
34 27 0.63
35 2 0.05
36 12 0.28
ACGTcount: A:0.15, C:0.11, G:0.20, T:0.55
Consensus pattern (36 bp):
TTCATTTATGTTCGGTAATATGTTCGTTTATGTGCG
Found at i:664539 original size:24 final size:24
Alignment explanation
Indices: 664488--664548 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
664478 TCGGTAATAT
* * *
664488 GTTCGTTTATGTTGGTTCATTTAT
1 GTTCGTTTATGTTCGTTCATGTAC
* *
664512 GTTCGTTTATGTTCGTTTATGTGC
1 GTTCGTTTATGTTCGTTCATGTAC
*
664536 GTTCATTTATGTT
1 GTTCGTTTATGTT
664549 TAGCTCAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.11, C:0.10, G:0.21, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCATGTAC
Found at i:664599 original size:25 final size:25
Alignment explanation
Indices: 664571--664625 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
664561 CCTAGACCCA
664571 TTTAAAATATAAAATCCCA-AAATAT
1 TTTAAAATATAAAA-CCCATAAATAT
* *
664596 TTT--AATCTAACACCCATAAATAT
1 TTTAAAATATAAAACCCATAAATAT
664619 TTTAAAA
1 TTTAAAA
664626 CTCAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.16
23 16 0.64
25 5 0.20
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.35
Consensus pattern (25 bp):
TTTAAAATATAAAACCCATAAATAT
Found at i:664750 original size:23 final size:23
Alignment explanation
Indices: 664721--664810 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 23
664711 ATTTCATTTA
* *
664721 TGTTCGTTTATGTCCATTTATTG
1 TGTTCGTTTACGTTCATTTATTG
*
664744 TGTTCGTTTACGTTCGTTCGT-TTG
1 TGTTCGTTTACGTTCATT--TATTG
* *
664768 TCTTCGTTTACGTTCTTTTATTG
1 TGTTCGTTTACGTTCATTTATTG
* * *
664791 TGTTTGTTTATGTTCGTTTA
1 TGTTCGTTTACGTTCATTTA
664811 CATCCGTTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
22 1 0.02
23 34 0.62
24 19 0.35
25 1 0.02
ACGTcount: A:0.09, C:0.13, G:0.19, T:0.59
Consensus pattern (23 bp):
TGTTCGTTTACGTTCATTTATTG
Found at i:665247 original size:7 final size:7
Alignment explanation
Indices: 665235--665271 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
665225 TCAAGTCAAT
665235 GTCGTAA
1 GTCGTAA
665242 GTCGTAA
1 GTCGTAA
665249 GTCGTAA
1 GTCGTAA
*
665256 GTCGCAA
1 GTCGTAA
665263 GTCGTAA
1 GTCGTAA
665270 GT
1 GT
665272 AATTGAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (7 bp):
GTCGTAA
Found at i:666572 original size:21 final size:21
Alignment explanation
Indices: 666546--666591 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
666536 GAGTTCTGGG
* *
666546 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
666567 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
666588 CAAG
1 CAAG
666592 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:667261 original size:22 final size:23
Alignment explanation
Indices: 667221--667265 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
667211 ATATGGCATG
*
667221 TGATATGAAGTGTATATGTGAAA
1 TGATATGAAGTATATATGTGAAA
667244 TGATATGAA-TATATATGTGAAA
1 TGATATGAAGTATATATGTGAAA
667266 ACAAGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (23 bp):
TGATATGAAGTATATATGTGAAA
Found at i:667550 original size:31 final size:31
Alignment explanation
Indices: 667480--667592 Score: 201
Period size: 31 Copynumber: 3.7 Consensus size: 31
667470 AGGGTCGAGG
*
667480 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
667511 G-TTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
667541 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
667572 GTTTACCTAGGTTCTTCGGAA
1 GTTTACCTATGTTCTTCGGAA
667593 ATCTATGGAC
Statistics
Matches: 79, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
30 29 0.37
31 50 0.63
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Found at i:670748 original size:21 final size:21
Alignment explanation
Indices: 670722--670767 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
670712 GAGTTCTGGG
* *
670722 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
670743 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
670764 CAAG
1 CAAG
670768 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:671442 original size:23 final size:24
Alignment explanation
Indices: 671399--671445 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
671389 ATATGGCATG
*
671399 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
671423 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
671446 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:671698 original size:31 final size:31
Alignment explanation
Indices: 671660--671784 Score: 216
Period size: 31 Copynumber: 4.0 Consensus size: 31
671650 AGGGTCGAGG
*
671660 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
671691 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
671722 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGAACATATGGACT
*
671753 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGAA-CATATGGACT
671784 G
1 G
671785 GTCCTTCGGG
Statistics
Matches: 91, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
31 90 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGAACATATGGACT
Done.