Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008511.1 Hibiscus syriacus cultivar Beakdansim tig00111366_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: 2221980
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 6 of 9
Found at i:1202964 original size:18 final size:20
Alignment explanation
Indices: 1202938--1202974 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
1202928 TGACTTTTCA
1202938 TTAAATAGC-TTG-TTTCTG
1 TTAAATAGCATTGCTTTCTG
*
1202956 TTAAGTAGCATTGCTTTCT
1 TTAAATAGCATTGCTTTCT
1202975 ACTTCGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (20 bp):
TTAAATAGCATTGCTTTCTG
Found at i:1216304 original size:40 final size:40
Alignment explanation
Indices: 1216260--1216389 Score: 105
Period size: 40 Copynumber: 3.4 Consensus size: 40
1216250 ACTCTAATTT
*
1216260 CGCAACAC-AGTTTT-CAAATTCGCAACTTGAATTTCTTTTC
1 CGCAACACGA-TTTTCCAAATTCGCAACTCG-ATTTCTTTTC
* *
1216300 CGCAACGCGATTTTCCAAATTCGCAACTCGATTTCTAAATT-
1 CGCAACACGATTTTCCAAATTCGCAACTCGATTTCT--TTTC
* * **
1216341 CGCAACTCGA-TTTCTAAATTCGCAACGAGATTT-TTTT-
1 CGCAACACGATTTTCCAAATTCGCAACTCGATTTCTTTTC
1216378 --CAACACGATTTT
1 CGCAACACGATTTT
1216390 TAAACTCGTA
Statistics
Matches: 76, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
35 7 0.09
36 3 0.04
37 2 0.03
39 1 0.01
40 37 0.49
41 24 0.32
42 2 0.03
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (40 bp):
CGCAACACGATTTTCCAAATTCGCAACTCGATTTCTTTTC
Found at i:1216372 original size:20 final size:20
Alignment explanation
Indices: 1216235--1216373 Score: 104
Period size: 20 Copynumber: 6.9 Consensus size: 20
1216225 AATAACCAAC
* **
1216235 AAATTCGCAACGCAAACTCT
1 AAATTCGCAACGCGATTTCT
* * *
1216255 AATTTCGCAACACAGTTTTC-
1 AAATTCGCAACGC-GATTTCT
**
1216275 AAATTCGCAACTTGAATTTCT
1 AAATTCGCAACGCG-ATTTCT
* *
1216296 --TTTCCGCAACGCGATTTTCC
1 AAATT-CGCAACGCGA-TTTCT
*
1216316 AAATTCGCAACTCGATTTCT
1 AAATTCGCAACGCGATTTCT
*
1216336 AAATTCGCAACTCGATTTCT
1 AAATTCGCAACGCGATTTCT
*
1216356 AAATTCGCAACGAGATTT
1 AAATTCGCAACGCGATTT
1216374 TTTTCAACAC
Statistics
Matches: 93, Mismatches: 19, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
19 4 0.04
20 76 0.82
21 11 0.12
22 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (20 bp):
AAATTCGCAACGCGATTTCT
Found at i:1216700 original size:19 final size:19
Alignment explanation
Indices: 1216676--1216714 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1216666 GAACTCGAAT
1216676 TTGCGAAACCAAAGCTGTG
1 TTGCGAAACCAAAGCTGTG
*
1216695 TTGCGAAATCAAAGCTGTG
1 TTGCGAAACCAAAGCTGTG
1216714 T
1 T
1216715 GGAGGAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (19 bp):
TTGCGAAACCAAAGCTGTG
Found at i:1217560 original size:21 final size:21
Alignment explanation
Indices: 1217521--1217601 Score: 67
Period size: 20 Copynumber: 3.9 Consensus size: 21
1217511 GATAATCAAA
*
1217521 CGCGTTGCAATTTTT-AAATT
1 CGCGTTGCGATTTTTAAAATT
1217541 CGCGTTGCGATTTTTAAAATT
1 CGCGTTGCGATTTTTAAAATT
* * * **
1217562 -GAGTTACGAATCTGGAAAATT
1 CGCGTTGCG-ATTTTTAAAATT
* *
1217583 CGCGTTGCGAATTTAAAAA
1 CGCGTTGCGATTTTTAAAA
1217602 CTGTGTTACG
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
20 20 0.43
21 20 0.43
22 6 0.13
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.36
Consensus pattern (21 bp):
CGCGTTGCGATTTTTAAAATT
Found at i:1217634 original size:40 final size:41
Alignment explanation
Indices: 1217536--1217636 Score: 125
Period size: 42 Copynumber: 2.5 Consensus size: 41
1217526 TGCAATTTTT
* * *
1217536 AAATTCGCGTTGCGATTTTTAAAATTGAGTTACGAATCTGG
1 AAATTCGCGTTGCGAATTTAAAAACTGAGTTACGAATCTGG
*
1217577 AAAATTCGCGTTGCGAATTTAAAAACTGTGTTACGAAAT-TGG
1 -AAATTCGCGTTGCGAATTTAAAAACTGAGTTACG-AATCTGG
*
1217619 -AGTTCGCGTTGCGAATTT
1 AAATTCGCGTTGCGAATTT
1217637 GTTGGTCATT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
40 17 0.32
42 33 0.62
43 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (41 bp):
AAATTCGCGTTGCGAATTTAAAAACTGAGTTACGAATCTGG
Found at i:1219081 original size:19 final size:20
Alignment explanation
Indices: 1219059--1219100 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1219049 ACAACATATT
1219059 TTTAAT-AATAAAAATAAAA
1 TTTAATAAATAAAAATAAAA
* *
1219078 TTTAATAAATATAGATAAAA
1 TTTAATAAATAAAAATAAAA
1219098 TTT
1 TTT
1219101 TAAGAACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TTTAATAAATAAAAATAAAA
Found at i:1219323 original size:39 final size:40
Alignment explanation
Indices: 1219267--1219347 Score: 130
Period size: 39 Copynumber: 2.0 Consensus size: 40
1219257 CACTAATGGA
*
1219267 CAGCAATCAAAGTTTCAATAAAA-AGTTTA-GGAACCAAAG
1 CAGCAATCAAAGCTTCAA-AAAAGAGTTTAGGGAACCAAAG
1219306 CAGCAATCAAAGCTTCAAAAAAGAGTTTAGGGAACCAAAG
1 CAGCAATCAAAGCTTCAAAAAAGAGTTTAGGGAACCAAAG
1219346 CA
1 CA
1219348 AGAATAAATA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
38 4 0.10
39 23 0.59
40 12 0.31
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.17
Consensus pattern (40 bp):
CAGCAATCAAAGCTTCAAAAAAGAGTTTAGGGAACCAAAG
Found at i:1228757 original size:13 final size:13
Alignment explanation
Indices: 1228739--1228784 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1228729 TTTCTATAAC
1228739 CATATATGATATA
1 CATATATGATATA
** *
1228752 CATATATTTTATT
1 CATATATGATATA
*
1228765 CATATGTGATATA
1 CATATATGATATA
1228778 CATATAT
1 CATATAT
1228785 TATGTAAAGT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.46
Consensus pattern (13 bp):
CATATATGATATA
Found at i:1229029 original size:467 final size:463
Alignment explanation
Indices: 1228105--1229014 Score: 1003
Period size: 467 Copynumber: 1.9 Consensus size: 463
1228095 GAGTAAAGCC
* *
1228105 AAAAAATTTCGAGTTAGTCGAGTTAATGAGTCCTATTTTATAATTCAAAATTTACATGAAAATTG
1 AAAAAATTTCGAGTTAGTCGAGTTAACGAGTCCTATTTTATAACTCAAAATTTACATGAAAATTG
* *
1228170 TTTGATTCGAGTCGAGTTGTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATGTTATG
66 TTTGATTCGAGTAGAGTGGTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATGTTATG
** * *
1228235 ATACTAATCGATTCCAATTAAAACAACTTTCTATAGTCATATACGATATACATATGTATTTCTTC
131 ATACTAATCGATTCCAATTAAAACAACTTTCTATAACCATATACGATATACATATATATTTATTC
* ** * *
1228300 ATATTTTTTCATATGTATGTATCATGTAGAATTGAAAGACTTCACTCAAACTTGAAAACCAATCC
196 ATA--TTGTCATATACATATATCATGTAGAATTGAAAGACTTCACTCAAACTTGAAAACCAATCA
* **
1228365 ACGAATTACTAAAATTTTCAAGTTATTCGAGTTTTATTTTATAACTCAAACTATATTTTGAATTT
259 ACGAATTACTAAAATTTTCAAGTTATTCAAGTCCTATTTTATAACTCAAACTATATTTTGAATTT
** * *
1228430 TTTTGAGCCGGTGCGAGCTTTCTAGTGTTGAGTCGAAAAAATTAATTTTTTCAAATAAAGTTTTG
324 TTTTGAGCCAATGCGAGCTTTCTAGCGTTGAGTCGAAAAAATTAATTTTTTAAAATAAAGTTTTG
***
1228495 CTTGCCCCTACTTATACCTTGAAGAAAAATCAAGTGATAAATGAAAAAAGAAAAATGCACAAGAA
389 CTCAACCCTACTTATACCTTGAAGAAAAATCAAGTGATAAATGAAAAAAGAAAAATG---AAGAA
1228560 GAGAGGACCTAAG
451 GAGAGGACCTAAG
* * * * * **
1228573 AAAAAATTTCGAGTTTGTTGAGTTGACGAGTCCTATTTTATAACTCGAACTTTATTTGAAAATT-
1 AAAAAATTTCGAGTTAGTCGAGTTAACGAGTCCTATTTTATAACTCAAAATTTACATGAAAATTG
* * *
1228637 TTTTAGTT-GAGTAGAGTGGTTCGAA-TTTCTGTTTAAATTTAATTGTAAATATTTATAATGTTA
66 TTTGA-TTCGAGTAGAGTGGTTC-AAGTTTCTATTTAAATTTAATTATAAATATTTATAATGTTA
* * * ** *
1228700 TGGTACTAATTGATTTCAACTT-AAACGGCTTTCTATAACCATATATGATATACATATAT-TTTA
129 TGATACTAATCGATTCCAA-TTAAAACAACTTTCTATAACCATATACGATATACATATATATTTA
* * ** *** ** * *
1228763 TTCATA-TGTGATATACATATATTATGTA-AAGTTGAGGGACTTGGTTCGCACTTGAAAATCTAT
193 TTCATATTGTCATATACATATATCATGTAGAA-TTGAAAGACTTCACTCAAACTTGAAAACCAAT
* * *
1228826 CAACTAATTACTAAAATTTT-GAGTTATTCAAGTCCTATTTTATAACTCAAACTTTATTTT-AAT
257 CAACGAATTACTAAAATTTTCAAGTTATTCAAGTCCTATTTTATAACTCAAACTATATTTTGAA-
* * * * *
1228889 TTTTTTTGTGTCAATGCGAGTTTTTTAGCGTTGAGTC-AAAAATTTCAATTTTTTTTAATTAAGT
321 TTTTTTTGAGCCAATGCGAGCTTTCTAGCGTTGAGTCGAAAAAATT-AA--TTTTTTAA--AA-T
* * * *
1228953 CGAGTCGAGTTTTTCTCAACCCTACTTATATCTTGAAGATAAATCAAGTGATAAATGAAAAA
380 --A---AAGTTTTGCTCAACCCTACTTATACCTTGAAGAAAAATCAAGTGATAAATGAAAAA
1229015 TGCACAAGAG
Statistics
Matches: 364, Mismatches: 62, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
461 9 0.02
462 69 0.19
463 57 0.16
464 7 0.02
466 11 0.03
467 100 0.27
468 61 0.17
469 1 0.00
472 49 0.13
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.40
Consensus pattern (463 bp):
AAAAAATTTCGAGTTAGTCGAGTTAACGAGTCCTATTTTATAACTCAAAATTTACATGAAAATTG
TTTGATTCGAGTAGAGTGGTTCAAGTTTCTATTTAAATTTAATTATAAATATTTATAATGTTATG
ATACTAATCGATTCCAATTAAAACAACTTTCTATAACCATATACGATATACATATATATTTATTC
ATATTGTCATATACATATATCATGTAGAATTGAAAGACTTCACTCAAACTTGAAAACCAATCAAC
GAATTACTAAAATTTTCAAGTTATTCAAGTCCTATTTTATAACTCAAACTATATTTTGAATTTTT
TTGAGCCAATGCGAGCTTTCTAGCGTTGAGTCGAAAAAATTAATTTTTTAAAATAAAGTTTTGCT
CAACCCTACTTATACCTTGAAGAAAAATCAAGTGATAAATGAAAAAAGAAAAATGAAGAAGAGAG
GACCTAAG
Found at i:1229991 original size:82 final size:80
Alignment explanation
Indices: 1229797--1230095 Score: 431
Period size: 80 Copynumber: 3.7 Consensus size: 80
1229787 CAACAAAAAG
* * ** *
1229797 GGGAGCCAACCTAAGGATATTCCTT-GGATCTACCCAAGGATATCCTTAGATCCGT-AGGTTTAC
1 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAA-GATATCCTTAGGTCCGTAAGG-TTAC
* *
1229860 CTTAAGCACACAGCTAA
64 CTTATGCACACAGCAAA
* * *
1229877 GGGAACCAATCTAAGGATATGCCTTGGGGCCTACCCAATACATCCTTAGGTCCGTAAGGTTACCT
1 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAAGGTTACCT
*
1229942 TATGCACACATCAAAAA
66 TATGCACACAGC--AAA
* *
1229959 GGGAACCAACCTAATGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAAGGTTACCT
1230024 TATGCACACAGCAAA
66 TATGCACACAGCAAA
1230039 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAA
1 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAA
1230096 TGACTTACAG
Statistics
Matches: 196, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
80 110 0.56
81 13 0.07
82 73 0.37
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAAGGTTACCT
TATGCACACAGCAAA
Found at i:1230055 original size:162 final size:163
Alignment explanation
Indices: 1229782--1230095 Score: 488
Period size: 162 Copynumber: 1.9 Consensus size: 163
1229772 CTTGCCCTCA
* * *
1229782 GCACACAACAAAAAGGGGAGCCAACCTAAGGATATTCCTTGGATCTACCCAAGGATATCCTTAGA
1 GCACACAACAAAAAGGGGAACCAACCTAAGGATATGCCTTGGACCTACCCAAGGATATCCTTAGA
* * *
1229847 TCCGTAGGTTTACCTTAAGCACACAGCTAAGGGAACCAATCTAAGGATATGCCTTGGGGCCTACC
66 TCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACC
*
1229912 CAATACATCCTTAGGTCCGTAAGGTTACCTTAT
131 CAAGACATCCTTAGGTCCGTAAGGTTACCTTAT
* * *
1229945 GCACACATCAAAAA-GGGAACCAACCTAATGATATGCCTTGGGGCCTACCCAA-GATATCCTTAG
1 GCACACAACAAAAAGGGGAACCAACCTAAGGATATGCCTT-GGACCTACCCAAGGATATCCTTAG
* *
1230008 GTCCGTAGGGTTACCTTATGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAC
65 ATCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTAC
*
1230073 CCAAGATATCCTTAGGTCCGTAA
130 CCAAGACATCCTTAGGTCCGTAA
1230096 TGACTTACAG
Statistics
Matches: 137, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
162 114 0.83
163 23 0.17
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (163 bp):
GCACACAACAAAAAGGGGAACCAACCTAAGGATATGCCTTGGACCTACCCAAGGATATCCTTAGA
TCCGTAGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACC
CAAGACATCCTTAGGTCCGTAAGGTTACCTTAT
Found at i:1235216 original size:30 final size:30
Alignment explanation
Indices: 1235182--1235287 Score: 185
Period size: 30 Copynumber: 3.5 Consensus size: 30
1235172 ATTAATGTTA
*
1235182 TCAATTTATAACAAATAAGATATTAGAATT
1 TCAATTTATAACAAATAAGATATTAGCATT
1235212 TCAATTTATAACAAATAAGATATTAGCATT
1 TCAATTTATAACAAATAAGATATTAGCATT
*
1235242 TCAATTTATAACAAATAATATATTAGCATT
1 TCAATTTATAACAAATAAGATATTAGCATT
*
1235272 TCAATTTATAATAAAT
1 TCAATTTATAACAAAT
1235288 CGGTCAATTG
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (30 bp):
TCAATTTATAACAAATAAGATATTAGCATT
Found at i:1235596 original size:21 final size:20
Alignment explanation
Indices: 1235516--1235597 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 20
1235506 CGCAAATCAG
1235516 TTTCCAGATTCGCAATGCGAT
1 TTTCCA-ATTCGCAATGCGAT
* * *
1235537 TAT-GACTATCGCAATGCGAT
1 TTTCCAAT-TCGCAATGCGAT
* **
1235557 TTTCCAATTTTGCGTTGCGAT
1 TTTCCAA-TTCGCAATGCGAT
1235578 TTTCCCAATTCGCAATGCGA
1 TTT-CCAATTCGCAATGCGA
1235598 ATAAGTAAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
19 1 0.02
20 15 0.33
21 24 0.53
22 5 0.11
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.35
Consensus pattern (20 bp):
TTTCCAATTCGCAATGCGAT
Found at i:1235658 original size:20 final size:20
Alignment explanation
Indices: 1235635--1235721 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
1235625 AAATCGTAAT
1235635 GCGATACTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
* *
1235655 GCGATAAT-ACAAAATCGCAAC
1 GCGATACTGAC--TATCGCAAC
*
1235676 GCGATACTGACTTTCGCAAC
1 GCGATACTGACTATCGCAAC
* *
1235696 GAGATTCTGACTATCGCAAC
1 GCGATACTGACTATCGCAAC
*
1235716 GAGATA
1 GCGATA
1235722 ATACAGAATC
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
19 2 0.04
20 36 0.65
21 15 0.27
22 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (20 bp):
GCGATACTGACTATCGCAAC
Found at i:1235894 original size:12 final size:12
Alignment explanation
Indices: 1235875--1235908 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1235865 CTCTCCGGTG
1235875 ACATCCGTTCCT
1 ACATCCGTTCCT
*
1235887 ATATCCGTTCCT
1 ACATCCGTTCCT
1235899 ACATCC-TTCC
1 ACATCCGTTCC
1235909 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:1236705 original size:12 final size:12
Alignment explanation
Indices: 1236688--1236712 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1236678 ATATAATCCT
1236688 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1236700 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1236712 G
1 G
1236713 TCCCCGAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1239002 original size:20 final size:20
Alignment explanation
Indices: 1238977--1239115 Score: 192
Period size: 20 Copynumber: 7.0 Consensus size: 20
1238967 ATTCATTTGA
1238977 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1238997 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1239017 TTATCGCAACGCTG-AAATGG
1 CTATCGCAACGC-GAAAATGG
1239037 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
1239057 CTATCGTAATGC-AGAAATGG
1 CTATCGCAACGCGA-AAATGG
* *
1239077 CTATCGCAATGCGGAAATGG
1 CTATCGCAACGCGAAAATGG
*
1239097 CTATCGCAATGCGAAAATG
1 CTATCGCAACGCGAAAATG
1239116 AAAATCACAT
Statistics
Matches: 108, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
19 2 0.02
20 105 0.97
21 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1240804 original size:41 final size:42
Alignment explanation
Indices: 1240750--1240841 Score: 150
Period size: 42 Copynumber: 2.2 Consensus size: 42
1240740 CCTCTTTAAC
* *
1240750 GATGACAGTGGCCTCTTGAACGA-TGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
*
1240791 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1240833 GATGACAGG
1 GATGACAGG
1240842 TGAGTCGGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 21 0.46
42 25 0.54
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
Found at i:1240806 original size:21 final size:21
Alignment explanation
Indices: 1240777--1240837 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1240767 GAACGATGGG
*
1240777 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
1240798 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
1240819 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
1240838 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:1241682 original size:18 final size:18
Alignment explanation
Indices: 1241659--1241706 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1241649 CGGGTCGATC
1241659 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1241677 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1241695 AGGTGATGGCTC
1 AGGTGATGGCTC
1241707 CCGATGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1243048 original size:20 final size:20
Alignment explanation
Indices: 1243023--1243096 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1243013 AATAGTTTCT
*
1243023 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1243043 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1243063 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
1243083 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1243097 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1243374 original size:22 final size:22
Alignment explanation
Indices: 1243347--1243401 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1243337 GGAGATAGAT
1243347 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
1243369 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCGCCGGAGATGGGGAC
*
1243391 GGATGTCGCCG
1 GGATTTCGCCG
1243402 TAGAGAGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.16, C:0.18, G:0.45, T:0.20
Consensus pattern (22 bp):
GGATTTCGCCGGAGATGGGGAC
Found at i:1243700 original size:20 final size:20
Alignment explanation
Indices: 1243586--1243699 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
1243576 GATTATGTAT
*
1243586 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1243606 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
1243626 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
1243646 TATCGCATTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1243667 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1243687 TATCGCATTGCGA
1 TATCGCGTTGCGA
1243700 TTTTCCCAAT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.77
21 13 0.16
22 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1243703 original size:41 final size:41
Alignment explanation
Indices: 1243569--1243701 Score: 189
Period size: 41 Copynumber: 3.3 Consensus size: 41
1243559 CTTTGAAAAT
*
1243569 GCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGTATC
1 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATC
* * *
1243610 GCGTTGCGA--AAGTAAGTATCGCGTTGCGAAAGTCAGTATC
1 GCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATC
* *
1243650 GCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATC
1 GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATC
1243691 GCATTGCGATT
1 GCATTGCGATT
1243702 TTCCCAATTC
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
39 3 0.04
40 32 0.40
41 43 0.54
42 2 0.03
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (41 bp):
GCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATC
Found at i:1243714 original size:41 final size:41
Alignment explanation
Indices: 1243586--1243721 Score: 143
Period size: 41 Copynumber: 3.3 Consensus size: 41
1243576 GATTATGTAT
* * * ***
1243586 TATCTCGTTGCGAAAGTCAGTATCGCGTTGCGAAAGT--AA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
* ** *
1243625 GTATCGCGTTGCGAAAGTCAGTATCGCATTGCGATTTTGTAT
1 -TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
1243667 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAA
1243709 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
1243722 TTACTTATTC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.39
41 48 0.58
42 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAA
Found at i:1243782 original size:21 final size:22
Alignment explanation
Indices: 1243733--1243782 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1243723 TACTTATTCG
*
1243733 CATTGCG-AATTGGGAAAATCG
1 CATTGCGAAATTGGGAAAATCA
**
1243754 CAACGCGAAATT-GGAAAATCA
1 CATTGCGAAATTGGGAAAATCA
1243775 CATTGCGA
1 CATTGCGA
1243783 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (22 bp):
CATTGCGAAATTGGGAAAATCA
Found at i:1246515 original size:2 final size:2
Alignment explanation
Indices: 1246434--1246499 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1246424 ACTTTACATG
1246434 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1246476 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
1246500 GCATATATCG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1246610 original size:24 final size:23
Alignment explanation
Indices: 1246582--1246639 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
1246572 TGATTAAATT
* *
1246582 TTAACATAAACTCGAACAATTTGA
1 TTAACTTAAACTC-AACAATTCGA
*
1246606 TTAACTTAAGACTCATCAATTCGA
1 TTAACTTAA-ACTCAACAATTCGA
1246630 TTAACTTAAA
1 TTAACTTAAA
1246640 AATATTTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 25 0.83
25 4 0.13
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (23 bp):
TTAACTTAAACTCAACAATTCGA
Found at i:1253892 original size:23 final size:22
Alignment explanation
Indices: 1253862--1253909 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
1253852 TATTTTATAA
1253862 AAAAAATAAAGAGATAAAATTAT
1 AAAAAATAAAGAGATAAAATT-T
*
1253885 AAAAAATAAAGAGGTAAAATTT
1 AAAAAATAAAGAGATAAAATTT
1253907 AAA
1 AAA
1253910 TTATTTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (22 bp):
AAAAAATAAAGAGATAAAATTT
Found at i:1267530 original size:11 final size:11
Alignment explanation
Indices: 1267504--1267535 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1267494 ATTTATTTAT
1267504 TATAAAATATA
1 TATAAAATATA
1267515 -A-AAAATATA
1 TATAAAATATA
1267524 TATAAAATATA
1 TATAAAATATA
1267535 T
1 T
1267536 GTTCCGTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 8 0.42
10 2 0.11
11 9 0.47
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TATAAAATATA
Found at i:1267933 original size:36 final size:36
Alignment explanation
Indices: 1267886--1267958 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1267876 GTCATTTGTG
1267886 AGTCAACTTTTAGAGTTCGATCGCATCCAAGAAAAC
1 AGTCAACTTTTAGAGTTCGATCGCATCCAAGAAAAC
1267922 AGTCAACTTTTAGAGTTCGATCGCATCCAAGAAAAC
1 AGTCAACTTTTAGAGTTCGATCGCATCCAAGAAAAC
1267958 A
1 A
1267959 ATCTCAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (36 bp):
AGTCAACTTTTAGAGTTCGATCGCATCCAAGAAAAC
Found at i:1269324 original size:24 final size:23
Alignment explanation
Indices: 1269297--1269352 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
1269287 CCACTAGGGG
*
1269297 CACTGAATATTTATCCCGAAAGAC
1 CACTG-ATATATATCCCGAAAGAC
* *
1269321 CACTG-TATATGTCCCGAAGGAC
1 CACTGATATATATCCCGAAAGAC
1269343 CACTG-TATAT
1 CACTGATATAT
1269353 CCCTCGACTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 24 0.83
24 5 0.17
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (23 bp):
CACTGATATATATCCCGAAAGAC
Found at i:1269338 original size:22 final size:22
Alignment explanation
Indices: 1269310--1269352 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1269300 TGAATATTTA
1269310 TCCCGAAAGACCACTGTATATG
1 TCCCGAAAGACCACTGTATATG
*
1269332 TCCCGAAGGACCACTGTATAT
1 TCCCGAAAGACCACTGTATAT
1269353 CCCTCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (22 bp):
TCCCGAAAGACCACTGTATATG
Found at i:1274900 original size:16 final size:15
Alignment explanation
Indices: 1274865--1274903 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1274855 TCCCCATCTC
*
1274865 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1274880 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1274896 TAATTTTT
1 TAATTTTT
1274904 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1275475 original size:12 final size:12
Alignment explanation
Indices: 1275454--1275488 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1275444 ACCATATTTC
*
1275454 CAATACCAAACA
1 CAATATCAAACA
1275466 CAATATCAAACA
1 CAATATCAAACA
*
1275478 CAATCTCAAAC
1 CAATATCAAAC
1275489 CCACAACCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.14
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:1277947 original size:18 final size:18
Alignment explanation
Indices: 1277924--1277959 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1277914 AAGCAAAAGG
*
1277924 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1277942 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1277960 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1278026 original size:22 final size:22
Alignment explanation
Indices: 1277999--1278043 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1277989 ACTTAGGTGA
1277999 TTTTTAAATGCAAACATTGTAT
1 TTTTTAAATGCAAACATTGTAT
1278021 TTTTTAAATGCAAACATTGTAT
1 TTTTTAAATGCAAACATTGTAT
1278043 T
1 T
1278044 ATGCGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (22 bp):
TTTTTAAATGCAAACATTGTAT
Found at i:1278337 original size:20 final size:20
Alignment explanation
Indices: 1278297--1278360 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1278287 AAATCGAAAA
*
1278297 TCGCGTTGCG-ATTTTAGCTT
1 TCGCGTTGCGAATTTGA-CTT
1278317 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
** * *
1278337 TTTCGTTGCAAATTTGACTA
1 TCGCGTTGCGAATTTGACTT
1278357 TCGC
1 TCGC
1278361 AACGCTTATT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 31 0.86
21 5 0.14
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:1279221 original size:38 final size:38
Alignment explanation
Indices: 1279160--1279245 Score: 147
Period size: 38 Copynumber: 2.2 Consensus size: 38
1279150 TCCGATGCTC
1279160 ATCAAAATCCAAAGTTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAAT-CAAAGTTCATATGGTGCCAAGCAAAAGGAA
1279199 ATCAAAATCAAA-TCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCAAAGT-TCATATGGTGCCAAGCAAAAGGAA
1279237 ATCAAAATC
1 ATCAAAATC
1279246 TACAACTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
37 1 0.02
38 37 0.80
39 8 0.17
ACGTcount: A:0.48, C:0.19, G:0.15, T:0.19
Consensus pattern (38 bp):
ATCAAAATCAAAGTTCATATGGTGCCAAGCAAAAGGAA
Found at i:1279477 original size:20 final size:20
Alignment explanation
Indices: 1279452--1279527 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
1279442 AAACCGAAAA
*
1279452 TCGCGTTGCGAATTTGGCTT
1 TCGCGTTGCGAATTTGACTT
1279472 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTT
** *
1279492 TCGCGTTATGAATTTAACTT
1 TCGCGTTGCGAATTTGACTT
1279512 TCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
1279528 TACCTTCAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTT
Found at i:1279691 original size:60 final size:62
Alignment explanation
Indices: 1279566--1279696 Score: 185
Period size: 61 Copynumber: 2.1 Consensus size: 62
1279556 GAATTGCTCA
*
1279566 AACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAAATTAAACAAATC
1 AACTTTTACAAATCAATT--A-AAGCAAAAAATAAATCTTATTTACACATCAAATTAAACAAATC
* * *
1279631 AACTTTTACAAATCAATT-AATCAAAAAATAAATCTTATTTCCTCATC-AATTAAACAAATC
1 AACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACACATCAAATTAAACAAATC
1279691 AACTTT
1 AACTTT
1279697 CAATGTAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
60 19 0.31
61 25 0.40
65 18 0.29
ACGTcount: A:0.50, C:0.18, G:0.01, T:0.32
Consensus pattern (62 bp):
AACTTTTACAAATCAATTAAAGCAAAAAATAAATCTTATTTACACATCAAATTAAACAAATC
Found at i:1281081 original size:21 final size:21
Alignment explanation
Indices: 1281057--1281155 Score: 85
Period size: 21 Copynumber: 4.7 Consensus size: 21
1281047 GCAGGCAGGA
*
1281057 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* *
1281078 CCTCTTGAACGGTGGGAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
1281099 CTTC-TGCGATGATGAGAGGGG
1 CCTCTTG-AACGATGAGAGGGG
* *
1281120 CCTCTTGAACGAT-AGGAAGTG
1 CCTCTTGAACGATGA-GAGGGG
*
1281141 CCTCTTGAATGATGA
1 CCTCTTGAACGATGA
1281156 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
20 3 0.05
21 54 0.90
22 3 0.05
ACGTcount: A:0.22, C:0.19, G:0.35, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:1281153 original size:42 final size:42
Alignment explanation
Indices: 1281037--1281155 Score: 114
Period size: 42 Copynumber: 2.8 Consensus size: 42
1281027 GTGAATCAGG
** * * *
1281037 CTCTTGAACGGCAGGCAGGACCTCTTGAACGATGACAGGGGC
1 CTCTTGAACGATAGGAAGGGCCTCTTGAATGATGACAGGGGC
* * * * * *
1281079 CTCTTGAACGGTGGGAGGGGCTTC-TGCGATGATGAGAGGGGC
1 CTCTTGAACGATAGGAAGGGCCTCTTG-AATGATGACAGGGGC
*
1281121 CTCTTGAACGATAGGAAGTGCCTCTTGAATGATGA
1 CTCTTGAACGATAGGAAGGGCCTCTTGAATGATGA
1281156 TAGGTGCATC
Statistics
Matches: 60, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
41 2 0.03
42 56 0.93
43 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.35, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGATAGGAAGGGCCTCTTGAATGATGACAGGGGC
Found at i:1281162 original size:21 final size:20
Alignment explanation
Indices: 1281107--1281162 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
1281097 GGCTTCTGCG
*
1281107 ATGATGAGAGGGGCCTCTTGA
1 ATGATGA-AGGTGCCTCTTGA
*
1281128 ACGATAGGAA-GTGCCTCTTGA
1 ATGAT--GAAGGTGCCTCTTGA
1281149 ATGATGATAGGTGC
1 ATGATGA-AGGTGC
1281163 ATCGGGCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
19 2 0.07
20 1 0.04
21 22 0.79
22 1 0.04
23 2 0.07
ACGTcount: A:0.27, C:0.14, G:0.34, T:0.25
Consensus pattern (20 bp):
ATGATGAAGGTGCCTCTTGA
Found at i:1283294 original size:20 final size:20
Alignment explanation
Indices: 1283284--1283334 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
1283274 ACTTAAATTT
* *
1283284 GCAACGCGAAAAAGAAAATC
1 GCAACGCGAAAATGAAAATA
1283304 GCAACGCGAAAATGAAAATA
1 GCAACGCGAAAATGAAAATA
1283324 GCAACGCGAAA
1 GCAACGCGAAA
1283335 CTAAAATCGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.53, C:0.20, G:0.22, T:0.06
Consensus pattern (20 bp):
GCAACGCGAAAATGAAAATA
Found at i:1283736 original size:43 final size:43
Alignment explanation
Indices: 1283688--1283780 Score: 177
Period size: 43 Copynumber: 2.2 Consensus size: 43
1283678 GTAGAGAGTG
1283688 AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
1 AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
*
1283731 AGAGATGGAGATGAGACTGAGTTGTGATTTAGGGTTTTAGGTT
1 AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
1283774 AGAGATG
1 AGAGATG
1283781 ATTTGCGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.27, C:0.03, G:0.38, T:0.32
Consensus pattern (43 bp):
AGAGATGGAGATGAGACTGAGTTGCGATTTAGGGTTTTAGGTT
Found at i:1283867 original size:20 final size:20
Alignment explanation
Indices: 1283842--1284009 Score: 182
Period size: 20 Copynumber: 8.4 Consensus size: 20
1283832 GCGTAAAAAC
1283842 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* * *
1283862 ATTTGACTATCGTGTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
1283882 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
*
1283901 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* *
1283922 ATTTGACTTTTGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1283942 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1283962 ATTTGACTTT-GTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1283981 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
1284001 ATTTAACTT
1 ATTTGACTT
1284010 ATGTGTTGCG
Statistics
Matches: 123, Mismatches: 18, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
18 2 0.02
19 23 0.19
20 89 0.72
21 7 0.06
22 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:1283899 original size:40 final size:39
Alignment explanation
Indices: 1283842--1284020 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 39
1283832 GCGTAAAAAC
* * *
1283842 ATTTGACTTTCGCGTTGCGAATTTGACTATCGTGTTACGA
1 ATTTGACTTT-GTGTTGCGAATTTGACTATCGCGTTGCGA
*
1283882 ATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
1283922 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGAC-TTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1283962 ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
*
1284001 ATTTAACTTATGTGTTGCGA
1 ATTTGACTT-TGTGTTGCGA
1284021 TTTACAAATT
Statistics
Matches: 126, Mismatches: 6, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
38 2 0.02
39 45 0.36
40 69 0.55
41 8 0.06
42 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (39 bp):
ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
Found at i:1284034 original size:40 final size:39
Alignment explanation
Indices: 1283842--1284040 Score: 235
Period size: 40 Copynumber: 5.0 Consensus size: 39
1283832 GCGTAAAAAC
* * * *
1283842 ATTTGACTTTCGCGTTGCGAATTTGACTATCGTGTTACGA
1 ATTTGACTTT-GTGTTGCGAATTTGACAATCGCGTTGCGA
1283882 ATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATTTGAC-AA-TCGCGTTGCGA
*
1283922 ATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGAC-TTTGTGTTGCGAATTTGACAATCGCGTTGCGA
*
1283962 ATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGA
1 ATTTGACTTTGTGTTGCGAATTTGACAATCGCGTTGCGA
*
1284001 ATTTAACTTATGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 ATTTGACTT-TGTGTTGCGAATTTGAC-AA-TCGCGTTGCGA
1284041 TTTATAGATT
Statistics
Matches: 143, Mismatches: 7, Indels: 18
0.85 0.04 0.11
Matches are distributed among these distances:
38 4 0.03
39 50 0.35
40 79 0.55
41 8 0.06
42 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (39 bp):
ATTTGACTTTGTGTTGCGAATTTGACAATCGCGTTGCGA
Found at i:1284034 original size:79 final size:80
Alignment explanation
Indices: 1283855--1284040 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 80
1283845 TGACTTTCGC
* * *
1283855 GTTGCGAATTTGACTATCGTGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGC
1 GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGC
* *
1283920 GAATTTGACTTTTGT
66 GAATTTAACTTATGT
* *
1283935 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGTGTTGCGAATTTGAC-TA-TCGCGTT
1 GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTT
1283997 GCGAATTTAACTTATGT
64 GCGAATTTAACTTATGT
1284014 GTTGCG-ATTT-ACAAATTCGCGTTGCGA
1 GTTGCGAATTTGAC-AA-TCGCGTTGCGA
1284041 TTTATAGATT
Statistics
Matches: 96, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
77 2 0.02
78 5 0.05
79 48 0.50
80 39 0.41
81 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (80 bp):
GTTGCGAATTTGACAATCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGC
GAATTTAACTTATGT
Found at i:1284057 original size:20 final size:20
Alignment explanation
Indices: 1284014--1284060 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
1284004 TAACTTATGT
**
1284014 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCAA
* *
1284034 GTTGCGATTTATAGATTCAA
1 GTTGCGATTTACAAATTCAA
1284054 GTTGCGA
1 GTTGCGA
1284061 AAATTGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCAA
Found at i:1284156 original size:20 final size:19
Alignment explanation
Indices: 1284107--1284160 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1284097 AATGCGACAT
1284107 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
1284126 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
1284146 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
1284161 TTTATTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:1290213 original size:2 final size:2
Alignment explanation
Indices: 1290202--1290279 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
1290192 GGCAGTGAAA
1290202 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1290243 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1290280 CAACTCATTC
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1293755 original size:12 final size:12
Alignment explanation
Indices: 1293730--1293799 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1293720 ACGAAGATAT
* *
1293730 CAGAAATCAAAA
1 CAGAATTCAGAA
1293742 CAGAATTCAGAA
1 CAGAATTCAGAA
1293754 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1293766 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1293778 CAGAAATCAGAA
1 CAGAATTCAGAA
1293790 CAGAATTCAG
1 CAGAATTCAG
1293800 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1293799 original size:48 final size:47
Alignment explanation
Indices: 1293728--1293836 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
1293718 AAACGAAGAT
*
1293728 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
1293775 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
1293823 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1293837 TAAATATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:1293834 original size:24 final size:25
Alignment explanation
Indices: 1293728--1293836 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
1293718 AAACGAAGAT
*
1293728 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
1293752 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
1293776 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
1293800 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
1293825 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1293837 TAAATATTTA
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:1295401 original size:31 final size:31
Alignment explanation
Indices: 1295366--1295465 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 31
1295356 TTAATTGCTT
1295366 TCTTAAACACTCTCTGATCTTGAAACGGTTC
1 TCTTAAACACTCTCTGATCTTGAAACGGTTC
* *
1295397 TCTTAACAGACT-TCTAGTATCCTTCACAAAC---TC
1 TCTTAA-ACACTCTCT-G-AT-CTT--GAAACGGTTC
1295430 T-TCT-AACACTCTCTGATCTTGAAACGGTTC
1 TCT-TAAACACTCTCTGATCTTGAAACGGTTC
1295460 TCTTAA
1 TCTTAA
1295466 CAAACTTCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 26
0.63 0.05 0.32
Matches are distributed among these distances:
27 4 0.08
29 3 0.06
30 6 0.12
31 16 0.31
32 10 0.19
33 6 0.12
34 3 0.06
36 4 0.08
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (31 bp):
TCTTAAACACTCTCTGATCTTGAAACGGTTC
Found at i:1295473 original size:63 final size:63
Alignment explanation
Indices: 1295371--1295493 Score: 237
Period size: 63 Copynumber: 2.0 Consensus size: 63
1295361 TGCTTTCTTA
*
1295371 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAGACTTCTAGTATCCTTCACAAACTCTTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAAACTTCTAGTATCCTTCACAAACTCTTCT
1295434 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAAACTTCTAGTATCCTTCACAAACTCT
1 AACACTCTCTGATCTTGAAACGGTTCTCTTAACAAACTTCTAGTATCCTTCACAAACTCT
1295494 CCTAGGATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (63 bp):
AACACTCTCTGATCTTGAAACGGTTCTCTTAACAAACTTCTAGTATCCTTCACAAACTCTTCT
Found at i:1296424 original size:7 final size:7
Alignment explanation
Indices: 1296412--1296443 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1296402 TGGTCAATTC
1296412 CGGTCAA
1 CGGTCAA
1296419 CGGTCAA
1 CGGTCAA
1296426 CGGGTCAA
1 C-GGTCAA
1296434 CGGTCAA
1 CGGTCAA
1296441 CGG
1 CGG
1296444 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1296453 original size:13 final size:13
Alignment explanation
Indices: 1296420--1296508 Score: 97
Period size: 13 Copynumber: 6.3 Consensus size: 13
1296410 TCCGGTCAAC
*
1296420 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1296435 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1296448 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1296461 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTC-----G
1296479 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1296492 GGTCAACGGGTCA
1 GGTCAACGGGTCG
1296505 GGTC
1 GGTC
1296509 GGGTTGTGAC
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
13 42 0.63
15 12 0.18
18 13 0.19
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1296464 original size:18 final size:18
Alignment explanation
Indices: 1296454--1296495 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1296444 GTCGGGTCAA
1296454 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1296472 CGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1296490 CGGGTC
1 CGGGTC
1296496 AACGGGTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1296482 original size:31 final size:31
Alignment explanation
Indices: 1296441--1296512 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
1296431 CAACGGTCAA
1296441 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
*
1296472 CGGGTTGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
*
1296503 CAGGTCGGGT
1 CGGGTCGGGT
1296513 TGTGACCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.12, C:0.21, G:0.49, T:0.18
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
Found at i:1296490 original size:8 final size:8
Alignment explanation
Indices: 1296413--1296472 Score: 64
Period size: 8 Copynumber: 8.5 Consensus size: 8
1296403 GGTCAATTCC
1296413 GGTCAAC-
1 GGTCAACG
1296420 GGTCAACG
1 GGTCAACG
1296428 GGTCAAC-
1 GGTCAACG
1296435 GGTCAACG
1 GGTCAACG
1296443 GGT---CG
1 GGTCAACG
1296448 GGTCAACG
1 GGTCAACG
1296456 GGT---CG
1 GGTCAACG
1296461 GGTCAACG
1 GGTCAACG
1296469 GGTC
1 GGTC
1296473 GGGTTGGGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
5 10 0.22
7 14 0.31
8 21 0.47
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1296508 original size:18 final size:17
Alignment explanation
Indices: 1296456--1296512 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
1296446 CGGGTCAACG
1296456 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
*
1296473 GGGTTGGGTCAAC--G--
1 -GGTCGGGTCAACGGGTC
1296487 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
1296504 AGGTCGGGT
1 -GGTCGGGT
1296513 TGTGACCGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 11 0.34
15 1 0.03
16 1 0.03
18 19 0.59
ACGTcount: A:0.12, C:0.19, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCAACGGGTC
Found at i:1298596 original size:12 final size:12
Alignment explanation
Indices: 1298571--1298640 Score: 79
Period size: 12 Copynumber: 5.8 Consensus size: 12
1298561 ACGAAGATAT
* *
1298571 CAGAAATCAAAA
1 CAGAATTCAGAA
1298583 CAGAATTCAGAA
1 CAGAATTCAGAA
1298595 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
1298607 CAGAATCCAGAT
1 CAGAATTCAGAA
*
1298619 CAGAAATCAGAA
1 CAGAATTCAGAA
1298631 CAGAATTCAG
1 CAGAATTCAG
1298641 GTCATTTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
11 2 0.04
12 44 0.92
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.16, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:1298640 original size:48 final size:47
Alignment explanation
Indices: 1298569--1298677 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 47
1298559 AAACGAAGAT
*
1298569 ATCAGAAATCAAAACAGAATTCAGAACAGATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
** ** *
1298616 GATCAGAAATCAGAACAGAATTCAGGTCATTTATCAGAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
*
1298664 AGTCGGAAATCAGA
1 A-TCAGAAATCAGA
1298678 TAAAATATTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 52 0.98
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCAGAACAGATATCAGAACAGAATCCA
Found at i:1298675 original size:24 final size:25
Alignment explanation
Indices: 1298569--1298677 Score: 109
Period size: 24 Copynumber: 4.5 Consensus size: 25
1298559 AAACGAAGAT
*
1298569 ATCAGAAATCAAAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* * *
1298593 AACAGATATCAGAACAGAA-TCCAG
1 ATCAGAAATCAGAACAGAATTCAAG
1298617 ATCAGAAATCAGAACAGAATTC-AG
1 ATCAGAAATCAGAACAGAATTCAAG
* ***
1298641 GTCATTTATCAGAACAGAATTCAAG
1 ATCAGAAATCAGAACAGAATTCAAG
*
1298666 -TCGGAAATCAGA
1 ATCAGAAATCAGA
1298678 TAAAATATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 63 0.91
25 4 0.06
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (25 bp):
ATCAGAAATCAGAACAGAATTCAAG
Found at i:1301267 original size:7 final size:7
Alignment explanation
Indices: 1301255--1301286 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1301245 TGGTCAATTC
1301255 CGGTCAA
1 CGGTCAA
1301262 CGGTCAA
1 CGGTCAA
1301269 CGGGTCAA
1 C-GGTCAA
1301277 CGGTCAA
1 CGGTCAA
1301284 CGG
1 CGG
1301287 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1301296 original size:13 final size:13
Alignment explanation
Indices: 1301263--1301351 Score: 97
Period size: 13 Copynumber: 6.3 Consensus size: 13
1301253 TCCGGTCAAC
*
1301263 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1301278 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1301291 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1301304 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTC-----G
1301322 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1301335 GGTCAACGGGTCA
1 GGTCAACGGGTCG
1301348 GGTC
1 GGTC
1301352 GGGTTGTGAC
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
13 42 0.63
15 12 0.18
18 13 0.19
ACGTcount: A:0.17, C:0.22, G:0.44, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1301307 original size:18 final size:18
Alignment explanation
Indices: 1301297--1301338 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
1301287 GTCGGGTCAA
1301297 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1301315 CGGGTTGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1301333 CGGGTC
1 CGGGTC
1301339 AACGGGTCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.21, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1301325 original size:31 final size:31
Alignment explanation
Indices: 1301284--1301355 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
1301274 CAACGGTCAA
1301284 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
*
1301315 CGGGTTGGGTCAACGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
*
1301346 CAGGTCGGGT
1 CGGGTCGGGT
1301356 TGTGACCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.12, C:0.21, G:0.49, T:0.18
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTCAACGGGT
Found at i:1301333 original size:8 final size:8
Alignment explanation
Indices: 1301256--1301315 Score: 64
Period size: 8 Copynumber: 8.5 Consensus size: 8
1301246 GGTCAATTCC
1301256 GGTCAAC-
1 GGTCAACG
1301263 GGTCAACG
1 GGTCAACG
1301271 GGTCAAC-
1 GGTCAACG
1301278 GGTCAACG
1 GGTCAACG
1301286 GGT---CG
1 GGTCAACG
1301291 GGTCAACG
1 GGTCAACG
1301299 GGT---CG
1 GGTCAACG
1301304 GGTCAACG
1 GGTCAACG
1301312 GGTC
1 GGTC
1301316 GGGTTGGGTC
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
5 10 0.22
7 14 0.31
8 21 0.47
ACGTcount: A:0.20, C:0.25, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1301351 original size:18 final size:17
Alignment explanation
Indices: 1301299--1301355 Score: 59
Period size: 18 Copynumber: 3.5 Consensus size: 17
1301289 CGGGTCAACG
1301299 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
*
1301316 GGGTTGGGTCAAC--G--
1 -GGTCGGGTCAACGGGTC
1301330 GGTCGGGTCAACGGGTC
1 GGTCGGGTCAACGGGTC
1301347 AGGTCGGGT
1 -GGTCGGGT
1301356 TGTGACCGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 11 0.34
15 1 0.03
16 1 0.03
18 19 0.59
ACGTcount: A:0.12, C:0.19, G:0.49, T:0.19
Consensus pattern (17 bp):
GGTCGGGTCAACGGGTC
Found at i:1302640 original size:20 final size:20
Alignment explanation
Indices: 1302612--1302649 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1302602 GTAAGTTTAA
*
1302612 AAAAATTTAATTTACTCACT
1 AAAAATTTAAATTACTCACT
*
1302632 AAAATTTTAAATTACTCA
1 AAAAATTTAAATTACTCA
1302650 TATTTTAATA
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:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATTTAAATTACTCACT
Found at i:1303752 original size:29 final size:29
Alignment explanation
Indices: 1303719--1303777 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
1303709 GAGAGAGAAG
* *
1303719 AAAGTTGACTGATGAATTATGTAATTTAC
1 AAAGTTGACAGATGAATTATGTAAATTAC
* *
1303748 AAAGTTGACAGGTGATTTATGTAAATTAC
1 AAAGTTGACAGATGAATTATGTAAATTAC
1303777 A
1 A
1303778 TTTTCTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.36
Consensus pattern (29 bp):
AAAGTTGACAGATGAATTATGTAAATTAC
Found at i:1308001 original size:29 final size:29
Alignment explanation
Indices: 1307965--1308023 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1307955 ATGTATTCCG
1307965 TAATTATTTTAAGATCAATCTATTACGTA
1 TAATTATTTTAAGATCAATCTATTACGTA
* *
1307994 TAATTATTTTAAGATCGATTTATTACGTA
1 TAATTATTTTAAGATCAATCTATTACGTA
1308023 T
1 T
1308024 GTTCAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.47
Consensus pattern (29 bp):
TAATTATTTTAAGATCAATCTATTACGTA
Found at i:1312363 original size:8 final size:8
Alignment explanation
Indices: 1312350--1312425 Score: 56
Period size: 8 Copynumber: 9.8 Consensus size: 8
1312340 CCATATGGTC
1312350 TTATTATA
1 TTATTATA
1312358 TTATTAGT-
1 TTATTA-TA
1312366 TTATTATAA
1 TTATTAT-A
1312375 TTATTA-A
1 TTATTATA
*
1312382 -CA-TATAA
1 TTATTAT-A
1312389 TTATTATA
1 TTATTATA
1312397 TTA-TATA
1 TTATTATA
*
1312404 TCATTATA
1 TTATTATA
1312412 TTAATTAT-
1 TT-ATTATA
1312420 TTATTA
1 TTATTA
1312426 ACTATAATTC
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
5 2 0.04
6 1 0.02
7 13 0.24
8 24 0.44
9 15 0.27
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (8 bp):
TTATTATA
Found at i:1312396 original size:23 final size:22
Alignment explanation
Indices: 1312366--1312434 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
1312356 TATTATTAGT
1312366 TTATTATAATTATTAACATATAA
1 TTATTAT-ATTATTAACATATAA
*
1312389 TTATTATATTATATATCAT-TATA
1 TTATTATATTAT-TAACATATA-A
1312412 TTAATTAT-TTATTAAC-TATAA
1 TT-ATTATATTATTAACATATAA
1312433 TT
1 TT
1312435 CAATCTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 4 0.10
22 12 0.30
23 19 0.47
24 5 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTATATTATTAACATATAA
Found at i:1314838 original size:229 final size:227
Alignment explanation
Indices: 1314428--1314876 Score: 781
Period size: 229 Copynumber: 2.0 Consensus size: 227
1314418 GTAAATTATC
* * * *
1314428 TATCCTTTTTATAAAAGTGTCTATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
1314493 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
1314558 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
1314623 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
1314656 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
1314721 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
1314786 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
1314851 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
1314877 GCAGTTTTAA
Statistics
Matches: 209, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
228 39 0.19
229 170 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:1314965 original size:20 final size:19
Alignment explanation
Indices: 1314942--1314987 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1314932 CGATATACCA
1314942 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1314962 GGTAACAAATGATAAAACC
1 GGTAAAAAATGATAAAACC
1314981 GGTAAAA
1 GGTAAAA
1314988 TTAAAAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1315130 original size:20 final size:19
Alignment explanation
Indices: 1315107--1315153 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1315097 CGATATAACA
*
1315107 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
1315127 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
1315147 GGTAAAA
1 GGTAAAA
1315154 TGATACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:1317492 original size:33 final size:33
Alignment explanation
Indices: 1317450--1317515 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1317440 AAATAGAAGG
*
1317450 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
1317483 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1317516 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1319354 original size:19 final size:19
Alignment explanation
Indices: 1319310--1319353 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1319300 AATGTCGAGT
1319310 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1319329 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1319348 T-ATTTT
1 TAATTTT
1319354 TTTATGTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1319969 original size:196 final size:198
Alignment explanation
Indices: 1319435--1320055 Score: 1133
Period size: 196 Copynumber: 3.1 Consensus size: 198
1319425 TTAAGTGTCA
*
1319435 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
1319500 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
1319565 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
1319630 ATG
196 ATG
1319633 TGTCGACACTAATATAGTTTGTGTCGATATTTTCTTTCCAGAATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTT-TTTCCAGAATGAATTAAAAACAAGGTGCATC
1319698 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCC-AAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
1319762 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1319827 AATG
195 AATG
*
1319831 TGTCGACACT-A-ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCATC
*
1319894 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
* * *
1319958 TAATATGTAATTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAATATGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
1320023 AATG
195 AATG
*
1320027 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
1320056 CTAATTTAAA
Statistics
Matches: 411, Mismatches: 7, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
195 33 0.08
196 155 0.38
197 2 0.00
198 137 0.33
199 84 0.20
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:1320874 original size:18 final size:18
Alignment explanation
Indices: 1320851--1320918 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 18
1320841 ATCGGTCGCA
1320851 GAAGATGAAGCTGACGAT
1 GAAGATGAAGCTGACGAT
* *
1320869 GAAGATGACGATGATGATGAT
1 GAAGATGA--A-GCTGACGAT
*
1320890 GATGACGATGAAGCTGGCGAT
1 GA--A-GATGAAGCTGACGAT
1320911 GAAGATGA
1 GAAGATGA
1320919 TGACGATGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
18 13 0.33
19 1 0.03
20 1 0.03
21 17 0.44
22 1 0.03
23 1 0.03
24 5 0.13
ACGTcount: A:0.37, C:0.09, G:0.35, T:0.19
Consensus pattern (18 bp):
GAAGATGAAGCTGACGAT
Found at i:1320875 original size:6 final size:6
Alignment explanation
Indices: 1320851--1320948 Score: 70
Period size: 6 Copynumber: 16.3 Consensus size: 6
1320841 ATCGGTCGCA
* * * * * *
1320851 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
1320899 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
1320947 GA
1 GA
1320949 TGATCCAAAC
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 74 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:1320886 original size:3 final size:3
Alignment explanation
Indices: 1320866--1320952 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
1320856 TGAAGCTGAC
* * * * * ** *
1320866 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
1320914 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1320953 CCAAACAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.36, C:0.06, G:0.34, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:1320901 original size:42 final size:42
Alignment explanation
Indices: 1320854--1320944 Score: 146
Period size: 42 Copynumber: 2.2 Consensus size: 42
1320844 GGTCGCAGAA
*
1320854 GATGAAGCTGACGATGAAGATGACGATGATGATGATGATGAC
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
* * *
1320896 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
1320938 GATGAAG
1 GATGAAG
1320945 ATGATGATCC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACGATGAAGATGACGACGATGATGATGATGAC
Found at i:1320952 original size:18 final size:18
Alignment explanation
Indices: 1320851--1320948 Score: 88
Period size: 18 Copynumber: 5.4 Consensus size: 18
1320841 ATCGGTCGCA
* *
1320851 GAAGATGAAGCTGACGAT
1 GAAGATGAAGATGATGAT
*
1320869 GAAGATGACGATGATGAT
1 GAAGATGAAGATGATGAT
* * * *
1320887 GATGATGACGATGAAGCT
1 GAAGATGAAGATGATGAT
** *
1320905 GGCGATGAAGATGATGAC
1 GAAGATGAAGATGATGAT
* *
1320923 GATGATGATGATGATGAT
1 GAAGATGAAGATGATGAT
1320941 GAAGATGA
1 GAAGATGA
1320949 TGATCCAAAC
Statistics
Matches: 63, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 63 1.00
ACGTcount: A:0.37, C:0.07, G:0.35, T:0.21
Consensus pattern (18 bp):
GAAGATGAAGATGATGAT
Found at i:1322732 original size:184 final size:184
Alignment explanation
Indices: 1322423--1322910 Score: 913
Period size: 184 Copynumber: 2.7 Consensus size: 184
1322413 CTTTCAACAT
**
1322423 ATTATAATAAAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1322488 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAAAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAAAAA
1322553 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
1322607 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
1322672 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAAAAA
*
1322737 AATGTGTCGATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
131 AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
* *
1322791 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATA
1 ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
*
1322856 GGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTACTTTATGTCCATA
66 GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
1322911 CCATTTAAAA
Statistics
Matches: 297, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
184 297 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (184 bp):
ATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATA
GGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAAAAA
AATGTGTCGATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATA
Found at i:1325498 original size:23 final size:23
Alignment explanation
Indices: 1325467--1325529 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1325457 ATAGGTAAAC
*
1325467 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1325490 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1325513 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1325530 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1325537 original size:23 final size:23
Alignment explanation
Indices: 1325467--1325539 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1325457 ATAGGTAAAC
* * **
1325467 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1325490 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1325513 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1325536 ATAT
1 ATAT
1325540 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1325928 original size:23 final size:23
Alignment explanation
Indices: 1325897--1325959 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
1325887 ATAGGTAAAC
*
1325897 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
1325920 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
1325943 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
1325960 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:1325967 original size:23 final size:23
Alignment explanation
Indices: 1325897--1325969 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
1325887 ATAGGTAAAC
* * **
1325897 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
1325920 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
1325943 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
1325966 ATAT
1 ATAT
1325970 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:1326168 original size:430 final size:431
Alignment explanation
Indices: 1325368--1326389 Score: 2030
Period size: 430 Copynumber: 2.4 Consensus size: 431
1325358 AATTCGCAGT
1325368 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1325433 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
1325498 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
1325563 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1325628 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
1325693 ATTAAATTTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAA-TTTTTGTGCA
326 ATTAAATTTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
1325757 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
1325798 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1325863 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
1325928 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
131 TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
1325993 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
196 AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
1326058 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
261 AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
1326123 ATTAAATTTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
326 ATTAAATTTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
1326188 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
391 AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
1326229 ACACTGTTAAAAAAATTGAAACATAAATTACATAAG-TTTAAAAAAAGTATCGATCCTTTTTATA
1 ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
1326293 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
66 AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
1326358 TAATAGGTATCGTTTATATAATGTAATAGGTA
131 TAATAGGTATCGTTTATATAATGTAATAGGTA
1326390 TCTATCTCGC
Statistics
Matches: 591, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
430 504 0.85
431 87 0.15
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (431 bp):
ACACTGTTAAAAAAATTGAAACATAAATTACATAAGTTTTAAAAAAAGTATCGATCCTTTTTATA
AAAAGTATGGACACTTTCAATATAATAGGTAAACATATGATGTAATAGGTAGCCCTTATATAATG
TAATAGGTATCGTTTATATAATGTAATAGGTAATGGTTATATTGTAAAGTGTCTATCCTTTTTAT
AAAAGTGTCCATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTT
AAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATT
ATTAAATTTAAAATTCTAAATAATATTTTATAAAATATAAAAACAATCAAATAATTTTTTGTGCA
AATGAAATTATTAAATCAATATTGTAGGTGGAAAACATGAA
Found at i:1326390 original size:23 final size:23
Alignment explanation
Indices: 1326327--1326391 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1326317 ATAGGTAAAC
* *
1326327 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCCCTT
**
1326350 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCCCTT
1326373 ATATAATGTAATAGGTATC
1 ATATAATGTAATAGGTATC
1326392 TATCTCGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCCCTT
Found at i:1326616 original size:18 final size:18
Alignment explanation
Indices: 1326595--1326631 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1326585 GTAATTGGAG
1326595 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1326613 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1326631 T
1 T
1326632 ATATATTCGG
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:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1335683 original size:2 final size:2
Alignment explanation
Indices: 1335676--1335730 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
1335666 TTTAAATTAA
* *
1335676 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CT AT AT AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1335716 AT TT AA AT AT AT AT A
1 AT AT AT AT AT AT AT A
1335731 CCTGTCCCGA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1335703 original size:51 final size:48
Alignment explanation
Indices: 1335623--1335723 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 48
1335613 CCCGATAAAT
1335623 ATTAAAAATAATTATTATATATATATAATAT-TAATAAATTTAATTTAA
1 ATTAAAAATAATTATTATATATATATAATATCT-ATAAATTTAATTTAA
* *
1335671 ATTAAATATATATATATATATATATATATAATATCTATATATTTAATTTAA
1 ATTAAAAATA-AT-TAT-TATATATATATAATATCTATAAATTTAATTTAA
1335722 AT
1 AT
1335724 ATATATACCT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
48 9 0.19
49 2 0.04
50 3 0.06
51 32 0.68
52 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (48 bp):
ATTAAAAATAATTATTATATATATATAATATCTATAAATTTAATTTAA
Found at i:1358055 original size:31 final size:31
Alignment explanation
Indices: 1358014--1358075 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
1358004 CAGTCACTGC
*
1358014 AGCAGGAAAAAAAAAGATCAACATGGATCTA
1 AGCAGAAAAAAAAAAGATCAACATGGATCTA
*
1358045 AGCAGAAAAAAAAAAGATCAACGTGGATCTA
1 AGCAGAAAAAAAAAAGATCAACATGGATCTA
1358076 TCTCAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.55, C:0.13, G:0.19, T:0.13
Consensus pattern (31 bp):
AGCAGAAAAAAAAAAGATCAACATGGATCTA
Found at i:1363273 original size:17 final size:17
Alignment explanation
Indices: 1363251--1363287 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1363241 TATTTAATAT
*
1363251 TTAATTTTTAAAAAAAA
1 TTAATTATTAAAAAAAA
*
1363268 TTAATTATTAATAAAAA
1 TTAATTATTAAAAAAAA
1363285 TTA
1 TTA
1363288 TATGATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTATTAAAAAAAA
Found at i:1364159 original size:17 final size:17
Alignment explanation
Indices: 1364137--1364171 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1364127 TTCAACATAC
1364137 TATATT-ATAAACAATAA
1 TATATTCATAAA-AATAA
1364154 TATATTCATAAAAATAA
1 TATATTCATAAAAATAA
1364171 T
1 T
1364172 TTTTGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
TATATTCATAAAAATAA
Found at i:1370842 original size:17 final size:18
Alignment explanation
Indices: 1370805--1370842 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1370795 TGTTAATTTT
*
1370805 ATGATGTGGACTAAATTAA
1 ATGATGTGGA-TAAATCAA
1370824 ATGATGTGG-TAAATCAA
1 ATGATGTGGATAAATCAA
1370841 AT
1 AT
1370843 TACGACATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (18 bp):
ATGATGTGGATAAATCAA
Found at i:1371616 original size:19 final size:19
Alignment explanation
Indices: 1371594--1371633 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1371584 TTTATTCAAT
*
1371594 AATGATAAAT-TTAAATTTA
1 AATGA-AAATATTAAAATTA
1371613 AATGAAAATATTAAAATTA
1 AATGAAAATATTAAAATTA
1371632 AA
1 AA
1371634 ACGAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
AATGAAAATATTAAAATTA
Found at i:1372268 original size:31 final size:31
Alignment explanation
Indices: 1372231--1372300 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1372221 CATTTGAAAC
1372231 TTGCAATACAGTCTCC-AAACATTTAGTCCGT
1 TTGCAATACAGT-TCCTAAACATTTAGTCCGT
*
1372262 TTGCAATACAGTTCCTCAACATTTAGTCCGT
1 TTGCAATACAGTTCCTAAACATTTAGTCCGT
*
1372293 TTACAATA
1 TTGCAATA
1372301 TGACCACCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 3 0.08
31 33 0.92
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (31 bp):
TTGCAATACAGTTCCTAAACATTTAGTCCGT
Found at i:1383942 original size:14 final size:14
Alignment explanation
Indices: 1383923--1383949 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1383913 TCACAGTAGA
1383923 TGATAAGATAAATG
1 TGATAAGATAAATG
1383937 TGATAAGATAAAT
1 TGATAAGATAAAT
1383950 TATTTTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.19, T:0.30
Consensus pattern (14 bp):
TGATAAGATAAATG
Found at i:1384458 original size:22 final size:22
Alignment explanation
Indices: 1384420--1384483 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
1384410 ATAAATATGT
*
1384420 CTTTATGACATGATTTTCTTTA-
1 CTTTATGACACGATTTT-TTTAG
*
1384442 CTTTATGACACGTTTTTTTTAG
1 CTTTATGACACGATTTTTTTAG
* * *
1384464 CTTTTTGGCACAATTTTTTT
1 CTTTATGACACGATTTTTTT
1384484 TGTTTTCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (22 bp):
CTTTATGACACGATTTTTTTAG
Found at i:1385846 original size:29 final size:29
Alignment explanation
Indices: 1385805--1385881 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
1385795 GAGGAGCAGG
1385805 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
1385834 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
1385863 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
1385882 TGCTGGGAAG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.23, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:1390312 original size:60 final size:60
Alignment explanation
Indices: 1390215--1390371 Score: 183
Period size: 60 Copynumber: 2.6 Consensus size: 60
1390205 GGATAGCTAA
* *
1390215 TCCTTAAACTTTTAAACATTCCAACTTCATCCTCAAACTCTGACTCTCATTCTAAATGAG
1 TCCTTAAACTTTTGAACATTCCAACTTCATCCTCAAACTATGACTCTCATTCTAAATGAG
** * **
1390275 TCCTTAAACTTTTGAACATTTTAATTTCAT-CTACAAACTATGACTCTCATTCTAAATTTG
1 TCCTTAAACTTTTGAACATTCCAACTTCATCCT-CAAACTATGACTCTCATTCTAAATGAG
* * * *
1390335 TCCTCAATCTTTTGAATC-TTCCAATTTCATCCCCAAA
1 TCCTTAAACTTTTGAA-CATTCCAACTTCATCCTCAAA
1390372 TCCATCCAAA
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.02
60 78 0.95
61 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (60 bp):
TCCTTAAACTTTTGAACATTCCAACTTCATCCTCAAACTATGACTCTCATTCTAAATGAG
Found at i:1390964 original size:19 final size:19
Alignment explanation
Indices: 1390929--1390966 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1390919 ATTTTAGATA
*
1390929 TAAAGTTAAACAATTAAAT
1 TAAAGTTAAAAAATTAAAT
1390948 TAAA-TTAAAAAAGTTAAAT
1 TAAAGTTAAAAAA-TTAAAT
1390967 ATTTTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
TAAAGTTAAAAAATTAAAT
Found at i:1392612 original size:2 final size:2
Alignment explanation
Indices: 1392607--1392641 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1392597 ACACACACAA
1392607 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1392642 ATTATCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1401230 original size:31 final size:31
Alignment explanation
Indices: 1401192--1401251 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1401182 GACAGTTCTA
* *
1401192 GATGCATAATTGATACTATCCCCTAATGCTG
1 GATGCATAACTGAAACTATCCCCTAATGCTG
1401223 GATGCATAACTGAAACTATCCCCTAATGC
1 GATGCATAACTGAAACTATCCCCTAATGC
1401252 ATAAAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (31 bp):
GATGCATAACTGAAACTATCCCCTAATGCTG
Found at i:1406525 original size:138 final size:138
Alignment explanation
Indices: 1406335--1406608 Score: 539
Period size: 138 Copynumber: 2.0 Consensus size: 138
1406325 AGAAACAAGA
1406335 ACTAGGATGTACATTTACTACTATGAACATAGGGCAGAAAACTGGAAGAATTTTTTCCAAATGCT
1 ACTAGGATGTACATTTACTACTATGAACATAGGGCAGAAAACTGGAAGAATTTTTTCCAAATGCT
*
1406400 ATCAAGAAAACTAATCTTAATTGCATTTGAATATCGCGGTACTGCTAACAACACAAACAGAACCT
66 ATCAAGAAAACTAATCTTAATTGCATTTGAATATCACGGTACTGCTAACAACACAAACAGAACCT
1406465 AACATACT
131 AACATACT
1406473 ACTAGGATGTACATTTACTACTATGAACATAGGGCAGAAAACTGGAAGAATTTTTTCCAAATGCT
1 ACTAGGATGTACATTTACTACTATGAACATAGGGCAGAAAACTGGAAGAATTTTTTCCAAATGCT
1406538 ATCAAGAAAACTAATCTTAATTGCATTTGAATATCACGGTACTGCTAACAACACAAACAGAACCT
66 ATCAAGAAAACTAATCTTAATTGCATTTGAATATCACGGTACTGCTAACAACACAAACAGAACCT
1406603 AACATA
131 AACATA
1406609 TAAACTTCTA
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 135 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (138 bp):
ACTAGGATGTACATTTACTACTATGAACATAGGGCAGAAAACTGGAAGAATTTTTTCCAAATGCT
ATCAAGAAAACTAATCTTAATTGCATTTGAATATCACGGTACTGCTAACAACACAAACAGAACCT
AACATACT
Found at i:1414678 original size:20 final size:20
Alignment explanation
Indices: 1414653--1414718 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
1414643 TTCGCTTTGT
1414653 GATTTACATATTATCGTTGC
1 GATTTACATATTATCGTTGC
* *
1414673 GATTTACCTATTCA-CGTTGT
1 GATTTACATATT-ATCGTTGC
* *
1414693 GAATTACATATTATTGTTGC
1 GATTTACATATTATCGTTGC
1414713 GATTTA
1 GATTTA
1414719 ACTATTCGCG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (20 bp):
GATTTACATATTATCGTTGC
Found at i:1414704 original size:40 final size:40
Alignment explanation
Indices: 1414649--1414731 Score: 130
Period size: 40 Copynumber: 2.1 Consensus size: 40
1414639 AGAATTCGCT
* *
1414649 TTGTGATTTACATATTATCGTTGCGATTTACCTATTCACG
1 TTGTGAATTACATATTATCGTTGCGATTTAACTATTCACG
* *
1414689 TTGTGAATTACATATTATTGTTGCGATTTAACTATTCGCG
1 TTGTGAATTACATATTATCGTTGCGATTTAACTATTCACG
1414729 TTG
1 TTG
1414732 CGAAATTCGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.46
Consensus pattern (40 bp):
TTGTGAATTACATATTATCGTTGCGATTTAACTATTCACG
Found at i:1414724 original size:20 final size:20
Alignment explanation
Indices: 1414661--1414734 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
1414651 GTGATTTACA
*
1414661 TATTATCGTTGCGATTTACC
1 TATTATCGTTGCGATTTAAC
* *
1414681 TATTCA-CGTTGTGAATT-AC
1 TATT-ATCGTTGCGATTTAAC
*
1414700 ATATTATTGTTGCGATTTAAC
1 -TATTATCGTTGCGATTTAAC
**
1414721 TATTCGCGTTGCGA
1 TATTATCGTTGCGA
1414735 AATTCGAGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
19 2 0.05
20 36 0.88
21 3 0.07
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (20 bp):
TATTATCGTTGCGATTTAAC
Found at i:1414792 original size:20 final size:20
Alignment explanation
Indices: 1414763--1414800 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1414753 GGAGAATTCG
1414763 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* *
1414783 CGTTGTGATTTACCTATT
1 CGTTGCGATTTACATATT
1414801 CGCAACGCGA
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:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:1414874 original size:63 final size:62
Alignment explanation
Indices: 1414807--1415003 Score: 143
Period size: 63 Copynumber: 3.1 Consensus size: 62
1414797 TATTCGCAAC
1414807 GCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTAACGTTGCAAAATTCGAGTT
1 GCGAATTTCGTTTTCGCAACGCTAATTACCTATATC-GTAATTAACGTTGCAAAATTCGAGTT
* ** * * * **** * *
1414870 GCGAATTTGGAGAATTCGCGTTACG--ATTTACATATTATCGTTGCGAA-TTTGGAAAA-TCGCA
1 GCGAATTT--CGTTTTCGC--AACGCTAATTACCTA-TATCGTAATTAACGTTGCAAAATTCG-A
**
1414931 -AC
60 GTT
* *
1414933 GCGAATTTCGTTTTCGCAACGCTAATTACCTATATCTGTAATTAGCGTTGCGAAATTCGAGTT
1 GCGAATTTCGTTTTCGCAACGCTAATTACCTATATC-GTAATTAACGTTGCAAAATTCGAGTT
1414996 GCGAATTT
1 GCGAATTT
1415004 GGAAAATTTG
Statistics
Matches: 92, Mismatches: 30, Indels: 24
0.63 0.21 0.16
Matches are distributed among these distances:
59 3 0.03
60 4 0.04
61 16 0.17
62 7 0.08
63 30 0.33
64 8 0.09
65 17 0.18
66 4 0.04
67 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (62 bp):
GCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGTAATTAACGTTGCAAAATTCGAGTT
Found at i:1414982 original size:126 final size:126
Alignment explanation
Indices: 1414726--1415046 Score: 511
Period size: 126 Copynumber: 2.6 Consensus size: 126
1414716 TTAACTATTC
*
1414726 GCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATTCGCGTTGCGATTTACATATTATCGTTGTG-
1 GCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATTCGCGTTGCGATTTACATATTATCGTTGCGA
** *
1414790 ATTTACCTATTCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTA
66 ATTTACAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTA
* * *
1414851 ACGTTGCAAAATTCGAGTTGCGAATTTGGAGAATTCGCGTTACGATTTACATATTATCGTTGCGA
1 GCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATTCGCGTTGCGATTTACATATTATCGTTGCGA
** *
1414916 ATTTGGAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCTGTAATTA
66 ATTTACAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTA
* * *
1414977 GCGTTGCGAAATTCGAGTTGCGAATTTGGAAAATTTGCGTTGTGATTTACATATTATCGTTGCG-
1 GCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATTCGCGTTGCGATTTACATATTATCGTTGCGA
1415041 ATTTAC
66 ATTTAC
1415047 CTATTCGCGT
Statistics
Matches: 177, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
125 64 0.36
126 113 0.64
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (126 bp):
GCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATTCGCGTTGCGATTTACATATTATCGTTGCGA
ATTTACAAAATCGCAACGCGAATTTCGTTTTCGCAACGCTAATTACCTATATCGGTAATTA
Done.