Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009605.1 Hibiscus syriacus cultivar Beakdansim tig00116989_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: 9158330
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 35
Found at i:2502222 original size:54 final size:53
Alignment explanation
Indices: 2502164--2502283 Score: 177
Period size: 54 Copynumber: 2.2 Consensus size: 53
2502154 ACCATCAGGC
* *
2502164 ATGTATCGATACCTGTAAACATCAAATTTAATTTGGGTACCGCTACCCCTTGTA
1 ATGTATCGATACCTGTAAACATCAAATTTAATTTGGGTACCGATACCCC-AGTA
* *
2502218 ATGTATCAATACCTGTAAACATCGAATTTAATTTGGGTACCGATACCCCAGTA
1 ATGTATCGATACCTGTAAACATCAAATTTAATTTGGGTACCGATACCCCAGTA
* *
2502271 GTGTATTGATACC
1 ATGTATCGATACC
2502284 CTTCTAAATG
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
53 13 0.22
54 46 0.78
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.33
Consensus pattern (53 bp):
ATGTATCGATACCTGTAAACATCAAATTTAATTTGGGTACCGATACCCCAGTA
Found at i:2502760 original size:59 final size:59
Alignment explanation
Indices: 2502687--2503094 Score: 645
Period size: 59 Copynumber: 6.9 Consensus size: 59
2502677 ATTACCAAAT
* * * *
2502687 GGCACTTTGTGTGCTAAAATGGTAAAGAAATTATACTAAGTGTATGAATTTCCATATAT
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * *
2502746 GACACTTTGTGTGCTAAAATTGTAAGGAAATCATATTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
2502805 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * *
2502864 GGCACTTCGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCTAGATAA
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
2502923 GGCACTTTGTGTGCTAAAATGGTAACGAAATCATACTAAGTGTATGAATTTCCAGACAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* *
2502982 GGCACTTTGTGTGCTAAAATGGTAATGAAATCATACTAAGTATATGAATTTCCAGATAG
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
* * * * *
2503041 GGCACTTTGTGTGCCAAAATGGTAAGGAAATCATATTGATTGTATGAAATTCCA
1 GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCA
2503095 ATTGAATTTA
Statistics
Matches: 321, Mismatches: 28, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 321 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (59 bp):
GGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGATAG
Found at i:2508438 original size:19 final size:19
Alignment explanation
Indices: 2508414--2508460 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
2508404 ACATATTATG
2508414 AGTTTTCAAACTTAGAAAT
1 AGTTTTCAAACTTAGAAAT
*
2508433 AGTTTTCAAACTTTGAAAT
1 AGTTTTCAAACTTAGAAAT
2508452 AGTTTTCAA
1 AGTTTTCAA
2508461 TTTTGCTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (19 bp):
AGTTTTCAAACTTAGAAAT
Found at i:2512957 original size:2 final size:2
Alignment explanation
Indices: 2512950--2513017 Score: 120
Period size: 2 Copynumber: 34.0 Consensus size: 2
2512940 AAATATAGTC
2512950 AT AT AT AT AT -T AT GAT 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
2512992 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
2513018 CGTGGCCTTG
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 61 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2513509 original size:21 final size:22
Alignment explanation
Indices: 2513483--2513536 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
2513473 AGAAACTATC
*
2513483 AGTATCGATACT-CTTATTTGG
1 AGTATCGATACTCCATATTTGG
*
2513504 AGTATCAATATCTCCATATTTGG
1 AGTATCGATA-CTCCATATTTGG
2513527 -GTATCGATAC
1 AGTATCGATAC
2513537 CATCATATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.36
22 10 0.36
23 8 0.29
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (22 bp):
AGTATCGATACTCCATATTTGG
Found at i:2527147 original size:20 final size:21
Alignment explanation
Indices: 2527109--2527147 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2527099 TAATTAAGGA
2527109 AGTATCGATACCTCCTTAACG
1 AGTATCGATACCTCCTTAACG
2527130 AGTATCGATACC-CCTTAA
1 AGTATCGATACCTCCTTAA
2527148 ACATCAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.28
Consensus pattern (21 bp):
AGTATCGATACCTCCTTAACG
Found at i:2527246 original size:302 final size:302
Alignment explanation
Indices: 2526683--2527286 Score: 992
Period size: 302 Copynumber: 2.0 Consensus size: 302
2526673 TCCAAGTTTT
2526683 CAAATATCAATTTTACTACTTACTTAAATGAAAAAATTGTGTTTCACAATTAAAGTATTTTTGAA
1 CAAATATCAATTTTACTACTTACTTAAATGAAAAAATTGTGTTTCACAATTAAAGTATTTTTGAA
*
2526748 ATAATTTTTACAAAGTATTTCGAACCATAATCGAGTAAAAAATAAGTTTTAAATAGGGAAATATC
66 ATAATTTTTACAAAGTATTTCGAACCATAATCGAGTAAAAAATAAGTTTTAAATAAGGAAATATC
*
2526813 GATACCTCCTTAACGAGTATCGATACCCCTTAAACATCGAATGCAAAAGAGGTACTCATACCCTA
131 GATACCTCCTTAACGAGTATCGATACCCCTTAAACATCAAATGCAAAAGAGGTACTCATACCCTA
* * * * *
2526878 TAGGGTATTGATACCCCTATATAAAATAGTACCGATACCTAGCCAAATGTATCAATACCTCTCCT
196 CAGGGTATCGATACCCCTATATAAAATAGTACCGATACCTAGCCAAAGGTACCAATACCACTCCT
***
2526943 TTTGATTTTGGCTCCGAGAAATAACAGAATGCAAAATGGGTA
261 TTTGATTTACACTCCGAGAAATAACAGAATGCAAAATGGGTA
* * ** *
2526985 CAAATATCAATTTTACTCCTTACTTAAATGAAAAATTTGTGTTTCACTCTTAAAGTATTTTTGCA
1 CAAATATCAATTTTACTACTTACTTAAATGAAAAAATTGTGTTTCACAATTAAAGTATTTTTGAA
* * * *
2527050 ATAATTTTTACAAAGTATTTCGAACCATAATCGAGTCAAAAATGAGTTTTAATTAAGGAAGTATC
66 ATAATTTTTACAAAGTATTTCGAACCATAATCGAGTAAAAAATAAGTTTTAAATAAGGAAATATC
* *
2527115 GATACCTCCTTAACGAGTATCGATACCCCTTAAACATCAAATGCAAAAGAGGTATTGATACCCTA
131 GATACCTCCTTAACGAGTATCGATACCCCTTAAACATCAAATGCAAAAGAGGTACTCATACCCTA
* *
2527180 CAGGGTATCGATACCCCTATATAAAGTAGTACCGATACCTAGCCAAAGGTACCGATACCACTCCT
196 CAGGGTATCGATACCCCTATATAAAATAGTACCGATACCTAGCCAAAGGTACCAATACCACTCCT
*
2527245 TTTGATTTACACTCTGAGAAATAACAGAATGCAAAATGGGTA
261 TTTGATTTACACTCCGAGAAATAACAGAATGCAAAATGGGTA
2527287 TTGATACCAT
Statistics
Matches: 278, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
302 278 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (302 bp):
CAAATATCAATTTTACTACTTACTTAAATGAAAAAATTGTGTTTCACAATTAAAGTATTTTTGAA
ATAATTTTTACAAAGTATTTCGAACCATAATCGAGTAAAAAATAAGTTTTAAATAAGGAAATATC
GATACCTCCTTAACGAGTATCGATACCCCTTAAACATCAAATGCAAAAGAGGTACTCATACCCTA
CAGGGTATCGATACCCCTATATAAAATAGTACCGATACCTAGCCAAAGGTACCAATACCACTCCT
TTTGATTTACACTCCGAGAAATAACAGAATGCAAAATGGGTA
Found at i:2543599 original size:40 final size:40
Alignment explanation
Indices: 2543482--2543758 Score: 354
Period size: 40 Copynumber: 7.1 Consensus size: 40
2543472 TATCGATTAA
*
2543482 GCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* *
2543522 GCACTTTGGTGCATA-GGT---CACAACC-TATGT-TAA-
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
*
2543555 GCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* *
2543595 GCACTTTGGTGCATATGGTGGGCACAACCTTATGTGTAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* * *
2543635 GCACTTCGGTACATATTGTGGACACGACCTTATGTGTAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* * * *
2543675 ACACTTCGGTGCATATGGTGGGAACAACCTTATGTATAAT
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
* * *
2543715 GCACTTCGATGCATATGGTGGGCATGACCTTATGCGTAA-
1 GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
2543754 GCACT
1 GCACT
2543759 AAAGTGCATA
Statistics
Matches: 202, Mismatches: 28, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
33 13 0.06
34 6 0.03
35 5 0.02
36 6 0.03
37 6 0.03
38 5 0.02
39 11 0.05
40 150 0.74
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (40 bp):
GCACTTCGGTGCATATGGTGGGCACGACCTTATGTGTAAT
Found at i:2543688 original size:80 final size:79
Alignment explanation
Indices: 2543478--2543758 Score: 407
Period size: 80 Copynumber: 3.6 Consensus size: 79
2543468 TGCATATCGA
2543478 TTAA-GCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAATGCACTTTGGTGCATA-GGT-
1 TTAATGCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAATGCACTTTGGTGCATATGGTG
2543540 --CACAACC-TATG
66 GGCACAACCTTATG
2543551 TTAA-GCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAATGCACTTTGGTGCATATGGTG
1 TTAATGCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAATGCACTTTGGTGCATATGGTG
2543615 GGCACAACCTTATG
66 GGCACAACCTTATG
* * * * * *
2543629 TGTAATGCACTTCGGTACATATTGTGGACACGACCTTATGTGTAATACACTTCGGTGCATATGGT
1 T-TAATGCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAATGCACTTTGGTGCATATGGT
*
2543694 GGGAACAACCTTATG
65 GGGCACAACCTTATG
* *
2543709 TATAATGCACTTCGATGCATATGGTGGGCATGACCTTATGCGTAA-GCACT
1 T-TAATGCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAATGCACT
2543759 AAAGTGCATA
Statistics
Matches: 186, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
73 59 0.32
74 3 0.02
77 7 0.04
78 5 0.03
79 7 0.04
80 105 0.56
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (79 bp):
TTAATGCACTTCGATGCATATGGTGGGCACGACCTTATGTGTAATGCACTTTGGTGCATATGGTG
GGCACAACCTTATG
Found at i:2545236 original size:22 final size:22
Alignment explanation
Indices: 2545189--2545237 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
2545179 TCAATTAACG
***
2545189 GAAA-TGCCTTAGCACTCTGAC
1 GAAAGTGCCTTAGCACTAAAAC
*
2545210 TAAAGTGCCTTAGCACTAAAAC
1 GAAAGTGCCTTAGCACTAAAAC
2545232 GAAAGT
1 GAAAGT
2545238 ACATTCGCAC
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.22
Consensus pattern (22 bp):
GAAAGTGCCTTAGCACTAAAAC
Found at i:2545538 original size:20 final size:19
Alignment explanation
Indices: 2545495--2545551 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
2545485 TATTATGAAG
* *
2545495 GTATCAATATAACCTTTCA
1 GTATCAATATCACCCTTCA
*
2545514 ATATCAATATCGACCCTTCA
1 GTATCAATATC-ACCCTTCA
*
2545534 GTATCGATACTCACCCTT
1 GTATCAATA-TCACCCTT
2545552 GGTATCGATA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 9 0.29
20 20 0.65
21 2 0.06
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (19 bp):
GTATCAATATCACCCTTCA
Found at i:2545841 original size:20 final size:20
Alignment explanation
Indices: 2545816--2545855 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2545806 AGTCAAAACC
2545816 CCTGGTTTCGAAACCCTATG
1 CCTGGTTTCGAAACCCTATG
**
2545836 CCTGGTTTTTAAACCCTATG
1 CCTGGTTTCGAAACCCTATG
2545856 TTCCAATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (20 bp):
CCTGGTTTCGAAACCCTATG
Found at i:2549041 original size:37 final size:37
Alignment explanation
Indices: 2548986--2549059 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
2548976 TATGAATGCG
*
2548986 ACTGAGCTGGGGATGCAACTCAAGCTGATAAGCAACA
1 ACTGAGCTGGGGAGGCAACTCAAGCTGATAAGCAACA
2549023 ACTGAGCTGGGGAGGCAACTCAAGCTGATAAGCAACA
1 ACTGAGCTGGGGAGGCAACTCAAGCTGATAAGCAACA
2549060 GGTCTGACTC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.35, C:0.22, G:0.28, T:0.15
Consensus pattern (37 bp):
ACTGAGCTGGGGAGGCAACTCAAGCTGATAAGCAACA
Found at i:2557218 original size:20 final size:20
Alignment explanation
Indices: 2557182--2557226 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
2557172 GATAAAAATT
*
2557182 AAAAGTTAAAAATGAAATAG
1 AAAAGTTAAAAATGAAAGAG
*
2557202 AAAAGTTAAGGAA-GAAAGAG
1 AAAAGTTAA-AAATGAAAGAG
2557222 AAAAG
1 AAAAG
2557227 AAAACGTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.13
Consensus pattern (20 bp):
AAAAGTTAAAAATGAAAGAG
Found at i:2570600 original size:15 final size:17
Alignment explanation
Indices: 2570575--2570607 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2570565 TAGTTATATA
2570575 TTTTACTTTATTT-TTG
1 TTTTACTTTATTTATTG
2570591 TTTT-CTTTATTTATTG
1 TTTTACTTTATTTATTG
2570607 T
1 T
2570608 AGGCATGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTACTTTATTTATTG
Found at i:2577574 original size:28 final size:28
Alignment explanation
Indices: 2577525--2577591 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
2577515 ATACACAAAA
*
2577525 ATCATATACAAAAATACCGT-AACCA-GT
1 ATCATATA-AAAAATACAGTAAACCAGGT
* *
2577552 GATCATATAAAAATGTACAGTAAATCAGGT
1 -ATCATATAAAAA-ATACAGTAAACCAGGT
2577582 ATCATATAAA
1 ATCATATAAA
2577592 CAGTATTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 4 0.12
28 13 0.39
29 14 0.42
30 2 0.06
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.25
Consensus pattern (28 bp):
ATCATATAAAAAATACAGTAAACCAGGT
Found at i:2578770 original size:29 final size:30
Alignment explanation
Indices: 2578738--2578794 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
2578728 TTTGGATCCA
*
2578738 AATTTAATCAAA-ATTTAATTTGGTCCTTG
1 AATTTAATCAAACATTTAATTTAGTCCTTG
* *
2578767 AATTTAATTAAACTTTTAATTTAGTCCT
1 AATTTAATCAAACATTTAATTTAGTCCT
2578795 CAGAATAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (30 bp):
AATTTAATCAAACATTTAATTTAGTCCTTG
Found at i:2579495 original size:17 final size:17
Alignment explanation
Indices: 2579473--2579514 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2579463 GGTGAAGGAT
2579473 GAAG-AACAAGAAGAAGA
1 GAAGAAACAAGAA-AAGA
*
2579490 GAAGAAAGAAGAAAAGA
1 GAAGAAACAAGAAAAGA
2579507 GAAAGAAA
1 G-AAGAAA
2579515 AGTGTCGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAGAAACAAGAAAAGA
Found at i:2579500 original size:15 final size:14
Alignment explanation
Indices: 2579480--2579513 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2579470 GATGAAGAAC
*
2579480 AAGAAGAAGAGAAGA
1 AAGAAGAAAAG-AGA
2579495 AAGAAGAAAAGAGA
1 AAGAAGAAAAGAGA
2579509 AAGAA
1 AAGAA
2579514 AAGTGTCGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAGAGA
Found at i:2579512 original size:18 final size:18
Alignment explanation
Indices: 2579480--2579514 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2579470 GATGAAGAAC
2579480 AAGAAGAAGAGAAGAAAG
1 AAGAAGAAGAGAAGAAAG
2579498 AAGAA-AAGAGAAAGAAA
1 AAGAAGAAGAG-AAGAAA
2579515 AGTGTCGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AAGAAGAAGAGAAGAAAG
Found at i:2581606 original size:20 final size:20
Alignment explanation
Indices: 2581581--2581633 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2581571 GCCCCTCTAA
2581581 CTGGTTTCTAAACTCCCTGC
1 CTGGTTTCTAAACTCCCTGC
*
2581601 CTGGTTTCTAAACTCCTTGC
1 CTGGTTTCTAAACTCCCTGC
*
2581621 CTGGTTTATAAAC
1 CTGGTTTCTAAAC
2581634 CCTATATTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.28, G:0.15, T:0.38
Consensus pattern (20 bp):
CTGGTTTCTAAACTCCCTGC
Found at i:2581967 original size:31 final size:31
Alignment explanation
Indices: 2581926--2581992 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2581916 TTTTTAAAGG
*
2581926 AGAGTGGTTCTAGTTTAGCCATAGAAAA-ACT
1 AGAGTAGTTCTAGTTTAGCCATAGAAAAGA-T
* * *
2581957 AGAGTAGTTCTATTTTATCCATTGAAAAGAT
1 AGAGTAGTTCTAGTTTAGCCATAGAAAAGAT
2581988 AGAGT
1 AGAGT
2581993 TGTAAGGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (31 bp):
AGAGTAGTTCTAGTTTAGCCATAGAAAAGAT
Found at i:2585671 original size:14 final size:13
Alignment explanation
Indices: 2585652--2585688 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2585642 TTTGTAGTTT
*
2585652 TTTTTTATCTGATA
1 TTTTTTAT-TAATA
2585666 TTTTTTATTAATA
1 TTTTTTATTAATA
2585679 TTTTTTATTA
1 TTTTTTATTA
2585689 TGTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (13 bp):
TTTTTTATTAATA
Found at i:2586843 original size:19 final size:21
Alignment explanation
Indices: 2586819--2586872 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
2586809 TGCATAAATG
2586819 GTATCGATACTATA-AT-GGA
1 GTATCGATACTATAGATAGGA
* *
2586838 GTATCGATACCATAGTATAGTA
1 GTATCGATACTATAG-ATAGGA
2586860 GTATCGATACTAT
1 GTATCGATACTAT
2586873 GGTAGGGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 13 0.45
21 2 0.07
22 14 0.48
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (21 bp):
GTATCGATACTATAGATAGGA
Found at i:2587309 original size:54 final size:54
Alignment explanation
Indices: 2587227--2587828 Score: 823
Period size: 54 Copynumber: 11.1 Consensus size: 54
2587217 ATAGGAACTC
* *
2587227 TGTGTGCAACCCACGTAATTCATCATGAGTTGATAAACAACCGTACAGGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
* *
2587281 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAAAAACCGTACATGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
* *
2587335 TGTGTACAACCCACGAAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
** * *
2587389 TGTGTGCAACCCACAAAATTCATCATGAGTTGATGAACAATCATACAGGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
* * * * *
2587443 TGTGTGCGACCCATGGAATTCATCACGAGTTGATGAAAAACCGTACATGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
* * *
2587497 TGTGTGAAACCCACGGAATTCATCATGAGTTCATGAACAACCGTACATGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
* * * *
2587551 TGTGTGCAACCCAAGAAATTCATCAAGAGTTGATGAACAACCGTACAGACACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
2587605 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
* * *
2587659 TGTGTGCAACCCACAGAATTCATCAT-ATGTTGATGAATAACCGTATAGGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGA-GTTGATGAACAACCGTACAGGCACTA
** * *
2587713 TGTGTGCAACTTACGGAATTCATCAT-ATGTTGATGAACAACCGTACATGCATTA
1 TGTGTGCAACCCACGGAATTCATCATGA-GTTGATGAACAACCGTACAGGCACTA
* * * * * * *
2587767 TGTGTACAACTCACGAAATTTATCAT-AGGTTGGTGAACGACCGTATAGGCACTA
1 TGTGTGCAACCCACGGAATTCATCATGA-GTTGATGAACAACCGTACAGGCACTA
*
2587821 CGTGTGCA
1 TGTGTGCA
2587829 TCTAAATAAA
Statistics
Matches: 487, Mismatches: 60, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
53 1 0.00
54 486 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (54 bp):
TGTGTGCAACCCACGGAATTCATCATGAGTTGATGAACAACCGTACAGGCACTA
Found at i:2590666 original size:18 final size:19
Alignment explanation
Indices: 2590631--2590667 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2590621 CACGGAATGT
2590631 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
2590651 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
2590668 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:2605788 original size:21 final size:22
Alignment explanation
Indices: 2605763--2605808 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
2605753 AATAGTTTGG
2605763 TTTCATG-AAATTTATCCTTA-A
1 TTTCATGTAAATTTA-CCTTATA
*
2605784 TTTCATGTTAATTTACCTTATA
1 TTTCATGTAAATTTACCTTATA
2605806 TTT
1 TTT
2605809 AAGCTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.54
Consensus pattern (22 bp):
TTTCATGTAAATTTACCTTATA
Found at i:2615884 original size:20 final size:20
Alignment explanation
Indices: 2615847--2615890 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2615837 ATTCTCTCTT
* *
2615847 GAAAACAAAATTAGATTTTG
1 GAAAACAAAATGAAATTTTG
*
2615867 GAAAGCAAAATGAAATTTT-
1 GAAAACAAAATGAAATTTTG
2615886 GAAAA
1 GAAAA
2615891 ATGATTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.55, C:0.05, G:0.16, T:0.25
Consensus pattern (20 bp):
GAAAACAAAATGAAATTTTG
Found at i:2620006 original size:21 final size:19
Alignment explanation
Indices: 2619982--2620029 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
2619972 ATAATTTAAA
2619982 TTGTTGTTAAGATAAATTAGT
1 TTGTTGTTAAGATAAA--AGT
* *
2620003 TTGTT-TAAAGATAAAATT
1 TTGTTGTTAAGATAAAAGT
2620021 TTGTTGTTA
1 TTGTTGTTA
2620030 GTCTCTATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 9 0.39
21 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (19 bp):
TTGTTGTTAAGATAAAAGT
Found at i:2626476 original size:18 final size:18
Alignment explanation
Indices: 2626452--2626515 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
2626442 GAAGGTCATA
*
2626452 ATCAATATCGTCACTATC
1 ATCAATATCGTCACTAGC
* *
2626470 GTCAATAGCGTCACTAGC
1 ATCAATATCGTCACTAGC
2626488 ATCAATATCGTCACTAGC
1 ATCAATATCGTCACTAGC
*
2626506 ACCAATATCG
1 ATCAATATCG
2626516 ATATCATCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (18 bp):
ATCAATATCGTCACTAGC
Found at i:2629008 original size:30 final size:29
Alignment explanation
Indices: 2628974--2629075 Score: 116
Period size: 29 Copynumber: 3.4 Consensus size: 29
2628964 TCATAATTTT
* *
2628974 TATTTTAGTCCCTTAAGTGTCTATATTTAC
1 TATTTTAGT-CCTTAAGTTTCTATTTTTAC
2629004 TA-TTTAGATCCTTAAGTTTCTATTTTTAC
1 TATTTTAG-TCCTTAAGTTTCTATTTTTAC
* * *
2629033 TATTATAGTCCTTAAACTTTCTATTTTTTAT
1 TATTTTAGTCCTT-AAGTTTCTA-TTTTTAC
2629064 TATTTTAGTCCT
1 TATTTTAGTCCT
2629076 AAGATGTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
29 30 0.48
30 15 0.24
31 17 0.27
ACGTcount: A:0.24, C:0.15, G:0.07, T:0.55
Consensus pattern (29 bp):
TATTTTAGTCCTTAAGTTTCTATTTTTAC
Found at i:2634585 original size:29 final size:28
Alignment explanation
Indices: 2634530--2634623 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 28
2634520 CTCTTGAAAC
2634530 AAATCTTTGAG--TATGTTCATTTAAAAAAA
1 AAATCTTTGAGTCTAT-TTC-TTT-AAAAAA
2634559 AAATCTTTGAGTCTATTTCTCTTAAAAAA
1 AAATCTTTGAGTCTATTTCT-TTAAAAAA
** *
2634588 TCATCTTTGAGTCTATTTCTTTAAAAAC
1 AAATCTTTGAGTCTATTTCTTTAAAAAA
2634616 AAAT-TTTG
1 AAATCTTTG
2634624 TCTCTCTTGA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
27 4 0.07
28 9 0.16
29 36 0.63
30 5 0.09
31 3 0.05
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.43
Consensus pattern (28 bp):
AAATCTTTGAGTCTATTTCTTTAAAAAA
Found at i:2635403 original size:3 final size:3
Alignment explanation
Indices: 2635389--2635429 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
2635379 TCTACAAAAC
2635389 ATT ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2635430 TACATAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2636900 original size:29 final size:28
Alignment explanation
Indices: 2636826--2636924 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 28
2636816 TTGTTTATAA
* *
2636826 TTTTTATTTTAGTCCCTTAAGTGTCTATAT
1 TTTTTATTATAGT-CCTTAAGTTTCTAT-T
**
2636856 TTGATATT-TAGATCCTTAAGTTTCTATT
1 TTTTTATTATAG-TCCTTAAGTTTCTATT
*
2636884 TTTTCTATTATAGTCCTTCAACTTTCCGT-TT
1 TTTT-TATTATAGTCCTT-AAGTTT-C-TATT
2636915 TTTTTATTAT
1 TTTTTATTAT
2636925 TTTAGTCCAA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
28 3 0.05
29 25 0.44
30 21 0.37
31 7 0.12
32 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (28 bp):
TTTTTATTATAGTCCTTAAGTTTCTATT
Found at i:2644827 original size:13 final size:13
Alignment explanation
Indices: 2644809--2644834 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2644799 ATACTATAAC
2644809 AGAAAACCAGATT
1 AGAAAACCAGATT
2644822 AGAAAACCAGATT
1 AGAAAACCAGATT
2644835 CATGCAGGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AGAAAACCAGATT
Found at i:2645540 original size:30 final size:29
Alignment explanation
Indices: 2645506--2645578 Score: 87
Period size: 30 Copynumber: 2.6 Consensus size: 29
2645496 TTTGGGTATA
* * **
2645506 AATTTAATTGAAATTTCATTTTGGTCCTC
1 AATTTAATTAAAATTTCAATTTAATCCTC
2645535 GAATTTAATTAAAATTTCAATTTAATCCTC
1 -AATTTAATTAAAATTTCAATTTAATCCTC
2645565 AATTTAA--AAAATTT
1 AATTTAATTAAAATTT
2645579 AGGCCCTCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
27 7 0.18
29 7 0.18
30 25 0.64
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.45
Consensus pattern (29 bp):
AATTTAATTAAAATTTCAATTTAATCCTC
Found at i:2647571 original size:21 final size:21
Alignment explanation
Indices: 2647529--2647571 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
2647519 ATTTATGAGA
2647529 AATCCTAAAAATACCATGAATG
1 AATCCTAAAAATACCA-GAATG
*
2647551 AATCTTAAAAATCACCA-AATG
1 AATCCTAAAAAT-ACCAGAATG
2647572 TCATTGCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.23
Consensus pattern (21 bp):
AATCCTAAAAATACCAGAATG
Found at i:2650763 original size:2 final size:2
Alignment explanation
Indices: 2650746--2650894 Score: 111
Period size: 2 Copynumber: 77.0 Consensus size: 2
2650736 CCTGTTATGC
* **
2650746 AT AT AT ACT AT A- AT AT AT AT AT -T AC AT A- AT AT GG AT A- AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2650785 A- AA AT AG AT AT AT AT -T CAC AT ACT AT AT AT AGC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT A-T AT AT AT A-T AT AT AT AT
2650826 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
*
2650868 AT A- AC ACT -T AT AT A- AT AT A- AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
2650895 GTACATGCAC
Statistics
Matches: 118, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
1 10 0.08
2 103 0.87
3 5 0.04
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2651377 original size:2 final size:2
Alignment explanation
Indices: 2651370--2651402 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2651360 TTTAGTTTTA
2651370 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2651403 TACAAGGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2652513 original size:2 final size:2
Alignment explanation
Indices: 2652508--2652535 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2652498 TCTAAAAAAC
2652508 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
2652536 TAGCCATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2652771 original size:2 final size:2
Alignment explanation
Indices: 2652764--2652796 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2652754 ATACGTAAAT
2652764 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2652797 CGTATTTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2654303 original size:13 final size:13
Alignment explanation
Indices: 2654285--2654326 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2654275 CCTGCATGTA
2654285 AATTAATAATAAT
1 AATTAATAATAAT
*
2654298 AATTAATACTAAT
1 AATTAATAATAAT
2654311 AA-TAATAA-AAT
1 AATTAATAATAAT
2654322 -ATTAA
1 AATTAA
2654327 AAACGAGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 6 0.23
12 5 0.19
13 14 0.54
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:2654778 original size:111 final size:111
Alignment explanation
Indices: 2654529--2655180 Score: 948
Period size: 111 Copynumber: 5.9 Consensus size: 111
2654519 TTCAGGGAAG
* * * *
2654529 ATTGAATCAGTGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGGAAGA-TAGTAAT
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAG-GAT
* *
2654593 CTGTTCCGCTTCTTATGAAGGGAATATCAGATCTGGGAAAGTTGATCC
65 CTGTTCCGCTTCCTCTG-AGGGAATATCAGATCTGGGAAAGTTGATCC
2654641 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
*
2654706 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
* *
2654752 ATTGAATCGGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
* * *
2654817 TGTTTCGTTTCTTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
* * *
2654863 ATTGAATCAGGGTAGACTTATTCTGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
** * * *
2654928 TGTTATGCTTTCTCTGAGGGAATATCATATATGGGAAAGTTGATCC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
* * *
2654974 ATTGAATCAGGGTAGACTTGTTTCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
* * *
2655039 TGTTCTGCTTCCTCTGAGGGAATATCAGATATGGGAAAGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
* * *
2655085 ATTGAATCAGGGTAGACTTGTTCCGCTGTTACTCAGGGAATATCAAAACTTGAAAAAG-AGTGAT
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAG-GAT
* * * * *
2655149 ATGTTCCACTTCTTCTGAAGAGAGTATCAGAT
65 CTGTTCCGCTTCCTCTG-AGGGAATATCAGAT
2655181 AGATGGATTT
Statistics
Matches: 496, Mismatches: 41, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
110 1 0.00
111 409 0.82
112 84 0.17
113 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (111 bp):
ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAAGGATC
TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATCC
Found at i:2655324 original size:79 final size:79
Alignment explanation
Indices: 2655181--2655349 Score: 205
Period size: 79 Copynumber: 2.1 Consensus size: 79
2655171 AGTATCAGAT
** * ** * *
2655181 AGATGGATTTGCTTCACTATTCTTCCGTGAAGGCTTAAAATGGCCCGGAGGACTTAATCGTCATG
1 AGATGGATTTGCTTCACTACACTTCCGTGAAAGCTTAAAATGGCCCAAAGGACTTAAGCATCATG
*
2655246 CTCGGAATG-CTTAC
66 CTC-GAAAGACTTAC
* * * * *
2655260 TGATGGATTTGCTTCAGTACACTTCGGTGAAAGCTTAAGATGGCCCAAAGGATTTAAGCATCATG
1 AGATGGATTTGCTTCACTACACTTCCGTGAAAGCTTAAAATGGCCCAAAGGACTTAAGCATCATG
2655325 CTCGAAAGACTTAC
66 CTCGAAAGACTTAC
2655339 AGATGGATTTG
1 AGATGGATTTG
2655350 ATCATCATGC
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
78 4 0.05
79 71 0.95
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (79 bp):
AGATGGATTTGCTTCACTACACTTCCGTGAAAGCTTAAAATGGCCCAAAGGACTTAAGCATCATG
CTCGAAAGACTTAC
Found at i:2655356 original size:34 final size:34
Alignment explanation
Indices: 2655309--2655411 Score: 170
Period size: 34 Copynumber: 3.0 Consensus size: 34
2655299 ATGGCCCAAA
* * * *
2655309 GGATTTAAGCATCATGCTCGAAAGACTTACAGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
2655343 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
2655377 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
1 GGATTTGATCATCATGCTCGGAAGACTTACTGAT
2655411 G
1 G
2655412 ACCCGAAGGA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.30
Consensus pattern (34 bp):
GGATTTGATCATCATGCTCGGAAGACTTACTGAT
Found at i:2659410 original size:21 final size:21
Alignment explanation
Indices: 2659384--2659432 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
2659374 TAATCTTTTT
2659384 CTTCTTTCTATTCTTTTTGGC
1 CTTCTTTCTATTCTTTTTGGC
2659405 CTTCTTTCTATTCTTTTTGGC
1 CTTCTTTCTATTCTTTTTGGC
2659426 CTTCTTT
1 CTTCTTT
2659433 ACTAGCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.04, C:0.24, G:0.08, T:0.63
Consensus pattern (21 bp):
CTTCTTTCTATTCTTTTTGGC
Found at i:2664411 original size:2 final size:2
Alignment explanation
Indices: 2664404--2664431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2664394 TAGTGTCTAC
2664404 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
2664432 TCGTATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2664504 original size:2 final size:2
Alignment explanation
Indices: 2664487--2664611 Score: 109
Period size: 2 Copynumber: 63.5 Consensus size: 2
2664477 CATGTTATGC
* **
2664487 AT AT AT ACT AT A- AT AT AT AT AT -T AC AT A- AT AT GG AT A- AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
2664526 A- AA AT AG AT AT AT AT -T CAC AT ACT AT AT AT AGC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT -AT AT A-T AT AT AT A-T AT AT AT AT
2664567 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
2664609 AT A
1 AT A
2664612 AACACTTAAA
Statistics
Matches: 100, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
1 6 0.06
2 89 0.89
3 5 0.05
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2665987 original size:13 final size:13
Alignment explanation
Indices: 2665965--2666006 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2665955 CCTGCATGTA
2665965 AATTAATAATAAT
1 AATTAATAATAAT
*
2665978 AATTATTAATAAT
1 AATTAATAATAAT
2665991 AA-TAATAA-AAT
1 AATTAATAATAAT
2666002 -ATTAA
1 AATTAA
2666007 AAAACGAGAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 1 0.04
11 6 0.23
12 5 0.19
13 14 0.54
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:2665987 original size:16 final size:16
Alignment explanation
Indices: 2665966--2665996 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2665956 CTGCATGTAA
2665966 ATTAATAATAATAATT
1 ATTAATAATAATAATT
2665982 ATTAATAATAATAAT
1 ATTAATAATAATAAT
2665997 AAAATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTAATAATAATAATT
Found at i:2669134 original size:29 final size:29
Alignment explanation
Indices: 2669102--2669168 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
2669092 CTGGGTATTT
* *
2669102 TAATAATTAAATCGGAATATTGGATAGT-C
1 TAATAATTAAATCGGAAGACTGGATA-TCC
*
2669131 TAATAATTAATTCGGAAGACTGGATATCC
1 TAATAATTAAATCGGAAGACTGGATATCC
2669160 TAATAATTA
1 TAATAATTA
2669169 TTTCTAAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 1 0.03
29 33 0.97
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (29 bp):
TAATAATTAAATCGGAAGACTGGATATCC
Found at i:2669439 original size:29 final size:29
Alignment explanation
Indices: 2669407--2669471 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
2669397 TAAAGGTTGA
* *
2669407 ATATTTTAAAAATTAACTCGGAGCACTGG
1 ATATTTTAAAAATAAACTCGGAACACTGG
** * *
2669436 ATATAATAATAATAAATTCGGAACACTGG
1 ATATTTTAAAAATAAACTCGGAACACTGG
2669465 ATATTTT
1 ATATTTT
2669472 GCTATTTAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (29 bp):
ATATTTTAAAAATAAACTCGGAACACTGG
Found at i:2670027 original size:27 final size:28
Alignment explanation
Indices: 2669925--2670038 Score: 131
Period size: 28 Copynumber: 4.1 Consensus size: 28
2669915 CTGATACATG
*
2669925 AACATGACATTTTAAAAATTAATTCCGA
1 AACAAGACATTTTAAAAATTAATTCCGA
** ** * *
2669953 AGTAAGACATTGCAAAATTTAATTCCCA
1 AACAAGACATTTTAAAAATTAATTCCGA
* *
2669981 AACAAGACATTTTGAAAATTAATTCTGA
1 AACAAGACATTTTAAAAATTAATTCCGA
*
2670009 AACAGGA-ATTTTAAAAATTAATTCCGA
1 AACAAGACATTTTAAAAATTAATTCCGA
2670036 AAC
1 AAC
2670039 GGAAAAATTT
Statistics
Matches: 68, Mismatches: 18, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
27 21 0.31
28 47 0.69
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (28 bp):
AACAAGACATTTTAAAAATTAATTCCGA
Found at i:2670052 original size:27 final size:27
Alignment explanation
Indices: 2669935--2670054 Score: 89
Period size: 28 Copynumber: 4.3 Consensus size: 27
2669925 AACATGACAT
** * *
2669935 TTTAAAAATTAATTCCGAAGTAAGACA
1 TTTAAAAATTAATTCCGAAACAGGAAA
* * * * *
2669962 TTGCAAAATTTAATTCCCAAACAAGACAT
1 TT-TAAAAATTAATTCCGAAACAGGA-AA
* * *
2669991 TTTGAAAATTAATTCTGAAACAGGAAT
1 TTTAAAAATTAATTCCGAAACAGGAAA
2670018 TTTAAAAATTAATTCCGAAAC-GGAAAAA
1 TTTAAAAATTAATTCCGAAACAGG--AAA
2670046 TTTAAAAAT
1 TTTAAAAAT
2670055 AATATTCCCA
Statistics
Matches: 73, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
26 2 0.03
27 23 0.32
28 46 0.63
29 2 0.03
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (27 bp):
TTTAAAAATTAATTCCGAAACAGGAAA
Found at i:2670863 original size:17 final size:17
Alignment explanation
Indices: 2670841--2670874 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2670831 TATGAATTCT
2670841 TTTAGAATTCATAAATG
1 TTTAGAATTCATAAATG
2670858 TTTAGAATTCATAAATG
1 TTTAGAATTCATAAATG
2670875 GTTATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTAGAATTCATAAATG
Found at i:2671794 original size:22 final size:22
Alignment explanation
Indices: 2671769--2671815 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2671759 GCTATGAAAT
*
2671769 TGAAATGTGAAAGTATTGAATA
1 TGAAATGTGAAAGTACTGAATA
*
2671791 TGAAATGTGAAAGTACTGATTA
1 TGAAATGTGAAAGTACTGAATA
2671813 TGA
1 TGA
2671816 GAACTTGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (22 bp):
TGAAATGTGAAAGTACTGAATA
Found at i:2672777 original size:29 final size:29
Alignment explanation
Indices: 2672744--2672804 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
2672734 AGTCCATTAT
2672744 TCTTTTACTCAACAGTGTTTAATCGTTCA
1 TCTTTTACTCAACAGTGTTTAATCGTTCA
2672773 TCTTTTACTCAACAGTGTTTAATCGTTCA
1 TCTTTTACTCAACAGTGTTTAATCGTTCA
2672802 TCT
1 TCT
2672805 AACTAGCATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (29 bp):
TCTTTTACTCAACAGTGTTTAATCGTTCA
Found at i:2672856 original size:110 final size:110
Alignment explanation
Indices: 2672701--2672995 Score: 412
Period size: 110 Copynumber: 2.7 Consensus size: 110
2672691 ATCTAGCTTT
* *
2672701 CATATTTGACACTTTTTTGTCTAATGCACAGCTAGTCCATTATTCTTTTACTCAACAGTGTTTAA
1 CATAATTGACACTTTTTTGTCAAATGCACAGCTAGTCCATTATTCTTTTACTCAACAGTGTTTAA
*
2672766 TCGTTCATCTTTTACTCAACAGTGTTTAA-TCGTTCATCTAACTAG
66 TCGTTCATCTTTTACTCAACAGTGTTTAACT-ATTCATCTAACTAG
* * *
2672811 CATAATTGACACTTTTTTGTCAAATACACAACTAGTCCATTATTCTTTTACTCAACAATGTTTAA
1 CATAATTGACACTTTTTTGTCAAATGCACAGCTAGTCCATTATTCTTTTACTCAACAGTGTTTAA
*
2672876 TCGTTCATCTTTTACTCAACAGTGTTTAACTATTCATCTAACTGG
66 TCGTTCATCTTTTACTCAACAGTGTTTAACTATTCATCTAACTAG
* * ** * * * * * **
2672921 CATAATTGGCAATTTCCTGTCAAATGCACAGCTAGTTCATTATTTTTTTCCTCAACGGTATTTCG
1 CATAATTGACACTTTTTTGTCAAATGCACAGCTAGTCCATTATTCTTTTACTCAACAGTGTTTAA
2672986 TCGTTCATCT
66 TCGTTCATCT
2672996 AACTGGCATA
Statistics
Matches: 163, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
110 162 0.99
111 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (110 bp):
CATAATTGACACTTTTTTGTCAAATGCACAGCTAGTCCATTATTCTTTTACTCAACAGTGTTTAA
TCGTTCATCTTTTACTCAACAGTGTTTAACTATTCATCTAACTAG
Found at i:2672911 original size:29 final size:29
Alignment explanation
Indices: 2672854--2672914 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
2672844 AGTCCATTAT
*
2672854 TCTTTTACTCAACAATGTTTAATCGTTCA
1 TCTTTTACTCAACAATGTTTAATCATTCA
*
2672883 TCTTTTACTCAACAGTGTTTAA-CTATTCA
1 TCTTTTACTCAACAATGTTTAATC-ATTCA
2672912 TCT
1 TCT
2672915 AACTGGCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (29 bp):
TCTTTTACTCAACAATGTTTAATCATTCA
Found at i:2673417 original size:12 final size:13
Alignment explanation
Indices: 2673388--2673422 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
2673378 ATCCTTAGTA
2673388 TCATTTTTCTTAT
1 TCATTTTTCTTAT
*
2673401 ACATTTTTCTT-T
1 TCATTTTTCTTAT
2673413 TCATTTTTCT
1 TCATTTTTCT
2673423 GTAGTAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTTCTTAT
Found at i:2673547 original size:34 final size:34
Alignment explanation
Indices: 2673509--2673718 Score: 145
Period size: 34 Copynumber: 5.8 Consensus size: 34
2673499 TTATGGCATC
2673509 CTTTTATGCCAATAATGCACCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
* * *** * *
2673543 CTTTTATGTCGATATATGCA-TTTTA-GCTATGGCATC
1 CTTTTATGCCAATA-ATGCACCCATATGC-AT--TATT
* * *
2673579 CTTTTATGCCAATAAGGTAGCCATATGCATTATT
1 CTTTTATGCCAATAATGCACCCATATGCATTATT
*
2673613 CTTTTATGTCAATAATGCACCCATATGCATTTCAGCTATGT
1 CTTTTATGCCAATAATGCACCCATATGCA--T----TAT-T
*
2673654 CATCCTTTCATACCAATAATGCACCCATATGCATTATT
1 C-T--TTT-ATGCCAATAATGCACCCATATGCATTATT
* *
2673692 CTTTAATGCCGATAATGCACCCATATG
1 CTTTTATGCCAATAATGCACCCATATG
2673719 TATTTCAGCT
Statistics
Matches: 134, Mismatches: 25, Indels: 34
0.69 0.13 0.18
Matches are distributed among these distances:
33 2 0.01
34 63 0.47
35 10 0.07
36 19 0.14
37 3 0.02
38 2 0.01
39 3 0.02
40 3 0.02
41 2 0.01
42 1 0.01
43 1 0.01
44 3 0.02
45 22 0.16
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (34 bp):
CTTTTATGCCAATAATGCACCCATATGCATTATT
Found at i:2673603 original size:70 final size:69
Alignment explanation
Indices: 2673488--2673710 Score: 230
Period size: 70 Copynumber: 3.1 Consensus size: 69
2673478 GCATCTTTTC
** *
2673488 ATGCATTTTATTTATGGCATCCTTTTATGCCAATAATGCACCCATATGCATTATTCTTTTATGTC
1 ATGCATTTTAGCTATGGCATCCTTTTATGCCAATAAGGCACCCATATGCATTATTCTTTTATGTC
*
2673553 GATA
66 AATA
* *
2673557 TATGCATTTTAGCTATGGCATCCTTTTATGCCAATAAGGTAGCCATATGCATTATTCTTTTATGT
1 -ATGCATTTTAGCTATGGCATCCTTTTATGCCAATAAGGCACCCATATGCATTATTCTTTTATGT
2673622 CAATA
65 CAATA
* * * *
2673627 ATGCACCCATATGCATTTCAGCTATGTCATCCTTTCATACCAATAATGCACCCATATGCATTATT
1 ATG----C--AT---TTT-AGCTATGGCATCCTTTTATGCCAATAAGGCACCCATATGCATTATT
* * *
2673692 CTTTAATGCCGATA
56 CTTTTATGTCAATA
2673706 ATGCA
1 ATGCA
2673711 CCCATATGTA
Statistics
Matches: 128, Mismatches: 15, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
69 3 0.02
70 63 0.49
73 2 0.02
75 3 0.02
78 3 0.02
79 54 0.42
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (69 bp):
ATGCATTTTAGCTATGGCATCCTTTTATGCCAATAAGGCACCCATATGCATTATTCTTTTATGTC
AATA
Found at i:2673652 original size:79 final size:79
Alignment explanation
Indices: 2673556--2673756 Score: 276
Period size: 79 Copynumber: 2.5 Consensus size: 79
2673546 TTATGTCGAT
* * * * *
2673556 ATATGCATTTTAGCTATGGCATCCTTTTATGCCAATAAGGTAGCCATATGCATTATTCTTTTATG
1 ATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAAGGCACCCATATGCATTATTCTTTAATG
*
2673621 TCAATAATGCACCC
66 CCAATAATGCACCC
* * *
2673635 ATATGCATTTCAGCTATGTCATCCTTTCATACCAATAATGCACCCATATGCATTATTCTTTAATG
1 ATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAAGGCACCCATATGCATTATTCTTTAATG
*
2673700 CCGATAATGCACCC
66 CCAATAATGCACCC
* * * *
2673714 ATATGTATTTCAGCTATGGCATCATTTCATGCTAATAATGCAC
1 ATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAAGGCAC
2673757 TCTTTTATGT
Statistics
Matches: 107, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 107 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (79 bp):
ATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAAGGCACCCATATGCATTATTCTTTAATG
CCAATAATGCACCC
Found at i:2673795 original size:34 final size:34
Alignment explanation
Indices: 2673757--2673822 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
2673747 AATAATGCAC
**
2673757 TCTTTTATGTCGATAATGCACCCATATGCATTAT
1 TCTTTTATACCGATAATGCACCCATATGCATTAT
2673791 TCTTTTATACCGATAATGCACCCATATGCATT
1 TCTTTTATACCGATAATGCACCCATATGCATT
2673823 TCAGCTATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.39
Consensus pattern (34 bp):
TCTTTTATACCGATAATGCACCCATATGCATTAT
Found at i:2674413 original size:95 final size:95
Alignment explanation
Indices: 2674261--2674470 Score: 312
Period size: 95 Copynumber: 2.2 Consensus size: 95
2674251 TCGATACTAC
* * * * *
2674261 TACCCTGGTACCGATACTTCTATACTATGGTACTGATACCCCCTTCCGATATTGATACCAATTTT
1 TACCATGGTATCGATACTACAATACTATGGTACTGATACCCCCTTCCGATATCGATACCAATTTT
*
2674326 AGCTTCGATGTTGCCTGATATCGATACCCT
66 AGATTCGATGTTGCCTGATATCGATACCCT
* * *
2674356 TACCATGGTATCGATACTACAATACTATGGTACTGATACCCTCTTCCGGTATCGATACTAATTTT
1 TACCATGGTATCGATACTACAATACTATGGTACTGATACCCCCTTCCGATATCGATACCAATTTT
* *
2674421 AGATTCGATGTTGTCTGGTATCGATACCCT
66 AGATTCGATGTTGCCTGATATCGATACCCT
*
2674451 TACCATGGTATCAATACTAC
1 TACCATGGTATCGATACTAC
2674471 CTAGTCGGTA
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
95 103 1.00
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (95 bp):
TACCATGGTATCGATACTACAATACTATGGTACTGATACCCCCTTCCGATATCGATACCAATTTT
AGATTCGATGTTGCCTGATATCGATACCCT
Found at i:2682767 original size:24 final size:24
Alignment explanation
Indices: 2682737--2682791 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
2682727 CTTAATATAT
2682737 TTTTGAAACAATTTTCATAAAGTA
1 TTTTGAAACAATTTTCATAAAGTA
2682761 TTTTGAAACAATTTTCATAAAGTA
1 TTTTGAAACAATTTTCATAAAGTA
2682785 TTTTGAA
1 TTTTGAA
2682792 CCAAAATCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (24 bp):
TTTTGAAACAATTTTCATAAAGTA
Found at i:2682851 original size:20 final size:20
Alignment explanation
Indices: 2682826--2682883 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
2682816 TTTCAGAGGA
*
2682826 ATGCACCTATACACCAATCC
1 ATGCACCGATACACCAATCC
*
2682846 ATGCACCGATGCACCAATCC
1 ATGCACCGATACACCAATCC
* *
2682866 ATGCATCGATGCACCAAT
1 ATGCACCGATACACCAAT
2682884 GAATAAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.33, C:0.36, G:0.12, T:0.19
Consensus pattern (20 bp):
ATGCACCGATACACCAATCC
Found at i:2682935 original size:19 final size:19
Alignment explanation
Indices: 2682911--2682964 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2682901 AATGCAATTT
2682911 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
2682930 ATGCATCGATGCACTCTCC
1 ATGCATCGATGCACTCTCC
*
2682949 ATGCATTGATGCACTC
1 ATGCATCGATGCACTC
2682965 AGGTTTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (19 bp):
ATGCATCGATGCACTCTCC
Found at i:2683007 original size:65 final size:64
Alignment explanation
Indices: 2682930--2683071 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 64
2682920 TGCACTCTCC
* * * * * * *
2682930 ATGCATCGATGCACTCTCCATGCATTGATGCACTCAGGTTTTAATGAAAACATCGATTGCATTTT
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGG-CTTAATCAAAACATCGAATGAATTTT
* *
2682995 ATGCATCGATGCACACACCATGCATCGATGCACTTAGGCTTATTCAAAACATCGAATGAATTTT
1 ATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAAAACATCGAATGAATTTT
2683059 ATGCATCGATGCA
1 ATGCATCGATGCA
2683072 AACTTAGTGC
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
64 34 0.50
65 34 0.50
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (64 bp):
ATGCATCGATGCACACACCATGCATCGATGCACTCAGGCTTAATCAAAACATCGAATGAATTTT
Found at i:2684465 original size:22 final size:24
Alignment explanation
Indices: 2684435--2684485 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
2684425 TAATTGCTTT
2684435 TATGATTATATATATAT-AATTAA
1 TATGATTATATATATATAAATTAA
* *
2684458 TATG-TTATTTATCTATAAATTAA
1 TATGATTATATATATATAAATTAA
*
2684481 AATGA
1 TATGA
2684486 AAGTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (24 bp):
TATGATTATATATATATAAATTAA
Found at i:2687780 original size:2 final size:2
Alignment explanation
Indices: 2687773--2687799 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2687763 GGGATATTAC
2687773 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 A
2687800 GCTTTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2697424 original size:3 final size:3
Alignment explanation
Indices: 2697416--2697512 Score: 180
Period size: 3 Copynumber: 33.0 Consensus size: 3
2697406 ATTCGTCTGT
2697416 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2697463 ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2697510 ATA
1 ATA
2697513 CGAACATAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.04
3 88 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2702992 original size:39 final size:39
Alignment explanation
Indices: 2702949--2703067 Score: 118
Period size: 39 Copynumber: 3.1 Consensus size: 39
2702939 CCGGTAAAGG
* *
2702949 CCTTATACACATAGCATAAGGA-CTTGTGGTAAGGACTTA
1 CCTTATACACAAAGCA-AAGGAGCCTGTGGTAAGGACTTA
* *
2702988 CCTTATGCACAAAGCAGAGGAGCCTGTGGTAAGGACTTA
1 CCTTATACACAAAGCAAAGGAGCCTGTGGTAAGGACTTA
* * * *
2703027 CCTTGA-GCACAAAGTC-GAGGAGCTTGTGGTAAGGATTTA
1 CCTT-ATACACAAAG-CAAAGGAGCCTGTGGTAAGGACTTA
2703066 CC
1 CC
2703068 CTGAGCACAA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
38 4 0.06
39 65 0.92
40 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (39 bp):
CCTTATACACAAAGCAAAGGAGCCTGTGGTAAGGACTTA
Found at i:2703073 original size:39 final size:39
Alignment explanation
Indices: 2702967--2703080 Score: 153
Period size: 39 Copynumber: 2.9 Consensus size: 39
2702957 ACATAGCATA
*
2702967 AGGA-CTTGTGGTAAGGACTTA-CCTTATGCACAAAGCAG
1 AGGAGCTTGTGGTAAGGACTTACCCTGA-GCACAAAGCAG
* *
2703005 AGGAGCCTGTGGTAAGGACTTACCTTGAGCACAAAGTC-G
1 AGGAGCTTGTGGTAAGGACTTACCCTGAGCACAAAG-CAG
*
2703044 AGGAGCTTGTGGTAAGGATTTACCCTGAGCACAAAGC
1 AGGAGCTTGTGGTAAGGACTTACCCTGAGCACAAAGC
2703081 CGATAAGCAT
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
38 5 0.07
39 58 0.87
40 4 0.06
ACGTcount: A:0.30, C:0.19, G:0.29, T:0.22
Consensus pattern (39 bp):
AGGAGCTTGTGGTAAGGACTTACCCTGAGCACAAAGCAG
Found at i:2703097 original size:39 final size:39
Alignment explanation
Indices: 2702976--2703105 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 39
2702966 AAGGACTTGT
* * * * *
2702976 GGTAAGGACTTA-CCTTATGCACAAAGCAGAGGAGCCTGT
1 GGTAAGGACTTACCCTGA-GCACAAAGCCGAGAAGCATGC
* * * * *
2703015 GGTAAGGACTTACCTTGAGCACAAAGTCGAGGAGCTTGT
1 GGTAAGGACTTACCCTGAGCACAAAGCCGAGAAGCATGC
* *
2703054 GGTAAGGATTTACCCTGAGCACAAAGCCGATAAGCATGC
1 GGTAAGGACTTACCCTGAGCACAAAGCCGAGAAGCATGC
*
2703093 GGTAATGACTTAC
1 GGTAAGGACTTAC
2703106 AAGTCATAGA
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 73 0.96
40 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.22
Consensus pattern (39 bp):
GGTAAGGACTTACCCTGAGCACAAAGCCGAGAAGCATGC
Found at i:2708692 original size:39 final size:39
Alignment explanation
Indices: 2708648--2708804 Score: 106
Period size: 39 Copynumber: 4.0 Consensus size: 39
2708638 CTAGTAAGGG
* * * *
2708648 CCTTATACGCATAGCATAAGG-GCTTGCGGTAAGGACTTA
1 CCTTATACACAAAGCA-AAGGAGCCTACGGTAAGGACTTA
* *
2708687 CCTTATGCACAAAGCAGAGGAGCCTACGGTAAGGACTTA
1 CCTTATACACAAAGCAAAGGAGCCTACGGTAAGGACTTA
* * *** * *
2708726 CCCTGA-GCACAAAGTTGAGGAGCCTGCGATAAGGACTTA
1 -CCTTATACACAAAGCAAAGGAGCCTACGGTAAGGACTTA
* * *
2708765 CCTTGA-GCACAAAGTC-AAGGAGCTTGCGGTAAGGACTTA
1 CCTT-ATACACAAAG-CAAAGGAGCCTACGGTAAGGACTTA
2708804 C
1 C
2708805 AAGTCATAGA
Statistics
Matches: 98, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
38 6 0.06
39 88 0.90
40 4 0.04
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (39 bp):
CCTTATACACAAAGCAAAGGAGCCTACGGTAAGGACTTA
Found at i:2709496 original size:17 final size:18
Alignment explanation
Indices: 2709474--2709507 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2709464 TTTAAAAAGC
2709474 GTCAAC-GTCGATCAACA
1 GTCAACGGTCGATCAACA
*
2709491 GTCAACGGTCGGTCAAC
1 GTCAACGGTCGATCAAC
2709508 GATCAATGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (18 bp):
GTCAACGGTCGATCAACA
Found at i:2716642 original size:12 final size:12
Alignment explanation
Indices: 2716610--2716644 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
2716600 GCTTTCGACT
2716610 TTTTTTCTTTTA
1 TTTTTTCTTTTA
*
2716622 TTTTCTTCTTTTG
1 TTTT-TTCTTTTA
2716635 TTTTTTCTTT
1 TTTTTTCTTT
2716645 GAGTATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTTTCTTTTA
Found at i:2718716 original size:22 final size:22
Alignment explanation
Indices: 2718691--2718737 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
2718681 GCTATGAAAT
2718691 TGAAAAGTGAAAGTATTGAATA
1 TGAAAAGTGAAAGTATTGAATA
* *
2718713 TGAAATGTGAAAGTATTGATTA
1 TGAAAAGTGAAAGTATTGAATA
2718735 TGA
1 TGA
2718738 GAACTGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
TGAAAAGTGAAAGTATTGAATA
Found at i:2718745 original size:22 final size:22
Alignment explanation
Indices: 2718698--2718745 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2718688 AATTGAAAAG
*
2718698 TGAAAGTATTGAATATGAAATG
1 TGAAAGTATTGAATATGAAATC
*
2718720 TGAAAGTATTGATTATGAGAA-C
1 TGAAAGTATTGAATATGA-AATC
2718742 TGAA
1 TGAA
2718746 TATGTGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.44, C:0.02, G:0.23, T:0.31
Consensus pattern (22 bp):
TGAAAGTATTGAATATGAAATC
Found at i:2720769 original size:16 final size:16
Alignment explanation
Indices: 2720748--2720833 Score: 145
Period size: 16 Copynumber: 5.4 Consensus size: 16
2720738 GTATTACCCA
2720748 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
2720764 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
* *
2720780 ACTTGTTTTTAACCTG
1 ACCTGTTTTCAACCTG
2720796 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
*
2720812 ACCTGTTTTTAACCTG
1 ACCTGTTTTCAACCTG
2720828 ACCTGT
1 ACCTGT
2720834 AAATGATCCA
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 65 1.00
ACGTcount: A:0.19, C:0.28, G:0.13, T:0.41
Consensus pattern (16 bp):
ACCTGTTTTCAACCTG
Found at i:2721325 original size:27 final size:26
Alignment explanation
Indices: 2721268--2721327 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
2721258 GTGCTAGTCT
*
2721268 ATTTA-AATTAGGGTTTATGGTTTAA
1 ATTTAGAATTAGGGTTTATGATTTAA
*
2721293 AGTTTAGAATTAGGGTTTATGATTTAGG
1 A-TTTAGAATTAGGGTTTATGATTTA-A
2721321 ATTTAGA
1 ATTTAGA
2721328 GTTTTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 4 0.13
27 24 0.80
28 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (26 bp):
ATTTAGAATTAGGGTTTATGATTTAA
Found at i:2721428 original size:17 final size:17
Alignment explanation
Indices: 2721406--2721443 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
2721396 TAATTTACTT
2721406 TATATAGTTTATATATA-
1 TATATAG-TTATATATAC
2721423 TATATAGTTATATATAC
1 TATATAGTTATATATAC
2721440 TATA
1 TATA
2721444 CTTGGTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (17 bp):
TATATAGTTATATATAC
Found at i:2721847 original size:21 final size:21
Alignment explanation
Indices: 2721823--2721862 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2721813 TAGTATTTGT
2721823 GGTTTAA-AGTTTAGGGTTTAG
1 GGTTTAAGA-TTTAGGGTTTAG
*
2721844 GGTTTATGATTTAGGGTTT
1 GGTTTAAGATTTAGGGTTT
2721863 CTATAACTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (21 bp):
GGTTTAAGATTTAGGGTTTAG
Found at i:2721944 original size:2 final size:2
Alignment explanation
Indices: 2721939--2721984 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
2721929 TTATATAGTT
* *
2721939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA GTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
2721982 TA T
1 TA T
2721985 TACATGGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 38 0.97
3 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2722025 original size:13 final size:13
Alignment explanation
Indices: 2722007--2722033 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2721997 ACATACATAT
2722007 ATAAAATTATTTA
1 ATAAAATTATTTA
2722020 ATAAAATTATTTA
1 ATAAAATTATTTA
2722033 A
1 A
2722034 ATGTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:2723309 original size:15 final size:13
Alignment explanation
Indices: 2723272--2723298 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2723262 TACATATTAT
2723272 ATAAAATTATTTA
1 ATAAAATTATTTA
2723285 ATAAAATTATTTA
1 ATAAAATTATTTA
2723298 A
1 A
2723299 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:2723619 original size:21 final size:21
Alignment explanation
Indices: 2723590--2723654 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
2723580 AGTCTATTTA
* *
2723590 TTAGGGTTTATGATTTAGTGT
1 TTAGTGTTTATGATTTAGAGT
* *
2723611 TTAGTGTTTGTGATTTAAAGT
1 TTAGTGTTTATGATTTAGAGT
*
2723632 TTA-TGGTTTATGATTTAGGGT
1 TTAGT-GTTTATGATTTAGAGT
2723653 TT
1 TT
2723655 CTATAAAATA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (21 bp):
TTAGTGTTTATGATTTAGAGT
Found at i:2723705 original size:48 final size:50
Alignment explanation
Indices: 2723637--2723746 Score: 136
Period size: 48 Copynumber: 2.2 Consensus size: 50
2723627 AAAGTTTATG
* ** *
2723637 GTTTATGATTTAGGGTTTCTATAAAATATATATTTTA-TTACTTTATATA
1 GTTTATGATATAGGGTTTCTATAAAATATATAAGTAATTTACTTTATATA
* *
2723686 GTTTATG-TATAGTGTTTCTATAAACTATATAAGTAATTTACTTTATATA
1 GTTTATGATATAGGGTTTCTATAAAATATATAAGTAATTTACTTTATATA
2723735 GTTTTAT-ATATA
1 G-TTTATGATATA
2723747 ATATATAGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
48 23 0.44
49 20 0.38
50 9 0.17
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.52
Consensus pattern (50 bp):
GTTTATGATATAGGGTTTCTATAAAATATATAAGTAATTTACTTTATATA
Found at i:2723760 original size:18 final size:19
Alignment explanation
Indices: 2723729--2723764 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2723719 TAATTTACTT
2723729 TATATAGTTTTATATATAA
1 TATATAGTTTTATATATAA
2723748 TATATAG-TTTATATATA
1 TATATAGTTTTATATATA
2723765 CTAATGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
TATATAGTTTTATATATAA
Found at i:2723805 original size:13 final size:13
Alignment explanation
Indices: 2723787--2723813 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2723777 ATACATATAT
2723787 ATAAAATTATTTA
1 ATAAAATTATTTA
2723800 ATAAAATTATTTA
1 ATAAAATTATTTA
2723813 A
1 A
2723814 ATGTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATAAAATTATTTA
Found at i:2723823 original size:15 final size:14
Alignment explanation
Indices: 2723787--2723829 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
2723777 ATACATATAT
2723787 ATAAAATTATTT-A
1 ATAAAATTATTTAA
2723800 ATAAAATTATTTAA
1 ATAAAATTATTTAA
* *
2723814 ATGTAAATTATATAA
1 AT-AAAATTATTTAA
2723829 A
1 A
2723830 ACATGATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 12 0.46
14 3 0.12
15 11 0.42
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
ATAAAATTATTTAA
Found at i:2724069 original size:36 final size:38
Alignment explanation
Indices: 2724029--2724111 Score: 118
Period size: 36 Copynumber: 2.3 Consensus size: 38
2724019 TAAATTATGC
* * *
2724029 ATAGTATTTCTATAAACTATAT-AAGTAATTTACTT-T
1 ATAGTATATATATAAACTATATAAAGTAAATTACTTAT
2724065 ATAGTATATATATAAACTATATAAAGTAAATTACTTAT
1 ATAGTATATATATAAACTATATAAAGTAAATTACTTAT
2724103 ATAGT-TATA
1 ATAGTATATA
2724112 GAAACACTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 20 0.48
37 16 0.38
38 6 0.14
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (38 bp):
ATAGTATATATATAAACTATATAAAGTAAATTACTTAT
Found at i:2724121 original size:37 final size:36
Alignment explanation
Indices: 2724040--2724121 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 36
2724030 TAGTATTTCT
* *
2724040 ATAAACTATATAAGTAATTTACTTTATAGTATATAT
1 ATAAACTATATAAGTAAATTACTTTATAGTATATAG
2724076 ATAAACTATATAAAGTAAATTACTTATATAGT-TATAG
1 ATAAACTATAT-AAGTAAATTACTT-TATAGTATATAG
2724113 A-AACACTAT
1 ATAA-ACTAT
2724122 GATATTACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
36 13 0.32
37 22 0.54
38 6 0.15
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (36 bp):
ATAAACTATATAAGTAAATTACTTTATAGTATATAG
Found at i:2724519 original size:22 final size:24
Alignment explanation
Indices: 2724489--2724544 Score: 80
Period size: 22 Copynumber: 2.4 Consensus size: 24
2724479 ATGCATACAT
2724489 ATTATATAAAATTATTGAAT-AAA
1 ATTATATAAAATTATTGAATGAAA
* *
2724512 ATTA-ATAAAATTATTTAATGTAA
1 ATTATATAAAATTATTGAATGAAA
2724535 ATTATATAAA
1 ATTATATAAA
2724545 CATGATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 14 0.48
23 10 0.34
24 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
ATTATATAAAATTATTGAATGAAA
Found at i:2725030 original size:161 final size:163
Alignment explanation
Indices: 2724832--2725156 Score: 604
Period size: 161 Copynumber: 2.0 Consensus size: 163
2724822 ACCTGAACTC
2724832 AATCCGTATCCGATAACATCCGACCCTGAATTTTATCTGTCAATGATGTGACTCGATCTGAACGA
1 AATCCGTATCCGATAACATCCGACCCTGAATTTTATCTGTCAATGATGTGACTCGATCTGAACGA
2724897 GATCCGACTAAAGTC-A-CCGAACCTGAATTAACATGGGTATTTATCTGCTTCGGA-CTGAATTG
66 GATCCGACTAAAGTCAACCCGAACCTGAATTAACAT-GGTATTTATCTGCTTCGGACCTGAATTG
2724959 TTTTGACCTGAACTGAAATCGATCCGAACTGAAA
130 TTTTGACCTGAACTGAAATCGATCCGAACTGAAA
2724993 AATCCGTATCCGATAAACATCCGA-CCTGAATTTTATCTGTCAATGATGTGACTCGATCTGAACG
1 AATCCGTATCCGAT-AACATCCGACCCTGAATTTTATCTGTCAATGATGTGACTCGATCTGAACG
2725057 AGATCCGACTAAAGTCAACCCGAACCTGAATTAACATGGTATTTATCTGCTTCGGACCTGAATTG
65 AGATCCGACTAAAGTCAACCCGAACCTGAATTAACATGGTATTTATCTGCTTCGGACCTGAATTG
2725122 TTTTGACCTGAACTGAAATCGATCCGAACTGAAA
130 TTTTGACCTGAACTGAAATCGATCCGAACTGAAA
2725156 A
1 A
2725157 TGACCCGACC
Statistics
Matches: 160, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
161 70 0.44
162 29 0.18
163 61 0.38
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.28
Consensus pattern (163 bp):
AATCCGTATCCGATAACATCCGACCCTGAATTTTATCTGTCAATGATGTGACTCGATCTGAACGA
GATCCGACTAAAGTCAACCCGAACCTGAATTAACATGGTATTTATCTGCTTCGGACCTGAATTGT
TTTGACCTGAACTGAAATCGATCCGAACTGAAA
Found at i:2726141 original size:26 final size:28
Alignment explanation
Indices: 2726081--2726142 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
2726071 GAGTATTGCT
*
2726081 GAGCTCGACTCGACTCGAAAATTCTGCAA
1 GAGCTCGACTCGACTCGAAAACTCTGC-A
2726110 TGGAGCTCGACTCGACTCGAAAACTC-GC-
1 --GAGCTCGACTCGACTCGAAAACTCTGCA
2726138 GAGCT
1 GAGCT
2726143 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 2 0.07
31 23 0.77
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGCA
Found at i:2727691 original size:15 final size:16
Alignment explanation
Indices: 2727657--2727698 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
2727647 TAATATAAAA
* *
2727657 ATTAAAATATCATTTT
1 ATTAAAATATTATATT
2727673 ATTAAAATATTA-ATT
1 ATTAAAATATTATATT
2727688 ATTAAAATATT
1 ATTAAAATATT
2727699 TAAAATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTAAAATATTATATT
Found at i:2727698 original size:23 final size:23
Alignment explanation
Indices: 2727674--2727737 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 23
2727664 TATCATTTTA
2727674 TTAAAATATTAATTATTAAAATAT
1 TTAAAATA-TAATTATTAAAATAT
* *
2727698 TTAAAATATATTTATTAATAT-T
1 TTAAAATATAATTATTAAAATAT
2727720 TATAATAATATAA-TATTA
1 T-TAA-AATATAATTATTA
2727738 TATTTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 2 0.06
23 19 0.54
24 14 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAAATATAATTATTAAAATAT
Found at i:2727718 original size:36 final size:34
Alignment explanation
Indices: 2727640--2727719 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 34
2727630 TTTTATGAAT
2727640 TTAATATTAATATAAAAATTAAAATATCATTTTA
1 TTAATATTAATATAAAAATTAAAATATCATTTTA
2727674 TTAAAATATTAATTATTAAAATATTTAAAATAT-A-TTTA
1 TT--AATATTAA-TA-TAAAA-A-TTAAAATATCATTTTA
2727712 TTAATATT
1 TTAATATT
2727720 TATAATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
34 2 0.05
36 14 0.35
37 2 0.05
38 11 0.28
39 2 0.05
40 9 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (34 bp):
TTAATATTAATATAAAAATTAAAATATCATTTTA
Found at i:2727735 original size:38 final size:40
Alignment explanation
Indices: 2727637--2727736 Score: 107
Period size: 38 Copynumber: 2.5 Consensus size: 40
2727627 TTATTTTATG
* *
2727637 AATTTAATATTAATATAAAAATTAAAATATCATTTTATTAA
1 AATTT-ATATTAATATAATATTTAAAATATCATTTTATTAA
* *
2727678 AATATTA-ATTATTAAAATATTTAAAATAT-A-TTTATTAA
1 AAT-TTATATTAATATAATATTTAAAATATCATTTTATTAA
* *
2727716 TATTTATAATAATATAATATT
1 AATTTATATTAATATAATATT
2727737 ATATTTTTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
37 3 0.06
38 21 0.43
39 1 0.02
40 18 0.37
41 4 0.08
42 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (40 bp):
AATTTATATTAATATAATATTTAAAATATCATTTTATTAA
Found at i:2727738 original size:26 final size:24
Alignment explanation
Indices: 2727674--2727738 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 24
2727664 TATCATTTTA
2727674 TTAAAATAT-TAATTATTAAAATAT
1 TTAAAATATAT-ATTATTAAAATAT
*
2727698 TTAAAATATAT-TTATTAATAT-T
1 TTAAAATATATATTATTAAAATAT
2727720 TATAATAATATAATATTAT
1 T-TAA-AATAT-ATATTAT
2727739 ATTTTTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.06
23 12 0.34
24 14 0.40
25 3 0.09
26 4 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAAAATATATATTATTAAAATAT
Found at i:2727740 original size:22 final size:22
Alignment explanation
Indices: 2727694--2727761 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
2727684 AATTATTAAA
* *
2727694 ATATTTAAAAT-ATAT-TTATT
1 ATATTTATAATAATATAATATT
2727714 AATATTTATAATAATATAATATT
1 -ATATTTATAATAATATAATATT
* * * *
2727737 ATATTTTTTATATTATAATAAT
1 ATATTTATAATAATATAATATT
2727759 ATA
1 ATA
2727762 CTCAATTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
21 10 0.26
22 25 0.64
23 4 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTTATAATAATATAATATT
Found at i:2727770 original size:32 final size:32
Alignment explanation
Indices: 2727704--2727784 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
2727694 ATATTTAAAA
2727704 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTTATTAATATTTATAATAATATAATAT
* *
2727736 TATATTT-TTTATA-TTATAATAATATACTCAAT
1 TATATTTATTAATATTTATAATAATATAAT--AT
*
2727768 TATATTATAATAATATT
1 TATATT-TATTAATATT
2727785 ATTTTTTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
30 14 0.35
31 5 0.12
32 15 0.38
33 1 0.03
34 4 0.10
35 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAATATAATAT
Found at i:2727793 original size:23 final size:22
Alignment explanation
Indices: 2727728--2727793 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
2727718 TTTATAATAA
*
2727728 TATAATATTATATTTTTTATAT
1 TATAATAATATATTTTTTATAT
***
2727750 TATAATAATATACTCAATTATAT
1 TATAATAATATA-TTTTTTATAT
2727773 TATAATAATATTATTTTTTAT
1 TATAATAATA-TATTTTTTAT
2727794 TTTTTATTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
22 11 0.31
23 22 0.63
24 2 0.06
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (22 bp):
TATAATAATATATTTTTTATAT
Found at i:2727823 original size:48 final size:53
Alignment explanation
Indices: 2727719--2727823 Score: 130
Period size: 53 Copynumber: 2.1 Consensus size: 53
2727709 TTATTAATAT
* *
2727719 TTATAATAATATAATATTATATTTTTTATATTATAATAATATACTCAATTATA
1 TTATAATAATATAATATTATATTTTTTATATTAGAATAATATACTCAATTAAA
* * *
2727772 TTATAATAATATTATTTTTTATTTTTTAT-TT-GAATAATATA-T-AA-TAAA
1 TTATAATAATATAATATTATATTTTTTATATTAGAATAATATACTCAATTAAA
2727820 TTAT
1 TTAT
2727824 TCTTACATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
48 7 0.15
49 2 0.04
50 1 0.02
51 9 0.19
52 2 0.04
53 26 0.55
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (53 bp):
TTATAATAATATAATATTATATTTTTTATATTAGAATAATATACTCAATTAAA
Found at i:2727915 original size:27 final size:27
Alignment explanation
Indices: 2727835--2727915 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
2727825 CTTACATTTT
* *
2727835 ATATTATTTAT-TAATTTCATAGAAATA
1 ATATTATTTATAT-ATTTTATATAAATA
*
2727862 ATATTA-TTA-A-ATTATTAATAATGAATA
1 ATATTATTTATATATT-TT-AT-ATAAATA
*
2727889 ATATTATTTATATATTTTATATCAATA
1 ATATTATTTATATATTTTATATAAATA
2727916 TATAATAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
24 3 0.07
25 1 0.02
26 5 0.12
27 23 0.53
28 5 0.12
29 3 0.07
30 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
ATATTATTTATATATTTTATATAAATA
Found at i:2728155 original size:22 final size:22
Alignment explanation
Indices: 2728130--2728179 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
2728120 TATTTCAAAA
2728130 ATAATAATATTAAATTTTTATT
1 ATAATAATATTAAATTTTTATT
*
2728152 ATAAATAATATTAATTTTTTATT
1 AT-AATAATATTAAATTTTTATT
2728175 -TAATA
1 ATAATA
2728180 TTTTTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 4 0.15
22 3 0.12
23 19 0.73
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAATAATATTAAATTTTTATT
Found at i:2728552 original size:7 final size:7
Alignment explanation
Indices: 2728542--2728566 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2728532 TTTTTTAATA
2728542 ATTTATC
1 ATTTATC
2728549 ATTTATC
1 ATTTATC
2728556 ATTTATC
1 ATTTATC
2728563 ATTT
1 ATTT
2728567 TATAACATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTATC
Found at i:2732235 original size:24 final size:24
Alignment explanation
Indices: 2732191--2732236 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2732181 TCTTTCTCTT
* *
2732191 TCTCTTTCCCGTTCCATATCTCGC
1 TCTCTATCCCGTTCCAGATCTCGC
2732215 TCTCTATCCCGTTCTC-GATCTC
1 TCTCTATCCCGTTC-CAGATCTC
2732237 TTCTTCTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 18 0.95
25 1 0.05
ACGTcount: A:0.09, C:0.41, G:0.09, T:0.41
Consensus pattern (24 bp):
TCTCTATCCCGTTCCAGATCTCGC
Found at i:2732571 original size:51 final size:51
Alignment explanation
Indices: 2732495--2732591 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
2732485 CTTCTCTCCC
*
2732495 TTAACCTTTTTCTAAATTGTTCCCTATTCGCAACGTGTCATATTCATTCAT
1 TTAACCTTTTTCTAAATTATTCCCTATTCGCAACGTGTCATATTCATTCAT
2732546 TTAACCTTTTTCTAAATTATTCCCTATTCGCAACGTGTCATATTCA
1 TTAACCTTTTTCTAAATTATTCCCTATTCGCAACGTGTCATATTCA
2732592 AAGGTTAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.25, C:0.24, G:0.07, T:0.44
Consensus pattern (51 bp):
TTAACCTTTTTCTAAATTATTCCCTATTCGCAACGTGTCATATTCATTCAT
Found at i:2737441 original size:15 final size:14
Alignment explanation
Indices: 2737421--2737454 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
2737411 AATTTCATTA
2737421 TTATAAAATTATTTT
1 TTATAAAATT-TTTT
2737436 TTATAAAATTTTTT
1 TTATAAAATTTTTT
*
2737450 GTATA
1 TTATA
2737455 TATTATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
TTATAAAATTTTTT
Found at i:2737576 original size:23 final size:23
Alignment explanation
Indices: 2737547--2737682 Score: 229
Period size: 23 Copynumber: 5.9 Consensus size: 23
2737537 TTCTATAATC
2737547 AACAAACTCAAAAT-ATAACACCA
1 AACAAACTC-AAATCATAACACCA
*
2737570 AGCAAACTCAAATCATAACACCA
1 AACAAACTCAAATCATAACACCA
2737593 AACAAACTCAAATCATAACACCA
1 AACAAACTCAAATCATAACACCA
*
2737616 AACAAACTCAAATCATAACATCA
1 AACAAACTCAAATCATAACACCA
*
2737639 AACAAACTCAAATCATAACATCA
1 AACAAACTCAAATCATAACACCA
2737662 AACAAACTCAAATCATAACAC
1 AACAAACTCAAATCATAACAC
2737683 TTGTAATAAC
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
22 4 0.04
23 104 0.96
ACGTcount: A:0.57, C:0.28, G:0.01, T:0.15
Consensus pattern (23 bp):
AACAAACTCAAATCATAACACCA
Found at i:2739640 original size:18 final size:18
Alignment explanation
Indices: 2739597--2739641 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
2739587 CCATGAGAAA
2739597 CCGATGAGAGGAAGAGAG
1 CCGATGAGAGGAAGAGAG
* *
2739615 CC-ATTGAGGGGAATAGAG
1 CCGA-TGAGAGGAAGAGAG
2739633 CCGATGAGA
1 CCGATGAGA
2739642 AGAGCTGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.36, C:0.13, G:0.40, T:0.11
Consensus pattern (18 bp):
CCGATGAGAGGAAGAGAG
Found at i:2741372 original size:7 final size:7
Alignment explanation
Indices: 2741360--2741389 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
2741350 TCTAAAGTAT
2741360 TTTTTGC
1 TTTTTGC
2741367 TTTTTGC
1 TTTTTGC
2741374 TTTTTGC
1 TTTTTGC
2741381 TTTTTGC
1 TTTTTGC
2741388 TT
1 TT
2741390 AAAGTAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.13, G:0.13, T:0.73
Consensus pattern (7 bp):
TTTTTGC
Found at i:2745912 original size:14 final size:14
Alignment explanation
Indices: 2745895--2745921 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2745885 AGTCTATACT
2745895 AACTATATAATATG
1 AACTATATAATATG
2745909 AACTATATAATAT
1 AACTATATAATAT
2745922 ACTAATTATT
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:0.07, G:0.04, T:0.37
Consensus pattern (14 bp):
AACTATATAATATG
Found at i:2745925 original size:12 final size:13
Alignment explanation
Indices: 2745894--2745947 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 13
2745884 TAGTCTATAC
2745894 TAACTATATAATA
1 TAACTATATAATA
2745907 TGAACTATATAATA
1 T-AACTATATAATA
* *
2745921 T-ACTA-ATTATT
1 TAACTATATAATA
*
2745932 TAA-TATCTAATA
1 TAACTATATAATA
2745944 TAAC
1 TAAC
2745948 ATGCAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
11 7 0.22
12 11 0.34
13 1 0.03
14 13 0.41
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (13 bp):
TAACTATATAATA
Found at i:2747328 original size:16 final size:17
Alignment explanation
Indices: 2747308--2747384 Score: 72
Period size: 17 Copynumber: 4.6 Consensus size: 17
2747298 TTTTCACCTT
2747308 TTTTTCTTCTATTTTTC
1 TTTTTCTTCTATTTTTC
*
2747325 TTTTTCTTCT-CTTTTC
1 TTTTTCTTCTATTTTTC
*
2747341 TTTTTTCTGC-A--TTTC
1 -TTTTTCTTCTATTTTTC
*
2747356 TTTTTCTTCTTCTTTTTC
1 TTTTTCTTC-TATTTTTC
2747374 ATTTTTCTTCT
1 -TTTTTCTTCT
2747385 TCCAAACTGC
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
14 8 0.16
15 4 0.08
16 5 0.10
17 18 0.37
18 5 0.10
19 9 0.18
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (17 bp):
TTTTTCTTCTATTTTTC
Found at i:2747330 original size:6 final size:6
Alignment explanation
Indices: 2747319--2747382 Score: 51
Period size: 6 Copynumber: 10.3 Consensus size: 6
2747309 TTTTCTTCTA
* * *
2747319 TTTTTC TTTTTC -TTCTC -TTTTC TTTTTTC TGCATTTC TTTTTC TTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC T--TTTTC TTTTTC TTTTTC
2747368 TTTTTC ATTTTTC TT
1 TTTTTC -TTTTTC TT
2747383 CTTCCAAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
5 8 0.17
6 23 0.49
7 11 0.23
8 5 0.11
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (6 bp):
TTTTTC
Found at i:2747345 original size:34 final size:34
Alignment explanation
Indices: 2747307--2747384 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 34
2747297 GTTTTCACCT
2747307 TTTTTTCTTCTATTT-TTCTTT-TTCTTCTCTTTTC
1 TTTTTTCTTCTATTTCTT-TTTCTTCTTCT-TTTTC
*
2747341 TTTTTTCTGC-ATTTCTTTTTCTTCTTCTTTTTC
1 TTTTTTCTTCTATTTCTTTTTCTTCTTCTTTTTC
*
2747374 ATTTTTCTTCT
1 TTTTTTCTTCT
2747385 TCCAAACTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
33 20 0.53
34 18 0.47
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (34 bp):
TTTTTTCTTCTATTTCTTTTTCTTCTTCTTTTTC
Done.