Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 126 of 214
Found at i:38407861 original size:24 final size:24
Alignment explanation
Indices: 38407833--38407884 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38407823 TTAGTAAGTC
*
38407833 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
38407857 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
38407881 AAAT
1 AAAT
38407885 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:38409829 original size:24 final size:24
Alignment explanation
Indices: 38409802--38409853 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38409792 TTAGTAAGTC
*
38409802 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
38409826 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
38409850 AAAT
1 AAAT
38409854 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:38424534 original size:15 final size:15
Alignment explanation
Indices: 38424502--38424557 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
38424492 AATTCAGTAT
* **
38424502 TTAAGTTTTCAATGC
1 TTAATTTTTCAACAC
38424517 TTAATTTTTCAACAC
1 TTAATTTTTCAACAC
* * *
38424532 TTATTTTTTCAGCAT
1 TTAATTTTTCAACAC
38424547 TTAATTTTTCA
1 TTAATTTTTCA
38424558 GTTTATCAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.27, C:0.14, G:0.05, T:0.54
Consensus pattern (15 bp):
TTAATTTTTCAACAC
Found at i:38424558 original size:15 final size:15
Alignment explanation
Indices: 38424516--38424558 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
38424506 GTTTTCAATG
*
38424516 CTTAATTTTTCAACA
1 CTTAATTTTTCAGCA
*
38424531 CTTATTTTTTCAGCA
1 CTTAATTTTTCAGCA
*
38424546 TTTAATTTTTCAG
1 CTTAATTTTTCAG
38424559 TTTATCAAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (15 bp):
CTTAATTTTTCAGCA
Found at i:38425228 original size:30 final size:30
Alignment explanation
Indices: 38425187--38425257 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
38425177 TTTTCAGGAT
*
38425187 CCACACAGGCTGGACACATGCCCGTGTGAG
1 CCACACGGGCTGGACACATGCCCGTGTGAG
38425217 CCACACGGGCTGGACACATGCCCGTGTGAG
1 CCACACGGGCTGGACACATGCCCGTGTGAG
38425247 CCACACGGGCT
1 CCACACGGGCT
38425258 AGCCAGATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.21, C:0.35, G:0.31, T:0.13
Consensus pattern (30 bp):
CCACACGGGCTGGACACATGCCCGTGTGAG
Found at i:38425268 original size:30 final size:30
Alignment explanation
Indices: 38425187--38425274 Score: 122
Period size: 30 Copynumber: 2.9 Consensus size: 30
38425177 TTTTCAGGAT
* *
38425187 CCACACAGGCTGGACACATGCCCGTGTGAG
1 CCACACGGGCTAGACACATGCCCGTGTGAG
*
38425217 CCACACGGGCTGGACACATGCCCGTGTGAG
1 CCACACGGGCTAGACACATGCCCGTGTGAG
* * *
38425247 CCACACGGGCTAGCCAGATGCCCATGTG
1 CCACACGGGCTAGACACATGCCCGTGTG
38425275 CTAGCCCGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.22, C:0.34, G:0.31, T:0.14
Consensus pattern (30 bp):
CCACACGGGCTAGACACATGCCCGTGTGAG
Found at i:38427522 original size:23 final size:25
Alignment explanation
Indices: 38427494--38427552 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 25
38427484 TTTTCTTTAT
38427494 TTTATTTATTATTTGT--TATAT-TA
1 TTTATTTATTATTTGTACTA-ATCTA
38427517 TTTATTT-TTA-TTGTACTAATCTA
1 TTTATTTATTATTTGTACTAATCTA
38427540 TTT-TTTATTATTT
1 TTTATTTATTATTT
38427553 TATTACTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
21 4 0.13
22 8 0.26
23 17 0.55
24 2 0.06
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (25 bp):
TTTATTTATTATTTGTACTAATCTA
Found at i:38427703 original size:12 final size:11
Alignment explanation
Indices: 38427672--38427702 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
38427662 ATTAAGTTTA
38427672 TTTCTTTTCTT
1 TTTCTTTTCTT
38427683 TTTCGTTTTCTT
1 TTTC-TTTTCTT
38427695 TTTCTTTT
1 TTTCTTTT
38427703 TATCTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:38447756 original size:44 final size:44
Alignment explanation
Indices: 38447702--38447797 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
38447692 TTGAAGTCAC
* * *
38447702 AGTGGGGCAGACTGAGGAAG-TATATCTTATCTCCCTGAGGTACT
1 AGTGGAGCAGACTGAAGAAGATA-ATCCTATCTCCCTGAGGTACT
* ** **
38447746 AGTGGAGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGT
1 AGTGGAGCAGACTGAAGAAGATAATCCTATCTCCCTGAGGTACT
38447790 AGTGGAGC
1 AGTGGAGC
38447798 GGGTTAACGT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
44 41 0.95
45 2 0.05
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (44 bp):
AGTGGAGCAGACTGAAGAAGATAATCCTATCTCCCTGAGGTACT
Found at i:38466914 original size:18 final size:18
Alignment explanation
Indices: 38466891--38466939 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
38466881 TATACCTATA
38466891 TATATGTGTATGTATATG
1 TATATGTGTATGTATATG
*
38466909 TATATGTATATGTATATG
1 TATATGTGTATGTATATG
38466927 TATATGTGTATGT
1 TATATGTGTATGT
38466940 GTGTGCGTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (18 bp):
TATATGTGTATGTATATG
Found at i:38466941 original size:6 final size:6
Alignment explanation
Indices: 38466891--38466939 Score: 80
Period size: 6 Copynumber: 8.2 Consensus size: 6
38466881 TATACCTATA
* *
38466891 TATATG TGTATG TATATG TATATG TATATG TATATG TATATG TGTATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
38466939 T
1 T
38466940 GTGTGCGTGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:38468412 original size:32 final size:31
Alignment explanation
Indices: 38468367--38468437 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 31
38468357 AGTTACAAAA
***
38468367 TGGTCACCCAATTATTTTAGTTTTTCTTTTT
1 TGGTCACCCAATTATACGAGTTTTTCTTTTT
* *
38468398 TGAGTCACCTAATTATACGATTTTTTCTTTTT
1 TG-GTCACCCAATTATACGAGTTTTTCTTTTT
38468430 TGGTCACC
1 TGGTCACC
38468438 AACTATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 8 0.24
32 26 0.76
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.52
Consensus pattern (31 bp):
TGGTCACCCAATTATACGAGTTTTTCTTTTT
Found at i:38474670 original size:23 final size:24
Alignment explanation
Indices: 38474622--38474670 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
38474612 TTTGGGTATG
*
38474622 GAACTATAGGCATGTGATGTATTC
1 GAACTATAGGCATGTGATATATTC
*
38474646 GAAC-ATAGGTATGT-ATATATGTC
1 GAACTATAGGCATGTGATATAT-TC
38474669 GA
1 GA
38474671 TAAAGTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (24 bp):
GAACTATAGGCATGTGATATATTC
Found at i:38474746 original size:14 final size:14
Alignment explanation
Indices: 38474727--38474753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
38474717 ATGTTCGAAT
38474727 AGATATATATATAA
1 AGATATATATATAA
38474741 AGATATATATATA
1 AGATATATATATA
38474754 TTTATGTATC
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:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (14 bp):
AGATATATATATAA
Found at i:38475378 original size:41 final size:41
Alignment explanation
Indices: 38475329--38475519 Score: 310
Period size: 41 Copynumber: 4.6 Consensus size: 41
38475319 GATTATACGT
38475329 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
38475370 CTAGCAGGCTAAGTACCTGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
38475411 CTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * *
38475452 CTAGCAGGCTAAGTGCCAGTGATCTGAATTAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
38475493 CTAGCAGGCTAAGTGCCGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
38475520 TTAAATTAAG
Statistics
Matches: 138, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
41 133 0.96
42 5 0.04
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:38481617 original size:19 final size:18
Alignment explanation
Indices: 38481587--38481640 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
38481577 TTGAATCAAA
*
38481587 TTTTAAAATTTTAATAAGT
1 TTTTAAATTTTTAATAA-T
*
38481606 TTTTAAATTTTTTATTAAT
1 TTTTAAA-TTTTTAATAAT
*
38481625 TTTACAAATTTTTAAT
1 TTT-TAAATTTTTAAT
38481641 TGTTTATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTTAAATTTTTAATAAT
Found at i:38483641 original size:9 final size:9
Alignment explanation
Indices: 38483624--38483660 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
38483614 TGAGTTTTCG
38483624 AATTCGAAT
1 AATTCGAAT
*
38483633 AACTCGAAT
1 AATTCGAAT
38483642 AATTCGAAT
1 AATTCGAAT
38483651 AATTCGAAT
1 AATTCGAAT
38483660 A
1 A
38483661 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:38484079 original size:20 final size:20
Alignment explanation
Indices: 38484040--38484079 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
38484030 TTATTCCCCA
* * *
38484040 AAACTTTTTCTTTTCCCCCT
1 AAACTTTTACTTCTCACCCT
38484060 AAACTTTTACTTCTCACCCT
1 AAACTTTTACTTCTCACCCT
38484080 TTACTCTCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (20 bp):
AAACTTTTACTTCTCACCCT
Found at i:38486686 original size:4 final size:4
Alignment explanation
Indices: 38486677--38486716 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
38486667 TGGCATGTCA
38486677 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
38486717 CCATATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:38498773 original size:133 final size:133
Alignment explanation
Indices: 38498532--38499357 Score: 1244
Period size: 133 Copynumber: 6.2 Consensus size: 133
38498522 CATGTTTCAC
* *
38498532 AGATAACAGATCCTATCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * *
38498596 CATACTGGTGGCGAAGTATATCGAATAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
38498661 CGA
131 CGA
* * * *
38498664 AGATAGCAGATCCTGTCTTCCTATATCGGTAGCGAAGTGGATCGAATATGTAGATCTTGCCTTCC
1 AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
*
38498729 CATACTGGTGGCGAAGTAGATCGGAA-AAAACAGATCTTGGCTTCATGTATTGGCGTGAAGTAGA
66 CATACTGGTGGCGAAGTAGATC-GAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
38498793 TCGA
130 TCGA
* * **
38498797 AGATGGCAAATGATGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * * * *
38498862 CATATTGATGGAGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
38498927 CGA
131 CGA
*
38498930 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* *
38498995 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAATAGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
38499060 CGA
131 CGA
* * * * *
38499063 AGATAGCAGATCCTGTCTTCCTATATCGGCAGCGAAGTGGATCGAAGTTGTAAATCTTGTCTTCC
1 AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * *
38499128 CATACTGGTGGCGAAGTAGATTGGAA-AAAACAGATCTTGACTTCATGTATTGGCCTGAAGTAGA
66 CATACTGGTGGCGAAGTAGA-TCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
38499192 TCGA
130 TCGA
* *
38499196 AGATAGCAGATTCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCC
1 AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* ** *
38499261 CATATTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGAAGTGGAT
66 CATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
38499326 CGA
131 CGA
* * *
38499329 AAATAACAGATCCTGTCTTCTTATATTGG
1 AGATAGCAGATCCTGTCTTCCTATATTGG
38499358 CAGTGAGGCA
Statistics
Matches: 624, Mismatches: 65, Indels: 9
0.89 0.09 0.01
Matches are distributed among these distances:
132 35 0.06
133 582 0.93
134 7 0.01
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (133 bp):
AGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
CATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
CGA
Found at i:38499302 original size:399 final size:398
Alignment explanation
Indices: 38498532--38499357 Score: 1411
Period size: 399 Copynumber: 2.1 Consensus size: 398
38498522 CATGTTTCAC
*
38498532 AGATAACAGATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCC
* * *
38498597 ATACTGGTGGCGAAGTATATCGAATAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATC
66 ATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAATAGATC
* *
38498662 GAAGATAGCAGATCCTGTCTTCCTATATCGGTAGCGAAGTGGATCGAATATGTAGATCTTGCCTT
131 GAAGATAGCAGATCCTGTCTTCCTATATCGGCAGCGAAGTGGATCGAATATGTAAATCTTGCCTT
* *
38498727 CCCATACTGGTGGCGAAGTAGATCGGAAAAAACAGATCTTGGCTTCATGTATTGGCGTGAAGTAG
196 CCCATACTGGTGGCGAAGTAGATCGGAAAAAACAGATCTTGACTTCATGTATTGGCCTGAAGTAG
* *
38498792 ATCGAAGATGGCAAATGATGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGT
261 ATCGAAGATAGCAAATGATGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGT
38498857 CTTCCCATATTGATGGAGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAG
326 CTTCCCATATTGATGGAGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAG
38498922 TAGATCGA
391 TAGATCGA
38498930 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCC
*
38498995 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAATAGAT
65 CATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAATAGAT
*
38499060 CGAAGATAGCAGATCCTGTCTTCCTATATCGGCAGCGAAGTGGATCGAAGT-TGTAAATCTTGTC
130 CGAAGATAGCAGATCCTGTCTTCCTATATCGGCAGCGAAGTGGATCGAA-TATGTAAATCTTGCC
*
38499124 TTCCCATACTGGTGGCGAAGTAGATTGGAAAAAACAGATCTTGACTTCATGTATTGGCCTGAAGT
194 TTCCCATACTGGTGGCGAAGTAGATCGGAAAAAACAGATCTTGACTTCATGTATTGGCCTGAAGT
* **
38499189 AGATCGAAGATAGCAGATTCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATCTT
259 AGATCGAAGATAGCAAATGATGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATCTT
* * * * *
38499254 GTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGCGTGA
324 GTCTTCCCATATTGATGGAGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGA
*
38499319 AGTGGATCGA
389 AGTAGATCGA
* *
38499329 AAATAACAGATCCTGTCTTCTTATATTGG
1 AGATAACAGATCCTGTCTTCCTATATTGG
38499358 CAGTGAGGCA
Statistics
Matches: 402, Mismatches: 24, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
398 31 0.08
399 370 0.92
400 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.30
Consensus pattern (398 bp):
AGATAACAGATCCTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCC
ATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAATAGATC
GAAGATAGCAGATCCTGTCTTCCTATATCGGCAGCGAAGTGGATCGAATATGTAAATCTTGCCTT
CCCATACTGGTGGCGAAGTAGATCGGAAAAAACAGATCTTGACTTCATGTATTGGCCTGAAGTAG
ATCGAAGATAGCAAATGATGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGT
CTTCCCATATTGATGGAGAAGTAGATCAAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAG
TAGATCGA
Found at i:38510000 original size:20 final size:18
Alignment explanation
Indices: 38509953--38510001 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
38509943 ACAAGATAAA
38509953 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
38509970 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
38509990 ATTAAATTAATA
1 ATTAAATTAATA
38510002 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:38510047 original size:37 final size:37
Alignment explanation
Indices: 38509951--38510056 Score: 96
Period size: 37 Copynumber: 2.9 Consensus size: 37
38509941 CAACAAGATA
*
38509951 AAATTAAATTAA-ATTTAA-TATTAAGATAATCACTTT
1 AAATTAAATTAATATTAAACTATTAAGATAATCAC-TT
*
38509987 AATATTAAATTAATA-AAATACTATTAAGATAAGT-A-TT
1 AA-ATTAAATTAATATTAA-ACTATTAAGATAA-TCACTT
* *
38510024 AAATTAAATTTAATATTAAACTATCAAAATAAT
1 AAATTAAA-TTAATATTAAACTATTAAGATAAT
38510057 AATATTTTTG
Statistics
Matches: 58, Mismatches: 5, Indels: 14
0.75 0.06 0.18
Matches are distributed among these distances:
36 9 0.16
37 32 0.55
38 4 0.07
39 12 0.21
40 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.39
Consensus pattern (37 bp):
AAATTAAATTAATATTAAACTATTAAGATAATCACTT
Found at i:38511659 original size:16 final size:16
Alignment explanation
Indices: 38511638--38511668 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38511628 CTATACATGC
*
38511638 AAAATATAAAAGACAA
1 AAAATACAAAAGACAA
38511654 AAAATACAAAAGACA
1 AAAATACAAAAGACA
38511669 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAA
Found at i:38514459 original size:20 final size:19
Alignment explanation
Indices: 38514419--38514473 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
38514409 TAAAAAATGC
*
38514419 ATAATAAAATAAAAGATATAA
1 ATAA-AAAATAAAA-AAATAA
*
38514440 ATCCAAAAATAAAAAAATAA
1 AT-AAAAAATAAAAAAATAA
38514460 ATAAAAAATAAAAA
1 ATAAAAAATAAAAA
38514474 TAGGGCTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.37
20 7 0.23
21 11 0.37
22 1 0.03
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (19 bp):
ATAAAAAATAAAAAAATAA
Found at i:38514699 original size:13 final size:14
Alignment explanation
Indices: 38514674--38514702 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38514664 TTTAAATAAC
38514674 AATAAAGTAAAATA
1 AATAAAGTAAAATA
38514688 AATAAA-TAAAATA
1 AATAAAGTAAAATA
38514701 AA
1 AA
38514703 AACACTCGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAAGTAAAATA
Found at i:38515116 original size:20 final size:21
Alignment explanation
Indices: 38515093--38515144 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
38515083 AAATGCAATA
38515093 ATTAAATTAAAA-ACAAAAA-T
1 ATTAAATTAAAATA-AAAAATT
38515113 ATTAAAATTAAAATAAAAAATT
1 ATT-AAATTAAAATAAAAAATT
*
38515135 GTTAAATTAA
1 ATTAAATTAA
38515145 TAGAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.11
21 21 0.75
22 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
ATTAAATTAAAATAAAAAATT
Found at i:38518300 original size:23 final size:23
Alignment explanation
Indices: 38518261--38518305 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
38518251 AATTTAACTT
38518261 AAAAAATAAAAACT-AAATTAAC
1 AAAAAATAAAAACTAAAATTAAC
* *
38518283 AAAAATATAAATATTAAAATTAA
1 AAAAA-ATAAAAACTAAAATTAA
38518306 ATTTATGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 7 0.37
24 7 0.37
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (23 bp):
AAAAAATAAAAACTAAAATTAAC
Found at i:38519154 original size:26 final size:26
Alignment explanation
Indices: 38519094--38519154 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
38519084 GTTAAGTTAT
38519094 TATTATGACTATTCCTCTGTATGTCAA
1 TATT-TGACTATTCCTCTGTATGTCAA
*
38519121 -ATAATGACTATTCCTCTGTATGTCAA
1 TAT-TTGACTATTCCTCTGTATGTCAA
38519147 TATTTGAC
1 TATTTGAC
38519155 ATACATATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (26 bp):
TATTTGACTATTCCTCTGTATGTCAA
Found at i:38522783 original size:18 final size:18
Alignment explanation
Indices: 38522760--38522811 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
38522750 ATTTTATATG
*
38522760 AAAATCCCAGAATGATTT
1 AAAATCCCAGAAGGATTT
38522778 AAAATCCCAGAAGGATTT
1 AAAATCCCAGAAGGATTT
*
38522796 AAAATCCCTGAAGGAT
1 AAAATCCCAGAAGGAT
38522812 ATAGAGCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (18 bp):
AAAATCCCAGAAGGATTT
Found at i:38543831 original size:11 final size:11
Alignment explanation
Indices: 38543815--38543913 Score: 60
Period size: 11 Copynumber: 9.9 Consensus size: 11
38543805 TAAAAATATT
38543815 TATTTTAAAAA
1 TATTTTAAAAA
38543826 TATTTT--AAA
1 TATTTTAAAAA
38543835 -A--TTAAAAA
1 TATTTTAAAAA
* *
38543843 -A-ATTAAAAG
1 TATTTTAAAAA
38543852 TATTTTAAAAA
1 TATTTTAAAAA
38543863 TATTTT--AAA
1 TATTTTAAAAA
38543872 -A-TTTAAAAA
1 TATTTTAAAAA
*
38543881 -ATTTAAAAAAA
1 TATTT-TAAAAA
*
38543892 TTATTTTAAAAG
1 -TATTTTAAAAA
38543904 TATTTTAAAA
1 TATTTTAAAA
38543914 TTTAAAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 22
0.72 0.06 0.22
Matches are distributed among these distances:
6 2 0.03
7 3 0.04
8 6 0.08
9 16 0.23
10 3 0.04
11 33 0.46
12 4 0.06
13 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:38543879 original size:29 final size:30
Alignment explanation
Indices: 38543840--38543929 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 30
38543830 TTAAAATTAA
* *
38543840 AAAAATTAAAAGTATTT-TAAAAA-TATTTT
1 AAAAATTAAAA-AATTTAAAAAAATTATTTT
*
38543869 AAAATTTAAAAAATTTAAAAAAATTATTTT
1 AAAAATTAAAAAATTTAAAAAAATTATTTT
**
38543899 AAAAGTATTTTAAAATTTAAAAAAAATTATT
1 AAAA--ATTAAAAAATTT-AAAAAAATTATT
38543930 GTATTCCGGC
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
28 4 0.08
29 15 0.30
30 10 0.20
32 9 0.18
33 12 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAAATTAAAAAATTTAAAAAAATTATTTT
Found at i:38543909 original size:41 final size:41
Alignment explanation
Indices: 38543782--38543923 Score: 175
Period size: 41 Copynumber: 3.5 Consensus size: 41
38543772 ACCAAAAATT
* * *
38543782 TATTTTAAAAATTAAAACAAAAATAAAAATATTTATTTTAAAAA
1 TATTTT-AAAATTTAAA-AAAATTAAAAA-AATTATTTTAAAAA
*
38543826 TATTTTAAAA-TTAAAAAAATT---AAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAATTATTTTAAAAA
* *
38543863 TATTTTAAAATTTAAAAAATTTAAAAAAATTATTTTAAAAG
1 TATTTTAAAATTTAAAAAAATTAAAAAAATTATTTTAAAAA
38543904 TATTTTAAAATTTAAAAAAA
1 TATTTTAAAATTTAAAAAAA
38543924 ATTATTGTAT
Statistics
Matches: 86, Mismatches: 8, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
37 22 0.26
38 12 0.14
41 38 0.44
42 4 0.05
43 4 0.05
44 6 0.07
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (41 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAATTATTTTAAAAA
Found at i:38549753 original size:18 final size:18
Alignment explanation
Indices: 38549730--38549770 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38549720 ATGTGTATCA
*
38549730 ATAAATA-ATTTAAAAATT
1 ATAAATATA-TTAAAAAAT
38549748 ATAAATATATTAAAAAAT
1 ATAAATATATTAAAAAAT
38549766 ATAAA
1 ATAAA
38549771 ATACTTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAATATATTAAAAAAT
Found at i:38567655 original size:16 final size:16
Alignment explanation
Indices: 38567634--38567665 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38567624 GAGAAAAGGA
38567634 ACCTTAAGAAATTAGC
1 ACCTTAAGAAATTAGC
38567650 ACCTTAAGAAATTAGC
1 ACCTTAAGAAATTAGC
38567666 CTCGCGCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
ACCTTAAGAAATTAGC
Found at i:38572637 original size:21 final size:21
Alignment explanation
Indices: 38572598--38572638 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38572588 ATTCCTAAGA
**
38572598 TATGAATTGCATTGTATTGAG
1 TATGAATTGCATTAAATTGAG
*
38572619 TATGAATTGTATTAAATTGA
1 TATGAATTGCATTAAATTGA
38572639 TGTTAAATCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (21 bp):
TATGAATTGCATTAAATTGAG
Found at i:38573192 original size:25 final size:26
Alignment explanation
Indices: 38573085--38573187 Score: 106
Period size: 26 Copynumber: 4.0 Consensus size: 26
38573075 ACAGCTCTTA
*
38573085 TGAGCGTCTCGA-TATATGGCTCTTCG
1 TGAGCTTCTCGATTA-ATGGCTCTTCG
* * * *
38573111 TGAGTTTCTCGATTAAAGGTTCTTTG
1 TGAGCTTCTCGATTAATGGCTCTTCG
38573137 TGAGCTTC-CTGATTAATGGCTC-TC-
1 TGAGCTTCTC-GATTAATGGCTCTTCG
38573161 TGGAGCTTCTCGATTAATGGCTCTTCG
1 T-GAGCTTCTCGATTAATGGCTCTTCG
38573188 AAGCTACCCG
Statistics
Matches: 62, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
24 1 0.02
25 21 0.34
26 38 0.61
27 2 0.03
ACGTcount: A:0.17, C:0.20, G:0.24, T:0.39
Consensus pattern (26 bp):
TGAGCTTCTCGATTAATGGCTCTTCG
Found at i:38578303 original size:16 final size:16
Alignment explanation
Indices: 38578269--38578318 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
38578259 ATGACATCAG
38578269 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
38578285 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
38578301 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
38578317 TC
1 TC
38578319 CTGAGTATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 5 0.18
16 19 0.68
17 4 0.14
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:38578560 original size:40 final size:41
Alignment explanation
Indices: 38578511--38578614 Score: 138
Period size: 41 Copynumber: 2.6 Consensus size: 41
38578501 ACCAATTTGG
* * *
38578511 CACCTAGTGTCTCATCGGATAATTC-GAAGTAGTAAATTGA
1 CACCCAGTGTCTCATCGGATAAATCTGAAGCAGTAAATTGA
**
38578551 CACCCAGTGTCTCATCAAATAAATCTGAAGCAGTAAATTGA
1 CACCCAGTGTCTCATCGGATAAATCTGAAGCAGTAAATTGA
* *
38578592 CAGCCAGTGTCTCATCGGTTAAA
1 CACCCAGTGTCTCATCGGATAAA
38578615 CAGAAGTAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 21 0.39
41 33 0.61
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGGATAAATCTGAAGCAGTAAATTGA
Found at i:38579532 original size:4 final size:4
Alignment explanation
Indices: 38579515--38579600 Score: 70
Period size: 4 Copynumber: 20.8 Consensus size: 4
38579505 ACCCTAGCCT
* *
38579515 TTTC TTTC -TCC TTTC TTTC TTTC TTTTT TTTC TTTTC TTTC TTTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTTC -TTTC TTTC -TTTC TTTC
*
38579565 TTTCC TTTC -TT- TTTC ATTTTG TTTC TTTC TTTC TTT
1 TTT-C TTTC TTTC TTTC --TTTC TTTC TTTC TTTC TTT
38579601 ATTCGTTTAC
Statistics
Matches: 67, Mismatches: 6, Indels: 18
0.74 0.07 0.20
Matches are distributed among these distances:
3 6 0.09
4 43 0.64
5 15 0.22
6 3 0.04
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:38579548 original size:9 final size:9
Alignment explanation
Indices: 38579515--38579600 Score: 88
Period size: 9 Copynumber: 9.3 Consensus size: 9
38579505 ACCCTAGCCT
38579515 TTTCTTTCTCC
1 TTTCTTT-T-C
38579526 TTTC-TTTC
1 TTTCTTTTC
*
38579534 TTTCTTTTT
1 TTTCTTTTC
38579543 TTTCTTTTC
1 TTTCTTTTC
38579552 TTTCTTTTC
1 TTTCTTTTC
*
38579561 TTTCTTTCC
1 TTTCTTTTC
38579570 TTTCTTTTTC
1 TTTC-TTTTC
38579580 ATTT-TGTTTC
1 -TTTCT-TTTC
38579590 TTTC-TTTC
1 TTTCTTTTC
38579598 TTT
1 TTT
38579601 ATTCGTTTAC
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
8 12 0.18
9 37 0.56
10 10 0.15
11 7 0.11
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:38579594 original size:42 final size:42
Alignment explanation
Indices: 38579513--38579600 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
38579503 AAACCCTAGC
*
38579513 CTTTTCTTTCTCCTTTCTTTCTTTCTTTTTTTTCTTTTCTTT
1 CTTTTCTTTCTCCTTTCTTTCTTTCTTTTGTTTCTTTTCTTT
38579555 CTTTTCTTTCTTTCCTTTC-TT-TTTCATTTTGTTTC-TTTCTTT
1 CTTTTCTTTC--TCCTTTCTTTCTTTC-TTTTGTTTCTTTTCTTT
38579597 CTTT
1 CTTT
38579601 ATTCGTTTAC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
42 25 0.60
43 10 0.24
44 7 0.17
ACGTcount: A:0.01, C:0.23, G:0.01, T:0.75
Consensus pattern (42 bp):
CTTTTCTTTCTCCTTTCTTTCTTTCTTTTGTTTCTTTTCTTT
Found at i:38584342 original size:39 final size:39
Alignment explanation
Indices: 38584212--38584347 Score: 130
Period size: 39 Copynumber: 3.4 Consensus size: 39
38584202 CATTTGGACA
* * *
38584212 AAAAACGCCGGTAAAAATTAAGCATTAGCGGCGCTTTCTGG
1 AAAAACGCCGCTAAAAA-TGAGCATTAGCGGCG-TTTTTGG
* * * * **
38584253 -AAATCGCCACTAAAGATTGAGCATTAGTGGCGTTTTTAA
1 AAAAACGCCGCTAAA-AATGAGCATTAGCGGCGTTTTTGG
**
38584292 AAAAATACCGCTAAAAATGAGCATTAGCGGCGTTTTTGG
1 AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTGG
*
38584331 AAAAGCGCCGCTAAAAA
1 AAAAACGCCGCTAAAAA
38584348 CATTTTATCT
Statistics
Matches: 73, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
39 38 0.52
40 34 0.47
41 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.24
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATGAGCATTAGCGGCGTTTTTGG
Found at i:38584586 original size:22 final size:22
Alignment explanation
Indices: 38584561--38584635 Score: 75
Period size: 21 Copynumber: 3.5 Consensus size: 22
38584551 GAGTTACTGT
38584561 TTTAAGGTTTATGGAGTATGGA
1 TTTAAGGTTTATGGAGTATGGA
* * *
38584583 TTTAAGGATTATGGATTAGGGA
1 TTTAAGGTTTATGGAGTATGGA
* *
38584605 -TTATGGTTTAAGG-GT-TGAGA
1 TTTAAGGTTTATGGAGTATG-GA
38584625 TTTAAGGTTTA
1 TTTAAGGTTTA
38584636 GGGGTTAGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.02
20 3 0.07
21 19 0.45
22 19 0.45
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (22 bp):
TTTAAGGTTTATGGAGTATGGA
Found at i:38584607 original size:14 final size:15
Alignment explanation
Indices: 38584577--38584617 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
38584567 GTTTATGGAG
38584577 TATGGATTTAAGGAT
1 TATGGATTTAAGGAT
*
38584592 TATGGA-TTAGGGAT
1 TATGGATTTAAGGAT
38584606 TATGG-TTTAAGG
1 TATGGATTTAAGG
38584618 GTTGAGATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (15 bp):
TATGGATTTAAGGAT
Found at i:38584656 original size:22 final size:22
Alignment explanation
Indices: 38584630--38584692 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
38584620 TGAGATTTAA
*
38584630 GGTTTAGGGGTT-AGTGGTTAGG
1 GGTTTAGGGGTTAAG-AGTTAGG
38584652 GGTTTAGGGGTTAAGAGTTAGG
1 GGTTTAGGGGTTAAGAGTTAGG
* * *
38584674 GATTTAGGGTTTATGAGTT
1 GGTTTAGGGGTTAAGAGTT
38584693 CATGGGTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
22 34 0.94
23 2 0.06
ACGTcount: A:0.19, C:0.00, G:0.43, T:0.38
Consensus pattern (22 bp):
GGTTTAGGGGTTAAGAGTTAGG
Found at i:38584744 original size:12 final size:12
Alignment explanation
Indices: 38584723--38584765 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
38584713 TGGGTTTAGA
38584723 TTAA-TTATTTT
1 TTAATTTATTTT
38584734 TTAATTTATTTT
1 TTAATTTATTTT
* *
38584746 TAAATAT-TTTT
1 TTAATTTATTTT
38584757 TTAATTTAT
1 TTAATTTAT
38584766 ATATTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 13 0.50
12 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TTAATTTATTTT
Found at i:38584760 original size:23 final size:24
Alignment explanation
Indices: 38584722--38584775 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
38584712 TTGGGTTTAG
*
38584722 ATTAATTA-TTTTTTAATTTAT-T
1 ATTAAATATTTTTTTAATTTATAT
*
38584744 TTTAAATATTTTTTTAATTTATAT
1 ATTAAATATTTTTTTAATTTATAT
38584768 ATTAAATA
1 ATTAAATA
38584776 ATTTCATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 6 0.22
23 13 0.48
24 8 0.30
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTAAATATTTTTTTAATTTATAT
Found at i:38585022 original size:21 final size:20
Alignment explanation
Indices: 38584970--38585023 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
38584960 TAGGATTTAA
38584970 GGTTTAGGGATTAAGAATTAG
1 GGTTTAGGG-TTAAGAATTAG
* *
38584991 GGGTTATGGGTTAAGAGTTAG
1 GGTTTA-GGGTTAAGAATTAG
38585012 GGATTTAGGGTT
1 GG-TTTAGGGTT
38585024 TCAAGGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.26, C:0.00, G:0.39, T:0.35
Consensus pattern (20 bp):
GGTTTAGGGTTAAGAATTAG
Found at i:38589659 original size:42 final size:43
Alignment explanation
Indices: 38589541--38589785 Score: 314
Period size: 43 Copynumber: 5.7 Consensus size: 43
38589531 ATGGCACTTT
** * * * *
38589541 TAGCGGCGTTTGTGAAAAAAACGTCGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *** *
38589584 TAGCGGCGTTTATAAAAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* *
38589627 TAGCGGCGTTTGT-GTAAAAGTGCCGCTAAAGGTCCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
* * *
38589669 TAGCGGCGTTTGTGGGAAAAGTGTCGCTAAAGGTTCTGATCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
38589712 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCT-
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
*
38589754 TAGCGGCATTTGTGGGAAAAGCGCCGCTAAAG
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
38589786 TTAGCGACGC
Statistics
Matches: 182, Mismatches: 19, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
42 69 0.38
43 113 0.62
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGATCTA
Found at i:38589666 original size:85 final size:85
Alignment explanation
Indices: 38589541--38589785 Score: 314
Period size: 85 Copynumber: 2.9 Consensus size: 85
38589531 ATGGCACTTT
* * * * * ***
38589541 TAGCGGCGTTTGTGAAAAAAACGTCGCTAAAAGTCATGATCTATAGCGGCGTTTATAAAAAAAGC
1 TAGCGGCGTTTGTG-AAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
38589606 GCCGCTAAAGG-TCTTGATCTA
65 GCCGCTAAAGGTTC-TGATCTA
* * *
38589627 TAGCGGCGTTTGTGTAAAAGTGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGTG
1 TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCG
*
38589692 TCGCTAAAGGTTCTGATCTA
66 CCGCTAAAGGTTCTGATCTA
* * *
38589712 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTCT-TAGCGGCATTTGTGGGAAAAGC
1 TAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGC
38589776 GCCGCTAAAG
65 GCCGCTAAAG
38589786 TTAGCGACGC
Statistics
Matches: 139, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
85 98 0.71
86 41 0.29
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (85 bp):
TAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAAAAGCG
CCGCTAAAGGTTCTGATCTA
Found at i:38590735 original size:19 final size:19
Alignment explanation
Indices: 38590707--38590748 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
38590697 TAATGGACTT
38590707 TATAGGATAA-TTTATTGG
1 TATAGGATAATTTTATTGG
38590725 TATAGGGATAATTTTTATTGG
1 TATA-GGATAA-TTTTATTGG
38590746 TAT
1 TAT
38590749 TTTTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
21 11 0.52
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (19 bp):
TATAGGATAATTTTATTGG
Found at i:38591138 original size:5 final size:5
Alignment explanation
Indices: 38591128--38591153 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38591118 CTACATTGTA
38591128 ATTTT ATTTT ATTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT A
38591154 AAGTCTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:38593305 original size:49 final size:49
Alignment explanation
Indices: 38593248--38593352 Score: 149
Period size: 49 Copynumber: 2.1 Consensus size: 49
38593238 TCATGCGTTA
* * * *
38593248 TAATTTTATACAGTGTTGA-GTTTGTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTT-TGATTCATGATATTAAACTCAATTT
*
38593297 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
38593346 TAATTTT
1 TAATTTT
38593353 TTTTTTCTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
49 47 0.94
50 3 0.06
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:38594794 original size:110 final size:117
Alignment explanation
Indices: 38594675--38594940 Score: 336
Period size: 122 Copynumber: 2.3 Consensus size: 117
38594665 AATAAAGTAG
*
38594675 ATTA-TAAATTATAATTTAATAATAATTA-GTTAAATTATATTTTATATTATTATATATTATGA-
1 ATTATTAAATTATAATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGAT
*
38594737 TT-TTAGTAAATTCATA-TAAGAATA-A-GA-ATTTTATTAAATTATATATT
66 TTATTAGTAAATTCATATTAAGAATATATAACATTTTATTAAATTATATATT
* *
38594784 ATTATTAAATTAT-ATTTAATAATAATTATTTTAAATTATATTTTATAGTGTTATATATTATGAT
1 ATTATTAAATTATAATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGA-
38594848 TTTATTAGTAAATTCATATTTAAGAATATTTATTAATCATTTTATTAAATTATATATT
65 TTTATTAGTAAATTCATA-TTAAGAATA--TA-TAA-CATTTTATTAAATTATATATT
* * * *
38594906 TTTATTAAATTAT-ATTTTAGAACAATTATGTTAAA
1 ATTATTAAATTATAATTTAATAATAATTATGTTAAA
38594941 ATATGATTAA
Statistics
Matches: 134, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
109 19 0.14
110 39 0.29
112 2 0.01
113 14 0.10
115 8 0.06
118 1 0.01
120 1 0.01
122 50 0.37
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (117 bp):
ATTATTAAATTATAATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGAT
TTATTAGTAAATTCATATTAAGAATATATAACATTTTATTAAATTATATATT
Found at i:38594817 original size:26 final size:28
Alignment explanation
Indices: 38594763--38594826 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
38594753 TAAGAATAAG
* * *
38594763 AATTTTATTAAATTATATATTATTATTA
1 AATTATATTTAATAATATATTATTATTA
38594791 AATTATATTTAATAATA-ATTATT-TTA
1 AATTATATTTAATAATATATTATTATTA
38594817 AATTATATTT
1 AATTATATTT
38594827 TATAGTGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (28 bp):
AATTATATTTAATAATATATTATTATTA
Found at i:38595112 original size:39 final size:41
Alignment explanation
Indices: 38595067--38595172 Score: 135
Period size: 44 Copynumber: 2.5 Consensus size: 41
38595057 TTTCCTTATG
* *
38595067 CTATTACACCTCTATTCCATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
38595107 C-ATTACGCCTCTATTCCATTACATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTCTATT-C----CATTCAACCAAACAAAAGAATTAC
38595152 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
38595173 ACACCTCTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
39 13 0.23
40 2 0.04
41 4 0.07
44 19 0.33
45 5 0.09
46 14 0.25
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:38595147 original size:44 final size:46
Alignment explanation
Indices: 38595084--38595175 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
38595074 ACCTCTATTC
*
38595084 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
38595128 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
38595174 CA
1 CA
38595176 CCTCTATTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 19 0.42
45 4 0.09
46 22 0.49
ACGTcount: A:0.39, C:0.30, G:0.04, T:0.26
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
Found at i:38595179 original size:16 final size:16
Alignment explanation
Indices: 38595154--38595191 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
38595144 AGAATTACCT
*
38595154 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
38595170 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
38595186 ATTACA
1 ATTACA
38595192 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:38596136 original size:9 final size:9
Alignment explanation
Indices: 38596122--38596152 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38596112 GTTAAACGAA
38596122 TCGAGTTAT
1 TCGAGTTAT
*
38596131 TCGAGTTAA
1 TCGAGTTAT
38596140 TCGAGTTAT
1 TCGAGTTAT
38596149 TCGA
1 TCGA
38596153 ATCAACTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:38597190 original size:10 final size:10
Alignment explanation
Indices: 38597155--38597222 Score: 50
Period size: 10 Copynumber: 7.0 Consensus size: 10
38597145 ATATATGTAA
*
38597155 GTATGTATAT
1 GTATATATAT
* *
38597165 ATATACATAT
1 GTATATATAT
*
38597175 ATATATATAT
1 GTATATATAT
*
38597185 GTATATAAAT
1 GTATATATAT
**
38597195 -TA-GCATAT
1 GTATATATAT
38597203 GTATATATAT
1 GTATATATAT
*
38597213 GTATGTATAT
1 GTATATATAT
38597223 AAAACTTATG
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
8 3 0.07
9 4 0.09
10 37 0.84
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (10 bp):
GTATATATAT
Found at i:38599607 original size:29 final size:29
Alignment explanation
Indices: 38599561--38599616 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
38599551 TGTGACTTGT
*
38599561 TTTAATAGTACAAGGACTAAATTGATTCA
1 TTTAATAGTACAAAGACTAAATTGATTCA
* * *
38599590 TTTAGTAGTAGAAAGACTAATTTGATT
1 TTTAATAGTACAAAGACTAAATTGATT
38599617 AGGTCCATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (29 bp):
TTTAATAGTACAAAGACTAAATTGATTCA
Found at i:38599783 original size:18 final size:18
Alignment explanation
Indices: 38599760--38599796 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38599750 GGGAGAAGTT
38599760 AGAAAAATTGTTTAGGAG
1 AGAAAAATTGTTTAGGAG
38599778 AGAAAAATTGTTTAGGAG
1 AGAAAAATTGTTTAGGAG
38599796 A
1 A
38599797 ATCGAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.27, T:0.27
Consensus pattern (18 bp):
AGAAAAATTGTTTAGGAG
Found at i:38602974 original size:8 final size:8
Alignment explanation
Indices: 38602961--38602991 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
38602951 GTTTTATTAT
38602961 TATAATAA
1 TATAATAA
*
38602969 TATAATAT
1 TATAATAA
38602977 TATAATAA
1 TATAATAA
38602985 TATAATA
1 TATAATA
38602992 TAACAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TATAATAA
Found at i:38602979 original size:16 final size:16
Alignment explanation
Indices: 38602958--38602992 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
38602948 CTTGTTTTAT
38602958 TATTATAATAATATAA
1 TATTATAATAATATAA
38602974 TATTATAATAATATAA
1 TATTATAATAATATAA
38602990 TAT
1 TAT
38602993 AACAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TATTATAATAATATAA
Found at i:38602993 original size:13 final size:15
Alignment explanation
Indices: 38602958--38603001 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
38602948 CTTGTTTTAT
38602958 TATTATAATAATATAA
1 TATTATAATAATAT-A
38602974 TATTATAATAATATA
1 TATTATAATAATATA
*
38602989 -A-TATAACAATATA
1 TATTATAATAATATA
38603002 CTTATTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.41
14 1 0.04
15 1 0.04
16 14 0.52
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TATTATAATAATATA
Found at i:38610106 original size:21 final size:21
Alignment explanation
Indices: 38610073--38610112 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38610063 TTTGATTTTT
* *
38610073 TTCATGATGAAAATGCTGAAA
1 TTCAAGATCAAAATGCTGAAA
38610094 TTCAAGATCAAAATGCTGA
1 TTCAAGATCAAAATGCTGA
38610113 TGTGGCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.28
Consensus pattern (21 bp):
TTCAAGATCAAAATGCTGAAA
Found at i:38618068 original size:15 final size:15
Alignment explanation
Indices: 38618033--38618084 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
38618023 TTAAGAATTT
*
38618033 TATTAAATTAT-ATA
1 TATTTAATTATAATA
38618047 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
38618061 TATTTAATAATAAT-
1 TATTTAATTATAATA
38618075 TATGTTAATT
1 TAT-TTAATT
38618085 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:38618112 original size:120 final size:120
Alignment explanation
Indices: 38617971--38618200 Score: 460
Period size: 120 Copynumber: 1.9 Consensus size: 120
38617961 TTTGAGTAAA
38617971 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
38618036 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
38618091 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
1 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
38618156 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
66 TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
38618201 TAAATATGAT
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 110 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.50
Consensus pattern (120 bp):
TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTAT
TAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATT
Found at i:38618166 original size:61 final size:61
Alignment explanation
Indices: 38617981--38618168 Score: 208
Period size: 61 Copynumber: 3.1 Consensus size: 61
38617971 TTATAGTATC
38617981 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
* * * * * * * * * *
38618042 ATATATTTTAATTAT-AATATATTTA-ATAATAAT-TATG-TTAATTTA-TATTTTA-TAGTATC
1 ATATATTATGATT-TGAGTAAATTCATATAAGAATAT-TGATT-ATTAAGAATTTTATTA-AATT
38618101 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
38618162 ATATATT
1 ATATATT
38618169 TTAATTATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 20
0.71 0.15 0.15
Matches are distributed among these distances:
58 3 0.03
59 29 0.30
60 26 0.27
61 36 0.37
62 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
Found at i:38618183 original size:16 final size:16
Alignment explanation
Indices: 38618162--38618203 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
38618152 TTATTAAATT
*
38618162 ATATATTTTAATTATA
1 ATATATTTTAATAATA
38618178 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
38618193 AT-TATGTTTAA
1 ATATAT-TTTAA
38618204 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:38618188 original size:15 final size:15
Alignment explanation
Indices: 38618153--38618194 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
38618143 TTAAGAATTT
*
38618153 TATTAAATTAT-ATA
1 TATTTAATTATAATA
38618167 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
38618181 TATTTAATAATAAT
1 TATTTAATTATAAT
38618195 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:38618430 original size:45 final size:43
Alignment explanation
Indices: 38618330--38618439 Score: 120
Period size: 45 Copynumber: 2.6 Consensus size: 43
38618320 TTTTCCATTA
38618330 TGCTATTACACCTCTATT-C---CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
* * ***
38618369 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCA-TACATTCAACCAAACACAAGA-T
38618414 TGCTATTACACCTCTATTCCAATACA
1 TGCTATTACACCTCTATTCC-ATACA
38618440 CCTCTAATCC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 23 0.40
46 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (43 bp):
TGCTATTACACCTCTATTCCATACATTCAACCAAACACAAGAT
Found at i:38618441 original size:16 final size:16
Alignment explanation
Indices: 38618420--38618487 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
38618410 GATTTGCTAT
*
38618420 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
*
38618436 TACACCTCTAATCCAT
1 TACACCTCTAATCCAA
38618452 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
38618468 TACACCTTTAATCCAA
1 TACACCTCTAATCCAA
38618484 TACA
1 TACA
38618488 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:38621236 original size:32 final size:32
Alignment explanation
Indices: 38621197--38621261 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
38621187 TCGTGAAAAG
38621197 TATGTATGATTTTTATTTATTTGTTATTTAAC
1 TATGTATGATTTTTATTTATTTGTTATTTAAC
38621229 TATGTATGATTTTTATTTATTTGTTATTTAAC
1 TATGTATGATTTTTATTTATTTGTTATTTAAC
38621261 T
1 T
38621262 GTGAAAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.03, G:0.09, T:0.63
Consensus pattern (32 bp):
TATGTATGATTTTTATTTATTTGTTATTTAAC
Found at i:38623573 original size:30 final size:29
Alignment explanation
Indices: 38623537--38623602 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
38623527 GCCCAAATAT
38623537 TATGTTATAAAACAT-ATTATATTAATTATA
1 TATGTTATAAAA-ATAATTATATTAATT-TA
* *
38623567 TATGTTA-AATAATAATTATATTTATTTA
1 TATGTTATAAAAATAATTATATTAATTTA
38623595 TAT-TTATA
1 TATGTTATA
38623603 TTAAATCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
28 8 0.25
29 14 0.44
30 7 0.22
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (29 bp):
TATGTTATAAAAATAATTATATTAATTTA
Found at i:38627812 original size:18 final size:18
Alignment explanation
Indices: 38627785--38627820 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
38627775 TCCAAAAGAA
*
38627785 ATATAAATATAAACTTAT
1 ATATAAATATAAAATTAT
*
38627803 ATATATATATAAAATTAT
1 ATATAAATATAAAATTAT
38627821 TGGTTTTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATAAATATAAAATTAT
Found at i:38637474 original size:19 final size:20
Alignment explanation
Indices: 38637446--38637485 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
38637436 TTCTAAATTA
*
38637446 TTATCCACATGA-TTTAAAT
1 TTATCAACATGATTTTAAAT
*
38637465 TTATCAACATTATTTTAAAT
1 TTATCAACATGATTTTAAAT
38637485 T
1 T
38637486 CTTTTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATCAACATGATTTTAAAT
Found at i:38637799 original size:26 final size:27
Alignment explanation
Indices: 38637769--38637819 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
38637759 TAGAATTTGT
38637769 TTGTTATTC-ATCAT-TTGCTTTGTATA
1 TTGTTATTCAATCATATTG-TTTGTATA
38637795 TTGTTATTCAATCATATTGTTTGTA
1 TTGTTATTCAATCATATTGTTTGTA
38637820 GGAATTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.39
27 11 0.48
28 3 0.13
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (27 bp):
TTGTTATTCAATCATATTGTTTGTATA
Found at i:38641217 original size:19 final size:18
Alignment explanation
Indices: 38641193--38641238 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
38641183 ACGCTCTTTT
*
38641193 TGCATTCATTTCATGCATA
1 TGCATTCATGTCAT-CATA
38641212 TGCATTGCATGTCATCATA
1 TGCATT-CATGTCATCATA
38641231 TGCATTCA
1 TGCATTCA
38641239 AGATTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 2 0.08
19 16 0.64
20 7 0.28
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (18 bp):
TGCATTCATGTCATCATA
Found at i:38643760 original size:35 final size:35
Alignment explanation
Indices: 38643721--38643790 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
38643711 GCTCCATATA
*
38643721 TATAAATTTAACAACCGCATATCACC-ATGTACATT
1 TATAAATTCAACAACCGCATAT-ACCAATGTACATT
*
38643756 TATAAATTCAATAACCGCATATACCTAATGTACAT
1 TATAAATTCAACAACCGCATATACC-AATGTACAT
38643791 ATGCCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.10
35 20 0.65
36 8 0.26
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (35 bp):
TATAAATTCAACAACCGCATATACCAATGTACATT
Found at i:38644068 original size:41 final size:41
Alignment explanation
Indices: 38644012--38644114 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
38644002 TGATTCGATA
* * * *
38644012 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
* * *
38644053 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
*
38644094 CACCGGTATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
38644115 GCACATAGCC
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
Found at i:38644128 original size:41 final size:41
Alignment explanation
Indices: 38644050--38644129 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
38644040 GTCCGAAATG
** *
38644050 TTTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTA
1 TTTCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTA
* * *
38644091 TTTCACCGGTATTAAGCCTGCTAGGCACATAGCCTGAAT
1 TTTCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAAT
38644130 AACTGAGATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (41 bp):
TTTCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTA
Found at i:38644763 original size:21 final size:21
Alignment explanation
Indices: 38644737--38644780 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
38644727 TAAAATCAAC
*
38644737 TTCAGCTTGTAGAACATAAAA
1 TTCAGCTTATAGAACATAAAA
38644758 TTCAGCTTATAGAACATAAAA
1 TTCAGCTTATAGAACATAAAA
38644779 TT
1 TT
38644781 TGCTATTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (21 bp):
TTCAGCTTATAGAACATAAAA
Found at i:38651346 original size:35 final size:35
Alignment explanation
Indices: 38651307--38651376 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
38651297 GCTCCATACA
*
38651307 TATAAATTTAACAACCGCATATCACC-ATGTACATT
1 TATAAATTCAACAACCGCATAT-ACCAATGTACATT
*
38651342 TATAAATTCAATAACCGCATATACCTAATGTACAT
1 TATAAATTCAACAACCGCATATACC-AATGTACAT
38651377 ATGCCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 3 0.10
35 20 0.65
36 8 0.26
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.31
Consensus pattern (35 bp):
TATAAATTCAACAACCGCATATACCAATGTACATT
Found at i:38651681 original size:41 final size:41
Alignment explanation
Indices: 38651598--38651700 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 41
38651588 TGATTCGATA
* * * *
38651598 CACCGGCTTTTAGCCTGCTAGACCTATAGTCCGAAATGTTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
* * * *
38651639 CATCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTATTT
1 CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
38651680 CACCGGCATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
38651701 GCACATAGCC
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACCTAAAGTCCGAAATATTT
Found at i:38651714 original size:41 final size:41
Alignment explanation
Indices: 38651636--38651715 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
38651626 GTCCGAAATG
* ** *
38651636 TTTCATCGGCATTAAGCCTGCTAGACGTAAAGTCTGAATTA
1 TTTCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTA
* *
38651677 TTTCACCGGCATTAAGCCTGCTAGGCACATAGCCTGAAT
1 TTTCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAAT
38651716 AACTGAGATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (41 bp):
TTTCACCGGCATTAAGCCTGCTAGACACAAAGCCTGAATTA
Found at i:38651990 original size:12 final size:12
Alignment explanation
Indices: 38651973--38652003 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
38651963 TTCTAACCTC
38651973 TTATATATATAT
1 TTATATATATAT
38651985 TTATATATATAT
1 TTATATATATAT
38651997 TTCATAT
1 TT-ATAT
38652004 CTTTTCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 14 0.78
13 4 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATATATATAT
Found at i:38652351 original size:21 final size:21
Alignment explanation
Indices: 38652325--38652368 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
38652315 TAAAATCAAC
*
38652325 TTCAGCTTGTAGAACATAAAA
1 TTCAGCTTATAGAACATAAAA
38652346 TTCAGCTTATAGAACATAAAA
1 TTCAGCTTATAGAACATAAAA
38652367 TT
1 TT
38652369 TGCTATTAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (21 bp):
TTCAGCTTATAGAACATAAAA
Found at i:38660285 original size:44 final size:44
Alignment explanation
Indices: 38660222--38660312 Score: 146
Period size: 44 Copynumber: 2.1 Consensus size: 44
38660212 ATCGCATCAA
*
38660222 ATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAG
1 ATTGAAGCTAGAAATCTTATCTCCCGGAGATTACAGCGGAGCAG
* * *
38660266 ATTGAAGCTAGTAATCTTATCTCGCGGAGATTACAGTGGAGCAG
1 ATTGAAGCTAGAAATCTTATCTCCCGGAGATTACAGCGGAGCAG
38660310 ATT
1 ATT
38660313 AAAATAAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
ATTGAAGCTAGAAATCTTATCTCCCGGAGATTACAGCGGAGCAG
Found at i:38660344 original size:44 final size:44
Alignment explanation
Indices: 38660234--38660346 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
38660224 TGAAGCTAGA
* **
38660234 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAAATAGT
* *
38660278 AATCTTATCTCGCGGAGATTACAGTGGAGCAGATT-AAAATAAAG-
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAAAT--AGT
*
38660322 AATCTTATCTCTCTGA-AGTTACAGT
1 AATCTTATCTCCCTGAGA-TTACAGT
38660347 AGAGTTGATC
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 4 0.07
44 53 0.90
45 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAAATAGT
Found at i:38660493 original size:50 final size:50
Alignment explanation
Indices: 38660439--38660723 Score: 204
Period size: 50 Copynumber: 5.6 Consensus size: 50
38660429 GCAGTGGAGC
*
38660439 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * ** *
38660489 AGATTAAAGCTACAAT-AGCGAATCTTAC-TCCCCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCAC-ATCGGTGAATCTTACTTCCCC-GAC-ATTGCAGTTAAAA
* * * * *
38660539 AGATTAAAGCCAGATCGGTGAAT-TTCGCCTCTCCGACATTGCAGCTAAAA
1 AGATTAAAGCCACATCGGTGAATCTT-ACTTCCCCGACATTGCAGTTAAAA
* * *
38660589 GGATTAAAGCCATATCGGTGAATCTCACTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACATCGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * ** * * **
38660639 GGATTAAAGCTGCCAGAAAGGGGAATCTTACTT-CCCTAGCGGTGCAGTTAAAA
1 AGATTAAA---GCCACATCGGTGAATCTTACTTCCCCGA-CATTGCAGTTAAAA
* * *
38660692 AGATTGAAGCTACAAT-GGCGAATCTTACTTCC
1 AGATTAAAGCCAC-ATCGGTGAATCTTACTTCC
38660724 TAAAAGTTGC
Statistics
Matches: 181, Mismatches: 40, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
49 10 0.06
50 122 0.67
51 10 0.06
52 4 0.02
53 35 0.19
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACATCGGTGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:38660612 original size:100 final size:100
Alignment explanation
Indices: 38660428--38660622 Score: 252
Period size: 100 Copynumber: 1.9 Consensus size: 100
38660418 TCCCAAGCAG
* * *
38660428 TGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCCTCCCCGACATTGCAGCTAAAAAGAT
*
38660493 TAAAGCTACAATAGCGAATCTTAC-TCCCCAGGCGA
66 TAAAGC-ACAATAGCGAATCTCACTTCCCCAGGCGA
* * *
38660528 TGCAGTGGAACAGATTAAAGCCAGATCGGTGAAT-TTCGCCTCTCCGACATTGCAGCTAAAAGGA
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTT-GCCTCCCCGACATTGCAGCTAAAAAGA
* *
38660592 TTAAAGC-CATATCGGTGAATCTCACTTCCCC
65 TTAAAGCACA-AT-AGCGAATCTCACTTCCCC
38660623 GACATTGCAG
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
98 2 0.02
99 4 0.05
100 71 0.87
101 5 0.06
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (100 bp):
TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCCTCCCCGACATTGCAGCTAAAAAGAT
TAAAGCACAATAGCGAATCTCACTTCCCCAGGCGA
Found at i:38660644 original size:100 final size:99
Alignment explanation
Indices: 38660428--38660648 Score: 227
Period size: 100 Copynumber: 2.2 Consensus size: 99
38660418 TCCCAAGCAG
** * *
38660428 TGCAGTGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAAAAGATTAAAGCCACATCGGTGAATCTTGCCTCCCCGACATTGCAGCTAAAAAGAT
* *
38660493 TAAAGCTACAATAGCGAATCTTACTCCCCAGGCGA
66 TAAAGC-ACAATAGCGAATCTCACTCCCCAGACGA
* * * *
38660528 TGCAGTGGAACAGATTAAAGCCAGATCGGTGAAT-TTCGCCTCTCCGACATTGCAGCTAAAAGGA
1 TGCAGTGGAAAAGATTAAAGCCACATCGGTGAATCTT-GCCTCCCCGACATTGCAGCTAAAAAGA
* *
38660592 TTAAAGC-CATATCGGTGAATCTCACTTCCCC-GAC-A
65 TTAAAGCACA-AT-AGCGAATCTCAC-TCCCCAGACGA
*
38660627 TTGCAGT-TAAAAGGATTAAAGC
1 -TGCAGTGGAAAA-GATTAAAGC
38660649 TGCCAGAAAG
Statistics
Matches: 103, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
98 2 0.02
99 8 0.08
100 88 0.85
101 5 0.05
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (99 bp):
TGCAGTGGAAAAGATTAAAGCCACATCGGTGAATCTTGCCTCCCCGACATTGCAGCTAAAAAGAT
TAAAGCACAATAGCGAATCTCACTCCCCAGACGA
Found at i:38662556 original size:19 final size:20
Alignment explanation
Indices: 38662528--38662567 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
38662518 TTCTAAATTA
*
38662528 TTATCCACATGA-TTTAAAT
1 TTATCAACATGATTTTAAAT
*
38662547 TTATCAACATTATTTTAAAT
1 TTATCAACATGATTTTAAAT
38662567 T
1 T
38662568 CTTTTTACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.03, T:0.47
Consensus pattern (20 bp):
TTATCAACATGATTTTAAAT
Found at i:38662879 original size:26 final size:27
Alignment explanation
Indices: 38662849--38662899 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
38662839 TAGAATTTGT
38662849 TTGTTATTC-ATCAT-TTGCTTTGTATA
1 TTGTTATTCAATCATATTG-TTTGTATA
38662875 TTGTTATTCAATCATATTGTTTGTA
1 TTGTTATTCAATCATATTGTTTGTA
38662900 AGAATTGCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 9 0.39
27 11 0.48
28 3 0.13
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (27 bp):
TTGTTATTCAATCATATTGTTTGTATA
Found at i:38673472 original size:51 final size:51
Alignment explanation
Indices: 38673396--38673559 Score: 283
Period size: 51 Copynumber: 3.2 Consensus size: 51
38673386 CTAATCAATG
38673396 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
* *
38673447 ACAAGTGATTAGTGGTTGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
* * *
38673498 ACAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGGGACAAGTG
1 ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
38673549 ACAAGTGATAA
1 ACAAGTGATAA
38673560 ATGTGATCCG
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 105 1.00
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (51 bp):
ACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTA
Found at i:38674470 original size:155 final size:156
Alignment explanation
Indices: 38674187--38674499 Score: 556
Period size: 155 Copynumber: 2.0 Consensus size: 156
38674177 CTATTCCGGT
38674187 GTTGGATACGGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGATA
1 GTTGGATACGGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGATA
* *
38674252 TGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAATCCTGATAATGCTCTGTAACCCT
66 TGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAACCCTGATAATGCTCTATAACCCT
*
38674317 GTTTTGGTAACAGACACGGGTTAGGG
131 GTTTCGGTAACAGACACGGGTTAGGG
*
38674343 GTTGGATACGGGTAAGGGGTGTTACAATATATGA-TTTTTATAAGTTTTATTATGAATATTGATA
1 GTTGGATACGGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGATA
*
38674407 TGTAATGAAACATTTGAAATTTCTATCTGATTGATCTGTAAACCCTGATAATGCTCTATAACCCT
66 TGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAACCCTGATAATGCTCTATAACCCT
* *
38674472 GTTTCGGTAACATATACGGGTTAGGG
131 GTTTCGGTAACAGACACGGGTTAGGG
38674498 GT
1 GT
38674500 GTTACAGGGA
Statistics
Matches: 150, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
155 117 0.78
156 33 0.22
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (156 bp):
GTTGGATACGGATAAGGGGTGTTACAATATATGATTTTTTATAAGTTTTATTATGAATATTGATA
TGTAATGAAACATTTGAAATTTCTATCTGATTGATCCGTAAACCCTGATAATGCTCTATAACCCT
GTTTCGGTAACAGACACGGGTTAGGG
Found at i:38675465 original size:20 final size:20
Alignment explanation
Indices: 38675434--38675545 Score: 68
Period size: 20 Copynumber: 5.6 Consensus size: 20
38675424 AGTACCGAAT
*
38675434 TACAAACAGGGGCACATATG
1 TACAATCAGGGGCACATATG
* *
38675454 TGCAATCAGGGGTATCGA-A-G
1 TACAATCAGGGGCA-C-ATATG
* *
38675474 TACAAACAGGGGCACGTATG
1 TACAATCAGGGGCACATATG
* * *
38675494 TACAATAAGGGGTA-TTGATG
1 TACAATCAGGGGCACAT-ATG
* * *
38675514 TACAAACAGGGGCACGTATA
1 TACAATCAGGGGCACATATG
*
38675534 TGCAATCAGGGG
1 TACAATCAGGGG
38675546 TACCGAAGTA
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
19 3 0.04
20 61 0.90
21 3 0.04
22 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (20 bp):
TACAATCAGGGGCACATATG
Found at i:38675487 original size:40 final size:40
Alignment explanation
Indices: 38675398--38675661 Score: 350
Period size: 40 Copynumber: 6.6 Consensus size: 40
38675388 GTCGAGGTAT
* * * * *
38675398 AAACAGGGGCACGAAAGTGCATTCA-GAGTACCGAATTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* *
38675437 AAACAGGGGCACATATGTGCAATCAGGGGTATCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* * ** *
38675477 AAACAGGGGCACGTATGTACAATAAGGGGTATTGATGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
*
38675517 AAACAGGGGCACGTATATGCAATCAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* * *
38675557 AAACAGGGGCATGTATGTGTAATTAGGGGTACCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
* * *
38675597 AAACAAGGTCACGTATGTGCAATCAGGGGTACCGGAGTAC
1 AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
38675637 AAACAGGGGCACGTATGTGCAATCA
1 AAACAGGGGCACGTATGTGCAATCA
38675662 TACAATAATT
Statistics
Matches: 194, Mismatches: 30, Indels: 1
0.86 0.13 0.00
Matches are distributed among these distances:
39 21 0.11
40 173 0.89
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (40 bp):
AAACAGGGGCACGTATGTGCAATCAGGGGTACCGAAGTAC
Found at i:38676928 original size:25 final size:25
Alignment explanation
Indices: 38676894--38676946 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
38676884 AAATAATTTC
38676894 TAAAATTAAATATAACAATTAATAA
1 TAAAATTAAATATAACAATTAATAA
* *
38676919 TAAATTTAAATATAATAATTAATAA
1 TAAAATTAAATATAACAATTAATAA
38676944 TAA
1 TAA
38676947 GTTTTCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (25 bp):
TAAAATTAAATATAACAATTAATAA
Found at i:38676942 original size:12 final size:12
Alignment explanation
Indices: 38676894--38676940 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
38676884 AAATAATTTC
38676894 TAAAATTAAATA
1 TAAAATTAAATA
38676906 TAACAATT-AATAA
1 TAA-AATTAAAT-A
*
38676919 TAAATTTAAATA
1 TAAAATTAAATA
38676931 TAATAATTAA
1 TAA-AATTAA
38676941 TAATAAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
12 13 0.45
13 16 0.55
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAAATTAAATA
Found at i:38682739 original size:21 final size:21
Alignment explanation
Indices: 38682713--38682753 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38682703 AGACGAGCAA
* *
38682713 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
38682734 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
38682754 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:38693062 original size:18 final size:19
Alignment explanation
Indices: 38693035--38693090 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
38693025 TTTTTTTTCA
*
38693035 AAAAAATTAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
38693054 -AAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
38693072 AAAAATTTTAAA-ATTTAT
1 AAAAATTTAAAATATTTAT
38693090 A
1 A
38693091 TTTTAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
17 4 0.12
18 19 0.58
19 10 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:38693085 original size:27 final size:24
Alignment explanation
Indices: 38693041--38693118 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 24
38693031 TTCAAAAAAA
38693041 TTAAAATAATTTTAAAATTTAAAATAT
1 TTAAAA-AATTTTAAAATTT-AAAT-T
*
38693068 TTATAAAAATTTTAAAATTTATATT
1 TTA-AAAAATTTTAAAATTTAAATT
38693093 TTAAAAAATTTTTAAAAATTGTAAAT
1 TTAAAAAA-TTTT-AAAATT-TAAAT
38693119 AATATATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
24 5 0.11
25 8 0.18
26 9 0.20
27 20 0.44
28 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (24 bp):
TTAAAAAATTTTAAAATTTAAATT
Found at i:38693125 original size:34 final size:34
Alignment explanation
Indices: 38693058--38693126 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
38693048 AATTTTAAAA
* * *
38693058 TTTAAAATATTTATAAAAATTTTAAAATTTATAT
1 TTTAAAAAATTTATAAAAATTGTAAAATATATAT
*
38693092 TTTAAAAAATTTTTAAAAATTGTAAATAATATATA
1 TTTAAAAAATTTATAAAAATTGT-AA-AATATATA
38693127 AAAAAAAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 20 0.69
35 2 0.07
36 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTAAAAAATTTATAAAAATTGTAAAATATATAT
Found at i:38694048 original size:31 final size:31
Alignment explanation
Indices: 38694011--38694074 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
38694001 TTGTAAAATG
* *
38694011 GTCACTGAACTATTCAAAAG-TTTTCATTTAA
1 GTCACTGAACTATACAAAAGCTCTT-ATTTAA
*
38694042 GTCACTGAATTATACAAAAGCTCTTATTTAA
1 GTCACTGAACTATACAAAAGCTCTTATTTAA
38694073 GT
1 GT
38694075 AGTTGGGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (31 bp):
GTCACTGAACTATACAAAAGCTCTTATTTAA
Found at i:38696669 original size:13 final size:15
Alignment explanation
Indices: 38696643--38696674 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
38696633 ATGTAATTTT
38696643 TTTTCTTTATTTTCC
1 TTTTCTTTATTTTCC
38696658 TTTTC-TTA-TTTCC
1 TTTTCTTTATTTTCC
38696671 TTTT
1 TTTT
38696675 GTTTTAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 3 0.18
15 5 0.29
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCTTTATTTTCC
Found at i:38697710 original size:30 final size:31
Alignment explanation
Indices: 38697671--38697730 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
38697661 GGAGGTGGAT
*
38697671 TGGGAAGGGAATAAAAGTTTTAGGG-GAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGAGAAAAG
*
38697702 TGGG-AGGGAGTAAAAATTTTGGGAGAAAA
1 TGGGAAGGGAATAAAAATTTTGGGAGAAAA
38697731 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGAGAAAAG
Found at i:38698040 original size:9 final size:9
Alignment explanation
Indices: 38698023--38698053 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
38698013 TCGAGTTGAT
38698023 TCGAATAAC
1 TCGAATAAC
*
38698032 TCGATTAAC
1 TCGAATAAC
38698041 TCGAATAAC
1 TCGAATAAC
38698050 TCGA
1 TCGA
38698054 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:38701168 original size:4 final size:4
Alignment explanation
Indices: 38701159--38701203 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
38701149 AATTAAAACT
38701159 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C
38701204 CTTGGGAGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:38703183 original size:182 final size:179
Alignment explanation
Indices: 38702988--38703335 Score: 493
Period size: 181 Copynumber: 1.9 Consensus size: 179
38702978 AAAAAATTCA
* * *
38702988 AATTTGAATATTCGAATCAATCGATTCAAACTCAAATTCGATCTCATCCAATTTGATCATTAAAA
1 AATTTGAATATTCGAATCAATCAATTCAAACTCAAATTC-ACCCCATCCAATTTGATCATTAAAA
** * *
38703053 AACTCAAACCACCTGACCTTAAA-TCCAAATTGAATTAAATTTGGATTAACTTGAACATAAAGTG
65 AACTCAAACCACCCAACCCTAAACT-CAAATTGAATTAAATTT-GAATAACTTGAACATAAAGTG
*
38703117 AGTAAAACTTGAACTGATTCGAACTTC-TTAATGACCCAATTTGGAAATATCTG
128 AGTAAAACCTGAACTGATTCGAAC--CATTAATGACCCAATTTGGAAATATCTG
* * *
38703170 AATTTGAATATTCGAATCGATCAATTCAAACTCCAATTCACCCCATCCTATTTGATCATTAAAAA
1 AATTTGAATATTCGAATCAATCAATTCAAACTCAAATTCACCCCATCCAATTTGATCATTAAAAA
* * * * *
38703235 TCTCAAACCACCCAACCCTAAACTCAAATTGAATTGAATTTGAATAACTTGAACGTGAAGTGATT
66 ACTCAAACCACCCAACCCTAAACTCAAATTGAATTAAATTTGAATAACTTGAACATAAAGTGAGT
38703300 AAAACCTGAACTGATTCGAACCATTAATGACCCAAT
131 AAAACCTGAACTGATTCGAACCATTAATGACCCAAT
38703336 CCAAAAAAAC
Statistics
Matches: 148, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
178 1 0.01
179 13 0.09
180 40 0.27
181 57 0.39
182 37 0.25
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (179 bp):
AATTTGAATATTCGAATCAATCAATTCAAACTCAAATTCACCCCATCCAATTTGATCATTAAAAA
ACTCAAACCACCCAACCCTAAACTCAAATTGAATTAAATTTGAATAACTTGAACATAAAGTGAGT
AAAACCTGAACTGATTCGAACCATTAATGACCCAATTTGGAAATATCTG
Found at i:38708928 original size:30 final size:32
Alignment explanation
Indices: 38708857--38708932 Score: 95
Period size: 30 Copynumber: 2.5 Consensus size: 32
38708847 GTAGCACTAA
38708857 ACATCTTTAAATTATAATTTTTATTCTAAATT
1 ACATCTTTAAATTATAATTTTTATTCTAAATT
** *
38708889 -GGTCTTTAAATT-TAATTTTTTTTCT-AATT
1 ACATCTTTAAATTATAATTTTTATTCTAAATT
*
38708918 ACATCATTAAATTAT
1 ACATCTTTAAATTAT
38708933 CGATGTTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 4 0.11
30 21 0.58
31 11 0.31
ACGTcount: A:0.34, C:0.09, G:0.03, T:0.54
Consensus pattern (32 bp):
ACATCTTTAAATTATAATTTTTATTCTAAATT
Found at i:38709918 original size:41 final size:41
Alignment explanation
Indices: 38709861--38710015 Score: 197
Period size: 41 Copynumber: 3.8 Consensus size: 41
38709851 GAGTTTTTGG
* *
38709861 GGTCTTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATTCTCA
1 GGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* * *
38709902 GGTCTTTAGCAGCGTTTTTTAATAAGCGCCGCTAATGCTCA
1 GGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
* * *
38709943 GGTCTTTAGCGGCGTTTTTTAATAAGCGCTGCTAATGCTC-
1 GGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
*
38709983 -GTACCTTTAGCGGCGTTTTTGAGGAAGCGCCGC
1 GGT--CTTTAGCGGCGTTTTTGAAGAAGCGCCGC
38710016 AAAAACATTT
Statistics
Matches: 101, Mismatches: 11, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
39 2 0.02
41 99 0.98
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (41 bp):
GGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCA
Found at i:38710160 original size:26 final size:26
Alignment explanation
Indices: 38710112--38710162 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
38710102 AAAATGGATA
** * *
38710112 AATTTGAAATAATGACACGTAGAAAT
1 AATTTGAAATAAAAAAACATAGAAAT
38710138 AATTTGAAATAAAAAAACATAGAAA
1 AATTTGAAATAAAAAAACATAGAAA
38710163 AATATTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAAAT
Found at i:38710608 original size:20 final size:21
Alignment explanation
Indices: 38710574--38710612 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38710564 TAAATAATAT
38710574 TTAGGGGTTAGGGATTTAGTG
1 TTAGGGGTTAGGGATTTAGTG
*
38710595 TTAGGGTTTA-GGATTTAG
1 TTAGGGGTTAGGGATTTAG
38710613 ATTAATTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (21 bp):
TTAGGGGTTAGGGATTTAGTG
Found at i:38710630 original size:80 final size:76
Alignment explanation
Indices: 38710510--38710663 Score: 209
Period size: 80 Copynumber: 2.0 Consensus size: 76
38710500 GGATTCGGTG
*
38710510 TTAGGTTAGAGTTTAGGGTTTAGACTAATTAATATATTTTAAATTATATAATATTAAATAATATT
1 TTAGGTTAGAGTTTAGGATTTAGACTAATTAATATATTTT-AATT-TAT-ATATTAAATAATATT
38710575 TAGGGGTTAGGGAT
63 TAGGGGTTAGGGAT
* * * * * *
38710589 TTAGTGTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTA
1 TTAG-GTTAGAGTTTAGGATTTAGACTAATTAATATATTTTAATTTATATATTAAATAATATTTA
38710654 GGGGTTAGGG
65 GGGGTTAGGG
38710664 GTTAGTGATT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
77 26 0.39
78 3 0.04
79 8 0.12
80 30 0.45
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (76 bp):
TTAGGTTAGAGTTTAGGATTTAGACTAATTAATATATTTTAATTTATATATTAAATAATATTTAG
GGGTTAGGGAT
Found at i:38710752 original size:87 final size:89
Alignment explanation
Indices: 38710594--38710842 Score: 439
Period size: 87 Copynumber: 2.8 Consensus size: 89
38710584 GGGATTTAGT
*
38710594 GTTAGGGTTTAGGATTTAGATTAATTAGTGTTTTTTAATTTATATATTAAATAATGTTTAGGGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGGT
38710659 TAGGGGTTAGTGATTCGGGGTCGA
66 TAGGGGTTAGTGATTCGGGGTCGA
38710683 GTTAGGGTTTAGGATTTAGATT-ATTAGTATTTTTTAATTTATATATT-AATAATGTTTAGGGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGGT
*
38710746 TAGGGGTTAGTGATTCGGGGTTGA
66 TAGGGGTTAGTGATTCGGGGTCGA
* *
38710770 GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTTAATTTATATATTAAATAATGTTTAAGGT
1 GTTAGGGTTTAGGATTTAGATTAATTAGTA-TTTTTTAATTTATATATTAAATAATGTTTAGGGG
38710835 TTAGGGGT
65 TTAGGGGT
38710843 AGGGGTTTAG
Statistics
Matches: 153, Mismatches: 4, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
87 61 0.40
88 31 0.20
89 40 0.26
90 21 0.14
ACGTcount: A:0.27, C:0.01, G:0.26, T:0.46
Consensus pattern (89 bp):
GTTAGGGTTTAGGATTTAGATTAATTAGTATTTTTTAATTTATATATTAAATAATGTTTAGGGGT
TAGGGGTTAGTGATTCGGGGTCGA
Found at i:38710887 original size:15 final size:14
Alignment explanation
Indices: 38710854--38710900 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
38710844 GGGGTTTAGA
38710854 GTTTAG-GATTAAG
1 GTTTAGAGATTAAG
*
38710867 AG-TTAGTGATTTAAG
1 -GTTTAGAGA-TTAAG
38710882 GTTTAGAGATTAAG
1 GTTTAGAGATTAAG
38710896 GTTTA
1 GTTTA
38710901 AGCTCAGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 4 0.14
14 14 0.48
15 11 0.38
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (14 bp):
GTTTAGAGATTAAG
Found at i:38711557 original size:21 final size:20
Alignment explanation
Indices: 38711518--38711561 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
38711508 GGACAAGACC
38711518 AAAATATAAGAAAAAATAAA
1 AAAATATAAGAAAAAATAAA
38711538 AAAATATAA-AAAGGAAATAAA
1 AAAATATAAGAAA--AAATAAA
38711559 AAA
1 AAA
38711562 GTAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (20 bp):
AAAATATAAGAAAAAATAAA
Done.