Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009617.1 Hibiscus syriacus cultivar Beakdansim tig00117005_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: 3386631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 16
Found at i:2653281 original size:20 final size:20
Alignment explanation
Indices: 2653256--2653303 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2653246 CTGGGGAACA
2653256 ACCATTCGCCTTGGCAGTAT
1 ACCATTCGCCTTGGCAGTAT
2653276 ACCATTCGCCTTGGCAGTAT
1 ACCATTCGCCTTGGCAGTAT
2653296 ACCATTCG
1 ACCATTCG
2653304 TCTGAATTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.21, C:0.31, G:0.19, T:0.29
Consensus pattern (20 bp):
ACCATTCGCCTTGGCAGTAT
Found at i:2653810 original size:11 final size:11
Alignment explanation
Indices: 2653794--2653836 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
2653784 AAAGAATATA
2653794 CTTTCTTCATT
1 CTTTCTTCATT
2653805 CTTTCTT-ATAT
1 CTTTCTTCAT-T
2653816 -TTTCTTCATT
1 CTTTCTTCATT
*
2653826 CTTTCTGCATT
1 CTTTCTTCATT
2653837 ATTCAACATG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.12, C:0.23, G:0.02, T:0.63
Consensus pattern (11 bp):
CTTTCTTCATT
Found at i:2653819 original size:21 final size:21
Alignment explanation
Indices: 2653790--2653831 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2653780 GAATAAAGAA
2653790 TATACTTTCTTCATTCTTTCT
1 TATACTTTCTTCATTCTTTCT
*
2653811 TATATTTTCTTCATTCTTTCT
1 TATACTTTCTTCATTCTTTCT
2653832 GCATTATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (21 bp):
TATACTTTCTTCATTCTTTCT
Found at i:2658860 original size:169 final size:170
Alignment explanation
Indices: 2658581--2658919 Score: 671
Period size: 169 Copynumber: 2.0 Consensus size: 170
2658571 TACCTCTTCA
2658581 TATTTCAATTTCTCAGTTAACAGTGATTGTTACTATGTATTTTGAATTGTGCATGTTTTATCATT
1 TATTTCAATTTCTCAGTTAACAGTGATTGTTACTATGTATTTTGAATTGTGCATGTTTTATCATT
2658646 CTAAAAAGAATGTTAAATTTGTCACATTATTCCATATATATGGAATTTGAATGTTTATCCCTCTA
66 CTAAAAAGAATGTTAAATTTGTCACATTATTCCATATATATGGAATTTGAATGTTTATCCCTCTA
2658711 CAATTTTTGTGTAAGTTTATGTAACTGTTTGTG-GTATTG
131 CAATTTTTGTGTAAGTTTATGTAACTGTTTGTGTGTATTG
2658750 TATTTCAATTTCTCAGTTAACAGTGATTGTTACTATGTATTTTGAATTGTGCATGTTTTATCATT
1 TATTTCAATTTCTCAGTTAACAGTGATTGTTACTATGTATTTTGAATTGTGCATGTTTTATCATT
2658815 CTAAAAAGAATGTTAAATTTGTCACATTATTCCATATATATGGAATTTGAATGTTTATCCCTCTA
66 CTAAAAAGAATGTTAAATTTGTCACATTATTCCATATATATGGAATTTGAATGTTTATCCCTCTA
2658880 CAATTTTTGTGTAAGTTTATGTAACTGTTTGTGTGTATTG
131 CAATTTTTGTGTAAGTTTATGTAACTGTTTGTGTGTATTG
2658920 ATGCAGATGA
Statistics
Matches: 169, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 163 0.96
170 6 0.04
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.47
Consensus pattern (170 bp):
TATTTCAATTTCTCAGTTAACAGTGATTGTTACTATGTATTTTGAATTGTGCATGTTTTATCATT
CTAAAAAGAATGTTAAATTTGTCACATTATTCCATATATATGGAATTTGAATGTTTATCCCTCTA
CAATTTTTGTGTAAGTTTATGTAACTGTTTGTGTGTATTG
Found at i:2659377 original size:85 final size:85
Alignment explanation
Indices: 2659282--2659439 Score: 271
Period size: 85 Copynumber: 1.9 Consensus size: 85
2659272 ACGACACATG
* *
2659282 AATGTGTGTCATTTTTATTTATGACGGGGGCTTCAATGACACGCAATATAAGTCATAAATGCGTG
1 AATGTGTGTCATATTTATTTATGACGGGGGCTTCAATGACACGCAATATAAGTCATAAATGCGCG
2659347 TCATAAATTTATGACATACA
66 TCATAAATTTATGACATACA
* * *
2659367 AATGTGTGTCATATTTATTTATGATGGGGGCTTCAATGACGCGCAATGTAAGTCATAAATGCGCG
1 AATGTGTGTCATATTTATTTATGACGGGGGCTTCAATGACACGCAATATAAGTCATAAATGCGCG
2659432 TCATAAAT
66 TCATAAAT
2659440 GCGTGTCATA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.34
Consensus pattern (85 bp):
AATGTGTGTCATATTTATTTATGACGGGGGCTTCAATGACACGCAATATAAGTCATAAATGCGCG
TCATAAATTTATGACATACA
Found at i:2659434 original size:13 final size:13
Alignment explanation
Indices: 2659418--2659452 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
2659408 CGCAATGTAA
2659418 GTCATAAATGCGC
1 GTCATAAATGCGC
*
2659431 GTCATAAATGCGT
1 GTCATAAATGCGC
2659444 GTCATAAAT
1 GTCATAAAT
2659453 TTATGACCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:2662466 original size:21 final size:21
Alignment explanation
Indices: 2662440--2662484 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2662430 GATTTCTGGG
* *
2662440 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2662461 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2662482 CAA
1 CAA
2662485 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2663334 original size:2 final size:2
Alignment explanation
Indices: 2663327--2663374 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2663317 ATAAATAGAG
2663327 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
*
2663369 AG AT AT
1 AT AT AT
2663375 GAAATGAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2664281 original size:149 final size:149
Alignment explanation
Indices: 2664100--2664405 Score: 576
Period size: 149 Copynumber: 2.1 Consensus size: 149
2664090 GAGTCGAGGG
2664100 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
2664165 ACTTGACCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGACCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
2664230 TATGGCACTACGGTGCAAT
131 TATGGCACTACAGTGCAAT
*
2664249 TCTACGCGGTCCTTCGGGATATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
2664314 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGACCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2664379 TATGGCACTACAGTGCAAT
131 TATGGCACTACAGTGCAAT
2664398 TCTACGCG
1 TCTACGCG
2664406 ACACTTCGGT
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGACCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACAGTGCAAT
Found at i:2681769 original size:44 final size:44
Alignment explanation
Indices: 2681700--2681830 Score: 208
Period size: 44 Copynumber: 3.0 Consensus size: 44
2681690 AAATTATACG
**
2681700 TCAATAATATCTTTAACTTTTTTGTTCGTTAACTAACAATCTTA
1 TCAATAATATCTTTAACTTCATTGTTCGTTAACTAACAATCTTA
* *
2681744 TCGATAATATCTTTAACTTCATTGTTAGTTAACTAACAATCTTA
1 TCAATAATATCTTTAACTTCATTGTTCGTTAACTAACAATCTTA
* *
2681788 TCAATAATATCTTTAACTTCATTTTTCGTTAACCAACAATCTT
1 TCAATAATATCTTTAACTTCATTGTTCGTTAACTAACAATCTT
2681831 GCACACCAAG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 79 1.00
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.45
Consensus pattern (44 bp):
TCAATAATATCTTTAACTTCATTGTTCGTTAACTAACAATCTTA
Found at i:2682089 original size:21 final size:20
Alignment explanation
Indices: 2682048--2682086 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2682038 AAAATACTTA
* *
2682048 TGTCTTTGTGACATGTTTTC
1 TGTCTTTATGACACGTTTTC
2682068 TGTCTTTATGACACGTTTT
1 TGTCTTTATGACACGTTTT
2682087 TCTCTGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.15, G:0.18, T:0.54
Consensus pattern (20 bp):
TGTCTTTATGACACGTTTTC
Found at i:2683141 original size:19 final size:20
Alignment explanation
Indices: 2683117--2683157 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2683107 TTGAGTTAGA
2683117 AAAAATAG-TTAATTAATAT
1 AAAAATAGTTTAATTAATAT
*
2683136 AAAAATAGTTTATTTAATAT
1 AAAAATAGTTTAATTAATAT
2683156 AA
1 AA
2683158 TAAAAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAAATAGTTTAATTAATAT
Found at i:2683409 original size:14 final size:14
Alignment explanation
Indices: 2683390--2683417 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2683380 CGCTGGGCAT
2683390 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2683404 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2683418 AAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:2683436 original size:44 final size:46
Alignment explanation
Indices: 2683386--2683486 Score: 161
Period size: 44 Copynumber: 2.2 Consensus size: 46
2683376 AACACGCTGG
2683386 GCATCCGAGGCCATCCGACCGAGGCCATCCGAA-AGC-ATCCGAGA
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACAGCTATCCGAGA
* *
2683430 GCATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGCTATGCGAGG
1 GCATCCGAGGCCATCCGACCGAGGCCATCCGAAC-AGCTATCCGAGA
2683477 GCATCCGAGG
1 GCATCCGAGG
2683487 GAAACCGAGC
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
44 33 0.63
46 3 0.06
47 16 0.31
ACGTcount: A:0.25, C:0.35, G:0.31, T:0.10
Consensus pattern (46 bp):
GCATCCGAGGCCATCCGACCGAGGCCATCCGAACAGCTATCCGAGA
Found at i:2683444 original size:20 final size:22
Alignment explanation
Indices: 2683385--2683461 Score: 79
Period size: 24 Copynumber: 3.4 Consensus size: 22
2683375 CAACACGCTG
2683385 GGCATCCGAGGCCATCCGACCGA
1 GGCATCCGAGGCCATCCGA-CGA
*
2683408 GGCCATCCGAAAG-CATCCGA-GA
1 GG-CATCCG-AGGCCATCCGACGA
2683430 -GCATCCGAGGCCATCCGACCGA
1 GGCATCCGAGGCCATCCGA-CGA
2683452 GGCCATCCGA
1 GG-CATCCGA
2683462 ACGAGCTATG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
19 2 0.04
20 13 0.29
21 1 0.02
22 4 0.09
23 3 0.07
24 20 0.44
25 2 0.04
ACGTcount: A:0.25, C:0.38, G:0.29, T:0.09
Consensus pattern (22 bp):
GGCATCCGAGGCCATCCGACGA
Found at i:2683453 original size:14 final size:14
Alignment explanation
Indices: 2683434--2683466 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2683424 CCGAGAGCAT
2683434 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
2683448 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
2683462 ACGAG
1 CCGAG
2683467 CTATGCGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.06
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:2683500 original size:33 final size:33
Alignment explanation
Indices: 2683458--2683532 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
2683448 CCGAGGCCAT
* *
2683458 CCGAACGAGCTATGCGAGGGCATCCGAGGGAAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAA
*
2683491 CCGAGCGAGCTATGCGAGGGAATCCGAGGGCAA
1 CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAA
2683524 CCGAGCGAG
1 CCGAGCGAG
2683533 GGTAGGTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.25, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGCGAGCTATGCGAGGGAATCCGAGGGAAA
Found at i:2683594 original size:33 final size:33
Alignment explanation
Indices: 2683542--2683604 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
2683532 GGGTAGGTCG
*
2683542 CCCTCAGATTCCCTCGCATAGCTCGCTCGGTTT
1 CCCTCAGATGCCCTCGCATAGCTCGCTCGGTTT
* * *
2683575 CCCTCGGATGCCCTTGCATAGCTCGTTCGG
1 CCCTCAGATGCCCTCGCATAGCTCGCTCGG
2683605 ATGGCCTCGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.11, C:0.38, G:0.22, T:0.29
Consensus pattern (33 bp):
CCCTCAGATGCCCTCGCATAGCTCGCTCGGTTT
Found at i:2683613 original size:33 final size:33
Alignment explanation
Indices: 2683541--2683614 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
2683531 AGGGTAGGTC
* * *
2683541 GCCCTCAGATTCCCTCGCATAGCTCGCTCGGTT
1 GCCCTCGGATGCCCTCGCATAGCTCGCTCGGAT
* * *
2683574 TCCCTCGGATGCCCTTGCATAGCTCGTTCGGAT
1 GCCCTCGGATGCCCTCGCATAGCTCGCTCGGAT
*
2683607 GGCCTCGG
1 GCCCTCGG
2683615 TCGGATGGCC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.11, C:0.36, G:0.26, T:0.27
Consensus pattern (33 bp):
GCCCTCGGATGCCCTCGCATAGCTCGCTCGGAT
Found at i:2683618 original size:14 final size:14
Alignment explanation
Indices: 2683596--2683642 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
2683586 CCTTGCATAG
*
2683596 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
2683610 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
2683624 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
2683638 CTCGG
1 CTCGG
2683643 ATGCTCTCGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.06, C:0.30, G:0.40, T:0.23
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:2683654 original size:20 final size:20
Alignment explanation
Indices: 2683629--2683682 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
2683619 ATGGCCTCGG
2683629 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
2683649 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
2683669 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
2683683 TCGGATGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:2683688 original size:14 final size:14
Alignment explanation
Indices: 2683669--2683696 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2683659 TCGGATGCTT
2683669 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
2683683 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
2683697 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:2683699 original size:10 final size:10
Alignment explanation
Indices: 2683629--2683682 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
2683619 ATGGCCTCGG
2683629 TCGGATGGCC
1 TCGGATGGCC
2683639 TCGGAT-GCTC
1 TCGGATGGC-C
2683649 TCGGATGGCC
1 TCGGATGGCC
*
2683659 TCGGAT-GCTT
1 TCGGATGGC-C
2683669 TCGGATGGCC
1 TCGGATGGCC
2683679 TCGG
1 TCGG
2683683 TCGGATGGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:2683871 original size:113 final size:113
Alignment explanation
Indices: 2683673--2683880 Score: 380
Period size: 113 Copynumber: 1.8 Consensus size: 113
2683663 ATGCTTTCGG
*
2683673 ATGGCCTCGGTCGGATGGCCTCGGATGCCCAGCGTGTTGGGACGTGCATGGAACATGCAATCTCT
1 ATGGCCTCGGTCGAATGGCCTCGGATGCCCAGCGTGTTGGGACGTGCATGGAACATGCAATCTCT
2683738 TGTAGATCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGAAGGC
66 TGTAGATCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGAAGGC
**
2683786 ATGGCCTCGGTCGAATGGCCTCGGATGCCCAGCGTGTTGGGACGTGCATGTCACATGCAATCTCT
1 ATGGCCTCGGTCGAATGGCCTCGGATGCCCAGCGTGTTGGGACGTGCATGGAACATGCAATCTCT
*
2683851 TGTAGCTCGCCGGGAAGACATGGCGACCTA
66 TGTAGATCGCCGGGAAGACATGGCGACCTA
2683881 CGGCCAACAT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 91 1.00
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (113 bp):
ATGGCCTCGGTCGAATGGCCTCGGATGCCCAGCGTGTTGGGACGTGCATGGAACATGCAATCTCT
TGTAGATCGCCGGGAAGACATGGCGACCTAGTAGGTCGCCCGGAAGGC
Found at i:2685588 original size:87 final size:87
Alignment explanation
Indices: 2685442--2685616 Score: 341
Period size: 87 Copynumber: 2.0 Consensus size: 87
2685432 TTTTCCATTT
*
2685442 TTTCTTTAACATATTATATTAAATTTAACTTTTTTTCCTAAATAATGAGGATGCATTTGACCCCT
1 TTTCTTTAACATATTATACTAAATTTAACTTTTTTTCCTAAATAATGAGGATGCATTTGACCCCT
2685507 AGGGGCTTAGTGCATCCGCCCC
66 AGGGGCTTAGTGCATCCGCCCC
2685529 TTTCTTTAACATATTATACTAAATTTAACTTTTTTTCCTAAATAATGAGGATGCATTTGACCCCT
1 TTTCTTTAACATATTATACTAAATTTAACTTTTTTTCCTAAATAATGAGGATGCATTTGACCCCT
2685594 AGGGGCTTAGTGCATCCGCCCC
66 AGGGGCTTAGTGCATCCGCCCC
2685616 T
1 T
2685617 GGCTACATCG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (87 bp):
TTTCTTTAACATATTATACTAAATTTAACTTTTTTTCCTAAATAATGAGGATGCATTTGACCCCT
AGGGGCTTAGTGCATCCGCCCC
Found at i:2690805 original size:27 final size:27
Alignment explanation
Indices: 2690772--2690824 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
2690762 AAGGTGCTGA
2690772 AAATTTTATGTAATTAATGTGACATAG
1 AAATTTTATGTAATTAATGTGACATAG
2690799 AAATTTTATGTAATTAATGTGACATA
1 AAATTTTATGTAATTAATGTGACATA
2690825 CTCATAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.42
Consensus pattern (27 bp):
AAATTTTATGTAATTAATGTGACATAG
Found at i:2692112 original size:18 final size:17
Alignment explanation
Indices: 2692089--2692135 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
2692079 CAAATGTTTA
2692089 TAGTTATCATACATTTT
1 TAGTTATCATACATTTT
*
2692106 GTAGTTATCAGACATTTT
1 -TAGTTATCATACATTTT
2692124 TCAGTTATCATA
1 T-AGTTATCATA
2692136 TGCTTTACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.47
Consensus pattern (17 bp):
TAGTTATCATACATTTT
Found at i:2693358 original size:23 final size:23
Alignment explanation
Indices: 2693327--2693395 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
2693317 CACCACAGCT
* *
2693327 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
2693350 CGTAGAAATGCACC-ATAATGCCA
1 CGTAGAAATGCACCGA-AGTGCCA
* * *
2693373 CGTAGAATTACACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2693396 TATAAAATGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2695011 original size:24 final size:20
Alignment explanation
Indices: 2694934--2695031 Score: 92
Period size: 20 Copynumber: 4.8 Consensus size: 20
2694924 TTTCCCTTGA
* *
2694934 AGTGCATAGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
2694954 AGTGTATCGATGCATCCTAC
1 AGTGCATCGATGCATCCTAC
*
2694974 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
2694997 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
2695018 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
2695032 TAATTGCATT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.01
19 12 0.18
20 32 0.47
21 3 0.04
22 1 0.01
23 4 0.06
24 14 0.21
25 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:2698777 original size:23 final size:23
Alignment explanation
Indices: 2698746--2698814 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
2698736 CACCACAGCT
* *
2698746 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
2698769 CGTAGAAATACACC-ATAGTGCCA
1 CGTAGAAATGCACCGA-AGTGCCA
* *
2698792 CGTAGAATTGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2698815 TATAAAATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2700382 original size:20 final size:20
Alignment explanation
Indices: 2700359--2700425 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
2700349 GAAGTGCATA
2700359 GATGCATTCTACAGTGTATC
1 GATGCATTCTACAGTGTATC
2700379 GATGCATTCTACAGTGTATC
1 GATGCATTCTACAGTGTATC
* *
2700399 GATGCATCCTACAGTGTATT
1 GATGCATTCTACAGTGTATC
2700419 GATGCAT
1 GATGCAT
2700426 CCCTTAACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
GATGCATTCTACAGTGTATC
Found at i:2700454 original size:24 final size:21
Alignment explanation
Indices: 2700351--2700487 Score: 103
Period size: 20 Copynumber: 6.7 Consensus size: 21
2700341 TTTCCCTTGA
* *
2700351 AGTGCATAGATGCATTC-TAC
1 AGTGCATCGATGCATCCTTAC
* *
2700371 AGTGTATCGATGCATTC-TAC
1 AGTGCATCGATGCATCCTTAC
*
2700391 AGTGTATCGATGCATCC-TAC
1 AGTGCATCGATGCATCCTTAC
* *
2700411 AGTGTATTGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CCTT-AC
2700434 ATGTGCATCGATGCACTCCTT--
1 A-GTGCATCGATGCA-TCCTTAC
2700455 A-TGCATCGATGCACTCCTT--
1 AGTGCATCGATGCA-TCCTTAC
2700474 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
2700488 TAATTGCATT
Statistics
Matches: 106, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.01
19 31 0.29
20 51 0.48
21 3 0.03
22 1 0.01
23 3 0.03
24 15 0.14
25 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (21 bp):
AGTGCATCGATGCATCCTTAC
Found at i:2700461 original size:19 final size:19
Alignment explanation
Indices: 2700437--2700486 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
2700427 CCTTAACATG
2700437 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2700456 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
2700475 TGCATCGATGCA
1 TGCATCGATGCA
2700487 TTAATTGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:2702109 original size:21 final size:21
Alignment explanation
Indices: 2702083--2702122 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2702073 GCTGTTTGTG
2702083 TTCCTTAGTGTTCCATGAGCT
1 TTCCTTAGTGTTCCATGAGCT
2702104 TTCCTTAGTGTTCCATGAG
1 TTCCTTAGTGTTCCATGAG
2702123 TTGCCTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (21 bp):
TTCCTTAGTGTTCCATGAGCT
Found at i:2706477 original size:23 final size:24
Alignment explanation
Indices: 2706428--2706480 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2706418 TTCTTTGCTT
* *
2706428 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
2706451 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
2706474 TTTCTTT
1 TTTCTTT
2706481 TTTGATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Found at i:2716462 original size:21 final size:21
Alignment explanation
Indices: 2716436--2716480 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2716426 GATTTCTGGG
* *
2716436 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2716457 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2716478 CAA
1 CAA
2716481 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2717503 original size:2 final size:2
Alignment explanation
Indices: 2717496--2717525 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2717486 AAACATGTGA
2717496 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
2717526 GTTTAAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2718196 original size:13 final size:13
Alignment explanation
Indices: 2718178--2718240 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
2718168 TTATATGGCA
2718178 CTACGGTGCAATT
1 CTACGGTGCAATT
2718191 CTACGG-GC-A--
1 CTACGGTGCAATT
*
2718200 CTTCGGTGCAATT
1 CTACGGTGCAATT
2718213 CTACGG-GC-A--
1 CTACGGTGCAATT
*
2718222 CTTCGGTGCAATT
1 CTACGGTGCAATT
2718235 CTACGG
1 CTACGG
2718241 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:2718206 original size:22 final size:22
Alignment explanation
Indices: 2718174--2718254 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
2718164 ATCATTATAT
*
2718174 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
2718196 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
2718218 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
2718241 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2718255 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:2721469 original size:21 final size:21
Alignment explanation
Indices: 2721426--2721470 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2721416 GATTTCTGGG
* *
2721426 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
2721447 CAAGGGGAACCGATAACCC-TT
1 CAAGGGGAACCGAT-ACCCATT
2721468 CAA
1 CAA
2721471 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.33, C:0.27, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2722489 original size:2 final size:2
Alignment explanation
Indices: 2722482--2722527 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2722472 GAACATGTGA
2722482 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
2722524 AT AT
1 AT AT
2722528 GTTTAAGAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2723211 original size:22 final size:22
Alignment explanation
Indices: 2723179--2723259 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
2723169 ATCATTATAT
*
2723179 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
2723201 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
*
2723223 GGCACTTCGGTGTAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
2723246 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
2723260 TTTATACGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 41 0.75
23 14 0.25
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:2724604 original size:27 final size:27
Alignment explanation
Indices: 2724574--2724633 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
2724564 AAATTATTTA
*
2724574 AATTTTTAGTTATTT-A-TAATTTATAC
1 AATTTTTA-TAATTTAATTAATTTATAC
*
2724600 TAATTTTTATAATTTAATTAATTTTTAC
1 -AATTTTTATAATTTAATTAATTTATAC
2724628 AATTTT
1 AATTTT
2724634 GTTGGATTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 5 0.17
27 15 0.52
28 9 0.31
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (27 bp):
AATTTTTATAATTTAATTAATTTATAC
Found at i:2724623 original size:18 final size:19
Alignment explanation
Indices: 2724586--2724632 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
2724576 TTTTTAGTTA
2724586 TTTATAATTTATACTAATT
1 TTTATAATTTATACTAATT
*
2724605 TTTATAATTTA-ATTAATT
1 TTTATAATTTATACTAATT
*
2724623 TTTACAATTT
1 TTTATAATTT
2724633 TGTTGGATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTATAATTTATACTAATT
Found at i:2724789 original size:200 final size:200
Alignment explanation
Indices: 2724543--2724941 Score: 629
Period size: 200 Copynumber: 2.0 Consensus size: 200
2724533 TTGACAGACA
2724543 TGCGATGAATATTATTTTAGTAAATTATTTAAATTTTTAGTTATTTATAATTTATACTAATTTTT
1 TGCGATGAATATTATTTTAGTAAATTATTTAAATTTTTAGTTATTTATAATTTATACTAATTTTT
* * ** * *
2724608 ATAATTTAATTAATTTTTACAATTTTGTTGGATTCTGTTTTGTGAGCCAGAGATCTACGGTTACT
66 ATAATTTAATTAATGTTTACAATTTTGTTAGATTCCATATTGTGAGCCAGAGATATACGGTTACT
* * **
2724673 GTCACCGGGATTTTTTTGAAGGCTTGGAGTTGTGGTGTGTCGTAATG-CTTTTGCTTCATTTTCC
131 GTCACCGAGATTTTTTTGAAGACTCAGAGTTGTGGTGTGTCGTAATGTC-TTTGCTTCATTTTCC
2724737 GATTGT
195 GATTGT
*
2724743 TGCGATGAATATTATTTTAGTAAATTATTTAAATTTTTATTTATTTATAATTTATACTAATTTTT
1 TGCGATGAATATTATTTTAGTAAATTATTTAAATTTTTAGTTATTTATAATTTATACTAATTTTT
** **
2724808 ATAATTTAATTAATGTTTACAATTTTGTTAGATTCCATATTGTGAGCTGGAGATATATTGTTACT
66 ATAATTTAATTAATGTTTACAATTTTGTTAGATTCCATATTGTGAGCCAGAGATATACGGTTACT
* *
2724873 GTCACCGAGATTTTTTTGAAGACTCATAGTTGTGGTGTGTCGTAATGTCTTTGCTTCATTTTTCG
131 GTCACCGAGATTTTTTTGAAGACTCAGAGTTGTGGTGTGTCGTAATGTCTTTGCTTCATTTTCCG
2724938 ATTG
196 ATTG
2724942 CTGAGATGTA
Statistics
Matches: 181, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
200 180 0.99
201 1 0.01
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (200 bp):
TGCGATGAATATTATTTTAGTAAATTATTTAAATTTTTAGTTATTTATAATTTATACTAATTTTT
ATAATTTAATTAATGTTTACAATTTTGTTAGATTCCATATTGTGAGCCAGAGATATACGGTTACT
GTCACCGAGATTTTTTTGAAGACTCAGAGTTGTGGTGTGTCGTAATGTCTTTGCTTCATTTTCCG
ATTGT
Found at i:2724826 original size:18 final size:19
Alignment explanation
Indices: 2724786--2724832 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
2724776 TTTTTATTTA
*
2724786 TTTATAATTTATACTAATT
1 TTTATAATTTATACTAATG
*
2724805 TTTATAATTTA-ATTAATG
1 TTTATAATTTATACTAATG
*
2724823 TTTACAATTT
1 TTTATAATTT
2724833 TGTTAGATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTATAATTTATACTAATG
Found at i:2725786 original size:15 final size:15
Alignment explanation
Indices: 2725768--2725799 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2725758 ATTATTATTA
2725768 TGTAATAAATTAGTT
1 TGTAATAAATTAGTT
*
2725783 TGTAATAAATTATTT
1 TGTAATAAATTAGTT
2725798 TG
1 TG
2725800 ATTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
TGTAATAAATTAGTT
Found at i:2726080 original size:16 final size:16
Alignment explanation
Indices: 2726061--2726115 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
2726051 CGAAAATCAA
*
2726061 TCGATCCGATATTGAC
1 TCGACCCGATATTGAC
2726077 TCGACCCGATATTGAC
1 TCGACCCGATATTGAC
2726093 TCGACCCGATATTGAC
1 TCGACCCGATATTGAC
2726109 TCGACCC
1 TCGACCC
2726116 AAAATCTAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (16 bp):
TCGACCCGATATTGAC
Found at i:2729398 original size:10 final size:10
Alignment explanation
Indices: 2729383--2729412 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2729373 GAGGGATAGA
2729383 TATACTTTGG
1 TATACTTTGG
2729393 TATACTTTGG
1 TATACTTTGG
2729403 TATACTTTGG
1 TATACTTTGG
2729413 GATCCTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.20, T:0.50
Consensus pattern (10 bp):
TATACTTTGG
Found at i:2729781 original size:21 final size:21
Alignment explanation
Indices: 2729755--2729795 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2729745 TAACCCAAAT
*
2729755 CGAAATTAACTTAAACCGAAC
1 CGAAATTAACTCAAACCGAAC
*
2729776 CGAAATTAACTCAAATCGAA
1 CGAAATTAACTCAAACCGAA
2729796 AAAAACCTGA
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:0.49, C:0.22, G:0.10, T:0.20
Consensus pattern (21 bp):
CGAAATTAACTCAAACCGAAC
Found at i:2729829 original size:32 final size:32
Alignment explanation
Indices: 2729793--2729871 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
2729783 AACTCAAATC
* *
2729793 GAAAA-AAACCTGAATCGAATTTTAAC-CGATCT
1 GAAAACAAACC-GAACCGAA-TTTAACTCGACCT
*
2729825 GAAAACAATCCGAACCGAATTTAACTCGACCT
1 GAAAACAAACCGAACCGAATTTAACTCGACCT
* *
2729857 GAAAGCAACCCGAAC
1 GAAAACAAACCGAAC
2729872 AAAAATTAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 30 0.75
33 4 0.10
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (32 bp):
GAAAACAAACCGAACCGAATTTAACTCGACCT
Found at i:2730547 original size:16 final size:16
Alignment explanation
Indices: 2730526--2730556 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2730516 ACCAAAAATC
*
2730526 AATCGATCCGATATTG
1 AATCGACCCGATATTG
2730542 AATCGACCCGATATT
1 AATCGACCCGATATT
2730557 AACCCGACCC
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:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (16 bp):
AATCGACCCGATATTG
Found at i:2731546 original size:37 final size:36
Alignment explanation
Indices: 2731487--2731560 Score: 103
Period size: 37 Copynumber: 2.0 Consensus size: 36
2731477 AAAGTTTACA
*
2731487 AAATATGACAACACATCTAAATTTATAAAAAGATGAC
1 AAATATGACAACACATCCAAATTTAT-AAAAGATGAC
* * *
2731524 AAATATGACAATATATCCAAATTTATACAAGATGAC
1 AAATATGACAACACATCCAAATTTATAAAAGATGAC
2731560 A
1 A
2731561 CTATTTTCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
36 10 0.30
37 23 0.70
ACGTcount: A:0.53, C:0.14, G:0.08, T:0.26
Consensus pattern (36 bp):
AAATATGACAACACATCCAAATTTATAAAAGATGAC
Found at i:2731704 original size:30 final size:30
Alignment explanation
Indices: 2731649--2731739 Score: 137
Period size: 30 Copynumber: 2.9 Consensus size: 30
2731639 CCAGTTAAGC
*
2731649 TTACTTACAAAAGATGGCAGCAACATGTCAAGT
1 TTACTTACAAAAGAT---TGCAACATGTCAAGT
2731682 TTACTTACAAAAGATTGCAACATGTCAAGT
1 TTACTTACAAAAGATTGCAACATGTCAAGT
*
2731712 TTACTTACAAAAGATTGAAACATGTCAA
1 TTACTTACAAAAGATTGCAACATGTCAA
2731740 ATTAAGTTCC
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
30 41 0.73
33 15 0.27
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.27
Consensus pattern (30 bp):
TTACTTACAAAAGATTGCAACATGTCAAGT
Found at i:2735037 original size:17 final size:17
Alignment explanation
Indices: 2735007--2735044 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2734997 AATTTATCCA
*
2735007 TTTATATTTGTCCCGAT
1 TTTATATTTGTCCCAAT
2735024 TTTATTATTT-TCCCAAT
1 TTTA-TATTTGTCCCAAT
2735041 TTTA
1 TTTA
2735045 GTTTTAGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.21, C:0.16, G:0.05, T:0.58
Consensus pattern (17 bp):
TTTATATTTGTCCCAAT
Found at i:2735227 original size:21 final size:20
Alignment explanation
Indices: 2735209--2735255 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2735199 ACCCTAAATT
2735209 CTAAATACTAAAATATAAACC
1 CTAAAT-CTAAAATATAAACC
*
2735230 CTAAATCTTAAATATTAAACC
1 CTAAATCTAAAATA-TAAACC
*
2735251 TTAAA
1 CTAAA
2735256 CCCTAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (20 bp):
CTAAATCTAAAATATAAACC
Found at i:2735241 original size:14 final size:14
Alignment explanation
Indices: 2735190--2735274 Score: 50
Period size: 14 Copynumber: 6.1 Consensus size: 14
2735180 TTGTTAACTT
2735190 TAAA-CTTAAACCC
1 TAAATCTTAAACCC
**
2735203 TAAAT-TCTAAATAC
1 TAAATCT-TAAACCC
*
2735217 TAAAAT-ATAAACCC
1 T-AAATCTTAAACCC
***
2735231 TAAATCTTAAATAT
1 TAAATCTTAAACCC
*
2735245 TAAACCTTAAACCC
1 TAAATCTTAAACCC
* *
2735259 TAAATTTTAAATCC
1 TAAATCTTAAACCC
2735273 TA
1 TA
2735275 TACCATAAAC
Statistics
Matches: 52, Mismatches: 16, Indels: 7
0.69 0.21 0.09
Matches are distributed among these distances:
13 9 0.17
14 39 0.75
15 4 0.08
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:2735262 original size:21 final size:21
Alignment explanation
Indices: 2735219--2735283 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
2735209 CTAAATACTA
* *
2735219 AAATA-TAAACCCTAAATCTT
1 AAATATTAAACCCTAAACCCT
*
2735239 AAATATTAAACCTTAAACCCT
1 AAATATTAAACCCTAAACCCT
* * * *
2735260 AAATTTTAAATCCTATACCAT
1 AAATATTAAACCCTAAACCCT
2735281 AAA
1 AAA
2735284 CTCTATCACA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 5 0.14
21 31 0.86
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.31
Consensus pattern (21 bp):
AAATATTAAACCCTAAACCCT
Found at i:2735283 original size:28 final size:28
Alignment explanation
Indices: 2735196--2735284 Score: 106
Period size: 28 Copynumber: 3.2 Consensus size: 28
2735186 ACTTTAAACT
* **
2735196 TAAACCCTAAATTCTAAATACTAAAATA
1 TAAACCCTAAATTTTAAATACTAAACCA
* * *
2735224 TAAACCCTAAATCTTAAATATTAAACCT
1 TAAACCCTAAATTTTAAATACTAAACCA
* *
2735252 TAAACCCTAAATTTTAAATCCTATACCA
1 TAAACCCTAAATTTTAAATACTAAACCA
2735280 TAAAC
1 TAAAC
2735285 TCTATCACAT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (28 bp):
TAAACCCTAAATTTTAAATACTAAACCA
Found at i:2736965 original size:7 final size:7
Alignment explanation
Indices: 2736953--2737075 Score: 51
Period size: 7 Copynumber: 17.6 Consensus size: 7
2736943 ATGTGCATAA
2736953 CTTAAAC
1 CTTAAAC
2736960 CTTAAAC
1 CTTAAAC
*
2736967 CCTAAA-
1 CTTAAAC
2736973 CTATAAAC
1 CT-TAAAC
*
2736981 CTTAAAT
1 CTTAAAC
* *
2736988 CAT-ATC
1 CTTAAAC
*
2736994 ACATAAA-
1 -CTTAAAC
2737001 CTCTAAAC
1 CT-TAAAC
2737009 CTTAAAC
1 CTTAAAC
*
2737016 TTTAAAC
1 CTTAAAC
*
2737023 TTTAAA-
1 CTTAAAC
2737029 CTCT-AAC
1 CT-TAAAC
*
2737036 TCATAAAC
1 -CTTAAAC
*
2737044 CCTAAAC
1 CTTAAAC
*
2737051 CTTAATAT
1 CTTAA-AC
2737059 C-TAAAC
1 CTTAAAC
*
2737065 CTTAAAT
1 CTTAAAC
2737072 CTTA
1 CTTA
2737076 TCAGATAAAC
Statistics
Matches: 88, Mismatches: 16, Indels: 24
0.69 0.12 0.19
Matches are distributed among these distances:
6 8 0.09
7 69 0.78
8 11 0.12
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (7 bp):
CTTAAAC
Found at i:2737008 original size:42 final size:41
Alignment explanation
Indices: 2736955--2737095 Score: 149
Period size: 42 Copynumber: 3.4 Consensus size: 41
2736945 GTGCATAACT
*
2736955 TAAACCTTAAACCCTAAACTATAAACCTTAAATCATATCACA
1 TAAACCCTAAACCCTAAACTATAAACCTTAAATC-TATCACA
* * * * * *
2736997 TAAACTCTAAACCTTAAACTTTAAACTTTAAACTCTAACTCA
1 TAAACCCTAAACCCTAAACTATAAACCTTAAA-TCTATCACA
* * *
2737039 TAAACCCTAAACCTTAATA-TCTAAACCTTAAATCTTATCAGA
1 TAAACCCTAAACCCTAA-ACTATAAACCTTAAATC-TATCACA
2737081 TAAACCCTAAACCCT
1 TAAACCCTAAACCCT
2737096 TAACATTAAC
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
41 2 0.02
42 77 0.94
43 3 0.04
ACGTcount: A:0.44, C:0.26, G:0.01, T:0.29
Consensus pattern (41 bp):
TAAACCCTAAACCCTAAACTATAAACCTTAAATCTATCACA
Found at i:2737014 original size:14 final size:14
Alignment explanation
Indices: 2736953--2737070 Score: 84
Period size: 14 Copynumber: 8.4 Consensus size: 14
2736943 ATGTGCATAA
2736953 CTTAAAC-CTTAAAC
1 CTTAAACTC-TAAAC
* *
2736967 CCTAAACTATAAAC
1 CTTAAACTCTAAAC
*
2736981 CTTAAA-TC-ATATC
1 CTTAAACTCTA-AAC
*
2736994 ACATAAACTCTAAAC
1 -CTTAAACTCTAAAC
*
2737009 CTTAAACTTTAAAC
1 CTTAAACTCTAAAC
*
2737023 TTTAAACTCT-AAC
1 CTTAAACTCTAAAC
* *
2737036 TCATAAACCCTAAAC
1 -CTTAAACTCTAAAC
2737051 CTTAATA-TCTAAAC
1 CTTAA-ACTCTAAAC
2737065 CTTAAA
1 CTTAAA
2737071 TCTTATCAGA
Statistics
Matches: 80, Mismatches: 16, Indels: 17
0.71 0.14 0.15
Matches are distributed among these distances:
12 1 0.01
13 7 0.09
14 63 0.79
15 8 0.10
16 1 0.01
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (14 bp):
CTTAAACTCTAAAC
Found at i:2737498 original size:14 final size:14
Alignment explanation
Indices: 2737481--2737521 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
2737471 TTTATTCATC
2737481 AATAATGTATTTTT
1 AATAATGTATTTTT
2737495 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
2737506 AATAATGTAATTTT
1 AATAATGTATTTTT
2737520 AA
1 AA
2737522 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:2741001 original size:17 final size:17
Alignment explanation
Indices: 2740979--2741011 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2740969 TAAGGTATTT
2740979 ATATTCGGTTTGTGTTC
1 ATATTCGGTTTGTGTTC
2740996 ATATTCGGTTTGTGTT
1 ATATTCGGTTTGTGTT
2741012 AGTTTAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.24, T:0.55
Consensus pattern (17 bp):
ATATTCGGTTTGTGTTC
Found at i:2741156 original size:34 final size:34
Alignment explanation
Indices: 2741118--2741196 Score: 106
Period size: 34 Copynumber: 2.3 Consensus size: 34
2741108 TTCATGAATG
2741118 TGTTCATTTAGCATTCATTTAACGT-TCGTGAACA
1 TGTTCATTTAGCATTCATTTAACGTAT-GTGAACA
* * * *
2741152 TGTTCATTTAGCGTTCGTTTATCGTATGTGAATA
1 TGTTCATTTAGCATTCATTTAACGTATGTGAACA
2741186 TGTTCATTTAG
1 TGTTCATTTAG
2741197 AATAAAAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 39 0.98
35 1 0.03
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.46
Consensus pattern (34 bp):
TGTTCATTTAGCATTCATTTAACGTATGTGAACA
Found at i:2741906 original size:17 final size:17
Alignment explanation
Indices: 2741882--2741919 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
2741872 TCATAACCAT
2741882 TTTTAAAAAAATTAT-A
1 TTTTAAAAAAATTATGA
2741898 TTTTAAAAAAATTATGA
1 TTTTAAAAAAATTATGA
2741915 TTTTA
1 TTTTA
2741920 TTGAAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.71
17 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TTTTAAAAAAATTATGA
Found at i:2742963 original size:23 final size:23
Alignment explanation
Indices: 2742916--2742969 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
2742906 AAACTGCATA
**
2742916 TAGAATTGCACCGAAGTGCTGCG
1 TAGAATTGCACCGAAGTGCAACG
2742939 TAGAATTGCACCGAAGTGCAACG
1 TAGAATTGCACCGAAGTGCAACG
*
2742962 TAAAATTG
1 TAGAATTG
2742970 TCCCAAAGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (23 bp):
TAGAATTGCACCGAAGTGCAACG
Found at i:2743001 original size:23 final size:23
Alignment explanation
Indices: 2742975--2743058 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
2742965 AATTGTCCCA
*
2742975 AAGGATCACATAGAAATGTCTCG
1 AAGGACCACATAGAAATGTCTCG
* *
2742998 AAGGACCGCTTAGAAATGTCTCG
1 AAGGACCACATAGAAATGTCTCG
* * * *
2743021 AAGGACCACGTAGAATTATCCCG
1 AAGGACCACATAGAAATGTCTCG
* *
2743044 TAGGACCGCATAGAA
1 AAGGACCACATAGAA
2743059 CCCTCAACTG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (23 bp):
AAGGACCACATAGAAATGTCTCG
Found at i:2744221 original size:60 final size:59
Alignment explanation
Indices: 2744128--2744294 Score: 183
Period size: 60 Copynumber: 2.8 Consensus size: 59
2744118 TGTACCGATG
* * * * *
2744128 TAAGTATGTATATTTTTAAATATCTTGGCACCTAAAAATAAACACATATTTACA-CTGGTA
1 TAAGTATGTATATATCT-AATATCTTGGTACCTAAAAATAAACACATATATACACCT-ATA
* * * *
2744188 TAAGTATGTATATATCTCGATATCTGGGTACCTAAACATAAACACATATATACACCTATG
1 TAAGTATGTATATATCT-AATATCTTGGTACCTAAAAATAAACACATATATACACCTATA
* * * *
2744248 TACGTATATACATATCTAAAATCTTGGTACCTAAAAATAAACACATA
1 TAAGTATGTATATATCTAATATCTTGGTACCTAAAAATAAACACATA
2744295 ATTATATTGG
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
59 26 0.29
60 61 0.69
61 2 0.02
ACGTcount: A:0.41, C:0.16, G:0.10, T:0.33
Consensus pattern (59 bp):
TAAGTATGTATATATCTAATATCTTGGTACCTAAAAATAAACACATATATACACCTATA
Found at i:2747047 original size:3 final size:3
Alignment explanation
Indices: 2747039--2747065 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2747029 TTTTATAAAT
2747039 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
2747066 TTTAATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2759070 original size:40 final size:40
Alignment explanation
Indices: 2759024--2759107 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
2759014 GACAATTTCG
* *
2759024 CAACACGAATTTCTTTTTCGCAA-ATCGATTTT-TAAATTCA
1 CAACACGAATTTCCTTTTCGCAACA-AGATTTTCT-AATTCA
*
2759064 CAACACGAGTTTCCTTTTCGCAACAAGATTTTCTAATTCA
1 CAACACGAATTTCCTTTTCGCAACAAGATTTTCTAATTCA
2759104 CAAC
1 CAAC
2759108 GCGGGGTTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
40 37 0.95
41 2 0.05
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (40 bp):
CAACACGAATTTCCTTTTCGCAACAAGATTTTCTAATTCA
Found at i:2760001 original size:12 final size:12
Alignment explanation
Indices: 2759980--2760013 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2759970 ACCACATTTC
*
2759980 CAATACCAAACA
1 CAATATCAAACA
2759992 CAATATCAAACA
1 CAATATCAAACA
*
2760004 CAATCTCAAA
1 CAATATCAAA
2760014 ATCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2760190 original size:24 final size:24
Alignment explanation
Indices: 2760139--2760192 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
2760129 GTATTCGAAA
**
2760139 TTTGATCTTGGTAAATACCCGGAC
1 TTTGATCTTGGTAAATACCCAAAC
* * *
2760163 TTTGATCTTGGTCAATACTCAAAT
1 TTTGATCTTGGTAAATACCCAAAC
2760187 TTTGAT
1 TTTGAT
2760193 GATGTTTCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTAAATACCCAAAC
Found at i:2762913 original size:20 final size:20
Alignment explanation
Indices: 2762884--2762926 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2762874 ATTCCACCAC
2762884 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGCTCCTAA
* * *
2762904 ATGCATCTATGTGGTCCTAA
1 ATGCAACTATATGCTCCTAA
2762924 ATG
1 ATG
2762927 AGCTCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGCTCCTAA
Found at i:2771298 original size:20 final size:20
Alignment explanation
Indices: 2771273--2771317 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2771263 TAATTCCACC
2771273 AAATGCAACTATATGCTCCT
1 AAATGCAACTATATGCTCCT
* * *
2771293 AAATGCATCTATGTGGTCCT
1 AAATGCAACTATATGCTCCT
2771313 AAATG
1 AAATG
2771318 AGCTCTTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (20 bp):
AAATGCAACTATATGCTCCT
Found at i:2772757 original size:18 final size:18
Alignment explanation
Indices: 2772734--2772775 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2772724 CAAGTAAAGG
2772734 AAAATCAAAATCGCAATC
1 AAAATCAAAATCGCAATC
*
2772752 AAAATCAAAATCTCAATC
1 AAAATCAAAATCGCAATC
*
2772770 ACAATC
1 AAAATC
2772776 GCCTTCACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.24, G:0.02, T:0.19
Consensus pattern (18 bp):
AAAATCAAAATCGCAATC
Found at i:2772958 original size:20 final size:20
Alignment explanation
Indices: 2772935--2772986 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
2772925 AACGCGATCC
2772935 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
2772955 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
2772975 CCAAAATCGCAA
1 CCAGAATCGCAA
2772987 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:2773067 original size:20 final size:20
Alignment explanation
Indices: 2773042--2773235 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
2773032 GATTTTCCAT
* *
2773042 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
2773062 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
2773082 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2773102 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
2773122 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
2773142 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
2773162 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
2773182 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
2773203 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
2773223 AATCGCAACGCGA
1 AATCGCAACGCGA
2773236 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:2773087 original size:40 final size:39
Alignment explanation
Indices: 2773038--2773235 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
2773028 TTGCGATTTT
* ** *
2773038 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
2773076 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
2773117 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
2773157 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
2773196 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
2773236 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:2773125 original size:60 final size:60
Alignment explanation
Indices: 2773042--2773234 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
2773032 GATTTTCCAT
* ** * *
2773042 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
2773102 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
2773162 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
2773223 AATCGCAACGCG
1 AATCGCAACGCG
2773235 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:2773655 original size:33 final size:33
Alignment explanation
Indices: 2773616--2773686 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
2773606 TTCACTTAGA
*
2773616 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2773649 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2773682 TTTCA
1 TTTCA
2773687 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2773826 original size:14 final size:14
Alignment explanation
Indices: 2773807--2773861 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
2773797 AGAATGACTG
2773807 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
2773821 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
2773840 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2773854 TCGCAACG
1 TCGCAACG
2773862 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:2773844 original size:33 final size:33
Alignment explanation
Indices: 2773807--2773877 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2773797 AGAATGACTG
**
2773807 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2773840 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
2773873 TCGCA
1 TCGCA
2773878 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:2773895 original size:19 final size:19
Alignment explanation
Indices: 2773873--2773937 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
2773863 GAAACCAAAA
*
2773873 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2773892 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2773906 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2773925 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2773938 CTCGTTGCGA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 22 0.58
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2773914 original size:14 final size:14
Alignment explanation
Indices: 2773895--2773982 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
2773885 TTTCATTTCG
2773895 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2773909 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2773928 CGTTGCGA-T-TCT
1 CGTTGCGATTCTCT
2773940 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
2773957 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
2773973 CGTTGCGATT
1 CGTTGCGATT
2773983 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 24
0.70 0.02 0.28
Matches are distributed among these distances:
12 10 0.17
14 18 0.30
15 1 0.02
16 7 0.12
17 5 0.08
18 1 0.02
19 18 0.30
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2773920 original size:33 final size:33
Alignment explanation
Indices: 2773878--2773990 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
2773868 CAAAATCGCA
2773878 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2773911 TTGCGATTTTCATTTCGCGTTGCGA-T-TCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
2773942 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2773975 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2773991 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
31 28 0.38
32 2 0.03
33 44 0.59
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2773964 original size:19 final size:18
Alignment explanation
Indices: 2773873--2773983 Score: 70
Period size: 19 Copynumber: 6.8 Consensus size: 18
2773863 GAAACCAAAA
* *
2773873 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
2773892 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
*
2773908 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATC
2773925 TCGCGTTGCGA--T--TC
1 TCGCGTTGCGATTTCATC
2773939 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATT-TCATC
2773956 TCGCGTTGCGA-TTC-TC
1 TCGCGTTGCGATTTCATC
2773972 T--CGTTGCGATTT
1 TCGCGTTGCGATTT
2773984 TCATTTCAAC
Statistics
Matches: 75, Mismatches: 4, Indels: 30
0.69 0.04 0.28
Matches are distributed among these distances:
12 8 0.11
14 18 0.24
15 3 0.04
16 9 0.12
17 10 0.13
18 1 0.01
19 26 0.35
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.43
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATC
Found at i:2775917 original size:185 final size:185
Alignment explanation
Indices: 2775687--2776157 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
2775677 TAGATTGCTT
*
2775687 AGTAAA-TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2775751 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
2775816 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2775871 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2775936 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
2776001 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2776056 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2776121 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
2776158 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 6 0.02
185 278 0.98
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2776000 original size:93 final size:93
Alignment explanation
Indices: 2775687--2776157 Score: 903
Period size: 92 Copynumber: 5.1 Consensus size: 93
2775677 TAGATTGCTT
*
2775687 AGTAAA-TTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2775751 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2775779 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2775843 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2775871 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2775936 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2775964 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2776028 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2776056 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2776121 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2776149 AGTAAATTT
1 AGTAAATTT
2776158 ATCCATTCAA
Statistics
Matches: 373, Mismatches: 3, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
92 189 0.51
93 184 0.49
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2776241 original size:19 final size:19
Alignment explanation
Indices: 2776201--2776327 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
2776191 TAGTTTACTT
* *
2776201 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2776221 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2776240 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
2776259 TCGCAA--CG--A-C--AA
1 TCGCAACGCGAAACCAAAA
2776271 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2776290 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2776304 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2776323 TCGCA
1 TCGCA
2776328 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 7, Indels: 25
0.73 0.06 0.21
Matches are distributed among these distances:
12 8 0.09
14 12 0.14
15 2 0.02
16 3 0.03
17 5 0.06
18 1 0.01
19 44 0.50
20 13 0.15
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2776276 original size:31 final size:32
Alignment explanation
Indices: 2776237--2776327 Score: 148
Period size: 31 Copynumber: 2.8 Consensus size: 32
2776227 CGCGAAACCA
**
2776237 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2776269 -AATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2776300 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2776328 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 29 0.53
32 1 0.02
33 25 0.45
ACGTcount: A:0.46, C:0.29, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2776345 original size:19 final size:19
Alignment explanation
Indices: 2776323--2776457 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
2776313 GAAACCAAAA
*
2776323 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2776342 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2776358 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2776375 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2776391 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
2776408 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
2776427 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2776447 TCGTGTTGCGA
1 TCGCGTTGCGA
2776458 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2776364 original size:14 final size:14
Alignment explanation
Indices: 2776345--2776401 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2776335 TTTCATTTCG
2776345 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2776359 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2776376 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2776392 CGTTGCGATT
1 CGTTGCGATT
2776402 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2776370 original size:33 final size:33
Alignment explanation
Indices: 2776328--2776420 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2776318 CAAAATCGCA
*
2776328 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2776361 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2776394 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2776421 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2778374 original size:14 final size:14
Alignment explanation
Indices: 2778355--2778390 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2778345 ATTGTTTAAT
2778355 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2778369 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2778383 TGATTTGT
1 TGATTTGT
2778391 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2778583 original size:20 final size:19
Alignment explanation
Indices: 2778497--2778597 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
2778487 AAAAATGACT
2778497 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2778516 ATCGCAATGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
*
2778534 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
2778548 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2778567 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2778587 ATCGCAATGCG
1 ATCGCAATGCG
2778598 TTTATAATTT
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 4 0.05
18 15 0.20
19 25 0.34
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2778650 original size:19 final size:19
Alignment explanation
Indices: 2778626--2778918 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
2778616 GATTATCTCG
2778626 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2778645 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2778664 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
2778678 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2778697 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2778716 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2778735 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2778754 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2778773 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2778792 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
*
2778806 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2778825 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2778844 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2778858 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2778878 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2778892 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2778911 TTGCGATT
1 TTGCGATT
2778919 GTATTTTCCG
Statistics
Matches: 243, Mismatches: 10, Indels: 42
0.82 0.03 0.14
Matches are distributed among these distances:
14 28 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 156 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2778666 original size:52 final size:52
Alignment explanation
Indices: 2778604--2778918 Score: 321
Period size: 52 Copynumber: 5.9 Consensus size: 52
2778594 TGCGTTTATA
*
2778604 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
2778656 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2778708 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2778765 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGTGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
2778817 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
2778869 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
2778919 GTATTTTCCG
Statistics
Matches: 239, Mismatches: 11, Indels: 25
0.87 0.04 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 127 0.53
53 18 0.08
54 6 0.03
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2778774 original size:128 final size:122
Alignment explanation
Indices: 2778626--2778890 Score: 185
Period size: 128 Copynumber: 2.1 Consensus size: 122
2778616 GATTATCTCG
*
2778626 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
2778688 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
2778752 CA
121 CA
* * * *
2778754 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGTGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
2778816 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
2778876 CA
121 CA
2778878 TTGCGATTTTCAT
1 TTGCGATTTTCAT
2778891 GTTGGGATTT
Statistics
Matches: 124, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.15
124 18 0.15
125 2 0.02
126 2 0.02
128 73 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:2781412 original size:24 final size:24
Alignment explanation
Indices: 2781378--2781424 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2781368 CTGAAACATC
2781378 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2781402 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2781425 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2782126 original size:20 final size:20
Alignment explanation
Indices: 2782098--2782466 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
2782088 AAATTTAAGT
* * * *
2782098 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2782118 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
2782138 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
2782158 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2782178 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2782198 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
2782218 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
2782238 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2782258 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2782278 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2782298 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
2782318 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
2782338 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
2782358 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
2782378 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
2782398 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
2782418 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
2782438 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
2782458 GTTGCGATT
1 GTTGCGATT
2782467 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:2782983 original size:20 final size:20
Alignment explanation
Indices: 2782927--2782985 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
2782917 ATAATGAATC
**
2782927 AAATTCGCAACTCGAAAATA
1 AAATTCGCAACTCGAATTTA
*
2782947 AAATTCGCAACTCGAATTTT
1 AAATTCGCAACTCGAATTTA
*
2782967 AAATTCACAACTCGAATTT
1 AAATTCGCAACTCGAATTT
2782986 CATTTTCGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (20 bp):
AAATTCGCAACTCGAATTTA
Found at i:2783012 original size:20 final size:20
Alignment explanation
Indices: 2782979--2783072 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
2782969 ATTCACAACT
*
2782979 CGAATTTCATTTTCGAGTTG
1 CGAATTTAATTTTCGAGTTG
* *
2782999 CGATTTTTATTTTCGAGTTG
1 CGAATTTAATTTTCGAGTTG
* *
2783019 TGAATTCAATTTTCGAGTTG
1 CGAATTTAATTTTCGAGTTG
2783039 CGAATTTAATTTTCGAGTTG
1 CGAATTTAATTTTCGAGTTG
*
2783059 CGAATTTGATTTTC
1 CGAATTTAATTTTC
2783073 TTGAAATAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (20 bp):
CGAATTTAATTTTCGAGTTG
Found at i:2789783 original size:24 final size:23
Alignment explanation
Indices: 2789746--2789792 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2789736 TTGTTGAAAA
* *
2789746 TATTTTTTTATTTTGAAATAATT
1 TATTTTTATATTTTGAAAAAATT
*
2789769 TATTTTATATATTTTTAAAAAATT
1 TATTTT-TATATTTTGAAAAAATT
2789793 CTAAAGTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TATTTTTATATTTTGAAAAAATT
Found at i:2790575 original size:19 final size:19
Alignment explanation
Indices: 2790551--2790587 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2790541 ATGACCAACA
*
2790551 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
2790570 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
2790588 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2790694 original size:21 final size:20
Alignment explanation
Indices: 2790669--2790739 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
2790659 ATTCTGACTG
2790669 TCGCAACGCGATAATACATAA
1 TCGCAACGCG-TAATACATAA
** *
2790690 TCGCAACGCGTTCTGAC-T-G
1 TCGCAACGCGTAAT-ACATAA
2790709 TCGCAACGCGTAAATACATAA
1 TCGCAACGCGT-AATACATAA
2790730 TCGCAACGCG
1 TCGCAACGCG
2790740 ATTCTGACCG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
19 13 0.32
20 5 0.12
21 22 0.55
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGTAATACATAA
Found at i:2790715 original size:40 final size:41
Alignment explanation
Indices: 2790618--2790758 Score: 209
Period size: 40 Copynumber: 3.5 Consensus size: 41
2790608 ATTTGCAATA
* *
2790618 CGATTCTGACTATCGCAACGTGATAATACATAAT--CAACG
1 CGATTCTGACTGTCGCAACGCGATAATACATAATCGCAACG
*
2790657 TGATTCTGACTGTCGCAACGCGATAATACATAATCGCAACG
1 CGATTCTGACTGTCGCAACGCGATAATACATAATCGCAACG
2790698 CG-TTCTGACTGTCGCAACGCG-TAAATACATAATCGCAACG
1 CGATTCTGACTGTCGCAACGCGAT-AATACATAATCGCAACG
*
2790738 CGATTCTGACCGTCGCAACGC
1 CGATTCTGACTGTCGCAACGC
2790759 TGAATTTCAA
Statistics
Matches: 93, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
39 32 0.34
40 38 0.41
41 23 0.25
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (41 bp):
CGATTCTGACTGTCGCAACGCGATAATACATAATCGCAACG
Found at i:2791595 original size:23 final size:23
Alignment explanation
Indices: 2791539--2791583 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2791529 AGTCGGTATT
*
2791539 CGAAATTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
2791562 CGAACTTTGATC-TGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
2791584 TCGGATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (23 bp):
CGAACTTTGATCTTGGTCAATAC
Found at i:2791837 original size:24 final size:24
Alignment explanation
Indices: 2791779--2791825 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
2791769 AGTCGGTATT
*
2791779 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
2791803 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
2791826 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:2791983 original size:14 final size:14
Alignment explanation
Indices: 2791966--2791992 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2791956 GAATAAGAAA
2791966 TCCCCGAAGAAAAG
1 TCCCCGAAGAAAAG
2791980 TCCCCGAAGAAAA
1 TCCCCGAAGAAAA
2791993 TGCCATGGGA
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:0.44, C:0.30, G:0.19, T:0.07
Consensus pattern (14 bp):
TCCCCGAAGAAAAG
Found at i:2794344 original size:140 final size:140
Alignment explanation
Indices: 2794032--2794450 Score: 747
Period size: 140 Copynumber: 3.0 Consensus size: 140
2794022 GCAAACGTTG
*
2794032 TATTATGTCTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCA--TATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
2794095 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATT--TTTGAATATCGCAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCAATTATTACACATTCATTTGAATATCGCAACG
2794158 CGAATTTGAC
131 CGAATTTGAC
*
2794168 TATTTTGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
2794233 TTGAACATTGCTATGATCTGTTCAGTTGTTATCATTTATTACACATTCATTTGAATATCACAACG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCAATTATTACACATTCATTTGAATATCGCAACG
2794298 CGAATTTGAC
131 CGAATTTGAC
2794308 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
2794373 TTGAACATTGCTATGATCTGTTCAGTTGTTATCAATTATTACACATTCATTTGAATATCGCAATG
66 TTGAACATTGCTATGATCTGTTCAGTTGTTATCAATTATTACACATTCATTTGAATATCGCAACG
2794438 CGAATTTGAC
131 CGAATTTGAC
2794448 TAT
1 TAT
2794451 CGTAACACGA
Statistics
Matches: 270, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
136 45 0.17
138 61 0.23
140 164 0.61
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTGTTCAGTTGTTATCAATTATTACACATTCATTTGAATATCGCAACG
CGAATTTGAC
Found at i:2794446 original size:20 final size:20
Alignment explanation
Indices: 2794421--2794557 Score: 184
Period size: 20 Copynumber: 6.8 Consensus size: 20
2794411 TTACACATTC
* *
2794421 ATTTGAATATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
2794441 ATTTGACTATCGTAACACGA
1 ATTTGACTATCGCAACGCGA
2794461 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
** *
2794481 ATTTGACTATCGCAGTGCAA
1 ATTTGACTATCGCAACGCGA
*
2794501 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
2794521 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
2794541 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
2794558 AGAAAATCGT
Statistics
Matches: 101, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2794642 original size:20 final size:20
Alignment explanation
Indices: 2794599--2794692 Score: 127
Period size: 20 Copynumber: 4.8 Consensus size: 20
2794589 ATGCGAATTA
*
2794599 ACTTTCGCGTTGCGA-TTTG
1 ACTTTCGCATTGCGATTTTG
* *
2794618 GCTTTCGCATTACGATTTTG
1 ACTTTCGCATTGCGATTTTG
2794638 ACTTTCGCATTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
2794658 ACTTTCGCATTGCGATTTTG
1 ACTTTCGCATTGCGATTTTG
* * *
2794678 AGTTTAGCGTTGCGA
1 ACTTTCGCATTGCGA
2794693 AAGTGTACCT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
19 12 0.18
20 54 0.82
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
ACTTTCGCATTGCGATTTTG
Found at i:2794847 original size:59 final size:60
Alignment explanation
Indices: 2794744--2794891 Score: 201
Period size: 61 Copynumber: 2.4 Consensus size: 60
2794734 TATTGAAATC
*
2794744 AACAAATCAACTTTTACATTTCAATCATTAAATAAGCACAAATAAGAATTA-TT-ACATCAATTA
1 AACAAATCAACTTTTACA-ATC-A--ATTAAATAAGCACAAATAAG-ATTATTTAACATCAATTA
*
2794807 AACAAATCAACTTTTACAATCAATTAAATAATCACAAATAAGATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAATCAATTAAATAAGCACAAATAAGATTATTTA-ACATCAATTA
2794868 AACAAATCAACTTTTACAAATCAA
1 AACAAATCAACTTTTAC-AATCAA
2794892 CTTTTACAAA
Statistics
Matches: 79, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
58 4 0.05
59 21 0.27
61 28 0.35
62 8 0.10
63 18 0.23
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (60 bp):
AACAAATCAACTTTTACAATCAATTAAATAAGCACAAATAAGATTATTTAACATCAATTA
Found at i:2794888 original size:14 final size:14
Alignment explanation
Indices: 2794869--2794905 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2794859 CATCAATTAA
2794869 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2794883 ACAAATCAACTTTT
1 ACAAATCAACTTTT
2794897 ACAAATCAA
1 ACAAATCAA
2794906 TTAAACAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:2796337 original size:42 final size:42
Alignment explanation
Indices: 2796278--2796370 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
2796268 ATGAATCGGG
*
2796278 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATTACAGGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATTACAGGGGC
* ** *
2796320 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATTATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATTACAGGGGC
2796362 CTC-TGAACG
1 CTCTTGAACG
2796371 ATAGGAAAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 6 0.13
42 35 0.78
43 4 0.09
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATTACAGGGGC
Found at i:2796338 original size:21 final size:21
Alignment explanation
Indices: 2796278--2796347 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
2796268 ATGAATCGGG
* *
2796278 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * ***
2796299 CTCTTCAACGATTACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
2796320 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
2796341 CTCTTGA
1 CTCTTGA
2796348 GGGATTATAG
Statistics
Matches: 36, Mismatches: 13, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:2796386 original size:41 final size:42
Alignment explanation
Indices: 2796308--2796388 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 42
2796298 CCTCTTCAAC
* * **
2796308 GATTACAGGGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATTACAGGGGCCTCTTGAACGATAGGAAAGGACTCTTGAGG
* *
2796350 GATTATAGGGGCCTC-TGAACGATAGGAAAGGCCTCTTGA
1 GATTACAGGGGCCTCTTGAACGATAGGAAAGGACTCTTGA
2796389 ACGATGACAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
41 19 0.58
42 14 0.42
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (42 bp):
GATTACAGGGGCCTCTTGAACGATAGGAAAGGACTCTTGAGG
Found at i:2796903 original size:18 final size:19
Alignment explanation
Indices: 2796873--2796912 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
2796863 ATAATTTCTG
2796873 AAACTTAAAATCGCAACAC
1 AAACTTAAAATCGCAACAC
*
2796892 AAACTT-AAATCGCAACGC
1 AAACTTAAAATCGCAACAC
2796910 AAA
1 AAA
2796913 TGACTATCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.53, C:0.25, G:0.07, T:0.15
Consensus pattern (19 bp):
AAACTTAAAATCGCAACAC
Found at i:2796921 original size:18 final size:20
Alignment explanation
Indices: 2796900--2796945 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2796890 ACAAACTTAA
2796900 ATCGCAACGC-AA-ATGACT
1 ATCGCAACGCGAATATGACT
*
2796918 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
2796938 ATCGCAAC
1 ATCGCAAC
2796946 TGGATAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 13 0.52
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Done.