Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008702.1 Hibiscus syriacus cultivar Beakdansim tig00111741_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: 3201804
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 14
Found at i:3079588 original size:9 final size:8
Alignment explanation
Indices: 3079576--3079788 Score: 103
Period size: 7 Copynumber: 28.8 Consensus size: 8
3079566 ATATACATAC
3079576 ATATACTT
1 ATATACTT
*
3079584 -TATATTT
1 ATATACTT
3079591 A-ATACTT
1 ATATACTT
3079598 ATATACTT
1 ATATACTT
*
3079606 -TATATTT
1 ATATACTT
3079613 A-ATACTT
1 ATATACTT
3079620 ATATACTT
1 ATATACTT
3079628 ATAT--TT
1 ATATACTT
*
3079634 A-ATGCTT
1 ATATACTT
3079641 ATATACTT
1 ATATACTT
*
3079649 -CATA-TT
1 ATATACTT
*
3079655 ATATACTA
1 ATATACTT
*
3079663 AAATACTT
1 ATATACTT
3079671 -TAGT-CTT
1 ATA-TACTT
*
3079678 -TATAATT
1 ATATACTT
* *
3079685 ATACATTTT
1 ATATA-CTT
3079694 ATATA-TAT
1 ATATACT-T
3079702 AATATAC--
1 -ATATACTT
3079709 ATATAC-T
1 ATATACTT
3079716 -TATACTT
1 ATATACTT
*
3079723 -TATATTT
1 ATATACTT
3079730 A-ATACTT
1 ATATACTT
3079737 ATATAC--
1 ATATACTT
*
3079743 CTATACTT
1 ATATACTT
3079751 A-ATACTT
1 ATATACTT
3079758 ATATACTTT
1 ATATAC-TT
3079767 ATATTA-TT
1 ATA-TACTT
*
3079775 ATATACCT
1 ATATACTT
3079783 ATATAC
1 ATATAC
3079789 AGTTTATACT
Statistics
Matches: 159, Mismatches: 20, Indels: 52
0.69 0.09 0.23
Matches are distributed among these distances:
5 2 0.01
6 22 0.14
7 64 0.40
8 53 0.33
9 16 0.10
10 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (8 bp):
ATATACTT
Found at i:3079601 original size:13 final size:13
Alignment explanation
Indices: 3079578--3079644 Score: 53
Period size: 13 Copynumber: 4.8 Consensus size: 13
3079568 ATACATACAT
3079578 ATACTTTATATTTA
1 ATAC-TTATATTTA
*
3079592 ATACTTATATACTTT
1 ATACTTATAT--TTA
* *
3079607 ATATTTAATACTTA
1 ATACTT-ATATTTA
3079621 TATACTTATATTTA
1 -ATACTTATATTTA
*
3079635 ATGCTTATAT
1 ATACTTATAT
3079645 ACTTCATATT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 15 0.36
14 12 0.29
15 12 0.29
16 3 0.07
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (13 bp):
ATACTTATATTTA
Found at i:3079648 original size:21 final size:22
Alignment explanation
Indices: 3079191--3079385 Score: 138
Period size: 22 Copynumber: 8.7 Consensus size: 22
3079181 AAGTATATAT
3079191 ATACTTATATACTTTATA-TTA
1 ATACTTATATACTTTATATTTA
*
3079212 TATACTTATATACTTTACA-TT-
1 -ATACTTATATACTTTATATTTA
* *
3079233 ATA--TATATA-TGTATGTATGT-
1 ATACTTATATACT-T-TATATTTA
*
3079253 ATACATATGTATACTTTATATTTA
1 ATAC-T-TATATACTTTATATTTA
*
3079277 ATAATTATATAC-TTATATTTA
1 ATACTTATATACTTTATATTTA
* *
3079298 ATTCTTATATACTTCATA-TTA
1 ATACTTATATACTTTATATTTA
*
3079319 TATATTTATATACTTTATATTATTA
1 -ATACTTATATACTTTATA-T-TTA
*
3079344 TATACATATATATACATTATATTTA
1 -ATAC-T-TATATACTTTATATTTA
3079369 TATACTTATATACTTTA
1 -ATACTTATATACTTTA
3079386 GTCTTTATAA
Statistics
Matches: 139, Mismatches: 18, Indels: 31
0.74 0.10 0.16
Matches are distributed among these distances:
17 1 0.01
18 7 0.05
19 2 0.01
20 7 0.05
21 22 0.16
22 44 0.32
23 16 0.12
24 10 0.07
25 16 0.12
26 2 0.01
27 12 0.09
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.52
Consensus pattern (22 bp):
ATACTTATATACTTTATATTTA
Found at i:3079800 original size:137 final size:135
Alignment explanation
Indices: 3079513--3079802 Score: 383
Period size: 137 Copynumber: 2.1 Consensus size: 135
3079503 TACTTACTTT
* * *
3079513 ATATTATATGCTTATATACTTTAGTCTTTATAATTATACTTTATATATATATAATATACATACAT
1 ATATTATATACTAAAATACTTTAGTCTTTATAATTATACTTTATATATATATAATATACATACAT
* * * *
3079578 ATACTTTATATTTAATACTTATATACTTTATATTTAATACTTATATACTTATATTTAATGCTTAT
66 ATACTTTATATTTAATACTTATATACTCTATACTTAATACTTATATACTTATATTTAATACCTAT
3079643 ATACTTC
131 ATA--TC
3079650 ATATTATATACTAAAATACTTTAGTCTTTATAATTATACATTT-TATATATATAATATACATATA
1 ATATTATATACTAAAATACTTTAGTCTTTATAATTATAC-TTTATATATATATAATATAC--ATA
*
3079714 CTTATACTTTATATTTAATACTTATATAC-CTATACTTAATACTTATATACTTTATATTATTATA
63 CATATACTTTATATTTAATACTTATATACTCTATACTTAATACTTATATAC-TTATA-T-TTA-A
3079778 TACCTATATA-C
124 TACCTATATATC
*
3079789 A-GTT-TATACTAAAA
1 ATATTATATACTAAAA
3079803 CTTTATATAT
Statistics
Matches: 137, Mismatches: 9, Indels: 14
0.86 0.06 0.09
Matches are distributed among these distances:
137 62 0.45
138 24 0.18
139 38 0.28
140 1 0.01
141 3 0.02
142 9 0.07
ACGTcount: A:0.39, C:0.11, G:0.02, T:0.49
Consensus pattern (135 bp):
ATATTATATACTAAAATACTTTAGTCTTTATAATTATACTTTATATATATATAATATACATACAT
ATACTTTATATTTAATACTTATATACTCTATACTTAATACTTATATACTTATATTTAATACCTAT
ATATC
Found at i:3079814 original size:117 final size:116
Alignment explanation
Indices: 3079599--3079815 Score: 273
Period size: 117 Copynumber: 1.9 Consensus size: 116
3079589 TTAATACTTA
* * *
3079599 TATACTTTATATTTAATACTTATATACTTATATTTAATGCTTATATACTTCATATTATATACTAA
1 TATACTTTATATTTAATACTTATATACCTATACTTAATACTTATATACTTCATATTATATACTAA
** * *
3079664 AATACTTTAGTCTTTATAATTATACATTTTATATATATAATATACATATACT
66 AATACTACAG-CTTTATAATAAAACATTTTATATATATAATATACATATACT
*
3079716 TATACTTTATATTTAATACTTATATACCTATACTTAATACTTATATACTTTATATTATTATA-TA
1 TATACTTTATATTTAATACTTATATACCTATACTTAATACTTATATACTTCATATTA-TATACTA
** *
3079780 CCTATA-TACAG-TTTATACTAAAAC--TTTATATATATA
65 -AAATACTACAGCTTTATAATAAAACATTTTATATATATA
3079816 CACACACACA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
113 12 0.14
115 10 0.11
117 58 0.67
118 7 0.08
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.49
Consensus pattern (116 bp):
TATACTTTATATTTAATACTTATATACCTATACTTAATACTTATATACTTCATATTATATACTAA
AATACTACAGCTTTATAATAAAACATTTTATATATATAATATACATATACT
Found at i:3079909 original size:37 final size:36
Alignment explanation
Indices: 3079835--3079914 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 36
3079825 ACTTTTTCTG
*
3079835 TATA-TATACTTTATATACTTATATACTTTAGTATT
1 TATATTATACTTTATATACTAATATACTTTAGTATT
3079870 TATAATTATACTTTATCTATA-TAATATAC-TTA-TACTT
1 TAT-ATTATACTTTA--TATACTAATATACTTTAGTA-TT
3079907 TATATTAT
1 TATATTAT
3079915 TATAAATGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
35 3 0.08
36 8 0.21
37 17 0.44
38 7 0.18
39 4 0.10
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (36 bp):
TATATTATACTTTATATACTAATATACTTTAGTATT
Found at i:3079947 original size:40 final size:42
Alignment explanation
Indices: 3079894--3079972 Score: 108
Period size: 40 Copynumber: 1.9 Consensus size: 42
3079884 ATCTATATAA
* * *
3079894 TATACTTATACTTTATAT-TAT-TATAAATGTATATATACTT
1 TATACTAAAACTTTATATATATATATAAATATATATATACTT
*
3079934 TATACTAAAACTTTATATATATATATATATATATATATA
1 TATACTAAAACTTTATATATATATATAAATATATATATA
3079973 TATAAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 16 0.48
41 3 0.09
42 14 0.42
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.49
Consensus pattern (42 bp):
TATACTAAAACTTTATATATATATATAAATATATATATACTT
Found at i:3079954 original size:2 final size:2
Alignment explanation
Indices: 3079947--3080104 Score: 94
Period size: 2 Copynumber: 77.5 Consensus size: 2
3079937 ACTAAAACTT
*
3079947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A GTA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * *
3079989 TA AA GTA TA TA -A TA TA TA TA AA GT- TT TA -A TG TA AA GTA TA
1 TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * *
3080029 TA TA CTT TA TA GTT TA TA TA TA TA CA TA TA -A TA TA CT- TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
3080070 CTT TA TA GTT TA TA TA TA TA TA TA TA TA TA TA TA T
1 -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
3080105 TACACTTTAT
Statistics
Matches: 120, Mismatches: 21, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
1 6 0.05
2 106 0.88
3 8 0.07
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3080071 original size:37 final size:39
Alignment explanation
Indices: 3080025--3080119 Score: 133
Period size: 37 Copynumber: 2.5 Consensus size: 39
3080015 TAATGTAAAG
3080025 TATA-TATACTTTATAGTTTATATATATACATATA-ATA
1 TATATTATACTTTATAGTTTATATATATACATATATATA
* *
3080062 TA-CTTATACTTTATAGTTTATATATATATATATATATA
1 TATATTATACTTTATAGTTTATATATATACATATATATA
* *
3080100 TATATTACACTTTATTGTTT
1 TATATTATACTTTATAGTTT
3080120 CACATCATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
37 31 0.62
38 5 0.10
39 14 0.28
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (39 bp):
TATATTATACTTTATAGTTTATATATATACATATATATA
Found at i:3080192 original size:2 final size:2
Alignment explanation
Indices: 3080185--3080285 Score: 54
Period size: 2 Copynumber: 52.0 Consensus size: 2
3080175 TAAATAAGTG
* *
3080185 TA TA TA TA TT TA TA TA CT- TA TA TA CT- TA TA TG TA TA TA CT-
1 TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA
* * * *
3080225 TT TA TA T- TA -A TT TA TA TA CT- TA TA TT TA TA TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
*
3080265 TG TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
3080286 ATTGTTTTAA
Statistics
Matches: 75, Mismatches: 13, Indels: 22
0.68 0.12 0.20
Matches are distributed among these distances:
1 7 0.09
2 64 0.85
3 4 0.05
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (2 bp):
TA
Found at i:3080200 original size:8 final size:8
Alignment explanation
Indices: 3080187--3080282 Score: 65
Period size: 8 Copynumber: 12.0 Consensus size: 8
3080177 AATAAGTGTA
3080187 TATATATT
1 TATATATT
*
3080195 TATATACT
1 TATATATT
*
3080203 TATATACT
1 TATATATT
* *
3080211 TATATGTA
1 TATATATT
3080219 TATACT-TT
1 TATA-TATT
3080227 TATATTAATT
1 TATA-T-ATT
*
3080237 TATATA-C
1 TATATATT
3080244 T-TATATT
1 TATATATT
3080251 TATAT-TT
1 TATATATT
*
3080258 ATATATATG
1 -TATATATT
*
3080267 TATATATA
1 TATATATT
3080275 TATATATT
1 TATATATT
3080283 ATAATTGTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 14
0.74 0.12 0.15
Matches are distributed among these distances:
6 4 0.06
7 4 0.06
8 53 0.76
9 3 0.04
10 6 0.09
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (8 bp):
TATATATT
Found at i:3080215 original size:42 final size:40
Alignment explanation
Indices: 3080160--3080281 Score: 131
Period size: 42 Copynumber: 3.0 Consensus size: 40
3080150 TTATACATTT
*
3080160 TTATATATGTATATTTAAATAAGTGTATATATATTTATATAC
1 TTATATAT-TATATTTATATAA-TGTATATATATTTATATAC
* * *
3080202 TTATATACTTATATGTATATACT-TTTATATTAATTTATATAC
1 TTATATA-TTATATTTATATAATGTATATA-T-ATTTATATAC
*
3080244 TTATAT-TTATATTTATATATATGTATATATATATATAT
1 TTATATATTATATTTATATA-ATGTATATATATTTATAT
3080282 TATAATTGTT
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
40 24 0.36
41 4 0.06
42 38 0.57
43 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (40 bp):
TTATATATTATATTTATATAATGTATATATATTTATATAC
Found at i:3080253 original size:14 final size:14
Alignment explanation
Indices: 3080189--3080255 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 14
3080179 TAAGTGTATA
3080189 TATATTTATATACT
1 TATATTTATATACT
*
3080203 TATATACTTATAT-GT
1 TATAT--TTATATACT
3080218 ATATACTTT-TATA-T
1 -TATA-TTTATATACT
3080232 TA-ATTTATATACT
1 TATATTTATATACT
3080245 TATATTTATAT
1 TATATTTATAT
3080256 TTATATATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 16
0.72 0.02 0.26
Matches are distributed among these distances:
11 3 0.07
12 5 0.11
13 5 0.11
14 17 0.39
15 3 0.07
16 10 0.23
17 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (14 bp):
TATATTTATATACT
Found at i:3081307 original size:538 final size:545
Alignment explanation
Indices: 3080267--3081577 Score: 1760
Period size: 561 Copynumber: 2.4 Consensus size: 545
3080257 TATATATATG
* * *
3080267 TATATATATATATATTATAATTGTTTTAATTTTCCTCAACTTTTGAAATTAATGCAAATCAATCC
1 TATATATATATATATTATAATTGTTTTAATTTTCCCCAACTTTTGAAATTAATGCAATTCAGTCC
* * * * *
3080332 ATTTTACAATTTTTCCTCACATTTTATAATTTTTTTATTTGAACCTTTTATGTTGTTTATTGTAT
66 ATTTTACAAATTTTCCTCACATTTTACAATTTTTTGATTTGATCCTTTTATGTTATTTATTGTAT
* ** * *
3080397 TTAAACTTTAATTTCCAATCTCATATTTTTTTCAATTTAGTCCTTCAAATTATATTTGTTTCTGA
131 TTAAATTTTAATTTGTAAT-TCATA-TTTGTTCAATTTAGTCCTTCAAATTATATTTGTATCTGA
* **
3080462 AATTGACCCATACTTATTTATATTTTTTTAATTTAGTTAAACCCTATAAAATGTAAATCACATAA
194 AATTGACCCATACTTATTCATATTTTTTTAATTTAAATAAACCCTATAAAATGTAAATCACATAA
* * ***
3080527 TAATTTTCTTTTCAAGTTTTGTTCACCAGGTTTTTAAATGTATGCAATTTAGGCCATTTTTATAT
259 TAAATTTCTTTTCAAGTTATGTTCACCAACCTTTTAAATGTATGCAATTTAGGCCATTTTTATAT
* * *
3080592 TAATATCAACTTCACGTTTTATAATTTCAATTTCATCCCTCATCAATGTGTGTTGCTTAATTTAT
324 TAATATCAACTTCACATTTTATAATTTCAATTTCATCCCTCATCAATGCGAGTTGCTTAATTTAT
* *
3080657 TCAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTAGTACTTTATATACATATATAAATTATA
389 TCAAATTTTTATTTCCAATTTCATGTTTGTTCAATTTAGTACTTTATATACATATATAAACTATA
* *
3080722 AAGATAAGTATATATGTATATATATAAAGTATAATGTGCATTATATATACAT-GCATCA-T-ATT
454 AAGATAAGTATAGA-GTATATATATAAAGTATAATGTG-A-TATATATACATAGCATAAGTAATT
3080784 ATCATA-AAAT-TC-A-T-T-AT-ACA-T-A
516 AT-ATATAAATATCGATTATCATAACATTCA
*
3080806 -ATATATATATATATTATAATTGTTTTAATTTTCCCCAACTTTTGGAATTAATGCAATTCAGTCC
1 TATATATATATATATTATAATTGTTTTAATTTTCCCCAACTTTTGAAATTAATGCAATTCAGTCC
* * *
3080870 ATTTTACAAAATTTCCTCACATTTTACAATTTTTTGATTTGATCCTTTTATGTCATTTAATGTAT
66 ATTTTACAAATTTTCCTCACATTTTACAATTTTTTGATTTGATCCTTTTATGTTATTTATTGTAT
*
3080935 TTAAATTTTAATTTGTAAGTTCATATTTGTTCAATTTAGTCCTTCAAATTATATTTGCATCTGAA
131 TTAAATTTTAATTTGTAA-TTCATATTTGTTCAATTTAGTCCTTCAAATTATATTTGTATCTGAA
*
3081000 ATTGACCCATAGTTATTCATA-TTTTTTAATTCACTTAAAATAAACCCTATAAAATGTAAATCAC
195 ATTGACCCATACTTATTCATATTTTTTTAA-T---TT-AAATAAACCCTATAAAATGTAAATCAC
*
3081064 ATAATAAATTTCTTTTCTAA-TTATGTTCACCAACCTTTTAAATGTATGCAATTTAGTCCATTTT
255 ATAATAAATTTCTTTTC-AAGTTATGTTCACCAACCTTTTAAATGTATGCAATTTAGGCCATTTT
* *
3081128 TATATTAATATCAGCTTCACATTTTATAATAAATTCAATTTCATCCCTCATCGATGCGAGTTGCT
319 TATATTAATATCAACTTCACATTTTATAAT---TTCAATTTCATCCCTCATCAATGCGAGTTGCT
*
3081193 TAATTTATTCAAATTTTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATAT
381 TAATTTATTCAAATTTTTATTTCCAATTTCATGTTTGTTCAATTTAGTACTTTATATACATATAT
* * * *
3081258 AAACTATAAAGTATAAGTATAGA-TATATATATATA-TAT-ATGTGTATATATATATAAAGTATA
446 AAACTATAAAG-ATAAGTATAGAGTATATATATAAAGTATAATGTG-ATATATATACATAGCATA
*
3081320 ATGTACATTATATATACATGCATCGTATTATCATAACATTCA
509 A-GTA-ATTATATATAAAT--ATCG-ATTATCATAACATTCA
* *
3081362 TTATACATATTATATATATTATAATTATTTTAATTTTTCCCCAACTTTTGAAATTAATGAAATTC
1 -TAT--ATA-TATATATATTATAATTGTTTTAA-TTTTCCCCAACTTTTGAAATTAATGCAATTC
** *
3081427 AGTCCATTTTAC-AATTTTCCTCACATTTTACAATTTTTTGATTTGATTATTTTATGTTTTTTAT
61 AGTCCATTTTACAAATTTTCCTCACATTTTACAATTTTTTGATTTGATCCTTTTATGTTATTTAT
* * *
3081491 TTTATTTAAATTTTAATTTGTAATTTCATATTTGTGCAATTTAGTCATTCAAATTATATTTGTAT
126 TGTATTTAAATTTTAATTTGTAA-TTCATATTTGTTCAATTTAGTCCTTCAAATTATATTTGTAT
*
3081556 TTGAAATTGACCCATACTTATT
190 CTGAAATTGACCCATACTTATT
3081578 TATTGTAACC
Statistics
Matches: 678, Mismatches: 60, Indels: 46
0.86 0.08 0.06
Matches are distributed among these distances:
536 8 0.01
537 57 0.08
538 137 0.20
539 1 0.00
540 11 0.02
541 118 0.17
542 5 0.01
543 12 0.02
544 105 0.15
545 18 0.03
548 2 0.00
550 1 0.00
551 1 0.00
552 1 0.00
553 2 0.00
554 3 0.00
555 1 0.00
556 1 0.00
558 2 0.00
560 3 0.00
561 148 0.22
562 41 0.06
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.48
Consensus pattern (545 bp):
TATATATATATATATTATAATTGTTTTAATTTTCCCCAACTTTTGAAATTAATGCAATTCAGTCC
ATTTTACAAATTTTCCTCACATTTTACAATTTTTTGATTTGATCCTTTTATGTTATTTATTGTAT
TTAAATTTTAATTTGTAATTCATATTTGTTCAATTTAGTCCTTCAAATTATATTTGTATCTGAAA
TTGACCCATACTTATTCATATTTTTTTAATTTAAATAAACCCTATAAAATGTAAATCACATAATA
AATTTCTTTTCAAGTTATGTTCACCAACCTTTTAAATGTATGCAATTTAGGCCATTTTTATATTA
ATATCAACTTCACATTTTATAATTTCAATTTCATCCCTCATCAATGCGAGTTGCTTAATTTATTC
AAATTTTTATTTCCAATTTCATGTTTGTTCAATTTAGTACTTTATATACATATATAAACTATAAA
GATAAGTATAGAGTATATATATAAAGTATAATGTGATATATATACATAGCATAAGTAATTATATA
TAAATATCGATTATCATAACATTCA
Found at i:3082460 original size:20 final size:20
Alignment explanation
Indices: 3082435--3082490 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
3082425 TATCCTATAT
3082435 CACTATAAAT-AAATAATTAG
1 CACTATAAATAAAAT-ATTAG
3082455 CACTATAAATAAAATATTAG
1 CACTATAAATAAAATATTAG
3082475 CACTA-AGAATAAAATA
1 CACTATA-AATAAAATA
3082491 AAATGAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.85
21 4 0.12
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (20 bp):
CACTATAAATAAAATATTAG
Found at i:3083039 original size:29 final size:29
Alignment explanation
Indices: 3083009--3083324 Score: 181
Period size: 29 Copynumber: 11.2 Consensus size: 29
3082999 ATTCTAGGAA
* *
3083009 TATTTTTAAAAGTGTGCTAGTTTCGTAAA
1 TATTTTTAAAAGTGTGCTATTTTCGTAAT
* *
3083038 TATGTTTAAAA-TGATGTTAGTTTT-GTAAT
1 TATTTTTAAAAGTG-TGCTA-TTTTCGTAAT
**** *
3083067 TGATTTCGGTAAGTGT--TATTTTCATAAT
1 T-ATTTTTAAAAGTGTGCTATTTTCGTAAT
* ** *
3083095 TATTTTTAAAAGGGCACTATTTTCCTAAT
1 TATTTTTAAAAGTGTGCTATTTTCGTAAT
*
3083124 TATTTTTAAAAG-GTGCTATTTTTGTAAT
1 TATTTTTAAAAGTGTGCTATTTTCGTAAT
* *
3083152 TATTTTTAAAAGAT-T-TTATTTTCATAAT
1 TATTTTTAAAAG-TGTGCTATTTTCGTAAT
* *
3083180 TATTTTTAAAA-TGT--TATTTTGGGAAT
1 TATTTTTAAAAGTGTGCTATTTTCGTAAT
* * *
3083206 TATTTTTAAAACG-GTGATATTTTGGGAAT
1 TATTTTTAAAA-GTGTGCTATTTTCGTAAT
* *** * *
3083235 TATTTTTACAACAATGATATTTTGGTAAT
1 TATTTTTAAAAGTGTGCTATTTTCGTAAT
** * *
3083264 TATTTTTAAAACAGTGATATTTTGGTAAT
1 TATTTTTAAAAGTGTGCTATTTTCGTAAT
** * *
3083293 TATTTAAAAAAG-GTGATATTTTTGTAA-
1 TATTTTTAAAAGTGTGCTATTTTCGTAAT
3083320 TATTT
1 TATTT
3083325 GACTTTGGAC
Statistics
Matches: 235, Mismatches: 37, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
26 21 0.09
27 20 0.09
28 68 0.29
29 115 0.49
30 9 0.04
31 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.50
Consensus pattern (29 bp):
TATTTTTAAAAGTGTGCTATTTTCGTAAT
Found at i:3083143 original size:28 final size:28
Alignment explanation
Indices: 3083091--3083324 Score: 226
Period size: 29 Copynumber: 8.3 Consensus size: 28
3083081 GTTATTTTCA
**
3083091 TAATTATTTTTAAAAGG-GCACTATTTTCC
1 TAATTATTTTTAAAAGGTG-A-TATTTTGG
* *
3083120 TAATTATTTTTAAAAGGTGCTATTTTTG
1 TAATTATTTTTAAAAGGTGATATTTTGG
* ** **
3083148 TAATTATTTTTAAAAGATTTTATTTTCA
1 TAATTATTTTTAAAAGGTGATATTTTGG
*
3083176 TAATTATTTTTAAAA--TGTTATTTTGG
1 TAATTATTTTTAAAAGGTGATATTTTGG
*
3083202 GAATTATTTTTAAAACGGTGATATTTTGG
1 TAATTATTTTTAAAA-GGTGATATTTTGG
* *
3083231 GAATTATTTTTACAACA-ATGATATTTTGG
1 TAATTATTTTTA-AA-AGGTGATATTTTGG
*
3083260 TAATTATTTTTAAAACAGTGATATTTTGG
1 TAATTATTTTTAAAA-GGTGATATTTTGG
** *
3083289 TAATTATTTAAAAAAGGTGATATTTTTG
1 TAATTATTTTTAAAAGGTGATATTTTGG
3083317 TAA-TATTT
1 TAATTATTT
3083325 GACTTTGGAC
Statistics
Matches: 177, Mismatches: 20, Indels: 18
0.82 0.09 0.08
Matches are distributed among these distances:
26 22 0.12
27 6 0.03
28 60 0.34
29 85 0.48
30 3 0.02
31 1 0.01
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.50
Consensus pattern (28 bp):
TAATTATTTTTAAAAGGTGATATTTTGG
Found at i:3093616 original size:16 final size:16
Alignment explanation
Indices: 3093465--3093617 Score: 97
Period size: 16 Copynumber: 9.7 Consensus size: 16
3093455 TAGTATTTTA
3093465 AATAATAATAATAA-T
1 AATAATAATAATAATT
* * * *
3093480 AAGCACTACTAACAATT
1 AA-TAATAATAATAATT
*
3093497 AAT-A-AAT-ATAAGT
1 AATAATAATAATAATT
*
3093510 AATAATAATTATAATT
1 AATAATAATAATAATT
3093526 AATAATAATAA-ATATT
1 AATAATAATAATA-ATT
* *
3093542 GATAACAATTAATAA-T
1 AATAATAA-TAATAATT
*
3093558 AATAATAATTAATATTT
1 AATAATAA-TAATAATT
* *
3093575 ATTAATTAT-ATAATT
1 AATAATAATAATAATT
3093590 AATAAATAATAATAA-T
1 AAT-AATAATAATAATT
3093606 AACTAATAATAA
1 AA-TAATAATAA
3093618 CCACTAATAA
Statistics
Matches: 105, Mismatches: 21, Indels: 23
0.70 0.14 0.15
Matches are distributed among these distances:
13 7 0.07
14 3 0.03
15 13 0.12
16 62 0.59
17 19 0.18
18 1 0.01
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAATAATAATAATT
Found at i:3093630 original size:3 final size:3
Alignment explanation
Indices: 3093465--3093617 Score: 85
Period size: 3 Copynumber: 47.7 Consensus size: 3
3093455 TAGTATTTTA
* * * *
3093465 AAT AAT AAT AAT AAT AAGC ACT ACT AAC AATT AAT AA- ATAT AAGT AAT
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AA-T AAT AAT A-AT AA-T AAT
* * * *
3093513 AAT AAT TAT AATT AAT AAT AAT AAAT ATT GAT AAC AATT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT AAT AA-T AAT AAT AAT
* * *
3093561 AAT AATT AAT ATTT ATT AAT TAT -AT AATT AAT AAAT AAT AAT AAT AACT
1 AAT AA-T AAT A-AT AAT AAT AAT AAT AA-T AAT -AAT AAT AAT AAT AA-T
3093610 AAT AAT AA
1 AAT AAT AA
3093618 CCACTAATAA
Statistics
Matches: 119, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
2 3 0.03
3 87 0.73
4 29 0.24
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:3093631 original size:13 final size:13
Alignment explanation
Indices: 3093596--3093633 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3093586 AATTAATAAA
*
3093596 TAATAATAATAAC
1 TAATAATAACAAC
*
3093609 TAATAATAACCAC
1 TAATAATAACAAC
3093622 TAATAATAACAA
1 TAATAATAACAA
3093634 GTTCCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (13 bp):
TAATAATAACAAC
Found at i:3099030 original size:40 final size:40
Alignment explanation
Indices: 3099006--3099104 Score: 189
Period size: 40 Copynumber: 2.5 Consensus size: 40
3098996 TTTTATGTTT
3099006 GTTTAATTAAATAAATGAATATGAATAAAATTTTATTCTC
1 GTTTAATTAAATAAATGAATATGAATAAAATTTTATTCTC
3099046 GTTTAATTAAATAAATGAATATGAATAAAATTTTATTCTC
1 GTTTAATTAAATAAATGAATATGAATAAAATTTTATTCTC
*
3099086 GTTTAATTAAATGAATGAA
1 GTTTAATTAAATAAATGAA
3099105 CATAAACAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 58 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.41
Consensus pattern (40 bp):
GTTTAATTAAATAAATGAATATGAATAAAATTTTATTCTC
Found at i:3099192 original size:32 final size:32
Alignment explanation
Indices: 3099151--3099213 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
3099141 TAACGTTTGC
* *
3099151 TAATTCGTTCATTTATGTT-CATTTATATTTAG
1 TAATACGTTCATTTA-GTTAAATTTATATTTAG
*
3099183 TAATACGTTCTTTTAGTTAAATTTATATTTA
1 TAATACGTTCATTTAGTTAAATTTATATTTA
3099214 TCTTTATATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.29, C:0.08, G:0.08, T:0.56
Consensus pattern (32 bp):
TAATACGTTCATTTAGTTAAATTTATATTTAG
Found at i:3103987 original size:15 final size:16
Alignment explanation
Indices: 3103969--3103998 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3103959 TCCTAGATGA
3103969 TGGGTTTA-ATTTGTT
1 TGGGTTTAGATTTGTT
3103984 TGGGTTTAGATTTGT
1 TGGGTTTAGATTTGT
3103999 AAATGAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (16 bp):
TGGGTTTAGATTTGTT
Found at i:3106498 original size:24 final size:24
Alignment explanation
Indices: 3106464--3106572 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
3106454 AAATGGAGAT
* *
3106464 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAGAACAGAATTCAG
* * *
3106488 ATCAGATATCAGAACAAAATCCAG
1 ATCAGAAATCAGAACAGAATTCAG
*
3106512 TTCAGAAATCAGAACAGAATTCA-
1 ATCAGAAATCAGAACAGAATTCAG
* * *
3106535 AGTAATG-AATCAAAATAGAATTCA-
1 A-TCA-GAAATCAGAACAGAATTCAG
3106559 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
3106573 TAAAATATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 65 0.97
25 1 0.01
ACGTcount: A:0.51, C:0.16, G:0.13, T:0.20
Consensus pattern (24 bp):
ATCAGAAATCAGAACAGAATTCAG
Found at i:3108835 original size:13 final size:13
Alignment explanation
Indices: 3108817--3108846 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3108807 ACTTTTTCGA
*
3108817 TCAAAGTCAATGG
1 TCAAAGTCAACGG
3108830 TCAAAGTCAACGG
1 TCAAAGTCAACGG
3108843 TCAA
1 TCAA
3108847 TGGCAGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (13 bp):
TCAAAGTCAACGG
Found at i:3112577 original size:2 final size:2
Alignment explanation
Indices: 3112570--3112594 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3112560 GGGTTTGAAG
3112570 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3112595 TAGGATCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3118290 original size:12 final size:12
Alignment explanation
Indices: 3118273--3118298 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3118263 AGGAACTCAT
3118273 CCTATTGGAGTG
1 CCTATTGGAGTG
3118285 CCTATTGGAGTG
1 CCTATTGGAGTG
3118297 CC
1 CC
3118299 GTGTTCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (12 bp):
CCTATTGGAGTG
Found at i:3125780 original size:12 final size:12
Alignment explanation
Indices: 3125763--3125792 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3125753 TTAATTGCGA
*
3125763 AAATTAGAATTT
1 AAATTAAAATTT
3125775 AAATTAAAATTT
1 AAATTAAAATTT
3125787 AAATTA
1 AAATTA
3125793 TTCGATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:3127390 original size:13 final size:13
Alignment explanation
Indices: 3127372--3127397 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3127362 GGTGAATAAT
3127372 AATAAATAAAAAC
1 AATAAATAAAAAC
3127385 AATAAATAAAAAC
1 AATAAATAAAAAC
3127398 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAC
Found at i:3127527 original size:33 final size:31
Alignment explanation
Indices: 3127446--3127546 Score: 125
Period size: 31 Copynumber: 3.2 Consensus size: 31
3127436 CTATATACTA
* *
3127446 TATATAAATTTTCAAAAATGTTTTTCAAAAAAC
1 TATAT-AATTTTTAAAAATGTTTTT-AAAAAAT
*
3127479 TA-ATAATTTTTAAAAATGTTCTTTTAAAAAT
1 TATATAATTTTTAAAAATGTT-TTTAAAAAAT
3127510 TATATAATTTTTTAAAAATG-TTTTAAAAAAT
1 TATATAA-TTTTTAAAAATGTTTTTAAAAAAT
3127541 TATATA
1 TATATA
3127547 TTATATATCA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
31 37 0.61
32 10 0.16
33 14 0.23
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.46
Consensus pattern (31 bp):
TATATAATTTTTAAAAATGTTTTTAAAAAAT
Found at i:3127552 original size:104 final size:104
Alignment explanation
Indices: 3127427--3127696 Score: 277
Period size: 104 Copynumber: 2.6 Consensus size: 104
3127417 AACTGTTTCT
* *
3127427 TTTTAAAAACTATATACTATATATAAATTTTCAAAAATGTTTTTCAAAAA-ACTA-A-TA-AT-T
1 TTTTAAAAA-TATATATTATATAT-AGTTTTCAAAAATGTTTTT-AAAAATA-TATATTATATGT
* *
3127487 TTTAAAAATGTTCTTTTAAAAATTATATA-ATTTTTTAAAAATG
62 TTTAAAAATGTT-TTTCAAAAATTATATATATATTTTAAAAATG
* *
3127530 TTTTAAAAAATTATATATTATATATCAGTTTTCAAAAATG-CTCTAAAAATTATATATTATATGT
1 TTTT-AAAAA-TATATATTATATAT-AGTTTTCAAAAATGTTTTTAAAAA-TATATATTATATGT
*
3127594 TTTCAAAATGTTTTTCAAAAATTATATATTATATTTTAAAAATG
62 TTTAAAAATGTTTTTCAAAAATTATATA-TATATTTTAAAAATG
* * * * *
3127638 TTTTGAAAATATATATAATATATAGTTTTTAAAAGTG-TTTTAAAAACCATATATTATAT
1 TTTTAAAAATATATATTATATATAGTTTTCAAAAATGTTTTTAAAAA-TATATATTATAT
3127697 ACGTATTTTC
Statistics
Matches: 141, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
102 5 0.04
103 8 0.06
104 33 0.23
105 32 0.23
106 30 0.21
107 16 0.11
108 17 0.12
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (104 bp):
TTTTAAAAATATATATTATATATAGTTTTCAAAAATGTTTTTAAAAATATATATTATATGTTTTA
AAAATGTTTTTCAAAAATTATATATATATTTTAAAAATG
Found at i:3127653 original size:108 final size:104
Alignment explanation
Indices: 3127486--3127696 Score: 264
Period size: 105 Copynumber: 2.0 Consensus size: 104
3127476 AACTAATAAT
* *
3127486 TTTTAAAAATGTTCTTTTAAAAATTATATAATTTTTTAAAAATGTTTTAAAAAATTATATATTAT
1 TTTTAAAAATGTTCTTTCAAAAATTATATAATATTTTAAAAATGTTTTAAAAAATTATATA--AT
**
3127551 ATATCAGTTTTCAAAAATGCTCTAAAAATTATATATTATATG
64 ATAT-AGTTTTCAAAAATGCTCTAAAAACCATATATTATATG
* *
3127593 TTTTCAAAATGTT-TTTCAAAAATTATATATTATATTTTAAAAATGTTTT-GAAAATATATATAA
1 TTTTAAAAATGTTCTTTCAAAAATTATATA--ATATTTTAAAAATGTTTTAAAAAAT-TATATAA
* * * *
3127656 TATATAGTTTTTAAAAGTGTTTTAAAAACCATATATTATAT
63 TATATAGTTTTCAAAAATGCTCTAAAAACCATATATTATAT
3127697 ACGTATTTTC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
105 30 0.33
106 21 0.23
107 17 0.19
108 23 0.25
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (104 bp):
TTTTAAAAATGTTCTTTCAAAAATTATATAATATTTTAAAAATGTTTTAAAAAATTATATAATAT
ATAGTTTTCAAAAATGCTCTAAAAACCATATATTATATG
Found at i:3127697 original size:36 final size:37
Alignment explanation
Indices: 3127508--3127697 Score: 164
Period size: 34 Copynumber: 5.2 Consensus size: 37
3127498 TCTTTTAAAA
*
3127508 ATTATATAATTTTTTAAAAATGTTTTAAAAAATTATAT
1 ATTATAT-AGTTTTTAAAAATGTTTTAAAAAATTATAT
* * *
3127546 ATTATATATCAGTTTTCAAAAATGCTCT-AAAAATTATAT
1 A-T-TATAT-AGTTTTTAAAAATGTTTTAAAAAATTATAT
* *
3127585 ATTATAT-G-TTTTCAAAATGTTTTTCAAAAATTATAT
1 ATTATATAGTTTTTAAAAATG-TTTTAAAAAATTATAT
*
3127621 A-T-TATA--TTTTAAAAATGTTTT-GAAAATATATAT
1 ATTATATAGTTTTTAAAAATGTTTTAAAAAAT-TATAT
* * **
3127654 AATATATAGTTTTTAAAAGTGTTTT-AAAAACCATAT
1 ATTATATAGTTTTTAAAAATGTTTTAAAAAATTATAT
3127690 ATTATATA
1 ATTATATA
3127698 CGTATTTTCA
Statistics
Matches: 126, Mismatches: 16, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
32 5 0.04
33 10 0.08
34 23 0.18
35 8 0.06
36 23 0.18
37 23 0.18
38 2 0.02
39 13 0.10
40 19 0.15
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (37 bp):
ATTATATAGTTTTTAAAAATGTTTTAAAAAATTATAT
Found at i:3128588 original size:30 final size:29
Alignment explanation
Indices: 3128542--3128624 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
3128532 ATCAAATTCG
3128542 AAGGTTTTGTGTTTCAAGAGAAAC-ATTTTCA
1 AAGGTTTT-T-TTTCAAGAGAAACAATTTT-A
3128573 AAGGGTTTTTTTTCAAGAGAAACAATTTTA
1 AA-GGTTTTTTTTCAAGAGAAACAATTTTA
**
3128603 AAGGTTTTTTTAAAAGAGAAAC
1 AAGGTTTTTTTTCAAGAGAAAC
3128625 TGTCTCAAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
29 18 0.38
30 16 0.33
31 8 0.17
32 6 0.12
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.37
Consensus pattern (29 bp):
AAGGTTTTTTTTCAAGAGAAACAATTTTA
Found at i:3128613 original size:31 final size:31
Alignment explanation
Indices: 3128542--3128613 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
3128532 ATCAAATTCG
* *
3128542 AAGGTTTTGTGTTTCAAGAGAAACATTTTCA
1 AAGGTTTTTTTTTTCAAGAGAAACATTTTCA
*
3128573 AAGG-GTTTTTTTTCAAGAGAAACAATTTT-A
1 AAGGTTTTTTTTTTCAAGAGAAAC-ATTTTCA
3128603 AAGGTTTTTTT
1 AAGGTTTTTTT
3128614 AAAAGAGAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 21 0.60
31 14 0.40
ACGTcount: A:0.32, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
AAGGTTTTTTTTTTCAAGAGAAACATTTTCA
Found at i:3128727 original size:36 final size:36
Alignment explanation
Indices: 3128620--3128804 Score: 255
Period size: 36 Copynumber: 5.1 Consensus size: 36
3128610 TTTTAAAAGA
* *
3128620 GAAACTGTCTCAAGGGAGACAGAATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGAC-GAAATTTGTTTCAAGG
* *
3128657 GAAACTGTTTCAA-AGATTGACAAAAATTTGTTTCAAGG
1 GAAACTGTCTCAAGAGA--GAC-GAAATTTGTTTCAAGG
* *
3128695 GAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGT
1 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGG
* *
3128731 GAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGG
3128767 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGG
3128803 GA
1 GA
3128805 GACGAAATTT
Statistics
Matches: 131, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
36 84 0.64
37 15 0.11
38 30 0.23
39 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGG
Found at i:3128776 original size:72 final size:73
Alignment explanation
Indices: 3128620--3128804 Score: 284
Period size: 72 Copynumber: 2.5 Consensus size: 73
3128610 TTTTAAAAGA
* * *
3128620 GAAACTGTCTCAAGGGAGACAGAATTTTGTTTCAAGGGAAACTGTTTCAAAGATTGACAAAAATT
1 GAAACTGTCTCAAGGGAGAC-GAAATTTGTTTCAAGGGAAACTGTCTCAAAGA-TGACAAAAATA
3128685 TGTTTCAAGG
64 TGTTTCAAGG
*
3128695 GAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGTGAAACTGTCTCAAGAGA-GAC-AAAATAT
1 GAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAA-AGATGACAAAAATAT
3128758 GTTTCAAGG
65 GTTTCAAGG
*
3128767 GAAACTGTCTCAAGAGAGACGAAATTTGTTTCAAGGGA
1 GAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGA
3128805 GACGAAATTT
Statistics
Matches: 103, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
72 51 0.50
73 3 0.03
74 26 0.25
75 23 0.22
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (73 bp):
GAAACTGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAAGATGACAAAAATATG
TTTCAAGG
Found at i:3128800 original size:21 final size:21
Alignment explanation
Indices: 3128776--3128861 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 21
3128766 GGAAACTGTC
3128776 TCAAGAGAGACGAAATTTGTT
1 TCAAGAGAGACGAAATTTGTT
*
3128797 TCAAGGGAGACGAAATTTGTT
1 TCAAGAGAGACGAAATTTGTT
* *
3128818 TC-A-AG-G--GAAA-CTGTC
1 TCAAGAGAGACGAAATTTGTT
*
3128833 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACGAAATTTGTT
3128854 TCAAGAGA
1 TCAAGAGA
3128862 AACTGTCTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
15 5 0.10
16 5 0.10
17 2 0.04
18 2 0.04
19 1 0.02
20 4 0.08
21 33 0.63
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACGAAATTTGTT
Found at i:3128807 original size:57 final size:57
Alignment explanation
Indices: 3128740--3128861 Score: 208
Period size: 57 Copynumber: 2.1 Consensus size: 57
3128730 TGAAACTGTC
*
3128740 TCAAGAGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTTGTT
1 TCAAGAGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
* * *
3128797 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
3128854 TCAAGAGA
1 TCAAGAGA
3128862 AACTGTCTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (57 bp):
TCAAGAGAGACAAAATATGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTT
Found at i:3128813 original size:93 final size:93
Alignment explanation
Indices: 3128704--3128894 Score: 330
Period size: 93 Copynumber: 2.1 Consensus size: 93
3128694 GGAAACTGTC
* *
3128704 TCAAGGGAGACGAAATTTGTTTCAAGTGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGGGA
1 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGAGA
*
3128769 AACTGTCTCAAGAGAGACGAAA-TTTGTT
66 AACTGTCTCAAGAGAGAC-AAATTTTATT
*
3128797 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGA
1 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGAGA
3128862 AACTGTCTCAAGAGAGACAAATTTTATT
66 AACTGTCTCAAGAGAGACAAATTTTATT
3128890 TCAAG
1 TCAAG
3128895 AAAAACAATC
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
92 3 0.03
93 90 0.97
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (93 bp):
TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATATGTTTCAAGAGA
AACTGTCTCAAGAGAGACAAATTTTATT
Found at i:3128837 original size:36 final size:35
Alignment explanation
Indices: 3128797--3128900 Score: 145
Period size: 36 Copynumber: 2.9 Consensus size: 35
3128787 GAAATTTGTT
* *
3128797 TCAAGGGAGACGAAATTTGTTTCAAGGGAAACTGTC
1 TCAAGAGAGAC-AAATTTGTTTCAAGAGAAACTGTC
3128833 TCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
1 TCAAGAGAGAC-AAATTTGTTTCAAGAGAAACTGTC
* *
3128869 TCAAGAGAGACAAATTTTATTTCAAGAAAAAC
1 TCAAGAGAGACAAA-TTTGTTTCAAGAGAAAC
3128901 AATCTCAAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 3 0.05
36 59 0.95
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.25
Consensus pattern (35 bp):
TCAAGAGAGACAAATTTGTTTCAAGAGAAACTGTC
Found at i:3129119 original size:84 final size:84
Alignment explanation
Indices: 3128999--3129542 Score: 695
Period size: 84 Copynumber: 6.5 Consensus size: 84
3128989 TCGGGGGTCT
* * *
3128999 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCC-TTGGAGCTGAGCGTAG
3129063 TCGAACTCAAAGGTCTTTTG
65 TCGAACTCAAAGGTCTTTTG
* * * * *
3129083 TTGGCAGACAACCCTTCTAGGCTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
3129148 CGAACTCAAAGGTCTTTTG
66 CGAACTCAAAGGTCTTTTG
* * * * *
3129167 TTGGCAGACAACCCTTCTAGGCTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* *
3129232 CGAACTCGAAGGTCTTTGG
66 CGAACTCAAAGGTCTTTTG
* * * * * *
3129251 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATAATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
***
3129316 TCGAACTCGGGGGTC---T-
65 TCGAACTCAAAGGTCTTTTG
* * *
3129332 TTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAG
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCC-TTGGAGCTGAGCGTAG
3129396 TCGAACTCAAAGGTCTTTTG
65 TCGAACTCAAAGGTCTTTTG
* * * * * *
3129416 TTAGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
3129481 CAAACTCGAAGGTCTTTGG
66 CGAACTCAAAGGTCTTTTG
3129500 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGAT
3129543 TTGTTTAAAA
Statistics
Matches: 400, Mismatches: 52, Indels: 16
0.85 0.11 0.03
Matches are distributed among these distances:
80 24 0.06
81 44 0.11
83 5 0.01
84 300 0.75
85 27 0.07
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCAAAGGTCTTTTG
Found at i:3129389 original size:249 final size:250
Alignment explanation
Indices: 3128904--3129539 Score: 840
Period size: 249 Copynumber: 2.6 Consensus size: 250
3128894 GAAAAACAAT
* * * * * * *
3128904 CTCAAAGGT-TTTTGTTGACAGATAACTCC-TCTAGCCTTGAGTTATGCTATAAATGATGTGCCC
1 CTCAAAGGTCTTTTGTTGGCAGACAAC-CCTTCTAGACTTAAGTTGTGCTACAAATGATATG-CC
* * * * ** * *
3128967 TCGGAGCTGAGTGGAATCGAACTCGGGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCT
64 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTT
* * * *
3129028 ATACTGCAAATGATGTGCCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGTTGGCAGACA
129 ATACTGCAAATAATGTGCCCTCGAGCTGAGCGTAATCGAACTCAAAGGTC--TTGTTGGCAGACA
* * * *
3129093 ACCCTTCTAGGCTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
192 ACCCTTCTAGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
* *
3129152 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGGCTTAAGTTGTGCTGCAAATGATATGCCTT
1 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTT
3129217 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
66 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* *** * *
3129282 ACTGCAAATAATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC-T-TTGGCAGATAGCC
131 ACTGCAAATAATGTGCCCTCG-AGCTGAGCGTAATCGAACTCAAAGGTCTTGTTGGCAGACAACC
* *
3129345 CTTCTCGACTTAAGCTATACTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCGAA
195 CTTCTAGACTTAAGCTATACTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAA
*
3129401 CTCAAAGGTCTTTTGTTAGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTT
1 CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTT
*
3129466 GGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
66 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
3129531 ACTGCAAAT
131 ACTGCAAAT
3129540 GATTTGTTTA
Statistics
Matches: 344, Mismatches: 36, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
248 38 0.11
249 233 0.68
250 4 0.01
252 47 0.14
253 22 0.06
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (250 bp):
CTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTACAAATGATATGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
ACTGCAAATAATGTGCCCTCGAGCTGAGCGTAATCGAACTCAAAGGTCTTGTTGGCAGACAACCC
TTCTAGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
Found at i:3130887 original size:95 final size:95
Alignment explanation
Indices: 3130720--3130906 Score: 286
Period size: 95 Copynumber: 2.0 Consensus size: 95
3130710 ATGTAAACAC
* * * * * *
3130720 CTTTATTAGGTTAGCTGAAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCCTTAGAGGGA
1 CTTTATCAGGCTAGCTGAAATATTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGGA
*
3130785 CAGCTCAAGCTTTATTGTATAGTATAATCAT
66 CAACTCAAGCTTTATTGTATA-TATAATCAT
*
3130816 CTTTATCAGGCTAGCTG-AATATTATCCATAAAGCCAGGGCATTTAACCAATTGCTTTAGAGGGA
1 CTTTATCAGGCTAGCTGAAATATTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGGA
3130880 CAACTCAAGCTTTATTGTATATATAAT
66 CAACTCAAGCTTTATTGTATATATAAT
3130907 AGTATAATCT
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
94 6 0.07
95 62 0.75
96 15 0.18
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (95 bp):
CTTTATCAGGCTAGCTGAAATATTATCCATAAAGCCAGGGCATTTAACCAATTGCCTTAGAGGGA
CAACTCAAGCTTTATTGTATATATAATCAT
Found at i:3134263 original size:12 final size:12
Alignment explanation
Indices: 3134246--3134275 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3134236 TTAATTGCGA
*
3134246 AAATTAGAATTT
1 AAATTAAAATTT
3134258 AAATTAAAATTT
1 AAATTAAAATTT
3134270 AAATTA
1 AAATTA
3134276 TTCGATCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
AAATTAAAATTT
Found at i:3135873 original size:13 final size:13
Alignment explanation
Indices: 3135855--3135880 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3135845 GTTGAATAAT
3135855 AATAAATAAAAAC
1 AATAAATAAAAAC
3135868 AATAAATAAAAAC
1 AATAAATAAAAAC
3135881 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAC
Found at i:3136000 original size:32 final size:31
Alignment explanation
Indices: 3135929--3136029 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
3135919 CTATATACTA
* *
3135929 TATATAAATTTTCAAAAATGTTTTTCAAAAAAC
1 TATAT-AATTTTTAAAAATGTTTTT-AAAAAAT
* *
3135962 TA-ATAATTTTTAAAAAGGTTCTTTTAAAAAT
1 TATATAATTTTTAAAAATGTT-TTTAAAAAAT
3135993 TATATAATTTTTTAAAAATG-TTTTAAAAAAT
1 TATATAA-TTTTTAAAAATGTTTTTAAAAAAT
3136024 TATATA
1 TATATA
3136030 TTATATATCA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
31 36 0.61
32 10 0.17
33 13 0.22
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
TATATAATTTTTAAAAATGTTTTTAAAAAAT
Found at i:3136104 original size:36 final size:36
Alignment explanation
Indices: 3136002--3136183 Score: 183
Period size: 36 Copynumber: 5.0 Consensus size: 36
3135992 TTATATAATT
*
3136002 TTTTAAAAATGTTTTAAAAAATTATATATTATATATCAG
1 TTTTAAAAATGTTTTTAAAAATTATATA-T-TATAT-AG
* *
3136041 TTTTCAAAAATG-CTCTAAAAATTATATATTATAT-G
1 TTTT-AAAAATGTTTTTAAAAATTATATATTATATAG
* *
3136076 TTTTCAAAATGTTTTTCAAAAATTATATATTATATAT
1 TTTTAAAAATGTTTTT-AAAAATTATATATTATATAG
* *
3136113 TTTTAAAAATG-TTTTGAAAATATATATAATATATAG
1 TTTTAAAAATGTTTTTAAAAAT-TATATATTATATAG
* **
3136149 TTTTTAAAA-GTGTTTTAAAAACCATATATTATATA
1 TTTTAAAAATGT-TTTTAAAAATTATATATTATATA
3136184 CGTATTTTCA
Statistics
Matches: 120, Mismatches: 16, Indels: 17
0.78 0.10 0.11
Matches are distributed among these distances:
34 6 0.05
35 13 0.11
36 53 0.44
37 23 0.19
38 1 0.01
39 17 0.14
40 7 0.06
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTTAAAAATGTTTTTAAAAATTATATATTATATAG
Found at i:3136176 original size:72 final size:72
Alignment explanation
Indices: 3135986--3136195 Score: 218
Period size: 72 Copynumber: 2.9 Consensus size: 72
3135976 AAGGTTCTTT
*
3135986 TAAAAATTATAT-A-AT-T-TTTTAAAAATGTTTTAAAAAATTATATATTATATATCAGTTTTCA
1 TAAAAATTATATAATATATGTTTTTAAAATGTTTTAAAAAATTATATATTATATAT-A-TTTTCA
3136047 AAAATGCTC
64 AAAATGCTC
* * *
3136056 TAAAAATTATATATTATATGTTTTCAAAATGTTTTTCAAAAATTATATATTATATAT-TTTT-AA
1 TAAAAATTATATAATATATGTTTTTAAAATG-TTTTAAAAAATTATATATTATATATATTTTCAA
* *
3136119 AAATGTTT
65 AAATGCTC
* **
3136127 TGAAAATATATATAATATATAGTTTTTAAAAGTGTTTT-AAAAACCATATATTATATACGTATTT
1 TAAAAAT-TATATAATATAT-GTTTTTAAAA-TGTTTTAAAAAATTATATATTATATA--TATTT
3136191 TCAAA
61 TCAAA
3136196 CCGCTTGCAA
Statistics
Matches: 118, Mismatches: 10, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
70 12 0.10
71 14 0.12
72 34 0.29
73 14 0.12
74 13 0.11
75 28 0.24
76 3 0.03
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (72 bp):
TAAAAATTATATAATATATGTTTTTAAAATGTTTTAAAAAATTATATATTATATATATTTTCAAA
AATGCTC
Found at i:3139483 original size:31 final size:31
Alignment explanation
Indices: 3139415--3139483 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
3139405 CAGTTGAGTG
* * *
3139415 ACCAATTTATTATAAATCGATAACGTTAGCA
1 ACCAATTAATTATAAATCGATAACATTAACA
* * *
3139446 ATCAATTAATTATAAATCGATAATATTAATA
1 ACCAATTAATTATAAATCGATAACATTAACA
3139477 ACCAATT
1 ACCAATT
3139484 TGTTACTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (31 bp):
ACCAATTAATTATAAATCGATAACATTAACA
Found at i:3140641 original size:2 final size:2
Alignment explanation
Indices: 3140636--3140676 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3140626 ATAATAACAT
3140636 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3140677 TATCTATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3140854 original size:38 final size:39
Alignment explanation
Indices: 3140812--3140977 Score: 175
Period size: 36 Copynumber: 4.3 Consensus size: 39
3140802 GGTTATGTAT
3140812 ATAGTTTTGAAAAATATATATATAGTATAATTTT-GAAA
1 ATAGTTTTGAAAAATATATATATAGTATAATTTTAGAAA
*
3140850 ATAGTTTT-AAAAA-ATACATATAGTATAATTTT-GAAA
1 ATAGTTTTGAAAAATATATATATAGTATAATTTTAGAAA
* *
3140886 ATAGTTTTGAAAAATATATATA-A-TATAGTTTTATAAA
1 ATAGTTTTGAAAAATATATATATAGTATAATTTTAGAAA
* * * * *
3140923 ATAAAAGTTTAG-AATATATATATATAATATAGTTTTAAAAAA
1 AT---AGTTTTGAAAAATATATATATAGTATAATTTT-AGAAA
3140965 ATAGTTTTGAAAA
1 ATAGTTTTGAAAA
3140978 CAAATATAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
36 38 0.35
37 16 0.15
38 14 0.13
39 17 0.16
40 9 0.08
41 9 0.08
42 6 0.06
ACGTcount: A:0.50, C:0.01, G:0.09, T:0.40
Consensus pattern (39 bp):
ATAGTTTTGAAAAATATATATATAGTATAATTTTAGAAA
Found at i:3140970 original size:14 final size:16
Alignment explanation
Indices: 3140951--3140983 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3140941 TATATATAAT
3140951 ATAGTTTT-AAAA-AA
1 ATAGTTTTGAAAACAA
3140965 ATAGTTTTGAAAACAA
1 ATAGTTTTGAAAACAA
3140981 ATA
1 ATA
3140984 TAAATATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 4 0.24
16 5 0.29
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (16 bp):
ATAGTTTTGAAAACAA
Found at i:3140985 original size:41 final size:38
Alignment explanation
Indices: 3140812--3141037 Score: 151
Period size: 36 Copynumber: 5.8 Consensus size: 38
3140802 GGTTATGTAT
* * *
3140812 ATAGTTTTGAAAAATATATATATAGTATAATTTTGAAA
1 ATAGTTTTGAAAAAAATATATATAATATAATTTTAAAA
* * *
3140850 ATAGTTTT--AAAAAATACATATAGTATAATTTTGAAA
1 ATAGTTTTGAAAAAAATATATATAATATAATTTTAAAA
*
3140886 ATAGTTTTG--AAAAATATATATAATATAGTTTTATAAA
1 ATAGTTTTGAAAAAAATATATATAATATAATTTTA-AAA
* * * *
3140923 ATAAAAGTTTAG-AATATATATATATAATATAGTTTTAAAAAA
1 AT---AGTTTTGAAAAAAATATATATAATATAATTTT--AAAA
* *
3140965 ATAGTTTTGAAAACAA-ATATA-AATATAAGTTATAAATA
1 ATAGTTTTGAAAAAAATATATATAATATAA-TTTTAAA-A
* * *
3141003 ATTGGTTTTTGAAATATAAATAAATATATTATAAT
1 A-TAG-TTTTGAAA-A-AAATATATATAATATAAT
3141038 ATGAGTTTAT
Statistics
Matches: 152, Mismatches: 19, Indels: 29
0.76 0.09 0.14
Matches are distributed among these distances:
36 54 0.36
37 8 0.05
38 16 0.11
39 16 0.11
40 17 0.11
41 22 0.14
42 7 0.05
43 6 0.04
44 6 0.04
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.40
Consensus pattern (38 bp):
ATAGTTTTGAAAAAAATATATATAATATAATTTTAAAA
Found at i:3141096 original size:3 final size:3
Alignment explanation
Indices: 3141090--3141162 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
3141080 ATAATAATAA
3141090 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3141138 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
3141163 GTAAAGTCCA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3154251 original size:75 final size:76
Alignment explanation
Indices: 3154082--3154288 Score: 283
Period size: 75 Copynumber: 2.7 Consensus size: 76
3154072 CAAAGCCAAA
* * * * **
3154082 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATCCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
3154147 TTTGACCCCGAG
65 TTTGACCCCGAG
*
3154159 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
3154224 TTG-CTCCGAG
66 TTGACCCCGAG
* * * *
3154234 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
3154289 CTTGTACAAC
Statistics
Matches: 117, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
74 17 0.15
75 39 0.33
76 36 0.31
77 25 0.21
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.19
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGACCCCGAG
Found at i:3160099 original size:21 final size:21
Alignment explanation
Indices: 3160063--3160144 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 21
3160053 TTTGGTGCAG
* *
3160063 AGGGAATCGA-TCCCCCCCTA
1 AGGGAACCGATTCCCCCCATA
**
3160083 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCCAT-A
3160105 AGGGGAACCGATTCCCCCCATA
1 A-GGGAACCGATTCCCCCCATA
* * *
3160127 GGGGAATCGATACCCCCC
1 AGGGAACCGATTCCCCCC
3160145 TGGGGTTCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 9 0.18
21 22 0.43
22 3 0.06
23 17 0.33
ACGTcount: A:0.24, C:0.37, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGAACCGATTCCCCCCATA
Found at i:3162391 original size:13 final size:13
Alignment explanation
Indices: 3162373--3162399 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3162363 TTGAAGAAGT
3162373 GTTAAAGTAAGGG
1 GTTAAAGTAAGGG
3162386 GTTAAAGTAAGGG
1 GTTAAAGTAAGGG
3162399 G
1 G
3162400 GAGTAATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (13 bp):
GTTAAAGTAAGGG
Found at i:3162852 original size:76 final size:77
Alignment explanation
Indices: 3162701--3162909 Score: 280
Period size: 76 Copynumber: 2.8 Consensus size: 77
3162691 CAAAGCCAAA
* * * * **
3162701 AATTACAGATTGCTCAGAGGGAACCAATTCCCCCCATAGGAGGAACCGA-TCCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
3162765 TTTGGCCCCGAG
66 TTTGGCCCCGAG
* *
3162777 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACTGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
3162842 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
3162853 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
3162910 TGTACAACGG
Statistics
Matches: 117, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
75 18 0.15
76 83 0.71
77 16 0.14
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:3165518 original size:2 final size:2
Alignment explanation
Indices: 3165511--3165535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3165501 TATTTAAATA
3165511 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3165536 ACAATTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3167398 original size:42 final size:43
Alignment explanation
Indices: 3167351--3167446 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
3167341 TTTATAATGT
*
3167351 TAAAATATATT-CTTTAAT-AGTAAAAAATATAGTAAATTATTA
1 TAAAATATATTACTTTAATCA-TAAAAAATATAATAAATTATTA
* **
3167393 TAAAATATATTATTTTAATCATTTAAAATATAATAAATTATTA
1 TAAAATATATTACTTTAATCATAAAAAATATAATAAATTATTA
*
3167436 T-AGATATATTA
1 TAAAATATATTA
3167447 TTATTATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 20 0.43
43 26 0.55
44 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (43 bp):
TAAAATATATTACTTTAATCATAAAAAATATAATAAATTATTA
Found at i:3167473 original size:18 final size:18
Alignment explanation
Indices: 3167429--3167466 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3167419 AATATAATAA
*
3167429 ATTATTA-TAGATATATT
1 ATTATTATTAAATATATT
3167446 ATTATTATTAAATATATT
1 ATTATTATTAAATATATT
3167464 ATT
1 ATT
3167467 TTAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
ATTATTATTAAATATATT
Found at i:3170295 original size:121 final size:122
Alignment explanation
Indices: 3169993--3170417 Score: 798
Period size: 122 Copynumber: 3.5 Consensus size: 122
3169983 TACTTAGAAT
*
3169993 CAAAATATATGTATTCAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTAATTTATACTT
1 CAAAATATATGTATTGAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTAATTTATACTT
3170058 CTTGATGAATATTTAATGGGAAAACATAAAACAAAGTTGAAAACTATTGTCTCGAAG
66 CTTGATGAATATTTAATGGGAAAACATAAAACAAAGTTGAAAACTATTGTCTCGAAG
3170115 CAAAATATATGTATTGAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTAATTTATACTT
1 CAAAATATATGTATTGAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTAATTTATACTT
*
3170180 CTTGATGAATATTTAATGGGAAAACATAAAA-AAAGGTGAAAACTATTGTCTCGAAG
66 CTTGATGAATATTTAATGGGAAAACATAAAACAAAGTTGAAAACTATTGTCTCGAAG
3170236 CAAAATATATGTATTGAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTAATTTATACTT
1 CAAAATATATGTATTGAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTAATTTATACTT
3170301 CTTGATGAATATTTAATGGGAAAACATAAAACAAAGTTGAAAACTATTGTCTCGAAG
66 CTTGATGAATATTTAATGGGAAAACATAAAACAAAGTTGAAAACTATTGTCTCGAAG
* *
3170358 CAAAATATATGTATTGAAAGAGCATTTATAGAACCTCCTGCAGTATATTCCACTAGATTT
1 CAAAATATATGTATTGAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTA-ATTT
3170418 GGCTTCCTTA
Statistics
Matches: 296, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
121 120 0.41
122 172 0.58
123 4 0.01
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (122 bp):
CAAAATATATGTATTGAAAGAGCATTTGTAGAACCTCCTGCAGTAGATTCCACTAATTTATACTT
CTTGATGAATATTTAATGGGAAAACATAAAACAAAGTTGAAAACTATTGTCTCGAAG
Found at i:3172575 original size:15 final size:15
Alignment explanation
Indices: 3172555--3172584 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3172545 AATGTGACAC
3172555 CTCAGATCAGATCGG
1 CTCAGATCAGATCGG
3172570 CTCAGATCAGATCGG
1 CTCAGATCAGATCGG
3172585 GTCACCCGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (15 bp):
CTCAGATCAGATCGG
Found at i:3179952 original size:5 final size:4
Alignment explanation
Indices: 3179922--3179978 Score: 50
Period size: 4 Copynumber: 14.2 Consensus size: 4
3179912 TTTTTGGTTG
3179922 TTTA TTTA TTTA TTTA TTTA TTTTA TATTA TATTA TATT- TTTA -TTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA T-TTA T-TTA T-TTA TTTA TTTA
3179968 -TTA TTT- TTTA T
1 TTTA TTTA TTTA T
3179979 ACATATTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
3 11 0.23
4 21 0.44
5 16 0.33
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:3180334 original size:10 final size:9
Alignment explanation
Indices: 3180305--3180377 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 9
3180295 CCATTAATTC
*
3180305 TTTTTTTCT
1 TTTTTTTAT
*
3180314 TTATCTTTAT
1 TT-TTTTTAT
3180324 TTTTATTTAT
1 TTTT-TTTAT
*
3180334 TTTTTTACCAT
1 TTTTTT--TAT
*
3180345 TTTATTTAT
1 TTTTTTTAT
*
3180354 TTTGTTTAT
1 TTTTTTTAT
3180363 TTTTTATTAT
1 TTTTT-TTAT
3180373 TTTTT
1 TTTTT
3180378 ACATGCTCTA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
9 19 0.37
10 25 0.49
11 7 0.14
ACGTcount: A:0.15, C:0.05, G:0.01, T:0.78
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:3180367 original size:20 final size:18
Alignment explanation
Indices: 3180319--3180377 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 18
3180309 TTTCTTTATC
3180319 TTTATTTTTATTTATTTT
1 TTTATTTTTATTTATTTT
*
3180337 TTTACCATTTTATTTATTTT
1 TTTA--TTTTTATTTATTTT
3180357 GTTTATTTTT-TATTATTTT
1 -TTTATTTTTAT-TTATTTT
3180376 TT
1 TT
3180378 ACATGCTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
18 7 0.20
19 11 0.31
20 13 0.37
21 4 0.11
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTATTTTTATTTATTTT
Found at i:3182555 original size:11 final size:11
Alignment explanation
Indices: 3182539--3182601 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
3182529 AAAATTACAT
3182539 TATTAAAAATA
1 TATTAAAAATA
*
3182550 TATTAAAACTA
1 TATTAAAAATA
* ***
3182561 CATTATTGATA
1 TATTAAAAATA
3182572 -ATTATAAAAT-
1 TATTA-AAAATA
3182582 T-TTAAAAATA
1 TATTAAAAATA
3182592 TATTAAAAAT
1 TATTAAAAAT
3182602 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 26 0.67
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:3182709 original size:15 final size:15
Alignment explanation
Indices: 3182673--3182712 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3182663 AAAATTTAAC
*
3182673 ATATTTCTAATAATA
1 ATATTTTTAATAATA
3182688 ATATTTTTAATAACTA
1 ATATTTTTAATAA-TA
3182704 AT-TTTTTAA
1 ATATTTTTAA
3182713 ATTGTTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTTTAATAATA
Found at i:3184820 original size:11 final size:11
Alignment explanation
Indices: 3184804--3184876 Score: 67
Period size: 11 Copynumber: 6.5 Consensus size: 11
3184794 AGTAGTTTCA
3184804 AGCTTGAATCG
1 AGCTTGAATCG
3184815 AGCTTGAATCG
1 AGCTTGAATCG
*
3184826 AGTTTGAATCG
1 AGCTTGAATCG
*
3184837 AGCTAT-AATTG
1 AGCT-TGAATCG
* *
3184848 AGTTTGAGTCTTG
1 AGCTTGAATC--G
*
3184861 AGCTTTAATCG
1 AGCTTGAATCG
3184872 AGCTT
1 AGCTT
3184877 TGATTTTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
10 1 0.02
11 39 0.80
12 1 0.02
13 8 0.16
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.36
Consensus pattern (11 bp):
AGCTTGAATCG
Found at i:3184835 original size:22 final size:21
Alignment explanation
Indices: 3184807--3184879 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 21
3184797 AGTTTCAAGC
3184807 TTGAATCGAGCTTGAATCGAGT
1 TTGAATCGAGCTT-AATCGAGT
*
3184829 TTGAATCGAGCTATAATTGAGT
1 TTGAATCGAGCT-TAATCGAGT
*
3184851 TTGAGTCTTGAGCTTTAATCGAGCT
1 TTGAATC--GAGC-TTAATCGAG-T
3184876 TTGA
1 TTGA
3184880 TTTTTTTTTG
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
22 25 0.58
23 1 0.02
24 11 0.26
25 6 0.14
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (21 bp):
TTGAATCGAGCTTAATCGAGT
Found at i:3185911 original size:3 final size:3
Alignment explanation
Indices: 3185900--3185960 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
3185890 TTTTTTTCCG
*
3185900 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCA TTA -TA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3185945 TTA TTA TTTA TTA TTA
1 TTA TTA -TTA TTA TTA
3185961 CAATTTTTGC
Statistics
Matches: 52, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
2 6 0.12
3 43 0.83
4 3 0.06
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3186116 original size:26 final size:25
Alignment explanation
Indices: 3186038--3186186 Score: 280
Period size: 25 Copynumber: 5.9 Consensus size: 25
3186028 ACCCACCAGA
3186038 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
3186063 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
3186088 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
3186114 TTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
3186140 TTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
3186165 TTAGGGTTTCAAACCCTAAATC
1 TTAGGGTTTCAAACCCTAAATC
3186187 CCCAACTGCA
Statistics
Matches: 123, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
25 72 0.59
26 51 0.41
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (25 bp):
TTAGGGTTTCAAACCCTAAATCAGT
Found at i:3186125 original size:51 final size:50
Alignment explanation
Indices: 3186038--3186186 Score: 280
Period size: 51 Copynumber: 2.9 Consensus size: 50
3186028 ACCCACCAGA
3186038 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAATCAGT
3186088 TTAGGGTTTCAAACCCTAAAATCAGTTTAGGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGTTTAGGGTTTCAAACCCT-AAATCAGT
3186140 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAATC
1 TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAATC
3186187 CCCAACTGCA
Statistics
Matches: 97, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
50 22 0.23
51 50 0.52
52 25 0.26
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (50 bp):
TTAGGGTTTCAAACCCTAAATCAGTTTAGGGTTTCAAACCCTAAATCAGT
Found at i:3187649 original size:30 final size:31
Alignment explanation
Indices: 3187609--3187693 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 31
3187599 TAGACTCATA
3187609 AGTTTCTATTTTTACTATTTTAATCCC-TTT
1 AGTTTCTATTTTTACTATTTTAATCCCTTTT
* * * *
3187639 AGTTTTTA-TTTCATCCATTTTGATCCCTTTT
1 AGTTTCTATTTTTA-CTATTTTAATCCCTTTT
* *
3187670 A-TTGCTATTTTTATTATTTTAATC
1 AGTTTCTATTTTTACTATTTTAATC
3187694 ATGTATGTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
29 4 0.10
30 30 0.71
31 8 0.19
ACGTcount: A:0.20, C:0.15, G:0.05, T:0.60
Consensus pattern (31 bp):
AGTTTCTATTTTTACTATTTTAATCCCTTTT
Found at i:3200957 original size:90 final size:87
Alignment explanation
Indices: 3200807--3201020 Score: 275
Period size: 90 Copynumber: 2.4 Consensus size: 87
3200797 CATCCCCAGA
* *
3200807 CCAGATCTCTTCATCACGTAGAGCCGTGTCACCATAGATAACCAGCCGTCCTCATCACGTAGGAA
1 CCAGATCTCTTCATCACGTAGAGCCGTGTCAACATAGATAACCAGCCGTCCTCATCACGTAAGAA
*
3200872 CCGTGTTATCACCTTTAGATGG
66 CCGAGTTATCACCTTTAGATGG
*
3200894 CCAGATCTCTTCATCATGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAA
1 CCAGATCTCTTCATCACGT-AGAGCCGTGTCAACA-TA-GATAACCAGCCGTCCTCATCACGTAA
* *
3200959 GAACCGAGTTATCACCCTTCCTAAAAATGA
63 GAACCGAGTTATCA-CCTT--T--AGATGG
* *
3200989 CCAGATCTCCTCATCACGTAGGAGCCATGTCA
1 CCAGATCTCTTCATCACGTA-GAGCCGTGTCA
3201021 CCCTTAGACG
Statistics
Matches: 109, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
87 18 0.17
88 14 0.13
89 2 0.02
90 38 0.35
91 4 0.04
93 1 0.01
94 1 0.01
95 31 0.28
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (87 bp):
CCAGATCTCTTCATCACGTAGAGCCGTGTCAACATAGATAACCAGCCGTCCTCATCACGTAAGAA
CCGAGTTATCACCTTTAGATGG
Found at i:3200959 original size:44 final size:43
Alignment explanation
Indices: 3200817--3200960 Score: 141
Period size: 46 Copynumber: 3.3 Consensus size: 43
3200807 CCAGATCTCT
3200817 TCATCACGT-AGAGCCGTGTCACCA-TAGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCACCATTAGATAACCAGCCGTCC
* * * ** * *
3200858 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-TCT
1 TCATCACGTAAGAGCCGTG---TCACCATTAGATAACCAG-CCGTCC
* *
3200904 TCATCATGTAAGAGCCGTGTCAACATTAGGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGTCACCATTA-GATAACCAGCCGTCC
3200948 TCATCACGTAAGA
1 TCATCACGTAAGA
3200961 ACCGAGTTAT
Statistics
Matches: 78, Mismatches: 17, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
41 9 0.12
42 7 0.09
43 8 0.10
44 21 0.27
45 5 0.06
46 27 0.35
47 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (43 bp):
TCATCACGTAAGAGCCGTGTCACCATTAGATAACCAGCCGTCC
Found at i:3201226 original size:3 final size:3
Alignment explanation
Indices: 3201214--3201269 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
3201204 TTTTTTTCCG
* *
3201214 TTA TTT TTA TTA TTA TTA TTA TTA TCA -TA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3201260 TTTA TTA TTA
1 -TTA TTA TTA
3201270 CAATTTTGCA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 3 0.07
3 40 0.87
4 3 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3201246 original size:11 final size:10
Alignment explanation
Indices: 3201214--3201269 Score: 71
Period size: 11 Copynumber: 5.6 Consensus size: 10
3201204 TTTTTTTCCG
3201214 TTATT-TTTA
1 TTATTATTTA
3201223 TTATTA-TTA
1 TTATTATTTA
*
3201232 TTATTATCATA
1 TTATTAT-TTA
3201243 TTATTATTTTA
1 TTATTA-TTTA
3201254 TTATTATTTA
1 TTATTATTTA
3201264 TTATTA
1 TTATTA
3201270 CAATTTTGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
9 14 0.34
10 10 0.24
11 16 0.39
12 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATTATTTA
Found at i:3201440 original size:49 final size:51
Alignment explanation
Indices: 3201346--3201462 Score: 183
Period size: 49 Copynumber: 2.4 Consensus size: 51
3201336 ACCCACCAGA
3201346 TTAGGGTTTC-AACCCT--AATCAGTTTAGGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCTAAAATCAGTTTAGGTTTCAAACCCTAAAATCAGT
3201394 TTAGGGTTTCAAACCCTAAAATCAG-TTAGGGTTTC-AACCCT-AAATCAGT
1 TTAGGGTTTCAAACCCTAAAATCAGTTTA-GGTTTCAAACCCTAAAATCAGT
3201443 TTAGGGTTTCAAACCCTAAA
1 TTAGGGTTTCAAACCCTAAA
3201463 TCCCCAACTG
Statistics
Matches: 65, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
48 10 0.15
49 34 0.52
50 9 0.14
51 12 0.18
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (51 bp):
TTAGGGTTTCAAACCCTAAAATCAGTTTAGGTTTCAAACCCTAAAATCAGT
Found at i:3201463 original size:25 final size:25
Alignment explanation
Indices: 3201346--3201464 Score: 185
Period size: 25 Copynumber: 4.9 Consensus size: 25
3201336 ACCCACCAGA
3201346 TTAGGGTTTC-AACCCT-AATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
3201369 TTA-GGTTTCAAACCCTAAAATCAGT
1 TTAGGGTTTCAAACCCT-AAATCAGT
3201394 TTAGGGTTTCAAACCCTAAAATCAG-
1 TTAGGGTTTCAAACCCT-AAATCAGT
3201419 TTAGGGTTTC-AACCCTAAATCAGT
1 TTAGGGTTTCAAACCCTAAATCAGT
3201443 TTAGGGTTTCAAACCCTAAATC
1 TTAGGGTTTCAAACCCTAAATC
3201465 CCCAACTGCA
Statistics
Matches: 90, Mismatches: 0, Indels: 10
0.90 0.00 0.10
Matches are distributed among these distances:
22 6 0.07
23 16 0.18
24 16 0.18
25 31 0.34
26 21 0.23
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (25 bp):
TTAGGGTTTCAAACCCTAAATCAGT
Done.