Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009623.1 Hibiscus syriacus cultivar Beakdansim tig00117012_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: 3488723
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 18
Found at i:1500950 original size:27 final size:27
Alignment explanation
Indices: 1500919--1501026 Score: 103
Period size: 25 Copynumber: 4.0 Consensus size: 27
1500909 TGTTACAAAT
* *
1500919 TATATAAGTATAAAATATATTATATAA
1 TATATAAATATAAAATATAGTATATAA
1500946 TATATAATATATATAAACTATAGTATATAA
1 TATATAA-ATATA-AAA-TATAGTATATAA
* * *
1500976 TATATAAATATCAACTATAGTATATAG
1 TATATAAATATAAAATATAGTATATAA
* * *
1501003 T-T-TATATATAAACTATAGTTTATA
1 TATATAAATATAAAATATAGTATATA
1501027 TAGTTTAGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
25 19 0.27
26 1 0.01
27 19 0.27
28 6 0.09
29 7 0.10
30 18 0.26
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.42
Consensus pattern (27 bp):
TATATAAATATAAAATATAGTATATAA
Found at i:1501001 original size:7 final size:7
Alignment explanation
Indices: 1500919--1500986 Score: 61
Period size: 7 Copynumber: 9.7 Consensus size: 7
1500909 TGTTACAAAT
1500919 TATATAA
1 TATATAA
1500926 GTATA-AA
1 -TATATAA
*
1500933 -ATATAT
1 TATATAA
1500939 TATATAA
1 TATATAA
1500946 TATATAA
1 TATATAA
1500953 TATATATA
1 TATATA-A
* *
1500961 AACTATAG
1 TA-TATAA
1500969 TATATAA
1 TATATAA
1500976 TATATAA
1 TATATAA
1500983 -ATAT
1 TATAT
1500987 CAACTATAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 3 0.06
6 5 0.10
7 31 0.62
8 7 0.14
9 4 0.08
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (7 bp):
TATATAA
Found at i:1501027 original size:27 final size:27
Alignment explanation
Indices: 1500953--1501152 Score: 151
Period size: 27 Copynumber: 7.3 Consensus size: 27
1500943 TAATATATAA
* *
1500953 TATATATAAACTATAGTATATAATA-TA
1 TATATATAAACTATAGTTTAT-ATAGTT
* *
1500980 TAAATATCAACTATAG--TATATAGTT
1 TATATATAAACTATAGTTTATATAGTT
1501005 TATATATAAACTATAGTTTATATAGTT
1 TATATATAAACTATAGTTTATATAGTT
* * **
1501032 TAGATATATA-TAATTTTTATATATAGTT
1 TATATATAAACT-ATAGTT-TATATAGTT
* * *
1501060 CATATGTAAACTATATATATATTATATAGTAT
1 TATATATAAAC--TATA-GT-TTATATAGT-T
* *
1501092 ATAAATATCAACTATAG--TATATAGTT
1 -TATATATAAACTATAGTTTATATAGTT
*
1501118 TATACATAAACTATAGTTTATATAGTT
1 TATATATAAACTATAGTTTATATAGTT
1501145 TATATATA
1 TATATATA
1501153 TATAGTTTTT
Statistics
Matches: 135, Mismatches: 24, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
24 3 0.02
25 31 0.23
26 2 0.01
27 59 0.44
28 15 0.11
30 2 0.01
31 14 0.10
32 2 0.01
33 7 0.05
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (27 bp):
TATATATAAACTATAGTTTATATAGTT
Found at i:1501087 original size:7 final size:6
Alignment explanation
Indices: 1500933--1501099 Score: 53
Period size: 7 Copynumber: 27.0 Consensus size: 6
1500923 TAAGTATAAA
*
1500933 ATATAT -TATAT A-ATAT ATA-AT ATATAT AAACTAT AGTATAT A-ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATA-TAT A-TATAT ATATAT
* * * *
1500979 ATAAAT ATCA-ACT ATAGTAT ATAGTTT ATATAT AAACTAT AGTTTAT
1 ATATAT AT-ATA-T ATA-TAT ATA-TAT ATATAT ATA-TAT A-TATAT
* * * * * *
1501026 ATAGTTT AGATAT ATATA- ATTTTT ATATAT AGT-TCAT ATGTAA ACTATAT
1 ATA-TAT ATATAT ATATAT ATATAT ATATAT A-TAT-AT ATATAT A-TATAT
*
1501076 ATATAT -TATAT AGTATAT AAATAT
1 ATATAT ATATAT A-TATAT ATATAT
1501100 CAACTATAGT
Statistics
Matches: 120, Mismatches: 21, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
5 28 0.23
6 41 0.34
7 49 0.41
8 2 0.02
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (6 bp):
ATATAT
Found at i:1501094 original size:9 final size:8
Alignment explanation
Indices: 1500933--1501099 Score: 53
Period size: 9 Copynumber: 20.2 Consensus size: 8
1500923 TAAGTATAAA
1500933 ATATAT-T
1 ATATATAT
1500940 ATATA-AT
1 ATATATAT
1500947 ATATA-AT
1 ATATATAT
*
1500954 ATATATAA
1 ATATATAT
1500962 ACTATAGTAT
1 A-TATA-TAT
1500972 ATA-ATAT
1 ATATATAT
*
1500979 ATAAATAT
1 ATATATAT
1500987 CA-ACTATAGT
1 -ATA-TATA-T
*
1500997 ATATAGTTT
1 ATATA-TAT
*
1501006 ATATATAA
1 ATATATAT
*
1501014 ACTATAGTTT
1 A-TATA-TAT
*
1501024 ATATAGTTT
1 ATATA-TAT
*
1501033 AGATATAT
1 ATATATAT
*
1501041 ATA-ATTT
1 ATATATAT
*
1501048 TTATATAT
1 ATATATAT
1501056 AGT-TCATAT
1 A-TAT-ATAT
* *
1501065 GTAAACTAT
1 ATATA-TAT
1501074 ATATATAT
1 ATATATAT
1501082 -TATATAGT
1 ATATATA-T
*
1501090 ATATAAAT
1 ATATATAT
1501098 AT
1 AT
1501100 CAACTATAGT
Statistics
Matches: 121, Mismatches: 20, Indels: 37
0.68 0.11 0.21
Matches are distributed among these distances:
7 35 0.29
8 27 0.22
9 51 0.42
10 8 0.07
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (8 bp):
ATATATAT
Found at i:1501120 original size:113 final size:113
Alignment explanation
Indices: 1500964--1501171 Score: 362
Period size: 113 Copynumber: 1.8 Consensus size: 113
1500954 ATATATAAAC
*
1500964 TATAGTATATAATATATAAATATCAACTATAGTATATAGTTTATATATAAACTATAGTTTATATA
1 TATAGTATATAATATATAAATATCAACTATAGTATATAGTTTATACATAAACTATAGTTTATATA
1501029 GTTTAGATATATATAATTTTTATATATAGTTCATATGTAAACTATATA
66 GTTTAGATATATATAATTTTTATATATAGTTCATATGTAAACTATATA
* *
1501077 TATATTATATAGTATATAAATATCAACTATAGTATATAGTTTATACATAAACTATAGTTTATATA
1 TATAGTATATAATATATAAATATCAACTATAGTATATAGTTTATACATAAACTATAGTTTATATA
* * *
1501142 GTTTATATATATATAGTTTTTATATGTAGT
66 GTTTAGATATATATAATTTTTATATATAGT
1501172 ATATACTATA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 89 1.00
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (113 bp):
TATAGTATATAATATATAAATATCAACTATAGTATATAGTTTATACATAAACTATAGTTTATATA
GTTTAGATATATATAATTTTTATATATAGTTCATATGTAAACTATATA
Found at i:1501278 original size:27 final size:25
Alignment explanation
Indices: 1501248--1501393 Score: 97
Period size: 25 Copynumber: 5.7 Consensus size: 25
1501238 TTTGAATTTA
* *
1501248 TATAGTATAAATTATATAAGTATCAAC
1 TATAGTATATAGTATATAA-TAT-AAC
* *
1501275 TATATTATATAGTATATAAATATAAA
1 TATAGTATATAGTATAT-AATATAAC
* *
1501301 TATA-AACTATA-TATATATATATATAG
1 TATAGTA-TATAGTATATA-ATATA-AC
* *
1501327 TTTA-TATATATTATA-AATATCAAC
1 TATAGTATATAGTATATAATAT-AAC
1501351 TATAGTATATAGTATATAAATATAAAC
1 TATAGTATATAGTATAT-AATAT-AAC
1501378 TATAGT-TATA-TATATA
1 TATAGTATATAGTATATA
1501394 GTTCATATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
24 10 0.10
25 32 0.33
26 23 0.23
27 31 0.32
28 2 0.02
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (25 bp):
TATAGTATATAGTATATAATATAAC
Found at i:1501288 original size:34 final size:33
Alignment explanation
Indices: 1501245--1501393 Score: 112
Period size: 34 Copynumber: 4.4 Consensus size: 33
1501235 TACTTTGAAT
* *
1501245 TTATATAGTATA-AATTATATAAGTATCAACTATA
1 TTATATAGTATATAA--ATATAAATATAAACTATA
1501279 TTATATAGTATATAAATATAAATATAAACTATA
1 TTATATAGTATATAAATATAAATATAAACTATA
* *
1501312 TATATATA-TATATAGTTTATATATATTATAAA-TATCA
1 T-TATATAGTATATA---AATATA-AATATAAACTAT-A
*
1501349 --ACTATAGTATATAGTATATAAATATAAACTATA
1 TTA-TATAGTATATA-AATATAAATATAAACTATA
1501382 GTTATATA-TATA
1 -TTATATAGTATA
1501394 GTTCATATTT
Statistics
Matches: 96, Mismatches: 6, Indels: 26
0.75 0.05 0.20
Matches are distributed among these distances:
33 31 0.32
34 32 0.33
35 10 0.10
36 15 0.16
37 8 0.08
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (33 bp):
TTATATAGTATATAAATATAAATATAAACTATA
Found at i:1501292 original size:2 final size:2
Alignment explanation
Indices: 1501275--1501682 Score: 88
Period size: 2 Copynumber: 206.0 Consensus size: 2
1501265 AAGTATCAAC
* * *
1501275 TA TA T- TA TA TA GTA TA TA AA TA TA AA TA TA AA CTA 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
* *
1501318 TA TA TA TA GTT TA TA TA TA T- TA TA AA TA TCA -A CTA TA GTA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA -TA TA
* * *
1501360 TA GTA TA TA AA TA TA AA CTA TA GT- TA TA TA TA TA GT- TCA TA TT
1 TA -TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA -TA T-A TA TA
* *
1501403 TA AA CTA TA TA GTA TA TA TA GT- TA -A TA TA TA GA GTA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* *
1501445 TA CTA TA TA GTT TA TA TA TA CTA -A TGA -A CTT TA TA -A TA TA TA
1 TA -TA TA TA -TA TA TA TA TA -TA TA T-A TA -TA TA TA TA TA TA TA
* * *
1501487 GTT TA T- TA -A TA TA -A T- TA TA TA AA CTA TA -A TT TA T- TA -A
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
1501524 TA TA AA CTA TA TA TA TA TA TA TA TA TA T- TA -A TA AA CCA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
1501566 GTT TA TA TA TA GT- TCA TA TA CA -A TA AA TA -A TT TA TA TA CA
1 -TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
* * **
1501606 -A TA TA TA -A AA CTA TA AA TA TA -A CC TA TA TA TA T- 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
*
1501645 TA T- TA TA T- TA -A AA TA TA TA TA TA TA T- TA -A TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1501681 TA
1 TA
1501683 ATTATTTTAA
Statistics
Matches: 296, Mismatches: 50, Indels: 120
0.64 0.11 0.26
Matches are distributed among these distances:
1 32 0.11
2 231 0.78
3 33 0.11
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1501453 original size:13 final size:12
Alignment explanation
Indices: 1501275--1501682 Score: 88
Period size: 13 Copynumber: 34.3 Consensus size: 12
1501265 AAGTATCAAC
1501275 TATAT-TATATA
1 TATATATATATA
*
1501286 GTATATAAATATA
1 -TATATATATATA
* *
1501299 AATATAAACTATA
1 TATATATA-TATA
1501312 TATATATATATA
1 TATATATATATA
*
1501324 TAGTTTATATATA
1 TA-TATATATATA
*
1501337 T-TATAAATATCA
1 TATATATATAT-A
1501349 -ACTATAGTATATA
1 TA-TATA-TATATA
*
1501362 GTATATAAATATA
1 -TATATATATATA
*
1501375 AACTATAGT-TATA
1 TA-TATA-TATATA
1501388 TATATAGT-TCATA
1 TATATA-TAT-ATA
* *
1501401 TTTAAACTATATA
1 TATATA-TATATA
1501414 GTATATATAGT-TA
1 -TATATATA-TATA
*
1501427 -ATATATAGAGTA
1 TATATATATA-TA
1501439 TATATATACTATA
1 TATATATA-TATA
*
1501452 TAGTTTATATATA
1 TA-TATATATATA
*
1501465 CTA-ATGA-ACTTTA
1 -TATAT-ATA-TATA
*
1501478 TA-ATATATAGTT
1 TATATATATA-TA
1501490 TAT-TA-ATATA
1 TATATATATATA
*
1501500 -AT-TATATAAA
1 TATATATATATA
*
1501510 CTATA-ATTTAT-
1 -TATATATATATA
*
1501521 TA-ATATAAACTA
1 TATATATATA-TA
1501533 TATATATATATA
1 TATATATATATA
1501545 TATATAT-TA-A
1 TATATATATATA
* * *
1501555 TAAACCATATAGTT
1 TATA-TATATA-TA
1501569 TATATATAGT-TCA
1 TATATATA-TAT-A
* *
1501582 TATACA-ATAAA
1 TATATATATATA
*
1501593 TA-ATTTATATA
1 TATATATATATA
*
1501604 CA-ATATATA-A
1 TATATATATATA
* *
1501614 AACTATAAATATA
1 TA-TATATATATA
**
1501627 -ACCTATATATA
1 TATATATATATA
1501638 T-TATATATAT-
1 TATATATATATA
*
1501648 TATAT-TA-AAA
1 TATATATATATA
1501658 TATATATATATA
1 TATATATATATA
1501670 T-TA-ATATAT-
1 TATATATATATA
1501679 TATA
1 TATA
1501683 ATTATTTTAA
Statistics
Matches: 292, Mismatches: 53, Indels: 104
0.65 0.12 0.23
Matches are distributed among these distances:
9 7 0.02
10 33 0.11
11 60 0.21
12 72 0.25
13 93 0.32
14 26 0.09
15 1 0.00
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.44
Consensus pattern (12 bp):
TATATATATATA
Found at i:1501496 original size:15 final size:14
Alignment explanation
Indices: 1501474--1501556 Score: 55
Period size: 15 Copynumber: 5.7 Consensus size: 14
1501464 ACTAATGAAC
1501474 TTTA-TAATATATA
1 TTTATTAATATATA
1501487 GTTTATTAATATA-A
1 -TTTATTAATATATA
*
1501501 TTATATAAACTATA-A
1 TT-TATTAA-TATATA
*
1501516 TTTATTAATATAAA
1 TTTATTAATATATA
*
1501530 CTATATATATATATATA
1 -TTTAT-TA-ATATATA
*
1501547 TATATTAATA
1 TTTATTAATA
1501557 AACCATATAG
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
13 6 0.10
14 19 0.33
15 20 0.34
16 7 0.12
17 6 0.10
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (14 bp):
TTTATTAATATATA
Found at i:1501663 original size:19 final size:19
Alignment explanation
Indices: 1501639--1501692 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1501629 CTATATATAT
1501639 TATATATATTATATTAAAA
1 TATATATATTATATTAAAA
*
1501658 TATATATA-TATATTAATA
1 TATATATATTATATTAAAA
*
1501676 TAT-TATAATTATTTTAA
1 TATATAT-ATTATATTAA
1501693 TTTTTTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 15 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TATATATATTATATTAAAA
Found at i:1501758 original size:19 final size:19
Alignment explanation
Indices: 1501717--1501758 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
1501707 GAAATGAATG
* *
1501717 TAATTTACTTTATTTTTTA
1 TAATTTACTTCACTTTTTA
1501736 -AATTTACTTCACTTTTTA
1 TAATTTACTTCACTTTTTA
1501754 TAATT
1 TAATT
1501759 ATTTTGATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.62
Consensus pattern (19 bp):
TAATTTACTTCACTTTTTA
Found at i:1507878 original size:20 final size:20
Alignment explanation
Indices: 1507850--1507900 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1507840 ACCGAACCGA
1507850 AAACCGAACCGTTTAAAGCC
1 AAACCGAACCGTTTAAAGCC
*
1507870 AAACAGAACCGTTTAAAGCC
1 AAACCGAACCGTTTAAAGCC
1507890 AAACCGAACCG
1 AAACCGAACCG
1507901 AACCGAACCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.29, G:0.16, T:0.12
Consensus pattern (20 bp):
AAACCGAACCGTTTAAAGCC
Found at i:1508512 original size:182 final size:182
Alignment explanation
Indices: 1508119--1508592 Score: 652
Period size: 182 Copynumber: 2.6 Consensus size: 182
1508109 GATCCAAATT
* * * * * **
1508119 AAAAATGTATCGATCCAA-AACGATATAACAAGTAAAACTATGACAAAAC-CAGTATTGAAATGA
1 AAAAATATATCGAT-CAACAACGATATAACAATTAAAAATATGATAAAACTGA-TATCAAAATGA
* * * * * *
1508182 TAAAACCGGTAAACCGGTATCGAATATATTTAAAGTGTTGGTACTTTAATATAAGGATCGACACT
64 TAAAACCGGTAAAACGATATCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACT
* *
1508247 TCGTTAATTTAAAAGAAAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
129 TCGTGAATTTAAAAGAAAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
* *
1508301 AAAAATATATCGATCAACAAGGATATAACAATTAAAAATATGATAAAACTGATATCAAAATGATG
1 AAAAATATATCGATCAACAACGATATAACAATTAAAAATATGATAAAACTGATATCAAAATGATA
* * * * *
1508366 AAACCGGTAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATATCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
1508430 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
131 GTGAATTTAAAAGAAAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
1508482 AAAAATATATCGATCAAACAACGATATAAC-ATGTAAAAATATGATAAAA-TCGATATCAAAATG
1 AAAAATATATCGATC-AACAACGATATAACAAT-TAAAAATATGATAAAACT-GATATCAAAATG
*
1508545 ATAAAACCGGTAAAATGATATCGGATATATTAAAAGTGTCGATACTTT
63 ATAAAACCGGTAAAACGATATCGGATATATTAAAAGTGTCGATACTTT
1508593 CGTAAGTACG
Statistics
Matches: 259, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
181 88 0.34
182 170 0.66
183 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.27
Consensus pattern (182 bp):
AAAAATATATCGATCAACAACGATATAACAATTAAAAATATGATAAAACTGATATCAAAATGATA
AAACCGGTAAAACGATATCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAAAAGCAGTTTTAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:1510722 original size:15 final size:15
Alignment explanation
Indices: 1510702--1510734 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1510692 TGGTTATATT
*
1510702 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
1510717 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
1510732 GGG
1 GGG
1510735 AAAACATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:1510843 original size:21 final size:21
Alignment explanation
Indices: 1510817--1510857 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1510807 AAGACAATCA
1510817 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
1510838 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
1510858 GAGGCATAAG
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:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:1510936 original size:33 final size:33
Alignment explanation
Indices: 1510894--1510959 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1510884 AAATAGATGG
*
1510894 AGTGGTGAAAGAAATAGAAGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAATAGAAGTGTTAAGGGGTGA
* * *
1510927 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAATAGAAGTGTTAAGGGGTGA
1510960 TCTTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAATAGAAGTGTTAAGGGGTGA
Found at i:1511184 original size:33 final size:33
Alignment explanation
Indices: 1511146--1511219 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
1511136 AAAAATATGA
*
1511146 AGAAGAAAAAAGGGAGGAGGAAGAAGAAGAGAT
1 AGAAGAAAAAAGGGAAGAGGAAGAAGAAGAGAT
* *
1511179 GGAAGAAAAGAGGGAAGAGGAAGAAGAAGAGAT
1 AGAAGAAAAAAGGGAAGAGGAAGAAGAAGAGAT
1511212 AGAAGAAA
1 AGAAGAAA
1511220 TGAGGAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.58, C:0.00, G:0.39, T:0.03
Consensus pattern (33 bp):
AGAAGAAAAAAGGGAAGAGGAAGAAGAAGAGAT
Found at i:1511233 original size:33 final size:33
Alignment explanation
Indices: 1511146--1511234 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
1511136 AAAAATATGA
*
1511146 AGAAGAAAAAAGGGAGG-AGGAAGAAGAAGAGAT
1 AGAAGAAAAGA-GGAGGAAGGAAGAAGAAGAGAT
* *
1511179 GGAAGAAAAGAGG-GAAGAGGAAGAAGAAGAGAT
1 AGAAGAAAAGAGGAGGA-AGGAAGAAGAAGAGAT
*
1511212 AGAAGAAATGAGGAGGAAGGAAG
1 AGAAGAAAAGAGGAGGAAGGAAG
1511235 TCGATGTCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
31 1 0.02
32 2 0.04
33 42 0.89
34 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.42, T:0.03
Consensus pattern (33 bp):
AGAAGAAAAGAGGAGGAAGGAAGAAGAAGAGAT
Found at i:1512744 original size:19 final size:20
Alignment explanation
Indices: 1512720--1512768 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
1512710 AATGTAGGGT
1512720 TAATTTTGTATTA-GATTTA
1 TAATTTTGTATTACGATTTA
1512739 TAATTTTGTA-TACGATTTA
1 TAATTTTGTATTACGATTTA
1512758 TAATTTTGTAT
1 TAATTTTGTAT
1512769 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.57
Consensus pattern (20 bp):
TAATTTTGTATTACGATTTA
Found at i:1513346 original size:200 final size:200
Alignment explanation
Indices: 1513003--1513390 Score: 713
Period size: 200 Copynumber: 1.9 Consensus size: 200
1512993 AATTTACAAT
1513003 ATGGCAAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
1 ATGGCAAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
** * *
1513068 TGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGATTT
66 CAAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACAGGTATAAGTATACCGGATTT
1513133 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
1513198 AATGA
196 AATGA
* *
1513203 ATGGCAAACATGGTGCAACCATAAAGTGTGGATCCATATATAAAAGGTGTCGATCCCAGAAACAT
1 ATGGCAAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
*
1513268 CAAAACCCATAAGTATAATATAATATGTAATTTTTCAATCTAACAGGTATAAGTATACCGGATTT
66 CAAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACAGGTATAAGTATACCGGATTT
1513333 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
131 ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
1513391 TTTAAATATC
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
200 181 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATGGCAAACATGGTGCAACCATAAAGTGTCGATCCATATATAAAAGGTGTCGATCCCAAAAACAT
CAAAACCCATAAGTATAATATAATAGGTAATTTTTCAATCTAACAGGTATAAGTATACCGGATTT
ATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCCAG
AATGA
Found at i:1515536 original size:182 final size:182
Alignment explanation
Indices: 1514890--1515907 Score: 1748
Period size: 182 Copynumber: 5.6 Consensus size: 182
1514880 TTTTACCTTT
* *
1514890 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
1514955 AACAATATAACAAGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
1515020 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGAAACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
1515072 TTTAAAAGAGAAG-AGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
1515136 AATAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1515201 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
1515251 -TTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1515315 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
1515380 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
1515433 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATTCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
1515498 AACAATATAACAGGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
1515563 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
1515615 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
1515680 AATAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
1515745 CAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTT-GAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
1515796 ATTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCG--A--TTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * * * **
1515857 TAATAATATAACATATAAAAATATGATAAAACCGATCTATAAATGACAAAA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAA
1515908 GGTGAACGCA
Statistics
Matches: 805, Mismatches: 25, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
178 70 0.09
179 18 0.02
180 153 0.19
181 158 0.20
182 402 0.50
183 4 0.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:1517515 original size:20 final size:20
Alignment explanation
Indices: 1517492--1517536 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1517482 ATGACCTTTA
1517492 ACTTTGACTTTTGA-TAGTTG
1 ACTTTGAC-TTTGACTAGTTG
*
1517512 ACTTTGACTTTGACTCGTTG
1 ACTTTGACTTTGACTAGTTG
1517532 ACTTT
1 ACTTT
1517537 TTTTGAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
ACTTTGACTTTGACTAGTTG
Found at i:1521429 original size:19 final size:19
Alignment explanation
Indices: 1521405--1521448 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1521395 AGGTAACTCA
*
1521405 TTTTTACGATTTTCTTTAT
1 TTTTTACGATTTTATTTAT
**
1521424 TTTTTATTATTTTATTTAT
1 TTTTTACGATTTTATTTAT
1521443 TATTTT
1 T-TTTT
1521449 CATTTTTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (19 bp):
TTTTTACGATTTTATTTAT
Found at i:1521439 original size:15 final size:15
Alignment explanation
Indices: 1521419--1521458 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 15
1521409 TACGATTTTC
1521419 TTTATTTTTTATTAT
1 TTTATTTTTTATTAT
1521434 TTTA---TTTATTAT
1 TTTATTTTTTATTAT
1521446 TTTCATTTTTTAT
1 TTT-ATTTTTTAT
1521459 GAACATCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 7
0.75 0.00 0.25
Matches are distributed among these distances:
12 11 0.52
13 1 0.05
15 4 0.19
16 5 0.24
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTATTTTTTATTAT
Found at i:1525369 original size:20 final size:20
Alignment explanation
Indices: 1525346--1525384 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1525336 CATTAAGGCC
*
1525346 TTTGTTGAAGCCATGAAATT
1 TTTGTTGAAGCCATAAAATT
*
1525366 TTTGTTGATGCCATAAAAT
1 TTTGTTGAAGCCATAAAAT
1525385 CTTATAGTGA
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:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (20 bp):
TTTGTTGAAGCCATAAAATT
Found at i:1525563 original size:63 final size:63
Alignment explanation
Indices: 1525495--1525621 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
1525485 AGAAATATTT
*
1525495 TAATGTGGCATGTTATGATTGCCTGGATGGTTGTTGTTGGTCCATTGATTACCCCAAGAAAAA
1 TAATGTGGCATGTTATGATTGCATGGATGGTTGTTGTTGGTCCATTGATTACCCCAAGAAAAA
1525558 TAATGTGGCATGTTATGATTGCATGGATGGTTGTTGTTGGTCCATTGATTACCCCAAGAAAAA
1 TAATGTGGCATGTTATGATTGCATGGATGGTTGTTGTTGGTCCATTGATTACCCCAAGAAAAA
1525621 T
1 T
1525622 TTGGATGTTG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.35
Consensus pattern (63 bp):
TAATGTGGCATGTTATGATTGCATGGATGGTTGTTGTTGGTCCATTGATTACCCCAAGAAAAA
Found at i:1527179 original size:45 final size:44
Alignment explanation
Indices: 1527084--1527181 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 44
1527074 GACCAGATGG
* * * *
1527084 AAAAAGTTTGGTAGAGGCAAGAAAAATTGTAAAGTGAAGAGAGT
1 AAAAAGTTTGGTAGAGGCAAGAAAAATTGCAAAGTAAACAGAAT
* *
1527128 AGAAAAGTTTTGTCGAGGCAAGAAAAATATGCAAAGGTAAACA-AAT
1 A-AAAAGTTTGGTAGAGGCAAGAAAAAT-TGCAAA-GTAAACAGAAT
1527174 AAAAAGTT
1 AAAAAGTT
1527182 GTCAAGGCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
44 1 0.02
45 31 0.69
46 8 0.18
47 5 0.11
ACGTcount: A:0.50, C:0.05, G:0.24, T:0.20
Consensus pattern (44 bp):
AAAAAGTTTGGTAGAGGCAAGAAAAATTGCAAAGTAAACAGAAT
Found at i:1528944 original size:4 final size:4
Alignment explanation
Indices: 1528935--1528963 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1528925 TCTTGCATTC
1528935 TTTA TTTA TTTA TTTA TTT- TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1528964 AAATTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTA
Found at i:1528957 original size:15 final size:16
Alignment explanation
Indices: 1528939--1528973 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1528929 GCATTCTTTA
*
1528939 TTTATTTATT-TATTT
1 TTTATTTATTAAATTT
1528954 TTTATTTATTAAATTT
1 TTTATTTATTAAATTT
1528970 TTTA
1 TTTA
1528974 AACCCCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTATTAAATTT
Found at i:1529741 original size:18 final size:20
Alignment explanation
Indices: 1529714--1529751 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1529704 CTTTGACCAA
1529714 ACCCATCTCGTTGA-CGTTG
1 ACCCATCTCGTTGATCGTTG
1529733 ACCCA-CTCGTTGATCGTTG
1 ACCCATCTCGTTGATCGTTG
1529752 GTTGTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.16, C:0.32, G:0.21, T:0.32
Consensus pattern (20 bp):
ACCCATCTCGTTGATCGTTG
Found at i:1529788 original size:26 final size:26
Alignment explanation
Indices: 1529759--1529812 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
1529749 TTGGTTGTTA
*
1529759 ACTTTTAACCATTGACTTTGACTTTG
1 ACTTTTAACCATTGACTTAGACTTTG
*
1529785 ACTTTTAATCATTGACTTAGACTTTG
1 ACTTTTAACCATTGACTTAGACTTTG
1529811 AC
1 AC
1529813 CCGTTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (26 bp):
ACTTTTAACCATTGACTTAGACTTTG
Found at i:1530471 original size:30 final size:30
Alignment explanation
Indices: 1530396--1530531 Score: 109
Period size: 30 Copynumber: 4.5 Consensus size: 30
1530386 AAGAGCATAA
**
1530396 TCCCCGTTTTGATTCTACATAGG-ACTATGT
1 TCCCCGTCCTGATTCTACAT-GGAACTATGT
** * *
1530426 TCCCTATTCAT-ATTCTACATGGAATTATGT
1 TCCC-CGTCCTGATTCTACATGGAACTATGT
1530456 TCCCCGTCCTGATTCTGCACA-GG-ACTATGT
1 TCCCCGTCCTGATTCT--ACATGGAACTATGT
* * *
1530486 TCCCCGTCCTGATTCAATATGGGACTATGT
1 TCCCCGTCCTGATTCTACATGGAACTATGT
* *
1530516 TCCCCGTTCTAATTCT
1 TCCCCGTCCTGATTCT
1530532 GAATGAGATT
Statistics
Matches: 85, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
28 2 0.02
29 7 0.08
30 69 0.81
31 4 0.05
32 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (30 bp):
TCCCCGTCCTGATTCTACATGGAACTATGT
Found at i:1535581 original size:14 final size:15
Alignment explanation
Indices: 1535559--1535594 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
1535549 TTTGTTGAGT
*
1535559 TTTTGAATGAGAC-A
1 TTTTAAATGAGACAA
1535573 TTTTAAATGAGACAA
1 TTTTAAATGAGACAA
1535588 TTTTAAA
1 TTTTAAA
1535595 AAACAAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (15 bp):
TTTTAAATGAGACAA
Found at i:1536378 original size:2 final size:2
Alignment explanation
Indices: 1536371--1536425 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1536361 TATTTCTTAA
1536371 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
1536413 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1536426 AAGTTCTAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1537953 original size:18 final size:20
Alignment explanation
Indices: 1537930--1537972 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
1537920 AGCCATTTTG
*
1537930 GTATCGATACT-TATG-AGA
1 GTATCGATACTATAGGTAGA
1537948 GTATCGATACTATAGGTAGA
1 GTATCGATACTATAGGTAGA
1537968 GTATC
1 GTATC
1537973 AATATCAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 11 0.50
19 3 0.14
20 8 0.36
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.33
Consensus pattern (20 bp):
GTATCGATACTATAGGTAGA
Found at i:1542062 original size:59 final size:59
Alignment explanation
Indices: 1541933--1542059 Score: 146
Period size: 59 Copynumber: 2.1 Consensus size: 59
1541923 ATAGTTGGGT
* * * *
1541933 GACCATTTTGTAACTTTTAATAGTCGAGTGACTCAACAATGCAACACTCTATAGTCAGG
1 GACCATTTTGTAACTTCTAATAATCGAGGGACTCAACAAAGCAACACTCTATAGTCAGG
* * * * * * *
1541992 GATCATTTTGTAACTTCTAATAATCGAGGGACTTAATAAAGTAATACTTTATAGTCCGG
1 GACCATTTTGTAACTTCTAATAATCGAGGGACTCAACAAAGCAACACTCTATAGTCAGG
1542051 AGACCATTT
1 -GACCATTT
1542060 GTATATTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
59 48 0.87
60 7 0.13
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (59 bp):
GACCATTTTGTAACTTCTAATAATCGAGGGACTCAACAAAGCAACACTCTATAGTCAGG
Found at i:1542963 original size:18 final size:17
Alignment explanation
Indices: 1542912--1542963 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
1542902 TTAGCATTTC
1542912 AAAAGAAAATAA-AACAT
1 AAAAGAAAATAAGAA-AT
**
1542929 AAAAGTAAAATTTGAAAT
1 AAAAG-AAAATAAGAAAT
1542947 GAAAAGAAAATAAGAAA
1 -AAAAGAAAATAAGAAA
1542964 ACTTTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 5 0.18
18 16 0.57
19 7 0.25
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAAGAAAATAAGAAAT
Found at i:1550856 original size:22 final size:21
Alignment explanation
Indices: 1550814--1550853 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1550804 GAGTTTATTT
*
1550814 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1550835 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1550854 ACAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1552927 original size:65 final size:64
Alignment explanation
Indices: 1552771--1552953 Score: 201
Period size: 65 Copynumber: 2.8 Consensus size: 64
1552761 CCGTTGGACT
* * *
1552771 CTCAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGAT-TTTTCAAAATAG
1 CTCAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAG
1552834 C
64 C
** * * *
1552835 CGGAGTGCATCGATGCATGGCTGGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-AT
1 CTCAGTGCATCGGTGCATGG-TAGTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAG
1552899 C
64 C
* * *
1552900 CTCAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCGTTTGATGTT
1 CTCAGTGCATCGGTGCATGGTA-GTGCATCGATGCATAAAATGCATTCGATGTT
1552954 CAATTTAATT
Statistics
Matches: 99, Mismatches: 15, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 41 0.41
65 53 0.54
66 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.30
Consensus pattern (64 bp):
CTCAGTGCATCGGTGCATGGTAGTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGC
Found at i:1552992 original size:65 final size:63
Alignment explanation
Indices: 1552794--1553001 Score: 183
Period size: 65 Copynumber: 3.2 Consensus size: 63
1552784 TGCACTAAGA
* * * * *
1552794 GTGCATCGATGCATCAAGTGCATTCGATTTTTCA-AAATAGC-CGGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
1552857 G
63 G
*
1552858 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
1552923 -
63 G
* * * **
1552923 GTGCATCGATGCATGAAATGCGTTTGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
1552986 TG
62 TG
*
1552988 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
1553002 CACTCTGAAA
Statistics
Matches: 121, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.39
65 62 0.51
66 5 0.04
67 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:1560393 original size:14 final size:14
Alignment explanation
Indices: 1560359--1560387 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1560349 ACTTAAAAGT
1560359 AAAAAAAAAGCAAA
1 AAAAAAAAAGCAAA
1560373 AAAAAAAAAGCAAA
1 AAAAAAAAAGCAAA
1560387 A
1 A
1560388 GGAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGCAAA
Found at i:1560868 original size:14 final size:14
Alignment explanation
Indices: 1560812--1560870 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1560802 TCCAAATCAA
1560812 CAACATAAACTAAT
1 CAACATAAACTAAT
*
1560826 CAACA-AGAAGTAATT
1 CAACATA-AACTAA-T
* * *
1560841 AAAGATAAAATAAT
1 CAACATAAACTAAT
1560855 CAACATAAACTAAT
1 CAACATAAACTAAT
1560869 CA
1 CA
1560871 TCACTTTTCT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
13 1 0.03
14 24 0.69
15 9 0.26
16 1 0.03
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.20
Consensus pattern (14 bp):
CAACATAAACTAAT
Found at i:1561271 original size:27 final size:27
Alignment explanation
Indices: 1561241--1561295 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1561231 CCTACTAGGA
1561241 TTCAAACTCCTAAAAATAGGATAGAGT
1 TTCAAACTCCTAAAAATAGGATAGAGT
1561268 TTCAAACTCCTAAAAATAGGATAGAGT
1 TTCAAACTCCTAAAAATAGGATAGAGT
1561295 T
1 T
1561296 CTACTATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (27 bp):
TTCAAACTCCTAAAAATAGGATAGAGT
Found at i:1562051 original size:21 final size:22
Alignment explanation
Indices: 1562027--1562068 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1562017 TCATTATATG
1562027 TATACTTT-TATA-TTTGGTTTA
1 TATA-TTTATATATTTTGGTTTA
*
1562048 TATATTTATTTATTTTGGTTT
1 TATATTTATATATTTTGGTTT
1562069 TTGGTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 7 0.39
22 8 0.44
ACGTcount: A:0.21, C:0.02, G:0.10, T:0.67
Consensus pattern (22 bp):
TATATTTATATATTTTGGTTTA
Found at i:1562161 original size:2 final size:2
Alignment explanation
Indices: 1562154--1562180 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1562144 TTTACTCATT
1562154 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 T
1562181 TAATATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1562223 original size:29 final size:30
Alignment explanation
Indices: 1562187--1562270 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 30
1562177 ATATTAATAT
*
1562187 TTCA-TTTATTTATTTATTTATTTTTCCTT-
1 TTCATTTTATTTATTTATTTATTTTT-ATTC
* *
1562216 TT-ATTTTATTTTTTTACTTATTTTTATTC
1 TTCATTTTATTTATTTATTTATTTTTATTC
*
1562245 TTCATTTT-TTTCATTTATTCATTTTT
1 TTCATTTTATTT-ATTTATTTATTTTT
1562271 TCCCTCTAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.07
29 26 0.58
30 16 0.36
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.74
Consensus pattern (30 bp):
TTCATTTTATTTATTTATTTATTTTTATTC
Found at i:1565295 original size:8 final size:8
Alignment explanation
Indices: 1565284--1565334 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
1565274 CAAAAAGGGT
1565284 AAAAAG-A
1 AAAAAGAA
1565291 AAAAAGAA
1 AAAAAGAA
*
1565299 AAGAAGCAA
1 AAAAAG-AA
*
1565308 AAAAGGAA
1 AAAAAGAA
*
1565316 AAAAATAA
1 AAAAAGAA
*
1565324 AAAAACAA
1 AAAAAGAA
1565332 AAA
1 AAA
1565335 GAAAGAACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
7 6 0.17
8 24 0.67
9 6 0.17
ACGTcount: A:0.82, C:0.04, G:0.12, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:1566052 original size:22 final size:22
Alignment explanation
Indices: 1565978--1566054 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
1565968 GGTACCCCAT
*
1565978 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
1566000 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1566022 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
1566044 CAAACCTTTGA
1 CAAACCTTTGA
1566055 CCAAACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:1566491 original size:18 final size:19
Alignment explanation
Indices: 1566468--1566504 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1566458 TCAACATCAA
*
1566468 ATATTGGGGTATT-TTTGG
1 ATATTGGGGCATTATTTGG
1566486 ATATTGGGGCATTATTTGG
1 ATATTGGGGCATTATTTGG
1566505 GGATTCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.19, C:0.03, G:0.32, T:0.46
Consensus pattern (19 bp):
ATATTGGGGCATTATTTGG
Found at i:1567050 original size:63 final size:63
Alignment explanation
Indices: 1566906--1567043 Score: 233
Period size: 63 Copynumber: 2.2 Consensus size: 63
1566896 ACAACGCAAG
*
1566906 TTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
1 TTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
* *
1566969 TTCAACTTCACGAA-GAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
1 TTCAACTTCAC-AATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
1567032 TTCAACTTCACA
1 TTCAACTTCACA
1567044 TCGAAGGATA
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
62 1 0.01
63 68 0.96
64 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.26
Consensus pattern (63 bp):
TTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAAT
Found at i:1567077 original size:169 final size:169
Alignment explanation
Indices: 1566798--1567148 Score: 621
Period size: 169 Copynumber: 2.1 Consensus size: 169
1566788 TCGAGAGTAG
*
1566798 ATTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
1 ATTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
*
1566863 TTCAACTTCACAGCGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACAATGAAGGGAC
66 TTCAACTTCACAGCGAAGAATATTGGACTCAAGACAACGCAAGTTCAACTTCACAATGAAGGGAC
*
1566928 CGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
131 CGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
*
1566967 ATTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAAT
1 ATTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
* * *
1567032 TTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGATGAAGGGAC
66 TTCAACTTCACAGCGAAGAATATTGGACTCAAGACAACGCAAGTTCAACTTCACAATGAAGGGAC
* *
1567097 CGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
131 CGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1567136 ATTTCAACTTCAC
1 ATTTCAACTTCAC
1567149 ATCGAAGGAT
Statistics
Matches: 173, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
169 173 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (169 bp):
ATTTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
TTCAACTTCACAGCGAAGAATATTGGACTCAAGACAACGCAAGTTCAACTTCACAATGAAGGGAC
CGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCA
Found at i:1567079 original size:106 final size:106
Alignment explanation
Indices: 1566969--1568221 Score: 1887
Period size: 106 Copynumber: 11.9 Consensus size: 106
1566959 CAGAGCCAAT
* *
1566969 TTCAACTTCACGAAGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
*
1567034 CAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
* *
1567075 TTCAACTTCACGATGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1567140 CAACTTCACATCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
*
1567181 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
*
1567246 CAACTTCACAGCGTAGGATATTGGACTCAAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
*
1567287 TTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1567352 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGTAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
* *
1567393 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* * *
1567458 TAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
* * * *
1567499 TTCAACTTCACGACGAAGGGACCGTTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
** *
1567564 CAACTTCACAATGAAGGATATTGGACTCAAGACAATGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
* *
1567605 TTCAACTTCACGACGAAGGGAACGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGTCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
*
1567670 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
* *
1567711 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTTAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
*
1567776 CAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
*
1567817 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* *
1567882 TAACTTCACAG-GATAGGATATTGGACTCAAGACAACGTAAG
66 CAACTTCACAGCGA-AGGATATTGGACTCAAGACAACGCAAG
1567923 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
* * * *
1567988 CAACTTCTCAGCGAAGGATCTTGGACCCAAGACAACACAAG
66 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
* * * ** * *
1568029 CTCAACTTCACGACGAAGGG-GCGACTGATTGTCAA-CGA-AA-TT-TC-A-TTCAGAGTCAATT
1 TTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATT
* * * *
1568087 TCAACTTCACAGCAAAGGATATTGGACTCGAGATAACACAAG
65 TCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
* * * * * **
1568129 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCC-GGTTCTAGAGCCAATT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTC-AGAGCCAATT
* *
1568193 TCAGCTTCAC-GACGGAGGATATTGGACTC
65 TCAACTTCACAG-CGAAGGATATTGGACTC
1568222 GGAACAATGC
Statistics
Matches: 1052, Mismatches: 84, Indels: 22
0.91 0.07 0.02
Matches are distributed among these distances:
100 76 0.07
101 3 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 9 0.01
106 952 0.90
107 2 0.00
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.24
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAG
Found at i:1569005 original size:37 final size:37
Alignment explanation
Indices: 1568952--1569056 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
1568942 CCTCTTTGTC
1568952 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1568989 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1569026 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
1569057 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1569564 original size:19 final size:19
Alignment explanation
Indices: 1569542--1569579 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1569532 ATTCATTTGG
*
1569542 TTATTTTTTA-ATACTATAT
1 TTATTATTTATATA-TATAT
1569561 TTATTATTTATATATATAT
1 TTATTATTTATATATATAT
1569580 ATATATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTATTTATATATATAT
Found at i:1569831 original size:12 final size:12
Alignment explanation
Indices: 1569785--1569841 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
1569775 TTTTTTTTGT
1569785 TTAT-ATTA-TA
1 TTATCATTATTA
1569795 TTAT-ATTA-TA
1 TTATCATTATTA
*
1569805 TTTTCA-TATTA
1 TTATCATTATTA
*
1569816 TTATCATTATTG
1 TTATCATTATTA
*
1569828 TTATGATTATTA
1 TTATCATTATTA
1569840 TT
1 TT
1569842 TTTCTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
10 15 0.38
11 8 0.21
12 16 0.41
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.61
Consensus pattern (12 bp):
TTATCATTATTA
Found at i:1569865 original size:2 final size:2
Alignment explanation
Indices: 1569858--1569887 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1569848 TTTACTCATT
1569858 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1569888 TTTATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1569958 original size:25 final size:23
Alignment explanation
Indices: 1569911--1569959 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
1569901 TTATTTTTCC
*
1569911 TTTTATTTTATTTTTTTACTTAT
1 TTTTATTTTATTTTTTCACTTAT
*
1569934 TTTTATTCTTCATTTTTTCATTTAT
1 TTTTATT-TT-ATTTTTTCACTTAT
1569959 T
1 T
1569960 CATTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 2 0.09
25 13 0.59
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTATTTTATTTTTTCACTTAT
Found at i:1574624 original size:29 final size:30
Alignment explanation
Indices: 1574590--1574664 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
1574580 TACGATCAAA
** *
1574590 AATCAATTTGACCACCGAACT-TTCAATTG
1 AATCAATCAGACCACCAAACTATTCAATTG
*
1574619 AATCAATCAGACCACCAAACTATTTAATTG
1 AATCAATCAGACCACCAAACTATTCAATTG
** *
1574649 GTTCAATCAAACCACC
1 AATCAATCAGACCACC
1574665 GACCGTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 18 0.47
30 20 0.53
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.27
Consensus pattern (30 bp):
AATCAATCAGACCACCAAACTATTCAATTG
Found at i:1575425 original size:29 final size:27
Alignment explanation
Indices: 1575383--1575436 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
1575373 TTTATTGTTT
*
1575383 TTAATTTTTATTAATGAAAGAAATAATTC
1 TTAACTTTTATTAAT-AAA-AAATAATTC
1575412 TTAACTTTTATTAATAAAAAATAAT
1 TTAACTTTTATTAATAAAAAATAAT
1575437 CTTTAGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
28 3 0.12
29 14 0.58
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (27 bp):
TTAACTTTTATTAATAAAAAATAATTC
Found at i:1575447 original size:27 final size:28
Alignment explanation
Indices: 1575381--1575450 Score: 90
Period size: 27 Copynumber: 2.5 Consensus size: 28
1575371 TTTTTATTGT
1575381 TTTTAATTTTTATTAATGAAAGAAATAA
1 TTTTAATTTTTATTAATGAAAGAAATAA
*
1575409 TTCTTAACTTTTATTAAT-AAA-AAATAA
1 TT-TTAATTTTTATTAATGAAAGAAATAA
*
1575436 TCTTTAGTTTTTATT
1 T-TTTAATTTTTATT
1575451 TATTAATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 17 0.46
28 6 0.16
29 14 0.38
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTTAATTTTTATTAATGAAAGAAATAA
Found at i:1575630 original size:74 final size:74
Alignment explanation
Indices: 1575484--1575622 Score: 208
Period size: 74 Copynumber: 1.9 Consensus size: 74
1575474 ATATATCTAT
* * * *
1575484 TAAATTATAATTAATAAATAAAATCAATAATTATTTATTCGATTAAAAATTTAAAATTTAAAATA
1 TAAATTATAATTAATAAATAAAATAAATAATTATTTATTCGACTAAAAATTTAAAAATAAAAATA
1575549 TAAAAATTG
66 TAAAAATTG
*
1575558 TAAATTATAATTAATAAATAAAAGTAAATAATTATTTATTCGACT-AAATTTTAAAACATAAAAA
1 TAAATTATAATTAATAAATAAAA-TAAATAATTATTTATTCGACTAAAAATTTAAAA-ATAAAAA
1575622 T
64 T
1575623 TGTAAATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
74 33 0.57
75 25 0.43
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (74 bp):
TAAATTATAATTAATAAATAAAATAAATAATTATTTATTCGACTAAAAATTTAAAAATAAAAATA
TAAAAATTG
Found at i:1576188 original size:3 final size:3
Alignment explanation
Indices: 1576175--1576217 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
1576165 ATAATACATA
1576175 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1576218 AACTAATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1577429 original size:30 final size:29
Alignment explanation
Indices: 1577395--1577478 Score: 78
Period size: 30 Copynumber: 2.8 Consensus size: 29
1577385 ATATTTAGGG
*
1577395 TTTAGTCCTTTAACTTTTTATTTTAACTAT
1 TTTAGTCCTTTAACTTTTTATTTT-ACCAT
* * * *
1577425 TTTAGTCCCTTAAATTTCTATTCTTGCCAT
1 TTTAGTCCTTTAACTTTTTATT-TTACCAT
* * *
1577455 TTTAGTTCTTTAACCTTTTGTTTT
1 TTTAGTCCTTTAACTTTTTATTTT
1577479 TGTATTTTGA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
29 2 0.05
30 38 0.90
31 2 0.05
ACGTcount: A:0.19, C:0.17, G:0.06, T:0.58
Consensus pattern (29 bp):
TTTAGTCCTTTAACTTTTTATTTTACCAT
Found at i:1577572 original size:2 final size:2
Alignment explanation
Indices: 1577565--1577593 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1577555 TTTACATTGT
1577565 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 T
1577594 TTACACTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1577646 original size:6 final size:6
Alignment explanation
Indices: 1577635--1577671 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1577625 ATTTTTCTTA
*
1577635 ATTTTT ATTTTT ATGTTT ATTTTT -TTTTT -TTTTT ATT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT
1577672 CTTAACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.84
Consensus pattern (6 bp):
ATTTTT
Found at i:1581706 original size:96 final size:98
Alignment explanation
Indices: 1581523--1581720 Score: 274
Period size: 96 Copynumber: 2.0 Consensus size: 98
1581513 TTATAATATT
***
1581523 ATATATATACAATAAAGCTTAAGTTGTCCCTCTACAGCTATTGGTTAAACGTCCCGACTTTATGG
1 ATATATATACAATAAAGCTTAAGTTGTCCCTCTACAAAAATTGGTTAAACGTCCCGACTTTATGG
1581588 ATAAGATTCACTAGCCTAATAAAGGTGATTATA
66 ATAAGATTCACTAGCCTAATAAAGGTGATTATA
* * * * *
1581621 ATATCTATACAATTAAGCTTGAGTTGTCCCTCTA-AAAAATTGGTTAAGCG-CCCGGCTTTATGG
1 ATATATATACAATAAAGCTTAAGTTGTCCCTCTACAAAAATTGGTTAAACGTCCCGACTTTATGG
* * * *
1581684 ATAAGATTTAGTAGCCTGATAAAGGTGGTTATA
66 ATAAGATTCACTAGCCTAATAAAGGTGATTATA
1581717 ATAT
1 ATAT
1581721 TGAGTTGTCC
Statistics
Matches: 88, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
96 45 0.51
97 12 0.14
98 31 0.35
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (98 bp):
ATATATATACAATAAAGCTTAAGTTGTCCCTCTACAAAAATTGGTTAAACGTCCCGACTTTATGG
ATAAGATTCACTAGCCTAATAAAGGTGATTATA
Found at i:1583034 original size:85 final size:84
Alignment explanation
Indices: 1582878--1583192 Score: 324
Period size: 85 Copynumber: 3.7 Consensus size: 84
1582868 TAAAGGAACT
* * * * * *
1582878 ATTTGCAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAGCAAAAACCTTCGAGTTCGATTCCAT
1 ATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
*
1582943 TAAGCTCAAGGACCTATCAA
66 TCAGCTCAAGG-CCTATCAA
* * * *
1582963 ATTTACAACATAGCTCAAGGCAAGAAGGGCTAACTGTCAACCACAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* *
1583028 TCAGCTCAAGGGCATGTCAA
66 TCAGCTCAA-GGCCTATCAA
* * * * * ** * * * *
1583048 ATTTACAGTATAACTTAAGTCGAGAAAAGCTATCTGTCAAGAGAAATCGTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* * *
1583113 TCAGCTCAAGGGCAACCAA
66 TCAGCTCAAGGCCTATCAA
* * * * *
1583132 ATTTACAGCATAGATCAAGGCAATAAGGGCTATCTGTCAACAAAAATCTTCAAGTTTGATT
1 ATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATT
1583193 CTATTAAGCT
Statistics
Matches: 182, Mismatches: 47, Indels: 3
0.78 0.20 0.01
Matches are distributed among these distances:
84 52 0.29
85 128 0.70
86 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (84 bp):
ATTTACAGCATAGCTCAAGGCAAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAGGCCTATCAA
Found at i:1583997 original size:5 final size:5
Alignment explanation
Indices: 1583987--1584016 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
1583977 GCATAATACA
1583987 TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT
1584017 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:1585134 original size:30 final size:30
Alignment explanation
Indices: 1585100--1585173 Score: 94
Period size: 30 Copynumber: 2.5 Consensus size: 30
1585090 ATATTTAGGG
**
1585100 TTTAGTCCTTTAACTTTCTATTTTAATTAT
1 TTTAGTCCTTTAACTTTCTATTTTAACCAT
* * *
1585130 TTTAGTCCCTTAAATTTCTATTTTCACCAT
1 TTTAGTCCTTTAACTTTCTATTTTAACCAT
*
1585160 TTTAGTTCTTTAAC
1 TTTAGTCCTTTAAC
1585174 CTTTTGTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.18, G:0.04, T:0.55
Consensus pattern (30 bp):
TTTAGTCCTTTAACTTTCTATTTTAACCAT
Found at i:1585346 original size:6 final size:6
Alignment explanation
Indices: 1585335--1585364 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1585325 ATTTTTCTTC
*
1585335 ATTTTT ATTTTT ATGTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1585365 TCTTTCTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:1586568 original size:17 final size:17
Alignment explanation
Indices: 1586546--1586578 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1586536 TGTTGTAAGG
1586546 CAAATAATTTATTTAAA
1 CAAATAATTTATTTAAA
*
1586563 CAAATAATTTGTTTAA
1 CAAATAATTTATTTAA
1586579 TTTTTTATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
CAAATAATTTATTTAAA
Found at i:1597691 original size:30 final size:30
Alignment explanation
Indices: 1597638--1597738 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
1597628 CTTATTAAAA
* * *
1597638 TAAAGGACT-AAATAACAAGAACAGAAATT
1 TAAAGGACTAAAATAATAAAAACAGAAACT
1597667 TACAA-GACTAAAATAATAAAAACAGAAACT
1 TA-AAGGACTAAAATAATAAAAACAGAAACT
* * * *
1597697 TAAAGGATTAAAATAGTAAAAATAGAAAAT
1 TAAAGGACTAAAATAATAAAAACAGAAACT
*
1597727 TAAAGGGCTAAA
1 TAAAGGACTAAA
1597739 CAATAATTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 8 0.13
30 52 0.87
ACGTcount: A:0.60, C:0.08, G:0.13, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAAATAATAAAAACAGAAACT
Found at i:1598693 original size:21 final size:20
Alignment explanation
Indices: 1598650--1598694 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1598640 AGTTTCTCCC
*
1598650 TTTCTCTTTTATCATTGTTT
1 TTTCTCTTTTATCATTATTT
* *
1598670 TTTCTTTTTTCATTATTATTT
1 TTTCTCTTTT-ATCATTATTT
1598691 TTTC
1 TTTC
1598695 GTTCAAGGCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.11, C:0.13, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTCTCTTTTATCATTATTT
Found at i:1599215 original size:11 final size:11
Alignment explanation
Indices: 1599201--1599243 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1599191 CCGGGTAAAG
1599201 TCTGGATCGGA
1 TCTGGATCGGA
1599212 TCTGGATCTGGA
1 TCTGGATC-GGA
* *
1599224 TCTTGGGTCGGG
1 TC-TGGATCGGA
1599236 TCTGGATC
1 TCTGGATC
1599244 CTCTTGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 13 0.48
12 9 0.33
13 5 0.19
ACGTcount: A:0.12, C:0.19, G:0.37, T:0.33
Consensus pattern (11 bp):
TCTGGATCGGA
Found at i:1599687 original size:40 final size:43
Alignment explanation
Indices: 1599588--1599695 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 43
1599578 TTTGGATTAG
* * *
1599588 GGATGACACGGTTCATACGCGATGAAGAGTTCTGGTCGTCTAA
1 GGATGACACGGTTCCTACGTGATGAAGAGATCTGGTCGTCTAA
* * * * *
1599631 GGGTGACACGGCTCCTACGTGATGATGAGATCTGGTTG-GT-A
1 GGATGACACGGTTCCTACGTGATGAAGAGATCTGGTCGTCTAA
1599672 -GATGACACGGTTCCTACGTGATGA
1 GGATGACACGGTTCCTACGTGATGA
1599696 GGATGTCAGA
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
40 22 0.40
41 1 0.02
42 1 0.02
43 31 0.56
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (43 bp):
GGATGACACGGTTCCTACGTGATGAAGAGATCTGGTCGTCTAA
Found at i:1599888 original size:131 final size:131
Alignment explanation
Indices: 1599631--1600139 Score: 532
Period size: 130 Copynumber: 3.9 Consensus size: 131
1599621 GGTCGTCTAA
* * **
1599631 GGGTGACACGGCTCCTACGTGATGATGAGATCTGGTTGGTAGATGACACGGTTCCTACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGGTAGATGACACAATTCCTACGTGATGA
* * * * * * *
1599696 GGATGTCAGACAATCTTTAG-GGATGATAACACGATTCCTACGTGATGAGGATGACTAGTTATTA
66 GGACGTTAGGCCATCTTTAGAGGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATTA
1599760 G
131 G
* * * *
1599761 GGGTGACACGGCTTCTACGTGATGAGGAGGTCTGGTCGGT-GATGACACAACTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGGTAGATGACACAATTCCTACGTGATGA
* * ** *
1599825 AGA-GTTTGGCCATCTTTAGAAAGGGCGATAACACGGTTCCTACGCGATGAGGACGACTGGTTAT
66 GGACGTTAGGCCATCTTTAG--AGGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTAT
1599889 CTAG
129 -TAG
* * * *
1599893 GGGTGACACTGCTCCTACGTGATGAGGAGGTTTGGTTGGTAGATGACACATTTCCTATGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGGTAGATGACACAATTCCTACGTGATGA
* * * *
1599958 GGACGGTAAGCCATCTTTAGA-GATGATAACTA-GGTTCCTACGTGAT-ATGGACGACCGATTAT
66 GGACGTTAGGCCATCTTTAGAGGATGATAAC-ACGGTTCCTACGTGATGA-GGACGACTGGTTAT
*
1600020 CAG
129 TAG
* ** * * * * * * *
1600023 GGGTGGCACAACTTCTACGTGATGAGGAAGTCTGATTGGTTGATGACATAGTTCCTATGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGGTAGATGACACAATTCCTACGTGATGA
* *
1600088 GGACGACT-GGCCATCTTT--AGGATGATAACACGGTTCCCACGTGATGAGGACG
66 GGACG-TTAGGCCATCTTTAGAGGATGATAACACGGTTCCTACGTGATGAGGACG
1600140 GCATGTTTTC
Statistics
Matches: 317, Mismatches: 50, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
128 14 0.04
129 49 0.15
130 109 0.34
131 69 0.22
132 41 0.13
133 22 0.07
134 13 0.04
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.27
Consensus pattern (131 bp):
GGGTGACACGGCTCCTACGTGATGAGGAGGTCTGGTTGGTAGATGACACAATTCCTACGTGATGA
GGACGTTAGGCCATCTTTAGAGGATGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATTA
G
Found at i:1600277 original size:32 final size:30
Alignment explanation
Indices: 1600227--1600326 Score: 87
Period size: 30 Copynumber: 3.3 Consensus size: 30
1600217 ACAAAATTTA
* *
1600227 TTTCAAGGGAAA-TGACTCAAAGATGATTTTG
1 TTTCAAGAGAAACAGACTCAAAGA--ATTTTG
* * *
1600258 TTTTAATAGAAACAGACTCAAAGACTTTTG
1 TTTCAAGAGAAACAGACTCAAAGAATTTTG
* * *
1600288 TTTCAAGAGAAACAAACTCAAA-TATATTG
1 TTTCAAGAGAAACAGACTCAAAGAATTTTG
*
1600317 TCTCAAGAGA
1 TTTCAAGAGA
1600327 GACAAAATTT
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
29 13 0.23
30 24 0.43
31 9 0.16
32 10 0.18
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (30 bp):
TTTCAAGAGAAACAGACTCAAAGAATTTTG
Found at i:1600289 original size:30 final size:30
Alignment explanation
Indices: 1600253--1600332 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
1600243 TCAAAGATGA
* * *
1600253 TTTTGTTTTAATAGAAACAGACTCAAAGAC
1 TTTTGTTTCAAGAGAAACAAACTCAAAGAC
*
1600283 TTTTGTTTCAAGAGAAACAAACTCAAATA-
1 TTTTGTTTCAAGAGAAACAAACTCAAAGAC
* * *
1600312 TATTGTCTCAAGAGAGACAAA
1 TTTTGTTTCAAGAGAAACAAA
1600333 ATTTTTTTCC
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 18 0.42
30 25 0.58
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (30 bp):
TTTTGTTTCAAGAGAAACAAACTCAAAGAC
Found at i:1602223 original size:2 final size:2
Alignment explanation
Indices: 1602218--1602244 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1602208 TGTGTGTGTG
1602218 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 T
1602245 GTTTACGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1606277 original size:29 final size:28
Alignment explanation
Indices: 1606208--1606318 Score: 105
Period size: 29 Copynumber: 3.8 Consensus size: 28
1606198 GCATGCTTAT
* * *
1606208 TAAAATAAAGGACTAAATAACAAGAACA
1 TAAATTAAAGGACTAAATAATAAAAACA
*
1606236 TAAATTAACAGGACTAAATAATAAAAATA
1 TAAATTAA-AGGACTAAATAATAAAAACA
* * *
1606265 GAAACTTAAAGGATTAAAATAGTAAAAACA
1 TAAA-TTAAAGGACT-AAATAATAAAAACA
* *
1606295 TAAAGTTAAAGGGCTAAACAATAA
1 TAAA-TTAAAGGACTAAATAATAA
1606319 TTACAAATAA
Statistics
Matches: 66, Mismatches: 14, Indels: 5
0.78 0.16 0.06
Matches are distributed among these distances:
28 7 0.11
29 32 0.48
30 27 0.41
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (28 bp):
TAAATTAAAGGACTAAATAATAAAAACA
Found at i:1608599 original size:7 final size:7
Alignment explanation
Indices: 1608589--1608613 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1608579 CAACGAATTC
1608589 AAATATT
1 AAATATT
1608596 AAATATT
1 AAATATT
1608603 AAATATT
1 AAATATT
1608610 AAAT
1 AAAT
1608614 GAAGACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATATT
Found at i:1613397 original size:36 final size:36
Alignment explanation
Indices: 1613345--1613633 Score: 226
Period size: 36 Copynumber: 8.2 Consensus size: 36
1613335 GATACTATTT
* *
1613345 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1613381 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
1613417 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
1613452 ACATCATCC-T--TCCATTACCATTCATCA--CC-A-A
1 TCATCA-CCATAGTCCATCACCATT-ATCACGCCTATA
* * * * *** * * *
1613483 T-AGCA--TTGGTTCCTTCTTAGTTTTAT-AAGATACTATTT
1 TCATCACCATAG-TCCATC--ACCATTATCACG--CCTA-TA
* *
1613521 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1613557 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
* *
1613593 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAGTCCATCACCATTATCACGCCTATA
*
1613628 ACATCA
1 TCATCA
1613634 TCCTTCCATT
Statistics
Matches: 201, Mismatches: 32, Indels: 41
0.73 0.12 0.15
Matches are distributed among these distances:
28 1 0.00
30 3 0.01
31 6 0.03
32 3 0.01
33 14 0.07
34 1 0.00
35 40 0.20
36 114 0.57
37 3 0.01
38 5 0.02
39 5 0.02
40 5 0.02
41 1 0.00
ACGTcount: A:0.31, C:0.34, G:0.04, T:0.31
Consensus pattern (36 bp):
TCATCACCATAGTCCATCACCATTATCACGCCTATA
Found at i:1613400 original size:13 final size:11
Alignment explanation
Indices: 1613345--1613443 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
1613335 GATACTATTT
1613345 TCATCACCATAA
1 TCATCACCAT-A
*
1613357 TCCATCTCCATTA
1 T-CATCACCA-TA
*
1613370 TCA-CGCCTATA
1 TCATCACC-ATA
1613381 TCATCACCATA
1 TCATCACCATA
1613392 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
1613406 TCA-CGCCTATA
1 TCATCACC-ATA
1613417 TCATCACCATA
1 TCATCACCATA
1613428 TTCCATCACCATA
1 -T-CATCACCATA
1613441 TCA
1 TCA
1613444 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:1613576 original size:13 final size:11
Alignment explanation
Indices: 1613521--1613619 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
1613511 GATACTATTT
1613521 TCATCACCATAA
1 TCATCACCAT-A
*
1613533 TCCATCTCCATTA
1 T-CATCACCA-TA
*
1613546 TCA-CGCCTATA
1 TCATCACC-ATA
1613557 TCATCACCATA
1 TCATCACCATA
1613568 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
1613582 TCA-CGCCTATA
1 TCATCACC-ATA
1613593 TCATCACCATA
1 TCATCACCATA
1613604 TTCCATCACCATA
1 -T-CATCACCATA
1613617 TCA
1 TCA
1613620 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:1613600 original size:176 final size:177
Alignment explanation
Indices: 1613306--1613658 Score: 699
Period size: 176 Copynumber: 2.0 Consensus size: 177
1613296 TTGCTCCTTT
1613306 ATAGCATTGGTTCCTTCTTAGTTTTATAAGATACTATTTTCATCACCATAATCCATCTCCATTAT
1 ATAGCATTGGTTCCTTCTTAGTTTTATAAGATACTATTTTCATCACCATAATCCATCTCCATTAT
1613371 CACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCA
66 CACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCA
1613436 CCATATCACGCCAATAACATCATCCTTCCATTACCA-TTCATCACCA
131 CCATATCACGCCAATAACATCATCCTTCCATTACCATTTCATCACCA
1613482 ATAGCATTGGTTCCTTCTTAGTTTTATAAGATACTATTTTCATCACCATAATCCATCTCCATTAT
1 ATAGCATTGGTTCCTTCTTAGTTTTATAAGATACTATTTTCATCACCATAATCCATCTCCATTAT
1613547 CACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCA
66 CACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCA
1613612 CCATATCACGCCAATAACATCATCCTTCCATTACCATTTCATCACCA
131 CCATATCACGCCAATAACATCATCCTTCCATTACCATTTCATCACCA
1613659 TTAAATCATC
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
176 166 0.94
177 10 0.06
ACGTcount: A:0.30, C:0.32, G:0.05, T:0.33
Consensus pattern (177 bp):
ATAGCATTGGTTCCTTCTTAGTTTTATAAGATACTATTTTCATCACCATAATCCATCTCCATTAT
CACGCCTATATCATCACCATAGTCCATCACCATTATCACGCCTATATCATCACCATATTCCATCA
CCATATCACGCCAATAACATCATCCTTCCATTACCATTTCATCACCA
Found at i:1613648 original size:33 final size:33
Alignment explanation
Indices: 1613533--1613672 Score: 97
Period size: 36 Copynumber: 4.1 Consensus size: 33
1613523 ATCACCATAA
* * *
1613533 TCCATCTCCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC-T
* *
1613567 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACGCCAATAACATCATCC---T
1613605 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
1613638 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
1613671 TC
1 TC
1613673 ATTCATTAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.08
35 17 0.18
36 43 0.46
38 2 0.02
ACGTcount: A:0.30, C:0.36, G:0.03, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:1620276 original size:21 final size:22
Alignment explanation
Indices: 1620250--1620296 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 22
1620240 TATGCCTTCT
1620250 AGTTCA-AGGGGAAGGCGTGCA
1 AGTTCAGAGGGGAAGGCGTGCA
1620271 AGTTCAGTAGGGGAAGGCGTGCA
1 AGTTCAG-AGGGGAAGGCGTGCA
1620294 AGT
1 AGT
1620297 AGTAGGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 6 0.25
23 18 0.75
ACGTcount: A:0.28, C:0.13, G:0.43, T:0.17
Consensus pattern (22 bp):
AGTTCAGAGGGGAAGGCGTGCA
Found at i:1622715 original size:130 final size:130
Alignment explanation
Indices: 1622566--1622816 Score: 484
Period size: 130 Copynumber: 1.9 Consensus size: 130
1622556 TGAAGATTAA
*
1622566 AAAAATGAACACAATCATTAAATTTTATCAAACTAATAACAATTTGGTATTTAAATACAACAAAC
1 AAAAACGAACACAATCATTAAATTTTATCAAACTAATAACAATTTGGTATTTAAATACAACAAAC
1622631 TTACAATAAGAATTAAATGGTAAATGATAACCAAATTACGATAACTGATATTAAATACAATCATT
66 TTACAATAAGAATTAAATGGTAAATGATAACCAAATTACGATAACTGATATTAAATACAATCATT
*
1622696 AAAAACGAACACAATCATTAAATTTTATCGAACTAATAACAATTTGGTATTTAAATACAACAAAC
1 AAAAACGAACACAATCATTAAATTTTATCAAACTAATAACAATTTGGTATTTAAATACAACAAAC
1622761 TTACAATAAGAATTAAATGGTAAATGATAACCAAATTACGATAACTGATATTAAAT
66 TTACAATAAGAATTAAATGGTAAATGATAACCAAATTACGATAACTGATATTAAAT
1622817 GGTAATAAAC
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 119 1.00
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (130 bp):
AAAAACGAACACAATCATTAAATTTTATCAAACTAATAACAATTTGGTATTTAAATACAACAAAC
TTACAATAAGAATTAAATGGTAAATGATAACCAAATTACGATAACTGATATTAAATACAATCATT
Found at i:1623069 original size:15 final size:15
Alignment explanation
Indices: 1623049--1623077 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1623039 TCCTCGATGT
1623049 CATCATCGTCGTCGA
1 CATCATCGTCGTCGA
1623064 CATCATCGTCGTCG
1 CATCATCGTCGTCG
1623078 TCGTCCTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.34, G:0.21, T:0.28
Consensus pattern (15 bp):
CATCATCGTCGTCGA
Found at i:1625106 original size:111 final size:111
Alignment explanation
Indices: 1624969--1625301 Score: 630
Period size: 111 Copynumber: 3.0 Consensus size: 111
1624959 ATTACAAAAA
1624969 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1625034 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
1625080 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
*
1625145 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAAATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
*
1625191 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
1625256 AATTAAAACGTTAAAATATTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
1625302 ATGATTTCTA
Statistics
Matches: 217, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 217 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTTGAGATAT
Found at i:1625383 original size:17 final size:18
Alignment explanation
Indices: 1625363--1625403 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1625353 GAATTATATT
*
1625363 AGTAAAATA-TTAAATAA
1 AGTAAAATACTAAAATAA
1625380 AGTAAAATACTAAAATAA
1 AGTAAAATACTAAAATAA
*
1625398 ATTAAA
1 AGTAAA
1625404 TACATAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (18 bp):
AGTAAAATACTAAAATAA
Found at i:1625472 original size:20 final size:19
Alignment explanation
Indices: 1625443--1625484 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
1625433 ACCTTAAAGA
*
1625443 TAGAGTATTTGAGAGAAATT
1 TAGAGAATTTGAGAG-AATT
1625463 TAGAGAATTTGAGAGAATT
1 TAGAGAATTTGAGAGAATT
1625482 TAG
1 TAG
1625485 TGTGATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.26, T:0.33
Consensus pattern (19 bp):
TAGAGAATTTGAGAGAATT
Found at i:1625659 original size:50 final size:49
Alignment explanation
Indices: 1625605--1625730 Score: 135
Period size: 50 Copynumber: 2.5 Consensus size: 49
1625595 AGATACCCAG
* *
1625605 GTATAGTGCGGATCAGGGGGCGCGCTATACCCACATGGCGCCAAATCACC
1 GTATA-TGCGGATCAGGGGGCGCGCTATACCCACATGACGCCAAATCAAC
** * * *
1625655 GTATATCGCGGGGCAGGGGACGCGCTATACCCACGTGACGCGAAATCAAC
1 GTATAT-GCGGATCAGGGGGCGCGCTATACCCACATGACGCCAAATCAAC
* * *
1625705 GTATAACGCGGTTCAGAGGGCGCGCT
1 GTAT-ATGCGGATCAGGGGGCGCGCT
1625731 TTACTACTAC
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
49 1 0.02
50 60 0.97
51 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.16
Consensus pattern (49 bp):
GTATATGCGGATCAGGGGGCGCGCTATACCCACATGACGCCAAATCAAC
Found at i:1626299 original size:38 final size:36
Alignment explanation
Indices: 1626257--1626333 Score: 82
Period size: 37 Copynumber: 2.1 Consensus size: 36
1626247 TTTATAATTA
*
1626257 AATAAATAAATGAACTAAAATAATATTTTTTATGTTAT
1 AATAAATAAATG-ACTAAAATAACATTTTTTATG-TAT
* * ** *
1626295 AATAATTTAATGTTTAAAGTAACATTTTTTATGTAT
1 AATAAATAAATGACTAAAATAACATTTTTTATGTAT
1626331 AAT
1 AAT
1626334 TTATTAATTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
36 6 0.18
37 17 0.52
38 10 0.30
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (36 bp):
AATAAATAAATGACTAAAATAACATTTTTTATGTAT
Found at i:1626789 original size:17 final size:18
Alignment explanation
Indices: 1626748--1626793 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1626738 ATTTCCGAGA
*
1626748 GAATTGGAATCTGTGAAG
1 GAATTAGAATCTGTGAAG
*
1626766 GAATTAGAATCTGT-CAG
1 GAATTAGAATCTGTGAAG
*
1626783 GATTTAGAATC
1 GAATTAGAATC
1626794 CAATTTCATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 12 0.48
18 13 0.52
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (18 bp):
GAATTAGAATCTGTGAAG
Found at i:1627373 original size:28 final size:28
Alignment explanation
Indices: 1627314--1627404 Score: 121
Period size: 28 Copynumber: 3.1 Consensus size: 28
1627304 TTCACCCTAA
1627314 ACCCGAATATCACACTTAAAAAAACATGACCCG
1 ACCCGAATATCACACTT--AAAAA-A--ACCCG
*
1627347 ACCCGAATATCACACTTAAAAAAACCCA
1 ACCCGAATATCACACTTAAAAAAACCCG
1627375 ACCCGAATATCACACTT-AAAAAACCCG
1 ACCCGAATATCACACTTAAAAAAACCCG
1627402 ACC
1 ACC
1627405 TGACCCGAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
27 12 0.21
28 21 0.38
30 1 0.02
31 5 0.09
33 17 0.30
ACGTcount: A:0.46, C:0.33, G:0.07, T:0.14
Consensus pattern (28 bp):
ACCCGAATATCACACTTAAAAAAACCCG
Found at i:1629548 original size:22 final size:22
Alignment explanation
Indices: 1629520--1629571 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1629510 TACCATAGCA
* *
1629520 TAGTATCGGTACCATAGTATGG
1 TAGTATCGATAACATAGTATGG
1629542 TAGTATCGATAACATAGTATGG
1 TAGTATCGATAACATAGTATGG
1629564 --GTATCGAT
1 TAGTATCGAT
1629572 TCTGAAGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 8 0.29
22 20 0.71
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.33
Consensus pattern (22 bp):
TAGTATCGATAACATAGTATGG
Found at i:1630265 original size:214 final size:215
Alignment explanation
Indices: 1629896--1630432 Score: 763
Period size: 214 Copynumber: 2.5 Consensus size: 215
1629886 GATTACCAAA
* * * * *
1629896 TCGACACTAAGTCTGCATTTCATGGAATTCATCCTATGTGGATGAATAATCGTTTCGACACTAAA
1 TCGACACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAG
* * *
1629961 TGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGTATTTCA
66 TGTGCATTTCACGAAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCA
* **
1630026 CGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCATGGAATTCATC
131 CGGAATTCATCCTATGTAGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCATC
*
1630091 C-TGTGGATGAATAATC-GTT
196 CATGTGGATGAATAA-CAATT
*
1630110 TCGACACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAG
1 TCGACACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAG
* * ** *
1630175 TGTGTATTTCACGAAATTCATCATGTGTGGATGAATAATTGTTTCGGCACTAAGTGTGCATTTCA
66 TGTGCATTTCACGAAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCA
*
1630240 CGGAATTCATCCTATGTAGATGAATAACTGTTTCGGCACTAAGTGTGCATTTCACAGAATTCATC
131 CGGAATTCATCCTATGTAGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCATC
1630305 CTATGTGGATGAATAACAATT
196 C-ATGTGGATGAATAACAATT
* * * *
1630326 TTGGCACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGAATGAATAACCGTTTCGGCACTATG
1 TCGACACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAG
*** * * ** *
1630391 TGTGCAAAACACGGAATTCATAATATGTTAATGAATGACCGT
66 TGTGCATTTCACGAAATTCATCATATGTGGATGAATAACCGT
1630433 ATGGGCACTA
Statistics
Matches: 285, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
214 179 0.63
215 1 0.00
216 105 0.37
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (215 bp):
TCGACACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAG
TGTGCATTTCACGAAATTCATCATATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATTTCA
CGGAATTCATCCTATGTAGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCATC
CATGTGGATGAATAACAATT
Found at i:1630432 original size:54 final size:54
Alignment explanation
Indices: 1629900--1630411 Score: 758
Period size: 54 Copynumber: 9.5 Consensus size: 54
1629890 ACCAAATCGA
* * * *
1629900 CACTAAGTCTGCATTTCATGGAATTCATCCTATGTGGATGAATAATCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* *
1629954 CACTAAATGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
*
1630008 CACTAAGTGTGTATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* * *
1630062 CACTAAGTGTGCATTTCATGGAATTCATCC--TGTGGATGAATAATCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1630114 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* * * * **
1630168 CACTAAGTGTGTATTTCACGAAATTCATCATGTGTGGATGAATAATTGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* *
1630222 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTAGATGAATAACTGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* ** *
1630276 CACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACAATTTTGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* *
1630330 CACTAAGTGTGCATTTCAAGGAATTCATCCTATGTGAATGAATAACCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
* ***
1630384 CACTATGTGTGCAAAACACGGAATTCAT
1 CACTAAGTGTGCATTTCACGGAATTCAT
1630412 AATATGTTAA
Statistics
Matches: 414, Mismatches: 42, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
52 49 0.12
54 365 0.88
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGG
Found at i:1630519 original size:2 final size:2
Alignment explanation
Indices: 1630512--1630604 Score: 179
Period size: 2 Copynumber: 47.0 Consensus size: 2
1630502 AAGAATAATG
1630512 AT AT AT AT AT AT AT AT AT A- 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
1630553 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
1630595 AT AT AT AT AT
1 AT AT AT AT AT
1630605 TGATTTCATT
Statistics
Matches: 90, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 89 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1632424 original size:20 final size:20
Alignment explanation
Indices: 1632399--1632436 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1632389 GTCGAGGGTT
*
1632399 CATAGGTCCTTCGGGACATA
1 CATAGGTCATTCGGGACATA
*
1632419 CATAGGTCATTTGGGACA
1 CATAGGTCATTCGGGACA
1632437 AATTTCACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
CATAGGTCATTCGGGACATA
Found at i:1632878 original size:200 final size:203
Alignment explanation
Indices: 1632526--1632933 Score: 741
Period size: 200 Copynumber: 2.0 Consensus size: 203
1632516 ACATGTGTAC
1632526 ATGGGCTATCTAAAAGATATTACATGAGTAAATTATATGTGATGTTATGTGTTTGTTTGGTGATA
1 ATGGGCTATCTAAAAGATATTACATGAGTAAATTATATGTGATGTTATGTGTTTGTTTGGTG--A
1632591 TGATATGATATGATGTGAATAAATGATAAGTATATGATTATACGATAAAAGGAATTAATGATAAT
64 TGATATGATATGATGTGAATAAATGATAAGTATATGATTATACGATAAAAGGAATTAATGATAAT
1632656 AATAAGATAATGATAGGAATGAAGATAATTATATGCATGTGTGGATTTGATGTATAAATGGATAT
129 AATAAGATAATGATAGGAATGAAGATAATTATATGCATGTGTGGATTTGATGTATAAATGGATAT
1632721 ATGCTGGTGT
194 ATGCTGGTGT
*
1632731 ATGGGCTATCTAAAAGATATTACATGAGTAAATTCTATGTGATGTTATGTGTTTGTTT-G-G-TG
1 ATGGGCTATCTAAAAGATATTACATGAGTAAATTATATGTGATGTTATGTGTTTGTTTGGTGATG
1632793 ATATGATATGATGTGAATAAATGATAAGTATATGATTATACGATAAAAGGAATTAATGATAATAA
66 ATATGATATGATGTGAATAAATGATAAGTATATGATTATACGATAAAAGGAATTAATGATAATAA
* *
1632858 TACGATAATGATATGAATGAAGATAATTATATGCATGTGTGGATTTGATGTATAAATGGATATAT
131 TAAGATAATGATAGGAATGAAGATAATTATATGCATGTGTGGATTTGATGTATAAATGGATATAT
*
1632923 GTTGGTGT
196 GCTGGTGT
1632931 ATG
1 ATG
1632934 ATATGATAGT
Statistics
Matches: 199, Mismatches: 4, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
200 140 0.70
203 1 0.01
204 1 0.01
205 57 0.29
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.37
Consensus pattern (203 bp):
ATGGGCTATCTAAAAGATATTACATGAGTAAATTATATGTGATGTTATGTGTTTGTTTGGTGATG
ATATGATATGATGTGAATAAATGATAAGTATATGATTATACGATAAAAGGAATTAATGATAATAA
TAAGATAATGATAGGAATGAAGATAATTATATGCATGTGTGGATTTGATGTATAAATGGATATAT
GCTGGTGT
Found at i:1637012 original size:40 final size:40
Alignment explanation
Indices: 1636967--1637051 Score: 125
Period size: 40 Copynumber: 2.1 Consensus size: 40
1636957 AGGTCTTTTA
* *
1636967 GGACATACAGAGGTCCTTCAGAATATATAGAGGTCCTTCG
1 GGACATACAGAGGTCCTTCAGAACATACAGAGGTCCTTCG
* * *
1637007 GGACATACAGAGGTCCTTCAGGACATACATATGTCCTTCG
1 GGACATACAGAGGTCCTTCAGAACATACAGAGGTCCTTCG
1637047 GGACA
1 GGACA
1637052 AATTTCACAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (40 bp):
GGACATACAGAGGTCCTTCAGAACATACAGAGGTCCTTCG
Found at i:1637050 original size:20 final size:20
Alignment explanation
Indices: 1636967--1637051 Score: 107
Period size: 20 Copynumber: 4.2 Consensus size: 20
1636957 AGGTCTTTTA
*
1636967 GGACATACAGAGGTCCTTCA
1 GGACATACAGAGGTCCTTCG
* * *
1636987 GAATATATAGAGGTCCTTCG
1 GGACATACAGAGGTCCTTCG
*
1637007 GGACATACAGAGGTCCTTCA
1 GGACATACAGAGGTCCTTCG
* *
1637027 GGACATACATATGTCCTTCG
1 GGACATACAGAGGTCCTTCG
1637047 GGACA
1 GGACA
1637052 AATTTCACAT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (20 bp):
GGACATACAGAGGTCCTTCG
Found at i:1642674 original size:29 final size:29
Alignment explanation
Indices: 1642641--1642733 Score: 152
Period size: 29 Copynumber: 3.2 Consensus size: 29
1642631 GGATTTATTC
1642641 GATTAAATGATAGATGATGAGAATGA-TTG
1 GATTAAATGATA-ATGATGAGAATGATTTG
1642670 GATTAAATGATAAATGATGAGAATGATTTG
1 GATTAAATGAT-AATGATGAGAATGATTTG
*
1642700 GATAAAATGATAATGATGAGAATGATTTG
1 GATTAAATGATAATGATGAGAATGATTTG
1642729 GATTA
1 GATTA
1642734 GTGGTTTAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
29 46 0.77
30 14 0.23
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.32
Consensus pattern (29 bp):
GATTAAATGATAATGATGAGAATGATTTG
Found at i:1644054 original size:53 final size:54
Alignment explanation
Indices: 1643842--1644068 Score: 325
Period size: 54 Copynumber: 4.2 Consensus size: 54
1643832 CCAAATCAGT
* * *
1643842 ACTACGTGTGCATTTCACGGAATTCATCCTATATGGATAAATAACCGTTTCGAC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
* * *
1643896 ATTAAGTGTGCATTTCACGGAATTCATCCTATGTTGATGAATAATCGTTTC-AGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGA-C
* * *
1643950 ACTAATTGTACATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGGC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
*
1644004 ACTAAGTGTGCATTTCACGGAATT-ATCCTATGTGGATGAATAATCGTTTCGAC
1 ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
1644057 ACTATA-TGTGCA
1 ACTA-AGTGTGCA
1644069 AAACACATAA
Statistics
Matches: 154, Mismatches: 16, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
53 38 0.25
54 116 0.75
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (54 bp):
ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCGAC
Found at i:1644090 original size:107 final size:108
Alignment explanation
Indices: 1643861--1644113 Score: 289
Period size: 107 Copynumber: 2.4 Consensus size: 108
1643851 GCATTTCACG
** * * * *
1643861 GAATTCATCCTATATGGATAAATAACCGTTTCGACATTAAGTGTGCATTTCACGGAATTCATCCT
1 GAATTCATAATATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCT
* *** *
1643926 ATGTTGATGAATAATCGTTTCAGCACTAATTGTACATTTCACG
66 ATGTGGATGAATAATCGTTTCAGCACTAATTGTACAAAACACA
**
1643969 GAATTCATCCTATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATT-ATCCT
1 GAATTCATAATATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCT
*
1644033 ATGTGGATGAATAATCGTTTC-GACACT-ATATGTGCAAAACACA
66 ATGTGGATGAATAATCGTTTCAG-CACTAAT-TGTACAAAACACA
* ** * *
1644076 TAATTCATAATATGTTTATGAATGACCGTAT-GGCACTA
1 GAATTCATAATATGTGGATGAATAACCGTTTCGGCACTA
1644114 TGGGCGCATT
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
106 10 0.08
107 61 0.48
108 55 0.44
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (108 bp):
GAATTCATAATATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCT
ATGTGGATGAATAATCGTTTCAGCACTAATTGTACAAAACACA
Found at i:1657320 original size:7 final size:7
Alignment explanation
Indices: 1657308--1657361 Score: 54
Period size: 7 Copynumber: 7.7 Consensus size: 7
1657298 GTTAGATTAC
1657308 ACCCTAA
1 ACCCTAA
*
1657315 ACCCTAT
1 ACCCTAA
*
1657322 ACTCTAA
1 ACCCTAA
*
1657329 ACCATAA
1 ACCCTAA
*
1657336 ACCATAA
1 ACCCTAA
* *
1657343 ATCTTAA
1 ACCCTAA
1657350 ACCCTAA
1 ACCCTAA
1657357 ACCCT
1 ACCCT
1657362 TAATATGATT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:1659685 original size:30 final size:31
Alignment explanation
Indices: 1659649--1659709 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
1659639 GGAACTTAAT
1659649 TTGACATGTTG-CAATCTTTTGTAAGTAAAC
1 TTGACATGTTGTCAATCTTTTGTAAGTAAAC
*
1659679 TTGACATGTTGCTTCCATCTTTTGTAAGTAA
1 TTGACATGTTG--TCAATCTTTTGTAAGTAA
1659710 GCTTAACTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.41
33 16 0.59
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (31 bp):
TTGACATGTTGTCAATCTTTTGTAAGTAAAC
Found at i:1659851 original size:37 final size:36
Alignment explanation
Indices: 1659800--1659872 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 36
1659790 AAAAATAGTG
*
1659800 TCATCTTATATAAATTTGGATATGTTGTCATATTTT
1 TCATCTTATATAAATTTAGATATGTTGTCATATTTT
* *
1659836 TCATCTTTTTATAAATTTAGATGTGTTGTCATATTTT
1 TCATC-TTATATAAATTTAGATATGTTGTCATATTTT
1659873 GTAAACTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 5 0.15
37 28 0.85
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (36 bp):
TCATCTTATATAAATTTAGATATGTTGTCATATTTT
Found at i:1660097 original size:17 final size:17
Alignment explanation
Indices: 1660075--1660111 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1660065 ATTCGAGTTT
1660075 GAGTTCGAGCTTGAACC
1 GAGTTCGAGCTTGAACC
*
1660092 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAACC
1660109 GAG
1 GAG
1660112 CTTGAATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (17 bp):
GAGTTCGAGCTTGAACC
Found at i:1660110 original size:11 final size:11
Alignment explanation
Indices: 1660096--1660145 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
1660086 TGAACCGAGT
1660096 TCGAGCTTGAA
1 TCGAGCTTGAA
1660107 TCGAGCTTGAA
1 TCGAGCTTGAA
* **
1660118 TTGAGCTCAAAA
1 TCGAGCT-TGAA
*
1660130 TCGAGCTTCAA
1 TCGAGCTTGAA
1660141 TCGAG
1 TCGAG
1660146 ATCGATTCTC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 24 0.75
12 8 0.25
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:1660162 original size:24 final size:24
Alignment explanation
Indices: 1660130--1660193 Score: 119
Period size: 24 Copynumber: 2.7 Consensus size: 24
1660120 GAGCTCAAAA
*
1660130 TCGAGCTTCAATCGAGATCGATTC
1 TCGAGCTTCAATCGAGATCGAGTC
1660154 TCGAGCTTCAATCGAGATCGAGTC
1 TCGAGCTTCAATCGAGATCGAGTC
1660178 TCGAGCTTCAATCGAG
1 TCGAGCTTCAATCGAG
1660194 CTCCTGTTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (24 bp):
TCGAGCTTCAATCGAGATCGAGTC
Found at i:1664893 original size:3 final size:3
Alignment explanation
Indices: 1664887--1664954 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
1664877 AATTTTTTAT
* *
1664887 TAA TAA TAA TAA TAA TAA TAA -AA TTA TAA -AA TAA TAA TAG TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
1664934 TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1664955 CAAATGGATG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1664925 original size:25 final size:23
Alignment explanation
Indices: 1664891--1664954 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 23
1664881 TTTTATTAAT
1664891 AATAATAATAATAATAAAATTATAA
1 AATAATAATAATAATAAAA-TA-AA
* *
1664916 AATAATAATAGTAAT-AAATAAC
1 AATAATAATAATAATAAAATAAA
1664938 AATAATAATAATAATAA
1 AATAATAATAATAATAA
1664955 CAAATGGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 15 0.43
23 3 0.09
24 3 0.09
25 14 0.40
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (23 bp):
AATAATAATAATAATAAAATAAA
Found at i:1664959 original size:25 final size:25
Alignment explanation
Indices: 1664888--1664959 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
1664878 ATTTTTTATT
* *
1664888 AATAATAATAATAATAATAAAATTAT
1 AATAATAATAATAATAA-AAAATAAC
* *
1664914 AA-AATAATAATAGTAATAAATAAC
1 AATAATAATAATAATAAAAAATAAC
*
1664938 AATAATAATAATAATAACAAAT
1 AATAATAATAATAATAAAAAAT
1664960 GGATGAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 7 0.18
25 30 0.77
26 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (25 bp):
AATAATAATAATAATAAAAAATAAC
Found at i:1665662 original size:111 final size:111
Alignment explanation
Indices: 1665306--1665734 Score: 483
Period size: 112 Copynumber: 3.8 Consensus size: 111
1665296 GAATTAAGGC
* *
1665306 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAATTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * ** *
1665370 TGAACACTTCTGAAAATGTTGATCTATCTCCTTCTGTGATAGAATCATGCAA
66 TGAACTCTACTGGAAATGTTGATCTA--T-C--GAGTGAT-GAATCAAGCAA
* * * *
1665422 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTT-TTCCGATAAGTACTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
1665486 TGAACTTTCT-CTGTAAAAGTTTATCCATCGAGTGATGAAATCAAGCGAA
66 TGAAC--TCTACTGGAAATGTTGATCTATCGAGTGATG-AATCAAGC-AA
* * *
1665535 AA-GTTAAACAAATTCTTCTCATTATGAATTTCCTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
1665598 TGAACTCTACTGGAAATGTTGATCTATCGAAG-GATGAATTCAAGTAA
66 TGAACTCTACTGGAAATGTTGATCTATCG-AGTGATGAA-TCAAGCAA
* *
1665645 AAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGACTTCTTCTCATTA
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
1665710 TGAACTCTACCTAGAAATATTGATC
66 TGAACTCTA-CTGGAAATGTTGATC
1665735 CATTGAATGT
Statistics
Matches: 272, Mismatches: 29, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
110 9 0.03
111 62 0.23
112 103 0.38
113 17 0.06
114 1 0.00
115 1 0.00
116 59 0.22
117 18 0.07
118 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (111 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTCTACTGGAAATGTTGATCTATCGAGTGATGAATCAAGCAA
Found at i:1667094 original size:18 final size:17
Alignment explanation
Indices: 1667071--1667143 Score: 92
Period size: 18 Copynumber: 4.1 Consensus size: 17
1667061 CATTTGCAAG
1667071 AATAAATTGAATTTCAGA
1 AATAAATTGAATTTC-GA
* *
1667089 AATAAATTGGACTTTGGA
1 AATAAATT-GAATTTCGA
*
1667107 AATATATTGAATTTCGAA
1 AATAAATTGAATTTCG-A
1667125 AATAAATTGAATTTCGA
1 AATAAATTGAATTTCGA
1667142 AA
1 AA
1667144 AGATAAACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
17 9 0.19
18 33 0.70
19 5 0.11
ACGTcount: A:0.47, C:0.05, G:0.14, T:0.34
Consensus pattern (17 bp):
AATAAATTGAATTTCGA
Done.