Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold36
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: 4808052
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18886 characters in sequence are not A, C, G, or T
File 11 of 28
Found at i:1721705 original size:21 final size:23
Alignment explanation
Indices: 1721664--1721705 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
1721654 TCATTTAATC
*
1721664 ATCAAATATTATTTTATAAATAT
1 ATCAAATATTATTTTAAAAATAT
1721687 ATCAAATA-T-TTTTAAAAAT
1 ATCAAATATTATTTTAAAAAT
1721706 TAAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 1 0.06
23 8 0.44
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (23 bp):
ATCAAATATTATTTTAAAAATAT
Found at i:1722342 original size:37 final size:37
Alignment explanation
Indices: 1722296--1722404 Score: 95
Period size: 37 Copynumber: 3.0 Consensus size: 37
1722286 GTTATGTTAG
* * *
1722296 TATTAAATTTAGTATATGTTTAATATAAATATAAATA
1 TATTTAATTTAATATATATTTAATATAAATATAAATA
**
1722333 TATTTAATTTTTTATATATTT-A-A-AAAT-T--ATA
1 TATTTAATTTAATATATATTTAATATAAATATAAATA
*
1722364 TATTTATATTTAAATATATATTAAATATAAATATTAAATA
1 TATTTA-ATTT-AATATATATTTAATATAAATA-TAAATA
1722404 T
1 T
1722405 TAATAATAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
31 9 0.16
32 4 0.07
33 9 0.16
34 5 0.09
35 2 0.04
36 5 0.09
37 17 0.30
38 1 0.02
40 4 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (37 bp):
TATTTAATTTAATATATATTTAATATAAATATAAATA
Found at i:1722392 original size:21 final size:21
Alignment explanation
Indices: 1722346--1722392 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
1722336 TTAATTTTTT
*
1722346 ATATATTTAAAAATTATATAT
1 ATATATTTAAAAATTATATAA
* *
1722367 TTATATTTAAATA-TATATTAA
1 ATATATTTAAAAATTATA-TAA
1722388 ATATA
1 ATATA
1722393 AATATTAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATATTTAAAAATTATATAA
Found at i:1722399 original size:13 final size:12
Alignment explanation
Indices: 1722373--1722414 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
1722363 ATATTTATAT
1722373 TTAAATAT-ATA
1 TTAAATATAATA
1722384 TTAAATATAAATA
1 TTAAATAT-AATA
1722397 TTAAATATTAATA
1 TTAAATA-TAATA
*
1722410 ATAAA
1 TTAAA
1722415 AAATTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 8 0.30
13 18 0.67
14 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTAAATATAATA
Found at i:1722544 original size:4 final size:4
Alignment explanation
Indices: 1722525--1722595 Score: 70
Period size: 4 Copynumber: 17.8 Consensus size: 4
1722515 GCAGTGCATG
* * * * * *
1722525 TATA TATG TATG TATA TATA TATA TATA TATT TGTA TAGA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* *
1722573 TATA TATA TATA GATA TGTA TAT
1 TATA TATA TATA TATA TATA TAT
1722596 TTATTAATTT
Statistics
Matches: 53, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:1722550 original size:10 final size:10
Alignment explanation
Indices: 1722525--1722595 Score: 70
Period size: 10 Copynumber: 7.1 Consensus size: 10
1722515 GCAGTGCATG
*
1722525 TATATATGTA
1 TATATATATA
*
1722535 TGTATATATA
1 TATATATATA
1722545 TATATATATA
1 TATATATATA
* * *
1722555 TTTGTATAGA
1 TATATATATA
*
1722565 TATGTATATA
1 TATATATATA
1722575 TATATATATA
1 TATATATATA
* *
1722585 GATATGTATA
1 TATATATATA
1722595 T
1 T
1722596 TTATTAATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 49 1.00
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (10 bp):
TATATATATA
Found at i:1722553 original size:22 final size:22
Alignment explanation
Indices: 1722522--1722595 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
1722512 TTAGCAGTGC
* *
1722522 ATGTATATATGTATGTATATAT
1 ATGTATATATATATGTATAGAT
* *
1722544 ATATATATATATTTGTATAGAT
1 ATGTATATATATATGTATAGAT
*
1722566 ATGTATATATATATATATAGAT
1 ATGTATATATATATGTATAGAT
1722588 ATGTATAT
1 ATGTATAT
1722596 TTATTAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (22 bp):
ATGTATATATATATGTATAGAT
Found at i:1725096 original size:12 final size:12
Alignment explanation
Indices: 1725045--1725100 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
1725035 GTATAATATC
*
1725045 TATTATAATTTA
1 TATTATATTTTA
* *
1725057 TATCATACTTTA
1 TATTATATTTTA
*
1725069 T-TTAATAGTATTA
1 TATT-ATA-TTTTA
1725082 TATTATATTTTA
1 TATTATATTTTA
1725094 TATTATA
1 TATTATA
1725101 ATATGTTAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
11 1 0.03
12 25 0.71
13 7 0.20
14 2 0.06
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (12 bp):
TATTATATTTTA
Found at i:1725104 original size:15 final size:15
Alignment explanation
Indices: 1725078--1725119 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1725068 ATTTAATAGT
*
1725078 ATTATATTATATTTTA
1 ATTATA-TATATGTTA
1725094 TATTATA-ATATGTTA
1 -ATTATATATATGTTA
1725109 ATTATATATAT
1 ATTATATATAT
1725120 AAACCCTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 11 0.48
17 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (15 bp):
ATTATATATATGTTA
Found at i:1725892 original size:26 final size:26
Alignment explanation
Indices: 1725856--1725905 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1725846 TTTTTCTATG
1725856 AGAAGTGAGATTTATGAAATGAAACA
1 AGAAGTGAGATTTATGAAATGAAACA
*
1725882 AGAAGTGAGATTTGTGAAATGAAA
1 AGAAGTGAGATTTATGAAATGAAA
1725906 AACAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.02, G:0.26, T:0.24
Consensus pattern (26 bp):
AGAAGTGAGATTTATGAAATGAAACA
Found at i:1726678 original size:169 final size:169
Alignment explanation
Indices: 1726399--1726707 Score: 573
Period size: 169 Copynumber: 1.8 Consensus size: 169
1726389 CACAAGTCAC
* *
1726399 ATGACTTGTAAGAACTTGATTATACTAATATTCTTTTTTGCATGCAACTCCTATTATTTAACTCT
1 ATGACTTGTAAGAACTTGATTATACTAATATTCTTTTTTGCATCCAACTCCTATTAGTTAACTCT
*
1726464 ATCAAACTTCAACTTTACGATTACTTTTGAAAATCTCAATAAATAATTATAGTTAATTTAATGGG
66 ATCAAACTTCAACTTTACGATTACTTTTGAAAATCTCAATAAATAATTATAGTTAATTTAATGGA
1726529 TTCAAAAACTTGATTGTTAAAAAGTCTTATGAACTTGTT
131 TTCAAAAACTTGATTGTTAAAAAGTCTTATGAACTTGTT
*
1726568 ATGACTTGTAAGAACTTGATTATACTAATTTTCTTTTTTGCATCCAACTCCTATTAGTTAACTCT
1 ATGACTTGTAAGAACTTGATTATACTAATATTCTTTTTTGCATCCAACTCCTATTAGTTAACTCT
*
1726633 ATCAAACTTCACCTTTACGATTACTTTTGAAAATCTCAATAAATAATTATAGTTAATTTAATGGA
66 ATCAAACTTCAACTTTACGATTACTTTTGAAAATCTCAATAAATAATTATAGTTAATTTAATGGA
1726698 TTCAAAAACT
131 TTCAAAAACT
1726708 AATGATTTTA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
169 135 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (169 bp):
ATGACTTGTAAGAACTTGATTATACTAATATTCTTTTTTGCATCCAACTCCTATTAGTTAACTCT
ATCAAACTTCAACTTTACGATTACTTTTGAAAATCTCAATAAATAATTATAGTTAATTTAATGGA
TTCAAAAACTTGATTGTTAAAAAGTCTTATGAACTTGTT
Found at i:1728035 original size:2 final size:2
Alignment explanation
Indices: 1728028--1728056 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1728018 AAGTATAAAT
1728028 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
1728057 TAAAGTTTAA
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:1731336 original size:5 final size:5
Alignment explanation
Indices: 1731328--1731380 Score: 54
Period size: 5 Copynumber: 9.8 Consensus size: 5
1731318 AATAAAATTC
1731328 TTTTA TTTTA TTTTA TTTTA -TTTA CTATTTA TTTTTA TTTTCA TTTTCA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -T-TTTA -TTTTA TTTT-A TTTT-A
1731377 TTTT
1 TTTT
1731381 CAATTATAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
4 4 0.09
5 19 0.44
6 15 0.35
7 5 0.12
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:1731387 original size:28 final size:27
Alignment explanation
Indices: 1731333--1731396 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
1731323 AATTCTTTTA
*
1731333 TTTTATTTTATTTTATTTACTATTTAT
1 TTTTATTTTATTTTATTTACTAATTAT
*
1731360 TTTTATTTTCATTTTCATTTTC-AATTAT
1 TTTTATTTT-ATTTT-ATTTACTAATTAT
**
1731388 AATTATTTT
1 TTTTATTTT
1731397 TTTATACTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
27 9 0.29
28 17 0.55
29 5 0.16
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTATTTTATTTTATTTACTAATTAT
Found at i:1733629 original size:26 final size:27
Alignment explanation
Indices: 1733600--1733650 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1733590 TTAGCTTTTT
* *
1733600 TAAAAATA-TAAAAAAATTATTATCAA
1 TAAAAAAAGTAAAAAAATTAATATCAA
*
1733626 TAAAAAAAGTAAAAAATTTAATATC
1 TAAAAAAAGTAAAAAAATTAATATC
1733651 CTCTTTAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (27 bp):
TAAAAAAAGTAAAAAAATTAATATCAA
Found at i:1735344 original size:10 final size:10
Alignment explanation
Indices: 1735308--1735424 Score: 71
Period size: 10 Copynumber: 11.4 Consensus size: 10
1735298 TTTGGTAAAC
*
1735308 TTTTAATATGA
1 TTTT-ATATAA
*
1735319 TTTTTTATAA
1 TTTTATATAA
1735329 TTTTTTATATAA
1 --TTTTATATAA
* *
1735341 TTTTGTA-AT
1 TTTTATATAA
*
1735350 TTTTATACAA
1 TTTTATATAA
*
1735360 GTTTAT-TAA
1 TTTTATATAA
*
1735369 GTTTTAATATGA
1 -TTTT-ATATAA
1735381 TTTT-TATAA
1 TTTTATATAA
*
1735390 TTTTGATATAG
1 TTTT-ATATAA
1735401 TTTTA-ATAAA
1 TTTTATAT-AA
1735411 TTTTATATAA
1 TTTTATATAA
1735421 TTTT
1 TTTT
1735425 GGGTAATTTA
Statistics
Matches: 82, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
9 19 0.23
10 32 0.39
11 20 0.24
12 11 0.13
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (10 bp):
TTTTATATAA
Found at i:1735433 original size:41 final size:39
Alignment explanation
Indices: 1735331--1735425 Score: 102
Period size: 41 Copynumber: 2.4 Consensus size: 39
1735321 TTTTATAATT
* * *
1735331 TTTTATATAATTTTGTAATTTTTATACAAGTTTATTAAG
1 TTTTATATAATTTTGTAATTTTGATACAAGTTTAATAAA
* * *
1735370 TTTTAATATGATTTTTATAATTTTGATA-TAGTTTTAATAAA
1 TTTT-ATAT-AATTTTGTAATTTTGATACAAG-TTTAATAAA
1735411 TTTTATATAATTTTG
1 TTTTATATAATTTTG
1735426 GGTAATTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
39 9 0.20
40 10 0.22
41 26 0.58
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.58
Consensus pattern (39 bp):
TTTTATATAATTTTGTAATTTTGATACAAGTTTAATAAA
Found at i:1736127 original size:18 final size:18
Alignment explanation
Indices: 1736084--1736127 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
1736074 TCATTTAATA
1736084 TAAAAA-TT-ATTATTTT
1 TAAAAACTTAATTATTTT
* *
1736100 TAATATCTTAATTATTTT
1 TAAAAACTTAATTATTTT
1736118 TAAAAACTTA
1 TAAAAACTTA
1736128 TTTGAACTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.18
17 2 0.09
18 16 0.73
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (18 bp):
TAAAAACTTAATTATTTT
Found at i:1736796 original size:235 final size:235
Alignment explanation
Indices: 1736318--1736797 Score: 650
Period size: 237 Copynumber: 2.0 Consensus size: 235
1736308 AATAAATTTT
* *
1736318 AAAGCAGTCTTTGAATCAAAATTGTCATCAAATTTCAATTAAATTAAAAATTCAACGTGTCTTTT
1 AAAGCA-TCTTTGAATCAAAATTGTCATCAAATTTCAATCAAATTAAAAATTCAACATGTCTTTT
* ** * * *
1736383 TTTCCCCGTTTTTATACTTCAAAGAAAAAGTATTCTAGCAACTGAATGTCCCAATTTGGTCCCCT
65 TTT-CCCGTTTTAATACTAAAAAAAAAAAGTAATCTAGCAACTGAATGTCACAATTTGGTCCCCT
1736448 TAACATAAACCTAATTTATGTAATAATTAACGTGAAATATATATACATATATATATATATAATGT
129 TAACATAAACCTAATTTATGTAATAATTAACGTGAAATATATATACATATATATATATATAATGT
* * *
1736513 TTGTTATCATGTCATATGTTACGTAGCCTTAAATTGAACTCCA
194 ATGTTAT-ATGTCATATGTTACGTAGCCTCAAATTAAACTCCA
* * *
1736556 AAAGCATCTTTGAATCAAAATTGTCATCAAATTTCAATCCAATTAATAATTTAACATGTCTGTTT
1 AAAGCATCTTTGAATCAAAATTGTCATCAAATTTCAATCAAATTAAAAATTCAACATGTCT-TTT
* *
1736621 TTT-TC-TTTTAATAC-AAAAAAAAAAAGTAATGTAGCTAA-TGAATGTCACAATTTGGTCCCCT
65 TTTCCCGTTTTAATACTAAAAAAAAAAAGTAATCTAGC-AACTGAATGTCACAATTTGGTCCCCT
* *
1736682 T-ACATAAACCTAATTTATGTAATAATTAATGTGAAATATATATATATATATACCTATATATGTA
129 TAACATAAACCTAATTTATGTAATAATTAACGTGAAATATATATACATATATA--TATATA--TA
*
1736746 ATGTAAT-TTGT-TGTCATATGTTACGTAGCCTCAAATTAAACTCCA
190 ATGT-ATGTTATATGTCATATGTTACGTAGCCTCAAATTAAACTCCA
1736791 AAAGCAT
1 AAAGCAT
1736798 GGAATCAAGA
Statistics
Matches: 216, Mismatches: 19, Indels: 17
0.86 0.08 0.07
Matches are distributed among these distances:
233 49 0.23
234 39 0.18
235 55 0.25
236 1 0.00
237 59 0.27
238 13 0.06
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (235 bp):
AAAGCATCTTTGAATCAAAATTGTCATCAAATTTCAATCAAATTAAAAATTCAACATGTCTTTTT
TTCCCGTTTTAATACTAAAAAAAAAAAGTAATCTAGCAACTGAATGTCACAATTTGGTCCCCTTA
ACATAAACCTAATTTATGTAATAATTAACGTGAAATATATATACATATATATATATATAATGTAT
GTTATATGTCATATGTTACGTAGCCTCAAATTAAACTCCA
Found at i:1737121 original size:2 final size:2
Alignment explanation
Indices: 1737114--1737138 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1737104 TTGTAAGAGC
1737114 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1737139 GTATGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1737460 original size:29 final size:29
Alignment explanation
Indices: 1737387--1737464 Score: 79
Period size: 32 Copynumber: 2.6 Consensus size: 29
1737377 TATTTTATAA
*
1737387 ATAT-TTAATATTTATATTACTTTTGAAAT
1 ATATATTAATA-TTATATGACTTTTGAAAT
*
1737416 ATTAATAATTTATATTATATGACTTTT-AAATT
1 A-T-AT-ATTAATATTATATGACTTTTGAAA-T
1737448 ATATATTAATATTATAT
1 ATATATTAATATTATAT
1737465 TTTAATAATT
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
29 13 0.32
30 3 0.07
31 6 0.15
32 14 0.34
33 5 0.12
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (29 bp):
ATATATTAATATTATATGACTTTTGAAAT
Found at i:1737698 original size:3 final size:3
Alignment explanation
Indices: 1737690--1737716 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1737680 ACCCTAATGA
1737690 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1737717 GGTGTTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1738234 original size:2 final size:2
Alignment explanation
Indices: 1738227--1738264 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1738217 TTTTGTTGAC
* *
1738227 CA CA CA CA CG CA CC CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1738265 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.53, G:0.03, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1738622 original size:15 final size:16
Alignment explanation
Indices: 1738602--1738636 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
1738592 AAGAATAAAA
1738602 ATAAGTTTAG-TTTTT
1 ATAAGTTTAGTTTTTT
1738617 ATAAGTTTAGTTTTTT
1 ATAAGTTTAGTTTTTT
1738633 ATAA
1 ATAA
1738637 AATAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.57
Consensus pattern (16 bp):
ATAAGTTTAGTTTTTT
Found at i:1743874 original size:2 final size:2
Alignment explanation
Indices: 1743867--1743896 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1743857 AAGATAAATG
*
1743867 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1743897 CACGTCATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1744114 original size:19 final size:20
Alignment explanation
Indices: 1744086--1744128 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1744076 TATTGAACTT
1744086 AAAAAATAAA-T-TTAAATA
1 AAAAAATAAACTGTTAAATA
*
1744104 AAAAAATTAAACTGTTCAATA
1 AAAAAA-TAAACTGTTAAATA
1744125 AAAA
1 AAAA
1744129 TAAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 1 0.05
21 10 0.48
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAAATAAACTGTTAAATA
Found at i:1744285 original size:20 final size:20
Alignment explanation
Indices: 1744235--1744271 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1744225 AAGATCAGTG
1744235 ATAATA-TTTTTAAAAAATA
1 ATAATATTTTTTAAAAAATA
1744254 ATAATATTTTTTAAAAAA
1 ATAATATTTTTTAAAAAA
1744272 AATTGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTTAAAAAATA
Found at i:1746759 original size:36 final size:34
Alignment explanation
Indices: 1746712--1746778 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 34
1746702 TAATATTTTT
* *
1746712 TAAATAATATTATATTTATTTTAAATATAAATATAA
1 TAAATAATATTATAATTA-ATT-AATATAAATATAA
*
1746748 TAAATATTATTATAATTAATTAATATAAATA
1 TAAATAATATTATAATTAATTAATATAAATA
1746779 AAAAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 10 0.36
35 2 0.07
36 16 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (34 bp):
TAAATAATATTATAATTAATTAATATAAATATAA
Found at i:1749403 original size:21 final size:20
Alignment explanation
Indices: 1749378--1749448 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 20
1749368 TGTCAAAGTT
*
1749378 TAAAAATTATCAAAATTATC
1 TAAAAATTATCAAAATTATA
*
1749398 TCAAAAATTATAAAAATTATA
1 T-AAAAATTATCAAAATTATA
*
1749419 TTTAAAATTA-CTAAAATTATA
1 -TAAAAATTATC-AAAATTATA
1749440 TAAAAATTA
1 TAAAAATTA
1749449 AAAAAAATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 9 0.21
21 33 0.77
22 1 0.02
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATTATCAAAATTATA
Found at i:1749418 original size:9 final size:9
Alignment explanation
Indices: 1749378--1749453 Score: 55
Period size: 9 Copynumber: 7.7 Consensus size: 9
1749368 TGTCAAAGTT
1749378 TAAAAATTA
1 TAAAAATTA
*
1749387 TCAAAATTA
1 TAAAAATTA
1749396 TCTCAAAAATTA
1 --T-AAAAATTA
1749408 TAAAAATTA
1 TAAAAATTA
1749417 TATTTAAAATTA
1 TA---AAAATTA
*
1749429 CTAAAATTATA
1 -TAAAAAT-TA
1749440 TAAAAATTA
1 TAAAAATTA
1749449 -AAAAA
1 TAAAAA
1749454 AATGTTATCT
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
8 5 0.09
9 20 0.36
10 11 0.20
11 3 0.05
12 14 0.25
13 2 0.04
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:1750145 original size:2 final size:2
Alignment explanation
Indices: 1750138--1750166 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1750128 ATTCATATTT
1750138 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
1750167 TATTTGAAAG
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:1754306 original size:2 final size:2
Alignment explanation
Indices: 1754301--1754417 Score: 180
Period size: 2 Copynumber: 58.5 Consensus size: 2
1754291 TCCTCTCTAA
* *
1754301 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT GT 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
* *
1754343 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT GT 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
* *
1754385 AT AT GT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1754418 ATCAGATTGC
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 103 1.00
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1754741 original size:29 final size:29
Alignment explanation
Indices: 1754687--1754787 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 29
1754677 AAATATAAAT
* *
1754687 AAAATTATATTTATGTTTAATAATAATTA
1 AAAATTATATTTATATTAAATAATAATTA
1754716 AAAATTATATTTATATTAAA-ATATAATTTTAAA
1 AAAATTATATTTATATTAAATA-ATAA--TT--A
1754749 GTAAATATTTATATTTATATTAAATAATAATTA
1 --AAA-A-TTATATTTATATTAAATAATAATTA
1754782 AAAATT
1 AAAATT
1754788 GTCAACATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
28 1 0.02
29 24 0.40
30 1 0.02
31 5 0.08
33 2 0.03
35 5 0.08
36 1 0.02
37 20 0.33
38 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
AAAATTATATTTATATTAAATAATAATTA
Found at i:1755900 original size:26 final size:26
Alignment explanation
Indices: 1755855--1755914 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
1755845 CTATAAAAAC
*
1755855 AATATTAAAGTTATCCCAAGTAAATT
1 AATATTAAAGTTATCCCAAGCAAATT
* *
1755881 AATATTAAAGTTA-CTTCAAGCAATTT
1 AATATTAAAGTTATC-CCAAGCAAATT
1755907 AATATTAA
1 AATATTAA
1755915 TTTAACATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 1 0.03
26 29 0.97
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (26 bp):
AATATTAAAGTTATCCCAAGCAAATT
Found at i:1756946 original size:17 final size:18
Alignment explanation
Indices: 1756924--1756975 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
1756914 TTTTTTGTCA
1756924 TATAATAATATTTATA-T
1 TATAATAATATTTATATT
*
1756941 TATAAT-ATATTAAATATT
1 TATAATAATATT-TATATT
*
1756959 TTTAAATAATATTTATA
1 TAT-AATAATATTTATA
1756976 AAAATTTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.18
17 9 0.32
18 3 0.11
19 6 0.21
20 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TATAATAATATTTATATT
Found at i:1757337 original size:21 final size:21
Alignment explanation
Indices: 1757299--1757346 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1757289 ATTATATGAC
*
1757299 ATAAAAAATAATTAAAATATG
1 ATAAAAAATAATTAAAATATA
* *
1757320 ATAAAAATTAA-TATAAATTTA
1 ATAAAAAATAATTA-AAATATA
1757341 ATAAAA
1 ATAAAA
1757347 TACATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (21 bp):
ATAAAAAATAATTAAAATATA
Found at i:1758085 original size:2 final size:2
Alignment explanation
Indices: 1758078--1758110 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1758068 AAAATAGCTT
1758078 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1758111 CATTTTCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1765848 original size:18 final size:18
Alignment explanation
Indices: 1765825--1765861 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1765815 AATATTCGCA
1765825 TAAATTAGTAGCATTTTT
1 TAAATTAGTAGCATTTTT
1765843 TAAATTAGTAGCATTTTT
1 TAAATTAGTAGCATTTTT
1765861 T
1 T
1765862 TTATAACGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TAAATTAGTAGCATTTTT
Found at i:1766530 original size:49 final size:49
Alignment explanation
Indices: 1766462--1766563 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
1766452 TTTAAAATAA
* * *
1766462 ATATATTTGTATTATTTTTAATTAGTAATAAAAACATATATATCTATAT
1 ATATATATATATTATTTTTAATTAGTAATAAAAACATATATATATATAT
1766511 ATATATATATATTATTTTTAATTAGTAATAAAAACATATATATATATAT
1 ATATATATATATTATTTTTAATTAGTAATAAAAACATATATATATATAT
1766560 ATAT
1 ATAT
1766564 TCAAGCTCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (49 bp):
ATATATATATATTATTTTTAATTAGTAATAAAAACATATATATATATAT
Found at i:1769463 original size:19 final size:20
Alignment explanation
Indices: 1769422--1769464 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
1769412 TGGTATTTGC
* *
1769422 TTATCTAATAATTTATGTAT
1 TTATATAATAATTTATATAT
*
1769442 TTATATAAT-ATTTATATTT
1 TTATATAATAATTTATATAT
1769461 TTAT
1 TTAT
1769465 CATATCATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATATAATAATTTATATAT
Found at i:1769558 original size:24 final size:25
Alignment explanation
Indices: 1769516--1769571 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
1769506 TTTTAATACA
*
1769516 TTAATAATTTATATTATATAG-ATT
1 TTAATAATATATATTATATAGTATT
*
1769540 TTAATAA-ATATATTCATATGGTATT
1 TTAATAATATATATT-ATATAGTATT
1769565 TTAATAA
1 TTAATAA
1769572 CTTTACGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.21
24 12 0.43
25 10 0.36
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (25 bp):
TTAATAATATATATTATATAGTATT
Found at i:1772762 original size:24 final size:24
Alignment explanation
Indices: 1772726--1772778 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1772716 AAATATAAAA
*
1772726 AATA-TAAATATTTAAATATAGTT
1 AATATTAAAAATTTAAATATAGTT
* *
1772749 AATATTAAAAATTTTAATATATTT
1 AATATTAAAAATTTAAATATAGTT
1772773 AATATT
1 AATATT
1772779 TTATGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 4 0.15
24 22 0.85
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
AATATTAAAAATTTAAATATAGTT
Found at i:1773503 original size:2 final size:2
Alignment explanation
Indices: 1773496--1773522 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1773486 AATACTGTAT
1773496 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1773523 ATATATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:1773527 original size:2 final size:2
Alignment explanation
Indices: 1773522--1773564 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1773512 TGTGTGTGTG
1773522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1773564 T
1 T
1773565 GAGAGAGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1773889 original size:20 final size:21
Alignment explanation
Indices: 1773864--1773903 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1773854 AGTATAACCT
*
1773864 AAAATAAT-AATAATAAAAAG
1 AAAATAATGAATAACAAAAAG
1773884 AAAATAATGAATAACAAAAA
1 AAAATAATGAATAACAAAAA
1773904 TCATACCCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAATAATGAATAACAAAAAG
Found at i:1774489 original size:2 final size:2
Alignment explanation
Indices: 1774482--1774507 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1774472 CCACCGACTC
1774482 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
1774508 TGTCTTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1777922 original size:6 final size:6
Alignment explanation
Indices: 1777911--1777944 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1777901 ATAAAAACAA
* *
1777911 TAAAAT TAAAAT TAAAAC TAAAAT TAAAAA TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAA
1777945 TATATAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (6 bp):
TAAAAT
Found at i:1778473 original size:21 final size:21
Alignment explanation
Indices: 1778437--1778488 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1778427 TAATAATTTG
**
1778437 TATTAGTTTGATATAATTTAAAT
1 TATTA-TTT-ATATAATAAAAAT
1778460 TATTATTTATATAATAAAAAT
1 TATTATTTATATAATAAAAAT
1778481 T-TTATTTA
1 TATTATTTA
1778489 AAATTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 12 0.44
22 3 0.11
23 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (21 bp):
TATTATTTATATAATAAAAAT
Found at i:1779810 original size:2 final size:2
Alignment explanation
Indices: 1779795--1779830 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1779785 GTATGTATGC
* *
1779795 AT AT AT AA AC 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
1779831 GTAATAAGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1780861 original size:2 final size:2
Alignment explanation
Indices: 1780854--1780890 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1780844 ATTTCAAGAA
1780854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1780891 AACACAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1781993 original size:15 final size:16
Alignment explanation
Indices: 1781973--1782011 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1781963 TTTTTTATTT
*
1781973 TTAAATTCA-ATTTAA
1 TTAAATTAACATTTAA
1781988 TTAAATTAACATTTAA
1 TTAAATTAACATTTAA
1782004 -TAAATTAA
1 TTAAATTAA
1782012 AAATTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATTAACATTTAA
Found at i:1782018 original size:15 final size:15
Alignment explanation
Indices: 1781984--1782023 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1781974 TAAATTCAAT
* *
1781984 TTAATTAAATTAACAT
1 TTAA-TAAATTAAAAA
1782000 TTAATAAATTAAAAA
1 TTAATAAATTAAAAA
1782015 TTAATAAAT
1 TTAATAAAT
1782024 AAATTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAATAAATTAAAAA
Found at i:1783531 original size:3 final size:3
Alignment explanation
Indices: 1783525--1783556 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1783515 AAATTTCATC
1783525 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1783557 ATTTTAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1784622 original size:2 final size:2
Alignment explanation
Indices: 1784615--1784643 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1784605 TGGAACATAC
1784615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1784644 AAATAAACAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1785712 original size:27 final size:27
Alignment explanation
Indices: 1785682--1785735 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1785672 AGTAAACTCT
1785682 ATTATTTATTTATAAAATTGTTGTTAA
1 ATTATTTATTTATAAAATTGTTGTTAA
1785709 ATTATTTATTTATAAAATTGTTGTTAA
1 ATTATTTATTTATAAAATTGTTGTTAA
1785736 GGCCACTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (27 bp):
ATTATTTATTTATAAAATTGTTGTTAA
Found at i:1789158 original size:10 final size:10
Alignment explanation
Indices: 1789153--1789193 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
1789143 GATTTTATAT
1789153 TTTTTTAAAA
1 TTTTTTAAAA
1789163 TTTTTTAAAA
1 TTTTTTAAAA
1789173 TTTTTT-AAA
1 TTTTTTAAAA
1789182 --TTTTAAAA
1 TTTTTTAAAA
1789190 TTTT
1 TTTT
1789194 CAATATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 4 0.14
8 3 0.11
9 3 0.11
10 18 0.64
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:1789166 original size:9 final size:9
Alignment explanation
Indices: 1789154--1789193 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
1789144 ATTTTATATT
1789154 TTTTTAAAA
1 TTTTTAAAA
1789163 TTTTTTAAAA
1 -TTTTTAAAA
*
1789173 TTTTTTAAA
1 TTTTTAAAA
1789182 -TTTTAAAA
1 TTTTTAAAA
1789190 TTTT
1 TTTT
1789194 CAATATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
8 7 0.26
9 11 0.41
10 9 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:1789215 original size:2 final size:2
Alignment explanation
Indices: 1789208--1789235 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1789198 ATTCAATTAA
1789208 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
1789236 TTTGATAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1791169 original size:20 final size:20
Alignment explanation
Indices: 1791130--1791169 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1791120 ATAATTTATT
*
1791130 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
1791150 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
1791170 TTTTAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:1792116 original size:16 final size:16
Alignment explanation
Indices: 1792069--1792116 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1792059 AAATTTATTT
1792069 TATTAATATATTTAAATA
1 TATTAA-ATA-TTAAATA
*
1792087 TA-TAAGTATATAAATA
1 TATTAAATAT-TAAATA
1792103 TATTAAATATTAAA
1 TATTAAATATTAAA
1792117 AAAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.54
17 9 0.35
18 2 0.08
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TATTAAATATTAAATA
Found at i:1792600 original size:17 final size:17
Alignment explanation
Indices: 1792558--1792626 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 17
1792548 GATTTAATTT
*
1792558 AATTTATTATATTTTAA
1 AATTTATTATATATTAA
***
1792575 AAAAAATTAT-TATTTAA
1 AATTTATTATATA-TTAA
*
1792592 AATTTATTAAATATTAA
1 AATTTATTATATATTAA
*
1792609 AATTTTATTTTATATTAA
1 AA-TTTATTATATATTAA
1792627 TAAATATTAT
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
16 1 0.03
17 23 0.59
18 15 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTATTATATATTAA
Found at i:1792623 original size:18 final size:17
Alignment explanation
Indices: 1792584--1792626 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
1792574 AAAAAAATTA
1792584 TTAT-TTAAAATTTATT
1 TTATATTAAAATTTATT
**
1792600 AAATATTAAAATTTTATT
1 TTATATTAAAA-TTTATT
1792618 TTATATTAA
1 TTATATTAA
1792627 TAAATATTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 2 0.10
17 6 0.29
18 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTAAAATTTATT
Found at i:1792640 original size:28 final size:25
Alignment explanation
Indices: 1792599--1792673 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 25
1792589 TAAAATTTAT
* *
1792599 TAAATATTAAAATTTTATTTTATATTAA
1 TAAATATTATAATTTTA-TTTA-AAT-A
*
1792627 TAAATATTATAATTATATTTAAATA
1 TAAATATTATAATTTTATTTAAATA
1792652 -AAATATTATAA-TTTA-TTAAATA
1 TAAATATTATAATTTTATTTAAATA
1792674 ATAATTTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.16
23 3 0.07
24 11 0.26
25 1 0.02
26 2 0.05
27 4 0.09
28 15 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATATTATAATTTTATTTAAATA
Found at i:1792673 original size:22 final size:22
Alignment explanation
Indices: 1792592--1792674 Score: 80
Period size: 24 Copynumber: 3.6 Consensus size: 22
1792582 TATTATTTAA
*
1792592 AATTTATTAAATATTAAA-ATTTT
1 AATTTATTAAATA--AAATATTAT
* *
1792615 ATTTTATATTAAT-AAATATTAT
1 AATTTAT-TAAATAAAATATTAT
1792637 AATTATATTTAAATAAAATATTAT
1 AATT-TA-TTAAATAAAATATTAT
1792661 AATTTATTAAATAA
1 AATTTATTAAATAA
1792675 TAATTTAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
21 3 0.06
22 15 0.30
23 14 0.28
24 18 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTATTAAATAAAATATTAT
Found at i:1793227 original size:18 final size:19
Alignment explanation
Indices: 1793192--1793228 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1793182 TAAAAATTAA
1793192 TTTTTTTTTGTTTCTTTCC
1 TTTTTTTTTGTTTCTTTCC
1793211 TTTTTTCTTT-TTT-TTTCC
1 TTTTTT-TTTGTTTCTTTCC
1793229 ATTCATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 9 0.53
20 3 0.18
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTGTTTCTTTCC
Found at i:1794765 original size:20 final size:20
Alignment explanation
Indices: 1794724--1794766 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
1794714 ATAAAATCAT
* *
1794724 TTATTTTTAGAAAATGAGAA
1 TTATTTTTAGAAAATAAAAA
1794744 TTATTTTTA-AACAATAAAAA
1 TTATTTTTAGAA-AATAAAAA
1794764 TTA
1 TTA
1794767 AATTCAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.42
Consensus pattern (20 bp):
TTATTTTTAGAAAATAAAAA
Found at i:1796416 original size:24 final size:24
Alignment explanation
Indices: 1796350--1796444 Score: 83
Period size: 24 Copynumber: 4.1 Consensus size: 24
1796340 GATAATTTAT
1796350 ATTTTAA-TTTATTAAATT-T--A
1 ATTTTAATTTTATTAAATTATAAA
*
1796370 ATATTAATTTTTATGTAAATTATAAA
1 ATTTTAA-TTTTAT-TAAATTATAAA
**
1796396 ATTTTAATTTTATTAAATTATATT
1 ATTTTAATTTTATTAAATTATAAA
** *
1796420 ATTAAAATTTTATT-AATAATAAA
1 ATTTTAATTTTATTAAATTATAAA
1796443 AT
1 AT
1796445 CAAATCAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
20 6 0.10
22 5 0.08
23 14 0.23
24 22 0.37
25 6 0.10
26 7 0.12
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
ATTTTAATTTTATTAAATTATAAA
Found at i:1796442 original size:47 final size:46
Alignment explanation
Indices: 1796350--1796444 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 46
1796340 GATAATTTAT
* *
1796350 ATTTTAATTTATTAAATTTAATATTAATTTTTATGTAAATTATAAA
1 ATTTTAATTTATTAAATTTAATATTAAATTTTATGTAAATAATAAA
*
1796396 ATTTTAATTTTATTAAATTATATTATTAAAATTTTAT-T-AATAATAAA
1 ATTTTAA-TTTATTAAATT-TAATATT-AAATTTTATGTAAATAATAAA
1796443 AT
1 AT
1796445 CAAATCAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
46 7 0.16
47 21 0.49
48 7 0.16
49 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (46 bp):
ATTTTAATTTATTAAATTTAATATTAAATTTTATGTAAATAATAAA
Found at i:1809161 original size:28 final size:25
Alignment explanation
Indices: 1809114--1809181 Score: 82
Period size: 28 Copynumber: 2.6 Consensus size: 25
1809104 TTAATATTAA
*
1809114 TATATTTTTATAAATAAATTTAAAT
1 TATATTATTATAAATAAATTTAAAT
1809139 TATATTATTATTAAATAATAATTTAAAT
1 TATATTATTA-TAAAT-A-AATTTAAAT
* *
1809167 TAAATTAATATAAAT
1 TATATTATTATAAAT
1809182 TTATAAAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 9 0.24
26 5 0.14
27 6 0.16
28 17 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TATATTATTATAAATAAATTTAAAT
Found at i:1817505 original size:2 final size:2
Alignment explanation
Indices: 1817498--1817526 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1817488 CAGAAAAAGA
1817498 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1817527 TATATATATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1821969 original size:13 final size:13
Alignment explanation
Indices: 1821947--1821981 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
1821937 GGTAGTTCAC
1821947 TCCATCCCATAAA
1 TCCATCCCATAAA
*
1821960 TCCATTCCATAAA
1 TCCATCCCATAAA
1821973 TCCATCCCA
1 TCCATCCCA
1821982 CTTCCCGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.34, C:0.40, G:0.00, T:0.26
Consensus pattern (13 bp):
TCCATCCCATAAA
Found at i:1823138 original size:2 final size:2
Alignment explanation
Indices: 1823131--1823180 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1823121 CTAATTAAGA
*
1823131 AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1823173 AG AG AG AG
1 AG AG AG AG
1823181 GGAAAATTAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1824738 original size:23 final size:22
Alignment explanation
Indices: 1824712--1824763 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
1824702 TTTTTAATTA
*
1824712 TATTCTTAATTTTATTATAATAT
1 TATTATTAATTTT-TTATAATAT
*
1824735 TATTATTAATTTTTTATTATAT
1 TATTATTAATTTTTTATAATAT
*
1824757 TAATATT
1 TATTATT
1824764 TTTTAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
TATTATTAATTTTTTATAATAT
Found at i:1824754 original size:17 final size:17
Alignment explanation
Indices: 1824732--1824766 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1824722 TTTATTATAA
1824732 TATTATTATTAAT-TTTT
1 TATTA-TATTAATATTTT
1824749 TATTATATTAATATTTT
1 TATTATATTAATATTTT
1824766 T
1 T
1824767 TAAATTAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTATATTAATATTTT
Found at i:1824867 original size:14 final size:14
Alignment explanation
Indices: 1824850--1824966 Score: 58
Period size: 14 Copynumber: 8.9 Consensus size: 14
1824840 TTAATAACAA
1824850 TAAATTTATTTATT
1 TAAATTTATTTATT
* *
1824864 TAAATTATAATTATA
1 TAAATT-TATTTATT
1824879 T-AA-TTA--T-TT
1 TAAATTTATTTATT
*
1824888 TAAA-ATATTTAATT
1 TAAATTTATTT-ATT
1824902 T-AATTTATTTAATT
1 TAAATTTATTT-ATT
*
1824916 TAAATTT-TTAATT
1 TAAATTTATTTATT
* *
1824929 TAAATTCTAATCATT
1 TAAATT-TATTTATT
1824944 T-AA-TTATTT-TT
1 TAAATTTATTTATT
*
1824955 TAAATTTTTTTA
1 TAAATTTATTTA
1824967 AAGAGAATGA
Statistics
Matches: 79, Mismatches: 11, Indels: 26
0.68 0.09 0.22
Matches are distributed among these distances:
9 2 0.03
10 5 0.06
11 3 0.04
12 8 0.10
13 18 0.23
14 26 0.33
15 17 0.22
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (14 bp):
TAAATTTATTTATT
Found at i:1824912 original size:23 final size:22
Alignment explanation
Indices: 1824852--1824913 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
1824842 AATAACAATA
1824852 AATTT-ATTTATTT-AAATTAT
1 AATTTAATTTATTTAAAATTAT
* *
1824872 AATTATATAATTATTTTAAAATATTT
1 AATT-TA-ATTTA-TTTAAAAT-TAT
1824898 AATTTAATTTATTTAA
1 AATTTAATTTATTTAA
1824914 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
23 9 0.27
24 7 0.21
25 6 0.18
26 6 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTAATTTATTTAAAATTAT
Found at i:1824961 original size:32 final size:30
Alignment explanation
Indices: 1824861--1824961 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 30
1824851 AAATTTATTT
* *
1824861 ATTTAAATTATAATTATATAATTATTTTAAA
1 ATTTAAATT-TAATTATTTAATTATTTTTAA
*
1824892 ATATTTAATTTAATTTATTTAATTTAAATTTTT-A
1 AT-TTAAATTTAA-TTATTTAA-TT--ATTTTTAA
*
1824926 ATTTAAATTCTAATCATTTAATTATTTTTTAA
1 ATTTAAATT-TAATTATTTAATTA-TTTTTAA
1824958 ATTT
1 ATTT
1824962 TTTTAAAGAG
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
30 1 0.02
31 10 0.18
32 20 0.35
33 15 0.26
34 6 0.11
35 5 0.09
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (30 bp):
ATTTAAATTTAATTATTTAATTATTTTTAA
Found at i:1825238 original size:19 final size:19
Alignment explanation
Indices: 1825169--1825238 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1825159 TTATTTTATT
*
1825169 TTTAAAAAAATAATTATAA
1 TTTAAATAAATAATTATAA
* *
1825188 GTTAAATTAAAT-ATTTTAA
1 TTTAAA-TAAATAATTATAA
* * *
1825207 ATTAATTATATAATTATAA
1 TTTAAATAAATAATTATAA
1825226 TTTAAATAAATAA
1 TTTAAATAAATAA
1825239 ATTTATTATC
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
18 4 0.10
19 31 0.79
20 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (19 bp):
TTTAAATAAATAATTATAA
Found at i:1825326 original size:19 final size:17
Alignment explanation
Indices: 1825289--1825327 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
1825279 TAAAAATTAT
1825289 TATTATATTTATAATAA
1 TATTATATTTATAATAA
*
1825306 TATTATACTTTACTCATAA
1 TATTATA-TTTA-TAATAA
1825325 TAT
1 TAT
1825328 AATCTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATATTTATAATAA
Found at i:1825576 original size:29 final size:28
Alignment explanation
Indices: 1825543--1825606 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
1825533 TTCTTACGTA
* *
1825543 TTAAAATAAT-TATATTTCATTAATTTATT
1 TTAAAATAATAT-TATTTCAATAA-TTAAT
* *
1825572 TTAAATTAATATTATTTTAATAATTAAT
1 TTAAAATAATATTATTTCAATAATTAAT
1825600 TTAAAAT
1 TTAAAAT
1825607 TTTTATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 10 0.34
29 18 0.62
30 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TTAAAATAATATTATTTCAATAATTAAT
Found at i:1825588 original size:16 final size:15
Alignment explanation
Indices: 1825561--1825602 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 15
1825551 ATTATATTTC
1825561 ATTAATTTATTTTAA
1 ATTAATTTATTTTAA
1825576 ATTAATATTATTTTAATA
1 ATTAAT-TTATTTT-A-A
1825594 ATTAATTTA
1 ATTAATTTA
1825603 AAATTTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 4 0.17
18 7 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTAATTTATTTTAA
Found at i:1825670 original size:25 final size:25
Alignment explanation
Indices: 1825567--1825671 Score: 70
Period size: 25 Copynumber: 4.0 Consensus size: 25
1825557 TTTCATTAAT
*
1825567 TTATTTTAAATTAATATTATTTTAATAA
1 TTATTTTAAATT-AT-TTATTAT-ATAA
*
1825595 TTAATTTAAAATT-TTTATT-TATATA
1 TT-ATTTTAAATTATTTATTATATA-A
* * *
1825620 TTATTATTTAATATATATATAAATATAA
1 TTATT-TTAAAT-TATTTAT-TATATAA
*
1825648 TTATTTTTAATTATTTATTATATA
1 TTATTTTAAATTATTTATTATATA
1825672 TACATATATT
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
24 6 0.10
25 13 0.21
26 12 0.19
27 11 0.17
28 8 0.13
29 13 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TTATTTTAAATTATTTATTATATAA
Found at i:1830762 original size:19 final size:19
Alignment explanation
Indices: 1830720--1830773 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 19
1830710 ATACAACCTA
*
1830720 TTTAATACATTTATCATT-TT
1 TTTAATA-ATTTAT-ATTATG
1830740 TTTAATAATTTATATTATG
1 TTTAATAATTTATATTATG
1830759 TTT-AT-ATTTATATTA
1 TTTAATAATTTATATTA
1830774 ATTGACATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
17 10 0.31
18 5 0.16
19 10 0.31
20 7 0.22
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTAATAATTTATATTATG
Found at i:1834354 original size:2 final size:2
Alignment explanation
Indices: 1834337--1834372 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
1834327 TATAATATTC
1834337 AT AT GAT AT A- 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
1834373 TATTTTTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1834356 original size:16 final size:15
Alignment explanation
Indices: 1834327--1834372 Score: 60
Period size: 14 Copynumber: 3.1 Consensus size: 15
1834317 GTCATTAAAT
1834327 TATAATAT-TCATATGA
1 TATAATATAT-ATAT-A
1834343 TATAATATATATATA
1 TATAATATATATATA
1834358 TAT-ATATATATATA
1 TATAATATATATATA
1834372 T
1 T
1834373 TATTTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.41
15 4 0.14
16 12 0.41
17 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
TATAATATATATATA
Found at i:1839832 original size:23 final size:23
Alignment explanation
Indices: 1839796--1839851 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
1839786 AAAGAAATAC
* *
1839796 ATATTT-TTTAATTTATCTTTTAT
1 ATATTTATTTAATTTAT-ATATAT
1839819 ATATTTATTT-ATTTATATATAT
1 ATATTTATTTAATTTATATATAT
1839841 ATATTTTATTT
1 ATA-TTTATTT
1839852 TAAAAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 7 0.24
23 19 0.66
24 3 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
ATATTTATTTAATTTATATATAT
Found at i:1839839 original size:18 final size:18
Alignment explanation
Indices: 1839806--1839851 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
1839796 ATATTTTTTA
* *
1839806 ATTTATCTTTTATATATTT
1 ATTTAT-TTATATATATAT
1839825 ATTTATTTATATATATAT
1 ATTTATTTATATATATAT
1839843 ATTTTATTT
1 A-TTTATTT
1839852 TAAAAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTATTTATATATATAT
Found at i:1840227 original size:2 final size:2
Alignment explanation
Indices: 1840220--1840250 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1840210 GCACAAAATT
1840220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1840251 CAGCGAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1843731 original size:37 final size:33
Alignment explanation
Indices: 1843653--1843731 Score: 79
Period size: 37 Copynumber: 2.3 Consensus size: 33
1843643 ATATTGTAAT
1843653 AATAAATTATTTAAAAATTAATTTTATATAACA
1 AATAAATTATTTAAAAATTAATTTTATATAACA
* * *
1843686 AATTAATTATATATATAAATATAGATTTTA-ATAAATA
1 AATAAATTAT-T-TAAAAAT-TA-ATTTTATAT-AACA
1843723 AATAAATTA
1 AATAAATTA
1843732 AAAATAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
33 9 0.24
34 1 0.03
35 6 0.16
36 4 0.11
37 17 0.46
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (33 bp):
AATAAATTATTTAAAAATTAATTTTATATAACA
Found at i:1848421 original size:19 final size:19
Alignment explanation
Indices: 1848371--1848421 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1848361 TTATTATAAT
*
1848371 ATTAATTATATAAAAATTTA
1 ATTAATTATAT-AAAATTAA
* *
1848391 TTTAAATATATAAAATTAA
1 ATTAATTATATAAAATTAA
*
1848410 ATTAATTTTATA
1 ATTAATTATATA
1848422 TTAATATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAATTATATAAAATTAA
Found at i:1851503 original size:3 final size:3
Alignment explanation
Indices: 1851495--1851519 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1851485 CCGTTAGCCT
1851495 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
1851520 GCTGTTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1852582 original size:20 final size:21
Alignment explanation
Indices: 1852559--1852607 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1852549 ATTAAATCAA
1852559 ATTTTAATT-TAAAAAAAACT
1 ATTTTAATTATAAAAAAAACT
* * * *
1852579 ATTTTTATTATATAAAATATT
1 ATTTTAATTATAAAAAAAACT
1852600 ATTTTAAT
1 ATTTTAAT
1852608 ATGTTGATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTAATTATAAAAAAAACT
Found at i:1854985 original size:25 final size:25
Alignment explanation
Indices: 1854957--1855010 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
1854947 AAATTATTCA
*
1854957 TTATCAATAAATTAAATAATTTAT-T
1 TTATCAA-AAATAAAATAATTTATAT
* *
1854982 TTATTAAAAATAAAATTATTTATAT
1 TTATCAAAAATAAAATAATTTATAT
1855007 TTAT
1 TTAT
1855011 TTTTAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATCAAAAATAAAATAATTTATAT
Found at i:1854997 original size:24 final size:24
Alignment explanation
Indices: 1854965--1855032 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
1854955 CATTATCAAT
*
1854965 AAATTAAATAATTTATTTTATTAA
1 AAATAAAATAATTTATTTTATTAA
* **
1854989 AAATAAAATTATTTATATTTATTTT
1 AAATAAAATAATTTAT-TTTATTAA
*
1855014 TAATAAAATAATATTATTT
1 AAATAAAATAAT-TTATTT
1855033 ATTTTATTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 14 0.39
25 18 0.50
26 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AAATAAAATAATTTATTTTATTAA
Found at i:1855011 original size:30 final size:30
Alignment explanation
Indices: 1854975--1855040 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
1854965 AAATTAAATA
*
1854975 ATTTA-TTTTATTAAAAATAAAATTATTTAT
1 ATTTATTTTTAAT-AAAATAAAATTATTTAT
*
1855005 ATTTATTTTTAATAAAATAATATTATTTAT
1 ATTTATTTTTAATAAAATAAAATTATTTAT
1855035 -TTTATT
1 ATTTATT
1855041 GATATCGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 6 0.18
30 21 0.64
31 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
ATTTATTTTTAATAAAATAAAATTATTTAT
Found at i:1855036 original size:24 final size:25
Alignment explanation
Indices: 1854990--1855037 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1854980 TTTTATTAAA
* *
1854990 AATAAAATTATTTATATTTATTTTT
1 AATAAAATAATATATATTTATTTTT
1855015 AATAAAATAATAT-TATTTATTTT
1 AATAAAATAATATATATTTATTTT
1855038 ATTGATATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
AATAAAATAATATATATTTATTTTT
Found at i:1855982 original size:18 final size:19
Alignment explanation
Indices: 1855937--1855982 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1855927 CATCTTGTCA
*
1855937 TCATCATTTATTTTACATC
1 TCATCATTAATTTTACATC
*
1855956 TAAAT-ATTAATTTTA-ATC
1 T-CATCATTAATTTTACATC
1855974 TCATCATTA
1 TCATCATTA
1855983 TAATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 2 0.09
18 8 0.36
19 10 0.45
20 2 0.09
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (19 bp):
TCATCATTAATTTTACATC
Found at i:1857209 original size:29 final size:28
Alignment explanation
Indices: 1857134--1857209 Score: 73
Period size: 29 Copynumber: 2.7 Consensus size: 28
1857124 TCAATTCATT
* * *
1857134 TTATATTTATAAAAAAATTAAAAATATC
1 TTATATTAATATAAAAATAAAAAATATC
***
1857162 TTATATTAATATTTTAATAAAAATATAT-
1 TTATATTAATATAAAAATAAAAA-ATATC
1857190 TCTATATTAATATAAAAATA
1 T-TATATTAATATAAAAATA
1857210 TTTCATGTAA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
28 18 0.49
29 19 0.51
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (28 bp):
TTATATTAATATAAAAATAAAAAATATC
Found at i:1858101 original size:16 final size:16
Alignment explanation
Indices: 1858057--1858148 Score: 73
Period size: 16 Copynumber: 5.7 Consensus size: 16
1858047 ATTAATTAAA
1858057 ATATAATATAAATATTT
1 ATATAATATAAA-ATTT
* * *
1858074 AAATATTTTAAAATTT
1 ATATAATATAAAATTT
1858090 ATATAATATAAAATATT
1 ATATAATATAAAAT-TT
*
1858107 A-AT-GTATCAAAATTT
1 ATATAATAT-AAAATTT
*
1858122 ATATCATATAAAATATT
1 ATATAATATAAAAT-TT
*
1858139 TTA-AATATAA
1 ATATAATATAA
1858149 TTATCACATG
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
15 6 0.10
16 35 0.58
17 19 0.32
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (16 bp):
ATATAATATAAAATTT
Found at i:1858124 original size:32 final size:33
Alignment explanation
Indices: 1858057--1858147 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 33
1858047 ATTAATTAAA
* *
1858057 ATATAATAT-AAATATTTAAATATTTTAAAATTT
1 ATATAATATAAAATA-TTAAATATATCAAAATTT
*
1858090 ATATAATATAAAATATT-AATGTATCAAAATTT
1 ATATAATATAAAATATTAAATATATCAAAATTT
*
1858122 ATATCATATAAAATATTTTAAATATA
1 ATATAATATAAAATA--TTAAATATA
1858148 ATTATCACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 26 0.53
33 11 0.22
34 7 0.14
35 5 0.10
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (33 bp):
ATATAATATAAAATATTAAATATATCAAAATTT
Found at i:1860743 original size:2 final size:2
Alignment explanation
Indices: 1860736--1860761 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1860726 GGGACTCTTT
1860736 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1860762 AAACACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1861197 original size:34 final size:34
Alignment explanation
Indices: 1861159--1861303 Score: 170
Period size: 34 Copynumber: 4.3 Consensus size: 34
1861149 CAACTTATTT
* * *
1861159 ATTTAATCAACAAT-GACAAACTATCAAATCTCTC
1 ATTTAATCAACAATAG-CAAACCACCAAATCACTC
*
1861193 ATTTAATCAACAATATCAAACCACCAAATCACTC
1 ATTTAATCAACAATAGCAAACCACCAAATCACTC
* * *
1861227 ATTTAATTAATAATAGCAAACTACCAAAT-ATCTC
1 ATTTAATCAACAATAGCAAACCACCAAATCA-CTC
* *
1861261 ATTTAGTCAACAATGGCAAACCACCAAATCAC-C
1 ATTTAATCAACAATAGCAAACCACCAAATCACTC
1861294 ATTTAATCAA
1 ATTTAATCAA
1861304 TAATTCTCCC
Statistics
Matches: 94, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
33 11 0.12
34 82 0.87
35 1 0.01
ACGTcount: A:0.46, C:0.24, G:0.03, T:0.27
Consensus pattern (34 bp):
ATTTAATCAACAATAGCAAACCACCAAATCACTC
Found at i:1861255 original size:68 final size:67
Alignment explanation
Indices: 1861159--1861307 Score: 210
Period size: 68 Copynumber: 2.2 Consensus size: 67
1861149 CAACTTATTT
* * * *
1861159 ATTTAATCAACAAT-GACAAACTATCAAATCTCTCATTTAATCAACAATATCAAACCACCAAATC
1 ATTTAATCAATAATAG-CAAACTACCAAATATCTCATTTAATCAACAATAGCAAACCACCAAATC
1861223 ACTC
65 AC-C
* * *
1861227 ATTTAATTAATAATAGCAAACTACCAAATATCTCATTTAGTCAACAATGGCAAACCACCAAATCA
1 ATTTAATCAATAATAGCAAACTACCAAATATCTCATTTAATCAACAATAGCAAACCACCAAATCA
1861292 CC
66 CC
1861294 ATTTAATCAATAAT
1 ATTTAATCAATAAT
1861308 TCTCCCACTT
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
67 14 0.19
68 57 0.79
69 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.28
Consensus pattern (67 bp):
ATTTAATCAATAATAGCAAACTACCAAATATCTCATTTAATCAACAATAGCAAACCACCAAATCA
CC
Found at i:1865389 original size:19 final size:19
Alignment explanation
Indices: 1865365--1865419 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
1865355 GTGCACATTA
*
1865365 CCGTATACGTAAATAGTAC
1 CCGTATACGTGAATAGTAC
*
1865384 CCGTATATGTGAATAGTAC
1 CCGTATACGTGAATAGTAC
**
1865403 CTATATACGTGAATAGT
1 CCGTATACGTGAATAGT
1865420 GCCTCGACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (19 bp):
CCGTATACGTGAATAGTAC
Found at i:1865768 original size:34 final size:34
Alignment explanation
Indices: 1865723--1865836 Score: 122
Period size: 34 Copynumber: 3.4 Consensus size: 34
1865713 GTTTGGTAAA
*
1865723 AAACTACCAAATCACCTATTTAATCAATAATGGT
1 AAACTATCAAATCACCTATTTAATCAATAATGGT
*** *
1865757 AAACTATCAAAT-TTTTCATTTAATCAATAATTGT
1 AAACTATCAAATCACCT-ATTTAATCAATAATGGT
* * * **
1865791 AAACCATCAAATCACCCATTTAATCAACAATGAC
1 AAACTATCAAATCACCTATTTAATCAATAATGGT
1865825 AAACTATCAAAT
1 AAACTATCAAAT
1865837 TTTTCGTTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
33 1 0.02
34 62 0.98
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.31
Consensus pattern (34 bp):
AAACTATCAAATCACCTATTTAATCAATAATGGT
Found at i:1865870 original size:68 final size:68
Alignment explanation
Indices: 1865723--1865872 Score: 192
Period size: 68 Copynumber: 2.2 Consensus size: 68
1865713 GTTTGGTAAA
* * ** *
1865723 AAACTACCAAATCACCTATTTAATCAATAATGGTAAACTATCAAATTTTTCATTTAATCAATAAT
1 AAACTACCAAATCACCCATTTAATCAACAATGACAAACTATCAAATTTTTCATTTAATCAACAAT
***
1865788 TGT
66 AAC
* * * *
1865791 AAACCATCAAATCACCCATTTAATCAACAATGACAAACTATCAAATTTTTCGTTTAGTCAACAAT
1 AAACTACCAAATCACCCATTTAATCAACAATGACAAACTATCAAATTTTTCATTTAATCAACAAT
1865856 AAC
66 AAC
1865859 AAACTACCAAATCA
1 AAACTACCAAATCA
1865873 TTATTTAATC
Statistics
Matches: 68, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.45, C:0.21, G:0.04, T:0.31
Consensus pattern (68 bp):
AAACTACCAAATCACCCATTTAATCAACAATGACAAACTATCAAATTTTTCATTTAATCAACAAT
AAC
Found at i:1870574 original size:2 final size:2
Alignment explanation
Indices: 1870567--1870599 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1870557 TATTAGACAC
1870567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1870600 TCTTATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1871928 original size:15 final size:16
Alignment explanation
Indices: 1871903--1871932 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1871893 CTTACATGAT
1871903 ATTTAAAAAATTTAAA
1 ATTTAAAAAATTTAAA
1871919 ATTT-AAAAATTTAA
1 ATTTAAAAAATTTAA
1871933 TTTAATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTTAAAAAATTTAAA
Found at i:1873480 original size:19 final size:18
Alignment explanation
Indices: 1873451--1873500 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
1873441 AAAGCCATAG
*
1873451 TTTTTTATTTTTCTATTT
1 TTTTTTTTTTTTCTATTT
*
1873469 TTTTTTCTTTTTTCTCTTT
1 TTTTTT-TTTTTTCTATTT
1873488 TTTTTTTTTTTTC
1 TTTTTTTTTTTTC
1873501 AACTTGTGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTTTTCTATTT
Found at i:1873752 original size:22 final size:22
Alignment explanation
Indices: 1873694--1873736 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1873684 TTAGCCACCT
*
1873694 CTTTC-TTCTTCTTCTCTCTCC
1 CTTTCATTTTTCTTCTCTCTCC
1873715 CTTTCATTTTTCTTCTCTCTCC
1 CTTTCATTTTTCTTCTCTCTCC
1873737 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (22 bp):
CTTTCATTTTTCTTCTCTCTCC
Found at i:1874233 original size:24 final size:26
Alignment explanation
Indices: 1874206--1874259 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1874196 GTTAAACTAA
1874206 TAAAAAAGTTAAT-TA-ATT-ATTTTT
1 TAAAAAA-TTAATATATATTAATTTTT
*
1874230 TAAAAAATTATTATATATTAATTTTT
1 TAAAAAATTAATATATATTAATTTTT
1874256 TAAA
1 TAAA
1874260 TTTATATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 9 0.35
25 3 0.12
26 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (26 bp):
TAAAAAATTAATATATATTAATTTTT
Found at i:1875685 original size:34 final size:33
Alignment explanation
Indices: 1875637--1875857 Score: 280
Period size: 34 Copynumber: 6.5 Consensus size: 33
1875627 TGGTAAAAAC
* *
1875637 CACCATTTAATCAACAATGGCAATCTACCAAAT
1 CACCATTTAATCAACAATGGTAAGCTACCAAAT
* *
1875670 CTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
1875704 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
**
1875738 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAAGCTACCAAAT
* * * * *
1875772 CTCCCATTTAGTCAACAATGGCAAACCACCAAAT
1 C-ACCATTTAATCAACAATGGTAAGCTACCAAAT
*
1875806 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAAGCTACCAAAT
1875840 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1875858 TCTCTCACTT
Statistics
Matches: 163, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
33 19 0.12
34 143 0.88
35 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAAGCTACCAAAT
Found at i:1875816 original size:102 final size:101
Alignment explanation
Indices: 1875637--1875857 Score: 352
Period size: 102 Copynumber: 2.2 Consensus size: 101
1875627 TGGTAAAAAC
* * *
1875637 CACCATTTAATCAACAATGGCAATCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1875702 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
1875738 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
1875803 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1875840 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1875858 TCTCTCACTT
Statistics
Matches: 108, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 16 0.15
102 92 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAAGCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1880308 original size:34 final size:33
Alignment explanation
Indices: 1880260--1880478 Score: 262
Period size: 34 Copynumber: 6.5 Consensus size: 33
1880250 TGGTAAAAAC
*
1880260 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
1880293 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
1880327 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
1880361 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
1880395 CTCCAATTTAGTCAACAATGGCAAACC-ACCAAAT
1 CACC-ATTTAATCAACAATGG-TAACCTACCAAAT
*
1880429 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
1880463 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1880479 CATCACTTAC
Statistics
Matches: 161, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
33 22 0.14
34 132 0.82
35 7 0.04
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:1880404 original size:102 final size:101
Alignment explanation
Indices: 1880260--1880478 Score: 341
Period size: 102 Copynumber: 2.2 Consensus size: 101
1880250 TGGTAAAAAC
* *
1880260 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
1880325 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** * *
1880361 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCT-CCAATTTAGTCAACAATGGCAAACCACC
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACC-ATTTAGTCAACAATGGCAAACCACC
1880425 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
64 AAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1880463 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1880479 CATCACTTAC
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
101 16 0.15
102 90 0.85
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:1881304 original size:21 final size:21
Alignment explanation
Indices: 1881280--1881323 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1881270 TTCTATCAAT
* * *
1881280 TATATCTTGACTTTTTTTATA
1 TATATATTGAATTTATTTATA
1881301 TATATATTGAATTTATTTATA
1 TATATATTGAATTTATTTATA
1881322 TA
1 TA
1881324 ATTTAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TATATATTGAATTTATTTATA
Found at i:1885731 original size:31 final size:31
Alignment explanation
Indices: 1885692--1885764 Score: 110
Period size: 31 Copynumber: 2.4 Consensus size: 31
1885682 TTAAAAAATA
1885692 TATCGATACATCTAGATAAAAAAACAGAATG
1 TATCGATACATCTAGATAAAAAAACAGAATG
* * * *
1885723 TATTGATACATTTTGGTAAAAAAACAGAATG
1 TATCGATACATCTAGATAAAAAAACAGAATG
1885754 TATCGATACAT
1 TATCGATACAT
1885765 GTACTGTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.29
Consensus pattern (31 bp):
TATCGATACATCTAGATAAAAAAACAGAATG
Found at i:1890914 original size:21 final size:21
Alignment explanation
Indices: 1890876--1890933 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
1890866 TATGATTGTT
* *
1890876 TTATATATGTATAATTTACTAAA
1 TTATATAT-TAT-TTTTACCAAA
1890899 TTATATATTATTTTTACCAAA
1 TTATATATTATTTTTACCAAA
* *
1890920 TTATTTATAATTTT
1 TTATATATTATTTT
1890934 ATATTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 20 0.65
22 3 0.10
23 8 0.26
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
TTATATATTATTTTTACCAAA
Found at i:1898576 original size:31 final size:32
Alignment explanation
Indices: 1898533--1898596 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1898523 GTTACGTATT
1898533 AAATAATATTAATTTAATAA-ATAATAATAAAA
1 AAATAATATTAATTTAATAAGATAA-AATAAAA
*
1898565 AAATAA-ATTAATTTATTAATGATAAAATAAAA
1 AAATAATATTAATTTAATAA-GATAAAATAAAA
1898597 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 12 0.41
32 13 0.45
33 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (32 bp):
AAATAATATTAATTTAATAAGATAAAATAAAA
Found at i:1898648 original size:14 final size:14
Alignment explanation
Indices: 1898629--1898658 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1898619 AATTTTTTTA
*
1898629 AAAAATTATTTATT
1 AAAAATTAATTATT
1898643 AAAAATTAATTATT
1 AAAAATTAATTATT
1898657 AA
1 AA
1898659 CTTAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAAAATTAATTATT
Done.