Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold156
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: 2697547
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 8 of 14
Found at i:1559437 original size:58 final size:60
Alignment explanation
Indices: 1559366--1559481 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 60
1559356 TAGATAGTAA
* *
1559366 TAATTTTTAATTTTGTAAATA-AGATTAAAA-AT-TATTATTTATTTTAATTTTTTTAAAT
1 TAATTTTTAATTTTGTAAATATAGATTAAAAGATGAATTATTT-TATTAATTTTTTTAAAT
* * *
1559424 TAATTTTTTATTTTTTAAATATATATTAAAAGTATGAATTATTTTATTAATTTTTTTA
1 TAATTTTTAATTTTGTAAATATAGATTAAAAG-ATGAATTATTTTATTAATTTTTTTA
1559482 TGAAATTTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
58 19 0.39
59 8 0.16
61 15 0.31
62 7 0.14
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (60 bp):
TAATTTTTAATTTTGTAAATATAGATTAAAAGATGAATTATTTTATTAATTTTTTTAAAT
Found at i:1564275 original size:30 final size:32
Alignment explanation
Indices: 1564213--1564280 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 32
1564203 CTCTATATTA
* *
1564213 AATTTAATAATATTAAGATTAATCATTATTTTT
1 AATTTAATAATATTAAAAATAA-CATTATTTTT
*
1564246 AATTTAATAGTATTAAAAATAA-ATT-TTTTT
1 AATTTAATAATATTAAAAATAACATTATTTTT
1564276 AATTT
1 AATTT
1564281 TTTTTTTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 10 0.31
31 3 0.09
33 19 0.59
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (32 bp):
AATTTAATAATATTAAAAATAACATTATTTTT
Found at i:1567906 original size:8 final size:8
Alignment explanation
Indices: 1567895--1567926 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1567885 TAAAGTATTA
1567895 ATTTATAT
1 ATTTATAT
1567903 ATTTAT-T
1 ATTTATAT
1567910 -TTTATAT
1 ATTTATAT
1567917 ATTTATAT
1 ATTTATAT
1567925 AT
1 AT
1567927 GTGGAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 5 0.23
7 2 0.09
8 15 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
ATTTATAT
Found at i:1567915 original size:14 final size:14
Alignment explanation
Indices: 1567896--1567922 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1567886 AAAGTATTAA
1567896 TTTATATATTTATT
1 TTTATATATTTATT
1567910 TTTATATATTTAT
1 TTTATATATTTAT
1567923 ATATGTGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATATATTTATT
Found at i:1569018 original size:21 final size:21
Alignment explanation
Indices: 1568994--1569045 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1568984 AATTTGTAAG
*
1568994 TTTATTTTACTATTTAT-TATA
1 TTTATTTTAATATTTATATA-A
*
1569015 TTTATATTAATATTTATATAA
1 TTTATTTTAATATTTATATAA
*
1569036 TTTAATTTAA
1 TTTATTTTAA
1569046 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTATTTTAATATTTATATAA
Found at i:1578698 original size:2 final size:2
Alignment explanation
Indices: 1578691--1578719 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1578681 TACAAACTTT
1578691 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
1578720 TTTATGCATC
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:1579463 original size:21 final size:21
Alignment explanation
Indices: 1579437--1579490 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1579427 TTGTTATTAA
* *
1579437 AAAATAAAAAAATTTAATGAT
1 AAAATAAAAAAATTAAATAAT
* *
1579458 AAAATAATATAATTAAATAAT
1 AAAATAAAAAAATTAAATAAT
1579479 AAAATAAAAAAA
1 AAAATAAAAAAA
1579491 ATTTCATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAAATAAAAAAATTAAATAAT
Found at i:1586737 original size:2 final size:2
Alignment explanation
Indices: 1586730--1586767 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1586720 CTACATACAA
1586730 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1586768 ATTTGACTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1588718 original size:27 final size:28
Alignment explanation
Indices: 1588687--1588749 Score: 119
Period size: 27 Copynumber: 2.3 Consensus size: 28
1588677 ATTTAAAATC
1588687 ATATGATGGGTTTTTTAT-TTGTTCATA
1 ATATGATGGGTTTTTTATATTGTTCATA
1588714 ATATGATGGGTTTTTTATATTGTTCATA
1 ATATGATGGGTTTTTTATATTGTTCATA
1588742 ATATGATG
1 ATATGATG
1588750 ATGGATTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.52
Consensus pattern (28 bp):
ATATGATGGGTTTTTTATATTGTTCATA
Found at i:1588759 original size:31 final size:29
Alignment explanation
Indices: 1588689--1588761 Score: 105
Period size: 28 Copynumber: 2.5 Consensus size: 29
1588679 TTAAAATCAT
1588689 ATGATGGGTTTTTTATTTGTTCATAATATG
1 ATGAT-GGTTTTTTATTTGTTCATAATATG
1588719 ATG--GGTTTTTTATATTGTTCATAATATG
1 ATGATGGTTTTTTAT-TTGTTCATAATATG
1588747 ATGATGGATTTTTTA
1 ATGATGG-TTTTTTA
1588762 AGTTGTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
27 10 0.26
28 17 0.44
30 5 0.13
31 7 0.18
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (29 bp):
ATGATGGTTTTTTATTTGTTCATAATATG
Found at i:1592228 original size:2 final size:2
Alignment explanation
Indices: 1592221--1592282 Score: 97
Period size: 2 Copynumber: 30.5 Consensus size: 2
1592211 TTTTTCGTGT
* *
1592221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
1592264 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1592283 TGTAGTGTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 53 0.96
3 2 0.04
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1593405 original size:14 final size:14
Alignment explanation
Indices: 1593386--1593415 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1593376 GATACGTTTA
1593386 AATATAATTAATAT
1 AATATAATTAATAT
*
1593400 AATATATTTAATAT
1 AATATAATTAATAT
1593414 AA
1 AA
1593416 ATATCACATT
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):
AATATAATTAATAT
Found at i:1595518 original size:22 final size:23
Alignment explanation
Indices: 1595493--1595548 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 23
1595483 AAAGTACGAG
* *
1595493 ATTAAATATAATATTATATAAA-
1 ATTAAATATAAAATAATATAAAT
1595515 ATT-AATATTAAAATAATATAAAT
1 ATTAAATA-TAAAATAATATAAAT
1595538 ATATAAATATA
1 AT-TAAATATA
1595549 TTAAAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 4 0.14
22 15 0.54
23 2 0.07
24 3 0.11
25 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTAAATATAAAATAATATAAAT
Found at i:1595529 original size:8 final size:8
Alignment explanation
Indices: 1595518--1595587 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
1595508 ATATAAAATT
1595518 AATATTAA
1 AATATTAA
*
1595526 AATAATATA
1 AATATTA-A
1595535 AATATATAA
1 AATAT-TAA
1595544 ATATATTAA
1 A-ATATTAA
1595553 AAT-TTATA
1 AATATTA-A
1595561 TAATA-TAA
1 -AATATTAA
*
1595569 ATTATTAA
1 AATATTAA
*
1595577 TATATTAA
1 AATATTAA
1595585 AAT
1 AAT
1595588 TTTATATAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
7 6 0.12
8 21 0.43
9 16 0.33
10 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AATATTAA
Found at i:1595552 original size:33 final size:32
Alignment explanation
Indices: 1595497--1595588 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 32
1595487 TACGAGATTA
*
1595497 AATATAATATTATATAA-A-ATTAATATTAAAAT
1 AATATAA-ATTATA-AATATATTAAAATTAAAAT
* *
1595529 AATATAAATATATAAATATATTAAAATTTATAT
1 AATATAAAT-TATAAATATATTAAAATTAAAAT
*
1595562 AATATAAATTATTAATATATTAAAATT
1 AATATAAATTATAAATATATTAAAATT
1595589 TTATATAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
31 4 0.08
32 29 0.55
33 20 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
AATATAAATTATAAATATATTAAAATTAAAAT
Found at i:1595553 original size:55 final size:58
Alignment explanation
Indices: 1595493--1595626 Score: 143
Period size: 61 Copynumber: 2.3 Consensus size: 58
1595483 AAAGTACGAG
*
1595493 ATTAAATATAATATTATATAAA-ATT-A-ATATTAAAA-TAATATAAATATATAAATAT
1 ATTAAATATAATATAATATAAATATTAATATATTAAAATTAATATAAATATAT-AATAT
* *
1595548 ATTAAA-ATTTATATAATATAAATTATTAATATATTAAAATTTTATATAAATATATAATAT
1 ATTAAATA-TAATATAATATAAA-TATTAATATATTAAAA-TTAATATAAATATATAATAT
* *
1595608 TTTGAATATAATTATAATA
1 ATTAAATATAA-TATAATA
1595627 CATGAAATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
54 1 0.02
55 18 0.28
57 3 0.05
58 1 0.02
59 9 0.14
60 11 0.17
61 21 0.33
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (58 bp):
ATTAAATATAATATAATATAAATATTAATATATTAAAATTAATATAAATATATAATAT
Found at i:1595584 original size:32 final size:32
Alignment explanation
Indices: 1595497--1595601 Score: 115
Period size: 33 Copynumber: 3.2 Consensus size: 32
1595487 TACGAGATTA
* * *
1595497 AATATAATATTATATAA-A-ATTAATATTAAAAT
1 AATATAA-ATTAT-TAATATATTAAAATTTATAT
*
1595529 AATATAAATATATAAATATATTAAAATTTATAT
1 AATATAAAT-TATTAATATATTAAAATTTATAT
1595562 AATATAAATTATTAATATATTAAAATTTTATAT
1 AATATAAATTATTAATATATTAAAA-TTTATAT
1595595 AAATATA
1 -AATATA
1595602 TAATATTTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
31 4 0.06
32 26 0.41
33 27 0.43
34 6 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (32 bp):
AATATAAATTATTAATATATTAAAATTTATAT
Found at i:1595592 original size:33 final size:33
Alignment explanation
Indices: 1595527--1595607 Score: 119
Period size: 33 Copynumber: 2.4 Consensus size: 33
1595517 TAATATTAAA
1595527 ATAATATAAATATATAAATATATTAAAATTTAT
1 ATAATATAAATATATAAATATATTAAAATTTAT
*
1595560 ATAATATAAAT-TATTAATATATTAAAATTTTAT
1 ATAATATAAATATATAAATATATTAAAA-TTTAT
1595593 ATAAATATATAATAT
1 AT-AATATA-AATAT
1595608 TTTGAATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
32 15 0.35
33 18 0.42
34 6 0.14
35 3 0.07
36 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATAATATAAATATATAAATATATTAAAATTTAT
Found at i:1595594 original size:15 final size:15
Alignment explanation
Indices: 1595544--1595595 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
1595534 AAATATATAA
1595544 ATATATTAAAA-TTT
1 ATATATTAAAATTTT
*
1595558 ATATAATATAAATTATT
1 ATATATTA-AAATT-TT
1595575 AATATATTAAAATTTT
1 -ATATATTAAAATTTT
1595591 ATATA
1 ATATA
1595596 AATATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.22
15 8 0.25
16 3 0.09
17 7 0.22
18 7 0.22
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATATTAAAATTTT
Found at i:1595626 original size:20 final size:18
Alignment explanation
Indices: 1595543--1595624 Score: 63
Period size: 17 Copynumber: 4.7 Consensus size: 18
1595533 TAAATATATA
1595543 AATAT-ATTA-AAA-TTT
1 AATATAATTATAAATTTT
1595558 -ATATAA-TATAAATTATT
1 AATATAATTATAAATT-TT
1595575 AATAT-ATTA-AAATTTT
1 AATATAATTATAAATTTT
1595591 -ATATAAATATATAATATTTT
1 AATAT-AAT-TATAA-ATTTT
1595611 GAATATAATTATAA
1 -AATATAATTATAA
1595625 TACATGAAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 21
0.72 0.00 0.28
Matches are distributed among these distances:
14 6 0.11
15 8 0.15
16 3 0.06
17 10 0.19
18 8 0.15
19 2 0.04
20 10 0.19
21 3 0.06
22 4 0.07
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.46
Consensus pattern (18 bp):
AATATAATTATAAATTTT
Found at i:1595986 original size:3 final size:3
Alignment explanation
Indices: 1595978--1596021 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1595968 CTTCATGACC
1595978 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1596022 ATTTGGAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1599801 original size:12 final size:14
Alignment explanation
Indices: 1599769--1599802 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1599759 TATTTACTCG
1599769 ATAAAAATATAAAT
1 ATAAAAATATAAAT
1599783 ATAAAAATAT-AAT
1 ATAAAAATATAAAT
1599796 -TAAAAAT
1 ATAAAAAT
1599803 GAATAGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 3 0.15
14 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
ATAAAAATATAAAT
Found at i:1600570 original size:21 final size:21
Alignment explanation
Indices: 1600544--1600692 Score: 88
Period size: 21 Copynumber: 7.2 Consensus size: 21
1600534 GATATATAAT
*
1600544 ATAACCTTTGATATGATTTTA
1 ATAACCTTTAATATGATTTTA
*
1600565 ATAACCTTAAATATGATTTTGA
1 ATAACCTTTAATATGATTTT-A
** *
1600587 A-AATTTTTTATATGATTTTA
1 ATAACCTTTAATATGATTTTA
* **** *
1600607 ATAATCTTCCGCATGATTTTT
1 ATAACCTTTAATATGATTTTA
* * *
1600628 ATAACTTTTATTATAATTTTA
1 ATAACCTTTAATATGATTTTA
* ** * *
1600649 GT-ATTTTTAATATAATTTTG
1 ATAACCTTTAATATGATTTTA
*
1600669 ATAACCTTT-ATATAATTTTA
1 ATAACCTTTAATATGATTTTA
1600689 ATAA
1 ATAA
1600693 AATTTTATGT
Statistics
Matches: 97, Mismatches: 28, Indels: 7
0.73 0.21 0.05
Matches are distributed among these distances:
20 32 0.33
21 63 0.65
22 2 0.02
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (21 bp):
ATAACCTTTAATATGATTTTA
Found at i:1600667 original size:11 final size:11
Alignment explanation
Indices: 1600627--1600699 Score: 55
Period size: 11 Copynumber: 6.9 Consensus size: 11
1600617 GCATGATTTT
*
1600627 TATAACTTTTAT
1 TATAA-TTTTAA
*
1600639 TATAATTTTAG
1 TATAATTTTAA
1600650 TAT--TTTTAA
1 TATAATTTTAA
*
1600659 TATAATTTTGA
1 TATAATTTTAA
**
1600670 TA-ACCTTT-A
1 TATAATTTTAA
1600679 TATAATTTTAA
1 TATAATTTTAA
*
1600690 TAAAATTTTA
1 TATAATTTTA
1600700 TGTAAGTTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
9 11 0.22
10 8 0.16
11 25 0.51
12 5 0.10
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (11 bp):
TATAATTTTAA
Found at i:1600728 original size:41 final size:42
Alignment explanation
Indices: 1600678--1600773 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 42
1600668 GATAACCTTT
*
1600678 ATATAATTTTAATAAAATTTTATGTAAGT-TGTTAAGTTTTG
1 ATATAATTTTAATAAAATTTTATGTAAGTCTGATAAGTTTTG
* * ** * * *
1600719 ATGTAATTTTGATAATCTTTTATGTAATTCTGATAATTTTTT
1 ATATAATTTTAATAAAATTTTATGTAAGTCTGATAAGTTTTG
1600761 ATATAATTTTAAT
1 ATATAATTTTAAT
1600774 CAGTAACATT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
41 24 0.55
42 20 0.45
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.54
Consensus pattern (42 bp):
ATATAATTTTAATAAAATTTTATGTAAGTCTGATAAGTTTTG
Found at i:1600730 original size:11 final size:11
Alignment explanation
Indices: 1600714--1600806 Score: 50
Period size: 11 Copynumber: 8.4 Consensus size: 11
1600704 AGTTGTTAAG
1600714 TTTTGATGTAA
1 TTTTGATGTAA
1600725 TTTTGA--TAA
1 TTTTGATGTAA
*
1600734 TCTTTTATGTAA
1 T-TTTGATGTAA
*
1600746 TTCTGA--TAA
1 TTTTGATGTAA
* *
1600755 TTTTTTATATAA
1 -TTTTGATGTAA
*
1600767 TTTTAATCAGTAA
1 TTTTGAT--GTAA
*
1600780 CATTTGATGTAA
1 -TTTTGATGTAA
*
1600792 ATTTGATGTAA
1 TTTTGATGTAA
1600803 TTTT
1 TTTT
1600807 AATAATTTTT
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
9 7 0.11
10 8 0.13
11 29 0.46
12 11 0.17
13 3 0.05
14 5 0.08
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (11 bp):
TTTTGATGTAA
Found at i:1600744 original size:21 final size:21
Alignment explanation
Indices: 1600661--1600770 Score: 91
Period size: 21 Copynumber: 5.3 Consensus size: 21
1600651 ATTTTTAATA
* *
1600661 TAATTTTGATAA-CCTTTATA
1 TAATTTTGATAATCTTTTATG
* **
1600681 TAATTTTAATAAAATTTTATG
1 TAATTTTGATAATCTTTTATG
* * *
1600702 TAA-GTTGTTAAGT-TTTGATG
1 TAATTTTGATAA-TCTTTTATG
1600722 TAATTTTGATAATCTTTTATG
1 TAATTTTGATAATCTTTTATG
* * *
1600743 TAATTCTGATAATTTTTTATA
1 TAATTTTGATAATCTTTTATG
1600764 TAATTTT
1 TAATTTT
1600771 AATCAGTAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
20 26 0.37
21 44 0.63
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.55
Consensus pattern (21 bp):
TAATTTTGATAATCTTTTATG
Found at i:1600869 original size:20 final size:20
Alignment explanation
Indices: 1600846--1600942 Score: 76
Period size: 20 Copynumber: 4.8 Consensus size: 20
1600836 TTAATATAGC
1600846 TTTGTAATAATTTTATAACA
1 TTTGTAATAATTTTATAACA
1600866 TTTGTAATAATTTGGT-TAAC-
1 TTTGTAATAATTT--TATAACA
* * *
1600886 TTTTTATATAA--TTCTAGCA
1 TTTGTA-ATAATTTTATAACA
**
1600905 TTTGTAATAATTTTGATAATT
1 TTTGTAATAATTTT-ATAACA
*
1600926 TTTGTTATAATTTTATA
1 TTTGTAATAATTTTATA
1600943 CCAAAATATA
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
17 1 0.02
18 7 0.11
19 6 0.10
20 23 0.38
21 23 0.38
22 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTGTAATAATTTTATAACA
Found at i:1601632 original size:3 final size:3
Alignment explanation
Indices: 1601624--1601650 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1601614 TTGATATAAA
1601624 AGC AGC AGC AGC AGC AGC AGC AGC AGC
1 AGC AGC AGC AGC AGC AGC AGC AGC AGC
1601651 GGCAAGGTCT
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:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:1604116 original size:15 final size:14
Alignment explanation
Indices: 1604083--1604115 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1604073 AGAAGAAGCC
1604083 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
1604097 TTTTTCCTTTT-TTT
1 TTTTT-CTTTTCTTT
1604111 TTTTT
1 TTTTT
1604116 TGCCTGTTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:1604635 original size:3 final size:3
Alignment explanation
Indices: 1604627--1604662 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1604617 CCCTAGATAT
1604627 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1604663 TATGTGGCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1606233 original size:2 final size:2
Alignment explanation
Indices: 1606226--1606257 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1606216 TGAGTTATGC
1606226 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
1606258 AGAAATGACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1607018 original size:11 final size:11
Alignment explanation
Indices: 1606980--1607016 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1606970 ATTCCAATTT
1606980 TTTTTACTTTTC
1 TTTTT-CTTTTC
1606992 TTTTTCTTTTC
1 TTTTTCTTTTC
1607003 TTTTT-TTTT-
1 TTTTTCTTTTC
1607012 TTTTT
1 TTTTT
1607017 TTGGAACGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.20
10 4 0.16
11 11 0.44
12 5 0.20
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTCTTTTC
Found at i:1607342 original size:21 final size:21
Alignment explanation
Indices: 1607325--1607365 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1607315 AATACATTTA
1607325 AAATAAAAATAATAACATGTT
1 AAATAAAAATAATAACATGTT
*
1607346 AAATAAAGATAATAACATGT
1 AAATAAAAATAATAACATGT
1607366 ACAATCTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (21 bp):
AAATAAAAATAATAACATGTT
Found at i:1612898 original size:12 final size:11
Alignment explanation
Indices: 1612849--1612898 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1612839 TTATATGTTG
1612849 ATTTTT-TTTA
1 ATTTTTATTTA
* *
1612859 ATTTGTCATTTC
1 ATTT-TTATTTA
1612871 A-TTTTATTTA
1 ATTTTTATTTA
1612881 ATTTTTATTTA
1 ATTTTTATTTA
1612892 TATTTTT
1 -ATTTTT
1612899 TAAAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 10 0.31
11 12 0.38
12 10 0.31
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (11 bp):
ATTTTTATTTA
Found at i:1613044 original size:16 final size:17
Alignment explanation
Indices: 1613025--1613056 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1613015 TGTTAAAAAA
1613025 TAAA-ATAAAAATTATG
1 TAAATATAAAAATTATG
1613041 TAAATATAAAAATTAT
1 TAAATATAAAAATTAT
1613057 TTTGAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
TAAATATAAAAATTATG
Found at i:1613863 original size:18 final size:18
Alignment explanation
Indices: 1613840--1613979 Score: 51
Period size: 18 Copynumber: 8.3 Consensus size: 18
1613830 TTAAATTATG
1613840 TAATATTAAATATTATTA
1 TAATATTAAATATTATTA
* * *
1613858 TAATA-TGAGTA-TAATA
1 TAATATTAAATATTATTA
*
1613874 TAA-A--AAATAATTAAAATA
1 TAATATTAAAT-ATT--ATTA
1613892 TAATA-TAAATA-TATTA
1 TAATATTAAATATTATTA
1613908 -ATATATTAAA-ATT-TATA
1 TA-ATATTAAATATTAT-TA
1613925 TAATA-T-AA-ATTATTA
1 TAATATTAAATATTATTA
* *
1613940 AAATATTAAAAATTA-TA
1 TAATATTAAATATTATTA
*
1613957 TAAATATAAAATATT-TTA
1 T-AATATTAAATATTATTA
1613975 -AATAT
1 TAATAT
1613980 AATTATAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 36
0.67 0.07 0.26
Matches are distributed among these distances:
14 2 0.02
15 14 0.15
16 24 0.25
17 18 0.19
18 31 0.33
19 2 0.02
20 4 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (18 bp):
TAATATTAAATATTATTA
Found at i:1613901 original size:11 final size:11
Alignment explanation
Indices: 1613856--1614020 Score: 68
Period size: 11 Copynumber: 15.4 Consensus size: 11
1613846 TAAATATTAT
* *
1613856 TATAATATGAG
1 TATAATATAAA
1613867 TATAATATAAAA
1 TATAATAT-AAA
*
1613879 AATAAT-TAAAA
1 TATAATAT-AAA
1613890 TATAATATAAA
1 TATAATATAAA
1613901 TAT-AT-TAATA
1 TATAATATAA-A
* **
1613911 TATTAAAATTTA
1 TA-TAATATAAA
1613923 TATAATATAAA
1 TATAATATAAA
*
1613934 T-TATTA-AAA
1 TATAATATAAA
1613943 TATTAA-A-AATTA
1 TA-TAATATAA--A
1613955 TATAAATATAAA
1 TAT-AATATAAA
* *
1613967 -ATATTTTAAA
1 TATAATATAAA
1613977 TATAATTATAAA
1 TATAA-TATAAA
1613989 -AT-A-ATAAA
1 TATAATATAAA
1613997 -AT-ATATAAA
1 TATAATATAAA
*
1614006 TATAACATAAA
1 TATAATATAAA
1614017 TATA
1 TATA
1614021 TAAATTATTA
Statistics
Matches: 119, Mismatches: 17, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
8 8 0.07
9 12 0.10
10 21 0.18
11 52 0.44
12 22 0.18
13 2 0.02
14 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1613931 original size:33 final size:33
Alignment explanation
Indices: 1613889--1614001 Score: 129
Period size: 32 Copynumber: 3.3 Consensus size: 33
1613879 AATAATTAAA
* *
1613889 ATATAATATAAATATATTAATATATTAAAATTT
1 ATATAATATAAATATATTAAAATATTAAAAATT
1613922 ATATAATATAAAT-TATTAAAATATTAAAAATT
1 ATATAATATAAATATATTAAAATATTAAAAATT
* *
1613954 ATATAAATATAAAATATTTTAAATATAATTATAAAATA
1 ATAT-AATAT-AAATATATTAAA-AT-ATTA-AAAATT
*
1613992 ATAAAATATA
1 ATATAATATA
1614002 TAAATATAAC
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
32 21 0.30
33 18 0.26
34 4 0.06
35 6 0.09
36 3 0.04
37 9 0.13
38 8 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (33 bp):
ATATAATATAAATATATTAAAATATTAAAAATT
Found at i:1613940 original size:24 final size:25
Alignment explanation
Indices: 1613867--1614032 Score: 92
Period size: 23 Copynumber: 7.0 Consensus size: 25
1613857 ATAATATGAG
*
1613867 TATAATATAA-A-AAATAATTAAAA
1 TATAATATAATATAAATTATTAAAA
1613890 TATAATATAAATATATTAATATATTAAAA
1 TATAATAT-AATATA--AAT-TATTAAAA
*
1613919 T-TTATATAATATAAATTATTAAAA
1 TATAATATAATATAAATTATTAAAA
* *
1613943 TATTAAAAATTATATAAA-TA-TAAAA
1 TA-T-AATATAATATAAATTATTAAAA
**
1613968 TATTTTA-AATAT-AATTA-TAAAA
1 TATAATATAATATAAATTATTAAAA
*
1613990 TAATAAAAT-ATATAAA-TA-T--AA
1 T-ATAATATAATATAAATTATTAAAA
*
1614011 CATAA-AT-ATATAAATTATTAAA
1 TATAATATAATATAAATTATTAAA
1614033 CCTATCAACT
Statistics
Matches: 113, Mismatches: 13, Indels: 34
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.08
20 6 0.05
21 5 0.04
22 12 0.11
23 20 0.18
24 14 0.12
25 11 0.10
26 4 0.04
27 16 0.14
28 8 0.07
29 8 0.07
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.39
Consensus pattern (25 bp):
TATAATATAATATAAATTATTAAAA
Found at i:1613946 original size:32 final size:32
Alignment explanation
Indices: 1613889--1613971 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 32
1613879 AATAATTAAA
* *
1613889 ATATAATATAAATATATTAATATATTAAAATTT
1 ATATAATATAAAT-TATTAAAATATTAAAAATT
1613922 ATATAATATAAATTATTAAAATATTAAAAATT
1 ATATAATATAAATTATTAAAATATTAAAAATT
*
1613954 ATATAAATATAAAATATT
1 ATAT-AATATAAATTATT
1613972 TTAAATATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
32 21 0.46
33 25 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (32 bp):
ATATAATATAAATTATTAAAATATTAAAAATT
Found at i:1613949 original size:8 final size:8
Alignment explanation
Indices: 1613877--1614005 Score: 55
Period size: 8 Copynumber: 16.4 Consensus size: 8
1613867 TATAATATAA
1613877 AAAATAATT
1 AAAAT-ATT
1613886 AAAATA-T
1 AAAATATT
1613893 --AATA-T
1 AAAATATT
1613898 AAATATATT
1 AAA-ATATT
*
1613907 AATATATT
1 AAAATATT
1613915 AAAAT-TT
1 AAAATATT
1613922 ATATAATA-T
1 A-A-AATATT
*
1613931 AAATTATT
1 AAAATATT
1613939 AAAATATT
1 AAAATATT
1613947 AAAA-ATT
1 AAAATATT
1613954 ATATAA-ATAT
1 A-A-AATAT-T
1613964 AAAATATTT
1 AAAATA-TT
*
1613973 TAAATA-T
1 AAAATATT
*
1613980 -AATTA-T
1 AAAATATT
*
1613986 AAAATAAT
1 AAAATATT
1613994 AAAATATAT
1 AAAATAT-T
1614003 AAA
1 AAA
1614006 TATAACATAA
Statistics
Matches: 96, Mismatches: 8, Indels: 32
0.71 0.06 0.24
Matches are distributed among these distances:
5 5 0.05
6 5 0.05
7 17 0.18
8 37 0.39
9 29 0.30
10 3 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAAATATT
Found at i:1613975 original size:27 final size:29
Alignment explanation
Indices: 1613867--1614010 Score: 95
Period size: 29 Copynumber: 4.9 Consensus size: 29
1613857 ATAATATGAG
* * *
1613867 TATAATATAAAAAATAATTAAA-AT-ATAA
1 TATAA-ATATAAAATATTTAAATATAATTA
*
1613895 TATAAATATATTAATATATTAAA-AT--TTA
1 TATAAATATA-AAATAT-TTAAATATAATTA
* *
1613923 TAT-AATATAAATTATTAAAATATTAAAAATTA
1 TATAAATATAAAATATTTAAATA-T---AATTA
1613955 TATAAATATAAAATATTTTAAATATAATTA
1 TATAAATATAAAATA-TTTAAATATAATTA
*
1613985 TA-AAATAATAAAATATATAAATATAA
1 TATAAAT-ATAAAATATTTAAATATAA
1614011 CATAAATATA
Statistics
Matches: 94, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
25 4 0.04
26 5 0.05
27 11 0.12
28 14 0.15
29 21 0.22
30 15 0.16
32 6 0.06
33 11 0.12
34 7 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TATAAATATAAAATATTTAAATATAATTA
Found at i:1614006 original size:8 final size:8
Alignment explanation
Indices: 1613894--1614025 Score: 69
Period size: 8 Copynumber: 16.0 Consensus size: 8
1613884 TTAAAATATA
1613894 ATATAAAT
1 ATATAAAT
*
1613902 ATATTAAT
1 ATATAAAT
1613910 ATATTAAA-
1 ATA-TAAAT
* *
1613918 ATTTATAT
1 ATATAAAT
1613926 AATATAAAT
1 -ATATAAAT
1613935 -TATTAAAAT
1 ATA-T-AAAT
*
1613944 ATTAAAAATT
1 A-TATAAA-T
1613954 ATATAAAT
1 ATATAAAT
1613962 ATA-AAAT
1 ATATAAAT
* *
1613969 ATTTTAA-
1 ATATAAAT
*
1613976 ATATAATT
1 ATATAAAT
1613984 ATA-AAAT
1 ATATAAAT
1613991 A-ATAAAAT
1 ATAT-AAAT
1613999 ATATAAAT
1 ATATAAAT
1614007 ATAACATAAAT
1 AT---ATAAAT
1614018 ATATAAAT
1 ATATAAAT
1614026 TATTAAACCT
Statistics
Matches: 94, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
6 1 0.01
7 19 0.20
8 39 0.41
9 23 0.24
10 2 0.02
11 10 0.11
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:1614017 original size:27 final size:26
Alignment explanation
Indices: 1613922--1614032 Score: 107
Period size: 27 Copynumber: 4.0 Consensus size: 26
1613912 ATTAAAATTT
*
1613922 ATATAATATAAATTATTAAAATATTAA
1 ATATAATATAAA-TAATAAAATATTAA
* *
1613949 AAATTATATAAAT-ATAAAATATTTTAA
1 ATATAATATAAATAATAAAATA--TTAA
1613976 ATATAATTATAAAATAATAAAATATATAA
1 ATATAA-TAT-AAATAATAAAATAT-TAA
* *
1614005 ATATAACATAAATATATAAATTATTAA
1 ATATAATATAAATA-ATAAAATATTAA
1614032 A
1 A
1614033 CCTATCAACT
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
25 7 0.10
26 1 0.01
27 27 0.39
28 14 0.20
29 13 0.19
30 8 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (26 bp):
ATATAATATAAATAATAAAATATTAA
Found at i:1614022 original size:19 final size:18
Alignment explanation
Indices: 1613983--1614025 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
1613973 TAAATATAAT
*
1613983 TATAAA-ATAATAAAATA
1 TATAAATATAACAAAATA
1614000 TATAAATATAACATAAATA
1 TATAAATATAACA-AAATA
1614019 TATAAAT
1 TATAAAT
1614026 TATTAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 12 0.52
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TATAAATATAACAAAATA
Found at i:1614710 original size:9 final size:9
Alignment explanation
Indices: 1614698--1614735 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1614688 ATAATAATAA
1614698 TTTTATTAT
1 TTTTATTAT
1614707 TTTTATTAT
1 TTTTATTAT
*
1614716 TATTATTAT
1 TTTTATTAT
*
1614725 TCTT-TTAT
1 TTTTATTAT
1614733 TTT
1 TTT
1614736 AGTCTTAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 6 0.23
9 20 0.77
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTATTAT
Found at i:1615767 original size:2 final size:2
Alignment explanation
Indices: 1615762--1615804 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1615752 TGGACTACTC
1615762 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
1615804 T
1 T
1615805 TCTGTTTGTT
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:1616618 original size:55 final size:55
Alignment explanation
Indices: 1616534--1616644 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
1616524 ATCATGGTTG
1616534 ATCTTTGCTAATACCAGAAGATTTTAGAGGTTTGGTCTTGAATCTGCCTTAGTTT
1 ATCTTTGCTAATACCAGAAGATTTTAGAGGTTTGGTCTTGAATCTGCCTTAGTTT
1616589 ATCTTTGCTAATACCAGAAGATTTTAGAGGTTTGGTCTTGAATCTGCCTTAGTTT
1 ATCTTTGCTAATACCAGAAGATTTTAGAGGTTTGGTCTTGAATCTGCCTTAGTTT
1616644 A
1 A
1616645 AGTATTCACG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.41
Consensus pattern (55 bp):
ATCTTTGCTAATACCAGAAGATTTTAGAGGTTTGGTCTTGAATCTGCCTTAGTTT
Found at i:1628089 original size:26 final size:27
Alignment explanation
Indices: 1628047--1628115 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
1628037 GATTCATTTG
1628047 AATAA-AAATATTTTTAAA-A-TTATATA
1 AATAATAAATA-TTTTAAATATTTA-ATA
*
1628073 AATAATAAATATATTAAATATTTAATA
1 AATAATAAATATTTTAAATATTTAATA
*
1628100 AA-AATATATATTTTAA
1 AATAATAAATATTTTAA
1628116 TTTAATAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 23 0.62
27 11 0.30
28 3 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AATAATAAATATTTTAAATATTTAATA
Found at i:1633755 original size:28 final size:27
Alignment explanation
Indices: 1633715--1633788 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 27
1633705 TTATTAATTC
*
1633715 TAAATTAAAAAATTTTAAATTTCAACAT
1 TAAATT-AAAAATTTTAAATTTCAACAA
* *
1633743 TAAAATTAAAAA-TTTAATATTTTATCAA
1 T-AAATTAAAAATTTTAA-ATTTCAACAA
*
1633771 TAAATTAAAAATTATAAA
1 TAAATTAAAAATTTTAAA
1633789 AATATATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 16 0.41
28 18 0.46
29 5 0.13
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (27 bp):
TAAATTAAAAATTTTAAATTTCAACAA
Found at i:1634375 original size:15 final size:15
Alignment explanation
Indices: 1634342--1634415 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
1634332 TTTTGTAAAT
**
1634342 ATTTTATATTTATTT
1 ATTTTATATTTATAA
*
1634357 ATTTTATATTTAAAA
1 ATTTTATATTTATAA
*
1634372 ATTTTAAATTT-TAA
1 ATTTTATATTTATAA
*
1634386 ATATTTATTATTTTTAA
1 AT-TTTA-TATTTATAA
1634403 A-TTTATATTTATA
1 ATTTTATATTTATA
1634416 TATAAACATA
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
14 11 0.22
15 30 0.61
16 4 0.08
17 4 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTTATATTTATAA
Found at i:1634531 original size:12 final size:12
Alignment explanation
Indices: 1634514--1634548 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
1634504 TATTAAAAAA
1634514 TTAAAAATATAT
1 TTAAAAATATAT
1634526 TTAAAAAATATAT
1 TT-AAAAATATAT
1634539 TTAAAAATAT
1 TTAAAAATAT
1634549 TGATAAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TTAAAAATATAT
Found at i:1641868 original size:52 final size:52
Alignment explanation
Indices: 1641782--1641884 Score: 179
Period size: 52 Copynumber: 2.0 Consensus size: 52
1641772 TATACCACAA
* * *
1641782 TATCAGATATTATTCTCTTTGAACTCATAGGCTCTCAAGCTCTTATTACCTG
1 TATCAGATATAATTCTCTTTGAACCCATAAGCTCTCAAGCTCTTATTACCTG
1641834 TATCAGATATAATTCTCTTTGAACCCATAAGCTCTCAAGCTCTTATTACCT
1 TATCAGATATAATTCTCTTTGAACCCATAAGCTCTCAAGCTCTTATTACCT
1641885 CTCAGGGTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (52 bp):
TATCAGATATAATTCTCTTTGAACCCATAAGCTCTCAAGCTCTTATTACCTG
Found at i:1643354 original size:23 final size:25
Alignment explanation
Indices: 1643313--1643359 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
1643303 ATCATTAAAA
* *
1643313 TTTTTAAGATAATAGTAAT-TAATT
1 TTTTTAAGATAAAAATAATATAATT
1643337 TTTTTAA-ATAAAAATAATATAAT
1 TTTTTAAGATAAAAATAATATAAT
1643360 ATATTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTTTAAGATAAAAATAATATAATT
Found at i:1652335 original size:11 final size:11
Alignment explanation
Indices: 1652304--1652336 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1652294 TTAGATATTT
1652304 TTATAAGTTAAA
1 TTATAA-TTAAA
1652316 TTA-AATTAAA
1 TTATAATTAAA
1652326 TTATAATTAAA
1 TTATAATTAAA
1652337 AAAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.40
11 9 0.45
12 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
TTATAATTAAA
Found at i:1652345 original size:21 final size:22
Alignment explanation
Indices: 1652304--1652348 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1652294 TTAGATATTT
*
1652304 TTATAAGTTAAATTAAATTAAA
1 TTATAAGTTAAATAAAATTAAA
1652326 TTATAA-TTAAA-AAAATTTAAA
1 TTATAAGTTAAATAAAA-TTAAA
1652347 TT
1 TT
1652349 TTTTAAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 12 0.57
22 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTATAAGTTAAATAAAATTAAA
Found at i:1652766 original size:34 final size:34
Alignment explanation
Indices: 1652714--1652914 Score: 251
Period size: 34 Copynumber: 5.9 Consensus size: 34
1652704 GCGCCGGGGT
* * *
1652714 GATTTAGTAGTTTACCATTGTTAATTAAATGGGT
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
* * * *
1652748 GATTTGGTGGTTTGCCATTGTTGACTAAAT-GAA
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
*
1652781 GATTTGGTAGCTTACCATTGTTGATTAAATGGGA
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
* * * *
1652815 AATTTGGTAGCTTACCATTATTGATTAAATGGGT
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
* *
1652849 GATTTGGTGGTTTACCATTGTTGACTAAATGGGA
1 GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
* *
1652883 GATTTGGTAGGTTGCCATTGTTGATTAAATGG
1 GATTTGGTAGTTTACCATTGTTGATTAAATGG
1652915 TGGTTTTTAC
Statistics
Matches: 141, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
33 27 0.19
34 114 0.81
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
GATTTGGTAGTTTACCATTGTTGATTAAATGGGA
Found at i:1653274 original size:19 final size:19
Alignment explanation
Indices: 1653218--1653280 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1653208 TGGTTGTCGA
**
1653218 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
1653237 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
1653256 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
1653275 GTTACT
1 GGTACT
1653281 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:1657415 original size:34 final size:34
Alignment explanation
Indices: 1657346--1657563 Score: 269
Period size: 34 Copynumber: 6.5 Consensus size: 34
1657336 AAGTGGGAGA
* *
1657346 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * * *
1657379 ATTGTTAATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
1657413 ATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* *
1657446 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
1657480 ATTATTGATTAAATGGGTGATTTGGTGGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
* * *
1657514 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
1657548 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
1657564 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
33 40 0.25
34 117 0.75
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGTTTACC
Found at i:1657457 original size:67 final size:66
Alignment explanation
Indices: 1657346--1657565 Score: 287
Period size: 67 Copynumber: 3.3 Consensus size: 66
1657336 AAGTGGGAGA
* * *
1657346 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTAATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGTGG-TTG
1657411 CC
65 CC
* ** * * * *
1657413 ATTGTTGACTAAATGAAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTTG
1657478 CC
65 CC
* * *
1657480 ATTATTGATTAAATGGGTGATTTGGTGGTTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGT-GGTT
1657545 GCC
64 GCC
1657548 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1657566 GTTTTTACCA
Statistics
Matches: 130, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
67 71 0.55
68 59 0.45
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (66 bp):
ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGGAGATTTGGTGGTTGC
C
Found at i:1657496 original size:101 final size:101
Alignment explanation
Indices: 1657346--1657565 Score: 336
Period size: 101 Copynumber: 2.2 Consensus size: 101
1657336 AAGTGGGAGA
* * *
1657346 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTAATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTATTAATTAAATGGGTGATTTGGTGGTTTA
1657411 CCATTGTTGACTAAAT-GAAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
* *
1657446 ATTGTTGATTAAATGG-GAAATTTGGTAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGTT
1 ATTGTTGATTAAATGGTG--ATTTAGTAGCTTACCATTATTAATTAAATGGGTGATTTGGTGGTT
* * *
1657510 TACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
64 TACCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
1657548 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
1657566 GTTTTTACCA
Statistics
Matches: 108, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
99 1 0.01
100 16 0.15
101 58 0.54
102 32 0.30
103 1 0.01
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGTGATTTAGTAGCTTACCATTATTAATTAAATGGGTGATTTGGTGGTTTA
CCATTGTTGACTAAATGGAAGATTTGGTAGCTTACC
Found at i:1665466 original size:24 final size:25
Alignment explanation
Indices: 1665405--1665455 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
1665395 CCATGTAAGT
*
1665405 TCCAAATTATGATCCTTTTTTCACC
1 TCCAAATTGTGATCCTTTTTTCACC
1665430 TCCAAATTGTGATCCTTTTTTCACC
1 TCCAAATTGTGATCCTTTTTTCACC
1665455 T
1 T
1665456 TTCAATGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.27, G:0.06, T:0.45
Consensus pattern (25 bp):
TCCAAATTGTGATCCTTTTTTCACC
Found at i:1671020 original size:14 final size:14
Alignment explanation
Indices: 1671001--1671038 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1670991 AGATCAAATT
1671001 AATTTAAATTTAAA
1 AATTTAAATTTAAA
*
1671015 AATTTATATTT-AA
1 AATTTAAATTTAAA
1671028 AATTT-AATTTA
1 AATTTAAATTTA
1671039 TTAGGTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 4 0.19
13 7 0.33
14 10 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTAAATTTAAA
Found at i:1672118 original size:15 final size:15
Alignment explanation
Indices: 1672082--1672135 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
1672072 TTTGAATTTG
1672082 AATTAATTT-AAA-T
1 AATTAATTTAAAATT
* *
1672095 AATAAATTTATAATT
1 AATTAATTTAAAATT
*
1672110 AATTTATTTAAAATT
1 AATTAATTTAAAATT
1672125 AATTAATTTAA
1 AATTAATTTAA
1672136 GTATTATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
13 8 0.24
14 2 0.06
15 23 0.70
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATTAATTTAAAATT
Found at i:1672249 original size:29 final size:33
Alignment explanation
Indices: 1672208--1672270 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 33
1672198 ACATAATTTG
*
1672208 ATTAATCTGAATA-AAAA-AT-TT-AAATTTAA
1 ATTAATCTCAATATAAAATATCTTAAAATTTAA
*
1672237 ATTAATGTCAATATAAAATATCTTAAAATTTAA
1 ATTAATCTCAATATAAAATATCTTAAAATTTAA
1672270 A
1 A
1672271 AAATTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 11 0.39
30 4 0.14
31 2 0.07
32 2 0.07
33 9 0.32
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
ATTAATCTCAATATAAAATATCTTAAAATTTAA
Found at i:1672308 original size:26 final size:26
Alignment explanation
Indices: 1672263--1672322 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
1672253 AATATCTTAA
*
1672263 AATTTAAAAAATTGAGATTT-AAAAT
1 AATTTAAAAAATTGAAATTTAAAAAT
1672288 AATTTAAAAAAGTAT-AAATTTAAAAAT
1 AATTTAAAAAA-T-TGAAATTTAAAAAT
*
1672315 AATCTAAA
1 AATTTAAA
1672323 TTTTTTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 11 0.37
26 6 0.20
27 13 0.43
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (26 bp):
AATTTAAAAAATTGAAATTTAAAAAT
Found at i:1672814 original size:13 final size:13
Alignment explanation
Indices: 1672796--1672833 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1672786 GACATAAAAA
1672796 ATAATAAAAATAT
1 ATAATAAAAATAT
*
1672809 ATAATAAAAAAAT
1 ATAATAAAAATAT
1672822 A-AATATAAAATA
1 ATAATA-AAAATA
1672834 AATACATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
ATAATAAAAATAT
Found at i:1672821 original size:15 final size:15
Alignment explanation
Indices: 1672789--1672837 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
1672779 TAAACATGAC
*
1672789 ATAAAAAATAATAAAA
1 ATAAATAATAA-AAAA
*
1672805 ATATATAATAAAAAA
1 ATAAATAATAAAAAA
1672820 ATAAAT-ATAAAATAA
1 ATAAATAATAAAA-AA
1672835 ATA
1 ATA
1672838 CATTAGCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 6 0.21
15 14 0.48
16 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAATAATAAAAAA
Found at i:1672895 original size:32 final size:33
Alignment explanation
Indices: 1672824--1672904 Score: 92
Period size: 32 Copynumber: 2.4 Consensus size: 33
1672814 AAAAAAATAA
*
1672824 ATATAAAATAAATACATTAGCATATTAAAATTC
1 ATATAAAATAAATACATTAACATATTAAAATTC
* * * *
1672857 ACATAAAATAAAT-TATTAATATATTAAAATTT
1 ATATAAAATAAATACATTAACATATTAAAATTC
1672889 ATATAAATATATAATA
1 ATATAAA-ATA-AATA
1672905 TTTTAAATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 21 0.54
33 15 0.38
34 3 0.08
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (33 bp):
ATATAAAATAAATACATTAACATATTAAAATTC
Found at i:1672920 original size:27 final size:27
Alignment explanation
Indices: 1672864--1672921 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
1672854 TTCACATAAA
*
1672864 ATAAATTATTAATATATTAAAATTTAT
1 ATAAATTATTAATATATTAAAATTAAT
*
1672891 ATAAA-TATATAATAT-TTTAAATTAATT
1 ATAAATTAT-TAATATATTAAAATTAA-T
1672918 ATAA
1 ATAA
1672922 TAAAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.41
27 16 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAAATTATTAATATATTAAAATTAAT
Found at i:1673532 original size:27 final size:27
Alignment explanation
Indices: 1673482--1673555 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1673472 AAACAACATG
*
1673482 CCACCATTTTTGACAAATAAAAAGAAA
1 CCACCATTTTTGACAAACAAAAAGAAA
* * * *
1673509 CCACCATTTTTTACATACACAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGAAA
**
1673536 CCATAATTTTTGACAAACAA
1 CCACCATTTTTGACAAACAA
1673556 TGGGTGGTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGAAA
Found at i:1675469 original size:21 final size:22
Alignment explanation
Indices: 1675431--1675476 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1675421 ATCTGTTGAA
* **
1675431 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1675452 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1675474 ACT
1 ACT
1675477 TGTCTAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1677963 original size:13 final size:13
Alignment explanation
Indices: 1677942--1677975 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
1677932 GAGGAATACA
*
1677942 AGAGAGGATGCTTG
1 AGAG-GGATACTTG
1677956 AGAGGGATACTTG
1 AGAGGGATACTTG
1677969 AGAGGGA
1 AGAGGGA
1677976 GGAGGGAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.32, C:0.06, G:0.44, T:0.18
Consensus pattern (13 bp):
AGAGGGATACTTG
Found at i:1678101 original size:27 final size:27
Alignment explanation
Indices: 1678051--1678124 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
1678041 AAACAACATG
* *
1678051 CTACCATTTTTGATAAATAAAAAGAAA
1 CTACCATTTTTGACAAACAAAAAGAAA
* *
1678078 CTACCATTTTTGACAAACACAAAGTAA
1 CTACCATTTTTGACAAACAAAAAGAAA
* **
1678105 CCATAATTTTTGACAAACAA
1 CTACCATTTTTGACAAACAA
1678125 TGAGTGGTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.47, C:0.18, G:0.07, T:0.28
Consensus pattern (27 bp):
CTACCATTTTTGACAAACAAAAAGAAA
Found at i:1683444 original size:16 final size:16
Alignment explanation
Indices: 1683425--1683517 Score: 73
Period size: 16 Copynumber: 5.8 Consensus size: 16
1683415 ACTTTTTATT
1683425 ATTTAAATTTAAAATA
1 ATTTAAATTTAAAATA
**
1683441 ATTTAAA-TTAATGTA
1 ATTTAAATTTAAAATA
* * *
1683456 AATTGAATTCGAAAA-A
1 ATTTAAATT-TAAAATA
* *
1683472 ATTTAAATATAAAAAA
1 ATTTAAATTTAAAATA
* *
1683488 ATTTAAATTTAAATTT
1 ATTTAAATTTAAAATA
1683504 ATTTAAATATTAAA
1 ATTTAAAT-TTAAA
1683518 TTTATAATTA
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
15 15 0.26
16 36 0.62
17 7 0.12
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (16 bp):
ATTTAAATTTAAAATA
Found at i:1683495 original size:6 final size:6
Alignment explanation
Indices: 1683486--1683526 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
1683476 AAATATAAAA
1683486 AAATTT AAATTT AAATTT --ATTT AAATATT AAATTT ATAATT
1 AAATTT AAATTT AAATTT AAATTT AAAT-TT AAATTT A-AATT
1683527 AATTTATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
4 4 0.13
6 17 0.55
7 10 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AAATTT
Found at i:1683518 original size:17 final size:16
Alignment explanation
Indices: 1683488--1683522 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 16
1683478 ATATAAAAAA
1683488 ATTTAAATTTAAATTT
1 ATTTAAATTTAAATTT
1683504 ATTTAAATATTAAATTT
1 ATTTAAAT-TTAAATTT
1683521 AT
1 AT
1683523 AATTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:1683520 original size:23 final size:23
Alignment explanation
Indices: 1683486--1683532 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
1683476 AAATATAAAA
*
1683486 AAATTTAAATTTA-AATTTATTT
1 AAATTTAAATTTATAATTAATTT
1683508 AAATATTAAATTTATAATTAATTT
1 AAAT-TTAAATTTATAATTAATTT
1683532 A
1 A
1683533 TTTAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.18
23 9 0.41
24 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTAAATTTATAATTAATTT
Found at i:1683528 original size:29 final size:26
Alignment explanation
Indices: 1683481--1683545 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 26
1683471 AATTTAAATA
1683481 TAAAA-AAATTTAAATTTAAATTTATT
1 TAAAATAAATTTAAATTT-AATTTATT
1683507 TAAATATTAAATTTATAA-TTAATTTATT
1 TAAA-A-TAAATTTA-AATTTAATTTATT
1683535 TAAAATAAATT
1 TAAAATAAATT
1683546 AATTTGAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 10 0.29
27 2 0.06
28 12 0.34
29 9 0.26
30 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAAATAAATTTAAATTTAATTTATT
Found at i:1683960 original size:16 final size:16
Alignment explanation
Indices: 1683939--1683983 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
1683929 TATGACTCAT
1683939 ATTTAAAATAATTTAA
1 ATTTAAAATAATTTAA
1683955 ATTTAAAATAATTTAA
1 ATTTAAAATAATTTAA
* *
1683971 ATCTAAATTAATT
1 ATTTAAAATAATT
1683984 CGAATAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTAAAATAATTTAA
Found at i:1684012 original size:15 final size:17
Alignment explanation
Indices: 1683976--1684017 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
1683966 TTTAAATCTA
1683976 AATTAATTCGAATAATT
1 AATTAATTCGAATAATT
*
1683993 GATTAATTC-AA-AATT
1 AATTAATTCGAATAATT
1684008 AATTAATTCG
1 AATTAATTCG
1684018 TATGTTGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 12 0.55
16 2 0.09
17 8 0.36
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (17 bp):
AATTAATTCGAATAATT
Found at i:1685736 original size:15 final size:16
Alignment explanation
Indices: 1685715--1685754 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1685705 CCTTTAGTGT
1685715 AATAAATTTAA-TTTA
1 AATAAATTTAATTTTA
* *
1685730 TATAAATTAAATTTTA
1 AATAAATTTAATTTTA
1685746 AATAAATTT
1 AATAAATTT
1685755 TTTAATTTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAATTTAATTTTA
Found at i:1703065 original size:2 final size:2
Alignment explanation
Indices: 1703058--1703082 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1703048 ATGTTTAGTT
1703058 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 A
1703083 TGTACAAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1706158 original size:16 final size:16
Alignment explanation
Indices: 1706139--1706171 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1706129 AAAATTTGCA
1706139 TTGTGCAAA-ATGTGAT
1 TTGTG-AAATATGTGAT
1706155 TTGTGAAATATGTGAT
1 TTGTGAAATATGTGAT
1706171 T
1 T
1706172 ATTGTTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.42
Consensus pattern (16 bp):
TTGTGAAATATGTGAT
Found at i:1706402 original size:38 final size:35
Alignment explanation
Indices: 1706318--1706419 Score: 100
Period size: 38 Copynumber: 2.8 Consensus size: 35
1706308 TTTTGAACTG
* *
1706318 TGTCATCGGTTAAGAATAGT-GATTTTTGTTTCAAA
1 TGTCACCGGTTAAGAATAGTAG-TTTTTATTTCAAA
1706353 TCGTACTACCGGTTAAGAATAGTAGTTTTTATTTCAACCTA
1 T-GT-C-ACCGGTTAAGAATAGTAGTTTTTATTTCAA---A
*
1706394 TGTCACCGG-TAAAAATAGTAGTTTTT
1 TGTCACCGGTTAAGAATAGTAGTTTTT
1706420 GTTTTGAACC
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
35 1 0.02
36 2 0.04
37 17 0.30
38 31 0.54
39 2 0.04
40 2 0.04
41 2 0.04
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (35 bp):
TGTCACCGGTTAAGAATAGTAGTTTTTATTTCAAA
Found at i:1706490 original size:38 final size:38
Alignment explanation
Indices: 1706403--1706498 Score: 111
Period size: 38 Copynumber: 2.5 Consensus size: 38
1706393 ATGTCACCGG
* *
1706403 TAAAAATAGTAGTTTTTGTTTTGAACCGTATCACCGAT
1 TAAAAATAGTAGTTTTTGTTTTGAACCGTACCACCGAC
* * * ** *
1706441 TAAAAACAGTAGTTTTTGTTTTGAATCGTGCCATTGGC
1 TAAAAATAGTAGTTTTTGTTTTGAACCGTACCACCGAC
*
1706479 TGAAAATAGTAGTTTTTGTT
1 TAAAAATAGTAGTTTTTGTT
1706499 CTTACCTATG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.42
Consensus pattern (38 bp):
TAAAAATAGTAGTTTTTGTTTTGAACCGTACCACCGAC
Found at i:1706672 original size:13 final size:14
Alignment explanation
Indices: 1706654--1706691 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 14
1706644 TATGAGATTA
1706654 TCAAATTTTATT-T
1 TCAAATTTTATTGT
1706667 TCAAATTATTATTGT
1 TCAAATT-TTATTGT
1706682 TCATAATTTT
1 TCA-AATTTT
1706692 GATCTAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.32
14 5 0.23
15 6 0.27
16 4 0.18
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.58
Consensus pattern (14 bp):
TCAAATTTTATTGT
Found at i:1708151 original size:50 final size:50
Alignment explanation
Indices: 1708097--1708299 Score: 298
Period size: 50 Copynumber: 4.1 Consensus size: 50
1708087 AAGTGATTTA
* * * *
1708097 ACTATTTTTCATCAACCTTTGACAATCGAGATAGGTGACCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTGACCGTAATTGTTG
* *
1708147 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTGACCGTAATTGTTG
* * * *
1708197 ACTATTCTTCACCAACCTTTAACAATCGAGAGGGGTGGCCATAATTGTCG
1 ACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTGACCGTAATTGTTG
* *
1708247 ACTATTTTTCACCAACCTTTAACAATCAAGAGAGGTGACCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTGACCGTAATTGTTG
1708297 ACT
1 ACT
1708300 TTAAGCATCT
Statistics
Matches: 139, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 139 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (50 bp):
ACTATTCTTCACCAACCTTTAACAATCGAGAGAGGTGACCGTAATTGTTG
Found at i:1708583 original size:19 final size:19
Alignment explanation
Indices: 1708539--1708584 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1708529 TGGTTGTTGA
*
1708539 GGTACTGTTCACATATACG
1 GGTACTGTTCACACATACG
*
1708558 GGCACTGTTCACACATACG
1 GGTACTGTTCACACATACG
*
1708577 GTTACTGT
1 GGTACTGT
1708585 GCATGTGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (19 bp):
GGTACTGTTCACACATACG
Found at i:1712765 original size:75 final size:75
Alignment explanation
Indices: 1712679--1712828 Score: 246
Period size: 75 Copynumber: 2.0 Consensus size: 75
1712669 AAGTGATTTG
*
1712679 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTTACCAA
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAA
1712744 CCTTTGACAA
66 CCTTTGACAA
* * * *
1712754 ACTATTCTTCACCAACCTTTTATAATTGAGAGAGGTGGCCGTAATTGTTGACTATTCTTCACCAA
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAA
*
1712819 TCTTTGACAA
66 CCTTTGACAA
1712829 TCGAGAGATG
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (75 bp):
ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTGACTATTCTTCACCAA
CCTTTGACAA
Found at i:1712835 original size:50 final size:50
Alignment explanation
Indices: 1712754--1712906 Score: 225
Period size: 50 Copynumber: 3.1 Consensus size: 50
1712744 CCTTTGACAA
* * *
1712754 ACTATTCTTCACCAACCTTTTATAATTGAGAGAGGTGGCCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTG
* * * * *
1712804 ACTATTCTTCACCAATCTTTGACAATCGAGAGATGTGGTCGTAATTCTCG
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTG
*
1712854 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTGTTG
1 ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTG
1712904 ACT
1 ACT
1712907 TTAAGCATCT
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 89 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (50 bp):
ACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGCCGTAATTGTTG
Found at i:1720971 original size:13 final size:13
Alignment explanation
Indices: 1720953--1720979 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1720943 ATATAAATTT
1720953 TACCAAATTTATA
1 TACCAAATTTATA
1720966 TACCAAATTTATA
1 TACCAAATTTATA
1720979 T
1 T
1720980 CTTTGAGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (13 bp):
TACCAAATTTATA
Found at i:1724343 original size:11 final size:11
Alignment explanation
Indices: 1724327--1724356 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1724317 CCGAAGCATC
1724327 ACTTTCTTGCG
1 ACTTTCTTGCG
*
1724338 ACTTTCTTGTG
1 ACTTTCTTGCG
1724349 ACTTTCTT
1 ACTTTCTT
1724357 CACGTATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.10, C:0.23, G:0.13, T:0.53
Consensus pattern (11 bp):
ACTTTCTTGCG
Found at i:1728566 original size:24 final size:26
Alignment explanation
Indices: 1728539--1728627 Score: 83
Period size: 27 Copynumber: 3.4 Consensus size: 26
1728529 AAAATTAGCT
*
1728539 ACCAATTTTGACAAACAATAA-G-CC
1 ACCAATTTTGACAAACAAAAAGGACC
* * *
1728563 ACCATTTTTTATAAACAAAAAGGAACC
1 ACCAATTTTGACAAACAAAAAGG-ACC
* *
1728590 ATCAATTTTGACAAACATAAAAGAACC
1 ACCAATTTTGACAAACA-AAAAGGACC
*
1728617 ACTAATTTTGA
1 ACCAATTTTGA
1728628 TAAATACAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 5
0.76 0.17 0.08
Matches are distributed among these distances:
24 17 0.34
25 1 0.02
27 27 0.54
28 5 0.10
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (26 bp):
ACCAATTTTGACAAACAAAAAGGACC
Found at i:1728611 original size:28 final size:26
Alignment explanation
Indices: 1728542--1728659 Score: 80
Period size: 27 Copynumber: 4.5 Consensus size: 26
1728532 ATTAGCTACC
* *
1728542 AATTTTGACAAACAATAAG--CCACC
1 AATTTTGACAAACAAAAAGAACCACT
* * *
1728566 ATTTTTTATAAACAAAAAGGAACCA-T
1 AATTTTGACAAACAAAAA-GAACCACT
1728592 CAATTTTGACAAACATAAAAGAACCACT
1 -AATTTTGACAAACA-AAAAGAACCACT
* * * *
1728620 AATTTTGATAAATACAAAGAAATCACT
1 AATTTTGACAAACAAAAAG-AACCACT
*
1728647 ATTTTTTGACAAA
1 A-ATTTTGACAAA
1728660 TATAAAGGGT
Statistics
Matches: 72, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
24 14 0.19
25 1 0.01
26 4 0.06
27 39 0.54
28 14 0.19
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.28
Consensus pattern (26 bp):
AATTTTGACAAACAAAAAGAACCACT
Found at i:1736916 original size:2 final size:2
Alignment explanation
Indices: 1736909--1736942 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1736899 TTACAGTGAA
1736909 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
1736943 GGATACTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1739818 original size:17 final size:17
Alignment explanation
Indices: 1739796--1739831 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1739786 ATTTAATAAA
*
1739796 CATATTACTTTCGAAAT
1 CATATTACTTTCAAAAT
1739813 CATATTACTTTCAAAAT
1 CATATTACTTTCAAAAT
1739830 CA
1 CA
1739832 GGTTTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.19, G:0.03, T:0.39
Consensus pattern (17 bp):
CATATTACTTTCAAAAT
Found at i:1740054 original size:75 final size:75
Alignment explanation
Indices: 1739968--1740106 Score: 215
Period size: 75 Copynumber: 1.9 Consensus size: 75
1739958 TGGTGATATA
* * * *
1739968 GTTCGAAACAAAAACCAGTATTCTTAATCAGTAAGACTGTTCAGAACAAAAATTACTATTTTTAC
1 GTTCGAAACAAAAACCACTATTCTAAATCAGTAACACAGTTCAGAACAAAAATTACTATTTTTAC
1740033 CGGTAGCATG
66 CGGTAGCATG
* * *
1740043 GTTCGAAACAAAAACTACTATTCTAAATCGGTAACTCAGTTCAGAACAAAAATTACTATTTTTA
1 GTTCGAAACAAAAACCACTATTCTAAATCAGTAACACAGTTCAGAACAAAAATTACTATTTTTA
1740107 TTGATGGCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 57 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (75 bp):
GTTCGAAACAAAAACCACTATTCTAAATCAGTAACACAGTTCAGAACAAAAATTACTATTTTTAC
CGGTAGCATG
Found at i:1740131 original size:75 final size:75
Alignment explanation
Indices: 1740006--1740144 Score: 165
Period size: 75 Copynumber: 1.9 Consensus size: 75
1739996 CAGTAAGACT
* ** * *
1740006 GTTCAGAACAAAAATTACTATTTTTACCGGTAGCATGGTTCGAAACAAAAA-CTACTATTCTAAA
1 GTTCAGAACAAAAATTACTATTTTTACCGATAGCATGACTCAAAACAAAAATC-ACTATTATAAA
1740070 TCGGTAACTCA
65 TCGGTAACTCA
** * *
1740081 GTTCAGAACAAAAATTACTATTTTTATTGATGGCACT-ACTCAAAATAAAAATCACTATTATAAA
1 GTTCAGAACAAAAATTACTATTTTTACCGATAGCA-TGACTCAAAACAAAAATCACTATTATAAA
1740145 CTAATGGCAT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
75 51 0.96
76 2 0.04
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (75 bp):
GTTCAGAACAAAAATTACTATTTTTACCGATAGCATGACTCAAAACAAAAATCACTATTATAAAT
CGGTAACTCA
Found at i:1740660 original size:15 final size:15
Alignment explanation
Indices: 1740637--1740666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1740627 ATTAATATTA
1740637 ATCACTTACCTGATT
1 ATCACTTACCTGATT
*
1740652 ATCATTTACCTGATT
1 ATCACTTACCTGATT
1740667 CTCTAAACTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (15 bp):
ATCACTTACCTGATT
Found at i:1740763 original size:20 final size:20
Alignment explanation
Indices: 1740734--1740771 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1740724 AAAGCATCTA
*
1740734 AATTATCACCTTAAGCTATC
1 AATTAGCACCTTAAGCTATC
1740754 AATTAGCACCTTAAGCTA
1 AATTAGCACCTTAAGCTA
1740772 ATTTTAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.32
Consensus pattern (20 bp):
AATTAGCACCTTAAGCTATC
Found at i:1741397 original size:21 final size:20
Alignment explanation
Indices: 1741373--1741411 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1741363 AAGCTTAATG
1741373 AGTTTTTTTAATTCAATTTTA
1 AGTTTTTTT-ATTCAATTTTA
1741394 AGTTTTTTTATTCAATTT
1 AGTTTTTTTATTCAATTT
1741412 GTATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.26, C:0.05, G:0.05, T:0.64
Consensus pattern (20 bp):
AGTTTTTTTATTCAATTTTA
Found at i:1745467 original size:7 final size:7
Alignment explanation
Indices: 1745458--1745492 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
1745448 GCACCTGCAC
*
1745458 GTGCCAC
1 GTGCCAA
1745465 GTGTCCAA
1 GTG-CCAA
1745473 GTGCCAA
1 GTGCCAA
1745480 GTGCCAA
1 GTGCCAA
1745487 GTGCCA
1 GTGCCA
1745493 TATAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.23, C:0.31, G:0.29, T:0.17
Consensus pattern (7 bp):
GTGCCAA
Found at i:1750768 original size:7 final size:7
Alignment explanation
Indices: 1750724--1750767 Score: 70
Period size: 7 Copynumber: 6.3 Consensus size: 7
1750714 TTTGCACCTG
1750724 CAGGTGC
1 CAGGTGC
1750731 CAGGTGC
1 CAGGTGC
*
1750738 CAGGTGT
1 CAGGTGC
1750745 CAGGTGC
1 CAGGTGC
1750752 CAGGTGC
1 CAGGTGC
*
1750759 CAAGTGC
1 CAGGTGC
1750766 CA
1 CA
1750768 AAAGTGGTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.18, C:0.27, G:0.39, T:0.16
Consensus pattern (7 bp):
CAGGTGC
Found at i:1750950 original size:166 final size:166
Alignment explanation
Indices: 1750581--1751757 Score: 1442
Period size: 180 Copynumber: 6.8 Consensus size: 166
1750571 ATATCTTAGT
1750581 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1750646 TATCCTTTCATAAAAAATAAT--AAA-AATAATAATAATAATATAATTAATTAATTAAAAAGTTA
66 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
* *
1750708 ATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTG
131 ATTAATTTTGCACCTGTAGGTGCCAGGTGCCAAGTG
* * * * * * * * *
1750744 TCAGGTGCCAGGTGCCAAGTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGA
1 CCA-----AAAGTG----GTGTC--TA-T-CTG--TAT-AG-ACACA----ATTATTTGTTCAGA
1750809 CAAGAATTGTCTGAACAAATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATAT
45 CAAGAATTGTCTGAACAAATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATAT
1750874 AATTAATTAATTAAAAAGTTAATTAATTTTGCACCTGTAGGTGCCAGGTGCCAAGTG
110 AATTAATTAATTAAAAAGTTAATTAATTTTGCACCTGTAGGTGCCAGGTGCCAAGTG
1750931 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1750996 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
66 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
1751061 ATTAATTTTGCACC------TG-CA---G----GTG
131 ATTAATTTTGCACCTGTAGGTGCCAGGTGCCAAGTG
1751083 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
*
1751148 TATCCTTTCACAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
66 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
1751213 ATTAATTTTGCACCTGCAGGTACCAGGTGCCAGGTGCCAGGTGCCAAGTG
131 ATTAATTTTGCA-C--C---T-----GT---AGGTGCCAGGTGCCAAGTG
* *
1751263 CCAAAAGTGGTGTCTA----TATGGACACAATTATTTGTTCAGACAAGAATTATCTGAACAAATA
1 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1751324 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
66 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
*
1751389 ATTAATTTTGCACCTGCAGGTGCCAAGTGCTAGGTGTCAGGTGCCAAGTG
131 ATTAA-TTT-----TGCA----CC---TG-TAGGTGCCAGGTGCCAAGTG
* * *
1751439 TCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAAAATTGTCTGAATAAATA
1 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1751504 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
66 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
1751569 ATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTGACAGGTGCCAAGTG
131 ATTAATTTTGCACCT----GT---AGGTG-C------CAGGTGCCAAGTG
*
1751619 CTAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
1 CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
** *
1751684 TATTTTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAATTA
66 TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
1751749 ATTAATTTT
131 ATTAATTTT
1751758 ACACTTGCAG
Statistics
Matches: 894, Mismatches: 40, Indels: 143
0.83 0.04 0.13
Matches are distributed among these distances:
152 144 0.16
153 1 0.00
155 1 0.00
156 1 0.00
159 2 0.00
160 2 0.00
163 2 0.00
166 114 0.13
167 1 0.00
168 4 0.00
170 6 0.01
171 2 0.00
172 9 0.01
173 7 0.01
174 7 0.01
175 2 0.00
176 149 0.17
177 3 0.00
178 8 0.01
179 5 0.01
180 278 0.31
182 8 0.01
183 4 0.00
184 56 0.06
185 1 0.00
186 3 0.00
187 74 0.08
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (166 bp):
CCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATA
TATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTA
ATTAATTTTGCACCTGTAGGTGCCAGGTGCCAAGTG
Found at i:1751097 original size:152 final size:152
Alignment explanation
Indices: 1750762--1751233 Score: 809
Period size: 152 Copynumber: 3.0 Consensus size: 152
1750752 CAGGTGCCAA
1750762 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
1 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
1750827 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
66 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
1750892 TTAATTAATTTTGCACCTGTAGGTGCCAGGTG
131 TTAATTAATTTTGCACC------TG-CA---G
1750924 CCAAGTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGA
1 ----GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGA
1750989 ACAAATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAA
62 ACAAATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAA
1751054 AAAGTTAATTAATTTTGCACCTGCAG
127 AAAGTTAATTAATTTTGCACCTGCAG
1751080 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
1 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
*
1751145 ATATATCCTTTCACAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
66 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
1751210 TTAATTAATTTTGCACCTGCAG
131 TTAATTAATTTTGCACCTGCAG
1751232 GT
1 GT
1751234 ACCAGGTGCC
Statistics
Matches: 305, Mismatches: 1, Indels: 14
0.95 0.00 0.04
Matches are distributed among these distances:
152 153 0.50
156 1 0.00
159 2 0.01
160 2 0.01
166 147 0.48
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (152 bp):
GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
TTAATTAATTTTGCACCTGCAG
Found at i:1751245 original size:7 final size:7
Alignment explanation
Indices: 1751229--1751265 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
1751219 TTTGCACCTG
*
1751229 CAGGTAC
1 CAGGTGC
1751236 CAGGTGC
1 CAGGTGC
1751243 CAGGTGC
1 CAGGTGC
1751250 CAGGTGC
1 CAGGTGC
*
1751257 CAAGTGC
1 CAGGTGC
1751264 CA
1 CA
1751266 AAAGTGGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.22, C:0.30, G:0.35, T:0.14
Consensus pattern (7 bp):
CAGGTGC
Found at i:1751514 original size:180 final size:180
Alignment explanation
Indices: 1751080--1751855 Score: 1240
Period size: 180 Copynumber: 4.3 Consensus size: 180
1751070 GCACCTGCAG
1751080 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
1 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
*
1751145 ATATATCCTTTCACAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
66 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
* *
1751210 TTAATTAATTTTGCACCTGCAGGTACCAGGTGCCAGGTGCCAGGTGCCAA
131 TTAATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTGTCAGGTGCCAA
* *
1751260 GTGCCAAAAGTGGTGTCTA----TATGGACACAATTATTTGTTCAGACAAGAATTATCTGAACAA
1 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
1751321 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
66 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
* *
1751386 TTAATTAATTTTGCACCTGCAGGTGCCAAGTGCTAGGTGTCAGGTGCCAA
131 TTAATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTGTCAGGTGCCAA
* * *
1751436 GTGTCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAAAATTGTCTGAATAA
1 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
1751501 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
66 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
*
1751566 TTAATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTGACAGGTGCCAA
131 TTAATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTGTCAGGTGCCAA
*
1751616 GTGCTAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
1 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
** *
1751681 ATATATTTTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAA
66 ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
* * * *
1751746 TTAATTAATTTTACACTTGCAGGTATCAGACTTGCAGGTGTCAAGTGTCAGGTGCCAA
131 TTAATTAATTTTGCACCTGCAGG--T--G-C---CAGGTGCCAGGTGTCAGGTGCCAA
* * *
1751804 ATGCCAAAAGTGATGTCTATCTATATAGACACAATTATTTGTTC--ACAAGAAT
1 GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAAT
1751856 CTAAGAGTTA
Statistics
Matches: 553, Mismatches: 31, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
176 168 0.30
180 313 0.57
182 1 0.00
184 1 0.00
185 1 0.00
186 8 0.01
188 61 0.11
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (180 bp):
GTGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAA
ATATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAG
TTAATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTGTCAGGTGCCAA
Found at i:1751597 original size:7 final size:7
Alignment explanation
Indices: 1751585--1751619 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1751575 TTTGCACCTG
1751585 CAGGTGC
1 CAGGTGC
1751592 CAGGTGC
1 CAGGTGC
*
1751599 CAGGTGA
1 CAGGTGC
1751606 CAGGTGC
1 CAGGTGC
*
1751613 CAAGTGC
1 CAGGTGC
1751620 TAAAAGTGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.20, C:0.26, G:0.40, T:0.14
Consensus pattern (7 bp):
CAGGTGC
Found at i:1751737 original size:356 final size:360
Alignment explanation
Indices: 1751081--1751848 Score: 1249
Period size: 356 Copynumber: 2.1 Consensus size: 360
1751071 CACCTGCAGG
*
1751081 TGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAA
1 TGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAAAATTGTCTGAACAAA
1751146 TATATCCTTTCACAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGT
66 TATATCCTTTCACAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGT
*
1751211 TAATTAATTTTGCACCTGCAGGTACCAGGTGCCAGGTGCCAGGTGCCAAGTGCCAAAAGTGGTGT
131 TAATTAATTTTGCACCTGCAGGTACCAGGTGCCAGGTGACAGGTGCCAAGTGCCAAAAGTGGTGT
*
1751276 CTATATGGACACAATTATTTGTTCAGACAAGAATTATCTGAACAAATATATCCTTTCATAAAAAA
196 CTATATAGACACAATTATTTGTTCAGACAAGAATTATCTGAACAAATATATCCTTTCATAAAAAA
* *
1751341 TAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGTTAATTAATTTTGCACCTGC
261 TAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAATTAATTAATTTTACACCTGC
* *
1751406 AGG-T-G-C-CAAGTG-CTAGGTGTCAGGTGCCAAG
326 AGGATAGACTCAAGTGTC-AAGTGTCAGGTGCCAAA
* *
1751437 TGTCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAAAATTGTCTGAATAAA
1 TGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAAAATTGTCTGAACAAA
*
1751502 TATATCCTTTCATAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGT
66 TATATCCTTTCACAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGT
* *
1751567 TAATTAATTTTGCACCTGCAGGTGCCAGGTGCCAGGTGACAGGTGCCAAGTGCTAAAAGTGGTGT
131 TAATTAATTTTGCACCTGCAGGTACCAGGTGCCAGGTGACAGGTGCCAAGTGCCAAAAGTGGTGT
* **
1751632 CTATCTGTATAGACACAATTATTTGTTCAGACAAGAATTGTCTGAACAAATATATTTTTTCATAA
196 CTA----TATAGACACAATTATTTGTTCAGACAAGAATTATCTGAACAAATATATCCTTTCATAA
1751697 AAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAATTAATTAATTTTACAC
257 AAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAATTAATTAATTTTACAC
* *
1751762 TTGCAGGTATCAGACTTGCAGGTGTCAAGTGTCAGGTGCCAAA
322 CTGCAGG-AT-AGAC-T-CAAGTGTCAAGTGTCAGGTGCCAAA
* *
1751805 TGCCAAAAGTGATGTCTATCTATATAGACACAATTATTTGTTCA
1 TGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCA
1751849 CAAGAATCTA
Statistics
Matches: 379, Mismatches: 20, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
356 191 0.50
360 123 0.32
362 1 0.00
364 1 0.00
365 1 0.00
368 61 0.16
369 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (360 bp):
TGCCAAAAGTGGTGTCTATCTGTATAGACACAATTATTTGTTCAGACAAAAATTGTCTGAACAAA
TATATCCTTTCACAAAAAATAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAGT
TAATTAATTTTGCACCTGCAGGTACCAGGTGCCAGGTGACAGGTGCCAAGTGCCAAAAGTGGTGT
CTATATAGACACAATTATTTGTTCAGACAAGAATTATCTGAACAAATATATCCTTTCATAAAAAA
TAATAAAAATAATAATAATAATAATATAATTAATTAATTAAAAAATTAATTAATTTTACACCTGC
AGGATAGACTCAAGTGTCAAGTGTCAGGTGCCAAA
Found at i:1752503 original size:38 final size:38
Alignment explanation
Indices: 1752452--1752527 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1752442 AACAATATGT
*
1752452 AAGTCAACCGTGCAGCTTCATCTGTTTGTGAAGCTACA
1 AAGTCAACCGTGCAGCTGCATCTGTTTGTGAAGCTACA
1752490 AAGTCAACCGTGCAGCTGCATCTGTTTGTGAAGCTACA
1 AAGTCAACCGTGCAGCTGCATCTGTTTGTGAAGCTACA
1752528 CAAACAAGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (38 bp):
AAGTCAACCGTGCAGCTGCATCTGTTTGTGAAGCTACA
Found at i:1753170 original size:24 final size:23
Alignment explanation
Indices: 1753143--1753194 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
1753133 AAAAAGGGGA
*
1753143 AAAAAACAAAGAAGGAAAAAAAAG
1 AAAAAACAAAGAAAG-AAAAAAAG
* *
1753167 AAAAAAGAAAGAAAGAAAAAGAG
1 AAAAAACAAAGAAAGAAAAAAAG
1753190 AAAAA
1 AAAAA
1753195 TTTAATGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAAAACAAAGAAAGAAAAAAAG
Found at i:1753172 original size:7 final size:7
Alignment explanation
Indices: 1753160--1753194 Score: 52
Period size: 8 Copynumber: 4.7 Consensus size: 7
1753150 AAAGAAGGAA
1753160 AAAAAAG
1 AAAAAAG
1753167 AAAAAAG
1 AAAAAAG
1753174 AAAGAAAG
1 AAA-AAAG
1753182 AAAAAGAG
1 AAAAA-AG
1753190 AAAAA
1 AAAAA
1753195 TTTAATGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 12 0.46
8 14 0.54
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1753176 original size:16 final size:16
Alignment explanation
Indices: 1753142--1753194 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1753132 AAAAAAGGGG
* *
1753142 AAAAAAACAAAGAAGGA
1 AAAAAAAGAAA-AAAGA
1753159 AAAAAAAGAAAAAAG-
1 AAAAAAAGAAAAAAGA
*
1753174 AAAGAAAGAAAAAGAGA
1 AAAAAAAGAAAAA-AGA
1753191 AAAA
1 AAAA
1753195 TTTAATGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 12 0.40
16 5 0.17
17 13 0.43
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAGA
Found at i:1753181 original size:15 final size:16
Alignment explanation
Indices: 1753163--1753192 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1753153 GAAGGAAAAA
1753163 AAAGAAAAA-AGAAAG
1 AAAGAAAAAGAGAAAG
1753178 AAAGAAAAAGAGAAA
1 AAAGAAAAAGAGAAA
1753193 AATTTAATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAGAAAG
Found at i:1753616 original size:17 final size:17
Alignment explanation
Indices: 1753594--1753628 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1753584 TTTCAGCAGC
1753594 CATGGGAAAGAGAAAGA
1 CATGGGAAAGAGAAAGA
1753611 CATGGGAAAGAGAAAGA
1 CATGGGAAAGAGAAAGA
1753628 C
1 C
1753629 GGAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.09, G:0.34, T:0.06
Consensus pattern (17 bp):
CATGGGAAAGAGAAAGA
Found at i:1753814 original size:11 final size:12
Alignment explanation
Indices: 1753779--1753816 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1753769 TATTCGTATC
1753779 ATATTCATTTTTT
1 ATATT-ATTTTTT
*
1753792 ATATTATGTTTT
1 ATATTATTTTTT
1753804 A-ATTATTTTTT
1 ATATTATTTTTT
1753815 AT
1 AT
1753817 GTCATGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
12 7 0.32
13 5 0.23
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (12 bp):
ATATTATTTTTT
Found at i:1754381 original size:18 final size:19
Alignment explanation
Indices: 1754348--1754383 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1754338 TATGTTTTAA
*
1754348 TTATTTTTTGTCATATTTT
1 TTATTTTTCGTCATATTTT
1754367 TTATTTTTCGT-ATATTT
1 TTATTTTTCGTCATATTT
1754384 AAAGTAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (19 bp):
TTATTTTTCGTCATATTTT
Found at i:1754601 original size:16 final size:17
Alignment explanation
Indices: 1754577--1754609 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1754567 ATTTTTATTA
1754577 AAAATAATTAAAAATAT
1 AAAATAATTAAAAATAT
1754594 AAAA-AATTAAAAATAT
1 AAAATAATTAAAAATAT
1754610 CATTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAATTAAAAATAT
Done.