Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1030567 original size:18 final size:18
Alignment explanation
Indices: 1030541--1030585 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1030531 GTCGATCAGA
*
1030541 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
1030559 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
1030577 TGATGGCTC
1 TGATGGCTC
1030586 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:1031927 original size:20 final size:20
Alignment explanation
Indices: 1031902--1031975 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
1031892 AATAGTTTCT
*
1031902 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
1031922 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
1031942 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
1031962 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
1031976 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:1032236 original size:22 final size:22
Alignment explanation
Indices: 1032209--1032252 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1032199 GATGGAGATA
1032209 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1032231 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1032253 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1032467 original size:20 final size:20
Alignment explanation
Indices: 1032441--1032513 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
1032431 GATTATGTAT
1032441 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1032461 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1032481 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
1032501 TATCTCGTTGCGA
1 TATCGCGTTGCGA
1032514 TTTTGTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1032551 original size:20 final size:20
Alignment explanation
Indices: 1032441--1032555 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
1032431 GATTATGTAT
*
1032441 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1032461 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
1032481 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* * *
1032501 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
* *
1032522 TATTGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
1032542 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
1032556 TTTCCCAATT
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.80
21 11 0.14
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:1032558 original size:41 final size:41
Alignment explanation
Indices: 1032421--1032556 Score: 150
Period size: 41 Copynumber: 3.3 Consensus size: 41
1032411 CGCTTTGAAA
*
1032421 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * *
1032462 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * * * * *
1032502 ATCTCGTTGCGATTTTGTATTATTGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
1032543 ATCGCATTGCGATT
1 ATCGCATTGCGATT
1032557 TTCCCAATTC
Statistics
Matches: 77, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 3 0.04
40 31 0.40
41 41 0.53
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1032573 original size:21 final size:21
Alignment explanation
Indices: 1032544--1032619 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1032534 ATAGTCAGTA
*
1032544 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
1032565 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
1032585 TCGCTTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
1032606 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
1032620 ACTTATTCGC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:1032574 original size:41 final size:41
Alignment explanation
Indices: 1032544--1032632 Score: 133
Period size: 41 Copynumber: 2.2 Consensus size: 41
1032534 ATAGTCAGTA
* *
1032544 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* * *
1032585 TCGCTTTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
1032626 TCGCATT
1 TCGCATT
1032633 ACGAATTGGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.43
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:1032588 original size:20 final size:20
Alignment explanation
Indices: 1032563--1032629 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1032553 GATTTTCCCA
1032563 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
1032583 ATTCGCTTTGCGATTTTCCCA
1 ATTCGCGTTGCGA-TTTACTT
1032604 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
1032624 ATTCGC
1 ATTCGC
1032630 ATTACGAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:1033871 original size:23 final size:23
Alignment explanation
Indices: 1033845--1033897 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1033835 CACCACAGCT
*
1033845 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
*
1033868 CGTAGAATTGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
1033891 CGTAGAA
1 CGTAGAA
1033898 TTACACCGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1033898 original size:23 final size:23
Alignment explanation
Indices: 1033853--1033905 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
1033843 CTCGTATAAA
1033853 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
1033876 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
1033899 TACACCG
1 TGCACCG
1033906 TAGTTCCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.26, C:0.32, G:0.25, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:1034637 original size:67 final size:66
Alignment explanation
Indices: 1034543--1034679 Score: 238
Period size: 67 Copynumber: 2.1 Consensus size: 66
1034533 TCGGTTCCCC
* *
1034543 CCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGTTGAGGGGGTATCGGT
1 CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTGAGGGGGTATCGGT
1034608 T
66 T
*
1034609 CCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGTTGAGGGGGTATCGG
1 CCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTGAGGGGGTATCGG
1034674 TT
65 TT
1034676 CCCC
1 CCCC
1034680 TTGAATGGGT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
66 7 0.10
67 60 0.90
ACGTcount: A:0.15, C:0.28, G:0.26, T:0.31
Consensus pattern (66 bp):
CCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTTGAGGGGGTATCGGT
T
Found at i:1040757 original size:23 final size:23
Alignment explanation
Indices: 1040739--1040798 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1040729 CTCGTATAAA
1040739 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
1040762 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
1040785 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1040799 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:1041521 original size:68 final size:67
Alignment explanation
Indices: 1041412--1041564 Score: 252
Period size: 68 Copynumber: 2.3 Consensus size: 67
1041402 TTTTTCTCAT
* * *
1041412 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTCTAGCATTCTGGAATTTCATATCCGT
1 GGGGGTATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGT
1041477 TGA
65 TGA
*
1041480 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTAGTATTCTGGAAATTCATATCCGT
1 GGGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGT
1041545 TGA
65 TGA
1041548 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
1041565 TTGAATGGGT
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
67 8 0.10
68 72 0.90
ACGTcount: A:0.14, C:0.28, G:0.28, T:0.29
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATCCGTT
GA
Found at i:1044252 original size:24 final size:20
Alignment explanation
Indices: 1044218--1044262 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 20
1044208 TTAATTATTT
1044218 AAAAAAATTAAATAAAAATATA
1 AAAAAAATT-AATAAAAA-ATA
1044240 AAAAAACATTTAATAAAAAATA
1 AAAAAA-A-TTAATAAAAAATA
1044262 A
1 A
1044263 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.48
23 9 0.43
24 2 0.10
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAAAATTAATAAAAAATA
Found at i:1044254 original size:23 final size:21
Alignment explanation
Indices: 1044218--1044262 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
1044208 TTAATTATTT
1044218 AAAAAAATTAAATAAAAATATA
1 AAAAAAATTAAATAAAAA-ATA
*
1044240 AAAAAACATTTAATAAAAAATA
1 AAAAAA-ATTAAATAAAAAATA
1044262 A
1 A
1044263 TTTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAAATTAAATAAAAAATA
Found at i:1044350 original size:24 final size:23
Alignment explanation
Indices: 1044323--1044371 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1044313 AAAAACCATA
*
1044323 AAATCAAGTAAAACAAAATGATTT
1 AAATCAACTAAAACAAAAT-ATTT
* *
1044347 AAATCAACTACAACATAATATTT
1 AAATCAACTAAAACAAAATATTT
1044370 AA
1 AA
1044372 GGTACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 6 0.27
24 16 0.73
ACGTcount: A:0.57, C:0.12, G:0.04, T:0.27
Consensus pattern (23 bp):
AAATCAACTAAAACAAAATATTT
Found at i:1048799 original size:2 final size:2
Alignment explanation
Indices: 1048792--1048817 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1048782 AAGGTCAAAG
1048792 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
1048818 GGACAATAGA
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:1049071 original size:2 final size:2
Alignment explanation
Indices: 1049064--1049107 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
1049054 AACGTTTGAA
*
1049064 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1049106 AT
1 AT
1049108 TATTGTCGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1055629 original size:13 final size:13
Alignment explanation
Indices: 1055611--1055635 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1055601 TCGTTTAAAA
1055611 AATTAATTATTTT
1 AATTAATTATTTT
1055624 AATTAATTATTT
1 AATTAATTATTT
1055636 ATTTTATTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTAATTATTTT
Found at i:1056559 original size:30 final size:29
Alignment explanation
Indices: 1056525--1056660 Score: 130
Period size: 30 Copynumber: 4.6 Consensus size: 29
1056515 ATTTTACATT
* *
1056525 TTAACATTAAAAATATATTTTATTTTTATA
1 TTAAC-TTAAAAATATATTTTATTCTTATC
* * *
1056555 TTAACTTATTAAATATATTTTAATCTTGTC
1 TTAACTTA-AAAATATATTTTATTCTTATC
* * * *
1056585 TTAACCTAAAAATACAATTTATTCTTATT
1 TTAACTTAAAAATATATTTTATTCTTATC
*
1056614 TTAACTTAAAATTATATTTTAGTAT-TTATC
1 TTAACTTAAAAATATATTTTA-T-TCTTATC
1056644 TTAACTTAAAAAATATA
1 TTAACTT-AAAAATATA
1056661 CATTTTATCT
Statistics
Matches: 84, Mismatches: 18, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
29 35 0.42
30 40 0.48
31 9 0.11
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.49
Consensus pattern (29 bp):
TTAACTTAAAAATATATTTTATTCTTATC
Found at i:1056646 original size:59 final size:58
Alignment explanation
Indices: 1056532--1056655 Score: 144
Period size: 59 Copynumber: 2.1 Consensus size: 58
1056522 ATTTTAACAT
* * * *
1056532 TAAAAATATATTTTATTTTTATATTAACTTATTAAATATATTTTAATCTTGTCTTAACC
1 TAAAAATACAATTTATTCTTATATTAACTTA-TAAATATATTTTAATCTTATCTTAACC
* *
1056591 TAAAAATACAATTTATTCTTATTTTAACTTA-AAATTATATTTTAGTAT-TTATCTTAACT
1 TAAAAATACAATTTATTCTTATATTAACTTATAAA-TATATTTTA--ATCTTATCTTAACC
1056650 TAAAAA
1 TAAAAA
1056656 ATATACATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
57 3 0.05
58 9 0.16
59 42 0.75
60 2 0.04
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (58 bp):
TAAAAATACAATTTATTCTTATATTAACTTATAAATATATTTTAATCTTATCTTAACC
Found at i:1058982 original size:30 final size:30
Alignment explanation
Indices: 1058948--1059051 Score: 129
Period size: 30 Copynumber: 3.5 Consensus size: 30
1058938 GGAGTTACTT
* *
1058948 TATTCTTATCTTAACTTATTACATAAATTA
1 TATTCTTATCTTAAATTATTAAATAAATTA
** *
1058978 TATTCTTAAATTAAATTATTAAATATATTA
1 TATTCTTATCTTAAATTATTAAATAAATTA
*
1059008 TATTCTTACCTTAAATTATTAAATATAATTA
1 TATTCTTATCTTAAATTATTAAATA-AATTA
*
1059039 -ATTCTTATTTTAA
1 TATTCTTATCTTAA
1059052 CTTAAAACAC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 59 0.94
31 4 0.06
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTCTTATCTTAAATTATTAAATAAATTA
Found at i:1058989 original size:13 final size:13
Alignment explanation
Indices: 1058971--1059008 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1058961 ACTTATTACA
*
1058971 TAAATTATATTCT
1 TAAATTATATTAT
*
1058984 TAAATTAAATTAT
1 TAAATTATATTAT
1058997 TAAA-TATATTAT
1 TAAATTATATTAT
1059009 ATTCTTACCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATTATATTAT
Found at i:1059105 original size:19 final size:20
Alignment explanation
Indices: 1059075--1059116 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
1059065 TTTTATTATA
1059075 TTAACTTAAAAATATATTTT
1 TTAACTTAAAAATATATTTT
1059095 TTAAC-TAAAAATATATTTT
1 TTAACTTAAAAATATATTTT
1059114 TTA
1 TTA
1059117 TTTTTATCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAACTTAAAAATATATTTT
Found at i:1059249 original size:30 final size:29
Alignment explanation
Indices: 1059172--1059305 Score: 110
Period size: 29 Copynumber: 4.6 Consensus size: 29
1059162 AAATATTATC
* *
1059172 AGAATAAAATATAAATATTTAAGTTAAGATA
1 AGAATAAAATAT-ATTTTTTAA-TTAAGATA
* * *
1059203 AGAATATATTACATTTTTTAATTGAAGATA
1 AGAATAAAATATATTTTTTAATT-AAGATA
* * *
1059233 AGATTAAAATATA-TTTTAAATTAAAATA
1 AGAATAAAATATATTTTTTAATTAAGATA
* * *
1059261 AGAATAAAATATA-TTTTTAGGTTACGAAA
1 AGAATAAAATATATTTTTTA-ATTAAGATA
*
1059290 ATAATAAAATATATTT
1 AGAATAAAATATATTT
1059306 AATATGTTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 7
0.77 0.17 0.07
Matches are distributed among these distances:
28 22 0.27
29 27 0.33
30 24 0.29
31 9 0.11
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.38
Consensus pattern (29 bp):
AGAATAAAATATATTTTTTAATTAAGATA
Found at i:1059329 original size:25 final size:27
Alignment explanation
Indices: 1059290--1059343 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
1059280 GGTTACGAAA
1059290 ATAATAAAATATATTTA-ATATGTTAAG
1 ATAATAAAATATATTTATA-ATGTTAAG
*
1059317 ATAA-AAAA-ATATTTTTAATGTTAAG
1 ATAATAAAATATATTTATAATGTTAAG
1059342 AT
1 AT
1059344 GTAAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 16 0.64
26 5 0.20
27 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
ATAATAAAATATATTTATAATGTTAAG
Found at i:1059349 original size:27 final size:27
Alignment explanation
Indices: 1059290--1059343 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1059280 GGTTACGAAA
*
1059290 ATAATAAAATATATTTAATATGTTAAG
1 ATAAAAAAATATATTTAATATGTTAAG
*
1059317 ATAAAAAAATAT-TTTTA-ATGTTAAG
1 ATAAAAAAATATATTTAATATGTTAAG
1059342 AT
1 AT
1059344 GTAAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.40
26 4 0.16
27 11 0.44
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (27 bp):
ATAAAAAAATATATTTAATATGTTAAG
Found at i:1060205 original size:28 final size:27
Alignment explanation
Indices: 1060153--1060209 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1060143 CAAATGATTC
*
1060153 TTAAATTTGACCCCAAAAATATTTTTT
1 TTAAATTTAACCCCAAAAATATTTTTT
*
1060180 TTAAATTTAACACCC-AAGATATTTTTT
1 TTAAATTTAAC-CCCAAAAATATTTTTT
1060207 TTA
1 TTA
1060210 GCTCCGCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 24 0.89
28 3 0.11
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.46
Consensus pattern (27 bp):
TTAAATTTAACCCCAAAAATATTTTTT
Found at i:1062663 original size:4 final size:4
Alignment explanation
Indices: 1062654--1062679 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1062644 TAAGATATAA
1062654 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
1062680 ACTACCAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:1063866 original size:19 final size:19
Alignment explanation
Indices: 1063821--1063875 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
1063811 TTTCTAATAC
* *
1063821 TTAATAATTAGAATAAAAA
1 TTAATAATCAAAATAAAAA
*
1063840 TTAGTAATCAAAATAAATAA
1 TTAATAATCAAAATAAA-AA
*
1063860 -TAATAAT-AATATAAAA
1 TTAATAATCAAAATAAAA
1063876 TAAGTTATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 1 0.03
18 7 0.23
19 20 0.67
20 2 0.07
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (19 bp):
TTAATAATCAAAATAAAAA
Found at i:1067344 original size:26 final size:27
Alignment explanation
Indices: 1067315--1067377 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 27
1067305 ACGAGAATTA
1067315 ACCG-TTGAGGTATTAAAATTGAACGG
1 ACCGATTGAGGTATTAAAATTGAACGG
*
1067341 ACCGATAATTTTAGGTATTAAAATTGAACGG
1 ACCG---A-TTGAGGTATTAAAATTGAACGG
1067372 ACCGAT
1 ACCGAT
1067378 AATTTTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
28 1 0.03
31 25 0.81
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.29
Consensus pattern (27 bp):
ACCGATTGAGGTATTAAAATTGAACGG
Found at i:1067359 original size:31 final size:31
Alignment explanation
Indices: 1067322--1067385 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
1067312 TTAACCGTTG
1067322 AGGTATTAAAATTGAACGGACCGATAATTTT
1 AGGTATTAAAATTGAACGGACCGATAATTTT
1067353 AGGTATTAAAATTGAACGGACCGATAATTTT
1 AGGTATTAAAATTGAACGGACCGATAATTTT
1067384 AG
1 AG
1067386 AAACTATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.31
Consensus pattern (31 bp):
AGGTATTAAAATTGAACGGACCGATAATTTT
Found at i:1069472 original size:27 final size:28
Alignment explanation
Indices: 1069423--1069475 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
1069413 GACTAAGAAA
*
1069423 TAAAATAAAATAATAAAAGAAAACAAGG
1 TAAAATAAAATAATAAAAAAAAACAAGG
1069451 TAAAAT-AAATAA-AAATAAAAAACAA
1 TAAAATAAAATAATAAA-AAAAAACAA
1069476 AAAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 3 0.13
27 14 0.61
28 6 0.26
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (28 bp):
TAAAATAAAATAATAAAAAAAAACAAGG
Found at i:1072137 original size:252 final size:252
Alignment explanation
Indices: 1071721--1072347 Score: 983
Period size: 252 Copynumber: 2.5 Consensus size: 252
1071711 TCGTATATGA
** *
1071721 CCCCTTCGTCGTGAAGTTGAGTATTAGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATGT
1 CCCCTTCGTCGTGAAGTTGA-TCCTGGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-GT
* * * * * *
1071786 AAGTTGCACTATTTCGAGGCCAATATCCTTCG-CTGTGAAGTTGAAATTGAC-CTTGAAACTGGA
64 AAGTTGTATTGTTTCGAGTCCAATATCCTCCGTC-GTGAAGTTGAAATTGGCTC-TGAAACTGGA
* *
1071849 ACGTTTGTTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCATGAAGTTGAAATCTAATC
127 ACGTTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCATGAAGTTGAAATCCAATC
*
1071914 TAGAGATGGATGATGCTTGTGTGCACGATTCCCTTCGTCGTGAAGTTAAAACCGC-AGGTGG
192 TAGAGAGGGATGATGCTTGTGTGCACGATTCCCTTCGTCGTGAAGTTAAAACCGCGA-GTGG
*
1071975 CCCCTTCGTCGTGAAGTTGATCCTGGAATTGGATATCCTTCGTCATGAAGTTGAAATCCAAGTAA
1 CCCCTTCGTCGTGAAGTTGATCCTGGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAA
*
1072040 GTTGTATTGTTTCGAGTCCAATATCCTCCGTCCTGAAGTTGAAATTGGCTCTGAAACTAGGAA-G
66 GTTGTATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACT-GGAACG
* *
1072104 TTTATTGACAGACACTCCTTCTTTTAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG
130 TTTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAG
* *
1072169 AGAGGGATGCTGCTTGTGTGCACGATTCCCTTCGTCGTGAAGTTGAAACCGCGAGTGG
195 AGAGGGATGATGCTTGTGTGCACGATTCCCTTCGTCGTGAAGTTAAAACCGCGAGTGG
* * *
1072227 CCCCTTCATCGTGAAGTTGAGCCTGGGATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAA
1 CCCCTTCGTCGTGAAGTTGATCCTGGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAA
1072292 GTTGTATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAA
66 GTTGTATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAA
1072348 TTGGGAAGCC
Statistics
Matches: 346, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
252 282 0.82
253 44 0.13
254 20 0.06
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (252 bp):
CCCCTTCGTCGTGAAGTTGATCCTGGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGTAA
GTTGTATTGTTTCGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACTGGAACGT
TTATTGACAGACACTCCTTCTTTGAGTTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTAGA
GAGGGATGATGCTTGTGTGCACGATTCCCTTCGTCGTGAAGTTAAAACCGCGAGTGG
Found at i:1072828 original size:110 final size:106
Alignment explanation
Indices: 1072634--1072833 Score: 267
Period size: 110 Copynumber: 1.8 Consensus size: 106
1072624 ATTTTGAGCT
* * *
1072634 CAATATCCTTCGCTGTGAAGTTGAAATTAACTCTGAAATTGGAAAGTTTATTCTTGACAGTCAGT
1 CAATATCATTCGCTGTGAAGTTGAAATTAACTCTGAAACTGAAAAGTTTATTCTTGACAGTCAGT
* *
1072699 CGCCCATTCGCTGTTAAGTTGAGCTTGTATTGTCTCGAGTC
66 CGCCCATTCGCTATGAAGTTGAGCTTGTATTGTCTCGAGTC
* * *
1072740 CAATATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGT-TTGTTGACAG
1 CAATATCATTCGCTGTGAAGTTGAAATTAACTC----TGAAACTGAAAAGTT-TATTCTTGACAG
*
1072804 TCAGTCGCCCCTTCGCTATGAAGTTGAGCT
61 TCAGTCGCCCATTCGCTATGAAGTTGAGCT
1072834 ACCACCATCA
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
106 30 0.38
110 49 0.61
111 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (106 bp):
CAATATCATTCGCTGTGAAGTTGAAATTAACTCTGAAACTGAAAAGTTTATTCTTGACAGTCAGT
CGCCCATTCGCTATGAAGTTGAGCTTGTATTGTCTCGAGTC
Found at i:1073316 original size:95 final size:94
Alignment explanation
Indices: 1073140--1073335 Score: 268
Period size: 95 Copynumber: 2.1 Consensus size: 94
1073130 GGACAACTCA
* * * * *
1073140 ATATCTAAACACCTTTATCAGGTTAACTGAATCTTATCTATAAAGCCGGGGAGTTTAACCAATTG
1 ATATATAATCACCTTTATCAGGTTAACCGAATATTATCCATAAAGCCGGGGAGTTTAACCAATTG
*
1073205 CCTTAGAGGGACAACTCAAACTTTATTGT
66 CCTTAGAGGGAAAACTCAAACTTTATTGT
* * *
1073234 ATAGTATAATCACCTTTATCAGGTTAGCCGAATATTATCCATAAAGTCGGGGCGTTTAACCAATT
1 ATA-TATAATCACCTTTATCAGGTTAACCGAATATTATCCATAAAGCCGGGGAGTTTAACCAATT
* *
1073299 -TCTCTAGAGGGAAAACTCAAGCTTTATTGT
65 GCCT-TAGAGGGAAAACTCAAACTTTATTGT
1073329 ATATATA
1 ATATATA
1073336 TAATATTATA
Statistics
Matches: 89, Mismatches: 11, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
94 9 0.10
95 80 0.90
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (94 bp):
ATATATAATCACCTTTATCAGGTTAACCGAATATTATCCATAAAGCCGGGGAGTTTAACCAATTG
CCTTAGAGGGAAAACTCAAACTTTATTGT
Found at i:1077438 original size:24 final size:23
Alignment explanation
Indices: 1077408--1077460 Score: 63
Period size: 27 Copynumber: 2.2 Consensus size: 23
1077398 ATTAAAAATC
1077408 ATAAA-AAAATAATGCAAAGGAGAA
1 ATAAATAAAATAATGCAAA-GA-AA
1077432 ATAAAAATAAAATAATGCAAAGAAA
1 AT--AAATAAAATAATGCAAAGAAA
1077457 ATAA
1 ATAA
1077461 GTTTATTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
23 2 0.08
24 2 0.08
25 4 0.15
26 5 0.19
27 13 0.50
ACGTcount: A:0.70, C:0.04, G:0.11, T:0.15
Consensus pattern (23 bp):
ATAAATAAAATAATGCAAAGAAA
Found at i:1077642 original size:18 final size:18
Alignment explanation
Indices: 1077591--1077649 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
1077581 AGAAAACAAG
1077591 ATAAAATAAATAAAAATA
1 ATAAAATAAATAAAAATA
*
1077609 A-AAAATGAAA-AGAAATA
1 ATAAAAT-AAATAAAAATA
1077626 ATAAAATAAATAAAAATA
1 ATAAAATAAATAAAAATA
*
1077644 ACAAAA
1 ATAAAA
1077650 CAAAATGAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
17 15 0.43
18 20 0.57
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (18 bp):
ATAAAATAAATAAAAATA
Found at i:1077726 original size:2 final size:2
Alignment explanation
Indices: 1077719--1077745 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1077709 AAATAAGATA
1077719 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 A
1077746 AAGTGATGAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1078008 original size:2 final size:2
Alignment explanation
Indices: 1078003--1078049 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1077993 AAAGGGTTGA
1078003 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1078043 AT TT AT A
1 AT AT AT A
1078050 AACAAATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1079480 original size:40 final size:40
Alignment explanation
Indices: 1079412--1079522 Score: 159
Period size: 40 Copynumber: 2.8 Consensus size: 40
1079402 ACATTTTCCA
* * *
1079412 AATTTGCAACACTGAATTTCAAATTCGCAACTCGATTTCTG
1 AATTCGCAACAC-GAATTTTAATTTCGCAACTCGATTTCTG
** *
1079453 AATTCGCAACACGAATTTTGTTTTCGCAACTCGATTTTTG
1 AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTCTG
1079493 AATTCGCAACACGAATTTTAATTTCGCAAC
1 AATTCGCAACACGAATTTTAATTTCGCAAC
1079523 AGGTTTTATT
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
40 51 0.82
41 11 0.18
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTAATTTCGCAACTCGATTTCTG
Found at i:1079523 original size:20 final size:21
Alignment explanation
Indices: 1079390--1079523 Score: 97
Period size: 20 Copynumber: 6.6 Consensus size: 21
1079380 ACGCAAACTC
1079390 CAATTTCGCAACAC--ATTTT
1 CAATTTCGCAACACGAATTTT
1079409 CCAAATTT-GCAACACTGAA-TTT
1 -C-AATTTCGCAACAC-GAATTTT
* *
1079431 CAAATTCGCAACTCG-ATTTCT
1 CAATTTCGCAACACGAATTT-T
*
1079452 GAA-TTCGCAACACGAATTTT
1 CAATTTCGCAACACGAATTTT
** * *
1079472 -GTTTTCGCAACTCGATTTTT
1 CAATTTCGCAACACGAATTTT
*
1079492 GAA-TTCGCAACACGAATTTT
1 CAATTTCGCAACACGAATTTT
1079512 -AATTTCGCAACA
1 CAATTTCGCAACA
1079524 GGTTTTATTT
Statistics
Matches: 91, Mismatches: 12, Indels: 22
0.73 0.10 0.18
Matches are distributed among these distances:
19 3 0.03
20 65 0.71
21 19 0.21
22 3 0.03
23 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.34
Consensus pattern (21 bp):
CAATTTCGCAACACGAATTTT
Found at i:1080518 original size:24 final size:24
Alignment explanation
Indices: 1080458--1080525 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
1080448 GTGAGTACTA
* *
1080458 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
* *
1080482 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
*
1080506 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
1080526 GATGCTTCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATCTTG
Found at i:1084666 original size:42 final size:42
Alignment explanation
Indices: 1084607--1084687 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
1084597 GTGAATCGGG
1084607 CTCTTGAACAGTGGGAGGGACCTCTTGAACGATGACAGGGGA
1 CTCTTGAACAGTGGGAGGGACCTCTTGAACGATGACAGGGGA
* * *
1084649 CTCTTGAATAGTGGGAGGGGCCTCTTGAATGATGACAGG
1 CTCTTGAACAGTGGGAGGGACCTCTTGAACGATGACAGG
1084688 TGAATCAGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACAGTGGGAGGGACCTCTTGAACGATGACAGGGGA
Found at i:1084678 original size:21 final size:21
Alignment explanation
Indices: 1084607--1084678 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
1084597 GTGAATCGGG
* *
1084607 CTCTTGAACAGTGGGAGGGAC
1 CTCTTGAATAGTGGGAGGGGC
* ** *
1084628 CTCTTGAA-CGATGACAGGGGA
1 CTCTTGAATAG-TGGGAGGGGC
1084649 CTCTTGAATAGTGGGAGGGGC
1 CTCTTGAATAGTGGGAGGGGC
1084670 CTCTTGAAT
1 CTCTTGAAT
1084679 GATGACAGGT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAATAGTGGGAGGGGC
Found at i:1084881 original size:21 final size:21
Alignment explanation
Indices: 1084857--1084906 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
1084847 ATCATTGTCG
*
1084857 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* * **
1084878 TCACGCAAAGCACTGATTTCA
1 TCACGTAAAGCACCGACCTCA
1084899 TCACGTAA
1 TCACGTAA
1084907 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1084903 original size:42 final size:42
Alignment explanation
Indices: 1084812--1084906 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
1084802 AGCATCTACC
* * *
1084812 TCATCACATAAAGACCGTACCTCATCACGCCATGCATCATTG
1 TCATCACGTAAAGACCGTACCTCATCACGCAAAGCATCATTG
* *
1084854 TCGTCACGTAAAGTACCG-ACCTCATCACGCAAAGCACTGATT-
1 TCATCACGTAAAG-ACCGTACCTCATCACGCAAAGCA-TCATTG
1084896 TCATCACGTAA
1 TCATCACGTAA
1084907 CTCCCCTAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 37 0.82
43 8 0.18
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.23
Consensus pattern (42 bp):
TCATCACGTAAAGACCGTACCTCATCACGCAAAGCATCATTG
Found at i:1086863 original size:22 final size:22
Alignment explanation
Indices: 1086833--1086890 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1086823 GAGATAGAGA
1086833 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
* *
1086855 GACTGATTTCATCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
1086877 GACGGATGTCGTCG
1 GACGGATTTCGTCG
1086891 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.19, C:0.16, G:0.41, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:1101350 original size:31 final size:30
Alignment explanation
Indices: 1101276--1101350 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 30
1101266 TTTATTTTTT
* *
1101276 ATTTGACCGTTAAAATTAGATAAAATATTA
1 ATTTGACCATTAAAATTAGATAAAATATCA
* * * *
1101306 TTTTGATCTTTAAACTTTAGATAAAATATCA
1 ATTTGACCATTAAA-ATTAGATAAAATATCA
1101337 ATTTGACCATTAAA
1 ATTTGACCATTAAA
1101351 TTCAACCATA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
30 11 0.31
31 25 0.69
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (30 bp):
ATTTGACCATTAAAATTAGATAAAATATCA
Found at i:1101485 original size:18 final size:19
Alignment explanation
Indices: 1101436--1101488 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
1101426 AATCGTCAAA
1101436 TCTCAAAATTTTTAATTCAC
1 TCTC-AAATTTTTAATTCAC
*
1101456 TCTCAAAATTTTTAGTTCAC
1 TCTC-AAATTTTTAATTCAC
*
1101476 TCTCAATTTTTTA
1 TCTCAAATTTTTA
1101489 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.26
20 23 0.74
ACGTcount: A:0.30, C:0.19, G:0.02, T:0.49
Consensus pattern (19 bp):
TCTCAAATTTTTAATTCAC
Found at i:1101487 original size:20 final size:20
Alignment explanation
Indices: 1101436--1101481 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1101426 AATCGTCAAA
1101436 TCTCAAAATTTTTAATTCAC
1 TCTCAAAATTTTTAATTCAC
*
1101456 TCTCAAAATTTTTAGTTCAC
1 TCTCAAAATTTTTAATTCAC
1101476 TCTCAA
1 TCTCAA
1101482 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43
Consensus pattern (20 bp):
TCTCAAAATTTTTAATTCAC
Found at i:1106300 original size:55 final size:53
Alignment explanation
Indices: 1106238--1106478 Score: 177
Period size: 51 Copynumber: 4.6 Consensus size: 53
1106228 ATTCATACTT
* * * *
1106238 AAAAAATGTAACACTTAACGCATACTTATACTGGTGTAAGTGAGTAAAATTTAAA
1 AAAAAATGTAACACTTAACGCATACTTACACCGATGTAAGTGAATAAAA--TAAA
* *
1106293 AAAAAATGTATCACTTAGCGCATACTTACACCGATGTAAGTGAATAAAAT--A
1 AAAAAATGTAACACTTAACGCATACTTACACCGATGTAAGTGAATAAAATAAA
* * * * * **
1106344 AAAAAATATAGA-ATTTAACACATATTTACATCGACATAAGTGAATAAAAT--A
1 AAAAAATGTA-ACACTTAACGCATACTTACACCGATGTAAGTGAATAAAATAAA
* *** * * * * *
1106395 ACAAAATGTAACACTTAATATATATTTACATCAAGGTAAGTGGATAAAATAAA
1 AAAAAATGTAACACTTAACGCATACTTACACCGATGTAAGTGAATAAAATAAA
* ** *
1106448 ATAAAAATATAGTACTTAACTCATACTTACA
1 A-AAAAATGTAACACTTAACGCATACTTACA
1106479 TCGGTGCAAG
Statistics
Matches: 149, Mismatches: 32, Indels: 11
0.78 0.17 0.06
Matches are distributed among these distances:
50 1 0.01
51 81 0.54
53 3 0.02
54 21 0.14
55 43 0.29
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.28
Consensus pattern (53 bp):
AAAAAATGTAACACTTAACGCATACTTACACCGATGTAAGTGAATAAAATAAA
Found at i:1106639 original size:12 final size:12
Alignment explanation
Indices: 1106622--1106649 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1106612 AAATATAATA
1106622 AATTAGAAATTT
1 AATTAGAAATTT
1106634 AATTAGAAATTT
1 AATTAGAAATTT
1106646 AATT
1 AATT
1106650 TATTAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
AATTAGAAATTT
Found at i:1106981 original size:35 final size:35
Alignment explanation
Indices: 1106935--1107004 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
1106925 AAAACAGTCC
* *
1106935 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
1106970 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
1107005 AATTCAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.40, C:0.24, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:1107563 original size:130 final size:130
Alignment explanation
Indices: 1107410--1107657 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
1107400 TATTTATATA
* ** *
1107410 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGAGATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
1107475 TTAGCACATGATCATGACACGTGTCATTGGCGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGCGACACATGTCACCACCTAATTATTTATATATGCT
1107540 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
1107605 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGCGACACATGTCACCACCTAATTA
1107658 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGCGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:1107688 original size:130 final size:129
Alignment explanation
Indices: 1107424--1107688 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
1107414 ATTTGGTCCT
* ** * *
1107424 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGAGATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
1107489 TGACACGTGTCATTGGCGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGCGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
1107554 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
1107619 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGCGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
1107683 -A
128 CA
1107684 AAATT
1 AAATT
1107689 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGCGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:1108010 original size:28 final size:27
Alignment explanation
Indices: 1107979--1108041 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
1107969 AGTTGATACA
*
1107979 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
1108007 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
1108035 ATATTTT
1 ATATTTT
1108042 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:1108138 original size:15 final size:17
Alignment explanation
Indices: 1108118--1108149 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1108108 ATTTCTTATT
1108118 AAAATA-AAAT-ATTCA
1 AAAATATAAATGATTCA
1108133 AAAATATAAATGATTCA
1 AAAATATAAATGATTCA
1108150 TACATTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.28
Consensus pattern (17 bp):
AAAATATAAATGATTCA
Found at i:1109312 original size:34 final size:33
Alignment explanation
Indices: 1109206--1109314 Score: 82
Period size: 34 Copynumber: 3.2 Consensus size: 33
1109196 ATTATTAATG
* *
1109206 TGATTTCACTTTATACCG-ATATTTTTGGTAATAA
1 TGATTTTACTTTATA-TGAATATTTTT-GTAATAA
* * *
1109240 TGATTTT-CTGTTAAAT-AATACTCTTTTGTTGAT-G
1 TGATTTTACT-TTATATGAATA-T-TTTTG-TAATAA
1109274 TGATTTTACTTTATATGAATATTTTTCGTAATAA
1 TGATTTTACTTTATATGAATATTTTT-GTAATAA
1109308 TGATTTT
1 TGATTTT
1109315 GGCCGTTACC
Statistics
Matches: 58, Mismatches: 8, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
33 12 0.21
34 33 0.57
35 13 0.22
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.52
Consensus pattern (33 bp):
TGATTTTACTTTATATGAATATTTTTGTAATAA
Found at i:1110633 original size:16 final size:16
Alignment explanation
Indices: 1110580--1110635 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
1110570 ATTTAAACAT
1110580 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
1110597 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
1110617 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
1110633 ATA
1 ATA
1110636 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:1110650 original size:37 final size:37
Alignment explanation
Indices: 1110580--1110650 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1110570 ATTTAAACAT
* *
1110580 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
1110617 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
1110651 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:1111880 original size:24 final size:24
Alignment explanation
Indices: 1111853--1111911 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
1111843 ATGTAATTTG
*
1111853 TAATATATTATA-TATTTTAATAAA
1 TAATATATTATATTATTATAAT-AA
1111877 TAATA-ATATATATTATTATAATAA
1 TAATATAT-TATATTATTATAATAA
1111901 TAATAT-TTATA
1 TAATATATTATA
1111912 ATAATAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 6 0.19
24 17 0.55
25 8 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TAATATATTATATTATTATAATAA
Found at i:1111883 original size:3 final size:3
Alignment explanation
Indices: 1111870--1111936 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
1111860 TTATATATTT
* * * *
1111870 TAA TAAA TAA TAA T-A TATA TTA TTA TAA TAA TAA TAT TTA TAA TAA
1 TAA T-AA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1111916 TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
1111937 ACAAAAAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.86
4 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:1111885 original size:18 final size:17
Alignment explanation
Indices: 1111864--1111936 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 17
1111854 AATATATTAT
1111864 ATATTTTAATAAATAATA
1 ATATTTTAAT-AATAATA
1111882 ATATATATTATTATAATAATA
1 ATAT-T-TTA--ATAATAATA
1111903 ATA-TTT-ATAATAATA
1 ATATTTTAATAATAATA
1111918 ATAATTTTAATAATAATA
1 AT-ATTTTAATAATAATA
1111936 A
1 A
1111937 ACAAAAAATT
Statistics
Matches: 48, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
15 11 0.23
16 1 0.02
17 3 0.06
18 16 0.33
19 2 0.04
20 3 0.06
21 10 0.21
22 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTTTAATAATAATA
Found at i:1111901 original size:21 final size:21
Alignment explanation
Indices: 1111853--1111922 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
1111843 ATGTAATTTG
*
1111853 TAAT-ATATTATATATT-TTAA
1 TAATAATAATATATATTATT-A
1111873 TAAATAATAATATATATTATTA
1 T-AATAATAATATATATTATTA
* * *
1111895 TAATAATAATATTTATAATAA
1 TAATAATAATATATATTATTA
1111916 TAATAAT
1 TAATAAT
1111923 TTTAATAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 1 0.02
21 27 0.63
22 13 0.30
23 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAATAATAATATATATTATTA
Found at i:1111936 original size:15 final size:16
Alignment explanation
Indices: 1111876--1111936 Score: 81
Period size: 15 Copynumber: 3.8 Consensus size: 16
1111866 ATTTTAATAA
*
1111876 ATAATAATATATATTATT
1 ATAATAATA-ATAAT-TT
1111894 ATAATAATAAT-ATTT
1 ATAATAATAATAATTT
1111909 ATAATAATAATAATTT
1 ATAATAATAATAATTT
1111925 -TAATAATAATAA
1 ATAATAATAATAA
1111937 ACAAAAAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
15 25 0.61
16 5 0.12
17 2 0.05
18 9 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATAATAATAATAATTT
Found at i:1112410 original size:77 final size:76
Alignment explanation
Indices: 1112082--1112489 Score: 714
Period size: 76 Copynumber: 5.4 Consensus size: 76
1112072 GAGGTCTTAA
* *
1112082 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1112147 AGGCTTTTTGG
66 AGGCTTTTTGG
1112158 -AA-ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1112221 AGGC-TTTTGG
66 AGGCTTTTTGG
1112231 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1112296 AGGCTTTTTGG
66 AGGCTTTTTGG
*
1112307 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1112372 AGGCTTTTTTGG
66 AGGC-TTTTTGG
* * *
1112384 AAACATCATGCACTGCAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1112449 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
1112460 AAACATCATGCACTGCAAGACTTACAGATG
1 AAACATCATGCACTGTAGGACTTACAGATG
1112490 TGGGAAATAG
Statistics
Matches: 321, Mismatches: 7, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
73 6 0.02
74 65 0.20
75 67 0.21
76 109 0.34
77 74 0.23
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:1112448 original size:153 final size:151
Alignment explanation
Indices: 1112082--1112489 Score: 712
Period size: 153 Copynumber: 2.7 Consensus size: 151
1112072 GAGGTCTTAA
*
1112082 AAACATCATGCACTGAAGGGCTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1112147 AGGCTTTTTGG-AA-ATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
*
1112210 AAAGCTCCCGAAGGCTTTTGG
131 AAAACTCCCGAAGGCTTTTGG
*
1112231 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1112296 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
1112361 AAAACTCCCGAAGGCTTTTTTGG
131 AAAACTCCCGAAGGC--TTTTGG
* * *
1112384 AAACATCATGCACTGCAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* *
1112449 AGGCTTTTTGGAAACATCATGCACTGCAAGACTTACAGATG
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1112490 TGGGAAATAG
Statistics
Matches: 247, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
149 74 0.30
150 2 0.01
151 64 0.26
153 107 0.43
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (151 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
AAAACTCCCGAAGGCTTTTGG
Found at i:1112743 original size:76 final size:76
Alignment explanation
Indices: 1112614--1112977 Score: 676
Period size: 76 Copynumber: 4.8 Consensus size: 76
1112604 TTAAAATAAC
*
1112614 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGGCCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1112679 AAGGCTTTGAA
66 AAGGCTTTGAA
*
1112690 AAAATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATTG-CCC
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGA-TGACCC
1112754 TAAGGCTTTGAA
65 TAAGGCTTTGAA
1112766 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1112831 AAGGCTTTGAA
66 AAGGCTTTGAA
* *
1112842 AACATCAAAAAACTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1112907 AAGGCTTTGAA
66 AAGGCTTTGAA
1112918 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1112978 TGGGAAATAG
Statistics
Matches: 280, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
75 2 0.01
76 276 0.99
77 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (76 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
AAGGCTTTGAA
Found at i:1113076 original size:488 final size:489
Alignment explanation
Indices: 1112128--1113162 Score: 1918
Period size: 488 Copynumber: 2.1 Consensus size: 489
1112118 AGGCTTTGAA
*
1112128 AACATCAAAAAGCTCCCGAAGGCTTTTTGG-AA-ATCATGCACTGTAGGACTTACAGATGACCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
* *
1112191 AAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGTAGGACTTAC
66 AAGGCTTTGAAAAAATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTAC
1112256 AGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACT
131 AGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACT
*
1112321 GTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTTGGAA
196 GCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTTGGAA
*
1112386 ACATCATGCACTGCAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAG
261 ACATCATGCACTACAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAG
*
1112451 GCTTTTTGGAAACATCATGCACTGCAAGACTTACAGATGTGGGAAATAGTTTACTAAGTAAGAAA
326 GCTTTTTGGAAACATCATGCACTGCAAGACTTACAGATGTGGGAAATAGTTTACAAAGTAAGAAA
*
1112516 CTATGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTATG
391 CTATGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTATG
1112581 GAAATCGTTTTCTCATTATTTTTTT-AAAATAAC
456 GAAATCGTTTTCTCATTATTTTTTTCAAAATAAC
*
1112614 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGGCCCT
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
1112679 AAGGCTTTGAAAAAATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTA
66 AAGGCTTTGAAAAAATCAAAAAGCTCCCGAAGGC-TTTTGGAAACATCATGCACTGCAGGACTTA
1112744 CAGATTG-CCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA
130 CAGA-TGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCA
1112808 CTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGC-TTTTTGG
194 CTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTTGG
* *
1112872 AAACATCATGCACTACAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
259 AAACATCATGCACTACAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGA
*
1112937 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGTGGGAAATAGTTTACAAAGTAAGA
324 AGGCTTTTTGGAAACATCATGCACTGCAAGACTTACAGATGTGGGAAATAGTTTACAAAGTAAGA
1113002 AACTATGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTA
389 AACTATGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTA
1113067 TGGAAATCGTTTTCTCATTATTTTTTTCAAAATAAC
454 TGGAAATCGTTTTCTCATTATTTTTTTCAAAATAAC
1113103 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1113163 TGGGAAATAG
Statistics
Matches: 533, Mismatches: 11, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
486 30 0.06
487 2 0.00
488 285 0.53
489 214 0.40
490 2 0.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (489 bp):
AACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCT
AAGGCTTTGAAAAAATCAAAAAGCTCCCGAAGGCTTTTGGAAACATCATGCACTGCAGGACTTAC
AGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACT
GCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTTGGAA
ACATCATGCACTACAGGACTTACAGATAACCCTAAGGCTTTGAAAACATCAAAAAACTCCCGAAG
GCTTTTTGGAAACATCATGCACTGCAAGACTTACAGATGTGGGAAATAGTTTACAAAGTAAGAAA
CTATGAAAATCATTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAAACTATG
GAAATCGTTTTCTCATTATTTTTTTCAAAATAAC
Found at i:1114060 original size:54 final size:54
Alignment explanation
Indices: 1113966--1114096 Score: 155
Period size: 54 Copynumber: 2.5 Consensus size: 54
1113956 AGAATAGCAG
* * * * *
1113966 GTTCGTAAAACATTTGACAGCGCATT-TATCATTTCCTGTGGCTTCTGCTCAGA
1 GTTCGTAAAACATTTGACAACACATTCTATCATCTCATGTGGCTTCAGCTCAGA
*
1114019 TGTTCGTAAAACATTTGACAACACATTCT-TCATCTCATGTGGTTTCAGCTCAGA
1 -GTTCGTAAAACATTTGACAACACATTCTATCATCTCATGTGGCTTCAGCTCAGA
*
1114073 --T-GTAAAACACTTGACAACACATTC
1 GTTCGTAAAACATTTGACAACACATTC
1114097 ATCCTTTTCT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 22 0.32
51 1 0.01
54 45 0.65
55 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCTATCATCTCATGTGGCTTCAGCTCAGA
Found at i:1114115 original size:40 final size:40
Alignment explanation
Indices: 1114071--1114150 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1114061 TTTCAGCTCA
1114071 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1114111 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1 GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
1114151 CTTCTGCTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (40 bp):
GATGTAAAACACTTGACAACACATTCATCCTTTTCTGTGG
Found at i:1116570 original size:111 final size:111
Alignment explanation
Indices: 1116263--1116598 Score: 466
Period size: 115 Copynumber: 3.0 Consensus size: 111
1116253 GATCATGCAG
* * * * *
1116263 TTCATCTTTTAATTCCAATGATTGGTTCTGTGGTTCCTACCGAACCATG-TCAGAT-AACTCAAA
1 TTCATCTTTCAAATCC-ATGATTGGTTTTG-GGTTCATACCAAACCA-GATCAGATAAACTCAAA
* *
1116326 GAACACTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACCATGAGCAAA
63 GAACACTTCCAGAAGATGCTATTGGG--TCTTTATTTCTACTATGAGCAAA
*
1116377 TTCATCTTTCAAATCTAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAAA-TCAAA
1 TTCATCTTTCAAATC-CATGATTGG-TTTT-GGGTTCATACCAAACCAGATCAGATAAACTCAAA
1116441 GAACACTTCCAGAAGATGCTATTGGGTCTTTA-TTCTACTATGAGCAAA
63 GAACACTTCCAGAAGATGCTATTGGGTCTTTATTTCTACTATGAGCAAA
1116489 TTCATCTTTCAAATCCATGATTGGTTTTAGGGTTCATACCAAACCAGATCAGATAAACTCAAAGA
1 TTCATCTTTCAAATCCATGATTGGTTTT-GGGTTCATACCAAACCAGATCAGATAAACTCAAAGA
*
1116554 ACACTTCCAGAAGATGCTATTGGGTCATCTATTTCTA-TATGAGCA
65 ACACTTCCAGAAGATGCTATTGGGTC-TTTATTTCTACTATGAGCA
1116599 CATGGCACTT
Statistics
Matches: 203, Mismatches: 11, Indels: 18
0.88 0.05 0.08
Matches are distributed among these distances:
110 32 0.16
111 41 0.20
112 41 0.20
113 10 0.05
114 22 0.11
115 54 0.27
116 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (111 bp):
TTCATCTTTCAAATCCATGATTGGTTTTGGGTTCATACCAAACCAGATCAGATAAACTCAAAGAA
CACTTCCAGAAGATGCTATTGGGTCTTTATTTCTACTATGAGCAAA
Found at i:1118869 original size:6 final size:7
Alignment explanation
Indices: 1118833--1118875 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
1118823 CTTGATTCAA
1118833 TTTTCCTT
1 TTTTCC-T
*
1118841 TTTTCCA
1 TTTTCCT
1118848 TTTT--T
1 TTTTCCT
1118853 TTTTCCT
1 TTTTCCT
1118860 TTTTCCT
1 TTTTCCT
1118867 TTTTCCT
1 TTTTCCT
1118874 TT
1 TT
1118876 CTTTGCTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.13
7 21 0.68
8 6 0.19
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCCT
Found at i:1118876 original size:19 final size:20
Alignment explanation
Indices: 1118834--1118876 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1118824 TTGATTCAAT
*
1118834 TTTCCTTTTTTCCATTTTTT
1 TTTCCTTTTTTCCATTTTTC
1118854 TTTCC-TTTTTCC-TTTTTCC
1 TTTCCTTTTTTCCATTTTT-C
1118873 TTTC
1 TTTC
1118877 TTTGCTGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTCCTTTTTTCCATTTTTC
Found at i:1118889 original size:27 final size:26
Alignment explanation
Indices: 1118859--1118909 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 26
1118849 TTTTTTTTCC
1118859 TTTTTCCTTT-TTCCTTTCTTTGCTGAA
1 TTTTT-CTTTCTT-CTTTCTTTGCTGAA
1118886 TTTTTCTTTCTTCTTTCTTTGCTG
1 TTTTTCTTTCTTCTTTCTTTGCTG
1118910 GATGAGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.04, C:0.22, G:0.08, T:0.67
Consensus pattern (26 bp):
TTTTTCTTTCTTCTTTCTTTGCTGAA
Found at i:1119965 original size:23 final size:23
Alignment explanation
Indices: 1119939--1119983 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1119929 CACCACAGCT
*
1119939 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1119962 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1119984 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1120222 original size:149 final size:149
Alignment explanation
Indices: 1119962--1120265 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
1119952 CGAAGTGCCC
* *
1119962 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAG
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAG
1120027 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
1120092 CATATGTCTCGAAGAACCG
131 CATATGTCTCGAAGAACCG
*
1120111 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAG
1120176 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
1120241 CATATGTCTCGAAGAACCG
131 CATATGTCTCGAAGAACCG
1120260 CGTAGA
1 CGTAGA
1120266 CCCGACTCTT
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAG
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
CATATGTCTCGAAGAACCG
Found at i:1121260 original size:18 final size:18
Alignment explanation
Indices: 1121239--1121273 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1121229 TCCCATCTAG
1121239 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1121257 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1121274 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1121874 original size:21 final size:21
Alignment explanation
Indices: 1121844--1121888 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1121834 ATTTTGTCGT
* *
1121844 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1121865 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1121886 TTG
1 TTG
1121889 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1125027 original size:23 final size:23
Alignment explanation
Indices: 1125001--1125045 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1124991 CACCACAGCT
*
1125001 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* * *
1125024 CGTAGAATTGTACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1125046 ATATAATGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1125299 original size:149 final size:147
Alignment explanation
Indices: 1125024--1125325 Score: 541
Period size: 149 Copynumber: 2.0 Consensus size: 147
1125014 CGAAGTGCCC
* * *
1125024 CGTAGAATTGTACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1125089 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
*
1125154 CATATGTCTTGAAGAACCG
131 C--ATGTCTCGAAGAACCG
*
1125173 CGTATAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1125238 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
1125303 CATGTCTCGAAGAACCG
131 CATGTCTCGAAGAACCG
1125320 CGTAGA
1 CGTAGA
1125326 CCCTCGACTC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
147 20 0.14
149 127 0.86
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (147 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATA
CATGTCTCGAAGAACCG
Found at i:1126322 original size:18 final size:18
Alignment explanation
Indices: 1126301--1126335 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1126291 TCCCATCTAG
1126301 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1126319 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1126336 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1126941 original size:21 final size:21
Alignment explanation
Indices: 1126911--1126955 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1126901 ATTTTGTCGT
* *
1126911 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1126932 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1126953 TTG
1 TTG
1126956 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1129865 original size:15 final size:15
Alignment explanation
Indices: 1129847--1129884 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1129837 TAAAAGTATG
1129847 AATGCAAAAATGAAA
1 AATGCAAAAATGAAA
* *
1129862 AATGCAAAGATGCAA
1 AATGCAAAAATGAAA
1129877 AATG-AAAA
1 AATGCAAAA
1129885 TGCATATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.63, C:0.08, G:0.16, T:0.13
Consensus pattern (15 bp):
AATGCAAAAATGAAA
Found at i:1133643 original size:16 final size:16
Alignment explanation
Indices: 1133590--1133645 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
1133580 ATTTAAACAT
1133590 ATAAAATTAAAATATAA
1 ATAAAATTAAAAT-TAA
1133607 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
1133627 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
1133643 ATA
1 ATA
1133646 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:1133660 original size:37 final size:37
Alignment explanation
Indices: 1133590--1133660 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1133580 ATTTAAACAT
* *
1133590 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
1133627 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
1133661 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Found at i:1134907 original size:3 final size:3
Alignment explanation
Indices: 1134899--1134973 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
1134889 TATATATATT
* * * * *
1134899 TAA TAA TAAA TAA TAA TAA T-A TTA TTA TAT TAA TAA TAA TAT TTA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
1134944 TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1134974 ACGAAAAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:1138813 original size:20 final size:21
Alignment explanation
Indices: 1138773--1138813 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1138763 TATTTTCTAT
**
1138773 TTTTTATAAATAAAATTATTA
1 TTTTTATAAATAAAAAAATTA
1138794 TTTTTA-AAATAAAAAAATTA
1 TTTTTATAAATAAAAAAATTA
1138814 AAAAAAATCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTTATAAATAAAAAAATTA
Found at i:1145667 original size:19 final size:20
Alignment explanation
Indices: 1145503--1145693 Score: 144
Period size: 20 Copynumber: 9.6 Consensus size: 20
1145493 AAATGACCAA
*
1145503 CAAATTCGCAACGCGAATTC
1 CAAATTCGCAACGCGAATTT
* * * *
1145523 CAATTTCTCAAC-CCAGTTT
1 CAAATTCGCAACGCGAATTT
*
1145542 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
** *
1145565 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
*
1145583 CCAAATTCGCAACGCG-ATAGT
1 -CAAATTCGCAACGCGAAT-TT
*
1145604 CAAATTCGCAACGCGGAA-GT
1 CAAATTCGCAACGC-GAATTT
**
1145624 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAATTT
*
1145644 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
1145663 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
1145683 -AATTTCGCAAC
1 CAAATTCGCAAC
1145694 AGGTTTTAGT
Statistics
Matches: 138, Mismatches: 21, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.01
19 34 0.25
20 85 0.62
21 15 0.11
22 2 0.01
23 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:1148918 original size:18 final size:18
Alignment explanation
Indices: 1148895--1148930 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1148885 AAGCAAAAGG
*
1148895 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1148913 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1148931 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1149241 original size:20 final size:20
Alignment explanation
Indices: 1149216--1149319 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 20
1149206 ATGTTGCGAT
1149216 CAACGCGAAAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
1149236 CAACGCGAAA-T--AA---G
1 CAACGCGAAAGTCAAATTCG
*** * * *
1149250 CGTTGCGATAGTTAAATCCG
1 CAACGCGAAAGTCAAATTCG
**
1149270 CAACGCGAAAGAGAAATTCG
1 CAACGCGAAAGTCAAATTCG
* * *
1149290 TAATGCGATAGTCAAATTCG
1 CAACGCGAAAGTCAAATTCG
1149310 CAACGCGAAA
1 CAACGCGAAA
1149320 TCGCAAACCG
Statistics
Matches: 59, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
14 7 0.12
15 1 0.02
17 4 0.07
19 1 0.02
20 46 0.78
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.17
Consensus pattern (20 bp):
CAACGCGAAAGTCAAATTCG
Found at i:1149458 original size:25 final size:25
Alignment explanation
Indices: 1149420--1149469 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1149410 AAATCAATTA
*
1149420 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1149445 AACATTGTTATGGGTACATTATTTG
1 AACATTGTTATGGGTACATTATTTG
1149470 GAAAAATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTG
Found at i:1149876 original size:18 final size:18
Alignment explanation
Indices: 1149855--1149891 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1149845 GTAATTGGAG
1149855 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1149873 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1149891 T
1 T
1149892 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1149898 original size:24 final size:24
Alignment explanation
Indices: 1149847--1149899 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1149837 TTTCATATGT
* * *
1149847 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1149871 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1149895 AATTT
1 AATTT
1149900 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1150284 original size:33 final size:33
Alignment explanation
Indices: 1150208--1150285 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
1150198 ATGCTCATTA
* *
1150208 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGG
1 AAATCCAAATCTCATATGGTGCAAAGCAAAAGG
1150241 AAATCCAAATCTCATATGGTGCAAAGCAAAAGG
1 AAATCCAAATCTCATATGGTGCAAAGCAAAAGG
*
1150274 AAATCAAAATCT
1 AAATCCAAATCT
1150286 AAAACTTGAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.18
Consensus pattern (33 bp):
AAATCCAAATCTCATATGGTGCAAAGCAAAAGG
Found at i:1150543 original size:20 final size:20
Alignment explanation
Indices: 1150498--1150536 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1150488 AATAAGCGTT
*
1150498 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
1150518 GCGAAAGTCAAATTCGCAA
1 GCGAAAGTCAAATTCGCAA
1150537 ACCGAAAATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.18
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:1150787 original size:60 final size:63
Alignment explanation
Indices: 1150656--1150792 Score: 165
Period size: 66 Copynumber: 2.2 Consensus size: 63
1150646 TAGAAACAAT
*
1150656 AAATCAACTTTTACAGATCAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATTAAA
1 AAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAATTCTTATTTACAAATCAAATTAAA
1150721 C
63 C
* * **
1150722 AAATCAACTTTTACAAATCAATT-AATC-AAAAAATGAA-TCTTATTTCCTCATC-AATTAAAC
1 AAATCAACTTTTACAAATCAATTAAAGCAAAAAAAT-AATTCTTATTTACAAATCAAATTAAAC
1150782 AAATCAACTTT
1 AAATCAACTTT
1150793 CAATGTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
60 19 0.29
61 19 0.29
62 5 0.08
66 22 0.34
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (63 bp):
AAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAATTCTTATTTACAAATCAAATTAAAC
Found at i:1152034 original size:21 final size:21
Alignment explanation
Indices: 1152010--1152105 Score: 63
Period size: 21 Copynumber: 4.6 Consensus size: 21
1152000 GGCGGGACCA
*
1152010 CTTGAATGATGACAAGGGCCT
1 CTTGAATGATGAGAAGGGCCT
* * * * *
1152031 CTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGAGAAGGGCCT
*
1152052 CTTCG-ATAATGA-AAGGGGCCT
1 CTT-GAATGATGAGAA-GGGCCT
* *
1152073 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAATGATGAGAAGG-GCCT
1152094 CTTGAATGATGA
1 CTTGAATGATGA
1152106 TAGGTGCATC
Statistics
Matches: 53, Mismatches: 16, Indels: 11
0.66 0.20 0.14
Matches are distributed among these distances:
20 5 0.09
21 46 0.87
22 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (21 bp):
CTTGAATGATGAGAAGGGCCT
Found at i:1152270 original size:4 final size:4
Alignment explanation
Indices: 1152249--1152290 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1152239 AGGCCGCTGA
* * *
1152249 AAAT AAAT TAAT ATAT AAAT AAGT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1152291 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:1154261 original size:20 final size:20
Alignment explanation
Indices: 1154249--1154299 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1154239 AAACTTAAAT
1154249 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1154269 TCGTAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
1154289 TCGCAACGCGA
1 TCGCAACGCGA
1154300 TTTTAGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1154751 original size:20 final size:20
Alignment explanation
Indices: 1154728--1154838 Score: 84
Period size: 20 Copynumber: 5.5 Consensus size: 20
1154718 TGACTTTTGC
*
1154728 GTTGTGAATTTGACTATCGT
1 GTTGCGAATTTGACTATCGT
*
1154748 GTTGCAAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATC-GT
*
1154768 GTTGCG-ATTT-ACAAATTCGT
1 GTTGCGAATTTGAC-TA-TCGT
* * *
1154788 GTTGCAAATTTGACTTTCGC
1 GTTGCGAATTTGACTATCGT
* * *
1154808 GTTGAGAATTTAACTATCGC
1 GTTGCGAATTTGACTATCGT
*
1154828 ATTGCGAATTT
1 GTTGCGAATTT
1154839 AGAAAATCGC
Statistics
Matches: 71, Mismatches: 14, Indels: 12
0.73 0.14 0.12
Matches are distributed among these distances:
18 2 0.03
19 6 0.08
20 55 0.77
21 6 0.08
22 2 0.03
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGT
Found at i:1154759 original size:40 final size:39
Alignment explanation
Indices: 1154715--1154826 Score: 127
Period size: 40 Copynumber: 2.8 Consensus size: 39
1154705 GCGTAAAAAT
*
1154715 ATTTGACTTTTGCGTTGTGAATTTGACTATCGTGTTGCAA
1 ATTTGACTTTTGCGTTGAGAATTT-ACTATCGTGTTGCAA
* * * *
1154755 ATTTGACTTCTGTGTTGCG-ATTTACAAATTCGTGTTGCAA
1 ATTTGACTTTTGCGTTGAGAATTTAC-TA-TCGTGTTGCAA
*
1154795 ATTTGACTTTCGCGTTGAGAATTTAACTATCG
1 ATTTGACTTTTGCGTTGAGAATTT-ACTATCG
1154827 CATTGCGAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
38 2 0.03
39 5 0.08
40 45 0.76
41 5 0.08
42 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (39 bp):
ATTTGACTTTTGCGTTGAGAATTTACTATCGTGTTGCAA
Found at i:1154849 original size:21 final size:21
Alignment explanation
Indices: 1154823--1154880 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1154813 GAATTTAACT
*
1154823 ATCGCATTGCGAATTTAGAAA
1 ATCGCAATGCGAATTTAGAAA
* *
1154844 ATCGCAACGCGAATTTGGAAA
1 ATCGCAATGCGAATTTAGAAA
1154865 ATCGCAATGCG-ATTTA
1 ATCGCAATGCGAATTTA
1154881 CATATTCGCG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 4 0.12
21 28 0.88
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (21 bp):
ATCGCAATGCGAATTTAGAAA
Found at i:1154933 original size:20 final size:20
Alignment explanation
Indices: 1154884--1154937 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1154874 CGATTTACAT
*
1154884 ATTCGCGTTGTGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
1154904 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
1154924 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
1154938 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:1155546 original size:17 final size:18
Alignment explanation
Indices: 1155524--1155572 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
1155514 TTATTTTATC
*
1155524 TTTTTATATTATGT-ATA
1 TTTTTATAATATGTAATA
*
1155541 TTTTTATACTAT-TAATA
1 TTTTTATAATATGTAATA
1155558 TTATTTATAATATGT
1 TT-TTTATAATATGT
1155573 TTATATTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 16 0.59
18 9 0.33
19 1 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
TTTTTATAATATGTAATA
Found at i:1155562 original size:20 final size:20
Alignment explanation
Indices: 1155539--1155630 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
1155529 ATATTATGTA
1155539 TATTTTTATACTATTAATAT
1 TATTTTTATACTATTAATAT
*
1155559 TATTTATAATATGTTTA-TATTCATAT
1 TATTT-T--TA----TACTATTAATAT
* *
1155585 AAATTTTTATACCATTAATAT
1 TA-TTTTTATACTATTAATAT
*
1155606 TATTTTTATATTA-TATATAT
1 TATTTTTATACTATTA-ATAT
1155626 TATTT
1 TATTT
1155631 ACAAATTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
19 2 0.04
20 25 0.45
21 9 0.16
23 2 0.04
24 2 0.04
26 10 0.18
27 5 0.09
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (20 bp):
TATTTTTATACTATTAATAT
Found at i:1155639 original size:37 final size:36
Alignment explanation
Indices: 1155572--1155656 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 36
1155562 TTATAATATG
* *
1155572 TTTATATTCATATAAATTTTTATACCATTAATATTATT-
1 TTTATATT-ATATAAATTTTTACACAATTAAT-TT-TTC
*
1155610 TTTATATTATATATATTATTTACA-AATTAATTTTTC
1 TTTATATTATATAAATT-TTTACACAATTAATTTTTC
1155646 TTTATA-TATAT
1 TTTATATTATAT
1155657 TTTCTCATGT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
35 7 0.17
36 8 0.19
37 14 0.33
38 13 0.31
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (36 bp):
TTTATATTATATAAATTTTTACACAATTAATTTTTC
Found at i:1161606 original size:8 final size:8
Alignment explanation
Indices: 1161593--1161633 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1161583 CTCATTTTCA
1161593 GAGAATTT
1 GAGAATTT
1161601 GAGAATTT
1 GAGAATTT
*
1161609 -AGAGTTT
1 GAGAATTT
*
1161616 GGGAATTT
1 GAGAATTT
1161624 GAGAATTT
1 GAGAATTT
1161632 GA
1 GA
1161634 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1161926 original size:126 final size:126
Alignment explanation
Indices: 1161701--1162428 Score: 1422
Period size: 126 Copynumber: 5.8 Consensus size: 126
1161691 CTATAATCGG
1161701 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1161766 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1161827 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1161892 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1161953 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1162017 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1162078 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1162143 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1162204 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1162269 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
* *
1162330 TTCACTATTCACATAAAGGCGCGTTCCCGGGGGCTCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1162395 TCATTGCCCTATTATGTCACTCATGTCCCTCGGG
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGG
1162429 AAATAACTTA
Statistics
Matches: 598, Mismatches: 3, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
125 125 0.21
126 473 0.79
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:1162145 original size:251 final size:252
Alignment explanation
Indices: 1161701--1162428 Score: 1422
Period size: 251 Copynumber: 2.9 Consensus size: 252
1161691 CTATAATCGG
1161701 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
1161766 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
1161831 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
1161896 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1161953 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1162017 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
1162082 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
1162147 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
196 TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
1162204 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1162269 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
* *
1162334 CTATTCACATAAAGGCGCGTTCCCGGGGGCTCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
131 CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
1162399 TGCCCTATTATGTCACTCATGTCCCTCGGG
196 TGCCCTATTATGTCACTCATGTCCCTCGGG
1162429 AAATAACTTA
Statistics
Matches: 472, Mismatches: 3, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
251 250 0.53
252 222 0.47
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (252 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTCA
CTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTATCAT
TGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:1162896 original size:32 final size:34
Alignment explanation
Indices: 1162818--1162915 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 34
1162808 AAATTTAATG
*
1162818 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
1162852 TTAAATTT-GAATAATATTATTT-T-TTTTTATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
1162883 TTAAATTTCGAATAATATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
1162916 AACATTTATC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
31 14 0.26
32 14 0.26
33 13 0.24
34 13 0.24
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1163523 original size:21 final size:21
Alignment explanation
Indices: 1163435--1163528 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1163425 TATGGTATAA
*
1163435 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1163456 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1163477 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1163498 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1163519 AACCCTGCGG
1 AACCCTGCGG
1163529 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1163558 original size:21 final size:21
Alignment explanation
Indices: 1163532--1163579 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1163522 CCTGCGGAGA
*
1163532 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1163553 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1163574 GGGCAT
1 TGGCAT
1163580 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1165336 original size:36 final size:33
Alignment explanation
Indices: 1165295--1165371 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 33
1165285 TAATAATTCT
*
1165295 AAATAATAATAATATATAAATATTATTTTAATA-AAA
1 AAATAATAAT-ATACATAAATA-TA--TTAATATAAA
*
1165331 AAATAAT-ATTTACATAAATATATTAATATAAA
1 AAATAATAATATACATAAATATATTAATATAAA
1165363 AAATAATAA
1 AAATAATAA
1165372 CTATTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
31 6 0.16
32 10 0.27
33 3 0.08
34 9 0.24
35 2 0.05
36 7 0.19
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (33 bp):
AAATAATAATATACATAAATATATTAATATAAA
Found at i:1169172 original size:45 final size:45
Alignment explanation
Indices: 1169117--1169206 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1169107 TGAACTGGTT
1169117 TTTTTCTTACATTTATAAATTAAATAAAGATTAAAATGAAATTAA
1 TTTTTCTTACATTTATAAATTAAATAAAGATTAAAATGAAATTAA
1169162 TTTTTCTTACATTTATAAATTAAATAAAGATTAAAATGAAATTAA
1 TTTTTCTTACATTTATAAATTAAATAAAGATTAAAATGAAATTAA
1169207 AGAAAGATGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (45 bp):
TTTTTCTTACATTTATAAATTAAATAAAGATTAAAATGAAATTAA
Found at i:1171298 original size:130 final size:130
Alignment explanation
Indices: 1171094--1171341 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
1171084 AATTTTCTTC
* * *
1171094 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAGCACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
1171159 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
1171224 TAATTAGGTGGTGACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
1171289 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1171342 TATATAAATA
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1171788 original size:35 final size:35
Alignment explanation
Indices: 1171738--1171813 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
1171728 AATTGAATTT
* *
1171738 AATTGAATTATTTTGGAATTTAGGA-TTTAGAATGA
1 AATTGAATTACTTTGGAAATT-GGAGTTTAGAATGA
1171773 AATTGAATTACTTTGGAAATTGGAGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTGGAGTTTAGAATGA
1171808 AATTGA
1 AATTGA
1171814 GGACTGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 3 0.08
35 35 0.92
ACGTcount: A:0.38, C:0.01, G:0.21, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTGGAGTTTAGAATGA
Found at i:1175022 original size:20 final size:20
Alignment explanation
Indices: 1174997--1175037 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1174987 ATAAACGTAC
1174997 AATATTAG-CTAAAATAATTA
1 AATATTAGTC-AAAATAATTA
*
1175017 AATATTTGTCAAAATAATTA
1 AATATTAGTCAAAATAATTA
1175037 A
1 A
1175038 TTAGTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
AATATTAGTCAAAATAATTA
Done.