Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold76
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: 1973630
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 106294 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:1330631 original size:26 final size:26
Alignment explanation
Indices: 1330595--1330671 Score: 93
Period size: 26 Copynumber: 2.9 Consensus size: 26
1330585 TTTGAGGTCA
1330595 GGCGAGCTGGTGTTCGTAGTAGGAC-T
1 GGCGAGCTGGTGTTCGTAGTAGG-CTT
* * *
1330621 GGCGAGTTGGTATTTGTAGTAGGCTT
1 GGCGAGCTGGTGTTCGTAGTAGGCTT
*
1330647 GACGAGCTGGTGTTCGTCAGTAGGC
1 GGCGAGCTGGTGTTCGT-AGTAGGC
1330672 CAGACAAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.02
26 34 0.81
27 7 0.17
ACGTcount: A:0.16, C:0.14, G:0.40, T:0.30
Consensus pattern (26 bp):
GGCGAGCTGGTGTTCGTAGTAGGCTT
Found at i:1333752 original size:18 final size:19
Alignment explanation
Indices: 1333729--1333768 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1333719 TAAATGTTTC
1333729 TCATTTCACTT-TTTCTAT
1 TCATTTCACTTATTTCTAT
*
1333747 TCATTTCATTTATTTCTAT
1 TCATTTCACTTATTTCTAT
1333766 TCA
1 TCA
1333769 AACACACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (19 bp):
TCATTTCACTTATTTCTAT
Found at i:1346921 original size:27 final size:26
Alignment explanation
Indices: 1346891--1346986 Score: 102
Period size: 27 Copynumber: 3.6 Consensus size: 26
1346881 CCCAATATTT
* *
1346891 GTAAAATGACCGTAATCCCCCTGTAGG
1 GTAAAATGACCGAAAT-CCCCTGAAGG
* * *
1346918 GTAAAATGACCAAAATACCCTAGAACG
1 GTAAAATGACCGAAATCCCCT-GAAGG
*
1346945 GTAAAATGATCGAAATACCCCTGAAGG
1 GTAAAATGACCGAAAT-CCCCTGAAGG
*
1346972 GTAAAATGATCGAAA
1 GTAAAATGACCGAAA
1346987 AGGGTAAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
26 4 0.07
27 50 0.86
28 4 0.07
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.19
Consensus pattern (26 bp):
GTAAAATGACCGAAATCCCCTGAAGG
Found at i:1347050 original size:27 final size:27
Alignment explanation
Indices: 1346985--1347052 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
1346975 AAATGATCGA
*
1346985 AAAGGGTAAAAAGAACCAAAAACCCGC
1 AAAGGGTAAAATGAACCAAAAACCCGC
* *
1347012 AAAGGGTAAAATGATCGAAAAATCCC-C
1 AAAGGGTAAAATGAACCAAAAA-CCCGC
*
1347039 ATAGGGTAAAATGA
1 AAAGGGTAAAATGA
1347053 CTGTAATGCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 33 0.92
28 3 0.08
ACGTcount: A:0.51, C:0.16, G:0.21, T:0.12
Consensus pattern (27 bp):
AAAGGGTAAAATGAACCAAAAACCCGC
Found at i:1347118 original size:43 final size:43
Alignment explanation
Indices: 1347030--1347120 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
1347020 AAATGATCGA
* ** *
1347030 AAAATCCCCATAGGGTAAAATGACTGTAATGCCCCTGTAGAGT
1 AAAATCCCCATAGGGTAAAATGACTGAAATAACCCTATAGAGT
* *
1347073 AAAATCCCCATAGGGTTAAATGACTGAAATAACCTTATA-AGGT
1 AAAATCCCCATAGGGTAAAATGACTGAAATAACCCTATAGA-GT
1347116 AAAAT
1 AAAAT
1347121 GTCTGTAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAATCCCCATAGGGTAAAATGACTGAAATAACCCTATAGAGT
Found at i:1347197 original size:24 final size:24
Alignment explanation
Indices: 1347166--1347262 Score: 106
Period size: 24 Copynumber: 4.0 Consensus size: 24
1347156 ACCCCTCGAG
* *
1347166 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
1347190 TGTAAATGAGTGATTTATCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
1347214 TTTAAATGACTAATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
1347238 T-TAGTATAACTGATTTGTCTGTGA
1 TGTA-AATGACTGATTTGTCTGTGA
1347262 T
1 T
1347263 TTGTATTACT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
23 2 0.03
24 60 0.97
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:1347493 original size:32 final size:32
Alignment explanation
Indices: 1347448--1347602 Score: 174
Period size: 32 Copynumber: 4.9 Consensus size: 32
1347438 GCTGCGATGC
**
1347448 TACTGATGGCTTTGTGTTGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTATCGT
*
1347480 TACTGATGACTTTGTGCCGATCATATTA-CTGT
1 TACTGATGGCTTTGTGCCGATCATATTATC-GT
*
1347512 TACTAATGGCTTTGTGCCGATCATATTATCG-
1 TACTGATGGCTTTGTGCCGATCATATTATCGT
* * * *
1347543 TACTGATAG-TTATGTGCCGGTCATATCA-CTGC
1 TACTGATGGCTT-TGTGCCGATCATATTATC-GT
*
1347575 TACTGATGGCTTTGTGCCAATCATATTA
1 TACTGATGGCTTTGTGCCGATCATATTA
1347603 CTGTACTTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
30 3 0.03
31 23 0.22
32 75 0.72
33 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTATCGT
Found at i:1347584 original size:63 final size:64
Alignment explanation
Indices: 1347445--1347602 Score: 221
Period size: 63 Copynumber: 2.5 Consensus size: 64
1347435 TTTGCTGCGA
** *
1347445 TGCTACTGATGGCTTTGTGTTGATCATATTATCGTTACTGATGACTTTGTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGACTTTGTGCCGATCATATCAC
* * * *
1347509 TGTTACTAATGGCTTTGTGCCGATCATATTATCG-TACTGAT-AGTTATGTGCCGGTCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGACTT-TGTGCCGATCATATCAC
*
1347572 TGCTACTGATGGCTTTGTGCCAATCATATTA
1 TGCTACTGATGGCTTTGTGCCGATCATATTA
1347603 CTGTACTTAT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
62 3 0.04
63 50 0.60
64 30 0.36
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTATCGTTACTGATGACTTTGTGCCGATCATATCAC
Found at i:1347634 original size:22 final size:22
Alignment explanation
Indices: 1347609--1347658 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
1347599 ATTACTGTAC
* *
1347609 TTATGGATTGTAGCCATTCTGT
1 TTATGGATTATAGCCATCCTGT
* * *
1347631 TTATAGCTTATAGCTATCCTGT
1 TTATGGATTATAGCCATCCTGT
1347653 TTATGG
1 TTATGG
1347659 CTCTTAGTCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (22 bp):
TTATGGATTATAGCCATCCTGT
Found at i:1347902 original size:46 final size:46
Alignment explanation
Indices: 1347833--1347920 Score: 124
Period size: 46 Copynumber: 1.9 Consensus size: 46
1347823 ATTGTTGCAT
* * *
1347833 TTCTATTACTGATTCTGTCACTGTATTGGGCTTAGGCCCACATGTA
1 TTCTATTACTGATTCTGTCACTGTAATGGGCTAAGACCCACATGTA
*
1347879 TTCTATTTCTGATTCTGAT-ACTGTAATGGGCTAAGACCCACA
1 TTCTATTACTGATTCTG-TCACTGTAATGGGCTAAGACCCACA
1347921 CTACACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 36 0.97
47 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (46 bp):
TTCTATTACTGATTCTGTCACTGTAATGGGCTAAGACCCACATGTA
Found at i:1369062 original size:20 final size:20
Alignment explanation
Indices: 1369010--1369062 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1369000 ACATTTGTGC
*
1369010 CTCTATTTGCACTTTGGTGT
1 CTCTATTTGCACTTTGATGT
* *
1369030 CTCTACTTACACTTTGATGT
1 CTCTATTTGCACTTTGATGT
*
1369050 CTCTGTTTGCACT
1 CTCTATTTGCACT
1369063 ACAGTGCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.13, C:0.25, G:0.15, T:0.47
Consensus pattern (20 bp):
CTCTATTTGCACTTTGATGT
Found at i:1376175 original size:43 final size:42
Alignment explanation
Indices: 1376103--1376215 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 42
1376093 TTTCGAGGTG
* * * *
1376103 TGATTTCGTGCAAGACCATGTCAGGGACATTGGCATCGGTATGA
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCA-CCGTAT-A
*
1376147 -GATTACGTGTAAGACCATGTCTGGGACATTGGCACCTTATA
1 TGATTACGTGTAAGACCATGTCTGGGACATTGGCACCGTATA
1376188 TGATCTA--TGTAAGACCATGTCTGGGACA
1 TGAT-TACGTGTAAGACCATGTCTGGGACA
1376216 AAGGCATTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
41 22 0.35
42 7 0.11
43 33 0.53
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTCTGGGACATTGGCACCGTATA
Found at i:1382147 original size:25 final size:25
Alignment explanation
Indices: 1382119--1382173 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
1382109 TTCCTGATAG
1382119 GGCTCGCTTGAA-CTTCCCGA-TATAT
1 GGCTCGC-TGAAGCTTCCCGATTA-AT
**
1382144 GGCTATCTGAAGCTTCCCGATTAAT
1 GGCTCGCTGAAGCTTCCCGATTAAT
1382169 GGCTC
1 GGCTC
1382174 TTAGGAGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 4 0.16
25 19 0.76
26 2 0.08
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (25 bp):
GGCTCGCTGAAGCTTCCCGATTAAT
Found at i:1386183 original size:5 final size:5
Alignment explanation
Indices: 1386169--1386224 Score: 82
Period size: 5 Copynumber: 11.8 Consensus size: 5
1386159 TAAATATACA
*
1386169 ATAT- ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG -TA-C
1 ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG ATATG
1386216 ATATG ATAT
1 ATATG ATAT
1386225 ATGTATATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
4 8 0.17
5 39 0.83
ACGTcount: A:0.41, C:0.02, G:0.16, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:1386600 original size:29 final size:30
Alignment explanation
Indices: 1386536--1386601 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
1386526 ATTTGGATTT
* * *
1386536 ATTTGATTCTTTTTAATAATATAAAAATTA
1 ATTTGATTCTATTTAATAATAGAAAAACTA
* **
1386566 AATTGATT-TATTTAATAATAGAATGACTA
1 ATTTGATTCTATTTAATAATAGAAAAACTA
1386595 ATTTGAT
1 ATTTGAT
1386602 CCAATTCTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 22 0.76
30 7 0.24
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (30 bp):
ATTTGATTCTATTTAATAATAGAAAAACTA
Found at i:1387654 original size:11 final size:11
Alignment explanation
Indices: 1387640--1387679 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
1387630 TATTTTCTTC
1387640 CTATTTTGCTA
1 CTATTTTGCTA
*
1387651 CTATTTTACTA
1 CTATTTTGCTA
* *
1387662 TTATGTTGCTA
1 CTATTTTGCTA
1387673 CTATTTT
1 CTATTTT
1387680 ATTGTTATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:1387777 original size:29 final size:30
Alignment explanation
Indices: 1387717--1387780 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
1387707 ACTTATTTTA
**
1387717 TTGTTAATTTTGTTATTATTTTAAAGGTAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
1387747 TTGTTAA-TTTGTTATTATTTTAGATACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
1387776 TTGTT
1 TTGTT
1387781 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 23 0.77
30 7 0.23
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.61
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:1396069 original size:7 final size:7
Alignment explanation
Indices: 1396022--1396068 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
1396012 TTTTTTGGTT
1396022 GTTTAGG
1 GTTTAGG
*
1396029 GTATTAGT
1 GT-TTAGG
1396037 GTATTAGG
1 GT-TTAGG
1396045 GTTTAGG
1 GTTTAGG
1396052 G-TTAGG
1 GTTTAGG
*
1396058 GTTTTGG
1 GTTTAGG
1396065 GTTT
1 GTTT
1396069 TAAATTGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 6 0.17
7 16 0.46
8 13 0.37
ACGTcount: A:0.15, C:0.00, G:0.38, T:0.47
Consensus pattern (7 bp):
GTTTAGG
Found at i:1403411 original size:17 final size:17
Alignment explanation
Indices: 1403391--1403425 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1403381 AGGAAATAAA
*
1403391 AAAATATATATGTATAT
1 AAAATATAAATGTATAT
*
1403408 AAAATGTAAATGTATAT
1 AAAATATAAATGTATAT
1403425 A
1 A
1403426 TATGTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (17 bp):
AAAATATAAATGTATAT
Found at i:1403562 original size:3 final size:3
Alignment explanation
Indices: 1403554--1403592 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1403544 GTATATATAG
* * *
1403554 TAA TAA TAA TAA TGA TGA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1403593 CTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1403600 original size:20 final size:20
Alignment explanation
Indices: 1403575--1403634 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
1403565 ATGATGATAA
1403575 TAATAACAATAATAATAACT
1 TAATAACAATAATAATAACT
* *
1403595 TAATAACAAGAA-AATCAAATT
1 TAATAACAATAATAAT--AACT
*
1403616 TAATAAAAATAAATAATAA
1 TAATAACAAT-AATAATAA
1403635 ATAAAAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
19 3 0.09
20 11 0.34
21 13 0.41
22 2 0.06
23 3 0.09
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.27
Consensus pattern (20 bp):
TAATAACAATAATAATAACT
Found at i:1403939 original size:23 final size:24
Alignment explanation
Indices: 1403909--1403955 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1403899 AAATTAAATC
1403909 TCTAAGATTACA-AAATCATATCT
1 TCTAAGATTACATAAATCATATCT
* *
1403932 TCTAAGATTGCATATATCATATCT
1 TCTAAGATTACATAAATCATATCT
1403956 AAGATCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (24 bp):
TCTAAGATTACATAAATCATATCT
Found at i:1403980 original size:14 final size:12
Alignment explanation
Indices: 1403947--1403972 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1403937 GATTGCATAT
1403947 ATCATATCTAAG
1 ATCATATCTAAG
1403959 ATCATATCTAAG
1 ATCATATCTAAG
1403971 AT
1 AT
1403973 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:1406695 original size:33 final size:33
Alignment explanation
Indices: 1406658--1406755 Score: 130
Period size: 32 Copynumber: 3.0 Consensus size: 33
1406648 CACACGGTTC
* * *
1406658 TGTGAAATGGTAACAAATATCAGCTTTTCATTT
1 TGTGAAATGATAACAAATATCAACTTTTAATTT
1406691 TGTGAAATGATAACAAAT-TACAAC-TTTAATTT
1 TGTGAAATGATAACAAATAT-CAACTTTTAATTT
*
1406723 TGTAAAATGATAACAAATATCAAC-TTTAATTT
1 TGTGAAATGATAACAAATATCAACTTTTAATTT
1406755 T
1 T
1406756 TTTTAAATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
32 38 0.64
33 21 0.36
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (33 bp):
TGTGAAATGATAACAAATATCAACTTTTAATTT
Found at i:1408980 original size:50 final size:49
Alignment explanation
Indices: 1408852--1408980 Score: 120
Period size: 49 Copynumber: 2.6 Consensus size: 49
1408842 AATAATAACA
* * * *
1408852 TGCCAAAGTCATGTCCCAA-ACATGGTCTTACATGAGATGTTTCCTGTAC
1 TGCCAATGCCATGT-CCAAGACATGGTCTTACATGAGATGTTTCATATAC
* ** *
1408901 TGCCAATGCCATATCCCTGATATGGTCTTACATGAGA-GTTCTCATAT-C
1 TGCCAATGCCATGTCCAAGACATGGTCTTACATGAGATGTT-TCATATAC
*
1408949 GGTGCCCATGCCATGTCCAAGACATGGTCTTA
1 --TGCCAATGCCATGTCCAAGACATGGTCTTA
1408981 TGGGGGACCT
Statistics
Matches: 63, Mismatches: 13, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
48 6 0.10
49 32 0.51
50 25 0.40
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (49 bp):
TGCCAATGCCATGTCCAAGACATGGTCTTACATGAGATGTTTCATATAC
Found at i:1409001 original size:50 final size:50
Alignment explanation
Indices: 1408942--1409040 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
1408932 ATGAGAGTTC
* *
1408942 TCATATCGGTGCCCATGCCATGTCCAAGACATGGTCTTATGGGGGACCTT
1 TCATATCGGTGCCAATGCCATGTCCAAGACACGGTCTTATGGGGGACCTT
* * * *
1408992 TCATCTCGGTGCGAATGCCATGTCCTAGACACGGTCTTATGTGGGACCT
1 TCATATCGGTGCCAATGCCATGTCCAAGACACGGTCTTATGGGGGACCT
1409041 CTTATAACCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (50 bp):
TCATATCGGTGCCAATGCCATGTCCAAGACACGGTCTTATGGGGGACCTT
Found at i:1409465 original size:29 final size:29
Alignment explanation
Indices: 1409432--1409487 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1409422 CCTTGACTCG
1409432 AACTTTGGCAAAATTACAATTTTCCCCTA
1 AACTTTGGCAAAATTACAATTTTCCCCTA
* * * *
1409461 AACTTTTGCATATTTACACTTTTCCCC
1 AACTTTGGCAAAATTACAATTTTCCCC
1409488 AAAGCTCGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.27, G:0.05, T:0.39
Consensus pattern (29 bp):
AACTTTGGCAAAATTACAATTTTCCCCTA
Found at i:1411807 original size:11 final size:12
Alignment explanation
Indices: 1411766--1411812 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
1411756 GAATTAATTT
1411766 TTAATAAAAAATA
1 TTAAT-AAAAATA
**
1411779 TTTTTAGAAAATA
1 TTAATA-AAAATA
1411792 TTAATAAAAATA
1 TTAATAAAAATA
1411804 -TAATAAAAA
1 TTAATAAAAA
1411813 ATAGAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 9 0.31
12 7 0.24
13 13 0.45
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
TTAATAAAAATA
Found at i:1411813 original size:12 final size:13
Alignment explanation
Indices: 1411766--1411815 Score: 59
Period size: 12 Copynumber: 4.0 Consensus size: 13
1411756 GAATTAATTT
1411766 TTAATAAAAAATA
1 TTAATAAAAAATA
** *
1411779 TTTTTAGAAAATA
1 TTAATAAAAAATA
1411792 TTAAT-AAAAATA
1 TTAATAAAAAATA
1411804 -TAATAAAAAATA
1 TTAATAAAAAATA
1411816 GAATTTAGAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
TTAATAAAAAATA
Found at i:1412342 original size:13 final size:13
Alignment explanation
Indices: 1412324--1412348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1412314 AAATATTAAT
1412324 AATTAATTTTGAA
1 AATTAATTTTGAA
1412337 AATTAATTTTGA
1 AATTAATTTTGA
1412349 GAACAATTGC
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
AATTAATTTTGAA
Found at i:1413815 original size:21 final size:21
Alignment explanation
Indices: 1413789--1413830 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1413779 TATGGTGTGG
1413789 ATGGAAGATGCTACCGAAACA
1 ATGGAAGATGCTACCGAAACA
1413810 ATGGAAGATGCTACCGAAACA
1 ATGGAAGATGCTACCGAAACA
1413831 TGTACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (21 bp):
ATGGAAGATGCTACCGAAACA
Found at i:1420277 original size:14 final size:14
Alignment explanation
Indices: 1420239--1420270 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1420229 AAAATTAGAA
*
1420239 TTAGGAATTAGGAC
1 TTAGGACTTAGGAC
1420253 TTAGGACTTAGGAC
1 TTAGGACTTAGGAC
1420267 TTAG
1 TTAG
1420271 TATTTAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.09, G:0.28, T:0.31
Consensus pattern (14 bp):
TTAGGACTTAGGAC
Found at i:1426975 original size:50 final size:48
Alignment explanation
Indices: 1426872--1427041 Score: 135
Period size: 50 Copynumber: 3.4 Consensus size: 48
1426862 AGGTCCCACA
* * * * * **
1426872 TAAGACCGTGTCTAGGACATGGCGCTGGCACCGAGATGAAAGGTCCCCCG
1 TAAGACCATGTCTAGGACATGGC-ATGGCACTGACATGAAA-CTCCCATG
*
1426922 TAAGACCATGTCTAGGACATGGCATGGGCACTGATATGAGAACTCCCATG
1 TAAGACCATGTCTAGGACATGGCAT-GGCACTGACATGA-AACTCCCATG
* * * * * *
1426972 TAAGACCATATCTGGGATATGACATTGGCAGT-ACAAGAAACATCCCATG
1 TAAGACCATGTCTAGGACATGGCA-TGGCACTGACATGAAAC-TCCCATG
* *
1427021 TAAGACCATGTTTGGGACATG
1 TAAGACCATGTCTAGGACATG
1427042 ACTTTGGCAT
Statistics
Matches: 99, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
48 3 0.03
49 30 0.30
50 63 0.64
51 3 0.03
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.21
Consensus pattern (48 bp):
TAAGACCATGTCTAGGACATGGCATGGCACTGACATGAAACTCCCATG
Found at i:1428665 original size:472 final size:472
Alignment explanation
Indices: 1427339--1429639 Score: 3659
Period size: 472 Copynumber: 4.9 Consensus size: 472
1427329 TCCATTTTAC
* * * *
1427339 GGGAGAATTTAACGAATTAACTGTGCTATTTGGCTAACCTAGAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
** * * *
1427404 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACTTATCTAAATTTAGAGTTTCGT-AACTCAA
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTT-TTAAACTCGA
*
1427468 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTAAAATAAATTA
130 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTA
* *
1427533 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGT
195 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGT
* *
1427598 TGCATGTTTTAGGGTCTTGAGGTCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
260 TGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
* *
1427663 TTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGTTCGACT-C
325 TTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCC
* *
1427727 TAGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAGTTGATTTCTAGTGAATAGAGGTCAGAA
390 GA-CAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAA
* * *
1427792 CAGTCGGACAGTGAAATAG
454 CCGTCAGACAGTGAAACAG
* * *
1427811 GGGAGAGTTTAACGAATTAACTTTACTATTTTGCTAACCCAAAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* * *
1427876 GAAGACATGTGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTTGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
*
1427941 TTATAATTAAATTAGTGAATGTCACG-AAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* *
1428005 TTTGATTTATTTAAGTATTTAGAAAATTTTTAATGTTCCAC-GTTTGGACCTAAACCATTTTTGT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCC-CGGTTTGGACCTGAACCATTTTTGT
* * * *
1428069 TGCATGTTTTAGGGTCTCGAGGTCCCTTTTTAGAGACATATTGATTGAGCGTGAGTGAATTAATT
260 TGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
* * *
1428134 TTAAAAATAAATTTTTATGCCCCGAACTAGTAAGTCAAGTCAGGTAACGCATCATGCTCGACTCC
325 TTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCC
*
1428199 GACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
390 GACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
*
1428264 CGTCAGACAGTGAAACAA
455 CGTCAGACAGTGAAACAG
* * *
1428282 GGGAGACTTTAACGAATTAACTGTAGTATTTCGCAAACCCAAAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* *
1428347 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCAAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
*
1428412 TTATAATGAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* * *
1428477 TTTGATTTATTTACGTATTCAGAAAATTTTTAATGTTCCCCGTTTGGACTTGAACCATTTTTGTT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
1428542 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
261 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
*
1428607 TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
326 TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCG
* *
1428672 ACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACC
391 ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACC
*
1428737 GTCAGACAGTGAAACAC
456 GTCAGACAGTGAAACAG
* * *
1428754 GGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAT
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* *
1428819 GAAGATATATGAGTCTACTTTTAGGAAAAATTTACGGATCTCAATTTCGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
* *
1428884 TTATAATTAAATTAGTGACTGTAACACAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
*
1428949 TTTGATTTATTTAAGTATTCAGAAATTTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
** * *
1429014 GCATGTTTTAGGGTCTTAAGGACCCTTTTTAGGGACATATTGATTGAACGTGAGAGAATTAATTT
261 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
* *
1429079 TAAAAGA-AAATTTTTATGCTCCAAACTAGTAAGTTAAGTCAAGTAACGCATCATGCTCGACTCC
326 TAAAA-ACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCC
*
1429143 GGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
390 GACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAAC
*
1429208 CGTCGGACAGTGAAACAG
455 CGTCAGACAGTGAAACAG
* *
1429226 GGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
*
1429291 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATTTAAATTTCGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
* *
1429356 TTATAATTAAATTAGTGACTGTCATGCAAGTGGACT-GTTTTATTGTGAATAGTGAAATAAATTA
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGA-TAGTTTTATTATGAATAGTGAAATAAATTA
* * * ** **
1429420 TTTTGATTTATTTAAGTATTC-GAAAAAATTTTAATGTTCCCGGTTTAGATCTGAACTGTTTCCG
195 TTTTGATTTATTTAAGTATTCAG-AAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTG
* * * *
1429484 TTGCATGTTTTAGTGTCTCGAGGGCCCTTTTTAAGGAC--ATTGATTGAACATGAGCAAATTAAT
259 TTGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAAT
* * *
1429547 TTTAAAAGCAAATTTTTATGATCCGAACTAGTAAGTTAAGTCAGGTAACTGC-TCGTGCTCGACT
324 TTTAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAAC-GCATCATGCTCGACT
* * *
1429611 CTGGCAACGGTCTCGAGTAAGGGGTGTTA
388 CCGACAACGGTCTCGGGTAAGGGGTGTTA
1429640 CATCCCAGAA
Statistics
Matches: 1700, Mismatches: 119, Indels: 22
0.92 0.06 0.01
Matches are distributed among these distances:
470 104 0.06
471 441 0.26
472 1153 0.68
473 2 0.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (472 bp):
GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATTTCGAGTTTTTAAACTCGAG
TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACCTGAACCATTTTTGTT
GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGCTCGACTCCG
ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAGAACC
GTCAGACAGTGAAACAG
Found at i:1429398 original size:944 final size:943
Alignment explanation
Indices: 1427339--1429639 Score: 3688
Period size: 943 Copynumber: 2.4 Consensus size: 943
1427329 TCCATTTTAC
* * * *
1427339 GGGAGAATTTAACGAATTAACTGTGCTATTTGGCTAACCTAGAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
** * * *
1427404 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACTTATCTAAATTTAGAGTTTCGT-AACTCAA
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTT-TTAAACTCGA
*
1427468 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTAAAATAAATTA
130 GTTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTA
* * *
1427533 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCTGGTTTGGACCTAAACCATTTTTGT
195 TTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACTTGAACCATTTTTGT
* *
1427598 TGCATGTTTTAGGGTCTTGAGGTCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
260 TGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATT
* *
1427663 TTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACGCATCATGTTCGACT-C
325 TTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCC
* * *
1427727 TAGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAGTTGATTTCTAGTGAATAGAGGTCAGAA
390 GA-CAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAA
* * * * * * *
1427792 CAGTCGGACAGTGAAATAGGGGAGAGTTTAACGAATTAACTTTACTATTTTGCTAACCCAAAAAT
454 CAGTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAAT
* *
1427857 TCTAGAAATTTTATGATAAGAAGACATGTGAGTCTAGTTTTAGGAAAAATTTACGGATCTAAATT
519 TCTAGAAATTTTATGATAAGAAGACATATGAGTCTACTTTTAGGAAAAATTTACGGATCTAAATT
*
1427922 TTGAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGTCACGAAGTGGATAGTTTTATTATG
584 TCGAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGTCACGAAGTGGATAGTTTTATTATG
*
1427987 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTTAGAAAATTTTTAATGTTCCACGTTTGG
649 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCACGTTTGG
* *
1428052 ACCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCGAGGTCCCTTTTTAGAGACATATTGATTGA
714 ACCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCAAGGACCCTTTTTAGAGACATATTGATTGA
* * * *
1428117 GCGTGAGTGAATTAATTTTAAAAATAAATTTTTATGCCCCGAACTAGTAAGTCAAGTCAGGTAAC
779 ACGTGAGAGAATTAATTTTAAAAATAAATTTTTATGCCCCAAACTAGTAAGTCAAGTCAAGTAAC
*
1428182 GCATCATGCTCGACTCCGACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAG
844 GCATCATGCTCGACTCCGACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAG
1428247 TGAATAGAGGTCAGAACCGTCAGACAGTGAAACAA
909 TGAATAGAGGTCAGAACCGTCAGACAGTGAAACAA
* * *
1428282 GGGAGACTTTAACGAATTAACTGTAGTATTTCGCAAACCCAAAAATTCTAGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
*
1428347 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCAAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTTTTAAACTCGAG
*
1428412 TTATAATGAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
* *
1428477 TTTGATTTATTTACGTATTCAGAAAATTTTTAATGTTCCCCGTTTGGACTTGAACCATTTTTGTT
196 TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACTTGAACCATTTTTGTT
1428542 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
261 GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
*
1428607 TAAAAACAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
326 TAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
* *
1428672 ACAATGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACC
391 ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACA
1428737 GTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTC
456 GTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTC
* * * *
1428802 TGGAAATTTTATGATATGAAGATATATGAGTCTACTTTTAGGAAAAATTTACGGATCTCAATTTC
521 TAGAAATTTTATGATAAGAAGACATATGAGTCTACTTTTAGGAAAAATTTACGGATCTAAATTTC
*
1428867 GAGTTTTTAAACTCGAGTTATAATTAAATTAGTGACTGTAACAC-AAGTGGATAGTTTTATTATG
586 GAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGT--CACGAAGTGGATAGTTTTATTATG
*
1428931 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAATTTTTTAATGTTCC-CGGTTTG
649 AATAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCAC-GTTTG
* * *
1428995 GACCTGAACCATTTTTGTTGCATGTTTTAGGGTCTTAAGGACCCTTTTTAGGGACATATTGATTG
713 GACCTAAACCATTTTTGTTGCATGTTTTAGGGTCTCAAGGACCCTTTTTAGAGACATATTGATTG
* *
1429060 AACGTGAGAGAATTAATTTTAAAAGA-AAATTTTTATGCTCCAAACTAGTAAGTTAAGTCAAGTA
778 AACGTGAGAGAATTAATTTTAAAA-ATAAATTTTTATGCCCCAAACTAGTAAGTCAAGTCAAGTA
*
1429124 ACGCATCATGCTCGACTCCGGCAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCT
842 ACGCATCATGCTCGACTCCGACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCT
* *
1429189 AGTGAATAGAGGTCAGAACCGTCGGACAGTGAAACAG
907 AGTGAATAGAGGTCAGAACCGTCAGACAGTGAAACAA
* *
1429226 GGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTCTGGAAATTTTATGATAA
1 GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
* *
1429291 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGGATTTAAATTTCGAGTTTTTAAACTCGAG
66 GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTTTTAAACTCGAG
* *
1429356 TTATAATTAAATTAGTGACTGTCATGCAAGTGGACT-GTTTTATTGTGAATAGTGAAATAAATTA
131 TTATAATTAAATTAGTGACTGTCACGCAAGTGGA-TAGTTTTATTATGAATAGTGAAATAAATTA
* * ** **
1429420 TTTTGATTTATTTAAGTATTC-GAAAAAATTTTAATGTTCCCGGTTTAGA-TCTGAACTGTTTCC
195 TTTTGATTTATTTAAGTATTCAG-AAAATTTTTAATGTTCCCGGTTTGGACT-TGAACCATTTTT
* * * *
1429483 GTTGCATGTTTTAGTGTCTCGAGGGCCCTTTTTAAGGAC--ATTGATTGAACATGAGCAAATTAA
258 GTTGCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAA
* *
1429546 TTTTAAAAGCAAATTTTTATGATCCGAACTAGTAAGTTAAGTCAGGTAACTGC-TCGTGCTCGAC
323 TTTTAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACT-CATCATGCTCGAC
* * *
1429610 TCTGGCAACGGTCTCGAGTAAGGGGTGTTA
387 TCCGACAACGGTCTCGGGTAAGGGGTGTTA
1429640 CATCCCAGAA
Statistics
Matches: 1256, Mismatches: 92, Indels: 21
0.92 0.07 0.02
Matches are distributed among these distances:
942 108 0.09
943 578 0.46
944 565 0.45
945 5 0.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (943 bp):
GGGAGACTTTAACGAATTAACTGTACTATTTGGCTAACCCAAAAATTCTAGAAATTTTATGATAA
GAAGATATATGAGTCTAGTTTTAGGAAAAATTTACGAATCTAAATTTCGAGTTTTTAAACTCGAG
TTATAATTAAATTAGTGACTGTCACGCAAGTGGATAGTTTTATTATGAATAGTGAAATAAATTAT
TTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCCGGTTTGGACTTGAACCATTTTTGTT
GCATGTTTTAGGGTCTCGAGGGCCCTTTTTAGGGACATATTGATTGAACGTGAGCGAATTAATTT
TAAAAGCAAATTTTTATGCTCCGAACTAGTAAGTTAAGTCAGGTAACTCATCATGCTCGACTCCG
ACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTGAATAGAGGTCAAAACA
GTCAGACAGTGAAACACGGGAGACTTTAACAAATTAACTGTACTATTTGGCTAACCCAAAAATTC
TAGAAATTTTATGATAAGAAGACATATGAGTCTACTTTTAGGAAAAATTTACGGATCTAAATTTC
GAGTTTTTAAACTCGAGTTATAATTAAATTAGTGAATGTCACGAAGTGGATAGTTTTATTATGAA
TAGTGAAATAAATTATTTTGATTTATTTAAGTATTCAGAAAATTTTTAATGTTCCACGTTTGGAC
CTAAACCATTTTTGTTGCATGTTTTAGGGTCTCAAGGACCCTTTTTAGAGACATATTGATTGAAC
GTGAGAGAATTAATTTTAAAAATAAATTTTTATGCCCCAAACTAGTAAGTCAAGTCAAGTAACGC
ATCATGCTCGACTCCGACAACGGTCTCGGGTAAGGGGTGTTATTTATGATAATTGATTTCTAGTG
AATAGAGGTCAGAACCGTCAGACAGTGAAACAA
Found at i:1433857 original size:13 final size:13
Alignment explanation
Indices: 1433802--1433858 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
1433792 TAATACTCGA
*
1433802 TTTTCAAGATATG
1 TTTTAAAGATATG
* *
1433815 TTTCT-AGGTTATG
1 TTT-TAAAGATATG
* *
1433828 TTTTTAAGTTATG
1 TTTTAAAGATATG
1433841 TTTTAAAGATATG
1 TTTTAAAGATATG
1433854 TTTTA
1 TTTTA
1433859 CGATGCTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 1 0.03
13 35 0.95
14 1 0.03
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.54
Consensus pattern (13 bp):
TTTTAAAGATATG
Found at i:1435158 original size:25 final size:23
Alignment explanation
Indices: 1435096--1435159 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 23
1435086 CGAACCCATG
*
1435096 TTTTTATGCGAACTCATATTTTA
1 TTTTTATGCGAACTCATATTGTA
* *
1435119 TGTTTTAGTGTGAACTCATGTTGTA
1 T-TTTTA-TGCGAACTCATATTGTA
1435144 CTTTTCTATGCGAACT
1 -TTTT-TATGCGAACT
1435160 ATAATAATAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 1 0.03
24 5 0.15
25 24 0.73
26 3 0.09
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.48
Consensus pattern (23 bp):
TTTTTATGCGAACTCATATTGTA
Found at i:1441539 original size:43 final size:43
Alignment explanation
Indices: 1441492--1441616 Score: 132
Period size: 41 Copynumber: 3.0 Consensus size: 43
1441482 CCCAGATATT
* * *
1441492 GTCTTATATGTTAACGCATATCGATGCCATTGTCCCAGACAGG
1 GTCTTATACGTTAACTCATATCGATGCCAATGTCCCAGACAGG
* *
1441535 GTCTTATACG--AA-TCATATACGATGCCAATATCCCAGACATG
1 GTCTTATACGTTAACTCATAT-CGATGCCAATGTCCCAGACAGG
* **
1441576 GTCTTACACGTTTTCTCACT-TCGATGCCAATGTCCCAGACA
1 GTCTTATACGTTAACTCA-TATCGATGCCAATGTCCCAGACA
1441617 TGATCTTACA
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
40 5 0.07
41 30 0.44
43 28 0.41
44 4 0.06
45 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
GTCTTATACGTTAACTCATATCGATGCCAATGTCCCAGACAGG
Found at i:1441879 original size:92 final size:92
Alignment explanation
Indices: 1441751--1442171 Score: 526
Period size: 92 Copynumber: 4.6 Consensus size: 92
1441741 ATCCAATGCT
* * * * *
1441751 CAAATCAATTC-AGCAGTATATATCCATATACGAATCAAATTTGGCAATGTATATTTATATACAA
1 CAAATCAATTCGA-CAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* *
1441815 ATC-AATTCGGCAATGAATATCCATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * * * *
1441842 CAATTCAAATTTGACAATGTATAACCATATACAAATCAAATTCGACAATATATATCTATATACAA
1 CAAATC-AATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
*
1441907 ATCAAATTCGACAATGTATATCTATATA
65 ATCAAATTCGGCAATGTATATCTATATA
* * *
1441935 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATACAAA
1 CAAATCAATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
1442000 TCAAATTCGGCAATGTATATCTATATA
66 TCAAATTCGGCAATGTATATCTATATA
* * * * * *
1442027 CAAATCAATTCGGCAATGTATATCTATAAACAATTCAAATTCGACAATGTATATCTATAAACAAA
1 CAAATCAATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
* * *
1442092 TCAATTTCGTCAATGTATATCTATAAA
66 TCAAATTCGGCAATGTATATCTATATA
* **
1442119 GAAATCAAATTC-AGCAATGTATATCTTTATACAAATC-AATTCGGCAATGTATA
1 CAAATC-AATTCGA-CAATGTATATCCATATACAAATCAAATTCGGCAATGTATA
1442172 AAACATATAC
Statistics
Matches: 287, Mismatches: 38, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
91 5 0.02
92 230 0.80
93 52 0.18
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (92 bp):
CAAATCAATTCGACAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
TCAAATTCGGCAATGTATATCTATATA
Found at i:1441894 original size:123 final size:122
Alignment explanation
Indices: 1441751--1442171 Score: 560
Period size: 123 Copynumber: 3.4 Consensus size: 122
1441741 ATCCAATGCT
* * * * *
1441751 CAAATC-AATTCAGCAGTATATATCCATATACGAATCAAATTTGGCAATGTATATTTATATACAA
1 CAAATCAAATTCAGCAATATATATCTATATACAAATC-AATTCGGCAATGTATATCTATATACAA
* *
1441815 ATCAATTCGGCAATGAATATCCATATACAATTCAAATTTGACAATGTATAACCATATA
65 ATCAATTCGGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
*
1441873 CAAATCAAATTC-GACAATATATATCTATATACAAATCAAATTCGACAATGTATATCTATATACA
1 CAAATCAAATTCAG-CAATATATATCTATATACAAATC-AATTCGGCAATGTATATCTATATACA
* *
1441937 AATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATAACCATATA
64 AATCAATTCGGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
* * * *
1441996 CAAATCAAATTCGGCAATGTATATCTATATACAAATCAATTCGGCAATGTATATCTATAAACAAT
1 CAAATCAAATTCAGCAATATATATCTATATACAAATCAATTCGGCAATGTATATCTATATACAAA
* * * * * * *
1442061 TCAAATTCGACAATGTATATCTATAAACAAATC-AATTTCGTCAATGTATATCTATAAA
66 TC-AATTCGGCAATGTATATCCATATACAAATCAAATTT-GACAATGTATAACCATATA
* * *
1442119 GAAATCAAATTCAGCAATGTATATCTTTATACAAATCAATTCGGCAATGTATA
1 CAAATCAAATTCAGCAATATATATCTATATACAAATCAATTCGGCAATGTATA
1442172 AAACATATAC
Statistics
Matches: 269, Mismatches: 25, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
122 38 0.14
123 230 0.86
124 1 0.00
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (122 bp):
CAAATCAAATTCAGCAATATATATCTATATACAAATCAATTCGGCAATGTATATCTATATACAAA
TCAATTCGGCAATGTATATCCATATACAAATCAAATTTGACAATGTATAACCATATA
Found at i:1442182 original size:31 final size:31
Alignment explanation
Indices: 1441751--1442171 Score: 537
Period size: 31 Copynumber: 13.7 Consensus size: 31
1441741 ATCCAATGCT
* * * *
1441751 CAAATC-AATTCAGCAGTATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
1441781 CGAATCAAATTTGGCAATGTATATTTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
1441812 CAAATC-AATTCGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * * * *
1441842 CAATTCAAATTTGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
1441873 CAAATCAAATTCGACAATATATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
1441904 CAAATCAAATTCGACAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
1441935 CAAATC-AATTCGGCAATGTATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
1441965 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
1441996 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
1442027 CAAATC-AATTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
1442057 CAATTCAAATTCGACAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
1442088 CAAATCAATTTCGTCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
1442119 GAAATCAAATTCAGCAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
1442150 CAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
1442172 AAACATATAC
Statistics
Matches: 345, Mismatches: 42, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
30 101 0.29
31 244 0.71
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:1443199 original size:4 final size:4
Alignment explanation
Indices: 1443190--1443216 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1443180 TTCTCATATA
1443190 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1 TTAT TTAT TTAT TTAT TTAT TTAT TTA
1443217 AAGTATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:1448926 original size:26 final size:26
Alignment explanation
Indices: 1448890--1448958 Score: 120
Period size: 26 Copynumber: 2.7 Consensus size: 26
1448880 CCCGTTATAT
*
1448890 GGCTCTTTGTGAGCTTCTTGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
1448916 GGCTCTTTGTGAGCTTCTCGATTAAA
1 GGCTCTTTGTGAGCTTCTCGATTAAA
*
1448942 GGCTTTTTGTGAGCTTC
1 GGCTCTTTGTGAGCTTC
1448959 CCAATATTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (26 bp):
GGCTCTTTGTGAGCTTCTCGATTAAA
Found at i:1453171 original size:10 final size:10
Alignment explanation
Indices: 1453156--1453183 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1453146 TAATATAAAT
1453156 ATTATAAACA
1 ATTATAAACA
1453166 ATTATAAACA
1 ATTATAAACA
1453176 ATTATAAA
1 ATTATAAA
1453184 TTAGATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (10 bp):
ATTATAAACA
Found at i:1459970 original size:62 final size:62
Alignment explanation
Indices: 1459870--1459993 Score: 185
Period size: 62 Copynumber: 2.0 Consensus size: 62
1459860 AAGTATGTCG
* * *
1459870 AGGCTGATCAAGTTATTTATGCTTTAAATATGGTTGAAGATATAAATGCAAACTAAGAGCCA
1 AGGCTGATCAAGTTACTTATGCTTTAAATATGGCTGAAGATATAAATGCAAACCAAGAGCCA
* * * *
1459932 AGGCTGATCTAGTTGCTTATGCTTTAAATGTGGCTGAAGATATAGATGCAAACCAAGAGCCA
1 AGGCTGATCAAGTTACTTATGCTTTAAATATGGCTGAAGATATAAATGCAAACCAAGAGCCA
1459994 TCTAATTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 55 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (62 bp):
AGGCTGATCAAGTTACTTATGCTTTAAATATGGCTGAAGATATAAATGCAAACCAAGAGCCA
Found at i:1461425 original size:15 final size:15
Alignment explanation
Indices: 1461407--1461445 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1461397 CGGTATCATT
1461407 TTGTTCGTGATAATA
1 TTGTTCGTGATAATA
* *
1461422 TTGTTCGTGGTGATA
1 TTGTTCGTGATAATA
1461437 TTGTT-GTGA
1 TTGTTCGTGA
1461446 GCAAAATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.18, C:0.05, G:0.28, T:0.49
Consensus pattern (15 bp):
TTGTTCGTGATAATA
Found at i:1465158 original size:43 final size:45
Alignment explanation
Indices: 1465095--1465182 Score: 162
Period size: 43 Copynumber: 2.0 Consensus size: 45
1465085 AGGAAAAATT
1465095 TAAAGTATTTATTTGACAAATAAACCTTAAAATTTAGAATTTTGG
1 TAAAGTATTTATTTGACAAATAAACCTTAAAATTTAGAATTTTGG
1465140 TAAAGTA-TT-TTTGACAAATAAACCTTAAAATTTAGAATTTTGG
1 TAAAGTATTTATTTGACAAATAAACCTTAAAATTTAGAATTTTGG
1465183 AGGGAAATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 34 0.79
44 2 0.05
45 7 0.16
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (45 bp):
TAAAGTATTTATTTGACAAATAAACCTTAAAATTTAGAATTTTGG
Found at i:1478380 original size:593 final size:594
Alignment explanation
Indices: 1477193--1478385 Score: 2325
Period size: 593 Copynumber: 2.0 Consensus size: 594
1477183 TATATAATAT
1477193 ATTACTATTATTATTAGTTAAAATAAAAGGAATAAAGTAAAGTAAGTAAATAAAAGAACAAGAAA
1 ATTA-TATTATTATTAGTTAAAATAAAAGGAATAAAGTAAAGTAAGTAAATAAAAGAACAAGAAA
1477258 AAGAAGAAGAACATAAAAGAAGCAGAGAACGAAAAGAAAACAAGGGAAGAAAAAGGAAAGAAAGA
65 AAGAAGAAGAACATAAAAGAAGCAGAGAACGAAAAGAAAACAAGGGAAGAAAAAGGAAAGAAAGA
1477323 AGAAAGGGAAAATTAGGGTTTTAAAGCTTGAAATTTAATTGGTAAGTTTAATCAAGTCCTTTTCT
130 AGAAAGGGAAAATTAGGGTTTTAAAGCTTGAAATTTAATTGGTAAGTTTAATCAAGTCCTTTTCT
1477388 TAAAAATTTGATGTTTTTGGAATCCTAGAGTGAGATACTATTGGATTTAAGTTGAAATTTTTAAA
195 TAAAAATTTGATGTTTTTGGAATCCTAGAGTGAGATACTATTGGATTTAAGTTGAAATTTTTAAA
1477453 GTTGGTAGATTTTTGAGTAGGGTTTATGTTGAAAAAAAAATGATGGAATTGAGGGTTTATTTGAT
260 GTTGGTAGATTTTTGAGTAGGGTTTATGTTGAAAAAAAAATGATGGAATTGAGGGTTTATTTGAT
* * *
1477518 AGAAATTTTGATTGGAATTGAATAAAGGATTGGATTGTAAACTAAGCTATAAGTGTTGAGTTTTA
325 AGAAATTTTGATTGGAATTGAATAAAGGATTGAATTGTAAACAAAGCTATAAGTGTTGAATTTTA
1477583 GGGATTAAATTGAAATAAATTCGAAATTATGAAAATATGATAAAAATTAGATAGTTAAATTTGAG
390 GGGATTAAATTGAAATAAATTCGAAATTATGAAAATATGATAAAAATTAGATAGTTAAATTTGAG
1477648 TTTGGCAAGAAATTGAGTAGCAAAAGGTTATAAATTGAGAAAGAAAAATATATAGGTTTAGTTAG
455 TTTGGCAAGAAATTGAGTAGCAAAAGGTTATAAATTGAGAAAGAAAAATATATAGGTTTAGTTAG
1477713 GATTCAAATTGAAATTAAATTAAAAGTTAGATAAAAATTTCAGCAATTAAATTGTGTTGTGCTAA
520 GATTCAAATTGAAATTAAATTAAAAGTTAGATAAAAATTTCAGCAATTAAATTGTGTTGTGCTAA
1477778 TGATTGTGAA
585 TGATTGTGAA
1477788 ATTATATTATTATTAGTTAAAATAAAAGGAATAAAGTAAAGTAAGTAAATAAAAGAACAAGAAAA
1 ATTATATTATTATTAGTTAAAATAAAAGGAATAAAGTAAAGTAAGTAAATAAAAGAACAAGAAAA
*
1477853 AGAAGAAGAACATAAAAGAAGCAGAGAACGAAACGAAAACAAGGGAAGAAAAAGGAAAGAAAGAA
66 AGAAGAAGAACATAAAAGAAGCAGAGAACGAAAAGAAAACAAGGGAAGAAAAAGGAAAGAAAGAA
1477918 GAAAGGGAAAATTAGGGTTTTAAAGCTTGAAATTTAATTGGTAAGTTTAATCAAGTCCTTTTCTT
131 GAAAGGGAAAATTAGGGTTTTAAAGCTTGAAATTTAATTGGTAAGTTTAATCAAGTCCTTTTCTT
1477983 AAAAATTTGATGTTTTTGGAATCCTAGAGTGAGATACTATTGGATTTAAGTTGAAATTTTTAAAG
196 AAAAATTTGATGTTTTTGGAATCCTAGAGTGAGATACTATTGGATTTAAGTTGAAATTTTTAAAG
1478048 TTGGTAGATTTTTGAGTAGGGTTTATGTTGAAAAAAAAA-GATGGAATTGAGGGTTTATTTGATA
261 TTGGTAGATTTTTGAGTAGGGTTTATGTTGAAAAAAAAATGATGGAATTGAGGGTTTATTTGATA
*
1478112 GAAATTTTGATTGGAATTGAATAAAGGATTGAATTGTAAACAAAGCTATAAGTTTTGAATTTTAG
326 GAAATTTTGATTGGAATTGAATAAAGGATTGAATTGTAAACAAAGCTATAAGTGTTGAATTTTAG
1478177 GGATTAAATTGAAATAAATTCGAAATTATGAAAATATGATAAAAATTAGATAGTTAAATTTGAGT
391 GGATTAAATTGAAATAAATTCGAAATTATGAAAATATGATAAAAATTAGATAGTTAAATTTGAGT
1478242 TTGGCAAGAAATTGAGTAGCAAAAGGTTATAAATTGAGAAAGAAAAATATATAGGTTTAGTTAGG
456 TTGGCAAGAAATTGAGTAGCAAAAGGTTATAAATTGAGAAAGAAAAATATATAGGTTTAGTTAGG
1478307 ATTCAAATTGAAATTAAATTAAAAGTTAGATAAAAATTTCAGCAATTAAATTGTGTTGTGCTAAT
521 ATTCAAATTGAAATTAAATTAAAAGTTAGATAAAAATTTCAGCAATTAAATTGTGTTGTGCTAAT
1478372 GATTGTGAA
586 GATTGTGAA
1478381 ATTAT
1 ATTAT
1478386 TTTAATTGTT
Statistics
Matches: 593, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
593 295 0.50
594 294 0.50
595 4 0.01
ACGTcount: A:0.45, C:0.04, G:0.20, T:0.31
Consensus pattern (594 bp):
ATTATATTATTATTAGTTAAAATAAAAGGAATAAAGTAAAGTAAGTAAATAAAAGAACAAGAAAA
AGAAGAAGAACATAAAAGAAGCAGAGAACGAAAAGAAAACAAGGGAAGAAAAAGGAAAGAAAGAA
GAAAGGGAAAATTAGGGTTTTAAAGCTTGAAATTTAATTGGTAAGTTTAATCAAGTCCTTTTCTT
AAAAATTTGATGTTTTTGGAATCCTAGAGTGAGATACTATTGGATTTAAGTTGAAATTTTTAAAG
TTGGTAGATTTTTGAGTAGGGTTTATGTTGAAAAAAAAATGATGGAATTGAGGGTTTATTTGATA
GAAATTTTGATTGGAATTGAATAAAGGATTGAATTGTAAACAAAGCTATAAGTGTTGAATTTTAG
GGATTAAATTGAAATAAATTCGAAATTATGAAAATATGATAAAAATTAGATAGTTAAATTTGAGT
TTGGCAAGAAATTGAGTAGCAAAAGGTTATAAATTGAGAAAGAAAAATATATAGGTTTAGTTAGG
ATTCAAATTGAAATTAAATTAAAAGTTAGATAAAAATTTCAGCAATTAAATTGTGTTGTGCTAAT
GATTGTGAA
Found at i:1478650 original size:40 final size:39
Alignment explanation
Indices: 1478602--1478697 Score: 106
Period size: 40 Copynumber: 2.4 Consensus size: 39
1478592 GAAATTGAGA
*
1478602 TTGA-TACTGCACTGAATTATGGAA-TACTGAATATTGTTT
1 TTGAGTACTGCATTGAATTAT-GAAGTACTGAATATT-TTT
* *
1478641 TTGAGTACTGAATTGAATTGTGAAGTTACTGAATATTTTT
1 TTGAGTACTGCATTGAATTATGAAG-TACTGAATATTTTT
* *
1478681 ATGTGTACTGCATTGAA
1 TTGAGTACTGCATTGAA
1478698 CTGTGAAATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
39 7 0.15
40 30 0.62
41 11 0.23
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (39 bp):
TTGAGTACTGCATTGAATTATGAAGTACTGAATATTTTT
Found at i:1478703 original size:40 final size:41
Alignment explanation
Indices: 1478626--1478709 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 41
1478616 AATTATGGAA
* * *
1478626 TACTGAATATTGTTTTTGAGTACTGAATTGAATTGTGAAGT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAT
* *
1478667 TACTGAATATT-TTTATGTGTACTGCATTGAACTGTGAAAT
1 TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAT
1478707 TAC
1 TAC
1478710 GGAAGTAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
40 27 0.71
41 11 0.29
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (41 bp):
TACTGAATATTGTTTATGAGTACTGAATTGAACTGTGAAAT
Found at i:1478986 original size:45 final size:44
Alignment explanation
Indices: 1478917--1479021 Score: 147
Period size: 45 Copynumber: 2.3 Consensus size: 44
1478907 GCCGACTATT
* *
1478917 GTTACTGTTACTGATTCAATACTTTGTGTGTCGAATACTGTTAGC
1 GTTACTGTTACT-ATTCAACACTTTGTGTGTCGAATACTATTAGC
* **
1478962 GTTACTGTTACATATTCAACACTTTGTGTGTTGAATACTATTATT
1 GTTACTGTTAC-TATTCAACACTTTGTGTGTCGAATACTATTAGC
1479007 GTTACTGTTACTATT
1 GTTACTGTTACTATT
1479022 ACTGATACCG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
44 4 0.07
45 49 0.91
46 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (44 bp):
GTTACTGTTACTATTCAACACTTTGTGTGTCGAATACTATTAGC
Found at i:1479020 original size:18 final size:18
Alignment explanation
Indices: 1478997--1479046 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
1478987 GTGTGTTGAA
* *
1478997 TACTATTATTGTTACTGT
1 TACTATTACTGTTACCGT
*
1479015 TACTATTACTGATACCGT
1 TACTATTACTGTTACCGT
1479033 TACTGATTACTGTT
1 TACT-ATTACTGTT
1479047 TAGGTGCTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 19 0.70
19 8 0.30
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (18 bp):
TACTATTACTGTTACCGT
Found at i:1479023 original size:12 final size:13
Alignment explanation
Indices: 1478997--1479046 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 13
1478987 GTGTGTTGAA
*
1478997 TACT-ATTATTGT
1 TACTGATTACTGT
*
1479009 TACTG-TTACTAT
1 TACTGATTACTGT
*
1479021 TACTGA-TACCGT
1 TACTGATTACTGT
1479033 TACTGATTACTGT
1 TACTGATTACTGT
1479046 T
1 T
1479047 TAGGTGCTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
TACTGATTACTGT
Found at i:1481800 original size:22 final size:22
Alignment explanation
Indices: 1481774--1481850 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 22
1481764 CTAAATTAAG
1481774 AATAAAGAATATAATGTATATT
1 AATAAAGAATATAATGTATATT
* * *
1481796 AATAATGTCATATAAAGTTAATAACAATT
1 AATAAAG-AATATAATG-T-AT----ATT
1481825 AATAAAGAATATAATGTATATT
1 AATAAAGAATATAATGTATATT
1481847 AATA
1 AATA
1481851 TATTAATTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
22 13 0.31
23 7 0.17
24 1 0.02
25 2 0.05
26 2 0.05
27 1 0.02
28 7 0.17
29 9 0.21
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.35
Consensus pattern (22 bp):
AATAAAGAATATAATGTATATT
Found at i:1485156 original size:50 final size:50
Alignment explanation
Indices: 1485030--1485271 Score: 211
Period size: 50 Copynumber: 4.7 Consensus size: 50
1485020 GATAATAACA
* * ** * * *
1485030 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGTATGTTTCCTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
1485079 TGCCAATGCCATATCACAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
1485129 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATATCGG
* * **
1485179 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
*
1485235 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1485272 TCTCATTCCC
Statistics
Matches: 155, Mismatches: 28, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
48 1 0.01
49 38 0.25
50 79 0.51
51 1 0.01
53 2 0.01
56 34 0.22
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:1497254 original size:25 final size:25
Alignment explanation
Indices: 1497226--1497284 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 25
1497216 AGCTATAAAC
*
1497226 AGTAAGCTCATACAAGTTGAATATT
1 AGTAAGCTCATACAAGCTGAATATT
* * *
1497251 AGTAAGGTCATGCGAGCTGAATATT
1 AGTAAGCTCATACAAGCTGAATATT
* *
1497276 GGCAAGCTC
1 AGTAAGCTC
1497285 TCTCGAGTTG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (25 bp):
AGTAAGCTCATACAAGCTGAATATT
Found at i:1505195 original size:27 final size:28
Alignment explanation
Indices: 1505165--1505461 Score: 219
Period size: 27 Copynumber: 11.1 Consensus size: 28
1505155 TAAAAGTTAG
**
1505165 TTTACCCTAT-GGGGGCGTTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
*
1505192 TTTACCC-ATCGAGGGTATTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* *
1505219 TTTACCCT-TCGGGGGTATTTTGGTAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
*
1505246 TTTA-CCAATCGGGGGTATTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
1505273 TTTACCCT-TC-GGGGTATTTC-AGTAAT
1 TTTACCCTATCGGGGGTATTTCGA-TAAT
* * * *
1505299 TTTACCC-ATCGAGGGTATTTTGGTAGT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* * ** * * *
1505326 TTTA-TCTACCAAGGGTATTTTGGTAAG
1 TTTACCCTATCGGGGGTATTTCGATAAT
* ** *
1505353 TTTACTC-ATC-GATGTATTTCGGTAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* *
1505379 TTTACCC-ATCGAGGGTATTTCGGTAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
* *
1505406 TTTA-CCTATCGAGAGTATTTC-AGTAAT
1 TTTACCCTATCGGGGGTATTTCGA-TAAT
** *
1505433 TTTACCC-ATCAAGGGTATTTTGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
1505460 TT
1 TT
1505462 AGGCCCATTA
Statistics
Matches: 221, Mismatches: 34, Indels: 30
0.78 0.12 0.11
Matches are distributed among these distances:
25 1 0.00
26 50 0.23
27 163 0.74
28 7 0.03
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.41
Consensus pattern (28 bp):
TTTACCCTATCGGGGGTATTTCGATAAT
Found at i:1505247 original size:54 final size:54
Alignment explanation
Indices: 1505188--1505461 Score: 295
Period size: 54 Copynumber: 5.1 Consensus size: 54
1505178 GGCGTTTCGA
**
1505188 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCGGGGGTATTTTGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
* * * **
1505242 TAATTTTACCAATCGGGGGTATTTCGATAATTTTACCCTTC-GGGGTATTTCAG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
* * * * *
1505295 TAATTTTACCCATCGAGGGTATTTTGGTAGTTTTA-TCTACCAAGGGTATTTTGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCT-TCAAGGGTATTTTGG
* * * * * * *
1505349 TAAGTTTACTCATCGA-TGTATTTCGGTAATTTTACCCATCGAGGGTATTTCGG
1 TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
* * * *
1505402 TAATTTTACCTATCGAGAGTATTTC-AGTAATTTTACCCATCAAGGGTATTTTGA
1 TAATTTTACCCATCGAGGGTATTTCGA-TAATTTTACCCTTCAAGGGTATTTTGG
1505456 TAATTT
1 TAATTT
1505462 AGGCCCATTA
Statistics
Matches: 183, Mismatches: 32, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
52 2 0.01
53 81 0.44
54 100 0.55
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (54 bp):
TAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCAAGGGTATTTTGG
Found at i:1505318 original size:80 final size:79
Alignment explanation
Indices: 1505182--1505461 Score: 319
Period size: 80 Copynumber: 3.5 Consensus size: 79
1505172 TATGGGGGCG
* *
1505182 TTTCGATAATTTTACCCATCGAGGGTATTTCGATAATTTTACCCTTCGGGGGTATTTTGGTAATT
1 TTTCGATAATTTTACCCATCG-GGGTATTTCG-TAATTTTACCCATCGAGGGTATTTTGGTAATT
* *
1505247 TTACCAATCGGGGGTA
64 TTACCTATCGAGGGTA
* *
1505263 TTTCGATAATTTTACCCTTCGGGGTATTTCAGTAATTTTACCCATCGAGGGTATTTTGGTAGTTT
1 TTTCGATAATTTTACCCATCGGGGTATTTC-GTAATTTTACCCATCGAGGGTATTTTGGTAATTT
* * *
1505328 TATCTACCAAGGGTA
65 TACCTATCGAGGGTA
* * * * ** *
1505343 TTTTGGTAAGTTTACTCATCGATGTATTTCGGTAATTTTACCCATCGAGGGTATTTCGGTAATTT
1 TTTCGATAATTTTACCCATCGGGGTATTTC-GTAATTTTACCCATCGAGGGTATTTTGGTAATTT
*
1505408 TACCTATCGAGAGTA
65 TACCTATCGAGGGTA
* *
1505423 TTTC-AGTAATTTTACCCATCAAGGGTATTTTGATAATTT
1 TTTCGA-TAATTTTACCCATC-GGGGTATTTCG-TAATTT
1505462 AGGCCCATTA
Statistics
Matches: 164, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
80 131 0.80
81 33 0.20
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.41
Consensus pattern (79 bp):
TTTCGATAATTTTACCCATCGGGGTATTTCGTAATTTTACCCATCGAGGGTATTTTGGTAATTTT
ACCTATCGAGGGTA
Found at i:1506676 original size:25 final size:25
Alignment explanation
Indices: 1506626--1506679 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1506616 TGAACCTCTA
* *
1506626 ACCTCCTTACCACACCTGTGATGCC
1 ACCTCATTACCACACCTATGATGCC
*
1506651 ACCTCATTGCCACACCTATG-TCGCC
1 ACCTCATTACCACACCTATGAT-GCC
1506676 ACCT
1 ACCT
1506680 TGGCACTACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.20, C:0.44, G:0.11, T:0.24
Consensus pattern (25 bp):
ACCTCATTACCACACCTATGATGCC
Found at i:1511663 original size:26 final size:26
Alignment explanation
Indices: 1511634--1511688 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
1511624 AACACACTAA
1511634 TATCGCAACAAAGCTACCAGTAACAG
1 TATCGCAACAAAGCTACCAGTAACAG
* * *
1511660 TATCGCAGCAAAGCTGCCAGTAATAG
1 TATCGCAACAAAGCTACCAGTAACAG
1511686 TAT
1 TAT
1511689 ACTTCCTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (26 bp):
TATCGCAACAAAGCTACCAGTAACAG
Found at i:1513249 original size:41 final size:41
Alignment explanation
Indices: 1513204--1513435 Score: 329
Period size: 41 Copynumber: 5.7 Consensus size: 41
1513194 GAACTGGATT
*
1513204 AGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATC
1 AGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATC
* * * * * *
1513245 AGGCTATAAACCTAGCAGGCTAAATGCCGGTGAACTGGATT
1 AGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATC
*
1513286 AGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATC
1 AGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATC
* * * *
1513327 AGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGAACTGGATT
1 AGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATC
1513368 AGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATC
1 AGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATC
* * *
1513409 AGGCTTTAAGCCTAACAAGCTAAGTGC
1 AGGCTATAAGCCTAGCAGGCTAAGTGC
1513436 CAGTGAATCT
Statistics
Matches: 165, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 165 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (41 bp):
AGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATC
Found at i:1513324 original size:82 final size:82
Alignment explanation
Indices: 1513187--1513442 Score: 449
Period size: 82 Copynumber: 3.1 Consensus size: 82
1513177 NNNNNNNNNN
1513187 TGCCGGTGAACTGGATTAGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTAT
1 TGCCGGTGAACTGGATTAGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTAT
* *
1513252 AAACCTAGCAGGCTAAA
66 AAGCCTAGCAGGCTAAG
1513269 TGCCGGTGAACTGGATTAGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTAT
1 TGCCGGTGAACTGGATTAGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTAT
1513334 AAGCCTAGCAGGCTAAG
66 AAGCCTAGCAGGCTAAG
* *
1513351 TGCCGGTGAACTGGATTAGGCTATAAGCCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTTT
1 TGCCGGTGAACTGGATTAGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTAT
* *
1513416 AAGCCTAACAAGCTAAG
66 AAGCCTAGCAGGCTAAG
*
1513433 TGCCAGTGAA
1 TGCCGGTGAA
1513443 TCTGTTTATA
Statistics
Matches: 167, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 167 1.00
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (82 bp):
TGCCGGTGAACTGGATTAGGCTATAAGTCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGCTAT
AAGCCTAGCAGGCTAAG
Found at i:1515499 original size:48 final size:48
Alignment explanation
Indices: 1515447--1515574 Score: 148
Period size: 48 Copynumber: 2.7 Consensus size: 48
1515437 TGTATATTTT
* * **
1515447 TTTCAAGCAACGAAAAGACTGGGAAAGAAAATGGACGGGAGTTTGGGA
1 TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAATGGACAAGAGTTTGGGA
* * * * * *
1515495 TTTCAAGTAAAGAGAAGTCTGGGAAAAAAAAGGGACAAGATTTTGGGG
1 TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAATGGACAAGAGTTTGGGA
* *
1515543 TTTCAGGCAAAGAAAAGTCTGAGAAAGAAAAT
1 TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAAT
1515575 AATTTGTGCG
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.19
Consensus pattern (48 bp):
TTTCAAGCAAAGAAAAGTCTGGGAAAGAAAATGGACAAGAGTTTGGGA
Found at i:1527234 original size:20 final size:20
Alignment explanation
Indices: 1527198--1527237 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1527188 TACTGCTGAG
*
1527198 CAGAGGCACCGTGGTGCAAA
1 CAGAGGCACAGTGGTGCAAA
1527218 CAGAGGCACTAGT-GTGCAAA
1 CAGAGGCAC-AGTGGTGCAAA
1527238 AAGGGGCACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.12
Consensus pattern (20 bp):
CAGAGGCACAGTGGTGCAAA
Found at i:1527254 original size:20 final size:20
Alignment explanation
Indices: 1527231--1527296 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
1527221 AGGCACTAGT
1527231 GTGCAAAAAGGGGCACCAAA
1 GTGCAAAAAGGGGCACCAAA
** * ***
1527251 GTGCAATGAGGGACATTGAA
1 GTGCAAAAAGGGGCACCAAA
* *
1527271 GTGCAAATAGAGGCACCAAA
1 GTGCAAAAAGGGGCACCAAA
1527291 GTGCAA
1 GTGCAA
1527297 TCTCGTACAA
Statistics
Matches: 33, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.30, T:0.12
Consensus pattern (20 bp):
GTGCAAAAAGGGGCACCAAA
Found at i:1538771 original size:22 final size:21
Alignment explanation
Indices: 1538736--1538850 Score: 71
Period size: 19 Copynumber: 5.7 Consensus size: 21
1538726 AAAAGGTATC
* * *
1538736 TACAAATTAAATCTCTAATAT
1 TACAAATCATATCTCTAAGAT
1538757 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
1538780 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
1538799 TACATATCATA--TCTATGAT
1 TACAAATCATATCTCTAAGAT
* * *
1538818 TGCATATCATA--TCTAAGAG
1 TACAAATCATATCTCTAAGAT
*
1538837 TACATATCATATCT
1 TACAAATCATATCT
1538851 AAGATTGCAT
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
19 51 0.65
21 4 0.05
22 15 0.19
23 9 0.11
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:1538796 original size:19 final size:19
Alignment explanation
Indices: 1538772--1538863 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
1538762 AATCATATCT
1538772 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
1538791 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
1538810 TCTATGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
1538829 TCTAAGAGTACATATCATA
1 TCTAAGATTGCATATCATA
1538848 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
1538864 CTTGAAGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1538825 original size:38 final size:38
Alignment explanation
Indices: 1538765--1538863 Score: 166
Period size: 38 Copynumber: 2.7 Consensus size: 38
1538755 ATTACAAAAT
*
1538765 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
*
1538801 CATATCATATCTATGATTGCATATCATATCTAAGAGTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
1538839 CATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTGCATATC
1538864 CTTGAAGATT
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 6 0.10
37 1 0.02
38 51 0.88
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.37
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGAGTA
Found at i:1538996 original size:15 final size:14
Alignment explanation
Indices: 1538965--1538995 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1538955 AATTTTGGAC
*
1538965 TTTGTTTTATTATT
1 TTTGGTTTATTATT
1538979 TTTGGTTTATTATT
1 TTTGGTTTATTATT
1538993 TTT
1 TTT
1538996 TTATGAGTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (14 bp):
TTTGGTTTATTATT
Found at i:1540015 original size:19 final size:19
Alignment explanation
Indices: 1539993--1540033 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1539983 TGGCCTCTCC
1539993 TTTTCCTCTTCTTCTTTCT
1 TTTTCCTCTTCTTCTTTCT
* * *
1540012 TTTTCTTTTTCTTTTTTCT
1 TTTTCCTCTTCTTCTTTCT
1540031 TTT
1 TTT
1540034 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCCTCTTCTTCTTTCT
Found at i:1540024 original size:12 final size:12
Alignment explanation
Indices: 1540001--1540044 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
1539991 CCTTTTCCTC
1540001 TTCTTCTTTCTTT
1 TTCTT-TTTCTTT
1540014 TTCTTTTTCTTT
1 TTCTTTTTCTTT
1540026 TT-TCTTTTCTTT
1 TTCT-TTTTCTTT
1540038 TTCTTTT
1 TTCTTTT
1540045 CCCTTTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.03
12 22 0.76
13 6 0.21
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTTTCTTT
Found at i:1540033 original size:18 final size:19
Alignment explanation
Indices: 1540001--1540044 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
1539991 CCTTTTCCTC
*
1540001 TTCTTCTTTCTTTTTCTTT
1 TTCTTTTTTCTTTTTCTTT
1540020 TTCTTTTTTC-TTTTCTTT
1 TTCTTTTTTCTTTTTCTTT
1540038 TTCTTTT
1 TTCTTTT
1540045 CCCTTTTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTCTTTTTTCTTTTTCTTT
Found at i:1540050 original size:18 final size:18
Alignment explanation
Indices: 1540012--1540051 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1540002 TCTTCTTTCT
**
1540012 TTTTCTTTTTCTTTTTTC
1 TTTTCTTTTTCTTTTCCC
1540030 TTTTCTTTTTCTTTTCCC
1 TTTTCTTTTTCTTTTCCC
1540048 TTTT
1 TTTT
1540052 TCCATCATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTCTTTTCCC
Found at i:1540051 original size:24 final size:23
Alignment explanation
Indices: 1539992--1540053 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 23
1539982 TTGGCCTCTC
*
1539992 CTTTTCCTCTTCTTCTTTCTTTTT
1 CTTTTCC-CTTTTTCTTTCTTTTT
* *
1540016 CTTTTTCTTTTTTCTTTTCTTTTT
1 CTTTTCCCTTTTTC-TTTCTTTTT
1540040 CTTTTCCCTTTTTC
1 CTTTTCCCTTTTTC
1540054 CATCATCATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 5 0.16
24 27 0.84
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (23 bp):
CTTTTCCCTTTTTCTTTCTTTTT
Found at i:1544985 original size:22 final size:20
Alignment explanation
Indices: 1544962--1545039 Score: 88
Period size: 19 Copynumber: 3.9 Consensus size: 20
1544952 CAAATTAAAT
*
1544962 CTCTAAGATTACAAAATCATA
1 CTCTAAGATTAC-ATATCATA
*
1544983 TCTTCTAAGATTGCATATCATA
1 -C-TCTAAGATTACATATCATA
1545005 -TCTAAGATTACATATCATA
1 CTCTAAGATTACATATCATA
*
1545024 C-CTAAGATTGCATATC
1 CTCTAAGATTACATATC
1545040 CTTGAATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
19 32 0.64
22 8 0.16
23 10 0.20
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (20 bp):
CTCTAAGATTACATATCATA
Found at i:1544993 original size:23 final size:22
Alignment explanation
Indices: 1544950--1545023 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 22
1544940 AAAAGATATC
* *
1544950 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
1544971 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
1544994 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
1545013 TACATATCATA
1 TACAAATCATA
1545024 CCTAAGATTG
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
19 18 0.39
21 3 0.07
22 15 0.33
23 10 0.22
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.35
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:1545010 original size:19 final size:19
Alignment explanation
Indices: 1544986--1545039 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
1544976 AATCATATCT
1544986 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
1545005 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
1545024 CCTAAGATTGCATATC
1 TCTAAGATTGCATATC
1545040 CTTGAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:1545036 original size:38 final size:41
Alignment explanation
Indices: 1544963--1545039 Score: 115
Period size: 38 Copynumber: 1.9 Consensus size: 41
1544953 AAATTAAATC
1544963 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTACAAAATCATATC-TCTAAGATTGCATATCATA
*
1545005 TCTAAGATTAC-ATATCATA-C-CTAAGATTGCATATC
1 TCTAAGATTACAAAATCATATCTCTAAGATTGCATATC
1545040 CTTGAATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 15 0.44
40 1 0.03
41 7 0.21
42 11 0.32
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.35
Consensus pattern (41 bp):
TCTAAGATTACAAAATCATATCTCTAAGATTGCATATCATA
Found at i:1546326 original size:16 final size:16
Alignment explanation
Indices: 1546305--1546346 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
1546295 TGTTTGGCTC
** *
1546305 GCTGTAATGGAATAGA
1 GCTGTAATAAAATAAA
1546321 GCTGTAATAAAATAAA
1 GCTGTAATAAAATAAA
1546337 GCTGTAATAA
1 GCTGTAATAA
1546347 GTAATTCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.21, T:0.26
Consensus pattern (16 bp):
GCTGTAATAAAATAAA
Found at i:1546640 original size:34 final size:35
Alignment explanation
Indices: 1546586--1546655 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
1546576 AATTTTTATT
1546586 AAAATATGAATTAATAAAAATCATAACATAATCTG
1 AAAATATGAATTAATAAAAATCATAACATAATCTG
1546621 AAAATATGAA-TAATAAAAATCATAACATAATCTG
1 AAAATATGAATTAATAAAAATCATAACATAATCTG
1546655 A
1 A
1546656 TGGGATCATA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 25 0.71
35 10 0.29
ACGTcount: A:0.59, C:0.09, G:0.06, T:0.27
Consensus pattern (35 bp):
AAAATATGAATTAATAAAAATCATAACATAATCTG
Found at i:1546650 original size:17 final size:17
Alignment explanation
Indices: 1546597--1546651 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
1546587 AAATATGAAT
1546597 TAATAAAAATCATAACA
1 TAATAAAAATCATAACA
* *
1546614 TAATCTGAAAAT-ATGA-A
1 TAA--TAAAAATCATAACA
1546631 TAATAAAAATCATAACA
1 TAATAAAAATCATAACA
1546648 TAAT
1 TAAT
1546652 CTGATGGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 6 0.20
16 3 0.10
17 12 0.40
18 3 0.10
19 6 0.20
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.27
Consensus pattern (17 bp):
TAATAAAAATCATAACA
Found at i:1548356 original size:15 final size:15
Alignment explanation
Indices: 1548336--1548367 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1548326 ATTGCACAAC
1548336 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
1548351 TTAATAGTAAAGCAT
1 TTAATAGTAAAGCAT
1548366 TT
1 TT
1548368 TCCTCCATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
TTAATAGTAAAGCAT
Found at i:1560392 original size:15 final size:15
Alignment explanation
Indices: 1560372--1560401 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1560362 ATTGAGGAGT
1560372 CAATTAATAATTAAC
1 CAATTAATAATTAAC
1560387 CAATTAATAATTAAC
1 CAATTAATAATTAAC
1560402 AAATGGACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
CAATTAATAATTAAC
Found at i:1564591 original size:10 final size:10
Alignment explanation
Indices: 1564578--1564608 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1564568 TAGATGAAAT
*
1564578 TTGAATTGAA
1 TTGAATCGAA
1564588 TTGAATCGAA
1 TTGAATCGAA
1564598 TTGAATCGAA
1 TTGAATCGAA
1564608 T
1 T
1564609 ATATTTGTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (10 bp):
TTGAATCGAA
Found at i:1564807 original size:1 final size:1
Alignment explanation
Indices: 1564803--1564840 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
1564793 AGCAAAAGTC
1564803 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1564841 CTAAACCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1572758 original size:16 final size:16
Alignment explanation
Indices: 1572737--1572770 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1572727 AGGAGGAGTG
*
1572737 TTGAGAATCTTTGATA
1 TTGAGAATCTTTCATA
1572753 TTGAGAATCTTTCATA
1 TTGAGAATCTTTCATA
1572769 TT
1 TT
1572771 ATTAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (16 bp):
TTGAGAATCTTTCATA
Found at i:1574571 original size:82 final size:82
Alignment explanation
Indices: 1574434--1574590 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 82
1574424 TCTCCGCCAA
* * *
1574434 TGATCACGAAGCAACTCAATTGTCTATTTATTACACCATTGGACATATTATTACCGAAAAATACA
1 TGATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACA
1574499 CAAAAAGAAACCACTAG
66 CAAAAAGAAACCACTAG
* * *
1574516 TGATCACGAAGCAACTCAACTGTCTATTTATTCCACCATTGGAAATATCATTACCGGAAAATGCA
1 TGATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACA
1574581 CAAAAAGAAA
66 CAAAAAGAAA
1574591 ACATTCAAAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (82 bp):
TGATCACGAAGCAACTCAACTGTCTATTTATTACACCATTGGAAATATCATTACCGAAAAATACA
CAAAAAGAAACCACTAG
Found at i:1576480 original size:5 final size:5
Alignment explanation
Indices: 1576470--1576498 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1576460 CACACTTCCA
1576470 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
1576499 ACTCTTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (5 bp):
TTTTG
Found at i:1585881 original size:23 final size:24
Alignment explanation
Indices: 1585851--1585958 Score: 150
Period size: 24 Copynumber: 4.6 Consensus size: 24
1585841 CATTATTGGG
*
1585851 AAAGGATGAATTGACGG-AAATGT
1 AAAGGATGAATTGAAGGAAAATGT
1585874 AAAGGATGAATTGAAGGAAAATGT
1 AAAGGATGAATTGAAGGAAAATGT
* *
1585898 AAAGGA-GAAACTGACGGAAAATGT
1 AAAGGATG-AATTGAAGGAAAATGT
*
1585922 AAAGGATGAATTGAAGG-TAATGT
1 AAAGGATGAATTGAAGGAAAATGT
1585945 AAAGGATGAATTGA
1 AAAGGATGAATTGA
1585959 TGACAAATTG
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
23 36 0.47
24 39 0.51
25 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.30, T:0.20
Consensus pattern (24 bp):
AAAGGATGAATTGAAGGAAAATGT
Found at i:1588574 original size:91 final size:92
Alignment explanation
Indices: 1588407--1588587 Score: 283
Period size: 91 Copynumber: 2.0 Consensus size: 92
1588397 TTTTTTTTTC
* ** *
1588407 TTTTTAATGGAATGTATTGAACCTTTTAACGTGAAGAGGGATGACAACCCAAGCACCCCACCCCG
1 TTTTTAA-GGAATGTATCGAACCTTTTAACAAGAAGAGAGATGACAACCCAAGCACCCCACCCCG
*
1588472 GTTACTGAGCCCAACACACTCTTAATTA
65 GTTACTCAGCCCAACACACTCTTAATTA
* *
1588500 TTTTTAA-GAATGTATCGAACCTTTTGACAAGAAGAGAGATGACAACCCAAGCACCCCACCTCGG
1 TTTTTAAGGAATGTATCGAACCTTTTAACAAGAAGAGAGATGACAACCCAAGCACCCCACCCCGG
1588564 TTACTCAGCCCAACACACTCTTAA
66 TTACTCAGCCCAACACACTCTTAA
1588588 AATAATTTAT
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
91 74 0.91
93 7 0.09
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (92 bp):
TTTTTAAGGAATGTATCGAACCTTTTAACAAGAAGAGAGATGACAACCCAAGCACCCCACCCCGG
TTACTCAGCCCAACACACTCTTAATTA
Found at i:1594754 original size:21 final size:19
Alignment explanation
Indices: 1594728--1594774 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
1594718 TCATTTTTAG
1594728 CAACTTCCTCTTCTTCAGCAA
1 CAACTT-CTC-TCTTCAGCAA
*
1594749 CAACTT-TCTCTTCTGCAA
1 CAACTTCTCTCTTCAGCAA
1594767 CAACTTCT
1 CAACTTCT
1594775 GCTTTTGCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 15 0.62
19 3 0.12
21 6 0.25
ACGTcount: A:0.23, C:0.36, G:0.04, T:0.36
Consensus pattern (19 bp):
CAACTTCTCTCTTCAGCAA
Found at i:1607771 original size:40 final size:41
Alignment explanation
Indices: 1607695--1607799 Score: 108
Period size: 40 Copynumber: 2.6 Consensus size: 41
1607685 GCTTAGATAA
*
1607695 AAAATACCGCTAAAAATCAAGCATTACCGGCGCTTTTA-AG
1 AAAATACCGCTAAAAATCAAGCATTACCGGCACTTTTAGAG
* * * * *
1607735 AAAATGCCGCTAAAGATCGAGTATTAGCGGCACTTTTAGAG
1 AAAATACCGCTAAAAATCAAGCATTACCGGCACTTTTAGAG
* * *
1607776 -AAACACTGCTAAAAAT-GAGCATTA
1 AAAATACCGCTAAAAATCAAGCATTA
1607800 GCGGTGTTTT
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
39 7 0.13
40 44 0.83
41 2 0.04
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (41 bp):
AAAATACCGCTAAAAATCAAGCATTACCGGCACTTTTAGAG
Found at i:1607919 original size:41 final size:41
Alignment explanation
Indices: 1607860--1608210 Score: 513
Period size: 41 Copynumber: 8.6 Consensus size: 41
1607850 TATTTGAGTT
* * *
1607860 CTCGGGTCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAGTT
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
1607901 TTCGGGTCTTTAGTGGCGTTTTTGAAGAAGAGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
1607942 TTTGGGTCTTTAGTGGCGTTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* *
1607983 CTCGGGTCTTTAGCGGCGTTTTTGGAGAATCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
*
1608024 CTCGGGTCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * * *
1608065 CTCGGGTCTTTAGCGGTGTTTTTAAAGAAGCACTGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* * *
1608106 CTCGGGTCTTTAGAGGCATTTTTGAAGAAGCGCTGCTAATG
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
* *
1608147 CTCAGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATT
1 CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
1608188 CTCGGGTCTTTAGCGGCGTTTTT
1 CTCGGGTCTTTAGCGGCGTTTTT
1608211 AAAAAAGCTT
Statistics
Matches: 278, Mismatches: 32, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 278 1.00
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (41 bp):
CTCGGGTCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG
Found at i:1613887 original size:43 final size:43
Alignment explanation
Indices: 1613840--1614132 Score: 302
Period size: 43 Copynumber: 6.8 Consensus size: 43
1613830 TTTTTAATAG
* * ** *
1613840 AAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTAGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
** * * * * *** *
1613883 AAGCGTAGCTGAAGGTCTTGTTCTTTAGCAGCGTTTTTAATAG
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
* * **
1613926 AAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
** * * * *
1613969 AAGCGTAGCTGAAGGTCTTGTTCTTTAGCAGCGTTTTTGGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
* *
1614012 AAGCGCCGCTAAAAGTCTTGGTCTTTAGCGGCGTTTGTGGGAG
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
*
1614055 AA-CGCCGCTAAAGGTCTTGGTCTTTAG-GGACATTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGG-CGTTTGTGGGAA
*
1614097 AAGGGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTT
1614133 TTTCTGGCGC
Statistics
Matches: 200, Mismatches: 47, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
41 2 0.01
42 36 0.18
43 160 0.80
44 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGGTCTTTAGCGGCGTTTGTGGGAA
Found at i:1613922 original size:86 final size:86
Alignment explanation
Indices: 1613822--1614081 Score: 371
Period size: 86 Copynumber: 3.0 Consensus size: 86
1613812 GTCAATGTTA
* *
1613822 TAGCGGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTAGGAAAAGC
1 TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
1613887 GTAGCTGAAGGTCTTGTTCTT
66 GTAGCTGAAGGTCTTGTTCTT
1613908 TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
1 TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
1613973 GTAGCTGAAGGTCTTGTTCTT
66 GTAGCTGAAGGTCTTGTTCTT
*** * * ** *
1613994 TAGCAGCGTTTTTGGGAAAAGCGCCGCTAAAAG-TCTTGGTCTTTAGCGGCGTTTGTGGGAGAA-
1 TAGCAGCGTTTTTAATAGAAGCGCCGCT-AAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAG
** * *
1614057 CGCCGCTAAAGGTCTTGGTCTT
65 CGTAGCTGAAGGTCTTGTTCTT
1614079 TAG
1 TAG
1614082 GGACATTTGT
Statistics
Matches: 159, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
85 21 0.13
86 134 0.84
87 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (86 bp):
TAGCAGCGTTTTTAATAGAAGCGCCGCTAAAGCTCATGACCTTTAGCGGCGTTTGTGGGAAAAGC
GTAGCTGAAGGTCTTGTTCTT
Found at i:1615310 original size:19 final size:19
Alignment explanation
Indices: 1615287--1615338 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
1615277 AAAAAAACTT
*
1615287 AAAAATCATTAAAATTTA-
1 AAAAATCATTAAAAATTAC
**
1615305 ATAAAAAAATTAAAAATTAC
1 A-AAAATCATTAAAAATTAC
1615325 AAAAATCA-TAAAAA
1 AAAAATCATTAAAAA
1615339 AAACTATAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 7 0.26
19 19 0.70
20 1 0.04
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (19 bp):
AAAAATCATTAAAAATTAC
Found at i:1615329 original size:29 final size:30
Alignment explanation
Indices: 1615274--1615330 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1615264 AATTATAAAA
**
1615274 AATAAAAAAACTTAAAAATCATTAAAATTT
1 AATAAAAAAACTTAAAAATCACAAAAATTT
*
1615304 AATAAAAAAA-TTAAAAATTACAAAAAT
1 AATAAAAAAACTTAAAAATCACAAAAAT
1615331 CATAAAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (30 bp):
AATAAAAAAACTTAAAAATCACAAAAATTT
Found at i:1615390 original size:30 final size:28
Alignment explanation
Indices: 1615305--1615378 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 28
1615295 TTAAAATTTA
1615305 ATAAAAAAATTA-AAAATTACAAAAATC
1 ATAAAAAAATTATAAAATTACAAAAATC
* *
1615332 ATAAAAAAAACTATAAAATTTTATAAAAATC
1 AT-AAAAAAATTATAAAA--TTACAAAAATC
1615363 ATAAAAAAATTATAAA
1 ATAAAAAAATTATAAA
1615379 CTTCACCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 2 0.05
28 9 0.22
29 4 0.10
30 13 0.32
31 12 0.30
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (28 bp):
ATAAAAAAATTATAAAATTACAAAAATC
Found at i:1615618 original size:21 final size:22
Alignment explanation
Indices: 1615561--1615618 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 22
1615551 TTGGTATGAT
1615561 AATTTTTATAATTTAT-TTTACG
1 AATTTTTATAATTT-TCTTTACG
*
1615583 AA-TCTTAT-A-TTTCTTTAC-
1 AATTTTTATAATTTTCTTTACG
1615601 AATTTTTATAATTTTCTT
1 AATTTTTATAATTTTCTT
1615619 ATGACTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
18 3 0.10
19 12 0.40
20 2 0.07
21 11 0.37
22 2 0.07
ACGTcount: A:0.29, C:0.09, G:0.02, T:0.60
Consensus pattern (22 bp):
AATTTTTATAATTTTCTTTACG
Found at i:1618385 original size:140 final size:140
Alignment explanation
Indices: 1618165--1618868 Score: 909
Period size: 140 Copynumber: 5.0 Consensus size: 140
1618155 TAGAAAACTA
*
1618165 AATTATATTCTTTCCAAAA-ACTATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
1618229 TATAATTGTTTATATTAATAAATTTGGCAAAATATATACAATTAATATTTTGAATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
1618294 TATATATATT
131 TATATATATT
* * *
1618304 AATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * *
1618369 TATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAACATTTTGTATGAATCAAA-T
66 TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
*
1618433 T-CATATATT
131 TATATATATT
* * *
1618442 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTTCAACGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
1618507 TATAACTATTTATATTAATAAATTCGGTAAAATATATATACAATTAATATTTTGTATGAATCAAA
66 TATAATTGTTTATATTAATAAATTTGGT-AAA-ATATATACAATTAATATTTTGTATGAATCAAA
*
1618572 -TT-CATATATT
129 TTTATATATATT
* * * *
1618582 AATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * *
1618647 TAT-ATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
66 TATAAT-TGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
*
1618711 TCATATATTAATTT
130 TTATATA-T-A-TT
* * ** * *
1618725 TATCTATGTTCTCTATTTGTGAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAAT
1 AAT-TAT-AT-TC---TT-TCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAAT
*
1618790 TAATTAATAT-ATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGA
59 TAATTAATATAAT-TGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGA
* * *
1618854 ACCACATTCATATAT
123 ATCAAATTTATATAT
1618869 TAATTTTATC
Statistics
Matches: 508, Mismatches: 41, Indels: 22
0.89 0.07 0.04
Matches are distributed among these distances:
138 119 0.23
139 28 0.06
140 224 0.44
141 1 0.00
142 1 0.00
143 4 0.01
144 3 0.01
145 1 0.00
146 1 0.00
149 3 0.01
150 123 0.24
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (140 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
TATATATATT
Found at i:1618683 original size:278 final size:277
Alignment explanation
Indices: 1618165--1618873 Score: 937
Period size: 278 Copynumber: 2.5 Consensus size: 277
1618155 TAGAAAACTA
* * *
1618165 AATTATATTCTTTCCAAAA-ACTATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTT-AACGAAATTAATTAA
* * *
1618229 TATAATTGTTTATATTAATAAATTTGG-CAAA-ATATATACAATTAATATTTTGAATGAATCAAA
65 TATAACTGTTTATATTAATAAATTTGGTAAAATATATATACAATTAATATTTTGTATGAATCAAA
* * * * * *
1618292 TTTATATATATTAATTATATTCTTTCCAAATGAATATTAATTTCTATATCTTTTATATTTTGACC
130 -TT-CATATATTAATTATATTATTTCAAAAAGAATATTAATTTCCATACCTTTTATATTTTGACC
*
1618357 GAAATTAATTAATATAATTGTTTGTATTAATAAATTCGATAAAATATATACAATTAACATTTTGT
193 GAAATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAACATTTTGT
*
1618422 ATGAATCAAATTCATATATT
258 ATGAACCAAATTCATATATT
1618442 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTTCAACGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTT-AACGAAATTAATTAA
* *
1618507 TATAACTATTTATATTAATAAATTCGGTAAAATATATATACAATTAATATTTTGTATGAATCAAA
65 TATAACTGTTTATATTAATAAATTTGGTAAAATATATATACAATTAATATTTTGTATGAATCAAA
* *
1618572 TTCATATATTAATTATATTATTTCAAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGA
130 TTCATATATTAATTATATTATTTCAAAAAGAATATTAATTTCCATACCTTTTATATTTTGACCGA
* * * *
1618637 AATTAATTAATAT-ATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTA
195 AATTAATTAATATAAT-TGTTTATATTAATAAATTCGATAAAATATATACAATTAACATTTTGTA
*
1618701 TGAACCACATTCATATATT
259 TGAACCAAATTCATATATT
** *
1618720 AATTTTATCTATGTTCTCTATTTGTGAAAAAGAATATTAATTTCCATG-CCTTTTATATTTTGAC
1 AA--TTA--TA---T-TC---TT-TCCAAAAGAATATTAATTTCCATGTCC-TTTATATTTTAAC
*
1618784 TGAAATTAATTAATATATCTGTTTATATTAATAAATTTGGTAAAATATATAT--AATTAATATTT
53 -GAAATTAATTAATATAACTGTTTATATTAATAAATTTGGTAAAATATATATACAATTAATATTT
* *
1618847 TGTATGAACCACATTCATATATTAATT
117 TGTATGAATCAAATTCATATATTAATT
1618874 TTATCTATGT
Statistics
Matches: 382, Mismatches: 32, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
277 21 0.05
278 195 0.51
279 5 0.01
280 34 0.09
282 2 0.01
285 1 0.00
286 2 0.01
288 36 0.09
289 6 0.02
290 80 0.21
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (277 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCCTTTATATTTTAACGAAATTAATTAAT
ATAACTGTTTATATTAATAAATTTGGTAAAATATATATACAATTAATATTTTGTATGAATCAAAT
TCATATATTAATTATATTATTTCAAAAAGAATATTAATTTCCATACCTTTTATATTTTGACCGAA
ATTAATTAATATAATTGTTTATATTAATAAATTCGATAAAATATATACAATTAACATTTTGTATG
AACCAAATTCATATATT
Found at i:1618717 original size:67 final size:67
Alignment explanation
Indices: 1618646--1618868 Score: 148
Period size: 67 Copynumber: 3.1 Consensus size: 67
1618636 AAATTAATTA
1618646 ATATATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
1 ATATATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
1618711 TC
66 TC
* ** ** * *
1618713 ATATAT-TAATTTTATCTATGTTCTCTATTTGTGAAAAAGA-ATATTAATTTCCATGCCTTTTAT
1 ATATATCT--GTTTA--TAT-TAATAAATTTG-GTAAAATATATA-TAA-TT--A--------AT
** *
1618776 ATTTTG-ACTGAAATTA-ATTA
48 ATTTTGTA-TG-AACCACATTC
1618796 ATATATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
1 ATATATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
1618861 TC
66 TC
1618863 ATATAT
1 ATATAT
1618869 TAATTTTATC
Statistics
Matches: 112, Mismatches: 20, Indels: 48
0.62 0.11 0.27
Matches are distributed among these distances:
66 4 0.04
67 25 0.22
68 5 0.04
70 3 0.03
71 10 0.09
72 9 0.08
73 2 0.02
75 2 0.02
77 2 0.02
78 9 0.08
79 10 0.09
80 3 0.03
82 5 0.04
83 19 0.17
84 4 0.04
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (67 bp):
ATATATCTGTTTATATTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACAT
TC
Found at i:1618867 original size:150 final size:150
Alignment explanation
Indices: 1618596--1618895 Score: 600
Period size: 150 Copynumber: 2.0 Consensus size: 150
1618586 ATATTATTTC
1618596 AAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAATATATCTGTTTATA
1 AAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAATATATCTGTTTATA
1618661 TTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACATTCATATATTAATTTT
66 TTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACATTCATATATTAATTTT
1618726 ATCTATGTTCTCTATTTGTG
131 ATCTATGTTCTCTATTTGTG
1618746 AAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAATATATCTGTTTATA
1 AAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAATATATCTGTTTATA
1618811 TTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACATTCATATATTAATTTT
66 TTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACATTCATATATTAATTTT
1618876 ATCTATGTTCTCTATTTGTG
131 ATCTATGTTCTCTATTTGTG
1618896 TACAACAAGT
Statistics
Matches: 150, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.47
Consensus pattern (150 bp):
AAAAAGAATATTAATTTCCATGCCTTTTATATTTTGACTGAAATTAATTAATATATCTGTTTATA
TTAATAAATTTGGTAAAATATATATAATTAATATTTTGTATGAACCACATTCATATATTAATTTT
ATCTATGTTCTCTATTTGTG
Found at i:1618959 original size:17 final size:17
Alignment explanation
Indices: 1618939--1618971 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1618929 TTTAACTATC
1618939 AAATTAAAT-TAATTCAA
1 AAATT-AATCTAATTCAA
1618956 AAATTAATCTAATTCA
1 AAATTAATCTAATTCA
1618972 TGTGACAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAATCTAATTCAA
Found at i:1623577 original size:18 final size:18
Alignment explanation
Indices: 1623533--1623577 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
1623523 GCAATAAGAA
1623533 AACGTTTTGAAATTGAAT
1 AACGTTTTGAAATTGAAT
*
1623551 AACGATTTGTAAA-TGAAT
1 AACGTTTTG-AAATTGAAT
*
1623569 AATGTTTTG
1 AACGTTTTG
1623578 GAAAAGAACG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 20 0.87
19 3 0.13
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (18 bp):
AACGTTTTGAAATTGAAT
Found at i:1626243 original size:27 final size:27
Alignment explanation
Indices: 1626189--1626252 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
1626179 TTTATCCCTA
*
1626189 GTAAAATTTT-GACCATTTTACCAGTG
1 GTAAAATTTTGGACCATTTTACCACTG
** *
1626215 GTAAAATTTTGGATGATTTTACCTCTG
1 GTAAAATTTTGGACCATTTTACCACTG
1626242 GTAAAATTTTG
1 GTAAAATTTTG
1626253 AGAAAATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (27 bp):
GTAAAATTTTGGACCATTTTACCACTG
Found at i:1627976 original size:23 final size:23
Alignment explanation
Indices: 1627946--1627994 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
1627936 TACGGAAGGA
1627946 AAACTTGTATTAGTAAATAAACT
1 AAACTTGTATTAGTAAATAAACT
*
1627969 AAACTTGTATTAGTAGATAAACT
1 AAACTTGTATTAGTAAATAAACT
1627992 AAA
1 AAA
1627995 TAAGATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (23 bp):
AAACTTGTATTAGTAAATAAACT
Found at i:1629925 original size:24 final size:24
Alignment explanation
Indices: 1629898--1629945 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1629888 AATTGATGTG
1629898 CAAATCAGTGAGTTAAAGGGAGCT
1 CAAATCAGTGAGTTAAAGGGAGCT
1629922 CAAATCAGTGAGTTAAAGGGAGCT
1 CAAATCAGTGAGTTAAAGGGAGCT
1629946 GAGGTGGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (24 bp):
CAAATCAGTGAGTTAAAGGGAGCT
Found at i:1631637 original size:33 final size:33
Alignment explanation
Indices: 1631610--1631685 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
1631600 ATAACTCGGT
1631610 TATGGTCTTATCATCAGAATGCTATAACCCAGC
1 TATGGTCTTATCATCAGAATGCTATAACCCAGC
* * * *
1631643 TATGGTCTTATCATCAGTATGCCATAGCCCAAC
1 TATGGTCTTATCATCAGAATGCTATAACCCAGC
1631676 TATGGTCTTA
1 TATGGTCTTA
1631686 CATATATACA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.33
Consensus pattern (33 bp):
TATGGTCTTATCATCAGAATGCTATAACCCAGC
Found at i:1643147 original size:41 final size:41
Alignment explanation
Indices: 1643006--1643147 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
1642996 TTTAAAATGA
* * *
1643006 TTCACTGGCATTAAGCCT-ACTAGACGTAAAGTCTAAAATAT
1 TTCACTAGCATTAAGCCTGA-TAGACGTAAAGTCTGAATTAT
* * *
1643047 TACACCAGCATTAAGCCTGCTAGACGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
**
1643088 TTCACTAGCATTAAGCCTGATAGGTGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
1643129 TTCACTAGCATTAAGCCTG
1 TTCACTAGCATTAAGCCTG
1643148 CTAAGCACAG
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (41 bp):
TTCACTAGCATTAAGCCTGATAGACGTAAAGTCTGAATTAT
Found at i:1643165 original size:41 final size:40
Alignment explanation
Indices: 1643006--1643166 Score: 146
Period size: 41 Copynumber: 3.9 Consensus size: 40
1642996 TTTAAAATGA
* * * *
1643006 TTCACTGGCATTAAGCCTACT-AGACGTAAAGTCTAAAATAT
1 TTCACTAGCATTAAGCCTGCTAAGAC--AAAGTCTGAATTAT
* *
1643047 TACACCAGCATTAAGCCTGCT-AGACGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGCTAAGAC--AAAGTCTGAATTAT
* * **
1643088 TTCACTAGCATTAAGCCTGATAGGTGTAAAGTCTGAATTAT
1 TTCACTAGCATTAAGCCTGCTAAG-ACAAAGTCTGAATTAT
* *
1643129 TTCACTAGCATTAAGCCTGCTAAGCACAGAGCCTGAAT
1 TTCACTAGCATTAAGCCTGCTAAG-ACAAAGTCTGAAT
1643167 AACTCAGATA
Statistics
Matches: 99, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
41 98 0.99
42 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (40 bp):
TTCACTAGCATTAAGCCTGCTAAGACAAAGTCTGAATTAT
Found at i:1646827 original size:13 final size:13
Alignment explanation
Indices: 1646809--1646833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1646799 ACAAACGATA
1646809 AAATTTTCACACG
1 AAATTTTCACACG
1646822 AAATTTTCACAC
1 AAATTTTCACAC
1646834 ATATCAATTC
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:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:1648770 original size:24 final size:24
Alignment explanation
Indices: 1648723--1648771 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1648713 GCCGCTATAG
**
1648723 AACATGACCTTTAGCGGTGCTTTT
1 AACATGACCTTTAGCGGCACTTTT
* *
1648747 AACATGACCTTTAGTGGCATTTTT
1 AACATGACCTTTAGCGGCACTTTT
1648771 A
1 A
1648772 TCACAAACGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (24 bp):
AACATGACCTTTAGCGGCACTTTT
Found at i:1648814 original size:43 final size:43
Alignment explanation
Indices: 1648747--1649014 Score: 373
Period size: 43 Copynumber: 6.2 Consensus size: 43
1648737 CGGTGCTTTT
* * * *
1648747 AACATGACCTTTAGTGGCA-TTTTTATCACAAACGCAGTTAAAG
1 AACATGACCTTTAGCGGCACTTCTT-TCACAAACGCCGCTAAAG
* *
1648790 AACATGATCTTTAGCGGCACTT-TTATCACAAACGCCGCTAAAT
1 AACATGACCTTTAGCGGCACTTCTT-TCACAAACGCCGCTAAAG
* *
1648833 AACATG-CCATTTAGCGGCACTT-TTATCATAAATGCCGCTAAAG
1 AACATGACC-TTTAGCGGCACTTCTT-TCACAAACGCCGCTAAAG
*
1648876 AACATGACCTTTAGCGGCGCTTCTTTCACAAACGCCGCTAAAG
1 AACATGACCTTTAGCGGCACTTCTTTCACAAACGCCGCTAAAG
*
1648919 AACATGACCTTTAGCGGCGCTTCTTTCACAAACGCCGCTAAAG
1 AACATGACCTTTAGCGGCACTTCTTTCACAAACGCCGCTAAAG
*
1648962 AACATGACCTTTAGCGGCGCTTCTTTCACAAACGCCGCTAAAG
1 AACATGACCTTTAGCGGCACTTCTTTCACAAACGCCGCTAAAG
1649005 AACATGACCT
1 AACATGACCT
1649015 GACTCTCCGA
Statistics
Matches: 209, Mismatches: 12, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
42 1 0.00
43 202 0.97
44 6 0.03
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (43 bp):
AACATGACCTTTAGCGGCACTTCTTTCACAAACGCCGCTAAAG
Found at i:1653505 original size:21 final size:21
Alignment explanation
Indices: 1653480--1653527 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1653470 AATTGAAGTA
*
1653480 ACAAATGATGTAAAGGCAGAG
1 ACAAATGATGCAAAGGCAGAG
* *
1653501 ACAAATGATGCAGAGGTAGAG
1 ACAAATGATGCAAAGGCAGAG
1653522 ACAAAT
1 ACAAAT
1653528 TTAATGATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.27, T:0.15
Consensus pattern (21 bp):
ACAAATGATGCAAAGGCAGAG
Found at i:1655376 original size:15 final size:15
Alignment explanation
Indices: 1655331--1655378 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
1655321 CTAAACCCCT
* *
1655331 AACCCTTAACCCATA
1 AACCCATAATCCATA
1655346 AA-CCATAATCTC-TA
1 AACCCATAATC-CATA
1655360 AACCCATAATCCATA
1 AACCCATAATCCATA
1655375 AACC
1 AACC
1655379 TTAGAATAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:1655414 original size:14 final size:14
Alignment explanation
Indices: 1655395--1655427 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1655385 TAGGAACTCT
*
1655395 TAAACCTTAAACCC
1 TAAACCATAAACCC
1655409 TAAACCATAAACCC
1 TAAACCATAAACCC
1655423 TAAAC
1 TAAAC
1655428 TATATAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.33, G:0.00, T:0.18
Consensus pattern (14 bp):
TAAACCATAAACCC
Found at i:1655588 original size:7 final size:7
Alignment explanation
Indices: 1655546--1655615 Score: 63
Period size: 7 Copynumber: 10.0 Consensus size: 7
1655536 AACCCCTATC
1655546 CCATAAA
1 CCATAAA
*
1655553 CCCTAAA
1 CCATAAA
*
1655560 TCATAAA
1 CCATAAA
*
1655567 ACATAAA
1 CCATAAA
**
1655574 CCCGAAA
1 CCATAAA
1655581 CCATAAA
1 CCATAAA
1655588 CC-TCAAA
1 CCAT-AAA
1655595 CC-TAAAA
1 CCAT-AAA
1655602 CCATAAA
1 CCATAAA
1655609 CCATAAA
1 CCATAAA
1655616 GCTCGATCTA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
6 1 0.02
7 49 0.96
8 1 0.02
ACGTcount: A:0.54, C:0.30, G:0.01, T:0.14
Consensus pattern (7 bp):
CCATAAA
Found at i:1655652 original size:17 final size:17
Alignment explanation
Indices: 1655627--1655666 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1655617 CTCGATCTAT
*
1655627 AGCGACATTTTTCGAAA
1 AGCGACATTTTCCGAAA
*
1655644 AGCGGCATTTTCCGAAA
1 AGCGACATTTTCCGAAA
1655661 AGCGAC
1 AGCGAC
1655667 GCTAATGCCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.23
Consensus pattern (17 bp):
AGCGACATTTTCCGAAA
Done.