Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 5 of 276
Found at i:1484770 original size:59 final size:59
Alignment explanation
Indices: 1484651--1484922 Score: 381
Period size: 59 Copynumber: 4.7 Consensus size: 59
1484641 TAAATGAATG
* *
1484651 ATTAATAAAAAATTAATTAATTATTCATAAAATTATTATGAAATGTGATTATTTA--T-
1 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* * *
1484707 -TTAATCAAAAAGTAATTAATTATTCATAATATTATTATGAAATATGATTATTTATTAA
1 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* **
1484765 ATTAATCAAAAATTAATTAATTATTCATAGAATTATTATGAAATATGATTAGATATTTA
1 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* *
1484824 ATTAATCGAAAATTAATTAATTATTCATAAAATTATTATGAAATATGAATATTTATTTA
1 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
* ** * *
1484883 ATTAATCAAGAATTCTTTAATTATTCAAAAAAATATTATG
1 ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
1484923 GATACGTTAT
Statistics
Matches: 190, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
55 50 0.26
59 140 0.74
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (59 bp):
ATTAATCAAAAATTAATTAATTATTCATAAAATTATTATGAAATATGATTATTTATTTA
Found at i:1486452 original size:25 final size:25
Alignment explanation
Indices: 1486394--1486488 Score: 91
Period size: 25 Copynumber: 3.8 Consensus size: 25
1486384 ACTTACACGG
* * *
1486394 CGATGCAGAAAAAGACTGTCGACGA
1 CGATGCAGCAAAGGACTGTCAACGA
*
1486419 CGATGCAGCAAAGGACTATCAACGA
1 CGATGCAGCAAAGGACTGTCAACGA
* * * *
1486444 TGATGCAGCAGAGGACTGTCAATGG
1 CGATGCAGCAAAGGACTGTCAACGA
* * *
1486469 CGATGCGGCAGAGGATTGTC
1 CGATGCAGCAAAGGACTGTC
1486489 GGTAGCAATG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.33, C:0.20, G:0.32, T:0.16
Consensus pattern (25 bp):
CGATGCAGCAAAGGACTGTCAACGA
Found at i:1495175 original size:27 final size:26
Alignment explanation
Indices: 1495143--1495208 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
1495133 CCTATACAAT
* *
1495143 ATCAGTACAGTCTAGGCCTTAGCCCT
1 ATCAGTACAGTCTAGGCCTAAGCCCA
* *
1495169 ATACAGTAACAGTGTGGGCCTAAGCCCA
1 AT-CAGT-ACAGTCTAGGCCTAAGCCCA
1495197 ATCAGTATCAGT
1 ATCAGTA-CAGT
1495209 ACAGTGTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 3 0.09
27 12 0.36
28 18 0.55
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (26 bp):
ATCAGTACAGTCTAGGCCTAAGCCCA
Found at i:1495605 original size:27 final size:26
Alignment explanation
Indices: 1495559--1495638 Score: 106
Period size: 27 Copynumber: 3.0 Consensus size: 26
1495549 GGGCATAATC
1495559 GTCATTTTACCTACAGGGGTATTACG
1 GTCATTTTACCTACAGGGGTATTACG
* *
1495585 GTTATTTTACCTTACAGGGGTATTACA
1 GTCATTTTACC-TACAGGGGTATTACG
* *
1495612 GTCATTTTACCCTATAGGGGCATTACG
1 GTCATTTTA-CCTACAGGGGTATTACG
1495639 ATCAGATAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 10 0.22
27 34 0.74
28 2 0.04
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (26 bp):
GTCATTTTACCTACAGGGGTATTACG
Found at i:1499031 original size:40 final size:38
Alignment explanation
Indices: 1498957--1499031 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 38
1498947 CATTTGGGGA
* *
1498957 ATTAATTTGGGGAAAAAATAAGGGATTTGGGGAAAATG
1 ATTAATTTGGGAAAAAAATAAGGGATTTGAGGAAAATG
* *
1498995 ATTAATTTAGGGAAAAAAACTAGGGGATTTTAGGAAA
1 ATTAATTT-GGGAAAAAAA-TAAGGGATTTGAGGAAA
1499032 CTGGGGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 8 0.26
39 9 0.29
40 14 0.45
ACGTcount: A:0.44, C:0.01, G:0.28, T:0.27
Consensus pattern (38 bp):
ATTAATTTGGGAAAAAAATAAGGGATTTGAGGAAAATG
Found at i:1499159 original size:40 final size:42
Alignment explanation
Indices: 1499092--1499171 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 42
1499082 AGGATATTCA
*
1499092 CGGTGTTTATGGGAAAAATGCTTCTATTGCTTTA-CTTTTAG
1 CGGTGTTTATGGAAAAAATGCTTCTATTGCTTTACCTTTTAG
1499133 CGGTGTTTAT-GAAAAAATG-TTGCTATTGCTTTACCTTTT
1 CGGTGTTTATGGAAAAAATGCTT-CTATTGCTTTACCTTTT
1499172 GCAACGTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 2 0.06
40 19 0.53
41 15 0.42
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (42 bp):
CGGTGTTTATGGAAAAAATGCTTCTATTGCTTTACCTTTTAG
Found at i:1499189 original size:41 final size:40
Alignment explanation
Indices: 1499096--1499212 Score: 103
Period size: 40 Copynumber: 2.9 Consensus size: 40
1499086 TATTCACGGT
* ***
1499096 GTTTATGGGAAAAATGCTTCTATTGCTTTACTTTTAGCGGT
1 GTTTAT-GAAAAAATGCTTCTATTGCTTTACTTTTAGCAAC
1499137 GTTTATGAAAAAATG-TTGCTATTGCTTTACCTTTT-GCAAC
1 GTTTATGAAAAAATGCTT-CTATTGCTTTA-CTTTTAGCAAC
* * ** *
1499177 GTTTATGCAAAAACGCCACTACTGCTTTACCTTTTA
1 GTTTATGAAAAAATGCTTCTATTGCTTTA-CTTTTA
1499213 CGGTATTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
39 2 0.03
40 50 0.79
41 11 0.17
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (40 bp):
GTTTATGAAAAAATGCTTCTATTGCTTTACTTTTAGCAAC
Found at i:1499501 original size:95 final size:95
Alignment explanation
Indices: 1499367--1499557 Score: 373
Period size: 95 Copynumber: 2.0 Consensus size: 95
1499357 CAAGATGTCA
1499367 TATTAGGAACCCCATTCATATCCTTACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACC
1 TATTAGGAACCCCATTCATATCCTTACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACC
*
1499432 AAATTTTTAAGCACTAAAATGGAATTTCCT
66 AAATTTTTAAGCACTAAAATGAAATTTCCT
1499462 TATTAGGAACCCCATTCATATCCTTACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACC
1 TATTAGGAACCCCATTCATATCCTTACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACC
1499527 AAATTTTTAAGCACTAAAATGAAATTTCCT
66 AAATTTTTAAGCACTAAAATGAAATTTCCT
1499557 T
1 T
1499558 TCGTAAAGAA
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (95 bp):
TATTAGGAACCCCATTCATATCCTTACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACC
AAATTTTTAAGCACTAAAATGAAATTTCCT
Found at i:1499599 original size:95 final size:95
Alignment explanation
Indices: 1499391--1499583 Score: 255
Period size: 95 Copynumber: 2.0 Consensus size: 95
1499381 TTCATATCCT
*
1499391 TACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACCAAATTTTTAAGCACTAAAATGGAA
1 TACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACCAAATTTTTAAGCACTAAAATGAAA
* * ** ****
1499456 TTTCCTTATTAGGAACCCCATTCATATCCT
66 TTTCCTTATTAAGAAACCCATAAATAGAAA
1499486 TACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACCAAATTTTTAAGCACTAAAATGAAA
1 TACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACCAAATTTTTAAGCACTAAAATGAAA
1499551 TTTCCTT-TCGTAAAGAAACCCA-AAATAAGAAA
66 TTTCCTTAT--T-AAGAAACCCATAAAT-AGAAA
1499583 T
1 T
1499584 CTCGACTTAT
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
94 1 0.01
95 71 0.84
96 3 0.04
97 10 0.12
ACGTcount: A:0.45, C:0.18, G:0.06, T:0.31
Consensus pattern (95 bp):
TACTCAAGCCATATAAAATAACAAATAATTAAATTTCTACCAAATTTTTAAGCACTAAAATGAAA
TTTCCTTATTAAGAAACCCATAAATAGAAA
Found at i:1504624 original size:16 final size:16
Alignment explanation
Indices: 1504603--1504633 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1504593 ACAAATAGTC
1504603 CAATTTACTTCCTCAA
1 CAATTTACTTCCTCAA
1504619 CAATTTACTTCCTCA
1 CAATTTACTTCCTCA
1504634 GCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (16 bp):
CAATTTACTTCCTCAA
Found at i:1507901 original size:27 final size:27
Alignment explanation
Indices: 1507859--1507961 Score: 138
Period size: 27 Copynumber: 3.9 Consensus size: 27
1507849 CTCTAATTGA
* *
1507859 TAAAATGACTATTTTGTCTTTATATGG
1 TAAAATGACTATTTTGCCCTTATATGG
1507886 TAAAATGACTGA-TTTGCCCTTATATGG
1 TAAAATGACT-ATTTTGCCCTTATATGG
*
1507913 TAAAATGACTATTTTGCCCCTATATGG
1 TAAAATGACTATTTTGCCCTTATATGG
* *
1507940 TAAGATGACTGTTTTG-CCTTAT
1 TAAAATGACTATTTTGCCCTTAT
1507962 GTGTATGTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 6 0.09
27 61 0.90
28 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATATGG
Found at i:1507941 original size:54 final size:53
Alignment explanation
Indices: 1507859--1507961 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 53
1507849 CTCTAATTGA
* **
1507859 TAAAATGACTATTTTGTCTTTATATGGTAAAATGACTGATTTGCCCTTATATGG
1 TAAAATGACTATTTTGCCCCTATATGGTAAAATGACTGATTTG-CCTTATATGG
* *
1507913 TAAAATGACTATTTTGCCCCTATATGGTAAGATGACTGTTTTGCCTTAT
1 TAAAATGACTATTTTGCCCCTATATGGTAAAATGACTGATTTGCCTTAT
1507962 GTGTATGTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 6 0.14
54 38 0.86
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (53 bp):
TAAAATGACTATTTTGCCCCTATATGGTAAAATGACTGATTTGCCTTATATGG
Found at i:1511306 original size:20 final size:19
Alignment explanation
Indices: 1511273--1511315 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1511263 CATGGCCTGA
*
1511273 GGCCGAATTAGGCCATAGTG
1 GGCCGAAATAGGCCAT-GTG
* *
1511293 GGCCGAAATGGGCCGTGTG
1 GGCCGAAATAGGCCATGTG
1511312 GGCC
1 GGCC
1511316 CCACAGGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.19, C:0.23, G:0.42, T:0.16
Consensus pattern (19 bp):
GGCCGAAATAGGCCATGTG
Found at i:1511593 original size:27 final size:27
Alignment explanation
Indices: 1511562--1511670 Score: 130
Period size: 27 Copynumber: 4.1 Consensus size: 27
1511552 GACCCCTAAT
*
1511562 TGGTAAAATGACTGTTTTGCCCTTATG
1 TGGTAAAATGACTATTTTGCCCTTATG
* *
1511589 TGGTAAAATGATTGTTTTGCCCTTATG
1 TGGTAAAATGACTATTTTGCCCTTATG
* * * *
1511616 TGGTAAACTAACTATTTTGCCCCTATA
1 TGGTAAAATGACTATTTTGCCCTTATG
* *
1511643 TGGTAAGATGACTATTCTGCCC-TATG
1 TGGTAAAATGACTATTTTGCCCTTATG
1511669 TG
1 TG
1511671 ATGTATATAT
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
26 5 0.07
27 65 0.93
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
TGGTAAAATGACTATTTTGCCCTTATG
Found at i:1513348 original size:16 final size:16
Alignment explanation
Indices: 1513307--1513351 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1513297 ATGTGTAAAA
*
1513307 AAATATAAATAGACATG
1 AAATATAAATA-AAATG
1513324 AAA-ATAAATAAAATG
1 AAATATAAATAAAATG
*
1513339 AAATAAAAATAAA
1 AAATATAAATAAA
1513352 TAAAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 15 0.60
17 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (16 bp):
AAATATAAATAAAATG
Found at i:1513357 original size:10 final size:10
Alignment explanation
Indices: 1513324--1513358 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1513314 AATAGACATG
1513324 AAAATAAAT-
1 AAAATAAATA
1513333 AAAATGAAATA
1 AAAAT-AAATA
1513344 AAAATAAATA
1 AAAATAAATA
1513354 AAAAT
1 AAAAT
1513359 TATACAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.21
10 14 0.58
11 5 0.21
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (10 bp):
AAAATAAATA
Found at i:1514045 original size:151 final size:147
Alignment explanation
Indices: 1513884--1514339 Score: 580
Period size: 151 Copynumber: 3.1 Consensus size: 147
1513874 CAAAATTTTC
* * * * * *
1513884 TTTAGAAAAAAACATTAATTTTCTTAAAAATCAAAAC-CTTATTTCGAAATAGTTAAAAAAATCA
1 TTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTATTT-GAAATAGTTAAAAAAATCA
* * *
1513948 AAACTTTATTTTAAAAATTTAAACTTTCCTTTAAAATGACATAAAAAAAACATAGATTTATTTTT
65 AAACTTTGTTTTAAAAATTTAAACTTTCTTTTAAAATAAC-T-AAAAAAACATAGATTTATTTTT
1514013 CAAAATCTAAACTTTCTCCTT
128 CAAAATCTAAACTTTCTCC-T
* *
1514034 TTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAGCTTTTATTTTGAAGTAGTTAAAAAAAAAA
1 TTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTA-TTTGAAATAGTT---AAAAAAA
* **
1514099 TCAAAACTTTGTTTTAAAAATTTAAACTTTCTTTTGAAATAACTAAAAAAACATATTTTTATTTT
62 TCAAAACTTTGTTTTAAAAATTTAAACTTTCTTTTAAAATAACTAAAAAAACATAGATTTATTTT
* * * *
1514164 TTAAAATTTAAAGTTTTTCCT
127 TCAAAATCTAAACTTTCTCCT
* * *
1514185 TTTAAAAAAACACACTATTTTTCTTAGAGATTAAAACTTTTACTTTGGAATAGTTAAAAAAATCA
1 TTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTA-TTTGAAATAGTTAAAAAAATCA
* * *
1514250 AAATTTTGTTTCAAAAATTTAAACTTTCTTTTAAAATAACT--AAAAAC-TAGATTTTTTTTTCA
65 AAACTTTGTTTTAAAAATTTAAACTTTCTTTTAAAATAACTAAAAAAACATAGATTTATTTTTCA
1514312 AAATCTAAACTTTCTCC-
130 AAATCTAAACTTTCTCCT
1514329 TTTAAAAAAAA
1 TTTAAAAAAAA
1514340 CTATTTTTCC
Statistics
Matches: 266, Mismatches: 35, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
144 10 0.04
145 25 0.09
146 6 0.02
148 48 0.18
150 31 0.12
151 61 0.23
152 38 0.14
153 1 0.00
154 46 0.17
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (147 bp):
TTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAACTTTTATTTGAAATAGTTAAAAAAATCAA
AACTTTGTTTTAAAAATTTAAACTTTCTTTTAAAATAACTAAAAAAACATAGATTTATTTTTCAA
AATCTAAACTTTCTCCT
Found at i:1514119 original size:20 final size:20
Alignment explanation
Indices: 1514094--1514133 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1514084 TAGTTAAAAA
*
1514094 AAAAATCAAAACTTTGTTTT
1 AAAAATCAAAACTTTCTTTT
**
1514114 AAAAATTTAAACTTTCTTTT
1 AAAAATCAAAACTTTCTTTT
1514134 GAAATAACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAAATCAAAACTTTCTTTT
Found at i:1515475 original size:27 final size:27
Alignment explanation
Indices: 1515435--1515492 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
1515425 TTCTTACCCC
1515435 GATCAAGACCCGAATCACGCTTCTCTT
1 GATCAAGACCCGAATCACGCTTCTCTT
*
1515462 GATCAAGACTCGAATCACGCTTCTCTT
1 GATCAAGACCCGAATCACGCTTCTCTT
1515489 GATC
1 GATC
1515493 TATACTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.28
Consensus pattern (27 bp):
GATCAAGACCCGAATCACGCTTCTCTT
Found at i:1517705 original size:23 final size:24
Alignment explanation
Indices: 1517644--1517752 Score: 95
Period size: 23 Copynumber: 4.8 Consensus size: 24
1517634 AATATTTGGC
*
1517644 ATGAATAGTGAAGATT-TGC-TA-G
1 ATGAACAGTGAAGATTCT-CTTACG
* * *
1517666 ATGAATAGTAAAAATTCTCTTAC-
1 ATGAACAGTGAAGATTCTCTTACG
* *
1517689 ATGAACAGTGGAGATTCT-TTGCG
1 ATGAACAGTGAAGATTCTCTTACG
*
1517712 ATGAACAGTGAAGATTCTC-TGCG
1 ATGAACAGTGAAGATTCTCTTACG
*
1517735 ATAAACAGTGAAGATTCT
1 ATGAACAGTGAAGATTCT
1517753 TTGAAAAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
22 18 0.25
23 55 0.75
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (24 bp):
ATGAACAGTGAAGATTCTCTTACG
Found at i:1517729 original size:46 final size:46
Alignment explanation
Indices: 1517665--1517755 Score: 112
Period size: 46 Copynumber: 2.0 Consensus size: 46
1517655 AGATTTGCTA
* * *
1517665 GATGAATAGTAAAAATTCTCTTAC-ATGAACAGTGGAGATTCTTTGC
1 GATGAACAGTAAAAATTCTC-TACGATAAACAGTGAAGATTCTTTGC
* * *
1517711 GATGAACAGTGAAGATTCTCTGCGATAAACAGTGAAGATTCTTTG
1 GATGAACAGTAAAAATTCTCTACGATAAACAGTGAAGATTCTTTG
1517756 AAAAAAAACA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (46 bp):
GATGAACAGTAAAAATTCTCTACGATAAACAGTGAAGATTCTTTGC
Found at i:1518020 original size:15 final size:16
Alignment explanation
Indices: 1518002--1518039 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
1517992 ATTTTTTAGC
1518002 TTTT-AAAAATTTAAT
1 TTTTCAAAAATTTAAT
*
1518017 TTTTCAAAATTTTAA-
1 TTTTCAAAAATTTAAT
1518032 TTTTCAAA
1 TTTTCAAA
1518040 TTATTATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTCAAAAATTTAAT
Found at i:1520150 original size:46 final size:48
Alignment explanation
Indices: 1520097--1520316 Score: 208
Period size: 46 Copynumber: 4.7 Consensus size: 48
1520087 CTATTGTGAA
1520097 CTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAG
1 CTAGTGTAAGACCATGTCTGGGACATGCATCGGCCACGA-TATGTAGAG
* * *
1520143 CTAGTGTAAGACCATGTCTGGGACATGCATCGACCTCGAAATGTA-AG
1 CTAGTGTAAGACCATGTCTGGGACATGCATCGGCCACGATATGTAGAG
* * * * *
1520190 -TCAGTGTAAGA-CATGTCAGGGACATGCATTGGCTACGAGATGT-G-T
1 CT-AGTGTAAGACCATGTCTGGGACATGCATCGGCCACGATATGTAGAG
* * *
1520235 C-AGTGTAAGACCATGTCTAGGACATGGCATCGG-CACAAATATGCTAAAG
1 CTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCAC-GATATG-TAGAG
*
1520284 CTTGTGTAAGACCATGTCTGGGACATGGCATCG
1 CTAGTGTAAGACCATGTCTGGGACAT-GCATCG
1520317 ACACCTTACC
Statistics
Matches: 141, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
44 9 0.06
45 14 0.10
46 48 0.34
47 38 0.27
48 2 0.01
49 1 0.01
50 29 0.21
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.24
Consensus pattern (48 bp):
CTAGTGTAAGACCATGTCTGGGACATGCATCGGCCACGATATGTAGAG
Found at i:1523133 original size:20 final size:19
Alignment explanation
Indices: 1523108--1523154 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1523098 ATCCATTTGC
1523108 AAACAGTAGCTCATCCATAT
1 AAACAGTA-CTCATCCATAT
* * *
1523128 AAACAGTATTTATCGATAT
1 AAACAGTACTCATCCATAT
1523147 AAACAGTA
1 AAACAGTA
1523155 TTTATGCCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.28
Consensus pattern (19 bp):
AAACAGTACTCATCCATAT
Found at i:1523369 original size:24 final size:22
Alignment explanation
Indices: 1523294--1523383 Score: 108
Period size: 23 Copynumber: 3.9 Consensus size: 22
1523284 GTTGAAGGAT
*
1523294 AGTAAGCTCTATTGAGCTGAAAC
1 AGTAAGCTCTA-CGAGCTGAAAC
*
1523317 GGTAAGCTCTGACGAGCTGAAAC
1 AGTAAGCTCT-ACGAGCTGAAAC
*
1523340 AGTAAGCTCATACGAGCTAGGAAC
1 AGTAAGCTC-TACGAGCT-GAAAC
1523364 AGTAAGCTCTTACGAGCTGA
1 AGTAAGCTC-TACGAGCTGA
1523384 TATATCAGTA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
23 35 0.60
24 23 0.40
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (22 bp):
AGTAAGCTCTACGAGCTGAAAC
Found at i:1535923 original size:47 final size:47
Alignment explanation
Indices: 1535851--1536016 Score: 193
Period size: 46 Copynumber: 3.6 Consensus size: 47
1535841 CTATTGTGAA
1535851 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCACATT-A-A-GAGAG
1 CTAGTGTAAGACATGTCTGGGACATGCATCGG-C-CATTGATACGAGAG
* *
1535897 CTAGTGTAAGACCAAGTCTGGGACATGGCATCGG-CATTGATACGAGTG
1 CTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCATTGATACGAGAG
*
1535945 CTAGTGTAAGACATGTCTGGGACATGCATCGG-C-TTCGAGACGTA-AG
1 CTAGTGTAAGACATGTCTGGGACATGCATCGGCCATT-GATACG-AGAG
*
1535991 TTAGTGTAAGACATGTCTGGGACATG
1 CTAGTGTAAGACATGTCTGGGACATG
1536017 TATTGGCTAC
Statistics
Matches: 107, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
45 6 0.06
46 51 0.48
47 28 0.26
48 22 0.21
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (47 bp):
CTAGTGTAAGACATGTCTGGGACATGCATCGGCCATTGATACGAGAG
Found at i:1536030 original size:46 final size:44
Alignment explanation
Indices: 1535852--1536076 Score: 181
Period size: 46 Copynumber: 4.9 Consensus size: 44
1535842 TATTGTGAAC
* * * *
1535852 TAGTGTAAGACATGTCTGGGACATGCATCGGCCACATTAAGA-GAGC
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCTAC---GAGATAAGT
* **
1535898 TAGTGTAAGACCAAGTCTGGGACATGGCATCGGC-A-TTGATACGAGT
1 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATA--AGT
*
1535944 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCTTCGAGACGTAAGT
1 --TAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGA--TAAGT
* * *
1535992 TAGTGTAAGACATGTCTGGGACATGTATTGGCTACGAGATATGT
1 TAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATAAGT
* *
1536036 CAGTGTAAGACCATGTATGGGACATGGCATCGGC-AC-AGATA
1 TAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATA
1536077 TGCTAGAGCC
Statistics
Matches: 149, Mismatches: 17, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
43 2 0.01
44 18 0.12
45 15 0.10
46 62 0.42
47 27 0.18
48 23 0.15
50 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (44 bp):
TAGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATAAGT
Found at i:1539106 original size:23 final size:23
Alignment explanation
Indices: 1539067--1539152 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
1539057 GCTGAAGGAT
* *
1539067 AGTAAGCT-ATATTGAGCTGAAAG
1 AGTAAGCTCATA-CGAGCTAAAAG
* *
1539090 GGTAAGCTC-TGACGAGCTAAAAT
1 AGTAAGCTCAT-ACGAGCTAAAAG
*
1539113 AGTAAGCTCATACGAGCTAAGAAC
1 AGTAAGCTCATACGAGCTAA-AAG
*
1539137 AGTAAGCTCTTACGAG
1 AGTAAGCTCATACGAG
1539153 TTGATATATC
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
23 33 0.63
24 19 0.37
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (23 bp):
AGTAAGCTCATACGAGCTAAAAG
Found at i:1539145 original size:24 final size:22
Alignment explanation
Indices: 1539091--1539152 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 22
1539081 AGCTGAAAGG
*
1539091 GTAAGCTCTGACGAGCTAAAATA
1 GTAAGCTCT-ACGAGCTAAAACA
1539114 GTAAGCTCATACGAGCTAAGAACA
1 GTAAGCTC-TACGAGCTAA-AACA
1539138 GTAAGCTCTTACGAG
1 GTAAGCTC-TACGAG
1539153 TTGATATATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 17 0.49
24 18 0.51
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
GTAAGCTCTACGAGCTAAAACA
Found at i:1544893 original size:40 final size:40
Alignment explanation
Indices: 1544837--1544981 Score: 193
Period size: 40 Copynumber: 3.6 Consensus size: 40
1544827 CATTTGAATG
*
1544837 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCGAGTTGA-T
* *
1544877 TTATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTGAT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCGAGTTGAT
* * *
1544917 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCGAGTTGAT
* * *
1544957 ATACCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCA
1544982 ATTGTGCTTG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 93 0.97
41 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTATGCGAGTTGAT
Found at i:1545000 original size:80 final size:80
Alignment explanation
Indices: 1544837--1545008 Score: 204
Period size: 80 Copynumber: 2.2 Consensus size: 80
1544827 CATTTGAATG
* * * * * *
1544837 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTTTATCCGGGCTAAGTCCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
* *
1544902 TTTGTGCGAGTTGAT
66 ATTGTGCGAGTGGAT
* *
1544917 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATACCCGGGTTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAG-TGACTATACCCGGGCTAAGACCCGAAGGC
** *
1544981 AATTGTGCTTGTGGTT
65 AATTGTGCGAGTGGAT
1544997 ATATCC-GGCTAA
1 ATATCCGGGCTAA
1545009 ATTCCGAAGA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 6 0.08
80 70 0.90
81 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTATGCGAGTGACTATACCCGGGCTAAGACCCGAAGGCA
ATTGTGCGAGTGGAT
Found at i:1549824 original size:20 final size:19
Alignment explanation
Indices: 1549799--1549845 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1549789 ATCCATTTGC
1549799 AAACAGTAGCTCATCCATAT
1 AAACAGTA-CTCATCCATAT
* * *
1549819 AAACAGTATTTATCGATAT
1 AAACAGTACTCATCCATAT
1549838 AAACAGTA
1 AAACAGTA
1549846 TTTATGCCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.28
Consensus pattern (19 bp):
AAACAGTACTCATCCATAT
Found at i:1550070 original size:24 final size:23
Alignment explanation
Indices: 1550020--1550099 Score: 81
Period size: 24 Copynumber: 3.4 Consensus size: 23
1550010 GTAAACTTTG
*
1550020 ACGAGCTGAAACACTAAGCT-CA
1 ACGAGCTGAAACAGTAAGCTCCA
*
1550042 TACGAGCTGAGAATAGTAAGCTCCA
1 -ACGAGCTGA-AACAGTAAGCTCCA
* **
1550067 ACGAGCTAAAAACAGTAAGCTCTT
1 ACGAGCT-GAAACAGTAAGCTCCA
1550091 ACGAGCTGA
1 ACGAGCTGA
1550100 TATATTAGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
23 10 0.21
24 34 0.72
25 3 0.06
ACGTcount: A:0.39, C:0.23, G:0.21, T:0.17
Consensus pattern (23 bp):
ACGAGCTGAAACAGTAAGCTCCA
Found at i:1550086 original size:48 final size:49
Alignment explanation
Indices: 1550020--1550114 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 49
1550010 GTAAACTTTG
*
1550020 ACGAGCTGAAACACTAAGCTCATACGAGCTGAGA-A-TAGTAAGCTCCA
1 ACGAGCTAAAACACTAAGCTCATACGAGCTGAGATATTAGTAAGCTCCA
* * *
1550067 ACGAGCTAAAAACAGTAAGCTCTTACGAGCTGATATATTAGTAAGCTC
1 ACGAGCT-AAAACACTAAGCTCATACGAGCTGAGATATTAGTAAGCTC
1550115 ATTTGAGCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
47 7 0.17
48 23 0.56
49 1 0.02
50 10 0.24
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (49 bp):
ACGAGCTAAAACACTAAGCTCATACGAGCTGAGATATTAGTAAGCTCCA
Found at i:1550828 original size:15 final size:15
Alignment explanation
Indices: 1550808--1550840 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1550798 GTTAAATATT
1550808 TAATAGTTCCAAATC
1 TAATAGTTCCAAATC
*
1550823 TAATAGTTTCAAATC
1 TAATAGTTCCAAATC
1550838 TAA
1 TAA
1550841 GGTACGGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (15 bp):
TAATAGTTCCAAATC
Found at i:1552367 original size:35 final size:35
Alignment explanation
Indices: 1552326--1552399 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
1552316 CCTAATCAAG
1552326 AACTGATTTGAATAAAATAAGAAAAGTTAAAAGAA
1 AACTGATTTGAATAAAATAAGAAAAGTTAAAAGAA
*
1552361 AACTGATTTGAATAAAATAAGAAAAGTTAAGAGAA
1 AACTGATTTGAATAAAATAAGAAAAGTTAAAAGAA
1552396 AACT
1 AACT
1552400 ATACTTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.23
Consensus pattern (35 bp):
AACTGATTTGAATAAAATAAGAAAAGTTAAAAGAA
Found at i:1553452 original size:57 final size:57
Alignment explanation
Indices: 1553359--1553478 Score: 213
Period size: 57 Copynumber: 2.1 Consensus size: 57
1553349 TTTATTTTTA
* *
1553359 TTTTGTTTCCCTCCATCCTTTTTCATTTTAAAATTTTGTTATATCTAAGATTGAAAG
1 TTTTCTTTCCCTCCATCCTTTTTCATTTTAAAATTTTGTTATACCTAAGATTGAAAG
*
1553416 TTTTCTTTCCCTCCATCTTTTTTCATTTTAAAATTTTGTTATACCTAAGATTGAAAG
1 TTTTCTTTCCCTCCATCCTTTTTCATTTTAAAATTTTGTTATACCTAAGATTGAAAG
1553473 TTTTCT
1 TTTTCT
1553479 CTAAAAAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.23, C:0.17, G:0.07, T:0.53
Consensus pattern (57 bp):
TTTTCTTTCCCTCCATCCTTTTTCATTTTAAAATTTTGTTATACCTAAGATTGAAAG
Found at i:1556341 original size:18 final size:18
Alignment explanation
Indices: 1556318--1556364 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
1556308 AAAATATGGT
1556318 CCCACATGCCCGTGTGAG
1 CCCACATGCCCGTGTGAG
1556336 CCCACATGCCCGTGTGAG
1 CCCACATGCCCGTGTGAG
*
1556354 TCCACATGCCC
1 CCCACATGCCC
1556365 AAATTGACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CCCACATGCCCGTGTGAG
Found at i:1564910 original size:38 final size:38
Alignment explanation
Indices: 1564859--1564938 Score: 151
Period size: 38 Copynumber: 2.1 Consensus size: 38
1564849 GAAGTGGTTT
1564859 ATTAGTTGGACTTGGAAAAAGATAAGGGTTATTTGGCA
1 ATTAGTTGGACTTGGAAAAAGATAAGGGTTATTTGGCA
*
1564897 ATTAGTTGGACTTGGAAAAAGATAAGGGTTGTTTGGCA
1 ATTAGTTGGACTTGGAAAAAGATAAGGGTTATTTGGCA
1564935 ATTA
1 ATTA
1564939 ACCCTTTTTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (38 bp):
ATTAGTTGGACTTGGAAAAAGATAAGGGTTATTTGGCA
Found at i:1565842 original size:15 final size:16
Alignment explanation
Indices: 1565822--1565855 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1565812 TCACATCAAC
1565822 AAAATAAAAATT-TTA
1 AAAATAAAAATTATTA
*
1565837 AAAATAAAAGTTATTA
1 AAAATAAAAATTATTA
1565853 AAA
1 AAA
1565856 TTTTGTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATAAAAATTATTA
Found at i:1568110 original size:10 final size:10
Alignment explanation
Indices: 1568092--1568121 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1568082 GCTAAAAAAG
*
1568092 CTTAGTTAAA
1 CTTATTTAAA
1568102 CTTATTTAAA
1 CTTATTTAAA
1568112 CTTATTTAAA
1 CTTATTTAAA
1568122 AGTCTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (10 bp):
CTTATTTAAA
Found at i:1569186 original size:158 final size:158
Alignment explanation
Indices: 1568930--1569227 Score: 560
Period size: 158 Copynumber: 1.9 Consensus size: 158
1568920 AACCTTTCAC
*
1568930 AAGAAGAATTAGTGTCCTAACCACTTTTACAGAGGCTTAATGAGTTAGGGATCACTCAAGGACCC
1 AAGAAGAATTAGTGTCCTAACCACTTTTACAGAGGCTCAATGAGTTAGGGATCACTCAAGGACCC
*
1568995 AAACGAAACAATTTGCAAAAAGGTACAAAAACTGTAAAAGTAGGGCCACACGATCATGTAGAGGG
66 AAACGAAACAATTTGCAAAAAGGTACAAAAACTGCAAAAGTAGGGCCACACGATCATGTAGAGGG
*
1569060 GTCTGGGCCACACGATCATGTAGACGGG
131 GTCTAGGCCACACGATCATGTAGACGGG
1569088 AAGAAGAATTAGTGTCCTAACCACTTTTACAGAGGCTCAATGAGTTAGGGATCACTCAAGGACCC
1 AAGAAGAATTAGTGTCCTAACCACTTTTACAGAGGCTCAATGAGTTAGGGATCACTCAAGGACCC
*
1569153 AAACGAAACAATTTGCAAAAAGGTGCAAAAACTGCAAAAGTAGGGCCACACGATCATGTAGAGGG
66 AAACGAAACAATTTGCAAAAAGGTACAAAAACTGCAAAAGTAGGGCCACACGATCATGTAGAGGG
1569218 GTCTAGGCCA
131 GTCTAGGCCA
1569228 TGTAGTAGGG
Statistics
Matches: 136, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
158 136 1.00
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.19
Consensus pattern (158 bp):
AAGAAGAATTAGTGTCCTAACCACTTTTACAGAGGCTCAATGAGTTAGGGATCACTCAAGGACCC
AAACGAAACAATTTGCAAAAAGGTACAAAAACTGCAAAAGTAGGGCCACACGATCATGTAGAGGG
GTCTAGGCCACACGATCATGTAGACGGG
Found at i:1570796 original size:56 final size:56
Alignment explanation
Indices: 1570710--1570826 Score: 193
Period size: 56 Copynumber: 2.1 Consensus size: 56
1570700 GTCGGAGCCA
*
1570710 TTCTATATGGAGTAATTGAGATCGGTGCAGTACCCGGA-AACAAATCAATGGCAAAC
1 TTCTATATGGAGTAATCGAGATCGGTGCAGTA-CCGGACAACAAATCAATGGCAAAC
*
1570766 TTCTATATGGAGTAATCGAGATCGGTGCAGTACCTGACAACAAATCAATGGCAAAC
1 TTCTATATGGAGTAATCGAGATCGGTGCAGTACCGGACAACAAATCAATGGCAAAC
1570822 -TCTAT
1 TTCTAT
1570827 CTCCCTGTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
55 9 0.16
56 49 0.84
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (56 bp):
TTCTATATGGAGTAATCGAGATCGGTGCAGTACCGGACAACAAATCAATGGCAAAC
Found at i:1586599 original size:5 final size:5
Alignment explanation
Indices: 1586591--1586619 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1586581 GAGGAAGAGA
1586591 AGAAG AGAAG AGAAG AGAAG AGAAG AGAA
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAA
1586620 AAAAACAGAG
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:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:1593583 original size:7 final size:7
Alignment explanation
Indices: 1593565--1593597 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
1593555 CCCAGTTAGA
1593565 TACAGA-
1 TACAGAT
1593571 TACAGAT
1 TACAGAT
1593578 TACAGAT
1 TACAGAT
1593585 TACAGAT
1 TACAGAT
1593592 T-CAGAT
1 TACAGAT
1593598 ATGCAAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 11 0.42
7 15 0.58
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.27
Consensus pattern (7 bp):
TACAGAT
Found at i:1593583 original size:13 final size:13
Alignment explanation
Indices: 1593565--1593598 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1593555 CCCAGTTAGA
1593565 TACAGATACAGAT
1 TACAGATACAGAT
1593578 TACAGATTACAGAT
1 TACAGA-TACAGAT
1593592 T-CAGATA
1 TACAGATA
1593599 TGCAAATCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 10 0.50
14 8 0.40
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (13 bp):
TACAGATACAGAT
Found at i:1595017 original size:47 final size:44
Alignment explanation
Indices: 1594910--1595076 Score: 181
Period size: 46 Copynumber: 3.6 Consensus size: 44
1594900 TTTGTGTGCT
* * * *
1594910 AGTGTAAGACATGTTTGGGACATGCATCGGCCATATTATAAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CAT-TGAGAAGAGCC
* *
1594956 AGTGGAAGACCATGTCTGGGACATGACATCAGCATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACATG-CATCAGCATTGAGA--AGAGCC
* * *
1595004 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATATAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGA-A-GAGCC
1595050 AGTGTAAGACATGTCTGGGACATGCAT
1 AGTGTAAGACATGTCTGGGACATGCAT
1595077 TGTCTATGAA
Statistics
Matches: 104, Mismatches: 12, Indels: 10
0.83 0.10 0.08
Matches are distributed among these distances:
45 1 0.01
46 53 0.51
47 32 0.31
48 18 0.17
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.23
Consensus pattern (44 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCATTGAGAAGAGCC
Found at i:1597970 original size:27 final size:26
Alignment explanation
Indices: 1597940--1598115 Score: 163
Period size: 27 Copynumber: 6.5 Consensus size: 26
1597930 AATTGTACAG
1597940 CACTAAGTGTGCGATTTGACTATGTTA
1 CACTAAGTGTGCGATTTGACTATG-TA
** * *
1597967 CACTAAGTGTGCGAAATGAATATGATG
1 CACTAAGTGTGCGATTTGACTATG-TA
* * **
1597994 CACTAAGTGTGCGAATTGACCATGCGG
1 CACTAAGTGTGCGATTTGACTATG-TA
1598021 CACTAAGTGTGCGAGTTTGACTATGTA
1 CACTAAGTGTGCGA-TTTGACTATGTA
* *
1598048 GCACTAAGTGTGCGATTTGATTACGTA
1 -CACTAAGTGTGCGATTTGACTATGTA
* * *
1598075 GCACTAAGTGTGCGAGTTGATTATATA
1 -CACTAAGTGTGCGATTTGACTATGTA
*
1598102 GCACTGAGTGTGCG
1 -CACTAAGTGTGCG
1598116 GACTCAATAT
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
27 105 0.83
28 22 0.17
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (26 bp):
CACTAAGTGTGCGATTTGACTATGTA
Found at i:1597999 original size:54 final size:54
Alignment explanation
Indices: 1597938--1598115 Score: 191
Period size: 54 Copynumber: 3.3 Consensus size: 54
1597928 TAAATTGTAC
*
1597938 AGCACTAAGTGTGCGATTTGACTATGTTACACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATTTGACTATG-TACACTAAGTGTGCGAATTGAATATGAT
* * ** * *
1597993 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG-T
1 AGCACTAAGTGTGCGATTTGACTATG-TACACTAAGTGTGCGA-ATTGAATATGAT
* * * *
1598047 AGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTTGACTATGTA-CACTAAGTGTGCGAATTGAATATGAT
*
1598101 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
1598116 GACTCAATAT
Statistics
Matches: 102, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
54 60 0.59
55 42 0.41
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTGACTATGTACACTAAGTGTGCGAATTGAATATGAT
Found at i:1598053 original size:82 final size:81
Alignment explanation
Indices: 1597939--1598094 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 81
1597929 AAATTGTACA
*
1597939 GCACTAAGTGTGCGATTTGACTATGTTACACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTTACACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
1598003 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
1598020 GCACTAAGTGTGCGAGTTTGACTATG-TAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTTA-CACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
1598084 GTGCGAGTTGA
64 GTGCGAATTGA
1598095 TTATATAGCA
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
81 17 0.25
82 49 0.73
83 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTTACACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:1598106 original size:82 final size:81
Alignment explanation
Indices: 1597935--1598115 Score: 222
Period size: 82 Copynumber: 2.2 Consensus size: 81
1597925 GATTAAATTG
*
1597935 TACAGCACTAAGTGTGCGATTTGACTATGTTACACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTTACACTAAGTGTGCGAAATGAATACGATGCACTAA
1598000 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
1598016 TGCGGCACTAAGTGTGCGAGTTTGACTATG-TAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTTA-CACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
1598079 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
1598098 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
1598116 GACTCAATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
81 20 0.24
82 64 0.76
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTTACACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:1603488 original size:24 final size:24
Alignment explanation
Indices: 1603461--1603509 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1603451 TTGGGAGATT
1603461 AAGCATTTGAGGAATAAGAGCATA
1 AAGCATTTGAGGAATAAGAGCATA
1603485 AAGCATTTGAGGAATAAGAGCATA
1 AAGCATTTGAGGAATAAGAGCATA
1603509 A
1 A
1603510 CACCTGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.24, T:0.20
Consensus pattern (24 bp):
AAGCATTTGAGGAATAAGAGCATA
Found at i:1604291 original size:41 final size:41
Alignment explanation
Indices: 1604246--1604327 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
1604236 ATGTGGTTGA
1604246 ATTGATATAGCATAAATTGCTTGTTTGTGGAAATGACTATG
1 ATTGATATAGCATAAATTGCTTGTTTGTGGAAATGACTATG
*
1604287 ATTGATATAGCATAGATTGCTTGTTTGTGGAAATGACTATG
1 ATTGATATAGCATAAATTGCTTGTTTGTGGAAATGACTATG
1604328 TATGGTGAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.39
Consensus pattern (41 bp):
ATTGATATAGCATAAATTGCTTGTTTGTGGAAATGACTATG
Found at i:1604488 original size:46 final size:46
Alignment explanation
Indices: 1604419--1604679 Score: 192
Period size: 46 Copynumber: 5.5 Consensus size: 46
1604409 TTTGTGTGCT
1604419 AGTGTAAGA-CATGTCTGGGACATGCATCAGCCTCGAGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-GCCTCGAGATGTAAGCC
* * * *
1604465 AGTGTAAGA-CATGTCTGGAACATGCATCGGCTACAAGATGT--GTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGCCT-CGAGATGTAAGCC
* * * *
1604509 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGCCTC-GAGATGT-A-AGCC
* ** ** **
1604559 AGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATTTCAATAGTA
1 AGTGTAAGACCATGTCTGGGACAT-GCATC-GCCTCGAGATGTA-AGCC
* * *
1604608 AGTGTAAGACCATGTCTGGGACATGGCATCGACT--TGATGGATAAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGCCTCGAGAT-G-TAAGCC
* *
1604655 AGTGTAGGACCATGTTTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
1604680 GCATTTGTAA
Statistics
Matches: 174, Mismatches: 30, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
44 11 0.06
45 17 0.10
46 49 0.28
47 24 0.14
48 4 0.02
49 32 0.18
50 34 0.20
51 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGCCTCGAGATGTAAGCC
Found at i:1606562 original size:43 final size:43
Alignment explanation
Indices: 1606474--1606638 Score: 183
Period size: 43 Copynumber: 3.9 Consensus size: 43
1606464 AATGTGATAT
* * * * *
1606474 TCGGGCCTC-GGCCTAGCAAGCTTTAA-GCTGGTGAATAATATTA
1 TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTG-A-AATAATA
*
1606517 TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAGATAATA
1 TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAATAATA
* * *
1606560 TCGGGCTTCGGGCCTAGCAAGCTATAATGCCAGTGAAATGATA
1 TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAATAATA
** *
1606603 TCGGGCTTCAAGCCTAGCAGGCGA-AATGCCGGTGAA
1 TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAA
1606639 TGAGTTCAGA
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 11 0.10
43 72 0.69
44 16 0.15
45 6 0.06
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (43 bp):
TCGGGCTTCGGGCCTAGCAGGCTATAATGCCGGTGAAATAATA
Found at i:1610778 original size:27 final size:27
Alignment explanation
Indices: 1610738--1610824 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
1610728 AGGAAGCGTC
*
1610738 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
1610765 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
1610792 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
*
1610819 ATGGTG
1 CTGGTG
1610825 ACTTCGTCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.15
27 44 0.83
28 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:1618786 original size:54 final size:54
Alignment explanation
Indices: 1618686--1618830 Score: 211
Period size: 54 Copynumber: 2.7 Consensus size: 54
1618676 TGGAGGAAGC
* *
1618686 GTCCTGGTGGCTATGCCACAATTTATCTAATCTGGTGGCTTTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAA-TTATCTGATCTGGTGGCTCTGCCACATATATCT
1618741 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
** * *
1618795 GTTTTGGTGGCTCTGGCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
1618831 ACTTCGTCAC
Statistics
Matches: 83, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
53 6 0.07
54 56 0.67
55 21 0.25
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:1618829 original size:27 final size:27
Alignment explanation
Indices: 1618689--1618847 Score: 148
Period size: 27 Copynumber: 5.9 Consensus size: 27
1618679 AGGAAGCGTC
*
1618689 CTGGTGGCTATGCCACAATTTATCT-AAT
1 CTGGTGGCTATGCCACAA--TATCTGTAT
* *
1618717 CTGGTGGCTTTGCCACATATATCTGT-C
1 CTGGTGGCTATGCCACA-ATATCTGTAT
1618744 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTATGCCACAA-TATCTGTAT
*
1618771 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACA-ATATCTGTAT
* * *
1618798 TTGGTGGCTCTGGCACAATATCTGTAT
1 CTGGTGGCTATGCCACAATATCTGTAT
* *
1618825 CTGGTGACT-TCGTCACAATATCT
1 CTGGTGGCTAT-GCCACAATATCT
1618848 AGAAGCCTCG
Statistics
Matches: 112, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
26 10 0.09
27 84 0.75
28 17 0.15
29 1 0.01
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATATCTGTAT
Found at i:1618842 original size:81 final size:81
Alignment explanation
Indices: 1618689--1618847 Score: 180
Period size: 81 Copynumber: 2.0 Consensus size: 81
1618679 AGGAAGCGTC
* * *
1618689 CTGGTGGCTATGCCACAATTTATCTAATCTGGTGGCTTTGCCACATATATCTGTCCTGGTGGCTA
1 CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTA
1618754 TGCCACAATTATCTGAT
66 TGCCACAA-TATCTGAT
* ** * * *
1618771 CTGGTGGCTCTGCCAC-ATATATCTGTTTTGGTGGCTCTGGCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTGCCACATATATCTGT-CCTGGTGACT
*
1618834 -TCGTCACAATATCT
65 AT-GCCACAATATCT
1618848 AGAAGCCTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
80 14 0.22
81 36 0.55
82 15 0.23
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (81 bp):
CTGGTGGCTATGCCACAATATATCTAATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGACTA
TGCCACAATATCTGAT
Found at i:1626259 original size:17 final size:17
Alignment explanation
Indices: 1626214--1626262 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
1626204 TATAAGGGAT
1626214 AAATCGATTGAAT-T-TG
1 AAAT-GATTGAATGTATG
*
1626230 -AATGA-TGATTGTATG
1 AAATGATTGAATGTATG
1626245 AAATGATTGAATGTATG
1 AAATGATTGAATGTATG
1626262 A
1 A
1626263 GAAAAGTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
13 4 0.15
14 3 0.11
15 5 0.19
16 5 0.19
17 10 0.37
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (17 bp):
AAATGATTGAATGTATG
Found at i:1642695 original size:28 final size:29
Alignment explanation
Indices: 1642651--1642705 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
1642641 AAAAAAACCA
*
1642651 TAAAATTTTATGAAAAA-AATAAAATTCT
1 TAAAATTTTATCAAAAATAATAAAATTCT
*
1642679 TAAAATTTT-TCATAAAATTATAAAATT
1 TAAAATTTTATCA-AAAATAATAAAATT
1642706 TTCCAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 13 0.57
29 8 0.35
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (29 bp):
TAAAATTTTATCAAAAATAATAAAATTCT
Found at i:1642704 original size:20 final size:21
Alignment explanation
Indices: 1642669--1642707 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1642659 TATGAAAAAA
*
1642669 ATAAAATTCTTAAAATTTTTC
1 ATAAAATTCATAAAATTTTTC
1642690 ATAAAATT-ATAAAATTTT
1 ATAAAATTCATAAAATTTT
1642708 CCAAACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAAATTCATAAAATTTTTC
Found at i:1642809 original size:20 final size:21
Alignment explanation
Indices: 1642766--1642809 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1642756 TTCACATACG
* **
1642766 TATAATTTTTAAAAATATTTT
1 TATAATTTTCAAAAATATGAT
1642787 TATAATTTTCAAAAATA-GAT
1 TATAATTTTCAAAAATATGAT
1642807 TAT
1 TAT
1642810 GTGTTTTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
TATAATTTTCAAAAATATGAT
Found at i:1642873 original size:22 final size:22
Alignment explanation
Indices: 1642848--1642894 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1642838 TTTTAATAAC
* *
1642848 TTTTTTTGGATTTTGTAAAGTT
1 TTTTTTTAGATTTTGTAAAATT
* *
1642870 TTTTTTTATATTTTTTAAAATT
1 TTTTTTTAGATTTTGTAAAATT
1642892 TTT
1 TTT
1642895 AAGTGAACAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTTTTAGATTTTGTAAAATT
Found at i:1644377 original size:31 final size:31
Alignment explanation
Indices: 1644339--1644407 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
1644329 TCACAAAATG
*
1644339 GTCACTAAACTATTGAAAAGTT-TTCATTCAA
1 GTCACTAAACTATTCAAAAGTTATT-ATTCAA
*
1644370 GTCACTAAACTATTCAAAAGTTATTATTTAA
1 GTCACTAAACTATTCAAAAGTTATTATTCAA
1644401 GTCACTA
1 GTCACTA
1644408 GGGTTTTAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (31 bp):
GTCACTAAACTATTCAAAAGTTATTATTCAA
Found at i:1647300 original size:45 final size:45
Alignment explanation
Indices: 1647199--1647325 Score: 129
Period size: 45 Copynumber: 2.9 Consensus size: 45
1647189 TTTTCTCAAA
* *
1647199 TCACCGGCATT-TCGCCTGTTAGGCTCG-AGGCCCG-ATATCAGT
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
* *
1647241 TCACCAGCATTATAGCCTGCTAGGCTCGAAGGCCTGAATAGT-A-T
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA-TCAGT
** * *
1647285 CTCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 -TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
1647326 ATCAAGTCAA
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
42 10 0.14
43 14 0.20
44 7 0.10
45 38 0.54
46 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.25
Consensus pattern (45 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATATCAGT
Found at i:1647720 original size:43 final size:43
Alignment explanation
Indices: 1647655--1647766 Score: 179
Period size: 43 Copynumber: 2.6 Consensus size: 43
1647645 CTTGCATTAC
* **
1647655 GCCTGCTAGGCACGAAGTCCCGAATACACATCATTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
1647698 GCCTGCTAGGCACGAAGGCCCGAATACATATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
1647741 GCCTGCTAGGCACAAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
1647767 TAATACCAGC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.30, C:0.31, G:0.25, T:0.13
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:1647866 original size:75 final size:76
Alignment explanation
Indices: 1647764--1647966 Score: 320
Period size: 75 Copynumber: 2.7 Consensus size: 76
1647754 AAAGGCCCGA
* * *
1647764 ATATAATACCAGCACTAGGCCTGCGGGATTTAACCCGGATATATTACCAGCACAAAGCCTGCGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACAAAGCCTGCGGG
1647829 ATTTAACCAGG
66 ATTTAACCAGG
* *
1647840 ATATATTA-CAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACTAGCACGAAGCCTGCGGG
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACAAAGCCTGCGGG
*
1647904 ATTTAACCCGG
66 ATTTAACCAGG
*
1647915 ATATATTACCAGCACGAAGCCTGCGGGAGTTAACCCGGATATAATT-CCAGCA
1 ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATAT-ATTACCAGCA
1647967 TATATCCTGC
Statistics
Matches: 117, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
75 70 0.60
76 44 0.38
77 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (76 bp):
ATATATTACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATTACCAGCACAAAGCCTGCGGG
ATTTAACCAGG
Found at i:1647979 original size:38 final size:38
Alignment explanation
Indices: 1647759--1647966 Score: 321
Period size: 38 Copynumber: 5.5 Consensus size: 38
1647749 GGCACAAAGG
* * * *
1647759 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
1647797 CCCGGATATATTACCAGCACAAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
1647835 CCAGGATATATTA-CAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
1647872 CCCGGATATATTACTAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
1647910 CCCGGATATATTACCAGCACGAAGCCTGCGGGAGTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
1647948 CCCGGATATAATT-CCAGCA
1 CCCGGATAT-ATTACCAGCA
1647967 TATATCCTGC
Statistics
Matches: 158, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
37 35 0.22
38 120 0.76
39 3 0.02
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (38 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:1648525 original size:49 final size:49
Alignment explanation
Indices: 1648453--1648551 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
1648443 CATGCATAAG
* *
1648453 TACATATCGTATACCTGAATAATTTACTTTACGGAATGAATCCACGTAT
1 TACATATCGCATACCTGAATAATTTACTTTACGAAATGAATCCACGTAT
1648502 TACATATCGCATACCTGAATAATTTACTTTACGAAATGAATCCACGTAT
1 TACATATCGCATACCTGAATAATTTACTTTACGAAATGAATCCACGTAT
1648551 T
1 T
1648552 GTATTAGCCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (49 bp):
TACATATCGCATACCTGAATAATTTACTTTACGAAATGAATCCACGTAT
Found at i:1653431 original size:43 final size:43
Alignment explanation
Indices: 1653366--1653688 Score: 272
Period size: 43 Copynumber: 7.5 Consensus size: 43
1653356 CCTACATTAC
* *
1653366 GCCTGCTAGGCACGAAGTCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
1653409 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
* * * *
1653452 GCCTGCTAGGCACGAAGGCCCGAATATA-AT-AC-CAGCACTAG
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGA-CACGAA
* ** * * * *
1653493 GCCTGC--GGGATTTAA--CCCGGAT--ATATTAC-CAGCACGAA
1 GCCTGCTAGGCA-CGAAGGCCCGAATACACATCACTGA-CACGAA
* * * *****
1653531 GCTTG-TGGGATTTAACCAGGATATATTAGAATACACATCACTGACACGAA
1 GCCTGCTAGG-------CACGA-AGGCCCGAATACACATCACTGACACGAA
1653581 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
1653624 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
*
1653667 GCCTGCTAGGCACGAAGACCCG
1 GCCTGCTAGGCACGAAGGCCCG
1653689 GATATATTAC
Statistics
Matches: 228, Mismatches: 32, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
36 1 0.00
37 2 0.01
38 19 0.08
39 5 0.02
40 3 0.01
41 12 0.05
42 2 0.01
43 155 0.68
44 4 0.02
45 1 0.00
46 2 0.01
48 3 0.01
50 15 0.07
51 4 0.02
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.15
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGACACGAA
Found at i:1653523 original size:38 final size:38
Alignment explanation
Indices: 1653470--1653558 Score: 115
Period size: 38 Copynumber: 2.3 Consensus size: 38
1653460 GGCACGAAGG
* * * *
1653470 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
* *
1653508 CCCGGATATATTACCAGCACGAAGCTTGTGGGATTTAA
1 CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
*
1653546 CCAGGATATATTA
1 CCCGGATATATTA
1653559 GAATACACAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (38 bp):
CCCGGATATATTACCAGCACGAAGCCTGCGGGATTTAA
Found at i:1655589 original size:89 final size:89
Alignment explanation
Indices: 1655438--1655615 Score: 302
Period size: 89 Copynumber: 2.0 Consensus size: 89
1655428 AGTTTCTAAC
* * *
1655438 TCATCTCCCACAATTTATGGTGATTTTCCAAAATCACATTACTGCTGCTGTCCCAAATAGATTTA
1 TCATCTCCCACAATTTATGGTGATTTTCCAAAATCACATTAATGCTGCTGTCCCAAACAGATTAA
1655503 TTACCAAATCACTCTTTCACACAT
66 TTACCAAATCACTCTTTCACACAT
* * *
1655527 TCATCTCCCACAATTTATGGTGATTTTCCAAATTCACGTTAATGCTGCTGTCCCAAGCAGATTAA
1 TCATCTCCCACAATTTATGGTGATTTTCCAAAATCACATTAATGCTGCTGTCCCAAACAGATTAA
1655592 TTACCAAATCACTCTTTCACACAT
66 TTACCAAATCACTCTTTCACACAT
1655616 ACCTTGCATG
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (89 bp):
TCATCTCCCACAATTTATGGTGATTTTCCAAAATCACATTAATGCTGCTGTCCCAAACAGATTAA
TTACCAAATCACTCTTTCACACAT
Found at i:1658049 original size:19 final size:19
Alignment explanation
Indices: 1658021--1658065 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1658011 TGGTGAGATT
1658021 TTTA-GGGATGAAAATTCC
1 TTTAGGGGATGAAAATTCC
*
1658039 TTTAGGGGATGAAAATTCT
1 TTTAGGGGATGAAAATTCC
1658058 TTTAGGGG
1 TTTAGGGG
1658066 GAGAGTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (19 bp):
TTTAGGGGATGAAAATTCC
Found at i:1661869 original size:26 final size:26
Alignment explanation
Indices: 1661840--1661891 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
1661830 GGATGATTAA
1661840 TTATGTAAATTAGTGAATTTGATGCT
1 TTATGTAAATTAGTGAATTTGATGCT
1661866 TTATGTAAATTAGTGAATTTGATGCT
1 TTATGTAAATTAGTGAATTTGATGCT
1661892 CCTAATCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.19, T:0.46
Consensus pattern (26 bp):
TTATGTAAATTAGTGAATTTGATGCT
Found at i:1673424 original size:40 final size:40
Alignment explanation
Indices: 1673380--1673466 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 40
1673370 TTGCACAATT
* **
1673380 AGTGCCACATATAGCCAAAGCTATAC-CAATTCGCACACTA
1 AGTGCCACATATAACCAAAGCTAT-CTCAAAACGCACACTA
* * **
1673420 AGTGCTATATATAACTGAAGCTATCTCAAAACGCACACTA
1 AGTGCCACATATAACCAAAGCTATCTCAAAACGCACACTA
1673460 AGTGCCA
1 AGTGCCA
1673467 AAAGTAGTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (40 bp):
AGTGCCACATATAACCAAAGCTATCTCAAAACGCACACTA
Found at i:1677151 original size:25 final size:25
Alignment explanation
Indices: 1677119--1677169 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1677109 TTTAGAAGTC
1677119 TGTGATACTTTCAAGATAAATGGTG
1 TGTGATACTTTCAAGATAAATGGTG
1677144 TGTGATACTTTCAAGATAAATGGTG
1 TGTGATACTTTCAAGATAAATGGTG
1677169 T
1 T
1677170 TTCTGACGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (25 bp):
TGTGATACTTTCAAGATAAATGGTG
Found at i:1681381 original size:40 final size:41
Alignment explanation
Indices: 1681296--1681406 Score: 120
Period size: 40 Copynumber: 2.8 Consensus size: 41
1681286 TGCGATGTTT
*
1681296 AGCACTTAGTGTGC-ATTTCAAGATAGCTTCAGCTATATAC
1 AGCACTTAGTGTGCGAATTCAAGATAGCTTCAGCTATATAC
* * **
1681336 AGCACTTAGTGTGCGAATTGAA-ATAGCTTCAGCTTTATGT
1 AGCACTTAGTGTGCGAATTCAAGATAGCTTCAGCTATATAC
* * *
1681376 GGCACTAAGTGTGCG-ATACCAAGATAGCTTC
1 AGCACTTAGTGTGCGAAT-TCAAGATAGCTTC
1681407 GATTCAATAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
39 2 0.03
40 44 0.75
41 13 0.22
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (41 bp):
AGCACTTAGTGTGCGAATTCAAGATAGCTTCAGCTATATAC
Found at i:1687744 original size:16 final size:16
Alignment explanation
Indices: 1687723--1687765 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1687713 ATGTATCGGC
* *
1687723 AAAAGCTGAAATGCTG
1 AAAAGCCGAAATGCCG
*
1687739 AAAAGCCAAAATGCCG
1 AAAAGCCGAAATGCCG
1687755 AAAAGCCGAAA
1 AAAAGCCGAAA
1687766 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.19, G:0.21, T:0.09
Consensus pattern (16 bp):
AAAAGCCGAAATGCCG
Found at i:1688015 original size:28 final size:29
Alignment explanation
Indices: 1687975--1688032 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
1687965 GTGAGCATGA
*
1687975 ATATGAATGTGA-TTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
*
1688003 ATATAAATGTGATTTGGGCTTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCC
1688032 A
1 A
1688033 GATACAGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCC
Found at i:1731421 original size:27 final size:26
Alignment explanation
Indices: 1731388--1732103 Score: 750
Period size: 27 Copynumber: 26.6 Consensus size: 26
1731378 ACATAGGGGT
* * *
1731388 AAAATAGTCATCTTACCATAAAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* *
1731415 AAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
** *
1731442 AAAACAACCATTTTACCTCATAAGGTC
1 AAAACAGTCATTTTACCT-ATAAGGGC
*
1731469 AAAACAATCATTTTACCTCATAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
1731496 AAAACAGTCATTTTACCTTATAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
1731523 AAAACAGTCATTTTACCTCATAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
* * *
1731550 AAAATAGTTATTTTACCTCAAAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
*
1731577 AAAATAGTCATTTTACCATATAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* *
1731604 AAAACAGTCATTTTACCACATAAGGGA
1 AAAACAGTCATTTTACC-TATAAGGGC
*
1731631 AAAATAGTCATTTTACCTCATAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
** *
1731658 AAAATTGTCATTTTACCTCACAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
*
1731685 AAAACAGTCATTTTACCATTTAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* * *
1731712 TAAACAGTCACTTTACCTCATAAAGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
*
1731739 AAAACAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* *
1731766 AAAATAGTCATTTTACCTCACAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
* * *
1731793 AAAACAGTTATTTTACC-ACAATGGC
1 AAAACAGTCATTTTACCTATAAGGGC
* *
1731818 AAAATAGTCATTTTACCTCACAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
* * * *
1731845 AAAATAGTCATTTTAGCTCACAAGGGA
1 AAAACAGTCATTTTACCT-ATAAGGGC
1731872 AAAACAGTCATATTTACCTTATAAGGGC
1 AAAACAGTCAT-TTTACC-TATAAGGGC
* *
1731900 AAAACAATCATCTTACCATATAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
*
1731927 AAAACAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
*
1731954 AAAATAGTCATTTTACCTCATAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
* * *
1731981 AAAATAGTTATTTTACCTCAAAAGGGC
1 AAAACAGTCATTTTACCT-ATAAGGGC
* *
1732008 AAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACC-TATAAGGGC
* *
1732035 AAAATAGTCATTTTACCCCATAAGGGC
1 AAAACAGTCATTTTA-CCTATAAGGGC
* *
1732062 AAAACAATCATTTTACCCTATAAGGGG
1 AAAACAGTCATTTTA-CCTATAAGGGC
*
1732089 AAAACAATCATTTTA
1 AAAACAGTCATTTTA
1732104 TTAATTTGGG
Statistics
Matches: 605, Mismatches: 68, Indels: 32
0.86 0.10 0.05
Matches are distributed among these distances:
25 22 0.04
26 2 0.00
27 554 0.92
28 26 0.04
29 1 0.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (26 bp):
AAAACAGTCATTTTACCTATAAGGGC
Found at i:1731436 original size:54 final size:54
Alignment explanation
Indices: 1731377--1732103 Score: 886
Period size: 54 Copynumber: 13.5 Consensus size: 54
1731367 AAACATACAT
* * * * *
1731377 CACATAGGGGTAAAATAGTCATCTTACCAT-AAAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACC-TCATAAGGGCAAAACAGTCATTTTAC
* ** * *
1731431 CACATAAGGGCAAAACAACCATTTTACCTCATAAGGTCAAAACAATCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * *
1731485 CTCATAAGGGCAAAACAGTCATTTTACCTTATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * * *
1731539 CTCATAAGGGCAAAATAGTTATTTTACCTCAAAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * * * *
1731593 CATATAAGGGCAAAACAGTCATTTTACCACATAAGGGAAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * *
1731647 CTCATAAGGGCAAAATTGTCATTTTACCTCACAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
** * * * *
1731701 CATTTAAGGGCTAAACAGTCACTTTACCTCATAAAGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* *
1731755 CACATAAGGGCAAAATAGTCATTTTACCTCACAAGGGCAAAACAGTTATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * * *
1731809 CAC--AATGGCAAAATAGTCATTTTACCTCACAAGGGCAAAATAGTCATTTTAG
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * * * * * *
1731861 CTCACAAGGGAAAAACAGTCATATTTACCTTATAAGGGCAAAACAATCATCTTAC
1 CACATAAGGGCAAAATAGTCAT-TTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * * *
1731916 CATATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * * *
1731970 CTCATAAGGGCAAAATAGTTATTTTACCTCAAAAGGGCAAAATAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* *
1732024 CACATAAGGGCAAAATAGTCATTTTACCCCATAAGGGCAAAACAATCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
* * *
1732078 C-CTATAAGGGGAAAACAATCATTTTA
1 CAC-ATAAGGGCAAAATAGTCATTTTA
1732104 TTAATTTGGG
Statistics
Matches: 577, Mismatches: 91, Indels: 10
0.85 0.13 0.01
Matches are distributed among these distances:
52 47 0.08
53 2 0.00
54 484 0.84
55 44 0.08
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (54 bp):
CACATAAGGGCAAAATAGTCATTTTACCTCATAAGGGCAAAACAGTCATTTTAC
Found at i:1731535 original size:81 final size:81
Alignment explanation
Indices: 1731409--1732103 Score: 876
Period size: 81 Copynumber: 8.6 Consensus size: 81
1731399 CTTACCATAA
** *
1731409 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAACCATTTTACCTCATAAGGTCAAAAC
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
*
1731474 AATCATTTTACCTCAT
66 AGTCATTTTACCTCAT
* ** *
1731490 AAGGGCAAAACAGTCATTTTACCTTATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAT
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
* *
1731555 AGTTATTTTACCTCAA
66 AGTCATTTTACCTCAT
* * * *
1731571 AAGGGCAAAATAGTCATTTTACCATATAAGGGCAAAACAGTCATTTTACCACATAAGGGAAAAAT
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
1731636 AGTCATTTTACCTCAT
66 AGTCATTTTACCTCAT
* * * * *
1731652 AAGGGCAAAATTGTCATTTTACCTCACAAGGGCAAAACAGTCATTTTACCAT-TTAAGGGCTAAA
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACC-TCATAAGGGCAAAA
*
1731716 CAGTCACTTTACCTCAT
65 CAGTCATTTTACCTCAT
* * * *
1731733 AAAGGCAAAACAGTCATTTTACCACATAAGGGCAAAATAGTCATTTTACCTCACAAGGGCAAAAC
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
* *
1731798 AGTTATTTTA-C-CAC
66 AGTCATTTTACCTCAT
* * * * * * *
1731812 AATGGCAAAATAGTCATTTTACCTCACAAGGGCAAAATAGTCATTTTAGCTCACAAGGGAAAAAC
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
*
1731877 AGTCATATTTACCTTAT
66 AGTCAT-TTTACCTCAT
* * * * * *
1731894 AAGGGCAAAACAATCATCTTACCATATAAGGGCAAAACAGTCATTTTACCACATAAGGGCAAAAT
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
1731959 AGTCATTTTACCTCAT
66 AGTCATTTTACCTCAT
* * * * * *
1731975 AAGGGCAAAATAGTTATTTTACCTCAAAAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAAT
1 AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
*
1732040 AGTCATTTTACCCCAT
66 AGTCATTTTACCTCAT
* * * *
1732056 AAGGGCAAAACAATCATTTTACC-CTATAAGGGGAAAACAATCATTTTA
1 AAGGGCAAAATAGTCATTTTACCAC-ATAAGGGCAAAACAGTCATTTTA
1732104 TTAATTTGGG
Statistics
Matches: 531, Mismatches: 77, Indels: 12
0.86 0.12 0.02
Matches are distributed among these distances:
79 66 0.12
80 7 0.01
81 399 0.75
82 59 0.11
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (81 bp):
AAGGGCAAAATAGTCATTTTACCACATAAGGGCAAAACAGTCATTTTACCTCATAAGGGCAAAAC
AGTCATTTTACCTCAT
Found at i:1733580 original size:40 final size:39
Alignment explanation
Indices: 1733531--1733693 Score: 188
Period size: 39 Copynumber: 4.1 Consensus size: 39
1733521 CTGAATTTAA
** *
1733531 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGG-CTTAGC
* * *
1733571 CCGGTTATAGTAACTCACACAAATGCCTTCGGGCTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
1733610 CCGGA-ATTAGTAACTCGCACAAATGCCTTCGGGCTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGCTTAGC
* *
1733649 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGTCTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGG-CTTAGC
1733689 CCGGA
1 CCGGA
1733694 CATCATTTGA
Statistics
Matches: 107, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
38 1 0.01
39 59 0.55
40 47 0.44
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGCTTAGC
Found at i:1737301 original size:30 final size:30
Alignment explanation
Indices: 1737267--1737330 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
1737257 ACTTCTCAAC
1737267 CACTCCAACTGCCCACTAGTATTAGAATTT
1 CACTCCAACTGCCCACTAGTATTAGAATTT
1737297 CACTCCAACTGCCCACTAGTATTAGAATTT
1 CACTCCAACTGCCCACTAGTATTAGAATTT
1737327 CACT
1 CACT
1737331 AACACACAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (30 bp):
CACTCCAACTGCCCACTAGTATTAGAATTT
Found at i:1738211 original size:20 final size:20
Alignment explanation
Indices: 1738186--1738223 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1738176 CCTTGTAACT
1738186 TAGAA-TTTATAGTTTTGACC
1 TAGAATTTTAT-GTTTTGACC
1738206 TAGAATTTTATGTTTTGA
1 TAGAATTTTATGTTTTGA
1738224 TTAGATTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.29, C:0.05, G:0.16, T:0.50
Consensus pattern (20 bp):
TAGAATTTTATGTTTTGACC
Found at i:1740220 original size:63 final size:60
Alignment explanation
Indices: 1740143--1740261 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
1740133 TCAAATTGTA
* *
1740143 TTAGATATTATAATTATTTAAGTTTATTTTTTTACCTAATTAATATTTAAATACTATTTATAC
1 TTAGATATTATAATTATTTAA-TTT-TATTTTTA-CAAATTAATATTTAAATACTATTTATAC
* *
1740206 TTAGATATTGTAATTATTTAATTTTATTTTTACAAATTAATATTTAGATACTATTT
1 TTAGATATTATAATTATTTAATTTTATTTTTACAAATTAATATTTAAATACTATTT
1740262 GTATTAGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
60 22 0.42
61 7 0.13
62 3 0.06
63 20 0.38
ACGTcount: A:0.36, C:0.05, G:0.04, T:0.55
Consensus pattern (60 bp):
TTAGATATTATAATTATTTAATTTTATTTTTACAAATTAATATTTAAATACTATTTATAC
Found at i:1749015 original size:43 final size:43
Alignment explanation
Indices: 1748954--1749036 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
1748944 CCCAGAATCA
1748954 AACACAAGACCTCAAGCAACCAACACTCCAATTAACCACCTTG
1 AACACAAGACCTCAAGCAACCAACACTCCAATTAACCACCTTG
* * *
1748997 AACACAAGACCTCAAGCAACCAGCACTCCACTTTACCACC
1 AACACAAGACCTCAAGCAACCAACACTCCAATTAACCACC
1749037 AGCCCGACAG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.13
Consensus pattern (43 bp):
AACACAAGACCTCAAGCAACCAACACTCCAATTAACCACCTTG
Found at i:1756267 original size:23 final size:24
Alignment explanation
Indices: 1756240--1756286 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1756230 CTTAAATTTT
1756240 AATAATAATAAAAT-A-TTAAAATA
1 AATAA-AATAAAATAATTTAAAATA
*
1756263 AATAAAGTAAAATAATTTAAAATA
1 AATAAAATAAAATAATTTAAAATA
1756287 CTCCTTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAAAATAAAATAATTTAAAATA
Found at i:1759084 original size:46 final size:46
Alignment explanation
Indices: 1759017--1759186 Score: 193
Period size: 46 Copynumber: 3.7 Consensus size: 46
1759007 TGTAACCCGC
* *
1759017 CCATAAGTGAACCCAGACTCAACTCAACGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
1759063 CCATAAGTGAACTTGGACTCAACTCAACGAGCTC-GG-ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGC-A--T
* *** * *
1759109 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
1759156 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
1759187 TTCAGATGCT
Statistics
Matches: 101, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 59 0.58
47 29 0.29
48 1 0.01
49 4 0.04
50 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:1760650 original size:21 final size:21
Alignment explanation
Indices: 1760612--1760651 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1760602 TGTGTGGAGG
*
1760612 AAGGCACACGACCGTGTGACA
1 AAGGCACACGACCATGTGACA
1760633 AAGGCACACG-CCTATGTGA
1 AAGGCACACGACC-ATGTGA
1760652 ACTAGGGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.33, C:0.28, G:0.28, T:0.12
Consensus pattern (21 bp):
AAGGCACACGACCATGTGACA
Found at i:1770185 original size:34 final size:34
Alignment explanation
Indices: 1770147--1770226 Score: 115
Period size: 34 Copynumber: 2.4 Consensus size: 34
1770137 CATGGCATCC
*
1770147 ATAGAGATAAGTCTACCAAGACAGTAAACACGAA
1 ATAGAGATAAGTCTACCAAGACAGTAAACACAAA
* * *
1770181 ATAGAGATAAGTCTATCAGGATAGTAAACACAAA
1 ATAGAGATAAGTCTACCAAGACAGTAAACACAAA
*
1770215 ATAGAGTTAAGT
1 ATAGAGATAAGT
1770227 TTGCTGGGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (34 bp):
ATAGAGATAAGTCTACCAAGACAGTAAACACAAA
Found at i:1773522 original size:18 final size:18
Alignment explanation
Indices: 1773499--1773546 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1773489 CGCCAAAATG
*
1773499 GTATTGATATTTATTTGA
1 GTATTGATACTTATTTGA
1773517 GTATTGATACTTATTTGA
1 GTATTGATACTTATTTGA
1773535 GTATTGATACTT
1 GTATTGATACTT
1773547 TTTCATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.52
Consensus pattern (18 bp):
GTATTGATACTTATTTGA
Found at i:1778290 original size:34 final size:34
Alignment explanation
Indices: 1778245--1778390 Score: 141
Period size: 34 Copynumber: 4.3 Consensus size: 34
1778235 CATGACATCC
***
1778245 ATAGAGATAAGTCCGTTGGGACAGAAAACACAGA
1 ATAGAGATAAGTCCGCCAGGACAGAAAACACAGA
* * * * * *
1778279 ATATAGATAAGTTCTCCAGGATAGTAAACATAGA
1 ATAGAGATAAGTCCGCCAGGACAGAAAACACAGA
* *
1778313 ATAGAGATAAGTCCGCCAGGATAGTAAAA-ATAGA
1 ATAGAGATAAGTCCGCCAGGACAG-AAAACACAGA
* * *
1778347 ATAGAGATAAGTCCGCTAGGACAGTAAACACAAA
1 ATAGAGATAAGTCCGCCAGGACAGAAAACACAGA
*
1778381 ATAAAGATAA
1 ATAGAGATAA
1778391 TGTAACAGCC
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
33 3 0.03
34 85 0.93
35 3 0.03
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (34 bp):
ATAGAGATAAGTCCGCCAGGACAGAAAACACAGA
Found at i:1778355 original size:68 final size:68
Alignment explanation
Indices: 1778245--1778390 Score: 159
Period size: 68 Copynumber: 2.1 Consensus size: 68
1778235 CATGACATCC
*** * * * * *
1778245 ATAGAGATAAGTCCGTTGGGACAGAAAACACAGAATATAGATAAGTTCTCCAGGATAGTAAACAT
1 ATAGAGATAAGTCCGCCAGGACAGAAAACACAGAATAGAGATAAGTCCGCCAGGACAGTAAACAC
*
1778310 AGA
66 AAA
* * *
1778313 ATAGAGATAAGTCCGCCAGGATAGTAAAA-ATAGAATAGAGATAAGTCCGCTAGGACAGTAAACA
1 ATAGAGATAAGTCCGCCAGGACAG-AAAACACAGAATAGAGATAAGTCCGCCAGGACAGTAAACA
1778377 CAAA
65 CAAA
*
1778381 ATAAAGATAA
1 ATAGAGATAA
1778391 TGTAACAGCC
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
68 60 0.94
69 4 0.06
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (68 bp):
ATAGAGATAAGTCCGCCAGGACAGAAAACACAGAATAGAGATAAGTCCGCCAGGACAGTAAACAC
AAA
Found at i:1778383 original size:39 final size:34
Alignment explanation
Indices: 1778245--1778374 Score: 145
Period size: 34 Copynumber: 3.8 Consensus size: 34
1778235 CATGACATCC
*** *
1778245 ATAGAGATAAGTCCGTTGGGACAG-AAAACACAGA
1 ATAGAGATAAGTCCGCCAGGACAGTAAAA-ATAGA
* * * * *
1778279 ATATAGATAAGTTCTCCAGGATAGTAAACATAGA
1 ATAGAGATAAGTCCGCCAGGACAGTAAAAATAGA
*
1778313 ATAGAGATAAGTCCGCCAGGATAGTAAAAATAGA
1 ATAGAGATAAGTCCGCCAGGACAGTAAAAATAGA
*
1778347 ATAGAGATAAGTCCGCTAGGACAGTAAA
1 ATAGAGATAAGTCCGCCAGGACAGTAAA
1778375 CACAAAATAA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
34 77 0.96
35 3 0.04
ACGTcount: A:0.45, C:0.13, G:0.23, T:0.19
Consensus pattern (34 bp):
ATAGAGATAAGTCCGCCAGGACAGTAAAAATAGA
Found at i:1790396 original size:56 final size:56
Alignment explanation
Indices: 1790304--1790414 Score: 195
Period size: 56 Copynumber: 2.0 Consensus size: 56
1790294 CAACGGGTAA
* * *
1790304 AGTTTTAACATGTCTACACTAAATTTGAGATTACTTGTTATGGAAATGTATGAGTT
1 AGTTTTAACATGTCTACACTAAACTTGAAATGACTTGTTATGGAAATGTATGAGTT
1790360 AGTTTTAACATGTCTACACTAAACTTGAAATGACTTGTTATGGAAATGTATGAGT
1 AGTTTTAACATGTCTACACTAAACTTGAAATGACTTGTTATGGAAATGTATGAGT
1790415 AATGTGAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (56 bp):
AGTTTTAACATGTCTACACTAAACTTGAAATGACTTGTTATGGAAATGTATGAGTT
Found at i:1793002 original size:15 final size:15
Alignment explanation
Indices: 1792982--1793012 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1792972 AATTGTTTTC
1792982 TATTTATTTGAACGA
1 TATTTATTTGAACGA
*
1792997 TATTTATTTTAACGA
1 TATTTATTTGAACGA
1793012 T
1 T
1793013 GAATAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (15 bp):
TATTTATTTGAACGA
Found at i:1803707 original size:46 final size:45
Alignment explanation
Indices: 1803612--1803710 Score: 108
Period size: 46 Copynumber: 2.2 Consensus size: 45
1803602 GCTGCAAACG
* * * *
1803612 GTAAGCTCCATTGTGATGAACAGTAAGCTCTTTCAAGCTAAATCG
1 GTAAGCTCCAATGAGATGAACAGTAAGCTCTTACAAGCTAAATCA
* * * * *
1803657 GTAAGCTCCAATGAGCTGAAACAGTAAGCTCTTACGAGTTGAATTA
1 GTAAGCTCCAATGAGATG-AACAGTAAGCTCTTACAAGCTAAATCA
1803703 GTAAGCTC
1 GTAAGCTC
1803711 ATACAAGCTG
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
45 15 0.34
46 29 0.66
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (45 bp):
GTAAGCTCCAATGAGATGAACAGTAAGCTCTTACAAGCTAAATCA
Found at i:1804630 original size:71 final size:70
Alignment explanation
Indices: 1804504--1804645 Score: 212
Period size: 71 Copynumber: 2.0 Consensus size: 70
1804494 TAGCTAATGA
* * * *
1804504 ACCATAGCCGAATGAAAATCTAGAGTTATTATTTTCTTCTTGCCAAATTCGGCTAAGGAAGATGA
1 ACCATAGCCGAATGAAAAACTAAAGTTATTATTTTCTCCTTGCCAAATTCAGCTAAGGAAGATGA
1804569 TGATG
66 TGATG
* * *
1804574 ACCATAGCCGAATGAAAAACTAAAGTTTCTTGTTTTCTCCTTGCCAAATTTAGCTAAGGAAGATG
1 ACCATAGCCGAATGAAAAACTAAAG-TTATTATTTTCTCCTTGCCAAATTCAGCTAAGGAAGATG
1804639 ATGATG
65 ATGATG
1804645 A
1 A
1804646 TATAAAATAA
Statistics
Matches: 64, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
70 23 0.36
71 41 0.64
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (70 bp):
ACCATAGCCGAATGAAAAACTAAAGTTATTATTTTCTCCTTGCCAAATTCAGCTAAGGAAGATGA
TGATG
Found at i:1812386 original size:38 final size:40
Alignment explanation
Indices: 1812342--1812419 Score: 106
Period size: 38 Copynumber: 2.0 Consensus size: 40
1812332 TGAAATCAAC
1812342 AATATATAAAAAATAATGTATAA-TATAAATTTT-AAAAT
1 AATATATAAAAAATAATGTATAAGTATAAATTTTGAAAAT
***
1812380 AATATATAATGTATAATGTATAATGTATAAATTTTGAAAA
1 AATATATAAAAAATAATGTATAA-GTATAAATTTTGAAAA
1812420 CAAAAACACA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 20 0.59
40 10 0.29
41 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (40 bp):
AATATATAAAAAATAATGTATAAGTATAAATTTTGAAAAT
Found at i:1812395 original size:14 final size:14
Alignment explanation
Indices: 1812378--1812409 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1812368 AAATTTTAAA
1812378 ATAATATATAATGT
1 ATAATATATAATGT
*
1812392 ATAATGTATAATGT
1 ATAATATATAATGT
1812406 ATAA
1 ATAA
1812410 ATTTTGAAAA
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:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (14 bp):
ATAATATATAATGT
Found at i:1812458 original size:14 final size:16
Alignment explanation
Indices: 1812439--1812471 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1812429 ATGTATAAAG
1812439 GAAATTTTA-A-AATA
1 GAAATTTTACATAATA
1812453 GAAATTTTACATAATA
1 GAAATTTTACATAATA
1812469 GAA
1 GAA
1812472 TAATTTAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 1 0.06
16 7 0.41
ACGTcount: A:0.55, C:0.03, G:0.09, T:0.33
Consensus pattern (16 bp):
GAAATTTTACATAATA
Found at i:1812576 original size:22 final size:22
Alignment explanation
Indices: 1812551--1812592 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1812541 TAAGATAATT
1812551 TTAAAAAAATAAT-AATAAAATC
1 TTAAAAAAA-AATGAATAAAATC
*
1812573 TTAAATAAAAATGAATAAAA
1 TTAAAAAAAAATGAATAAAA
1812593 ACATAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
TTAAAAAAAAATGAATAAAATC
Found at i:1812599 original size:22 final size:23
Alignment explanation
Indices: 1812564--1812606 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1812554 AAAAAATAAT
* *
1812564 AATAAAATCTTAAA-TAAAAATG
1 AATAAAAACATAAATTAAAAATG
1812586 AATAAAAACATAAATTAAAAA
1 AATAAAAACATAAATTAAAAA
1812607 AACTCGATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (23 bp):
AATAAAAACATAAATTAAAAATG
Found at i:1813803 original size:28 final size:29
Alignment explanation
Indices: 1813730--1813817 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
1813720 AGCATGGCTG
* * * *
1813730 CCAGATACAGA-AA-ATGTGACAGAGTCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
*
1813757 CCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAATTTGTGGCA-TAGCCA
1813786 CCAGA-ACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAATTTGTGGCATAGCCA
1813814 CCAG
1 CCAG
1813818 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
27 12 0.24
28 25 0.49
29 14 0.27
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (29 bp):
CCAGATACAGATAATTTGTGGCATAGCCA
Found at i:1813970 original size:28 final size:28
Alignment explanation
Indices: 1813923--1813987 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1813913 AAATTAACCC
*
1813923 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
1813951 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
1813979 TAGGGGTAT
1 TAGGGGTAT
1813988 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:1821649 original size:55 final size:56
Alignment explanation
Indices: 1821584--1821698 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
1821574 AGCATGGCTG
* * *
1821584 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
1821640 CCAGA-ACAGATATACGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
1821695 CCAG
1 CCAG
1821699 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.57
56 21 0.41
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (56 bp):
CCAGATACAGATAAACGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:1821695 original size:28 final size:27
Alignment explanation
Indices: 1821609--1821698 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
1821599 GTGACAGAGT
*
1821609 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
** *
1821638 CACCAGAACAGAT-ATACGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
1821665 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
1821693 CACCAG
1 CACCAG
1821699 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 23 0.44
28 22 0.42
29 7 0.13
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:1821851 original size:28 final size:28
Alignment explanation
Indices: 1821804--1821868 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1821794 AAATTAACCC
*
1821804 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
1821832 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
1821860 TAGGGGTAT
1 TAGGGGTAT
1821869 TCTAGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:1825090 original size:43 final size:45
Alignment explanation
Indices: 1825009--1825103 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 45
1824999 CTGCTTAGGG
** * *
1825009 AGATAAGATCTTCAATCTTCAGTCTACTTTCTTACTACCTTAGAA
1 AGATAAGATCTTCAATCTTCAACCTACTCTCTTACTACCTCAGAA
* * *
1825054 AGATAAGA-C-TCAATCTTCAACCTGCTCTCTTGCTACCTCAGAG
1 AGATAAGATCTTCAATCTTCAACCTACTCTCTTACTACCTCAGAA
1825097 AGATAAG
1 AGATAAG
1825104 GCTAGTAGCT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 34 0.79
44 1 0.02
45 8 0.19
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.32
Consensus pattern (45 bp):
AGATAAGATCTTCAATCTTCAACCTACTCTCTTACTACCTCAGAA
Found at i:1825235 original size:176 final size:176
Alignment explanation
Indices: 1824904--1825239 Score: 469
Period size: 176 Copynumber: 1.9 Consensus size: 176
1824894 AGACTACAAA
* * * * *
1824904 CTCTTGCTACCTTAGAGAGATAAGGCTAATGGCTAAAATTTGCTCCATTGCCGGTACATGGAGAT
1 CTCTTGCTACCTCAGAGAGATAAGGCTAATAGCTAAAATCTGCTCCATTACCGATACATGGAGAT
* * * *
1824969 AAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTCAATCTTCAGTCT
66 AAGATTCGCCATCTTCGATCTACCCCACTACTGCCTAGGGAGATAAGATCTTAAATCTTCAGTCT
* ***
1825034 ACTTTCTTACTACCTTAGAAAGATAAGACTCAATCTTCAACCTGCT
131 ACTTCCTTACTACAACAGAAAGATAAGACTCAATCTTCAACCTGCT
*
1825080 CTCTTGCTACCTCAGAGAGATAAGGCTAGTAGCTAAAATCTGCTCCATTACCGATACATGGAGAT
1 CTCTTGCTACCTCAGAGAGATAAGGCTAATAGCTAAAATCTGCTCCATTACCGATACATGGAGAT
*
1825145 AAGATTCGCCATC-TCTGATCTACCCCACTACTGCCTAGGGAGATAAGATCTGTAAAT-TTTAGT
66 AAGATTCGCCATCTTC-GATCTACCCCACTACTGCCTAGGGAGATAAGATCT-TAAATCTTCAGT
* * * *
1825208 CTGCTTCCTTGCTATAACAGGAAGATAAGACT
129 CTACTTCCTTACTACAACAGAAAGATAAGACT
1825240 TGTATATTGA
Statistics
Matches: 139, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
175 2 0.01
176 133 0.96
177 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (176 bp):
CTCTTGCTACCTCAGAGAGATAAGGCTAATAGCTAAAATCTGCTCCATTACCGATACATGGAGAT
AAGATTCGCCATCTTCGATCTACCCCACTACTGCCTAGGGAGATAAGATCTTAAATCTTCAGTCT
ACTTCCTTACTACAACAGAAAGATAAGACTCAATCTTCAACCTGCT
Found at i:1825643 original size:64 final size:63
Alignment explanation
Indices: 1825538--1825719 Score: 285
Period size: 64 Copynumber: 2.8 Consensus size: 63
1825528 TGCTTATGGA
* *
1825538 AAATAATTAGGATGCTATGATCAAAATGAATCAAATACTCCTAACTAAATGTGACGCTGATGTC
1 AAATAATTAGGATGCTATGATC-AAATGAATCAAATGCTCCTAACTAGATGTGACGCTGATGTC
* *
1825602 AAATAATTAGGACGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTGATGCTGATGTC
1 AAATAATTAGGATGCTATGATC-AAATGAATCAAATGCTCCTAACTAGATGTGACGCTGATGTC
1825666 AAATAATTAGGATGCTATGATCAAAGTGAATCAAATG-TGCCTAACTAGATGTGA
1 AAATAATTAGGATGCTATGATCAAA-TGAATCAAATGCT-CCTAACTAGATGTGA
1825720 TGTGAATGAT
Statistics
Matches: 110, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
63 4 0.04
64 106 0.96
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (63 bp):
AAATAATTAGGATGCTATGATCAAATGAATCAAATGCTCCTAACTAGATGTGACGCTGATGTC
Found at i:1826801 original size:20 final size:18
Alignment explanation
Indices: 1826774--1826823 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
1826764 CTTTTCTTTC
*
1826774 TTTT-TTTTTATTTTTATA
1 TTTTCTTTTT-TTTTTAAA
1826792 TTTTCCTTTTCTTTTTTAAA
1 TTTT-CTTTT-TTTTTTAAA
1826812 TTTTCTTTTTTT
1 TTTTCTTTTTTT
1826824 GTTTTGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.25
19 5 0.18
20 15 0.54
21 1 0.04
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTTTTTAAA
Found at i:1826828 original size:20 final size:20
Alignment explanation
Indices: 1826784--1826820 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1826774 TTTTTTTTTA
*
1826784 TTTTTATATTTTCCTTTTCT
1 TTTTTAAATTTTCCTTTTCT
1826804 TTTTTAAATTTT-CTTTT
1 TTTTTAAATTTTCCTTTT
1826821 TTTGTTTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTAAATTTTCCTTTTCT
Found at i:1833098 original size:14 final size:15
Alignment explanation
Indices: 1833069--1833101 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1833059 ATGGTAAGGT
*
1833069 TTTTCTTTTCTTTTG
1 TTTTCCTTTCTTTTG
1833084 TTTTCCTTT-TTTTG
1 TTTTCCTTTCTTTTG
1833098 TTTT
1 TTTT
1833102 AAATGCGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (15 bp):
TTTTCCTTTCTTTTG
Found at i:1834014 original size:45 final size:46
Alignment explanation
Indices: 1833927--1834062 Score: 134
Period size: 46 Copynumber: 2.9 Consensus size: 46
1833917 AAGCTCCTCT
* * * * *
1833927 TGAGCTAATAAATAGTAAGCTCATT-GAGCTGCAAACGGTAAGCTCTAT
1 TGAGCT-A-AAATAGTAAGCTCTTTCGAGATG-AATCGATAAGCTCTAA
* *
1833975 TGAGCT-GAATAGTAAGCTCTTTCGAGTTGAATCGATAAGCTCTAA
1 TGAGCTAAAATAGTAAGCTCTTTCGAGATGAATCGATAAGCTCTAA
* *
1834020 TGAGCTAAAACAGTAAGCTCTTACGAGATGAATC-AGTAAGCTC
1 TGAGCTAAAATAGTAAGCTCTTTCGAGATGAATCGA-TAAGCTC
1834063 ATATGCGCTG
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
45 34 0.45
46 35 0.47
48 6 0.08
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (46 bp):
TGAGCTAAAATAGTAAGCTCTTTCGAGATGAATCGATAAGCTCTAA
Found at i:1834056 original size:23 final size:23
Alignment explanation
Indices: 1833980--1834062 Score: 80
Period size: 23 Copynumber: 3.7 Consensus size: 23
1833970 TCTATTGAGC
* *
1833980 TGAAT-AGTAAGCTCTTTCGAGT
1 TGAATCAGTAAGCTCTTACGAGA
* * *
1834002 TGAATC-GATAAGCTCTAATGAGC
1 TGAATCAG-TAAGCTCTTACGAGA
* *
1834025 TAAAACAGTAAGCTCTTACGAGA
1 TGAATCAGTAAGCTCTTACGAGA
1834048 TGAATCAGTAAGCTC
1 TGAATCAGTAAGCTC
1834063 ATATGCGCTG
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
22 6 0.13
23 40 0.85
24 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (23 bp):
TGAATCAGTAAGCTCTTACGAGA
Found at i:1836983 original size:27 final size:26
Alignment explanation
Indices: 1836953--1837017 Score: 112
Period size: 27 Copynumber: 2.5 Consensus size: 26
1836943 ATTATTGAGG
*
1836953 TTATTAGTTTATCGATAAATAAATATT
1 TTATTAATTTATCGATAAATAAATA-T
1836980 TTATTAATTTATCGATAAATAAATAT
1 TTATTAATTTATCGATAAATAAATAT
1837006 TTATTAATTTAT
1 TTATTAATTTAT
1837018 AGAATATTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 13 0.35
27 24 0.65
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATAAATAT
Found at i:1837134 original size:35 final size:38
Alignment explanation
Indices: 1837094--1837165 Score: 123
Period size: 35 Copynumber: 2.0 Consensus size: 38
1837084 ACTCAACGTC
1837094 AATTGGTTCATGTAA-C-AAAA-AAAAAAGAGTTAATT
1 AATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAATT
1837129 AATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAAT
1 AATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAAT
1837166 GGTTTCAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
35 15 0.44
36 1 0.03
37 4 0.12
38 14 0.41
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.26
Consensus pattern (38 bp):
AATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAATT
Done.