Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 75 of 240
Found at i:23935065 original size:40 final size:41
Alignment explanation
Indices: 23934978--23935067 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
23934968 GAAAAAACGA
* * *
23934978 TATATGAAATGGTTATATGAAAAAATGATATGTGTAATGGT
1 TATATGAATTGGTTACATGAAAAAATGATATATGTAATGGT
*
23935019 TATATGAATTGGTTACATGGAAAAATGAT-TATGTAATGGT
1 TATATGAATTGGTTACATGAAAAAATGATATATGTAATGGT
23935059 TATATGAAT
1 TATATGAAT
23935068 AAGTTATGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 19 0.42
41 26 0.58
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.38
Consensus pattern (41 bp):
TATATGAATTGGTTACATGAAAAAATGATATATGTAATGGT
Found at i:23941792 original size:21 final size:21
Alignment explanation
Indices: 23941767--23941810 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
23941757 AACATTACGG
*
23941767 CACCAAACTACTATGTCATGA
1 CACCAAACTACTATGTCACGA
* *
23941788 CACCACACTCCTATGTCACGA
1 CACCAAACTACTATGTCACGA
23941809 CA
1 CA
23941811 TGGACAACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.36, G:0.09, T:0.20
Consensus pattern (21 bp):
CACCAAACTACTATGTCACGA
Found at i:23945058 original size:40 final size:39
Alignment explanation
Indices: 23944974--23945158 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
23944964 TTGAATGATG
* * * *
23944974 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
23945014 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAAA
*
23945054 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* *
23945093 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGTTACTA-AA
**
23945134 -CCGGGCTATCTCCCGAAGGCATTTG
1 TCCGGGCTAAGT-CCGAAGGCATTTG
23945159 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
39 35 0.28
40 78 0.63
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:23945110 original size:79 final size:80
Alignment explanation
Indices: 23944974--23945158 Score: 207
Period size: 79 Copynumber: 2.3 Consensus size: 80
23944964 TTGAATGATG
* *
23944974 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAG-CCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
23945038 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
23945053 TTCCGGGCTAAGCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAA
1 -TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAA
*
23945116 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* **
23945133 ACCGGGCTATCTCCCGAAGGCATTTG
1 TCCGGGCTA-AGCCCGAAGGCATTTG
23945159 AACGAGTAGC
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 56 0.62
80 33 0.37
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATA
Found at i:23945180 original size:79 final size:79
Alignment explanation
Indices: 23945027--23945181 Score: 190
Period size: 79 Copynumber: 2.0 Consensus size: 79
23945017 GGACTAAGAT
* * **
23945027 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
23945092 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* **
23945106 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATCTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTA-AGCCCGAAGGCATTTGAACGAGTTA-C
*
23945169 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
23945182 ATTCTGAAGG
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
78 2 0.03
79 38 0.58
80 25 0.38
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:23948651 original size:156 final size:156
Alignment explanation
Indices: 23948367--23948673 Score: 544
Period size: 156 Copynumber: 2.0 Consensus size: 156
23948357 CATATTTGTA
*
23948367 AATTAGAAGGTGTATTAAATGAATATTGGTCGCTATGACACAACACATATGACTCGATGTCGCAA
1 AATTAGAAGGTGTATTAAATGAATATTGGTCGCTATGACACAACACAGATGACTCGATGTCGCAA
*
23948432 CATAAGGAAAAGAATGGAGAAAAATCAACTCTGGCTTTGATGTCATGACACAGACTGAGGGTGTC
66 CATAAGGAAAAGAATGGAGAAAAATCAACTCTGGCTTTGATGTCACGACACAGACTGAGGGTGTC
23948497 GCGACATACCCCTGAAGATAGCTGAT
131 GCGACATACCCCTGAAGATAGCTGAT
23948523 AATTAGAAGGTGTATTAAATGAATATTGGTCGCTATGACACAACACAGATGACTCGATGTCGCAA
1 AATTAGAAGGTGTATTAAATGAATATTGGTCGCTATGACACAACACAGATGACTCGATGTCGCAA
* * * *
23948588 CAT-AGAGAACAGAATGGAGAAAAATCAAGTTTGGCTTTGATGTCACGACATAGACTGAGGGTGT
66 CATAAG-GAAAAGAATGGAGAAAAATCAACTCTGGCTTTGATGTCACGACACAGACTGAGGGTGT
23948652 CGCGACATACCCCTGAAGATAG
130 CGCGACATACCCCTGAAGATAG
23948674 ATGAAAAGAA
Statistics
Matches: 144, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
155 2 0.01
156 142 0.99
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (156 bp):
AATTAGAAGGTGTATTAAATGAATATTGGTCGCTATGACACAACACAGATGACTCGATGTCGCAA
CATAAGGAAAAGAATGGAGAAAAATCAACTCTGGCTTTGATGTCACGACACAGACTGAGGGTGTC
GCGACATACCCCTGAAGATAGCTGAT
Found at i:23967594 original size:20 final size:21
Alignment explanation
Indices: 23967545--23967595 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
23967535 GTATCGATCC
23967545 GGTATCGATA-ATTTTCTTAA
1 GGTATCGATATATTTTCTTAA
*
23967565 GGTACCGATATATTTTC-TAA
1 GGTATCGATATATTTTCTTAA
*
23967585 GGTATTGATAT
1 GGTATCGATAT
23967596 TCCTGCTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (21 bp):
GGTATCGATATATTTTCTTAA
Found at i:23970297 original size:66 final size:66
Alignment explanation
Indices: 23970220--23970346 Score: 191
Period size: 66 Copynumber: 1.9 Consensus size: 66
23970210 TGTGAAAAAT
*** *
23970220 TTAACACAATTTTAGAACCAAAGAAGACACGGTCATGTGACTGAATGACACACTCATGTGACAGA
1 TTAACACAATTTTAGAACCAAAGAAGACACAACCATGTGACTGAATGACACACCCATGTGACAGA
23970285 A
66 A
* * *
23970286 TTAACACAATTTTAGAAGCAGAGAAGACACAACCATGTGACTGAATGATACACCCATGTGA
1 TTAACACAATTTTAGAACCAAAGAAGACACAACCATGTGACTGAATGACACACCCATGTGA
23970347 TAGTGATGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (66 bp):
TTAACACAATTTTAGAACCAAAGAAGACACAACCATGTGACTGAATGACACACCCATGTGACAGA
A
Found at i:23971544 original size:31 final size:32
Alignment explanation
Indices: 23971508--23971572 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
23971498 CTTAGATAAT
23971508 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
23971539 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
23971571 TT
1 TT
23971573 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:23977719 original size:31 final size:32
Alignment explanation
Indices: 23977683--23977747 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
23977673 CTTAGATAAT
23977683 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
23977714 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
23977746 TT
1 TT
23977748 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:23979968 original size:40 final size:40
Alignment explanation
Indices: 23979931--23980116 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
23979921 GCTACTCGTT
* *
23979931 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
23979971 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
23980011 CAAATGCCTTCGGGACTTAACTCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * * *
23980051 CAAATGCCTTC-GGATCTTAGTCCGAATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
23980092 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
23980117 CATCATTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
39 3 0.02
40 113 0.88
41 13 0.10
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:23983101 original size:88 final size:88
Alignment explanation
Indices: 23982952--23983127 Score: 352
Period size: 88 Copynumber: 2.0 Consensus size: 88
23982942 AACGTTTCAA
23982952 ATCGTTGTACATTTTTGTACTCCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAA
1 ATCGTTGTACATTTTTGTACTCCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAA
23983017 TCATCGAAATGAGTTCCGAATTC
66 TCATCGAAATGAGTTCCGAATTC
23983040 ATCGTTGTACATTTTTGTACTCCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAA
1 ATCGTTGTACATTTTTGTACTCCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAA
23983105 TCATCGAAATGAGTTCCGAATTC
66 TCATCGAAATGAGTTCCGAATTC
23983128 CTTGGAACAC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 88 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (88 bp):
ATCGTTGTACATTTTTGTACTCCCCGGGTGAATTGACATTCGGCTACAATGGGCTTCGTTCAGAA
TCATCGAAATGAGTTCCGAATTC
Found at i:23988027 original size:40 final size:40
Alignment explanation
Indices: 23987990--23988175 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
23987980 GCTACTCGTT
* *
23987990 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
23988030 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
23988070 CAAATGCTTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
23988110 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
23988151 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
23988176 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 13 0.10
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:23996464 original size:19 final size:20
Alignment explanation
Indices: 23996440--23996500 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
23996430 ATATGAAGGA
23996440 GAGACACAC-CCGTGTGACT
1 GAGACACACACCGTGTGACT
*
23996459 GAGACACACGACCGTGTGGCT
1 GAGACACAC-ACCGTGTGACT
*
23996480 AAGACACACACCTGTGTGACT
1 GAGACACACACC-GTGTGACT
23996501 AGGTTACATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 9 0.25
20 3 0.08
21 24 0.67
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGACACACACCGTGTGACT
Found at i:24002783 original size:24 final size:24
Alignment explanation
Indices: 24002750--24002803 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
24002740 TATTTATACA
* *
24002750 ATTTTATATATCAAATATTAAATT
1 ATTTTATATATAAAAAATTAAATT
* *
24002774 ATTTTTTATATAAAAAATTAAAAT
1 ATTTTATATATAAAAAATTAAATT
24002798 -TTTTAT
1 ATTTTAT
24002804 TTAAAACTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
ATTTTATATATAAAAAATTAAATT
Found at i:24011031 original size:4 final size:4
Alignment explanation
Indices: 24011024--24011055 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
24011014 CTTAATAAAT
24011024 ATTA ATTA ATTA A-TA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
24011056 AATATCACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
ATTA
Found at i:24011044 original size:15 final size:14
Alignment explanation
Indices: 24011015--24011052 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
24011005 TACTAAAATC
*
24011015 TTAATAAATATTAA
1 TTAATTAATATTAA
24011029 TTAATTAATAATTAA
1 TTAATTAAT-ATTAA
24011044 TTAATTAAT
1 TTAATTAAT
24011053 TAAAATATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TTAATTAATATTAA
Found at i:24015451 original size:24 final size:25
Alignment explanation
Indices: 24015423--24015469 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
24015413 TCATATTTTT
*
24015423 AAAATGATAATA-TGTAAAAGAATA
1 AAAATGATAAAATTGTAAAAGAATA
*
24015447 AAAATTATAAAATTGTAAAAGAA
1 AAAATGATAAAATTGTAAAAGAA
24015470 ATTCTAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.26
Consensus pattern (25 bp):
AAAATGATAAAATTGTAAAAGAATA
Found at i:24016733 original size:11 final size:11
Alignment explanation
Indices: 24016707--24016790 Score: 82
Period size: 11 Copynumber: 7.5 Consensus size: 11
24016697 ATTTTAAAAA
24016707 TTAAAAA-A-T
1 TTAAAAATATT
24016716 TTAAAAAGTATT
1 TTAAAAA-TATT
24016728 TTAAAAATATT
1 TTAAAAATATT
* **
24016739 TTAAAATTAAAAA
1 TTAAAA--ATATT
* *
24016752 ATAAAAAAATT
1 TTAAAAATATT
24016763 TTAAAAATATT
1 TTAAAAATATT
24016774 TTAAAAATATT
1 TTAAAAATATT
24016785 TTAAAA
1 TTAAAA
24016791 TTAAAAAATA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
9 7 0.11
11 40 0.65
12 8 0.13
13 7 0.11
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:24016762 original size:46 final size:46
Alignment explanation
Indices: 24016702--24016802 Score: 177
Period size: 46 Copynumber: 2.2 Consensus size: 46
24016692 AATTTATTTT
*
24016702 AAAAATTAAAAAA-TTTAAAAAGTATTTTAAAAATATTTTAAAATTA
1 AAAAATAAAAAAATTTTAAAAA-TATTTTAAAAATATTTTAAAATTA
24016748 AAAAATAAAAAAATTTTAAAAATATTTTAAAAATATTTTAAAATTA
1 AAAAATAAAAAAATTTTAAAAATATTTTAAAAATATTTTAAAATTA
24016794 AAAAATAAA
1 AAAAATAAA
24016803 TATATTTATT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
46 45 0.85
47 8 0.15
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (46 bp):
AAAAATAAAAAAATTTTAAAAATATTTTAAAAATATTTTAAAATTA
Found at i:24021473 original size:13 final size:13
Alignment explanation
Indices: 24021455--24021494 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
24021445 AGTTCTTCAT
24021455 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
24021468 TGCTTTTTAGAAG
1 TGCTTTTGAAAAG
24021481 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
24021494 T
1 T
24021495 TTGGTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:24026180 original size:21 final size:19
Alignment explanation
Indices: 24026155--24026202 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
24026145 GTTGATTAAT
* *
24026155 TTAATTAATTATGTTTTTATC
1 TTAATTAATCAT-ATTTTA-C
24026176 TTAATTAATCATATTTTAC
1 TTAATTAATCATATTTTAC
24026195 TTAATTAA
1 TTAATTAA
24026203 GCAACAAGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 9 0.36
20 5 0.20
21 11 0.44
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (19 bp):
TTAATTAATCATATTTTAC
Found at i:24029151 original size:12 final size:12
Alignment explanation
Indices: 24029134--24029158 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
24029124 CAGAGGCTAT
24029134 TAACAATATTTA
1 TAACAATATTTA
24029146 TAACAATATTTA
1 TAACAATATTTA
24029158 T
1 T
24029159 GTTATAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TAACAATATTTA
Found at i:24032025 original size:21 final size:22
Alignment explanation
Indices: 24031977--24032029 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
24031967 CTTGGGTCAT
* *
24031977 ATGGCCGTGTGCCTCCCTTTAC
1 ATGGGCGTGTGCCTCCCTTCAC
*
24031999 ACGGGCGTGTGCCT-CCTTCAC
1 ATGGGCGTGTGCCTCCCTTCAC
24032020 ATGGGCGTGT
1 ATGGGCGTGT
24032030 AGACCCTCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.09, C:0.32, G:0.30, T:0.28
Consensus pattern (22 bp):
ATGGGCGTGTGCCTCCCTTCAC
Found at i:24033999 original size:4 final size:4
Alignment explanation
Indices: 24033990--24034021 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
24033980 TCATAATATT
24033990 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
24034022 GCAGACATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTA
Found at i:24035420 original size:36 final size:36
Alignment explanation
Indices: 24035368--24035444 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
24035358 AAATTAATAC
* * *
24035368 AGTTCGTCATATTAATATAGA-TCACCAATTTAACAT
1 AGTTCGCCATAATAATATA-ATTCACCAAGTTAACAT
*
24035404 AGTTCGCCATAATAATATAATTTACCAAGTTAACAT
1 AGTTCGCCATAATAATATAATTCACCAAGTTAACAT
*
24035440 GGTTC
1 AGTTC
24035445 ACAATATAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (36 bp):
AGTTCGCCATAATAATATAATTCACCAAGTTAACAT
Found at i:24041793 original size:47 final size:46
Alignment explanation
Indices: 24041689--24041794 Score: 106
Period size: 47 Copynumber: 2.3 Consensus size: 46
24041679 ATATTATAAT
* * * *
24041689 ATATTATTATTCTAAATTTATCATTAACATTATTTTAGGTTTATCAT
1 ATATTATTATT-TAAAGTTAACATTAACATTATTTTAGATTTATCAC
* * **
24041736 GTATTTTTATTTAAAGTTAACATATATTATTATTTT-GAATTTATCAC
1 ATATTATTATTTAAAGTTAACAT-TAACATTATTTTAG-ATTTATCAC
24041783 ATATTATTATTT
1 ATATTATTATTT
24041795 TTTAAAAATT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
46 11 0.23
47 36 0.77
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (46 bp):
ATATTATTATTTAAAGTTAACATTAACATTATTTTAGATTTATCAC
Found at i:24041806 original size:27 final size:26
Alignment explanation
Indices: 24041755--24041808 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
24041745 TTTAAAGTTA
* *
24041755 ACATATATTATTATTTTGAATTTATC
1 ACATATATTATTATTTTAAAATTATC
24041781 ACATATTATTATT-TTTTAAAAATTATC
1 ACATA-TATTATTATTTT-AAAATTATC
24041808 A
1 A
24041809 TCAAAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (26 bp):
ACATATATTATTATTTTAAAATTATC
Found at i:24042171 original size:15 final size:15
Alignment explanation
Indices: 24042133--24042171 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
24042123 TTACTTGTAA
*
24042133 TTTTAAATGATTTTT
1 TTTTAATTGATTTTT
*
24042148 TTTAAAATTGATTTTT
1 TTT-TAATTGATTTTT
24042164 TTTTAATT
1 TTTTAATT
24042172 CGTTTCATGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTTAATTGATTTTT
Found at i:24047396 original size:37 final size:37
Alignment explanation
Indices: 24047333--24047515 Score: 140
Period size: 37 Copynumber: 4.7 Consensus size: 37
24047323 ATAGTATTAT
*
24047333 ATATTATG-ATTTTATTAAATTCATATAATAATATTTA
1 ATATTAAGAATTTTATTAAATT-ATATAATAATATTTA
* ** *
24047370 ATATTAAGAATTTTATTAAATTATATATTTTTATTAAATT
1 ATATTAAGAATTTTATTAAATTATATAATAATATT---TA
* * *
24047410 ATATTTAATAATAATTATTTTAAATTATATTAT-ATAGTATTA
1 ATA-TTAAGAAT--TT-TATTAAATTATATAATAATA-T-TTA
* *
24047452 TATATTATG-ATTTTATTAAATTCATATAAGAATATTTA
1 -ATATTAAGAATTTTATTAAATT-ATATAATAATATTTA
24047490 ATATTAAGAA-TTTATTAAATTATATA
1 ATATTAAGAATTTTATTAAATTATATA
24047516 TTTTTATTAA
Statistics
Matches: 115, Mismatches: 17, Indels: 29
0.71 0.11 0.18
Matches are distributed among these distances:
36 5 0.04
37 35 0.30
38 25 0.22
39 8 0.07
40 7 0.06
41 9 0.08
42 4 0.03
43 7 0.06
44 14 0.12
45 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (37 bp):
ATATTAAGAATTTTATTAAATTATATAATAATATTTA
Found at i:24047518 original size:16 final size:17
Alignment explanation
Indices: 24047379--24047532 Score: 72
Period size: 18 Copynumber: 9.0 Consensus size: 17
24047369 AATATTAAGA
24047379 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
24047396 ATTTTTATTAAA-T-TAT
1 A-TTTTATTAAATTATAT
* *
24047412 A-TTTAAT-AATAAT-T
1 ATTTTATTAAATTATAT
*
24047426 ATTTTAAATTATATTATAT
1 ATTTT--ATTAAATTATAT
* * *
24047445 AGTATTA-TATATTAT-G
1 A-TTTTATTAAATTATAT
24047461 ATTTTATTAAATTCATAT
1 ATTTTATTAAATT-ATAT
*** *
24047479 AAGAATATTTAATATTA-AG
1 -ATTTTA-TTAA-ATTATAT
*
24047498 AATTTATTAAATTATAT
1 ATTTTATTAAATTATAT
24047515 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
24047533 TTAATAATAA
Statistics
Matches: 101, Mismatches: 19, Indels: 33
0.66 0.12 0.22
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 8 0.08
16 14 0.14
17 20 0.20
18 33 0.33
19 6 0.06
20 8 0.08
21 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:24047568 original size:119 final size:120
Alignment explanation
Indices: 24047315--24047674 Score: 598
Period size: 119 Copynumber: 3.0 Consensus size: 120
24047305 ATTATTAATC
*
24047315 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAATAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
*
24047380 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
24047435 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
24047500 -TTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * * * * * *
24047554 TATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAATAA
1 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
*
24047619 TTTTATTAAATTATATATTTTAATTATAA-TATATTTAATAATAATTATGTTTAAAT
66 TTTTATTAAATTATATATTTTTATTA-AATTATATTTAATAATAATTATG-TTAAAT
24047675 ATGATTAAAT
Statistics
Matches: 227, Mismatches: 10, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
119 111 0.49
120 108 0.48
121 8 0.04
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
Found at i:24047652 original size:16 final size:16
Alignment explanation
Indices: 24047613--24047672 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
24047603 TATTGATTAT
*
24047613 TAATA-ATTTTATTAAA
1 TAATATATTTTAAT-AA
* *
24047629 TTATATATTTTAATTA
1 TAATATATTTTAATAA
24047645 TAATATA-TTTAATAA
1 TAATATATTTTAATAA
24047660 TAAT-TATGTTTAA
1 TAATATAT-TTTAA
24047673 ATATGATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 2 0.06
15 11 0.31
16 16 0.44
17 7 0.19
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TAATATATTTTAATAA
Found at i:24047657 original size:15 final size:15
Alignment explanation
Indices: 24047622--24047663 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24047612 TTAATAATTT
*
24047622 TATTAAATTAT-ATA
1 TATTTAATTATAATA
24047636 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
24047650 TATTTAATAATAAT
1 TATTTAATTATAAT
24047664 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:24047841 original size:39 final size:40
Alignment explanation
Indices: 24047798--24047904 Score: 128
Period size: 45 Copynumber: 2.6 Consensus size: 40
24047788 TTTTCCATTA
*
24047798 TGCTATTACACCTCTATTCCATTCAACCAAACACA-AGA-T
1 TGCTATTACGCCTCTATTCCATTCAACCAAACA-ATAGATT
*
24047837 TGCTATTACGCCTCTATTCCATTACATTCAACCAAACAATTGATT
1 TGCTATTACGCCTCTATT-C----CATTCAACCAAACAATAGATT
24047882 TGCTATTACGCCTCTATTCCATT
1 TGCTATTACGCCTCTATTCCATT
24047905 ACGCCTCTAA
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
39 17 0.29
40 5 0.08
43 1 0.02
44 17 0.29
45 19 0.32
ACGTcount: A:0.30, C:0.29, G:0.07, T:0.35
Consensus pattern (40 bp):
TGCTATTACGCCTCTATTCCATTCAACCAAACAATAGATT
Found at i:24047894 original size:45 final size:44
Alignment explanation
Indices: 24047817--24047906 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 44
24047807 ACCTCTATTC
24047817 CATTCAACCAAACACAAGATTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTGCTATTACGCCTCTATTCCATTA
*
24047861 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACA-AGA-TTGCTATTACGCCTCTATTCCATTA
24047906 C
1 C
24047907 GCCTCTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.37
45 26 0.60
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTGCTATTACGCCTCTATTCCATTA
Found at i:24047907 original size:16 final size:16
Alignment explanation
Indices: 24047886--24047934 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
24047876 TTGATTTGCT
24047886 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
24047902 ATTACGCCTCTAATCC
1 ATTACGCCTCTATTCC
24047918 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
24047934 A
1 A
24047935 ATACAGCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:24048135 original size:17 final size:17
Alignment explanation
Indices: 24048109--24048142 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24048099 GGATTGTTGG
*
24048109 ATTTTTTTATTGTTATT
1 ATTTTCTTATTGTTATT
*
24048126 ATTTTCTTATTTTTATT
1 ATTTTCTTATTGTTATT
24048143 TTAATTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (17 bp):
ATTTTCTTATTGTTATT
Found at i:24053735 original size:50 final size:50
Alignment explanation
Indices: 24053673--24053907 Score: 227
Period size: 50 Copynumber: 4.6 Consensus size: 50
24053663 CAATGTCATA
* * ** * *
24053673 TCCCAAATATGGTCTTACATTGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
** * * *
24053723 TCCCAAACATGGTCTTACGGGGGACCTCTCATTTTGGTGCCAACGCTATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* * *
24053773 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCAAG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* * * *
24053823 TCCCAGACATGGTCTTACATGAGACCTCTCATAGTCTCAATGATGCCAATGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATA---TC---GGTGCCAACGCCATG
* * *
24053879 TCCTAGACATGGTCTTACATGGGATCTCT
1 TCCCAAACATGGTCTTACATGGGACCTCT
24053908 TTACCCAAAT
Statistics
Matches: 153, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 113 0.74
53 2 0.01
56 38 0.25
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:24059648 original size:71 final size:72
Alignment explanation
Indices: 24059561--24059694 Score: 216
Period size: 71 Copynumber: 1.9 Consensus size: 72
24059551 TTTATTATTG
* *
24059561 TTATTATTGTAAATTATATGATTTGATGTTTTAAATTCATCAATCGAAAAT-TATTCACTTGAAG
1 TTATTATTGTAAATTATATAATTTGATGTTTTAAACTCATCAATCGAAAATATATTCACTTGAAG
24059625 TTATTTA
66 TTATTTA
* **
24059632 TTATTATTGTGAATTATATAATTTGATGTTTTAAACTCATCAATTTAAAATATATTCACTTGA
1 TTATTATTGTAAATTATATAATTTGATGTTTTAAACTCATCAATCGAAAATATATTCACTTGA
24059695 TATTTTTAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
71 46 0.81
72 11 0.19
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (72 bp):
TTATTATTGTAAATTATATAATTTGATGTTTTAAACTCATCAATCGAAAATATATTCACTTGAAG
TTATTTA
Found at i:24071815 original size:17 final size:17
Alignment explanation
Indices: 24071793--24071832 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
24071783 TATAACCGTG
*
24071793 TGGGCCACACGGGCATA
1 TGGGCCACACGGGAATA
24071810 TGGGCCACACGGGAATA
1 TGGGCCACACGGGAATA
24071827 TGGGCC
1 TGGGCC
24071833 CATATGAACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.12
Consensus pattern (17 bp):
TGGGCCACACGGGAATA
Found at i:24071880 original size:35 final size:35
Alignment explanation
Indices: 24071790--24071881 Score: 96
Period size: 35 Copynumber: 2.7 Consensus size: 35
24071780 GGGTATAACC
** *
24071790 GTGTGGG-CCACACGGGCATATGGGCCACACGGGA
1 GTGTGGGCCCACACGAACGTATGGGCCACACGGGA
* * * * *
24071824 ATATGGGCCCATATGAACGTATGGGCCACATGGGA
1 GTGTGGGCCCACACGAACGTATGGGCCACACGGGA
*
24071859 GTGTGGGCCCACACGATCGTATG
1 GTGTGGGCCCACACGAACGTATG
24071882 TGTTTGGGCC
Statistics
Matches: 44, Mismatches: 13, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
34 5 0.11
35 39 0.89
ACGTcount: A:0.23, C:0.24, G:0.36, T:0.17
Consensus pattern (35 bp):
GTGTGGGCCCACACGAACGTATGGGCCACACGGGA
Found at i:24073392 original size:15 final size:15
Alignment explanation
Indices: 24073374--24073418 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
24073364 AACTTTAACT
*
24073374 CAAAAAATCCAAACC
1 CAAAAAATTCAAACC
24073389 CAAAAAATTTCAAA-C
1 CAAAAAA-TTCAAACC
24073404 CAAAAGAATTCAAAC
1 CAAAA-AATTCAAAC
24073419 AAAATCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.60, C:0.24, G:0.02, T:0.13
Consensus pattern (15 bp):
CAAAAAATTCAAACC
Found at i:24079781 original size:11 final size:11
Alignment explanation
Indices: 24079765--24079796 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
24079755 ACCCCAAACA
24079765 TATACATATCT
1 TATACATATCT
24079776 TATACATATCT
1 TATACATATCT
*
24079787 TATACTTATC
1 TATACATATC
24079797 ATGATCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (11 bp):
TATACATATCT
Found at i:24088906 original size:20 final size:20
Alignment explanation
Indices: 24088881--24088918 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24088871 ATAAAAAATT
*
24088881 AAAAAAATTAATTGAGCTAA
1 AAAAAAATTAATAGAGCTAA
*
24088901 AAAAAACTTAATAGAGCT
1 AAAAAAATTAATAGAGCT
24088919 TTCAATGCCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.24
Consensus pattern (20 bp):
AAAAAAATTAATAGAGCTAA
Found at i:24089408 original size:3 final size:3
Alignment explanation
Indices: 24089400--24089424 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
24089390 AACTACATAA
24089400 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
24089425 TGATAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:24091403 original size:24 final size:24
Alignment explanation
Indices: 24091376--24091453 Score: 86
Period size: 24 Copynumber: 3.2 Consensus size: 24
24091366 TTTGGTATAC
24091376 GAACCCCCATATGTTTTAATTTGT
1 GAACCCCCATATGTTTTAATTTGT
** * * * *
24091400 GAACCCTAATATGATTTAGTATAT
1 GAACCCCCATATGTTTTAATTTGT
24091424 GAACCCCCATATGTTTT-ATTATGT
1 GAACCCCCATATGTTTTAATT-TGT
24091448 GAACCC
1 GAACCC
24091454 TTATGGATTT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (24 bp):
GAACCCCCATATGTTTTAATTTGT
Found at i:24091422 original size:48 final size:47
Alignment explanation
Indices: 24091364--24091516 Score: 166
Period size: 48 Copynumber: 3.2 Consensus size: 47
24091354 AACACTTATG
*
24091364 GATTTGGTATACGAACCCCCATATGTTTTAATT-TGTGAACCCTAATAT
1 GATTTAGTATACGAACCCCCATATGTTTT-ATTATGTGAACCCT-ATAT
*
24091412 GATTTAGTATATGAACCCCCATATGTTTTATTATGTGAACCCT-TAT
1 GATTTAGTATACGAACCCCCATATGTTTTATTATGTGAACCCTATAT
* * ** * * * *
24091458 GGATTTAATATGCGAACCCTTATGTGATTTATTATGCGAACCCTCATGT
1 -GATTTAGTATACGAACCCCCATATGTTTTATTATGTGAACCCT-ATAT
24091507 GATTTAGTAT
1 GATTTAGTAT
24091517 GTAAACCTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
46 3 0.03
47 38 0.43
48 46 0.52
49 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (47 bp):
GATTTAGTATACGAACCCCCATATGTTTTATTATGTGAACCCTATAT
Found at i:24091518 original size:71 final size:70
Alignment explanation
Indices: 24091390--24091527 Score: 159
Period size: 71 Copynumber: 2.0 Consensus size: 70
24091380 CCCCATATGT
* * * * * *
24091390 TTTAATTTGTGAACCCTAATATGATTTAGTATATGAACCCCCATATGTTTTATTATGTGAACCCT
1 TTTAATATGCGAACCCTAATATGATTTAGTATACGAACCCCCATATGATTTAGTATGT-AAACCT
24091455 TATGGA
65 TATGGA
* * * * * *
24091461 TTTAATATGCGAACCCTTATGTGATTTATTATGCGAACCCTCATGTGATTTAGTATGTAAACCTT
1 TTTAATATGCGAACCCTAATATGATTTAGTATACGAACCCCCATATGATTTAGTATGTAAACCTT
24091526 AT
66 AT
24091528 ATGCGAACCA
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
70 8 0.15
71 47 0.85
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (70 bp):
TTTAATATGCGAACCCTAATATGATTTAGTATACGAACCCCCATATGATTTAGTATGTAAACCTT
ATGGA
Found at i:24091523 original size:24 final size:24
Alignment explanation
Indices: 24091397--24091523 Score: 121
Period size: 24 Copynumber: 5.3 Consensus size: 24
24091387 TGTTTTAATT
* *
24091397 TGTGAACCCTAATATGATTTAGTA
1 TGTGAACCCTCATGTGATTTAGTA
* * * * *
24091421 TATGAACCCCCATATGTTTTATTA
1 TGTGAACCCTCATGTGATTTAGTA
* *
24091445 TGTGAACCCTTATG-GATTTAATA
1 TGTGAACCCTCATGTGATTTAGTA
* * *
24091468 TGCGAACCCTTATGTGATTTATTA
1 TGTGAACCCTCATGTGATTTAGTA
*
24091492 TGCGAACCCTCATGTGATTTAGTA
1 TGTGAACCCTCATGTGATTTAGTA
*
24091516 TGTAAACC
1 TGTGAACC
24091524 TTATATGCGA
Statistics
Matches: 85, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
23 20 0.24
24 65 0.76
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (24 bp):
TGTGAACCCTCATGTGATTTAGTA
Found at i:24091526 original size:47 final size:47
Alignment explanation
Indices: 24091438--24091527 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
24091428 CCCCATATGT
* * *
24091438 TTTATTATGTGAACCCTTATGGATTTAATATGCGAACCCTTATGTGA
1 TTTATTATGCGAACCCTCATGGATTTAATATGCGAAACCTTATGTGA
* *
24091485 TTTATTATGCGAACCCTCATGTGATTTAGTATG-TAAACCTTAT
1 TTTATTATGCGAACCCTCATG-GATTTAATATGCGAAACCTTAT
24091528 ATGCGAACCA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
47 27 0.73
48 10 0.27
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (47 bp):
TTTATTATGCGAACCCTCATGGATTTAATATGCGAAACCTTATGTGA
Found at i:24092363 original size:3 final size:3
Alignment explanation
Indices: 24092355--24092434 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
24092345 AGCATCTAGT
24092355 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24092403 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
24092435 TCCATTGAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:24093033 original size:37 final size:40
Alignment explanation
Indices: 24092987--24093078 Score: 106
Period size: 37 Copynumber: 2.4 Consensus size: 40
24092977 AAATTTGTGC
*
24092987 TTAAAAATAACAT-ATAATAA-ATAATAAA-ATGTATGAT-
1 TTAAAAATAA-ATAATAATAACACAATAAATATGTATGATA
* *
24093024 TTAAAAATAATTAATAATAACACATTAAATATGTATGATA
1 TTAAAAATAAATAATAATAACACAATAAATATGTATGATA
24093064 TT-AAAATAAA-AATAA
1 TTAAAAATAAATAATAA
24093079 ATTAAATTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 1 0.02
37 17 0.36
38 11 0.23
39 16 0.34
40 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (40 bp):
TTAAAAATAAATAATAATAACACAATAAATATGTATGATA
Found at i:24097174 original size:25 final size:26
Alignment explanation
Indices: 24097144--24097201 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
24097134 ACAGCTCTTA
24097144 TGAGCTTCCCGATT-A-TGGCTCTTTG
1 TGAGCTTCCCG-TTAATTGGCTCTTTG
*
24097169 TGAGCTTCTCGTTAATTGGCTCTTTG
1 TGAGCTTCCCGTTAATTGGCTCTTTG
24097195 TGAGCTT
1 TGAGCTT
24097202 TTCTATAAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 2 0.07
25 11 0.37
26 17 0.57
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (26 bp):
TGAGCTTCCCGTTAATTGGCTCTTTG
Found at i:24097309 original size:24 final size:25
Alignment explanation
Indices: 24097277--24097325 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
24097267 AGAGCTACCC
24097277 AATATTGGCTCGCATGAGCTTCCTG
1 AATATTGGCTCGCATGAGCTTCCTG
**
24097302 AATA-TGGCTCTTATGAGCTTCCTG
1 AATATTGGCTCGCATGAGCTTCCTG
24097326 TTATACAGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (25 bp):
AATATTGGCTCGCATGAGCTTCCTG
Found at i:24099500 original size:35 final size:35
Alignment explanation
Indices: 24099452--24099523 Score: 108
Period size: 35 Copynumber: 2.1 Consensus size: 35
24099442 ATTCCACAAC
* *
24099452 ATAAACCCATCATTGGAATCGGTCTTTGTTTATGG
1 ATAAACCCATCATTGGAATCAGTCTTTGTCTATGG
* *
24099487 ATAAACTCGTCATTGGAATCAGTCTTTGTCTATGG
1 ATAAACCCATCATTGGAATCAGTCTTTGTCTATGG
24099522 AT
1 AT
24099524 TCACAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (35 bp):
ATAAACCCATCATTGGAATCAGTCTTTGTCTATGG
Found at i:24100917 original size:42 final size:43
Alignment explanation
Indices: 24100844--24100928 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 43
24100834 TATGTTCTAT
*
24100844 AACCACACGGGCATAGGACAAAGGCATGTGTCCAAGCCGTGTG
1 AACCACACGGGCATAGGACAAAGGCATGTGTCCAAGCCATGTG
** * *
24100887 AACCACACGGGCA-AGGACATGGGCGTGTGTCCAGGCCATGTG
1 AACCACACGGGCATAGGACAAAGGCATGTGTCCAAGCCATGTG
24100929 GCATATAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 24 0.65
43 13 0.35
ACGTcount: A:0.27, C:0.26, G:0.33, T:0.14
Consensus pattern (43 bp):
AACCACACGGGCATAGGACAAAGGCATGTGTCCAAGCCATGTG
Found at i:24109867 original size:31 final size:32
Alignment explanation
Indices: 24109832--24109900 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
24109822 GTATAACAAT
24109832 ATTTTGAGATAAATATTA-AATTT-ATACATAA
1 ATTTTGAGATAAATA-TACAATTTAATACATAA
* *
24109863 ATTTTG-GTTTAATATACAATTTAATACATAA
1 ATTTTGAGATAAATATACAATTTAATACATAA
24109894 ATTTTGA
1 ATTTTGA
24109901 TTTGACGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 2 0.06
30 11 0.33
31 20 0.61
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.45
Consensus pattern (32 bp):
ATTTTGAGATAAATATACAATTTAATACATAA
Found at i:24110152 original size:37 final size:37
Alignment explanation
Indices: 24110102--24110177 Score: 109
Period size: 37 Copynumber: 2.1 Consensus size: 37
24110092 TATTTAGCTC
*
24110102 AACAATGAATGTCATATTACTTGGGAAA-GTCACATGG
1 AACAATAAATGTCATATTA-TTGGGAAACGTCACATGG
* *
24110139 AACAATAAATGTCATATTATTTGGAAACTTCACATGG
1 AACAATAAATGTCATATTATTGGGAAACGTCACATGG
24110176 AA
1 AA
24110178 GGTTAGATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (37 bp):
AACAATAAATGTCATATTATTGGGAAACGTCACATGG
Found at i:24111494 original size:28 final size:28
Alignment explanation
Indices: 24111454--24111510 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
24111444 ATAAATAAAG
24111454 TAAATTTCACATTTCATTATTATGTATT
1 TAAATTTCACATTTCATTATTATGTATT
24111482 TAAATTTCACATTTCATTATTATGTATT
1 TAAATTTCACATTTCATTATTATGTATT
24111510 T
1 T
24111511 TGTGTTTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.54
Consensus pattern (28 bp):
TAAATTTCACATTTCATTATTATGTATT
Found at i:24113253 original size:61 final size:61
Alignment explanation
Indices: 24113120--24113250 Score: 196
Period size: 61 Copynumber: 2.2 Consensus size: 61
24113110 CAAAAATAAT
* * **
24113120 ATTATTTTAATAGTTTTAATATTAAATTTAATCTAATAATTATCTTATAGATAAGTATTCT
1 ATTAATTTAATAGATTTAATATTAAATTTAATCTAATAATTATCTTATAGATAAGTATTAA
*
24113181 ATTAATTTAATAGATTTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAGTATTAA
1 ATTAATTTAATAGATTTAATATTAAATTTAATCTAATAATTATCTTATAGATAAGTATTAA
24113239 ATTAATTTAATA
1 ATTAATTTAATA
24113251 ATAAAGTGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
58 22 0.34
59 1 0.02
60 1 0.02
61 41 0.63
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.50
Consensus pattern (61 bp):
ATTAATTTAATAGATTTAATATTAAATTTAATCTAATAATTATCTTATAGATAAGTATTAA
Found at i:24114421 original size:68 final size:68
Alignment explanation
Indices: 24114165--24114413 Score: 372
Period size: 68 Copynumber: 3.7 Consensus size: 68
24114155 TCCGTTAGGT
* **
24114165 AATAAACATGGGATCATATTGTGTAAGACCACAACTAGGCTATGGCAACATATGAAGTTTTCCAG
1 AATAAACATGGGATCATATTGTGTAAGACCACAACTAGGCTATGGCAACATATAAAGTTCGCCAG
*
24114230 GAC
66 AAC
* * * *
24114233 AACAAAAATGGGATCATATTGTGTAAGACCACAACTAGGCTATGGCAACATATAAAGTCCGCCAA
1 AATAAACATGGGATCATATTGTGTAAGACCACAACTAGGCTATGGCAACATATAAAGTTCGCCAG
24114298 AAC
66 AAC
* * * *
24114301 AATAAACATGGGATCATATTGTGTAAAACCACAACTATGCTATAGTAACATATAAAGTTCGCCAG
1 AATAAACATGGGATCATATTGTGTAAGACCACAACTAGGCTATGGCAACATATAAAGTTCGCCAG
24114366 AAC
66 AAC
* *
24114369 AATAAACATGGGATCATATTGTTTAAGACCACAGCTAGGCTATGG
1 AATAAACATGGGATCATATTGTGTAAGACCACAACTAGGCTATGG
24114414 TGCCATATGA
Statistics
Matches: 160, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 160 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (68 bp):
AATAAACATGGGATCATATTGTGTAAGACCACAACTAGGCTATGGCAACATATAAAGTTCGCCAG
AAC
Found at i:24117110 original size:21 final size:21
Alignment explanation
Indices: 24117085--24117141 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 21
24117075 ACCAAGAAGT
*
24117085 GGTATCAATACTTTGGGTA-AG
1 GGTATCAATACTTT-GATAGAG
* * *
24117106 GGTATTATTACCTT-ATAGAG
1 GGTATCAATACTTTGATAGAG
24117126 GGTATCAATACTTTGA
1 GGTATCAATACTTTGA
24117142 CCCTTGGGAG
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
19 2 0.07
20 13 0.48
21 12 0.44
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.37
Consensus pattern (21 bp):
GGTATCAATACTTTGATAGAG
Found at i:24120932 original size:23 final size:25
Alignment explanation
Indices: 24120891--24120938 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
24120881 TTATCTTTTG
* *
24120891 TATTATTATATTAAGTTTCTTCATA
1 TATTAATATATTAAGTTTCATCATA
24120916 TATTAATAT-TTAA-TTTCATCATA
1 TATTAATATATTAAGTTTCATCATA
24120939 AATCATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.54
Consensus pattern (25 bp):
TATTAATATATTAAGTTTCATCATA
Found at i:24124160 original size:24 final size:24
Alignment explanation
Indices: 24124128--24124176 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
24124118 AAAAAAAACA
24124128 CATAAAAAATTTCTTTCTATTCTT
1 CATAAAAAATTTCTTTCTATTCTT
24124152 CATAAAAAATTTCTTTCTATTCTT
1 CATAAAAAATTTCTTTCTATTCTT
24124176 C
1 C
24124177 CACTATCTTT
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:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (24 bp):
CATAAAAAATTTCTTTCTATTCTT
Found at i:24125789 original size:21 final size:21
Alignment explanation
Indices: 24125764--24125814 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
24125754 CTTGCACAAA
24125764 GTATCAATATCTTTGTAATAC
1 GTATCAATATCTTTGTAATAC
* * * *
24125785 GTATCAATATTTTTTTATTAG
1 GTATCAATATCTTTGTAATAC
24125806 GTATCAATA
1 GTATCAATA
24125815 CCAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (21 bp):
GTATCAATATCTTTGTAATAC
Found at i:24128444 original size:17 final size:17
Alignment explanation
Indices: 24128418--24128453 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24128408 AAAATTAAAT
* *
24128418 ATTTTGATATGACACTA
1 ATTTTAATATAACACTA
24128435 ATTTTAATATAACACTA
1 ATTTTAATATAACACTA
24128452 AT
1 AT
24128454 GACTTTGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (17 bp):
ATTTTAATATAACACTA
Found at i:24129269 original size:26 final size:26
Alignment explanation
Indices: 24129213--24129269 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
24129203 GTGATTATGT
*
24129213 ATTATCCACACAAACATCTTTCATTC
1 ATTATCCACACAAACATCTTTCATCC
* *
24129239 ATTATCCACTCACACA-CTTTTCATCC
1 ATTATCCACACAAACATC-TTTCATCC
*
24129265 TTTAT
1 ATTAT
24129270 AGAGGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.39
Consensus pattern (26 bp):
ATTATCCACACAAACATCTTTCATCC
Found at i:24152124 original size:41 final size:46
Alignment explanation
Indices: 24152051--24152234 Score: 155
Period size: 51 Copynumber: 3.9 Consensus size: 46
24152041 TTGAGATCAT
*
24152051 GAGAGGTCCCATGTAAGATCATGTTTGGGACATGGCGTTGGCA-CGA
1 GAGAGGTCCCATGTAAGATCATGTCT-GGACATGGCGTTGGCACCGA
24152097 GAGAGGT-CCATG-AAGA-CATGTCT-GACATGGCGTTGGCACCGAGA
1 GAGAGGTCCCATGTAAGATCATGTCTGGACATGGCGTTGGCACC--GA
* * * *
24152141 TGAGAGGTCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATA
1 -GAGAGGTCCCATGTAAGATCATGTCT-GGACATGGCGTTGGCACCG--A
** * *
24152190 TGAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -GAG-AGGTCCCATGTAAGATCATGTCT-GGACATGGCGTTGGCA
24152235 TGTTATGATC
Statistics
Matches: 116, Mismatches: 9, Indels: 21
0.79 0.06 0.14
Matches are distributed among these distances:
41 15 0.13
42 1 0.01
43 6 0.05
44 6 0.05
45 13 0.11
46 13 0.11
47 8 0.07
49 20 0.17
50 5 0.04
51 29 0.25
ACGTcount: A:0.26, C:0.21, G:0.32, T:0.21
Consensus pattern (46 bp):
GAGAGGTCCCATGTAAGATCATGTCTGGACATGGCGTTGGCACCGA
Found at i:24162454 original size:34 final size:34
Alignment explanation
Indices: 24162411--24162478 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
24162401 CTATGGCTGC
*
24162411 ATTTCGAAAGCGGTCCACTATCCTGCACGGAGGT
1 ATTTCGAAAGCAGTCCACTATCCTGCACGGAGGT
*
24162445 ATTTCGAAAGCAGTCCACTATCCTGCATGGAGGT
1 ATTTCGAAAGCAGTCCACTATCCTGCACGGAGGT
24162479 GAAAACCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (34 bp):
ATTTCGAAAGCAGTCCACTATCCTGCACGGAGGT
Found at i:24163592 original size:28 final size:28
Alignment explanation
Indices: 24163561--24163653 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
24163551 ATTTAAGAAA
**
24163561 TAAATATAATATATGTAAATT-AAAATAT
1 TAAA-ATAATATAAATAAATTAAAAATAT
*
24163589 TAAAATAAATTTAAATAAATTAAAAATAT
1 TAAAAT-AATATAAATAAATTAAAAATAT
* * *
24163618 TAAAATAAGT-TGAAATGAATTAAAGATTT
1 TAAAATAA-TAT-AAATAAATTAAAAATAT
24163647 TAAAATA
1 TAAAATA
24163654 TTTGAAAGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
27 2 0.04
28 18 0.33
29 35 0.64
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (28 bp):
TAAAATAATATAAATAAATTAAAAATAT
Found at i:24163599 original size:18 final size:19
Alignment explanation
Indices: 24163576--24163653 Score: 54
Period size: 19 Copynumber: 4.1 Consensus size: 19
24163566 ATAATATATG
24163576 TAAATTAAA-ATATTAAAA
1 TAAATTAAAGATATTAAAA
* *
24163594 TAAATTTAAATAAATTAAAA
1 TAAA-TTAAAGATATTAAAA
* *
24163614 -ATATTAAA-ATAAGTTGAAA
1 TAAATTAAAGAT-A-TTAAAA
* *
24163633 TGAATTAAAGATTTTAAAA
1 TAAATTAAAGATATTAAAA
24163652 TA
1 TA
24163654 TTTGAAAGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
17 1 0.02
18 10 0.22
19 18 0.40
20 14 0.31
21 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAATTAAAGATATTAAAA
Found at i:24163614 original size:29 final size:29
Alignment explanation
Indices: 24163576--24163669 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
24163566 ATAATATATG
*
24163576 TAAATT-AAAATATTAAAATAAATTTAAA
1 TAAATTAAAAATATTAAAATAAATTGAAA
*
24163604 TAAATTAAAAATATTAAAATAAGTTGAAA
1 TAAATTAAAAATATTAAAATAAATTGAAA
* * * *
24163633 TGAATTAAAGATTTTAAAAT-ATTTGAAA
1 TAAATTAAAAATATTAAAATAAATTGAAA
*
24163661 GAAA-TAAAA
1 TAAATTAAAA
24163670 TATCTATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
27 4 0.07
28 15 0.27
29 37 0.66
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (29 bp):
TAAATTAAAAATATTAAAATAAATTGAAA
Found at i:24163615 original size:11 final size:10
Alignment explanation
Indices: 24163576--24163641 Score: 66
Period size: 10 Copynumber: 6.9 Consensus size: 10
24163566 ATAATATATG
24163576 TAAATTAAAA
1 TAAATTAAAA
24163586 T--ATTAAAA
1 TAAATTAAAA
*
24163594 TAAATTTAAA
1 TAAATTAAAA
24163604 TAAATTAAAA
1 TAAATTAAAA
*
24163614 -ATATTAAAA
1 TAAATTAAAA
* *
24163623 TAAGTTGAAA
1 TAAATTAAAA
*
24163633 TGAATTAAA
1 TAAATTAAA
24163642 GATTTTAAAA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
8 8 0.18
9 8 0.18
10 28 0.64
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (10 bp):
TAAATTAAAA
Found at i:24163625 original size:19 final size:20
Alignment explanation
Indices: 24163576--24163641 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 20
24163566 ATAATATATG
24163576 TAAATTAAAAT--ATTAAAA
1 TAAATTAAAATAAATTAAAA
*
24163594 TAAATTTAAATAAATTAAAA
1 TAAATTAAAATAAATTAAAA
* * *
24163614 -ATATTAAAATAAGTTGAAA
1 TAAATTAAAATAAATTAAAA
*
24163633 TGAATTAAA
1 TAAATTAAA
24163642 GATTTTAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 10 0.26
19 15 0.39
20 13 0.34
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
TAAATTAAAATAAATTAAAA
Found at i:24182900 original size:14 final size:14
Alignment explanation
Indices: 24182872--24182900 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
24182862 GCTTAGTGGC
24182872 TTTTGACTTGATTT
1 TTTTGACTTGATTT
24182886 TTTTG-CTTGATTT
1 TTTTGACTTGATTT
24182899 TT
1 TT
24182901 AAGCAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.10, C:0.07, G:0.14, T:0.69
Consensus pattern (14 bp):
TTTTGACTTGATTT
Found at i:24185387 original size:21 final size:21
Alignment explanation
Indices: 24185363--24185407 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
24185353 TCCTTGAACA
24185363 TATCGCCCCTTCAGATTTACT
1 TATCGCCCCTTCAGATTTACT
24185384 TATCGCCCCTTCAGATTTACT
1 TATCGCCCCTTCAGATTTACT
24185405 TAT
1 TAT
24185408 GTTTTAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.31, G:0.09, T:0.40
Consensus pattern (21 bp):
TATCGCCCCTTCAGATTTACT
Found at i:24193249 original size:13 final size:13
Alignment explanation
Indices: 24193231--24193260 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
24193221 CTGACAAGGC
*
24193231 TGCTTTGTTCCTT
1 TGCTTTGCTCCTT
24193244 TGCTTTGCTCCTT
1 TGCTTTGCTCCTT
24193257 TGCT
1 TGCT
24193261 GATGGCTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.17, T:0.57
Consensus pattern (13 bp):
TGCTTTGCTCCTT
Found at i:24193420 original size:22 final size:22
Alignment explanation
Indices: 24193395--24193436 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
24193385 GAGGAGTGAA
*
24193395 TGAGGAATGGTTGAGGGATGCT
1 TGAGGAATGGTTCAGGGATGCT
* *
24193417 TGAGGGATGTTTCAGGGATG
1 TGAGGAATGGTTCAGGGATG
24193437 TTTTAGTGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.45, T:0.29
Consensus pattern (22 bp):
TGAGGAATGGTTCAGGGATGCT
Found at i:24198244 original size:22 final size:22
Alignment explanation
Indices: 24198214--24198262 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
24198204 TATATCTATT
*
24198214 TATTATAATCATGTTAACATAA
1 TATTTTAATCATGTTAACATAA
*
24198236 TATTTTAATCATTTTAACATAA
1 TATTTTAATCATGTTAACATAA
24198258 TATTT
1 TATTT
24198263 CCAAACTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (22 bp):
TATTTTAATCATGTTAACATAA
Found at i:24204957 original size:21 final size:22
Alignment explanation
Indices: 24204933--24204980 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
24204923 AAAATAATCT
* *
24204933 AAAC-TAATCAGAGTTTAATTG
1 AAACATAAACAGAGTTTAACTG
24204954 AAACAAATAAACAGAGTTTAACTG
1 AAAC--ATAAACAGAGTTTAACTG
24204978 AAA
1 AAA
24204981 AAATATTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 4 0.18
24 18 0.82
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.25
Consensus pattern (22 bp):
AAACATAAACAGAGTTTAACTG
Found at i:24204972 original size:24 final size:23
Alignment explanation
Indices: 24204941--24204985 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
24204931 CTAAACTAAT
*
24204941 CAGAGTTTAATTGAAACAAATAAA
1 CAGAGTTTAACTGAAA-AAATAAA
24204965 CAGAGTTTAACTGAAAAAATA
1 CAGAGTTTAACTGAAAAAATA
24204986 TTTCTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.24
Consensus pattern (23 bp):
CAGAGTTTAACTGAAAAAATAAA
Found at i:24210321 original size:17 final size:17
Alignment explanation
Indices: 24210295--24210327 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24210285 CAATGTTTAC
24210295 AACTAAATAAA-AGATT
1 AACTAAATAAACAGATT
24210311 AACTGAAATAAACAGAT
1 AACT-AAATAAACAGAT
24210328 ATTCAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.21
Consensus pattern (17 bp):
AACTAAATAAACAGATT
Found at i:24213093 original size:15 final size:16
Alignment explanation
Indices: 24213073--24213102 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
24213063 AGAAAAAGGC
24213073 AAGATTAAAT-GAAAA
1 AAGATTAAATCGAAAA
24213088 AAGATTAAATCGAAA
1 AAGATTAAATCGAAA
24213103 CCATAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.03, G:0.13, T:0.20
Consensus pattern (16 bp):
AAGATTAAATCGAAAA
Found at i:24214192 original size:18 final size:17
Alignment explanation
Indices: 24214171--24214213 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
24214161 ATTGTTTCTG
*
24214171 CTCTTTTTGTTTTCTGTT
1 CTCTTTTTATTTTCT-TT
*
24214189 CTCTGCTTTATTTTCTTT
1 CTCT-TTTTATTTTCTTT
24214207 CTCTTTT
1 CTCTTTT
24214214 GTAGGTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 2 0.10
18 10 0.48
19 9 0.43
ACGTcount: A:0.02, C:0.21, G:0.07, T:0.70
Consensus pattern (17 bp):
CTCTTTTTATTTTCTTT
Found at i:24214890 original size:94 final size:94
Alignment explanation
Indices: 24214769--24215048 Score: 273
Period size: 94 Copynumber: 3.0 Consensus size: 94
24214759 CAATTTCAAA
* * * * *
24214769 GAGATAAGATTTGTTGTAGTAGATTCAATCTGATCCACTGCAACTTTAGGAGTATAGGATTTGTA
1 GAGATAAGATTCGCTATAGTAGATTCAATCTGACCCACTGCAACTTAAGGAGTATAGGATTTGTA
*
24214834 GCTTCAATCTGCTTCACTACAACTTCAGG
66 GCTTCAATCTGATTCACTACAACTTCAGG
*
24214863 GAGATAAGATTCGCTATGGTAGATTCAAT-TAGACCCACTGCAACTTCAAGGA-TAT-GAGATTT
1 GAGATAAGATTCGCTATAGTAGATTCAATCT-GACCCACTGCAACTT-AAGGAGTATAG-GATTT
* * * *
24214925 GTAGCTTC-ATCTTGTTTTACTGCAACTTTAGG
63 GTAGCTTCAATC-TGATTCACTACAACTTCAGG
* * * * * ** * * * *
24214957 GAGATAAGATTCGCCATCGCAGTTTCATTCCAACCCACTACAACTTCACGG-GTATAGAAATTGT
1 GAGATAAGATTCGCTATAGTAGATTCAATCTGACCCACTGCAACTT-AAGGAGTATAGGATTTGT
*
24215021 AGCTTTAATCTGATTCACTACAACTTCA
65 AGCTTCAATCTGATTCACTACAACTTCA
24215049 AGGATATAGG
Statistics
Matches: 152, Mismatches: 26, Indels: 16
0.78 0.13 0.08
Matches are distributed among these distances:
93 5 0.03
94 139 0.91
95 8 0.05
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (94 bp):
GAGATAAGATTCGCTATAGTAGATTCAATCTGACCCACTGCAACTTAAGGAGTATAGGATTTGTA
GCTTCAATCTGATTCACTACAACTTCAGG
Found at i:24223185 original size:40 final size:40
Alignment explanation
Indices: 24222947--24223171 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
24222937 TCGAATGATG
* * * *
24222947 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * *
24222987 TTCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24223027 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24223066 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
24223106 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
24223147 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
24223172 AACGAGTAGC
Statistics
Matches: 163, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.21
40 119 0.73
41 10 0.06
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:24230104 original size:32 final size:30
Alignment explanation
Indices: 24230044--24230110 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 30
24230034 TTATGGGGTA
* ** *
24230044 AAAATAAAAAAATAAAAAAGGAGTAGGACG
1 AAAATAAAAAAACAAAAAAGGAAAAGGACC
24230074 AAAATAAAAAGGAACAAAAAAGGAAAAGGACC
1 AAAATAAAAA--AACAAAAAAGGAAAAGGACC
24230106 AAAAT
1 AAAAT
24230111 GGAAATTACC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 10 0.32
32 21 0.68
ACGTcount: A:0.69, C:0.06, G:0.18, T:0.07
Consensus pattern (30 bp):
AAAATAAAAAAACAAAAAAGGAAAAGGACC
Found at i:24236651 original size:12 final size:12
Alignment explanation
Indices: 24236621--24236651 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
24236611 AAACTGGTTT
*
24236621 GGGTAAAGTTGA
1 GGGTAAGGTTGA
24236633 GGGTAAGGTTGA
1 GGGTAAGGTTGA
24236645 GGGTAAG
1 GGGTAAG
24236652 TTTCGTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (12 bp):
GGGTAAGGTTGA
Found at i:24239704 original size:8 final size:8
Alignment explanation
Indices: 24239691--24239716 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
24239681 AAATTTTTAT
24239691 TTTTAAAA
1 TTTTAAAA
24239699 TTTTAAAA
1 TTTTAAAA
24239707 TTTTAAAA
1 TTTTAAAA
24239715 TT
1 TT
24239717 AATCAATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
TTTTAAAA
Found at i:24244081 original size:18 final size:18
Alignment explanation
Indices: 24244058--24244106 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
24244048 TTTAGATTAA
24244058 TTAGAGTTTCATTACATT
1 TTAGAGTTTCATTACATT
* *
24244076 TTAGAGTTTTATTATATT
1 TTAGAGTTTCATTACATT
*
24244094 TTATAGTTTCATT
1 TTAGAGTTTCATT
24244107 TAGAGGTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.57
Consensus pattern (18 bp):
TTAGAGTTTCATTACATT
Found at i:24245955 original size:22 final size:24
Alignment explanation
Indices: 24245913--24245956 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
24245903 TGATAATATG
24245913 TTTTGATATAATAAATTAAAGTGA
1 TTTTGATATAATAAATTAAAGTGA
*
24245937 TTTTGA-ATAA-AAGTTAAAGT
1 TTTTGATATAATAAATTAAAGT
24245957 TGAACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (24 bp):
TTTTGATATAATAAATTAAAGTGA
Found at i:24266293 original size:3 final size:3
Alignment explanation
Indices: 24266285--24266313 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
24266275 GTATTGCCAT
24266285 TGA TGA TGA TGA TGA TGA TGA TGA T-A TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
24266314 ATAAGCAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:24270789 original size:21 final size:24
Alignment explanation
Indices: 24270763--24270814 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 24
24270753 TATTTCTATT
24270763 TAATTTTATTA-ATTTTTA-G-AG
1 TAATTTTATTATATTTTTATGTAG
* *
24270784 TAATTTTTTTATTTTTTTATGTAG
1 TAATTTTATTATATTTTTATGTAG
24270808 TAATTTT
1 TAATTTT
24270815 TTTTATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 10 0.38
22 6 0.23
23 1 0.04
24 9 0.35
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (24 bp):
TAATTTTATTATATTTTTATGTAG
Found at i:24270809 original size:24 final size:23
Alignment explanation
Indices: 24270766--24270817 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
24270756 TTCTATTTAA
24270766 TTTTATTAATTTTTAGAGTAATTT
1 TTTTATT-ATTTTTAGAGTAATTT
24270790 TTTTATT-TTTTTATGTAGTAATTT
1 TTTTATTATTTTTA-G-AGTAATTT
24270814 TTTT
1 TTTT
24270818 TATGTTTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.23
23 1 0.04
24 19 0.73
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (23 bp):
TTTTATTATTTTTAGAGTAATTT
Found at i:24270825 original size:25 final size:22
Alignment explanation
Indices: 24270775--24270825 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 22
24270765 ATTTTATTAA
*
24270775 TTTTTAGAGTAATTTTTTTATT
1 TTTTTAGAGTAATTTTTTTATG
24270797 TTTTTATGTAGTAATTTTTTTTATG
1 TTTTTA-G-AGTAA-TTTTTTTATG
24270822 TTTT
1 TTTT
24270826 GTTTATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 1 0.04
24 5 0.20
25 13 0.52
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.71
Consensus pattern (22 bp):
TTTTTAGAGTAATTTTTTTATG
Found at i:24273617 original size:28 final size:29
Alignment explanation
Indices: 24273561--24273622 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
24273551 AATTACTTGA
* *
24273561 CCATTCTTCAATATATTTTTATATTAACT
1 CCATACTTCAATATATTTTTATAGTAACT
*
24273590 TCATACTTCAATATA-TTTTATAGTAACT
1 CCATACTTCAATATATTTTTATAGTAACT
24273618 CCATA
1 CCATA
24273623 AATATTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.47
Consensus pattern (29 bp):
CCATACTTCAATATATTTTTATAGTAACT
Found at i:24274492 original size:18 final size:18
Alignment explanation
Indices: 24274471--24274505 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
24274461 TCTTATTCTA
*
24274471 TTACAGATTCTAACACAC
1 TTACACATTCTAACACAC
24274489 TTACACATTCTAACACA
1 TTACACATTCTAACACA
24274506 TTATGAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.29
Consensus pattern (18 bp):
TTACACATTCTAACACAC
Found at i:24274632 original size:22 final size:22
Alignment explanation
Indices: 24274606--24274650 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
24274596 ATACGTTCTC
*
24274606 CCAATATGATCTTATTTTATCT
1 CCAATATAATCTTATTTTATCT
24274628 CCAATATAATCTTATTTTATCT
1 CCAATATAATCTTATTTTATCT
24274650 C
1 C
24274651 ATGGTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.02, T:0.49
Consensus pattern (22 bp):
CCAATATAATCTTATTTTATCT
Found at i:24275924 original size:64 final size:64
Alignment explanation
Indices: 24275843--24275969 Score: 245
Period size: 64 Copynumber: 2.0 Consensus size: 64
24275833 AAAAGCACAC
24275843 CATAAATAATAAAAAGCATCATTATTATTTTATTTAAAATTTTAATTCTTTAAAATAGATTTTG
1 CATAAATAATAAAAAGCATCATTATTATTTTATTTAAAATTTTAATTCTTTAAAATAGATTTTG
*
24275907 CATAAATAATGAAAAGCATCATTATTATTTTATTTAAAATTTTAATTCTTTAAAATAGATTTT
1 CATAAATAATAAAAAGCATCATTATTATTTTATTTAAAATTTTAATTCTTTAAAATAGATTTT
24275970 ATGCAAGTGC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (64 bp):
CATAAATAATAAAAAGCATCATTATTATTTTATTTAAAATTTTAATTCTTTAAAATAGATTTTG
Found at i:24276830 original size:20 final size:21
Alignment explanation
Indices: 24276791--24276830 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24276781 GATAAAATTG
* *
24276791 TTTTCTTTTAAGAATCTAAAT
1 TTTTCTTATAAAAATCTAAAT
24276812 TTTTCTTATAAAAAT-TAAA
1 TTTTCTTATAAAAATCTAAA
24276831 GTAATTTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTCTTATAAAAATCTAAAT
Found at i:24277209 original size:30 final size:31
Alignment explanation
Indices: 24277160--24277222 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
24277150 TGTACAAAAT
*
24277160 CAAAATTTATATATTAAATT-ATATATTATAA
1 CAAAATGTATATATTAAATTCATAT-TTATAA
*
24277191 CAAAATGTATCTA-TAAATTCGATATTTATAA
1 CAAAATGTATATATTAAATTC-ATATTTATAA
24277222 C
1 C
24277223 TTGATTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.21
31 18 0.64
32 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (31 bp):
CAAAATGTATATATTAAATTCATATTTATAA
Found at i:24288914 original size:16 final size:16
Alignment explanation
Indices: 24288893--24288938 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
24288883 TTATTAAATT
24288893 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
24288909 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
24288924 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
24288939 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:24288947 original size:107 final size:108
Alignment explanation
Indices: 24288833--24289043 Score: 388
Period size: 107 Copynumber: 2.0 Consensus size: 108
24288823 TATAGTATTA
* * *
24288833 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTGAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
24288898 TTTTAATTATAATATATTTAATAATAATTATG-TTAAATTATC
66 TTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATC
24288940 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
24289005 TTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
66 TTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
24289044 ATGATTAAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
107 94 0.94
108 6 0.06
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.49
Consensus pattern (108 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
TTTTAATTATAATATATTTAATAATAATTATGTTTAAATTATC
Found at i:24289021 original size:16 final size:16
Alignment explanation
Indices: 24289000--24289041 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
24288990 TTATTAAATT
*
24289000 ATATATTTTAATTATA
1 ATATATTTTAATAATA
24289016 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
24289031 AT-TATGTTTAA
1 ATATAT-TTTAA
24289042 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:24289026 original size:15 final size:15
Alignment explanation
Indices: 24288991--24289032 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
24288981 TTAAGAATTT
*
24288991 TATTAAATTAT-ATA
1 TATTTAATTATAATA
24289005 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
24289019 TATTTAATAATAAT
1 TATTTAATTATAAT
24289033 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:24289276 original size:16 final size:16
Alignment explanation
Indices: 24289255--24289308 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
24289245 TTGATTTGCT
* *
24289255 ATTACACCTCTATTTC
1 ATTACACCTCTAATCC
24289271 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* *
24289287 AATACACCTCGAATCC
1 ATTACACCTCTAATCC
*
24289303 AATACA
1 ATTACA
24289309 GTGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:24303282 original size:20 final size:21
Alignment explanation
Indices: 24303243--24303282 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
24303233 GATAAAATTG
* *
24303243 TTTTCTTTTAAGAATCTAAAT
1 TTTTCTTATAAAAATCTAAAT
24303264 TTTTCTTATAAAAAT-TAAA
1 TTTTCTTATAAAAATCTAAA
24303283 GTAATTTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (21 bp):
TTTTCTTATAAAAATCTAAAT
Found at i:24303656 original size:30 final size:31
Alignment explanation
Indices: 24303607--24303669 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
24303597 TGTACAAAAT
*
24303607 CAAAATTTATATATTAAATT-ATATATTATAA
1 CAAAATGTATATATTAAATTCATAT-TTATAA
*
24303638 CAAAATGTATCTA-TAAATTCGATATTTATAA
1 CAAAATGTATATATTAAATTC-ATATTTATAA
24303669 C
1 C
24303670 TTGATTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.21
31 18 0.64
32 4 0.14
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (31 bp):
CAAAATGTATATATTAAATTCATATTTATAA
Found at i:24315099 original size:16 final size:16
Alignment explanation
Indices: 24315078--24315123 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
24315068 TTATTAAATT
24315078 ATATATTTTAATTATA
1 ATATATTTTAATTATA
*
24315094 ATATA-TTTAATAATA
1 ATATATTTTAATTATA
*
24315109 AT-TATGTTAAATTAT
1 ATATAT-TTTAATTAT
24315124 CTATATTATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATTATA
Found at i:24315132 original size:107 final size:107
Alignment explanation
Indices: 24315018--24315223 Score: 385
Period size: 107 Copynumber: 1.9 Consensus size: 107
24315008 TATAGTATTA
* * *
24315018 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTGAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
24315083 TTTTAATTATAATATATTTAATAATAATTATGTTAAATTATC
66 TTTTAATTATAATATATTTAATAATAATTATGTTAAATTATC
24315125 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
1 TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
24315190 TTTTAATTATAATATATTTAATAATAATTATGTT
66 TTTTAATTATAATATATTTAATAATAATTATGTT
24315224 TAATATGATT
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 96 1.00
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (107 bp):
TATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTATATA
TTTTAATTATAATATATTTAATAATAATTATGTTAAATTATC
Found at i:24315206 original size:16 final size:16
Alignment explanation
Indices: 24315185--24315228 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
24315175 TTATTAAATT
*
24315185 ATATATTTTAATTATA
1 ATATATTTTAATAATA
24315201 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
24315216 AT-TATGTTTAATA
1 ATATAT-TTTAATA
24315229 TGATTAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 11 0.44
16 12 0.48
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:24315460 original size:16 final size:16
Alignment explanation
Indices: 24315439--24315492 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
24315429 TTGATTTGCT
* *
24315439 ATTACACCTCTATTTC
1 ATTACACCTCTAATCC
24315455 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
* *
24315471 AATACACCTCGAATCC
1 ATTACACCTCTAATCC
*
24315487 AATACA
1 ATTACA
24315493 GTGAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.33, G:0.02, T:0.30
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:24321450 original size:61 final size:60
Alignment explanation
Indices: 24321335--24321457 Score: 167
Period size: 61 Copynumber: 2.0 Consensus size: 60
24321325 AAATGCATAC
*
24321335 GAATGGTGATTCCAATACAGGTACCATGGTGATTCCAACATAATATTAAAATTTTGCAAAT
1 GAATGGTGATTCCAATACAGGTACCATGGTGATTCCAACAT-ATACTAAAATTTTGCAAAT
* * * *
24321396 GAATGGTGCTTCCAATATAGTTACCATGGTGATTCCAATGCAT-TACTAAGATTTTGCAAAT
1 GAATGGTGATTCCAATACAGGTACCATGGTGATTCCAA--CATATACTAAAATTTTGCAAAT
24321457 G
1 G
24321458 CAAATGAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
61 52 0.95
63 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (60 bp):
GAATGGTGATTCCAATACAGGTACCATGGTGATTCCAACATATACTAAAATTTTGCAAAT
Found at i:24321491 original size:23 final size:23
Alignment explanation
Indices: 24321465--24321524 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
24321455 ATGCAAATGA
*
24321465 ATAGTGATTCCAATACAATTATC
1 ATAGTGATTCCAATACAATTACC
*
24321488 ATAGTGATTGCAATACAATTACC
1 ATAGTGATTCCAATACAATTACC
*
24321511 ATGGTGATTCCAAT
1 ATAGTGATTCCAAT
24321525 GTAGTACTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (23 bp):
ATAGTGATTCCAATACAATTACC
Found at i:24321752 original size:17 final size:17
Alignment explanation
Indices: 24321730--24321808 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 17
24321720 AATACTTAGT
24321730 GTTATGACCATTTTGAG
1 GTTATGACCATTTTGAG
*
24321747 GTTATGACCTTTTTGA-
1 GTTATGACCATTTTGAG
* *
24321763 --AATGA-CA-CTT-AG
1 GTTATGACCATTTTGAG
24321775 TGTTATGACCATTTTGAG
1 -GTTATGACCATTTTGAG
*
24321793 GTTATGACCTTTTTGA
1 GTTATGACCATTTTGA
24321809 AATAACACTT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
11 1 0.02
12 2 0.04
13 1 0.02
14 4 0.08
15 4 0.08
16 2 0.04
17 32 0.67
18 2 0.04
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (17 bp):
GTTATGACCATTTTGAG
Found at i:24321777 original size:46 final size:46
Alignment explanation
Indices: 24321723--24321864 Score: 232
Period size: 46 Copynumber: 3.1 Consensus size: 46
24321713 CTAAAACAAT
24321723 ACTTAGTGTTATGACCATTTTGAGGTTATGACCTTTTTGAAATGAC
1 ACTTAGTGTTATGACCATTTTGAGGTTATGACCTTTTTGAAATGAC
*
24321769 ACTTAGTGTTATGACCATTTTGAGGTTATGACCTTTTTGAAATAAC
1 ACTTAGTGTTATGACCATTTTGAGGTTATGACCTTTTTGAAATGAC
* * *
24321815 ACTTAGTGTTATGACCTTTTTGAGGTTATGA-CTTTTCTAAAAGGAC
1 ACTTAGTGTTATGACCATTTTGAGGTTATGACCTTTT-TGAAATGAC
24321861 ACTT
1 ACTT
24321865 TATGATCATT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 5 0.06
46 85 0.94
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (46 bp):
ACTTAGTGTTATGACCATTTTGAGGTTATGACCTTTTTGAAATGAC
Found at i:24323979 original size:23 final size:23
Alignment explanation
Indices: 24323936--24323979 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
24323926 TTCGGTACTA
*
24323936 CTGTTACTTGCACTTTAGTGCTC
1 CTGTTACTTGCACTATAGTGCTC
* *
24323959 CTGTTCCTTGCACTATGGTGC
1 CTGTTACTTGCACTATAGTGC
24323980 GATCCTAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.41
Consensus pattern (23 bp):
CTGTTACTTGCACTATAGTGCTC
Found at i:24325749 original size:25 final size:25
Alignment explanation
Indices: 24325715--24325766 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
24325705 TAAGTATTAG
24325715 TAAGTTAAAATAGAATATCTAAACT
1 TAAGTTAAAATAGAATATCTAAACT
24325740 TAAGTTAAAATAGAATATCTAAACT
1 TAAGTTAAAATAGAATATCTAAACT
24325765 TA
1 TA
24325767 CCTTAATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.33
Consensus pattern (25 bp):
TAAGTTAAAATAGAATATCTAAACT
Found at i:24325772 original size:25 final size:25
Alignment explanation
Indices: 24325719--24325772 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
24325709 TATTAGTAAG
*
24325719 TTAAAATAGAATATCTAAACTTAAG
1 TTAAAATAGAATATCTAAACTTAAC
*
24325744 TTAAAATAGAATATCTAAACTTACC
1 TTAAAATAGAATATCTAAACTTAAC
24325769 TTAA
1 TTAA
24325773 TCCATTAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (25 bp):
TTAAAATAGAATATCTAAACTTAAC
Done.