Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold442
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: 369669
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:313991 original size:17 final size:19
Alignment explanation
Indices: 313953--313997 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
313943 AAAAAAATTA
*
313953 TAAAAATA-AAAATTATTT
1 TAAAAATATAAAATTATTG
313971 TAAAAATATAAAA-TA-TG
1 TAAAAATATAAAATTATTG
*
313988 TAAAATTATA
1 TAAAAATATA
313998 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
TAAAAATATAAAATTATTG
Found at i:314018 original size:42 final size:41
Alignment explanation
Indices: 313971--314055 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 41
313961 AAAATTATTT
313971 TAAAAATATAAAATATGT-AAAATTATATTTTAAAAAATATAA
1 TAAAAATATAAAAT-TGTAAAAATTATATTTTAAAAAAT-TAA
* * * *
314013 TAAAAATTTTAAATTTTAAAAATTATATTTTTAAAAATTAA
1 TAAAAATATAAAATTGTAAAAATTATATTTTAAAAAATTAA
314054 TA
1 TA
314056 TATGATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 7 0.18
42 31 0.82
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (41 bp):
TAAAAATATAAAATTGTAAAAATTATATTTTAAAAAATTAA
Found at i:314034 original size:16 final size:15
Alignment explanation
Indices: 313967--314052 Score: 65
Period size: 15 Copynumber: 5.9 Consensus size: 15
313957 AATAAAAATT
*
313967 ATTTTAAAAATATAAA
1 ATTTTAAAAAT-TATA
*
313983 ATATGT-AAAATTAT-
1 AT-TTTAAAAATTATA
*
313997 ATTTTAAAAAATATA
1 ATTTTAAAAATTATA
*
314012 A---TAAAAATTTTAA
1 ATTTTAAAAATTAT-A
314025 ATTTTAAAAATTATA
1 ATTTTAAAAATTATA
*
314040 TTTTTAAAAATTA
1 ATTTTAAAAATTA
314053 ATATATGATT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
12 8 0.15
13 4 0.07
14 9 0.16
15 16 0.29
16 16 0.29
17 2 0.04
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (15 bp):
ATTTTAAAAATTATA
Found at i:314073 original size:41 final size:42
Alignment explanation
Indices: 313989--314079 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
313979 TAAAATATGT
*
313989 AAAATTATATTTTAAAAAATATAATAAAAATTTTAAATTTTA
1 AAAATTATATTTTAAAAAATATAATAAAAATTTTAAATCTTA
* ** *
314031 AAAATTATATTTTTAAAAAT-TAATATATGATTTTTAA-CTTA
1 AAAATTATATTTTAAAAAATATAATA-AAAATTTTAAATCTTA
314072 AAAATTAT
1 AAAATTAT
314080 TTATTATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
41 16 0.37
42 27 0.63
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (42 bp):
AAAATTATATTTTAAAAAATATAATAAAAATTTTAAATCTTA
Found at i:314097 original size:25 final size:27
Alignment explanation
Indices: 314041--314100 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
314031 AAAATTATAT
314041 TTTTAAAAATTAATATATGATTTTTAA
1 TTTTAAAAATTAATATATGATTTTTAA
* * *
314068 -CTTAAAAATT-ATTTATTA-TTTTAA
1 TTTTAAAAATTAATATATGATTTTTAA
314092 TTTTAAAAA
1 TTTTAAAAA
314101 AAATATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 6 0.21
25 13 0.46
26 9 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTTAAAAATTAATATATGATTTTTAA
Found at i:314167 original size:26 final size:26
Alignment explanation
Indices: 314103--314181 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
314093 TTTAAAAAAA
**
314103 ATATTTTTAAAAAATGTATATTAATTTT
1 ATATTTTTAAAAAAT-TAT-TTAAAATT
* *
314131 TTCTTTATTAAAAAATTATTTAAAATT
1 ATATTT-TTAAAAAATTATTTAAAATT
*
314158 ATATTTTTAAAAAATT-TATAAAAT
1 ATATTTTTAAAAAATTATTTAAAAT
314182 ATTTGAATTT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
25 7 0.16
26 10 0.23
27 10 0.23
28 7 0.16
29 9 0.21
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
ATATTTTTAAAAAATTATTTAAAATT
Found at i:314206 original size:28 final size:28
Alignment explanation
Indices: 314175--314242 Score: 70
Period size: 27 Copynumber: 2.4 Consensus size: 28
314165 TAAAAAATTT
314175 ATAAAATATTTGAATTTTA-AAATTA-AAA
1 ATAAAATATTT--ATTTTAGAAATTACAAA
*
314203 AT-AAATAATTATTTTAGAAATTACAAA
1 ATAAAATATTTATTTTAGAAATTACAAA
*
314230 ATTAACATATTTA
1 A-TAAAATATTTA
314243 AGTAAACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 6 0.18
26 6 0.18
27 11 0.33
28 3 0.09
29 7 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (28 bp):
ATAAAATATTTATTTTAGAAATTACAAA
Found at i:314847 original size:23 final size:22
Alignment explanation
Indices: 314755--314850 Score: 110
Period size: 23 Copynumber: 4.5 Consensus size: 22
314745 TTAAATTTCA
*
314755 AATTATTTTTAAAAATACAAAT
1 AATTATTTTTAAAAATAAAAAT
* *
314777 AATTATTCTT-CAAA-AAAAAT
1 AATTATTTTTAAAAATAAAAAT
*
314797 --TTATCTTTAAAAATAAAAAT
1 AATTATTTTTAAAAATAAAAAT
314817 AATTAATTTTTAAAAATAAAAAT
1 AATT-ATTTTTAAAAATAAAAAT
314840 AATTAATTTTT
1 AATT-ATTTTT
314851 TGTTAATACA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
18 6 0.10
19 3 0.05
20 11 0.18
21 3 0.05
22 11 0.18
23 28 0.45
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
AATTATTTTTAAAAATAAAAAT
Found at i:316953 original size:4 final size:4
Alignment explanation
Indices: 316944--316972 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
316934 TTTGCTGCAC
316944 CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT C
316973 ACTATTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:324575 original size:17 final size:17
Alignment explanation
Indices: 324555--324610 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
324545 AATTTTATTT
324555 TAAAAATATTAATTTAA
1 TAAAAATATTAATTTAA
* *
324572 TAAAAATAATAATTACAA
1 TAAAAATATTAATT-TAA
* *
324590 CATAAAATATTAATTTTA
1 TA-AAAATATTAATTTAA
324608 TAA
1 TAA
324611 CTTATAGTTA
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 14 0.47
18 5 0.17
19 11 0.37
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAATATTAATTTAA
Found at i:325121 original size:24 final size:24
Alignment explanation
Indices: 325062--325121 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
325052 ACATATTATA
*
325062 TAAAAGAAAT-ATATTATTTTTACTT
1 TAAAA-AAATAAT-TTATTTTTACTG
*
325087 TAAAAATATAATTTATTTTTA-TG
1 TAAAAAAATAATTTATTTTTACTG
325110 TAATAAAAATAA
1 TAA-AAAAATAA
325122 AATATACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 4 0.13
24 19 0.63
25 7 0.23
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (24 bp):
TAAAAAAATAATTTATTTTTACTG
Found at i:325267 original size:18 final size:18
Alignment explanation
Indices: 325241--325276 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
325231 ATTGACACAT
*
325241 AAATTTTATAATAAATTA
1 AAATATTATAATAAATTA
*
325259 AAATATTATGATAAATTA
1 AAATATTATAATAAATTA
325277 TGTAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AAATATTATAATAAATTA
Found at i:325663 original size:38 final size:36
Alignment explanation
Indices: 325617--325701 Score: 86
Period size: 37 Copynumber: 2.3 Consensus size: 36
325607 ATACATGTAC
325617 ATAT-AAAAATATACATGAAATAAA-ATAA-ATTATTAA
1 ATATAAAAAATATACAT-AAA-AAATATAATATT-TTAA
* * *
325653 TATGTAAAAAATTTATATAAAAAATATAATATTTTAA
1 -ATATAAAAAATATACATAAAAAATATAATATTTTAA
325690 ATATAAAAAATA
1 ATATAAAAAATA
325702 ACACAAATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
36 13 0.32
37 14 0.35
38 13 0.32
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.34
Consensus pattern (36 bp):
ATATAAAAAATATACATAAAAAATATAATATTTTAA
Found at i:325745 original size:15 final size:14
Alignment explanation
Indices: 325722--325757 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
325712 GAATGCATAA
*
325722 TTTTTTTCTTTTTC
1 TTTTTTTCTATTTC
325736 TTTCTTTTCTATTTC
1 TTT-TTTTCTATTTC
325751 TTTTTTT
1 TTTTTTT
325758 ATCAAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTCTATTTC
Found at i:326176 original size:11 final size:12
Alignment explanation
Indices: 326125--326177 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
326115 AAATATATGA
326125 AATATAAAAATAT
1 AATAT-AAAATAT
* *
326138 GACATAAAATATT
1 AATATAAAATA-T
326151 AAT-TAAAATAT
1 AATATAAAATAT
326162 AATATAAAATA-
1 AATATAAAATAT
326173 AATAT
1 AATAT
326178 GATACGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 9 0.26
12 20 0.59
13 5 0.15
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (12 bp):
AATATAAAATAT
Found at i:326327 original size:8 final size:8
Alignment explanation
Indices: 326307--326336 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
326297 CTCTTTCTCC
326307 TTTTCTTT
1 TTTTCTTT
326315 CTTTTCTTT
1 -TTTTCTTT
326324 TTTTCTTT
1 TTTTCTTT
326332 TTTTC
1 TTTTC
326337 CTTTCCATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTCTTT
Found at i:326340 original size:17 final size:17
Alignment explanation
Indices: 326286--326336 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
326276 CACATTAATT
*
326286 TTTTTTTATTTCTCTTTC
1 TTTTTTTCTTTCT-TTTC
**
326304 TCCTTTTCTTTCTTTTC
1 TTTTTTTCTTTCTTTTC
326321 TTTTTTTCTTT-TTTTC
1 TTTTTTTCTTTCTTTTC
326337 CTTTCCATCT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 5 0.18
17 13 0.46
18 10 0.36
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTTTCTTTCTTTTC
Found at i:326676 original size:14 final size:15
Alignment explanation
Indices: 326650--326690 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
326640 AAGTTTTTTT
326650 CTTTTTCTT-TCTTTA
1 CTTTTT-TTCTCTTTA
*
326665 C-TTTTTTCTCTTTT
1 CTTTTTTTCTCTTTA
326679 CTTTTTTTCTCT
1 CTTTTTTTCTCT
326691 CTTTCCCTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 2 0.09
14 10 0.43
15 11 0.48
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTTTTCTCTTTA
Found at i:326835 original size:11 final size:11
Alignment explanation
Indices: 326795--326839 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
326785 ATAGATAAAT
326795 AAATAGATATAA
1 AAATA-ATATAA
326807 AAA-AAT-TAA
1 AAATAATATAA
326816 AATATAATATAA
1 AA-ATAATATAA
326828 AAATAATATAA
1 AAATAATATAA
326839 A
1 A
326840 TACTGTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 14 0.47
12 8 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (11 bp):
AAATAATATAA
Found at i:326840 original size:22 final size:21
Alignment explanation
Indices: 326789--326841 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
326779 TATTAGATAG
*
326789 ATAA-ATAAATAGATATAAAA
1 ATAATATAAATAAATATAAAA
326809 A-AAT-TAAAATATAATATAAAA
1 ATAATAT-AAATA-AATATAAAA
326830 ATAATATAAATA
1 ATAATATAAATA
326842 CTGTACAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
19 3 0.11
20 6 0.22
21 9 0.33
22 8 0.30
23 1 0.04
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
ATAATATAAATAAATATAAAA
Found at i:327037 original size:38 final size:40
Alignment explanation
Indices: 326966--327067 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 40
326956 AATATTTAAA
* *
326966 ACATA-ATATAAAAATGATATG-T-ACATAATATAAA-TA-T
1 ACATATATATAAAAAT-ATA-GATAAAATAAAATAAATTATT
327003 ACATATATATAAAAATATAGATAAAATAAAATAAATTATT
1 ACATATATATAAAAATATAGATAAAATAAAATAAATTATT
*
327043 A-ATATATA-AAAAATATATA-AAAATA
1 ACATATATATAAAAATATAGATAAAATA
327068 TCATATTTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
36 1 0.02
37 15 0.26
38 30 0.53
39 9 0.16
40 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (40 bp):
ACATATATATAAAAATATAGATAAAATAAAATAAATTATT
Found at i:330100 original size:21 final size:21
Alignment explanation
Indices: 330082--330141 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
330072 TATTAAAAGT
*
330082 TGCATTTTTTCATCCAAAAAA
1 TGCATTCTTTCATCCAAAAAA
**
330103 TGCATTCTTTCATCCAACCAA
1 TGCATTCTTTCATCCAAAAAA
* *
330124 TGCATTATTTCATTCAAA
1 TGCATTCTTTCATCCAAA
330142 GATACTTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.38
Consensus pattern (21 bp):
TGCATTCTTTCATCCAAAAAA
Found at i:331028 original size:2 final size:2
Alignment explanation
Indices: 331021--331058 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
331011 CATTTTGCTT
331021 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
331059 GCTACCAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:334986 original size:2 final size:2
Alignment explanation
Indices: 334981--335028 Score: 53
Period size: 2 Copynumber: 24.0 Consensus size: 2
334971 AATTCCTCTC
* * *
334981 AT AT AT AT AT AT AT AT AT AT AT -T AT AT TT AT TT AT AT ACT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
335023 AT AT AT
1 AT AT AT
335029 TTAAATTAGC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:335027 original size:21 final size:21
Alignment explanation
Indices: 334981--335031 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
334971 AATTCCTCTC
*
334981 ATATATATATATATATATATA
1 ATATATTTATATATATATATA
* *
335002 TTATATTTATTTATATACTA-A
1 ATATATTTATATATATA-TATA
335023 ATATATTTA
1 ATATATTTA
335032 AATTAGCTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATTTATATATATATATA
Found at i:335029 original size:17 final size:17
Alignment explanation
Indices: 334989--335031 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
334979 TCATATATAT
* * *
334989 ATATATATATATATTAT
1 ATATATTTATATACTAA
*
335006 ATTTATTTATATACTAA
1 ATATATTTATATACTAA
335023 ATATATTTA
1 ATATATTTA
335032 AATTAGCTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTTATATACTAA
Found at i:338858 original size:22 final size:22
Alignment explanation
Indices: 338830--338886 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
338820 AAAATCGAGA
* *
338830 ATGTATCAATACAATTGTAAGT
1 ATGTATCGATACAATTGTAAGC
*
338852 ATGTATCGATACAATTGTGAGC
1 ATGTATCGATACAATTGTAAGC
338874 ATGTATCGATACA
1 ATGTATCGATACA
338887 TTGACTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (22 bp):
ATGTATCGATACAATTGTAAGC
Found at i:339001 original size:21 final size:20
Alignment explanation
Indices: 338954--339007 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
338944 CATTTTAGGC
* *
338954 ATGTATCGATACATTCATTT
1 ATGTATCGATACATTCACTA
338974 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
338994 ATTGTATCGATACA
1 A-TGTATCGATACA
339008 AATCGTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:340751 original size:16 final size:16
Alignment explanation
Indices: 340723--340757 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
340713 ATCTAAAACA
340723 AAAGATAATATATAATT
1 AAAGATAATATAT-ATT
340740 AAAGAT-ATATATATT
1 AAAGATAATATATATT
340755 AAA
1 AAA
340758 TCATAAACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 6 0.33
17 6 0.33
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (16 bp):
AAAGATAATATATATT
Found at i:345723 original size:73 final size:72
Alignment explanation
Indices: 345600--345808 Score: 213
Period size: 79 Copynumber: 2.8 Consensus size: 72
345590 AAAGAGGCAG
* * * * *
345600 GGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCGTCGATATGAAAACATTTTGGAAAT
1 GGTTGGAATATCCCCTTGAAAATAACGGGGTTGGAGTATCCTCGAGATGAAAA-ATTTTGGAAAT
*
345665 AAAAACGT
65 AAAAACGA
* *
345673 GGTTGGAATAT-CCCTTTAGAAATAACGGGGTTGGAGTATCCTCAAGATGAAAATTTTAATATTT
1 GGTTGGAATATCCCCTTGA-AAATAACGGGGTTGGAGTATCCTCGAGATG--AA----AA-ATTT
*
345737 TGGAAATAAAAGCGA
58 TGGAAATAAAAACGA
* * * *
345752 GGTTGGAGTATCCCCTTGAAAATAACGGGATTGGAGTATCTTCGTGATGAAAAATTT
1 GGTTGGAATATCCCCTTGAAAATAACGGGGTTGGAGTATCCTCGAGATGAAAAATTT
345809 GATATTTTTG
Statistics
Matches: 112, Mismatches: 16, Indels: 17
0.77 0.11 0.12
Matches are distributed among these distances:
72 9 0.08
73 38 0.34
75 2 0.02
77 2 0.02
79 55 0.49
80 6 0.05
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.29
Consensus pattern (72 bp):
GGTTGGAATATCCCCTTGAAAATAACGGGGTTGGAGTATCCTCGAGATGAAAAATTTTGGAAATA
AAAACGA
Found at i:345764 original size:79 final size:78
Alignment explanation
Indices: 345654--345869 Score: 247
Period size: 79 Copynumber: 2.7 Consensus size: 78
345644 ATATGAAAAC
* *
345654 ATTTTGGAAATAAAAACGTGGTTGGAATATCCCTTTAGAAATAACGGGGTTGGAGTATCCTCAAG
1 ATTTTGGAAAT-AAAACGAGGTTGGAGTATCCCTTTAGAAATAACGGGGTTGGAGTATCCTCAAG
*
345719 ATGAAAATTTTAAT
65 ATGAAAAATTTAAT
* * * **
345733 ATTTTGGAAATAAAAGCGAGGTTGGAGTATCCCCTT-GAAAATAACGGGATTGGAGTATCTTCGT
1 ATTTTGGAAATAAAA-CGAGGTTGGAGTATCCCTTTAG-AAATAACGGGGTTGGAGTATCCTCAA
*
345797 GATGAAAAATTTGAT
64 GATGAAAAATTTAAT
** * *
345812 ATTTTTGGAAATAAAAATAGGATTAGAGTAT-CCTCTTAGAAATAACTGGGTTGGAGTA
1 A-TTTTGGAAATAAAACGAGG-TTGGAGTATCCCT-TTAGAAATAACGGGGTTGGAGTA
345870 ATCCCGAGAA
Statistics
Matches: 116, Mismatches: 15, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
78 5 0.04
79 69 0.59
80 41 0.35
81 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.31
Consensus pattern (78 bp):
ATTTTGGAAATAAAACGAGGTTGGAGTATCCCTTTAGAAATAACGGGGTTGGAGTATCCTCAAGA
TGAAAAATTTAAT
Found at i:348722 original size:21 final size:22
Alignment explanation
Indices: 348697--348745 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
348687 TTATAATAAA
348697 TTATAGTAT-A-AATCTAATAT
1 TTATAGTATAATAATCTAATAT
*
348717 TATATATTATAATTAATCTAATAT
1 T-TATAGTATAA-TAATCTAATAT
348741 TTATA
1 TTATA
348746 AAATATTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 7 0.29
22 1 0.04
23 4 0.17
24 11 0.46
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (22 bp):
TTATAGTATAATAATCTAATAT
Found at i:349802 original size:3 final size:3
Alignment explanation
Indices: 349796--349836 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
349786 CAACAACAAC
349796 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
349837 AGGGGTGATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:352560 original size:15 final size:13
Alignment explanation
Indices: 352524--352589 Score: 66
Period size: 12 Copynumber: 5.2 Consensus size: 13
352514 ATTTAATTAC
*
352524 AAATAAATAT-AT
1 AAATAAAAATAAT
352536 AAATAAAAATAAT
1 AAATAAAAATAAT
*
352549 AAATTAAAA-AAT
1 AAATAAAAATAAT
* *
352561 AAATAATAATTA-
1 AAATAAAAATAAT
352573 AAATATAAAATAAT
1 AAATA-AAAATAAT
352587 AAA
1 AAA
352590 AATCATAAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
12 24 0.56
13 16 0.37
14 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATAAAAATAAT
Found at i:352566 original size:19 final size:20
Alignment explanation
Indices: 352536--352589 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
352526 ATAAATATAT
352536 AAATAAAAATAATAAATTAAA
1 AAAT-AAAATAATAAATTAAA
352557 AAAT-AAATAAT-AATTAAA
1 AAATAAAATAATAAATTAAA
*
352575 ATATAAAATAATAAA
1 AAATAAAATAATAAA
352590 AATCATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 10 0.33
19 14 0.47
20 2 0.07
21 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAATAAAATAATAAATTAAA
Found at i:352590 original size:33 final size:33
Alignment explanation
Indices: 352524--352591 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
352514 ATTTAATTAC
*
352524 AAATAAATATATAAATAAAAATAATAAATTAAA
1 AAATAAATATATAAATAAAAATAATAAAATAAA
*
352557 AAATAAATA-ATAATTAAAATATAA-AATAATAAA
1 AAATAAATATATAAATAAAA-ATAATAA-AATAAA
352590 AA
1 AA
352592 TCATAAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.35
33 20 0.65
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (33 bp):
AAATAAATATATAAATAAAAATAATAAAATAAA
Found at i:352599 original size:16 final size:15
Alignment explanation
Indices: 352528--352599 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
352518 AATTACAAAT
*
352528 AAATATATA-AATAA
1 AAATATAAATAATAA
*
352542 AAATAATAAATTA-AA
1 AAAT-ATAAATAATAA
* *
352557 AAATAAATAATAATTA
1 AAATATA-AATAATAA
352573 AAATATAAAATAATAA
1 AAATAT-AAATAATAA
352589 AAATCATAAAT
1 AAAT-ATAAAT
352600 CAAATATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.13
15 14 0.31
16 22 0.49
17 3 0.07
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATATAAATAATAA
Found at i:362026 original size:16 final size:16
Alignment explanation
Indices: 362005--362041 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
361995 GTCCCTTGTT
362005 TTGGTTTTGGTTAAAA
1 TTGGTTTTGGTTAAAA
362021 TTGGTTTTGGTTAAAA
1 TTGGTTTTGGTTAAAA
362037 TTGGT
1 TTGGT
362042 ATATTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (16 bp):
TTGGTTTTGGTTAAAA
Found at i:366211 original size:79 final size:79
Alignment explanation
Indices: 366072--366241 Score: 214
Period size: 79 Copynumber: 2.2 Consensus size: 79
366062 ATAACAACAG
** * *
366072 GGTTGGAGTATCCCTGATTATAGAAAATCGGTATTTTGAAAATAAAATCGGGATTAGAGTATCCC
1 GGTTGGAGTATCCCCAATTATAGAAAATCGATACTTTGAAAATAAAATCGGGATTAGAGTATCCC
*
366137 TGCGAAAATAACGA
66 CGCGAAAATAACGA
* * * ** * *
366151 GGTTGGAGTATCCCCAATTGTGGAAAATCGATGCTTTGAAAATAAGGTCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCCCAATTATAGAAAATCGATACTTTGAAAATAAAATCGGGATTAGAGTATCCC
* *
366216 CGTGAAAATAATGA
66 CGCGAAAATAACGA
366230 GGTTGGAGTATC
1 GGTTGGAGTATC
366242 TCTTAGAAAT
Statistics
Matches: 77, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (79 bp):
GGTTGGAGTATCCCCAATTATAGAAAATCGATACTTTGAAAATAAAATCGGGATTAGAGTATCCC
CGCGAAAATAACGA
Found at i:366250 original size:28 final size:26
Alignment explanation
Indices: 366201--366299 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 26
366191 AATAAGGTCG
* *
366201 GGGTTGGAGTATCCCCGTGAAAATAAT
1 GGGTTGGAGTAT-CTCTTGAAAATAAT
*
366228 GAGGTTGGAGTATCTCTTAGAAATAAAAT
1 G-GGTTGGAGTATCTCTT-GAAA-ATAAT
* *
366257 CGGAGTTGGAGTATCTCCTTGGAAATAAC
1 -GG-GTTGGAGTATCT-CTTGAAAATAAT
366286 GGGATTGGAGTATC
1 GGG-TTGGAGTATC
366300 CTCGATGACA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
27 5 0.08
28 27 0.46
29 8 0.14
30 16 0.27
31 3 0.05
ACGTcount: A:0.30, C:0.12, G:0.29, T:0.28
Consensus pattern (26 bp):
GGGTTGGAGTATCTCTTGAAAATAAT
Found at i:366419 original size:28 final size:29
Alignment explanation
Indices: 366367--366442 Score: 86
Period size: 28 Copynumber: 2.7 Consensus size: 29
366357 ATATAAAGCT
*
366367 AGGGTTGGAGTATCCC-CTCGAAAATAAC
1 AGGGTTGGAGTATCCCAATCGAAAATAAC
366395 AGGGTTGGAGTATCTCCAAT-G-AAATAAC
1 AGGGTTGGAGTATC-CCAATCGAAAATAAC
* *
366423 GGGGTTGGAATATCACCAAT
1 AGGGTTGGAGTATC-CCAAT
366443 TATGAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 38 0.90
29 3 0.07
30 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (29 bp):
AGGGTTGGAGTATCCCAATCGAAAATAAC
Found at i:366545 original size:51 final size:51
Alignment explanation
Indices: 366463--366593 Score: 176
Period size: 51 Copynumber: 2.6 Consensus size: 51
366453 TGGTGTTTTG
* * **
366463 GAAATAAAATCGGAG-TGGAGTATCCCTGATTACGGTAAATCGATGCTTTA
1 GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATCGATGCTTTA
* * *
366513 GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTG
1 GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATCGATGCTTTA
366564 GAAATAAAATCGG-GATTGGAGTATCCCCGA
1 GAAATAAAATCGGAG-TTGGAGTATCCCCGA
366594 GATGAAAAAT
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
50 16 0.22
51 56 0.78
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (51 bp):
GAAATAAAATCGGAGTTGGAGTATCCCCGATTAAGAAAAATCGATGCTTTA
Found at i:368905 original size:20 final size:19
Alignment explanation
Indices: 368876--369017 Score: 104
Period size: 20 Copynumber: 6.8 Consensus size: 19
368866 AAAATGCCTG
* *
368876 AATGTTTCGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
368896 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
368916 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
*
368936 AATGTATCGATACATTTAAGTAA
1 AATGTATCGATACA---ATG-AA
*
368959 ACCCAGAGTATCGATACAATGAA
1 A---A-TGTATCGATACAATGAA
*
368982 CAATATATCGATACAATGAA
1 -AATGTATCGATACAATGAA
*
369002 CAATGTATCAATACAA
1 -AATGTATCGATACAA
369018 ATTGTAAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.01
20 75 0.75
21 2 0.02
23 7 0.07
24 3 0.03
26 1 0.01
27 11 0.11
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Done.