Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1910
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: 98447
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Found at i:3502 original size:19 final size:19
Alignment explanation
Indices: 3478--3518 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3468 CAAAAAAGAA
3478 AATAATAAAAATAATAA-AT
1 AATAATAAAAA-AATAATAT
*
3497 AATAATAAATAAATAATAT
1 AATAATAAAAAAATAATAT
3516 AAT
1 AAT
3519 TAAAGTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AATAATAAAAAAATAATAT
Found at i:15158 original size:11 final size:11
Alignment explanation
Indices: 15142--15166 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
15132 TTTAAGTTAA
15142 TAAACGAAAAT
1 TAAACGAAAAT
15153 TAAACGAAAAT
1 TAAACGAAAAT
15164 TAA
1 TAA
15167 CAGAATCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (11 bp):
TAAACGAAAAT
Found at i:18647 original size:25 final size:24
Alignment explanation
Indices: 18599--18647 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
18589 TAGTACGGAT
* *
18599 AATTTTTTTTAATTTAATATTTAA
1 AATTTTTTTCAATTTAATACTTAA
*
18623 AATTTTTTTCAATTTGATACCTTAA
1 AATTTTTTTCAATTTAATA-CTTAA
18648 TTTGACAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
AATTTTTTTCAATTTAATACTTAA
Found at i:26072 original size:15 final size:15
Alignment explanation
Indices: 26025--26070 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 15
26015 TTTTTAACAC
26025 TTAAAATTAATAATATT
1 TTAAAATT--TAATATT
26042 TT--AATTTAATATT
1 TTAAAATTTAATATT
26055 TTAAAATTT-ATATT
1 TTAAAATTTAATATT
26069 TT
1 TT
26071 TACTATTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 9 0.33
14 7 0.26
15 9 0.33
17 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTAAAATTTAATATT
Found at i:31403 original size:15 final size:15
Alignment explanation
Indices: 31384--31418 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
31374 AAAAAAACCA
31384 AAAAAAAGAAAGAAAG
1 AAAAAAAGAAA-AAAG
*
31400 AAAAAAAGGAAAAAG
1 AAAAAAAGAAAAAAG
31415 AAAA
1 AAAA
31419 CGGATGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:44039 original size:6 final size:6
Alignment explanation
Indices: 44030--44084 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
44020 TTCATCTCCT
* * *
44030 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCCTCA CCCTCA CCCTCA
1 CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA CCTTCA
*
44078 CCCTCA C
1 CCTTCA C
44085 ACTCGCCTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.16, C:0.58, G:0.00, T:0.25
Consensus pattern (6 bp):
CCTTCA
Found at i:44040 original size:18 final size:18
Alignment explanation
Indices: 44019--44079 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
44009 GCTTCTTCCT
* *
44019 CTTCATCTCCTCCTTCAC
1 CTTCACCTCCACCTTCAC
*
44037 CTTCACCTTCACCTTCAC
1 CTTCACCTCCACCTTCAC
*
44055 CTTCACC-CTCACCCTCAC
1 CTTCACCTC-CACCTTCAC
*
44073 CCTCACC
1 CTTCACC
44080 CTCACACTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.15, C:0.56, G:0.00, T:0.30
Consensus pattern (18 bp):
CTTCACCTCCACCTTCAC
Found at i:44045 original size:12 final size:12
Alignment explanation
Indices: 44030--44094 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
44020 TTCATCTCCT
*
44030 CCTTCACCTTCA
1 CCTTCACCCTCA
*
44042 CCTTCACCTTCA
1 CCTTCACCCTCA
44054 CCTTCACCCTCA
1 CCTTCACCCTCA
*
44066 CCCTCACCCTCA
1 CCTTCACCCTCA
* * *
44078 CCCTCACACTCG
1 CCTTCACCCTCA
44090 CCTTC
1 CCTTC
44095 TGCTTCTTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 48 1.00
ACGTcount: A:0.15, C:0.57, G:0.02, T:0.26
Consensus pattern (12 bp):
CCTTCACCCTCA
Found at i:44080 original size:18 final size:18
Alignment explanation
Indices: 44033--44094 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
44023 ATCTCCTCCT
* *
44033 TCACCTTCACCTTCACCT
1 TCACCTTCACCCTCACCC
44051 TCACCTTCACCCTCACCC
1 TCACCTTCACCCTCACCC
* *
44069 TCACCCTCACCCTCACAC
1 TCACCTTCACCCTCACCC
*
44087 TCGCCTTC
1 TCACCTTC
44095 TGCTTCTTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.16, C:0.56, G:0.02, T:0.26
Consensus pattern (18 bp):
TCACCTTCACCCTCACCC
Found at i:46318 original size:3 final size:3
Alignment explanation
Indices: 46310--46347 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
46300 AATCAAAAAT
* *
46310 AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAA AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
46348 TCTTATTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:46324 original size:9 final size:9
Alignment explanation
Indices: 46304--46347 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
46294 ACCATTAATC
*
46304 AAAAATAAG
1 AAAAAGAAG
*
46313 AAGAAGAAG
1 AAAAAGAAG
*
46322 AAGAAGAAG
1 AAAAAGAAG
46331 AAAAAGAAG
1 AAAAAGAAG
46340 AAAAAGAA
1 AAAAAGAA
46348 TCTTATTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:50236 original size:10 final size:10
Alignment explanation
Indices: 50221--50245 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
50211 TCCTAACCGT
50221 TAACTGCTGC
1 TAACTGCTGC
50231 TAACTGCTGC
1 TAACTGCTGC
50241 TAACT
1 TAACT
50246 ACCACAGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (10 bp):
TAACTGCTGC
Found at i:54660 original size:10 final size:10
Alignment explanation
Indices: 54645--54669 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54635 TCCTAACCGT
54645 TAACTGCTGC
1 TAACTGCTGC
54655 TAACTGCTGC
1 TAACTGCTGC
54665 TAACT
1 TAACT
54670 ACCACAGCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (10 bp):
TAACTGCTGC
Found at i:57751 original size:69 final size:68
Alignment explanation
Indices: 57500--57751 Score: 197
Period size: 69 Copynumber: 3.7 Consensus size: 68
57490 TACATAGGTG
* * * * *
57500 ACATGTTCCATGGGAAAAGCTCGTCTATTTTTGCGGATTCTATTCCAAGCAGC-CCTGCTTAT--
1 ACATGTT-CAAGGGGAAAGCTCGTCTATTTTTGCAGATTCTGTTCCAAGCA-CTCCTGCCTATGC
*
57562 A-AAA
64 AGATA
* * *
57566 ACAATCTTCAAGGGGAAAAGCTCATCTATTTTTGCAGATTCTGTTCCTAGCACTCCTGCCTATGC
1 AC-ATGTTCAAGGGG-AAAGCTCGTCTATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGC
57631 AGATA
64 AGATA
* ** * * * * * * * * *
57636 ACATGTTCATGGGGAAGAATTCGGCCATATTTGCAGAATATATTCCAAGCTCTCCTGTCTATGCG
1 ACATGTTCAAGGGGAA-AGCTCGTCTATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCA
57701 GATA
65 GATA
** **
57705 AGTTGTTCAAGGGGCAAAGCTCGTCTATTTTTGTTGATTCTGTTCCA
1 ACATGTTCAAGGGG-AAAGCTCGTCTATTTTTGCAGATTCTGTTCCA
57752 GGTACCCCTG
Statistics
Matches: 141, Mismatches: 37, Indels: 13
0.74 0.19 0.07
Matches are distributed among these distances:
66 8 0.06
67 44 0.31
68 2 0.01
69 81 0.57
70 6 0.04
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (68 bp):
ACATGTTCAAGGGGAAAGCTCGTCTATTTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAG
ATA
Found at i:64894 original size:105 final size:105
Alignment explanation
Indices: 64712--64900 Score: 335
Period size: 105 Copynumber: 1.8 Consensus size: 105
64702 AAATTATTAT
*
64712 GGAAATAATGTTGGTCAAAATTGTTTTGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
1 GGAAATAATGTTGGTCAAAATTGTTTAGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
64777 GTGTGCTGATGGCTATAATGGTTTTCTGGAACAACGTGCA
66 GTGTGCTGATGGCTATAATGGTTTTCTGGAACAACGTGCA
* *
64817 GGAAATAATGTTGGTCAAAATTAGTTTAGGGG-TGGTCAAACTAATTGTGTTTCTGGTCAAAATG
1 GGAAATAATGTTGGTCAAAATT-GTTTAGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATG
64881 TGTGTGCTGATGGCTATAAT
65 TGTGTGCTGATGGCTATAAT
64901 TGTGCAGGAC
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
105 72 0.90
106 8 0.10
ACGTcount: A:0.28, C:0.09, G:0.28, T:0.35
Consensus pattern (105 bp):
GGAAATAATGTTGGTCAAAATTGTTTAGGGGTTGGTCAAAATAATGGTGTTTCTGGTCAAAATGT
GTGTGCTGATGGCTATAATGGTTTTCTGGAACAACGTGCA
Found at i:73350 original size:39 final size:39
Alignment explanation
Indices: 73296--73381 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
73286 CCAAAGGCGT
73296 CTGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
1 CTGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
73335 CTGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
1 CTGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
*
73374 CTAACACT
1 CTGACACT
73382 GATGTTTCAG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.20, C:0.36, G:0.23, T:0.21
Consensus pattern (39 bp):
CTGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
Found at i:73510 original size:234 final size:233
Alignment explanation
Indices: 73101--73533 Score: 830
Period size: 234 Copynumber: 1.9 Consensus size: 233
73091 GATTCTTCGT
*
73101 CTGACACTTGCGTGTCACCAGCAGATATGACCGCCTCGCCTGACACTGATGTTTCAGGAACTTTT
1 CTGACACTTGCGTGTCACCAGCAGATATGACCGCCTCGCCTAACACTGATGTTTCAGGAACTTTT
73166 CGTGACAGTGAATCTGCTCCTCTACTCTCCTCTGAGCATCTGATATAGGGTCAAGTGCCGTGTGT
66 CGTGACAGTGAATCTGCTCCTCTACTCTCCTCTGAGCATCTGATATAGGGTCAAGTGCCGTGTGT
73231 GTCTTTGGGAAATATACATGCTATGGTTACACGGTCAAAAGCAGGCATTTTCAAACCAAAGGCGT
131 GTCTTTGGGAAATATACATGCTATGGTTACACGGTCAAAAGCAGGCATTTTCAAACCAAAGGCGT
73296 CTGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
196 -TGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
* *
73335 CTGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGCCTAACACTGATGTTTCAGGAGCTTTT
1 CTGACACTTGCGTGTCACCAGCAGATATGACCGCCTCGCCTAACACTGATGTTTCAGGAACTTTT
73400 CGTGACAGTGAATCTGCTCCTCTACTCTCCTCTGAGCATCTGATATAGGGTCAAGTGCCGTGTGT
66 CGTGACAGTGAATCTGCTCCTCTACTCTCCTCTGAGCATCTGATATAGGGTCAAGTGCCGTGTGT
73465 GTCTTTGGGAAATATACATGCTATGGTTACACGGTCAAAAGCAGGCATTTTCAAACCAAAGGCGT
131 GTCTTTGGGAAATATACATGCTATGGTTACACGGTCAAAAGCAGGCATTTTCAAACCAAAGGCGT
73530 TGAC
196 TGAC
73534 CGCCGAAGCT
Statistics
Matches: 196, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
233 4 0.02
234 192 0.98
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.27
Consensus pattern (233 bp):
CTGACACTTGCGTGTCACCAGCAGATATGACCGCCTCGCCTAACACTGATGTTTCAGGAACTTTT
CGTGACAGTGAATCTGCTCCTCTACTCTCCTCTGAGCATCTGATATAGGGTCAAGTGCCGTGTGT
GTCTTTGGGAAATATACATGCTATGGTTACACGGTCAAAAGCAGGCATTTTCAAACCAAAGGCGT
TGACACTTGCGTGTCACCAGCAGATGTGACCGCCTCGC
Found at i:80117 original size:15 final size:15
Alignment explanation
Indices: 80097--80126 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
80087 ATGGATCAAA
80097 TAGCACTAGCTACTC
1 TAGCACTAGCTACTC
80112 TAGCACTAGCTACTC
1 TAGCACTAGCTACTC
80127 CATCAGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (15 bp):
TAGCACTAGCTACTC
Found at i:81853 original size:9 final size:10
Alignment explanation
Indices: 81842--81903 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 10
81832 GGTACAAATA
81842 AATAAATAA-
1 AATAAATAAT
*
81851 AATGCAATAAT
1 AAT-AAATAAT
81862 AATGATAATAAT
1 AAT-A-AATAAT
81874 AAT-AATAAT
1 AATAAATAAT
81883 AATAAACTCAAT
1 AATAAA-T-AAT
81895 AATAAATAA
1 AATAAATAA
81904 AATGATAGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
9 12 0.27
10 9 0.20
11 6 0.13
12 18 0.40
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (10 bp):
AATAAATAAT
Found at i:81899 original size:3 final size:3
Alignment explanation
Indices: 81856--81887 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
81846 AATAAAATGC
*
81856 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
81888 ACTCAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:83333 original size:87 final size:87
Alignment explanation
Indices: 83223--83384 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
83213 AGACCTGATG
* * * * *
83223 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACC
83287 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * * *
83310 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
83375 CAGGGAGATA
66 CAGGGAGATA
83385 AGATCTGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 63 0.98
88 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (87 bp):
CGATCTACTCCGCTGTAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:83445 original size:131 final size:131
Alignment explanation
Indices: 83310--83608 Score: 315
Period size: 131 Copynumber: 2.3 Consensus size: 131
83300 ATAGTGTCTT
* * *
83310 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC-TGGCTTCAATCTGCTCCACTGTAACC
1 CGATCTGCTCCACTGTAA-CTCAGGGAGATAAGATCTCTTGACTTCAATCCGCTCCACTGTAACC
*
83374 TCAGGGAGATAAGATCTGAAAT-TCTTTAG-TCTGTTCCACTGTAATCTCAGGGAAATAAGA-C-
65 TCAGGGAGATAAGA--T--AATGTC-TTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCT
83435 CTGG-TG
125 CTGGCTG
* * * * * *
83441 CGATCTGCTCTACTGTAACTTCAGGGAGATAAGATC-CTTTATTTTAATCCGTTCCACTGTAACT
1 CGATCTGCTCCACTGTAAC-TCAGGGAGATAAGATCTCTTGACTTCAATCCGCTCCACTGTAACC
* * * * *
83505 TCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGC
65 TCAGGGAGATAAGATAATGTCTTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTCTGGC
*
83570 TT
130 TG
* *
83572 CAATCTGCTCCACTGTGACCTCAGGGAGATAAGATCT
1 CGATCTGCTCCACTGT-AACTCAGGGAGATAAGATCT
83609 GAAATTCTTT
Statistics
Matches: 140, Mismatches: 19, Indels: 17
0.80 0.11 0.10
Matches are distributed among these distances:
127 5 0.04
128 30 0.21
129 2 0.01
130 6 0.04
131 95 0.68
132 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (131 bp):
CGATCTGCTCCACTGTAACTCAGGGAGATAAGATCTCTTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAAGATAATGTCTTAGATCTGCTCCACTGTAATCTCAGGGAAATAAGATCTCTGGCT
G
Found at i:83447 original size:87 final size:85
Alignment explanation
Indices: 83312--83607 Score: 272
Period size: 87 Copynumber: 3.4 Consensus size: 85
83302 AGTGTCTTCG
* * *
83312 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCA
1 ATCTGTTCCACTGTAATCTCAGGGAGATAAGATC-CTGG-TTCGATCTGCTCCACTGTAACCTCA
83377 GGGAGATAAGATCTGAAATTCTTTA
64 GGGAGATAAGATCT-AAA-T-TTTA
* * * * *
83402 GTCTGTTCCACTGTAATCTCAGGGAAATAAGA-CCTGGTGCGATCTGCTCTACTGTAACTTCAGG
1 ATCTGTTCCACTGTAATCTCAGGGAGATAAGATCCTGGTTCGATCTGCTCCACTGTAACCTCAGG
**
83466 GAGATAAGATCCTTTATTTTA
66 GAGATAAGAT-CTAAATTTTA
* * ** * * *
83487 ATCCGTTCCACTGTAA-CTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCA
1 ATCTGTTCCACTGTAATC-TCAGGGAGATAAGATCCTG-GTTCGATCTGCTCCACTGTAACCTCA
**** *
83551 GGGAGATAAGATCTCTGGCTTCA
64 GGGAGATAAGATCT-AAATTTTA
* * *
83574 ATCTGCTCCACTGTGACCTCAGGGAGATAAGATC
1 ATCTGTTCCACTGTAATCTCAGGGAGATAAGATC
83608 TGAAATTCTT
Statistics
Matches: 169, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
84 1 0.01
85 30 0.18
86 5 0.03
87 97 0.57
88 7 0.04
89 1 0.01
90 28 0.17
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (85 bp):
ATCTGTTCCACTGTAATCTCAGGGAGATAAGATCCTGGTTCGATCTGCTCCACTGTAACCTCAGG
GAGATAAGATCTAAATTTTA
Found at i:83567 original size:218 final size:218
Alignment explanation
Indices: 83183--83654 Score: 838
Period size: 218 Copynumber: 2.2 Consensus size: 218
83173 TGTTGTGTTC
* * *
83183 AGTCTATTCCACTG-CATCTTCAGGGAAATAAGACCTGATGCGATCTACTCTGCTGTAACCTCAG
1 AGTCTGTTCCACTGTAATC-TCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAG
83247 AGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCG
65 AGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCG
83312 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCA
130 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCA
83377 GGGAGATAAGATCTGAAATTCTTT
195 GGGAGATAAGATCTGAAATTCTTT
* * * *
83401 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGG
1 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGA
*
83466 GAGATAAGATCCTTTATTTTAATCCGTTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGA
66 GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGA
*
83531 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTGACCTCAG
131 TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAG
83596 GGAGATAAGATCTGAAATTCTTT
196 GGAGATAAGATCTGAAATTCTTT
*
83619 AGTCTGTTCCACTGTAATCTCAGGGGAATAAGACCT
1 AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCT
83655 TTTATAATGA
Statistics
Matches: 243, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
218 240 0.99
219 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (218 bp):
AGTCTGTTCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGA
GAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGA
TCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAG
GGAGATAAGATCTGAAATTCTTT
Found at i:83608 original size:44 final size:44
Alignment explanation
Indices: 83235--83608 Score: 287
Period size: 44 Copynumber: 8.6 Consensus size: 44
83225 ATCTACTCTG
* *** * *
83235 CTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTC-TGGCTTCAATCTGCTCCA
* * ** * * *
83279 CTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
*
83322 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
* * * * *
83366 CTGTAACCTCAGGGAGATAAGATCTGAAAT-TCTTTAGTCTGTTCCA
1 CTGTAACCTCAGGGAGATAAGATCT---CTGGCTTCAATCTGCTCCA
* * * * *
83412 CTGTAATCTCAGGGAAATAAGA-C-CTGG-TGCGATCTGCTCTA
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
* *** * * *
83453 CTGTAACTTCAGGGAGATAAGATC-CTTTATTTTAATCCGTTCCA
1 CTGTAACCTCAGGGAGATAAGATCTC-TGGCTTCAATCTGCTCCA
* * ** * * *
83497 CTGTAACTTCAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
*
83540 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
*
83584 CTGTGACCTCAGGGAGATAAGATCT
1 CTGTAACCTCAGGGAGATAAGATCT
83609 GAAATTCTTT
Statistics
Matches: 253, Mismatches: 66, Indels: 22
0.74 0.19 0.06
Matches are distributed among these distances:
41 28 0.11
42 2 0.01
43 62 0.25
44 127 0.50
45 1 0.00
46 32 0.13
47 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
CTGTAACCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
Found at i:84860 original size:1 final size:1
Alignment explanation
Indices: 84856--84887 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
84846 AAAGTCCCCC
84856 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
84888 AGGAAGCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:95954 original size:21 final size:20
Alignment explanation
Indices: 95909--95955 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
95899 ATAATAGACG
*
95909 AATAAAAATCTAAAGCATTC
1 AATAAAAATATAAAGCATTC
*
95929 CATAAAAATAATAAACGC-TTC
1 AATAAAAAT-ATAAA-GCATTC
95950 AATAAA
1 AATAAA
95956 TGAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.36
21 12 0.55
22 2 0.09
ACGTcount: A:0.57, C:0.15, G:0.04, T:0.23
Consensus pattern (20 bp):
AATAAAAATATAAAGCATTC
Found at i:96224 original size:3 final size:3
Alignment explanation
Indices: 96216--96247 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
96206 AATAAAATGC
*
96216 AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
96248 ACTCAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Done.