Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_pilon, whole genome shotgun sequence
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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 12
Found at i:2963873 original size:103 final size:103
Alignment explanation
Indices: 2963694--2963895 Score: 359
Period size: 103 Copynumber: 2.0 Consensus size: 103
2963684 CTACACGGTC
*
2963694 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTT
1 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCAT
* *
2963759 GGCATGTGTATATGATTCTTAAGGAATGATATGTGGTT
66 AGCATATGTATATGATTCTTAAGGAATGATATGTGGTT
*
2963797 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGATACACATACTTGATCCAT
1 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCAT
*
2963862 AGTATATGTATATGATTCTTAAGGAATGATATGT
66 AGCATATGTATATGATTCTTAAGGAATGATATGT
2963896 AGTCCTTATG
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.37
Consensus pattern (103 bp):
CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCAT
AGCATATGTATATGATTCTTAAGGAATGATATGTGGTT
Found at i:2963952 original size:23 final size:23
Alignment explanation
Indices: 2963919--2963986 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
2963909 ATTATTTTAT
2963919 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* ** *
2963942 GGCACTCCGGTATAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
2963965 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2963987 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2967455 original size:20 final size:20
Alignment explanation
Indices: 2967426--2967463 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2967416 ATAATGTCAT
*
2967426 TAGGGTATCGATACCCCCAG
1 TAGGGAATCGATACCCCCAG
2967446 TAGGGAATCGATACCCCC
1 TAGGGAATCGATACCCCC
2967464 TAAAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (20 bp):
TAGGGAATCGATACCCCCAG
Found at i:2969242 original size:103 final size:103
Alignment explanation
Indices: 2969063--2969260 Score: 360
Period size: 103 Copynumber: 1.9 Consensus size: 103
2969053 GCGGTCCTTC
* * *
2969063 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCTTGGCA
1 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATACTTGATCCCTAGCA
2969128 TATGTATATGATTCTTAAGGAATGATATGTGGTCATTT
66 TATGTATATGATTCTTAAGGAATGATATGTGGTCATTT
*
2969166 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATACTTGATCCCTAGTA
1 GGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATACTTGATCCCTAGCA
2969231 TATGTATATGATTCTTAAGGAATGATATGT
66 TATGTATATGATTCTTAAGGAATGATATGT
2969261 AGTCCTTATG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 91 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (103 bp):
GGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATACTTGATCCCTAGCA
TATGTATATGATTCTTAAGGAATGATATGTGGTCATTT
Found at i:2969317 original size:23 final size:23
Alignment explanation
Indices: 2969284--2969351 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
2969274 ATTATTATAT
2969284 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2969307 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * * *
2969330 TGCACTTCAGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2969352 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2973770 original size:33 final size:33
Alignment explanation
Indices: 2973732--2973797 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2973722 CTATGCGAGA
2973732 TTGTTGAATTTTGTAGTGAAAATTTAAAATTGT
1 TTGTTGAATTTTGTAGTGAAAATTTAAAATTGT
2973765 TTGTTGAATTTTGTAGTGAAAATTTAAAATTGT
1 TTGTTGAATTTTGTAGTGAAAATTTAAAATTGT
2973798 AGTTTTAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGTTGAATTTTGTAGTGAAAATTTAAAATTGT
Found at i:2990237 original size:20 final size:21
Alignment explanation
Indices: 2990198--2990237 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2990188 AAAATGGTGA
2990198 AAATTGAAATCATCGGTAGAG
1 AAATTGAAATCATCGGTAGAG
* *
2990219 AAATTGTAATGAT-GGTAGA
1 AAATTGAAATCATCGGTAGA
2990238 TTAAGCGGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (21 bp):
AAATTGAAATCATCGGTAGAG
Found at i:2991985 original size:31 final size:32
Alignment explanation
Indices: 2991950--2992009 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
2991940 TATTTAAATG
* * *
2991950 TTATTTCAATTTTATTAATCAT-ATTATTTGA
1 TTATTTAAATGTTATCAATCATCATTATTTGA
*
2991981 TTATTTAAATGTTATCAGTCATCATTATT
1 TTATTTAAATGTTATCAATCATCATTATT
2992010 ATTTGTAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 18 0.75
32 6 0.25
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (32 bp):
TTATTTAAATGTTATCAATCATCATTATTTGA
Found at i:2992315 original size:25 final size:27
Alignment explanation
Indices: 2992282--2992331 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
2992272 AAATTAACAA
2992282 AATGATTTTAATTAAATAA-ATATAAT
1 AATGATTTTAATTAAATAATATATAAT
*
2992308 AATG-TTTTTATTAAATAATATATA
1 AATGATTTTAATTAAATAATATATA
2992332 TTATAAACCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (27 bp):
AATGATTTTAATTAAATAATATATAAT
Found at i:2992416 original size:23 final size:24
Alignment explanation
Indices: 2992390--2992440 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
2992380 ATAATTATGT
*
2992390 TTTTATAACATGT-TTTCT-TATAC
1 TTTTATAACACGTCTTTCTCTAT-C
2992413 TTTTATAACACGTCTTTCTCTATC
1 TTTTATAACACGTCTTTCTCTATC
2992437 TTTT
1 TTTT
2992441 GACATGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 12 0.48
24 10 0.40
25 3 0.12
ACGTcount: A:0.22, C:0.18, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTATAACACGTCTTTCTCTATC
Found at i:2995732 original size:18 final size:18
Alignment explanation
Indices: 2995709--2995744 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2995699 ATCATGTAAA
*
2995709 GGTTGAATAAGTTCTGTT
1 GGTTGAATAAGTTATGTT
2995727 GGTTGAATAAGTTATGTT
1 GGTTGAATAAGTTATGTT
2995745 CATTCTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.44
Consensus pattern (18 bp):
GGTTGAATAAGTTATGTT
Found at i:2995950 original size:113 final size:113
Alignment explanation
Indices: 2995749--2996154 Score: 677
Period size: 113 Copynumber: 3.6 Consensus size: 113
2995739 TATGTTCATT
* * *
2995749 CTTCTTCATATGAGTTCTTCTCATTATGAATTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
1 CTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
* * *
2995814 TCAAAGAAAAGATTTGAATAAATTCTTCTTATTATGAATTTCTTCTTC
66 TCAAACAAAAGGTTTGAACAAATTCTTCTTATTATGAATTTCTTCTTC
*
2995862 CTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
1 CTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
2995927 TCAAACAAAAGGTTTGAACAAATTCTTCTTATTATGAATTTCTTCTTC
66 TCAAACAAAAGGTTTGAACAAATTCTTCTTATTATGAATTTCTTCTTC
* * *
2995975 CTTCTTCAGATAAGTTATTCTCATTGTGAATTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
1 CTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
* * *
2996040 TCAAACAAAAGGTTTGAACAAATTTTTCTCATTATGAATTTCTTCTTA
66 TCAAACAAAAGGTTTGAACAAATTCTTCTTATTATGAATTTCTTCTTC
* *
2996088 CTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGACCCATCGAATGATGGAT
1 CTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
2996153 TC
66 TC
2996155 GAATCTTTGC
Statistics
Matches: 276, Mismatches: 17, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
113 276 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (113 bp):
CTTCTTCAGATGAGTTATTCTCATTATGAACTTCTCTGGAAAAGTTGATCCATCGAATGATGAAT
TCAAACAAAAGGTTTGAACAAATTCTTCTTATTATGAATTTCTTCTTC
Found at i:2997729 original size:14 final size:14
Alignment explanation
Indices: 2997706--2997741 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2997696 ATTTTTTCTC
*
2997706 TCTTTTTTCATTTT
1 TCTTTCTTCATTTT
2997720 TCTTTCTTCATTTT
1 TCTTTCTTCATTTT
*
2997734 TTTTTCTT
1 TCTTTCTT
2997742 TCTTCTTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (14 bp):
TCTTTCTTCATTTT
Found at i:3004816 original size:16 final size:16
Alignment explanation
Indices: 3004795--3004832 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
3004785 TGCAATACTG
3004795 GCTTCAATTTTCTCTA
1 GCTTCAATTTTCTCTA
3004811 GCTTCAATTTTCTCTA
1 GCTTCAATTTTCTCTA
3004827 GCTTCA
1 GCTTCA
3004833 TTCTCATCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.18, C:0.26, G:0.08, T:0.47
Consensus pattern (16 bp):
GCTTCAATTTTCTCTA
Found at i:3005075 original size:15 final size:15
Alignment explanation
Indices: 3005052--3005083 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3005042 TGCAATGAAT
3005052 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
3005067 AATGCATGTATGCAA
1 AATGAATGTATGCAA
3005082 AA
1 AA
3005084 GGTATTGATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:3008405 original size:20 final size:22
Alignment explanation
Indices: 3008359--3008410 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
3008349 ATTTAATAAT
*
3008359 TGAAAATAAAATAAAACATTAA
1 TGAAAATAATATAAAACATTAA
*
3008381 T-AAAATAATAT-AAATATT-A
1 TGAAAATAATATAAAACATTAA
3008400 TGAAAATAATA
1 TGAAAATAATA
3008411 AGTATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.07
20 15 0.56
21 9 0.33
22 1 0.04
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
TGAAAATAATATAAAACATTAA
Found at i:3010068 original size:3 final size:3
Alignment explanation
Indices: 3010060--3010094 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
3010050 TTCTTTGGTT
3010060 TTG TTG TTG TTG TTG TTG TTG TTG TTG -TG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
3010095 GTTCCCTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:3015755 original size:2 final size:2
Alignment explanation
Indices: 3015748--3015841 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
3015738 TCAAATAATT
3015748 TA TA 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 TA TA
3015790 TA TA 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 TA TA
3015832 TA TA TA TA TA
1 TA TA TA TA TA
3015842 AAAGAACTTG
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3017985 original size:136 final size:135
Alignment explanation
Indices: 3017610--3018100 Score: 779
Period size: 136 Copynumber: 3.6 Consensus size: 135
3017600 TTGTTAGATT
* * * * *
3017610 GAACAAGTTCTTCGCATTATGAAATTCTTCTCTCT-TTTGGATGAGTTTTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * *
3017674 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTGA
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTC-ATGAATCGAGTGA
3017738 TAGGTC
130 TAGGTC
*
3017744 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
3017809 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
3017874 AGGTC
131 AGGTC
*
3017879 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTT-GGATGAGTTCTTCTCATTATGAACT
* ** *
3017944 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
65 CTCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
3018009 TAGGTC
130 TAGGTC
*
3018015 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCT-TTGGATGAGTTCTTCTCATTATGAACT
3018080 CTCCATTGAAAATGTTGATCC
65 CTCCATTGAAAATGTTGATCC
3018101 ACCTATTTTT
Statistics
Matches: 329, Mismatches: 24, Indels: 6
0.92 0.07 0.02
Matches are distributed among these distances:
134 31 0.09
135 126 0.38
136 171 0.52
137 1 0.00
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.35
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:3019111 original size:26 final size:25
Alignment explanation
Indices: 3019061--3019118 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
3019051 CGAACCCTCC
*
3019061 TTCTTCATTTTTTCTTTCTTTTTTT
1 TTCTTCATTTTTTCTTTCATTTTTT
* *
3019086 TTCTTCTTTTTATTTTTTCATTTTTT
1 TTCTTCATTTT-TTCTTTCATTTTTT
3019112 TTCTTCA
1 TTCTTCA
3019119 AGCATAGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (25 bp):
TTCTTCATTTTTTCTTTCATTTTTT
Found at i:3019113 original size:17 final size:16
Alignment explanation
Indices: 3019067--3019104 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
3019057 CTCCTTCTTC
*
3019067 ATTTTTTCTT-TCTTT
1 ATTTTTTCTTCTTTTT
3019082 -TTTTTTCTTCTTTTT
1 ATTTTTTCTTCTTTTT
3019097 ATTTTTTC
1 ATTTTTTC
3019105 ATTTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 4 0.20
16 7 0.35
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (16 bp):
ATTTTTTCTTCTTTTT
Found at i:3019118 original size:13 final size:13
Alignment explanation
Indices: 3019061--3019118 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
3019051 CGAACCCTCC
3019061 TTCTTCATTTTTT
1 TTCTTCATTTTTT
* *
3019074 CT-TTCTTTTTTT
1 TTCTTCATTTTTT
3019086 TTCTTC-TTTTTAT
1 TTCTTCATTTTT-T
*
3019099 TTTTTCATTTTTT
1 TTCTTCATTTTTT
3019112 TTCTTCA
1 TTCTTCA
3019119 AGCATAGTAC
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
12 15 0.41
13 17 0.46
14 5 0.14
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTCATTTTTT
Found at i:3031132 original size:2 final size:2
Alignment explanation
Indices: 3031125--3031211 Score: 167
Period size: 2 Copynumber: 44.0 Consensus size: 2
3031115 TCAAATAATT
3031125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3031166 TA TA 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 TA TA
3031208 TA TA
1 TA TA
3031212 AAGAACTTGA
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 83 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3033207 original size:133 final size:135
Alignment explanation
Indices: 3032966--3033452 Score: 725
Period size: 133 Copynumber: 3.6 Consensus size: 135
3032956 TTGTTAGATT
* * * * * *
3032966 GAACAAGTTCTTCGCATTATGAAATTCTTCTCTCT-TTTGGATGAGTT-TTTTCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
* * * * * *
3033029 TTCACTGAAAATGTTGATCCCTCAAGCGAGGCGTCCCTGACTCGAAATG-CTGTGAATCGAGTGA
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTC-ATGAATCGAGTGA
3033093 TAGGTC
130 TAGGTC
3033099 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTC-T-TCATTATGAACTC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
3033162 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
66 TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
3033227 AGGTC
131 AGGTC
**
3033232 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTTTTTCGGATGAG-TCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTT-GGATGAGTTCTTCTCATTATGAACT
* ** *
3033296 CTCCATTGGAAATGTCAATTCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
65 CTCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGA
3033361 TAGGTC
130 TAGGTC
*
3033367 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGAGTTCTTCTCATTATGAACT
*
3033432 CTCCATTGAAAATGCTGATCC
65 CTCCATTGAAAATGTTGATCC
3033453 ACCTATTTTT
Statistics
Matches: 321, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
133 145 0.45
134 21 0.07
135 121 0.38
136 34 0.11
ACGTcount: A:0.25, C:0.22, G:0.18, T:0.34
Consensus pattern (135 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTC
TCCATTGAAAATGTTGATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCATGAATCGAGTGAT
AGGTC
Found at i:3034422 original size:13 final size:13
Alignment explanation
Indices: 3034404--3034450 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
3034394 TCCTTCTTCA
3034404 TTTTTTCTTTCTT
1 TTTTTTCTTTCTT
3034417 TTTTTTC-TTCTT
1 TTTTTTCTTTCTT
*
3034429 TTTATTT-TTTCAT
1 TTT-TTTCTTTCTT
3034442 TTTTTTCTT
1 TTTTTTCTT
3034451 CAAGCATAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTTTCTT
Found at i:3034445 original size:25 final size:24
Alignment explanation
Indices: 3034397--3034452 Score: 76
Period size: 25 Copynumber: 2.3 Consensus size: 24
3034387 CGAACCCTCC
*
3034397 TTCTTCATTTTTTCTTTCTTTTTT
1 TTCTTCATTTTTTCTTTCATTTTT
* *
3034421 TTCTTCTTTTTATTTTTTCATTTTT
1 TTCTTCATTTT-TTCTTTCATTTTT
3034446 TTCTTCA
1 TTCTTCA
3034453 AGCATAGTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (24 bp):
TTCTTCATTTTTTCTTTCATTTTT
Done.