Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012888.1 Corchorus olitorius cultivar O-4 contig12921, 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: 7198
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Found at i:653 original size:11 final size:11
Alignment explanation
Indices: 637--661 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
627 ATTTGTTTCC
637 TTTTGTTTTTT
1 TTTTGTTTTTT
648 TTTTGTTTTTT
1 TTTTGTTTTTT
659 TTT
1 TTT
662 AAATTTCCTT
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:961 original size:33 final size:34
Alignment explanation
Indices: 856--967 Score: 111
Period size: 34 Copynumber: 3.3 Consensus size: 34
846 TGATATTGTT
* * * * *
856 AAACATGAATTTGATGATTTTCTTTGTAC-TGGAA
1 AAACATGAATTTCATAATGTTGTGTGTACTTGG-A
* * * *
890 AAACATGTATTTGATAATGTTGTTTGTAATTGGA
1 AAACATGAATTTCATAATGTTGTGTGTACTTGGA
*
924 AAACATGAATTTCATATTGTTG-GTGTACTTGGA
1 AAACATGAATTTCATAATGTTGTGTGTACTTGGA
957 AAACATGAATT
1 AAACATGAATT
968 CTGTTGTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
33 20 0.30
34 44 0.66
35 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (34 bp):
AAACATGAATTTCATAATGTTGTGTGTACTTGGA
Found at i:1013 original size:32 final size:32
Alignment explanation
Indices: 976--1058 Score: 130
Period size: 32 Copynumber: 2.6 Consensus size: 32
966 TTCTGTTGTA
976 TATGGTATTTATGTGTTATGACAATGTTGTTT
1 TATGGTATTTATGTGTTATGACAATGTTGTTT
* *
1008 TATGGTATTCATGTGTTATGACAGTGTTGTTT
1 TATGGTATTTATGTGTTATGACAATGTTGTTT
* *
1040 TTTAGTATTTATGTGTTAT
1 TATGGTATTTATGTGTTAT
1059 ATGGTAGTCA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.20, C:0.04, G:0.22, T:0.54
Consensus pattern (32 bp):
TATGGTATTTATGTGTTATGACAATGTTGTTT
Found at i:3066 original size:4 final size:4
Alignment explanation
Indices: 3057--3270 Score: 76
Period size: 4 Copynumber: 55.5 Consensus size: 4
3047 AAAATTATTA
* * * *
3057 AAAT AAAT AAGT -AAT AGAT AAAT ATAT AAAT AGAA- AAAT AAGT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
* * * * *
3103 AAAT -AAT AGAT GAAT AAA- AGAAT AAAT ATAT -AAT AGAT AAAT AGAT
1 AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT
** * * ** *
3149 AGGT AAA- AAAA ATAAT AAAT AAAT AGAT -AAT AGCT AAAT TAAT AAAT
1 AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * ** * *
3196 AAA- AAGAT AAAT -AGT AAAT AAAT AGAT -AAT AGTT CAAT TAAT AAAT
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* *
3242 AAA- AAGAT AAAT -AGT AAAT AAAT AGAT AA
1 AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AA
3271 TAGTTCAATT
Statistics
Matches: 148, Mismatches: 44, Indels: 36
0.65 0.19 0.16
Matches are distributed among these distances:
3 28 0.19
4 110 0.74
5 10 0.07
ACGTcount: A:0.64, C:0.01, G:0.09, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:3106 original size:27 final size:26
Alignment explanation
Indices: 3076--3145 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 26
3066 AGTAATAGAT
3076 AAATATATAAATAGAAAAATAAGTAAA
1 AAATATATAAATAGAAAAATAAG-AAA
* * *
3103 AAATA-ATAGAT-GAATAA-AAGAAT
1 AAATATATAAATAGAAAAATAAGAAA
*
3126 AAATATAT-AATAGATAAATA
1 AAATATATAAATAGAAAAATA
3146 GATAGGTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
23 9 0.26
24 9 0.26
25 6 0.18
26 5 0.15
27 5 0.15
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (26 bp):
AAATATATAAATAGAAAAATAAGAAA
Found at i:3137 original size:19 final size:17
Alignment explanation
Indices: 3094--3170 Score: 57
Period size: 19 Copynumber: 4.2 Consensus size: 17
3084 AAATAGAAAA
3094 ATAAGTAAAAAATAATAG
1 ATAA-TAAAAAATAATAG
*
3112 ATGAATAAAAGAATAAATAT
1 AT-AATAAAA-AAT-AATAG
*
3132 ATAATAGATAAATAGATAG
1 ATAATA-AAAAATA-ATAG
* *
3151 GTAA-AAAAAATAATAA
1 ATAATAAAAAATAATAG
3167 ATAA
1 ATAA
3171 ATAGATAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
16 6 0.13
17 6 0.13
18 9 0.19
19 18 0.38
20 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.23
Consensus pattern (17 bp):
ATAATAAAAAATAATAG
Found at i:3198 original size:27 final size:25
Alignment explanation
Indices: 3158--3262 Score: 96
Period size: 27 Copynumber: 4.2 Consensus size: 25
3148 TAGGTAAAAA
3158 AAATAATAAATAAATAGATAATAGCT
1 AAATAATAAATAAATAGATAATAG-T
3184 AAAT--T-AATAAATA-A-AA-AGAT
1 AAATAATAAATAAATAGATAATAG-T
*
3204 AAATAGTAAATAAATAGATAATAGTT
1 AAATAATAAATAAATAGATAATAG-T
* *
3230 CAATTAATAAATAAAAAGATAAATAGT
1 -AAATAATAAATAAATAGAT-AATAGT
3257 AAATAA
1 AAATAA
3263 ATAGATAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
20 7 0.11
21 2 0.03
22 2 0.03
23 16 0.25
24 2 0.03
25 2 0.03
26 12 0.18
27 17 0.26
28 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.08, T:0.27
Consensus pattern (25 bp):
AAATAATAAATAAATAGATAATAGT
Found at i:3213 original size:19 final size:19
Alignment explanation
Indices: 3191--3274 Score: 62
Period size: 19 Copynumber: 4.1 Consensus size: 19
3181 GCTAAATTAA
3191 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
* *
3210 TAAATAAATAGATAATAGTTCAATTAA
1 TAAATAAA-A-A-GATA----AA-TAG
3237 TAAATAAAAAGATAAATAG
1 TAAATAAAAAGATAAATAG
*
3256 TAAATAAATAGAT-AATAG
1 TAAATAAAAAGATAAATAG
3274 T
1 T
3275 TCAATTTAAC
Statistics
Matches: 52, Mismatches: 5, Indels: 17
0.70 0.07 0.23
Matches are distributed among these distances:
18 6 0.12
19 22 0.42
20 3 0.06
21 1 0.02
22 3 0.06
24 3 0.06
25 1 0.02
26 3 0.06
27 10 0.19
ACGTcount: A:0.62, C:0.01, G:0.10, T:0.27
Consensus pattern (19 bp):
TAAATAAAAAGATAAATAG
Found at i:3265 original size:27 final size:27
Alignment explanation
Indices: 3210--3270 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
3200 AGATAAATAG
* * *
3210 TAAATAAATAGATAATAGTTCAATTAA
1 TAAATAAAAAGATAATAGTTAAATAAA
3237 TAAATAAAAAGATAAATAG-TAAATAAA
1 TAAATAAAAAGAT-AATAGTTAAATAAA
*
3264 TAGATAA
1 TAAATAA
3271 TAGTTCAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 24 0.83
28 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (27 bp):
TAAATAAAAAGATAATAGTTAAATAAA
Found at i:3274 original size:46 final size:46
Alignment explanation
Indices: 3158--3280 Score: 219
Period size: 46 Copynumber: 2.7 Consensus size: 46
3148 TAGGTAAAAA
* * *
3158 AAATAATAAATAAATAGATAATAGCTAAATTAATAAATAAAAAGAT
1 AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
3204 AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
1 AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
3250 AAATAGTAAATAAATAGATAATAGTTCAATT
1 AAATAGTAAATAAATAGATAATAGTTCAATT
3281 TAACAAAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 74 1.00
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.28
Consensus pattern (46 bp):
AAATAGTAAATAAATAGATAATAGTTCAATTAATAAATAAAAAGAT
Found at i:5109 original size:213 final size:214
Alignment explanation
Indices: 4612--5133 Score: 529
Period size: 213 Copynumber: 2.4 Consensus size: 214
4602 CGGAATCAAA
* * * *
4612 TTGGAGATCAACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATCTGGAGATCAA
1 TTGGAGATCAACTCTGAACATTGAAAACTTCTTGGAACGACCGCACTGGATCATCTGGAGATCAA
* * * *
4676 CTCTGATCTTCGAAAACTTCTTGAAACGACCATAATGGATCATCTGAAGATCAACTCTAATCTTC
66 CTCTGATCATCGAAAACTTCTTG-AATGACCACAATGGATCATCTGAAGATCAACTCTAATCATC
* * *
4741 GAAAATTTCTTGAAACGACAGCACCAGATCATCTGGAGATCAACTTAGATCTTTGAAAACTTCTA
130 -AAAACTTCTTGAAACGACAGCACCAGATCATCTGGAGATCAACTTAGACCATTGAAAACTTCTA
*
4806 GGAAGAACCGCACCGGATCAT
194 GGAAGAACCGCACCGGACCAT
* * * ** *
4827 CTGGACATCAACTCTGAAC-TTCGAAAACTT-TTCGGAAGGATTGTACTGGATCATCTGGAGATC
1 TTGGAGATCAACTCTGAACATT-GAAAACTTCTT-GGAACGACCGCACTGGATCATCTGGAGATC
* * * *
4890 AACTCTGATCATCAAAAACTTCTTAGAATGACCGCAA-GGAATCATCTGAGGATCAACTCTGATC
64 AACTCTGATCATCGAAAACTTCTT-GAATGACCACAATGG-ATCATCTGAAGATCAACTCTAATC
* * * ** * * *
4954 AT-AAAACTTCTTGGAATGACCGCACTGGAT-TTTTGGCGATCAACTCT-GACCATTGAAAACTT
127 ATCAAAACTTCTTGAAACGACAGCACCAGATCATCTGGAGATCAACT-TAGACCATTGAAAACTT
* * * *
5016 CTTGGAATG-ACTGCACTGGACCTT
191 CTAGGAA-GAACCGCACCGGACCAT
* * * * * *
5040 TTGGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCTTTTGGGGATCAA
1 TTGGAGATCAACTCTGAACATTGAAAACTTCTTGGAACGACCGCACTGGATCATCTGGAGATCAA
* *
5105 CTCTGACCATTGAAAACTTCTTGGAATGA
66 CTCTGATCATCGAAAACTTCTT-GAATGA
5134 GATCAACTCT
Statistics
Matches: 249, Mismatches: 49, Indels: 20
0.78 0.15 0.06
Matches are distributed among these distances:
213 115 0.46
214 31 0.12
215 25 0.10
216 77 0.31
217 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (214 bp):
TTGGAGATCAACTCTGAACATTGAAAACTTCTTGGAACGACCGCACTGGATCATCTGGAGATCAA
CTCTGATCATCGAAAACTTCTTGAATGACCACAATGGATCATCTGAAGATCAACTCTAATCATCA
AAACTTCTTGAAACGACAGCACCAGATCATCTGGAGATCAACTTAGACCATTGAAAACTTCTAGG
AAGAACCGCACCGGACCAT
Found at i:5128 original size:54 final size:54
Alignment explanation
Indices: 4613--5133 Score: 490
Period size: 54 Copynumber: 9.7 Consensus size: 54
4603 GGAATCAAAT
* * * *
4613 TGGAGATCAACTCTGATCATCGGAAACTTCTT-GAACGACCACACTGGATCATC
1 TGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATC
* * ** *
4666 TGGAGATCAACTCTGATC-TTCGAAAACTTCTTGAAACGACCATAATGGATCATC
1 TGGAGATCAACTCTGATCATT-GAAAACTTCTTGGAATGACCGCACTGGATCATC
* * * * * * **
4720 TGAAGATCAACTCTAATC-TTCGAAAATTTCTTGAAACGACAGCACCAGATCATC
1 TGGAGATCAACTCTGATCATT-GAAAACTTCTTGGAATGACCGCACTGGATCATC
* * *
4774 TGGAGATCAACT-TAGATCTTTGAAAACTTCTAGGAA-GAACCGCACCGGATCATC
1 TGGAGATCAACTCT-GATCATTGAAAACTTCTTGGAATG-ACCGCACTGGATCATC
* * * ** *
4828 TGGACATCAACTCTGAAC-TTCGAAAACTT-TTCGGAAGGATTGTACTGGATCATC
1 TGGAGATCAACTCTGATCATT-GAAAACTTCTT-GGAATGACCGCACTGGATCATC
** * *
4882 TGGAGATCAACTCTGATCATCAAAAACTTCTTAGAATGACCGCA-AGGAATCATC
1 TGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGG-ATCATC
* *
4936 T-GAGGATCAACTCTGATCA-T-AAAACTTCTTGGAATGACCGCACTGGAT-TTT
1 TGGA-GATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATC
* * * * * *
4987 TGGCGATCAACTCTGACCATTGAAAACTTCTTGGAATGACTGCACTGGACCTTT
1 TGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATC
* * * *
5041 TGGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGACCGCACTGGATCTTT
1 TGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATC
* *
5095 TGGGGATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 TGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGA
5134 GATCAACTCT
Statistics
Matches: 400, Mismatches: 50, Indels: 35
0.82 0.10 0.07
Matches are distributed among these distances:
51 16 0.04
52 26 0.06
53 65 0.16
54 286 0.71
55 7 0.02
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (54 bp):
TGGAGATCAACTCTGATCATTGAAAACTTCTTGGAATGACCGCACTGGATCATC
Found at i:5138 original size:35 final size:35
Alignment explanation
Indices: 5099--5665 Score: 796
Period size: 35 Copynumber: 16.0 Consensus size: 35
5089 ATCTTTTGGG
* ** *
5099 GATCAACTCTGACCATTGAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
5134 GATCAACTCTGATCATAAAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGA
*
5170 GATCAACTCTGATCATCAAAAACTTCTTGAAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* * *
5205 GATCAACTCTGATAATCAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
5240 GATCAACTCTGATCATCAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
5275 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* **
5310 GATCAACTCTGATCCTCGAAAACTTCTT-AGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGA-AATGA
**
5345 GATCAACTCTGATCCA-CGAAAACTTCTTGAAATGA
1 GATCAACTCTGAT-CATAAAAAACTTCTTGAAATGA
*
5380 GATCAACTCTGATCATAAAAAACTTCTTGGAATGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
*
5415 GATCAACTCTGATCATAAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT--AAAAAACTTCTTGAAATGA
*
5452 GATCAACTCTGATCATAAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGA
*
5488 GATCAACTCTGATCATAAAAAAACTTCTTGAAAGGA
1 GATCAACTCTGATCAT-AAAAAACTTCTTGAAATGA
*
5524 GATCAACTCTGATCATAAAAAACTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
5559 GATCAACTCTGATCATAAAAAGCCTTCTTGAAAGGA
1 GATCAACTCTGATCATAAAAA-ACTTCTTGAAATGA
* *
5595 GATCAACTCTGATCATAAAAAGCTTCTTGAAACGA
1 GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
* *
5630 GATCAACTCTGATCAATAAAAAACTTCATGGAATGA
1 GATCAACTCTGATC-ATAAAAAACTTCTTGAAATGA
5666 CTGCACCGGT
Statistics
Matches: 492, Mismatches: 31, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
34 3 0.01
35 301 0.61
36 155 0.32
37 33 0.07
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.26
Consensus pattern (35 bp):
GATCAACTCTGATCATAAAAAACTTCTTGAAATGA
Found at i:5734 original size:54 final size:54
Alignment explanation
Indices: 5630--5979 Score: 398
Period size: 54 Copynumber: 6.5 Consensus size: 54
5620 CTTGAAACGA
** * * * *
5630 GATCAACTCTGATCAATAAAAAACTTCATGGAATGACTGCACCGGTTCATCTGGG
1 GATCAACTCTGATCTCT-AAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
*
5685 GATCAACTCTGATCTCTAAAAACTTCCTGGAATGACCGCACTGGATCATCTGGG
1 GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * * * *
5739 GATCAACTCCGATCACTGAAAACTTCTTTTGAATGATCGCACTGAATCATCTAGG
1 GATCAACTCTGATCTCTAAAAACTTC-TTGGAATGACCGCACTGGATCATCTGGG
* * * *
5794 GATCAACTCTGATCTCT-AAAACTTATAGGAATGACCGCATTGGATCATCTAGG
1 GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * * *
5847 GATCAACTCTGATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTGGG
1 GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
* * * * *
5901 GATCAACTCTAATCAT-TCAAAACTTCTTGGAATGATCTCACTGGACCATCTGGG
1 GATCAACTCTGATC-TCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
5955 GATCAACTCTGATCTCTAAAAACTT
1 GATCAACTCTGATCTCTAAAAACTT
5980 TTATGAAAGA
Statistics
Matches: 250, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
53 40 0.16
54 157 0.63
55 53 0.21
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (54 bp):
GATCAACTCTGATCTCTAAAAACTTCTTGGAATGACCGCACTGGATCATCTGGG
Found at i:5979 original size:162 final size:163
Alignment explanation
Indices: 5630--5979 Score: 454
Period size: 162 Copynumber: 2.2 Consensus size: 163
5620 CTTGAAACGA
** * * *
5630 GATCAACTCTGATCAATAAAAAACTTCATGGAATGACTGCACCGGTTCATCTGGGGATCAACTCT
1 GATCAACTCTGATCTCT-AAAAACTTCATGGAATGACCGCACCGGATCATCTAGGGATCAACTCT
* * * * *
5695 GATCTCTAAAAACTTCCTGGAATGACCGCACTGGATCATCTGGGGATCAACTCCGATCACTGAAA
65 GATCACTAAAAACTTCCTGAAATGACCGCACTAGATCATCTGGGGATCAACTCCAATCACTCAAA
* *
5760 ACTTCTTTTGAATGATCGCACTGAATCATCTAGG
130 ACTTCTTTGGAATGATCGCACTGAACCATCTAGG
**
5794 GATCAACTCTGATCTCT-AAAACTT-ATAGGAATGACCGCATTGGATCATCTAGGGATCAACTCT
1 GATCAACTCTGATCTCTAAAAACTTCAT-GGAATGACCGCACCGGATCATCTAGGGATCAACTCT
* * * * * *
5857 GATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTGGGGATCAACTCTAATCATTCAAA
65 GATCACTAAAAACTTCCTGAAATGACCGCACTAGATCATCTGGGGATCAACTCCAATCACTCAAA
* * *
5922 ACTTC-TTGGAATGATCTCACTGGACCATCTGGG
130 ACTTCTTTGGAATGATCGCACTGAACCATCTAGG
5955 GATCAACTCTGATCTCTAAAAACTT
1 GATCAACTCTGATCTCTAAAAACTT
5980 TTATGAAAGA
Statistics
Matches: 161, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
161 42 0.26
162 104 0.65
164 15 0.09
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (163 bp):
GATCAACTCTGATCTCTAAAAACTTCATGGAATGACCGCACCGGATCATCTAGGGATCAACTCTG
ATCACTAAAAACTTCCTGAAATGACCGCACTAGATCATCTGGGGATCAACTCCAATCACTCAAAA
CTTCTTTGGAATGATCGCACTGAACCATCTAGG
Found at i:6005 original size:54 final size:52
Alignment explanation
Indices: 5630--6146 Score: 348
Period size: 54 Copynumber: 9.6 Consensus size: 52
5620 CTTGAAACGA
** * * * *
5630 GATCAACTCTGATCAATAAAAAACTTCATGGAATGACTGCACCGGTTCATCTGGG
1 GATCAACTCTGATCTCT-GAAAACTTC-TTGAATGAC-GCACTGGATCATCTGGG
* *
5685 GATCAACTCTGATCTCTAAAAACTTCCTGGAATGACCGCACTGGATCATCTGGG
1 GATCAACTCTGATCTCTGAAAACTT-CTTGAATGA-CGCACTGGATCATCTGGG
* * * *
5739 GATCAACTCCGATCACTGAAAACTTCTTTTGAATGATCGCACTGAATCATCTAGG
1 GATCAACTCTGATCTCTGAAAACTTC--TTGAATGA-CGCACTGGATCATCTGGG
* * * *
5794 GATCAACTCTGATCTCT-AAAACTTATAGGAATGACCGCATTGGATCATCTAGG
1 GATCAACTCTGATCTCTGAAAACTTCT-TGAATGA-CGCACTGGATCATCTGGG
* * *
5847 GATCAACTCTGATCACTGAAAACTTCTTGAAATGATCGCACTAGATCATTTGGG
1 GATCAACTCTGATCTCTGAAAACTTCTTG-AATGA-CGCACTGGATCATCTGGG
* * * *
5901 GATCAACTCTAATCAT-TCAAAACTTCTTGGAATGATCTCACTGGACCATCTGGG
1 GATCAACTCTGATC-TCTGAAAACTTCTT-GAATGA-CGCACTGGATCATCTGGG
* * * * * **
5955 GATCAACTCTGATCTCTAAAAACTTTTATGAAAGACAACAC-CGAGTCATCTGAA
1 GATCAACTCTGATCTCTGAAAACTTCT-TGAATGAC-GCACTGGA-TCATCTGGG
* * * ***
6009 GATCAACT-T-ATCTCTGAAAGCTTCTATGAAAGACCGCACAAGG-TCATCTTAA
1 GATCAACTCTGATCTCTGAAAACTTCT-TGAATGA-CGCAC-TGGATCATCTGGG
* * * * * **
6061 AATCAACT-TAGATCTCTGAAAAATTCTATGAAAGACCGGACTGGGTCATCTGAA
1 GATCAACTCT-GATCTCTGAAAACTTCT-TGAATGA-CGCACTGGATCATCTGGG
*
6115 GATCAACT-TAGATCTCTGAAAGCTTCTATGAA
1 GATCAACTCT-GATCTCTGAAAACTTCT-TGAA
6147 AGACCGCCCA
Statistics
Matches: 386, Mismatches: 57, Indels: 39
0.80 0.12 0.08
Matches are distributed among these distances:
52 41 0.11
53 48 0.12
54 240 0.62
55 57 0.15
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (52 bp):
GATCAACTCTGATCTCTGAAAACTTCTTGAATGACGCACTGGATCATCTGGG
Found at i:6015 original size:162 final size:162
Alignment explanation
Indices: 5669--6057 Score: 439
Period size: 162 Copynumber: 2.4 Consensus size: 162
5659 GGAATGACTG
* * * * * *
5669 CACCGGTTCATCTGGGGATCAACTCTGATCTCTAAAAACTTCCTGGAATGACCGCACTGGATCAT
1 CACCGGATCATCTGAGGATCAACTCTGATCTCTGAAAACTTCTTGAAATGACCGCACTAGATCAT
* * * *
5734 CTGGGGATCAACTCCGATCACTGAAAACTTCTTTTGAATGATCGCACTGAATCATCTAGGGATCA
66 CTGGGGATCAACTCCAATCACTCAAAACTTCTTTGGAATGATCGCACTGAACCATCTAGGGATCA
* **
5799 ACTCTGATCTCTAAAACTTATAGGAATGACCG
131 ACTCTGATCTCTAAAACTTATAGGAAAGACAA
** * *
5831 CATTGGATCATCT-AGGGATCAACTCTGATCACTGAAAACTTCTTGAAATGATCGCACTAGATCA
1 CACCGGATCATCTGA-GGATCAACTCTGATCTCTGAAAACTTCTTGAAATGACCGCACTAGATCA
* * * * * *
5895 TTTGGGGATCAACTCTAATCATTCAAAACTTC-TTGGAATGATCTCACTGGACCATCTGGGGATC
65 TCTGGGGATCAACTCCAATCACTCAAAACTTCTTTGGAATGATCGCACTGAACCATCTAGGGATC
* *
5959 AACTCTGATCTCTAAAAACTTTTATGAAAGACAA
130 AACTCTGATCTCT-AAAACTTATAGGAAAGACAA
* * * *
5993 CACC-GAGTCATCTGAAGATCAACT-T-ATCTCTGAAAGCTTCTATGAAA-GACCGCACAAGGTC
1 CACCGGA-TCATCTGAGGATCAACTCTGATCTCTGAAAACTTCT-TGAAATGACCGCACTAGATC
6054 ATCT
64 ATCT
6058 TAAAATCAAC
Statistics
Matches: 188, Mismatches: 34, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
160 28 0.15
161 48 0.26
162 111 0.59
163 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (162 bp):
CACCGGATCATCTGAGGATCAACTCTGATCTCTGAAAACTTCTTGAAATGACCGCACTAGATCAT
CTGGGGATCAACTCCAATCACTCAAAACTTCTTTGGAATGATCGCACTGAACCATCTAGGGATCA
ACTCTGATCTCTAAAACTTATAGGAAAGACAA
Found at i:6076 original size:106 final size:107
Alignment explanation
Indices: 5956--6153 Score: 294
Period size: 106 Copynumber: 1.9 Consensus size: 107
5946 CCATCTGGGG
*
5956 ATCAACTCTGATCTCT-AAAAACTTTTATGAAAGACAACACCGAGTCATCTGAAGATCAACTT-A
1 ATCAACTCTGATCTCTGAAAAA-TTCTATGAAAGACAACACCGAGTCATCTGAAGATCAACTTAA
6019 TCTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
65 TCTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
*** * *
6062 ATCAACT-TAGATCTCTGAAAAATTCTATGAAAGACCGGACTGGGTCATCTGAAGATCAACTTAG
1 ATCAACTCT-GATCTCTGAAAAATTCTATGAAAGACAACACCGAGTCATCTGAAGATCAACTTA-
6126 ATCTCTGAAAGCTTCTATGAAAGACCGC
64 ATCTCTGAAAGCTTCTATGAAAGACCGC
6154 CCAGGGCTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
105 1 0.01
106 48 0.59
107 5 0.06
108 28 0.34
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (107 bp):
ATCAACTCTGATCTCTGAAAAATTCTATGAAAGACAACACCGAGTCATCTGAAGATCAACTTAAT
CTCTGAAAGCTTCTATGAAAGACCGCACAAGGTCATCTTAAA
Found at i:6226 original size:93 final size:93
Alignment explanation
Indices: 6067--6252 Score: 275
Period size: 93 Copynumber: 2.0 Consensus size: 93
6057 TTAAAATCAA
* ** *
6067 CTTAGATCTCTGAAAAATTCTATGAAAGACCGGACTGGGTCATCTGAAGATCAACTTAGATCTCT
1 CTTAGATCTCTGAAAAATTCTATGAAAGACCGAAAAGGGTCATCTGAAGATCAACTTAAATCTCT
* *
6132 GAAAGCTTCTATGAAAGACCGCCCAGGG
66 GAAAACTTCTATGAAAGACCGCACAGGG
** *
6160 CTTAGATCTCTGAAAGCTTCTATGAAAGACCGCAAAAGGGTC-TCTTAAGATCAACTTAAATCTC
1 CTTAGATCTCTGAAAAATTCTATGAAAGACCG-AAAAGGGTCATCTGAAGATCAACTTAAATCTC
6224 TGAAAACTTCTATGAAAGACCGCACAGGG
65 TGAAAACTTCTATGAAAGACCGCACAGGG
6253 TGCTTGAAGG
Statistics
Matches: 83, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 77 0.93
94 6 0.07
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (93 bp):
CTTAGATCTCTGAAAAATTCTATGAAAGACCGAAAAGGGTCATCTGAAGATCAACTTAAATCTCT
GAAAACTTCTATGAAAGACCGCACAGGG
Done.