Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018738.1 Corchorus olitorius cultivar O-4 contig18771, 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: 63196
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:942 original size:12 final size:12
Alignment explanation
Indices: 927--964 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
917 TTATTCCTTA
927 TTTCCTTTTCTT
1 TTTCCTTTTCTT
939 TTTCCTTTTCTT
1 TTTCCTTTTCTT
*
951 CTTT-CTCTTCTT
1 -TTTCCTTTTCTT
963 TT
1 TT
965 CTCTTTCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 2 0.08
12 19 0.79
13 3 0.12
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCCTTTTCTT
Found at i:2820 original size:2 final size:2
Alignment explanation
Indices: 2813--2850 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2803 TAATAGCACT
2813 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
2851 CAAGTTAACA
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:5361 original size:29 final size:30
Alignment explanation
Indices: 5306--5382 Score: 106
Period size: 30 Copynumber: 2.7 Consensus size: 30
5296 ACTTGTAGCG
* *
5306 TTTGGG-CGTTTTGCCCCC-GGACTTCAAT
1 TTTGGGACATTTTGCCCCCTGAACTTCAAT
5334 TTT-GGACATTTTGCCCCCTGAACTTCAAT
1 TTTGGGACATTTTGCCCCCTGAACTTCAAT
*
5363 TTTGGGACGTTTTGCCCCCT
1 TTTGGGACATTTTGCCCCCT
5383 CAACCTAACG
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 2 0.05
28 14 0.33
29 12 0.28
30 15 0.35
ACGTcount: A:0.13, C:0.29, G:0.21, T:0.38
Consensus pattern (30 bp):
TTTGGGACATTTTGCCCCCTGAACTTCAAT
Found at i:5627 original size:21 final size:19
Alignment explanation
Indices: 5603--5641 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
5593 AAAATTAAAT
5603 AAAAATAAAAGAAAATGAGAG
1 AAAAA-AAAA-AAAATGAGAG
*
5624 AAAAAGAAAAAAATGAGA
1 AAAAAAAAAAAAATGAGA
5642 AGGGGATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (19 bp):
AAAAAAAAAAAAATGAGAG
Found at i:12987 original size:65 final size:64
Alignment explanation
Indices: 12859--12987 Score: 152
Period size: 65 Copynumber: 2.0 Consensus size: 64
12849 GGAAAAACTG
* * ** * * *
12859 GTCCTACCCATGCATGGGGTACCCTGGCCACCCCACGCCTGGGCTAGTGCAGAAAGTTTGAATC
1 GTCCAACCAATGCATGGGGTACCCTGGCCACCCCACGCAAGGGCTAGTGCAAAAAATTGGAATC
* *
12923 GTCCAACCAATGCATGGGGTATCCTTGGCCTA-CCCATGCAAGGGCTAGTGCAAAAAATTGGAAT
1 GTCCAACCAATGCATGGGGTA-CCCTGGCC-ACCCCACGCAAGGGCTAGTGCAAAAAATTGGAAT
12987 C
64 C
12988 AATAGCAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
64 19 0.35
65 34 0.63
66 1 0.02
ACGTcount: A:0.25, C:0.29, G:0.26, T:0.21
Consensus pattern (64 bp):
GTCCAACCAATGCATGGGGTACCCTGGCCACCCCACGCAAGGGCTAGTGCAAAAAATTGGAATC
Found at i:15607 original size:13 final size:13
Alignment explanation
Indices: 15589--15624 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
15579 GGGATCGTGA
15589 TGATTGTGATTAT
1 TGATTGTGATTAT
15602 TGATTGTGATTAT
1 TGATTGTGATTAT
*
15615 TGATTATGAT
1 TGATTGTGAT
15625 ACCAATGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (13 bp):
TGATTGTGATTAT
Found at i:24914 original size:107 final size:104
Alignment explanation
Indices: 24683--24944 Score: 384
Period size: 107 Copynumber: 2.5 Consensus size: 104
24673 AATTTTTTTA
* ** * *
24683 ACCCTTAAAATAAAATTTTAATTTTAATTTAGACTAAACTTAGTG-AATTAGTTATATATTTTAT
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
*
24747 TTCTAAAACCCTATAACAATATTATTAATTATGGAATTT
66 TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
* *
24786 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAGTGAAATTAGTTATATATTTTA
*
24851 TTTCTAAAACCCTATAACAATAAATTATTAATTTTGAAATTT
65 TTTCTAAAACCCTATAACAAT--ATTATTAATTATGAAATTT
24893 ACCCTTAAAATAAAAATAAAATTTTAATTTAGGGCTAAACTT-GTTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTT-GGGCTAAACTTAG-TGAAATTA
24945 AGGGTAAACA
Statistics
Matches: 144, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
103 27 0.19
104 13 0.09
105 37 0.26
106 1 0.01
107 66 0.46
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.41
Consensus pattern (104 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGCTAAACTTAGTGAAATTAGTTATATATTTTAT
TTCTAAAACCCTATAACAATATTATTAATTATGAAATTT
Found at i:43290 original size:35 final size:35
Alignment explanation
Indices: 43227--43293 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
43217 TGTATTTGAA
43227 AACTTCCAAACAAAACAGAGTTGAAAGTTACTGTT
1 AACTTCCAAACAAAACAGAGTTGAAAGTTACTGTT
* * *
43262 AACTTCC-AACAAAGCAAGATTTGGAAGTTACT
1 AACTTCCAAACAAAAC-AGAGTTGAAAGTTACT
43294 TAGTACATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.25
35 21 0.75
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (35 bp):
AACTTCCAAACAAAACAGAGTTGAAAGTTACTGTT
Found at i:44506 original size:129 final size:132
Alignment explanation
Indices: 44362--44624 Score: 406
Period size: 129 Copynumber: 2.0 Consensus size: 132
44352 GCCATTAGAC
44362 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* * * *
44427 TTTAATTTTTACCATTTTACTATTTTAA-TT-AAAAACTTATATATATTAG-AATTTTTAAATAT
66 TTTAATTTTTACCAATTTACTAATTTAATTTAAAAAACTTAGATATATTAGAAATTTTAAAATAT
44489 AT
131 AT
* * * * *
44491 TTTTATAGTTTTACTCAACTAAAAACTCTTTTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
* *
44556 TTTTATTTTTATCAATTTACTAATTTAATTTAAAAAACTTAGATATATTAGAAATTTTAAAATAT
66 TTTAATTTTTACCAATTTACTAATTTAATTTAAAAAACTTAGATATATTAGAAATTTTAAAATAT
44621 AT
131 AT
44623 TT
1 TT
44625 CTTAAATGAC
Statistics
Matches: 120, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
129 84 0.70
130 2 0.02
131 18 0.15
132 16 0.13
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.49
Consensus pattern (132 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATCTTTATTTAATTAAATATAATATCCTCATAACTA
TTTAATTTTTACCAATTTACTAATTTAATTTAAAAAACTTAGATATATTAGAAATTTTAAAATAT
AT
Found at i:45807 original size:27 final size:27
Alignment explanation
Indices: 45775--45826 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
45765 TTTTTTTAAT
45775 ATATTTCTAAAT-TACCATTATTAAATA
1 ATATTT-TAAATATACCATTATTAAATA
*
45802 ATATTTTAAATATTCCATTATTAAA
1 ATATTTTAAATATACCATTATTAAA
45827 ATGAAATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (27 bp):
ATATTTTAAATATACCATTATTAAATA
Found at i:45920 original size:149 final size:149
Alignment explanation
Indices: 45766--46042 Score: 473
Period size: 149 Copynumber: 1.9 Consensus size: 149
45756 ATTGTATCTT
* *
45766 TTTTTTAATATATTTCTAAATTACCATTATTAAATAATATTTTAAATATTCCATTATTAAAATGA
1 TTTTTTAATATATTTATAAATTACCATTATTAAATAATATTTTAAATATTCCATTATTAAAATAA
* *
45831 AATGAAAAATTAGATTATCCTCATTATTTAGGATCCAACGTGACCAATAGGAATGCTGCACATTA
66 AATGAAAAATTAGATTATCCTCATTATTTAGGATCCAACGTGACCAATAAGAATGCTCCACATTA
45896 TGGTTTCCGATTGCACCCA
131 TGGTTTCCGATTGCACCCA
** * **
45915 TTTTTTAATATATTTATAAATTGTCATTATTAAATCATATTTTAGTTATTCCATTATTAAAATAA
1 TTTTTTAATATATTTATAAATTACCATTATTAAATAATATTTTAAATATTCCATTATTAAAATAA
45980 AATGAAAAATTAGATTATCCTCATTATTTAGGATCCAACGTGACCAATAAGAATGCTCCACAT
66 AATGAAAAATTAGATTATCCTCATTATTTAGGATCCAACGTGACCAATAAGAATGCTCCACAT
46043 CATCTTTAGC
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
149 119 1.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (149 bp):
TTTTTTAATATATTTATAAATTACCATTATTAAATAATATTTTAAATATTCCATTATTAAAATAA
AATGAAAAATTAGATTATCCTCATTATTTAGGATCCAACGTGACCAATAAGAATGCTCCACATTA
TGGTTTCCGATTGCACCCA
Found at i:46854 original size:151 final size:155
Alignment explanation
Indices: 46659--46962 Score: 463
Period size: 151 Copynumber: 1.9 Consensus size: 155
46649 TATATATATT
46659 ATTGGCCAACCCAATTTCTACTATATATATTATTATTTATTTATGACTTAATTTTAAGTTTAAAA
1 ATTGGCCAACCCAATTTCTA-TATATATATTATTATTTATTTATGACTTAATTTTAAGTTTAAAA
46724 TTTTAAATCCTACTCAAAC-TATAT-TATATATATTTCTAACTACTTATTATCCAAATTATTAAC
65 TTTTAAATCCTACTCAAACTTATATATATATATATTTCTAACTACTTATTATCCAAATTATTAAC
46787 GATGATAATAAATATGTATTTTCTTA
130 GATGATAATAAATATGTATTTTCTTA
*
46813 ATTGGCCAACCCAATTT-T-TATATATATTATTATTTATTTATGACTTAATTTTTAGTTTAAAAT
1 ATTGGCCAACCCAATTTCTATATATATATTATTATTTATTTATGACTTAATTTTAAGTTTAAAAT
**
46876 TTTAAATTTTACTCAAACTATATTATATATATATATATATATTTCTAACTACTTATTATCCAAAT
66 TTTAAATCCTACTCAAAC-------T-TATATATATATATATTTCTAACTACTTATTATCCAAAT
*
46941 TATTAACGATGATGATAAATAT
123 TATTAACGATGATAATAAATAT
46963 ATGATTGTTG
Statistics
Matches: 136, Mismatches: 4, Indels: 13
0.89 0.03 0.08
Matches are distributed among these distances:
151 60 0.44
153 1 0.01
154 17 0.12
160 5 0.04
161 53 0.39
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.46
Consensus pattern (155 bp):
ATTGGCCAACCCAATTTCTATATATATATTATTATTTATTTATGACTTAATTTTAAGTTTAAAAT
TTTAAATCCTACTCAAACTTATATATATATATATTTCTAACTACTTATTATCCAAATTATTAACG
ATGATAATAAATATGTATTTTCTTA
Found at i:47657 original size:23 final size:21
Alignment explanation
Indices: 47612--47711 Score: 64
Period size: 22 Copynumber: 4.6 Consensus size: 21
47602 CATTGGGAAT
47612 GTTA-CAAAATTTCATAAGAAG
1 GTTATCAAAATTTCAT-AGAAG
* *
47633 GTTTATTAAAATTTCATAGTTAG
1 G-TTATCAAAATTTCATAG-AAG
*
47656 GTTATCAAAGTTTCATATGGAA-
1 GTTATCAAAATTTCATA--GAAG
* *
47678 TTTATCACAATTTCATAGGTAA-
1 GTTATCAAAATTTCATA-G-AAG
47700 -TTATCAAAATTT
1 GTTATCAAAATTT
47712 TTCATATCGT
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 14 0.22
22 35 0.55
23 14 0.22
24 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGAAG
Found at i:47880 original size:22 final size:22
Alignment explanation
Indices: 47852--48083 Score: 145
Period size: 22 Copynumber: 10.5 Consensus size: 22
47842 TTGCATTGTG
* *
47852 TGGTTATCAAAAGTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
47874 TGGTTATTACAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
* *
47897 -GGTTATCAAAATTGCATTGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
47918 TGGTTACCAAAA-TCCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
*
47940 -AGTTATCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
*
47961 AGGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
47983 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGGA
** * *
48005 TCAAATTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* ** *
48029 AGGTTATTGAAATTTCAAAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* * *
48051 TGGTTATCACAATTTTATAGAAA
1 TGGTTATCAAAATTTCATAG-GA
48074 T-GTTATCAAA
1 TGGTTATCAAA
48084 GAGATTATAA
Statistics
Matches: 160, Mismatches: 37, Indels: 26
0.72 0.17 0.12
Matches are distributed among these distances:
21 19 0.12
22 119 0.74
23 6 0.04
24 16 0.10
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:47968 original size:65 final size:65
Alignment explanation
Indices: 47842--48035 Score: 221
Period size: 65 Copynumber: 2.9 Consensus size: 65
47832 AAGTACGATT
* * * *
47842 TTGCATTGTGTGGTTATCAAAAGTTCATAAGATGGTTATTACAATTTCATGAGG-AGGTTATCAA
1 TTGCATTGTGTGGTTACCAAAAGTTCATAGGA-AGTTATTAAAATTTCAT-AGGAAGGTTATCAA
47906 AA
64 AA
* *
47908 TTGCATTGTGTGGTTACCAAAA-TCCATATGGAAGTTATCAAAATTTCATAGGAAGGTTATCAAA
1 TTGCATTGTGTGGTTACCAAAAGTTCATA-GGAAGTTATTAAAATTTCATAGGAAGGTTATCAAA
47972 A
65 A
* * * * *
47973 TTTCATAGTGTGGTTACCAAAATTTCATAGGATCAAATTATTAAAATTTCTTAGGAAGGTTAT
1 TTGCATTGTGTGGTTACCAAAAGTTCATAGG---AAGTTATTAAAATTTCATAGGAAGGTTAT
48036 TGAAATTTCA
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
64 3 0.03
65 53 0.48
66 28 0.25
68 26 0.24
ACGTcount: A:0.35, C:0.10, G:0.19, T:0.36
Consensus pattern (65 bp):
TTGCATTGTGTGGTTACCAAAAGTTCATAGGAAGTTATTAAAATTTCATAGGAAGGTTATCAAAA
Found at i:48042 original size:68 final size:65
Alignment explanation
Indices: 47849--48074 Score: 206
Period size: 68 Copynumber: 3.4 Consensus size: 65
47839 ATTTTGCATT
* * * ** * * *
47849 GTGTGGTTATCAAAAGTTCATAAGATGGTTATTACAATTTCATGAGG-AGGTTATCAAAATTGCA
1 GTGTGGTTACCAAAATTTCATAGGA-AATTATTAAAATTTC-TTAGGAAGGTTATCAAAATTTCA
*
47913 TT
64 TA
* * * *
47915 GTGTGGTTACCAAAA-TCCATATGGAAGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT
1 GTGTGGTTACCAAAATTTCATA-GGAAATTATTAAAATTTCTTAGGAAGGTTATCAAAATTTCAT
47979 A
65 A
**
47980 GTGTGGTTACCAAAATTTCATAGGATCAAATTATTAAAATTTCTTAGGAAGGTTATTGAAATTTC
1 GTGTGGTTACCAAAATTTCATAGG---AAATTATTAAAATTTCTTAGGAAGGTTATCAAAATTTC
*
48045 AAA
63 ATA
* * *
48048 GTGTGGTTATCACAATTTTATA-GAAAT
1 GTGTGGTTACCAAAATTTCATAGGAAAT
48075 GTTATCAAAG
Statistics
Matches: 134, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
64 7 0.05
65 51 0.38
66 21 0.16
67 1 0.01
68 54 0.40
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (65 bp):
GTGTGGTTACCAAAATTTCATAGGAAATTATTAAAATTTCTTAGGAAGGTTATCAAAATTTCATA
Found at i:48133 original size:22 final size:22
Alignment explanation
Indices: 48108--48231 Score: 103
Period size: 22 Copynumber: 5.6 Consensus size: 22
48098 GTCATAGCAA
48108 GGTTAT-AAGAATTTTATAGTGT
1 GGTTATCAA-AATTTTATAGTGT
** * *
48130 GGTTAAAAAAATTTCATAAG-GA
1 GGTTATCAAAATTTTAT-AGTGT
* * * *
48152 GGTTATTAATATTTTAT-GGGAA
1 GGTTATCAAAATTTTATAGTG-T
*
48174 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTTATAGTGT
48196 GGTTATCAAAAATTTT-TAGTGT
1 GGTTATC-AAAATTTTATAGTGT
48218 GGTTATCAAAATTT
1 GGTTATCAAAATTT
48232 CATATAAAGG
Statistics
Matches: 83, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.01
21 8 0.10
22 61 0.73
23 13 0.16
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.41
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGTGT
Found at i:48155 original size:44 final size:44
Alignment explanation
Indices: 48107--48235 Score: 131
Period size: 44 Copynumber: 2.9 Consensus size: 44
48097 TGTCATAGCA
**
48107 AGGTTATAAGAATTTTATAGTGTGGTTAAAAAAATTTCATAAG-G
1 AGGTTATAA-AATTTTATAGTGTGGTTATCAAAATTTCATAAGTG
* * *
48151 AGGTTATTAATATTTTAT-GGGAAGGTTATCAAAATTTCAT-AGTG
1 AGGTTA-TAAAATTTTATAGTG-TGGTTATCAAAATTTCATAAGTG
*
48195 TGGTTATCAAAAATTTT-TAGTGTGGTTATCAAAATTTCATA
1 AGGTTAT--AAAATTTTATAGTGTGGTTATCAAAATTTCATA
48236 TAAAGGTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
43 5 0.07
44 52 0.75
45 12 0.17
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (44 bp):
AGGTTATAAAATTTTATAGTGTGGTTATCAAAATTTCATAAGTG
Found at i:48243 original size:22 final size:22
Alignment explanation
Indices: 48218--48483 Score: 94
Period size: 22 Copynumber: 11.7 Consensus size: 22
48208 TTTTTAGTGT
48218 GGTTATCAAAATTTCATATAAA
1 GGTTATCAAAATTTCATATAAA
* *
48240 GGTTAT-AAAAGTCTCAATTTCATAA
1 GGTTATCAAAA-TTTC-ATAT-A-AA
* * * *
48265 GGAGTACCAAAATTTGATA-GAA
1 GG-TTATCAAAATTTCATATAAA
* * **
48287 GGTTATC-AAATCTCATAGAGT
1 GGTTATCAAAATTTCATATAAA
* * * *
48308 GATTATCGAAATTTCATAGAGATC
1 GGTTATCAAAATTTCATATA-A-A
*
48332 GGATTATAAAAATTT-ATAGCTAGGAA
1 GG-TTATCAAAATTTCATA--TA--AA
* **
48358 GATTATCAAAATTTCATAGT-GT
1 GGTTATCAAAATTTCATA-TAAA
* * ***
48380 TGTTATCAAAATTTCAAAGCGA
1 GGTTATCAAAATTTCATATAAA
* **
48402 GGTTATCAAAATTTCATAGAGG
1 GGTTATCAAAATTTCATATAAA
* *
48424 GGTCAACAAAATTTCATATAAA
1 GGTTATCAAAATTTCATATAAA
*
48446 GGTTATCAAAATTTCTTA-AAGA
1 GGTTATCAAAATTTCATATAA-A
*
48468 GGTTATCAAATTTTCA
1 GGTTATCAAAATTTCA
48484 AAATGTGATT
Statistics
Matches: 179, Mismatches: 48, Indels: 34
0.69 0.18 0.13
Matches are distributed among these distances:
20 8 0.04
21 15 0.08
22 105 0.59
23 3 0.02
24 5 0.03
25 28 0.16
26 9 0.05
27 6 0.03
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (22 bp):
GGTTATCAAAATTTCATATAAA
Found at i:48244 original size:44 final size:43
Alignment explanation
Indices: 48088--48249 Score: 123
Period size: 44 Copynumber: 3.7 Consensus size: 43
48078 ATCAAAGAGA
* ** *
48088 TTATAAAAATGTCATAGCAAGGTTATAAGAATTTTATAGTGTGG
1 TTATAAAAATTTCATATAAAGGTTATAAAAATTTT-TAGTGTGG
* * * * * *
48132 TTAAAAAAATTTCATA-AGGAGGTTATTAATA-TTTTATGGGAAGG
1 TTATAAAAATTTCATATA-AAGGTTATAAAAATTTTTA-GTG-TGG
* **
48176 TTATCAAAATTTCATAGT-GTGGTTATCAAAAATTTTTAGTGTGG
1 TTATAAAAATTTCATA-TAAAGGTTAT-AAAAATTTTTAGTGTGG
*
48220 TTATCAAAATTTCATATAAAGGTTATAAAA
1 TTATAAAAATTTCATATAAAGGTTATAAAA
48250 GTCTCAATTT
Statistics
Matches: 92, Mismatches: 18, Indels: 17
0.72 0.14 0.13
Matches are distributed among these distances:
42 2 0.02
43 10 0.11
44 70 0.76
45 5 0.05
46 5 0.05
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (43 bp):
TTATAAAAATTTCATATAAAGGTTATAAAAATTTTTAGTGTGG
Found at i:48410 original size:44 final size:44
Alignment explanation
Indices: 48360--48508 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 44
48350 GCTAGGAAGA
* ** **
48360 TTATCAAAATTTCATAGTGTTGTTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCAAAAAGAGG
* * * *
48404 TTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATATAA-AGG
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCA-AAAAGAGG
* * * * * *
48448 TTATCAAAATTTCTTAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCAAAAAGAGG
*
48492 TTACCAAAATTTCATAG
1 TTATCAAAATTTCATAG
48509 TGGTATTTCT
Statistics
Matches: 82, Mismatches: 21, Indels: 4
0.77 0.20 0.04
Matches are distributed among these distances:
43 2 0.02
44 79 0.96
45 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCAAAAAGAGG
Found at i:48634 original size:22 final size:22
Alignment explanation
Indices: 48607--48750 Score: 105
Period size: 22 Copynumber: 6.5 Consensus size: 22
48597 TGAGGGATGA
48607 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
48629 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
48651 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
48673 TATCAGAATTTCATAGGACGAT
1 TATCAAAATTTCATATGAAGGT
*
48695 TAACAAAATTTTACA-ATG-AGGT
1 TATCAAAA-TTT-CATATGAAGGT
** * *
48717 TATCAAAAAATCATAGGGTAGGT
1 TATCAAAATTTCATA-TGAAGGT
48740 TATCAAAATTT
1 TATCAAAATTT
48751 GTATTTATTT
Statistics
Matches: 92, Mismatches: 23, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 66 0.72
23 20 0.22
24 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:48799 original size:23 final size:23
Alignment explanation
Indices: 48772--48853 Score: 96
Period size: 22 Copynumber: 3.7 Consensus size: 23
48762 GATTTCATTA
*
48772 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAGGGAGGTTT
* *
48795 ATCAAAATTTTA-AGGAAGGTTT
1 ATCAAAATTTCATAGGGAGGTTT
* *
48817 ATCAAAATTTCATAGCGA-GATT
1 ATCAAAATTTCATAGGGAGGTTT
*
48839 ATCACAATTTCATAG
1 ATCAAAATTTCATAG
48854 TGTGATTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 37 0.71
23 15 0.29
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (23 bp):
ATCAAAATTTCATAGGGAGGTTT
Found at i:48840 original size:22 final size:21
Alignment explanation
Indices: 48772--49008 Score: 86
Period size: 22 Copynumber: 10.7 Consensus size: 21
48762 GATTTCATTA
* *
48772 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-GGA-GATT
* *
48795 ATCAAAATTTTA-AGGAAGGTTT
1 ATCAAAATTTCATAGG-A-GATT
48817 ATCAAAATTTCATAGCGAGATT
1 ATCAAAATTTCATAG-GAGATT
* *
48839 ATCACAATTTCATAGTGTGATT
1 ATCAAAATTTCATAG-GAGATT
* * *
48861 ATCAAGATTTCAGAGTGTGATT
1 ATCAAAATTTCATAG-GAGATT
48883 A-CTAACAA-TTCATATGGAGATT
1 ATC-AA-AATTTCATA-GGAGATT
* * * * * *
48905 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCAT-AGGAGATT
* * *
48927 ATCAATATATCATATGGAGATG
1 ATCAAAATTTCATA-GGAGATT
* * * *
48949 ATCAACATCTCATAGTGTTGGTT
1 ATCAAAATTTCATAG-G-AGATT
* *
48972 ATCAAAATTTTATTGG-GAAGTT
1 ATCAAAATTTCATAGGAG-A-TT
48994 ATCAAAATTTCATAG
1 ATCAAAATTTCATAG
49009 TGAGGTCTTC
Statistics
Matches: 162, Mismatches: 38, Indels: 29
0.71 0.17 0.13
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 123 0.76
23 31 0.19
24 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGATT
Found at i:56008 original size:2 final size:2
Alignment explanation
Indices: 55996--56063 Score: 77
Period size: 2 Copynumber: 34.5 Consensus size: 2
55986 ATTATACTTT
* * *
55996 TA TA T- TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TCC TC
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
*
56038 CA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
56064 CTAAAACTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.04
2 54 0.95
3 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.