Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014754.1 Corchorus capsularis cultivar CVL-1 contig14775, 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: 67627
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:69 original size:22 final size:22
Alignment explanation
Indices: 18--246 Score: 157
Period size: 22 Copynumber: 10.4 Consensus size: 22
8 AGGAGTAGCA
*
18 AAAATTTGATAGAAG-G-TTATC
1 AAAATTTCATA-AAGTGATTATC
*
39 -AAATCTCATAAAGTGATTATC
1 AAAATTTCATAAAGTGATTATC
* *
60 GAAATTTCATAGAGATCGGATTATC
1 AAAATTTCATAAAG-T--GATTATC
85 AAAATTT-ATAGAAG-GATTATC
1 AAAATTTCATA-AAGTGATTATC
** *
106 AAAATTTCATAGTGTTATTATC
1 AAAATTTCATAAAGTGATTATC
*
128 AAAATTTC--AAAGCGAGGTTATC
1 AAAATTTCATAAAGTGA--TTATC
* *
150 AAAATTACATAATGTGATTATC
1 AAAATTTCATAAAGTGATTATC
* * * * *
172 AGAATTTCATAAAGGGGTCAAC
1 AAAATTTCATAAAGTGATTATC
* * *
194 AAAATTTTATAAAGAGGTTATC
1 AAAATTTCATAAAGTGATTATC
* *
216 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAAAGTGATTATC
*
238 AAATTTTCA
1 AAAATTTCA
247 AACAAAATTT
Statistics
Matches: 165, Mismatches: 30, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.02
20 12 0.07
21 20 0.12
22 106 0.64
23 1 0.01
24 8 0.05
25 15 0.09
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (22 bp):
AAAATTTCATAAAGTGATTATC
Found at i:253 original size:34 final size:34
Alignment explanation
Indices: 215--280 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
205 AAGAGGTTAT
*
215 CAAAATTTCATAAAGAGGTTATCAAATTTTCAAA
1 CAAAATTTCATAAAGAGGTTATCAAAATTTCAAA
*
249 CAAAATTTTATAAAGAGGTTATCAAAATTTCA
1 CAAAATTTCATAAAGAGGTTATCAAAATTTCA
281 TAAAGAGGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (34 bp):
CAAAATTTCATAAAGAGGTTATCAAAATTTCAAA
Found at i:277 original size:56 final size:56
Alignment explanation
Indices: 191--304 Score: 228
Period size: 56 Copynumber: 2.0 Consensus size: 56
181 TAAAGGGGTC
191 AACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 AACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
247 AACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 AACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
303 AA
1 AA
305 ATGTGATTAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 58 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (56 bp):
AACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
Found at i:299 original size:21 final size:22
Alignment explanation
Indices: 249--302 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
239 AATTTTCAAA
*
249 CAAAATTTTATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
271 CAAAATTTCATAAAGAGGTTAT
1 CAAAATTTCATAAAGAGGTTAT
*
293 CAAATTTTCA
1 CAAAATTTCA
303 AAATGTGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
CAAAATTTCATAAAGAGGTTAT
Found at i:324 original size:78 final size:78
Alignment explanation
Indices: 174--324 Score: 189
Period size: 78 Copynumber: 1.9 Consensus size: 78
164 TGATTATCAG
* * *
174 AATTTCATAAAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCA
1 AATTTCATAAAGAGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAGAGATTATCA
*
239 AATTTTCAAACAA
66 AAATTTCAAACAA
* * * * *
252 AATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA-AAATGTGATTA-C
1 AATTTCATAAAGAGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAA-GAGATTATC
315 AAAAATTTCA
65 -AAAATTTCA
325 TAGTGGTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 4 0.06
78 58 0.94
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (78 bp):
AATTTCATAAAGAGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAGAGATTATCA
AAATTTCAAACAA
Found at i:456 original size:22 final size:22
Alignment explanation
Indices: 428--921 Score: 128
Period size: 22 Copynumber: 22.6 Consensus size: 22
418 CAACGAGGAA
* *
428 ATCAAAATTCCATATGAAGGTT
1 ATCAAAATTTCATATGTAGGTT
*
450 ATCAAAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATA-TGTAGGTT
* * *
472 TTCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATGTAGGT-T
* * *
494 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATATGTAGGTT
*
516 AACAAAATTTCATAATG-AGGTT
1 ATCAAAATTTCAT-ATGTAGGTT
538 ATCAAAA--T--T-TGTA-GTT
1 ATCAAAATTTCATATGTAGGTT
* * * *
554 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCATATGTAGGTT
* * * *
576 ATCAAAATTTTATAGGGAGATTT
1 ATCAAAATTTCATATGTAG-GTT
* * * *
599 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATATGTAG-GTT
* *
622 ATCAAAATTTCATA-GCGAAGTT
1 ATCAAAATTTCATATG-TAGGTT
* * *
644 ATCACAATTTCATGGTGT-GATT
1 ATCAAAATTTCAT-ATGTAGGTT
* *
666 ATCAAAATTTCAGAGTGTA-ATT
1 ATCAAAATTTCATA-TGTAGGTT
* *
688 A-CTAACAATTT-AGATGGAGGTT
1 ATC-AA-AATTTCATATGTAGGTT
* * * **
710 TTTAAATTTTCATA-ACATGGTT
1 ATCAAAATTTCATATGTA-GGTT
* * *
732 ATCAACATATCATAGTGTTGGTT
1 ATCAAAATTTCATA-TGTAGGTT
* *
755 ATCAAAATTTCAT-TGGAAAGTT
1 ATCAAAATTTCATAT-GTAGGTT
*
777 ATCAAAATTTCACAT-TGAGGTCT
1 ATCAAAATTTCATATGT-AGGT-T
* * * *
800 -TCAAAATTCCTTAGGGAGGTT
1 ATCAAAATTTCATATGTAGGTT
* * * * * *
821 ACCCAAATTTTATAAGAAGATT
1 ATCAAAATTTCATATGTAGGTT
** ***
843 AAAAAAATTT-ATAAAAAGGTT
1 ATCAAAATTTCATATGTAGGTT
* * **
864 CTAAAAATTTCATA-GTATCATT
1 ATCAAAATTTCATATGTA-GGTT
* * *
886 ATTAAAATTTCATAGGAAGGTT
1 ATCAAAATTTCATATGTAGGTT
908 ATCAAAATTTCATA
1 ATCAAAATTTCATA
922 ATGGGATCAT
Statistics
Matches: 346, Mismatches: 91, Indels: 70
0.68 0.18 0.14
Matches are distributed among these distances:
16 11 0.03
17 1 0.00
18 2 0.01
20 4 0.01
21 33 0.10
22 225 0.65
23 69 0.20
24 1 0.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (22 bp):
ATCAAAATTTCATATGTAGGTT
Found at i:542 original size:44 final size:45
Alignment explanation
Indices: 428--656 Score: 164
Period size: 44 Copynumber: 5.3 Consensus size: 45
418 CAACGAGGAA
* **
428 ATCAAAATTCCAT-ATGAAGGTTATCAAAATTTCATAGTTTAG-TT
1 ATCAAAATTTCATAATGAAGGTTATCAAAATTTCATAG-GGAGATT
* *
472 TTCAAAATTTCATAGTATGTA-G--ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATA--ATGAAGGTTATCAAAATTTCATAGGGAGATT
* *
516 AACAAAATTTCATAATG-AGGTTATCAAAA-TT--T--GTAG-TT
1 ATCAAAATTTCATAATGAAGGTTATCAAAATTTCATAGGGAGATT
* * *
554 ATCAAGATTTCATAA-GAAAGTTATCAAAATTTTATAGGGAGATTT
1 ATCAAAATTTCATAATGAAGGTTATCAAAATTTCATAGGGAGA-TT
* * * *
599 ATCAAAATTTTAT-AGGAAGATTTATCAAAATTTCATAGCGA-AGTT
1 ATCAAAATTTCATAATGAAG-GTTATCAAAATTTCATAGGGAGA-TT
*
644 ATCACAATTTCAT
1 ATCAAAATTTCAT
657 GGTGTGATTA
Statistics
Matches: 147, Mismatches: 21, Indels: 33
0.73 0.10 0.16
Matches are distributed among these distances:
37 1 0.01
38 26 0.18
39 5 0.03
41 3 0.02
42 4 0.03
43 7 0.05
44 48 0.33
45 30 0.20
46 19 0.13
47 4 0.03
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (45 bp):
ATCAAAATTTCATAATGAAGGTTATCAAAATTTCATAGGGAGATT
Found at i:3300 original size:2 final size:2
Alignment explanation
Indices: 3235--3286 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
3225 CAATTGCCTT
* *
3235 TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TT TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3276 TA TA T- TA TA TA
1 TA TA TA TA TA TA
3287 CACTTACTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3337 original size:12 final size:12
Alignment explanation
Indices: 3316--3359 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
3306 TCTCTCTATA
*
3316 TATATATATATC
1 TATATCTATATC
3328 TATATCTATATC
1 TATATCTATATC
3340 TATATC--TATC
1 TATATCTATATC
3350 TATA-CTATAT
1 TATATCTATAT
3360 TAAAAAGTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
9 1 0.03
10 8 0.28
11 3 0.10
12 17 0.59
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (12 bp):
TATATCTATATC
Found at i:3529 original size:70 final size:70
Alignment explanation
Indices: 3447--3679 Score: 288
Period size: 70 Copynumber: 3.2 Consensus size: 70
3437 CTGTTTAGGT
* *
3447 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTACAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTACAATT
3511 ATTTTA
65 ATTTTA
3517 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-AC-A
*
3582 TTATATTTTACCA
62 AT-TATTTT---A
* * * * *
3595 TTTTACTATTTTACTCAGCTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTACAATTA
*
3660 TTATA
66 TTTTA
*
3665 TTTTACAATTTTACT
1 TTTTACTATTTTACT
3680 ATTTTAGTTA
Statistics
Matches: 143, Mismatches: 11, Indels: 18
0.83 0.06 0.10
Matches are distributed among these distances:
70 64 0.45
71 5 0.03
72 1 0.01
73 7 0.05
74 3 0.02
75 7 0.05
76 1 0.01
77 2 0.01
78 53 0.37
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTACAATTA
TTTTA
Found at i:3529 original size:78 final size:77
Alignment explanation
Indices: 3447--3685 Score: 350
Period size: 78 Copynumber: 3.2 Consensus size: 77
3437 CTGTTTAGGT
* *
3447 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-AC-
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
3507 AAT-TATTTT--A
65 ATTATATTTTACA
3517 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
3582 TTATATTTTACCA
66 TTATATTTTA-CA
* *
3595 TTTTACTATTTTACTCAGCTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
3660 TTATATTTTACAA
66 TTATATTTTAC-A
3673 TTTTACTATTTTA
1 TTTTACTATTTTA
3686 GTTAAAAAAA
Statistics
Matches: 154, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 49 0.32
71 5 0.03
72 1 0.01
73 2 0.01
74 2 0.01
75 6 0.04
77 1 0.01
78 88 0.57
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACA
Found at i:8366 original size:298 final size:298
Alignment explanation
Indices: 7830--8425 Score: 1138
Period size: 298 Copynumber: 2.0 Consensus size: 298
7820 AGTGTGTCCA
*
7830 TACTATTTGTTTTCTAGCTGCTAGTCGCTTTAATCTCCAAATCATTAATCCCACTAACATCTTCA
1 TACTATTTGTTTTCTAGATGCTAGTCGCTTTAATCTCCAAATCATTAATCCCACTAACATCTTCA
7895 AGTTTTCTTCTAATCTTCAAAATTCTGTCTTAACTTGAGTATTCTTCCAATCTCCTTGGTTGATT
66 AGTTTTCTTCTAATCTTCAAAATTCTGTCTTAACTTGAGTATTCTTCCAATCTCCTTGGTTGATT
*
7960 ACTCAACTTTAATTCTGATCTTTGCCTTCTAGAATTGCTTCCTTTGGTTTCAAATGGTCTTTCCT
131 ACTCAACTTTAATTCTGATCTTTGCCTTCTAGAATTGCTTCCTTTGGCTTCAAATGGTCTTTCCT
8025 TGAGACTTTGAGCTCTTCATGCGCCTAAGGCTATGTGGCATCCTTCTACATTAGTGTCATTGATG
196 TGAGACTTTGAGCTCTTCATGCGCCTAAGGCTATGTGGCATCCTTCTACATTAGTGTCATTGATG
8090 AAGCTTTCTTTTTAAGAGTCTTCAATGCTCAACCTTTC
261 AAGCTTTCTTTTTAAGAGTCTTCAATGCTCAACCTTTC
* * *
8128 TACTATTTGTTTTCTAGATGCTAGTCGCTTTAATCTCCAGATCATTGATCCCACTAACATCTTCC
1 TACTATTTGTTTTCTAGATGCTAGTCGCTTTAATCTCCAAATCATTAATCCCACTAACATCTTCA
*
8193 AGTTTTCTTCTAATCTTCAAAATTCTGTCTTGACTTGAGTATTCTTCCAATCTCCTTGGTTGATT
66 AGTTTTCTTCTAATCTTCAAAATTCTGTCTTAACTTGAGTATTCTTCCAATCTCCTTGGTTGATT
8258 ACTCAACTTTAATTCTGATCTTTGCCTTCTAGAATTGCTTCCTTTGGCTTCAAATGGTCTTTCCT
131 ACTCAACTTTAATTCTGATCTTTGCCTTCTAGAATTGCTTCCTTTGGCTTCAAATGGTCTTTCCT
8323 TGAGACTTTGAGCTCTTCATGCGCCTAAGGCTATGTGGCATCCTTCTACATTAGTGTCATTGATG
196 TGAGACTTTGAGCTCTTCATGCGCCTAAGGCTATGTGGCATCCTTCTACATTAGTGTCATTGATG
8388 AAGCTTTCTTTTTAAGAGTCTTCAATGCTCAACCTTTC
261 AAGCTTTCTTTTTAAGAGTCTTCAATGCTCAACCTTTC
8426 AACTGTTAAA
Statistics
Matches: 292, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
298 292 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (298 bp):
TACTATTTGTTTTCTAGATGCTAGTCGCTTTAATCTCCAAATCATTAATCCCACTAACATCTTCA
AGTTTTCTTCTAATCTTCAAAATTCTGTCTTAACTTGAGTATTCTTCCAATCTCCTTGGTTGATT
ACTCAACTTTAATTCTGATCTTTGCCTTCTAGAATTGCTTCCTTTGGCTTCAAATGGTCTTTCCT
TGAGACTTTGAGCTCTTCATGCGCCTAAGGCTATGTGGCATCCTTCTACATTAGTGTCATTGATG
AAGCTTTCTTTTTAAGAGTCTTCAATGCTCAACCTTTC
Found at i:15181 original size:35 final size:36
Alignment explanation
Indices: 15135--15334 Score: 230
Period size: 35 Copynumber: 5.7 Consensus size: 36
15125 TAAGCCATTT
* ***
15135 ATTTACTTAATTACATCGAATTAAGC-CAATTATTG
1 ATTTACTTAATTACACCGAATTAAGCTCAATTACCA
*
15170 ATTTACTTAATTACACCGAATTAA-CTTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGCTCAATTACCA
**
15205 ATTTACTTAATTACACCGAATTAAG-TTGATTACCA
1 ATTTACTTAATTACACCGAATTAAGCTCAATTACCA
* *
15240 AATTACTTAATTACACCGAATTAAG-TTAATTACCA
1 ATTTACTTAATTACACCGAATTAAGCTCAATTACCA
* * * *
15275 ATTTGCTTAATCACACCGAATTAAG-TTATTTACCA
1 ATTTACTTAATTACACCGAATTAAGCTCAATTACCA
**
15310 AACTACTTAATTACACCGAATTAAG
1 ATTTACTTAATTACACCGAATTAAG
15335 TTGATTACCA
Statistics
Matches: 147, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
34 1 0.01
35 146 0.99
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (36 bp):
ATTTACTTAATTACACCGAATTAAGCTCAATTACCA
Found at i:15215 original size:70 final size:70
Alignment explanation
Indices: 15135--15383 Score: 298
Period size: 70 Copynumber: 3.7 Consensus size: 70
15125 TAAGCCATTT
* ** *** * *
15135 ATTTACTTAATTACATCGAATTAAGCCAATTATTGATTTACTTAATTACACCGAATTAACTTAAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTAAT
15200 TACCA
66 TACCA
*
15205 ATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTACACCGAATTAAGTTAAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTAAT
15270 TACCA
66 TACCA
* * * * *
15275 ATTTGCTTAATCACACCGAATTAAGTTATTTACCAAACTACTTAATTACACCGAATTAAGTTGAT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTAAT
15340 TACC-
66 TACCA
* *
15344 ----A---AATTACACCGAATTAAGTTGATTACCAAACTACTTAATT
1 ATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACTTAATT
15384 TAATTACAAA
Statistics
Matches: 160, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
62 36 0.22
70 124 0.77
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (70 bp):
ATTTACTTAATTACACCGAATTAAGTTAATTACCAAATTACTTAATTACACCGAATTAAGTTAAT
TACCA
Found at i:15262 original size:105 final size:105
Alignment explanation
Indices: 15137--15350 Score: 320
Period size: 105 Copynumber: 2.0 Consensus size: 105
15127 AGCCATTTAT
* *** *
15137 TTACTTAATTACATCGAATTAAGCCAATTATTGATTTACTTAATTACACCGAATTAACTTAATTA
1 TTACTTAATTACACCGAATTAAGCCAATTACCAATTTACTTAATCACACCGAATTAACTTAATTA
**
15202 CCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAA
66 CCAAACTACTTAATTACACCGAATTAAGTTGATTACCAAA
** * * *
15242 TTACTTAATTACACCGAATTAAGTTAATTACCAATTTGCTTAATCACACCGAATTAAGTTATTTA
1 TTACTTAATTACACCGAATTAAGCCAATTACCAATTTACTTAATCACACCGAATTAACTTAATTA
15307 CCAAACTACTTAATTACACCGAATTAAGTTGATTACCAAA
66 CCAAACTACTTAATTACACCGAATTAAGTTGATTACCAAA
15347 TTAC
1 TTAC
15351 ACCGAATTAA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 97 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (105 bp):
TTACTTAATTACACCGAATTAAGCCAATTACCAATTTACTTAATCACACCGAATTAACTTAATTA
CCAAACTACTTAATTACACCGAATTAAGTTGATTACCAAA
Found at i:15335 original size:35 final size:35
Alignment explanation
Indices: 15173--15383 Score: 260
Period size: 35 Copynumber: 6.3 Consensus size: 35
15163 ATTATTGATT
* * **
15173 TACTTAATTACACCGAATTAACTTAATTACCAATT
1 TACTTAATTACACCGAATTAAGTTGATTACCAAAC
*
15208 TACTTAATTACACCGAATTAAGTTGATTACCAAAT
1 TACTTAATTACACCGAATTAAGTTGATTACCAAAC
* **
15243 TACTTAATTACACCGAATTAAGTTAATTACCAATT
1 TACTTAATTACACCGAATTAAGTTGATTACCAAAC
* *
15278 TGCTTAATCACACCGAATTAAGTT-ATTTACCAAAC
1 TACTTAATTACACCGAATTAAGTTGA-TTACCAAAC
15313 TACTTAATTACACCGAATTAAGTTGATTA-C---C
1 TACTTAATTACACCGAATTAAGTTGATTACCAAAC
15344 -A---AATTACACCGAATTAAGTTGATTACCAAAC
1 TACTTAATTACACCGAATTAAGTTGATTACCAAAC
15375 TACTTAATT
1 TACTTAATT
15384 TAATTACAAA
Statistics
Matches: 155, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
27 24 0.15
28 1 0.01
30 1 0.01
31 2 0.01
32 1 0.01
34 2 0.01
35 123 0.79
36 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (35 bp):
TACTTAATTACACCGAATTAAGTTGATTACCAAAC
Found at i:15356 original size:27 final size:27
Alignment explanation
Indices: 15318--15373 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
15308 CAAACTACTT
15318 AATTACACCGAATTAAGTTGATTACCA
1 AATTACACCGAATTAAGTTGATTACCA
15345 AATTACACCGAATTAAGTTGATTACCA
1 AATTACACCGAATTAAGTTGATTACCA
15372 AA
1 AA
15374 CTACTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (27 bp):
AATTACACCGAATTAAGTTGATTACCA
Found at i:15389 original size:21 final size:21
Alignment explanation
Indices: 15365--15404 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
15355 AATTAAGTTG
15365 ATTACCAAA-CTACTTAATTTA
1 ATTA-CAAATCTACTTAATTTA
*
15386 ATTACAAATTTACTTAATT
1 ATTACAAATCTACTTAATT
15405 ACACCGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTACAAATCTACTTAATTTA
Found at i:15425 original size:35 final size:35
Alignment explanation
Indices: 15386--15460 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
15376 ACTTAATTTA
* * *
15386 ATTACAAATTTACTTAATTACACCGAATTATGTTG
1 ATTACAAATTCACTTAATTACACCGAATTAAGCTG
*
15421 ATTACCAATTCACTTAATTACACCGAATTAAGCTG
1 ATTACAAATTCACTTAATTACACCGAATTAAGCTG
15456 ATTAC
1 ATTAC
15461 TGATTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (35 bp):
ATTACAAATTCACTTAATTACACCGAATTAAGCTG
Found at i:16649 original size:35 final size:35
Alignment explanation
Indices: 16609--16679 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
16599 CACAAATGAA
16609 CCCTCCGAATAAAACCTAAGTCTCTGAAACCTTCG
1 CCCTCCGAATAAAACCTAAGTCTCTGAAACCTTCG
16644 CCCTCCGAATAAAACCTAAGTCTCTGAAACCTTCG
1 CCCTCCGAATAAAACCTAAGTCTCTGAAACCTTCG
16679 C
1 C
16680 TTCTTCCCTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.31, C:0.35, G:0.11, T:0.23
Consensus pattern (35 bp):
CCCTCCGAATAAAACCTAAGTCTCTGAAACCTTCG
Found at i:18735 original size:40 final size:40
Alignment explanation
Indices: 18680--18755 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
18670 CTGCATGGAA
18680 TCATGGACCATGCGAATGCAATTAAATTATACCAATTATT
1 TCATGGACCATGCGAATGCAATTAAATTATACCAATTATT
*
18720 TCATGGACCATGCGAATGCAATTAAATTATGCCAAT
1 TCATGGACCATGCGAATGCAATTAAATTATACCAAT
18756 GCGAATATGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.30
Consensus pattern (40 bp):
TCATGGACCATGCGAATGCAATTAAATTATACCAATTATT
Found at i:18962 original size:22 final size:23
Alignment explanation
Indices: 18921--18963 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
18911 ATAAGCTATG
18921 CTAAATGCCAAAGAGTGAATTTA
1 CTAAATGCCAAAGAGTGAATTTA
18944 CTAAATGCCAAA-AGTGAATT
1 CTAAATGCCAAAGAGTGAATT
18964 AGAAAATGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (23 bp):
CTAAATGCCAAAGAGTGAATTTA
Found at i:19930 original size:20 final size:22
Alignment explanation
Indices: 19887--19932 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
19877 TTGCCATAGA
*
19887 TTTAGATTTAATTTACTTTGTT
1 TTTAGATTTAATTTACTTTCTT
*
19909 TTTAG-TTTAA-TTGCTTTCTT
1 TTTAGATTTAATTTACTTTCTT
19929 TTTA
1 TTTA
19933 ATTGATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 5 0.23
22 5 0.23
ACGTcount: A:0.20, C:0.07, G:0.09, T:0.65
Consensus pattern (22 bp):
TTTAGATTTAATTTACTTTCTT
Found at i:26230 original size:22 final size:23
Alignment explanation
Indices: 26205--26252 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
26195 AAAAAGCAAT
* *
26205 TAAATAAAAGTAAAGTAAAA-AC
1 TAAATAAAACTAAACTAAAATAC
*
26227 TAAATTAAACTAAACTAAAATAC
1 TAAATAAAACTAAACTAAAATAC
26250 TAA
1 TAA
26253 TTAAGAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.65, C:0.08, G:0.04, T:0.23
Consensus pattern (23 bp):
TAAATAAAACTAAACTAAAATAC
Found at i:27217 original size:17 final size:17
Alignment explanation
Indices: 27195--27228 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
27185 GAAAATAGAG
27195 AAAACCCGAAGTCTGGC
1 AAAACCCGAAGTCTGGC
27212 AAAACCCGAAGTCTGGC
1 AAAACCCGAAGTCTGGC
27229 CCAAGACAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.29, G:0.24, T:0.12
Consensus pattern (17 bp):
AAAACCCGAAGTCTGGC
Found at i:27669 original size:12 final size:12
Alignment explanation
Indices: 27652--27676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27642 GTCTTCAATC
27652 ACGCATATTTTT
1 ACGCATATTTTT
27664 ACGCATATTTTT
1 ACGCATATTTTT
27676 A
1 A
27677 TAGCTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (12 bp):
ACGCATATTTTT
Found at i:58093 original size:22 final size:22
Alignment explanation
Indices: 58065--58109 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
58055 TTTCCCACAA
* *
58065 CAAGTCCTGAGTAGGAGTTGTC
1 CAAGTCCTGAGCAGGACTTGTC
*
58087 CAAGTCCTGGGCAGGACTTGTC
1 CAAGTCCTGAGCAGGACTTGTC
58109 C
1 C
58110 TACAATTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (22 bp):
CAAGTCCTGAGCAGGACTTGTC
Found at i:61654 original size:12 final size:12
Alignment explanation
Indices: 61633--61665 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
61623 TCAATTGCAG
*
61633 CAAAAGCTTTCC
1 CAAAATCTTTCC
61645 CAAAATCTTTCC
1 CAAAATCTTTCC
61657 CAAAATCTT
1 CAAAATCTT
61666 AAAACAACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.30
Consensus pattern (12 bp):
CAAAATCTTTCC
Found at i:65833 original size:12 final size:13
Alignment explanation
Indices: 65803--65844 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
65793 TTTATTACCG
65803 TTTTATTAATATG-
1 TTTTATTAA-ATGA
65816 TTTTA-TAAATGA
1 TTTTATTAAATGA
65828 TTTTATTAAATGA
1 TTTTATTAAATGA
65841 TTTT
1 TTTT
65845 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.11
12 8 0.30
13 16 0.59
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (13 bp):
TTTTATTAAATGA
Found at i:66888 original size:33 final size:33
Alignment explanation
Indices: 66754--66975 Score: 169
Period size: 33 Copynumber: 6.6 Consensus size: 33
66744 CACAATTATA
* *
66754 TGACACCAGAAGTTGTCATGATAAATCTCCAAC
1 TGACACCAGAAGTTGTCATGATAAATCTTCAAT
* ** * * * * *
66787 TGACATCTTAAGTTGTCAAGATTTTACTTTGTCATT
1 TGACACCAGAAGTTGTCATGA--TAAATCT-TCAAT
*
66823 TGACACCAGAAGTTGTCATGAT-AATCTCCAAT
1 TGACACCAGAAGTTGTCATGATAAATCTTCAAT
*
66855 TGACACGAGAAGTTGTCATGATAAATCTTCAAT
1 TGACACCAGAAGTTGTCATGATAAATCTTCAAT
* * * ** *
66888 TAACACCTGAAGTTGTCATAATTTTACTTTTTCAAT
1 TGACACCAGAAGTTGTCATGA---TAAATCTTCAAT
** *
66924 TGACACTGGAAGTTGTCATAATAAAT-TTCCAAT
1 TGACACCAGAAGTTGTCATGATAAATCTT-CAAT
*
66957 TGACACCTGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
66976 AATTTTACTT
Statistics
Matches: 147, Mismatches: 34, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
32 26 0.18
33 70 0.48
34 1 0.01
35 4 0.03
36 46 0.31
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
TGACACCAGAAGTTGTCATGATAAATCTTCAAT
Found at i:66901 original size:101 final size:102
Alignment explanation
Indices: 66754--66975 Score: 304
Period size: 101 Copynumber: 2.2 Consensus size: 102
66744 CACAATTATA
* * *
66754 TGACACCAGAAGTTGTCATGATAAATCTCCAACTGACATCTTAAGTTGTCA-AGATTTTACTTTG
1 TGACACCAGAAGTTGTCATGATAAATCTCCAACTAACACCTGAAGTTGTCATA-ATTTTACTTTG
* *
66818 TCATTTGACACCAGAAGTTGTCATGAT-AATCTCCAAT
65 TCAATTGACACCAGAAGTTGTCATAATAAATCTCCAAT
* * * *
66855 TGACACGAGAAGTTGTCATGATAAATCTTCAATTAACACCTGAAGTTGTCATAATTTTACTTTTT
1 TGACACCAGAAGTTGTCATGATAAATCTCCAACTAACACCTGAAGTTGTCATAATTTTACTTTGT
** *
66920 CAATTGACACTGGAAGTTGTCATAATAAATTTCCAAT
66 CAATTGACACCAGAAGTTGTCATAATAAATCTCCAAT
*
66957 TGACACCTGAAGTTGTCAT
1 TGACACCAGAAGTTGTCAT
66976 AATTTTACTT
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
101 78 0.74
102 27 0.26
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (102 bp):
TGACACCAGAAGTTGTCATGATAAATCTCCAACTAACACCTGAAGTTGTCATAATTTTACTTTGT
CAATTGACACCAGAAGTTGTCATAATAAATCTCCAAT
Found at i:66936 original size:36 final size:35
Alignment explanation
Indices: 66882--67050 Score: 164
Period size: 36 Copynumber: 4.7 Consensus size: 35
66872 ATGATAAATC
*
66882 TTCAATTAACACCTGAAGTTGTCATAATTTTACTTT
1 TTCAATTGACA-CTGAAGTTGTCATAATTTTACTTT
**
66918 TTCAATTGACACTGGAAGTTGTCATAA---TAAATT
1 TTCAATTGACACT-GAAGTTGTCATAATTTTACTTT
*
66951 TCCAATTGACACCTGAAGTTGTCATAATTTTACTTT
1 TTCAATTGACA-CTGAAGTTGTCATAATTTTACTTT
* * ** *
66987 TTTAATTAACACTTGAAAATGTCATAATTTTATTTTT
1 TTCAATTGACAC-TGAAGTTGTCATAATTTTA-CTTT
* *
67024 TTCAATTGACGCAAGAAGTTGTCATAA
1 TTCAATTGACAC-TGAAGTTGTCATAA
67051 CGATATTTGA
Statistics
Matches: 107, Mismatches: 19, Indels: 13
0.77 0.14 0.09
Matches are distributed among these distances:
33 27 0.25
34 2 0.02
35 3 0.03
36 52 0.49
37 23 0.21
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.41
Consensus pattern (35 bp):
TTCAATTGACACTGAAGTTGTCATAATTTTACTTT
Found at i:66937 original size:69 final size:70
Alignment explanation
Indices: 66851--66999 Score: 232
Period size: 69 Copynumber: 2.2 Consensus size: 70
66841 TGATAATCTC
*
66851 CAATTGACAC-GAGAAGTTGTCATGATAAATCTT-CAATTAACACCTGAAGTTGTCATAATTTTA
1 CAATTGACACTGAGAAGTTGTCATAATAAAT-TTCCAATTAACACCTGAAGTTGTCATAATTTTA
66914 CTTTTT
65 CTTTTT
*
66920 CAATTGACACTG-GAAGTTGTCATAATAAATTTCCAATTGACACCTGAAGTTGTCATAATTTTAC
1 CAATTGACACTGAGAAGTTGTCATAATAAATTTCCAATTAACACCTGAAGTTGTCATAATTTTAC
66984 TTTTT
66 TTTTT
* *
66989 TAATTAACACT
1 CAATTGACACT
67000 TGAAAATGTC
Statistics
Matches: 74, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
68 2 0.03
69 71 0.96
70 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (70 bp):
CAATTGACACTGAGAAGTTGTCATAATAAATTTCCAATTAACACCTGAAGTTGTCATAATTTTAC
TTTTT
Found at i:67010 original size:69 final size:69
Alignment explanation
Indices: 66868--67014 Score: 215
Period size: 69 Copynumber: 2.1 Consensus size: 69
66858 CACGAGAAGT
* *
66868 TGTCATGATAAATCTTCAATTAACACCTGAAGTTGTCATAATTTTACTTTTTCAATTGACACTGG
1 TGTCATAATAAATCTTCAATTAACACCTGAAGTTGTCATAATTTTACTTTTTCAATTAACACTGG
**
66933 AAGT
66 AAAA
* * *
66937 TGTCATAATAAAT-TTCCAATTGACACCTGAAGTTGTCATAATTTTACTTTTTTAATTAACACTT
1 TGTCATAATAAATCTT-CAATTAACACCTGAAGTTGTCATAATTTTACTTTTTCAATTAACACTG
67001 GAAAA
65 GAAAA
67006 TGTCATAAT
1 TGTCATAAT
67015 TTTATTTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
68 2 0.03
69 68 0.97
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (69 bp):
TGTCATAATAAATCTTCAATTAACACCTGAAGTTGTCATAATTTTACTTTTTCAATTAACACTGG
AAAA
Done.