Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008340.1 Corchorus capsularis cultivar CVL-1 contig08361, 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: 60522
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:114 original size:33 final size:32
Alignment explanation
Indices: 70--214 Score: 163
Period size: 33 Copynumber: 4.4 Consensus size: 32
60 GGTGTCGTCC
70 CCCTGGGGGCGG-CTGAGCCATGGCCAAGCCGCC-
1 CCCT-GGGGCGGCCT-A-CCATGGCCAAGCCGCCT
*
103 CTCCTGGGGCGGCACTACCATGGCCAGGCCGCCT
1 C-CCTGGGGCGGC-CTACCATGGCCAAGCCGCCT
137 CCCTGGGGCGGCCCTACCATGGCCAAGCCGCCT
1 CCCTGGGGCGG-CCTACCATGGCCAAGCCGCCT
*
170 CCCTGGGGCGGCCCTACCATGG--ATAGACCGCCC
1 CCCTGGGGCGG-CCTACCATGGCCA-AG-CCGCCT
203 CCCTGGGGCGGC
1 CCCTGGGGCGGC
215 ACCGGTACTA
Statistics
Matches: 102, Mismatches: 3, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
31 1 0.01
32 3 0.03
33 90 0.88
34 6 0.06
35 2 0.02
ACGTcount: A:0.12, C:0.42, G:0.34, T:0.12
Consensus pattern (32 bp):
CCCTGGGGCGGCCTACCATGGCCAAGCCGCCT
Found at i:177 original size:66 final size:66
Alignment explanation
Indices: 87--214 Score: 195
Period size: 66 Copynumber: 1.9 Consensus size: 66
77 GGCGGCTGAG
* * *
87 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTACCATGGCCAGGCCGCCTCCCTGGGGCGGCCCT
1 CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTACCATGGACAGACCGCCCCCCTGGGGCGGCCCT
152 A
66 A
* *
153 CCATGGCCAAGCCG-CCTCCCTGGGGCGGCCCTACCATGGATAGACCGCCCCCCTGGGGCGGC
1 CCATGGCCAAGCCGCCCT-CCTGGGGCGGCACTACCATGGACAGACCGCCCCCCTGGGGCGGC
215 ACCGGTACTA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 3 0.05
66 53 0.95
ACGTcount: A:0.12, C:0.44, G:0.32, T:0.12
Consensus pattern (66 bp):
CCATGGCCAAGCCGCCCTCCTGGGGCGGCACTACCATGGACAGACCGCCCCCCTGGGGCGGCCCT
A
Found at i:340 original size:33 final size:33
Alignment explanation
Indices: 277--370 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
267 AAAAAGCCTT
* * *
277 GCCGCCCTAGTGGGGCGGCT-AGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
309 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
*
342 GCCGTCCTAGTGGGGAGACTCCG-CGTGGC
1 GCCGTCCTAGTGGGGAGGCTCCGCCGTGGC
371 TAAGGGCAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
32 24 0.42
33 33 0.58
ACGTcount: A:0.12, C:0.31, G:0.43, T:0.15
Consensus pattern (33 bp):
GCCGTCCTAGTGGGGAGGCTCCGCCGTGGCAGA
Found at i:1269 original size:18 final size:18
Alignment explanation
Indices: 1248--1284 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1238 AGATTTCTAC
*
1248 TACCTATTAACTACCCGA
1 TACCTAATAACTACCCGA
*
1266 TACCTAATAATTACCCGA
1 TACCTAATAACTACCCGA
1284 T
1 T
1285 TAAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.30, G:0.05, T:0.30
Consensus pattern (18 bp):
TACCTAATAACTACCCGA
Found at i:8095 original size:103 final size:103
Alignment explanation
Indices: 7916--8123 Score: 389
Period size: 103 Copynumber: 2.0 Consensus size: 103
7906 TATGTAAATG
* *
7916 GTTTGAAAATGATGAATTAGCTAGAATGGAGGACAAGAATTTCATTCTGTTAAGAAATAAAATAT
1 GTTTGAAAATGATGAATTAGCTAGAATGGAGGACAAAAATTCCATTCTGTTAAGAAATAAAATAT
7981 GTAAGGAAATAATTGGTTACTTTCGGTCTTATAGTCTA
66 GTAAGGAAATAATTGGTTACTTTCGGTCTTATAGTCTA
*
8019 GTTTGCAAATGATGAATTAGCTAGAATGGAGGACAAAAATTCCATTCTGTTAAGAAATAAAATAT
1 GTTTGAAAATGATGAATTAGCTAGAATGGAGGACAAAAATTCCATTCTGTTAAGAAATAAAATAT
8084 GTAAGGAAATAATTGGTTACTTTCGGTCTTATAGTCTA
66 GTAAGGAAATAATTGGTTACTTTCGGTCTTATAGTCTA
8122 GT
1 GT
8124 GTAGTTTTGC
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.38, C:0.09, G:0.20, T:0.34
Consensus pattern (103 bp):
GTTTGAAAATGATGAATTAGCTAGAATGGAGGACAAAAATTCCATTCTGTTAAGAAATAAAATAT
GTAAGGAAATAATTGGTTACTTTCGGTCTTATAGTCTA
Found at i:13865 original size:51 final size:51
Alignment explanation
Indices: 13810--13936 Score: 254
Period size: 51 Copynumber: 2.5 Consensus size: 51
13800 TTGTCGGGCA
13810 CAACATCGAGCTCCGAGAGAGGCCTTGTTGAGGCCAAATAATATCGAGACC
1 CAACATCGAGCTCCGAGAGAGGCCTTGTTGAGGCCAAATAATATCGAGACC
13861 CAACATCGAGCTCCGAGAGAGGCCTTGTTGAGGCCAAATAATATCGAGACC
1 CAACATCGAGCTCCGAGAGAGGCCTTGTTGAGGCCAAATAATATCGAGACC
13912 CAACATCGAGCTCCGAGAGAGGCCT
1 CAACATCGAGCTCCGAGAGAGGCCT
13937 GCAAGAGAGC
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.31, C:0.27, G:0.26, T:0.17
Consensus pattern (51 bp):
CAACATCGAGCTCCGAGAGAGGCCTTGTTGAGGCCAAATAATATCGAGACC
Found at i:17405 original size:20 final size:21
Alignment explanation
Indices: 17380--17418 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
17370 TTTAGAAGCA
17380 ATTAATTAAAAA-CATTAAAT
1 ATTAATTAAAAACCATTAAAT
17400 ATTAATTAAAAACCATTAA
1 ATTAATTAAAAACCATTAA
17419 GGAAGGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAATTAAAAACCATTAAAT
Found at i:17511 original size:74 final size:74
Alignment explanation
Indices: 17425--17581 Score: 253
Period size: 74 Copynumber: 2.1 Consensus size: 74
17415 TTAAGGAAGG
* * *
17425 GAAATGTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATGGGGGAAACTCATAGAGGGGCTTTT
1 GAAAAGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
17490 TAGTCATCC-
66 TAGTCA-CCT
* *
17499 GAAAAGTGTAATTACAAAAAATGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGTGGCTTTT
1 GAAAAGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
17564 TAGTCACCT
66 TAGTCACCT
17573 GAAAAGTGT
1 GAAAAGTGT
17582 GAAAAGACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 2 0.03
74 75 0.97
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (74 bp):
GAAAAGTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTT
TAGTCACCT
Found at i:18830 original size:20 final size:21
Alignment explanation
Indices: 18797--18840 Score: 56
Period size: 19 Copynumber: 2.1 Consensus size: 21
18787 TGTATCTTAA
18797 TTTTTGATACAAAG-TTT-TT
1 TTTTTGATACAAAGCTTTCTT
*
18816 TTTTTGGTACAAAAGCTTTCTT
1 TTTTTGATAC-AAAGCTTTCTT
18838 TTT
1 TTT
18841 CTTTAATTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 4 0.19
21 3 0.14
22 5 0.24
ACGTcount: A:0.23, C:0.09, G:0.11, T:0.57
Consensus pattern (21 bp):
TTTTTGATACAAAGCTTTCTT
Found at i:22035 original size:22 final size:22
Alignment explanation
Indices: 22010--22056 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
22000 ATTTATTCAT
*
22010 TATTAATTAACTATTAATTATA
1 TATTAATTAACTATTAATTAGA
*
22032 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
22054 TAT
1 TAT
22057 AGTATAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:22052 original size:11 final size:11
Alignment explanation
Indices: 22010--22052 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
22000 ATTTATTCAT
*
22010 TATTAATTAAC
1 TATTAATTAGC
**
22021 TATTAATTATA
1 TATTAATTAGC
22032 TATTAATTAGC
1 TATTAATTAGC
22043 TATTAATTAG
1 TATTAATTAG
22053 ATATAGTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.49
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:22247 original size:22 final size:22
Alignment explanation
Indices: 22219--22265 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
22209 ATTTATTCAT
22219 TATTAATTAACTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
*
22241 TATTAATTAGCTATTAATTAGA
1 TATTAATTAACTATTAATTAGA
22263 TAT
1 TAT
22266 GGTATAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (22 bp):
TATTAATTAACTATTAATTAGA
Found at i:22261 original size:11 final size:11
Alignment explanation
Indices: 22219--22261 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
22209 ATTTATTCAT
*
22219 TATTAATTAAC
1 TATTAATTAGC
*
22230 TATTAATTAGA
1 TATTAATTAGC
22241 TATTAATTAGC
1 TATTAATTAGC
22252 TATTAATTAG
1 TATTAATTAG
22262 ATATGGTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (11 bp):
TATTAATTAGC
Found at i:22353 original size:209 final size:209
Alignment explanation
Indices: 21993--22415 Score: 783
Period size: 209 Copynumber: 2.0 Consensus size: 209
21983 TTAATCAATC
*
21993 ATATTGAATTTATTCATTATTAATTAACTATTAATTATATATTAATTAGCTATTAATTAGATATA
1 ATATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAATTAGCTATTAATTAGATATA
*
22058 GTATAATGGATGATTAAGGAGGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGG
66 GTATAATGGATGATTAAGGAAGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGG
22123 GGCAATAAGGTGACACCAGATTAAAAATTGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAA
131 GGCAATAAGGTGACACCAGATTAAAAATTGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAA
22188 ATAATATATAGTAT
196 ATAATATATAGTAT
*
22202 ATATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAATTAGCTATTAATTAGATATG
1 ATATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAATTAGCTATTAATTAGATATA
*
22267 GTATAATGGATGATTAAGGAAGGGTTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGG
66 GTATAATGGATGATTAAGGAAGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGG
* * *
22332 GGCGATAAGGTGGCACCAGATTAAAAGTTGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAA
131 GGCAATAAGGTGACACCAGATTAAAAATTGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAA
22397 ATAATATATAGTAT
196 ATAATATATAGTAT
22411 ATATT
1 ATATT
22416 CTACTTGTAA
Statistics
Matches: 207, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
209 207 1.00
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (209 bp):
ATATTGAATTTATTCATTATTAATTAACTATTAATTAGATATTAATTAGCTATTAATTAGATATA
GTATAATGGATGATTAAGGAAGGGCTTTAAATTAATATGTTAGATGTGAGAAATTACCAAAATGG
GGCAATAAGGTGACACCAGATTAAAAATTGAAAGGGCTTGTTAGTAATTTCCATAGGGGACAAAA
ATAATATATAGTAT
Found at i:39192 original size:12 final size:12
Alignment explanation
Indices: 39175--39199 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39165 AAATTCTCTC
39175 AATTTTTTTTTT
1 AATTTTTTTTTT
39187 AATTTTTTTTTT
1 AATTTTTTTTTT
39199 A
1 A
39200 CATCAAGAAA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (12 bp):
AATTTTTTTTTT
Found at i:44689 original size:18 final size:19
Alignment explanation
Indices: 44670--44705 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44660 AATTAATTAT
44670 TTTA-ATATTA-ATTTTTA
1 TTTATATATTATATTTTTA
44687 TTTATATATTATATTTTTA
1 TTTATATATTATATTTTTA
44706 CTTAAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 6 0.35
19 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATATATTATATTTTTA
Found at i:52013 original size:15 final size:13
Alignment explanation
Indices: 51989--52031 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
51979 AAAGTTTATA
51989 ATTTTTTTTAAATT
1 ATTTTTTTTAAA-T
*
52003 ATTTTTCTTTATAT
1 ATTTTT-TTTAAAT
52017 ATTTTTTTATAAAT
1 ATTTTTTT-TAAAT
52031 A
1 A
52032 ATGGTCAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 2 0.08
14 18 0.72
15 5 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTTTTTTTAAAT
Found at i:52100 original size:19 final size:19
Alignment explanation
Indices: 52073--52132 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
52063 AAAAGACAAA
* *
52073 TAATTAGGAATGGAGGGAG
1 TAATAAGGAACGGAGGGAG
* *
52092 TAATAAGGAAAGGGGGGGAG
1 TAATAAGG-AACGGAGGGAG
*
52112 TAATAAGAAACGGAGGGAG
1 TAATAAGGAACGGAGGGAG
52131 TA
1 TA
52133 TCGAACTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.42, C:0.02, G:0.42, T:0.15
Consensus pattern (19 bp):
TAATAAGGAACGGAGGGAG
Found at i:52112 original size:20 final size:20
Alignment explanation
Indices: 52087--52199 Score: 86
Period size: 20 Copynumber: 5.3 Consensus size: 20
52077 TAGGAATGGA
52087 GGGAGTAATAAGGAAAGGGG
1 GGGAGTAATAAGGAAAGGGG
52107 GGGAGTAATAA-GAAACGGAGG
1 GGGAGTAATAAGGAAA-GG-GG
* * *
52128 GAGTATCGAACTAATTAGGAAAGGGA
1 G-G----G-AGTAATAAGGAAAGGGG
*
52154 AGGAGTAATAAGGAAAGGGG
1 GGGAGTAATAAGGAAAGGGG
* *
52174 GGGAGTAATAA-GAAACGGA
1 GGGAGTAATAAGGAAAGGGG
52193 GGGAGTA
1 GGGAGTA
52200 TCGAATAAGA
Statistics
Matches: 74, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
19 17 0.23
20 37 0.50
21 4 0.05
22 1 0.01
25 1 0.01
26 2 0.03
27 8 0.11
28 4 0.05
ACGTcount: A:0.42, C:0.04, G:0.42, T:0.12
Consensus pattern (20 bp):
GGGAGTAATAAGGAAAGGGG
Found at i:52180 original size:67 final size:66
Alignment explanation
Indices: 52073--52204 Score: 237
Period size: 67 Copynumber: 2.0 Consensus size: 66
52063 AAAAGACAAA
* *
52073 TAATTAGGAATGGAGGGAGTAATAAGGAAAGGGGGGGAGTAATAAGAAACGGAGGGAGTATCGAA
1 TAATTAGGAAGGGAAGGAGTAATAAGGAAAGGGGGGGAGTAATAAGAAACGGAGGGAGTATCGAA
52138 C
66 C
52139 TAATTAGGAAAGGGAAGGAGTAATAAGGAAAGGGGGGGAGTAATAAGAAACGGAGGGAGTATCGA
1 TAATTAGG-AAGGGAAGGAGTAATAAGGAAAGGGGGGGAGTAATAAGAAACGGAGGGAGTATCGA
52204 A
65 A
52205 TAAGAAATTA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
66 8 0.13
67 55 0.87
ACGTcount: A:0.42, C:0.04, G:0.39, T:0.14
Consensus pattern (66 bp):
TAATTAGGAAGGGAAGGAGTAATAAGGAAAGGGGGGGAGTAATAAGAAACGGAGGGAGTATCGAA
C
Found at i:55797 original size:18 final size:18
Alignment explanation
Indices: 55774--55808 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55764 AAGAGGGAGA
55774 GAGGAGAAAAAGAAGAAG
1 GAGGAGAAAAAGAAGAAG
*
55792 GAGGAGAAGAAGAAGAA
1 GAGGAGAAAAAGAAGAA
55809 AGATAGAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (18 bp):
GAGGAGAAAAAGAAGAAG
Found at i:57372 original size:58 final size:58
Alignment explanation
Indices: 57279--57393 Score: 176
Period size: 58 Copynumber: 2.0 Consensus size: 58
57269 TCCCAATGGA
* * *
57279 AACATGTACAAAACTACAAATATTGTATCATATCTTTGCTTTTAAAAAAATGTAGAAT
1 AACATGTACAAAACTACAAATATTGCATCACATCTTTGCTTTTAAAAAAATATAGAAT
** *
57337 AACATGTACACTACTACAAATATTGCATCACATCTTTGCTTTTTAAAAAATATAGAA
1 AACATGTACAAAACTACAAATATTGCATCACATCTTTGCTTTTAAAAAAATATAGAA
57394 AAAAAGTATA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (58 bp):
AACATGTACAAAACTACAAATATTGCATCACATCTTTGCTTTTAAAAAAATATAGAAT
Found at i:58670 original size:161 final size:162
Alignment explanation
Indices: 58463--58788 Score: 591
Period size: 162 Copynumber: 2.0 Consensus size: 162
58453 AGGGTTTATT
* *
58463 ATGAAATGTGTAACTTTAACCACAATAAAAGCATATAATCATATCATATGATCATAATTACAA-T
1 ATGAAATGTGTAACTGTAACAACAATAAAAGCATATAATCATATCATATGATCATAATTACAATT
*
58527 TTAAATAATTAATTAAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGTAACGT
66 TTAAATAATTAATTAAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGCAACGT
* *
58592 ACATGTAAACATCTAATGACAATTAATATAGA
131 ACATGTAAACATCCAATGACAATTAATATAAA
58624 ATGAAATGTGTAACTGTAACAACAATAAAAGCATATAATCATATCATATGATCATAATTACAATT
1 ATGAAATGTGTAACTGTAACAACAATAAAAGCATATAATCATATCATATGATCATAATTACAATT
*
58689 TTAAATAATTAATTGAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGCAACGT
66 TTAAATAATTAATTAAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGCAACGT
58754 ACATGTAAACATCCAATGACAATTAATATAAA
131 ACATGTAAACATCCAATGACAATTAATATAAA
58786 ATG
1 ATG
58789 TAATTTTTTG
Statistics
Matches: 158, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
161 61 0.39
162 97 0.61
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.31
Consensus pattern (162 bp):
ATGAAATGTGTAACTGTAACAACAATAAAAGCATATAATCATATCATATGATCATAATTACAATT
TTAAATAATTAATTAAGAAGATGGAAAACATATTAAGTTACAAAATTTAATTTAGAATGCAACGT
ACATGTAAACATCCAATGACAATTAATATAAA
Found at i:58944 original size:30 final size:32
Alignment explanation
Indices: 58890--58955 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
58880 AACTTTATGT
*
58890 TTTCCAATTGTACCCTTATTTTTAAAA-CATA
1 TTTCCAATTGTACCATTATTTTTAAAAGCATA
58921 TTTCCAATTGTACCATT-TTTTTAAAAGCATA
1 TTTCCAATTGTACCATTATTTTTAAAAGCATA
58952 TTTC
1 TTTC
58956 TAAATTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (32 bp):
TTTCCAATTGTACCATTATTTTTAAAAGCATA
Found at i:58967 original size:30 final size:29
Alignment explanation
Indices: 58890--58967 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 29
58880 AACTTTATGT
* *
58890 TTTCCAATTGTACCCTTATTTTTAAAACATA
1 TTTCAAATTG-ACCATT-TTTTTAAAACATA
*
58921 TTTCCAATTGTACCATTTTTTTAAAAGCATA
1 TTTCAAATTG-ACCATTTTTTTAAAA-CATA
58952 TTTCTAAATTG-CCATT
1 TTTC-AAATTGACCATT
58968 ACTAAATAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 14 0.33
31 24 0.56
32 5 0.12
ACGTcount: A:0.31, C:0.18, G:0.05, T:0.46
Consensus pattern (29 bp):
TTTCAAATTGACCATTTTTTTAAAACATA
Found at i:59045 original size:15 final size:16
Alignment explanation
Indices: 59004--59045 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
58994 TATTTTTTAA
*
59004 TCATAAATTATTCCAT
1 TCATAAATTACTCCAT
59020 TCATAAATTACTCCAT
1 TCATAAATTACTCCAT
*
59036 T-ATTAATTAC
1 TCATAAATTAC
59046 ACGAATAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (16 bp):
TCATAAATTACTCCAT
Found at i:59128 original size:30 final size:32
Alignment explanation
Indices: 59068--59132 Score: 107
Period size: 30 Copynumber: 2.1 Consensus size: 32
59058 AAACTTTAGT
*
59068 TTTTCCAATTGTACCATTATTTTTAAAACATA
1 TTTTCCAATTGTACCATTATTTTAAAAACATA
59100 TTTT-CAATTGTACCATT-TTTTAAAAACATA
1 TTTTCCAATTGTACCATTATTTTAAAAACATA
59130 TTT
1 TTT
59133 CTAAATTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 15 0.47
31 13 0.41
32 4 0.12
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (32 bp):
TTTTCCAATTGTACCATTATTTTAAAAACATA
Found at i:59140 original size:31 final size:31
Alignment explanation
Indices: 59074--59140 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
59064 TAGTTTTTCC
* *
59074 AATTGTACCATTATTTTTAAAACATATTTTC
1 AATTGTACCATTATTTTAAAAACATATTTTA
59105 AATTGTACCATT-TTTTAAAAACATATTTCTA
1 AATTGTACCATTATTTTAAAAACATATTT-TA
59136 AATTG
1 AATTG
59141 CTATTACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.46
Consensus pattern (31 bp):
AATTGTACCATTATTTTAAAAACATATTTTA
Found at i:59324 original size:37 final size:36
Alignment explanation
Indices: 59235--59324 Score: 117
Period size: 37 Copynumber: 2.4 Consensus size: 36
59225 AACTTTTTGT
*
59235 TTCCAACGTCCTATTTAATTTTGCCTTTTGTCTTTG
1 TTCCAACGTCCTATTTAATTTTGCCTTTTGTCTTCG
* ** *
59271 TTTCAATCGTTGTATTTAATTTTGCTTTTTGTCTTCG
1 TTCCAA-CGTCCTATTTAATTTTGCCTTTTGTCTTCG
59308 TCTCCAACGTCCTATTT
1 T-TCCAACGTCCTATTT
59325 GGTCTTAGAT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
36 5 0.11
37 35 0.80
38 4 0.09
ACGTcount: A:0.14, C:0.21, G:0.11, T:0.53
Consensus pattern (36 bp):
TTCCAACGTCCTATTTAATTTTGCCTTTTGTCTTCG
Found at i:59410 original size:22 final size:22
Alignment explanation
Indices: 59378--59438 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
59368 TGGATGGTCC
59378 AATT-TCAAAATTTCA-AATCG-
1 AATTATCAAAATTTCATAAT-GT
*
59398 AAGTTATCAAAATTACATAATGT
1 AA-TTATCAAAATTTCATAATGT
*
59421 CATTATCAAAATTTCATA
1 AATTATCAAAATTTCATA
59439 GAGGGGCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 2 0.06
22 26 0.76
23 4 0.12
ACGTcount: A:0.46, C:0.13, G:0.05, T:0.36
Consensus pattern (22 bp):
AATTATCAAAATTTCATAATGT
Found at i:59477 original size:21 final size:22
Alignment explanation
Indices: 59451--59501 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
59441 GGGGCCAACA
*
59451 AAAATTT-ATAGAGAGGTTATT
1 AAAATTTCATAAAGAGGTTATT
*
59472 AAAATTTCATAAAGAGGTTATC
1 AAAATTTCATAAAGAGGTTATT
*
59494 AAATTTTC
1 AAAATTTC
59502 GAAATGTGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (22 bp):
AAAATTTCATAAAGAGGTTATT
Found at i:59655 original size:22 final size:22
Alignment explanation
Indices: 59627--59879 Score: 118
Period size: 22 Copynumber: 11.7 Consensus size: 22
59617 TCAGGGAGGA
*
59627 TATCAAAATTTCATATGAATGT
1 TATCAAAATTTCATAGGAATGT
* **
59649 TATCAAAGTTTCATATTTTAAT-T
1 TATCAAAATTTCATA--GGAATGT
* **
59672 T-TCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATAGGAATGT
*
59693 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATAGGAATGT
* *
59714 GCATCAAAATTTCATAGGGA-GAT
1 -TATCAAAATTTCATAGGAATG-T
* * * *
59737 TAACAAAATTTCTTAATG-AGGT
1 TATCAAAATTTCAT-AGGAATGT
** * *
59759 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATAGGAATGT
*
59781 TATCAAAA-TT--T--GTA-GT
1 TATCAAAATTTCATAGGAATGT
* *
59797 TATCAAGATTTCATAAGG-AGGT
1 TATCAAAATTTCAT-AGGAATGT
*
59819 TATCAAAATTTTATAGGGAGAT-T
1 TATCAAAATTTCATA-GGA-ATGT
*
59842 TATCAAAATTTTATAGGAATGTT
1 TATCAAAATTTCATAGGAATG-T
*
59865 TATCCAAATTTCATA
1 TATCAAAATTTCATA
59880 ACGAGATTAT
Statistics
Matches: 180, Mismatches: 29, Indels: 43
0.71 0.12 0.17
Matches are distributed among these distances:
16 9 0.05
17 4 0.02
19 2 0.01
20 1 0.01
21 12 0.07
22 109 0.61
23 38 0.21
24 5 0.03
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (22 bp):
TATCAAAATTTCATAGGAATGT
Found at i:60035 original size:23 final size:23
Alignment explanation
Indices: 59795--60037 Score: 73
Period size: 22 Copynumber: 10.9 Consensus size: 23
59785 AAAATTTGTA
* * *
59795 GTTATCAAGATTTCATA-AGGAG
1 GTTATCAAAATTTCATAGTGGTG
* *
59817 GTTATCAAAATTTTATAG-GGAG
1 GTTATCAAAATTTCATAGTGGTG
* * *
59839 ATTTATCAAAATTTTATAG-GAATG
1 -GTTATCAAAATTTCATAGTG-GTG
* * ** *
59863 TTTATCCAAATTTCATA-ACGAG
1 GTTATCAAAATTTCATAGTGGTG
*
59885 ATTAT-AACAATTTCATAGT-GTG
1 GTTATCAA-AATTTCATAGTGGTG
59907 AG-TATCAAAATTTC-TAAGT-GTG
1 -GTTATCAAAATTTCAT-AGTGGTG
* * * *
59929 ATTACTGACAA-TTCATA-TGGAG
1 GTTA-TCAAAATTTCATAGTGGTG
* * * **
59951 GTTTTTAAATTTTCATA-ACGTG
1 GTTATCAAAATTTCATAGTGGTG
* * *
59973 GTTATCAATATATCATA-TGGAG
1 GTTATCAAAATTTCATAGTGGTG
* *
59995 GTTATCAACATCTT-ATAGTGTTG
1 GTTATCAAAAT-TTCATAGTGGTG
60018 GTTATCAAAATTTCATAGTG
1 GTTATCAAAATTTCATAGTG
60038 AGATCTTCAA
Statistics
Matches: 164, Mismatches: 40, Indels: 33
0.69 0.17 0.14
Matches are distributed among these distances:
21 6 0.04
22 97 0.59
23 60 0.37
24 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (23 bp):
GTTATCAAAATTTCATAGTGGTG
Found at i:60205 original size:62 final size:62
Alignment explanation
Indices: 60132--60283 Score: 277
Period size: 62 Copynumber: 2.5 Consensus size: 62
60122 TCGTTATTGA
*
60132 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATAGTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
60194 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
1 AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
* *
60256 AATTTAATAGGAAGGTTATCATAATTTC
1 AATTTCATAGGAAGGTTATCAAAATTTC
60284 GTATCAATAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 87 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.34
Consensus pattern (62 bp):
AATTTCATAGGAAGGTTATCAAAATTTCATAAGGACGTCATAAAAAATACTGTAATTATCAT
Found at i:60212 original size:22 final size:22
Alignment explanation
Indices: 60187--60283 Score: 69
Period size: 22 Copynumber: 4.6 Consensus size: 22
60177 AATAGTGTAA
60187 TTATCATAATTTCATAGGAAGG
1 TTATCATAATTTCATAGGAAGG
* *
60209 TTATCAAAATTTCATAAGG-ACG
1 TTATCATAATTTCAT-AGGAAGG
* * * * * *
60231 TCATAAAAAATAC-T-GTAA--
1 TTATCATAATTTCATAGGAAGG
*
60249 TTATCATAATTTAATAGGAAGG
1 TTATCATAATTTCATAGGAAGG
60271 TTATCATAATTTC
1 TTATCATAATTTC
60284 GTATCAATAT
Statistics
Matches: 54, Mismatches: 15, Indels: 12
0.67 0.19 0.15
Matches are distributed among these distances:
18 7 0.13
19 2 0.04
20 4 0.07
21 1 0.02
22 37 0.69
23 3 0.06
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
TTATCATAATTTCATAGGAAGG
Done.