Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014084.1 Corchorus capsularis cultivar CVL-1 contig14105, 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: 117664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3663 original size:48 final size:48
Alignment explanation
Indices: 3592--3689 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
3582 ACACTTATAA
3592 TTCTTTCCGGTATTGGTATATGGTGGTGGTGGCTGATGCTGAATATGG
1 TTCTTTCCGGTATTGGTATATGGTGGTGGTGGCTGATGCTGAATATGG
3640 TTCTTTCCGGTATTGGTATATGGTGGTGGTGGCTGATGCTGAATATGG
1 TTCTTTCCGGTATTGGTATATGGTGGTGGTGGCTGATGCTGAATATGG
3688 TT
1 TT
3690 TGGCCCGGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.14, C:0.10, G:0.35, T:0.41
Consensus pattern (48 bp):
TTCTTTCCGGTATTGGTATATGGTGGTGGTGGCTGATGCTGAATATGG
Found at i:3741 original size:69 final size:69
Alignment explanation
Indices: 3666--3882 Score: 353
Period size: 69 Copynumber: 3.1 Consensus size: 69
3656 TATATGGTGG
** * *
3666 TGGTGGCTGATGCTGAATATGGTTTGGCCCGGGGTAACCACCATACGCTGTATTCATCTGCACCG
1 TGGTGGCTGACACTGGATAGGGTTTGGCCCGGGGTAACCACCATACGCTGTATTCATCTGCACCG
3731 GATT
66 GATT
* *
3735 TGGTGGCTGACACTGGATAGGGTTTGGCCTGGGGTAACCACCATACGCTGTATTCATCTGCGCCG
1 TGGTGGCTGACACTGGATAGGGTTTGGCCCGGGGTAACCACCATACGCTGTATTCATCTGCACCG
3800 GATT
66 GATT
* * *
3804 TGGTGGCTGCCACTGGATAGGGTTTGGCCCGGGGTAAACACCATACGCTGTATTCATCTGAACCG
1 TGGTGGCTGACACTGGATAGGGTTTGGCCCGGGGTAACCACCATACGCTGTATTCATCTGCACCG
3869 GATT
66 GATT
3873 TGGTGGCTGA
1 TGGTGGCTGA
3883 TCCGATGACT
Statistics
Matches: 136, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 136 1.00
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (69 bp):
TGGTGGCTGACACTGGATAGGGTTTGGCCCGGGGTAACCACCATACGCTGTATTCATCTGCACCG
GATT
Found at i:14316 original size:26 final size:26
Alignment explanation
Indices: 14283--14343 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
14273 GAAAATATGG
14283 TTTGTTGTAACTTAGAAAGATATCGT
1 TTTGTTGTAACTTAGAAAGATATCGT
14309 TTTGTTGTAACTTAGAAAGATATCGT
1 TTTGTTGTAACTTAGAAAGATATCGT
14335 TTTGTTGTA
1 TTTGTTGTA
14344 TATATGGATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.46
Consensus pattern (26 bp):
TTTGTTGTAACTTAGAAAGATATCGT
Found at i:20057 original size:31 final size:31
Alignment explanation
Indices: 20019--20087 Score: 120
Period size: 31 Copynumber: 2.2 Consensus size: 31
20009 AGTTTTATAA
*
20019 AACTTTTGAAACGCCTATTGTATCCTTATTT
1 AACTTTTGAAACGCCTATTATATCCTTATTT
*
20050 AACTTTTGAAATGCCTATTATATCCTTATTT
1 AACTTTTGAAACGCCTATTATATCCTTATTT
20081 AACTTTT
1 AACTTTT
20088 ACAGTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (31 bp):
AACTTTTGAAACGCCTATTATATCCTTATTT
Found at i:21820 original size:21 final size:19
Alignment explanation
Indices: 21775--21822 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
21765 AAGTAAAATA
21775 TATAAGCTTTTTAGAAACT
1 TATAAGCTTTTTAGAAACT
* *
21794 TCATAAGCATTTTTATTAATCT
1 T-ATAAGC-TTTTTA-GAAACT
21816 TATAAGC
1 TATAAGC
21823 CTTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 12 0.50
22 5 0.21
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (19 bp):
TATAAGCTTTTTAGAAACT
Found at i:27689 original size:18 final size:18
Alignment explanation
Indices: 27666--27702 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
27656 TCTTGGGCTT
27666 TTTTGCTCAAGGAATACA
1 TTTTGCTCAAGGAATACA
*
27684 TTTTGCTTAAGGAATACA
1 TTTTGCTCAAGGAATACA
27702 T
1 T
27703 CACTCAGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (18 bp):
TTTTGCTCAAGGAATACA
Found at i:27753 original size:17 final size:17
Alignment explanation
Indices: 27731--27767 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
27721 ATACGTTTCC
27731 AAGTTATTCCAATTCAT
1 AAGTTATTCCAATTCAT
27748 AAGTTATTCCAATTCAT
1 AAGTTATTCCAATTCAT
27765 AAG
1 AAG
27768 AATCTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (17 bp):
AAGTTATTCCAATTCAT
Found at i:34978 original size:1 final size:1
Alignment explanation
Indices: 34972--35012 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
34962 CTAAAGTTTG
34972 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35013 CAACTAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:37699 original size:20 final size:19
Alignment explanation
Indices: 37662--37700 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
37652 TTTATGAGGC
*
37662 CAAAGATTGAAGTAACAAG
1 CAAAGATTAAAGTAACAAG
*
37681 CAAAGAATTAAAGTGACAAG
1 CAAAG-ATTAAAGTAACAAG
37701 AGAAGCTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.54, C:0.10, G:0.21, T:0.15
Consensus pattern (19 bp):
CAAAGATTAAAGTAACAAG
Found at i:56849 original size:267 final size:267
Alignment explanation
Indices: 56367--56880 Score: 897
Period size: 267 Copynumber: 1.9 Consensus size: 267
56357 ATATATATTA
*
56367 ATTTTTTTCTTTTTATTTATTTTTGGGTCAAAGTCATGCATGCATGATGCAATTAGGAGTAATTA
1 ATTTTTTTCTTTTTATTTATTTTCGGGTCAAAGTCATGCATGCATGATGCAATTAGGAGTAATTA
*
56432 GTGGTTTGATGCTTGTTTTCTCTAAAAGATTTTGAATTTATGACTTATGAATTATAAATAAAAAA
66 GTGGTTTGATGCTTGTTTCCTCTAAAAGATTTTGAATTTATGACTTATGAATTATAAATAAAAAA
*
56497 AAACTATTATCATGAGAAATTTATTGTCATAGTAAACCAACCTAGCTCGGACAAGATTAGTGATA
131 AAACTATTATCATGAGAAATTTATTGTCATAGTAAACCAACCTAGCTCGGACAAGATCAGTGATA
56562 AACTATTGAGTATGGATTCATACTTATATGCTTTACTTTATTAAAAAAAAAGACAATCTAATTAT
196 AACTATTGAGTATGGATTCATACTTATATGCTTTACTTTA-TAAAAAAAAAGACAATCTAATTAT
56627 AATTATAT
260 AATTATAT
*
56635 ATTTTTTTCTTTTTATTTA-TTTCGGGTCAAAGTCATGCATGCATGATGCAATTAGGAGTAGTTA
1 ATTTTTTTCTTTTTATTTATTTTCGGGTCAAAGTCATGCATGCATGATGCAATTAGGAGTAATTA
* * *
56699 GTGGTTTGATGCTTGTTTCCTCTAAAAGATTTTGAATTTGTGACTTATGAGTTATGAATAAAAAA
66 GTGGTTTGATGCTTGTTTCCTCTAAAAGATTTTGAATTTATGACTTATGAATTATAAATAAAAAA
*
56764 AAACTATTCTCATGAGAAATTTATTGTCATAGTAAACCAACCTAAG-TCGGACAAGATCAGTGAT
131 AAACTATTATCATGAGAAATTTATTGTCATAGTAAACCAACCT-AGCTCGGACAAGATCAGTGAT
* * *
56828 AAACTGTTGAGTATTGATTCATATTTATATGCTTTACTTTATAAAAAAAAAGA
195 AAACTATTGAGTATGGATTCATACTTATATGCTTTACTTTATAAAAAAAAAGA
56881 AAAAAAAAGA
Statistics
Matches: 234, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
266 12 0.05
267 201 0.86
268 21 0.09
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (267 bp):
ATTTTTTTCTTTTTATTTATTTTCGGGTCAAAGTCATGCATGCATGATGCAATTAGGAGTAATTA
GTGGTTTGATGCTTGTTTCCTCTAAAAGATTTTGAATTTATGACTTATGAATTATAAATAAAAAA
AAACTATTATCATGAGAAATTTATTGTCATAGTAAACCAACCTAGCTCGGACAAGATCAGTGATA
AACTATTGAGTATGGATTCATACTTATATGCTTTACTTTATAAAAAAAAAGACAATCTAATTATA
ATTATAT
Found at i:58748 original size:30 final size:30
Alignment explanation
Indices: 58714--58792 Score: 131
Period size: 30 Copynumber: 2.6 Consensus size: 30
58704 CTCATTCTTA
58714 TGCTCTTACAATTCTCTTTTCATCTTACCG
1 TGCTCTTACAATTCTCTTTTCATCTTACCG
*
58744 TGCTCTTAGAATTCTCTTTTCATCTTACCG
1 TGCTCTTACAATTCTCTTTTCATCTTACCG
* *
58774 TGCACTTATAATTCTCTTT
1 TGCTCTTACAATTCTCTTT
58793 AATATAGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.18, C:0.27, G:0.08, T:0.48
Consensus pattern (30 bp):
TGCTCTTACAATTCTCTTTTCATCTTACCG
Found at i:58999 original size:2 final size:2
Alignment explanation
Indices: 58992--59020 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
58982 TGAGAGGCCA
58992 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59021 TAATTATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:70351 original size:61 final size:60
Alignment explanation
Indices: 70281--70433 Score: 168
Period size: 60 Copynumber: 2.5 Consensus size: 60
70271 CTAATTACTC
* * * *
70281 AAATA-GGTCCTTAACT-TATGTGAAAATGCTCAATTTAGGG-TTGATGCTTTTAATTTGATA
1 AAATAGGGTCC-TAA-TGTATGCGAAAATGCTCAATTCAGGGCCT-ATACTTTTAATTTGATA
* *
70341 AAATAGGGTCCTAATGTATGCGAAAATGCTCAATTCAGGGCCTATACTTTTAATTTGGTT
1 AAATAGGGTCCTAATGTATGCGAAAATGCTCAATTCAGGGCCTATACTTTTAATTTGATA
** * *
70401 AAATAGGACCCTAATGTATACGGAAATGCTCAA
1 AAATAGGGTCCTAATGTATGCGAAAATGCTCAA
70434 ATAAGGGCTC
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
59 1 0.01
60 73 0.91
61 6 0.08
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (60 bp):
AAATAGGGTCCTAATGTATGCGAAAATGCTCAATTCAGGGCCTATACTTTTAATTTGATA
Found at i:76808 original size:21 final size:21
Alignment explanation
Indices: 76761--76811 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
76751 AAAATTCAAA
* *
76761 ATAAAATAAAAACTACCTATT
1 ATAAGATAAAAACTACCCATT
*
76782 -TTAGATAAAAACTACCCATT
1 ATAAGATAAAAACTACCCATT
76802 ATAAGATAAA
1 ATAAGATAAA
76812 TATAATATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.55, C:0.14, G:0.04, T:0.27
Consensus pattern (21 bp):
ATAAGATAAAAACTACCCATT
Found at i:78247 original size:16 final size:16
Alignment explanation
Indices: 78219--78303 Score: 102
Period size: 16 Copynumber: 5.4 Consensus size: 16
78209 TTCCCTTGTC
*
78219 CTATTTCGGTAATTGA
1 CTATTTTGGTAATTGA
* *
78235 CTACTTTGGTAA-TAA
1 CTATTTTGGTAATTGA
*
78250 ATATTTTGGTAATTGA
1 CTATTTTGGTAATTGA
*
78266 CTATTTTGGTAA-TAA
1 CTATTTTGGTAATTGA
*
78281 ATATTTTGGTAATTGA
1 CTATTTTGGTAATTGA
78297 CTATTTT
1 CTATTTT
78304 AATAGTAAAT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
15 25 0.45
16 31 0.55
ACGTcount: A:0.29, C:0.07, G:0.15, T:0.48
Consensus pattern (16 bp):
CTATTTTGGTAATTGA
Found at i:78259 original size:15 final size:15
Alignment explanation
Indices: 78239--78293 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
78229 AATTGACTAC
78239 TTTGGTAATAAATAT
1 TTTGGTAATAAATAT
* *
78254 TTTGGTAATTGACTAT
1 TTTGGTAA-TAAATAT
78270 TTTGGTAATAAATAT
1 TTTGGTAATAAATAT
78285 TTTGGTAAT
1 TTTGGTAAT
78294 TGACTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 22 0.63
16 13 0.37
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (15 bp):
TTTGGTAATAAATAT
Found at i:78316 original size:31 final size:31
Alignment explanation
Indices: 78220--78303 Score: 150
Period size: 31 Copynumber: 2.7 Consensus size: 31
78210 TCCCTTGTCC
* *
78220 TATTTCGGTAATTGACTACTTTGGTAATAAA
1 TATTTTGGTAATTGACTATTTTGGTAATAAA
78251 TATTTTGGTAATTGACTATTTTGGTAATAAA
1 TATTTTGGTAATTGACTATTTTGGTAATAAA
78282 TATTTTGGTAATTGACTATTTT
1 TATTTTGGTAATTGACTATTTT
78304 AATAGTAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (31 bp):
TATTTTGGTAATTGACTATTTTGGTAATAAA
Found at i:78421 original size:83 final size:83
Alignment explanation
Indices: 78282--78492 Score: 343
Period size: 83 Copynumber: 2.5 Consensus size: 83
78272 TGGTAATAAA
* *
78282 TATTTTGGTAATTGACTATTTTAATAGTAAATATTGTCAGTAATAGTCCTTTAATTAGTTTCTTA
1 TATTTTGGTAATTGACTATTTTAATAGTAAATAGTGTCAGTAATAGTCCTTCAATTAGTTTCTTA
*
78347 CACTTTCTTCCCCTG-CTC
66 CACTTTCTCCCCCTGTC-C
78365 TATTTTGGTAATTGACTATTTTAATAGTAAATAGTGTCAGTAATAGTCCTTCAATTAGTTTCTTA
1 TATTTTGGTAATTGACTATTTTAATAGTAAATAGTGTCAGTAATAGTCCTTCAATTAGTTTCTTA
78430 CACTTTCTCCCCCTGTCC
66 CACTTTCTCCCCCTGTCC
** * *
78448 TATTTTGGTAATTGACTATTTTTGTAATAAATAGTGTCATTAATA
1 TATTTTGGTAATTGACTATTTTAATAGTAAATAGTGTCAGTAATA
78493 TATAATAATT
Statistics
Matches: 120, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 119 0.99
84 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (83 bp):
TATTTTGGTAATTGACTATTTTAATAGTAAATAGTGTCAGTAATAGTCCTTCAATTAGTTTCTTA
CACTTTCTCCCCCTGTCC
Found at i:81022 original size:75 final size:75
Alignment explanation
Indices: 80891--81200 Score: 365
Period size: 73 Copynumber: 4.2 Consensus size: 75
80881 GTTACAAATC
* * *** * * *
80891 TTTAGTAATTTGGATGTCACATGCATGGCAT-TTATTTGGACGGTTACAAGTACTTGTAACGTCT
1 TTTAGTAATTTGGAGGTTACATGCACAACATCATATTTGGACAGTTACAAATACTTGTAACGTCT
*
80955 ATTCAAGGTA
66 CTTCAAGGTA
* * * *
80965 TTTAATAATTTGAAGGTTACATGCACAACATCATATTCGGGCAGTTACAAATACTTGTAACGTCT
1 TTTAGTAATTTGGAGGTTACATGCACAACATCATATTTGGACAGTTACAAATACTTGTAACGTCT
*
81030 C-TCAAAGTA
66 CTTCAAGGTA
* * *
81039 TGTAGTAA-TTGGAGGTTACATGCACAACATCATATTTGGACAGTTACAAATGCTTGTAACCTCT
1 TTTAGTAATTTGGAGGTTACATGCACAACATCATATTTGGACAGTTACAAATACTTGTAACGTCT
81103 CTTCAAGGTA
66 CTTCAAGGTA
* * * ** *
81113 TCTAGTAATTTGGAGGTTACATGCGCAATATCATATTTTGGTTAGTTACAAATATTTGTAACGTC
1 TTTAGTAATTTGGAGGTTACATGCACAACATCATA-TTTGGACAGTTACAAATACTTGTAACGTC
*
81178 TCTTCAAGATA
65 TCTTCAAGGTA
*
81189 TTTACTAATTTG
1 TTTAGTAATTTG
81201 TCTCTTCAAG
Statistics
Matches: 199, Mismatches: 33, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
73 52 0.26
74 51 0.26
75 52 0.26
76 44 0.22
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (75 bp):
TTTAGTAATTTGGAGGTTACATGCACAACATCATATTTGGACAGTTACAAATACTTGTAACGTCT
CTTCAAGGTA
Found at i:81205 original size:25 final size:25
Alignment explanation
Indices: 81175--81225 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
81165 TATTTGTAAC
81175 GTCTCTTCAAGATATTTACTAATTT
1 GTCTCTTCAAGATATTTACTAATTT
81200 GTCTCTTCAAGATATTTACTAATTT
1 GTCTCTTCAAGATATTTACTAATTT
81225 G
1 G
81226 GAGATTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (25 bp):
GTCTCTTCAAGATATTTACTAATTT
Found at i:81346 original size:175 final size:176
Alignment explanation
Indices: 81047--81375 Score: 516
Period size: 175 Copynumber: 1.9 Consensus size: 176
81037 TATGTAGTAA
* * * *
81047 TTGGAGGTTACATGCACAACATCATATTTGGACAGTTACAAATGCTTGTAACCTCTCTTCAAGGT
1 TTGGAGATTACATGCACAACATCATATTCGGACAGTTACAAATACTTGTAACCTCTCTTCAAAGT
* * * * *
81112 ATCTAGTAATTTGGAGGTTACATGCGCAATATCATATTTTGGTTAGTTACAAATATTTGTAACGT
66 ATCTAGTAATTTGGAGGTTACATGCACAACATCATATTTTGATCAGTTACAAATATTTGTAACAT
81177 CTCTTCAAGATATTTACTAATTTGTCTCTTCAAGATATTTACTAAT
131 CTCTTCAAGATATTTACTAATTTGTCTCTTCAAGATATTTACTAAT
* * *
81223 TTGGAGATTACATGCATAACATCATATTCGGGCAGTTACAAATACTTGTAACGTCTC-TCAAAGT
1 TTGGAGATTACATGCACAACATCATATTCGGACAGTTACAAATACTTGTAACCTCTCTTCAAAGT
* *
81287 ATGTAGTAATTTGGAGGTTACATGCACAACATCATATTTTGATCCGTTACAAATATTTGTAACAT
66 ATCTAGTAATTTGGAGGTTACATGCACAACATCATATTTTGATCAGTTACAAATATTTGTAACAT
*
81352 CTCTTCAAGGTATTTACTAATTTG
131 CTCTTCAAGATATTTACTAATTTG
81376 GAGGTTATAT
Statistics
Matches: 138, Mismatches: 15, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
175 87 0.63
176 51 0.37
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (176 bp):
TTGGAGATTACATGCACAACATCATATTCGGACAGTTACAAATACTTGTAACCTCTCTTCAAAGT
ATCTAGTAATTTGGAGGTTACATGCACAACATCATATTTTGATCAGTTACAAATATTTGTAACAT
CTCTTCAAGATATTTACTAATTTGTCTCTTCAAGATATTTACTAAT
Found at i:81391 original size:76 final size:76
Alignment explanation
Indices: 81201--81439 Score: 304
Period size: 75 Copynumber: 3.2 Consensus size: 76
81191 TACTAATTTG
* * * * **
81201 TCTCTTCAAGATATTTACTAATTTGGAGATTACATGCATAACATCATA-TTCGGGCAGTTACAAA
1 TCTCTTCAAGGTATTTACTAATTTGGAGGTTACATGCACAACATCATATTTAGATCAGTTACAAA
*
81265 TACTTGTAACG
66 TACTTGTAACA
* * * * *
81276 TCTC-TCAAAGTATGTAGTAATTTGGAGGTTACATGCACAACATCATATTTTGATCCGTTACAAA
1 TCTCTTCAAGGTATTTACTAATTTGGAGGTTACATGCACAACATCATATTTAGATCAGTTACAAA
*
81340 TATTTGTAACA
66 TACTTGTAACA
* *
81351 TCTCTTCAAGGTATTTACTAATTTGGAGGTTATATGCACAACATCATATTTAGAT-GGTTACAAA
1 TCTCTTCAAGGTATTTACTAATTTGGAGGTTACATGCACAACATCATATTTAGATCAGTTACAAA
81415 TACTTGTAACA
66 TACTTGTAACA
* *
81426 TTTTTTCAAGGTAT
1 TCTCTTCAAGGTAT
81440 ATAAATGCAC
Statistics
Matches: 141, Mismatches: 21, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
74 37 0.26
75 59 0.42
76 45 0.32
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (76 bp):
TCTCTTCAAGGTATTTACTAATTTGGAGGTTACATGCACAACATCATATTTAGATCAGTTACAAA
TACTTGTAACA
Found at i:82232 original size:16 final size:16
Alignment explanation
Indices: 82188--82295 Score: 91
Period size: 16 Copynumber: 6.9 Consensus size: 16
82178 TTGGGCAGGT
*
82188 TTCGGG-TTCGGCTCA
1 TTCGGGTTTCGGGTCA
* *
82203 TTTGGG-TCCGGGTCA
1 TTCGGGTTTCGGGTCA
82218 TTCGGGTTTCGGGTCA
1 TTCGGGTTTCGGGTCA
* *
82234 -TCTGAG-TTCGGGTAA
1 TTC-GGGTTTCGGGTCA
* *
82249 TTCGGGTCTCGGGTCG
1 TTCGGGTTTCGGGTCA
82265 TTCGGGTCTT-GGGTCA
1 TTCGGGT-TTCGGGTCA
*
82281 TTCGGGTCTCGGGTC
1 TTCGGGTTTCGGGTC
82296 TACCGGGTCT
Statistics
Matches: 73, Mismatches: 14, Indels: 11
0.74 0.14 0.11
Matches are distributed among these distances:
15 30 0.41
16 42 0.58
17 1 0.01
ACGTcount: A:0.06, C:0.21, G:0.38, T:0.34
Consensus pattern (16 bp):
TTCGGGTTTCGGGTCA
Found at i:82246 original size:31 final size:30
Alignment explanation
Indices: 82188--82295 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 30
82178 TTGGGCAGGT
* *
82188 TTCGGGT-TCGGCTCATTTGGGTCCGGGTCA
1 TTCGGGTCTCGGGTCA-TTGGGTTCGGGTCA
* * *
82218 TTCGGGTTTCGGGTCATCTGAGTTCGGGTAA
1 TTCGGGTCTCGGGTCAT-TGGGTTCGGGTCA
* *
82249 TTCGGGTCTCGGGTCGTTCGGGTCTTGGGTCA
1 TTCGGGTCTCGGGTCATT-GGGT-TCGGGTCA
82281 TTCGGGTCTCGGGTC
1 TTCGGGTCTCGGGTC
82296 TACCGGGTCT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
30 9 0.14
31 35 0.54
32 21 0.32
ACGTcount: A:0.06, C:0.21, G:0.38, T:0.34
Consensus pattern (30 bp):
TTCGGGTCTCGGGTCATTGGGTTCGGGTCA
Found at i:82269 original size:9 final size:8
Alignment explanation
Indices: 82249--82310 Score: 60
Period size: 7 Copynumber: 7.9 Consensus size: 8
82239 GTTCGGGTAA
82249 TTCGGGTC
1 TTCGGGTC
82257 -TCGGGTC
1 TTCGGGTC
82264 GTTCGGGTC
1 -TTCGGGTC
82273 TT-GGGTC
1 TTCGGGTC
82280 ATTCGGGTC
1 -TTCGGGTC
82289 -TCGGGTC
1 TTCGGGTC
*
82296 TACCGGGTC
1 T-TCGGGTC
82305 -TCGGGT
1 TTCGGGT
82311 TGGGCGGGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
7 24 0.52
8 4 0.09
9 18 0.39
ACGTcount: A:0.03, C:0.24, G:0.40, T:0.32
Consensus pattern (8 bp):
TTCGGGTC
Found at i:82302 original size:16 final size:16
Alignment explanation
Indices: 82250--82310 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
82240 TTCGGGTAAT
82250 TCGGGTCTCGGGTCGT-
1 TCGGGTCTCGGGTC-TA
*
82266 TCGGGTCTTGGGTC-A
1 TCGGGTCTCGGGTCTA
82281 TTCGGGTCTCGGGTCTA
1 -TCGGGTCTCGGGTCTA
*
82298 CCGGGTCTCGGGT
1 TCGGGTCTCGGGT
82311 TGGGCGGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
16 38 0.97
17 1 0.03
ACGTcount: A:0.03, C:0.25, G:0.41, T:0.31
Consensus pattern (16 bp):
TCGGGTCTCGGGTCTA
Found at i:82303 original size:32 final size:32
Alignment explanation
Indices: 82206--82310 Score: 110
Period size: 32 Copynumber: 3.3 Consensus size: 32
82196 CGGCTCATTT
* *
82206 GGGTC-CGGGTCATTCGGGTTTCGGGTC-ATCT
1 GGGTCTCGGGTCATTCGGGTCTCGGGTCTA-CC
* * *
82237 GAGT-TCGGGTAATTCGGGTCTCGGGTCGT-TC
1 GGGTCTCGGGTCATTCGGGTCTCGGGTC-TACC
*
82268 GGGTCTTGGGTCATTCGGGTCTCGGGTCTACC
1 GGGTCTCGGGTCATTCGGGTCTCGGGTCTACC
82300 GGGTCTCGGGT
1 GGGTCTCGGGT
82311 TGGGCGGGTT
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
31 27 0.46
32 32 0.54
ACGTcount: A:0.07, C:0.22, G:0.40, T:0.31
Consensus pattern (32 bp):
GGGTCTCGGGTCATTCGGGTCTCGGGTCTACC
Found at i:82781 original size:21 final size:21
Alignment explanation
Indices: 82756--82803 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
82746 TAGCCAATTT
82756 ATAATAGGCAAAATCATAACA
1 ATAATAGGCAAAATCATAACA
* * *
82777 ATAATTGGTAAAATTATAACA
1 ATAATAGGCAAAATCATAACA
82798 ATAATA
1 ATAATA
82804 TAAATTGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.27
Consensus pattern (21 bp):
ATAATAGGCAAAATCATAACA
Found at i:82958 original size:48 final size:48
Alignment explanation
Indices: 82887--83023 Score: 145
Period size: 48 Copynumber: 2.9 Consensus size: 48
82877 TATATAATAT
* *
82887 TTTCGGGTCATTCGGGTTTCGGGTCATACAGGTCTTGGGTCAT-TCGGG
1 TTTCGGGTCATTCGGGTTACGGGTCATACAGGTCTCGGGTCATAT-GGG
***
82935 TTTCGGGTCA-TCTGGGTTACGGGTCATTTGGGTCTCGGGTCATATGGG
1 TTTCGGGTCATTC-GGGTTACGGGTCATACAGGTCTCGGGTCATATGGG
* * * *
82983 TTGCGGGTCATTCGGGTCACGGGTTCGT-CGGGTCTCGGGTC
1 TTTCGGGTCATTCGGGTTACGGG-TCATACAGGTCTCGGGTC
83024 GGGCGGGTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
47 2 0.03
48 68 0.89
49 6 0.08
ACGTcount: A:0.09, C:0.20, G:0.38, T:0.34
Consensus pattern (48 bp):
TTTCGGGTCATTCGGGTTACGGGTCATACAGGTCTCGGGTCATATGGG
Found at i:83000 original size:32 final size:31
Alignment explanation
Indices: 82888--83006 Score: 139
Period size: 32 Copynumber: 3.7 Consensus size: 31
82878 ATATAATATT
* **
82888 TTCGGGTCATTCGGGTTTCGGGTCATACAGG
1 TTCGGGTCATTCGGGTCTCGGGTCATATGGG
* * *
82919 TCTTGGGTCATTCGGGTTTCGGGTCATCTGGG
1 T-TCGGGTCATTCGGGTCTCGGGTCATATGGG
*
82951 TTACGGGTCATTTGGGTCTCGGGTCATATGGG
1 TT-CGGGTCATTCGGGTCTCGGGTCATATGGG
*
82983 TTGCGGGTCATTCGGGTCACGGGT
1 TT-CGGGTCATTCGGGTCTCGGGT
83007 TCGTCGGGTC
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
31 2 0.03
32 73 0.97
ACGTcount: A:0.10, C:0.18, G:0.38, T:0.34
Consensus pattern (31 bp):
TTCGGGTCATTCGGGTCTCGGGTCATATGGG
Found at i:83006 original size:16 final size:16
Alignment explanation
Indices: 82887--82999 Score: 124
Period size: 16 Copynumber: 7.1 Consensus size: 16
82877 TATATAATAT
82887 TTTCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
* *
82903 TTTCGGGTCATACAGG
1 TTTCGGGTCATTCGGG
82919 TCTT-GGGTCATTCGGG
1 T-TTCGGGTCATTCGGG
82935 TTTCGGGTCA-TCTGGG
1 TTTCGGGTCATTC-GGG
* *
82951 TTACGGGTCATTTGGG
1 TTTCGGGTCATTCGGG
*
82967 TCTCGGGTCATAT-GGG
1 TTTCGGGTCAT-TCGGG
*
82983 TTGCGGGTCATTCGGG
1 TTTCGGGTCATTCGGG
82999 T
1 T
83000 CACGGGTTCG
Statistics
Matches: 81, Mismatches: 10, Indels: 12
0.79 0.10 0.12
Matches are distributed among these distances:
15 5 0.06
16 72 0.89
17 4 0.05
ACGTcount: A:0.10, C:0.18, G:0.37, T:0.35
Consensus pattern (16 bp):
TTTCGGGTCATTCGGG
Found at i:83022 original size:32 final size:31
Alignment explanation
Indices: 82888--83023 Score: 132
Period size: 32 Copynumber: 4.3 Consensus size: 31
82878 ATATAATATT
* *
82888 TTCGGGTCATTCGGGTTTCGGGTCATACAGG
1 TTCGGGTCATTCGGGTCTCGGGTCATACGGG
* *
82919 TCTTGGGTCATTCGGGTTTCGGGTCAT-CTGGG
1 T-TCGGGTCATTCGGGTCTCGGGTCATAC-GGG
* *
82951 TTACGGGTCATTTGGGTCTCGGGTCATATGGG
1 TT-CGGGTCATTCGGGTCTCGGGTCATACGGG
* *
82983 TTGCGGGTCATTCGGGTCACGGGTTCGT-CGGG
1 TT-CGGGTCATTCGGGTCTCGGG-TCATACGGG
83015 TCTCGGGTC
1 T-TCGGGTC
83024 GGGCGGGTTC
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
31 3 0.03
32 81 0.92
33 4 0.05
ACGTcount: A:0.09, C:0.20, G:0.38, T:0.33
Consensus pattern (31 bp):
TTCGGGTCATTCGGGTCTCGGGTCATACGGG
Found at i:83087 original size:17 final size:18
Alignment explanation
Indices: 83065--83102 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
83055 AAATCGAATT
83065 GGGCGGGTTA-CGGATTC
1 GGGCGGGTTATCGGATTC
*
83082 GGGCGGGTTATCGGGTTC
1 GGGCGGGTTATCGGATTC
83100 GGG
1 GGG
83103 TCAGTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.08, C:0.16, G:0.53, T:0.24
Consensus pattern (18 bp):
GGGCGGGTTATCGGATTC
Found at i:84448 original size:149 final size:145
Alignment explanation
Indices: 84205--84538 Score: 445
Period size: 149 Copynumber: 2.3 Consensus size: 145
84195 GTCTATATAT
* *
84205 CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATATGATGTTGCGCACGTCCAAATTAGTA
1 CTTGAAAAGACGTTACAAGTACTTGTAACCGTCCAAATATGATGTTGCGCACGTCCAAATTAGTA
*
84270 AATACCTTGAAGAGACGTTACAAATATTTGTAA-TCACCCAAATATGATGTTCTGCATATAACCT
66 AATACCTTAAAGAGACGTTACAAATATTTGTAACT-ACCCAAATATGATGTTCTGCATATAACCT
*
84334 CCAAATTACTGAATAC
130 CCAAATTACTAAATAC
* * * * * *
84350 CTTGAAAAGAGGTTACAAGTAGTTGTAACTGTCCAAATATGATGTTGTGCATGTAACCTCTAATT
1 CTTGAAAAGACGTTACAAGTACTTGTAACCGTCCAAATATGATGTTGCGCACGT---C-CAAATT
* * * * * *
84415 ATTAAATACCTTAAAGAGACGTTACAAGTATTTGTAACTGCCCAAATATGATGTTGTGGATGTAA
62 AGTAAATACCTTAAAGAGACGTTACAAATATTTGTAACTACCCAAATATGATGTTCTGCATATAA
* *
84480 CCTCCAAATTATTAAATAT
127 CCTCCAAATTACTAAATAC
*
84499 CTTGAATAGACGTTACAAGTACTTGTAACCGTCCAAATAT
1 CTTGAAAAGACGTTACAAGTACTTGTAACCGTCCAAATAT
84539 AATGACATTC
Statistics
Matches: 163, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
145 48 0.29
148 1 0.01
149 113 0.69
150 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (145 bp):
CTTGAAAAGACGTTACAAGTACTTGTAACCGTCCAAATATGATGTTGCGCACGTCCAAATTAGTA
AATACCTTAAAGAGACGTTACAAATATTTGTAACTACCCAAATATGATGTTCTGCATATAACCTC
CAAATTACTAAATAC
Found at i:84555 original size:75 final size:74
Alignment explanation
Indices: 84205--84538 Score: 390
Period size: 75 Copynumber: 4.5 Consensus size: 74
84195 GTCTATATAT
* *
84205 CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATATGATGT-TGC--G-CACGTCCAAATT
1 CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATATGATGTCTGCATGTAACCTCCAAATT
*
84266 AGTAAATAC
66 ATTAAATAC
* * ** *
84275 CTTGAAGAGACGTTACAAATATTTGTAATCACCCAAATATGATGTTCTGCATATAACCTCCAAAT
1 CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATATGATG-TCTGCATGTAACCTCCAAAT
* *
84340 TACTGAATAC
65 TATTAAATAC
* * * * * *
84350 CTTGAAAAGAGGTTACAAGTAGTTGTAACTGTCCAAATATGATGTTGTGCATGTAACCT-CTAAT
1 CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATATGATG-TCTGCATGTAACCTCCAAAT
84414 TATTAAATAC
65 TATTAAATAC
* * * * *
84424 CTTAAAGAGACGTTACAAGTATTTGTAACTGCCCAAATATGATGTTGTGGATGTAACCTCCAAAT
1 CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATATGATG-TCTGCATGTAACCTCCAAAT
*
84489 TATTAAATAT
65 TATTAAATAC
* *
84499 CTTGAATAGACGTTACAAGTACTTGTAACCGTCCAAATAT
1 CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATAT
84539 AATGACATTC
Statistics
Matches: 223, Mismatches: 35, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
70 40 0.18
71 1 0.00
72 3 0.01
74 65 0.29
75 114 0.51
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (74 bp):
CTTGAAGAGACGTTACAAGTATTTGTAACCGTCCAAATATGATGTCTGCATGTAACCTCCAAATT
ATTAAATAC
Found at i:85887 original size:10 final size:10
Alignment explanation
Indices: 85872--85897 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
85862 GAGGACTCTA
85872 GAATTTTCTG
1 GAATTTTCTG
85882 GAATTTTCTG
1 GAATTTTCTG
85892 GAATTT
1 GAATTT
85898 GGCAGCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:93605 original size:22 final size:20
Alignment explanation
Indices: 93564--93606 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
93554 TAAAAACACC
*
93564 TATAAAAATAGCAAAAAGTA
1 TATAAAAATAACAAAAAGTA
93584 TATAAAAATAACTATAAAAGTA
1 TATAAAAATAAC-A-AAAAGTA
93606 T
1 T
93607 GCATAATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.26
Consensus pattern (20 bp):
TATAAAAATAACAAAAAGTA
Found at i:96145 original size:16 final size:16
Alignment explanation
Indices: 96124--96177 Score: 108
Period size: 16 Copynumber: 3.4 Consensus size: 16
96114 CCATGCGTGA
96124 CTTCACCTTGAAGCCT
1 CTTCACCTTGAAGCCT
96140 CTTCACCTTGAAGCCT
1 CTTCACCTTGAAGCCT
96156 CTTCACCTTGAAGCCT
1 CTTCACCTTGAAGCCT
96172 CTTCAC
1 CTTCAC
96178 TTGTTTCCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.19, C:0.39, G:0.11, T:0.31
Consensus pattern (16 bp):
CTTCACCTTGAAGCCT
Found at i:99565 original size:21 final size:21
Alignment explanation
Indices: 99526--99574 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
99516 TCAATGCTTT
**
99526 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
99548 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
99569 A-GAAGC
1 AGGAAGC
99575 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:109952 original size:18 final size:19
Alignment explanation
Indices: 109918--109956 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
109908 TGAAGATTTC
109918 TTGAAGATAATTTGAAGAA
1 TTGAAGATAATTTGAAGAA
*
109937 TTGAAGATTA-TTGAAGAA
1 TTGAAGATAATTTGAAGAA
109955 TT
1 TT
109957 ATTTCAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (19 bp):
TTGAAGATAATTTGAAGAA
Found at i:115322 original size:32 final size:32
Alignment explanation
Indices: 115263--115324 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
115253 AGTATATCCC
* * *
115263 AAACATAAGTAATAAGCCCAGTCCTAAATTGT
1 AAACATAAATAAAAAGCCCAATCCTAAATTGT
* *
115295 AAACATAAATAAAAAGCTCAATTCTAAATT
1 AAACATAAATAAAAAGCCCAATCCTAAATT
115325 CTAATTAACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (32 bp):
AAACATAAATAAAAAGCCCAATCCTAAATTGT
Done.