Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022193.1 Corchorus olitorius cultivar O-4 contig22226, 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: 39289
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--30 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31 GCATTGACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2292 original size:11 final size:11
Alignment explanation
Indices: 2278--2315 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
2268 ATTCATAACA
2278 AATTTATAATT
1 AATTTATAATT
2289 AATTTATAATT
1 AATTTATAATT
2300 -ATTTGATAATT
1 AATTT-ATAATT
*
2311 TATTT
1 AATTT
2316 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:3233 original size:23 final size:21
Alignment explanation
Indices: 3190--3231 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
3180 TAAGTCCTAA
3190 CTACACACTCCAATATTTTTT
1 CTACACACTCCAATATTTTTT
*
3211 CTACACACTCCAACATTTTTT
1 CTACACACTCCAATATTTTTT
3232 TTTTGAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.40
Consensus pattern (21 bp):
CTACACACTCCAATATTTTTT
Found at i:3328 original size:32 final size:32
Alignment explanation
Indices: 3292--3354 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
3282 AGAGCAGGGC
** *
3292 AACCCATTCAGTTTGGGATTTTGCAGTTTTTT
1 AACCCATTCAGTTTGAAATTCTGCAGTTTTTT
3324 AACCCATTCAGTTTGAAATTCTGCAGTTTTT
1 AACCCATTCAGTTTGAAATTCTGCAGTTTTT
3355 CGGAATTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.44
Consensus pattern (32 bp):
AACCCATTCAGTTTGAAATTCTGCAGTTTTTT
Found at i:8234 original size:19 final size:21
Alignment explanation
Indices: 8196--8234 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
8186 TAAGAATCTC
*
8196 TCTTTTTCCTTCTATTTTTTT
1 TCTTTTTCCTTCTATATTTTT
8217 TCTTTTT-C-TCTATATTTT
1 TCTTTTTCCTTCTATATTTT
8235 CACTGCTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (21 bp):
TCTTTTTCCTTCTATATTTTT
Found at i:9349 original size:139 final size:138
Alignment explanation
Indices: 9092--9361 Score: 414
Period size: 139 Copynumber: 1.9 Consensus size: 138
9082 GATTCACCAG
*
9092 ATCAAACTTTGAAGAAATACTGCACCAAATTAACTTGATTCTCCGAATCAAACTTTGAAGAAATA
1 ATCAAACTTTGAAGAAATACTGCACCAAATTAACTTGATTCACCGAATCAAACTTTGAAGAAATA
* * * *
9157 CTGCACTAAATTAACTTGATTCACCGAATGAAACTTTGAAGAAATACTGCACCGCAGTAACTTGA
66 CTGCACCAAAGTAACTTGATTCACCGAATCAAACTTTGAAGAAATAATGCACCGCAGTAACTTGA
9222 TTTACCGA
131 TTTACCGA
* ** *
9230 ATCAAACTTTTGAAGAAATATTGCACTGAATTAACTTGATTCACCGAATCAGACTTTGAAGAAAT
1 ATCAAAC-TTTGAAGAAATACTGCACCAAATTAACTTGATTCACCGAATCAAACTTTGAAGAAAT
** * *
9295 ACTGCACCGCAGTAACTTGATTCACTGAATCAAACTTTGAAGAAATAATGCACCGCATTAACTTG
65 ACTGCACCAAAGTAACTTGATTCACCGAATCAAACTTTGAAGAAATAATGCACCGCAGTAACTTG
9360 AT
130 AT
9362 CTACTTAATC
Statistics
Matches: 118, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
138 7 0.06
139 111 0.94
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.28
Consensus pattern (138 bp):
ATCAAACTTTGAAGAAATACTGCACCAAATTAACTTGATTCACCGAATCAAACTTTGAAGAAATA
CTGCACCAAAGTAACTTGATTCACCGAATCAAACTTTGAAGAAATAATGCACCGCAGTAACTTGA
TTTACCGA
Found at i:9372 original size:46 final size:46
Alignment explanation
Indices: 9055--9361 Score: 400
Period size: 46 Copynumber: 6.7 Consensus size: 46
9045 GGTTCGCAAA
* * * * *
9055 TGAAGAAATGCCGCATCGAATTAGCTCGATTCACC-AGATCAAACTT
1 TGAAGAAATACTGCACCGAATTAACTTGATTCACCGA-ATCAAACTT
* *
9101 TGAAGAAATACTGCACCAAATTAACTTGATTCTCCGAATCAAACTT
1 TGAAGAAATACTGCACCGAATTAACTTGATTCACCGAATCAAACTT
** *
9147 TGAAGAAATACTGCACTAAATTAACTTGATTCACCGAATGAAACTT
1 TGAAGAAATACTGCACCGAATTAACTTGATTCACCGAATCAAACTT
* * *
9193 TGAAGAAATACTGCACCGCAGTAACTTGATTTACCGAATCAAACTTT
1 TGAAGAAATACTGCACCGAATTAACTTGATTCACCGAATCAAAC-TT
* * *
9240 TGAAGAAATATTGCACTGAATTAACTTGATTCACCGAATCAGACTT
1 TGAAGAAATACTGCACCGAATTAACTTGATTCACCGAATCAAACTT
* * *
9286 TGAAGAAATACTGCACCGCAGTAACTTGATTCACTGAATCAAACTT
1 TGAAGAAATACTGCACCGAATTAACTTGATTCACCGAATCAAACTT
* *
9332 TGAAGAAATAATGCACCGCATTAACTTGAT
1 TGAAGAAATACTGCACCGAATTAACTTGAT
9362 CTACTTAATC
Statistics
Matches: 229, Mismatches: 30, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
46 188 0.82
47 41 0.18
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (46 bp):
TGAAGAAATACTGCACCGAATTAACTTGATTCACCGAATCAAACTT
Found at i:9585 original size:91 final size:91
Alignment explanation
Indices: 9316--9571 Score: 367
Period size: 91 Copynumber: 2.8 Consensus size: 91
9306 GTAACTTGAT
* * **
9316 TCACTGAATCAAACTTTGAAGAAATAATGCACCGCATTAACTTGA-TCTACTTAATCATCCTGAA
1 TCACCGAATCCAACTTTGAAGAAATAATGCACCGCATTAACTTGATTC-ACCGAATCATCCTGAA
9380 CTGTC-TGAAAATGTACTGCACCGAGC
65 CTGTCTTGAAAATGTACTGCACCGAGC
* *
9406 TCACCGAATCCAACCTTGAAGAAATTAATGCACTGCATTAACTTGATTCACCGAATCATCCTGAA
1 TCACCGAATCCAACTTTGAAGAAA-TAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAA
*
9471 TTGT-TTGAAAATGTACTGCACCGAGC
65 CTGTCTTGAAAATGTACTGCACCGAGC
* *
9497 TCACCGAATCCAACTTTGAAGAAATAATGCGCCGCATTGACTTGATTCACCGAATCAAT-CTGAA
1 TCACCGAATCCAACTTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATC-ATCCTGAA
*
9561 CTATCTTGAAA
65 CTGTCTTGAAA
9572 GTTATCTTGA
Statistics
Matches: 148, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
90 57 0.39
91 89 0.60
92 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (91 bp):
TCACCGAATCCAACTTTGAAGAAATAATGCACCGCATTAACTTGATTCACCGAATCATCCTGAAC
TGTCTTGAAAATGTACTGCACCGAGC
Found at i:9702 original size:54 final size:54
Alignment explanation
Indices: 9601--10319 Score: 494
Period size: 54 Copynumber: 13.9 Consensus size: 54
9591 TTGGATCACT
* * *
9601 TTAAACCACTGGAAACTATCTTGATTGACCTGCACTAGATCGCTTGAAGATAAAG
1 TTAAACCACTGGAAACTTTCTTGATTGACC-GCACTGGATCACTTGAAGATAAAG
* * * * * *
9656 TTAAACCACTGTAAACTTTTTTGACTGACTGCAATGGATCGC-T-----T---G
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAG
* *
9701 --AAACCACCGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAC
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAG
* * * * *
9753 TTAAACCACTGGAAACTTTCTTAACTGACTGCACTGGATCACTTGAGGATAAAT
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAG
* * *
9807 TTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTTGAGGATAAAT
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAAG
** * * *
9862 TTAAACCACTATAAACTTTCTTGATTAACCGCACTGGGTCGC-T-----T---G
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAG
** * * * * *
9907 --AAACCACCAGTAACTTTCTTGATTGACTGCTCCGGATCACTTGAAGATAAAT
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAG
* * * *
9959 TTAAACCACTGGAAACTTCCTTGATTGACCGCACTAGATCACTTGAAAATAAAC
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAG
* * *
10013 TTAAACCGCTGGAAACTTCCTTGATTGACCGCACTGGATCACTTG-AGAATAAAC
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAG-ATAAAG
** * * **
10067 TTAAACCGGTGGAAACTTCCTTGATTGACCGCACTGGACCACTTGAAGA-AATTT
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAA-AG
* ** *
10121 TTAAACCACTGTAAA----CTTGATTGATTGCACTGGATCACTTTGAAGATAAAC
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAAG
* ** * * ***
10172 TTAAGCCACTATAAA----CTTGATTGATCGCACTGGATCATTTTGAAGGA-ATTC
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCA-CTTGAA-GATAAAG
* ** *
10223 TTAAACCACTGTAAA----CTTGATTGATTGCACTGGATCACTTTGAAGATAAAC
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGATAAAG
* * * *
10274 TTAAGCCACTGTAAA----CTTGATTGATCACACTGGATCACTTTGAAGA
1 TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAAGA
10320 AATTTTTTAA
Statistics
Matches: 552, Mismatches: 80, Indels: 68
0.79 0.11 0.10
Matches are distributed among these distances:
43 64 0.12
44 2 0.00
45 1 0.00
48 2 0.00
49 2 0.00
50 22 0.04
51 132 0.24
52 4 0.01
53 5 0.01
54 241 0.44
55 77 0.14
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (54 bp):
TTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAAGATAAAG
Found at i:9737 original size:43 final size:43
Alignment explanation
Indices: 9658--9745 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
9648 AGATAAAGTT
* * * * *
9658 AAACCACTGTAAACTTTTTTGACTGACTGCAATGGATCGCTTG
1 AAACCACCGGAAACTTTCTTGACTGACCGCAATGGATCACTTG
* *
9701 AAACCACCGGAAACTTTCTTGATTGACCGCACTGGATCACTTG
1 AAACCACCGGAAACTTTCTTGACTGACCGCAATGGATCACTTG
9744 AA
1 AA
9746 GATAAACTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
AAACCACCGGAAACTTTCTTGACTGACCGCAATGGATCACTTG
Found at i:9949 original size:152 final size:151
Alignment explanation
Indices: 9766--10058 Score: 415
Period size: 152 Copynumber: 1.9 Consensus size: 151
9756 AACCACTGGA
* * * *
9766 AACTTTCTTAACTGACTGCACTGGATCACTTGAGGATAAATTTAAACCACTGTAAACTTTCTTGA
1 AACTTTCTTAACTGACTGCACCGGATCACTTGAAGATAAATTTAAACCACTGGAAACTTCCTTGA
* ** * * *
9831 TTGACCGCACTGGATCACTTTGAGGATAAATTTAAACCACTATAAACTTTCTTGATTAACCGCAC
66 TTGACCGCACTAGATCAC-TTGAAAATAAACTTAAACCACTAGAAACTTCCTTGATTAACCGCAC
* *
9896 TGGGTCGCTTGAAACCACCAGT
130 TGGATCACTTGAAACCACCAGT
* * *
9918 AACTTTCTTGATTGACTGCTCCGGATCACTTGAAGATAAATTTAAACCACTGGAAACTTCCTTGA
1 AACTTTCTTAACTGACTGCACCGGATCACTTGAAGATAAATTTAAACCACTGGAAACTTCCTTGA
* * *
9983 TTGACCGCACTAGATCACTTGAAAATAAACTTAAACCGCTGGAAACTTCCTTGATTGACCGCACT
66 TTGACCGCACTAGATCACTTGAAAATAAACTTAAACCACTAGAAACTTCCTTGATTAACCGCACT
10048 GGATCACTTGA
131 GGATCACTTGA
10059 GAATAAACTT
Statistics
Matches: 123, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
151 48 0.39
152 75 0.61
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (151 bp):
AACTTTCTTAACTGACTGCACCGGATCACTTGAAGATAAATTTAAACCACTGGAAACTTCCTTGA
TTGACCGCACTAGATCACTTGAAAATAAACTTAAACCACTAGAAACTTCCTTGATTAACCGCACT
GGATCACTTGAAACCACCAGT
Found at i:9954 original size:206 final size:205
Alignment explanation
Indices: 9600--10113 Score: 677
Period size: 206 Copynumber: 2.5 Consensus size: 205
9590 ATTGGATCAC
* * * * *
9600 TTTAAACCACTGGAAACTATCTTGATTGACCTGCACTAGATCGCTTGAAGATAAAGTTAAACCAC
1 TTTAAACCACTGGAAACTTTCTTGATTGACC-GCACTGGATCACTTGAGGATAAACTTAAACCAC
* * * * *
9665 TGTAAACTTTTTTGACTGACTGCAATGGATCGCTTGAAACCACCGGAAACTTTCTTGATTGACCG
65 TGTAAACTTTCTTGATTGACCGCACTGGATCGCTTGAAACCACCAGAAACTTTCTTGATTGACCG
* * * *
9730 CACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTAACTGACTGCACTGGATCAC
130 CACCGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTCCTTAACTGACCGCACTAGATCAC
**
9795 TTGAGGATAAA
195 TTGAAAATAAA
* *
9806 TTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCACTTTGAGGATAAATTTAAACCAC
1 TTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCAC-TTGAGGATAAACTTAAACCAC
* * * * *
9871 TATAAACTTTCTTGATTAACCGCACTGGGTCGCTTGAAACCACCAGTAACTTTCTTGATTGACTG
65 TGTAAACTTTCTTGATTGACCGCACTGGATCGCTTGAAACCACCAGAAACTTTCTTGATTGACCG
* * * *
9936 CTCCGGATCACTTGAAGATAAATTTAAACCACTGGAAACTTCCTTGATTGACCGCACTAGATCAC
130 CACCGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTCCTTAACTGACCGCACTAGATCAC
10001 TTGAAAATAAA
195 TTGAAAATAAA
* * * * **
10012 CTTAAACCGCTGGAAACTTCCTTGATTGACCGCACTGGATCACTTGAGAATAAACTTAAACCGGT
1 TTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAGGATAAACTTAAACCACT
* * * *
10077 GGAAACTTCCTTGATTGACCGCACTGGACCACTTGAA
66 GTAAACTTTCTTGATTGACCGCACTGGATCGCTTGAA
10114 GAAATTTTTA
Statistics
Matches: 266, Mismatches: 41, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
205 58 0.22
206 208 0.78
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (205 bp):
TTTAAACCACTGGAAACTTTCTTGATTGACCGCACTGGATCACTTGAGGATAAACTTAAACCACT
GTAAACTTTCTTGATTGACCGCACTGGATCGCTTGAAACCACCAGAAACTTTCTTGATTGACCGC
ACCGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTCCTTAACTGACCGCACTAGATCACT
TGAAAATAAA
Found at i:10187 original size:51 final size:50
Alignment explanation
Indices: 9978--10364 Score: 366
Period size: 51 Copynumber: 7.5 Consensus size: 50
9968 TGGAAACTTC
* * * * * *
9978 CTTGATTGACCGCACTAGATCAC-TTGAAAATAAACTTAAACCGCTGGAAA
1 CTTGATTGATCGCACTGGATCACTTTGAAGA-AATCTTAAACCACTGTAAA
* * * ** *
10028 CTTCCTTGATTGACCGCACTGGATCACTTGAGAATAAA-CTTAAACCGGTGGAAA
1 ----CTTGATTGATCGCACTGGATCACTT-TGAAGAAATCTTAAACCACTGTAAA
* * *
10082 CTTCCTTGATTGACCGCACTGGACCAC-TTGAAGAAATTTTTAAACCACTGTAAA
1 ----CTTGATTGATCGCACTGGATCACTTTGAAGAAA-TCTTAAACCACTGTAAA
* * * *
10136 CTTGATTGATTGCACTGGATCACTTTGAAGATAAACTTAAGCCACTATAAA
1 CTTGATTGATCGCACTGGATCACTTTGAAGA-AATCTTAAACCACTGTAAA
* *
10187 CTTGATTGATCGCACTGGATCATTTTGAAGGAATTCTTAAACCACTGTAAA
1 CTTGATTGATCGCACTGGATCACTTTGAA-GAAATCTTAAACCACTGTAAA
* * *
10238 CTTGATTGATTGCACTGGATCACTTTGAAGATAAACTTAAGCCACTGTAAA
1 CTTGATTGATCGCACTGGATCACTTTGAAGA-AATCTTAAACCACTGTAAA
* * *
10289 CTTGATTGATCACACTGGATCACTTTGAAGAAATTTTTTAACCACTGTAAA
1 CTTGATTGATCGCACTGGATCACTTTGAAGAAA-TCTTAAACCACTGTAAA
*
10340 CTTGATTGATCACACTGGATCACTT
1 CTTGATTGATCGCACTGGATCACTT
10365 AAAATTCAGC
Statistics
Matches: 289, Mismatches: 35, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
50 24 0.08
51 172 0.60
52 10 0.03
53 1 0.00
54 75 0.26
55 3 0.01
56 4 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (50 bp):
CTTGATTGATCGCACTGGATCACTTTGAAGAAATCTTAAACCACTGTAAA
Found at i:10239 original size:102 final size:101
Alignment explanation
Indices: 10086--10364 Score: 450
Period size: 102 Copynumber: 2.7 Consensus size: 101
10076 TGGAAACTTC
* * *
10086 CTTGATTGACCGCACTGGACCACTTGAAGAAATTTTTAAACCACTGTAAACTTGATTGATTGCAC
1 CTTGATTGATCGCACTGGATCATTTGAAGAAATTTTTAAACCACTGTAAACTTGATTGATTGCAC
10151 TGGATCACTTTGAAGATAAACTTAAGCCACTATAAA
66 TGGATCACTTTGAAGATAAACTTAAGCCACTATAAA
* *
10187 CTTGATTGATCGCACTGGATCATTTTGAAGGAATTCTTAAACCACTGTAAACTTGATTGATTGCA
1 CTTGATTGATCGCACTGGATCA-TTTGAAGAAATTTTTAAACCACTGTAAACTTGATTGATTGCA
*
10252 CTGGATCACTTTGAAGATAAACTTAAGCCACTGTAAA
65 CTGGATCACTTTGAAGATAAACTTAAGCCACTATAAA
* * **
10289 CTTGATTGATCACACTGGATCACTTTGAAGAAATTTTTTAACCACTGTAAACTTGATTGATCACA
1 CTTGATTGATCGCACTGGATCA-TTTGAAGAAATTTTTAAACCACTGTAAACTTGATTGATTGCA
10354 CTGGATCACTT
65 CTGGATCACTT
10365 AAAATTCAGC
Statistics
Matches: 164, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
101 20 0.12
102 144 0.88
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (101 bp):
CTTGATTGATCGCACTGGATCATTTGAAGAAATTTTTAAACCACTGTAAACTTGATTGATTGCAC
TGGATCACTTTGAAGATAAACTTAAGCCACTATAAA
Found at i:10244 original size:260 final size:254
Alignment explanation
Indices: 9718--10291 Score: 602
Period size: 260 Copynumber: 2.2 Consensus size: 254
9708 CGGAAACTTT
* *
9718 CTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTTCTTAACTGACT
1 CTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTCCTTAACTGACC
* * * * *
9783 GCACTGGATCACTTGAGGATAAATTTAAACCACTGTAAACTTTCTTGATTGACCGCACTGGATCA
66 GCACTGGATCACTTGAGAATAAACTTAAACCACTGGAAACTTCCTTGATTGACCGCACTGGACCA
* ** * * **
9848 CTTTGAGGATAAATTTAAACCACTATAAACTTTCTTGATTAACCGCACTGGGTCGCTTGAAACCA
131 CTTTGAAGATAAATTTAAACCACTATAAACTTGATTGATT-A--GCACTGGATCACTTGAAAAAA
* * * * *
9913 CCAGTAACTTTCTTGATTGACTGCTCCGGATCACTTGAAGATAAATTTAAACCACTGGAAACTTC
193 CAAGCAACTTACTTGATTGACTGCACCGGATCACTTGAAGAGAAATTTAAACCACTGGAAA---C
* * * * *
9978 CTTGATTGACCGCACTAGATCACTTGAAAATAAACTTAAACCGCTGGAAACTTCCTTGATTGACC
1 CTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTCCTTAACTGACC
**
10043 GCACTGGATCACTTGAGAATAAACTTAAACCGGTGGAAACTTCCTTGATTGACCGCACTGGACCA
66 GCACTGGATCACTTGAGAATAAACTTAAACCACTGGAAACTTCCTTGATTGACCGCACTGGACCA
* *
10108 C-TTGAAGA-AATTTTTAAACCACTGTAAACTTGATTGATT-GCACTGGATCACTTTGAAGATAA
131 CTTTGAAGATAA-ATTTAAACCACTATAAACTTGATTGATTAGCACTGGATCAC-TTGAA-A-AA
* * * *
10170 ACTTAAGCCACTATAAACTTGATTGA-TCGCACTGGATCATTTTGAAG-GAATTCTTAAACCACT
192 AC--AAGCAACT-T--ACTTGATTGACT-GCACCGGATCA-CTTGAAGAGAAAT-TTAAACCACT
*
10233 GTAAA-
249 GGAAAC
** * *
10238 CTTGATTGATTGCACTGGATCACTTTGAAGATAAACTTAAGCCACTGTAAACTT
1 CTTGATTGACCGCACTGGATCAC-TTGAAGATAAACTTAAACCACTGGAAACTT
10292 GATTGATCAC
Statistics
Matches: 261, Mismatches: 40, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
255 10 0.04
256 5 0.02
257 1 0.00
258 4 0.02
259 30 0.11
260 142 0.54
261 27 0.10
262 1 0.00
263 21 0.08
264 20 0.08
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (254 bp):
CTTGATTGACCGCACTGGATCACTTGAAGATAAACTTAAACCACTGGAAACTTCCTTAACTGACC
GCACTGGATCACTTGAGAATAAACTTAAACCACTGGAAACTTCCTTGATTGACCGCACTGGACCA
CTTTGAAGATAAATTTAAACCACTATAAACTTGATTGATTAGCACTGGATCACTTGAAAAAACAA
GCAACTTACTTGATTGACTGCACCGGATCACTTGAAGAGAAATTTAAACCACTGGAAAC
Found at i:11480 original size:13 final size:13
Alignment explanation
Indices: 11462--11487 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11452 GGAATGCAAT
11462 TCATTTTCAAAAC
1 TCATTTTCAAAAC
11475 TCATTTTCAAAAC
1 TCATTTTCAAAAC
11488 ATTTACAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
TCATTTTCAAAAC
Found at i:11924 original size:19 final size:20
Alignment explanation
Indices: 11888--11925 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11878 CCTTTTTGAG
* *
11888 AAAACATTTTTTCTTTTTAA
1 AAAACAATTTTTCATTTTAA
11908 AAAACAATTTTT-ATTTTA
1 AAAACAATTTTTCATTTTA
11926 GGGACTATCC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (20 bp):
AAAACAATTTTTCATTTTAA
Found at i:12725 original size:19 final size:20
Alignment explanation
Indices: 12696--12733 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
12686 GCAATTTGAT
12696 TTCTCTTTCTTTTTTTTTCA
1 TTCTCTTTCTTTTTTTTTCA
12716 TTCT-TTTCTTTTTTTTTC
1 TTCTCTTTCTTTTTTTTTC
12734 TTTTTCTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (20 bp):
TTCTCTTTCTTTTTTTTTCA
Found at i:12732 original size:10 final size:10
Alignment explanation
Indices: 12701--12738 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
12691 TTGATTTCTC
12701 TTTCTTTTTT
1 TTTCTTTTTT
* *
12711 TTTC-ATTCT
1 TTTCTTTTTT
12720 TTTCTTTTTT
1 TTTCTTTTTT
12730 TTTCTTTTT
1 TTTCTTTTT
12739 CTGATGGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:15538 original size:66 final size:63
Alignment explanation
Indices: 15364--15688 Score: 246
Period size: 65 Copynumber: 5.0 Consensus size: 63
15354 TTCGGGAGAC
* * ** * * *
15364 AAAACTAAACTTAGACGCAGAAATATAAAAAACTGGCCCTTTGATCGAAAGGCTATTTCTGGAAA
1 AAAACTAAACTTAGATG--GAAAAATATGAAACT-GACCTTTGATCGAAAGGGTATTTTTGGAAA
15429 TA
63 -A
* * * * *
15431 AAAACTAAACTTAGATGCAGAAAGACGAAACTGACCTTTTGATCGAAGGGGTATTTTATGGAAAA
1 AAAACTAAACTTAGATGGAAAAATATGAAACTGACC-TTTGATCGAAAGGGTATTTT-TGGAAAA
* * *
15496 CAAAATTAAACCTAGATGTGAAAAATATGAAACTGACCTTTGACCGAAAGGGTATTTTTGGAAAA
1 -AAAACTAAACTTAGATG-GAAAAATATGAAACTGACCTTTGATCGAAAGGGTATTTTTGGAAAA
* * * ** * * *
15561 GGAAACTAAACTTAGATACGAAAAATATGAAACTAACCCTTTGGCCGAAAGAGT-GTTTTGG--G
1 -AAAACTAAACTTAGAT-GGAAAAATATGAAACTGA-CCTTTGATCGAAAGGGTATTTTTGGAAA
15623 A
63 A
* * * * *
15624 AAAA--AAACTTAGATACGAAAAAGATGAAACTAACCCTTTGACCGAACGGGTATTTTTGGAAAA
1 AAAACTAAACTTAGAT-GGAAAAATATGAAACTGA-CCTTTGATCGAAAGGGTATTTTTGGAAAA
15687 AA
1 AA
15689 GAAAATACTA
Statistics
Matches: 213, Mismatches: 36, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
60 43 0.20
61 6 0.03
62 3 0.01
63 4 0.02
64 3 0.01
65 69 0.32
66 54 0.25
67 31 0.15
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (63 bp):
AAAACTAAACTTAGATGGAAAAATATGAAACTGACCTTTGATCGAAAGGGTATTTTTGGAAAA
Found at i:15584 original size:65 final size:64
Alignment explanation
Indices: 15249--15688 Score: 300
Period size: 66 Copynumber: 6.7 Consensus size: 64
15239 CTTAAATGTG
* *** * * *
15249 AAAATATGACAAGCTTGACCCTTTGACCGAAAGGGCATTTTTGGAAATTGGAAGTAAACTCAAAT
1 AAAATATGA-AA-C-TGA-CCTTTGACCGAAAGGGTATTTTTGGAAA-AAAAACTAAACTTAGAT
15314 GCG-
61 GCGA
* * * * * * * * *
15317 AAAATGAAGAAACTGAACCTTTCACTGAAGGGGCATTTTCGGGAGACAAAACTAAACTTAGACGC
1 AAAAT-ATGAAACTG-ACCTTTGACCGAAAGGGTATTTT-TGGAAAAAAAACTAAACTTAGATGC
15382 AGA
63 -GA
* ** * * * *
15385 AATATAAAAAACTGGCCCTTTGATCGAAAGGCTATTTCTGGAAATAAAAACTAAACTTAGATGC-
1 AAAATATGAAACT-GACCTTTGACCGAAAGGGTATTTTTGGAAA-AAAAACTAAACTTAGATGCG
15449 A
64 A
* * * * * * * *
15450 GAAAGACGAAACTGACCTTTTGATCGAAGGGGTATTTTATGGAAAACAAAATTAAACCTAGATGT
1 AAAATATGAAACTGACC-TTTGACCGAAAGGGTATTTT-TGGAAAA-AAAACTAAACTTAGATGC
15515 GA
63 GA
* *
15517 AAAATATGAAACTGACCTTTGACCGAAAGGGTATTTTTGGAAAAGGAAACTAAACTTAGATACGA
1 AAAATATGAAACTGACCTTTGACCGAAAGGGTATTTTTGGAAAA-AAAACTAAACTTAGATGCGA
* * * * * *
15582 AAAATATGAAACTAACCCTTTGGCCGAAAGAGT-GTTTTGG--GAAAAA--AAACTTAGATACGA
1 AAAATATGAAACTGA-CCTTTGACCGAAAGGGTATTTTTGGAAAAAAAACTAAACTTAGATGCGA
* * *
15642 AAAAGATGAAACTAACCCTTTGACCGAACGGGTATTTTTGGAAAAAA
1 AAAATATGAAACTGA-CCTTTGACCGAAAGGGTATTTTTGGAAAAAA
15689 GAAAATACTA
Statistics
Matches: 295, Mismatches: 62, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
60 43 0.15
61 6 0.02
62 3 0.01
63 4 0.01
64 3 0.01
65 69 0.23
66 91 0.31
67 61 0.21
68 12 0.04
69 3 0.01
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (64 bp):
AAAATATGAAACTGACCTTTGACCGAAAGGGTATTTTTGGAAAAAAAACTAAACTTAGATGCGA
Found at i:15651 original size:60 final size:60
Alignment explanation
Indices: 15515--15688 Score: 197
Period size: 60 Copynumber: 2.8 Consensus size: 60
15505 ACCTAGATGT
* * * *
15515 GAAAAATATGAAACTGA-CCTTTGACCGAAAGGGTATTTTTGGAAAAGGAAACTAAACTTAGATA
1 GAAAAAGATGAAACTAACCCTTTGACCGAAAGAGTA-TTTTGG-GAA--AAA--AAACTTAGATA
15579 C
60 C
* * *
15580 GAAAAATATGAAACTAACCCTTTGGCCGAAAGAGTGTTTTGGGAAAAAAAACTTAGATAC
1 GAAAAAGATGAAACTAACCCTTTGACCGAAAGAGTATTTTGGGAAAAAAAACTTAGATAC
* * *
15640 GAAAAAGATGAAACTAACCCTTTGACCGAACGGGTATTTTTGGAAAAAA
1 GAAAAAGATGAAACTAACCCTTTGACCGAAAGAGTATTTTGGGAAAAAA
15689 GAAAATACTA
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
60 55 0.57
62 3 0.03
64 2 0.02
65 22 0.23
66 15 0.15
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (60 bp):
GAAAAAGATGAAACTAACCCTTTGACCGAAAGAGTATTTTGGGAAAAAAAACTTAGATAC
Found at i:22486 original size:9 final size:9
Alignment explanation
Indices: 22472--22500 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
22462 TACTTGATTG
22472 CTTGTGAAT
1 CTTGTGAAT
22481 CTTGTGAAT
1 CTTGTGAAT
22490 CTTGTG-AT
1 CTTGTGAAT
22498 CTT
1 CTT
22501 AGGTGTTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 5 0.25
9 15 0.75
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (9 bp):
CTTGTGAAT
Found at i:22756 original size:25 final size:24
Alignment explanation
Indices: 22720--22766 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
22710 TCCTTCTATT
22720 CATCTATCATC-AAGTTTTTCATC
1 CATCTATCATCAAAGTTTTTCATC
22743 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATCAAAGTTTTTCA
22767 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (24 bp):
CATCTATCATCAAAGTTTTTCATC
Found at i:23731 original size:15 final size:15
Alignment explanation
Indices: 23711--23739 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
23701 TGGATGTTCG
23711 AAATCAACAAGCTCA
1 AAATCAACAAGCTCA
23726 AAATCAACAAGCTC
1 AAATCAACAAGCTC
23740 CACTTAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.28, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATCAACAAGCTCA
Found at i:26258 original size:21 final size:21
Alignment explanation
Indices: 26232--26323 Score: 141
Period size: 21 Copynumber: 4.4 Consensus size: 21
26222 TGCTAGGAGT
26232 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
* *
26253 TCATTGTAGAAGGTTCCAAGT
1 TCATTGGAGAAGGTTCCAAGC
26274 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
26295 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
26316 TCATTGGA
1 TCATTGGA
26324 ATTGCCTAAG
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
20 2 0.03
21 63 0.97
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Found at i:34878 original size:16 final size:16
Alignment explanation
Indices: 34857--34895 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
34847 AGGTTGACAG
34857 AAAACAATTAAACAAA
1 AAAACAATTAAACAAA
* *
34873 AAAACAATTAAACTAG
1 AAAACAATTAAACAAA
34889 AAAACAA
1 AAAACAA
34896 AACAAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.72, C:0.13, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAACAATTAAACAAA
Found at i:35660 original size:11 final size:11
Alignment explanation
Indices: 35644--35669 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35634 CCTTTGCCTA
35644 AAAACTAGAAG
1 AAAACTAGAAG
35655 AAAACTAGAAG
1 AAAACTAGAAG
35666 AAAA
1 AAAA
35670 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Done.