Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009106.1 Corchorus capsularis cultivar CVL-1 contig09127, 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: 20159
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:834 original size:17 final size:17
Alignment explanation
Indices: 812--845 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
802 GAATCGGCTA
812 TGAATTTTTGAAGTTTC
1 TGAATTTTTGAAGTTTC
*
829 TGAATTTTTGAATTTTC
1 TGAATTTTTGAAGTTTC
846 AAGAAGGGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTC
Found at i:1455 original size:22 final size:22
Alignment explanation
Indices: 1425--1468 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1415 CTTTCCCGTA
*
1425 ACAACTTCTGTCCCGAAGTTGT
1 ACAACTTCTGGCCCGAAGTTGT
* *
1447 ACAAGTTCTGGGCCGAAGTTGT
1 ACAACTTCTGGCCCGAAGTTGT
1469 CCTGAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
ACAACTTCTGGCCCGAAGTTGT
Found at i:3175 original size:15 final size:16
Alignment explanation
Indices: 3155--3185 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3145 CTGGTCGAAA
3155 ATTTTTTTT-TATTTT
1 ATTTTTTTTATATTTT
3170 ATTTTTTTTATATTTT
1 ATTTTTTTTATATTTT
3186 TCGATATGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (16 bp):
ATTTTTTTTATATTTT
Found at i:3293 original size:9 final size:8
Alignment explanation
Indices: 3259--3292 Score: 59
Period size: 8 Copynumber: 4.1 Consensus size: 8
3249 GAATCAGCTA
3259 TGAATTTT
1 TGAATTTT
3267 TGAAGTTTT
1 TGAA-TTTT
3276 TGAATTTT
1 TGAATTTT
3284 TGAATTTT
1 TGAATTTT
3292 T
1 T
3293 TCAAGAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
8 17 0.68
9 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (8 bp):
TGAATTTT
Found at i:3293 original size:17 final size:17
Alignment explanation
Indices: 3259--3292 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3249 GAATCAGCTA
3259 TGAATTTTTGAAGTTTT
1 TGAATTTTTGAAGTTTT
3276 TGAATTTTTGAA-TTTT
1 TGAATTTTTGAAGTTTT
3292 T
1 T
3293 TCAAGAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.15, T:0.62
Consensus pattern (17 bp):
TGAATTTTTGAAGTTTT
Found at i:3669 original size:30 final size:30
Alignment explanation
Indices: 3633--3720 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
3623 TTGCTAGGAC
3633 CCTAAGTTTGCTCAAACTAGAACAATGAAG
1 CCTAAGTTTGCTCAAACTAGAACAATGAAG
* ** *
3663 CCTAAGTTTGCT---ACAAGATGAA-GAAC
1 CCTAAGTTTGCTCAAACTAGAACAATGAAG
3689 CCTAAGTTTGCTCAAACTAGAACAATGAAG
1 CCTAAGTTTGCTCAAACTAGAACAATGAAG
3719 CC
1 CC
3721 AAAGAAATCG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
26 15 0.33
27 7 0.15
29 7 0.15
30 17 0.37
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.23
Consensus pattern (30 bp):
CCTAAGTTTGCTCAAACTAGAACAATGAAG
Found at i:4313 original size:23 final size:23
Alignment explanation
Indices: 4283--4338 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
4273 TGTCCGGTTG
4283 TGGCCGGTTGGTGCGCCTAGCGA
1 TGGCCGGTTGGTGCGCCTAGCGA
4306 TGGCCGGTTGGTGCGCCTAGCGA
1 TGGCCGGTTGGTGCGCCTAGCGA
4329 TGGCCGGTTG
1 TGGCCGGTTG
4339 TGGCCGGACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.07, C:0.25, G:0.45, T:0.23
Consensus pattern (23 bp):
TGGCCGGTTGGTGCGCCTAGCGA
Found at i:7979 original size:11 final size:11
Alignment explanation
Indices: 7958--7996 Score: 55
Period size: 10 Copynumber: 3.7 Consensus size: 11
7948 AGGGATAAGT
7958 GAAAAAA-AAA
1 GAAAAAAGAAA
7968 GAAAAAAGAAA
1 GAAAAAAGAAA
*
7979 GAAAAGAGAAA
1 GAAAAAAGAAA
7990 -AAAAAAG
1 GAAAAAAG
7997 CAACGATGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:7983 original size:16 final size:17
Alignment explanation
Indices: 7959--7996 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
7949 GGGATAAGTG
7959 AAAAA-AAAAGA-AAAA
1 AAAAAGAAAAGAGAAAA
*
7974 AGAAAGAAAAGAGAAAA
1 AAAAAGAAAAGAGAAAA
7991 AAAAAG
1 AAAAAG
7997 CAACGATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 4 0.21
16 6 0.32
17 9 0.47
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAGAAAA
Found at i:8052 original size:44 final size:44
Alignment explanation
Indices: 8002--8157 Score: 168
Period size: 44 Copynumber: 3.3 Consensus size: 44
7992 AAAAGCAACG
*
8002 ATGGTTTTCAAAAACAGTCATGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAA
* * * * *
8046 AAGGTTTTCACAAAGAGTCTTGGTTTTCAAAAGGTTTTAATAAA
1 ATGGTTTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAA
8090 ATGGTTTTCAAAAAAAAAAAAAGGGGTCATGGTTTTCAAAAGGTTTTGATAAA
1 ATGGTTTTC------AAAAAAA---GTCATGGTTTTCAAAAGGTTTTGATAAA
*
8143 ATGGTTTTCCAAAAA
1 ATGGTTTTCAAAAAA
8158 TGATTTTAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
44 47 0.51
47 5 0.05
50 5 0.05
53 35 0.38
ACGTcount: A:0.39, C:0.08, G:0.19, T:0.34
Consensus pattern (44 bp):
ATGGTTTTCAAAAAAAGTCATGGTTTTCAAAAGGTTTTGATAAA
Found at i:8502 original size:28 final size:29
Alignment explanation
Indices: 8471--8530 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
8461 AAGTCAAAAT
* * *
8471 AAAAAAGGTG-AAAATTGAAAGTGAAAGG
1 AAAAAAAGTGAAAAAATAAAAGTGAAAGG
*
8499 AAAAAAATTGAAAAAATAAAAGTGAAAGG
1 AAAAAAAGTGAAAAAATAAAAGTGAAAGG
8528 AAA
1 AAA
8531 GGTGAAGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (29 bp):
AAAAAAAGTGAAAAAATAAAAGTGAAAGG
Found at i:8816 original size:5 final size:5
Alignment explanation
Indices: 8808--8858 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
8798 GTGCACTGAA
*
8808 AAAAA AAAAG AAAAG AAAAG AAAAG AAAA- AGAAAG -AAAG -AAAG -AAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG AAAAG AAAAG
8855 AAAA
1 AAAA
8859 ATGAATGATG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
4 13 0.31
5 29 0.69
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:8876 original size:22 final size:22
Alignment explanation
Indices: 8807--8878 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
8797 AGTGCACTGA
*
8807 AAAAAAAAAAGAAA-AGAA-AAG
1 AAAAGAAAAAGAAAGA-AAGAAG
8828 AAAAGAAAAAGAAAGAAAGAA-
1 AAAAGAAAAAGAAAGAAAGAAG
* *
8849 AGAAAGAAAAATGAATG-ATGAAG
1 A-AAAGAAAAA-GAAAGAAAGAAG
8872 AAAAGAA
1 AAAAGAA
8879 GCTCTATGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
21 16 0.37
22 22 0.51
23 5 0.12
ACGTcount: A:0.76, C:0.00, G:0.19, T:0.04
Consensus pattern (22 bp):
AAAAGAAAAAGAAAGAAAGAAG
Found at i:10077 original size:36 final size:36
Alignment explanation
Indices: 10028--10135 Score: 128
Period size: 36 Copynumber: 3.0 Consensus size: 36
10018 CAGTTCACCC
*
10028 AGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* * * * *
10064 AGGGTGGTCTTTCTTTAGTTTATTTCGG-TTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
* **
10099 AGGGCGGTCTTTCTTCAGTTTATGTAAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
10135 A
1 A
10136 TTCAGTCGAC
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 27 0.47
36 30 0.53
ACGTcount: A:0.18, C:0.14, G:0.28, T:0.41
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTCAGTTTATGTCGGAATGATCG
Found at i:10119 original size:35 final size:36
Alignment explanation
Indices: 10024--10123 Score: 130
Period size: 36 Copynumber: 2.8 Consensus size: 36
10014 GATTCAGTTC
*
10024 ACCCAGGGTGGTTTTTCTTCAGTTTATGTCGGAATG
1 ACCCAGGGTGGTCTTTCTTCAGTTTATGTCGGAATG
* * * * *
10060 ATCGAGGGTGGTCTTTCTTTAGTTTATTTCGG-TTG
1 ACCCAGGGTGGTCTTTCTTCAGTTTATGTCGGAATG
*
10095 ACCCAGGGCGGTCTTTCTTCAGTTTATGT
1 ACCCAGGGTGGTCTTTCTTCAGTTTATGT
10124 AAGAATGATC
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
35 26 0.49
36 27 0.51
ACGTcount: A:0.14, C:0.17, G:0.27, T:0.42
Consensus pattern (36 bp):
ACCCAGGGTGGTCTTTCTTCAGTTTATGTCGGAATG
Found at i:10299 original size:261 final size:261
Alignment explanation
Indices: 9943--10830 Score: 1411
Period size: 261 Copynumber: 3.4 Consensus size: 261
9933 ATCTTCAATG
* * * * * * *
9943 CGATTCGGTCGACCCAAGGTGGTCTTTCTTCAATTGTTTTCAAGTTTATCTAAGATTATGTCGGA
1 CGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATCCAAGTTTATGTCAGA
*
10008 ATGATCGATTCAGTTCACCCAGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTC
66 ATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTC
*
10073 TTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTCAGTTTATGTAAGAATGATCGATT
131 TTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTCAGTTTATGTTAGAATGATCGATT
*
10138 CAGTCGACCCAGGGCGGTCTTTTCTTCAATTTTTTTCAAGTTTATTCGAAGTTTATGTCAGAATG
196 CAGTCGACCCAGGGCGGTC-TTTCTTCAATTATTTTCAAGTTTATTCGAAGTTTATGTCAGAATG
10203 AT
260 AT
* * *
10205 CGATTCAGTCAACCCAGGGCGATCTTTCTTCAGTTG-TTTCAAGATTATCCAAGTTTATGTCAGA
1 CGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATCCAAGTTTATGTCAGA
* * *
10269 ATGATTGATTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTTATGTCAGAATGATCGAGGGTGGTC
66 ATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTC
* * * *
10334 TATCTTTAGTTTATTTCAGTTGACCCATGGCAGTCTTTCTTCAGTTTATGTTAGAATGATCGATT
131 TTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTCAGTTTATGTTAGAATGATCGATT
*
10399 CAGTCGACCCAGGGCGGTCTTTCTTCAATTGTTTTCAAGTTTATTCGAAGTTTATGTCAGAATGA
196 CAGTCGACCCAGGGCGGTCTTTCTTCAATTATTTTCAAGTTTATTCGAAGTTTATGTCAGAATGA
10464 T
261 T
*
10465 CGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTTATCCAAGTTTATGTCAGA
1 CGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATCCAAGTTTATGTCAGA
* * *
10530 ATGATCGATTCAGTTGACCTAGGGTGGTTTTTCTTAAGTTTATGTCGGAATGATCGAGGGTGATC
66 ATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTC
* * * *
10595 TTTCTTTAGATTATTTCGGTTAACCTAGGGCGGTCTTTCTTTAGTTTATGTTAGAATGAAT-GAT
131 TTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTCAGTTTATGTTAGAATG-ATCGAT
* * *
10659 TCAGTCGACCCAGGGCGGTCTTTCTTTAGTTATTTTCAAGTTTATTCGAAGTTTATGTCAAAATG
195 TCAGTCGACCCAGGGCGGTCTTTCTTCAATTATTTTCAAGTTTATTCGAAGTTTATGTCAGAATG
10724 AT
260 AT
* *
10726 CGATTCAGCCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATTCCAAGTTTATATCAG
1 CGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTA-TCCAAGTTTATGTCAG
* *
10791 AATGATCGATTCAGTCGACCCAGGGTGGTATTTCTTCAGT
65 AATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGT
10831 AGTTTCCATG
Statistics
Matches: 576, Mismatches: 47, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
260 80 0.14
261 413 0.72
262 83 0.14
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.39
Consensus pattern (261 bp):
CGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTTATCCAAGTTTATGTCAGA
ATGATCGATTCAGTTGACCCAGGGTGGTTTTTCTTCAGTTTATGTCGGAATGATCGAGGGTGGTC
TTTCTTTAGTTTATTTCGGTTGACCCAGGGCGGTCTTTCTTCAGTTTATGTTAGAATGATCGATT
CAGTCGACCCAGGGCGGTCTTTCTTCAATTATTTTCAAGTTTATTCGAAGTTTATGTCAGAATGA
T
Found at i:10302 original size:69 final size:70
Alignment explanation
Indices: 10115--10308 Score: 255
Period size: 69 Copynumber: 2.8 Consensus size: 70
10105 GTCTTTCTTC
* * * *
10115 AGTTTATGTAAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTTCTTCAATTTTTTTCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGT-TTTTCTTC-AGTTGTTTCAAGAT
*
10180 TATTCGA
64 TATTCCA
* * *
10187 AGTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGCGATCTTTCTTCAGTTGTTTCAAGATTA
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTTTTTCTTCAGTTGTTTCAAGATTA
10252 -TCCA
66 TTCCA
* * * *
10256 AGTTTATGTCAGAATGATTGATTCAGTTGACCTAGGGTGGTTTTTCTTCAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTTTTTCTTCAGTT
10309 TATGTCAGAA
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
69 49 0.46
70 13 0.12
71 7 0.07
72 38 0.36
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (70 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTTTTTCTTCAGTTGTTTCAAGATTA
TTCCA
Found at i:10345 original size:36 final size:36
Alignment explanation
Indices: 10289--10396 Score: 110
Period size: 36 Copynumber: 3.0 Consensus size: 36
10279 CAGTTGACCT
*
10289 AGGGTGGTTTTTCTTCAGTTTATGTCAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCAGAATGATCG
* * * * * *
10325 AGGGTGGTCTATCTTTAGTTTATTTCAG-TTGACCC
1 AGGGTGGTCTTTCTTCAGTTTATGTCAGAATGATCG
* ** *
10360 ATGGCAGTCTTTCTTCAGTTTATGTTAGAATGATCG
1 AGGGTGGTCTTTCTTCAGTTTATGTCAGAATGATCG
10396 A
1 A
10397 TTCAGTCGAC
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
35 25 0.46
36 29 0.54
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (36 bp):
AGGGTGGTCTTTCTTCAGTTTATGTCAGAATGATCG
Found at i:10563 original size:70 final size:71
Alignment explanation
Indices: 10376--10569 Score: 300
Period size: 71 Copynumber: 2.7 Consensus size: 71
10366 GTCTTTCTTC
* * *
10376 AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAATTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
*
10441 ATTCGA
66 ATTCCA
10447 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
10512 A-TCCA
66 ATTCCA
* * * * *
10517 AGTTTATGTCAGAATGATCGATTCAGTTGACCTAGGGTGGTTTTTCTTAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTT
10570 TATGTCGGAA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
70 51 0.45
71 63 0.55
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (71 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATTCCA
Found at i:10623 original size:332 final size:322
Alignment explanation
Indices: 10115--10918 Score: 795
Period size: 332 Copynumber: 2.4 Consensus size: 322
10105 GTCTTTCTTC
* * * *
10115 AGTTTATGTAAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTTCTTCAATTTTTTTCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTC-TTTCTTCAGTTGTTTCCAAGTT
* *
10180 TATTCGAAGTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGCGATCTTTCTTCAGTTGTTTC
65 TA-TCCAAGTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGCGATCTTTCTTAAGTTGTTTC
* * * * *
10245 AAGATTATCCAAGTTTATGTCAGAATGATTGATTCAGTTGACCTAGGGTGGTTTTTCTTCAGTTT
129 AAGATGATCCAAGTATATGTCAGAATGATTGATTCAGTTAACCTAGGGCGGTCTTTCTTCAGTTT
* *
10310 ATG-T-CA-GAATG-A-TCG-AGGGTGGTCTATCTTTAGTTTATTTCAGTTGACCCATGGCAGTC
194 ATGTTAAATGAATGTAGTCGCAGGGCGGTCTATCTTTAG-TTA-TT---TT----CA----AG--
* * * *
10369 TTTCTTC-AGTTTATGTTAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAATTGTTT
244 TTTATTCAAGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCTTCAATTGTTT
*
10433 TCAAGTTTATTCGA
309 TCAAGTTTATTCCA
10447 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
** * * * *
10512 ATCCAAGTTTATGTCAGAATGATCGATTCAGTTGACCTAGGGTGGTTTTTCTTAAGTT-TATGTC
66 ATCCAAGTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGCGATCTTTCTTAAGTTGT-T-TC
* * * * * *** * *
10576 -GGAATGATCGAGGGTGATCTTTCTTTA-GATT-ATTTCGGTTAACCTAGGGCGGTCTTTCTTTA
129 AAG-ATGATCCA-AGT-ATATGTCAGAATGATTGA-TTCAGTTAACCTAGGGCGGTCTTTCTTCA
*
10638 GTTTATGTTAGAATGAATGATTCAGTCGACCCAGGGCGGTCTTTCTTTAGTTATTTTCAAGTTTA
190 GTTTATGTTA-AATGAATG--T-AGTCG---CAGGGCGGTCTATCTTTAGTTATTTTCAAGTTTA
*
10703 TTCGAAGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCA
248 TTC-AAGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCTTCAATTGTTTTCA
10768 AGTTTATTCCA
312 AGTTTATTCCA
* * * * *
10779 AGTTTATATCAGAATGATCGATTCAGTCGACCCAGGGTGGTATTTCTTCAGTAGTTTCCATGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
* * * * * *
10844 ATCCAAGTTTATGTCAGAATGATTGATTCAGTCGACTCAGGGCGGT-TTCTCATCAGTTGTTTCC
66 ATCCAAGTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGCGATCTT-TCTTAAGTTGTTT-C
*
10908 AAGTTGATCCA
129 AAGATGATCCA
10919 GGGTGGTCTT
Statistics
Matches: 396, Mismatches: 51, Indels: 50
0.80 0.10 0.10
Matches are distributed among these distances:
329 1 0.00
330 57 0.14
331 33 0.08
332 262 0.66
333 8 0.02
335 1 0.00
336 7 0.02
340 3 0.01
341 3 0.01
343 2 0.01
344 3 0.01
345 16 0.04
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (322 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATCCAAGTTTATGTCAGAATGATCGATTCAGTCAACCCAGGGCGATCTTTCTTAAGTTGTTTCAA
GATGATCCAAGTATATGTCAGAATGATTGATTCAGTTAACCTAGGGCGGTCTTTCTTCAGTTTAT
GTTAAATGAATGTAGTCGCAGGGCGGTCTATCTTTAGTTATTTTCAAGTTTATTCAAGTTTATGT
CAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCTTCAATTGTTTTCAAGTTTATTCCA
Found at i:10905 original size:141 final size:142
Alignment explanation
Indices: 10637--10912 Score: 371
Period size: 141 Copynumber: 2.0 Consensus size: 142
10627 GTCTTTCTTT
* * * * *
10637 AGTTTATGTTAGAATGAATGATTCAGTCGACCCAGGGCGGTCTTTCTTTAGTTATTTTCAAGTTT
1 AGTTTATATCAGAATGAATGATTCAGTCGACCCAGGGCGGTATTTCTTCAGTTATTTCCAAGTTT
* * *
10702 ATTCGAAGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTC
66 ATTCCAAGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCATCAGTTGTTTCC
10767 AAGTTTATTCCA
131 AAGTTTATTCCA
* *
10779 AGTTTATATCAGAATG-ATCGATTCAGTCGACCCAGGGTGGTATTTCTTCAG-TAGTTTCCATGT
1 AGTTTATATCAGAATGAAT-GATTCAGTCGACCCAGGGCGGTATTTCTTCAGTTA-TTTCCAAGT
* * * *
10842 TTA-TCCAAGTTTATGTCAGAATGATTGATTCAGTCGACTCAGGGCGGT-TTCTCATCAGTTGTT
64 TTATTCCAAGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTT-TCATCAGTTGTT
10905 TCCAAGTT
128 TCCAAGTT
10913 GATCCAGGGT
Statistics
Matches: 117, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
140 2 0.02
141 62 0.53
142 53 0.45
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (142 bp):
AGTTTATATCAGAATGAATGATTCAGTCGACCCAGGGCGGTATTTCTTCAGTTATTTCCAAGTTT
ATTCCAAGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCATCAGTTGTTTCC
AAGTTTATTCCA
Found at i:10918 original size:70 final size:71
Alignment explanation
Indices: 10637--10912 Score: 369
Period size: 71 Copynumber: 3.9 Consensus size: 71
10627 GTCTTTCTTT
* * * *
10637 AGTTTATGTTAGAATGAAT-GATTCAGTCGACCCAGGGCGGTCTTTCTTTAGTTATTTTCAAGTT
1 AGTTTATGTCAGAATG-ATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTT
*
10701 TATTCGA
65 TATTCCA
* * *
10708 AGTTTATGTCAAAATGATCGATTCAGCCGACCCAGGGCGGTCTTTCTTCAGTTGTTTTCAAGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
10773 ATTCCA
66 ATTCCA
* * * * *
10779 AGTTTATATCAGAATGATCGATTCAGTCGACCCAGGGTGGTATTTCTTCAGTAGTTTCCATGTTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
10844 A-TCCA
66 ATTCCA
* * *
10849 AGTTTATGTCAGAATGATTGATTCAGTCGACTCAGGGCGGT-TTCTCATCAGTTGTTTCCAAGTT
1 AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTT-TCTTCAGTTGTTTCCAAGTT
10913 GATCCAGGGT
Statistics
Matches: 182, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
69 2 0.01
70 60 0.33
71 120 0.66
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (71 bp):
AGTTTATGTCAGAATGATCGATTCAGTCGACCCAGGGCGGTCTTTCTTCAGTTGTTTCCAAGTTT
ATTCCA
Found at i:16459 original size:33 final size:33
Alignment explanation
Indices: 16417--16526 Score: 116
Period size: 33 Copynumber: 3.3 Consensus size: 33
16407 AGCACAAGTG
* *
16417 ACCGGCCATGCGACTTGGAGATATCC-GCACAAC
1 ACCGGCCATGCGACATGGAGATACCCGGC-CAAC
* * *
16450 ACCGGCCATGTGACATGGAGATGCCCGGCCATC
1 ACCGGCCATGCGACATGGAGATACCCGGCCAAC
** *
16483 ACCGGCCATGCGACATGGCCATGCCCGGCC-AC
1 ACCGGCCATGCGACATGGAGATACCCGGCCAAC
16515 ACCCGGCCATGC
1 A-CCGGCCATGC
16527 CCGGCCACAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.03
33 62 0.94
34 2 0.03
ACGTcount: A:0.22, C:0.38, G:0.27, T:0.13
Consensus pattern (33 bp):
ACCGGCCATGCGACATGGAGATACCCGGCCAAC
Found at i:16489 original size:10 final size:11
Alignment explanation
Indices: 16470--16573 Score: 70
Period size: 10 Copynumber: 10.1 Consensus size: 11
16460 TGACATGGAG
16470 ATGC-CCGGCC
1 ATGCACCGGCC
16480 AT-CACCGGCC
1 ATGCACCGGCC
*
16490 ATGCGACATGGCC
1 ATGC-AC-CGGCC
16503 ATGC-CCGGCC
1 ATGCACCGGCC
16513 A--CACCCGGCC
1 ATGCA-CCGGCC
16523 ATGC-CCGGCC
1 ATGCACCGGCC
16533 A--CACCCGGCC
1 ATGCA-CCGGCC
16543 ATGC-CCGGCC
1 ATGCACCGGCC
16553 A--CACCCGGCC
1 ATGCA-CCGGCC
16563 ATGC-CCGGCC
1 ATGCACCGGCC
16573 A
1 A
16574 CAACCGGCCA
Statistics
Matches: 76, Mismatches: 2, Indels: 32
0.69 0.02 0.29
Matches are distributed among these distances:
8 3 0.04
9 1 0.01
10 57 0.75
11 2 0.03
12 5 0.07
13 8 0.11
ACGTcount: A:0.16, C:0.50, G:0.26, T:0.08
Consensus pattern (11 bp):
ATGCACCGGCC
Found at i:16524 original size:20 final size:20
Alignment explanation
Indices: 16499--16584 Score: 163
Period size: 20 Copynumber: 4.3 Consensus size: 20
16489 CATGCGACAT
16499 GGCCATGCCCGGCCACACCC
1 GGCCATGCCCGGCCACACCC
16519 GGCCATGCCCGGCCACACCC
1 GGCCATGCCCGGCCACACCC
16539 GGCCATGCCCGGCCACACCC
1 GGCCATGCCCGGCCACACCC
*
16559 GGCCATGCCCGGCCACAACC
1 GGCCATGCCCGGCCACACCC
16579 GGCCAT
1 GGCCAT
16585 ATGATCCTTT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 65 1.00
ACGTcount: A:0.16, C:0.52, G:0.26, T:0.06
Consensus pattern (20 bp):
GGCCATGCCCGGCCACACCC
Found at i:16580 original size:10 final size:10
Alignment explanation
Indices: 16506--16583 Score: 93
Period size: 10 Copynumber: 7.8 Consensus size: 10
16496 CATGGCCATG
16506 CCCGGCCACA
1 CCCGGCCACA
**
16516 CCCGGCCATG
1 CCCGGCCACA
16526 CCCGGCCACA
1 CCCGGCCACA
**
16536 CCCGGCCATG
1 CCCGGCCACA
16546 CCCGGCCACA
1 CCCGGCCACA
**
16556 CCCGGCCATG
1 CCCGGCCACA
16566 CCCGGCCACA
1 CCCGGCCACA
*
16576 ACCGGCCA
1 CCCGGCCA
16584 TATGATCCTT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 55 1.00
ACGTcount: A:0.17, C:0.55, G:0.24, T:0.04
Consensus pattern (10 bp):
CCCGGCCACA
Found at i:17513 original size:17 final size:17
Alignment explanation
Indices: 17491--17523 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17481 ACCTTCTTGA
17491 AAACTTCAAAAATTCAG
1 AAACTTCAAAAATTCAG
17508 AAACTTCAAAAATTCA
1 AAACTTCAAAAATTCA
17524 TAGCCAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (17 bp):
AAACTTCAAAAATTCAG
Found at i:19234 original size:30 final size:31
Alignment explanation
Indices: 19131--19251 Score: 127
Period size: 33 Copynumber: 3.8 Consensus size: 31
19121 CTAATTGTGA
*
19131 TGAAAACAATTCTGTTTTGGTTGAACATAGCAT
1 TGAAAATAATTCTGTTTTGGTTG-ACA-AGCAT
* *
19164 TAAAAATAATTTTGTTTTGGTTGATCATAGCAT
1 TGAAAATAATTCTGTTTTGGTTGA-CA-AGCAT
* * *
19197 TGCAAATAATCCTGTTTTGGTTGAC-GGCAT
1 TGAAAATAATTCTGTTTTGGTTGACAAGCAT
* *
19227 TGAAAATAAATCTGTTTTGGGTGAC
1 TGAAAATAATTCTGTTTTGGTTGAC
19252 GAGAAAGAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
30 25 0.33
32 2 0.03
33 48 0.64
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (31 bp):
TGAAAATAATTCTGTTTTGGTTGACAAGCAT
Found at i:19252 original size:30 final size:30
Alignment explanation
Indices: 19193--19252 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
19183 GTTGATCATA
* *
19193 GCATTGCAAATAATCCTGTTTTGGTTGACG
1 GCATTGAAAATAATCCTGTTTTGGGTGACG
19223 GCATTGAAAATAAAT-CTGTTTTGGGTGACG
1 GCATTGAAAAT-AATCCTGTTTTGGGTGACG
19253 AGAAAGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (30 bp):
GCATTGAAAATAATCCTGTTTTGGGTGACG
Done.