Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012588.1 Corchorus olitorius cultivar O-4 contig12621, 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: 12004
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Found at i:459 original size:154 final size:153
Alignment explanation
Indices: 1--1732 Score: 2641
Period size: 154 Copynumber: 11.3 Consensus size: 153
* * *
1 AATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* *
66 ATCGAATACGATTCAAAACGGAACTAAT-GGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAA-GTGTTCCAAAT
130 GAGCTAAAAACTTCACAGTGGACT
130 GAGCTAAAAACTTCACAGTGGACT
* *
154 AATCTCACCAAAATGAGTATAGTTAGGCCATAAACAATGGAAAGAAAGGCATTGAGGGTTG-CAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* *
218 ATCGAAGAGGATTCAAAACTTG-ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
66 ATCGAAGACGATTCAAAAC-GGAACTAATGGGCCCCGATAGGCCCAAAATAA-AAGTGTTCCAAA
*
282 TGAGCTAAAAACTTCACATTGGACT
129 TGAGCTAAAAACTTCACAGTGGACT
*
307 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAATCATTGAGGGTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
**
372 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTGAAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA-AAGTGTTCCAAAT
437 GAGCTAAAAACATT-ACAGTGGACT
130 GAGCTAAAAAC-TTCACAGTGGACT
* * *
461 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCATTGAGGTTTGCCTA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* *
526 ATCGAAAACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAA-GTGTTCCAAAT
591 GAGCTAAAAACTTCACAGTGGACT
130 GAGCTAAAAACTTCACAGTGGACT
* *
615 AATCTCACCAAAATGATTATAGTTAGCCCATAAACAATGGAAAGAAAGGCATTGAGGGTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* ** ** *
680 AGCGAAGACGATTCAAAACGTCACTAATGGGCCCTAATAGGCTCAAAATAAAAGTGTTCCAAATG
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAGTGTTCCAAATG
745 AGCTAAAAACTTCACAGTGGACT
131 AGCTAAAAACTTCACAGTGGACT
* *
768 AATCTCACCAAAATGATTATAGTTAGGACATAAACAATGGAAAGAAAAGCATTGACGGTTTGCCA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGGTTGCCA
* ** * *
833 AATCGAAGACGATTGAAAACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCCAAT
65 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT-AAAAGTGTTCCAAA
*
898 TGAGCTAAAAACTTCACAGAGGACT
129 TGAGCTAAAAACTTCACAGTGGACT
* * *
923 AATCTCACCAAAATTATTACAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* * * * *
988 ATCGTAGACGATTCAAAACGGAACTAACGGGCCCTGATAGGCACAATATAAAGAGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAA-AGTGTTCCAAAT
*
1053 TAGCTAAAAACTTCACAGTGGACT
130 GAGCTAAAAACTTCACAGTGGACT
* * * *
1077 GATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATCGAGGATTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* *
1142 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATGGGCCAAAAATAACAAGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA-AAGTGTTCCAAAT
* *
1207 -ATGCTAAGAACATCACAGTGGACT
130 GA-GCTAAAAACTTCACAGTGGACT
*
1231 AATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATAT-AGGGTTGCCA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-TGAGGGTTGCCA
* * * *
1295 AATCGAAGACAATTCAAAATGGAACTAATGAGCCCCGATAGGCACAAAATAAAAGTGTTCCAAAT
65 AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAGTGTTCCAAAT
* *
1360 TACCTAAAAACTTCACAGTGGACT
130 GAGCTAAAAACTTCACAGTGGACT
1384 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
** *
1448 ATCGAAGACGATTCAAAACAGTCACTAATGGGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAA
66 ATCGAAGACGATTCAAAAC-GGAACTAATGGGCCCCGATAGGCCCAAAATAA-AAGTGTTCCAAA
1513 TGAGCTAAAAACTTCACAGTGGACT
129 TGAGCTAAAAACTTCACAGTGGACT
* * * * *
1538 AACCTCAGCAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* * *
1603 ATTGAATACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAA-GTGTTCCAAAT
1668 GAGCTAAAAACTTCACAGTGGACT
130 GAGCTAAAAACTTCACAGTGGACT
* *
1692 AATCTCACCAAAATGATTATAGTTAGACCGTAAACAATGGA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
1733 GAGCAAGGAA
Statistics
Matches: 1437, Mismatches: 122, Indels: 39
0.90 0.08 0.02
Matches are distributed among these distances:
151 1 0.00
152 60 0.04
153 372 0.26
154 878 0.61
155 126 0.09
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.21
Consensus pattern (153 bp):
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTGGACT
Found at i:1561 original size:461 final size:460
Alignment explanation
Indices: 1--1732 Score: 2647
Period size: 461 Copynumber: 3.8 Consensus size: 460
* * *
1 AATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCTA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
*
66 ATCGAATACGATTCAAAACGGAACTAAT-GGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
*
130 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAGTATAGTTAGGCCATAAACAATGGA
131 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* * *
195 AAGAAAGGCATTGAGGGTTG-CAAATCGAAGAGGATTCAAAACTTG-ACTAATGGGCCCCGATAG
196 AAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC-GGAACTAATGGGCCCCGATAG
*
258 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACATTGGACTAATCTCACCAAAATGA
260 GCCCAAAATAA-AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
323 TTATAGTTAGGCCATAAACAATGGAAAGAAAATCATTGAGGGTTGCCAAATCGAAGACGATTCAA
324 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAA
** *
388 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTGAAAATGAGCTAAAAACATT-A
389 AACGGAACTAATGGGCCCCGATAGGCCCAAAATAA-AAGTGTTCCAAATTAGCTAAAAAC-TTCA
452 CAGTGGACT
452 CAGTGGACT
* * *
461 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGCATTGAGGTTTGCCTA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
*
526 ATCGAAAACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
*
591 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGCCCATAAACAATGGA
131 GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* * ** **
656 AAGAAAGGCATTGAGGGTTGCCAAAGCGAAGACGATTCAAAACGTCACTAATGGGCCCTAATAGG
196 AAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGG
*
721 CTCAAAATAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
261 CCCAAAATAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * *
786 ATAGTTAGGACATAAACAATGGAAAGAAAAGCATTGACGGTTTGCCAAATCGAAGACGATTGAAA
326 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GGGTTGCCAAATCGAAGACGATTCAAA
** *
851 ACGTCACTAATGGGCCCCGATTGGCCCAAAATAAAAAGTGTTCC-AATTGAGCTAAAAACTTCAC
390 ACGGAACTAATGGGCCCCGATAGGCCCAAAAT-AAAAGTGTTCCAAATT-AGCTAAAAACTTCAC
*
915 AGAGGACT
453 AGTGGACT
* * *
923 AATCTCACCAAAATTATTACAGTTACGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
* * * * *
988 ATCGTAGACGATTCAAAACGGAACTAACGGGCCCTGATAGGCACAATATAAAGA-GTGTTCCAAA
66 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAAA-ATGTGTTCCAAA
* * *
1052 TTAGCTAAAAACTTCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGG
130 TGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
* * *
1117 AAAGAAAAGCATCGAGGATTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATGG
195 AAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAG
* * * *
1182 GCCAAAAATAACAAGTGTTCCAAAT-ATGCTAAGAACATCACAGTGGACTAATTTCACCAAAATG
260 GCCCAAAATAA-AAGTGTTCCAAATGA-GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
*
1246 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATAT-AGGGTTGCCAAATCGAAGACAATTC
323 ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTC
* * * *
1310 AAAATGGAACTAATGAGCCCCGATAGGCACAAAATAAAAGTGTTCCAAATTACCTAAAAACTTCA
387 AAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAGTGTTCCAAATTAGCTAAAAACTTCA
1375 CAGTGGACT
452 CAGTGGACT
1384 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGAGGGTTGCCAA
1 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
** * *
1448 ATCGAAGACGATTCAAAACAGTCACTAATGGGCCCCGATAGGCTCAAAATAACAA-GTGTTCCAA
66 ATCGAAGACGATTCAAAAC-GGAACTAATGGGCCCAGATAGGCCCAAAATAA-AATGTGTTCCAA
* * *
1512 ATGAGCTAAAAACTTCACAGTGGACTAACCTCAGCAAAATGATTATAGTTAGGCTATAAACAATG
129 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
* * * * *
1577 GAAAGAAAAGCATTGAGGTTTGCCTAATTGAATACGATTCAAAACGGAACTAATGGGCCCAGATA
194 GAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA
1642 GGCCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
259 GGCCCAAAATAAAA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
* *
1707 ATTATAGTTAGACCGTAAACAATGGA
323 ATTATAGTTAGGCCATAAACAATGGA
1733 GAGCAAGGAA
Statistics
Matches: 1161, Mismatches: 95, Indels: 31
0.90 0.07 0.02
Matches are distributed among these distances:
460 130 0.11
461 519 0.45
462 424 0.37
463 87 0.07
464 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.21
Consensus pattern (460 bp):
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAA
ATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCCCAAAATAAAATGTGTTCCAAAT
GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGG
CCCAAAATAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
CGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGT
GGACT
Found at i:3180 original size:21 final size:21
Alignment explanation
Indices: 3154--3194 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3144 TTGAAGCCTT
3154 ATTGGAGACAAGTGGTACTAA
1 ATTGGAGACAAGTGGTACTAA
* *
3175 ATTGGATATAAGTGGTACTA
1 ATTGGAGACAAGTGGTACTA
3195 GGGTTTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.07, G:0.27, T:0.29
Consensus pattern (21 bp):
ATTGGAGACAAGTGGTACTAA
Found at i:3790 original size:21 final size:21
Alignment explanation
Indices: 3751--3790 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3741 AGGAGATGCC
*
3751 AAAGATGCCATTTGATCCATT
1 AAAGATGCCATTAGATCCATT
*
3772 AAAGATGCCATTAGGTCCA
1 AAAGATGCCATTAGATCCA
3791 ATGACAAGAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (21 bp):
AAAGATGCCATTAGATCCATT
Found at i:5097 original size:22 final size:22
Alignment explanation
Indices: 5069--5111 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5059 TTTTCCGCAA
* *
5069 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
5091 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
5112 TCTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:5166 original size:21 final size:21
Alignment explanation
Indices: 5142--5183 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5132 TCAACAGAGC
5142 AAGTCCTGGGCAGGAGTTGTT
1 AAGTCCTGGGCAGGAGTTGTT
5163 AAGTCCTGGGCAGGAGTTGTT
1 AAGTCCTGGGCAGGAGTTGTT
5184 CTGATTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.38, T:0.29
Consensus pattern (21 bp):
AAGTCCTGGGCAGGAGTTGTT
Found at i:5183 original size:71 final size:72
Alignment explanation
Indices: 5069--5239 Score: 211
Period size: 71 Copynumber: 2.3 Consensus size: 72
5059 TTTTCCGCAA
* * *
5069 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGAATTT-TCTTCCTTTTTT
1 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTG-ATTTCTATTCCGTCTTT
5133 CAACAGAG
65 CAACAGAG
* * *
5141 CAAGTCCTGGGCAGGAGTTGT-TAAGTCCTGGGCAGGAGTTGTTCTGATTTCTATTCCGTCTTTC
1 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGATTTCTATTCCGTCTTTC
5205 AACAGAG
66 AACAGAG
*
5212 TCTCAGCAGTCCTGGGCAGGACTTGTCC
1 ---CA--AGTCCTGGGCAGGAGTTGTCC
5240 TGTTTTTAGG
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
70 4 0.05
71 39 0.46
72 21 0.25
74 2 0.02
76 18 0.21
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (72 bp):
CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTCTGATTTCTATTCCGTCTTTC
AACAGAG
Found at i:7368 original size:33 final size:33
Alignment explanation
Indices: 7323--7445 Score: 115
Period size: 33 Copynumber: 3.8 Consensus size: 33
7313 TCCAAAGCAG
*
7323 AATTT-GTTTCATCACAAACAACACCTAAAACA
1 AATTTAGTGTCATCACAAACAACACCTAAAACA
* **
7355 AATTTAGTGTCATCACAAACAACACTTAAATTA
1 AATTTAGTGTCATCACAAACAACACCTAAAACA
** * * *
7388 GGTTTAGTATCATCACTAACAACATCTAAAACA
1 AATTTAGTGTCATCACAAACAACACCTAAAACA
* **
7421 GATTTCA-TGTCATTGCAAACAACAC
1 AATTT-AGTGTCATCACAAACAACAC
7446 TCAAATCAGG
Statistics
Matches: 71, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
32 5 0.07
33 65 0.92
34 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (33 bp):
AATTTAGTGTCATCACAAACAACACCTAAAACA
Found at i:8063 original size:15 final size:15
Alignment explanation
Indices: 8043--8074 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
8033 AAACTAAGTG
8043 GAGCTTGTCGATTTT
1 GAGCTTGTCGATTTT
*
8058 GAGCTTGTTGATTTT
1 GAGCTTGTCGATTTT
8073 GA
1 GA
8075 ACCCCCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47
Consensus pattern (15 bp):
GAGCTTGTCGATTTT
Found at i:9597 original size:22 final size:22
Alignment explanation
Indices: 9569--9611 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
9559 TTTTCCGCAA
* *
9569 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGACAGGACTTGTC
9591 CAAGTCCTGGACAGGACTTGT
1 CAAGTCCTGGACAGGACTTGT
9612 TTTGAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.23, G:0.33, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGACAGGACTTGTC
Found at i:9667 original size:21 final size:21
Alignment explanation
Indices: 9641--9682 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9631 TTCAACAGAC
9641 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
9662 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGAGTTGT
9683 TCTGAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGAGTTGT
Found at i:9683 original size:71 final size:71
Alignment explanation
Indices: 9569--9753 Score: 316
Period size: 71 Copynumber: 2.6 Consensus size: 71
9559 TTTTCCGCAA
* * * *
9569 CAAGTCCTGGGCAGGAGTTGTCCAAGTCCTGGACAGGACTTGTTTTGAATTTTCTTCCGTTTTTC
1 CAAGTCCTGGGCAGGAGTTGT-CAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTCCCGTATTTC
9634 AACAGAC
65 AACAGAC
*
9641 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGAGTTGTTCTGAATTTTCTCCCGTATTTCA
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTCCCGTATTTCA
9706 ACAGAC
66 ACAGAC
9712 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGT
9754 CCTGTTTTTA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 86 0.80
72 21 0.20
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (71 bp):
CAAGTCCTGGGCAGGAGTTGTCAAGTCCTGGGCAGGACTTGTTCTGAATTTTCTCCCGTATTTCA
ACAGAC
Found at i:9738 original size:21 final size:21
Alignment explanation
Indices: 9712--9754 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
9702 TTCAACAGAC
*
9712 CAAGTCCTGGGCAGGAGTTGT
1 CAAGTCCTGGGCAGGACTTGT
9733 CAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGACTTGT
9754 C
1 C
9755 CTGTTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (21 bp):
CAAGTCCTGGGCAGGACTTGT
Found at i:10591 original size:154 final size:152
Alignment explanation
Indices: 10098--11998 Score: 2564
Period size: 154 Copynumber: 12.4 Consensus size: 152
10088 TGGCGCATCA
* * *
10098 ATAAACAATGGAAAGAAAAGCATTGAGTGTTGCCAAATCGAAGACGAATCAAAACAGAACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGAG-GTTGCCAAATCGAAGACGATTCAAAAC-GCACTAATG
* * *
10163 GGCCCCGA-AGGCCCAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCT
64 GGCCCAGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
10227 CACCAAAATGATTATAGTTAGGCC
129 CACCAAAATGATTATAGTTAGGCC
* * *
10251 ATAAAAAATGGAAAGAAAGGCATTGAGGGTTGCCAAAGCAAAGACGATTCAAAACGTCACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACGATTCAAAACG-CACTAATG
* * *
10316 GGCCCCGATAGGCTCAAAATAACAAGTGTTCCAAATGAG-TTAAAACATCACAGTGGACTAATCT
64 GGCCCAGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
10380 CACCAAAATGATTATAGTTAGGCC
129 CACCAAAATGATTATAGTTAGGCC
* * * *
10404 ATAAACAATGGATAGAAAAGCATTGAGGTTTGCCTAATCGAAGACGATTCAAAACAGAACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGAGG-TTGCCAAATCGAAGACGATTCAAAAC-GCACTAATG
* * * *
10469 GGCCCAGATAGGCCCAAAATAA-AATGTGTTGCAAATGAGCTAAAAACTTCATAGTGGAATAATC
64 GGCCCAGATAGGCTCAAAATAACAA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
10533 TCACCAAAATGATTATAGTTAGGCC
128 TCACCAAAATGATTATAGTTAGGCC
** * **
10558 ATAAACAATGGAAAGAAAGGCATTGACGGTTGCCAAAGAGAAGACGATACAAAAATTCACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACGATTC-AAAACGCACTAATG
* *
10623 GGCCCTA-ATAGACTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACATTGGACTAATC
64 GGCCC-AGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
10687 TCACCAAAATGATTATAGTTAGGCC
128 TCACCAAAATGATTATAGTTAGGCC
* * *
10712 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCGAAACGGAACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACGATTCAAAAC-GCACTAATG
* ** *
10777 GGCCCCGATAGGCGAAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCT
64 GGCCCAGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCT
10842 CACCAAAATGATTATAGTTAGGCC
129 CACCAAAATGATTATAGTTAGGCC
* * * *
10866 ATAAACAATGGAAAGAAAGGCATTGACGGTTGCCAAAGCGAAGATGATTCAAAACTTCACTATTG
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACGATTCAAAAC-GCACTAATG
* *
10931 GGCCCTA-ACAGTCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
64 GGCCC-AGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
*
10995 TCACCAAAATGATTATAGTTAGGCT
128 TCACCAAAATGATTATAGTTAGGCC
* * * * *
11020 ATAAACAATGGAGAGAAAAGCATTGAGGTTTGCCTAATCGAATACGATTCAAAACGGAACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGAGG-TTGCCAAATCGAAGACGATTCAAAAC-GCACTAATG
* * *
11085 GGCCTAGATAGGC-CAAAATAAAAATGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACAAATC
64 GGCCCAGATAGGCTCAAAATAACAA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
11149 TCACCAAAATGATTATAGTTAGGCC
128 TCACCAAAATGATTATAGTTAGGCC
* *
11174 ATAAACAATGGAAAGAAAGGCATTGAGGGTT-ACAAATCGAAGAGGATTCAAAACGTCACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACGATTCAAAACG-CACTAATG
* *
11238 GGTCCC-GATAGGCTC-----AACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACTAATT
64 GG-CCCAGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
11297 TCACCAAAATGATTATAGTTAGGCC
128 TCACCAAAATGATTATAGTTAGGCC
* * *
11322 ATAAACAATGGAAAGAAAGGCATTGACGGTTGCCAAAGCGAAGATGATTCAAAACTTCACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACGATTCAAAAC-GCACTAATG
* * * *
11387 GGCCCCA-ATAGTCTCAAAATAATAAGTGTTGCAAATGAGATAAAAACTTCACAGTGGACTAATC
64 GG-CCCAGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
11451 TCACCAAAATGATTATAGTTAGGCC
128 TCACCAAAATGATTATAGTTAGGCC
* * * * *
11476 ATAAACAATGGAAAGAAAGGCATTAAGGGTTACCAAAGCGAAGATGATTCAAAACGTTACTAATG
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACGATTCAAAACG-CACTAATG
* * *
11541 GG-CCACGATAGGTTAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACATTGGACTAATC
64 GGCCCA-GATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
11605 TCACCAAAATGATTATAGTTAGGCC
128 TCACCAAAATGATTATAGTTAGGCC
* *
11630 ATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGA-GAATTCAAAACGGAACTAAT
1 ATAAACAATGGAAAGAAAGGCATTGA-GGTTGCCAAATCGAAGACG-ATTCAAAAC-GCACTAAT
* * * * *
11694 GGCCCCCGATAGGCACAAAATAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGAACTAA-C
63 GGGCCCAGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* *
11758 ATTACCAAAATGATAATAGTTAGGCC
128 -TCACCAAAATGATTATAGTTAGGCC
* * *
11784 CTAAACAATGGAAAGAAAAGGAATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTGAT
1 ATAAACAATGGAAAG-AAAGGCATTGAGG-TTGCCAAATCGAAGACGATTCAAAACG-CACTAAT
*
11849 GGGCCC-GAAAGGC-CGAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
63 GGGCCCAGATAGGCTC-AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
11912 CTCACCAAAATGATTATAGTTAGGCC
127 CTCACCAAAATGATTATAGTTAGGCC
* * *
11938 ATAATCAATGGAATGAAAAG-ATTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACT
1 ATAAACAATGGAAAGAAAGGCA-TTGAGG-TTGCCAAATCGAAGACGATTCAAAACG-CACT
11999 GATAGG
Statistics
Matches: 1553, Mismatches: 152, Indels: 86
0.87 0.08 0.05
Matches are distributed among these distances:
148 91 0.06
149 44 0.03
152 10 0.01
153 293 0.19
154 1056 0.68
155 58 0.04
156 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (152 bp):
ATAAACAATGGAAAGAAAGGCATTGAGGTTGCCAAATCGAAGACGATTCAAAACGCACTAATGGG
CCCAGATAGGCTCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCA
CCAAAATGATTATAGTTAGGCC
Done.