Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016487.1 Corchorus olitorius cultivar O-4 contig16520, 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: 109821
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:770 original size:307 final size:311
Alignment explanation
Indices: 4--1125 Score: 1032
Period size: 307 Copynumber: 3.6 Consensus size: 311
1 CAA
* * * *
4 ACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGTCATATTGGATTTAAGGATTTTTTTT
1 ACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GATTT-A-GA--ATTTTA
* * * * * *
69 ACAAGCATCTGAATCATGTTTCGATTTAATCAGAAATTTATTCAGAATAAAATAGGAAAAATGAT
61 ACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTAGAAAAAAATAGGAAAAA-CAT
* *
134 ATT-GAAAGCGTGAAAAACCCTTCAATCTTTTTTGCGTTGAATTATATATTTTTTATTATGAGTA
125 ATTAG-AAGCGTGAAAAACCCTTCAATATTTTTT-CGTTGAATTATATA---TTT-TTCTGAGTA
* * *
198 TTGT-GTTTAAAATTGAGGAAAATTCTTTCACGGTCAA----T-------T--T-T--TACCATC
184 TTGTAGCTAAAAATTGAGGAAAAATCTTTC-CGGTCAATTTTTGCCGAAATCATGTACTACCATC
* * * *
246 ACGATTTTTGGCTAAAAACGCATTTCAGGGCACCGGCTTAGTTTTACATGATTTTTGGCGCCACG
248 ACGATTTTTGGCTAAAAACGCATTCCAGGGCACCGACTTAGTTTTACATGA-CTTTGGCGCCAAG
* * *
311 ACTCGTTGAATTATCTATATTCATCTAACCAAATCTCAGCTACATTGGATATTGGATTTAAGAAA
1 ACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGC--C-----ACATT-GATTT-AG-AA
* * * *
376 TTTTTTTTTACGAGCATCTAAATCATGTTTCGATTTAATAAAAAATT-ATTTCAGAATAAAATAG
56 ----TTTTAACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTT-AGAAAAAAATAG
440 GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTTCTGTTGAATTATATATATTTT-
116 GAAAAAC-ATATTAGAAGCGTGAAAAACCCTTCAATATTTTTTC-GTTGAATTATATAT-TTTTC
* * *
504 TTAGTATTGT-GTCT-AAAATTGAGGAAAAATCTTT-CGAGTCAATTTTTGCTGAAATCATGTAT
178 TGAGTATTGTAG-CTAAAAATTGAGGAAAAATCTTTCCG-GTCAATTTTTGCCGAAATCATGTAC
* * * * * *
566 TAACCATCACGATTTTTGGCTGAAAACGCATTTCGGGGCACC-AGTTTCGTTTTACATGATTTTT
241 T-ACCATCACGATTTTTGGCTAAAAACGCATTCCAGGGCACCGA-CTTAGTTTTACATGA-CTTT
630 GGCGCCAAG
303 GGCGCCAAG
** * *
639 ACTTGTTGAATTATCTATATTCATCTAACCTAAA-CTCAG-C-CA-T-ATTT-G-A-TTTAAGGA
1 ACTCATTGAAATATCTATATTCATCTAACC-AAATCTCAGCCACATTGATTTAGAATTTTAACGA
* * * *
696 GTATCTGAATCATGTTTCGATTTAATCAGAAATTAATTTAGAAAAAAATAAGAAAAATTATATTA
65 GCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTAGAAAAAAATAGGAAAAA-CATATTA
* * ** *
761 GAAGCGTGAAAAGCCCTTCAATCTTTTCGGCATTGAATTATATACTTTTTCTGAGTATTGTAGCT
129 GAAGCGTGAAAAACCCTTCAATATTTT-TTCGTTGAATTATATA-TTTTTCTGAGTATTGTAGCT
*
826 AAAAATTGAGGAAAAATCTTTCCGGTCAATTTTTGCCGAAATCGTGTACTACCATCACGATTTTT
192 AAAAATTGAGGAAAAATCTTTCCGGTCAATTTTTGCCGAAATCATGTACTACCATCACGATTTTT
* * *
891 TGCTAAAAACGCGTTCCAGGGCACCGACTTAGTTTTGCATGACTTTGGCGCCAAG
257 GGCTAAAAACGCATTCCAGGGCACCGACTTAGTTTTACATGACTTTGGCGCCAAG
* *
946 ACTCATTGAAATATCTATATTCATGTAACCAAATCTCAGCCACATTGGATTTAAGAATTTTTTTT
1 ACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATT-GATTT-AGAA---TTTTA
* * *
1011 ACGAGCATCTGAATCATATTTCGATTTAATCATAAATTAATTCA-AGAAAAAATAGGAAAAACAT
61 ACGAGCATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTAGA-AAAAAATAGGAAAAACA-
* * *
1075 TATTAGAAGCGTGAAAATCCCTTCAATCTTTTTGGCGTTGAATTATATATT
124 TATTAGAAGCGTGAAAAACCCTTCAATATTTTT-TCGTTGAATTATATATT
1126 GCTAATAATT
Statistics
Matches: 688, Mismatches: 64, Indels: 115
0.79 0.07 0.13
Matches are distributed among these distances:
306 3 0.00
307 179 0.26
308 65 0.09
309 48 0.07
310 5 0.01
311 5 0.01
312 34 0.05
313 5 0.01
314 18 0.03
315 6 0.01
316 106 0.15
317 1 0.00
318 5 0.01
319 102 0.15
322 1 0.00
324 1 0.00
325 2 0.00
327 1 0.00
328 98 0.14
329 3 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (311 bp):
ACTCATTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGATTTAGAATTTTAACGAG
CATCTGAATCATGTTTCGATTTAATCAAAAATTAATTTAGAAAAAAATAGGAAAAACATATTAGA
AGCGTGAAAAACCCTTCAATATTTTTTCGTTGAATTATATATTTTTCTGAGTATTGTAGCTAAAA
ATTGAGGAAAAATCTTTCCGGTCAATTTTTGCCGAAATCATGTACTACCATCACGATTTTTGGCT
AAAAACGCATTCCAGGGCACCGACTTAGTTTTACATGACTTTGGCGCCAAG
Found at i:2021 original size:14 final size:14
Alignment explanation
Indices: 2002--2030 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1992 GCAAAGTTTA
2002 ACTGACTTTTGTCG
1 ACTGACTTTTGTCG
2016 ACTGACTTTTGTCG
1 ACTGACTTTTGTCG
2030 A
1 A
2031 TGTCACATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.21, G:0.21, T:0.41
Consensus pattern (14 bp):
ACTGACTTTTGTCG
Found at i:9118 original size:178 final size:178
Alignment explanation
Indices: 8814--9143 Score: 509
Period size: 178 Copynumber: 1.9 Consensus size: 178
8804 TAAACTCAAA
* * * * * * * *
8814 TTATGTAATATTAAGTAGATCGTTTATTTCCGTTAATCGAAATAACTAATTTTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
* *
8879 TTTATACCTTGAGCATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
66 TTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
8944 CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAG
131 CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAG
*
8992 TTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
*
9057 TTGATA-CTTGAAACATTGAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAA
66 TTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAA
* * *
9121 TCTTTTAATAGACACTTGAATCA
130 CCTTTCAAGAGACACTTGAATCA
9144 CCTTAATTGG
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
177 4 0.03
178 132 0.97
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
TTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAG
Found at i:9172 original size:178 final size:178
Alignment explanation
Indices: 8814--9183 Score: 492
Period size: 178 Copynumber: 2.1 Consensus size: 178
8804 TAAACTCAAA
* * * * * * * *
8814 TTATGTAATATTAAGTAGATCGTTTATTTCCGTTAATCGAAATAACTAATTTTTTGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
* *
8879 TTTATACCTTGAGCATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
66 TTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
* * * *
8944 CTTTCAAGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAG
131 CTTTCAAGAGACACTTGAATCACCTCAATCAGACAACCGAAGCAAAAG
*
8992 TTATATAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
1 TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
*
9057 TTGATA-CTTGAAACATTGAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAA
66 TTGATACCTTG-AACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAA
* * * * ** *
9121 TCTTTTAATAGACACTTGAATCACCTTAATTGGATAACCGAAG-AGAAAG
130 CCTTTCAAGAGACACTTGAATCACCTCAATCAGACAACCGAAGCA-AAAG
*
9170 TTATATAATGTTAA
1 TTATATAATATTAA
9184 ATATATCGTT
Statistics
Matches: 166, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
177 5 0.03
178 161 0.97
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (178 bp):
TTATATAATATTAAGTAGACCGTCTATTCCCGTTAACCGAAACAACAAATTTTTCGGAAGCATTT
TTGATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAACAAC
CTTTCAAGAGACACTTGAATCACCTCAATCAGACAACCGAAGCAAAAG
Found at i:9477 original size:3 final size:3
Alignment explanation
Indices: 9469--9498 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
9459 ATGAAAGATT
9469 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9499 AATAATGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:22814 original size:29 final size:30
Alignment explanation
Indices: 22772--22845 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
22762 TATACAGTTT
* *
22772 AGTATGGTACATGCCTGGCCA-AAAAAAAA
1 AGTATAGTACATGCATGGCCATAAAAAAAA
* **
22801 AGTATAGTACATGCATTGTTATAAAAAAAA
1 AGTATAGTACATGCATGGCCATAAAAAAAA
22831 AGTATAGTACATGCA
1 AGTATAGTACATGCA
22846 AATATTGTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 16 0.41
30 23 0.59
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (30 bp):
AGTATAGTACATGCATGGCCATAAAAAAAA
Found at i:27004 original size:20 final size:20
Alignment explanation
Indices: 26979--27020 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
26969 GGATTGAAAA
26979 TAACGTTGCCTCTTTGTGTT
1 TAACGTTGCCTCTTTGTGTT
*
26999 TAACGTTGCCTCTTTGTTTT
1 TAACGTTGCCTCTTTGTGTT
27019 TA
1 TA
27021 TCTAACGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.17, T:0.52
Consensus pattern (20 bp):
TAACGTTGCCTCTTTGTGTT
Found at i:31930 original size:41 final size:41
Alignment explanation
Indices: 31873--31959 Score: 174
Period size: 41 Copynumber: 2.1 Consensus size: 41
31863 TGAATGGCTT
31873 AGCACGAACCTGTTAATTCGAAACTATAATGCTTGTATTAA
1 AGCACGAACCTGTTAATTCGAAACTATAATGCTTGTATTAA
31914 AGCACGAACCTGTTAATTCGAAACTATAATGCTTGTATTAA
1 AGCACGAACCTGTTAATTCGAAACTATAATGCTTGTATTAA
31955 AGCAC
1 AGCAC
31960 AAACTTGGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (41 bp):
AGCACGAACCTGTTAATTCGAAACTATAATGCTTGTATTAA
Found at i:31972 original size:41 final size:41
Alignment explanation
Indices: 31873--31972 Score: 155
Period size: 41 Copynumber: 2.4 Consensus size: 41
31863 TGAATGGCTT
* *
31873 AGCACGAACCTGTTAATTCGAAACTATAATGCTTGTATTAA
1 AGCACAAACCTGGTAATTCGAAACTATAATGCTTGTATTAA
* *
31914 AGCACGAACCTGTTAATTCGAAACTATAATGCTTGTATTAA
1 AGCACAAACCTGGTAATTCGAAACTATAATGCTTGTATTAA
*
31955 AGCACAAACTTGGTAATT
1 AGCACAAACCTGGTAATT
31973 AAACCATTAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (41 bp):
AGCACAAACCTGGTAATTCGAAACTATAATGCTTGTATTAA
Found at i:32477 original size:27 final size:27
Alignment explanation
Indices: 32446--32499 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
32436 TCTTCCAGGC
32446 TTGGTTCCAGCAAAAGTCGAGAACAAG
1 TTGGTTCCAGCAAAAGTCGAGAACAAG
32473 TTGGTTCCAGCAAAAGTCGAGAACAAG
1 TTGGTTCCAGCAAAAGTCGAGAACAAG
32500 CATATATAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (27 bp):
TTGGTTCCAGCAAAAGTCGAGAACAAG
Found at i:36633 original size:5 final size:5
Alignment explanation
Indices: 36618--36648 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
36608 TAAATGTTTT
36618 TCTTAA TCTTA TCTTA TCTTA TCTTA TCTTA
1 TCTT-A TCTTA TCTTA TCTTA TCTTA TCTTA
36649 CTATTATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.84
6 4 0.16
ACGTcount: A:0.23, C:0.19, G:0.00, T:0.58
Consensus pattern (5 bp):
TCTTA
Found at i:39565 original size:334 final size:328
Alignment explanation
Indices: 38525--39636 Score: 1118
Period size: 334 Copynumber: 3.3 Consensus size: 328
38515 ATACATTACA
* * * * * * *
38525 TCATCTAACCAAATCTCAGCAACATTGGATTTGAGA-ATTTCTTTTTACGAGTATCTGAATCTTA
1 TCATCTAATCAAATCTAAGCCACATTGGATTT-AAATATTTGTTTTTACGAGCATCTGAATCTTG
* *
38589 TTTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATACGATATTAAAAGCGTA-AAAAAC
65 TTTCGATTTAATTAGAAATTAATTTAG-AAAAATAGGAAAAACGATATTAAAA-CG-ACAAAAAC
* ** * * ** * *
38653 CCTCCAATCTTTTTGGCAATGAATTATATATTTTTATGAGTATTTTAGGTAAAAATTGAGGAGAA
127 CATCCAATCTTTTTGGCGTTAAATTATATAATTTTATGAGTATTTTAGCCAAAAATCGAGGAAAA
* * * * ** ** * * * * *
38718 ATATTT-GGTGTCAATTTTTGCAAAATTTTTGCTGAGTTAGT-AACAGTAAAGCCATTACGGTTT
192 ATCTTTCAG-GTCAA-TTTTACAAAATTTTAGCCAAAATCGTGTA-A-TTAA-CCATCACAGTTT
* * * * * * *
38781 CT-GACTAAAAACGCGTTTCGGGGACTCGACTCAATTTTGCATGATTTTTGGCTCCGAGACTACT
252 TTAG-CTAAAAACGCGTTTCCGGGCCCCGACTCAATTTTGCATGATTTTT-GCGCCGAAACTCCT
*
38845 TGAAATATCTATAT
315 TAAAATATCTATAT
* * *
38859 TCATCTAATCAATTCTCAGCCACATTGGATTTAAATATTTGTTTTGACGAGCA-CATGAATCTTG
1 TCATCTAATCAAATCTAAGCCACATTGGATTTAAATATTTGTTTTTACGAGCATC-TGAATCTTG
* *
38923 TTTCGATTTAATTAGAAATTAATTTGGAAAAATAGGAAAAACGATATTAGAAACGTCAAAAACCA
65 TTTCGATTTAATTAGAAATTAATTTAGAAAAATAGGAAAAACGATATTA-AAACGACAAAAACCA
* * * * * * * **
38988 TTCAATTTTTTTGGTGTTGAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGGTATTAT
129 TCCAATCTTTTTGGCGTTAAATTATATAATTTTATGAGTATTTTAGCCAAAAATCGAGGAAAAAT
* * *
39053 CTTTCGGGTCAATTTTACAAAATTTTAGCCGAAATCGTGTAATTAACCATCACAGTTTTTAGATG
194 CTTTCAGGTCAATTTTACAAAATTTTAGCCAAAATCGTGTAATTAACCATCACAGTTTTTAGCT-
* * * *
39118 AAAAA-GCG-TTCTGGGCCCCGGCTCACTTTTGCATGATTTTTTTGCGCC-AAGACTCCTTAAGA
258 AAAAACGCGTTTCCGGGCCCCGACTCAATTTTGCATGA--TTTTTGCGCCGAA-ACTCCTTAAAA
*
39180 TATCCATAT
320 TATCTATAT
* ** * *
39189 TCATCTAATCAAATCTAAGTCACATTGGATTTATGTATTTGTTTTTACAAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTAAGCCACATTGGATTTAAATATTTGTTTTTACGAGCATCTGAATCTTGT
* * * *
39254 TTCGATTTAATTAATTAGAATTTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAG
66 TTCGA--T--TTAATTAGAAATTAATTTAGAAAAATAGGAAAAACGATATTAAAA-CGACAAAA-
*
39319 TCC-TCCAATCTTTTTGGCGTTAAATTATATAAATTTTATGAGTATTTTAG-CATAAAATCGAGG
125 ACCATCCAATCTTTTTGGCGTTAAATTATAT-AATTTTATGAGTATTTTAGCCA-AAAATCGAGG
* * * *
39382 AAAAATTTTTCAGGTCATTTTTTGC-AAATTCTTAGCCAAAATCGTGTAA-TAACCATCATAGTT
188 AAAAATCTTTCAGGTCA-ATTTTACAAAATT-TTAGCCAAAATCGTGTAATTAACCATCACAGTT
* * * *
39445 TTTTGCTAAAAACGCGTTTCCGAGCCCCAACTCAGTTTTGCATGATTTTTGCCGCCGAAACTCCT
251 TTTAGCTAAAAACGCGTTTCCGGGCCCCGACTCAATTTTGCATGATTTTTG-CGCCGAAACTCCT
39510 TAAAATATCTATAT
315 TAAAATATCTATAT
* * * * *
39524 TCATCTAAT-AAATCTTAGCCGCATTGCATTTAAAAATTTGTTTTTACGAGCATCTGAATTTTGT
1 TCATCTAATCAAATCTAAGCCACATTGGATTTAAATATTTGTTTTTACGAGCATCTGAATCTTGT
39588 TTCGATTTAATTAGAAATTAATTTAGAAAAATAGGAAAAACGATATTAA
66 TTCGATTTAATTAGAAATTAATTTAGAAAAATAGGAAAAACGATATTAA
39637 TCTTTTTGGC
Statistics
Matches: 652, Mismatches: 100, Indels: 56
0.81 0.12 0.07
Matches are distributed among these distances:
329 24 0.04
330 135 0.21
331 15 0.02
332 23 0.04
333 98 0.15
334 212 0.33
335 98 0.15
336 47 0.07
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (328 bp):
TCATCTAATCAAATCTAAGCCACATTGGATTTAAATATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTTAGAAAAATAGGAAAAACGATATTAAAACGACAAAAACCATC
CAATCTTTTTGGCGTTAAATTATATAATTTTATGAGTATTTTAGCCAAAAATCGAGGAAAAATCT
TTCAGGTCAATTTTACAAAATTTTAGCCAAAATCGTGTAATTAACCATCACAGTTTTTAGCTAAA
AACGCGTTTCCGGGCCCCGACTCAATTTTGCATGATTTTTGCGCCGAAACTCCTTAAAATATCTA
TAT
Found at i:44835 original size:13 final size:13
Alignment explanation
Indices: 44817--44843 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44807 ACGTTACCTC
44817 ATATTACTTGATG
1 ATATTACTTGATG
44830 ATATTACTTGATG
1 ATATTACTTGATG
44843 A
1 A
44844 GAATACTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
ATATTACTTGATG
Found at i:48959 original size:62 final size:62
Alignment explanation
Indices: 48884--49003 Score: 222
Period size: 62 Copynumber: 1.9 Consensus size: 62
48874 CTCTCTTTGT
* *
48884 TTCTCTCACTTTCCCACGAAATTCCAGTCGATTTAACCTGGGTTCATTCTAAAATTTTGAAG
1 TTCTCTCACTTTCCCAAGAAATTCCAGTCGATTTAACCTGGGATCATTCTAAAATTTTGAAG
48946 TTCTCTCACTTTCCCAAGAAATTCCAGTCGATTTAACCTGGGATCATTCTAAAATTTT
1 TTCTCTCACTTTCCCAAGAAATTCCAGTCGATTTAACCTGGGATCATTCTAAAATTTT
49004 AAAGAATGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.38
Consensus pattern (62 bp):
TTCTCTCACTTTCCCAAGAAATTCCAGTCGATTTAACCTGGGATCATTCTAAAATTTTGAAG
Found at i:51688 original size:26 final size:26
Alignment explanation
Indices: 51656--51709 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
51646 TGATAATGAG
51656 GGTGATCAATTAGCTGATGATATTCA
1 GGTGATCAATTAGCTGATGATATTCA
51682 GGTGATCAATTAGCTGATGATATTCA
1 GGTGATCAATTAGCTGATGATATTCA
51708 GG
1 GG
51710 CATCTAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (26 bp):
GGTGATCAATTAGCTGATGATATTCA
Found at i:52452 original size:47 final size:47
Alignment explanation
Indices: 52392--52553 Score: 243
Period size: 47 Copynumber: 3.4 Consensus size: 47
52382 ATTAATTAAG
* **
52392 GATCAACTCAAACTAACAAGCGATAGGAAGTCCCAAACATCAATATT
1 GATCAACTCAAACTAACAAGCAATAGGAAGTCCCAAACATCAATACC
*
52439 GATCAACTCAAACTAACAAGCAATAGGAAGTCCTAAACATCAATACC
1 GATCAACTCAAACTAACAAGCAATAGGAAGTCCCAAACATCAATACC
* * *
52486 GATCAACTCAAACTAACAATCAATAGAAAGTCTCAAACATCAATACC
1 GATCAACTCAAACTAACAAGCAATAGGAAGTCCCAAACATCAATACC
* *
52533 AATTAACTCAAACTAACAAGC
1 GATCAACTCAAACTAACAAGC
52554 TAAATTGTTG
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 104 1.00
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.19
Consensus pattern (47 bp):
GATCAACTCAAACTAACAAGCAATAGGAAGTCCCAAACATCAATACC
Found at i:52757 original size:30 final size:30
Alignment explanation
Indices: 52721--52789 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
52711 CACGTCAGCA
52721 AAATTGACG-GTT-CAATTAAACAGAGGGATT
1 AAATTGACGTGTTCCAA-T-AACAGAGGGATT
* *
52751 AAATTGATCGTTTTCCAATAATAGAGGGATT
1 AAATTGA-CGTGTTCCAATAACAGAGGGATT
52782 AAATTGAC
1 AAATTGAC
52790 TGATTTCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 8 0.24
31 20 0.59
32 3 0.09
33 3 0.09
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.30
Consensus pattern (30 bp):
AAATTGACGTGTTCCAATAACAGAGGGATT
Found at i:56654 original size:20 final size:19
Alignment explanation
Indices: 56609--56655 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
56599 ATTCAAAATA
**
56609 AAATAAAAACTACCCATTTT
1 AAAT-AAAACTACCCATTAC
56629 AAATAAAACTACCCATTAC
1 AAATAAAACTACCCATTAC
56648 AAGATAAA
1 AA-ATAAA
56656 TATAAGTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.23
Consensus pattern (19 bp):
AAATAAAACTACCCATTAC
Found at i:58627 original size:10 final size:9
Alignment explanation
Indices: 58609--58641 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
58599 TGGTGTCTAG
58609 TTTTTTTCT
1 TTTTTTTCT
58618 TTTCTTTTCT
1 TTT-TTTTCT
58628 TTTTTTT-T
1 TTTTTTTCT
58636 TTTTTT
1 TTTTTT
58642 GACGAGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 7 0.30
9 7 0.30
10 9 0.39
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTCT
Found at i:62241 original size:32 final size:31
Alignment explanation
Indices: 62186--62302 Score: 198
Period size: 31 Copynumber: 3.7 Consensus size: 31
62176 AGCGTGACAT
*
62186 GCCACGTGTACCAAAAAGTGACATGTGGCAC
1 GCCACGTGTACCAAAAAGCGACATGTGGCAC
62217 GCCACGTGTACCAAAAAAGCGACATGTGGCAC
1 GCCACGTGTACC-AAAAAGCGACATGTGGCAC
62249 GCCACGTGTACCAAAAAGCGACATGTGGCAC
1 GCCACGTGTACCAAAAAGCGACATGTGGCAC
* *
62280 ACCACGTGTACCAAAAAGTGACA
1 GCCACGTGTACCAAAAAGCGACA
62303 CGTATCATGC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
31 52 0.63
32 30 0.37
ACGTcount: A:0.35, C:0.27, G:0.24, T:0.14
Consensus pattern (31 bp):
GCCACGTGTACCAAAAAGCGACATGTGGCAC
Found at i:62328 original size:63 final size:63
Alignment explanation
Indices: 62186--62327 Score: 178
Period size: 63 Copynumber: 2.3 Consensus size: 63
62176 AGCGTGACAT
* * * * *
62186 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACGTGTACCAAAAAAGCGACATGTGGCAC
1 GCCACATGTACCAAAAAGCGACATGTGGCACACCACGTGTACCAAAAAAGCGACACGTAGCAC
* * * *
62249 GCCACGTGTACCAAAAAGCGACATGTGGCACACCACGTGTACC-AAAAAGTGACACGTATCAT
1 GCCACATGTACCAAAAAGCGACATGTGGCACACCACGTGTACCAAAAAAGCGACACGTAGCAC
* *
62311 GCTATATGTACCAAAAA
1 GCCACATGTACCAAAAA
62328 ATGACACGTG
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
62 28 0.41
63 41 0.59
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (63 bp):
GCCACATGTACCAAAAAGCGACATGTGGCACACCACGTGTACCAAAAAAGCGACACGTAGCAC
Found at i:62365 original size:30 final size:31
Alignment explanation
Indices: 62178--62367 Score: 148
Period size: 31 Copynumber: 6.1 Consensus size: 31
62168 CGATGTCCAG
* **
62178 CGTGACATGCCACGTGTACCAAAAAGTGACA
1 CGTGGCATGCCATATGTACCAAAAAGTGACA
* * ** *
62209 TGTGGCACGCCACGTGTACCAAAAAAGCGACA
1 CGTGGCATGCCATATGTACC-AAAAAGTGACA
* * ** *
62241 TGTGGCACGCCACGTGTACCAAAAAGCGACA
1 CGTGGCATGCCATATGTACCAAAAAGTGACA
* ** **
62272 TGTGGCACACCACGTGTACCAAAAAGTGACA
1 CGTGGCATGCCATATGTACCAAAAAGTGACA
** * *
62303 CGTATCATGCTATATGTACCAAAAAATGACA
1 CGTGGCATGCCATATGTACCAAAAAGTGACA
**
62334 CGTGGCATGCCATATGTTTC-AAAAGTGACA
1 CGTGGCATGCCATATGTACCAAAAAGTGACA
62364 CGTG
1 CGTG
62368 CACAAAAGGA
Statistics
Matches: 137, Mismatches: 21, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
30 13 0.09
31 94 0.69
32 30 0.22
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (31 bp):
CGTGGCATGCCATATGTACCAAAAAGTGACA
Found at i:66200 original size:17 final size:17
Alignment explanation
Indices: 66178--66213 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
66168 TAAATTGGCA
66178 AACAACAGAAAAATGAT
1 AACAACAGAAAAATGAT
66195 AACAACAGAAAAATGAT
1 AACAACAGAAAAATGAT
66212 AA
1 AA
66214 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.11, G:0.11, T:0.11
Consensus pattern (17 bp):
AACAACAGAAAAATGAT
Done.