Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023846.1 Corchorus olitorius cultivar O-4 contig23879, 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: 9164
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:656 original size:325 final size:320
Alignment explanation
Indices: 54--1132 Score: 1358
Period size: 325 Copynumber: 3.3 Consensus size: 320
44 ATTCGTGAAC
* ** * *
54 TAACCATCACTGTTTTTTGCTAAAAACGCGTTTCGGAGATCCGGCTAAGTTCTGCATGA-TTTTT
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCCGGCTTAGTTTTGCATGATTTTTT
* * * *
118 G-GCATTGAGACTCCTTGCACTATCTATATTCATCTAATCAAATCTCAGCACATTGCATTGAAGG
66 GCGCA--GAGACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGCACATTGCATT-AATG
* *
182 ATTTGTTTGTACGAGCATTTGAATCTTGTTTCGATTTAATGAGAAATTAATGCGAAAAAAATATG
128 ATTTGTTTGTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AAAAAAATATG
* * * *
247 AAAAATGATATTAAAAGCGAGAAAAGTCCTCCAATCTTTTTGGTGTTAAATTATATATTTTTTAT
192 AAAAACGATATTAAAAGC-TGAAAAGT-CTCCAATCTTTTTGGAGTTAAATTATATATATTTTAT
*
312 GACTATTTTAGCCAAAAATTGAGTAGAAATTTTTTGGGCCATTTTCTGCAAAAGTTAAGCTGGAA
255 GACTATTTTAGCCAAAAATTGAGTAGAAATTTTTTGGGCCATTTTCTGCAAAATTTAAGCTGGAA
377 T
320 T
* * *
378 TAACCATCATGGTTTTTAGCTAAATACGCGTTTCAGG-GCCCCGGCTTAGTTTTGCATGATTTTT
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTTC-GGAGCCCCGGCTTAGTTTTGCATGATTTTT
* *
442 TTCGCAGAGACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGCGACATTTGAATTCAAT
65 TGCGCAGAGACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGC-ACA-TTGCATT-AAT
* * *
507 GATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAAAAAAATATG
127 GATTTGTTTGTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATG
* * * * *
572 AAAAACGATATTAAAAGCTCGAAAAGTCTTTCAACCTTTTTGGCGTTAAATTATATATCTTTCAT
192 AAAAACGATATTAAAAGCT-GAAAAGTC-TCCAATCTTTTTGGAGTTAAATTATATATATTTTAT
* * * * ** * * * *
637 GAGTATTTTAGCGAAAAATTGA-TGAAAAATTTTTCGGGTGATTTTTTGCAAAATTTTAGATGAA
255 GACTATTTTAGCCAAAAATTGAGT-AGAAATTTTTTGGGCCATTTTCTGCAAAATTTAAGCTGGA
701 AT
319 AT
** *
703 CGTGAA-CATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCTGCGGCTCAGTTTTGCATGATTT
1 --T-AACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCCGGCTTAGTTTTGCATGATTT
* ** * * *
767 TTGGCGTTGAGACTCCTTGAAATATCTATATTCATCTAATCAAATATCAGCACATTGCATTTATG
63 TTTGCGCAGAGACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGCACATTGCATTAAT-
* * *
832 GATTTGTTTGTACGAGCATTTAAATCTTGTTTCGATTTAATTAGAAATCAATTCAGAAAAATATG
127 GATTTGTTTGTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATG
*
897 AAAAACGATATTAAAAGCGTGGAAAGTACTCCAATCTTTTTGGAGTTAAATTATATATATTTTAT
192 AAAAACGATATTAAAAGC-TGAAAAGT-CTCCAATCTTTTTGGAGTTAAATTATATATATTTTAT
*
962 GACTATTTTAGCCAAAAATTGAGGAGAAATTTTTTGGGCCATTTTCTGCAAAATTTAAGCTGGAA
255 GACTATTTTAGCCAAAAATTGAGTAGAAATTTTTTGGGCCATTTTCTGCAAAATTTAAGCTGG-A
1027 TCGTGTAT
319 ------AT
* * *
1035 TAACCATCACGGTTTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTT
1 TAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCCGGCTTAGTTTTGCATGATTTTTT
* * *
1100 GCACCGAAACTCCTTGAAATATCTATACTCATC
66 GCGCAGAGACTCCTTGAAATATCTATACTCATC
1133 ATGAGTATTT
Statistics
Matches: 644, Mismatches: 87, Indels: 42
0.83 0.11 0.05
Matches are distributed among these distances:
324 92 0.14
325 300 0.47
326 68 0.11
327 95 0.15
328 2 0.00
329 2 0.00
330 83 0.13
332 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (320 bp):
TAACCATCACGGTTTTTTGCTAAAAACGCGTTTCGGAGCCCCGGCTTAGTTTTGCATGATTTTTT
GCGCAGAGACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGCACATTGCATTAATGATT
TGTTTGTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAAATATGAAAA
ACGATATTAAAAGCTGAAAAGTCTCCAATCTTTTTGGAGTTAAATTATATATATTTTATGACTAT
TTTAGCCAAAAATTGAGTAGAAATTTTTTGGGCCATTTTCTGCAAAATTTAAGCTGGAAT
Found at i:2013 original size:262 final size:259
Alignment explanation
Indices: 1537--2050 Score: 886
Period size: 262 Copynumber: 2.0 Consensus size: 259
1527 GTGTCACGGT
*
1537 TTTTGGCTAAAAACGCATTTCGGGGCCTCGGCTTAGTTTTGCATGATTTTTTGCACCGAAACTCC
1 TTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTTGCACCGAAACTCC
* *
1602 TTGAAATATCTATACTCATCTAATCAAATCTCAGCCACATTTGAATTTAATGATTTTTTTTTACG
66 TTGAAATATCTATACTCATCTAATCAAATCTAAGCCACATTTGAATTTAATGATTTGTTTTTACG
**
1667 AGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCTGAAAAATATGAAAAACGATATTAA
131 AGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAA
*
1732 AAGCTCGAAAAGTCCTTCAACCTTTTTGGCGTTAAATTATATATATTTCATGAGTATTTCATCGG
196 AAGCTCGAAAAGCCCTTCAACCTTTTTGGCGTTAAA-T-TATATATTTCATGAGTATTTCATCGG
1797 A
259 A
* * * *
1798 TTTTGGTTAAAAACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATCTTTTT-CGCCGAGACTC
1 TTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTTAGTTTTGCATGAT-TTTTTGCACCGAAACTC
1862 CTTGAAATATCTATACTCATCTAATCAAATCTAAGCCCACATTTGAATTTAATGATTTGTTTTTA
65 CTTGAAATATCTATACTCATCTAATCAAATCTAAG-CCACATTTGAATTTAATGATTTGTTTTTA
*
1927 CGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATT
129 CGAGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATT
1992 AAAAGCTCGAAAAGCCCTTCAACCTTTTTGGCGTTAAATTATATATTTCATGAGTATTT
194 AAAAGCTCGAAAAGCCCTTCAACCTTTTTGGCGTTAAATTATATATTTCATGAGTATTT
2051 TAGCGAAAAT
Statistics
Matches: 240, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
260 20 0.08
261 88 0.37
262 132 0.55
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (259 bp):
TTTTGGCTAAAAACGCATTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTTGCACCGAAACTCC
TTGAAATATCTATACTCATCTAATCAAATCTAAGCCACATTTGAATTTAATGATTTGTTTTTACG
AGCATCTCAATCTTGTTTTGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAA
AAGCTCGAAAAGCCCTTCAACCTTTTTGGCGTTAAATTATATATTTCATGAGTATTTCATCGGA
Found at i:2395 original size:91 final size:89
Alignment explanation
Indices: 2266--2436 Score: 225
Period size: 89 Copynumber: 1.9 Consensus size: 89
2256 CGAGCGTCTA
* * ** *
2266 AATCTTGTTTTGATTTTATTGGAAATAAATTTAGAAAAAAAAAAAGGAAAAACGATATTGGAAGC
1 AATCTTGTTTCGATTTAATTAAAAATAAATTTAG--AAAAAAAAAGGAAAAACGATATTAGAAGC
2331 GTGAAAAACCCTTCAATCGTGATTTG
64 GTGAAAAACCCTTCAATCGTGATTTG
* * **
2357 AATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAAAGTAGGAAAAACGATATTAGAAGCGT
1 AATCTTGTTTCGATTTAATTAAAAATAAATTTAGAAAAAAAAAGGAAAAACGATATTAGAAGCGT
* *
2422 GAGAAGCCCTTCAAT
66 GAAAAACCCTTCAAT
2437 TTTTTTGGCA
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
89 41 0.59
91 28 0.41
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.30
Consensus pattern (89 bp):
AATCTTGTTTCGATTTAATTAAAAATAAATTTAGAAAAAAAAAGGAAAAACGATATTAGAAGCGT
GAAAAACCCTTCAATCGTGATTTG
Found at i:2562 original size:422 final size:417
Alignment explanation
Indices: 1935--2703 Score: 1073
Period size: 422 Copynumber: 1.8 Consensus size: 417
1925 TACGAGCATC
* * *
1935 TGAATCTTGTTTTGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCTC
1 TGAATCTTGTTTCGATTTAATTAAAAATTAATTCAAAAAAATAGGAAAAACGATATTAAAAGCTC
* *
2000 GAAAAGCCCTTCAACCTTTTTGGCGTTAAATTATATATTTCATGAGTATTTTAGCGAAAATTTGA
66 GAAAAGCCCTTCAACCTTTTTGGCATTAAATTATATATTTCATGAGTATTGTAGCGAAAATTTGA
* * * * *
2065 AGAAAAATTTTCCAGGTCATTTATTGCAAAATTTTAGCCGAAATCGTGAACTAACCATCACGGTT
131 AAAAAAATTTTCCAGGTCATTTATTGCAAAACTTCAGCCAAAATCGT--A-TAACCATCACAGTT
*
2130 TTTTGCTAAAAACGCGTTCCGTG-GCCTCCACT-CAGTTTTGCATGGTTTTTGGCATAAAGACTC
193 TTTTGCTAAAAACGCGTTCCG-GAGCCTCCA-TGCAGTTTTGCATGGTTTTTGACATAAAGACTC
* * * * *
2193 CTTGAAATATCTATATTCAAGTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
256 CTTGAAATACCTATAATCAACTAACCAAATCCCAGCCACATTGGATTTAAGGATTTGTTTTTACA
* *
2258 AGCGTCTAAATCTTGTTTTGATTTTATTGGAAATAAATTTAGAAAAAAAAAAAGGAAAAACGATA
321 AGCATCTAAATCTTGTTTCGATTTTATTGGAAATAAATTTAGAAAAAAAAAAAGGAAAAACGATA
2323 TTGGAAGCGTGAAAAACCCTTCAATCGTGATT
386 TTGGAAGCGTGAAAAACCCTTCAATCGTGATT
* * *
2355 TGAATCTTGTTTCGATTTAATTAAAAATTAATTTGGAAAAAAGTAGGAAAAACGATATTAGAAGC
1 TGAATCTTGTTTCGATTTAATTAAAAATTAA-TT-CAAAAAAATAGGAAAAACGATATTAAAAGC
* ** * * * *
2420 GT-GAGAAGCCCTTCAATTTTTTTGGCATTAGATTATATATTTTTTATGATTATTGTGGCTG-AA
64 -TCGAAAAGCCCTTCAACCTTTTTGGCATTAAATTATATA--TTTCATGAGTATTGTAGC-GAAA
* * *
2483 ATTTGAGAAAAAAATATTT-CAGGTCATTTTTTGCAAAACTTCAGCTAAAATCGT-TTACCATCA
125 ATTTGA-AAAAAAAT-TTTCCAGGTCATTTATTGCAAAACTTCAGCCAAAATCGTATAACCATCA
*
2546 CAGTTTTTTGGCTAAAAACGCGTTCCGGAGCCTCGATGCAGTTTTGCATGGTTTTTGACATAAAG
188 CAGTTTTTT-GCTAAAAACGCGTTCCGGAGCCTCCATGCAGTTTTGCATGGTTTTTGACATAAAG
*
2611 ACTCCTTGAAATACCTATAATCATCTAACCAAATCCCAGCCACATTGGATTTAAGGATTTGTTTT
252 ACTCCTTGAAATACCTATAATCAACTAACCAAATCCCAGCCACATTGGATTTAAGGATTTGTTTT
2676 TACAAGCATCTAAATCTTGTTTCGATTT
317 TACAAGCATCTAAATCTTGTTTCGATTT
2704 AATAAGAATT
Statistics
Matches: 305, Mismatches: 33, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
420 29 0.10
421 20 0.07
422 192 0.63
423 1 0.00
424 22 0.07
425 38 0.12
426 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (417 bp):
TGAATCTTGTTTCGATTTAATTAAAAATTAATTCAAAAAAATAGGAAAAACGATATTAAAAGCTC
GAAAAGCCCTTCAACCTTTTTGGCATTAAATTATATATTTCATGAGTATTGTAGCGAAAATTTGA
AAAAAAATTTTCCAGGTCATTTATTGCAAAACTTCAGCCAAAATCGTATAACCATCACAGTTTTT
TGCTAAAAACGCGTTCCGGAGCCTCCATGCAGTTTTGCATGGTTTTTGACATAAAGACTCCTTGA
AATACCTATAATCAACTAACCAAATCCCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGCAT
CTAAATCTTGTTTCGATTTTATTGGAAATAAATTTAGAAAAAAAAAAAGGAAAAACGATATTGGA
AGCGTGAAAAACCCTTCAATCGTGATT
Found at i:2958 original size:321 final size:321
Alignment explanation
Indices: 2550--3173 Score: 773
Period size: 321 Copynumber: 1.9 Consensus size: 321
2540 CCATCACAGT
* * * *
2550 TTTTTGGCTAAAAACGCGTTCCGGAGCCTCGATGCAGTTTTGCATGGTTTTTGACATAAAGACTC
1 TTTTTGCCTAAAAACGCGTTCCGGACCCCCGATGCAGTTTTGCATGATTTTTGACATAAAGACTC
* * *
2615 CTTGAAATACCTATAATCATCTAACCAAATCCCAGCCACA-TTGGATTTAAGGATTTGTTTTTAC
66 CTTGAAATACCTACAATCATCTAACCAAATCACAGCCACATTTGAATTTAAGGATTTGTTTTTAC
*
2679 AAGCATCTAAATCTTGTTTCGATTTAATAAG-AATTAAATTCGGAAAAA-ACTGGAAAAACAATA
131 AAGCATCTAAATCTTGTTTCGATTTAATAAGAAATT-AATTCAGAAAAATA-TGG-AAAACAATA
* * *
2742 TTAAAAGCGTAAAAAATCGTTCAAT-TTTTTGGT-GTTGAATTATATAT-TCTTTCTGAGTATTG
193 TTAAAAGCGTAAAAAATCATCCAATCTTTTT-GTAGTTGAATTATATATAT-TTTATGAGTATTG
2804 CGGC-AGAAAATTGAGGGAAAAACT-TTTCGGGTC-AGTTTTTGCAAAATTTAAGCTGGAATCGT
256 CGGCTA-AAAATTGA-GGAAAAA-TATTTCGGGTCTA-TTTTTGCAAAATTTAAGCTGGAATCGT
2866 GACGG
317 GACGG
* * * * * **
2871 TTTTTGCCTAAAAACGCGTTTCGGGACCCCCGCT-TAGTTTTGCATGATTTTTGGCGTCGAGACT
1 TTTTTGCCTAAAAACGCG-TTCCGGACCCCCGATGCAGTTTTGCATGATTTTTGACATAAAGACT
* * * * * *
2935 CTTTGAAATATCTACACTCATCTAATCAAATCACAGCCATATTTGAATTTAATGATTTGTTTTTA
65 CCTTGAAATACCTACAATCATCTAACCAAATCACAGCCACATTTGAATTTAAGGATTTGTTTTTA
* * * * * *
3000 CGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTGATTCAGAAAAATATGGAAAACGATATT
130 CAAGCATCTAAATCTTGTTTCGATTTAATAAGAAATTAATTCAGAAAAATATGGAAAACAATATT
* * * * *
3065 AAAAGCGTGAAAAGTTATCCAATCTTTTTGTAGTTGAATTATATGTATTTTATGAGTATTGTGGC
195 AAAAGCGTAAAAAATCATCCAATCTTTTTGTAGTTGAATTATATATATTTTATGAGTATTGCGGC
3130 TAAAAATTGAGGAAAAATATTTCGGGTCTATTTTTGCAAAATTT
260 TAAAAATTGAGGAAAAATATTTCGGGTCTATTTTTGCAAAATTT
3174 TAGCCGAAAT
Statistics
Matches: 258, Mismatches: 35, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
320 1 0.00
321 135 0.52
322 115 0.45
323 7 0.03
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (321 bp):
TTTTTGCCTAAAAACGCGTTCCGGACCCCCGATGCAGTTTTGCATGATTTTTGACATAAAGACTC
CTTGAAATACCTACAATCATCTAACCAAATCACAGCCACATTTGAATTTAAGGATTTGTTTTTAC
AAGCATCTAAATCTTGTTTCGATTTAATAAGAAATTAATTCAGAAAAATATGGAAAACAATATTA
AAAGCGTAAAAAATCATCCAATCTTTTTGTAGTTGAATTATATATATTTTATGAGTATTGCGGCT
AAAAATTGAGGAAAAATATTTCGGGTCTATTTTTGCAAAATTTAAGCTGGAATCGTGACGG
Found at i:4131 original size:62 final size:58
Alignment explanation
Indices: 4027--4150 Score: 176
Period size: 62 Copynumber: 2.1 Consensus size: 58
4017 AAGACCCTCG
* * * *
4027 AATCAAATCAAACTCCCAAGTCATCAATTCAAGATCAAGTCATTCGACCCTTGAATCA
1 AATCAAATCAAACTCCAAAATCATCAATTCAAAATCAAGTCATTCGACCCTTGAAGCA
4085 AATCAAATCAAACTCTCAAATTATCATCAAGTTCAAAATCAAGTCATTCGACCCTTGAAGCA
1 AATCAAATCAAACTC-CAAA--ATCATCAA-TTCAAAATCAAGTCATTCGACCCTTGAAGCA
4147 AATC
1 AATC
4151 TTGAGGCATA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
58 15 0.26
59 3 0.05
61 7 0.12
62 33 0.57
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.25
Consensus pattern (58 bp):
AATCAAATCAAACTCCAAAATCATCAATTCAAAATCAAGTCATTCGACCCTTGAAGCA
Found at i:5005 original size:327 final size:328
Alignment explanation
Indices: 4311--5015 Score: 872
Period size: 327 Copynumber: 2.1 Consensus size: 328
4301 TGTGTGTTAC
* * * * * *
4311 ACGAGCATTTGAATCATGTTTCGATTTAATTAAAAATTAATTT-GAAAATTTAAAAAAAAAACGA
1 ACGAGCATATAAATCTTATTTCGATTTAATTAGAAATTAATTTAG-AAATTAAAAAAAAAAACGA
*
4375 TATTAGAAGCGTGATAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTG
65 TATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTG
** * *
4440 TGGCTAAAAATTGAGATAAATATTTAGGGTCAAATTTTTCAAAATTTTAGCCGAAATCGTGTACT
130 TCACTAAAAATTGAGAAAAATATTTAGGGTCAAATTTTTCAAAATTTTAACCGAAATCGTG-A-T
* * * *
4505 ATCACGGTTTTTTGGCTAAAACGCGTTTTGGGGCCCCATGTCAGTTTTGCATGATTTTTTACGCC
193 ATCACGGTTTTTTGGCTAAAACGCGTTTCGGGGCCACAGGTCAGTTTTGCATGATTTTTTACACC
* * *
4570 AAGACTCCTTAAAATATATCTTTATTCATGTAACCAAATCTCAGCCACATTGTATTTAAGAATTT
258 AAGACTCCTTAAAATATATCTCTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTT
4635 GTTTTT
323 GTTTTT
* * *
4641 ACGAGCATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAA-TAAAATAGAAAAAACG
1 ACGAGCATATAAATCTTATTTCGATTTAATTAGAAATTAATTTAGAAATTAAAA-A-AAAAAACG
* * * * * *
4705 ATATTAGAAGCGTGAAAAAGGCTTTCAATTTTTTTGGTGTTGATTTATATA-TTTTTCTGAGTAT
64 ATATTAGAAGCGTG-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTAT
* * * *
4769 TTTCACTAGAAATTGAGGAAAAATCTTTTGGGTC-AATTTTTACAAAATTTTAACCGAAATCGTG
128 TGTCACTAAAAATTGA-GAAAAATATTTAGGGTCAAATTTTT-CAAAATTTTAACCGAAATCGTG
** *
4833 -TATCACGG-TTTTTGGCTAAAAACGCGTTTCGGGGCCAC-GGCTTTGTTTTGCATGATTTTTTG
191 ATATCACGGTTTTTTGGCT-AAAACGCGTTTCGGGGCCACAGG-TCAGTTTTGCATGATTTTTTA
* * *
4895 CACCAAGACTCCTT-GAA-ATATCTCTATTCATCTAATCAAATCTCATCCACATTGGATTTAAGA
254 CACCAAGACTCCTTAAAATATATCTCTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGA
*
4958 ATTTTTTTTT
319 ATTTGTTTTT
* * *
4968 ACGTA-CATATGAATCTTATTTTGATTTAATTAGAAATTAATTCAGAAA
1 ACG-AGCATATAAATCTTATTTCGATTTAATTAGAAATTAATTTAGAAA
5016 AAATAAAAAT
Statistics
Matches: 325, Mismatches: 41, Indels: 21
0.84 0.11 0.05
Matches are distributed among these distances:
327 90 0.28
328 13 0.04
329 61 0.19
330 42 0.13
331 54 0.17
332 65 0.20
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (328 bp):
ACGAGCATATAAATCTTATTTCGATTTAATTAGAAATTAATTTAGAAATTAAAAAAAAAAACGAT
ATTAGAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT
CACTAAAAATTGAGAAAAATATTTAGGGTCAAATTTTTCAAAATTTTAACCGAAATCGTGATATC
ACGGTTTTTTGGCTAAAACGCGTTTCGGGGCCACAGGTCAGTTTTGCATGATTTTTTACACCAAG
ACTCCTTAAAATATATCTCTATTCATCTAACCAAATCTCAGCCACATTGGATTTAAGAATTTGTT
TTT
Found at i:9073 original size:38 final size:38
Alignment explanation
Indices: 9030--9164 Score: 191
Period size: 38 Copynumber: 3.6 Consensus size: 38
9020 ACTTTCAACA
* ** * *
9030 AAGCGATCAAATTT-ATTATTCGTTTTTGATCAAGACCC
1 AAGCGATC-AATTTCATTATTCGCTTAGGACCAAGACCT
* *
9068 AAGCGATCAATTTCATCATTCGCTTGGGACCAAGACCT
1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCT
9106 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCT
1 AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCT
9144 AAGCGATCAATTTCATTATTC
1 AAGCGATCAATTTCATTATTC
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
37 5 0.06
38 83 0.94
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (38 bp):
AAGCGATCAATTTCATTATTCGCTTAGGACCAAGACCT
Done.