Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016392.1 Corchorus olitorius cultivar O-4 contig16425, 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: 102210
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:436 original size:11 final size:12
Alignment explanation
Indices: 415--439 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
405 GTGAGATTTG
415 TGGGAAAAAAAT
1 TGGGAAAAAAAT
427 TGGGAAAAAAAT
1 TGGGAAAAAAAT
439 T
1 T
440 TTCACAGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (12 bp):
TGGGAAAAAAAT
Found at i:938 original size:335 final size:333
Alignment explanation
Indices: 11--1011 Score: 1286
Period size: 335 Copynumber: 3.0 Consensus size: 333
1 AAAAAATTGA
*
11 AAAAACGATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCT
1 AAAAACGATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATAATTTTT-T
* * *
76 GGGTACTGTGGCCTAAAAGTTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAACTTTTAGCCGAA
65 GAGTACTGTGGCCTAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAA
* *
141 ATTGTGTATGTTACATTACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGACTAAGTTTTCGA
130 ATCGTGTATGTTACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGACTAAGTTTTCGA
206 AGTTATTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAATTCAAATCTTAGACACATTTG
195 AGTTATTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAATTCAAATCTTAGACACATTTG
*
271 ATTTTAGGA-TT-TTTTTACAAGCATCTGAATCTTATTTCGATTTAATTAGAAATAAATTCCGCA
260 ATTTTAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCCGCA
334 AAAAGATGG
325 AAAAGATGG
* * * * *
343 AAAAACGATATTAGAAGCGTG-AAAATCCGTCAATTTTTTTGGCGTTGAATTATTTAATATTTGT
1 AAAAACGATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATAAT-TTTTT
* *** * * **
407 GAG-ATTTGTGGGAAAAAAATTG-GGAAAAAAATTTTC---ACAG----T-C-AGTTTTTAGCCG
65 GAGTA-CTGTGGCCTAAAAATTGAGG-AAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCG
* * * * *
461 AAA-C-TAGTACTGTTACATCACGGTTTTTGGCTGAAAACGCGATTCGGGGCCCCGCCTCAGTTT
128 AAATCGT-GTA-TGTTACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGACTAAGTTT
* * * * * * *
524 T-GCA-TGAGTTTTGCATAAAGACTCCTTGAAATATCTATATTCATCTAA-GCAAATCTCAGCCA
191 TCGAAGTTA-TTTGGCGTAAAGACTCCTTGAAATATCTATATTCATC-AATTCAAATCTTAGACA
* * * * * *
586 CACTGGAATTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGGTTTAATTAGAAATAAAT
254 CATTTGATTTTAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAAT
* *
651 TCAGAAAAAAGAATGG
319 TCCGCAAAAAG-ATGG
** *
667 AAAAACGATATCAGAAGCGTGAAAAACCCTTCAACCTTTTTGGCGTTAAATTATATAATTTTTTA
1 AAAAACGATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATAATTTTTT-
* *
732 GAGTACTGTGGCCTAAAATTTGAGGAAAAATTTTTCGGGTTAGTTTTTGCAAAATTTTAGCCGAA
65 GAGTACTGTGGCCTAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAA
* ** *
797 ATCGTGTAT-TAACCATCACACTTTTTGCCTAAAAACGCGTTTCGGGACCCCGACTAAGTTTTCG
130 ATCGTGTATGTTA-CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGACTAAGTTTTCG
* *
861 AAGTTATTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCGATTCAAATCTTAGGCACATTT
194 AAGTTATTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAATTCAAATCTTAGACACATTT
*
926 GATTTTAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCAATTTAATTAGAAATAAATTCCGC
259 GATTTTAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCCGC
991 AAAAAGATGG
324 AAAAAGATGG
*
1001 AAAAATGATAT
1 AAAAACGATAT
1012 TATTTCTGTT
Statistics
Matches: 556, Mismatches: 84, Indels: 56
0.80 0.12 0.08
Matches are distributed among these distances:
320 3 0.01
321 62 0.11
322 65 0.12
323 53 0.10
324 29 0.05
325 56 0.10
326 3 0.01
328 5 0.01
330 3 0.01
331 58 0.10
332 24 0.04
333 3 0.01
334 70 0.13
335 119 0.21
336 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (333 bp):
AAAAACGATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATAATTTTTTG
AGTACTGTGGCCTAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAA
TCGTGTATGTTACATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCCGACTAAGTTTTCGAA
GTTATTTGGCGTAAAGACTCCTTGAAATATCTATATTCATCAATTCAAATCTTAGACACATTTGA
TTTTAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCCGCAA
AAAGATGG
Found at i:3835 original size:333 final size:320
Alignment explanation
Indices: 3076--5114 Score: 1991
Period size: 333 Copynumber: 6.3 Consensus size: 320
3066 TTAGCCGCAA
* * * * * * *
3076 CACGGTTTTTGGCTTAAAACACGCTTCGGGGCCC-CAGCTCAGTTTTGCAT-ATTTTTGGCATAA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCTGA-CTAAGTTTTGCATGATTTTTGGCGTAA
* * *
3139 AGACTCCTTGAAATATTTATATTCATCTAAGCAAATCTCAGCCACACTGGAATTAAGGATTTGTT
65 AGACTCCTTGAAATATCTATATTCATCGAA-CAAATCTCAGCTACACTGGAATTAAGGATTTGTT
* *
3204 TTTACGAGCATCTGAATCTTGTTTCGGTTTAATTAGAAATAAATTCAGAAAAAAAAAATTGGAAA
129 TTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-G---GAAAAAA-TGGAAA
* * *
3269 AACGATATCAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTAAATTATTTAATTTTTT-AGA
189 AACGATATCAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTTCAGA
* ** *
3333 GTATTGTGGC-AAAAATTGGGAAAAAAACTTTTCATGTCAGTTTTTA-CCGAAACCGTGTACTAA
253 GTATTGTGGCAAAAAATTGAGAAAAAAA-TTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAA
3396 CCAT
317 CCAT
* * * * * * *
3400 CACGGTTTTTGGTTTAAAACGTGTTTC-GGAGCGCC-GGCTAAGTTTGGCATGATTTTTGTCATA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGGGA-C-CCTGACTAAGTTTTGCATGATTTTTGGCGTA
* * * *
3463 AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAACTACAATGGAATTAAGGATTTAT
64 AAGACTCCTTGAAATATCTATATTCATCGAA-CAAATCTCAGCTACACTGGAATTAAGGATTTGT
*
3528 TTTTACGAGCATCTGAATCTTGTTTCGGTTTAATTAGAAATAAATTC-GAAAGAAACTGGAAAAA
128 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAA-AAA-TGGAAAAA
* * * *
3592 CAATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGGGTA
191 CGATATCAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCAGAGTA
* * * *
3657 CTGTGGCAAAAAAATTGAGGAAAAATTTTTCGGGTCAGTTTTTGCAAAATTTTAGCTGAAATCGT
256 TTGTGGC-AAAAAATTGAGAAAAAAATTTTCGGGTCAG----T------TTTTAGCCGAAATCGT
* *
3722 GTATTAACAAT
310 GTACTAACCAT
* *
3733 CACGGTTTTTGGCTAAAAACGCATTTCGGGACCCTGACTAAGTTTT-CGAAG-TTATTTGGCGTA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCTGACTAAGTTTTGC-ATGATT-TTTGGCGTA
* *
3796 AAGACTCCTTGAAATATCTATATTCATCTAACAAAATCTCAGCAACACTGGAATTAAGGATTTGT
64 AAGACTCCTTGAAATATCTATATTCATCGAAC-AAATCTCAGCTACACTGGAATTAAGGATTTGT
* * * * *
3861 TTTTACGAGCATCTGAATCTTGTTTCGATTTGATTAAAAATATATTTGGAAAAAAATAGAAAAAC
128 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAATGGAAAAAC
* *
3926 GATATCAGAAGCGTGAAAAACCCTTCAATTTTTTTTTGCGTTGAATTATATATTTTTTCA-AG-A
192 GATATCAGAAGCGTGAAAAACCCTTCAA-TCTTTTTGGCGTTGAATTATATATTTTTTCAGAGTA
* * * * *
3989 CTGTGGAAAAAAAATCGAGCAAAAATTTTTCGGGTCAGATTTTGTAAAATTTTAGCCGAAATCGT
256 TTGTGG-CAAAAAATTGAGAAAAAAATTTTCGGGTC--A----GT----TTTTAGCCGAAATCGT
* *
4054 GGATTAACCAT
310 GTACTAACCAT
* * * * *
4065 CACGGTTTTTTGGCTAAAAACGCGTTCCGGG-GCCTCGGCTAAGTTTTGTATGATTTTTAGCGTA
1 CACGG-TTTTTGGCTAAAAACGCGTTTCGGGACCCT-GACTAAGTTTTGCATGATTTTTGGCGTA
* * * * ** *
4129 AAGACTCCTTGAAATATTTTTATTCATCGAGTCGAATC-CTAGCCGCACT----CT----ATTTG
64 AAGACTCCTTGAAATATCTATATTCATCGA-ACAAATCTC-AGCTACACTGGAATTAAGGATTTG
* *
4185 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAATGGCAAAAC
127 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAAAC
* * * * ** * * *
4249 GATATAAAAAGCGTGAAAACCCCTTCAATCTTTTGGGAATTGAATTGTTTAGTTTTTCAGAGTAT
192 GATATCAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCAGAGTAT
4314 TGTGGCAAAAAATTTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAAATCGTGTACTAACCA
257 TGTGGCAAAAAA-TTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCG-AAATCGTGTACTAACCA
4379 T
320 T
* * * * *
4380 CACGGTTTTTGGCTAAAAACGTGTTTCGAGACCTTGACTCAGTTTTACATGATTTTTGGCGTAAA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCTGACTAAGTTTTGCATGATTTTTGGCGTAAA
* * * * *
4445 GACTCCATGAAATATCTATATTCATCGAGACAAAT-TCTAGCCACATTCGATTTAAGGATTTGTT
66 GACTCCTTGAAATATCTATATTCATCGA-ACAAATCTC-AGCTACACTGGAATTAAGGATTTGTT
* * *
4509 TTTACGAGCATCTGAATCTTGTTTC--TGTTAGATTATAATTTAATTCGTGAAAAAATGGAAAAA
129 TTTACGAGCATCTGAATCTTGTTTCGAT-TTA-ATTAGAAATAAATTCG-GAAAAAATGGAAAAA
* * * * * *
4572 CGAGATTAGAAGCGTGAAAAAACCCTTCAATCTCTTTGGTGTTTAATTTTATATATTTTTTCAGC
191 CGATATCAGAAGCGTG-AAAAACCCTTCAATCTTTTTGGCGTTGAA--TTATATATTTTTTCAGA
* * * * * * *
4637 GTATTGTGGCAAAACATTGAGAAAAAAAATTCTCCGATCAGTTTTTAGCTGAAATCGCGAACTAA
253 GTATTGTGGCAAAAAATTGAG-AAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAA
*
4702 CAAT
317 CCAT
* * * *
4706 CATGGTTTTTGGCTAAAAACGCGTTTCAGGG-CCTTGACTCAGTTTTGCATGATTTTTGGTGTAA
1 CACGGTTTTTGGCTAAAAACGCGTTTC-GGGACCCTGACTAAGTTTTGCATGATTTTTGGCGTAA
* * * * * * * * * *
4770 AGATTCCCTGAAATAACTATGTTTATCGAACCACAT-TCCAG-TCGCATTCGATTTAAGGATTTG
65 AGACTCCTTGAAATATCTATATTCATCGAA-CAAATCT-CAGCT-ACACTGGAATTAAGGATTTG
* * * *
4833 TTTTTACGAACATCTTAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAA
127 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAAAATGGAAAAA
* * * * * * * *
4898 CGATATTAGAAGCGTGAGAAACCCTTCAATCTTTTGGGCATTAAATTGTTTAGTTTTTT-AGATT
191 CGATATCAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA-TTTTTTCAGAGT
* *
4962 ATTGTGGCAAAAAATTGAGAAAAAAATTCTCGGGTCAGTTTTTAGCCGAAATCGTGTACTATCCA
255 ATTGTGGCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCA
5027 T
320 T
* * * *
5028 CACGGTTTTTGGCTAAAAACGCGTTTCGGGA-CCTCGACT-CGATTTTACATGATCTTTGACGTA
1 CACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCT-GACTAAG-TTTTGCATGATTTTTGGCGTA
* *
5091 AAAACTCTTTGAAATATCTATATT
64 AAGACTCCTTGAAATATCTATATT
5115 TCAGAAGCAT
Statistics
Matches: 1449, Mismatches: 194, Indels: 146
0.81 0.11 0.08
Matches are distributed among these distances:
314 95 0.07
315 23 0.02
318 3 0.00
320 11 0.01
321 77 0.05
322 185 0.13
323 88 0.06
324 91 0.06
325 217 0.15
326 195 0.13
327 59 0.04
328 1 0.00
329 1 0.00
332 81 0.06
333 277 0.19
334 41 0.03
335 3 0.00
338 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (320 bp):
CACGGTTTTTGGCTAAAAACGCGTTTCGGGACCCTGACTAAGTTTTGCATGATTTTTGGCGTAAA
GACTCCTTGAAATATCTATATTCATCGAACAAATCTCAGCTACACTGGAATTAAGGATTTGTTTT
TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAATGGAAAAACGATA
TCAGAAGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTCAGAGTATTGTG
GCAAAAAATTGAGAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCAT
Found at i:19644 original size:38 final size:39
Alignment explanation
Indices: 19592--19671 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 39
19582 ATTTGAGCCG
* *
19592 GATTTTCTTGGCCATGAATTAAGTTAT-TTATTATTCATT
1 GATTTTCTTGGCCATGAATCAA-TCATGTTATTATTCATT
*
19631 GATTTT-TTGGCCATGAGTCAATCATGTTATTATTCATT
1 GATTTTCTTGGCCATGAATCAATCATGTTATTATTCATT
19669 GAT
1 GAT
19672 GACATTGATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 3 0.08
38 28 0.76
39 6 0.16
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (39 bp):
GATTTTCTTGGCCATGAATCAATCATGTTATTATTCATT
Found at i:20555 original size:3 final size:3
Alignment explanation
Indices: 20547--20624 Score: 113
Period size: 3 Copynumber: 26.0 Consensus size: 3
20537 CTTGTACTGC
20547 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
20595 TAT TA- TAT GAT TAAT TAT GAT GAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
20625 AAAGTTTAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.03
3 64 0.93
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:28473 original size:2 final size:2
Alignment explanation
Indices: 28468--28500 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28458 TTAAGAAATG
*
28468 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28501 CACACACTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:30642 original size:2 final size:2
Alignment explanation
Indices: 30635--30680 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
30625 CCAAGAATAC
* * * *
30635 AT AT AT AT AT AT AT AT AT AA AT AT AG AT AT AG AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30677 AT AT
1 AT AT
30681 GATAGGATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (2 bp):
AT
Found at i:30652 original size:12 final size:12
Alignment explanation
Indices: 30637--30685 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
30627 AAGAATACAT
*
30637 ATATATATATAT
1 ATATATATATAG
*
30649 ATATAAATATAG
1 ATATATATATAG
*
30661 ATATAGATATAG
1 ATATATATATAG
30673 ATATATATGATAG
1 ATATATAT-ATAG
30686 GATTTAATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 28 0.88
13 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (12 bp):
ATATATATATAG
Found at i:40060 original size:14 final size:14
Alignment explanation
Indices: 40019--40063 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
40009 TGTTTATGTG
40019 TAAAGAAAATGAAA
1 TAAAGAAAATGAAA
*** *
40033 TAATTTAAAGGAAA
1 TAAAGAAAATGAAA
40047 TAAAGAAAATGAAA
1 TAAAGAAAATGAAA
40061 TAA
1 TAA
40064 TTTGCAACAA
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (14 bp):
TAAAGAAAATGAAA
Found at i:44902 original size:2 final size:2
Alignment explanation
Indices: 44897--44931 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
44887 AAGGTTTCTT
44897 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
44932 TTAGTTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52155 original size:41 final size:41
Alignment explanation
Indices: 52110--52189 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
52100 TATGCCCAAA
*
52110 CATCTAAATGAGAATTCAACCCAAACTATAAACTATACCGG
1 CATCTAAATGAGAATTCAACCCAAACTAGAAACTATACCGG
52151 CATCTAAATGAGAATTCAACCCAAACTAGAAACTATACC
1 CATCTAAATGAGAATTCAACCCAAACTAGAAACTATACC
52190 ATAAATAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.21
Consensus pattern (41 bp):
CATCTAAATGAGAATTCAACCCAAACTAGAAACTATACCGG
Found at i:52400 original size:16 final size:16
Alignment explanation
Indices: 52379--52409 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
52369 AAAATGTCTT
52379 TTATATATATATATAA
1 TTATATATATATATAA
52395 TTATATATATATATA
1 TTATATATATATATA
52410 TCCCTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATATATATATATAA
Found at i:71288 original size:12 final size:12
Alignment explanation
Indices: 71271--71297 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
71261 TCATTTCTTC
71271 TTTTTTTATTGG
1 TTTTTTTATTGG
71283 TTTTTTTATTGG
1 TTTTTTTATTGG
71295 TTT
1 TTT
71298 ATCAGACCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.78
Consensus pattern (12 bp):
TTTTTTTATTGG
Found at i:98203 original size:122 final size:119
Alignment explanation
Indices: 98016--98242 Score: 325
Period size: 122 Copynumber: 1.9 Consensus size: 119
98006 AAATTATATA
*
98016 AACAAAAGCATATTATACACGCAGTCACCTGATTTGATGGTAGAGTGTTATATTTTTAGATTTAG
1 AACAAAAGCATATTATACACGCAGTCACCTGATCTGATGGTAGAGTGTTATATTTTTAGATTTAG
* * *
98081 TGATTAGAT-ATTGATTCCAAGCAATCTCATAAGTTTTTTTTTCTTTTATGTATG
66 TGATTAG-TCATTAATCCCAAACAATCTCATAAGTTTTTTTTTCTTTTATGTATG
* *
98135 AACAAAAGCATATTATGCACGCTATTAGTCACGTGATCTGATGGT-GAGTGTTAGT-TTTTTAGA
1 AACAAAAGCATATTATACACGC----AGTCACCTGATCTGATGGTAGAGTGTTA-TATTTTTAGA
98198 TTTAGTGATTAGTCATTAATCCCAAACAATCTCATAAGTTTTTTT
61 TTTAGTGATTAGTCATTAATCCCAAACAATCTCATAAGTTTTTTT
98243 ATGCCCTATT
Statistics
Matches: 96, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
119 21 0.22
121 1 0.01
122 56 0.58
123 18 0.19
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (119 bp):
AACAAAAGCATATTATACACGCAGTCACCTGATCTGATGGTAGAGTGTTATATTTTTAGATTTAG
TGATTAGTCATTAATCCCAAACAATCTCATAAGTTTTTTTTTCTTTTATGTATG
Found at i:99351 original size:29 final size:29
Alignment explanation
Indices: 99319--99391 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
99309 TCGTCTCCAA
*
99319 TCGCCATGGGCTCTTTGCTCTGTTGATCG
1 TCGCCATGGGCTCTTTGCTCTGTGGATCG
*
99348 TCGCCATGGACTCTTTGCTCTGTGGATCG
1 TCGCCATGGGCTCTTTGCTCTGTGGATCG
*
99377 GCGCCATGGGGCTCT
1 TCGCCAT-GGGCTCT
99392 CAGTTTCTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 33 0.85
30 6 0.15
ACGTcount: A:0.08, C:0.29, G:0.30, T:0.33
Consensus pattern (29 bp):
TCGCCATGGGCTCTTTGCTCTGTGGATCG
Found at i:99632 original size:84 final size:86
Alignment explanation
Indices: 99523--99678 Score: 271
Period size: 85 Copynumber: 1.8 Consensus size: 86
99513 TCAATTTGGT
*
99523 TTTGACAAAGTTTTTTCTGAAATTTCAAAACCCT-ATGTTTTTACCGGCGGAGCCTATGACCCAA
1 TTTGACAAAGTTTTTTCTGAAATTTCAAAACCCTAATATTTTTACCGGCGGAGCCTATGACCCAA
99587 ATTCATACTTGTGTTTTCAAG
66 ATTCATACTTGTGTTTTCAAG
* *
99608 TTTGACAAAG-TTTTTCTGAAATTTCAAAACCCTAATATTTTTATCGGCGGAGCCTATGACCCGA
1 TTTGACAAAGTTTTTTCTGAAATTTCAAAACCCTAATATTTTTACCGGCGGAGCCTATGACCCAA
99672 ATTCATA
66 ATTCATA
99679 TTATGCTTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
84 23 0.34
85 44 0.66
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (86 bp):
TTTGACAAAGTTTTTTCTGAAATTTCAAAACCCTAATATTTTTACCGGCGGAGCCTATGACCCAA
ATTCATACTTGTGTTTTCAAG
Found at i:101389 original size:92 final size:92
Alignment explanation
Indices: 101232--101450 Score: 402
Period size: 92 Copynumber: 2.4 Consensus size: 92
101222 GCAAAAGGGA
101232 TGGCATTCCTATTATACATCAAGGTATAATGGTGCATCCAAATAAAGGTTGGTAATGAGAATTCT
1 TGGCATTCCTATTATACATCAAGGTATAATGGTGCATCCAAATAAAGGTTGGTAATGAGAATTCT
101297 ATTTATGCAATAAAAGGCACAATGTGG
66 ATTTATGCAATAAAAGGCACAATGTGG
101324 TGGCATTCCTATTATACATCAAGGTATAATGGTGCATCCAAATAAAGGTTGGTAATGAGAATTCT
1 TGGCATTCCTATTATACATCAAGGTATAATGGTGCATCCAAATAAAGGTTGGTAATGAGAATTCT
*
101389 ATTTATGCAATTAAAGGCACAATGTGG
66 ATTTATGCAATAAAAGGCACAATGTGG
* * *
101416 TGGCATTCCTACTATACATAAAGGTATAGTGGTGC
1 TGGCATTCCTATTATACATCAAGGTATAATGGTGC
101451 CAGTTCATGT
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 123 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (92 bp):
TGGCATTCCTATTATACATCAAGGTATAATGGTGCATCCAAATAAAGGTTGGTAATGAGAATTCT
ATTTATGCAATAAAAGGCACAATGTGG
Done.