Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022456.1 Corchorus olitorius cultivar O-4 contig22489, 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: 83095
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:14363 original size:24 final size:23
Alignment explanation
Indices: 14303--14364 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
14293 TGAAGCAGCA
*
14303 GGGGTAGAAGGAGGAGGAGCAGAT
1 GGGGTAGCAGG-GGAGGAGCAGAT
* *
14327 GGGGTGGCA--GGAGGAGGAGAT
1 GGGGTAGCAGGGGAGGAGCAGAT
14348 GGGGTAGCAGGTGGAGG
1 GGGGTAGCAGG-GGAGG
14365 TGAAGGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 19 0.61
24 12 0.39
ACGTcount: A:0.26, C:0.05, G:0.60, T:0.10
Consensus pattern (23 bp):
GGGGTAGCAGGGGAGGAGCAGAT
Found at i:14364 original size:21 final size:21
Alignment explanation
Indices: 14314--14364 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
14304 GGGTAGAAGG
* *
14314 AGGAGGAGCAGATGGGGTGGC
1 AGGAGGAGGAGATGGGGTAGC
14335 AGGAGGAGGAGATGGGGTAGC
1 AGGAGGAGGAGATGGGGTAGC
*
14356 AGGTGGAGG
1 AGGAGGAGG
14365 TGAAGGAGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.06, G:0.59, T:0.10
Consensus pattern (21 bp):
AGGAGGAGGAGATGGGGTAGC
Found at i:16359 original size:19 final size:19
Alignment explanation
Indices: 16319--16355 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16309 AATGTTTAAG
16319 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
16338 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
16356 ATAATTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:17290 original size:12 final size:13
Alignment explanation
Indices: 17267--17296 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
17257 CATTAACCAC
17267 AAAAAAGAAAATG
1 AAAAAAGAAAATG
17280 AAAAAAG-AAATG
1 AAAAAAGAAAATG
17292 AAAAA
1 AAAAA
17297 GTATTTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (13 bp):
AAAAAAGAAAATG
Found at i:22938 original size:30 final size:32
Alignment explanation
Indices: 22876--22940 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
22866 AAATCATCTT
*
22876 TCTCTTTCCTCCTCCTGCTCCTTTCTCTCCGC
1 TCTCTTTACTCCTCCTGCTCCTTTCTCTCCGC
22908 TCTCTTTACTCTCTCCT-C-CCTTTC-CTCCGC
1 TCTCTTTACTC-CTCCTGCTCCTTTCTCTCCGC
22938 TCT
1 TCT
22941 TCTCCGCCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 9 0.29
31 6 0.19
32 11 0.35
33 5 0.16
ACGTcount: A:0.02, C:0.49, G:0.05, T:0.45
Consensus pattern (32 bp):
TCTCTTTACTCCTCCTGCTCCTTTCTCTCCGC
Found at i:24599 original size:27 final size:27
Alignment explanation
Indices: 24569--24627 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
24559 GTCATGCCTC
**
24569 CCATGGTTGTACCCATCATCATGATCA
1 CCATGGTCATACCCATCATCATGATCA
* *
24596 CCATGGTCATGCTCATCATCATGATCA
1 CCATGGTCATACCCATCATCATGATCA
*
24623 TCATG
1 CCATG
24628 ATCACCATGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (27 bp):
CCATGGTCATACCCATCATCATGATCA
Found at i:24600 original size:9 final size:9
Alignment explanation
Indices: 24583--24664 Score: 78
Period size: 9 Copynumber: 9.1 Consensus size: 9
24573 GGTTGTACCC
24583 ATCATCATG
1 ATCATCATG
*
24592 ATCACCATG
1 ATCATCATG
* *
24601 GTCATGC-TC
1 ATCAT-CATG
24610 ATCATCATG
1 ATCATCATG
24619 ATCATCATG
1 ATCATCATG
*
24628 ATCACCATG
1 ATCATCATG
* *
24637 GTCATGC-TC
1 ATCAT-CATG
24646 ATCATCATG
1 ATCATCATG
24655 ATCATCATG
1 ATCATCATG
24664 A
1 A
24665 CCACCGACAC
Statistics
Matches: 57, Mismatches: 12, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
8 2 0.04
9 53 0.93
10 2 0.04
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.30
Consensus pattern (9 bp):
ATCATCATG
Found at i:24630 original size:36 final size:36
Alignment explanation
Indices: 24583--24669 Score: 165
Period size: 36 Copynumber: 2.4 Consensus size: 36
24573 GGTTGTACCC
24583 ATCATCATGATCACCATGGTCATGCTCATCATCATG
1 ATCATCATGATCACCATGGTCATGCTCATCATCATG
24619 ATCATCATGATCACCATGGTCATGCTCATCATCATG
1 ATCATCATGATCACCATGGTCATGCTCATCATCATG
*
24655 ATCATCATGACCACC
1 ATCATCATGATCACC
24670 GACACGAACA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 50 1.00
ACGTcount: A:0.29, C:0.30, G:0.13, T:0.29
Consensus pattern (36 bp):
ATCATCATGATCACCATGGTCATGCTCATCATCATG
Found at i:45062 original size:14 final size:13
Alignment explanation
Indices: 45043--45081 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
45033 AAATTGTAAA
45043 ATTTAAAAAATTT
1 ATTTAAAAAATTT
* *
45056 CATTTAAGAAATAT
1 -ATTTAAAAAATTT
45070 ATTTAAAAAATT
1 ATTTAAAAAATT
45082 CTAATGTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (13 bp):
ATTTAAAAAATTT
Found at i:45275 original size:123 final size:128
Alignment explanation
Indices: 45067--45313 Score: 396
Period size: 123 Copynumber: 1.9 Consensus size: 128
45057 ATTTAAGAAA
*
45067 TATATTTAAAAAATTCTAATGTATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAAA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT---
*
45132 ATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTGTAAA
63 ATA-GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAAA
45197 AG
127 AG
*
45199 TATATTTAAATAATTCTAATATATATAAG-TTTTTTAATTAAAATAGTAAAATGGTAAAAAT-TA
1 TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
45262 -TA-AA-GATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAAC
66 GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAAC
45314 AATAAAAGAT
Statistics
Matches: 112, Mismatches: 3, Indels: 9
0.90 0.02 0.07
Matches are distributed among these distances:
123 47 0.42
124 2 0.02
125 2 0.02
127 2 0.02
131 32 0.29
132 27 0.24
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (128 bp):
TATATTTAAAAAATTCTAATATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATATA
GTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTGTAAAAG
Found at i:46944 original size:22 final size:22
Alignment explanation
Indices: 46919--46969 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
46909 CGTGCGACGA
**
46919 TCGCGACCTGGTCATGGCCCAG
1 TCGCGACCTGACCATGGCCCAG
**
46941 TCGCGACCTGACCATGGCCTGG
1 TCGCGACCTGACCATGGCCCAG
46963 TCGCGAC
1 TCGCGAC
46970 ACGCACGCGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.14, C:0.37, G:0.31, T:0.18
Consensus pattern (22 bp):
TCGCGACCTGACCATGGCCCAG
Found at i:50879 original size:19 final size:19
Alignment explanation
Indices: 50844--50881 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
50834 ATGCTTCATA
*
50844 TATTATATACTCTTATATT
1 TATTATATACTATTATATT
50863 TATTATATA-TATATATATT
1 TATTATATACTAT-TATATT
50882 ATTTTCAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTATATACTATTATATT
Found at i:65490 original size:29 final size:30
Alignment explanation
Indices: 65420--65492 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
65410 AGTTGAGGGG
*
65420 CAAAATGTTCCAAAATTGGAATTCAAGGAGC
1 CAAAATG-TCCAAAATTGGAATTCAAGGAGA
*
65451 CAAAATGTCCAAAATT-GAAGTTC-ATGAGA
1 CAAAATGTCCAAAATTGGAA-TTCAAGGAGA
*
65480 TAAAATGTCCAAA
1 CAAAATGTCCAAA
65493 CACTACAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 19 0.50
30 12 0.32
31 7 0.18
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.23
Consensus pattern (30 bp):
CAAAATGTCCAAAATTGGAATTCAAGGAGA
Found at i:69275 original size:338 final size:328
Alignment explanation
Indices: 68537--69576 Score: 1116
Period size: 338 Copynumber: 3.1 Consensus size: 328
68527 ACTATTTTTT
* *
68537 AATTAATTTCTAATTAAATCGAAACAAAATTTAAATGCTCGTAAAAACAAATCCTTAAATCCAAT
1 AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
* * * *
68602 ATGCCTGACATTTGATTAGATG-ATATAGATATTTCAAGGAGTCTCGATG-TCAAAAATCATGCA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCG--GCACAAAAATCATGCA
* * * * *
68665 AAACTTAGTCGGGGCCCCGGAACGCATTTTTAGCCAACAACTGTGATGG--TTAGTACACGATTT
129 AAACTGA-ACCGGGCCCCGGAACGCGTTTTTAGCCAA-AACCGTGATGGTATTAGTACACGATTT
* * * * * *
68728 CGGCTAAAATTTTGCAAAAATTGGCTC-GAAATATATTTCCTCAATTTTTGTCTAAAATACTCAT
192 CGGCTAAAATTTTGCAAAAATTGAC-CAAAAAT-TTTTTTCTCAATTTTAG-C-CAAATACTCAT
* * * *
68792 AAAAGATATATAA-TTAGATGTAAAAAAAATTGAAGGGC--TTTCAACACTTCTAATATTGTTTT
253 AAAA-ATATATAATTTA-ACGCAAAAAAAATTGAA-GGCTTTTTC-ACGCTTCTAATATCGTTTT
68854 TCCTATTTTTTTTCC
314 TCCTATTTTTTTTCC
* *
68869 GAATTAGTTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA
1 -AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAA
*
68934 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACAAAAAATCATGCA
65 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCAC-AAAAATCATGCA
* *
68999 AAACTGAACCGAGCCCCGGAACGCGTTTTTAGCCGAAAACCGTGATGGTAATTAGTATACGATTT
129 AAACTGAACCGGGCCCCGGAACGCGTTTTTAGCC-AAAACCGTGATGGT-ATTAGTACACGATTT
*
69064 CGGCTAAAATTTTGCAAAAATTGACGCAAAAGATTTTTTTCTCAATTTCTAGCGAAACTACTCAT
192 CGGCTAAAATTTTGCAAAAATTGAC-CAAAA-ATTTTTTTCTCAATTT-TAGCCAAA-TACTCAT
* * *
69129 AAGAAATATATAATTTAACACCAAAAAAATTGAATGTCTTTTTCACGCTTCTAATATCGTTTTTC
253 AA-AAATATATAATTTAACGCAAAAAAAATTGAA-GGCTTTTTCACGCTTCTAATATCGTTTTTC
*
69194 CTATTTTATTTCC
316 CTATTTTTTTTCC
* * * *
69207 ATATTAATTTCTGATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTTAATACAA
1 A-ATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAA
* *
69272 TGTGGATGAGATTTGATTAGATGAATATAGATATATTTTAAGGAGTCTCGACGC-CAAAAATCAT
65 TGTGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTCG--GCACAAAAATCAT
* * * * * *** * * *
69336 TC-AAACTGACCCGGGGCCCCGAAACGCGTTTTTAGTCAAAAACAAAATCGTGATGA-TACATGA
126 GCAAAACTGAACC-GGGCCCCGGAACGCGTTTTTAGCCAAAACCGTGATGGT-ATTAGTACACGA
* * *
69399 TTTCGGCTAAAATTTTGTAAAAATTGACCCAAAATATTTTTCTCAACTTTTAGCCACAATACTCA
189 TTTCGGCTAAAATTTTGCAAAAATTGACCAAAAATTTTTTTCTCAA-TTTTAGCCA-AATACTCA
* * * *
69464 TAAAAAATATATATATAATTCAACGCAAAAAAAAATTGAAGGGTTTCTCATGTTTCTAATATCGT
252 T-AAAAATATATA-AT--TT-AACGC-AAAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGT
* **
69529 ATTT-CT-TTTTTTTTAAA
311 TTTTCCTATTTTTTTT-CC
*
69546 AATTAATTTCTAATTAAATCGAAACATGATT
1 AATTAATTTCTAATTAAATCGAAACAAGATT
69577 CACGCTTTTA
Statistics
Matches: 605, Mismatches: 72, Indels: 55
0.83 0.10 0.08
Matches are distributed among these distances:
332 1 0.00
333 114 0.19
334 43 0.07
336 74 0.12
337 61 0.10
338 193 0.32
339 30 0.05
340 74 0.12
341 13 0.02
342 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (328 bp):
AATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAAT
GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCACAAAAATCATGCAAA
ACTGAACCGGGCCCCGGAACGCGTTTTTAGCCAAAACCGTGATGGTATTAGTACACGATTTCGGC
TAAAATTTTGCAAAAATTGACCAAAAATTTTTTTCTCAATTTTAGCCAAATACTCATAAAAATAT
ATAATTTAACGCAAAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTT
TCC
Found at i:77599 original size:325 final size:322
Alignment explanation
Indices: 76726--77976 Score: 1518
Period size: 324 Copynumber: 3.9 Consensus size: 322
76716 TGGTAAAAAT
* * * * * *
76726 GACCAAAAAGATTTTTTCTCAATTTTTGGCAAAAACACTCATAAAAATATATATAATTCAACGCC
1 GACCCAAAA-ATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAATTCAACGCC
* * * * **
76791 AAAAAGATTGGA-GGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTT-CTAAAAAATTT
64 AAAAAGATT-GACGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCCGAATTAATTT
* * * * *
76854 CTAATTAAATCGAAACAAGATTCTGATGCACGTAAAAAA-AAATCCTTAAATCCAATGTGGCCT-
128 CTAATTAAATCGAAACAAGATTCAGATGCTCG-AAAAAACAAATCCTTATATCCAATAT-GACTG
* ** * *
76917 AGATTTGATTAGACT-AATAA-AGATATTTCAAGGAGTCTCAG-GACCAAAAACCATGCAAAACA
191 AGATTTGATTCGA-TGAA-AATAGATATTTCAAGGAGTCTTTGCG-CCAAAAATCATGCAAAACT
** * * * * * *
76979 GAG-CGGTAACCCCGGAAGGCGTTTTTAGACAAAATCCGTGATGGTTAGTACACGATTTCGGCTG
253 GAGCCGG-GGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
*
77043 AAAACT
317 AAAACC
** * * * * * *
77049 GA-CCTGAAAGTTTCTATCAATTTTTTGCCACAATACT-AAAAAAAAAATATAATTCAACTCCAA
1 GACCCAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA
* *
77112 AAAGATTAACGGGCTTTTCATGCTTCTAATATCG-TTTTCATTTTTTTTTCCGAATTAATTTCTA
66 AAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCCGAATTAATTTCTA
* * * * * *
77176 ATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTCATATCCAATGTGGCTGACATT
131 ATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGATT
* ** * * *
77241 TGATTCGATGAATATAGATAAATGAAGGAGTCTTTGCGCCAAAAATCATGTAAAATTGAGCCGGG
196 TGATTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGG
* *
77306 GCTCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGATTAGTACACGATTTTGGCTAAAAACC
261 GCTCCGAAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACC
*
77369 GACCCAAAAATTTTTATCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCA
1 GACCCAAAAATTTTT-TCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
* * *
77434 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCCCGAATTGATTTCT
65 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCCGAATTAATTTCT
* *
77499 AATTAAATCGAAACAATTATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGA
130 AATTAAATCGAAACAA-GATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGA
* * * * *
77564 TTTGGTTCGATGAAAATAGATATTTAAAGGAGTCTTTGCGCCAAAAGTCATGAAAAATTGAGCCG
194 TTTGATTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCG
* * *
77629 GGGATCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACG
259 GGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACC
* * * *
77693 GACCCGAAAAGTTTTTTCTCAAATTTTTGCCACAATACTCAGAAATAATATATAATTCAACGCCT
1 GACCC-AAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
77758 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTTCCGAATTAATTTC
65 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCG-TTTTTCATTTTTTTTTCCGAATTAATTTC
* * * * *
77823 TAACTAAGTCGAAACAAGATTGAGATGCTCGAAAAAACAAATCCATATATTCAATATGACTGAGA
129 TAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGA
* * * * ** *
77888 TTTGGTTCCATGAATATAGATATTTCAAGGAGCCTTTATGCCAAAAATCTTGCAAAACTGAGCCG
194 TTTGATTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCG
*
77953 GGGC-CCGAAATGCGTTTTTAGCCA
259 GGGCTCCGAAACGCGTTTTTAGCCA
77977 TAAGTCGTGA
Statistics
Matches: 801, Mismatches: 111, Indels: 32
0.85 0.12 0.03
Matches are distributed among these distances:
318 25 0.03
319 163 0.20
320 47 0.06
321 30 0.04
322 25 0.03
323 74 0.09
324 266 0.33
325 171 0.21
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (322 bp):
GACCCAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAA
AAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTTTCCGAATTAATTTCTA
ATTAAATCGAAACAAGATTCAGATGCTCGAAAAAACAAATCCTTATATCCAATATGACTGAGATT
TGATTCGATGAAAATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGGG
GCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACC
Found at i:78991 original size:323 final size:316
Alignment explanation
Indices: 78275--79159 Score: 1041
Period size: 323 Copynumber: 2.8 Consensus size: 316
78265 AAACACTCAT
* * * *
78275 AAAAAT-ATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTT-TAATATCGTTTT
1 AAAAATAATATATAATTCAACACCAAAAAGATT-AAGGGCTTTTCACG-TTTCTAATATCTTTTT
* * ** *
78338 TCATATTTTTTTCTAAAAAATTTCTAATTAAATCGAAACAAGATTCTGATGCAT-GTAAAAACAA
64 TCAT-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAA
* * * **
78402 ATCCTTAAATCCAATGTGGCCT-AGATTTGATTAGACT-AATAAAGATATTTCAAGGAGTCTCAG
127 ATCC-TATATCCAATGTGG-CTGAGATTTGATTCGA-TGAATATAGATATTTCAAGGAGTCTTTG
* * * * * *
78465 CAG-CAAAAACCATG-AAAAAAGAGCGGTGACCCCGGAAGGCGTTTTTAGACAAAATCCGTGATG
189 C-GCCAAAAATCATGCAAAAATGAGCGG-GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
* *
78528 GTTAGTACACGATTTCGGCTGAAAACTGACCCGAAAGTTTCTATCAATTTTTTGCCACAAAACTC
252 GTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAGTTTCTATCAAATTTTTGCCACAAAACTC
* * *
78593 AAAAAAAATATATAATTCAACTCCAAAAAGATTAATGGGCTTTTCACGCTTCTAATATCATTTTT
1 AAAAATAATATATAATTCAACACCAAAAAGATTAA-GGGCTTTTCACGTTTCTAATATC-TTTTT
*
78658 TCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTCGTAAAAACAAA
64 TCA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* ** *
78723 TCCTCATATCCAATGTGGCTGACATTTGATTCGATGAATATAGATAAATGAAGGAGTCTTTGCGC
128 TCCT-ATATCCAATGTGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGCGC
* * *
78788 CAAAAATCATGCAAAATTGAGTCGGGGCTCCGGAACGCGTATTTAGCCAAAAACCGTGATGGTTA
192 CAAAAATCATGCAAAAATGAG-CGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
* * *
78853 GTACACGATTTCGGCTAAAAACTGGA-CCGAAAAGTTTTTTCTCAAATTTTTGCCACAATACTC
256 GTACACGATTTCGGCTAAAAACT-GACCCG-AAAG-TTTCTATCAAATTTTTGCCACAAAACTC
* *
78916 AGAAATAATATATAATTCAACACCTAAAAGATTAACGGGCTTTTCACGTTTCTAATATCTTTTTT
1 AAAAATAATATATAATTCAACACCAAAAAGATTAA-GGGCTTTTCACGTTTCTAATATC-TTTTT
* * * *
78981 TCGATTTTTTTCCGAATTAATTTCTAACTAAGTCGAAACAAGATTGAGATGCTCGAAAAAACAAA
64 TC-ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * * * *
79046 TCCATATATTCAATATGACTGAGATTT-AGTTCCATGAATATAGATATTTCAAGGAGCCTTTACG
128 TCC-TATATCCAATGTGGCTGAGATTTGA-TTCGATGAATATAGATATTTCAAGGAGTCTTTGCG
* * *
79110 CCAAAAATCTTGCAAAACTGAGCCGGGGCCCCGGAATGCGTTTTTAGCCA
191 CCAAAAATCATGCAAAAATGAG-CGGGGCCCCGGAACGCGTTTTTAGCCA
79160 TAAGCTGTGA
Statistics
Matches: 486, Mismatches: 63, Indels: 31
0.84 0.11 0.05
Matches are distributed among these distances:
318 8 0.02
319 49 0.10
320 116 0.24
321 67 0.14
322 10 0.02
323 234 0.48
324 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (316 bp):
AAAAATAATATATAATTCAACACCAAAAAGATTAAGGGCTTTTCACGTTTCTAATATCTTTTTTC
ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
TATATCCAATGTGGCTGAGATTTGATTCGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAA
AATCATGCAAAAATGAGCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
CGATTTCGGCTAAAAACTGACCCGAAAGTTTCTATCAAATTTTTGCCACAAAACTC
Found at i:80595 original size:327 final size:321
Alignment explanation
Indices: 79621--80887 Score: 1330
Period size: 327 Copynumber: 3.9 Consensus size: 321
79611 TTAGCCAAAC
* ** *
79621 GTACACGATTTT-GGCTAAAAATTGAGACGAAAATTTTTTTTCTCAATTTTTTGTG--ACAATAT
1 GTACACGATTTTCGGCTAAAAACTGACCCG--AATTTTTTTTCTCAATTTTTT-TGCCACAATAC
* * * * *
79683 TCATAAAAAATATATAATTTAACGCCAAAAAAATTGAAGGATTTTTCACACTTCTAATATCATTT
63 TCAGAAAAAATATATAATTCAACACCAAAAAAATTGATGG-TTTTTCACGCTT-TAATATCATTT
* * *
79748 TTACATTTTTTT-TGAATTAATTTCTAATTAAAACGAAACAAGATTCAGATGCTCGTAAAAATAA
126 TT-CATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
** * ** *
79812 ATTGTTAAATCGAATTTGGCTGGGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACG
190 ATCCTTAAATCGAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACG
* * * * * *
79877 CC-AAAATCATGCAAAACTGAGCCGGAGTCCCGGAACATG-G-TTTT-AGCAAAAAACCGTGATG
255 CCAAAAATCATGCAAAACTGAGCCGG-GCCCCCGAA-ACGCGTTTTTAACCCAAAAACCATGATG
79938 GTTA
318 GTTA
* * * *
79942 GTACAGGATTTCAGCGAAAGTTTTGCAAAAACTGACTC-AGA--TTTTTTCTCAATTTTTTTGCC
1 GTACACGATTT--TCG---G--CT--AAAAACTGACCCGA-ATTTTTTTTCTCAATTTTTTTGCC
* * * * * *
80004 ACAATATTCAGAAAAAATACACAATTCAATGCA-AAAAAAAATTGAAAT-ATTTTTCTCGCTTTA
56 ACAATACTCAGAAAAAATATATAATTCAA--CACCAAAAAAATTG--ATGGTTTTTCACGCTTT-
* * *
80067 AAGATCATTTTTCTATTTTTTTCCGAATCT-ATTTCTAATTACATCGAAACAATATTCAGATGCT
116 AATATCATTTTTC-ATTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* *
80131 CGTAAAAACAAATCCTTAAATCTAATGTGGCTAAGATCCTGAGATTGGTTAGATGAATATAGATA
179 CGTAAAAACAAATCCTTAAATCGAATGTGGCT--GA--C--A-TTTGGTTAGATGAATATAGATA
*
80196 TTTCAAGGAGTCTTT-CTGCCAAAAATCATACAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTT
237 TTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAACTGAGCC-GGGCCCCCGAAACGCGTTTTT
*
80260 AGCCCAAAAACCATGATGGTTA
300 AACCCAAAAACCATGATGGTTA
* *
80282 GTACACGATTTTCGGCTAAAAACTTACCCGAATTTTTTTGTTCTGAATTTTTTTGCCACAATACT
1 GTACACGATTTTCGGCTAAAAACTGACCCGAA-TTTTTT-TTCTCAATTTTTTTGCCACAATACT
* *
80347 CAGAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTATATCATTTTT
64 CAGAAAAAATATATAATTCAACACCAAAAAAATTGATGGT-TTTTCACGCTTTAATATCATTTTT
* *
80412 CCAATTTTTTCCCGAATTAATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAA
128 -C-ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* *
80477 TCCTTATATCCAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTG
191 TCCTTAAATCGAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTAC-G
*
80541 CCAAAAATCATGCAAAACTGAGCCGAGGCCCCTGAAACGCGTTTTTAACCCAAAAACCATGATGG
255 CCAAAAATCATGCAAAACTGAGCCG-GGCCCCCGAAACGCGTTTTTAACCCAAAAACCATGATGG
80606 TTA
319 TTA
* *
80609 GTACACAATTTTCGGCTAAAAACTGACCCGGAATTTTTTTTCTGAA-TTTTTTGCCACAATACTC
1 GTACACGATTTTCGGCTAAAAACTGACCC-GAATTTTTTTTCTCAATTTTTTTGCCACAATACTC
* * * * * * * *
80673 AGAAAAAACATATAATTCAACGCCAAAAAGATTGACGGGCTTCTCACGATTCT-A-ATCGTTTTT
65 AGAAAAAATATATAATTCAACACCAAAAAAATTGA-TGGTTTTTCACGCTT-TAATATC-ATTTT
* *
80736 TCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCCTCGTAAAAACAAA
127 TCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG-CTCGTAAAAACAAA
* * ** * ** * * * *
80801 TACTTAAATCGAACGTGGCTGGGATTTTGTTCCATGGATATTGATATTTCAAGGAGTATTTACGT
191 TCCTTAAATCGAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGC
80866 CAAAAATCATGCAAAACTGAGC
256 CAAAAATCATGCAAAACTGAGC
80888 TAGTGCTAAA
Statistics
Matches: 807, Mismatches: 88, Indels: 99
0.81 0.09 0.10
Matches are distributed among these distances:
321 10 0.01
323 46 0.06
324 91 0.11
325 67 0.08
326 13 0.02
327 153 0.19
328 32 0.04
329 41 0.05
330 64 0.08
331 22 0.03
332 6 0.01
333 15 0.02
334 99 0.12
335 43 0.05
336 2 0.00
337 40 0.05
338 30 0.04
339 6 0.01
340 27 0.03
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (321 bp):
GTACACGATTTTCGGCTAAAAACTGACCCGAATTTTTTTTCTCAATTTTTTTGCCACAATACTCA
GAAAAAATATATAATTCAACACCAAAAAAATTGATGGTTTTTCACGCTTTAATATCATTTTTCAT
TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
AAATCGAATGTGGCTGACATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAA
ATCATGCAAAACTGAGCCGGGCCCCCGAAACGCGTTTTTAACCCAAAAACCATGATGGTTA
Done.