Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007774.1 Corchorus capsularis cultivar CVL-1 contig07795, 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: 73908
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Found at i:863 original size:334 final size:331
Alignment explanation
Indices: 1--1207 Score: 1480
Period size: 332 Copynumber: 3.6 Consensus size: 331
*
1 TGAAAATATATAATTCAACTCCAAAAAAAATTGAAGTGCATTTCACGCTTTTAATATCATTTTTC
1 TGAAAATATATAATTCAACT--ACAAAAAATTGAAGTGCATTTCACGCTTTTAATATCATTTTTC
66 CATTTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAACTTCTGAAACTCAT-AGAAAAAA
64 CA-TTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAACTTCTGAAACTCATGA-AAAAAA
* *
130 AATCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTTCAATGAGTCTTTGC
127 AATCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTTCAATAAGTCTTGGC
* * * *
195 ACCGAAAATCATGCAAAACTGAGACGGGGCCCCAGAATGCATATTTAGCAAAAAACAGTGATGGT
192 ACCGAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCATTTTTAGCAAAAAACCGTGAT-G-
* ** * * **
260 GTTAGTACACGATTTCGGCTAAAATTTTTCAAAAATTAACCAAAACAATTTTTCCTCAATTTTTG
255 GTTAGTACACGATTTCGGAT-AAATTTCGCAAAAAATGACCCGAA-AATTTTTCCTCAATTTTTG
325 GCCACAATACTCTA
318 GCCACAATACTCTA
* ** * * * *
339 TTAAAATATATAATTCTTCGCTAAAAAAAATTGAAGTGCATTTCACACTTTCAATAACATTTTTC
1 TGAAAATATATAATTC--AACTACAAAAAATTGAAGTGCATTTCACGCTTTTAATATCATTTTTC
* ** * *
404 CATTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACTAGTTTCTGAAACTCGTGGAAAAAAAA
64 CATTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAACTTCTGAAACTCATGAAAAAAAAA
* * * * *
469 TCCTTCAATCCAATGTCCTTGAAATTTGTTTTGATGAATATAGATACTTCAATGAGTCTTGGCAC
129 TCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTTCAATAAGTCTTGGCAC
* * *
534 CGAAAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGGAAAAAAACCGTGATGGTT
194 CGAAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCATTTTTA-GCAAAAAACCGTGATGGTT
* * *
599 AGTTCACGATTTCAGATAAATTTCGCAAAAAATGACCCGAAAATTTTTTTCTTCAATTTTTGGCC
258 AGTACACGATTTCGGATAAATTTCGCAAAAAATGACCCGAAAA--TTTTTCCTCAATTTTTGGCC
*
664 ACAATACTCCA
321 ACAATACTCTA
675 TGAAAATATATAATTCAACT-CAAAAAATTGAAGTGCATTTCACGCTTTTAATATCATTTTTCCA
1 TGAAAATATATAATTCAACTACAAAAAATTGAAGTGCATTTCACGCTTTTAATATCATTTTTCCA
739 -TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAACTTCTGAAACTCAATAGAAAAAAAAA
66 TTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAACTTCTGAAACTC-AT-GAAAAAAAAA
* *
803 TCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAAATATTTCAATAAGTCTTGGTAC
129 TCCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTTCAATAAGTCTTGGCAC
* * * *** * * *
868 CAAAAATAATGAAAAACTGA-ACTGGGG-TGTGGAACGAATTTTTAGCTAAAAACCGTGATAGTT
194 CGAAAATCATGCAAAACTGAGAC-GGGGCCCCGGAACGCATTTTTAGCAAAAAACCGTGATGGTT
* * * *
931 AGTACACGATTTCGGCTTAAATTTCGCATAAACTGACCCAGAAAAATTTTCCTCAATTTTTGGCC
258 AGTACACGATTTCGG-ATAAATTTCGCAAAAAATGACCC-GAAAATTTTTCCTCAATTTTTGGCC
* *
996 ATAATACACTA
321 ACAATACTCTA
* * ** *
1007 TTAAAATATAAAATTCAACGCCAACAAAATTGAAGTGCATTTCACGCTTTAAATATCA-TTTTCC
1 TGAAAATATATAATTCAACTACAA-AAAATTGAAGTGCATTTCACGCTTTTAATATCATTTTTCC
* * ** * * * *
1071 A--TTTTTTCCAAATTAATATCTAATTAAATCAAAACCAGTTTTTGAAACTCGT-AAATACAAAT
65 ATTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAACTTCTGAAACTCATGAAAAAAAAAT
* * * * * * *
1133 TCATAAATCCAATGTGCTTGAAATTTATTCAAATAAATATAGATATTTCAA-AGAGTCTTGGCGC
130 CCTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTTCAATA-AGTCTTGGCAC
*
1197 AGAAAATCATG
194 CGAAAATCATG
1208 AATATACTGA
Statistics
Matches: 756, Mismatches: 99, Indels: 37
0.85 0.11 0.04
Matches are distributed among these distances:
328 1 0.00
329 69 0.09
331 1 0.00
332 163 0.22
333 84 0.11
334 129 0.17
335 18 0.02
336 61 0.08
337 158 0.21
338 70 0.09
340 2 0.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (331 bp):
TGAAAATATATAATTCAACTACAAAAAATTGAAGTGCATTTCACGCTTTTAATATCATTTTTCCA
TTTTTTTTCCAAATTAATTTCTAATTAAATCGAAACCAACTTCTGAAACTCATGAAAAAAAAATC
CTTAAATCCAATGTGCTTGAAATTTGTTTAGATGAATATAGATATTTCAATAAGTCTTGGCACCG
AAAATCATGCAAAACTGAGACGGGGCCCCGGAACGCATTTTTAGCAAAAAACCGTGATGGTTAGT
ACACGATTTCGGATAAATTTCGCAAAAAATGACCCGAAAATTTTTCCTCAATTTTTGGCCACAAT
ACTCTA
Found at i:1241 original size:26 final size:26
Alignment explanation
Indices: 1212--2264 Score: 1177
Period size: 26 Copynumber: 40.4 Consensus size: 26
1202 ATCATGAATA
1212 TACTGAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* **
1238 TACTGAATATGCAACAATATGTCCCC
1 TACTGAATATGCAACTATATGAGCCC
* **
1264 TACTGAATATGCGACTATATGTCCCC
1 TACTGAATATGCAACTATATGAGCCC
* **
1290 TACTGAATATGCGACTATATGTCCCC
1 TACTGAATATGCAACTATATGAGCCC
* *
1316 TACTGAATATGCCACTATATGAGTCC
1 TACTGAATATGCAACTATATGAGCCC
* *
1342 TACTGAATATGAAAC--TATG-TCTCC
1 TACTGAATATGCAACTATATGAGC-CC
1366 TACTGAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
1392 TACTGAATATGCAACTATATGTA-CCC
1 TACTGAATATGCAACTATATG-AGCCC
*
1418 TACTGAATATGCAACTATATGAGCTCA
1 TACTGAATATGCAACTATATGAGC-CC
*
1445 TACTGAATATGCAACTATATGAGCCT
1 TACTGAATATGCAACTATATGAGCCC
*
1471 TACTGAATATACAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* * *
1497 TACTGAATAGGCAACTAAATG-TCTCC
1 TACTGAATATGCAACTATATGAGC-CC
*
1523 TACTGAATATG---C----GGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* *
1542 TACTGAAAATGCAGCTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
**
1568 TACTGAATATGCAACTATATGTCCCC
1 TACTGAATATGCAACTATATGAGCCC
**
1594 TACTGAATATGCAACTATATGCCCCC
1 TACTGAATATGCAACTATATGAGCCC
* *
1620 TACTGAATATGCAACTAAAAGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* * *
1646 TAATGAATTTGCAACTAGATGAGCCCTAGCCCC
1 TACTGAATATGCAACTATAT--G----AG-CCC
*
1679 TACTGAATATGCAACTATATGAGCCA
1 TACTGAATATGCAACTATATGAGCCC
1705 TACTGAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* * *
1731 TACTGAATATGTATCTATATGACCCC
1 TACTGAATATGCAACTATATGAGCCC
*
1757 TACTCAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* *
1783 AACTGAATATGCAACTCTATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* **
1809 AACTGAATATGCAACTATATGTCCCC
1 TACTGAATATGCAACTATATGAGCCC
1835 TACTGAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
**
1861 TACTGAATATGCAACTATATGTTCCC
1 TACTGAATATGCAACTATATGAGCCC
*
1887 TATTGAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
*
1913 TACTGAATATGCTACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* *
1939 TACTGCATATGCAACTATATGTGCCC
1 TACTGAATATGCAACTATATGAGCCC
* *
1965 TACCGAATATGCAACTATATGACCCC
1 TACTGAATATGCAACTATATGAGCCC
* **
1991 TACTGAATATGCAACTAAATGTCCCC
1 TACTGAATATGCAACTATATGAGCCC
*
2017 TACTGAATATGCAACTATATGAGCTC
1 TACTGAATATGCAACTATATGAGCCC
2043 TACTGAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
* *
2069 TACTGAATATGCAAATATATG-TCTCC
1 TACTGAATATGCAACTATATGAGC-CC
2095 TACTGAATATGCAACTATATGAGCCC
1 TACTGAATATGCAACTATATGAGCCC
**
2121 TACTGAATATGCAACTATATGTCCCC
1 TACTGAATATGCAACTATATGAGCCC
* * * ** *
2147 TATATGAGCCCTACTGGATAACTGCATGA-TCC
1 TA-CTGA---ATA-T-G-CAACTATATGAGCCC
* *
2179 TACTGAATGTGCAACTACATGA-CCC
1 TACTGAATATGCAACTATATGAGCCC
* * *
2204 TACTGATTATGCAACTACATGA-TCC
1 TACTGAATATGCAACTATATGAGCCC
* *
2229 TACTAAATATGCAACTACATGA-CCC
1 TACTGAATATGCAACTATATGAGCCC
*
2254 TACTGATTATG
1 TACTGAATATG
2265 ATTTACATGA
Statistics
Matches: 884, Mismatches: 111, Indels: 65
0.83 0.10 0.06
Matches are distributed among these distances:
19 13 0.01
20 1 0.00
22 1 0.00
23 1 0.00
24 20 0.02
25 67 0.08
26 704 0.80
27 34 0.04
28 2 0.00
30 2 0.00
31 5 0.01
32 7 0.01
33 27 0.03
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (26 bp):
TACTGAATATGCAACTATATGAGCCC
Found at i:1548 original size:45 final size:45
Alignment explanation
Indices: 1491--1579 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
1481 ACAACTATAT
* *
1491 GAGCCCTACTGAATAGGCAACTAAATG-TCTCCTACTGAATATGCG
1 GAGCCCTACTGAAAAGGCAACTAAATGAGC-CCTACTGAATATGCG
* * *
1536 GAGCCCTACTGAAAATGCAGCTATATGAGCCCTACTGAATATGC
1 GAGCCCTACTGAAAAGGCAACTAAATGAGCCCTACTGAATATGC
1580 AACTATATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
45 37 0.97
46 1 0.03
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (45 bp):
GAGCCCTACTGAAAAGGCAACTAAATGAGCCCTACTGAATATGCG
Found at i:2194 original size:25 final size:25
Alignment explanation
Indices: 2166--2264 Score: 135
Period size: 25 Copynumber: 4.0 Consensus size: 25
2156 CCTACTGGAT
* * *
2166 AACTGCATGATCCTACTGAATGTGC
1 AACTACATGACCCTACTGAATATGC
*
2191 AACTACATGACCCTACTGATTATGC
1 AACTACATGACCCTACTGAATATGC
* *
2216 AACTACATGATCCTACTAAATATGC
1 AACTACATGACCCTACTGAATATGC
*
2241 AACTACATGACCCTACTGATTATG
1 AACTACATGACCCTACTGAATATG
2265 ATTTACATGA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 64 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (25 bp):
AACTACATGACCCTACTGAATATGC
Found at i:2228 original size:50 final size:50
Alignment explanation
Indices: 2166--2264 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
2156 CCTACTGGAT
* * *
2166 AACTGCATGATCCTACTGAATGTGCAACTACATGACCCTACTGATTATGC
1 AACTACATGATCCTACTAAATATGCAACTACATGACCCTACTGATTATGC
2216 AACTACATGATCCTACTAAATATGCAACTACATGACCCTACTGATTATG
1 AACTACATGATCCTACTAAATATGCAACTACATGACCCTACTGATTATG
2265 ATTTACATGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (50 bp):
AACTACATGATCCTACTAAATATGCAACTACATGACCCTACTGATTATGC
Found at i:2380 original size:71 final size:71
Alignment explanation
Indices: 2279--2411 Score: 196
Period size: 71 Copynumber: 1.9 Consensus size: 71
2269 ACATGATGTT
* *
2279 GATGGCCCTAGTGAGTATAAACAACATGATGCATAT-AGCCCTACTGAATATGAACTACGTGACG
1 GATGGCCCTACTGAATATAAACAACATGATGCATATGA-CCCTACTGAATATGAACTACGTGACG
2343 TGGTGTA
65 TGGTGTA
* * * *
2350 GATGGCCCTACTGAATATGAACTACGTGATGCATATGACCCTACTGAATATGAGCTACGTGA
1 GATGGCCCTACTGAATATAAACAACATGATGCATATGACCCTACTGAATATGAACTACGTGA
2412 TGCATATTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 54 0.98
72 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.26
Consensus pattern (71 bp):
GATGGCCCTACTGAATATAAACAACATGATGCATATGACCCTACTGAATATGAACTACGTGACGT
GGTGTA
Found at i:2387 original size:18 final size:18
Alignment explanation
Indices: 2364--2418 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
2354 GCCCTACTGA
2364 ATATGAACTACGTGATGC
1 ATATGAACTACGTGATGC
*
2382 ATATGACCCTAC-TGA---
1 ATATGA-ACTACGTGATGC
*
2397 ATATGAGCTACGTGATGC
1 ATATGAACTACGTGATGC
2415 ATAT
1 ATAT
2419 TACCCTAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 4 0.13
15 9 0.30
18 13 0.43
19 4 0.13
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (18 bp):
ATATGAACTACGTGATGC
Found at i:2392 original size:33 final size:33
Alignment explanation
Indices: 2247--2432 Score: 142
Period size: 33 Copynumber: 5.5 Consensus size: 33
2237 ATGCAACTAC
* ** * *
2247 ATGACCCTACTGATTATGATTTACATGATG-TT
1 ATGACCCTACTGAATATGAACTACGTGATGCAT
* * * * * *
2279 GATGGCCCTAGTGAGTATAAACAACATGATGCAT
1 -ATGACCCTACTGAATATGAACTACGTGATGCAT
* *
2313 AT-AGCCCTACTGAATATGAACTACGTGACGTGGTGTAG
1 ATGA-CCCTACTGAATATGAACTACGTGA-----TGCAT
*
2351 ATGGCCCTACTGAATATGAACTACGTGATGCAT
1 ATGACCCTACTGAATATGAACTACGTGATGCAT
*
2384 ATGACCCTACTGAATATGAGCTACGTGATGCAT
1 ATGACCCTACTGAATATGAACTACGTGATGCAT
* *
2417 ATTACCCTAGTGAATA
1 ATGACCCTACTGAATA
2433 ACATGTGCAG
Statistics
Matches: 122, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
33 92 0.75
34 1 0.01
38 29 0.24
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (33 bp):
ATGACCCTACTGAATATGAACTACGTGATGCAT
Found at i:16548 original size:109 final size:109
Alignment explanation
Indices: 16395--16690 Score: 432
Period size: 109 Copynumber: 2.7 Consensus size: 109
16385 TAAATTAAAA
** * *
16395 TGGTAAAAATAAAAAAAATTATATAAAATATT-GAATTTAATTAAATGAAAATAGAATTTTTAGT
1 TGGTAAAAAT-AAAGTAATTATA-AAGATATTAG-ATTTAATTAAATGAAAATAGAGTTTTTAGT
* *
16459 AGAATAAAATTGTATATTAGAAAGAATTTTAATATATCCAATTTTTT
63 AGAATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
16506 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
*
16571 ATAAAATTGTATATTAGAAAAAATTTTAGTATATCCAAATTTTT
66 ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
* *
16615 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTTAATTGAATAAAAATAGAGTTTCTA
1 TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAA-TT-A---AATGAAAATAGAGTTTTTA
16680 GTAGAATAAAA
61 GTAGAATAAAA
16691 CTATAATAGT
Statistics
Matches: 170, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
109 118 0.69
110 13 0.08
111 11 0.06
114 28 0.16
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.38
Consensus pattern (109 bp):
TGGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAAATGAAAATAGAGTTTTTAGTAGA
ATAAAATTGTATATTAGAAAAAATTTTAATATATCCAAATTTTT
Found at i:16871 original size:50 final size:50
Alignment explanation
Indices: 16812--16912 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
16802 ATATAGATAT
16812 ACTTCAACCCATTCTTGTATTAGCACATAGACAGGCTAAGATTGAGCTAG
1 ACTTCAACCCATTCTTGTATTAGCACATAGACAGGCTAAGATTGAGCTAG
*
16862 ACTTCAACCCATTCTTGTATTAGCACATAGACAGGCTAAGGTTGAGCTAG
1 ACTTCAACCCATTCTTGTATTAGCACATAGACAGGCTAAGATTGAGCTAG
16912 A
1 A
16913 TAATGTGTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.28
Consensus pattern (50 bp):
ACTTCAACCCATTCTTGTATTAGCACATAGACAGGCTAAGATTGAGCTAG
Found at i:18916 original size:21 final size:21
Alignment explanation
Indices: 18890--18948 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
18880 TGTTGCAGAA
* *
18890 GTAGAACCGGCCCTTGTCATT
1 GTAGAACCAGCCATTGTCATT
*
18911 GTAGAAGCAGCCATTGTCATT
1 GTAGAACCAGCCATTGTCATT
* *
18932 GTAGAAGCAGCCTTTGT
1 GTAGAACCAGCCATTGT
18949 TGCAGCTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (21 bp):
GTAGAACCAGCCATTGTCATT
Found at i:22043 original size:27 final size:24
Alignment explanation
Indices: 21995--22079 Score: 125
Period size: 24 Copynumber: 3.4 Consensus size: 24
21985 TGTGGGGCTT
*
21995 CATTTAAACCCTCACTACCTACTG
1 CATTTAAACCCTCACCACCTACTG
*
22019 CATTTATACCCGGTTCACCACCTACTG
1 CATTTAAACCC---TCACCACCTACTG
22046 CATTTAAACCCTCACCACCTACTG
1 CATTTAAACCCTCACCACCTACTG
22070 CATTTAAACC
1 CATTTAAACC
22080 ATCATCTACT
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
24 33 0.60
27 22 0.40
ACGTcount: A:0.28, C:0.38, G:0.06, T:0.28
Consensus pattern (24 bp):
CATTTAAACCCTCACCACCTACTG
Found at i:27156 original size:3 final size:3
Alignment explanation
Indices: 27148--27177 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
27138 GTAAAATACC
27148 ATA ATA ATAA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA AT
27178 GTAAAATCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35366 original size:32 final size:31
Alignment explanation
Indices: 35318--35389 Score: 101
Period size: 32 Copynumber: 2.3 Consensus size: 31
35308 AAGCCCTTGA
35318 TTGACCTTGAGCAATTTTCTTTCTTGGCCGG
1 TTGACCTTGAGCAATTTTCTTTCTTGGCCGG
* * *
35349 TTGACCTTTGAGTAATTTTTTTTTTTGGCCGG
1 TTGACC-TTGAGCAATTTTCTTTCTTGGCCGG
35381 TTGA-CTTGA
1 TTGACCTTGA
35390 CCTTGAGTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 7 0.19
32 26 0.70
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (31 bp):
TTGACCTTGAGCAATTTTCTTTCTTGGCCGG
Found at i:42720 original size:26 final size:26
Alignment explanation
Indices: 42691--42743 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
42681 AAGAGTTGAA
* *
42691 AAGATTTTCGTGAGTTTTACTTCTTT
1 AAGACTTTCGTCAGTTTTACTTCTTT
42717 AAGACTTTCGTCAGTTTTACTTCTTT
1 AAGACTTTCGTCAGTTTTACTTCTTT
42743 A
1 A
42744 TTTTTGGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (26 bp):
AAGACTTTCGTCAGTTTTACTTCTTT
Found at i:69633 original size:2 final size:2
Alignment explanation
Indices: 69628--69658 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
69618 AAAAAAAAAA
69628 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69659 CAAAGATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73333 original size:3 final size:3
Alignment explanation
Indices: 73325--73358 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
73315 CTTTAAAAAG
*
73325 GAA GAA GAA GAA GAA GAA GAA GAAA CAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA GAA
73359 AACCCACCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.68, C:0.03, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Done.