Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009491.1 Corchorus capsularis cultivar CVL-1 contig09512, 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: 23803
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:933 original size:332 final size:330
Alignment explanation
Indices: 1--3404 Score: 3980
Period size: 331 Copynumber: 10.3 Consensus size: 330
* * * * *
1 TGAAAAGCCCTTCAAAATTTTTTGGCTTTGAATAATTTA-TTTTTATTAGTATTTTGACCAAAAA
1 TGAAAAGCCCTTC--AATTTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAA
** * *
65 CTT-AGGAAAAATCTTTCGGGTCAATTTTTGCTCAATTTTTGCCAAAATCGTGTATTAACCATCA
64 -TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCA
* * * * * * * * *
129 CGCTATTTAGCTGAAGACCCGTTCCGGGTCCCGGTTCAGTTTTGCATGATTTTTGGAAACAAGCC
128 CGGTTTTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGAC
* * * * * * *
194 TCCTTGAGATATCTATATTCAACTAACCAAATGTCAGCCCTACTGGATTTAAGGAATTGTTTTTA
193 TCCTTGAAAAATATATATTCATCTAACCAAATCTAAGCCCTATTGGATTTAAGGAATTGTTTTTA
* *
259 CGAGCATCAGAATCATGTTTCGATTTAATTAAAAATTAATCCTC-GAAAAAATAGG-AAAACTGA
258 CGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAAT--TCAGAAAAAATAGGAAAAAC-GA
322 TATTAGAAGCG
320 TATTAGAAGCG
* * *
333 TGAAAAGCCCTTCAATTGTTTGGCATTGAATTATTCA-TTTTTATTAGTATTTTGTCCAAAAATT
1 TGAAAAGCCCTTCAATTTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAATT
* ** * * *
397 GAGAAAAAATCTTTCAAGTAAAGTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACTATCACGG
66 GAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGG
* * * * ** *
462 TTGTTGGATGAACACGCGTTCCGGTTCCTTGTTCAGTTTTGCATGATTTTTGGCACCAAGACTCC
131 TTTTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCC
* * * ** * ** * **
527 TTGAGATATCTATATTCATCTAACCAAATCTAAGCCAC-ATTATACTTAAATATTTGTTTAAACG
196 TTGAAAAATATATATTCATCTAACCAAATCTAAGCC-CTATTGGATTTAAGGAATTGTTTTTACG
* * *
591 AGCATCAGAATCTTGTTTCGATTTAATTATAAATTAATTCAG-AAAAATAGGAAAAATGATATCA
260 AGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTA
655 GAAGCG
325 GAAGCG
* * * *
661 TGCAAAGCCCTTCAATCTTTTTGGCGTTGAATTATAT-ATTTTTTTAATAATATTATGGCCAAAA
1 TGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTAT-TCA-TTTTTTATTAATATTTTGGCCAAAA
* * * * *
725 TTTGAGGAGAAATCTTTCGGGTCAATTTTTGCAAAATTCTTCCCGAAATCGTATACTAACCATCA
63 ATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCA
* ** * *
790 CGGTTTTTGACTGAAAACGCGTTTTTGGATCCCGCCTCAGTTTTGCATGATTTTTGGCACCAAGA
128 CGGTTTTTGGCTGAAAACGCG-TTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGA
* * * * * *
855 CTCGTTGAAAAATATATATTCAACTGACCGAATCTCAGCCCTACTGGATTTAAGGAATTGTTTTT
192 CTCCTTGAAAAATATATATTCATCTAACCAAATCTAAGCCCTATTGGATTTAAGGAATTGTTTTT
* * * * * *
920 ACGAGCATCAGAATCATGTTTTGATTTAATTAAAAATTAATCCTGAAAAAAAAATA-GTAAAACT
257 ACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAAT--T-CAGAAAAAATAGGAAAAAC-
*
984 GATACTAGAAGCG
318 GATATTAGAAGCG
* *
997 TGAAAAGCCCTTCAATTTTTTTGGCATTGAATTATTCATTTTTTATTAGTATTTTGTCCAAAAAT
1 TGAAAAGCCCTTCAA-TTTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAAT
** * * * * * *
1062 TGACAAAAAATCTTTCGGCTCAATTTTTGTAAAATTTTTGCCGAAGTCGTCTACTGACCACCACG
65 TGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACG
* * *
1127 GTTTTTGGCTGAAAACGCGTTCCGGTTCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGATTC
130 GTTTTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTC
* * *
1192 CTTGAAAAATATATATTCAAT-TGACCAAATCTCAGCCCTACTGGATTTAAGGAATTGTTTTTAC
195 CTTGAAAAATATATATTC-ATCTAACCAAATCTAAGCCCTATTGGATTTAAGGAATTGTTTTTAC
* * *
1256 GAGCATCAGAATCATGTTTCGATTTAATTAAAAATTAATCCTCA-AAAAAATAGG-AAAACTAAT
259 GAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAAT--TCAGAAAAAATAGGAAAAAC-GAT
*
1319 CTTAGAAGCG
321 ATTAGAAGCG
* * ** * *
1329 TGAAAAGCCCTTCAAATTTTTTGGCATTGAATTAGTCATTTTTTATTAGTATTTTGATCGAAAAC
1 TGAAAAGCCCTTC-AATTTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAAT
* **
1394 TGAGGAAAAATATTTCGGGAAAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACG
65 TGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACG
* * * *
1459 GTTTTCGGCTGAAAACGCATTCCGGTTCCCGGTTCAGTTTTGCATGATTTTTGGCACCAAGACTC
130 GTTTTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTC
* * * * * * * **
1524 CTTGAGATATCTATATTCATCTAACAAAATCTAAGTCAC-ATTAGATTTAAGGATTTGTTTAAAC
195 CTTGAAAAATATATATTCATCTAACCAAATCTAAG-CCCTATTGGATTTAAGGAATTGTTTTTAC
* * * *
1588 GAGCATCAGAATCTTATATCGATTTAATTATAAATTAATTCAGAAAAAATAGGAAAAACGATATC
259 GAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATT
*
1653 AGAAGTG
324 AGAAGCG
* * * *
1660 TGAAAACCCCTTCAATATTTTGGGCATTGAATTATAT-ATTTTTTAATAATATTATGGCCAAAAA
1 TGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTAT-TCATTTTTTATTAATATTTTGGCCAAAAA
* *
1724 TTGAGGAAAAATATTTCTGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCAC
64 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCAC
* * * * * *
1789 CGTTTTTGGCTGAAAACGCGTTCTGGGTCCCGGCTTAGTTTTGCATAATTTTTGGCAACAAGCCT
129 GGTTTTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACT
* * * * * * **
1854 -CTTTAAGATATCTATATTCAACTAACCAAATCTAAGCCAC-ATTAGATTTAAGGATTTGTTTAA
194 CCTTGAA-AAATATATATTCATCTAACCAAATCTAAGCC-CTATTGGATTTAAGGAATTGTTTTT
* *
1917 ACCAGCATCAGAATCTTGTTTCGATTTAATTAGAATTTAATTCAGAAAAAATAGGAAAAACGATA
257 ACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATA
*
1982 TTAGAAGCT
322 TTAGAAGCG
* * * *
1991 TGAAAAGCCCTTCAATATTTTTGGCATTGAATTATAT-ATTTTTTAATAATATTATGTCCAAGAA
1 TGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTAT-TCATTTTTTATTAATATTTTGGCCAAAAA
* *
2055 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTATTGCCGAAATCGTGGACT----A--AC
64 TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCAC
* *
2114 --TTTTTGGCTAAAAATGCGTTCCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGAC
129 GGTTTTTGGCTGAAAACGCGTTCC-GGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGAC
* * *
2177 TCCTTGAAAAATATATATTCATCTAACCAAATCTTAGCCCTATTGGATTTAAGGAGTTATTTTTA
193 TCCTTGAAAAATATATATTCATCTAACCAAATCTAAGCCCTATTGGATTTAAGGAATTGTTTTTA
* * * * * *
2242 CAAGCATCAAAATTTTGTTTCGAATTAATTAGAAATTAATTCGGAAAAAATAAGAAAAACGATAT
258 CGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATAT
*
2307 TACAAGCG
323 TAGAAGCG
* * *
2315 TGAAAAGCCCTTTAATCTTTTTGGCATTGAATTATTCATTTTTTATTAGTATTTTGGCCAAAATT
1 TGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAAT
* ** *
2380 TGAGGAAATATCTTTCGGGATCAATTTTTGCAAAATTTTAACCGAAATCGTTTACTAACC-TCAC
65 TGAGGAAAAATCTTTCGGG-TCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCAC
* * * *
2444 GGTTTTTGGCT-AAATCGCGTTCCGGGGTCCCAGCTCAATTTTGCATGATTTTTGGCACCGAGAC
129 GGTTTTTGGCTGAAAACGCGTTCC-GGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGAC
* ** **
2508 TCCTAT-AAAAATATATATTCACCTAACCAAATCTAAATCCTATTGGATTTAAGGAATTAATTTT
193 TCCT-TGAAAAATATATATTCATCTAACCAAATCTAAGCCCTATTGGATTTAAGGAATTGTTTTT
* * * * *
2572 AGGAGCATTACAATCTTGTTTCGATTTAATTAGAAATTGATTCAGAAAAAATAGGAAAAATGATA
257 ACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATA
*
2637 TTAGAAACG
322 TTAGAAGCG
* * * * *
2646 TGAAAAACCCTTCAATATTTTTGGCGTTGAATTATTCA-TTTCTATTAGTATTTTGGCAAAAAAT
1 TGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAAT
* * *
2710 TGAGCAAAAATCTTTCGGGTCAATTTTCGCAAAATTTTTGCCGAAATCGTATACTAACCATCACG
65 TGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACG
* * * * * *
2775 GTTTTTTGCTGAAATCACGTTTCCAGGTCCCGGCTCAGCTTTGCATGATTTTTGGCACCAATACT
130 GTTTTTGGCTGAAAACGCG-TTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACT
* *
2840 CCTTGAAAAATATATATTCATCTAACGAAATCTCAA-CCCTATTGGATTTAAGGAATTATTTTTA
194 CCTTGAAAAATATATATTCATCTAACCAAATCT-AAGCCCTATTGGATTTAAGGAATTGTTTTTA
* *
2904 CGAGCATCAGAATCTTGTTTCGA-TTAAGTTAGAAAATAATTCCGAAAAAAATAGGAAAAAACGA
258 CGAGCATCAGAATCTTGTTTCGATTTAA-TTAGAAATTAATTCAG-AAAAAATAGG-AAAAACGA
*
2968 TATTAGAAGCA
320 TATTAGAAGCG
* * * *
2979 TGAAAAGCCCTTCAAATATTTTGGCATTGAATTATTCATTTTTTATTAGTGTTTTGGCCAAAAAA
1 TGAAAAGCCCTTC-AATTTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAAT
* * * * *
3044 TAAGGAAAAATATTTCGGGTCAATTTTCT-CAAATTTTTTGCCG--ATCATGTACTAACCGTCAC
65 TGAGGAAAAATCTTTCGGGTCAATTTT-TGCAAAATTTTTGCCGAAATCGTGTACTAACCATCAC
* *
3106 GGTTTTTGACTGAAAACGCGTTCCGGGTCCCGACTCAGTTTTGCATGATTTTTGGCACCAAGACT
129 GGTTTTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACT
* * ** * * ** *
3171 CCTTGATATATCCGCATATTCATCTAACCAAATATAAGCCAC-ATTAGATTTAAGGTTTTGTTTA
194 CCTTGAAAAAT--ATATATTCATCTAACCAAATCTAAGCC-CTATTGGATTTAAGGAATTGTTTT
* * * *
3235 AACGACCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAAACGTT
256 TACGAGCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGAT
3300 ATTAGAAGCG
321 ATTAGAAGCG
* * * *
3310 TGAAAAGCCCTTCACTCTTTTTGGCGTTGAATTTTTCATTTTTTATTATTATTTTGGCCAAAAAT
1 TGAAAAGCCCTTCAAT-TTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAAT
*
3375 TGAGGAAAAATCTTTCAGGTCAATTTTTGC
65 TGAGGAAAAATCTTTCGGGTCAATTTTTGC
3405 CGAAATCGTG
Statistics
Matches: 2649, Mismatches: 363, Indels: 121
0.85 0.12 0.04
Matches are distributed among these distances:
323 21 0.01
324 220 0.08
325 38 0.01
327 1 0.00
328 38 0.01
329 60 0.02
330 312 0.12
331 985 0.37
332 485 0.18
333 127 0.05
334 209 0.08
335 102 0.04
336 50 0.02
337 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (330 bp):
TGAAAAGCCCTTCAATTTTTTGGCATTGAATTATTCATTTTTTATTAATATTTTGGCCAAAAATT
GAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACCATCACGG
TTTTTGGCTGAAAACGCGTTCCGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCACCAAGACTCC
TTGAAAAATATATATTCATCTAACCAAATCTAAGCCCTATTGGATTTAAGGAATTGTTTTTACGA
GCATCAGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTAG
AAGCG
Found at i:7128 original size:6 final size:6
Alignment explanation
Indices: 7117--7154 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
7107 TTATGTTATC
*
7117 ATTACT ATTACT ATTACT ATTACT ATTTATT ATTACT A
1 ATTACT ATTACT ATTACT ATTACT A-TTACT ATTACT A
7155 ATATATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.83
7 5 0.17
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (6 bp):
ATTACT
Found at i:7323 original size:65 final size:65
Alignment explanation
Indices: 7248--7372 Score: 162
Period size: 65 Copynumber: 1.9 Consensus size: 65
7238 ATTTTTTTAT
* * * *
7248 TTATCAAAATTTTATGAAGAGGTTATTAAAATTTTCATAGTGCGGTTA-CCAATTTTATAGTGTG
1 TTATCAAAATTTTATGAAGAGATTATCAAAA-TTTCACAGTGCGGTTATCAAATTTTATAGTGTG
7312 A
65 A
** * *
7313 TTATCAAAATTTTATGGGGAGATTCTCAAAATTTCACAGTGTGGTTATCAAATTTTATAG
1 TTATCAAAATTTTATGAAGAGATTATCAAAATTTCACAGTGCGGTTATCAAATTTTATAG
7373 GTTATAGAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
64 14 0.27
65 37 0.73
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.41
Consensus pattern (65 bp):
TTATCAAAATTTTATGAAGAGATTATCAAAATTTCACAGTGCGGTTATCAAATTTTATAGTGTGA
Found at i:7325 original size:22 final size:22
Alignment explanation
Indices: 7248--7372 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
7238 ATTTTTTTAT
*
7248 TTATCAAAATTTTATGAAGAG-G-
1 TTATCAAAATTTTAT--AGTGTGA
* * *
7270 TTATTAAAATTTTCATAGTGCGG
1 TTATCAAAATTTT-ATAGTGTGA
*
7293 TTA-C-CAATTTTATAGTGTGA
1 TTATCAAAATTTTATAGTGTGA
* * *
7313 TTATCAAAATTTTATGGGGAGA
1 TTATCAAAATTTTATAGTGTGA
* * * *
7335 TTCTCAAAATTTCACAGTGTGG
1 TTATCAAAATTTTATAGTGTGA
7357 TTATC-AAATTTTATAG
1 TTATCAAAATTTTATAG
7373 GTTATAGAAA
Statistics
Matches: 78, Mismatches: 20, Indels: 11
0.72 0.18 0.10
Matches are distributed among these distances:
20 10 0.13
21 19 0.24
22 44 0.56
23 5 0.06
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTTATAGTGTGA
Found at i:11704 original size:2 final size:2
Alignment explanation
Indices: 11697--11739 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
11687 TGATAATTTA
* *
11697 AT AT AT AT AT AT AT AT AT AT A- AT CT AT AT CT AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
11739 A
1 A
11740 AAAGTACGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
1 1 0.03
2 32 0.91
3 2 0.06
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15971 original size:6 final size:6
Alignment explanation
Indices: 15960--15984 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15950 TGTTGGCGGC
15960 CGAGTT CGAGTT CGAGTT CGAGTT C
1 CGAGTT CGAGTT CGAGTT CGAGTT C
15985 TTTCTTGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.20, G:0.32, T:0.32
Consensus pattern (6 bp):
CGAGTT
Found at i:16575 original size:13 final size:13
Alignment explanation
Indices: 16559--16606 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
16549 ACTAAGTTTG
16559 TGAATTTTATTAT
1 TGAATTTTATTAT
* *
16572 TGAATTTTTTTGT
1 TGAATTTTATTAT
16585 TGAGATATATTATTAT
1 TGA-AT-T-TTATTAT
16601 TGAATT
1 TGAATT
16607 AATCAAAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
13 14 0.50
14 3 0.11
15 3 0.11
16 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.58
Consensus pattern (13 bp):
TGAATTTTATTAT
Found at i:16720 original size:37 final size:37
Alignment explanation
Indices: 16679--16792 Score: 149
Period size: 37 Copynumber: 3.1 Consensus size: 37
16669 AACTGTGCAC
*
16679 ATTTTATTTTAATTAATCCACTGATCAAAGTTCTAGT
1 ATTTTATTTTAATTAATCCATTGATCAAAGTTCTAGT
* *
16716 ATTTTATTTTAATTAATCCATTGATCAAATTTCTCGT
1 ATTTTATTTTAATTAATCCATTGATCAAAGTTCTAGT
* * * *
16753 -TAATCATTTTAATTAATCCGTTGATCAAAGTTTTAGT
1 AT-TTTATTTTAATTAATCCATTGATCAAAGTTCTAGT
16790 ATT
1 ATT
16793 GGAATTGACT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
36 1 0.02
37 63 0.97
38 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (37 bp):
ATTTTATTTTAATTAATCCATTGATCAAAGTTCTAGT
Found at i:20461 original size:18 final size:18
Alignment explanation
Indices: 20440--20488 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
20430 ACATTTAAAC
*
20440 CATTGTCATCATTATTTA
1 CATTGTCACCATTATTTA
20458 CATTGTCACCATTATTTA
1 CATTGTCACCATTATTTA
*
20476 CATTCTCACCATT
1 CATTGTCACCATT
20489 CTGACCATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (18 bp):
CATTGTCACCATTATTTA
Found at i:21212 original size:60 final size:60
Alignment explanation
Indices: 21123--21286 Score: 319
Period size: 60 Copynumber: 2.7 Consensus size: 60
21113 AAAATTTACC
21123 ATATTATGTTCGAATACAAAACCCAACACATAAAACAAAAAAAAATTACAAATATCCCAT
1 ATATTATGTTCGAATACAAAACCCAACACATAAAACAAAAAAAAATTACAAATATCCCAT
21183 ATATTATGTTCGAATACAAAACCCAACACATAAAACAAAAAAAAATTACAAATATCCCAT
1 ATATTATGTTCGAATACAAAACCCAACACATAAAACAAAAAAAAATTACAAATATCCCAT
*
21243 ATATTATATTCGAATACAAAACCCAACACATAAAACAAAAAAAA
1 ATATTATGTTCGAATACAAAACCCAACACATAAAACAAAAAAAA
21287 GATTCCAACT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 103 1.00
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.21
Consensus pattern (60 bp):
ATATTATGTTCGAATACAAAACCCAACACATAAAACAAAAAAAAATTACAAATATCCCAT
Found at i:21888 original size:12 final size:13
Alignment explanation
Indices: 21858--21887 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
21848 TAAAAATGTC
*
21858 ATTTTCTTTTTTT
1 ATTTTCTGTTTTT
21871 ATTTTCTGTTTTT
1 ATTTTCTGTTTTT
21884 ATTT
1 ATTT
21888 CAATTACTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (13 bp):
ATTTTCTGTTTTT
Found at i:22882 original size:42 final size:42
Alignment explanation
Indices: 22800--22882 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
22790 GCAATGTGTT
* *
22800 TTTGGAGGTTGAGCTTCGGAAGAGAGAAATAGTTTCTTGGTG
1 TTTGGAGGTTGAGCTTCGAAAGAGAGAAATAGTTTATTGGTG
22842 TTTGGAGGTTGAGCTT-GAAGAGAGAGAAAT-GATTTATTGGT
1 TTTGGAGGTTGAGCTTCGAA-AGAGAGAAATAG-TTTATTGGT
22883 ATTGGCGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.27, C:0.05, G:0.35, T:0.34
Consensus pattern (42 bp):
TTTGGAGGTTGAGCTTCGAAAGAGAGAAATAGTTTATTGGTG
Found at i:23010 original size:29 final size:28
Alignment explanation
Indices: 22966--23021 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
22956 AATATTTATA
*
22966 TCAATCAAACGGTTGGATTATGTTGATT
1 TCAATCAAACAGTTGGATTATGTTGATT
22994 TCAATCAAAACAGTTGGATTATGTTGAT
1 TCAATC-AAACAGTTGGATTATGTTGAT
23022 AGGTTTGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 6 0.23
29 20 0.77
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.38
Consensus pattern (28 bp):
TCAATCAAACAGTTGGATTATGTTGATT
Found at i:23186 original size:66 final size:66
Alignment explanation
Indices: 23007--23205 Score: 224
Period size: 66 Copynumber: 3.0 Consensus size: 66
22997 ATCAAAACAG
* * *
23007 TTGGATTATGTTGATAGGTTTGTACAGTTTATGTTTGTGAATTTGGTAATATAAATCACAAACTA
1 TTGGATTATGTTGATAGGTTCGTACAGTTTATGTTTGTGAATTTGGTAATGTAAATCACAACCTA
23072 T
66 T
** * ** * * * *
23073 TTATATCA-AATGGT-GGTTGGATTA-TGTTGATGTTTGTGAATTTGGTAATGTAAATCACAACC
1 TTGGATTATGTTGATAGGTTCG--TACAGTTTATGTTTGTGAATTTGGTAATGTAAATCACAACC
23135 TAT
64 TAT
* * *
23138 TTGGATTATGTTGATAGGTTCGTACAGTTTATGTTTGCGAATTTGGTAAAGTAAATCACAGCCTA
1 TTGGATTATGTTGATAGGTTCGTACAGTTTATGTTTGTGAATTTGGTAATGTAAATCACAACCTA
23203 T
66 T
23204 TT
1 TT
23206 ATATCAAACG
Statistics
Matches: 105, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
64 5 0.05
65 47 0.45
66 48 0.46
67 5 0.05
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (66 bp):
TTGGATTATGTTGATAGGTTCGTACAGTTTATGTTTGTGAATTTGGTAATGTAAATCACAACCTA
T
Found at i:23351 original size:44 final size:42
Alignment explanation
Indices: 23282--23397 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 42
23272 AATCAAAGGG
* * **
23282 TTTATTATTGAATTACTCCAGTGATCAAAGTT-GAAAGTTCTAGTAT
1 TTTATT-TT-AATTAATCCATTGATCAAA-TTCGAAA-TT-TACCAT
23328 TTTATTTTAATTAATCCATTGATCAAATTCGAAATTTACCAT
1 TTTATTTTAATTAATCCATTGATCAAATTCGAAATTTACCAT
*
23370 TAATCATTTTAATTAATCCATTGATCAA
1 T--TTATTTTAATTAATCCATTGATCAA
23398 TAGTCTTGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
42 5 0.08
43 4 0.06
44 45 0.73
45 2 0.03
46 6 0.10
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (42 bp):
TTTATTTTAATTAATCCATTGATCAAATTCGAAATTTACCAT
Done.