Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008850.1 Corchorus capsularis cultivar CVL-1 contig08871, 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: 41350
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:160 original size:22 final size:22
Alignment explanation
Indices: 135--369 Score: 71
Period size: 22 Copynumber: 10.8 Consensus size: 22
125 ATGACGTCCT
135 TATGAAATTTTGATAACCTTTC
1 TATGAAATTTTGATAACCTTTC
** *
157 TATGAAATTAAGATAA--TTAC
1 TATGAAATTTTGATAACCTTTC
* * * *
177 -ACT--ATTTTTTATTACGTCTT-
1 TA-TGAAATTTTGATAACCT-TTC
*
197 TATGAAATTTCGATAACC-TTC
1 TATGAAATTTTGATAACCTTTC
** ** *
218 TTATGAAATTTCAATAACGATAC
1 -TATGAAATTTTGATAACCTTTC
* *
241 TATGGAATTTTTGATAACCTTTT
1 TAT-GAAATTTTGATAACCTTTC
**
264 TAT-AAATCTTTTTTAACC-TTC
1 TATGAAAT-TTTGATAACCTTTC
* **
285 TTATGAAATTTTGTTAAACC-CCC
1 -TATGAAATTTTGAT-AACCTTTC
* * **
308 TAAGGAATTTTGA-AGACCTCAC
1 TATGAAATTTTGATA-ACCTTTC
*
330 TATGAAATTTTGATAA-CTTCC
1 TATGAAATTTTGATAACCTTTC
*
351 AAATGAAATTTTGATAACC
1 -TATGAAATTTTGATAACC
370 AACACTATAA
Statistics
Matches: 153, Mismatches: 40, Indels: 39
0.66 0.17 0.17
Matches are distributed among these distances:
18 6 0.04
19 1 0.01
20 9 0.06
21 13 0.08
22 96 0.63
23 28 0.18
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTTC
Found at i:173 original size:62 final size:62
Alignment explanation
Indices: 76--227 Score: 225
Period size: 62 Copynumber: 2.5 Consensus size: 62
66 ATATTGATAC
* * * *
76 GAAATTATGATAACCTTCCTATTAAATTATGATAATTACACTATTTTTTATGACGTCCTTAT
1 GAAATTTTGATAACCTTTCTATGAAATTAAGATAATTACACTATTTTTTATGACGTCCTTAT
* *
138 GAAATTTTGATAACCTTTCTATGAAATTAAGATAATTACACTATTTTTTATTACGTCTTTAT
1 GAAATTTTGATAACCTTTCTATGAAATTAAGATAATTACACTATTTTTTATGACGTCCTTAT
*
200 GAAATTTCGATAACC-TTCTTATGAAATT
1 GAAATTTTGATAACCTTTC-TATGAAATT
228 TCAATAACGA
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
61 3 0.04
62 79 0.96
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (62 bp):
GAAATTTTGATAACCTTTCTATGAAATTAAGATAATTACACTATTTTTTATGACGTCCTTAT
Found at i:409 original size:22 final size:22
Alignment explanation
Indices: 197--782 Score: 209
Period size: 22 Copynumber: 26.9 Consensus size: 22
187 ATTACGTCTT
* * *
197 TATGAAATTTCGATAACCTTCT
1 TATGAAATTTTGATAACCTCCA
** * *
219 TATGAAATTTCAATAACGATAC-
1 TATGAAATTTTGATAAC-CTCCA
* ***
241 TATGGAATTTTTGATAACCTTTT
1 TAT-GAAATTTTGATAACCTCCA
** * *
264 TAT-AAATCTTTTTTAACCTTCT
1 TATGAAAT-TTTGATAACCTCCA
* *
286 TATGAAATTTTGTTAAACC-CCC
1 TATGAAATTTTGAT-AACCTCCA
* *
308 TAAGGAATTTTGA-AGACCT-CA
1 TATGAAATTTTGATA-ACCTCCA
*
329 CTATGAAATTTTGATAACTTCCA
1 -TATGAAATTTTGATAACCTCCA
* **
352 AATGAAATTTTGATAACCAACA
1 TATGAAATTTTGATAACCTCCA
*
374 CTAT-AATATGTTGATAACCTCCA
1 -TATGAA-ATTTTGATAACCTCCA
* * ****
397 TATGATATATTGATAACCAAGT
1 TATGAAATTTTGATAACCTCCA
* * *
419 TATGAAAATTTAAAAACCTCCA
1 TATGAAATTTTGATAACCTCCA
* *
441 TATG-AATTGTCAGTAA--TCACA
1 TATGAAATTTTGA-TAACCTC-CA
* *
462 CTTTGAAATTTTGAT-A-CTCATA
1 -TATGAAATTTTGATAACCTC-CA
*
484 CTATGAAATTGTT-ATAATCT-CA
1 -TATGAAATT-TTGATAACCTCCA
*
506 TTATGAAATTTTGATAAACCTTTC-
1 -TATGAAATTTTGAT-AACC-TCCA
* * *
530 TATAAAATTTTGATAACATCCT
1 TATGAAATTTTGATAACCTCCA
552 TATGAAATTTTGATAA----C-
1 TATGAAATTTTGATAACCTCCA
* *
569 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCA
**
590 TATGATTTTTTGATAACCT-CA
1 TATGAAATTTTGATAACCTCCA
* * * *
611 TTATGAAATCTTGTTAATCTCCC
1 -TATGAAATTTTGATAACCTCCA
* * *
634 TATGAAATTTTGATCTACATAC-
1 TATGAAATTTTGAT-AACCTCCA
*
656 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CA
* **
678 TATGAAATTTTGA-AAACTAAA
1 TATGAAATTTTGATAACCTCCA
* *
699 CTATGAAACTTTGATAACCTTCA
1 -TATGAAATTTTGATAACCTCCA
*
722 TATGAAATTTTGATATCCTCC-
1 TATGAAATTTTGATAACCTCCA
*
743 T-TGAAATTTTGATTA-CTCCA
1 TATGAAATTTTGATAACCTCCA
* * *
763 TGATAAAAGTTTAATAACCT
1 T-ATGAAATTTTGATAACCT
783 TCCTAATTTG
Statistics
Matches: 420, Mismatches: 99, Indels: 89
0.69 0.16 0.15
Matches are distributed among these distances:
16 12 0.03
17 2 0.00
18 1 0.00
19 4 0.01
20 17 0.04
21 29 0.07
22 272 0.65
23 79 0.19
24 3 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCA
Found at i:594 original size:38 final size:38
Alignment explanation
Indices: 534--606 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
524 CCTTTCTATA
*
534 AAATTTTGATAACATCCTTATGAAATTTTGATAACTAC
1 AAATTTTGATAACATCCCTATGAAATTTTGATAACTAC
* **
572 AAATTTTGATAACCTCCCTATGATTTTTTGATAAC
1 AAATTTTGATAACATCCCTATGAAATTTTGATAAC
607 CTCATTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (38 bp):
AAATTTTGATAACATCCCTATGAAATTTTGATAACTAC
Found at i:887 original size:22 final size:22
Alignment explanation
Indices: 862--981 Score: 100
Period size: 22 Copynumber: 5.5 Consensus size: 22
852 ATCACATTTC
* *
862 GAAAATTTGATAACCTCTTTAT
1 GAAATTTTGATAACCTCTCTAT
*
884 GAAATTTTAATAACCTCTCTAT
1 GAAATTTTGATAACCTCTCTAT
* * *
906 -AAATTTTTGTTGACCCCTCTAT
1 GAAA-TTTTGATAACCTCTCTAT
* *
928 GAAATTTTGATAATCACAT-TAT
1 GAAATTTTGATAACCTC-TCTAT
* ** *
950 GTAATTTTGATAACCTCGATTT
1 GAAATTTTGATAACCTCTCTAT
972 GAAATTTTGA
1 GAAATTTTGA
982 AATTGGATCA
Statistics
Matches: 77, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
21 3 0.04
22 70 0.91
23 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
GAAATTTTGATAACCTCTCTAT
Found at i:1130 original size:37 final size:37
Alignment explanation
Indices: 1039--1133 Score: 129
Period size: 37 Copynumber: 2.6 Consensus size: 37
1029 ATCTAAGGCC
* *
1039 AAATAGGACGTTGGAGACGAAGACAAAAAGCAAAATT
1 AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
** *
1076 AAATACAACGATT-GAAACAAAGACAAAAGGCAAAATT
1 AAATAGGACG-TTGGAAACAAAGACAAAAAGCAAAATT
1113 AAATAGGACGTTGGAAACAAA
1 AAATAGGACGTTGGAAACAAA
1134 AAGGCAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
36 2 0.04
37 45 0.92
38 2 0.04
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.14
Consensus pattern (37 bp):
AAATAGGACGTTGGAAACAAAGACAAAAAGCAAAATT
Found at i:1286 original size:31 final size:32
Alignment explanation
Indices: 1250--1322 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
1240 TTAGTAATGG
* *
1250 CAATTTAGAAA-TATGTTTTTAAAA-AAGGGTA
1 CAATTT-GAAAGTATGTTTTAAAAATAAAGGTA
1281 CAATTTGAAAGTATGTTTTAAAAATAAAGGTA
1 CAATTTGAAAGTATGTTTTAAAAATAAAGGTA
*
1313 CAATTGGAAA
1 CAATTTGAAA
1323 ACATAAAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.11
31 18 0.49
32 15 0.41
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (32 bp):
CAATTTGAAAGTATGTTTTAAAAATAAAGGTA
Found at i:1461 original size:31 final size:31
Alignment explanation
Indices: 1426--1491 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
1416 TGGCGATTTA
* *
1426 GAAATATTTTTTTTAAAA-AAGGGTACAATTG
1 GAAATA-TGTTTTAAAAATAAGGGTACAATTG
1457 GAAATATGTTTTAAAAATAAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
1488 GAAA
1 GAAA
1492 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 9 0.28
31 23 0.72
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.33
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:1467 original size:169 final size:169
Alignment explanation
Indices: 1183--1515 Score: 589
Period size: 169 Copynumber: 2.0 Consensus size: 169
1173 TATAATCTAA
1183 TAATTAATAATGGAATAATTTATGATTAAAAAAACAATGGAATAATTAAAATATTATTTAGTAAT
1 TAATTAATAATGGAATAATTTATGATTAAAAAAACAATGGAATAATTAAAATATTATTTAGTAAT
*
1248 GGCAATTTAGAAATATGTTTTTAAAAAAGGGTACAATTTGAAAGTATGTTTTAAAAATAAAGGTA
66 GGCAATTTAGAAATATGTTTTTAAAAAAGGGTACAATTGGAAAGTATGTTTTAAAAATAAAGGTA
1313 CAATTGGAAAACATAAAGTTTCCCCTTATTCGTAATACT
131 CAATTGGAAAACATAAAGTTTCCCCTTATTCGTAATACT
1352 TAATTAATAATGGAATAATTTATGATT-AAAAAACTAATGGAATAATTAAAATATTATTTAGTAA
1 TAATTAATAATGGAATAATTTATGATTAAAAAAAC-AATGGAATAATTAAAATATTATTTAGTAA
* * *
1416 TGGCGATTTAGAAATATTTTTTTTAAAAAAGGGTACAATTGGAAA-TATGTTTTAAAAATAAGGG
65 TGGCAATTTAGAAATA-TGTTTTTAAAAAAGGGTACAATTGGAAAGTATGTTTTAAAAATAAAGG
*
1480 TACAATTGGAAAACATAAAGTTTCTCCTTATTCGTA
129 TACAATTGGAAAACATAAAGTTTCCCCTTATTCGTA
1516 CTTTTATATA
Statistics
Matches: 157, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
168 7 0.04
169 124 0.79
170 26 0.17
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.36
Consensus pattern (169 bp):
TAATTAATAATGGAATAATTTATGATTAAAAAAACAATGGAATAATTAAAATATTATTTAGTAAT
GGCAATTTAGAAATATGTTTTTAAAAAAGGGTACAATTGGAAAGTATGTTTTAAAAATAAAGGTA
CAATTGGAAAACATAAAGTTTCCCCTTATTCGTAATACT
Found at i:3461 original size:27 final size:27
Alignment explanation
Indices: 3416--3497 Score: 119
Period size: 27 Copynumber: 3.0 Consensus size: 27
3406 GATCACATAT
* * *
3416 CTACAAGGGTGTGACGAACTTCTCCAC
1 CTACAAGGGTGTGAAGAACGTCACCAC
* *
3443 CTCCAAGGGTGTGAAGAACGTCCCCAC
1 CTACAAGGGTGTGAAGAACGTCACCAC
3470 CTACAAGGGTGTGAAGAACGTCACCAC
1 CTACAAGGGTGTGAAGAACGTCACCAC
3497 C
1 C
3498 CTCACGCTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.28, C:0.30, G:0.24, T:0.17
Consensus pattern (27 bp):
CTACAAGGGTGTGAAGAACGTCACCAC
Found at i:4389 original size:103 final size:103
Alignment explanation
Indices: 4210--4415 Score: 376
Period size: 103 Copynumber: 2.0 Consensus size: 103
4200 AAAAATAAGT
*
4210 CAACGTCCAGGACTCCTCTGGGAGAACGACGCCTCCATATTCTAAGGAGCGTGCGACGACCAGGA
1 CAACGTCCAGGACTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGCGTGCGACGACCAGGA
*
4275 CTCCTCCGGGAGAACGTCTCGTATACACTTGTATGGAC
66 CTCCTCCGGGAGAACGTCTCGTATACACTTGGATGGAC
*
4313 CAACGTCCAGGACTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGCGTGCGATGACCAGGA
1 CAACGTCCAGGACTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGCGTGCGACGACCAGGA
*
4378 CTCCTCCGGGAGAACGTCTCGTATACGCTTGGATGGAC
66 CTCCTCCGGGAGAACGTCTCGTATACACTTGGATGGAC
4416 GAGTCTCATT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.19
Consensus pattern (103 bp):
CAACGTCCAGGACTCCTCCGGGAGAACGACGCCTCCATATTCTAAGGAGCGTGCGACGACCAGGA
CTCCTCCGGGAGAACGTCTCGTATACACTTGGATGGAC
Found at i:4572 original size:54 final size:54
Alignment explanation
Indices: 4490--4598 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
4480 AAGAAAGTAT
* * *
4490 GCAAGTATGACGATCACCCAAACGAAGATGATAAAAAAGATGAAATTGAAGTTG
1 GCAAGCATGACGATCACCCAAACGAAGATCATAAAAAAGATGAAATTGAAATTG
* * * **
4544 GCAAGCATGACGATCACCTAAATGAAGATCATAGATGAGATGAAATTGAAATTG
1 GCAAGCATGACGATCACCCAAACGAAGATCATAAAAAAGATGAAATTGAAATTG
4598 G
1 G
4599 TAAGATTATC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.20
Consensus pattern (54 bp):
GCAAGCATGACGATCACCCAAACGAAGATCATAAAAAAGATGAAATTGAAATTG
Found at i:4708 original size:96 final size:96
Alignment explanation
Indices: 4567--4771 Score: 383
Period size: 96 Copynumber: 2.1 Consensus size: 96
4557 TCACCTAAAT
**
4567 GAAGATCATAGATGAGATGAAATTGAAATTGGTAAGATTATCTCCCAAACGTAGACCACAGAAGA
1 GAAGATCATAGATGAGACAAAATTGAAATTGGTAAGATTATCTCCCAAACGTAGACCACAGAAGA
*
4632 GATGAAATGCAAGTATGATGACCATCTAAGC
66 GATGAAATCCAAGTATGATGACCATCTAAGC
4663 GAAGATCATAGATGAGACAAAATTGAAATTGGTAAGATTATCTCCCAAACGTAGACCACAGAAGA
1 GAAGATCATAGATGAGACAAAATTGAAATTGGTAAGATTATCTCCCAAACGTAGACCACAGAAGA
4728 GATGAAATCCAAGTATGATGACCATCTAAGC
66 GATGAAATCCAAGTATGATGACCATCTAAGC
4759 GAAGATCATAGAT
1 GAAGATCATAGAT
4772 ACTAAATCTA
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 106 1.00
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (96 bp):
GAAGATCATAGATGAGACAAAATTGAAATTGGTAAGATTATCTCCCAAACGTAGACCACAGAAGA
GATGAAATCCAAGTATGATGACCATCTAAGC
Found at i:5001 original size:75 final size:76
Alignment explanation
Indices: 4885--5397 Score: 482
Period size: 75 Copynumber: 6.8 Consensus size: 76
4875 TCTCTTACAT
* *
4885 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
1 GAAGGATGATCTTCCCTATGAAGAACAACCAATCTCTCATATAATAAATTCATGAAGATCGTCGG
*
4950 TCCCCGCATGAA
66 TCCCCACATG-A
* * ** * * *
4962 GAAGGATGGTC-TCACTATGAAGAAC-GTCAATATGC-CATATCAA-AAATTAATGAAGATCGTT
1 GAAGGATGATCTTCCCTATGAAGAACAACCAATCT-CTCATAT-AATAAATTCATGAAGATCGTC
*
5023 GGTCTCCTACATGA
64 GGTC-CCCACATGA
* *
5037 -AA-GATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
1 GAAGGATGATCTTCCCTATGAAGAACAACCAATCTCTCATATAATAAATTCATGAAGATCGTCGG
*
5100 TCCCCGCATGAA
66 TCCCCACATG-A
* * * ** * * *
5112 GAAGGATGGTCGT-ACTATGAAGAAC-GTCAATCTCCCATATCAA-AAATTAATGAAGATCGTTG
1 GAAGGATGATCTTCCCTATGAAGAACAACCAATCTCTCATAT-AATAAATTCATGAAGATCGTCG
* **
5174 GTGTCTTACAT--
65 GT-CCCCACATGA
* * * *
5185 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATCATAAATTAATGAAGATCTTCGG
1 GAAGGATGATCTTCCCTATGAAGAACAACCAATCTCTCATATAATAAATTCATGAAGATCGTCGG
*
5250 TCTCCTACAT--
66 TC-CCCACATGA
* *
5260 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCGTATAATAAATTCATGAAGATCGTCGG
1 GAAGGATGATCTTCCCTATGAAGAACAACCAATCTCTCATATAATAAATTCATGAAGATCGTCGG
*
5325 T-CCCGCATGAA
66 TCCCCACATG-A
* * ** * *
5336 GAAGGATGGTC-TCTCTATGAAGAAC-GTCAATCTCCCATATTATAAATTCATGAAGATCGTCG
1 GAAGGATGATCTTCCCTATGAAGAACAACCAATCTCTCATATAATAAATTCATGAAGATCGTCG
5398 TCTTATAAAA
Statistics
Matches: 355, Mismatches: 62, Indels: 41
0.78 0.14 0.09
Matches are distributed among these distances:
73 22 0.06
74 67 0.19
75 198 0.56
76 51 0.14
77 17 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (76 bp):
GAAGGATGATCTTCCCTATGAAGAACAACCAATCTCTCATATAATAAATTCATGAAGATCGTCGG
TCCCCACATGA
Found at i:5068 original size:150 final size:150
Alignment explanation
Indices: 4861--5251 Score: 660
Period size: 150 Copynumber: 2.6 Consensus size: 150
4851 TCAATCTACC
*
4861 ATGAAGATC-TTCAGTCTCTTACATGAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCAT
1 ATGAAGATCGTT-GGTCTCTTACATGAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCAT
4925 ATAATAAATTCATGAAGACCGTCGGTCCCCGCATGAAGAAGGATGGTC-TCACTATGAAGAACGT
65 ATAATAAATTCATGAAGACCGTCGGTCCCCGCATGAAGAAGGATGGTCGT-ACTATGAAGAACGT
*
4989 CAATATGCCATATCAAAAATTA
129 CAATATCCCATATCAAAAATTA
* *
5011 ATGAAGATCGTTGGTCTCCTACATGAAAGATGATCTTCCCTATGAAGAACAACCGATCTCTCATA
1 ATGAAGATCGTTGGTCTCTTACATGAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATA
5076 TAATAAATTCATGAAGACCGTCGGTCCCCGCATGAAGAAGGATGGTCGTACTATGAAGAACGTCA
66 TAATAAATTCATGAAGACCGTCGGTCCCCGCATGAAGAAGGATGGTCGTACTATGAAGAACGTCA
*
5141 ATCTCCCATATCAAAAATTA
131 ATATCCCATATCAAAAATTA
*
5161 ATGAAGATCGTTGGTGTCTTACATGAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATA
1 ATGAAGATCGTTGGTCTCTTACATGAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATA
* * * *
5226 TCATAAATTAATGAAGATCTTCGGTC
66 TAATAAATTCATGAAGACCGTCGGTC
5252 TCCTACATGA
Statistics
Matches: 227, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
150 224 0.99
151 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (150 bp):
ATGAAGATCGTTGGTCTCTTACATGAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATA
TAATAAATTCATGAAGACCGTCGGTCCCCGCATGAAGAAGGATGGTCGTACTATGAAGAACGTCA
ATATCCCATATCAAAAATTA
Found at i:5354 original size:150 final size:148
Alignment explanation
Indices: 4885--5397 Score: 571
Period size: 150 Copynumber: 3.4 Consensus size: 148
4875 TCTCTTACAT
4885 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
1 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
*
4950 TCCCCGCATGAAGAAGGATGGTCTCACTATGAAGAACGTCAATATGCCATATCAAAAATTAATGA
66 TCCCCGCAT--AGAAGGATGGTCTCACTATGAAGAACGTCAATCT-CCATATCAAAAATTAATGA
5015 AGATCGTTGGTCTCCTACATG-A
128 AGATCGTTGGTC-CC-ACATGAA
5037 -AA-GATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
1 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
5100 TCCCCGCATGAAGAAGGATGGTCGT-ACTATGAAGAACGTCAATCTCCCATATCAAAAATTAATG
66 TCCCCGCAT--AGAAGGATGGTC-TCACTATGAAGAACGTCAATCT-CCATATCAAAAATTAATG
**
5164 AAGATCGTTGGTGTCTTACAT---
127 AAGATCGTT-G-GTCCCACATGAA
* * * *
5185 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATCATAAATTAATGAAGATCTTCGG
1 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
** * * ** * * *
5250 TCTCCTACAT-GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCGTAT-AATAAATTCAT
66 TC-CCCGCATAGAAGGATGGTC-TCACTATGAAGAAC-GTCAATCTC-CATATCAA-AAATTAAT
* *
5313 GAAGATCGTCGGTCCCGCATGAA
126 GAAGATCGTTGGTCCCACATGAA
* * ** * * * *
5336 GAAGGATGGTC-TCTCTATGAAGAAC-GTCAATCTCCCATATTATAAATTCATGAAGATCGTCG
1 GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCG
5398 TCTTATAAAA
Statistics
Matches: 317, Mismatches: 31, Indels: 29
0.84 0.08 0.08
Matches are distributed among these distances:
148 17 0.05
149 47 0.15
150 231 0.73
151 19 0.06
152 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (148 bp):
GAAGGATGATCTTCCCTATGAAGAACAACCGATCTCTCATATAATAAATTCATGAAGACCGTCGG
TCCCCGCATAGAAGGATGGTCTCACTATGAAGAACGTCAATCTCCATATCAAAAATTAATGAAGA
TCGTTGGTCCCACATGAA
Found at i:5484 original size:68 final size:68
Alignment explanation
Indices: 5405--5623 Score: 307
Period size: 68 Copynumber: 3.2 Consensus size: 68
5395 TCGTCTTATA
* * *
5405 AAAAATCAAACGATCTATGCATCGCAATTTCAAATAAGATGAACGTCTCCTTTGAGACCGTTTTA
1 AAAAATCAAACGATCCATGCATCGAAATTTCAAATAAGACGAACGTCTCCTTTGAGACCGTTTTA
5470 TCC
66 TCC
* * * * *
5473 AAAAATCAAACGATCCATGAATCAAAATTTCAAATAAGACGAACGTGTCCCTTGAGACCGTCTTA
1 AAAAATCAAACGATCCATGCATCGAAATTTCAAATAAGACGAACGTCTCCTTTGAGACCGTTTTA
*
5538 TCTA
66 TC-C
* *
5542 AAAAATCAAACGATCCATGCATCGTAATTTCAAATAAGACGAACGTCTCCTTTGAGACCGTTCTA
1 AAAAATCAAACGATCCATGCATCGAAATTTCAAATAAGACGAACGTCTCCTTTGAGACCGTTTTA
5607 -CC
66 TCC
5609 AAAAAAT-AAACGATC
1 -AAAAATCAAACGATC
5624 GCTCCAATAA
Statistics
Matches: 132, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
67 8 0.06
68 66 0.50
69 58 0.44
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (68 bp):
AAAAATCAAACGATCCATGCATCGAAATTTCAAATAAGACGAACGTCTCCTTTGAGACCGTTTTA
TCC
Found at i:6485 original size:27 final size:27
Alignment explanation
Indices: 6447--6530 Score: 98
Period size: 27 Copynumber: 3.1 Consensus size: 27
6437 TTGATCACAT
* *
6447 ACCTACAAGGGTGTGATGAACTTCGCC
1 ACCTACAAGGGTGTGAAGAACTTCACC
* * *
6474 ACCTCCAGGGGTGTGAAGAA-TGTCCCC
1 ACCTACAAGGGTGTGAAGAACT-TCACC
*
6501 ACCTACAAGGGTGTGAAGAACGTCACC
1 ACCTACAAGGGTGTGAAGAACTTCACC
6528 ACC
1 ACC
6531 CTCACGCTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (27 bp):
ACCTACAAGGGTGTGAAGAACTTCACC
Found at i:7829 original size:15 final size:16
Alignment explanation
Indices: 7809--7867 Score: 93
Period size: 15 Copynumber: 3.7 Consensus size: 16
7799 TTCATGCGGG
7809 TTCGGGTTCGGGTA-T
1 TTCGGGTTCGGGTATT
7824 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
*
7840 TTTGGGTTCGGGTATTT
1 TTCGGGTTCGGGTA-TT
7857 TTCGGGTTCGG
1 TTCGGGTTCGG
7868 ATCGGGTTCG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.35
16 14 0.35
17 12 0.30
ACGTcount: A:0.05, C:0.12, G:0.39, T:0.44
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:7848 original size:16 final size:16
Alignment explanation
Indices: 7812--7867 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
7802 ATGCGGGTTC
*
7812 GGGTTCGGGTA-TTTC
1 GGGTTCGGGTATTTTT
7827 GGGTTCGGGTATTTTT
1 GGGTTCGGGTATTTTT
7843 GGGTTCGGGTATTTTT
1 GGGTTCGGGTATTTTT
7859 CGGGTTCGG
1 -GGGTTCGG
7868 ATCGGGTTCG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
15 11 0.29
16 19 0.50
17 8 0.21
ACGTcount: A:0.05, C:0.11, G:0.41, T:0.43
Consensus pattern (16 bp):
GGGTTCGGGTATTTTT
Found at i:9699 original size:27 final size:27
Alignment explanation
Indices: 9669--9722 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
9659 AATTATTTTA
9669 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
9696 AGAAAATTCAGTTAAGAAATGAAATTT
1 AGAAAATTCAGTTAAGAAATGAAATTT
9723 TGTTGTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.30
Consensus pattern (27 bp):
AGAAAATTCAGTTAAGAAATGAAATTT
Found at i:9715 original size:13 final size:14
Alignment explanation
Indices: 9666--9714 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
9656 ATAAATTATT
9666 TTAAGAAAATTCAG
1 TTAAGAAAATTCAG
** *
9680 TTAAG-AAATGAAA
1 TTAAGAAAATTCAG
*
9693 TTTAGAAAATTCAG
1 TTAAGAAAATTCAG
9707 TTAAGAAA
1 TTAAGAAA
9715 TGAAATTTTG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (14 bp):
TTAAGAAAATTCAG
Found at i:10041 original size:11 final size:11
Alignment explanation
Indices: 10027--10064 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
10017 ATTCATAACA
10027 AATTTATAATT
1 AATTTATAATT
10038 AATTTATAATT
1 AATTTATAATT
10049 -ATTTGATAATT
1 AATTT-ATAATT
*
10060 TATTT
1 AATTT
10065 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:15425 original size:3 final size:3
Alignment explanation
Indices: 15419--15479 Score: 50
Period size: 3 Copynumber: 20.3 Consensus size: 3
15409 ACCACCACCA
* * * * * * *
15419 CCT CCT CCT CCT CCT CCT CCC CCG CCT CCA CCT CCA CCT CCC CCA CCC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT
*
15467 CCT CCA CCT CCT C
1 CCT CCT CCT CCT C
15480 AACTACTTTC
Statistics
Matches: 45, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.07, C:0.72, G:0.02, T:0.20
Consensus pattern (3 bp):
CCT
Found at i:15431 original size:9 final size:9
Alignment explanation
Indices: 15416--15479 Score: 56
Period size: 9 Copynumber: 7.1 Consensus size: 9
15406 ACCACCACCA
15416 CCACCTCCT
1 CCACCTCCT
*
15425 CCTCCTCCT
1 CCACCTCCT
* * *
15434 CCTCCCCCG
1 CCACCTCCT
* *
15443 CCTCCACCT
1 CCACCTCCT
*
15452 CCACCTCCC
1 CCACCTCCT
*
15461 CCACCCCCT
1 CCACCTCCT
15470 CCACCTCCT
1 CCACCTCCT
15479 C
1 C
15480 AACTACTTTC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 44 1.00
ACGTcount: A:0.08, C:0.72, G:0.02, T:0.19
Consensus pattern (9 bp):
CCACCTCCT
Found at i:15452 original size:21 final size:21
Alignment explanation
Indices: 15404--15477 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 21
15394 TGGATCCCCA
* * * *
15404 CCACCACCACCACCACCTCCT
1 CCACCTCCACCTCCCCCGCCT
* *
15425 CCTCCTCCTCCTCCCCCGCCT
1 CCACCTCCACCTCCCCCGCCT
*
15446 CCACCTCCACCTCCCCC-AC-
1 CCACCTCCACCTCCCCCGCCT
15465 CC-CCTCCACCTCC
1 CCACCTCCACCTCC
15478 TCAACTACTT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
18 11 0.25
19 2 0.05
20 1 0.02
21 30 0.68
ACGTcount: A:0.12, C:0.72, G:0.01, T:0.15
Consensus pattern (21 bp):
CCACCTCCACCTCCCCCGCCT
Found at i:19535 original size:20 final size:20
Alignment explanation
Indices: 19494--19531 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19484 ATAAATATGC
*
19494 TTATCATTTGTTTCATAATA
1 TTATCATTTGTTACATAATA
*
19514 TTATTATTTGTTAC-TAAT
1 TTATCATTTGTTACATAAT
19532 TATTCATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.29, C:0.08, G:0.05, T:0.58
Consensus pattern (20 bp):
TTATCATTTGTTACATAATA
Found at i:20025 original size:12 final size:12
Alignment explanation
Indices: 20008--20033 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19998 TATAAGAAAC
20008 AATAATAATAGA
1 AATAATAATAGA
20020 AATAATAATAGA
1 AATAATAATAGA
20032 AA
1 AA
20034 GTGAAATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (12 bp):
AATAATAATAGA
Found at i:20217 original size:61 final size:61
Alignment explanation
Indices: 20142--20266 Score: 234
Period size: 61 Copynumber: 2.0 Consensus size: 61
20132 AAACAATAAT
20142 AATAGAAAGTGAAATTACCTAAAAACCAAT-TCAACCTTAACTTCTCATGAATTGAAGAACA
1 AATAGAAAGTGAAATTACCTAAAAACCAATCT-AACCTTAACTTCTCATGAATTGAAGAACA
20203 AATAGAAAGTGAAATTACCTAAAAACCAATCTAACCTTAACTTCTCATGAATTGAAGAACA
1 AATAGAAAGTGAAATTACCTAAAAACCAATCTAACCTTAACTTCTCATGAATTGAAGAACA
20264 AAT
1 AAT
20267 GAAGAGGGGT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 62 0.98
62 1 0.02
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.25
Consensus pattern (61 bp):
AATAGAAAGTGAAATTACCTAAAAACCAATCTAACCTTAACTTCTCATGAATTGAAGAACA
Found at i:21412 original size:438 final size:436
Alignment explanation
Indices: 20522--21524 Score: 1193
Period size: 439 Copynumber: 2.3 Consensus size: 436
20512 TATCTGTCTG
* ** * * *
20522 ATTAAGGTGATTCAAGTGTATGCTAAAAGGTAATTTCATGATCTACAATTTTCATGAAGAACTCA
1 ATTAAGGTGATTC-AGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTAA
* * * * *
20587 AAAGCCAATTTTAATGTTTTGATTCTAAAAAATGCTTTCGAAATTTTGTGGTTTTGATTGCCGGT
65 AAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTTCTAAATTTTGT-GTTTCGATTGCCGGT
*** * * * * *
20652 CAATTTAATATTGTATAATTTTTTGTTCACATGTCCTATTGAAGTTATTGAAGTGTCAGGTAAAA
129 CAATTTAATACCATATAATTTTTCGTCCACATGTCCGATTAAAGTTATTCAAGTGTCAGGTAAAA
* * * *
20717 GGTTATTGCATGATTTACGACTTTCATGAAGGATCCGAAAACTAAATTTGATCTACGAGTTTCAT
194 GGTTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCAT
* * *
20782 GAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATCTCTATTAACAAACATTTTCTTATTTGGAT
259 GAAGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACATTTTCTTATTTGAAT
* ** * *
20847 TATTTATCAAATGATTCTCATATTTTTCTACTTTATACTACTTAATTCTTTACAAATTCTATCTT
324 TAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAAGTCTTTACAAATTCTATCTT
* *
20912 AATCTAATGTTTAAGATTTATTTTTTTTATTCTTTGTTTTATTTGTCAA
389 AATCT-ATGTTTAAGATTTATTTTTTTTATTATTTGTTATATTTGTCAA
* *
20961 ATTAAGTTGATTCATGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTTA
1 ATTAAGGTGATTCA-GTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTAA
* * **
21026 AAAGCAAATTTTTAGGTTTTAATTCAAAAAAATGCTTTCTAAATTTTGTCGTTTCGATTGTTGGT
65 AAAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTTCTAAATTTTGT-GTTTCGATTGCCGGT
** *
21091 TTATTTAATACCATATAA-TTTTCGATCCACATGTCCGATTAAAGTTATTCAAGTGTC-GATTAA
129 CAATTTAATACCATATAATTTTTCG-TCCACATGTCCGATTAAAGTTATTCAAGTGTCAG-GTAA
* * * * *
21154 AAGGTTACTGTATGATCTATGACTTTCTTGAAGAACCCG-AAAGTTAATTTGATCTACGAGTTTC
192 AAGGTTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTC
* *
21218 ATGAAGGGTTCAAAAGCGGAA-TTTTATGTTTCAAGATATCCATT-ACGAAATATTTTCTTATTT
257 ATGAAGGGTTCAAAAG-GGAATTTTTATGCTTCAAGATATCCATTAAC-AAACATTTTCTTATTT
*
21281 GAATTAGTTATCAAATGACCCTCATACTTTTCTATTTTATACTACTT-AGTCATTTACAAATTCT
320 GAATTAGTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAAGTC-TTTACAAATTCT
* *
21345 ATCTT-AT-T-TGATTTAACG-CTTATTTTTTTTTATTTTATTTGTTATATTTGTCCA
384 ATCTTAATCTATG-TTTAA-GATTTA-TTTTTTTTA--TTATTTGTTATATTTGTCAA
* ** * *
21399 ATTAAGGTGATTCAGATATCTATTAAAAGGTAATTTTGTGATTTACAACTTTCATGAAAAGACTA
1 ATTAAGGTGATTCAG-TGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATG-AAGGACTA
* * * *
21464 AAAAGCTAATTTTCATGTTTCAATTCCAAAAAAA-ACTTT-TGAAATTTTGTGATTTCGATTG
64 AAAAGCAAATTTTAATGTTTTAATT-CAAAAAAATGCTTTCT-AAATTTTGTG-TTTCGATTG
21525 ATAATATATA
Statistics
Matches: 484, Mismatches: 64, Indels: 32
0.83 0.11 0.06
Matches are distributed among these distances:
434 2 0.00
435 8 0.02
436 11 0.02
437 8 0.02
438 207 0.43
439 240 0.50
440 8 0.02
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (436 bp):
ATTAAGGTGATTCAGTGTCTATTAAAAGGTAATTTCATGATCTACAACTTTCATGAAGGACTAAA
AAGCAAATTTTAATGTTTTAATTCAAAAAAATGCTTTCTAAATTTTGTGTTTCGATTGCCGGTCA
ATTTAATACCATATAATTTTTCGTCCACATGTCCGATTAAAGTTATTCAAGTGTCAGGTAAAAGG
TTACTGCATGATCTACGACTTTCATGAAGAACCCGAAAACTAAATTTGATCTACGAGTTTCATGA
AGGGTTCAAAAGGGAATTTTTATGCTTCAAGATATCCATTAACAAACATTTTCTTATTTGAATTA
GTTATCAAATGACCCTCATACTTTTCTACTTTATACTACTTAAGTCTTTACAAATTCTATCTTAA
TCTATGTTTAAGATTTATTTTTTTTATTATTTGTTATATTTGTCAA
Found at i:21927 original size:15 final size:16
Alignment explanation
Indices: 21901--21974 Score: 75
Period size: 15 Copynumber: 4.7 Consensus size: 16
21891 CTCTTGTGTA
21901 ATAATAATAATATATAT
1 ATAAT-ATAATATATAT
* *
21918 AT-ATATAATATGTAGC
1 ATAATATAATATATA-T
21934 A-AA-ATAATAATATAT
1 ATAATATAAT-ATATAT
21949 ATAATATAATATA-AT
1 ATAATATAATATATAT
21964 ATAATATAATA
1 ATAATATAATA
21975 ACAATTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
15 28 0.58
16 13 0.27
17 7 0.15
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (16 bp):
ATAATATAATATATAT
Found at i:21957 original size:5 final size:5
Alignment explanation
Indices: 21940--21974 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
21930 TAGCAAAATA
21940 ATAAT AT-AT ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
21975 ACAATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:21967 original size:27 final size:27
Alignment explanation
Indices: 21901--21969 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
21891 CTCTTGTGTA
21901 ATAATAATAATAT-AT-ATATATATAAT
1 ATAAT-ATAATATAATAATATATATAAT
* * *
21927 AT-GTAGCAAAATAATAATATATATAAT
1 ATAATA-TAATATAATAATATATATAAT
21954 ATAATATAATATAATA
1 ATAATATAATATAATA
21970 TAATAACAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
24 1 0.03
25 5 0.15
26 4 0.12
27 21 0.64
28 2 0.06
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (27 bp):
ATAATATAATATAATAATATATATAAT
Found at i:27785 original size:20 final size:21
Alignment explanation
Indices: 27750--27795 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
27740 AAATATTATA
27750 TTTATCCTATAATGGGTAGTT
1 TTTATCCTATAATGGGTAGTT
*
27771 TTTATCTTA-AATGGGTAGTT
1 TTTATCCTATAATGGGTAGTT
27791 TTTAT
1 TTTAT
27796 TTTATTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.24, C:0.07, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTATCCTATAATGGGTAGTT
Found at i:27962 original size:19 final size:20
Alignment explanation
Indices: 27940--27986 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
27930 ACAGGTAGGT
27940 TTTTTTTTTA-AATGAGTAG
1 TTTTTTTTTATAATGAGTAG
* * *
27959 -TTTTATTTATGATGGGTAG
1 TTTTTTTTTATAATGAGTAG
27978 TTTTTTTTT
1 TTTTTTTTT
27987 TATTATGAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
18 8 0.36
19 7 0.32
20 7 0.32
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (20 bp):
TTTTTTTTTATAATGAGTAG
Found at i:31683 original size:24 final size:24
Alignment explanation
Indices: 31651--31699 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
31641 TGTAGAAAGT
31651 GAAGAAGAAGAAGAAGACTATTCC
1 GAAGAAGAAGAAGAAGACTATTCC
31675 GAAGAAGAAGAAGAAGACTATTCC
1 GAAGAAGAAGAAGAAGACTATTCC
31699 G
1 G
31700 TTTCCTGGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.49, C:0.12, G:0.27, T:0.12
Consensus pattern (24 bp):
GAAGAAGAAGAAGAAGACTATTCC
Found at i:37609 original size:35 final size:35
Alignment explanation
Indices: 37563--37634 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
37553 ACTCTTAGTT
37563 TCAGTCTACCCAGACCATGAGGTCTTGGGTTCAAC
1 TCAGTCTACCCAGACCATGAGGTCTTGGGTTCAAC
37598 TCAGTCTACCCAGACCATGAGGTCTTGGGTTCAAC
1 TCAGTCTACCCAGACCATGAGGTCTTGGGTTCAAC
37633 TC
1 TC
37635 TCACGGAATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (35 bp):
TCAGTCTACCCAGACCATGAGGTCTTGGGTTCAAC
Found at i:37841 original size:35 final size:35
Alignment explanation
Indices: 37795--37867 Score: 137
Period size: 35 Copynumber: 2.1 Consensus size: 35
37785 AGGGGTTTGT
*
37795 GGCTCATAGATTAGCTAATCATATAGCGGTGTATG
1 GGCTCATAGATTAGCTAATCATATAGCGGTGTACG
37830 GGCTCATAGATTAGCTAATCATATAGCGGTGTACG
1 GGCTCATAGATTAGCTAATCATATAGCGGTGTACG
37865 GGC
1 GGC
37868 GGTGTACGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (35 bp):
GGCTCATAGATTAGCTAATCATATAGCGGTGTACG
Done.