Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021334.1 Corchorus olitorius cultivar O-4 contig21367, 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: 55778
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1379 original size:42 final size:41
Alignment explanation
Indices: 1312--1500 Score: 229
Period size: 41 Copynumber: 4.6 Consensus size: 41
1302 AAATAGTAAG
* *
1312 TATTAACCTCAATCAAGGATG-AAATCGAACCAATTAAAAAGA
1 TATTAACATCAATCAGGGA-GCAAATCGAACCAATT-AAAAGA
* * *
1354 TAATAACCTCAATTAGGGAGCAAATCGAACCAATTAAAAGA
1 TATTAACATCAATCAGGGAGCAAATCGAACCAATTAAAAGA
* *
1395 TATTAACATCAATCAGGGGGCAAATCAAACCAATTAAAAGA
1 TATTAACATCAATCAGGGAGCAAATCGAACCAATTAAAAGA
* *
1436 TATTAACATCAATCA-GGAGTAAATCGAATCAATTAAAAGA
1 TATTAACATCAATCAGGGAGCAAATCGAACCAATTAAAAGA
* * * *
1476 CATCAACATCAACCAAGGAGCAAAT
1 TATTAACATCAATCAGGGAGCAAAT
1501 TGAAGAAGAA
Statistics
Matches: 129, Mismatches: 16, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
40 33 0.26
41 66 0.51
42 30 0.23
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.20
Consensus pattern (41 bp):
TATTAACATCAATCAGGGAGCAAATCGAACCAATTAAAAGA
Found at i:1384 original size:83 final size:81
Alignment explanation
Indices: 1291--1500 Score: 210
Period size: 81 Copynumber: 2.6 Consensus size: 81
1281 TTTCAAGAGT
* * * * *
1291 CAAATTGAACCAAATAGTAAG-TATTAACCTCAATCAAGGATG-AAATCGAACCAATTAAAAAGA
1 CAAATCGAACCAAATA-AAAGATATTAACATCAATC-AGGAGGCAAATCAAACCAATT-AAAAGA
* *
1354 TAATAACCTCAATTAGGGAG
63 TAATAACATCAATCA-GGAG
* * *
1374 CAAATCGAACCAATTAAAAGATATTAACATCAATCAGGGGGCAAATCAAACCAATTAAAAGATAT
1 CAAATCGAACCAAATAAAAGATATTAACATCAATCAGGAGGCAAATCAAACCAATTAAAAGATAA
1439 TAACATCAATCAGGAG
66 TAACATCAATCAGGAG
* * * * * *
1455 TAAATCGAATCAATTAAAAGACATCAACATCAACCAAGGA-GCAAAT
1 CAAATCGAACCAAATAAAAGATATTAACATCAATC-AGGAGGCAAAT
1501 TGAAGAAGAA
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
81 40 0.37
82 28 0.26
83 40 0.37
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (81 bp):
CAAATCGAACCAAATAAAAGATATTAACATCAATCAGGAGGCAAATCAAACCAATTAAAAGATAA
TAACATCAATCAGGAG
Found at i:1484 original size:81 final size:83
Alignment explanation
Indices: 1333--1487 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 83
1323 ATCAAGGATG
* * * *
1333 AAATCGAACCAATTAAAAAGATAATAACCTCAATTAGGGAGCAAATCGAACCAATTAAAAGATAT
1 AAATCAAACCAATTAAAAAGATAATAACATCAATCAGGGAGCAAATCGAACCAATTAAAAGACAT
*
1398 TAACATCAATCAGGGGGC
66 CAACATCAATCAGGGGGC
* * *
1416 AAATCAAACCAATT-AAAAGATATTAACATCAATCA-GGAGTAAATCGAATCAATTAAAAGACAT
1 AAATCAAACCAATTAAAAAGATAATAACATCAATCAGGGAGCAAATCGAACCAATTAAAAGACAT
1479 CAACATCAA
66 CAACATCAA
1488 CCAAGGAGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
81 33 0.52
82 18 0.28
83 13 0.20
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (83 bp):
AAATCAAACCAATTAAAAAGATAATAACATCAATCAGGGAGCAAATCGAACCAATTAAAAGACAT
CAACATCAATCAGGGGGC
Found at i:1907 original size:194 final size:194
Alignment explanation
Indices: 1578--2165 Score: 1050
Period size: 194 Copynumber: 3.0 Consensus size: 194
1568 TATATGAAGT
*
1578 AAATGACAGATTACACATGCAATTGAGGACTAAATTGAAAAGGGTTGTAAGTTTTACCTGAATAT
1 AAATGACAAATTACACATGCAATTGAGGACTAAATTGAAAAGGGTTGTAAGTTTTACCTGAATAT
* *
1643 AAAAGGGGATTCTTCTTCTTCGCTTTCAACTCAGCCTCTTCCTCAAAACCCTAGCGCCGCCTCTG
66 AAAAGGGGATTCTTCTTCTTCGCTTTCAACTCAGCCTCTTCCTCAAAACCCTATCGCCGCCGCTG
* *
1708 TCACCAAAGGTATCCGCCGCAGATCCGGTGATTTTAATCGTCAAAACGCCTTCAAACTCCCCTG
131 TCACCAAAGGTCTCCGCCGCAGATCCGGCGATTTTAATCGTCAAAACGCCTTCAAACTCCCCTG
*
1772 AAATGACAAATTACACATGCAATTGAGGACTAAATTGAAAAGGGTTGTAAGTTCTACCTGAATAT
1 AAATGACAAATTACACATGCAATTGAGGACTAAATTGAAAAGGGTTGTAAGTTTTACCTGAATAT
*
1837 AAAAGGGGATTCTTCTTCTTCGCTTTCAACTCAGCCTCTTCCTCAAAACCCTATCGTCGCCGCTG
66 AAAAGGGGATTCTTCTTCTTCGCTTTCAACTCAGCCTCTTCCTCAAAACCCTATCGCCGCCGCTG
*
1902 TCACCAAAGGTCTCCGCCGCAGATCCAGCGATTTTAATCGTCAAAACGCCTTCAAACTCCCCTG
131 TCACCAAAGGTCTCCGCCGCAGATCCGGCGATTTTAATCGTCAAAACGCCTTCAAACTCCCCTG
*
1966 AAATGACAAATTACACATGCAATTGAGGACTAAATTGAAAAGGGTTATAAGTTTTACCTGAATAT
1 AAATGACAAATTACACATGCAATTGAGGACTAAATTGAAAAGGGTTGTAAGTTTTACCTGAATAT
*
2031 AAAAGGGGATTCTTCTTCTTCGCTTTCAACTCAACCTCTTCCTCAAAACCCTATCGCCGCCGCTG
66 AAAAGGGGATTCTTCTTCTTCGCTTTCAACTCAGCCTCTTCCTCAAAACCCTATCGCCGCCGCTG
* * * *
2096 TCACCAAAGGTCTCCGCCGCATATCCGGCGATTTTAACCGTTAAGACGCCTTCAAACTCCCCTG
131 TCACCAAAGGTCTCCGCCGCAGATCCGGCGATTTTAATCGTCAAAACGCCTTCAAACTCCCCTG
2160 AAATGA
1 AAATGA
2166 TCACCACCGT
Statistics
Matches: 377, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
194 377 1.00
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (194 bp):
AAATGACAAATTACACATGCAATTGAGGACTAAATTGAAAAGGGTTGTAAGTTTTACCTGAATAT
AAAAGGGGATTCTTCTTCTTCGCTTTCAACTCAGCCTCTTCCTCAAAACCCTATCGCCGCCGCTG
TCACCAAAGGTCTCCGCCGCAGATCCGGCGATTTTAATCGTCAAAACGCCTTCAAACTCCCCTG
Found at i:4734 original size:29 final size:29
Alignment explanation
Indices: 4692--5110 Score: 243
Period size: 29 Copynumber: 14.4 Consensus size: 29
4682 TTAAAGCATT
* *
4692 AAAAATGCCCAAAATGCCCCTGAATATGC
1 AAAAATGACCAAAATGCCCCTGAATGTGC
* *
4721 AAAAATGACCAAAATGCCCTTGGATGTGC
1 AAAAATGACCAAAATGCCCCTGAATGTGC
* * * *
4750 AAAGATTAACAAAATGCTCCTAGACA--TGC
1 AAAAATGACCAAAATGCCCCT-GA-ATGTGC
* *
4779 AAAAATGACCATAATGTCCCTGAATGTGC
1 AAAAATGACCAAAATGCCCCTGAATGTGC
* *
4808 AAAAATTGACCAAAATG-CCCTTAGATGTGT
1 AAAAA-TGACCAAAATGCCCCTGA-ATGTGC
** ** ** *
4838 AAACCTGATAAAAAT-AACCTAGGATGTGC
1 AAAAATGACCAAAATGCCCCT-GAATGTGC
* * *
4867 AAAAATGACCAGAATGCCCCTG-AGGAAGC
1 AAAAATGACCAAAATGCCCCTGAATG-TGC
*
4896 AAAAATGACCAGAATGCCCCT-AA-GTAAGC
1 AAAAATGACCAAAATGCCCCTGAATGT--GC
*
4925 AAAAATGACCAAAATGCCCTTGGAA-GTGC
1 AAAAATGACCAAAATGCCCCT-GAATGTGC
* ** * *
4954 AAATATGATAAAAATG-CCATGGGATGTGC
1 AAAAATGACCAAAATGCCCCT-GAATGTGC
* * * *
4983 AAATATGATCAAAATG-CCCTAGGATGTAC
1 AAAAATGACCAAAATGCCCCT-GAATGTGC
* * *
5012 AAAAATGACCAGAATGCCCCTG-AGGAAGC
1 AAAAATGACCAAAATGCCCCTGAATG-TGC
*
5041 AAAAAGGACCAAAATGCCCCT-AA-GTAAGC
1 AAAAATGACCAAAATGCCCCTGAATGT--GC
* * **
5070 AAAAATGACCAAAATTCCCCTGGACCTGC
1 AAAAATGACCAAAATGCCCCTGAATGTGC
*
5099 AAATATGACCAA
1 AAAAATGACCAA
5111 TTAAGAAAAA
Statistics
Matches: 305, Mismatches: 62, Indels: 46
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.00
28 14 0.05
29 257 0.84
30 27 0.09
31 6 0.02
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (29 bp):
AAAAATGACCAAAATGCCCCTGAATGTGC
Found at i:5100 original size:116 final size:115
Alignment explanation
Indices: 4895--5106 Score: 275
Period size: 116 Copynumber: 1.8 Consensus size: 115
4885 CCTGAGGAAG
* * * *
4895 CAAAAATGACCAGAATGCCCCTAAGTAAGCAAAAATGACCAAAATGCCCTTGGAAGTGCAAATAT
1 CAAAAATGACCAGAATGCCCCTAAGGAAGCAAAAAGGACCAAAATGCCCCT-GAAGTGCAAAAAT
* * **
4960 GATAAAAATGCCATGGGATGTGCAAATATGATCAAAATGCCCTAGGATGTA
65 GACAAAAATCCCATGGGACCTGCAAATATGATCAAAATGCCCTAGGATGTA
*
5011 CAAAAATGACCAGAATGCCCCTGAGGAAGCAAAAAGGACCAAAATGCCCCT-AAGTAAGCAAAAA
1 CAAAAATGACCAGAATGCCCCTAAGGAAGCAAAAAGGACCAAAATGCCCCTGAAGT--GCAAAAA
* *
5075 TGACCAAAATTCCCCT-GGACCTGCAAATATGA
64 TGA-CAAAAATCCCATGGGACCTGCAAATATGA
5107 CCAATTAAGA
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
114 4 0.05
116 70 0.85
117 8 0.10
ACGTcount: A:0.43, C:0.21, G:0.19, T:0.17
Consensus pattern (115 bp):
CAAAAATGACCAGAATGCCCCTAAGGAAGCAAAAAGGACCAAAATGCCCCTGAAGTGCAAAAATG
ACAAAAATCCCATGGGACCTGCAAATATGATCAAAATGCCCTAGGATGTA
Found at i:7325 original size:22 final size:22
Alignment explanation
Indices: 7300--7345 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
7290 TAGAATTTGA
7300 TTGTTTTTGGATTAATCTTATT
1 TTGTTTTTGGATTAATCTTATT
7322 TTGTTTTTGGATTAATCTTATT
1 TTGTTTTTGGATTAATCTTATT
7344 TT
1 TT
7346 CCCCAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.65
Consensus pattern (22 bp):
TTGTTTTTGGATTAATCTTATT
Found at i:17773 original size:15 final size:15
Alignment explanation
Indices: 17729--17777 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
17719 TGCACCGTTT
*
17729 CATTGTTGTTCACAC
1 CATTGTTGTTCGCAC
*
17744 CATTGTTATTCGCAC
1 CATTGTTGTTCGCAC
*
17759 CATTGTTGTTTGCAC
1 CATTGTTGTTCGCAC
17774 CATT
1 CATT
17778 CACCCTAGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.14, T:0.43
Consensus pattern (15 bp):
CATTGTTGTTCGCAC
Found at i:18670 original size:48 final size:47
Alignment explanation
Indices: 18595--18717 Score: 140
Period size: 48 Copynumber: 2.6 Consensus size: 47
18585 GAGCGTGCCA
* * * * *
18595 ATCAATTTTGTCCAAAAATTAATAAAAAG-TGCAATGAAAATTAAAAG
1 ATCAATTTTGTCTAAAAATTGAGAAAAAGATGCAA-CAAAAATAAAAG
18642 ATCAATTTTGTCTTAAAAATTGAGAAAAAGATGCAACAAAAATAAAAG
1 ATCAATTTTGTC-TAAAAATTGAGAAAAAGATGCAACAAAAATAAAAG
* * *
18690 TTCAATTTTGTAGTAAAAATAGAGAAAA
1 ATCAATTTTGT-CTAAAAATTGAGAAAA
18718 GGTGTAGTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
47 12 0.18
48 48 0.74
49 5 0.08
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (47 bp):
ATCAATTTTGTCTAAAAATTGAGAAAAAGATGCAACAAAAATAAAAG
Found at i:20789 original size:19 final size:18
Alignment explanation
Indices: 20765--20800 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20755 TGACGACTTA
20765 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
20784 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
20801 ATTATCTCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:21429 original size:18 final size:19
Alignment explanation
Indices: 21401--21437 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
21391 CTCTTCTTCT
21401 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
21420 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
21438 GGCTAGGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:24836 original size:14 final size:14
Alignment explanation
Indices: 24817--24843 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
24807 AATATGTAAA
24817 TAATCAAGAAAAAG
1 TAATCAAGAAAAAG
24831 TAATCAAGAAAAA
1 TAATCAAGAAAAA
24844 TAGAAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.07, G:0.11, T:0.15
Consensus pattern (14 bp):
TAATCAAGAAAAAG
Found at i:27876 original size:2 final size:2
Alignment explanation
Indices: 27871--27901 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
27861 TACTCCCCCC
27871 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 T
27902 TATTTGCTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 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):
TA
Found at i:28112 original size:4 final size:4
Alignment explanation
Indices: 28105--28147 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
28095 ATTCATACAT
* *
28105 ATAC ATAC ATA- ATATT ATAT ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATA-C ATAC ATAC ATAC ATAC ATAC ATAC ATA
28148 TATATATATA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
3 3 0.08
4 30 0.83
5 3 0.08
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (4 bp):
ATAC
Found at i:33062 original size:47 final size:47
Alignment explanation
Indices: 32993--33129 Score: 161
Period size: 47 Copynumber: 2.9 Consensus size: 47
32983 TTTTCCGCTC
* * *
32993 TGTTTGACCTCTT-GGTCCCGTTTTTTGCCTGTTTGACCTCTTGGTCA
1 TGTTTGACCT-TTCGGTCCCGTTTTCTGCCTGTTTGACCTATTCGTCA
* * *
33040 TGTTTGTCCTTTCGGTCCCGTTTTCTACCTATTTGACCTATTCGTCA
1 TGTTTGACCTTTCGGTCCCGTTTTCTGCCTGTTTGACCTATTCGTCA
* * * *
33087 TGTTTGACCTTACGATCCCGTTTTCTGCATGTTTGGCCT-TTCG
1 TGTTTGACCTTTCGGTCCCGTTTTCTGCCTGTTTGACCTATTCG
33130 ATCCCGTTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
46 6 0.08
47 70 0.92
ACGTcount: A:0.09, C:0.26, G:0.19, T:0.46
Consensus pattern (47 bp):
TGTTTGACCTTTCGGTCCCGTTTTCTGCCTGTTTGACCTATTCGTCA
Found at i:33117 original size:29 final size:29
Alignment explanation
Indices: 33085--33154 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
33075 ACCTATTCGT
*
33085 CATGTTTGACCTTACGATCCCGTTTTCTG
1 CATGTTTGACCTTACGATCCCGTTTTCTA
* *
33114 CATGTTTGGCCTTTCGATCCCGTTTTCTA
1 CATGTTTGACCTTACGATCCCGTTTTCTA
*
33143 CCTGTTTGACCT
1 CATGTTTGACCT
33155 CTTGACCCTG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.11, C:0.29, G:0.17, T:0.43
Consensus pattern (29 bp):
CATGTTTGACCTTACGATCCCGTTTTCTA
Found at i:33127 original size:76 final size:76
Alignment explanation
Indices: 33038--33188 Score: 214
Period size: 76 Copynumber: 2.0 Consensus size: 76
33028 ACCTCTTGGT
* * *
33038 CATGTTTGTCCTTTCGGTCCCGTTTTCTACCTATTTGACCTATTCG-TCATGTTTGACCTTACGA
1 CATGTTTGGCCTTTCGATCCCGTTTTCTACCTATTTGACCTATT-GACCATGTTTGACCTTACGA
33102 TCCCGTTTTCTG
65 TCCCGTTTTCTG
* * * * *
33114 CATGTTTGGCCTTTCGATCCCGTTTTCTACCTGTTTGACCTCTTGACCCTGTTTGACCTTTCGGT
1 CATGTTTGGCCTTTCGATCCCGTTTTCTACCTATTTGACCTATTGACCATGTTTGACCTTACGAT
33179 CCCGTTTTCT
66 CCCGTTTTCT
33189 TTCTTTGATC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
75 1 0.02
76 65 0.98
ACGTcount: A:0.10, C:0.29, G:0.17, T:0.44
Consensus pattern (76 bp):
CATGTTTGGCCTTTCGATCCCGTTTTCTACCTATTTGACCTATTGACCATGTTTGACCTTACGAT
CCCGTTTTCTG
Found at i:33262 original size:57 final size:57
Alignment explanation
Indices: 33164--33319 Score: 215
Period size: 57 Copynumber: 2.7 Consensus size: 57
33154 TCTTGACCCT
* * * * *
33164 GTTTGACCTTTCGGTCCCGTTTTCTTTCTTTGATCTAATGATCCCGTATTTCGGCTCC
1 GTTTG-CCTTTCGATCCTGTTTTCTTCCATTGATCTGATGATCCCGTATTTCGGCTCC
* *
33222 GTTTGCCTTTCGATCTTGTTTTCTTCCATTGATCTGATGATCCCGTATTTCGGCTCT
1 GTTTGCCTTTCGATCCTGTTTTCTTCCATTGATCTGATGATCCCGTATTTCGGCTCC
*
33279 GTTTGCCTTTCGATCCTGTTTT-TTGCCCTTGATCTGATGAT
1 GTTTGCCTTTCGATCCTGTTTTCTT-CCATTGATCTGATGAT
33320 TCCGCTCTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
56 2 0.02
57 81 0.92
58 5 0.06
ACGTcount: A:0.10, C:0.25, G:0.18, T:0.47
Consensus pattern (57 bp):
GTTTGCCTTTCGATCCTGTTTTCTTCCATTGATCTGATGATCCCGTATTTCGGCTCC
Found at i:35801 original size:11 final size:11
Alignment explanation
Indices: 35785--35818 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
35775 TAATCCTTAA
35785 TCGGGCTGGGC
1 TCGGGCTGGGC
35796 TCGGGCTGGGC
1 TCGGGCTGGGC
*
35807 TCGGGCCGGGC
1 TCGGGCTGGGC
35818 T
1 T
35819 TGGGTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.29, G:0.53, T:0.18
Consensus pattern (11 bp):
TCGGGCTGGGC
Found at i:40326 original size:16 final size:15
Alignment explanation
Indices: 40307--40382 Score: 62
Period size: 16 Copynumber: 4.8 Consensus size: 15
40297 TTTAAGGTTT
40307 GGGTTCGGGTTTTATC
1 GGGTTCGGGTTTT-TC
* *
40323 GGGTTCTAGATTTTTC
1 GGGTTC-GGGTTTTTC
* **
40339 GGGTTTGACCTTTTTC
1 GGGTTCG-GGTTTTTC
*
40355 GGGTTCGGGTTTTTTT
1 GGGTTCGGG-TTTTTC
40371 GGGTTCGGGTTT
1 GGGTTCGGGTTT
40383 GGACGGGTTC
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.06
16 39 0.83
17 5 0.11
ACGTcount: A:0.05, C:0.12, G:0.34, T:0.49
Consensus pattern (15 bp):
GGGTTCGGGTTTTTC
Found at i:42350 original size:14 final size:15
Alignment explanation
Indices: 42331--42360 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42321 AACTAGGAAA
42331 AATAAAT-AACAAGG
1 AATAAATAAACAAGG
42345 AATAAATAAACAAGG
1 AATAAATAAACAAGG
42360 A
1 A
42361 TTGGACTTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (15 bp):
AATAAATAAACAAGG
Found at i:43375 original size:22 final size:21
Alignment explanation
Indices: 43350--43962 Score: 191
Period size: 22 Copynumber: 28.3 Consensus size: 21
43340 ATTTTTTATG
43350 ACCTCCTTATGAAATTTTGATA
1 ACCTCC-TATGAAATTTTGATA
*
43372 ACCTTCCTATGAAAAATTTTAATA
1 ACC-TCCTATG--AAATTTTGATA
* * * * *
43396 ACGATACTATGGAATTTCGAGA
1 AC-CTCCTATGAAATTTTGATA
** * **
43418 ACCTTTTTAT-AATTTTTTTTTA
1 ACC-TCCTATGAA-ATTTTGATA
* *
43440 ACCTTCTTATGAAATTTTGTTA
1 ACC-TCCTATGAAATTTTGATA
* **
43462 ACCTCCCTAAGGGATTTTGA-A
1 ACCT-CCTATGAAATTTTGATA
*
43483 GACCTCACTATAAAATTTTGATA
1 -ACCTC-CTATGAAATTTTGATA
* * * *
43506 ACTTCCCAACGAAATTGTGATA
1 ACCT-CCTATGAAATTTTGATA
* * *
43528 ACCAACACTATGAGATGTTGATA
1 ACC-TC-CTATGAAATTTTGATA
* *
43551 ACCTCCATATGATATATTGATA
1 ACCTCC-TATGAAATTTTGATA
* * * * *
43573 ACCACGTTATGAAAATTTAAAA
1 ACCTC-CTATGAAATTTTGATA
43595 ACCTCCATATG-AATTGTT-AGTA
1 ACCTCC-TATGAAATT-TTGA-TA
* *
43617 A-TTACACTCTGAAATTTTGATA
1 ACCT-C-CTATGAAATTTTGATA
* * *
43639 ATCACACTATGAAATTGTGATA
1 ACCTC-CTATGAAATTTTGATA
43661 ACCTCGCTATGAAATTTTGATAA
1 ACCTC-CTATGAAATTTTGAT-A
* *
43684 ACCTCCCTATAAAATTTAGATA
1 ACCT-CCTATGAAATTTTGATA
*
43706 ACCTCCTTATGAAATCTTGATA
1 ACCTCC-TATGAAATTTTGATA
*
43728 A----CTA-CAAATTTTGATA
1 ACCTCCTATGAAATTTTGATA
**
43744 ACCTCCCTATGATTTTTTGATA
1 ACCT-CCTATGAAATTTTGATA
* * *
43766 ACCTCATTATGAAATTTAGTTA
1 ACCTC-CTATGAAATTTTGATA
* *
43788 ATCTCCCTATGAAATTTTGATCT
1 ACCT-CCTATGAAATTTTGAT-A
* ** *
43811 ACATATTCTGAAATTTTGA-A
1 ACCTCCTATGAAATTTTGATA
* * **
43831 AACTAAACTATGAAATTTTTTTA
1 ACCT--CCTATGAAATTTTGATA
*
43854 ACCTTCATATGAAATTTTGATA
1 ACC-TCCTATGAAATTTTGATA
* * *
43876 TCCTCC-CTGAAATTTTGATT
1 ACCTCCTATGAAATTTTGATA
* * *
43896 A-CTCCATAATAAAAGTTTAATA
1 ACCTCC-T-ATGAAATTTTGATA
*
43918 ACCTTCC--T--AA-TTTGGTA
1 ACC-TCCTATGAAATTTTGATA
*
43935 ACCATACTATGAAATTTTGATA
1 ACC-TCCTATGAAATTTTGATA
43957 ACCTCC
1 ACCTCC
43963 CCTGAAATAC
Statistics
Matches: 424, Mismatches: 117, Indels: 101
0.66 0.18 0.16
Matches are distributed among these distances:
16 11 0.03
17 12 0.03
18 3 0.01
19 5 0.01
20 15 0.04
21 22 0.05
22 281 0.66
23 52 0.12
24 23 0.05
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (21 bp):
ACCTCCTATGAAATTTTGATA
Found at i:43755 original size:83 final size:82
Alignment explanation
Indices: 43650--43808 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 82
43640 TCACACTATG
* * *
43650 AAATTGTGATAACCTCGCTATGAAATTTTGATAAACCTCCCTATAAAATTTAGATAACCTCCTTA
1 AAATTGTGATAACCTCCCTATGAAATTTTGAT-AACCTCACTATAAAATTTAGATAACCTCCCTA
43715 TGAAATCTTGATAACTAC
65 TGAAATCTTGATAACTAC
* ** * * * *
43733 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGAAATTTAGTTAATCTCCCTAT
1 AAATTGTGATAACCTCCCTATGAAATTTTGATAACCTCACTATAAAATTTAGATAACCTCCCTAT
*
43798 GAAATTTTGAT
66 GAAATCTTGAT
43809 CTACATATTC
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
82 37 0.57
83 28 0.43
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (82 bp):
AAATTGTGATAACCTCCCTATGAAATTTTGATAACCTCACTATAAAATTTAGATAACCTCCCTAT
GAAATCTTGATAACTAC
Found at i:44150 original size:201 final size:200
Alignment explanation
Indices: 43894--44295 Score: 718
Period size: 201 Copynumber: 2.0 Consensus size: 200
43884 GAAATTTTGA
43894 TTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATAAC
1 TTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATAAC
* * *
43959 CTCCCCTGAAATACCACTATGAAATTCTTATAAGCTCGTTATGACATTTTGGTAATCTCTTTGAT
66 CTCCCCAGAAATACCACTATGAAATTCTTATAACCTCGTTATGACATTTTGATAATCTCTTTGAT
44024 AACCTTTCTAT-AAAATTGTGAT-ACCATACTATATAATTTCAATAACCTTGCTAAGAAATTTTA
131 AACCTTTCTATAAAAATTGTGATAACC--ACTATATAATTTCAATAACCTTGCTAAGAAATTTTA
44087 ATAACAC
194 ATAACAC
44094 TTACTCCATAATAAAAGTTTAATAACCTTTCCTAATTTGGTAACCATACTATGAAATTTTGATAA
1 TTACTCCATAATAAAAGTTTAATAACC-TTCCTAATTTGGTAACCATACTATGAAATTTTGATAA
* *
44159 CCTTCCCAGAAATACCACTATGAAATTCTTATAACCTTGTTATGACATTTTGATAATCTCTTTGA
65 CCTCCCCAGAAATACCACTATGAAATTCTTATAACCTCGTTATGACATTTTGATAATCTCTTTGA
44224 TAACCTTTCTATAAAAATTGTGATAACCACTATATAATTTCAATAACCTTGCTAAGAAATTTTAA
130 TAACCTTTCTATAAAAATTGTGATAACCACTATATAATTTCAATAACCTTGCTAAGAAATTTTAA
44289 TAACAC
195 TAACAC
44295 T
1 T
44296 ATGAAATTTT
Statistics
Matches: 194, Mismatches: 5, Indels: 5
0.95 0.02 0.02
Matches are distributed among these distances:
200 27 0.14
201 153 0.79
202 11 0.06
203 3 0.02
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (200 bp):
TTACTCCATAATAAAAGTTTAATAACCTTCCTAATTTGGTAACCATACTATGAAATTTTGATAAC
CTCCCCAGAAATACCACTATGAAATTCTTATAACCTCGTTATGACATTTTGATAATCTCTTTGAT
AACCTTTCTATAAAAATTGTGATAACCACTATATAATTTCAATAACCTTGCTAAGAAATTTTAAT
AACAC
Found at i:44304 original size:41 final size:43
Alignment explanation
Indices: 44223--44314 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 43
44213 AATCTCTTTG
* *
44223 ATAACCTTTCTATAAAAATTGTGATAACCACTATATAATTTCA
1 ATAACCTTGCTATAAAAATTGTAATAACCACTATATAATTTCA
* * **
44266 ATAACCTTGCTA-AGAAATTTTAATAA-CACTATGA-AATTTTG
1 ATAACCTTGCTATAAAAATTGTAATAACCACTAT-ATAATTTCA
44307 ATAACCTT
1 ATAACCTT
44315 CCCATGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
41 19 0.45
42 12 0.29
43 11 0.26
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (43 bp):
ATAACCTTGCTATAAAAATTGTAATAACCACTATATAATTTCA
Found at i:44324 original size:22 final size:22
Alignment explanation
Indices: 44296--44391 Score: 88
Period size: 22 Copynumber: 4.4 Consensus size: 22
44286 TAATAACACT
44296 ATGAAATTTTGATAACCTTCC-C
1 ATGAAATTTTGATAA-CTTCCAC
* *
44318 ATGAAATTTCGATAACTTCCAT
1 ATGAAATTTTGATAACTTCCAC
* *
44340 ATGAAATTTTGGTAA-TTACAC
1 ATGAAATTTTGATAACTTCCAC
* * * *
44361 TATGGAATTTTGATTACGTCCTC
1 -ATGAAATTTTGATAACTTCCAC
44384 ATGAAATT
1 ATGAAATT
44392 ATAATAACCA
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
21 9 0.16
22 46 0.79
23 3 0.05
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
ATGAAATTTTGATAACTTCCAC
Found at i:44399 original size:66 final size:66
Alignment explanation
Indices: 44286--44420 Score: 159
Period size: 66 Copynumber: 2.0 Consensus size: 66
44276 TAAGAAATTT
* * *
44286 TAATAACACTATGAAATTTTGATAACCTTCCCATGAAATTTCGATAA-CTTCCATATGAAATTTT
1 TAATAACACTATGAAATTTTGATAACCGTCCCATGAAATTTCAATAACCAT-CATATGAAATTTT
44350 GG
65 GG
* * * *
44352 TAATTACACTATGGAATTTTGATTA-CGTCCTCATGAAATTAT-AATAACCATCTTATGAAATTT
1 TAATAACACTATGAAATTTTGATAACCGTCC-CATGAAATT-TCAATAACCATCATATGAAATTT
44415 TGG
64 TGG
44418 TAA
1 TAA
44421 CCACAAAGAG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
65 4 0.07
66 52 0.88
67 3 0.05
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (66 bp):
TAATAACACTATGAAATTTTGATAACCGTCCCATGAAATTTCAATAACCATCATATGAAATTTTG
G
Found at i:47743 original size:27 final size:26
Alignment explanation
Indices: 47690--47751 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
47680 CTAAATTTTC
47690 ATTATTTAATAATGAAATAATTAAAAT
1 ATTATTTAATAATGAAAT-ATTAAAAT
*
47717 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAAT-GAAATATTA-AAAT
47744 A-TATTTAA
1 ATTATTTAA
47752 GAAAAGGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 10 0.31
27 18 0.56
28 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (26 bp):
ATTATTTAATAATGAAATATTAAAAT
Found at i:48245 original size:17 final size:17
Alignment explanation
Indices: 48219--48252 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48209 GAAATGCTTC
* *
48219 TAAAAGATAATGATAAT
1 TAAAAAATAATAATAAT
48236 TAAAAAATAATAATAAT
1 TAAAAAATAATAATAAT
48253 GAAACCTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAAAAAATAATAATAAT
Found at i:50149 original size:72 final size:72
Alignment explanation
Indices: 50032--50176 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
50022 TCAGAAAACA
50032 ATATTTTCATAAAGCTATAAACAAAATATGTTCACAAGTTATTTAGCTTATGTGCAAATCTCTTG
1 ATATTTTCATAAAGCTATAAACAAAATATGTTCACAAGTTATTTAGCTTATGTGCAAATCTCTTG
50097 CTCTTCG
66 CTCTTCG
50104 ATATTTTCATAAAGCTATAAACAAAATATGTTCACAAGTTATTTAGCTTATGTGCAAATCTCTTG
1 ATATTTTCATAAAGCTATAAACAAAATATGTTCACAAGTTATTTAGCTTATGTGCAAATCTCTTG
50169 CTCTTCG
66 CTCTTCG
50176 A
1 A
50177 GTTGTATAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.39
Consensus pattern (72 bp):
ATATTTTCATAAAGCTATAAACAAAATATGTTCACAAGTTATTTAGCTTATGTGCAAATCTCTTG
CTCTTCG
Found at i:53073 original size:124 final size:125
Alignment explanation
Indices: 52910--53357 Score: 523
Period size: 124 Copynumber: 3.6 Consensus size: 125
52900 TTCTAAATAC
* * * * *
52910 AATAGCGGCGTTTCTCCTATGAA-ACGCCGCGAAATAGTGGCATTTCTAGAGTAAACGCCGCTAT
1 AATAGCGGCGTTTCTCCAATAAATACGCCGCTAAATAGTGGCGTTTCTAAAGTAAACGCCGCTAT
* *
52974 ATATAATCTTATCGAAAGAATAGAAATTTAGTGAAACTAAAAACATTATTTCTTGTTGAG
66 ATATAATCTTATCAAAAGAATAGAAATTTGGTGAAACTAAAAACATTATTTCTTGTTGAG
* *
53034 AATAGCGGCGTTTCT-CACA-AAATACGCCGCTAAATAGTGGCGTTTCTAAAGCAAACGCAGCTA
1 AATAGCGGCGTTTCTCCA-ATAAATACGCCGCTAAATAGTGGCGTTTCTAAAGTAAACGCCGCTA
* * ** * *
53097 TATATAATCTTATCCAAAGAATAGAAATTTGGCGAAACTAATAAAAACACCATTTCTTGATGGG
65 TATATAATCTTATCAAAAGAATAGAAATTTGGTGAAAC---TAAAAACATTATTTCTTGTTGAG
* * *
53161 AATAGCGGCGTTTCTCCTATGAAAT--GCC-ATGAAATAGTGGCGTTTCTAGAGTAAACGCCGCT
1 AATAGCGGCGTTTCTCCAAT-AAATACGCCGCT-AAATAGTGGCGTTTCTAAAGTAAACGCCGCT
*
53223 ATATATAATCTTATCAAAAAAATAGAAATTTGGTGAAACTAAAAACATTATTTCTTGTTGAG
64 ATATATAATCTTATCAAAAGAATAGAAATTTGGTGAAACTAAAAACATTATTTCTTGTTGAG
* * * * * * * * *
53285 AATAG-GCACATTTCTCACAAAAAAAACGCCGCTAAATAATGACGTTTCTAAAATAAACACCGCC
1 AATAGCG-GCGTTTCTC-CAATAAATACGCCGCTAAATAGTGGCGTTTCTAAAGTAAACGCCGCT
53349 ATATATAAT
64 ATATATAAT
53358 TTCTATTTTG
Statistics
Matches: 272, Mismatches: 38, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
123 4 0.01
124 120 0.44
125 2 0.01
126 38 0.14
127 103 0.38
128 1 0.00
129 4 0.01
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (125 bp):
AATAGCGGCGTTTCTCCAATAAATACGCCGCTAAATAGTGGCGTTTCTAAAGTAAACGCCGCTAT
ATATAATCTTATCAAAAGAATAGAAATTTGGTGAAACTAAAAACATTATTTCTTGTTGAG
Found at i:54304 original size:30 final size:30
Alignment explanation
Indices: 54270--54327 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
54260 CTTAGGCCGC
54270 ATTTTTATTGTGAACAGAAATACGTAGCTG
1 ATTTTTATTGTGAACAGAAATACGTAGCTG
54300 ATTTTTATTGTGAACAGAAATACGTAGC
1 ATTTTTATTGTGAACAGAAATACGTAGC
54328 AAGGAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (30 bp):
ATTTTTATTGTGAACAGAAATACGTAGCTG
Done.