Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020681.1 Corchorus olitorius cultivar O-4 contig20714, 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: 48400
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:400 original size:16 final size:16
Alignment explanation
Indices: 379--410 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
369 TTTTACATAA
379 ATTGATTCCATGTATT
1 ATTGATTCCATGTATT
395 ATTGATTCCATGTATT
1 ATTGATTCCATGTATT
411 TTTATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (16 bp):
ATTGATTCCATGTATT
Found at i:2362 original size:2 final size:2
Alignment explanation
Indices: 2355--2384 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2345 AGTTCATTGT
2355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2385 AAAATAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3139 original size:30 final size:30
Alignment explanation
Indices: 3100--3167 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 30
3090 AAGAATGAAG
3100 TGTTAAGAGTTAAGAAACAATGCAGTGGAGC
1 TGTT-AGAGTTAAGAAACAATGCAGTGGAGC
*
3131 TGTTAGAGTTAAGAAACAATGCGGTGGAGC
1 TGTTAGAGTTAAGAAACAATGCAGTGGAGC
*
3161 TGCTAGA
1 TGTTAGA
3168 ATCAAAGGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.35, C:0.10, G:0.31, T:0.24
Consensus pattern (30 bp):
TGTTAGAGTTAAGAAACAATGCAGTGGAGC
Found at i:9814 original size:16 final size:16
Alignment explanation
Indices: 9756--9815 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
9746 TCCCGAACCC
9756 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
* *
9772 ACACGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
* *
9788 ACCTGAGCCCGAAAAT
1 ACCCGAACCCGAAAAT
9804 ACCCGAACCCGA
1 ACCCGAACCCGA
9816 CCGAGACCGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.40, C:0.37, G:0.17, T:0.07
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:9844 original size:17 final size:17
Alignment explanation
Indices: 9822--9854 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9812 CCGACCGAGA
*
9822 CCGAGCCCGATCCCGAC
1 CCGAGCCCGAACCCGAC
9839 CCGAGCCCGAACCCGA
1 CCGAGCCCGAACCCGA
9855 ACTCGAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.24, T:0.03
Consensus pattern (17 bp):
CCGAGCCCGAACCCGAC
Found at i:9847 original size:11 final size:11
Alignment explanation
Indices: 9804--9854 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
9794 GCCCGAAAAT
*
9804 ACCCGAACCCG
1 ACCCGAGCCCG
*
9815 A-CCGAGACCG
1 ACCCGAGCCCG
*
9825 AGCCCGATCCCG
1 A-CCCGAGCCCG
9837 ACCCGAGCCCG
1 ACCCGAGCCCG
9848 AACCCGA
1 -ACCCGA
9855 ACTCGAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.25
11 10 0.31
12 14 0.44
ACGTcount: A:0.25, C:0.49, G:0.24, T:0.02
Consensus pattern (11 bp):
ACCCGAGCCCG
Found at i:9848 original size:23 final size:22
Alignment explanation
Indices: 9804--9856 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
9794 GCCCGAAAAT
9804 ACCCGAACCCGACCGAGACCGA
1 ACCCGAACCCGACCGAGACCGA
* * *
9826 GCCCGATCCCGACCCGAGCCCGA
1 ACCCGAACCCGA-CCGAGACCGA
9849 ACCCGAAC
1 ACCCGAAC
9857 TCGAAATAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.40
23 15 0.60
ACGTcount: A:0.26, C:0.49, G:0.23, T:0.02
Consensus pattern (22 bp):
ACCCGAACCCGACCGAGACCGA
Found at i:10081 original size:2 final size:2
Alignment explanation
Indices: 10038--10072 Score: 54
Period size: 2 Copynumber: 17.5 Consensus size: 2
10028 AAACTACTAA
10038 AT AT AT AT A- AT GAT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A
10073 ACTTATATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 28 0.90
3 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:10381 original size:31 final size:31
Alignment explanation
Indices: 10310--10381 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
10300 GTCTATCAGC
*
10310 TTTTAATTTGTTTAATTTAAGACTTTGATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
10341 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
10371 GTTTTAATTTG
1 -TTTTAATTTG
10382 CCATAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 8 0.24
31 23 0.68
32 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:10814 original size:17 final size:17
Alignment explanation
Indices: 10794--10853 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
10784 AATCAAACTT
10794 GAGCCCGAACCAAACCC
1 GAGCCCGAACCAAACCC
*
10811 GAGCCC--ACCGAACCC
1 GAGCCCGAACCAAACCC
* **
10826 GAACCCGAACCCTACCC
1 GAGCCCGAACCAAACCC
*
10843 GAGACCGAACC
1 GAGCCCGAACC
10854 CGAAAATACC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 13 0.37
17 22 0.63
ACGTcount: A:0.32, C:0.48, G:0.18, T:0.02
Consensus pattern (17 bp):
GAGCCCGAACCAAACCC
Found at i:10843 original size:32 final size:33
Alignment explanation
Indices: 10797--10883 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 33
10787 CAAACTTGAG
*
10797 CCCGAACCAAACCCGAGCCCACCGAACCCG-A-A
1 CCCGAACC-CACCCGAGCCCACCGAACCCGAATA
10829 CCCGAACCCTACCCGAG---ACCGAACCCGAAAATA
1 CCCGAACCC-ACCCGAGCCCACCGAACCCG--AATA
*
10862 CCCGAACCCGCCCGAGCCCACC
1 CCCGAACCCACCCGAGCCCACC
10884 CAATTGCCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
29 10 0.22
32 22 0.49
33 10 0.22
35 3 0.07
ACGTcount: A:0.31, C:0.51, G:0.16, T:0.02
Consensus pattern (33 bp):
CCCGAACCCACCCGAGCCCACCGAACCCGAATA
Found at i:10844 original size:11 final size:11
Alignment explanation
Indices: 10797--10857 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 11
10787 CAAACTTGAG
*
10797 CCCGAACCAAA
1 CCCGAACCCAA
*
10808 CCCGAGCCC-A
1 CCCGAACCCAA
10818 -CCGAACCCGAA
1 CCCGAACCC-AA
*
10829 CCCGAACCCTA
1 CCCGAACCCAA
*
10840 CCCGAGACCGAA
1 CCCGA-ACCCAA
10852 CCCGAA
1 CCCGAA
10858 AATACCCGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
9 7 0.17
10 1 0.03
11 15 0.38
12 17 0.43
ACGTcount: A:0.33, C:0.49, G:0.16, T:0.02
Consensus pattern (11 bp):
CCCGAACCCAA
Found at i:18791 original size:58 final size:58
Alignment explanation
Indices: 18696--18818 Score: 239
Period size: 58 Copynumber: 2.1 Consensus size: 58
18686 ACATTTTAGA
18696 AATTT-CAGCGTACACGGCCAGTGGTGTCCAGTTCACTTTACATGAAATGTTGTGATT
1 AATTTGCAGCGTACACGGCCAGTGGTGTCCAGTTCACTTTACATGAAATGTTGTGATT
18753 AATTTGCAGCGTACACGGCCAGTGGTGTCCAGTTCACTTTACATGAAATGTTGTGATT
1 AATTTGCAGCGTACACGGCCAGTGGTGTCCAGTTCACTTTACATGAAATGTTGTGATT
18811 AATTTGCA
1 AATTTGCA
18819 TTGTCCAGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 5 0.08
58 60 0.92
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (58 bp):
AATTTGCAGCGTACACGGCCAGTGGTGTCCAGTTCACTTTACATGAAATGTTGTGATT
Found at i:19270 original size:18 final size:18
Alignment explanation
Indices: 19247--19282 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
19237 TCTAGAAAGA
19247 GCTACCGTGTTCAAACGG
1 GCTACCGTGTTCAAACGG
19265 GCTACCGTGTTCAAACGG
1 GCTACCGTGTTCAAACGG
19283 ACATTTTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (18 bp):
GCTACCGTGTTCAAACGG
Found at i:20160 original size:340 final size:337
Alignment explanation
Indices: 19540--20217 Score: 1018
Period size: 340 Copynumber: 2.0 Consensus size: 337
19530 TCTTATATTG
* * * *
19540 ATGGAGATGACCGGTTTCTTAGACACAGAGGTTACCCAATTGATGGATTGGCTGAGAGTTCCACC
1 ATGGAGATGACCGGTTTCTTAGACACAGAGGTTACCCAATTGAAGGATTCGCTGAGAATTCCAAC
*
19605 TTCTTGGAAGTTGCCTACCTTTTGAGTAAGCTTTAATCAAGTTTTAGACTTTTTTTTATGTCTTC
66 TTCTTGGAAGTTGCCTACCTTTTGAGTAAGCTTTAATCAACTTTTAGACTTTTTTTTATGTCTTC
* **
19670 CTTGCCTTGAAAAATACATATTAAATTAGAAAATCTTGGTCTAGGAAACACCAACTGACAAGAAT
131 CTTGCCTTGAAAAATACAGATTAAATTAGAAAATCTCAGTCTAGGAAACACCAACTGACAAGAAT
* *
19735 TATCATTTGGTTAATTAAAGCGATTGATTTTGAAGTTCAAATGGTTTGCTTGGCATGTTTCCGTT
196 AACCATTTGGTTAATTAAAGCGATTGATTTTGAAGTTCAAATGGTTTGCTTGGCATGTTTCCGTT
19800 GTACAATTACTCTATTATTTCTAGCTATCATT-ACACCTTTTAAATTTGGTCATTAGAAAGAAGT
261 GTACAATTACTCTATTATTTCTAGCTATCATTGA-ACCTTTTAAATTTGGTCATTAGAAAGAAGT
*
19864 CTCCCTTATTCTA
325 CTCCCTTATGCTA
* *
19877 ATGGAGATGACTGGTTTCTTAGATACAGAGGTTACCCAATTGAAGGATTCGCTGAGAATTCCAAC
1 ATGGAGATGACCGGTTTCTTAGACACAGAGGTTACCCAATTGAAGGATTCGCTGAGAATTCCAAC
*
19942 TTCTTGGAAGTTGCCTACCTTTTGAGTAAGCTTTAATGAACTTTTAGACTTATTTTTCTTATGTC
66 TTCTTGGAAGTTGCCTACCTTTTGAGTAAGCTTTAATCAACTTTTAGAC-T-TTTTT-TTATGTC
* * * * * * * *
20007 TT-TTGTGCCTTGAAAAATACAGATTAAATTAGTAAGTGTCAGTTTAGGGAACATCAACTGACCA
128 TTCCT-TGCCTTGAAAAATACAGATTAAATTAGAAAATCTCAGTCTAGGAAACACCAACTGACAA
* *
20071 TAATAACCATTTGGTTAATTAAAGCGATTGATTTTGAGGTTCAAATGGTTTGCTTGGCATGTTTC
192 GAATAACCATTTGGTTAATTAAAGCGATTGATTTTGAAGTTCAAATGGTTTGCTTGGCATGTTTC
* * * * * * *
20136 CGTTGTGCAGTTGCTCTGTTATTTCTAGCTATCCTTGAATCTTTTAAATTTGGTCTTTAGAAAGA
257 CGTTGTACAATTACTCTATTATTTCTAGCTATCATTGAACCTTTTAAATTTGGTCATTAGAAAGA
20201 AGTCTCCCTTATGCTA
322 AGTCTCCCTTATGCTA
20217 A
1 A
20218 CTTTTGTTAC
Statistics
Matches: 305, Mismatches: 31, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
337 106 0.35
338 1 0.00
339 6 0.02
340 191 0.63
341 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (337 bp):
ATGGAGATGACCGGTTTCTTAGACACAGAGGTTACCCAATTGAAGGATTCGCTGAGAATTCCAAC
TTCTTGGAAGTTGCCTACCTTTTGAGTAAGCTTTAATCAACTTTTAGACTTTTTTTTATGTCTTC
CTTGCCTTGAAAAATACAGATTAAATTAGAAAATCTCAGTCTAGGAAACACCAACTGACAAGAAT
AACCATTTGGTTAATTAAAGCGATTGATTTTGAAGTTCAAATGGTTTGCTTGGCATGTTTCCGTT
GTACAATTACTCTATTATTTCTAGCTATCATTGAACCTTTTAAATTTGGTCATTAGAAAGAAGTC
TCCCTTATGCTA
Found at i:21905 original size:20 final size:21
Alignment explanation
Indices: 21875--21914 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
21865 TCTCTAGGTA
21875 ATTCATCAAAATAAAGCTAAT
1 ATTCATCAAAATAAAGCTAAT
21896 ATTC-TCAAAATAAAGCTAA
1 ATTCATCAAAATAAAGCTAA
21915 CATTAATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.28
Consensus pattern (21 bp):
ATTCATCAAAATAAAGCTAAT
Found at i:28686 original size:13 final size:13
Alignment explanation
Indices: 28665--28701 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
28655 GAAAATTGGG
28665 TTTTTTCTTTTT-
1 TTTTTTCTTTTTC
28677 TTTCTTTCTTTTTC
1 TTT-TTTCTTTTTC
28691 TTTTTT-TTTTT
1 TTTTTTCTTTTT
28702 ACCAAGCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.35
13 12 0.52
14 3 0.13
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTTTTCTTTTTC
Found at i:28688 original size:10 final size:9
Alignment explanation
Indices: 28665--28698 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
28655 GAAAATTGGG
28665 TTTTTTCTT
1 TTTTTTCTT
28674 TTTTTTCTT
1 TTTTTTCTT
28683 TCTTTTTCTT
1 T-TTTTTCTT
28693 TTTTTT
1 TTTTTT
28699 TTTACCAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:28699 original size:10 final size:10
Alignment explanation
Indices: 28665--28699 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28655 GAAAATTGGG
28665 TTTTTTC-TT
1 TTTTTTCTTT
28674 TTTTTTCTTT
1 TTTTTTCTTT
*
28684 CTTTTTCTTT
1 TTTTTTCTTT
28694 TTTTTT
1 TTTTTT
28700 TTACCAAGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.30
10 16 0.70
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:34183 original size:15 final size:15
Alignment explanation
Indices: 34132--34183 Score: 50
Period size: 17 Copynumber: 3.3 Consensus size: 15
34122 AATCTGAAAT
*
34132 AATATATAATAAAATA
1 AATATAT-ATAATATA
*
34148 AATATATATTATATAA
1 AATATATATAATAT-A
*
34164 TAATATATGTAATATA
1 -AATATATATAATATA
34180 AATA
1 AATA
34184 CCTAATCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 9 0.30
16 9 0.30
17 12 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AATATATATAATATA
Found at i:35004 original size:16 final size:16
Alignment explanation
Indices: 34983--35026 Score: 65
Period size: 14 Copynumber: 2.9 Consensus size: 16
34973 TATCAGATAT
34983 TGGAGTCATGATTTAG
1 TGGAGTCATGATTTAG
*
34999 TGGAGTC-TTA-TTAG
1 TGGAGTCATGATTTAG
35013 TGGAGTCATGATTT
1 TGGAGTCATGATTT
35027 GGTTGTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 11 0.46
15 4 0.17
16 9 0.38
ACGTcount: A:0.23, C:0.07, G:0.30, T:0.41
Consensus pattern (16 bp):
TGGAGTCATGATTTAG
Found at i:44132 original size:36 final size:36
Alignment explanation
Indices: 44085--44154 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
44075 TTCAATAACC
* *
44085 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
44121 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
44155 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:44316 original size:72 final size:72
Alignment explanation
Indices: 44208--44347 Score: 262
Period size: 72 Copynumber: 1.9 Consensus size: 72
44198 CAAATTTCCA
*
44208 TATAAGGTTATAACTTATAACTAAACTTAATGCAACATAAGGAAGTATAAAATTAGGTGTACAAA
1 TATAAGGTTATAACTTATAACTAAACTTAATGCAACATAAGGAAGTATAAAATTAGGTCTACAAA
44273 ATTTAGT
66 ATTTAGT
*
44280 TATAAGGTTTTAACTTATAACTAAACTTAATGCAACATAAGGAAGTATAAAATTAGGTCTACAAA
1 TATAAGGTTATAACTTATAACTAAACTTAATGCAACATAAGGAAGTATAAAATTAGGTCTACAAA
44345 ATT
66 ATT
44348 GGTTCCTAGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (72 bp):
TATAAGGTTATAACTTATAACTAAACTTAATGCAACATAAGGAAGTATAAAATTAGGTCTACAAA
ATTTAGT
Found at i:46224 original size:202 final size:200
Alignment explanation
Indices: 45878--46286 Score: 719
Period size: 202 Copynumber: 2.0 Consensus size: 200
45868 GCTTAATAAC
*
45878 TTTATCAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
* * *
45943 GATACAACACATTATTATTATATATAAAATTATACCAAAAATAATTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
46008 AATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATC
131 AATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAG--ATTAAAGATC
46073 CGATTTA
194 CGATTTA
*
46080 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
1 TTTATCAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
* *
46145 GATAGAACACATTACTATTATATATAGAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
66 GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
* *
46210 ATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTAAATATCCG
131 AATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTAAAGATCCG
46275 ATTTA
196 ATTTA
46280 TTTATCA
1 TTTATCA
46287 TTAAGGAAAC
Statistics
Matches: 198, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
200 23 0.12
202 175 0.88
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAATTCTTTAAGTCTAAGATTACTAACAAAGTTGTAGTAAATAA
GATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGGTTG
AATTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATTAAAGATCCG
ATTTA
Found at i:46372 original size:25 final size:25
Alignment explanation
Indices: 46325--46374 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
46315 ATACGTTTGC
46325 AAAAATACCTAAGAATTTGAATTAA
1 AAAAATACCTAAGAATTTGAATTAA
46350 AAAAATTACCTAAGAATTT-AATTAA
1 AAAAA-TACCTAAGAATTTGAATTAA
46375 TGTAAGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (25 bp):
AAAAATACCTAAGAATTTGAATTAA
Found at i:46419 original size:39 final size:40
Alignment explanation
Indices: 46365--46445 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
46355 TTACCTAAGA
*
46365 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
46404 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
46444 AT
1 AT
46446 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Done.