Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018822.1 Corchorus olitorius cultivar O-4 contig18855, 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: 39838
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:5990 original size:48 final size:48
Alignment explanation
Indices: 5926--7217 Score: 1063
Period size: 48 Copynumber: 27.0 Consensus size: 48
5916 TCCCCCTCCT
* * *
5926 TCTCCATCACCTCCTCCTCCTTATGTCTATC-AGTCTCCACCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTA-CAAGTCTCCACCACCACCA
* * * * * *
5974 TCACCTTCGCCACCTCCGCCATATGTCTACAATTCCCCTCCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * *
6022 TCTCCATCACCCCCACCACCTTATGTCTACCAGTCTCCACCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * *
6070 TCACCTTCACCACCTCCTCCATATGTCTACAATTCTCCTCCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * * * * *
6118 TCCCCATCACCCCCTCCACCTTATGTCTACCAA-TCCCCGCCTCCTCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTA-CAAGTCTCCACCACCACCA
* * * * * * *
6166 TCTCCATCCCCACCACCTCCTTATGTTTATAAGTCCCCACCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * *
6214 TCACCTTCACCACCTCCTCCATATGTCTACCAA-TCACCGCCTCCCCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTA-CAAGTCTCCACCACCACCA
* * * * *
6262 TCACCTTCACCACCTCCACCATATGTGTACAAGTCTCCACCACCTCCT
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * * * * * *
6310 TCTCCTTCACCTCCCCCACCTTATATTTACAAGTCACCACCTCCTCCT
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * * *
6358 TCTCCATCTCCACCACCTCCTTATGTGTACAAATCTCCACCACCGCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * * *
6406 TCACCTTCCCCACCTCCACCTTATGTATACAAGTCTCCACCTCCTCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * ** *
6454 TCTCCATCCCCACCACCTCCATACATTTACAAGTCTCCACCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * *
6502 TCACCTTCACCACCTCCTCCTTATGTCTACAAGTCCCCTCCACCTCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * *
6550 TCTCCATCACCTCCTCCTCCATATGTCTATAAGTCACCACCTCCTCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * ** *
6598 TCTCCATCCCCACCACCTCCATACATTTACAAGTCTCCACCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * **
6646 TCCCCTTCACCACCTCCTCCATATGTCTATAAGTCTCCACC-CCGGCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * ** *
6693 TCTCCATCCCCACCACCTCCATACATTTACAAGTCTCCACCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * *
6741 TCCCCTTCACCTCCTCCTCCATATGTCTATAAGTCACCACCTCCTCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * ** *
6789 TCTCCATCCCCACCACCTCCATACATTTACAAGTCTCCACCACCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* *
6837 TCCCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCCCCACCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * *
6885 TCACCCTCACCTCCTCCTCCATATGTCTACAAGTCTCCACCTCCTCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * ** *
6933 TCCCCATCACCTCC-CGCTCCTTACATTTACAAGTCTCCACCACCACCA
1 TCTCCTTCACCACCTC-CTCCATATGTCTACAAGTCTCCACCACCACCA
* * * *
6981 TCGCCTTCACCACCACCTCCATATGTCTACAAGTC-CCCCCTCCTA-CA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACC-ACCA
* * * ** *
7028 TCTCCATCACCTCCTCC-CCTTACATCTACAAGTCTCCACCACCCCCA
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * * *
7075 TCCCCTTCACCACCTCCTCCATATGTCTATAAATCTCCCCCACCTCCT
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * ** * * *
7123 TCTCCGTCACCACCTCCCCCTTACATTTACAAATCTCCACCACCACCG
1 TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
* * * * *
7171 TCATCC-TCACCCCCTCGTCCATACGTGTACAAGTCCCCACCACCACC
1 TC-TCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACC
7218 TTCACCCGCC
Statistics
Matches: 983, Mismatches: 248, Indels: 26
0.78 0.20 0.02
Matches are distributed among these distances:
46 14 0.01
47 87 0.09
48 873 0.89
49 9 0.01
ACGTcount: A:0.22, C:0.50, G:0.04, T:0.25
Consensus pattern (48 bp):
TCTCCTTCACCACCTCCTCCATATGTCTACAAGTCTCCACCACCACCA
Found at i:6876 original size:27 final size:27
Alignment explanation
Indices: 6846--6933 Score: 80
Period size: 27 Copynumber: 3.5 Consensus size: 27
6836 ATCCCCTTCA
6846 CCACCTCCTCCATATGTCTACAAGTCT
1 CCACCTCCTCCATATGTCTACAAGTCT
* * ** *
6873 CCACCCCCACC--A--TC-AC-CCTCA
1 CCACCTCCTCCATATGTCTACAAGTCT
*
6894 CCTCCTCCTCCATATGTCTACAAGTCT
1 CCACCTCCTCCATATGTCTACAAGTCT
6921 CCACCTCCTCCAT
1 CCACCTCCTCCAT
6934 CCCCATCACC
Statistics
Matches: 43, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
21 10 0.23
22 2 0.05
23 3 0.07
25 3 0.07
26 2 0.05
27 23 0.53
ACGTcount: A:0.20, C:0.50, G:0.05, T:0.25
Consensus pattern (27 bp):
CCACCTCCTCCATATGTCTACAAGTCT
Found at i:7277 original size:75 final size:75
Alignment explanation
Indices: 7236--7412 Score: 268
Period size: 75 Copynumber: 2.4 Consensus size: 75
7226 CCCATCCACG
*
7236 TCCATACCACTATAAATCACCTCCTCCTCCCCGTCATTACAAGTCCCCAGTACCTCCATCTCACT
1 TCCATACCACTATAAATCACCTCCTCCTCCCCGCCATTACAAGTCCCCAGTACCTCCATCTCAC-
*
7301 ATGCACAT-CC
65 CTGCACATCCC
* * *
7311 TCCATACCGCTATAAATCACCTCCTCCTCCTCGCCATTACAAGTCTCCAGTACCTCCATCTCACC
1 TCCATACCACTATAAATCACCTCCTCCTCCCCGCCATTACAAGTCCCCAGTACCTCCATCTCACC
7376 ATGCACA-CCC
66 -TGCACATCCC
*
7386 TCCATACCTCTATAAATCACCTCCTCC
1 TCCATACCACTATAAATCACCTCCTCC
7413 ACCATCCTAC
Statistics
Matches: 94, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.25, C:0.45, G:0.05, T:0.25
Consensus pattern (75 bp):
TCCATACCACTATAAATCACCTCCTCCTCCCCGCCATTACAAGTCCCCAGTACCTCCATCTCACC
TGCACATCCC
Found at i:7412 original size:24 final size:23
Alignment explanation
Indices: 7384--7461 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
7374 CCATGCACAC
7384 CCTCCATACCTCTATAAATCACCT
1 CCTCCATACCTCTA-AAATCACCT
** *
7408 CCTCC--ACCATCCTACCATGCACAT
1 CCTCCATACC-T-CTAAAAT-CACCT
*
7432 CCTCCATACCTCTACAAGTCACCT
1 CCTCCATACCTCTA-AAATCACCT
7456 CCTCCA
1 CCTCCA
7462 CCATCCAAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
22 3 0.07
23 3 0.07
24 30 0.73
25 2 0.05
26 3 0.07
ACGTcount: A:0.26, C:0.47, G:0.03, T:0.24
Consensus pattern (23 bp):
CCTCCATACCTCTAAAATCACCT
Found at i:7418 original size:48 final size:48
Alignment explanation
Indices: 7373--7467 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
7363 CCTCCATCTC
*
7373 ACCATGCACACCCTCCATACCTCTATAAATCACCTCCTCCACCATCCT
1 ACCATGCACACCCTCCATACCTCTACAAATCACCTCCTCCACCATCCT
* *
7421 ACCATGCACATCCTCCATACCTCTACAAGTCACCTCCTCCACCATCC
1 ACCATGCACACCCTCCATACCTCTACAAATCACCTCCTCCACCATCC
7468 AAGTCTCCTC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.26, C:0.48, G:0.03, T:0.22
Consensus pattern (48 bp):
ACCATGCACACCCTCCATACCTCTACAAATCACCTCCTCCACCATCCT
Found at i:22330 original size:2 final size:2
Alignment explanation
Indices: 22323--22362 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
22313 AGCAAAAATA
*
22323 AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
22363 AAAGTACGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 33 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22714 original size:94 final size:94
Alignment explanation
Indices: 22610--22787 Score: 320
Period size: 94 Copynumber: 1.9 Consensus size: 94
22600 TTCAATTAAA
*
22610 TTCAATATTTTGATAATTATTTTATTTTTACTAGTTTAATTTAAAAGTTTATTTCTACCATTTTA
1 TTCAATATTTTGATAATTATTTTATTTTTACCAGTTTAATTTAAAAGTTTATTTCTACCATTTTA
22675 CTATTTTTCATTAAAAACTTGGATATATT
66 CTATTTTTCATTAAAAACTTGGATATATT
* * *
22704 TTCACTATTTTTATAATTATTTTATTTTTACCATTTTAATTTAAAAGTTTATTTCTACCATTTTA
1 TTCAATATTTTGATAATTATTTTATTTTTACCAGTTTAATTTAAAAGTTTATTTCTACCATTTTA
22769 CTATTTTTCATTAAAAACT
66 CTATTTTTCATTAAAAACT
22788 AAAACTTGGA
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 80 1.00
ACGTcount: A:0.31, C:0.10, G:0.03, T:0.55
Consensus pattern (94 bp):
TTCAATATTTTGATAATTATTTTATTTTTACCAGTTTAATTTAAAAGTTTATTTCTACCATTTTA
CTATTTTTCATTAAAAACTTGGATATATT
Found at i:23821 original size:43 final size:43
Alignment explanation
Indices: 23765--23877 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 43
23755 GGTTACCAAG
* * * *
23765 ATTTTAAAGTGAGGTTATC-AAA-TTCAGAGTGTGGTTATCCGAA
1 ATTTCAAA-TGAGGTTATCAAAATTTCACAGTGTGGATAT-CAAA
23808 ATTTCATAATGAGGTTATCAAAATTTCACAGTGTGGATATCAAA
1 ATTTCA-AATGAGGTTATCAAAATTTCACAGTGTGGATATCAAA
* *
23852 ATTTCAAAGGAGGTTA-CAAGATTTCA
1 ATTTCAAATGAGGTTATCAAAATTTCA
23878 TAAACAAACT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
42 9 0.15
43 24 0.39
44 14 0.23
45 14 0.23
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (43 bp):
ATTTCAAATGAGGTTATCAAAATTTCACAGTGTGGATATCAAA
Found at i:23831 original size:22 final size:22
Alignment explanation
Indices: 23735--23880 Score: 113
Period size: 22 Copynumber: 6.8 Consensus size: 22
23725 AGAGATTAGA
*
23735 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAATGAGG
* * *
23757 TTACCAAGATTTTA-AAGTGAGG
1 TTATCAAAATTTCATAA-TGAGG
* * *
23779 TTATC-AAA-TTCAGAGTGTGG
1 TTATCAAAATTTCATAATGAGG
*
23799 TTATCCGAAATTTCATAATGAGG
1 TTAT-CAAAATTTCATAATGAGG
* * *
23822 TTATCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAATGAGG
* *
23844 ATATCAAAATTTCA-AAGGAGG
1 TTATCAAAATTTCATAATGAGG
*
23865 TTA-CAAGATTTCATAA
1 TTATCAAAATTTCATAA
23881 ACAAACTTTT
Statistics
Matches: 96, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
20 20 0.21
21 14 0.15
22 49 0.51
23 13 0.14
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGAGG
Found at i:24083 original size:21 final size:22
Alignment explanation
Indices: 24057--24218 Score: 93
Period size: 22 Copynumber: 7.3 Consensus size: 22
24047 TTGTGGAGTA
*
24057 ATCAAAATTTTATA-GGAGGTT
1 ATCAAAATTTCATATGGAGGTT
*
24078 ATCAAAATTACATATGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
* **
24100 ATCAAAATTTCACAGTTTA-GTT
1 ATCAAAATTTCATA-TGGAGGTT
* * *
24122 TTCGAAATTTCATATGGTGGTT
1 ATCAAAATTTCATATGGAGGTT
*
24144 ATAAAAAAATTTCATAGTGTGTA-G--
1 AT--CAAAATTTCATA-TG-G-AGGTT
*
24168 ATCGAAATTTCATCAT-GAGGTT
1 ATCAAAATTTCAT-ATGGAGGTT
* ** *
24190 ATGAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATATGGAGGTT
24212 ATCAAAA
1 ATCAAAA
24219 CTTGTGATTA
Statistics
Matches: 104, Mismatches: 24, Indels: 25
0.68 0.16 0.16
Matches are distributed among these distances:
19 1 0.01
20 2 0.02
21 14 0.13
22 68 0.65
23 3 0.03
24 12 0.12
25 2 0.02
26 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATATGGAGGTT
Found at i:24282 original size:23 final size:23
Alignment explanation
Indices: 24248--24304 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
24238 CATAAACAAG
24248 TTATCAAAATTTTA-CAAGAAGGT
1 TTATCAAAATTTTATC-AGAAGGT
* *
24271 TTATCAATATTTTATCGGAAGGT
1 TTATCAAAATTTTATCAGAAGGT
24294 TTATCAAAATT
1 TTATCAAAATT
24305 CAAAATTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATCAGAAGGT
Found at i:24378 original size:22 final size:22
Alignment explanation
Indices: 24304--24531 Score: 114
Period size: 22 Copynumber: 10.4 Consensus size: 22
24294 TTATCAAAAT
*
24304 TCAAAATTTC-TATAGTGAGGTTC
1 TCAAAATTTCATA-AG-GAGGTTA
* *
24327 TCAAAATTTTCACAATGA--TTA
1 TCAAAA-TTTCATAAGGAGGTTA
*
24348 -CAAACATTTCATAAGGAGGTTC
1 TCAAA-ATTTCATAAGGAGGTTA
* * *
24370 TCAAAATTTCA-CAGCGTGCTTA
1 TCAAAATTTCATAAG-GAGGTTA
* * * *
24392 CCAACATTTCACAAGGAGATTA
1 TCAAAATTTCATAAGGAGGTTA
* *
24414 TCAAAATTTCAT-TGTGTGGTTA
1 TCAAAATTTCATAAG-GAGGTTA
* * *
24436 TCGAAATTTCAT-TGCATGGTTA
1 TCAAAATTTCATAAGGA-GGTTA
**
24458 TCAAAATTTCAT-TTGAGGTTA
1 TCAAAATTTCATAAGGAGGTTA
*
24479 TCAAAATTTCAT-AGTGAGGTTT
1 TCAAAATTTCATAAG-GAGGTTA
* * *
24501 TTAAAATTTCATAGGGAGGCTA
1 TCAAAATTTCATAAGGAGGTTA
*
24523 ACAAAATTT
1 TCAAAATTT
24532 TATTGGAAGG
Statistics
Matches: 157, Mismatches: 36, Indels: 25
0.72 0.17 0.11
Matches are distributed among these distances:
20 13 0.08
21 23 0.15
22 100 0.64
23 15 0.10
24 5 0.03
25 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAAGGAGGTTA
Found at i:24400 original size:44 final size:42
Alignment explanation
Indices: 24320--24424 Score: 129
Period size: 44 Copynumber: 2.4 Consensus size: 42
24310 TTTCTATAGT
*
24320 GAGGTTCTCAAAATTTTCACAATGATTACAAACATTTCATAAG
1 GAGGTTCTCAAAA-TTTCACAATGATTACAAACATTTCACAAG
* * *
24363 GAGGTTCTCAAAATTTCACAGCGTGCTTACCAACATTTCACAAG
1 GAGGTTCTCAAAATTTCACA--ATGATTACAAACATTTCACAAG
* *
24407 GAGATTATCAAAATTTCA
1 GAGGTTCTCAAAATTTCA
24425 TTGTGTGGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
42 7 0.13
43 13 0.24
44 34 0.63
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.30
Consensus pattern (42 bp):
GAGGTTCTCAAAATTTCACAATGATTACAAACATTTCACAAG
Found at i:24445 original size:44 final size:43
Alignment explanation
Indices: 24348--24512 Score: 134
Period size: 44 Copynumber: 3.7 Consensus size: 43
24338 ACAATGATTA
* ** * * *
24348 CAAACATTTCATAAGGAGGTTCTCAAAATTTCACAGCGTGCTTAC
1 CAAA-ATTTCA-AAGGAGGTTATCAAAATTTCATTGTGTGGTTAT
* *
24393 CAACATTTCACAAGGAGATTATCAAAATTTCATTGTGTGGTTAT
1 CAAAATTTCA-AAGGAGGTTATCAAAATTTCATTGTGTGGTTAT
* ** * *
24437 CGAAATTTCATTGCATGGTTATCAAAATTTCATT-TGAGGTTAT
1 CAAAATTTCAAAGGA-GGTTATCAAAATTTCATTGTGTGGTTAT
* * *
24480 CAAAATTTCATAGTGAGGTTTTTAAAATTTCAT
1 CAAAATTTCAAAG-GAGGTTATCAAAATTTCAT
24513 AGGGAGGCTA
Statistics
Matches: 97, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
43 36 0.37
44 58 0.60
45 3 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (43 bp):
CAAAATTTCAAAGGAGGTTATCAAAATTTCATTGTGTGGTTAT
Found at i:24631 original size:22 final size:21
Alignment explanation
Indices: 24603--24658 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
24593 AATTCCATAA
24603 TTATCAAAATTTCATAAGAAAG
1 TTATCAAAATTTCAT-AGAAAG
* * **
24625 TTATCAAATTTTTATAGGTAG
1 TTATCAAAATTTCATAGAAAG
24646 -TATCAAAATTTCA
1 TTATCAAAATTTCA
24659 AAATGTTCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 11 0.39
21 4 0.14
22 13 0.46
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (21 bp):
TTATCAAAATTTCATAGAAAG
Found at i:24840 original size:28 final size:30
Alignment explanation
Indices: 24782--24852 Score: 92
Period size: 29 Copynumber: 2.4 Consensus size: 30
24772 ATACCGTACA
*
24782 GGTCCCTCTACTTACAAAAAGGGATCGATTT
1 GGTCCCTCTAC-TACAAAAAGGGATCAATTT
**
24813 GGTCCC-CTACTACAAAAATTG-TCAATTT
1 GGTCCCTCTACTACAAAAAGGGATCAATTT
24841 GGTCCCTCTACT
1 GGTCCCTCTACT
24853 TATATTTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.33
29 14 0.39
30 4 0.11
31 6 0.17
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (30 bp):
GGTCCCTCTACTACAAAAAGGGATCAATTT
Found at i:25188 original size:30 final size:30
Alignment explanation
Indices: 25121--25188 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
25111 CACCAAATTG
* * *
25121 TAAGTAGAGGGACCAAATTGACAGTTTTTA
1 TAAGTAGAGAGACCAAATTAACACTTTTTA
*
25151 TAA-TAGAGAGACCAAATTAATC-CTTTTTT
1 TAAGTAGAGAGACCAAATTAA-CACTTTTTA
25180 TAAGTAGAG
1 TAAGTAGAG
25189 GGACATGTAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.32
Consensus pattern (30 bp):
TAAGTAGAGAGACCAAATTAACACTTTTTA
Found at i:32093 original size:21 final size:21
Alignment explanation
Indices: 32068--32108 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
32058 TCTCCTCCTC
*
32068 TTTTAGAGCATATTGTTTTTT
1 TTTTAGAGCATATTGCTTTTT
32089 TTTTAGAGCATATTGCTTTT
1 TTTTAGAGCATATTGCTTTT
32109 ACTCTGATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.15, T:0.59
Consensus pattern (21 bp):
TTTTAGAGCATATTGCTTTTT
Found at i:33113 original size:45 final size:45
Alignment explanation
Indices: 33047--33147 Score: 148
Period size: 45 Copynumber: 2.2 Consensus size: 45
33037 TCATCCCCGC
* * * * *
33047 CGCCACCACCAAAGCACCCATACAAGCCACCAGGCCACTATAAGT
1 CGCCACCACCTAAGAAACCATACAACCCACCAGGCCACTACAAGT
*
33092 CGCCACCACCTAAGAAACCATACCACCCACCAGGCCACTACAAGT
1 CGCCACCACCTAAGAAACCATACAACCCACCAGGCCACTACAAGT
33137 CGCCACCACCT
1 CGCCACCACCT
33148 CCTAAGCGGT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.34, C:0.46, G:0.12, T:0.09
Consensus pattern (45 bp):
CGCCACCACCTAAGAAACCATACAACCCACCAGGCCACTACAAGT
Found at i:33227 original size:48 final size:48
Alignment explanation
Indices: 33175--33531 Score: 362
Period size: 48 Copynumber: 7.5 Consensus size: 48
33165 ACCAGCTTAT
* * * * *
33175 CACTACAAGTCACCTCCTCCCCCAGTGAAATCTCCACCTCCACCATAC
1 CACTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
** * * ** *
33223 CACTACACCTCCCCACCTCCACCAAAGAAATCTCCACCTCCTCCATAT
1 CACTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
** * ** * * * *
33271 GTCTACAAGTCTCCACCACCACCTGTCCACTCCCCACCTCCTCCCTAT
1 CACTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
** * *
33319 GTCTACAAGTCTCCACCACCACCAGTGAAATCCCCACCTCCTCCCTAC
1 CACTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
**
33367 GTCTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
1 CACTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
**
33415 CACTACACA-TCTCCACCACCACCAAAGAAATCTCCACCTCCTCCATAC
1 CACTACA-AGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
* * **
33463 TACTACAAGTCCCCACCACCACCAAAGAAATCTCCA---CCTCCATAC
1 CACTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
* *
33508 TACTACAAGTCCCCACCACCACCA
1 CACTACAAGTCTCCACCACCACCA
33532 AAATACAAGC
Statistics
Matches: 271, Mismatches: 36, Indels: 7
0.86 0.11 0.02
Matches are distributed among these distances:
45 33 0.12
47 1 0.00
48 236 0.87
49 1 0.00
ACGTcount: A:0.28, C:0.48, G:0.05, T:0.18
Consensus pattern (48 bp):
CACTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATAC
Found at i:33277 original size:96 final size:96
Alignment explanation
Indices: 33177--33533 Score: 400
Period size: 96 Copynumber: 3.8 Consensus size: 96
33167 CAGCTTATCA
* * * * * ** *
33177 CTACAAGTCACCTCCTCCCCCAGTGAAATCTCCACCTCCACCATACCACTACACCTCCCCACCTC
1 CTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATACCACTACAAGTCCCCACCAC
33242 CACCAAAGAAATCTCCACCTCCTCCATATGT
66 CACCAAAGAAATCTCCACCTCCTCCATATGT
* ** * * * *** *
33273 CTACAAGTCTCCACCACCACCTGTCCACTCCCCACCTCCTCCCTATGTCTACAAGTCTCCACCAC
1 CTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATACCACTACAAGTCCCCACCAC
** * * *
33338 CACCAGTGAAATCCCCACCTCCTCCCTACGT
66 CACCAAAGAAATCTCCACCTCCTCCATATGT
*
33369 CTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATACCACTACACA-TCTCCACCA
1 CTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATACCACTACA-AGTCCCCACCA
*
33433 CCACCAAAGAAATCTCCACCTCCTCCATACT-A
65 CCACCAAAGAAATCTCCACCTCCTCCATA-TGT
* ** *
33465 CTACAAGTCCCCACCACCACCAAAGAAATCTCCA---CCTCCATACTACTACAAGTCCCCACCAC
1 CTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATACCACTACAAGTCCCCACCAC
33527 CACCAAA
66 CACCAAA
33534 ATACAAGCCC
Statistics
Matches: 215, Mismatches: 43, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
92 1 0.00
93 31 0.14
96 182 0.85
97 1 0.00
ACGTcount: A:0.29, C:0.48, G:0.05, T:0.18
Consensus pattern (96 bp):
CTACAAGTCTCCACCACCACCAGTGAAATCTCCACCTCCTCCATACCACTACAAGTCCCCACCAC
CACCAAAGAAATCTCCACCTCCTCCATATGT
Found at i:33286 original size:27 final size:26
Alignment explanation
Indices: 33253--33383 Score: 84
Period size: 27 Copynumber: 5.3 Consensus size: 26
33243 ACCAAAGAAA
33253 TCTCCACCTCCTCCATATGTCTACAAG
1 TCTCCACCTCCTCC-TATGTCTACAAG
* * *
33280 TCTCCACCACCACC--TGTC--C-AC
1 TCTCCACCTCCTCCTATGTCTACAAG
*
33301 TCCCCACCTCCTCCCTATGTCTACAAG
1 TCTCCACCTCCT-CCTATGTCTACAAG
* * *
33328 TCTCCACCACCACC-A-GT-GA-AA-
1 TCTCCACCTCCTCCTATGTCTACAAG
* *
33349 TCCCCACCTCCTCCCTACGTCTACAAG
1 TCTCCACCTCCT-CCTATGTCTACAAG
33376 TCTCCACC
1 TCTCCACC
33384 ACCACCAGTG
Statistics
Matches: 76, Mismatches: 16, Indels: 24
0.66 0.14 0.21
Matches are distributed among these distances:
21 19 0.25
22 7 0.09
23 2 0.03
24 12 0.16
25 2 0.03
26 5 0.07
27 29 0.38
ACGTcount: A:0.21, C:0.49, G:0.07, T:0.23
Consensus pattern (26 bp):
TCTCCACCTCCTCCTATGTCTACAAG
Found at i:33400 original size:21 final size:21
Alignment explanation
Indices: 33328--33404 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 21
33318 TGTCTACAAG
33328 TCTCCACCACCACCAGTGAAA
1 TCTCCACCACCACCAGTGAAA
* * * *
33349 TCCCCACCTCCTCCCTACGTCTACAA
1 TCTCCACCACC-ACC-A-GT-GA-AA
33375 GTCTCCACCACCACCAGTGAAA
1 -TCTCCACCACCACCAGTGAAA
33397 TCTCCACC
1 TCTCCACC
33405 TCCTCCATAC
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
21 17 0.40
22 4 0.10
23 2 0.05
24 4 0.10
25 2 0.05
26 4 0.10
27 9 0.21
ACGTcount: A:0.26, C:0.48, G:0.08, T:0.18
Consensus pattern (21 bp):
TCTCCACCACCACCAGTGAAA
Found at i:33447 original size:21 final size:21
Alignment explanation
Indices: 33423--33500 Score: 66
Period size: 21 Copynumber: 3.4 Consensus size: 21
33413 ACCACTACAC
33423 ATCTCCACCACCACCAAAGAA
1 ATCTCCACCACCACCAAAGAA
* * *
33444 ATCTCCACCTCCTCCATACTACTACA
1 ATCTCCACCACCACCA-A--A-GA-A
*
33470 AGTCCCCACCACCACCAAAGAA
1 A-TCTCCACCACCACCAAAGAA
33492 ATCTCCACC
1 ATCTCCACC
33501 TCCATACTAC
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
21 21 0.49
22 3 0.07
23 1 0.02
24 2 0.05
25 1 0.02
26 3 0.07
27 12 0.28
ACGTcount: A:0.35, C:0.46, G:0.04, T:0.15
Consensus pattern (21 bp):
ATCTCCACCACCACCAAAGAA
Found at i:34578 original size:27 final size:27
Alignment explanation
Indices: 34548--34601 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
34538 GTTCACTTTT
34548 ATTCATCGTTTTTGGACATAAAATATC
1 ATTCATCGTTTTTGGACATAAAATATC
34575 ATTCATCGTTTTTGGACATAAAATATC
1 ATTCATCGTTTTTGGACATAAAATATC
34602 TTATTTCCAA
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:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (27 bp):
ATTCATCGTTTTTGGACATAAAATATC
Found at i:38177 original size:6 final size:6
Alignment explanation
Indices: 38166--38195 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
38156 TAAGGTATTT
38166 TATTAA TATTAA TATTAA TATTAA TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA
38196 GGATAAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATTAA
Found at i:39413 original size:48 final size:48
Alignment explanation
Indices: 39373--39835 Score: 658
Period size: 48 Copynumber: 9.7 Consensus size: 48
39363 ACCAGTACAT
* *
39373 TCACCACCTCCTCCATATGTGTACAAGTCCCCTCCACCACCCGTCCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
* * * * *
39421 TCTCCACCCCCTCCTTATGTCTACAAGTCCCCTCCACCACCAGCCCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
* * * *
39469 TCACCACCTCCTCCATATGTATACAAGTCTCCACCACCACCCGTCCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
* *
39517 TCCCCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCAGTCCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
* * * *
39565 TCCCCACCTCCTCCCTATGTCTACAAGTCCTCACCACCACCCGTTCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
* *
39613 TCACCACCTCCTCCTTATGTATACAAGTCCCCTCCACCACCCGTCCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
*
39661 TCTCCACC-CCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
* * * * *
39708 TCCCCACCACCTCCCTATGTCTATAAGTCCCCACCACCACCCGTTCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
* * *
39756 TCACCACCCCCTCCTTATGTATACAAGTCCCCTCCACCACCCGTCCAC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
*
39804 TCTCCACCTCCTCCCTATGTCTACAAGTCCCC
1 TCACCACCTCCTCCCTATGTCTACAAGTCCCC
39836 GCC
Statistics
Matches: 366, Mismatches: 48, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
47 44 0.12
48 322 0.88
ACGTcount: A:0.20, C:0.52, G:0.06, T:0.22
Consensus pattern (48 bp):
TCACCACCTCCTCCCTATGTCTACAAGTCCCCTCCACCACCCGTCCAC
Done.