Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023983.1 Corchorus olitorius cultivar O-4 contig24016, 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: 32923
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:1688 original size:27 final size:27
Alignment explanation
Indices: 1636--1688 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1626 TGAAAAATAG
* * *
1636 TAAAATGGTAGAAATAAACTTTTAAAT
1 TAAAATGGTAGAAAAAAAATTATAAAT
1663 TAAAATGGTA-AAAAAATAATTATAAA
1 TAAAATGGTAGAAAAAA-AATTATAAA
1689 AATATTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (27 bp):
TAAAATGGTAGAAAAAAAATTATAAAT
Found at i:2083 original size:17 final size:17
Alignment explanation
Indices: 2032--2091 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
2022 AAAAAAAACT
2032 ATTTCAATAATAGTAAAA
1 ATTT-AATAATAGTAAAA
* * *
2050 TTTTTAA-AAGATTTAAAA
1 -ATTTAATAATA-GTAAAA
2068 ATTTAATAATAGTAAAA
1 ATTTAATAATAGTAAAA
*
2085 TTTTAAT
1 ATTTAAT
2092 TACCATGTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
17 19 0.59
18 10 0.31
19 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (17 bp):
ATTTAATAATAGTAAAA
Found at i:3225 original size:2 final size:2
Alignment explanation
Indices: 3218--3257 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
3208 GAGACATGTT
3218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3257 T
1 T
3258 TCAGGTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:5017 original size:23 final size:23
Alignment explanation
Indices: 4991--5053 Score: 117
Period size: 23 Copynumber: 2.7 Consensus size: 23
4981 TGATGGAGTC
4991 CAACTGGGAGCCCGATTACCCCT
1 CAACTGGGAGCCCGATTACCCCT
5014 CAACTGGGAGCCCGATTACCCCT
1 CAACTGGGAGCCCGATTACCCCT
*
5037 CAACTGGGGGCCCGATT
1 CAACTGGGAGCCCGATT
5054 GAAACCTCCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (23 bp):
CAACTGGGAGCCCGATTACCCCT
Found at i:7366 original size:9 final size:9
Alignment explanation
Indices: 7352--7387 Score: 72
Period size: 9 Copynumber: 4.0 Consensus size: 9
7342 CCAAACCCGA
7352 AACCCGTCC
1 AACCCGTCC
7361 AACCCGTCC
1 AACCCGTCC
7370 AACCCGTCC
1 AACCCGTCC
7379 AACCCGTCC
1 AACCCGTCC
7388 GATTGACTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.22, C:0.56, G:0.11, T:0.11
Consensus pattern (9 bp):
AACCCGTCC
Found at i:7634 original size:12 final size:12
Alignment explanation
Indices: 7619--7644 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
7609 ACTTTTAAAC
7619 TTGATAATAATA
1 TTGATAATAATA
7631 TTGATAATAATA
1 TTGATAATAATA
7643 TT
1 TT
7645 TCTTTTATTG
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (12 bp):
TTGATAATAATA
Found at i:7734 original size:70 final size:70
Alignment explanation
Indices: 7660--7875 Score: 187
Period size: 70 Copynumber: 3.1 Consensus size: 70
7650 TATTGAAAAT
*
7660 TAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAATAAATTTTTTAG
1 TAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAATAAACTTTTTAG
7725 TTAAG
66 TTAAG
* * * * **
7730 TAAAACT-ATAAAAGTAAAATA-GTAATATGG-TA--A-ATAT-ATCT-AATATATCTAAACTTT
1 TAAAA-TGGTAAAAATAAAATAGGT-ATAAGGATATTAGATTTAAT-TAAATA-AAATAAACTTT
*
7787 TTAATTAAATTAG
62 TTAGTT--A--AG
* * * *
7800 TAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAATATAGAGTATTTA
1 TAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAA-ATAAACTTTTTA
7865 GTTAAG
65 GTTAAG
7871 TAAAA
1 TAAAA
7876 CTATAAATGT
Statistics
Matches: 109, Mismatches: 20, Indels: 33
0.67 0.12 0.20
Matches are distributed among these distances:
65 6 0.06
66 17 0.16
67 1 0.01
68 1 0.01
69 5 0.05
70 45 0.41
71 11 0.10
73 2 0.02
74 5 0.05
75 16 0.15
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.36
Consensus pattern (70 bp):
TAAAATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAATAAACTTTTTAG
TTAAG
Found at i:7894 original size:22 final size:22
Alignment explanation
Indices: 7869--7915 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
7859 TATTTAGTTA
*
7869 AGTAAAACTA-TAAATGTAAAAT
1 AGTAAAA-TAGTAAATATAAAAT
7891 AGTAAAATAGTAAATATAAAAT
1 AGTAAAATAGTAAATATAAAAT
7913 AGT
1 AGT
7916 TATAAGGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.60, C:0.02, G:0.11, T:0.28
Consensus pattern (22 bp):
AGTAAAATAGTAAATATAAAAT
Found at i:7905 original size:7 final size:8
Alignment explanation
Indices: 7880--7915 Score: 51
Period size: 7 Copynumber: 4.9 Consensus size: 8
7870 GTAAAACTAT
7880 AAAT-GTA
1 AAATAGTA
7887 AAATAGTA
1 AAATAGTA
7895 AAATAGT-
1 AAATAGTA
7902 AAATA-TA
1 AAATAGTA
7909 AAATAGT
1 AAATAGT
7916 TATAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
6 1 0.04
7 14 0.54
8 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (8 bp):
AAATAGTA
Found at i:7910 original size:93 final size:93
Alignment explanation
Indices: 7792--7975 Score: 287
Period size: 93 Copynumber: 2.0 Consensus size: 93
7782 ACTTTTTAAT
* * * *
7792 TAAATTAGTAATATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAATATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
*
7857 AGTATTTAGTTAAGTAAAACTATAAATG
66 AGTATTTAGTTAACTAAAACTATAAATG
* *
7885 TAAAATAGTAAAATAGTAAATATAAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAG
1 TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
* *
7950 AGTTTTTAGTTGACTAAAACTATAAA
66 AGTATTTAGTTAACTAAAACTATAAA
7976 AGTTTAAACA
Statistics
Matches: 82, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 82 1.00
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.34
Consensus pattern (93 bp):
TAAAATAGTAAAATAGTAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAG
AGTATTTAGTTAACTAAAACTATAAATG
Found at i:9487 original size:13 final size:13
Alignment explanation
Indices: 9469--9493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9459 TACTTTTAAT
9469 ATAGTATAGATAG
1 ATAGTATAGATAG
9482 ATAGTATAGATA
1 ATAGTATAGATA
9494 TAGATAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (13 bp):
ATAGTATAGATAG
Found at i:9543 original size:23 final size:23
Alignment explanation
Indices: 9517--9566 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
9507 TCTTCATCCA
**
9517 AAAAGAAAAATATTTTTTGACAC
1 AAAAGAAAAATATAATTTGACAC
* * *
9540 AAAATAAAACTCTAATTTGACAC
1 AAAAGAAAAATATAATTTGACAC
9563 AAAA
1 AAAA
9567 TACCCCTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (23 bp):
AAAAGAAAAATATAATTTGACAC
Found at i:10328 original size:19 final size:19
Alignment explanation
Indices: 10283--10340 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
10273 ATTGCTCTAA
* *
10283 TAATCTCATCTGTACAGTACC
1 TAATCTAATCTGTACAGT--G
*
10304 TAATCTAATTTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
10323 TAATCTTATCTGTACAGT
1 TAATCTAATCTGTACAGT
10341 TACTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 16 0.50
21 16 0.50
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:14483 original size:42 final size:42
Alignment explanation
Indices: 14423--14539 Score: 198
Period size: 42 Copynumber: 2.8 Consensus size: 42
14413 CTTACCATTA
*
14423 CCTTCACTATGGTCAGGAGGTTCATATTCATCAGACTCATCT
1 CCTTCACTATGGGCAGGAGGTTCATATTCATCAGACTCATCT
* *
14465 GCTTCACTATGGGCAGGAGGATCATATTCATCAGACTCATCT
1 CCTTCACTATGGGCAGGAGGTTCATATTCATCAGACTCATCT
*
14507 CCTTCACTATGCGCAGGAGGTTCATATTCATCA
1 CCTTCACTATGGGCAGGAGGTTCATATTCATCA
14540 AACACAAGAT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (42 bp):
CCTTCACTATGGGCAGGAGGTTCATATTCATCAGACTCATCT
Found at i:17482 original size:28 final size:28
Alignment explanation
Indices: 17447--17504 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
17437 ATCCTAATAC
*
17447 ATTATTATAAACTATTAAATAAAATAGT
1 ATTATTATAAACCATTAAATAAAATAGT
17475 ATTATTATAAACCATTAAATAAAATAGT
1 ATTATTATAAACCATTAAATAAAATAGT
17503 AT
1 AT
17505 GATGTCAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.38
Consensus pattern (28 bp):
ATTATTATAAACCATTAAATAAAATAGT
Found at i:18325 original size:3 final size:3
Alignment explanation
Indices: 18317--18341 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
18307 CAATTGGTCG
18317 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
18342 GTGATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:25615 original size:22 final size:22
Alignment explanation
Indices: 25577--25775 Score: 160
Period size: 22 Copynumber: 9.1 Consensus size: 22
25567 TCAAAAAATT
* * *
25577 ATAGGGAGATTAACAAAATCTC
1 ATAGGAAGATTATCAAAATTTC
*
25599 ATAAGGAAG-TTATCAAAA-ATC
1 AT-AGGAAGATTATCAAAATTTC
25620 ATAGGAAGATTA-CAAAATTTC
1 ATAGGAAGATTATCAAAATTTC
* *
25641 ATAGGAAGGTTTATTAAAATTTC
1 ATAGGAA-GATTATCAAAATTTC
** *
25664 ATAGTTAGGTTATCAAAATTTC
1 ATAGGAAGATTATCAAAATTTC
* *
25686 ATATGG-AGTTTATCACAATTTC
1 ATA-GGAAGATTATCAAAATTTC
* *
25708 ATAGGTA-ATTATCAGAATTTC
1 ATAGGAAGATTATCAAAATTTC
* *
25729 ATAGCG-TGATTATCAAAATTTA
1 ATAG-GAAGATTATCAAAATTTC
*
25751 ATATGGCAG-TTATCAAAATTTC
1 ATA-GGAAGATTATCAAAATTTC
25773 ATA
1 ATA
25776 AAAATATTTA
Statistics
Matches: 146, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
20 11 0.08
21 34 0.23
22 80 0.55
23 21 0.14
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (22 bp):
ATAGGAAGATTATCAAAATTTC
Found at i:25627 original size:20 final size:21
Alignment explanation
Indices: 25568--25648 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
25558 ACTATAGCAT
* * *
25568 CAAAAAATTATAGGGAGATTAA
1 CAAAATATCATAGGAAGATT-A
*
25590 CAAAATCTCATAAGGAAG-TTA
1 CAAAATATCAT-AGGAAGATTA
25611 TCAAAA-ATCATAGGAAGATTA
1 -CAAAATATCATAGGAAGATTA
*
25632 CAAAATTTCATAGGAAG
1 CAAAATATCATAGGAAG
25649 GTTTATTAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
20 11 0.22
21 18 0.37
22 15 0.31
23 5 0.10
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.23
Consensus pattern (21 bp):
CAAAATATCATAGGAAGATTA
Found at i:26838 original size:22 final size:21
Alignment explanation
Indices: 26813--26891 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 21
26803 GGGAGATTAA
*
26813 CAAAATCTCATAAGGAAGTTAT
1 CAAAATTTCAT-AGGAAGTTAT
*
26835 CAAAA-ATCATAGGAAGGTTTAT
1 CAAAATTTCATAGGAA-G-TTAT
* * *
26857 TAAAATTTCATAGTTAGGTTAT
1 CAAAATTTCATAG-GAAGTTAT
26879 CAAAATTTCATAG
1 CAAAATTTCATAG
26892 CTTGATTATC
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.11
21 5 0.11
22 29 0.62
23 7 0.15
24 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (21 bp):
CAAAATTTCATAGGAAGTTAT
Found at i:26850 original size:20 final size:21
Alignment explanation
Indices: 26788--26850 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
26778 CATACTATAG
* *
26788 TATCAAAAAATTATAGGGAGAT
1 TATC-AAAAATCATAGGAAGAT
* *
26810 TAACAAAATCTCATAAGGAAG-T
1 TATCAAAA-ATCAT-AGGAAGAT
26832 TATCAAAAATCATAGGAAG
1 TATCAAAAATCATAGGAAG
26851 GTTTATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 6 0.18
21 8 0.24
22 14 0.42
23 5 0.15
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.24
Consensus pattern (21 bp):
TATCAAAAATCATAGGAAGAT
Found at i:26875 original size:23 final size:22
Alignment explanation
Indices: 26830--26891 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
26820 TCATAAGGAA
* **
26830 GTTATCAAAA-ATCATAGGAAG
1 GTTATCAAAATTTCATAGTTAG
*
26851 GTTTATTAAAATTTCATAGTTAG
1 G-TTATCAAAATTTCATAGTTAG
26874 GTTATCAAAATTTCATAG
1 GTTATCAAAATTTCATAG
26892 CTTGATTATC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.03
22 24 0.71
23 9 0.26
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTTAG
Found at i:26900 original size:22 final size:22
Alignment explanation
Indices: 26853--26901 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
26843 ATAGGAAGGT
* *
26853 TTATTAAAATTTCATAGTTAGG
1 TTATCAAAATTTCATAGTTAGA
26875 TTATCAAAATTTCATAGCTT-GA
1 TTATCAAAATTTCATAG-TTAGA
26897 TTATC
1 TTATC
26902 GATAGTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTTAGA
Found at i:26961 original size:2 final size:2
Alignment explanation
Indices: 26954--26990 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
26944 GTTGGGCCAC
26954 AT AT AT AT AT AT AT AT 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 AT A
26991 CTAGTCTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27086 original size:22 final size:22
Alignment explanation
Indices: 27044--27099 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
27034 TATTTTTATT
* *
27044 AAATTTTAATAATCACACTATG
1 AAATTTTGATAATCACACTATA
*
27066 AAATTTTGATAATTATC-CTATA
1 AAATTTTGATAATCA-CACTATA
*
27088 AAATTCTGATAA
1 AAATTTTGATAA
27100 ACTCCCAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (22 bp):
AAATTTTGATAATCACACTATA
Found at i:27370 original size:22 final size:21
Alignment explanation
Indices: 27345--27442 Score: 72
Period size: 22 Copynumber: 4.5 Consensus size: 21
27335 CTCCTACTTA
*
27345 CTATGAAATTTTGATAATCTC
1 CTATGAAATTTTGATAACCTC
*
27366 GCTAT-ATTATTTTGATAACCTCC
1 -CTATGA-AATTTTGATAACCT-C
** *
27389 CTAAAAAATTGTGATAACCTC
1 CTATGAAATTTTGATAACCTC
* *
27410 CTTGTGAAACTTTGATAACCTC
1 C-TATGAAATTTTGATAACCTC
*
27432 TATATGAAATT
1 -CTATGAAATT
27443 AATTTTGATG
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
21 3 0.05
22 53 0.91
23 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (21 bp):
CTATGAAATTTTGATAACCTC
Found at i:27555 original size:22 final size:22
Alignment explanation
Indices: 27506--27721 Score: 138
Period size: 22 Copynumber: 9.9 Consensus size: 22
27496 TGATTTGGTA
*
27506 CACTATGAAATTTGGATAACCAT
1 CACTATGAAATTTTGATAACC-T
*
27529 -ACTATAAAATTTTGATAACCT
1 CACTATGAAATTTTGATAACCT
* * * *
27550 CCCTATGGAATGTTGATAACTT
1 CACTATGAAATTTTGATAACCT
* * *
27572 CCCTAT-AGAATTTTGTTAATCT
1 CACTATGA-AATTTTGATAACCT
* * * *
27594 CACTGTGAAATTTTGATCAGCA
1 CACTATGAAATTTTGATAACCT
* *
27616 CAATATGAAATTTTGATTACCTT
1 CACTATGAAATTTTGATAACC-T
27639 CA--ATGAAATTTTTG-TAACCAT
1 CACTATGAAA-TTTTGATAACC-T
* *
27660 -ATTATGAAATTTTGATAACCA
1 CACTATGAAATTTTGATAACCT
* * ** *
27681 CATTATGAAATTTTGGTAGGCA
1 CACTATGAAATTTTGATAACCT
*
27703 CACTATGAAATTTCGATAA
1 CACTATGAAATTTTGATAA
27722 TCCATTAATC
Statistics
Matches: 151, Mismatches: 33, Indels: 19
0.74 0.16 0.09
Matches are distributed among these distances:
20 1 0.01
21 17 0.11
22 130 0.86
23 3 0.02
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (22 bp):
CACTATGAAATTTTGATAACCT
Found at i:28205 original size:2 final size:2
Alignment explanation
Indices: 28198--28225 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28188 TATTCGTATT
28198 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
28226 CATACTAGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29761 original size:58 final size:59
Alignment explanation
Indices: 29664--29783 Score: 206
Period size: 58 Copynumber: 2.1 Consensus size: 59
29654 GTCCAAATGG
* *
29664 AAACATGTACAATACTACAAATATTGCATCATATTTTTGCTTTTAAAAAAA-TGTAGAA
1 AAACATGTACAATACTACAAATATTGCATCACATCTTTGCTTTTAAAAAAATTGTAGAA
*
29722 AAACATGTACACTACTACAAATATTGCATCACATCTTTGCTTTTAAAAAAATTGTAGAA
1 AAACATGTACAATACTACAAATATTGCATCACATCTTTGCTTTTAAAAAAATTGTAGAA
29781 AAA
1 AAA
29784 ACATATATGA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
58 48 0.83
59 10 0.17
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (59 bp):
AAACATGTACAATACTACAAATATTGCATCACATCTTTGCTTTTAAAAAAATTGTAGAA
Found at i:31283 original size:3 final size:3
Alignment explanation
Indices: 31270--31305 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
31260 GACTTTTATG
31270 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31306 GGTCAACTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Done.