Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013105.1 Corchorus olitorius cultivar O-4 contig13138, 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: 26829
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:497 original size:31 final size:31
Alignment explanation
Indices: 426--497 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
416 GTCTATCAGC
*
426 TTTTAATTTGTTTAATTTAAGACTTTCATTT
1 TTTTAATTTGTTTAATTTAAGACTTTAATTT
*
457 TAATT-ATTTGTTTAATTTAATG-C-TTAATTT
1 T-TTTAATTTGTTTAATTTAA-GACTTTAATTT
487 GTTTTAATTTG
1 -TTTTAATTTG
498 CAATAATTTA
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:0.04, G:0.08, T:0.61
Consensus pattern (31 bp):
TTTTAATTTGTTTAATTTAAGACTTTAATTT
Found at i:786 original size:12 final size:12
Alignment explanation
Indices: 769--810 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
759 ATCAAAATCA
769 AACCCGAGCCCG
1 AACCCGAGCCCG
**
781 AACCCGAATCC-
1 AACCCGAGCCCG
*
792 TACCCGAGCCCG
1 AACCCGAGCCCG
804 AACCCGA
1 AACCCGA
811 AAATACCCGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.29, C:0.48, G:0.19, T:0.05
Consensus pattern (12 bp):
AACCCGAGCCCG
Found at i:790 original size:23 final size:23
Alignment explanation
Indices: 764--811 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
754 ATCGAATCAA
764 AATCAAACCCGAGCCCGAACCCG
1 AATCAAACCCGAGCCCGAACCCG
**
787 AATCCTACCCGAGCCCGAACCCG
1 AATCAAACCCGAGCCCGAACCCG
810 AA
1 AA
812 AATACCCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.44, G:0.17, T:0.06
Consensus pattern (23 bp):
AATCAAACCCGAGCCCGAACCCG
Found at i:820 original size:22 final size:23
Alignment explanation
Indices: 770--826 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
760 TCAAAATCAA
**
770 ACCCGAGCCCGAACCCGAATCCT
1 ACCCGAGCCCGAACCCGAATAAT
793 ACCCGAGCCCGAACCCGAA-AAT
1 ACCCGAGCCCGAACCCGAATAAT
*
815 ACCCGAACCCGA
1 ACCCGAGCCCGA
827 CATAACCCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 12 0.39
23 19 0.61
ACGTcount: A:0.32, C:0.46, G:0.18, T:0.05
Consensus pattern (23 bp):
ACCCGAGCCCGAACCCGAATAAT
Found at i:821 original size:16 final size:16
Alignment explanation
Indices: 800--936 Score: 215
Period size: 16 Copynumber: 8.6 Consensus size: 16
790 CCTACCCGAG
800 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
816 CCCGAACCCG-ACATAA
1 CCCGAACCCGAAAAT-A
*
832 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
*
848 CCCGAGCCCGAAAATA
1 CCCGAACCCGAAAATA
864 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
880 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
896 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
912 CCCGAACCCG-AAGTA
1 CCCGAACCCGAAAATA
927 CCCGAACCCG
1 CCCGAACCCG
937 CCCAATTGCC
Statistics
Matches: 114, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.15
16 94 0.82
17 3 0.03
ACGTcount: A:0.39, C:0.40, G:0.15, T:0.06
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:1522 original size:3 final size:3
Alignment explanation
Indices: 1514--1566 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
1504 AATAAGTTTC
1514 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1562 ATT AT
1 ATT AT
1567 ATATGTGGGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6658 original size:23 final size:23
Alignment explanation
Indices: 6610--6711 Score: 120
Period size: 23 Copynumber: 4.5 Consensus size: 23
6600 TCACACTATG
* *
6610 AAATTGTGAT-AACCTCGC-TATG
1 AAATTTTGATAAACCTC-CTTATA
6632 AAATTTTGATAAACCTCCTTATA
1 AAATTTTGATAAACCTCCTTATA
*
6655 AAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAACCTCCTTATA
* *
6678 AAATTTTGAT-AATCTCCTTATG
1 AAATTTTGATAAACCTCCTTATA
*
6700 AAATCTTGATAA
1 AAATTTTGATAA
6712 CTACAAATTT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
22 28 0.40
23 42 0.60
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (23 bp):
AAATTTTGATAAACCTCCTTATA
Found at i:6853 original size:88 final size:88
Alignment explanation
Indices: 6756--6967 Score: 343
Period size: 88 Copynumber: 2.4 Consensus size: 88
6746 ATAACCTCAT
* * * * * * *
6756 TATGAAATTTTGTTCATCTCCCTATGGAATTTTGATCTACATACTATGAAATTTTGATAATCCTC
1 TATGAAATTTTGATAACCTCCATATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTC
6821 TTATGAAATTTTGAAAACTAAAC
66 TTATGAAATTTTGAAAACTAAAC
*
6844 TATGAAATTTTGATAACCTTCATATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTC
1 TATGAAATTTTGATAACCTCCATATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTC
6909 TTATGAAATTTTGAAAACTAAAC
66 TTATGAAATTTTGAAAACTAAAC
*
6932 TATGAAATTTTGATAACCTTCATATGAAATTTTGAT
1 TATGAAATTTTGATAACCTCCATATGAAATTTTGAT
6968 ATCCTCCTTG
Statistics
Matches: 116, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 116 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (88 bp):
TATGAAATTTTGATAACCTCCATATGAAATTTTGATCTACATACTATAAAATTTTGATAACCCTC
TTATGAAATTTTGAAAACTAAAC
Found at i:6981 original size:20 final size:22
Alignment explanation
Indices: 6305--6987 Score: 234
Period size: 22 Copynumber: 31.3 Consensus size: 22
6295 ATTACACTAT
* * *
6305 TTTTGATGACCTCCTTATGAAA
1 TTTTGATAACCTTCATATGAAA
* * *
6327 TTTTGATAACATTCCTATCAAA
1 TTTTGATAACCTTCATATGAAA
* **
6349 TTTTAATAACGAT-ACTAT-AGAA
1 TTTTGATAACCTTCA-TATGA-AA
* ** *
6371 TTTCGATAACCTTTTTAT-AAT
1 TTTTGATAACCTTCATATGAAA
** *
6392 TTTTTTTAACCTTCTTATGAAA
1 TTTTGATAACCTTCATATGAAA
* * * * *
6414 TTTTGTTAACCTCCCTAAGGAA
1 TTTTGATAACCTTCATATGAAA
6436 TTTTGA-AGACC-TCATTATGAAA
1 TTTTGATA-ACCTTCA-TATGAAA
6458 TTTTGATAA-CTTCCCAT-TGAAA
1 TTTTGATAACCTT--CATATGAAA
** *
6480 TTTTGATAACCAACACTATGAGA
1 TTTTGATAACCTTCA-TATGAAA
* * *
6503 TGTTGATAACCTCCATATGATA
1 TTTTGATAACCTTCATATGAAA
* *
6525 TATTGATAACAACGT--TATGAAA
1 TTTTGATAAC--CTTCATATGAAA
* * * *
6547 ATTTAAAAACCTCCATATG-AA
1 TTTTGATAACCTTCATATGAAA
* * *
6568 TTGTT-AGTAATC-ACACTCTGAAA
1 TT-TTGA-TAACCTTCA-TATGAAA
* *
6591 TTTTGATAATC-ACACTATGAAA
1 TTTTGATAACCTTCA-TATGAAA
* *
6613 TTGTGATAACC-TCGCTATGAAA
1 TTTTGATAACCTTC-ATATGAAA
* * *
6635 TTTTGATAAACCTCCTTATAAAA
1 TTTTGAT-AACCTTCATATGAAA
* * *
6658 TTTTGATAAACCTCCCTATAAAA
1 TTTTGAT-AACCTTCATATGAAA
* * *
6681 TTTTGATAATCTCCTTATGAAA
1 TTTTGATAACCTTCATATGAAA
* *
6703 TCTTGATAA----C-TA-CAAA
1 TTTTGATAACCTTCATATGAAA
* * * * **
6719 TTTTTAAAACCTCCCTATGATT
1 TTTTGATAACCTTCATATGAAA
*
6741 TTTTTATAACC-TCATTATGAAA
1 TTTTGATAACCTTCA-TATGAAA
* * * * * *
6763 TTTTGTTCATCTCCCTATGGAA
1 TTTTGATAACCTTCATATGAAA
* * *
6785 TTTTGATCTACATAC-TATGAAA
1 TTTTGAT-AACCTTCATATGAAA
*
6807 TTTTGATAATCC-TCTTATGAAA
1 TTTTGATAA-CCTTCATATGAAA
* **
6829 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCTTCA-TATGAAA
6851 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTCATATGAAA
* * * *
6873 TTTTGATCTACATAC-TATAAAA
1 TTTTGAT-AACCTTCATATGAAA
* *
6895 TTTTGATAACCCTCTTATGAAA
1 TTTTGATAACCTTCATATGAAA
* **
6917 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCTTCA-TATGAAA
6939 TTTTGATAACCTTCATATGAAA
1 TTTTGATAACCTTCATATGAAA
* *
6961 TTTTGATATCC-TCCT-TGAAA
1 TTTTGATAACCTTCATATGAAA
6981 TTTTGAT
1 TTTTGAT
6988 TACTCTAGAA
Statistics
Matches: 498, Mismatches: 120, Indels: 88
0.71 0.17 0.12
Matches are distributed among these distances:
16 9 0.02
17 2 0.00
18 1 0.00
20 15 0.03
21 43 0.09
22 343 0.69
23 81 0.16
24 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TTTTGATAACCTTCATATGAAA
Found at i:7450 original size:22 final size:21
Alignment explanation
Indices: 7093--7463 Score: 137
Period size: 22 Copynumber: 16.7 Consensus size: 21
7083 AATTACATTT
* *
7093 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTC-CTA
7115 TGAAATTTTGATAACCTCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * * *
7137 TAAAATTTCGTTGACCCCTCTA
1 TGAAATTTTGATAACCTC-CTA
* * * *
7159 TAAAAATTTTGATAATCACATTA
1 T-GAAATTTTGATAACCTC-CTA
* *
7182 TGTAATTTTGATAACCTCGCTT
1 TGAAATTTTGATAACCTC-CTA
**
7204 TGAAATTTTTGATAACAACACTA
1 TGAAA-TTTTGATAACCTC-CTA
*
7227 TGAAATTTTGATAATCTTCCTA
1 TGAAATTTTGATAA-CCTCCTA
7249 T-AAATTTTGATAATCCGATCTCTA
1 TGAAATTTTGATAA-CC--TC-CTA
**
7273 TGAAATTTCAATAATCACT-CTA
1 TGAAATTTTGATAA-C-CTCCTA
* * *
7295 TGAGA-TTTGATAATCTTCTA
1 TGAAATTTTGATAACCTCCTA
* * *
7315 T-CAATGTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCC-TA
* *
7334 TGAAATTGACACTTTTATAACCTTCTTA
1 TGAAA-T-----TTTGATAACC-TCCTA
*
7362 TGAAATTTTGATAACCTCCCCA
1 TGAAATTTTGATAACCT-CCTA
*
7384 TGAAATATT-AGTAACCTCCTTA
1 TGAAATTTTGA-TAACCTCC-TA
* *
7406 TGAAATTTTGTTAACCACACTA
1 TGAAATTTTGATAACCTC-CTA
7428 TGAAATTCTT-ATAACCTCGCTA
1 TGAAATT-TTGATAACCTC-CTA
* *
7450 TGACATTTCGATAA
1 TGAAATTTTGATAA
7464 TCTCTTTGAT
Statistics
Matches: 263, Mismatches: 58, Indels: 56
0.70 0.15 0.15
Matches are distributed among these distances:
18 3 0.01
19 7 0.03
20 10 0.04
21 26 0.10
22 144 0.55
23 40 0.15
24 5 0.02
25 12 0.05
26 4 0.02
27 2 0.01
28 8 0.03
29 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (21 bp):
TGAAATTTTGATAACCTCCTA
Found at i:7578 original size:22 final size:22
Alignment explanation
Indices: 7481--7704 Score: 156
Period size: 22 Copynumber: 10.0 Consensus size: 22
7471 GATAACCTTT
*
7481 CTATAAAATTTGTGATAACCACA
1 CTATGAAATTT-TGATAACCACA
** *
7504 CTATGAAATTTCAATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
* * *
7526 CTAAGAAATTTTAATAA-CATGA
1 CTATGAAATTTTGATAACCA-CA
*
7548 TCCTATGAAATTTTGGTAACCACA
1 --CTATGAAATTTTGATAACCACA
*
7572 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
7594 CCATGAAATTTTGATAACTTC-CA
1 CTATGAAATTTTGATAAC--CACA
*
7617 -TATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
* * *
7638 CTACGGAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
7659 CTCATGAAATTATAATAACCATC-
1 CT-ATGAAATTTTGATAACCA-CA
*
7682 TTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
7704 C
1 C
7705 AGAGACAAGA
Statistics
Matches: 156, Mismatches: 30, Indels: 31
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 117 0.75
23 14 0.09
24 16 0.10
25 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:7650 original size:66 final size:66
Alignment explanation
Indices: 7472--7704 Score: 272
Period size: 66 Copynumber: 3.5 Consensus size: 66
7462 AATCTCTTTG
* * ** * *
7472 ATAACCTTTCTATAAAATTTGTGATAACCACACTATGAAATTTCAATAACCTTCCTAAGAAATTT
1 ATAACCTTCCTATGAAATTT-TGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTT
7537 TA
65 TA
* *
7539 ATAACATGATCCTATGAAATTTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
1 ATAACCT--TCCTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATT
*
7604 TTG
64 TTA
* * *
7607 ATAA-CTTCCATATGAAATTTTGGTAACCACACTACGGAATTTTGATAACC-TCCTCATGAAATT
1 ATAACCTTCC-TATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCC-CATGAAATT
*
7670 ATA
64 TTA
* *
7673 ATAACCATCTTATGAAATTTTGATAACCACAC
1 ATAACCTTCCTATGAAATTTTGATAACCACAC
7705 AGAGACAAGA
Statistics
Matches: 144, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
65 6 0.04
66 73 0.51
67 10 0.07
68 44 0.31
69 11 0.08
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (66 bp):
ATAACCTTCCTATGAAATTTTGATAACCACACTATGAAATTTTGATAACCTTCCCATGAAATTTT
A
Found at i:7700 original size:44 final size:43
Alignment explanation
Indices: 7468--7700 Score: 191
Period size: 44 Copynumber: 5.2 Consensus size: 43
7458 CGATAATCTC
* * *
7468 TTTGATAACCTTTCTATAAAATTTGTGATAACCA-CACTATGAAAT
1 TTTGATAACC-TCCTATGAAATTT-TAATAACCATC-CTATGAAAT
** * *
7513 TTCAATAACCTTCCTAAGAAATTTTAATAACATGATCCTATGAAAT
1 TTTGATAACC-TCCTATGAAATTTTAATAAC--CATCCTATGAAAT
* * * * *
7559 TTTGGTAACCACACTATGAAATTTTGATAACCTTCCCATGAAAT
1 TTTGATAACCTC-CTATGAAATTTTAATAACCATCCTATGAAAT
* ** * *
7603 TTTGATAACTTCCATATGAAATTTTGGTAACCA-CACTACGGAAT
1 TTTGATAACCTCC-TATGAAATTTTAATAACCATC-CTATGAAAT
* *
7647 TTTGATAACCTCCTCATGAAATTATAATAACCATCTTATGAAAT
1 TTTGATAACCTCCT-ATGAAATTTTAATAACCATCCTATGAAAT
7691 TTTGATAACC
1 TTTGATAACC
7701 ACACAGAGAC
Statistics
Matches: 149, Mismatches: 31, Indels: 17
0.76 0.16 0.09
Matches are distributed among these distances:
43 3 0.02
44 91 0.61
45 21 0.14
46 33 0.22
47 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (43 bp):
TTTGATAACCTCCTATGAAATTTTAATAACCATCCTATGAAAT
Found at i:9323 original size:29 final size:30
Alignment explanation
Indices: 9263--9324 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
9253 AAAAGAAAAA
* *
9263 GAAAACAAAAAAAATTTCATTTCTCTTGTC
1 GAAAACAAAAAAAATTTCATATCTCTTCTC
*
9293 GAAAA-AAAAAAAATTTCATGAT-TGTTCTC
1 GAAAACAAAAAAAATTTCAT-ATCTCTTCTC
9322 GAA
1 GAA
9325 GATAAACATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.31
Consensus pattern (30 bp):
GAAAACAAAAAAAATTTCATATCTCTTCTC
Found at i:11448 original size:2 final size:2
Alignment explanation
Indices: 11443--11483 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11433 CATATGTGTG
11443 TA TA TA TA TA 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 TA TA TA TA TA T
11484 TCTATGCCCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16656 original size:73 final size:73
Alignment explanation
Indices: 16537--16684 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
16527 CAAAAAAAGA
16537 CTCTCCTCTATCTTCCATCTTTTACCAATGTGGGATATGAGATAGTTTACAAAGCTTGACACACT
1 CTCTCCTCTATCTTCCATCTTTTACCAATGTGGGATATGAGATAGTTTACAAAGCTTGACACACT
16602 CCTTTGTT
66 CCTTTGTT
16610 CTCTCCTCTATCTTCCATCTTTTACCAATGTGGGATATGAGATAGTTTACAAAGCTTGACACACT
1 CTCTCCTCTATCTTCCATCTTTTACCAATGTGGGATATGAGATAGTTTACAAAGCTTGACACACT
16675 CCTTTGTT
66 CCTTTGTT
16683 CT
1 CT
16685 TTATCTTTCT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (73 bp):
CTCTCCTCTATCTTCCATCTTTTACCAATGTGGGATATGAGATAGTTTACAAAGCTTGACACACT
CCTTTGTT
Found at i:17113 original size:107 final size:107
Alignment explanation
Indices: 16903--17092 Score: 278
Period size: 106 Copynumber: 1.8 Consensus size: 107
16893 TTTATATATT
* ** * * *
16903 TTTTTCTAAAACCCTATGATAATGGGTTTTAAAATTTAAGATTTACCCTTAAAAAAACAAATATT
1 TTTTTCTAAAACCCTATGATAATGGGTCTTAAAATAAAAAATTTACCCTTAAAAAAACAAACAAT
16968 TTTATAATTGGGGCTAAACCTAGTAATAAGTGTTTAAATTTA
66 TTTATAATTGGGGCTAAACCTAGTAATAAGTGTTTAAATTTA
* **
17010 TTTTTGTAAAACCCTATGATAATGGGTCTT-AAATAAAAAATTTACCCTTAAAAAAATTAACAAT
1 TTTTTCTAAAACCCTATGATAATGGGTCTTAAAATAAAAAATTTACCCTTAAAAAAACAAACAAT
17074 TTT-TAATT-GGGCTAAACCT
66 TTTATAATTGGGGCTAAACCT
17093 TGGTGACTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
104 11 0.15
105 5 0.07
106 30 0.41
107 28 0.38
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.38
Consensus pattern (107 bp):
TTTTTCTAAAACCCTATGATAATGGGTCTTAAAATAAAAAATTTACCCTTAAAAAAACAAACAAT
TTTATAATTGGGGCTAAACCTAGTAATAAGTGTTTAAATTTA
Found at i:22772 original size:2 final size:2
Alignment explanation
Indices: 22761--22790 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
22751 AATAGTGTCT
22761 CA CA -A CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
22791 GCTTGTTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:24835 original size:63 final size:63
Alignment explanation
Indices: 24736--24859 Score: 248
Period size: 63 Copynumber: 2.0 Consensus size: 63
24726 TAATTCTTAG
24736 TTGTTCAATTATGAATTGTTCTACGAAATTGTGATGATGACTTTGTATTTATAGGCACCTAAA
1 TTGTTCAATTATGAATTGTTCTACGAAATTGTGATGATGACTTTGTATTTATAGGCACCTAAA
24799 TTGTTCAATTATGAATTGTTCTACGAAATTGTGATGATGACTTTGTATTTATAGGCACCTA
1 TTGTTCAATTATGAATTGTTCTACGAAATTGTGATGATGACTTTGTATTTATAGGCACCTA
24860 GGTCGGTTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.42
Consensus pattern (63 bp):
TTGTTCAATTATGAATTGTTCTACGAAATTGTGATGATGACTTTGTATTTATAGGCACCTAAA
Done.