Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007864.1 Corchorus capsularis cultivar CVL-1 contig07885, 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: 37607
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4429 original size:975 final size:975
Alignment explanation
Indices: 1578--4505 Score: 5536
Period size: 974 Copynumber: 3.0 Consensus size: 975
1568 TTACCAATTG
1578 ATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAATCA
1 ATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAATCA
1643 CCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCGTCGGCCTT
66 CCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCGTCGGCCTT
1708 AGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACCAAGCAATC
131 AGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACCAAGCAATC
*
1773 ACAACTTAATTGTTTGCTAGGACTCTACAAGATTGGAGAACCCTAAGTTTGCTCAAACTAGAACA
196 ACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAACTAGAACA
1838 ATGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTCAACT
261 ATGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTCAACT
1903 TTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCCTA
326 TTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCCTA
1968 ATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCAAACTTG-CCAACTAGGAAAAGGAAA
391 ATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGT-C---CTTGCCCAACTAGGAAAAGGAAA
2032 TAAAGACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAAC
452 TAAAGACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAAC
* *
2097 TTAAAAATAAGCTAATCTAAGATAGAATTAAGCCCAAACAAAGATAACTAATGATAATGGGTTCA
517 TTAAAAATAAGCTAATCTAAGATTGAATTAAGCCCAAACAAAGATAACTAATGATAATGGGCTCA
2162 TGCCATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATT
582 TGCCATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATT
* *
2227 TGTAATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTAAATTTCAATGGTCTTCAAGTCTTC
647 TGTAATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTC
2292 AAGATGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTTTTAGCTCTTCCTCTTGTCATCG
712 AAGATGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTTTTAGCTCTTCCTCTTGTCATCG
*
2357 GACCTAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTAAATTGCGACT
777 GACCTAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTGCGACT
*
2422 CCATTCTCTCCTTTAAACTTGTCCACGCTTCTTTGCAGCCCTTGATCATCCGTTCCATGTTCTCC
842 CCATTCTCTCCTTTAAACTTGTCCACGCTTCTTTGCAGCCCTTGATCATCCGTTCCATGCTCTCC
2487 ATGCTTGTCTTCAAGTCTATAATATGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTTGGGCG
907 ATGCTTGTCTTCAAGTCTATAATATGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTTGGGCG
2552 CATC
972 CATC
2556 ATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAATCA
1 ATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAATCA
* *
2621 CCAAACTTCTAGATGTGTATGTCGACAATCTTAACTTGATAAATCATCCTTCGTTCGTCGGCCTT
66 CCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCGTCGGCCTT
*
2686 AGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGTTTCACAAACAACCAAGCAATC
131 AGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACCAAGCAATC
2751 ACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAACTAGAACA
196 ACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAACTAGAACA
*
2816 ATGAAGCTAAGATAGTCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTCAACT
261 ATGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTCAACT
*
2881 TTTACAAGAGATATTGCTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCCTA
326 TTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCCTA
2946 ATTTT-GTCCAAATATAAGGGCTAGGGAAAAACTAGTCCTTGCCCAACTAGGAAAAGGAAATAAA
391 ATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCTTGCCCAACTAGGAAAAGGAAATAAA
3010 GACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAACTTAA
456 GACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAACTTAA
* *
3075 AAATAAGCTAATCTAAGATTGAATTAAACCCAAACATAGATAACTAATGATAATGGGCTCATGCC
521 AAATAAGCTAATCTAAGATTGAATTAAGCCCAAACAAAGATAACTAATGATAATGGGCTCATGCC
3140 ATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTA
586 ATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTA
3205 ATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGA
651 ATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGA
3270 TGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTTTTAGCTCTTCCTCTTGTCATCGGACC
716 TGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTTTTAGCTCTTCCTCTTGTCATCGGACC
3335 TAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTGCGACTCCAT
781 TAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTGCGACTCCAT
3400 TCTCTCCTTTAAACTTGTCCACGCTTCTTTGCAGCCCTTGATCATCCGTTCCATGCTCTCCATGC
846 TCTCTCCTTTAAACTTGTCCACGCTTCTTTGCAGCCCTTGATCATCCGTTCCATGCTCTCCATGC
3465 TTGTCTTCAAGTCTATAATATGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTTGGGCGCATC
911 TTGTCTTCAAGTCTATAATATGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTTGGGCGCATC
3530 ATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAATCA
1 ATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAATCA
*
3595 CCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCATCGGCCTT
66 CCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCGTCGGCCTT
*
3660 AGACCTCCAAATCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACCAAGCAATC
131 AGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACCAAGCAATC
*
3725 ACAACTTAATTGTTTGCTAGGACTCTATAAGATTGAAGAACCCTAAGTTTGCTCAAACTAGAACA
196 ACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAACTAGAACA
* *
3790 ATGAAACTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACCTCAACT
261 ATGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTCAACT
3855 TTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCCTA
326 TTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCCTA
3920 ATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCTTGCCCAACTAGGAAAAGGAAATAAA
391 ATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCTTGCCCAACTAGGAAAAGGAAATAAA
3985 GACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAACTTAA
456 GACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAACTTAA
4050 AAATAAGCTAATCTAAGATTGAATTAAGCCCAAACAAAGATAACTAATGATAATGGGCTCATGCC
521 AAATAAGCTAATCTAAGATTGAATTAAGCCCAAACAAAGATAACTAATGATAATGGGCTCATGCC
*
4115 ATGATGTCAATTCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTA
586 ATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTA
4180 ATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGA
651 ATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGA
* *
4245 TGAGTTCGAATAAGGCCCATGAGTGCATCCTTGAATCTTTTAACTCTTCCTCTTGTCATCGGACC
716 TGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTTTTAGCTCTTCCTCTTGTCATCGGACC
* * *
4310 TAATGGCATTTTTAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTGCGATTCCAT
781 TAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTGCGACTCCAT
* *
4375 TCTCTCCTTTAAACTTGTCCACGCTTCTTTGCAGCCTTTGATCATCCTTTCCATGCTCTCCATGC
846 TCTCTCCTTTAAACTTGTCCACGCTTCTTTGCAGCCCTTGATCATCCGTTCCATGCTCTCCATGC
** *
4440 TTGTCTTCAAGTCTATAATATGTCCTTAACGCATAATTCCTTCCATGATAAGCTTTGGGCGCATC
911 TTGTCTTCAAGTCTATAATATGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTTGGGCGCATC
4505 A
1 A
4506 GATGTCATTA
Statistics
Matches: 1911, Mismatches: 37, Indels: 7
0.98 0.02 0.00
Matches are distributed among these distances:
973 4 0.00
974 919 0.48
975 567 0.30
976 1 0.00
977 31 0.02
978 389 0.20
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (975 bp):
ATACGAATCTAGTTGTAATTGGTCCAAATCCACCTTAGAGACCCGCCTAAGATCAACTTGAATCA
CCAAACTTCTAGATGTGTATGTCGACAATCTTCACTTGATAAATCTTCCTTCGTTCGTCGGCCTT
AGACCTCCAAGTCGACCTGCACTTGAACACCTAAGATCACAAGATTCACAAACAACCAAGCAATC
ACAACTTAATTGTTTGCTAGGACTCTACAAGATTGAAGAACCCTAAGTTTGCTCAAACTAGAACA
ATGAAGCTAAGATAATCAATTTGGGAAAATAATCCTCAACTTTATTAATCAACTCAACTTCAACT
TTTACAAGAGATATTGGTGGCCTTATATAGTGATAGGGTCAACCAAAATCCTAAAATAAATCCTA
ATTTTCGTCCAAATATAAGGGCTAGGGAAAAACTAGTCCTTGCCCAACTAGGAAAAGGAAATAAA
GACATAATTAAACAAGGATTGGACTTAGTCAACCAAGGCCCAATCCAAATAAGGTCCAAACTTAA
AAATAAGCTAATCTAAGATTGAATTAAGCCCAAACAAAGATAACTAATGATAATGGGCTCATGCC
ATGATGTCAATCCGGCCATCTAGAATCAATAGCAAGCAATGTGATGAACTTGTAATTGATTTGTA
ATTTCTTGCCCAAATCATCACCAAAGCTCTTCAATTGAACTTCAATGGTCTTCAAGTCTTCAAGA
TGAGTTCGAACAAGGCCCATGAGTGCATCCTTGAATCTTTTAGCTCTTCCTCTTGTCATCGGACC
TAATGGCATCTTCAAAGGATCAAATGGCATCTTAATGGCATCTTCTTGGTGAATTGCGACTCCAT
TCTCTCCTTTAAACTTGTCCACGCTTCTTTGCAGCCCTTGATCATCCGTTCCATGCTCTCCATGC
TTGTCTTCAAGTCTATAATATGTCCTTGGCGCATAATTCCTTCCATGATAAGCCTTGGGCGCATC
Found at i:5096 original size:7 final size:7
Alignment explanation
Indices: 5084--5110 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5074 TCGAACTCCC
5084 TCCCAAG
1 TCCCAAG
5091 TCCCAAG
1 TCCCAAG
5098 TCCCAAG
1 TCCCAAG
5105 TCCCAA
1 TCCCAA
5111 CTCCATTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.44, G:0.11, T:0.15
Consensus pattern (7 bp):
TCCCAAG
Found at i:22077 original size:22 final size:22
Alignment explanation
Indices: 22052--22653 Score: 231
Period size: 22 Copynumber: 27.9 Consensus size: 22
22042 ATGATCCCAT
22052 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
* **
22074 TATGAAATTTTAATAA-C--GA
1 TATGAAATTTTGATAACCTTCC
* * * **
22093 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* ** *
22115 TAT-AATTTTTTTTTAACCTTCT
1 TATGAA-ATTTTGATAACCTTCC
* *
22137 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
22159 TAAGGAATTTTGA-AGACC-TCAA
1 TATGAAATTTTGATA-ACCTTC-C
22181 TATGAAATTTTGATAA-CTTCCC
1 TATGAAATTTTGATAACCTT-CC
* * *
22203 AATGAAATTATGATAACCTACAC
1 TATGAAATTTTGATAACCTTC-C
* *
22226 TATGAGATGTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
22247 ATATGATATATTGATAATCACGT--
1 -TATGAAATTTTGATAA-C-CTTCC
* * * *
22270 TATAAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
22291 ATATG-AATTGTT-AGTAATC-ACAC
1 -TATGAAATT-TTGA-TAACCTTC-C
* * *
22314 TCTGAAATTTTGATAATC-ACAC
1 TATGAAATTTTGATAACCTTC-C
*
22336 TATGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
22358 TATGAAATTTTGATAAATCTTTC
1 TATGAAATTTTGAT-AACCTTCC
* *
22381 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTTCC
* * *
22404 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTTCC
*
22426 TATGAAATCTTGATAA-----C
1 TATGAAATTTTGATAACCTTCC
* *
22443 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
22464 TATGATTTTTTGATAACC-TCAA
1 TATGAAATTTTGATAACCTTC-C
* * *
22486 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* *
22508 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
22530 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
*
22552 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
*
22574 TATGAAATTTTGATTA-C-TCC
1 TATGAAATTTTGATAACCTTCC
* * *
22594 ATAATAAAAGTTTAATAACCTTCC
1 -T-ATGAAATTTTGATAACCTTCC
* * *
22618 --T--AA-TTTGGTAACCATAC
1 TATGAAATTTTGATAACCTTCC
22635 TATGAAATTTTGATAACCT
1 TATGAAATTTTGATAACCT
22654 CCCAGAAATA
Statistics
Matches: 428, Mismatches: 107, Indels: 90
0.68 0.17 0.14
Matches are distributed among these distances:
16 11 0.03
17 12 0.03
18 2 0.00
19 14 0.03
20 5 0.01
21 22 0.05
22 285 0.67
23 71 0.17
24 5 0.01
25 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:22388 original size:23 final size:22
Alignment explanation
Indices: 22357--22441 Score: 91
Period size: 23 Copynumber: 3.8 Consensus size: 22
22347 GATAACCTCG
*
22357 CTATGAAATTTTGATAAATCTTT
1 CTATAAAATTTTGATAAA-CTTT
**
22380 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAA-CTTT
22403 CTATAAAATTTTGAT-AACTTT
1 CTATAAAATTTTGATAAACTTT
* *
22424 CTTATGAAATCTTGATAA
1 C-TATAAAATTTTGATAA
22442 CTACAAATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.06
22 14 0.27
23 35 0.67
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (22 bp):
CTATAAAATTTTGATAAACTTT
Found at i:22440 original size:45 final size:45
Alignment explanation
Indices: 22318--22441 Score: 130
Period size: 45 Copynumber: 2.8 Consensus size: 45
22308 TCACACTCTG
*** * *
22318 AAATTTTGAT-AATCACACTATGAAATTGTGAT-AACCTCGCTATG
1 AAATTTTGATAAATCTTTCTATGAAATT-TGATAAACCTCCCTATA
*
22362 AAATTTTGATAAATCTTTCTATAAAATTTTGATAAACCTCCCTATA
1 AAATTTTGATAAATCTTTCTATGAAA-TTTGATAAACCTCCCTATA
22408 AAATTTTGAT-AA-CTTTCTTATGAAATCTTGATAA
1 AAATTTTGATAAATCTTTC-TATGAAAT-TTGATAA
22442 CTACAAATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
44 16 0.24
45 30 0.44
46 22 0.32
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.40
Consensus pattern (45 bp):
AAATTTTGATAAATCTTTCTATGAAATTTGATAAACCTCCCTATA
Found at i:22675 original size:33 final size:34
Alignment explanation
Indices: 22633--22712 Score: 144
Period size: 34 Copynumber: 2.4 Consensus size: 34
22623 TGGTAACCAT
22633 ACTATGAAATTTTGATAACCT-CCCAGAAATACC
1 ACTATGAAATTTTGATAACCTCCCCAGAAATACC
*
22666 ACTATGAAATTTTGATAACCTCCCCTGAAATACC
1 ACTATGAAATTTTGATAACCTCCCCAGAAATACC
22700 ACTATGAAATTTT
1 ACTATGAAATTTT
22713 TGTAATCACA
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 21 0.47
34 24 0.53
ACGTcount: A:0.38, C:0.23, G:0.09, T:0.31
Consensus pattern (34 bp):
ACTATGAAATTTTGATAACCTCCCCAGAAATACC
Found at i:22751 original size:22 final size:22
Alignment explanation
Indices: 22726--22777 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
22716 AATCACATTT
22726 TGAAAATTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
*
22748 TGAAATTTTGATAACCTCTTTA
1 TGAAAATTTGATAACCTCTTTA
22770 T-AAAATTT
1 TGAAAATTT
22778 TCACTACAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.37, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
TGAAAATTTGATAACCTCTTTA
Found at i:25991 original size:27 final size:27
Alignment explanation
Indices: 25940--25992 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
25930 CGTATAATCC
* *
25940 AATTAGATTTACAATTTTGACAAAAAA
1 AATTAGATTCACAATTATGACAAAAAA
25967 AATTAGATTCACAATTAATGA-AAAAA
1 AATTAGATTCACAATT-ATGACAAAAA
25993 CAAAGAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.30
Consensus pattern (27 bp):
AATTAGATTCACAATTATGACAAAAAA
Found at i:26027 original size:12 final size:13
Alignment explanation
Indices: 26010--26038 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
26000 CAATAGATTC
26010 TTTTTTCT-TTCT
1 TTTTTTCTCTTCT
26022 TTTTTTCTCTTCT
1 TTTTTTCTCTTCT
26035 TTTT
1 TTTT
26039 GAAATATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTCTCTTCT
Found at i:27533 original size:22 final size:21
Alignment explanation
Indices: 27498--27656 Score: 100
Period size: 22 Copynumber: 7.4 Consensus size: 21
27488 TTGACCCCTC
*
27498 TATGAAATTCTGATAATCACAT
1 TATGAAATTTTGATAATC-CAT
*
27520 TAT-ATAATTTTGAT-ATCGAT
1 TATGA-AATTTTGATAATCCAT
27540 T-TGAAATTTTGATAA-CAACAT
1 TATGAAATTTTGATAATC--CAT
**
27561 TATGAAATTTTGATAATCTTT
1 TATGAAATTTTGATAATCCAT
27582 CTAT-AAATTTTGATAATCCGATCT
1 -TATGAAATTTTGATAATCC-A--T
*
27606 CTATGAAATTTTGATAA-CCTT
1 -TATGAAATTTTGATAATCCAT
* *
27627 CTATCAAATTTTTG-TACTCC-T
1 -TATGAAA-TTTTGATAATCCAT
27648 TATGAAATT
1 TATGAAATT
27657 GAGACTTTTA
Statistics
Matches: 112, Mismatches: 11, Indels: 31
0.73 0.07 0.20
Matches are distributed among these distances:
19 13 0.12
20 11 0.10
21 33 0.29
22 35 0.31
23 1 0.01
24 7 0.06
25 12 0.11
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (21 bp):
TATGAAATTTTGATAATCCAT
Found at i:27615 original size:25 final size:22
Alignment explanation
Indices: 27495--27638 Score: 90
Period size: 21 Copynumber: 6.6 Consensus size: 22
27485 TTGTTGACCC
* *
27495 CTCTATGAAATTCTGATAATCA
1 CTCTATGAAATTTTGATAATCT
*
27517 CAT-TAT-ATAATTTTGAT-ATCG
1 C-TCTATGA-AATTTTGATAATCT
* *
27538 AT-T-TGAAATTTTGATAA-CAA
1 CTCTATGAAATTTTGATAATC-T
27558 CAT-TATGAAATTTTGATAATCT
1 C-TCTATGAAATTTTGATAATCT
*
27580 TTCTAT-AAATTTTGATAATCCGAT
1 CTCTATGAAATTTTGATAAT-C--T
*
27604 CTCTATGAAATTTTGATAACCT
1 CTCTATGAAATTTTGATAATCT
*
27626 -TCTATCAAATTTT
1 CTCTATGAAATTTT
27639 TGTACTCCTT
Statistics
Matches: 99, Mismatches: 10, Indels: 27
0.73 0.07 0.20
Matches are distributed among these distances:
19 11 0.11
20 4 0.04
21 32 0.32
22 31 0.31
23 2 0.02
24 7 0.07
25 12 0.12
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (22 bp):
CTCTATGAAATTTTGATAATCT
Found at i:27703 original size:22 final size:22
Alignment explanation
Indices: 27678--27795 Score: 114
Period size: 22 Copynumber: 5.4 Consensus size: 22
27668 AACCTTCATA
* *
27678 TTTGATAACCACACTATAAAAT
1 TTTGATAACCTCACTATGAAAT
*
27700 TTTGATAACCTCCCTATGAAAT
1 TTTGATAACCTCACTATGAAAT
*
27722 ATT-AGTAACCTC-CTAATGAAAT
1 TTTGA-TAACCTCACT-ATGAAAT
* * *
27744 TTTGTTAACCACACTGTGAAAT
1 TTTGATAACCTCACTATGAAAT
* * *
27766 TTTTATAACCTCGCTATGACAT
1 TTTGATAACCTCACTATGAAAT
27788 TTTGATAA
1 TTTGATAA
27796 TGGCCTAATG
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.04
22 72 0.94
23 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (22 bp):
TTTGATAACCTCACTATGAAAT
Found at i:28377 original size:30 final size:31
Alignment explanation
Indices: 28343--28407 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
28333 TGGCAATTTA
*
28343 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
28373 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
28404 GAAA
1 GAAA
28408 ACATAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:28772 original size:2 final size:2
Alignment explanation
Indices: 28765--28802 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
28755 TCCGTACTTT
*
28765 TA TA TA TA GTA TA AA 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 T
28803 GTGATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:29371 original size:59 final size:59
Alignment explanation
Indices: 29257--29371 Score: 128
Period size: 59 Copynumber: 1.9 Consensus size: 59
29247 GTATATGGGG
** **
29257 TGAAAGTTTCAAATTAAAAGTTTAAGGAGAAAATTGTTCCATTTTGATATTTTAAGAAT
1 TGAAAGTACCAAATTAAAAGTTTAAGGAGAAAATTGTTCCATTTTGATAAGTTAAGAAT
* *
29316 TGAAAGTACCAAATTAAAAG-TTCAGGAAGGAAAA-TG-TCCCTTTTGTATAAGTTAAG
1 TGAAAGTACCAAATTAAAAGTTTAAGG-A-GAAAATTGTTCCATTTTG-ATAAGTTAAG
29372 GGGGGCAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
58 13 0.28
59 29 0.62
60 5 0.11
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (59 bp):
TGAAAGTACCAAATTAAAAGTTTAAGGAGAAAATTGTTCCATTTTGATAAGTTAAGAAT
Found at i:30161 original size:70 final size:70
Alignment explanation
Indices: 30079--30311 Score: 306
Period size: 70 Copynumber: 3.2 Consensus size: 70
30069 TTGTTTAGGT
* * *
30079 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCTTTATAATT
30143 ATTTTA
65 ATTTTA
30149 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
30214 TTATATTTTACCA
62 AT-TATTTT---A
* *
30227 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
30292 TTATA
66 TTTTA
*
30297 TTTTACAATTTTACT
1 TTTTACTATTTTACT
30312 ATTTTAGTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
70 63 0.43
71 5 0.03
72 1 0.01
73 6 0.04
74 5 0.03
75 7 0.05
76 1 0.01
77 2 0.01
78 55 0.38
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:30161 original size:78 final size:77
Alignment explanation
Indices: 30079--30317 Score: 359
Period size: 78 Copynumber: 3.2 Consensus size: 77
30069 TTGTTTAGGT
* * *
30079 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
*
30139 AAT-TATTTT--A
65 ATTATATTTTACA
30149 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
30214 TTATATTTTACCA
66 TTATATTTTA-CA
30227 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
30292 TTATATTTTACAA
66 TTATATTTTAC-A
30305 TTTTACTATTTTA
1 TTTTACTATTTTA
30318 GTTAAAACAA
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
70 48 0.31
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 90 0.58
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACA
Found at i:31440 original size:17 final size:17
Alignment explanation
Indices: 31418--31451 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31408 GTTTGATTGA
*
31418 AGGGGTTGCAAGGGGTG
1 AGGGGTAGCAAGGGGTG
*
31435 AGGGGTAGGAAGGGGTG
1 AGGGGTAGCAAGGGGTG
31452 GTCATCACCC
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:0.21, C:0.03, G:0.62, T:0.15
Consensus pattern (17 bp):
AGGGGTAGCAAGGGGTG
Done.