Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017341.1 Corchorus olitorius cultivar O-4 contig17374, 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: 44431
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:7964 original size:17 final size:17
Alignment explanation
Indices: 7942--7983 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
7932 AAGTAAATAG
7942 ATTGCAAATATCAGATA
1 ATTGCAAATATCAGATA
7959 ATTGCAAATATCAGATA
1 ATTGCAAATATCAGATA
7976 ATTGCAAA
1 ATTGCAAA
7984 CATCCAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (17 bp):
ATTGCAAATATCAGATA
Found at i:11494 original size:59 final size:57
Alignment explanation
Indices: 11332--11672 Score: 415
Period size: 59 Copynumber: 5.9 Consensus size: 57
11322 GGTCACTTAA
* * *
11332 AGGGGCATTTT-GATCATTTT-GCATAACCAGGGGCATTTTGGTCATTTTGCATAACC
1 AGGGGCATTTTAG-TCATTTTCGCATATCCAGGGGCATTTTGGTCATTTTGCACATCC
* *
11388 AGGGGCATTTTGGTCATTTT-GCATATCAAGGGGCATTTTGGTCATTTTGCACATCC
1 AGGGGCATTTTAGTCATTTTCGCATATCCAGGGGCATTTTGGTCATTTTGCACATCC
11444 AGGGGACATTTTAGTCACTTTTCGCATATCCAGGGGCATTTTGGTCATTTTGCACATCC
1 AGGGG-CATTTTAGTCA-TTTTCGCATATCCAGGGGCATTTTGGTCATTTTGCACATCC
*
11503 AGGGGACATTTTAGTCACTTTTCGCATATCTAGGGGCATTTTGGTCATTTTGCACATCC
1 AGGGG-CATTTTAGTCA-TTTTCGCATATCCAGGGGCATTTTGGTCATTTTGCACATCC
* * * * *
11562 AAGGGTATTTTTGTCATTTTCGCATATCCAAGGGCATTTTGGTCATTTTTGCACAATTC
1 AGGGGCATTTTAGTCATTTTCGCATATCCAGGGGCATTTTGGTCA-TTTTGCAC-ATCC
* * * *
11621 AGGGGCATTTGA-TC-GTTTCTGCACATCC-GAAGGCATTTTGGTCATTTGTGCA
1 AGGGGCATTTTAGTCATTTTC-GCATATCCAG-GGGCATTTTGGTCATTT-TGCA
11673 TACTCGGGGT
Statistics
Matches: 255, Mismatches: 21, Indels: 16
0.87 0.07 0.05
Matches are distributed among these distances:
56 55 0.22
57 45 0.18
58 47 0.18
59 108 0.42
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (57 bp):
AGGGGCATTTTAGTCATTTTCGCATATCCAGGGGCATTTTGGTCATTTTGCACATCC
Found at i:11512 original size:29 final size:28
Alignment explanation
Indices: 11332--11674 Score: 384
Period size: 28 Copynumber: 11.9 Consensus size: 28
11322 GGTCACTTAA
* *
11332 AGGGGCATTTTGATCATTTTGCATAACC
1 AGGGGCATTTTGGTCATTTTGCATATCC
*
11360 AGGGGCATTTTGGTCATTTTGCATAACC
1 AGGGGCATTTTGGTCATTTTGCATATCC
*
11388 AGGGGCATTTTGGTCATTTTGCATATCA
1 AGGGGCATTTTGGTCATTTTGCATATCC
*
11416 AGGGGCATTTTGGTCATTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
*
11444 AGGGGACATTTTAGTCACTTTTCGCATATCC
1 AGGGG-CATTTTGGTCA-TTTT-GCATATCC
*
11475 AGGGGCATTTTGGTCATTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
* *
11503 AGGGGACATTTTAGTCACTTTTCGCATATCT
1 AGGGG-CATTTTGGTCA-TTTT-GCATATCC
*
11534 AGGGGCATTTTGGTCATTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
* * *
11562 AAGGGTATTTTTGTCATTTTCGCATATCC
1 AGGGGCATTTTGGTCATTTT-GCATATCC
* * *
11591 AAGGGCATTTTGGTCATTTTTGCACAATTC
1 AGGGGCATTTTGGTCA-TTTTGCA-TATCC
* * *
11621 AGGGGCA-TTTGATCGTTTCTGCACATCC
1 AGGGGCATTTTGGTCATTT-TGCATATCC
*
11649 -GAAGGCATTTTGGTCATTTGTGCATA
1 AG-GGGCATTTTGGTCATTT-TGCATA
11675 CTCGGGGTTC
Statistics
Matches: 270, Mismatches: 33, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
27 1 0.00
28 129 0.48
29 76 0.28
30 41 0.15
31 23 0.09
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCATATCC
Found at i:11644 original size:87 final size:84
Alignment explanation
Indices: 11334--11674 Score: 357
Period size: 87 Copynumber: 3.9 Consensus size: 84
11324 TCACTTAAAG
* * * * * * *
11334 GGGCATTTTGATCATTTTGCATAACCAGGGGCATTTTGGTCATTTTGCATAACCAGGGGCATTTT
1 GGGCATTTTGGTCATTTTGCACATCCAGGGGCATTTTGATCATTTTGCACATCCAAGGGCATTTT
11399 GGTCATTTTGCATAT-CAA
66 GGTCATTTTGCATATCCAA
* *
11417 GGGGCATTTTGGTCATTTTGCACATCCAGGGGACATTTT-AGTCACTTTTCGCATATCCAGGGGC
1 -GGGCATTTTGGTCATTTTGCACATCCAGGGG-CATTTTGA-TCA-TTTT-GCACATCCAAGGGC
* *
11481 ATTTTGGTCATTTTGCACATCCAG
61 ATTTTGGTCATTTTGCATATCCAA
* * * * *
11505 GGGACATTTTAGTCACTTTTCGCATATCTAGGGGCATTTTGGTCATTTTGCACATCCAAGGGTAT
1 GGG-CATTTTGGTCA-TTTT-GCACATCCAGGGGCATTTTGATCATTTTGCACATCCAAGGGCAT
*
11570 TTTTGTCATTTTCGCATATCCAA
63 TTTGGTCATTTT-GCATATCCAA
* *
11593 GGGCATTTTGGTCATTTTTGCACAATTCAGGGGCA-TTTGATCGTTTCTGCACATCCGAA-GGCA
1 GGGCATTTTGGTCA-TTTTGCAC-ATCCAGGGGCATTTTGATCATTT-TGCACATCC-AAGGGCA
11656 TTTTGGTCATTTGTGCATA
62 TTTTGGTCATTT-TGCATA
11675 CTCGGGGTTC
Statistics
Matches: 217, Mismatches: 26, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
84 28 0.13
85 9 0.04
86 16 0.07
87 110 0.51
88 30 0.14
89 13 0.06
90 11 0.05
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.38
Consensus pattern (84 bp):
GGGCATTTTGGTCATTTTGCACATCCAGGGGCATTTTGATCATTTTGCACATCCAAGGGCATTTT
GGTCATTTTGCATATCCAA
Found at i:15733 original size:26 final size:27
Alignment explanation
Indices: 15685--15735 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
15675 CAAAAGAAGA
* *
15685 TTTTGGAAATAAATAAAATTGGTAAGT
1 TTTTAGAAAAAAATAAAATTGGTAAGT
*
15712 TTTTAGAAAAAAATCAAA-TGGTAA
1 TTTTAGAAAAAAATAAAATTGGTAA
15736 AAAGATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (27 bp):
TTTTAGAAAAAAATAAAATTGGTAAGT
Found at i:16768 original size:21 final size:22
Alignment explanation
Indices: 16738--16780 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
16728 TTAAGTTTCT
16738 GGGGTCACCCGGGGCTGGGTAG
1 GGGGTCACCCGGGGCTGGGTAG
16760 GGGGT-ACCCGGGGCTGGGTAG
1 GGGGTCACCCGGGGCTGGGTAG
16781 CCTCAGATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.09, C:0.21, G:0.56, T:0.14
Consensus pattern (22 bp):
GGGGTCACCCGGGGCTGGGTAG
Found at i:17211 original size:29 final size:29
Alignment explanation
Indices: 17169--17228 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
17159 TGAATGGCTA
17169 GTAAAGCCAATGCCCTTGTTGTTGCCGTG
1 GTAAAGCCAATGCCCTTGTTGTTGCCGTG
17198 GTAAAGCCAATGCCCTTGTTGTTGCCGTG
1 GTAAAGCCAATGCCCTTGTTGTTGCCGTG
17227 GT
1 GT
17229 GGATTTGTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.17, C:0.23, G:0.28, T:0.32
Consensus pattern (29 bp):
GTAAAGCCAATGCCCTTGTTGTTGCCGTG
Found at i:18426 original size:24 final size:25
Alignment explanation
Indices: 18398--18448 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
18388 AAAGAGTAAC
*
18398 AATAAAA-TAAATAAGCAAGA-AAAT
1 AATAAAATTAAA-AAACAAGATAAAT
18422 AATAAAATTAAAAAACAAGATAAAT
1 AATAAAATTAAAAAACAAGATAAAT
18447 AA
1 AA
18449 ATACTCCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.18
Consensus pattern (25 bp):
AATAAAATTAAAAAACAAGATAAAT
Found at i:19402 original size:21 final size:22
Alignment explanation
Indices: 19363--19403 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19353 GCGTTCCTGA
*
19363 GGGTACCCGGGGCCGGGTAGGG
1 GGGTACCCGGGGCCAGGTAGGG
19385 GGGTACCC-GGGCCAGGTAG
1 GGGTACCCGGGGCCAGGTAG
19404 CCTCAGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.12, C:0.24, G:0.54, T:0.10
Consensus pattern (22 bp):
GGGTACCCGGGGCCAGGTAGGG
Found at i:21592 original size:2 final size:2
Alignment explanation
Indices: 21540--21580 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
21530 ATGATTCTCT
*
21540 TA TA GA 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
21581 TACTACTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:23273 original size:22 final size:22
Alignment explanation
Indices: 23221--23283 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
23211 AAATGTCCGC
**
23221 TTATCAAAATTTCCTAGAGAGG
1 TTATCAAAATTTTATAGAGAGG
* *
23243 TTAACAAAATTTTATAGGGAGG
1 TTATCAAAATTTTATAGAGAGG
*
23265 TTATGAAAAATATTTATAG
1 TTAT-CAAAAT-TTTATAG
23284 TATAATCCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 21 0.64
23 5 0.15
24 7 0.21
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTTATAGAGAGG
Found at i:23630 original size:22 final size:22
Alignment explanation
Indices: 23393--23641 Score: 145
Period size: 22 Copynumber: 11.4 Consensus size: 22
23383 AGTTTCATTC
* *
23393 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGAGGTTATCAAAATT
* * *
23415 GCATGGTGTA-GCTATCAAAATT
1 TCATAGTG-AGGTTATCAAAATT
*
23437 T--TA-TTAGGTTATCAAAATTT
1 TCATAGTGAGGTTATCAAAA-TT
* *
23457 TCATAGTGCGGTTA-C-CAATT
1 TCATAGTGAGGTTATCAAAATT
* * * *
23477 TTATAGCGTGATTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
* **
23499 TCATAGGGAAATTATCAAAATT
1 TCATAGTGAGGTTATCAAAATT
* * *
23521 TCACACTGAGAGGTTATCAGAA-T
1 TCATA--GTGAGGTTATCAAAATT
* *
23544 TGATTAGTGTGGTTATCAAAATT
1 TCA-TAGTGAGGTTATCAAAATT
* * *
23567 CCACAGTGTGGTTATC-AAATT
1 TCATAGTGAGGTTATCAAAATT
*
23588 TGCATAGGGAGGTTATCAAAATT
1 T-CATAGTGAGGTTATCAAAATT
*
23611 TCATAATGAGGTTATCAAAAGTT
1 TCATAGTGAGGTTATCAAAA-TT
*
23634 TCACAGTG
1 TCATAGTG
23642 CGATTGTCAA
Statistics
Matches: 170, Mismatches: 42, Indels: 29
0.71 0.17 0.12
Matches are distributed among these distances:
18 1 0.01
19 10 0.06
20 16 0.09
21 8 0.05
22 97 0.57
23 26 0.15
24 12 0.07
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.35
Consensus pattern (22 bp):
TCATAGTGAGGTTATCAAAATT
Found at i:26557 original size:22 final size:23
Alignment explanation
Indices: 26527--27096 Score: 168
Period size: 22 Copynumber: 25.6 Consensus size: 23
26517 CATAGGAAGT
26527 TTATCAAAATTTCATAATGTA-G
1 TTATCAAAATTTCATAATGTAGG
*
26549 TTA-CAAAAATTTCAT-ATGGAGG
1 TTATC-AAAATTTCATAATGTAGG
* *
26571 TTATCAAAACTTCA-AA-GTATAG
1 TTATCAAAATTTCATAATGTA-GG
26593 TTATCAAAATTTCATACA-G-AGG
1 TTATCAAAATTTCATA-ATGTAGG
* **
26615 TTACCAAAATTTCATAA-AAAGG
1 TTATCAAAATTTCATAATGTAGG
* * *
26637 TTATCAAAATTTC-TTAGGGAGG
1 TTATCAAAATTTCATAATGTAGG
* * *
26659 TTAACAAAATTTCAT-ACGAAGG
1 TTATCAAAATTTCATAATGTAGG
* *
26681 TTATCGAAAGTTT-ATAGTGT-GG
1 TTATC-AAAATTTCATAATGTAGG
**
26703 TTATCAAAATTTCATAA-AAAGG
1 TTATCAAAATTTCATAATGTAGG
* * * * *
26725 TTAACAAAATATCATAGGGAGGGAGA
1 TTATCAAAATTTCATA---ATGTAGG
*
26751 TTATCAAAATTTCCT-A-G-AGG
1 TTATCAAAATTTCATAATGTAGG
* *
26771 TTAAT-AAAATTTCAT-AGGGAGG
1 TT-ATCAAAATTTCATAATGTAGG
* * *
26793 TTATGAAAATTTTATGGA-G-AGG
1 TTATCAAAATTTCAT-AATGTAGG
26815 TTATCAAAA-TT-ATATATAG-AGG
1 TTATCAAAATTTCATA-AT-GTAGG
* * * *
26837 ATATCATAATTTCATTCTCATAGGGAGG
1 TTATCAAAATTTCA---T-A-ATGTAGG
* * *
26865 TTATCGAAATTTCACAGTGTA-G
1 TTATCAAAATTTCATAATGTAGG
* *
26887 TTATCAAAATTTTCATAGTG-CGG
1 TTATCAAAA-TTTCATAATGTAGG
* * *
26910 TTA-C-CAATTAT-ATAGTGT-GA
1 TTATCAAAATT-TCATAATGTAGG
* * *
26930 TTATCAAAATTTCAT-AGGGAGA
1 TTATCAAAATTTCATAATGTAGG
* * *
26952 TTATCAAAATTTTACACTG-AGG
1 TTATCAAAATTTCATAATGTAGG
* *
26974 TTATCAAAATTTTATAGTGT-GG
1 TTATCAAAATTTCATAATGTAGG
* * *
26996 TTATCAAAATTTCACAGTGT-TG
1 TTATCAAAATTTCATAATGTAGG
* * * *
27018 TTATCAAACTTCCAT-AGGAAGG
1 TTATCAAAATTTCATAATGTAGG
* * * *
27040 TAATCGAAGTTTCATAATG-AAG
1 TTATCAAAATTTCATAATGTAGG
* * *
27062 TTATCAAATTTTCATAGTGT-TG
1 TTATCAAAATTTCATAATGTAGG
*
27084 TTATCAATATTTC
1 TTATCAAAATTTC
27097 TACGTTTGAG
Statistics
Matches: 415, Mismatches: 86, Indels: 94
0.70 0.14 0.16
Matches are distributed among these distances:
20 29 0.07
21 31 0.07
22 284 0.68
23 32 0.08
24 5 0.01
25 1 0.00
26 14 0.03
27 2 0.00
28 17 0.04
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (23 bp):
TTATCAAAATTTCATAATGTAGG
Found at i:26575 original size:44 final size:43
Alignment explanation
Indices: 26509--26804 Score: 187
Period size: 44 Copynumber: 6.7 Consensus size: 43
26499 ACAATCAAAC
* * *
26509 CAAAATTACATAGGAAGTTTATCAAAATTTCATAATGTAGTTA-
1 CAAAATTTCATAGG-AGGTTATCAAAATTTCATAATATAGTTAT
*
26552 CAAAAATTTCATATGGAGGTTATCAAAACTTCA-AAGTATAGTTAT
1 C-AAAATTTCATA-GGAGGTTATCAAAATTTCATAA-TATAGTTAT
* * *
26597 CAAAATTTCATACAGAGGTTACCAAAATTTCATAA-AAAGGTTAT
1 CAAAATTTCATA-GGAGGTTATCAAAATTTCATAATATA-GTTAT
* * **
26641 CAAAATTTCTTAGGGAGGTTAACAAAATTTCATACGA-AGGTTAT
1 CAAAATTTCATA-GGAGGTTATCAAAATTTCATAATATA-GTTAT
* * * *
26685 CGAAAGTTT-ATAGTGTGGTTATCAAAATTTCATAA-AAAGGTTAA
1 C-AAAATTTCATAG-GAGGTTATCAAAATTTCATAATATA-GTTAT
* * * *
26729 CAAAATATCATAGGGAGGGAGATTATCAAAATTTCCT-AGA-GGTTAAT
1 CAAAATTTCATA-GGA--G-G-TTATCAAAATTTCATAATATAGTT-AT
*
26776 -AAAATTTCATAGGGAGGTTATGAAAATTT
1 CAAAATTTCATA-GGAGGTTATCAAAATTT
26805 TATGGAGAGG
Statistics
Matches: 207, Mismatches: 28, Indels: 37
0.76 0.10 0.14
Matches are distributed among these distances:
42 11 0.05
43 13 0.06
44 134 0.65
45 13 0.06
46 18 0.09
47 3 0.01
48 15 0.07
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.32
Consensus pattern (43 bp):
CAAAATTTCATAGGAGGTTATCAAAATTTCATAATATAGTTAT
Found at i:26786 original size:46 final size:47
Alignment explanation
Indices: 26703--26792 Score: 128
Period size: 46 Copynumber: 1.9 Consensus size: 47
26693 TATAGTGTGG
26703 TTATCAAAATTTCATAAAAAGGTTAACAAAATATCATAGGGAGGGAGA
1 TTATCAAAATTTCAT-AAAAGGTTAACAAAATATCATAGGGAGGGAGA
* * * *
26751 TTATCAAAATTTCCT-AGAGGTTAATAAAATTTCATAGGGAGG
1 TTATCAAAATTTCATAAAAGGTTAACAAAATATCATAGGGAGG
26793 TTATGAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 24 0.63
48 14 0.37
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (47 bp):
TTATCAAAATTTCATAAAAGGTTAACAAAATATCATAGGGAGGGAGA
Found at i:27007 original size:66 final size:66
Alignment explanation
Indices: 26509--27009 Score: 281
Period size: 66 Copynumber: 7.5 Consensus size: 66
26499 ACAATCAAAC
* * * * * *
26509 CAAAATTACATAGGAAGTTTATCAAAATTTCATAATGTA-GTTA-CAAAAATTTCATA-TGGAGG
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCAT-AGGGAGGTTATC-AAAATTTTATACT-GAGG
26571 TTAT
63 TTAT
* * * * ** * * ***
26575 CAAAACTTCA-AAGTATAGTTATCAAAATTTCATACAGAGGTTACCAAAATTTCATAAAAAGGTT
1 CAAAATTTCATAGGGA-GGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTTATACTGAGGTT
26639 AT
65 AT
* * * * * * * *
26641 CAAAATTTCTTAGGGAGGTTAACAAAATTTCATACGAAGGTTATCGAAAGTTTATAGTGTGGTTA
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTTATACTGAGGTTA
26706 T
66 T
*** * * **
26707 CAAAATTTCATAAAAAGGTTAACAAAATATCATAGGGAGGGAGATTATCAAAATTTCCTA--GAG
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGA--G-G-TTATCAAAATTTTATACTGAG
26770 GTTAAT
62 GTT-AT
* * * *
26776 -AAAATTTCATAGGGAGGTTATGAAAATTTTAT-GGAGAGGTTATCAAAATTATATA-TAGAGGA
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCATAGG-GAGGTTATCAAAATTTTATACT-GAGGT
26838 TAT
64 TAT
* * * *
26841 CATAATTTCATTCTCATAGGGAGGTTATCGAAATTTCACAGTGTA-GTTATCAAAATTTTCATAG
1 CA-AA----ATT-TCATAGGGAGGTTATCAAAATTTCATAG-GGAGGTTATCAAAATTTT-ATAC
*
26905 TGCGGTTA-
58 TGAGGTTAT
* * * * * *
26913 C-CAATTAT-ATAGTGTGATTATCAAAATTTCATAGGGAGATTATCAAAATTTTACACTGAGGTT
1 CAAAATT-TCATAGGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTTATACTGAGGTT
26976 AT
65 AT
* * *
26978 CAAAATTTTATAGTGTGGTTATCAAAATTTCA
1 CAAAATTTCATAGGGAGGTTATCAAAATTTCA
27010 CAGTGTTGTT
Statistics
Matches: 335, Mismatches: 72, Indels: 56
0.72 0.16 0.12
Matches are distributed among these distances:
64 24 0.07
65 44 0.13
66 159 0.47
67 8 0.02
68 33 0.10
69 3 0.01
70 13 0.04
71 3 0.01
72 36 0.11
73 10 0.03
74 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (66 bp):
CAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTTATACTGAGGTTA
T
Found at i:28563 original size:2 final size:2
Alignment explanation
Indices: 28556--28580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28546 AAAGTACTAG
28556 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 T
28581 GATTGGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31606 original size:144 final size:144
Alignment explanation
Indices: 31336--31633 Score: 411
Period size: 144 Copynumber: 2.1 Consensus size: 144
31326 CCAAGTGAAA
* *
31336 TAGGATTGCTCCAATCTCTTTTTACGTTGCAGTTGCAGCTTAACAAACTCACTGGTGTCATCCCT
1 TAGGATTGCTCCAATCTCTTTTGACGTTGCAGTTGCAGCATAACAAACTCACTGGTGTCATCCCT
** * ** * * * *
31401 ACTTCAATAGGAAACTTGACCGCTTTATTCAGTCTTTTTCTTTACGAAAATATACTCTCTGGGCC
66 ACTTCAATAGGAAACTTGACCAATTTAGTCAGTCTTCATCTTCAAGAAAACAGACTCTCTGGGCC
31466 GATT-CCTCGAGAGG
131 -ATTACCTCGAGAGG
31480 TAGGATTGCTCCAATCTCTTTTGACGTTGCAGTTGCAGCATAACAAACTCACTGGTGTCATCCCT
1 TAGGATTGCTCCAATCTCTTTTGACGTTGCAGTTGCAGCATAACAAACTCACTGGTGTCATCCCT
* * * * *
31545 ACTTCAATAGGAAACTTGACCAATTTGGTCGGTCTTCATCTTCAAGAGAACAGGA-TTTCTGGTC
66 ACTTCAATAGGAAACTTGACCAATTTAGTCAGTCTTCATCTTCAAGAAAACA-GACTCTCTGGGC
31609 CATTACCTCGAGAGG
130 CATTACCTCGAGAGG
*
31624 TAGGAATGCT
1 TAGGATTGCT
31634 AATATCTCTC
Statistics
Matches: 135, Mismatches: 17, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
143 3 0.02
144 131 0.97
145 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (144 bp):
TAGGATTGCTCCAATCTCTTTTGACGTTGCAGTTGCAGCATAACAAACTCACTGGTGTCATCCCT
ACTTCAATAGGAAACTTGACCAATTTAGTCAGTCTTCATCTTCAAGAAAACAGACTCTCTGGGCC
ATTACCTCGAGAGG
Found at i:37674 original size:36 final size:37
Alignment explanation
Indices: 37633--37705 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
37623 ATTATTTTGA
37633 GGGATAC-TTTTTTTTATTAAAATAGGAGTATCTTTT
1 GGGATACTTTTTTTTTATTAAAATAGGAGTATCTTTT
*
37669 GGGATACTTTTTTTTTATTAAAATAGGAGTATTTTTT
1 GGGATACTTTTTTTTTATTAAAATAGGAGTATCTTTT
37706 TGGTAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 7 0.20
37 28 0.80
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.52
Consensus pattern (37 bp):
GGGATACTTTTTTTTTATTAAAATAGGAGTATCTTTT
Found at i:38005 original size:36 final size:36
Alignment explanation
Indices: 37965--38036 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
37955 AAATGAGAAT
37965 TCAACCAAAACTAGAAACTATACCATAAATAAACTA
1 TCAACCAAAACTAGAAACTATACCATAAATAAACTA
38001 TCAACCAAAACTAGAAACTATACCATAAATAAACTA
1 TCAACCAAAACTAGAAACTATACCATAAATAAACTA
38037 CCTACCTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (36 bp):
TCAACCAAAACTAGAAACTATACCATAAATAAACTA
Found at i:38007 original size:18 final size:16
Alignment explanation
Indices: 37979--38036 Score: 64
Period size: 16 Copynumber: 3.4 Consensus size: 16
37969 CCAAAACTAG
37979 AAACTATACCATAAAT
1 AAACTATACCATAAAT
37995 AAACTATCAACCA-AAACT
1 AAACTAT--ACCATAAA-T
38013 AGAAACTATACCATAAAT
1 --AAACTATACCATAAAT
38031 AAACTA
1 AAACTA
38037 CCTACCTACC
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
16 13 0.36
17 3 0.08
18 10 0.28
19 3 0.08
20 7 0.19
ACGTcount: A:0.57, C:0.21, G:0.02, T:0.21
Consensus pattern (16 bp):
AAACTATACCATAAAT
Found at i:38042 original size:18 final size:17
Alignment explanation
Indices: 37979--38042 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 17
37969 CCAAAACTAG
37979 AAACTA-TACCATAAAT
1 AAACTACTACCATAAAT
*
37995 AAACTATCAACCA-AAACT
1 AAACTA-CTACCATAAA-T
38013 AGAAACTA-TACCATAAAT
1 --AAACTACTACCATAAAT
38031 AAACTACCTACC
1 AAACTA-CTACC
38043 TACCAAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
16 12 0.32
17 3 0.08
18 14 0.37
19 3 0.08
20 6 0.16
ACGTcount: A:0.53, C:0.25, G:0.02, T:0.20
Consensus pattern (17 bp):
AAACTACTACCATAAAT
Found at i:40683 original size:16 final size:16
Alignment explanation
Indices: 40662--40695 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40652 TTTTTGTGGA
40662 TTTTTGTC-TTTTCTTC
1 TTTTTGTCATTTT-TTC
40678 TTTTTGTCATTTTTTC
1 TTTTTGTCATTTTTTC
40694 TT
1 TT
40696 CAACTTTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTTGTCATTTTTTC
Found at i:43362 original size:22 final size:23
Alignment explanation
Indices: 43337--43380 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
43327 AATTCAGTCC
* *
43337 CCAATGATAAG-ATTCCCATTTT
1 CCAAAGATAAGAATCCCCATTTT
43359 CCAAAGATAAGAATCCCCATTT
1 CCAAAGATAAGAATCCCCATTT
43381 GCCAGCTGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.36, C:0.25, G:0.09, T:0.30
Consensus pattern (23 bp):
CCAAAGATAAGAATCCCCATTTT
Done.