Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015036.1 Corchorus olitorius cultivar O-4 contig15069, 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: 70558
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:2601 original size:432 final size:427
Alignment explanation
Indices: 1595--2647 Score: 1182
Period size: 430 Copynumber: 2.5 Consensus size: 427
1585 TATTTTTGTA
* *
1595 TTTT-TTT-TTCTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAATGGTAATTTCATGACC
1 TTTTCTTTGTTCTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
* * ** *
1658 TACAA-TTTACAT-TAAGAACTAAAAAG-TCAATTTTAATGTTTTGATTCTAAAAAATGCTTCCG
66 TACAACTTT-CATGAAAG-ACTCAAAAGCT-AATTTTAATGTTTAAATTCTAAAAAATGCTTCTG
* * * * * * * *
1720 AAATTTTATGGTTTTGATTATCGGT-TAATTTAACATCGTATAATTTTTTG-CCCACATGTCCGA
128 AAATTTTGTGATTTCGATTGTTGGTCT-ATTTAATATCATATAA-TTTTTGATCCACATGTCCGA
* * * * * *
1783 TTGAAGTTATTGAACTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGACCCGA
191 TTAAAGTTATTGAACTATCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATGAAGAACCCGA
* ** *
1848 AAGCTAAATTTGATCTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAGATCTC
256 AAGCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGAAAATTTTTATATTTCAAGATCTC
* * *
1913 CATTAACAAACATTTTCTTATTTGGATTATTTATCAAATGACCCTCTACTTTATACTACTTAGTC
321 CATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCTACTTTATACTACTTAGTC
* *
1978 CTTTACAAATTCTATCTTAATCTAACGTTTAAGCTTTATTTTTT
386 CTTTACAAATTCTATCTTAATCTAAC-TTTAAACTTCA-TTTTT
* * *
2022 TTATTCTTTGTTCTATTTGTCCGATTAAGTTGATTCATGTGTCTATTGAAAGGTAATTTCATGAT
1 TT-TTCTTTGTTCTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGAT
* * * * *
2087 CTACAACTTTCATGAAGGATTCAAAAGCAAATTTTAATGTTTCAATTCAAAAAAATGCTTCCT-A
65 CTACAACTTTCATGAAAGACTCAAAAGCTAATTTTAATGTTTAAATTCTAAAAAATGCTT-CTGA
* * * *
2151 AA-TTTGTTAGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCACATGTCCAATT
129 AATTTTGTGA-TTTCGATTGTTGGTCTATTTAATATCATATAATTTTTGATCCACATGTCCGATT
* * *
2215 AAAGTTATTTAAGTATCGGTTAAAAGGTTACTGTATAATCTACGACTTTCATGAAGAACCCGAAA
193 AAAGTTATTGAACTATCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATGAAGAACCCGAAA
* *
2280 G-TTAATTTGATCTACGAGTTTTATGAAGGGTTCAAAAGAAAATTTTTATATTTCAAGATCTCCA
258 GCTAAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGAAAATTTTTATATTTCAAGATCTCCA
* * * *
2344 TTAACAAATATTTTCTTA-TTGAATTAGTTATTAAATCACTCTTATACTTTTCTATTTTATGCTA
323 TTAACAAACATTTTCTTATTTGAATTAGTTATCAAATCAC-C-----C---TCTACTTTATACTA
* * *
2408 -TTCAGTCCTTTCCAAATTCTATCTTACT-TGA-TTTAACACTTCA-TTTT
379 CTT-AGTCCTTTACAAATTCTATCTTAATCTAACTTTAA-ACTTCATTTTT
* * * * * * *
2455 TTTTCTTTGTTCTATTTGTCCAATTAAGGTAATTCAGGTATCTATTAAAAAGTAATTTTATGATC
1 TTTTCTTTGTTCTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
* * *
2520 TACAACTTTCATGAAAGACTCAAAAGCTAATTTTTATATTTAAATTCTAAAAAATGCTTTTGAAA
66 TACAACTTTCATGAAAGACTCAAAAGCTAATTTTAATGTTTAAATTCTAAAAAATGCTTCTGAAA
* ** * * *
2585 TTTTGTGATTTCGATTGATAATCTATTTACTATCATATTATTTTTGATCCAGATGTCCGATTA
131 TTTTGTGATTTCGATTGTTGGTCTATTTAATATCATATAATTTTTGATCCACATGTCCGATTA
2648 TCAAATTCAC
Statistics
Matches: 524, Mismatches: 79, Indels: 41
0.81 0.12 0.06
Matches are distributed among these distances:
427 2 0.00
428 19 0.04
429 87 0.17
430 191 0.36
431 8 0.02
432 156 0.30
433 12 0.02
434 6 0.01
435 4 0.01
436 4 0.01
437 35 0.07
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (427 bp):
TTTTCTTTGTTCTATTTGTCCGATTAAGATGATTCAAGTGTCTATTAAAAGGTAATTTCATGATC
TACAACTTTCATGAAAGACTCAAAAGCTAATTTTAATGTTTAAATTCTAAAAAATGCTTCTGAAA
TTTTGTGATTTCGATTGTTGGTCTATTTAATATCATATAATTTTTGATCCACATGTCCGATTAAA
GTTATTGAACTATCGGTTAAAAGGTTACTGCATAATCTACGACTTTCATGAAGAACCCGAAAGCT
AAATTTGATCTACGAGTTTCATGAAGGGTTCAAAAGAAAATTTTTATATTTCAAGATCTCCATTA
ACAAACATTTTCTTATTTGAATTAGTTATCAAATCACCCTCTACTTTATACTACTTAGTCCTTTA
CAAATTCTATCTTAATCTAACTTTAAACTTCATTTTT
Found at i:2939 original size:31 final size:31
Alignment explanation
Indices: 2902--3073 Score: 166
Period size: 31 Copynumber: 5.5 Consensus size: 31
2892 ACGGTGTCCG
* *
2902 ACGTGGCATGCCACGTGTACCAAAAAGCGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * *
2933 ATGTGGCACGCCACGTGTACAAAAAAGCGAT
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
** *
2964 ATATGACACGCCACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
** *
2995 ACGTATCACGCCATGTGTACCCAAAAA-TGAC
1 ACGTGGCACGCCACGTGTA-CCAAAAAGTGAC
* * * **
3026 ACGTGGCATGTCATGTGTTTCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
*
3057 ACGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
3074 CACAAAAGGA
Statistics
Matches: 117, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
30 6 0.05
31 104 0.89
32 7 0.06
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.19
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:8826 original size:22 final size:22
Alignment explanation
Indices: 8625--9847 Score: 479
Period size: 22 Copynumber: 56.0 Consensus size: 22
8615 AACAGAAGGG
* * * *
8625 TATGAAATTCTAGTAATTTCCT
1 TATGAAATTTTGGTAACTTCCC
* * * *
8647 TGTGAAATTTGGGTAATTTCTC
1 TATGAAATTTTGGTAACTTCCC
* **
8669 TATGAAA-CTTGAGTAACTTTAC
1 TATGAAATTTTG-GTAACTTCCC
* * * * *
8691 TAAGAAATTCTAGTAATTTACC
1 TATGAAATTTTGGTAACTTCCC
* * * *
8713 TATAAAATTTTGCTAACCTACC
1 TATGAAATTTTGGTAACTTCCC
* **
8735 TAAGAAATTTCAGTAA-TATCCC
1 TATGAAATTTTGGTAACT-TCCC
* * *
8757 TATCAAATTCAT-GTAACTTTCC
1 TATGAAATT-TTGGTAACTTCCC
* * ** *
8779 TATAAAATTCTATTAA-TCTCCT
1 TATGAAATTTTGGTAACT-TCCC
8801 TATGAAATTTTGGTAACTTCCC
1 TATGAAATTTTGGTAACTTCCC
** * **
8823 TATGAAATACTAGTAACTTCAA
1 TATGAAATTTTGGTAACTTCCC
* * *
8845 TATGAAATTTCGATAACATCCC
1 TATGAAATTTTGGTAACTTCCC
* * * * *
8867 TTTGAAA-TCTAGTAACCTACC
1 TATGAAATTTTGGTAACTTCCC
* * *
8888 TATAAAATTCTGGTAACCTT-GC
1 TATGAAATTTTGGTAA-CTTCCC
*** * * *
8910 TATTTTATTTCGGTAACCTCCT
1 TATGAAATTTTGGTAACTTCCC
* * *
8932 TATGAAATTCTAGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* ** *
8954 TCTGAAATTCCGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* * *
8976 TCTGAAATTCTT-GTAACCTCAC
1 TATGAAATT-TTGGTAACTTCCC
* * *
8998 TATAAAATTCTGCTAACTTCCC
1 TATGAAATTTTGGTAACTTCCC
* *
9020 TATG-AATTTTAGTAACCTT-AC
1 TATGAAATTTTGGTAA-CTTCCC
* * *
9041 TATGAAATTCTAGTAACTTACC
1 TATGAAATTTTGGTAACTTCCC
* * *
9063 TATGAAATTCTAGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* *
9085 TAAGTAATTTTGGTAA-TCTCCC
1 TATGAAATTTTGGTAACT-TCCC
***
9107 TATGAAA-TTCACTAAGC-TCCC
1 TATGAAATTTTGGTAA-CTTCCC
* *
9128 TATGAAATTCTGGTAACCTT-CT
1 TATGAAATTTTGGTAA-CTTCCC
* * *
9150 TATGAAATTTTAGTAACCTCCA
1 TATGAAATTTTGGTAACTTCCC
* **
9172 TATGAAATTTCGGTAACCACCC
1 TATGAAATTTTGGTAACTTCCC
* *
9194 TATGAAATTTTAGTAACCTT-AC
1 TATGAAATTTTGGTAA-CTTCCC
* * **
9216 TATGGAATTATGGTAACTTAGC
1 TATGAAATTTTGGTAACTTCCC
* * * * * *
9238 TATTAAATTCTAGTGACCTCCT
1 TATGAAATTTTGGTAACTTCCC
* * *
9260 TATTAACTTTTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* * * * *
9282 TGTGAAATTGTGATAACCTCCT
1 TATGAAATTTTGGTAACTTCCC
* * *
9304 TGTGAAATTCTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* * *
9326 TGTGAAATTTTAGTAACCTT-AC
1 TATGAAATTTTGGTAA-CTTCCC
** *
9348 TATGAAATTCAGGTAACTTACC
1 TATGAAATTTTGGTAACTTCCC
* * *
9370 TATGAAATTCTAGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
9392 TATGAAAATTTT-GTAATCTT-CC
1 TATG-AAATTTTGGTAA-CTTCCC
*
9414 TATGAAATTTTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* * *
9436 TATAAAATTTTGGTAACCTCCT
1 TATGAAATTTTGGTAACTTCCC
* * *
9458 TGTGAAATTTCGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* *
9480 TTTGAAATTCTGGTAACTTCCC
1 TATGAAATTTTGGTAACTTCCC
* *
9502 TAT--AATTCTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* *
9522 TATGAAATTTCGGTAA-TATCCA
1 TATGAAATTTTGGTAACT-TCCC
** * **
9544 TACAAAATTTTAGTAACCTT-AG
1 TATGAAATTTTGGTAA-CTTCCC
* * *
9566 TATGAAATTCTAGTAACTT-AC
1 TATGAAATTTTGGTAACTTCCC
* **
9587 TAATGAAATTCTAATAACTTCCC
1 T-ATGAAATTTTGGTAACTTCCC
* *
9610 TAT-AAAATTTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* * * *
9631 AATGAAATTCTGGGAAC--CTC
1 TATGAAATTTTGGTAACTTCCC
* *
9651 -ATGAAATTTCT-GTTACCTCCC
1 TATGAAATTT-TGGTAACTTCCC
* *
9672 TATGAAATTTTAGTAACTT-AC
1 TATGAAATTTTGGTAACTTCCC
* * * * *
9693 TATGAAATTCTAGTAACCTACT
1 TATGAAATTTTGGTAACTTCCC
* * *
9715 TAGGAAATTCTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* * *
9737 TATGTAATTTTAGTAACCTT-AC
1 TATGAAATTTTGGTAA-CTTCCC
* * * * *
9759 TATGAACTTCTGATAATTTACC
1 TATGAAATTTTGGTAACTTCCC
* *
9781 TATGAAATTCTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
* * * *
9803 AAAGAAATTTTGGTAACCTACC
1 TATGAAATTTTGGTAACTTCCC
* *
9825 TATGAAATTCTGGTAACCTCCC
1 TATGAAATTTTGGTAACTTCCC
9847 T
1 T
9848 GACCTTACTA
Statistics
Matches: 895, Mismatches: 260, Indels: 92
0.72 0.21 0.07
Matches are distributed among these distances:
19 11 0.01
20 22 0.02
21 112 0.13
22 727 0.81
23 22 0.02
24 1 0.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGGTAACTTCCC
Found at i:8968 original size:44 final size:44
Alignment explanation
Indices: 8753--10258 Score: 996
Period size: 44 Copynumber: 34.3 Consensus size: 44
8743 TTCAGTAATA
* * * * ** *
8753 TCCCTATCAAATTC-ATGTAACTTTCCTATAAAATTCTATTAATC
1 TCCCTATGAAATTCTA-GTAACCTCCCTATGAAATTCTGGTAACC
* * * * * * *
8797 TCCTTATGAAATTTTGGTAACTTCCCTATGAAATACTAGTAACT
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
** * * * *
8841 TCAATATGAAATT-TCGATAACATCCCTTTGAAA-TCTAGTAACC
1 TCCCTATGAAATTCTAG-TAACCTCCCTATGAAATTCTGGTAACC
* * * ** ***
8884 TACCTATAAAATTCTGGTAACCTTGCTATTTTATT-TCGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCT-GGTAACC
* * *
8928 TCCTTATGAAATTCTAGTAACCTCCCTCTGAAATTCCGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * * * *
8972 TCCCTCTGAAATTCTTGTAACCTCACTATAAAATTCTGCTAACT
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* ** * *
9016 TCCCTATG-AATTTTAGTAACCTTACTATGAAATTCTAGTAACT
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * * *
9059 TACCTATGAAATTCTAGTAACCTCCCTAAGTAATTTTGGTAATC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* *
9103 TCCCTATGAAATTC-ACTAAGCTCCCTATGAAATTCTGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * *
9146 TTCTTATGAAATTTTAGTAACCTCCATATGAAATT-TCGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCT-GGTAACC
* * ** * * *
9190 ACCCTATGAAATTTTAGTAACCTTACTATGGAATTATGGTAACT
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
** * * * * * *
9234 TAGCTATTAAATTCTAGTGACCTCCTTATTAACTTTTGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * *
9278 TCCCTGTGAAATTGT-GATAACCTCCTTGTGAAATTCTGGTAACC
1 TCCCTATGAAATTCTAG-TAACCTCCCTATGAAATTCTGGTAACC
* * ** * *
9322 TCCCTGTGAAATTTTAGTAACCTTACTATGAAATTCAGGTAACT
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * *
9366 TACCTATGAAATTCTAGTAACCTCCCTATGAAAATT-TTGTAATC
1 TCCCTATGAAATTCTAGTAACCTCCCTATG-AAATTCTGGTAACC
* * * * *
9410 TTCCTATGAAATTTTGGTAACCTCCCTATAAAATTTTGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * * *
9454 TCCTTGTGAAATT-TCGGTAACCTCCCTTTGAAATTCTGGTAACT
1 TCCCTATGAAATTCT-AGTAACCTCCCTATGAAATTCTGGTAACC
* **
9498 TCCCTAT--AATTCTGGTAACCTCCCTATGAAATT-TCGGTAATA
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCT-GGTAACC
* ** * *** *
9540 TCCATACAAAATTTTAGTAACCTTAGTATGAAATTCTAGTAA-C
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
** * * *
9583 TTACTAATGAAATTCTAATAACTTCCCTATAAAATT-TGGTAACC
1 TCCCT-ATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * *
9627 TCCCAATGAAATTCTGGGAACCT--C-ATGAAATTTCT-GTTACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAA-TTCTGGTAACC
* ** *
9668 TCCCTATGAAATTTTAGTAA-CTTACTATGAAATTCTAGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * * * * *
9711 TACTTAGGAAATTCTGGTAACCTCCCTATGTAATTTTAGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
** * ** *
9755 TTACTATGAACTTCT-GATAATTTACCTATGAAATTCTGGTAACC
1 TCCCTATGAAATTCTAG-TAACCTCCCTATGAAATTCTGGTAACC
* * * * *
9799 TCCCAAAGAAATTTTGGTAACCTACCTATGAAATTCTGGTAACCTCCC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAA----CC
* * * *
9847 TGACCTTACTATAAAATTCTAGTAACTTTCCTATGAAATTCTAGTAACC
1 T--CC---CTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * * * *
9896 TTCTTATGAAATTTTGGTAACCTACCTATGAAA-TCTGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
**
9939 TCCCTATGAAA-TCCGGTAACCT-CCTATGAAATTCTGGTAACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
** * * * *
9981 TCGATATGAAATTTTAGTAACCTCCTTATGAAATTATGGTTACC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* * ** * * *
10025 TCCCAATGAAATTTTTAGTAACCTTACGATGAAATTCTGATAACT
1 TCCCTATGAAA-TTCTAGTAACCTCCCTATGAAATTCTGGTAACC
*** * * *
10070 TATATATGAAATTTTCGTAACCTCCCTATGAAATTTTGGTAA-C
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
* **
10113 TACCCTATGAAATTCTAGTAACCTCCTTATGAAATTCT-GTCAATG
1 T-CCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGT-AACC
* * * * *
10158 TCACTATGAAATTCTAGCAACGTCCCTATGAAATAT-TAGTAATC
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAAT-TCTGGTAACC
* * ** * *
10202 TCCCTATGAAAATCCAGTAACCTCCCTAAAAAATTTTGGTAACT
1 TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
**
10246 TCATTATGAAATT
1 TCCCTATGAAATT
10259 TTGTAAATAA
Statistics
Matches: 1126, Mismatches: 286, Indels: 100
0.74 0.19 0.07
Matches are distributed among these distances:
40 7 0.01
41 34 0.03
42 67 0.06
43 186 0.17
44 747 0.66
45 45 0.04
47 1 0.00
48 3 0.00
49 3 0.00
50 2 0.00
53 31 0.03
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (44 bp):
TCCCTATGAAATTCTAGTAACCTCCCTATGAAATTCTGGTAACC
Found at i:8992 original size:66 final size:66
Alignment explanation
Indices: 8777--10212 Score: 919
Period size: 66 Copynumber: 21.8 Consensus size: 66
8767 ATGTAACTTT
* * * * * * * ** * *
8777 CCTATAAAATTCTATTAATCTCCTTATGAAATTTTGGTAACTTCCCTATGAAATACTAGTAACTT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
8842 C
66 C
** * * * * * *
8843 AATATGAAATT-TCGATAACATCCCTTTGAAA-TCTAGTAACCTACCTATAAAATTCTGGTAACC
1 CCTATGAAATTCTAG-TAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACC
*
8906 TT
65 TC
* *** * * * **
8908 GCTATTTTATT-TCGGTAACCTCCTTATGAAATTCTAGTAACCTCCCTCTGAAATTCCGGTAACC
1 CCTATGAAATTCT-AGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACC
8972 TC
65 TC
* * * * * *
8974 CCTCTGAAATTCTTGTAACCTCACTATAAAATTCT-GCTAACTTCCCTATG-AATTTTAGTAACC
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAG-TAACCTCCCTATGAAATTTTGGTAACC
*
9037 TT
65 TC
* * * * * *
9039 ACTATGAAATTCTAGTAACTTACCTATGAAATTCTAGTAACCTCCCTAAGTAATTTTGGTAATCT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
9104 C
66 C
* * * * * *
9105 CCTATGAAATTC-ACTAAGCTCCCTATGAAATTCTGGTAACCTTCTTATGAAATTTTAGTAACCT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
9169 C
66 C
* * * * ** * * *
9170 CATATGAAATT-TCGGTAACCACCCTATGAAATTTTAGTAACCTTACTATGGAATTATGGTAACT
1 CCTATGAAATTCT-AGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACC
*
9234 TA
65 TC
* * * * * * * * * * *
9236 GCTATTAAATTCTAGTGACCTCCTTATTAACTTTTGGTAACCTCCCTGTGAAATTGTGATAACCT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
9301 C
66 C
* * * * * ** ** *
9302 CTTGTGAAATTCTGGTAACCTCCCTGTGAAATTTTAGTAACCTTACTATGAAATTCAGGTAACTT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
*
9367 A
66 C
* * *
9368 CCTATGAAATTCTAGTAACCTCCCTATGAAAATT-TTGTAATCTTCCTATGAAATTTTGGTAACC
1 CCTATGAAATTCTAGTAACCTCCCTATG-AAATTCTAGTAACCTCCCTATGAAATTTTGGTAACC
9432 TC
65 TC
* * * * * * * * *
9434 CCTATAAAATTTTGGTAACCTCCTTGTGAAATT-TCGGTAACCTCCCTTTGAAATTCTGGTAACT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCT-AGTAACCTCCCTATGAAATTTTGGTAACC
9498 TC
65 TC
* * ** * ** *
9500 CCTAT--AATTCTGGTAACCTCCCTATGAAATT-TCGGTAATATCCATACAAAATTTTAGTAACC
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCT-AGTAACCTCCCTATGAAATTTTGGTAACC
*
9562 TT
65 TC
** ** * * *
9564 AGTATGAAATTCTAGTAA-CTTACTAATGAAATTCTAATAACTTCCCTAT-AAAATTTGGTAACC
1 CCTATGAAATTCTAGTAACCTCCCT-ATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACC
9627 TC
65 TC
* * * * *
9629 CCAATGAAATTCTGGGAACCT--C-ATGAAATTTCT-GTTACCTCCCTATGAAATTTTAGTAA-C
1 CCTATGAAATTCTAGTAACCTCCCTATGAAA-TTCTAGTAACCTCCCTATGAAATTTTGGTAACC
*
9689 TT
65 TC
* * * * * * *
9691 ACTATGAAATTCTAGTAACCTACTTAGGAAATTCTGGTAACCTCCCTATGTAATTTTAGTAACCT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
*
9756 T
66 C
* * ** * * * *
9757 ACTATGAACTTCT-GATAATTTACCTATGAAATTCTGGTAACCTCCCAAAGAAATTTTGGTAACC
1 CCTATGAAATTCTAG-TAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACC
*
9821 TA
65 TC
* * * * *
9823 CCTATGAAATTCTGGTAACCTCCCTGACCTTACTATAAAATTCTAGTAACTTTCCTATGAAATTC
1 CCTATGAAATTCTAGTAA----CCT--CC---CTATGAAATTCTAGTAACCTCCCTATGAAATTT
* *
9888 TAGTAACCTT
57 TGGTAACCTC
* * * * * **
9898 CTTATGAAATTTTGGTAACCTACCTATGAAA-TCTGGTAACCTCCCTATGAAA-TCCGGTAACCT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
9961 -
66 C
* ** * * * *
9961 CCTATGAAATTCTGGTAACCTCGATATGAAATTTTAGTAACCTCCTTATGAAATTATGGTTACCT
1 CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
10026 C
66 C
* * ** * * *** *
10027 CCAATGAAATTTTTAGTAACCTTACGATGAAATTCT-GATAACTTATATATGAAATTTTCGTAAC
1 CCTATGAAA-TTCTAGTAACCTCCCTATGAAATTCTAG-TAACCTCCCTATGAAATTTTGGTAAC
10091 CTC
64 CTC
* * * * *
10094 CCTATGAAATTTTGGTAA-CTACCCTATGAAATTCTAGTAACCTCCTTATGAAATTCT-GTCAAT
1 CCTATGAAATTCTAGTAACCT-CCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGT-AAC
*
10157 GTC
64 CTC
* * * *
10160 ACTATGAAATTCTAGCAACGTCCCTATGAAATAT-TAGTAATCTCCCTATGAAA
1 CCTATGAAATTCTAGTAACCTCCCTATGAAAT-TCTAGTAACCTCCCTATGAAA
10213 ATCCAGTAAC
Statistics
Matches: 1057, Mismatches: 268, Indels: 90
0.75 0.19 0.06
Matches are distributed among these distances:
62 35 0.03
63 40 0.04
64 81 0.08
65 245 0.23
66 539 0.51
67 61 0.06
69 1 0.00
70 1 0.00
71 3 0.00
72 1 0.00
75 50 0.05
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (66 bp):
CCTATGAAATTCTAGTAACCTCCCTATGAAATTCTAGTAACCTCCCTATGAAATTTTGGTAACCT
C
Found at i:9885 original size:22 final size:22
Alignment explanation
Indices: 9849--10229 Score: 230
Period size: 22 Copynumber: 17.4 Consensus size: 22
9839 AACCTCCCTG
* *
9849 ACCTTACTATAAAATTCTAGTA
1 ACCTTCCTATGAAATTCTAGTA
*
9871 ACTTTCCTATGAAATTCTAGTA
1 ACCTTCCTATGAAATTCTAGTA
* * *
9893 ACCTTCTTATGAAATTTTGGTA
1 ACCTTCCTATGAAATTCTAGTA
* *
9915 ACCTACCTATGAAA-TCTGGTA
1 ACCTTCCTATGAAATTCTAGTA
* **
9936 ACCTCCCTATGAAA-TCCGGTA
1 ACCTTCCTATGAAATTCTAGTA
*
9957 ACC-TCCTATGAAATTCTGGTA
1 ACCTTCCTATGAAATTCTAGTA
* *
9978 ACC-TCGATATGAAATTTTAGTA
1 ACCTTC-CTATGAAATTCTAGTA
* * *
10000 ACC-TCCTTATGAAATTATGGTT
1 ACCTTCC-TATGAAATTCTAGTA
* * *
10022 ACCTCCCAATGAAATTTTTAGTA
1 ACCTTCCTATGAAA-TTCTAGTA
* *
10045 ACCTTACGATGAAATTCT-GATA
1 ACCTTCCTATGAAATTCTAG-TA
** * *
10067 A-CTTATATATGAAATTTTCGTA
1 ACCTT-CCTATGAAATTCTAGTA
* * *
10089 ACCTCCCTATGAAATTTTGGTA
1 ACCTTCCTATGAAATTCTAGTA
*
10111 A-CTACCCTATGAAATTCTAGTA
1 ACCT-TCCTATGAAATTCTAGTA
10133 ACC-TCCTTATGAAATTCT-GTCA
1 ACCTTCC-TATGAAATTCTAGT-A
*
10155 A--TGTCACTATGAAATTCTAGCA
1 ACCT-TC-CTATGAAATTCTAGTA
* *
10177 ACGTCCCTATGAAATAT-TAGTA
1 ACCTTCCTATGAAAT-TCTAGTA
* * * *
10199 ATCTCCCTATGAAAATCCAGTA
1 ACCTTCCTATGAAATTCTAGTA
*
10221 ACCTCCCTA
1 ACCTTCCTA
10230 AAAAATTTTG
Statistics
Matches: 289, Mismatches: 49, Indels: 42
0.76 0.13 0.11
Matches are distributed among these distances:
20 9 0.03
21 50 0.17
22 203 0.70
23 26 0.09
24 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (22 bp):
ACCTTCCTATGAAATTCTAGTA
Found at i:9918 original size:97 final size:96
Alignment explanation
Indices: 9752--9943 Score: 280
Period size: 97 Copynumber: 2.0 Consensus size: 96
9742 AATTTTAGTA
* * *
9752 ACCTTACTATGAACTTCTGATAATTTACCTATGAAATTCTGGTAACCTCCCAAAGAAATTTTGGT
1 ACCTTACTATAAAATTCTGATAATTTACCTATGAAATTCTAGTAACCTCCCAAAGAAATTTTGGT
9817 AACCTACCTATGAAATTCTGGTAACCTCCCTG
66 AACCTACCTATGAAA-TCTGGTAACCTCCCTG
* ** *
9849 ACCTTACTATAAAATTCT-AGTAACTTT-CCTATGAAATTCTAGTAACCTTCTTATGAAATTTTG
1 ACCTTACTATAAAATTCTGA-TAA-TTTACCTATGAAATTCTAGTAACCTCCCAAAGAAATTTTG
9912 GTAACCTACCTATGAAATCTGGTAACCTCCCT
64 GTAACCTACCTATGAAATCTGGTAACCTCCCT
9944 ATGAAATCCG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
96 16 0.19
97 67 0.78
98 3 0.03
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (96 bp):
ACCTTACTATAAAATTCTGATAATTTACCTATGAAATTCTAGTAACCTCCCAAAGAAATTTTGGT
AACCTACCTATGAAATCTGGTAACCTCCCTG
Found at i:10080 original size:89 final size:87
Alignment explanation
Indices: 9855--10136 Score: 279
Period size: 89 Copynumber: 3.2 Consensus size: 87
9845 CCTGACCTTA
* * * * *
9855 CTATAAAATTCTAGTAACTTTCCTATGAAATTCT-AGTAACCTTCT-TATGAAATTTTGGTAACC
1 CTATGAAATTCTAGTAACCTTACGATGAAATTCTGA-TAA-CTTCTATATGAAATTTTAGTAACC
* *
9918 TACCTATGAAA-TCTGGTAACCTCC
64 T-CCTATGAAATTATGGTTACCTCC
** * * * * *
9942 CTATGAAA-TCCGGTAACC-TCCTATGAAATTCTGGTAACCTCGATATGAAATTTTAGTAACCTC
1 CTATGAAATTCTAGTAACCTTACGATGAAATTCTGATAACTTCTATATGAAATTTTAGTAACCTC
10005 CTTATGAAATTATGGTTACCTCC
66 C-TATGAAATTATGGTTACCTCC
* * * *
10028 CAATGAAATTTTTAGTAACCTTACGATGAAATTCTGATAACTTATATATGAAATTTTCGTAACCT
1 CTATGAAA-TTCTAGTAACCTTACGATGAAATTCTGATAACTTCTATATGAAATTTTAGTAACCT
* *
10093 CCCTATGAAATTTTGG-TAACTACC
65 -CCTATGAAATTATGGTTACCT-CC
10117 CTATGAAATTCTAGTAACCT
1 CTATGAAATTCTAGTAACCT
10137 CCTTATGAAA
Statistics
Matches: 161, Mismatches: 25, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
84 5 0.03
85 42 0.26
86 25 0.16
87 7 0.04
88 22 0.14
89 58 0.36
90 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (87 bp):
CTATGAAATTCTAGTAACCTTACGATGAAATTCTGATAACTTCTATATGAAATTTTAGTAACCTC
CTATGAAATTATGGTTACCTCC
Found at i:10290 original size:36 final size:37
Alignment explanation
Indices: 10231--10301 Score: 101
Period size: 36 Copynumber: 1.9 Consensus size: 37
10221 ACCTCCCTAA
* *
10231 AAAATTTTGGTAACTTCATTATGAAATTTT-GTAAAT
1 AAAATTCTGATAACTTCATTATGAAATTTTAGTAAAT
10267 AAAATTCTGATAACCTTCA-TATGAAATTTTAGTAA
1 AAAATTCTGATAA-CTTCATTATGAAATTTTAGTAA
10302 CCTTTCTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 22 0.71
37 9 0.29
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (37 bp):
AAAATTCTGATAACTTCATTATGAAATTTTAGTAAAT
Found at i:15618 original size:18 final size:19
Alignment explanation
Indices: 15576--15618 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
15566 TATATCAATT
*
15576 CTTTTTACATGAACTGATT
1 CTTTTTACATGAACTGATG
* *
15595 CTTTTTACATGGATTGATG
1 CTTTTTACATGAACTGATG
15614 CTTTT
1 CTTTT
15619 GTTTTTCCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.51
Consensus pattern (19 bp):
CTTTTTACATGAACTGATG
Found at i:18704 original size:22 final size:22
Alignment explanation
Indices: 18665--18845 Score: 127
Period size: 22 Copynumber: 8.2 Consensus size: 22
18655 TCAAACCTTA
* * *
18665 CATAGAAAGATTATCAAAATTT
1 CATAGTAAGGTTACCAAAATTT
*
18687 CATAGTATGGTTACCAAAATTT
1 CATAGTAAGGTTACCAAAATTT
* *
18709 CATA-TAGAGGTTATCAAAACTT
1 CATAGTA-AGGTTACCAAAATTT
* *
18731 CATAGTGTA-GTTATCAAAATTT
1 CATAGT-AAGGTTACCAAAATTT
*
18753 CATA-CAGAGGTTACCAAAATTT
1 CATAGTA-AGGTTACCAAAATTT
**
18775 CATAAAAAGGTTACCAAAATTT
1 CATAGTAAGGTTACCAAAATTT
* ** * **
18797 CTTAGGGATGTTAATAAAATTT
1 CATAGTAAGGTTACCAAAATTT
* *
18819 CATA-TGAAAGTTAACAAAATTT
1 CATAGT-AAGGTTACCAAAATTT
18841 CATAG
1 CATAG
18846 GGAGGGAGGT
Statistics
Matches: 126, Mismatches: 25, Indels: 15
0.76 0.15 0.09
Matches are distributed among these distances:
21 3 0.02
22 120 0.95
23 3 0.02
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.33
Consensus pattern (22 bp):
CATAGTAAGGTTACCAAAATTT
Found at i:18733 original size:44 final size:44
Alignment explanation
Indices: 18675--18797 Score: 165
Period size: 44 Copynumber: 2.8 Consensus size: 44
18665 CATAGAAAGA
*
18675 TTATCAAAATTTCATAGTATGGTTACCAAAATTTCATATAGAGG
1 TTATCAAAATTTCATAGTATGGTTACCAAAATTTCATACAGAGG
* * * *
18719 TTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATACAGAGG
1 TTATCAAAATTTCATAGTATGGTTACCAAAATTTCATACAGAGG
* ** *
18763 TTACCAAAATTTCATAAAAAGGTTACCAAAATTTC
1 TTATCAAAATTTCATAGTATGGTTACCAAAATTTC
18798 TTAGGGATGT
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTATGGTTACCAAAATTTCATACAGAGG
Found at i:18771 original size:66 final size:66
Alignment explanation
Indices: 18675--18844 Score: 186
Period size: 66 Copynumber: 2.6 Consensus size: 66
18665 CATAGAAAGA
* * * * *
18675 TTATCAAAATTTCAT-AGTATGGTTACCAAAATTTCATATAGAGGTTATCAAAACTTCATAGTG-
1 TTATCAAAATTTCATAAG-AAGGTTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGGA
18738 TAG
65 T-G
* *
18741 TTATCAAAATTTCATACAG-AGGTTACCAAAATTTCATAAAAAGGTTACCAAAATTTCTTAGGGA
1 TTATCAAAATTTCATA-AGAAGGTTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGGA
18805 TG
65 TG
* * *
18807 TTAAT-AAAATTTCATATGAAAGTTAACAAAATTTCATA
1 TT-ATCAAAATTTCATAAGAAGGTTACCAAAATTTCATA
18845 GGGAGGGAGG
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
65 1 0.01
66 83 0.93
67 3 0.03
68 2 0.02
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTTCATAAGAAGGTTACCAAAATTTCATAAAAAGGTTACCAAAACTTCATAGGGAT
G
Found at i:18939 original size:22 final size:22
Alignment explanation
Indices: 18871--18947 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
18861 AATTTTGTGC
* **
18871 TTATCAAAATTTCCTAGGGAGG
1 TTATGAAAATTTTATAGGGAGG
* *
18893 TTAAGAAAACTTTATAGGGAGG
1 TTATGAAAATTTTATAGGGAGG
*
18915 TTATGAAAATTTTAT-GGAGATG
1 TTATGAAAATTTTATAGG-GAGG
18937 TTATCGAAAAT
1 TTAT-GAAAAT
18948 ACATAGAGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
21 2 0.04
22 37 0.82
23 6 0.13
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (22 bp):
TTATGAAAATTTTATAGGGAGG
Found at i:19101 original size:22 final size:22
Alignment explanation
Indices: 19054--19220 Score: 120
Period size: 22 Copynumber: 7.6 Consensus size: 22
19044 TTTAGTATGA
* **
19054 TTATTAAAATTTCATAG-GTAAA
1 TTATCAAAATTTCATAGTG-AGG
* *
19076 TTATCAAAATTTCACATTGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
19098 TTATCGAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* *
19120 TTACCAAAATTTCATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
* * * *
19142 CTATCAAATTTTTATAGGGAGG
1 TTATCAAAATTTCATAGTGAGG
* * *
19164 TTATCGAAATTTTATAATGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
19186 TAATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCATAGTGAGG
*
19208 TTATCAATATTTC
1 TTATCAAAATTTC
19221 TACATTGGAG
Statistics
Matches: 113, Mismatches: 31, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
22 112 0.99
23 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:19147 original size:66 final size:66
Alignment explanation
Indices: 19077--19227 Score: 158
Period size: 66 Copynumber: 2.3 Consensus size: 66
19067 ATAGGTAAAT
* * * * *
19077 TATCAAAATTTCACATTGAGGTTATCGAAATTTCATAGTGTGGTTACCAAAATTTCATAGTGTGG
1 TATCAAAATTTCACATTGAGGTTATCGAAATTTCATAATGAGGTAACCAAAATTTCAAAATGTGG
19142 C
66 C
* * * ** * * *
19143 TATCAAATTTTTATAGGGAGGTTATCGAAATTTTATAATGAGGTAATCAAATTTTCAAAATGTGG
1 TATCAAAATTTCACATTGAGGTTATCGAAATTTCATAATGAGGTAACCAAAATTTCAAAATGTGG
*
19208 T
66 C
*
19209 TATCAATATTTCTACATTG
1 TATCAAAATTTC-ACATTG
19228 GAGTATGAAA
Statistics
Matches: 64, Mismatches: 20, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
66 61 0.95
67 3 0.05
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (66 bp):
TATCAAAATTTCACATTGAGGTTATCGAAATTTCATAATGAGGTAACCAAAATTTCAAAATGTGG
C
Found at i:20894 original size:20 final size:20
Alignment explanation
Indices: 20850--20895 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
20840 TCAAGGAAAC
*
20850 AACCCGTTGAAACCCGGTGT
1 AACCCGTTGAAACCCGATGT
*
20870 GACCCGTTGAAACCCGAAT-T
1 AACCCGTTGAAACCCG-ATGT
20890 AACCCG
1 AACCCG
20896 GTGACCCGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (20 bp):
AACCCGTTGAAACCCGATGT
Found at i:21328 original size:9 final size:9
Alignment explanation
Indices: 21314--21342 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
21304 ATTAATCCGC
21314 ATTGACCCG
1 ATTGACCCG
21323 ATTGACCCG
1 ATTGACCCG
21332 ATTGACCCG
1 ATTGACCCG
21341 AT
1 AT
21343 GGTTAAACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (9 bp):
ATTGACCCG
Found at i:27116 original size:23 final size:23
Alignment explanation
Indices: 27089--27197 Score: 78
Period size: 23 Copynumber: 4.6 Consensus size: 23
27079 GGTTTCAACC
27089 TGGCCCCAACTTGAGGGGTAAGT
1 TGGCCCCAACTTGAGGGGTAAGT
* *
27112 TGGCCCCAACTT-AGGACAGAAAGGT
1 TGGCCCCAACTTGAGG--GGTAA-GT
* * ** **
27137 T-GCACAAACTTTGAAGGTTTCAACC
1 TGGCCCCAAC-TTG-AGGGGT-AAGT
27162 TGGCCCCAACTTGAGGGGTAAGT
1 TGGCCCCAACTTGAGGGGTAAGT
27185 TGGCCCCAACTTG
1 TGGCCCCAACTTG
27198 GACTTCGTCA
Statistics
Matches: 63, Mismatches: 15, Indels: 16
0.67 0.16 0.17
Matches are distributed among these distances:
22 3 0.05
23 27 0.43
24 13 0.21
25 9 0.14
26 8 0.13
27 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
TGGCCCCAACTTGAGGGGTAAGT
Found at i:27161 original size:73 final size:73
Alignment explanation
Indices: 27042--27200 Score: 293
Period size: 73 Copynumber: 2.2 Consensus size: 73
27032 GTCAACCCGA
* *
27042 CCCCAACTTAGGACAGAAGGGTTGCGCAAACTTTGAAGGTTTCAACCTGGCCCCAACTTGAGGGG
1 CCCCAACTTAGGACAGAAAGGTTGCACAAACTTTGAAGGTTTCAACCTGGCCCCAACTTGAGGGG
27107 TAAGTTGG
66 TAAGTTGG
27115 CCCCAACTTAGGACAGAAAGGTTGCACAAACTTTGAAGGTTTCAACCTGGCCCCAACTTGAGGGG
1 CCCCAACTTAGGACAGAAAGGTTGCACAAACTTTGAAGGTTTCAACCTGGCCCCAACTTGAGGGG
27180 TAAGTTGG
66 TAAGTTGG
27188 CCCCAACTT-GGAC
1 CCCCAACTTAGGAC
27201 TTCGTCAAGA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
72 4 0.05
73 80 0.95
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.21
Consensus pattern (73 bp):
CCCCAACTTAGGACAGAAAGGTTGCACAAACTTTGAAGGTTTCAACCTGGCCCCAACTTGAGGGG
TAAGTTGG
Found at i:29043 original size:18 final size:19
Alignment explanation
Indices: 29015--29053 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
29005 AGAAAAACGA
*
29015 AAAATATGCAAATAAAAAC
1 AAAATATGCAAAAAAAAAC
29034 AAAA-ATGCAAAAAAAAAC
1 AAAATATGCAAAAAAAAAC
29052 AA
1 AA
29054 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.74, C:0.10, G:0.05, T:0.10
Consensus pattern (19 bp):
AAAATATGCAAAAAAAAAC
Found at i:32489 original size:21 final size:23
Alignment explanation
Indices: 32449--32491 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
32439 TCAAGACAAT
32449 TAAAAACTAAGAGCAATTAAATTA
1 TAAAAAC-AAGAGCAATTAAATTA
32473 TAAAAAC-AGAG-AATTAAAT
1 TAAAAACAAGAGCAATTAAAT
32492 AAGATGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
24 7 0.37
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.23
Consensus pattern (23 bp):
TAAAAACAAGAGCAATTAAATTA
Found at i:37006 original size:23 final size:23
Alignment explanation
Indices: 36980--37025 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
36970 ATATGTTATC
36980 AATTGAACATCATGTAAATAAAT
1 AATTGAACATCATGTAAATAAAT
37003 AATTGAACATCATGTAAATAAAT
1 AATTGAACATCATGTAAATAAAT
37026 GGTGGTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (23 bp):
AATTGAACATCATGTAAATAAAT
Found at i:39234 original size:52 final size:53
Alignment explanation
Indices: 39172--39302 Score: 201
Period size: 53 Copynumber: 2.5 Consensus size: 53
39162 CATATCCCAA
* ** *
39172 ATCAGACAACAAATTCAAACCAGAAATACAAAAAT-CGAAAGTGGGTTTGATG
1 ATCAGACAACAAATTCAAACAAGAAATACAAAAATAAAAAAGTAGGTTTGATG
* *
39224 ATCAGACAACAAATTCAAACAAGAAATGCAAATATAAAAAAGTAGGTTTGATG
1 ATCAGACAACAAATTCAAACAAGAAATACAAAAATAAAAAAGTAGGTTTGATG
39277 ATCAGACAACAAATTCAAACAAGAAA
1 ATCAGACAACAAATTCAAACAAGAAA
39303 GCCTTAAAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 32 0.44
53 40 0.56
ACGTcount: A:0.53, C:0.15, G:0.15, T:0.18
Consensus pattern (53 bp):
ATCAGACAACAAATTCAAACAAGAAATACAAAAATAAAAAAGTAGGTTTGATG
Found at i:39443 original size:85 final size:85
Alignment explanation
Indices: 39296--39474 Score: 322
Period size: 85 Copynumber: 2.1 Consensus size: 85
39286 CAAATTCAAA
*
39296 CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACAAAACAAATAAATCCTAACC
1 CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACAAAACAAATAAACCCTAACC
39361 CTAGCAGAGAAATCAAACGT
66 CTAGCAGAGAAATCAAACGT
* *
39381 CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAACCCAAACAAATAAACCCTAACC
1 CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACAAAACAAATAAACCCTAACC
*
39446 GTAGCAGAGAAATCAAACGT
66 CTAGCAGAGAAATCAAACGT
39466 CAAGAAAGC
1 CAAGAAAGC
39475 TAACCTGATA
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 90 1.00
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.18
Consensus pattern (85 bp):
CAAGAAAGCCTTAAAAACACACATTTGTTTAATCATTACAAAAACAAAACAAATAAACCCTAACC
CTAGCAGAGAAATCAAACGT
Found at i:39812 original size:17 final size:17
Alignment explanation
Indices: 39783--39836 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
39773 TTCCCCCAAT
*
39783 TTATTACTA-ATTTTTTA
1 TTATT-CTATATTTATTA
39800 TTATTCTATATTTATTA
1 TTATTCTATATTTATTA
39817 TT-TTC--TATTTATTA
1 TTATTCTATATTTATTA
39831 TCTATT
1 T-TATT
39837 AATTCTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 8 0.24
17 14 0.42
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTCTATATTTATTA
Found at i:39813 original size:14 final size:14
Alignment explanation
Indices: 39796--39835 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
39786 TTACTAATTT
39796 TTTATTATTCTATA
1 TTTATTATTCTATA
* *
39810 TTTATTATTTTCTA
1 TTTATTATTCTATA
39824 TTTATTA-TCTAT
1 TTTATTATTCTAT
39836 TAATTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 3 0.14
14 19 0.86
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATTATTCTATA
Found at i:45895 original size:2 final size:2
Alignment explanation
Indices: 45883--45911 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
45873 ACCAATTATT
45883 TA TA T- 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 TA
45912 CGATATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46386 original size:16 final size:17
Alignment explanation
Indices: 46355--46389 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
46345 ACGAAATGCA
46355 TGTTTAGTTCATTTGTT
1 TGTTTAGTTCATTTGTT
*
46372 TGTTTA-TTTATTTGTT
1 TGTTTAGTTCATTTGTT
46388 TG
1 TG
46390 ATAGGTAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.11, C:0.03, G:0.17, T:0.69
Consensus pattern (17 bp):
TGTTTAGTTCATTTGTT
Found at i:47599 original size:17 final size:19
Alignment explanation
Indices: 47557--47599 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
47547 ACGGTTAAAG
47557 ATAAAAAATTAAAATTAAT
1 ATAAAAAATTAAAATTAAT
*
47576 A-ATAAAA-TAAAA-TAAT
1 ATAAAAAATTAAAATTAAT
47592 ATAAAAAA
1 ATAAAAAA
47600 GCTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 5 0.24
17 10 0.48
18 5 0.24
19 1 0.05
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
ATAAAAAATTAAAATTAAT
Found at i:53356 original size:12 final size:12
Alignment explanation
Indices: 53339--53363 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
53329 TTATGGGGTG
53339 AAATAATGGAGA
1 AAATAATGGAGA
53351 AAATAATGGAGA
1 AAATAATGGAGA
53363 A
1 A
53364 TCATTTGACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AAATAATGGAGA
Found at i:57603 original size:15 final size:16
Alignment explanation
Indices: 57585--57617 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
57575 GAAAGAAAGT
57585 AATTAAAC-AGAAAAC
1 AATTAAACTAGAAAAC
*
57600 AATTATACTAGAAAAC
1 AATTAAACTAGAAAAC
57616 AA
1 AA
57618 AGCAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (16 bp):
AATTAAACTAGAAAAC
Found at i:58413 original size:17 final size:18
Alignment explanation
Indices: 58376--58413 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
58366 ACCCTTGTCT
*
58376 AAAACTAGAAGAAAACTA
1 AAAACTAGAAGAAAACGA
58394 AAAACTAGAAGAAAA-GA
1 AAAACTAGAAGAAAACGA
58411 AAA
1 AAA
58414 TATCTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.71, C:0.08, G:0.13, T:0.08
Consensus pattern (18 bp):
AAAACTAGAAGAAAACGA
Found at i:61593 original size:2 final size:2
Alignment explanation
Indices: 61586--61616 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
61576 ACAAGATGAT
61586 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61617 AACATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:61606 original size:15 final size:15
Alignment explanation
Indices: 61586--61614 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
61576 ACAAGATGAT
61586 TATATATATATATAA
1 TATATATATATATAA
61601 TATATATATATATA
1 TATATATATATATA
61615 TAAACATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATATATATATATAA
Found at i:61859 original size:2 final size:2
Alignment explanation
Indices: 61852--61876 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
61842 AAAGGAATGC
61852 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 A
61877 CTACATATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63819 original size:42 final size:42
Alignment explanation
Indices: 63760--63850 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
63750 AACAACAATT
* *
63760 AATATTAGCTTTATTTTGATGAATTATCTAGATATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
63802 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
63844 AAT-TTAG
1 AATATTAG
63851 GTAATACACT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:63825 original size:21 final size:21
Alignment explanation
Indices: 63760--63825 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 21
63750 AACAACAATT
63760 AATATTAGCTTTATTTTGATG
1 AATATTAGCTTTATTTTGATG
* ** * *
63781 -A-ATTATCTAGATATGGAGTAG
1 AATATTAGCTTTATTTTGA-T-G
63802 AATATTAGCTTTATTTTGATG
1 AATATTAGCTTTATTTTGATG
63823 AAT
1 AAT
63826 TACCTAGAGA
Statistics
Matches: 31, Mismatches: 10, Indels: 8
0.63 0.20 0.16
Matches are distributed among these distances:
19 11 0.35
20 2 0.06
21 5 0.16
22 2 0.06
23 11 0.35
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (21 bp):
AATATTAGCTTTATTTTGATG
Found at i:65948 original size:43 final size:43
Alignment explanation
Indices: 65900--65986 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
65890 GTAGTGATAA
* *
65900 AATAATTGATACAAATTGTGCAATTTAAGAGAATAATAATACC
1 AATAATTGATACAAATTGTACAATTTAAAAGAATAATAATACC
*
65943 AATAATTGATACAAATTGTACAATTTAAAAGGATAATAATACC
1 AATAATTGATACAAATTGTACAATTTAAAAGAATAATAATACC
65986 A
1 A
65987 CTGAACTTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.51, C:0.09, G:0.10, T:0.30
Consensus pattern (43 bp):
AATAATTGATACAAATTGTACAATTTAAAAGAATAATAATACC
Done.