Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010928.1 Corchorus capsularis cultivar CVL-1 contig10949, 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: 21447
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:2345 original size:43 final size:43
Alignment explanation
Indices: 2298--2403 Score: 176
Period size: 43 Copynumber: 2.5 Consensus size: 43
2288 ACAACATTGT
* *
2298 AGATCGGCAGAAGTGTCAGAACATAGGAGAACAGAAACCTCGA
1 AGATCGGCAGAAGTGTCAGAACATAGAAGAACAGAAACATCGA
*
2341 AGATCGGCAGAAGTGTAAGAACATAGAAGAACAGAAACATCGA
1 AGATCGGCAGAAGTGTCAGAACATAGAAGAACAGAAACATCGA
*
2384 AGATCGACAGAAGTGTCAGA
1 AGATCGGCAGAAGTGTCAGA
2404 TATGTAGATT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.44, C:0.16, G:0.27, T:0.12
Consensus pattern (43 bp):
AGATCGGCAGAAGTGTCAGAACATAGAAGAACAGAAACATCGA
Found at i:2787 original size:165 final size:165
Alignment explanation
Indices: 2602--3159 Score: 904
Period size: 165 Copynumber: 3.4 Consensus size: 165
2592 TTAAACGCCG
* *
2602 TAGAACACGAACATGGTAGAACGATAACATCAAAGATCGGCAGAAGTGTCAGATATGGAGATCCC
1 TAGAACACGAACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTGTCAGATATGGAGATCCC
* * *
2667 GTAGAACATGAACATGGTAGAACGACAACGTCAAAGATAGGAAGAGTATCAGTTATGGAAATCCT
66 GTAGAACATGAACATGGTAGAACGACAACGTCAAAGATCGGCAGAGTATCAGATATGGAAATCCT
2732 TACGTTGGTTACAAGCTTGAAAGATTTGATGGTGA
131 TACGTTGGTTACAAGCTTGAAAGATTTGATGGTGA
* * *
2767 TAGAACACGGACATGGTAGAACGACAACATCGAAGATCGACAGAAGTGTTAGATATGGAGATCCC
1 TAGAACACGAACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTGTCAGATATGGAGATCCC
*
2832 ATAGAACATGAACATGGTAGAACGACAACGTCAAAGATCGGCAGAGTATCAGATATGGAAATCCT
66 GTAGAACATGAACATGGTAGAACGACAACGTCAAAGATCGGCAGAGTATCAGATATGGAAATCCT
2897 TACGTTGGTTACAAGCTTGAAAGATTTGATGGTGA
131 TACGTTGGTTACAAGCTTGAAAGATTTGATGGTGA
*
2932 TAGAACACGGACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTG-CTAGATATGGAGATCC
1 TAGAACACGAACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTGTC-AGATATGGAGATCC
* * * * *
2996 CGTAGAACATGAACATGGTAAAACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCC
65 CGTAGAACATGAACATGGTAGAACGACAACGTCAAAGATCGGCAGAGTATCAGATATGGAAATCC
* *
3061 TTACATTGGTTACAAGCTTGAAAGATCTGATGGTGA
130 TTACGTTGGTTACAAGCTTGAAAGATTTGATGGTGA
* * * *
3097 TAGAACCCGAACATGGAAGAACAACAACATCGAAGATCAGCAG-AGTGTCAGATATGGAGATCC
1 TAGAACACGAACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTGTCAGATATGGAGATCC
3160 TTACGTTGGT
Statistics
Matches: 367, Mismatches: 24, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
164 18 0.05
165 349 0.95
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (165 bp):
TAGAACACGAACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTGTCAGATATGGAGATCCC
GTAGAACATGAACATGGTAGAACGACAACGTCAAAGATCGGCAGAGTATCAGATATGGAAATCCT
TACGTTGGTTACAAGCTTGAAAGATTTGATGGTGA
Found at i:3038 original size:66 final size:65
Alignment explanation
Indices: 2932--3060 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 65
2922 TTGATGGTGA
* *
2932 TAGAACACGGACATGGTAGAACGACAACATCGAAGATCGGCAGAAGTG-CTAGATATGGAGATCC
1 TAGAACACGAACATGGTAAAACGACAACATCGAAGATCGGCAG-AGTGTC-AGATATGGAGATCC
2996 CG
64 CG
*
2998 TAGAACATGAACATGGTAAAACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCC
1 TAGAACACGAACATGGTAAAACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCC
3061 TTACATTGGT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
65 18 0.31
66 41 0.69
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (65 bp):
TAGAACACGAACATGGTAAAACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCCCG
Found at i:3169 original size:99 final size:99
Alignment explanation
Indices: 3006--3258 Score: 427
Period size: 99 Copynumber: 2.5 Consensus size: 99
2996 CGTAGAACAT
3006 GAACATGGTAA-AACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCCTTACATTGG
1 GAACATGG-AAGAACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCCTTACATTGG
3070 TTACAAGCTTGAAAGATCTGATGGTGATAGAACCC
65 TTACAAGCTTGAAAGATCTGATGGTGATAGAACCC
* * *
3105 GAACATGGAAGAACAACAACATCGAAGATCAGCAGAGTGTCAGATATGGAGATCCTTACGTTGGT
1 GAACATGGAAGAACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCCTTACATTGGT
*
3170 TACAAGCTTGAAAGATTTGATGGTGATAGAACCC
66 TACAAGCTTGAAAGATCTGATGGTGATAGAACCC
* *
3204 GAACATGGAAGAACGACAACATCGAAGATTGGCAGAGGTTTCAGATATGGAGATC
1 GAACATGGAAGAACGACAACATCGAAGATCGGCAGA-GTGTCAGATATGGAGATC
3259 TTCCCCACAA
Statistics
Matches: 144, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
98 2 0.01
99 125 0.87
100 17 0.12
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.21
Consensus pattern (99 bp):
GAACATGGAAGAACGACAACATCGAAGATCGGCAGAGTGTCAGATATGGAGATCCTTACATTGGT
TACAAGCTTGAAAGATCTGATGGTGATAGAACCC
Found at i:6000 original size:233 final size:233
Alignment explanation
Indices: 5593--6022 Score: 616
Period size: 233 Copynumber: 1.8 Consensus size: 233
5583 AAAAAAATTA
*
5593 GATGATCAAGATAGTGGAGTACTTGAAAAAGATCAATCCTCTCTCTGATCCAAAAGTCACGACCG
1 GATGATCAAGATAGTGGAGTACTTGAAAAAGATCAATCCTCTCTCTAATCCAAAAGTCACGACCG
* * * * * * *
5658 CTAGACCATGAAGAGTGGCAAGGTAAGTGTTGATTGATGATGAACTATATAAAAAATCCTTCACC
66 CTAGACCACGAAGAGCGGCAAGGTAAGTGTTGATTAATAATGAAATATATAAAAAAGCATTCACC
**** *
5723 CTTTATTTTTTGAAGTATGTAGACCTAGATAAAGTTGTCTATGTGTT-AAGGGAGATCCACGAAG
131 CTTTATTTTTTGAAGTATGTAGACCTAGATAAAGCCAACTATGTGTTGAA-GAAGATCCACGAAG
5787 GTGGAGAACCCCCAAACGTAAGTCTGATCCACGAAGGTG
195 GTGGAGAACCCCCAAACGTAAGTCTGATCCACGAAGGTG
*
5826 GATGATCGAGATAGTGGAGTACTTGAAAAAGATCAATCCTCTCTCTAATCCAAAAGTCACGACCG
1 GATGATCAAGATAGTGGAGTACTTGAAAAAGATCAATCCTCTCTCTAATCCAAAAGTCACGACCG
* * * *
5891 CTAGACTACGAAGAGCGGCAAGGTATGTGTTGGTTAATAATGAAATATATAAGAAAGCATTCA-C
66 CTAGACCACGAAGAGCGGCAAGGTAAGTGTTGATTAATAATGAAATATATAAAAAAGCATTCACC
* *
5955 CTTTCCTTTTTTGAAGT-TCGTAGA-CTCAGATGAAGCCAACTATGTGTTGAAGAAGATCCACGA
131 CTTT-ATTTTTTGAAGTAT-GTAGACCT-AGATAAAGCCAACTATGTGTTGAAGAAGATCCACGA
6018 AGGTG
193 AGGTG
6023 TATGTGGCAA
Statistics
Matches: 173, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
232 8 0.05
233 163 0.94
234 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (233 bp):
GATGATCAAGATAGTGGAGTACTTGAAAAAGATCAATCCTCTCTCTAATCCAAAAGTCACGACCG
CTAGACCACGAAGAGCGGCAAGGTAAGTGTTGATTAATAATGAAATATATAAAAAAGCATTCACC
CTTTATTTTTTGAAGTATGTAGACCTAGATAAAGCCAACTATGTGTTGAAGAAGATCCACGAAGG
TGGAGAACCCCCAAACGTAAGTCTGATCCACGAAGGTG
Found at i:6523 original size:99 final size:99
Alignment explanation
Indices: 6352--6773 Score: 738
Period size: 99 Copynumber: 4.3 Consensus size: 99
6342 ATTTATGAAA
* * *
6352 GACCTTAGATTTTGATCCGGACTCCCAGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
1 GACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
*
6417 TGGACTCTTTGTGAGAATGGCTAAGTTCGTAATT
66 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
*
6451 GACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATTGAAACTAAGTTGGCCGAACGTAAGCCC
1 GACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
*
6516 TGGACTCTTTGTGAGAACGGCTAAATTCGTAATT
66 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
*
6550 GACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATCGAAACTAAGTTGACCGAACGTAAGCCC
1 GACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
6615 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
66 TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
* * *
6649 GACCTTAGATTTCGATCTAGACTCCCCGTGAGAACATAGAAACTAAGTTGGCCGAACGTAAGCTC
1 GACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
6714 TGGACTCTTTGTGAGAACGGC-AACGTTCGTAATT
66 TGGACTCTTTGTGAGAACGGCTAA-GTTCGTAATT
6748 GACCTTAGATTTCGATCTGGACTCCC
1 GACCTTAGATTTCGATCTGGACTCCC
6774 TGATCGTGTC
Statistics
Matches: 308, Mismatches: 14, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
98 2 0.01
99 306 0.99
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (99 bp):
GACCTTAGATTTCGATCTGGACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCC
TGGACTCTTTGTGAGAACGGCTAAGTTCGTAATT
Found at i:6629 original size:48 final size:48
Alignment explanation
Indices: 6379--6632 Score: 129
Period size: 48 Copynumber: 5.2 Consensus size: 48
6369 CGGACTCCCA
*
6379 GTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTT
1 GTGAGAACATCGAAACTAAGTTGACCGAACGTAAGCCCTGGACTCTTT
*** * * * * ** ** ***
6427 GTGAGAATGGCTAAGTTCGTAA-TTGACCTTAGA-TTTCGATCTGGACTCCCC
1 GTGAGAACATCGAA--AC-TAAGTTGACC-GA-ACGTAAGCCCTGGACTCTTT
* *
6478 GTGAGAACATTGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTT
1 GTGAGAACATCGAAACTAAGTTGACCGAACGTAAGCCCTGGACTCTTT
** * * * ** ** ***
6526 GTGAGAACGGCTAAATTCGTAA-TTGACCTTAGA-TTTCGATCTGGACTCCCC
1 GTGAGAACATCGAAA--C-TAAGTTGACC-GA-ACGTAAGCCCTGGACTCTTT
6577 GTGAGAACATCGAAACTAAGTTGACCGAACGTAAGCCCTGGACTCTTT
1 GTGAGAACATCGAAACTAAGTTGACCGAACGTAAGCCCTGGACTCTTT
6625 GTGAGAAC
1 GTGAGAAC
6633 GGCTAAGTTC
Statistics
Matches: 135, Mismatches: 57, Indels: 28
0.61 0.26 0.13
Matches are distributed among these distances:
47 2 0.01
48 57 0.42
49 13 0.10
50 12 0.09
51 49 0.36
52 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (48 bp):
GTGAGAACATCGAAACTAAGTTGACCGAACGTAAGCCCTGGACTCTTT
Found at i:6999 original size:6 final size:6
Alignment explanation
Indices: 6988--7012 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6978 AGTAAATTAG
6988 ATCTAA ATCTAA ATCTAA ATCTAA A
1 ATCTAA ATCTAA ATCTAA ATCTAA A
7013 GCAGATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATCTAA
Found at i:8392 original size:19 final size:18
Alignment explanation
Indices: 8360--8395 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
8350 TTGAAATAAT
*
8360 TCTTCAATTGTCTTCAAA
1 TCTTCAATTATCTTCAAA
8378 TCTTCAAATTATCTTCAA
1 TCTTC-AATTATCTTCAA
8396 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (18 bp):
TCTTCAATTATCTTCAAA
Found at i:10474 original size:99 final size:99
Alignment explanation
Indices: 10255--10734 Score: 598
Period size: 99 Copynumber: 4.9 Consensus size: 99
10245 TGGCTCGATC
* *
10255 ACTCCCCGTGAGAACATCGAAACTAAGTTGTGGCCGAACGTGAGCCCTGGACTCTTTGTGAGAAC
1 ACTCCCCGTGAGAACATCGAAACTAAG-T-TGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAAT
*
10320 GGCTAAGTTCGT-TTTGACCTTAGATTTCGATCTGG
64 GGCTAAGTTCGTATTTGACCTTAGATTTCGATCCGG
* *
10355 ACTCCCCGTGAGAACATCGAAACTAAGTTGGCTGAACGTAAGCCCCGGACTCTTTGTGAGAATGG
1 ACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAATGG
*
10420 CTAAGTTCGTAATTGACCTTAGATTTCGATCCGG
66 CTAAGTTCGTATTTGACCTTAGATTTCGATCCGG
* * *
10454 ACTCCCCGTGAGAACGTCGAAACTATGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAACGG
1 ACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAATGG
*
10519 CTAAGTTCGTAATTGACCTTAGATTTCGATCCGG
66 CTAAGTTCGTATTTGACCTTAGATTTCGATCCGG
** * * * * * *
10553 ACTCGTCATGAGGACATCGAAACTAAGTTGTGGTCGAGCGTAAGCCCT-GAATATTTTGTGAGAA
1 ACTCCCCGTGAGAACATCGAAACTAAG-T-TGGCCGAACGTAAGCCCTGGACT-CTTTGTGAGAA
*
10617 TGGCTAAGTTCGTATTTGACC------TTCGATTCGG
63 TGGCTAAGTTCGTATTTGACCTTAGATTTCGATCCGG
*** * * * *
10648 ACTTGTCATGAGAACATCGAAACTAAGTTGTGGCCGAGCGTAAGCCCTGAACACTTTGTGAGAAT
1 ACTCCCCGTGAGAACATCGAAACTAAG-T-TGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAAT
*
10713 GGCTAAGTTCATATTTGACCTT
64 GGCTAAGTTCGTATTTGACCTT
10735 CGATCCGGAC
Statistics
Matches: 341, Mismatches: 32, Indels: 17
0.87 0.08 0.04
Matches are distributed among these distances:
95 84 0.25
96 1 0.00
98 43 0.13
99 137 0.40
100 31 0.09
101 45 0.13
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (99 bp):
ACTCCCCGTGAGAACATCGAAACTAAGTTGGCCGAACGTAAGCCCTGGACTCTTTGTGAGAATGG
CTAAGTTCGTATTTGACCTTAGATTTCGATCCGG
Found at i:10842 original size:47 final size:46
Alignment explanation
Indices: 10788--10877 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 46
10778 TCTACGTTGG
* *
10788 ACGTTCTCCCAACTTTAGAGATCTTGCCGAA-TTGTTAGTATTTATAA
1 ACGTTCTCCCAACTTTAGACATC-TGCC-AACTTGTTAATATTTATAA
*
10835 ACGTTCTCCCAACTTTCGACATCTGCCAACTTGTTAATATTTA
1 ACGTTCTCCCAACTTTAGACATCTGCCAACTTGTTAATATTTA
10878 CAAGGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
45 2 0.05
46 16 0.41
47 21 0.54
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (46 bp):
ACGTTCTCCCAACTTTAGACATCTGCCAACTTGTTAATATTTATAA
Found at i:15688 original size:19 final size:19
Alignment explanation
Indices: 15628--15691 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
15618 AATTTTTAAG
*
15628 GAATTTGTGAATAAAGATT
1 GAATTTGTGAATAATGATT
* *
15647 GAATCTT-TTAGATAAT-TTGT
1 GAAT-TTGTGA-ATAATGAT-T
15667 GAATTTGTGAATAATGATT
1 GAATTTGTGAATAATGATT
15686 GAATTT
1 GAATTT
15692 TTAATTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
19 21 0.60
20 14 0.40
ACGTcount: A:0.36, C:0.02, G:0.19, T:0.44
Consensus pattern (19 bp):
GAATTTGTGAATAATGATT
Found at i:15802 original size:49 final size:49
Alignment explanation
Indices: 15722--15870 Score: 126
Period size: 50 Copynumber: 3.0 Consensus size: 49
15712 TTAAGTAATT
* * * *
15722 TTTGTAAATAAAGATTGAACCTTT-AAGTAAAAGATGAAATCTTTGAATAA
1 TTTG-AAATAAAAATGGAATCTTTGAACTAAAAGATGAAAT-TTTGAATAA
* *
15772 TTTGAAATAAAAATGGAATCTTTGAA-TAAAAGGCT-AAACTTTTTGATTAA
1 TTTGAAATAAAAATGGAATCTTTGAACTAAAA-GATGAAA--TTTTGAATAA
** *
15822 GGTGAAATAAAAATAGG-ATCTTTGAACTAAATGATGAAATTTGTGAATA
1 TTTGAAATAAAAAT-GGAATCTTTGAACTAAAAGATGAAATTT-TGAATA
15871 GTTAATAAGA
Statistics
Matches: 81, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
49 27 0.33
50 44 0.54
51 10 0.12
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (49 bp):
TTTGAAATAAAAATGGAATCTTTGAACTAAAAGATGAAATTTTGAATAA
Found at i:16512 original size:41 final size:41
Alignment explanation
Indices: 16467--17091 Score: 440
Period size: 41 Copynumber: 14.6 Consensus size: 41
16457 CCCAATCTGT
* *
16467 CCTTCCCCATCGGAAGATGTTGTTTAGTTTTCCC-GTATTGC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGT-TTGC
* *
16508 CCTT-CCCAGTCGGAAGGTGTTGTCTTGTTGTTTAGTTTTTCCAGTTTGC
1 CCTTCCCCA-CCGGAA---G--G---TGTTGTTTAGTTTTCCCAGTTTGC
* * **
16557 CCTTCCTCATCGGAAGGTGTTGTTTA--AATCCCAGTTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
* * * *
16596 CCTTTCTCATCAGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
* * * *
16637 CCTTCCTCACCGGAAGGTGTTGTTTAGATTACCCAGTTTAC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
* * * *
16678 CCTTCCCTACCGGAAGGTGTTGTCTAGATTTCCCAATTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
*
16719 CCTTCCCTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCA-TCTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTT-AG--T---TTTCCCAGT-TTGC
* *
16766 CCTTCCCCACCGGAAGGTGTTATTTAGATTTCCCAGTTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
* * * *
16807 CTTTCCCCACCGGAAGGCGTTGTCTAGATTTCCCAGTTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
* * ** *
16848 CTTTTCTTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCATTTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTT-AG--T---TTTCCCAGTTTGC
**
16895 CCTTCCCCACCATAAGGTGTTGTTTAG-TTTCCCAGTTTGC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
* * * *
16935 CCTTCCTCATCGGAAGGTGTTGTTTAATTGTCTAATTACCAGTTTAC
1 CCTTCCCCACCGGAAGGTGTTGTTT-A--GT-T--TTCCCAGTTTGC
* * * *
16982 CCTTCCCCATCGGAAGGTGCTGTTTAG-TTTCCCAATTTTC
1 CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
* * *
17022 CCTTCCCCCGCCGGAAAGG-GTTCTTTAGTTGCCTTATTCCCATTTTGC
1 CCTT-CCCCACCGG-AAGGTGTTGTTTA---G--TT-TTCCCAGTTTGC
*
17070 CCTTCCCC-TCGGAAGGTGTTGT
1 CCTTCCCCACCGGAAGGTGTTGT
17092 CTAAGTTGCC
Statistics
Matches: 476, Mismatches: 64, Indels: 83
0.76 0.10 0.13
Matches are distributed among these distances:
39 34 0.07
40 50 0.11
41 206 0.43
42 10 0.02
43 1 0.00
44 4 0.01
45 5 0.01
46 14 0.03
47 103 0.22
48 14 0.03
49 30 0.06
50 5 0.01
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (41 bp):
CCTTCCCCACCGGAAGGTGTTGTTTAGTTTTCCCAGTTTGC
Found at i:16537 original size:49 final size:49
Alignment explanation
Indices: 16484--16579 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 49
16474 CATCGGAAGA
*
16484 TGTTGTTTAG-TTTTCCCGTATTGCCCTTCC-CAGTCGGAAGGTGTTGTCT
1 TGTTGTTTAGTTTTTCCAGT-TTGCCCTTCCTCA-TCGGAAGGTGTTGTCT
16533 TGTTGTTTAGTTTTTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
1 TGTTGTTTAGTTTTTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT
16580 TTAAATCCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
49 34 0.77
50 10 0.23
ACGTcount: A:0.10, C:0.21, G:0.24, T:0.45
Consensus pattern (49 bp):
TGTTGTTTAGTTTTTCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTCT
Found at i:16596 original size:88 final size:88
Alignment explanation
Indices: 16406--17028 Score: 310
Period size: 88 Copynumber: 7.2 Consensus size: 88
16396 GCCTTGTCTA
* * * * ** * * *
16406 ATTCCCGGTTTTGCCCTTCCAAGTCGGAAGGTGTTGTCTAGTTG-TCA-AATTCCCAATCTGTCC
1 ATTCCCAG-TTTGCCCTTCCCA-TCGGAAGGTGTTGTCTTGTTGTTTAGTTTTCCCAGTTTGCCC
* *
16469 TTCCCCATCGGAAGATGTTGTTTAG
64 TTCCTCATCGGAAGGTGTTGTTTAG
* *
16494 TTTTCCC-GTATTGCCCTTCCCAGTCGGAAGGTGTTGTCTTGTTGTTTAGTTTTTCCAGTTTGCC
1 -ATTCCCAGT-TTGCCCTTCCCA-TCGGAAGGTGTTGTCTTGTTGTTTAGTTTTCCCAGTTTGCC
16558 CTTCCTCATCGGAAGGTGTTGTTTA-
63 CTTCCTCATCGGAAGGTGTTGTTTAG
* * *
16583 AATCCCAGTTTGCCCTTTCTCATCAGAA---G--G---TGTTGTTTAGTTTTCCCAGTTTGCCCT
1 ATTCCCAGTTTGCCC-TTCCCATCGGAAGGTGTTGTCTTGTTGTTTAGTTTTCCCAGTTTGCCCT
*
16640 TCCTCACCGGAAGGTGTTGTTTAG
65 TCCTCATCGGAAGGTGTTGTTTAG
* * * *
16664 ATTACCCAGTTTACCCTTCCCTACCGGAAGGTGTTGTC--------TAGATTTCCCAATTTGCCC
1 ATT-CCCAGTTTGCCCTTCCC-ATCGGAAGGTGTTGTCTTGTTGTTTAGTTTTCCCAGTTTGCCC
*
16721 TTCC-CTACCGGAAGGTGTTGTTTAAGTTTG
64 TTCCTC-ATCGGAAGGTGTTGTTT-A----G
* * *
16751 CATTTCCCA-TCTTGCCCTTCCCCACCGGAA---G--G---TGTTATTTAGATTTCCCAGTTTGC
1 -A-TTCCCAGT-TTGCCCTT-CCCATCGGAAGGTGTTGTCTTGTTGTTTAGTTTTCCCAGTTTGC
* * * * *
16807 CTTTCCCCACCGGAAGGCGTTGTCTAG
62 CCTTCCTCATCGGAAGGTGTTGTTTAG
* ** * ** * *
16834 ATTTCCCAGTTTGCCTTTTCTTACCGGAAGGTGTTGT-TT-AAGTTT-GCATTTCCCATTTTGCC
1 A-TTCCCAGTTTGCC-CTTCCCATCGGAAGGTGTTGTCTTGTTGTTTAG-TTTTCCCAGTTTGCC
* * **
16896 CTTCCCCACCATAAGGTGTTGTTTAG
63 CTTCCTCATCGGAAGGTGTTGTTTAG
* * * * * *
16922 TTTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT-TTAATTGTCTA--ATTACCAGTTTACCC
1 ATTCCCAGTTTGCCCTTCC-CATCGGAAGGTGTTGTCTT-GTTGTTTAGTTTTCCCAGTTTGCCC
* *
16984 TTCCCCATCGGAAGGTGCTGTTTAG
64 TTCCTCATCGGAAGGTGTTGTTTAG
* * *
17009 TTTCCCAATTTTCCCTTCCC
1 ATTCCCAGTTTGCCCTTCCC
17029 CCGCCGGAAA
Statistics
Matches: 427, Mismatches: 60, Indels: 97
0.73 0.10 0.17
Matches are distributed among these distances:
80 48 0.11
81 7 0.02
82 75 0.18
83 7 0.02
85 4 0.01
86 4 0.01
87 85 0.20
88 141 0.33
89 24 0.06
90 32 0.07
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.38
Consensus pattern (88 bp):
ATTCCCAGTTTGCCCTTCCCATCGGAAGGTGTTGTCTTGTTGTTTAGTTTTCCCAGTTTGCCCTT
CCTCATCGGAAGGTGTTGTTTAG
Found at i:16757 original size:129 final size:128
Alignment explanation
Indices: 16533--16957 Score: 505
Period size: 129 Copynumber: 3.4 Consensus size: 128
16523 GGTGTTGTCT
* * * * * *
16533 TGTTGTTTAGTTTTTCCAGTTTGCCCTT-CCTCATCGGAAGGTGTTGTTTA-A-ATCCCAGTTTG
1 TGTTGTTTAGATTTCCCAGTTTGCCCTTCCCT-ACCGGAAGGTGTTGTCTAGATTTCCCAATTTG
* * * *
16595 CCCTT-TCTCATCAGAAGGTGTTGTTT-AG--T---TTTCCCAGTTTGCCCTTCCTCACCGGAAG
65 CCCTTCCCT-ACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCA-TTTGCCCTTCCCCACCGGAAG
16653 G
128 G
* *
16654 TGTTGTTTAGATTACCCAGTTTACCCTTCCCTACCGGAAGGTGTTGTCTAGATTTCCCAATTTGC
1 TGTTGTTTAGATTTCCCAGTTTGCCCTTCCCTACCGGAAGGTGTTGTCTAGATTTCCCAATTTGC
16719 CCTTCCCTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCATCTTGCCCTTCCCCACCGGAAGG
66 CCTTCCCTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCAT-TTGCCCTTCCCCACCGGAAGG
* * * * *
16783 TGTTATTTAGATTTCCCAGTTTGCCTTTCCCCACCGGAAGGCGTTGTCTAGATTTCCCAGTTTGC
1 TGTTGTTTAGATTTCCCAGTTTGCCCTTCCCTACCGGAAGGTGTTGTCTAGATTTCCCAATTTGC
* * * **
16848 CTTTTCTTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCATTTTGCCCTTCCCCACCATAAGG
66 CCTTCCCTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCA-TTTGCCCTTCCCCACCGGAAGG
*
16912 TGTTGTTTAG-TTTCCCAGTTTGCCCTT-CCTCATCGGAAGGTGTTGT
1 TGTTGTTTAGATTTCCCAGTTTGCCCTTCCCT-ACCGGAAGGTGTTGT
16958 TTAATTGTCT
Statistics
Matches: 262, Mismatches: 29, Indels: 19
0.85 0.09 0.06
Matches are distributed among these distances:
121 40 0.15
122 4 0.02
123 29 0.11
124 4 0.02
126 1 0.00
127 2 0.01
128 30 0.11
129 151 0.58
130 1 0.00
ACGTcount: A:0.16, C:0.26, G:0.20, T:0.39
Consensus pattern (128 bp):
TGTTGTTTAGATTTCCCAGTTTGCCCTTCCCTACCGGAAGGTGTTGTCTAGATTTCCCAATTTGC
CCTTCCCTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCATTTGCCCTTCCCCACCGGAAGG
Found at i:17082 original size:87 final size:87
Alignment explanation
Indices: 16625--17087 Score: 274
Period size: 88 Copynumber: 5.4 Consensus size: 87
16615 TTGTTTAGTT
* * * * * * * *
16625 TTCCCAGTTTGCCCTTCCTCACCGGAAGGTGTTGTTTAGATTACCCAGTTTACCCTTCCCTACCG
1 TTCCCATTTTGCCCTTCCCCATCGGAAGGTGCTGTTTAG-TTTCCCAATTTGCCCTTCCCCACCG
* * *
16690 GAAGGTGTTGTCT-A--G---AT
65 GAAGGTGTTCTTTAATTGCCTAA
* * * * *
16707 TTCCCAATTTGCCCTTCCCTACCGGAAGGTGTTGTTTAAGTTTGCATTTCCCATCTTGCCCTTCC
1 TTCCCATTTTGCCCTTCCCCATCGGAAGGTGCTGTTT-AGTTT-C----CCAAT-TTGCCCTTCC
* *
16772 CCACCGGAAGGTGTTATTT-A--G---AT
59 CCACCGGAAGGTGTTCTTTAATTGCCTAA
* * * * * * * * * **
16795 TTCCCAGTTTGCCTTTCCCCACCGGAAGGCGTTGTCTAGATTTCCCAGTTTGCCTTTTCTTACCG
1 TTCCCATTTTGCCCTTCCCCATCGGAAGGTGCTGTTTAG-TTTCCCAATTTGCCCTTCCCCACCG
* *
16860 GAAGGTGTTGTTTAAGTTTG-C-AT
65 GAAGGTGTTCTTTAA--TTGCCTAA
* ** * * * *
16883 TTCCCATTTTGCCCTTCCCCACCATAAGGTGTTGTTTAGTTTCCCAGTTTGCCCTTCCTCATCGG
1 TTCCCATTTTGCCCTTCCCCATCGGAAGGTGCTGTTTAGTTTCCCAATTTGCCCTTCCCCACCGG
* *
16948 AAGGTGTTGTTTAATTGTCTAA
66 AAGGTGTTCTTTAATTGCCTAA
* * * * *
16970 TTACCAGTTTACCCTTCCCCATCGGAAGGTGCTGTTTAGTTTCCCAATTTTCCCTTCCCCCGCCG
1 TTCCCATTTTGCCCTTCCCCATCGGAAGGTGCTGTTTAGTTTCCCAATTTGCCCTT-CCCCACCG
* *
17035 GAAAGG-GTTCTTTAGTTGCCTTA
65 G-AAGGTGTTCTTTAATTGCCTAA
17058 TTCCCATTTTGCCCTTCCCC-TCGGAAGGTG
1 TTCCCATTTTGCCCTTCCCCATCGGAAGGTG
17088 TTGTCTAAGT
Statistics
Matches: 311, Mismatches: 52, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
82 60 0.19
83 7 0.02
85 3 0.01
86 1 0.00
87 101 0.32
88 135 0.43
89 4 0.01
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (87 bp):
TTCCCATTTTGCCCTTCCCCATCGGAAGGTGCTGTTTAGTTTCCCAATTTGCCCTTCCCCACCGG
AAGGTGTTCTTTAATTGCCTAA
Found at i:17168 original size:49 final size:48
Alignment explanation
Indices: 17054--17284 Score: 256
Period size: 49 Copynumber: 4.8 Consensus size: 48
17044 CTTTAGTTGC
* * * * *
17054 CTTATTCCCATTTTGCCCTTCCCC-TCGGAAGGTGTTGTCTAA-GTTGC
1 CTTATT-CCGTTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAATTTTGT
*
17101 CTTAGTCCCGTTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAATTTTGT
1 CTTA-TTCCGTTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAATTTTGT
*
17150 CTTATTCTCGTTTTGCCCTTCCCCA-CAGGAAGGTATTGTTTAATTTTGT
1 CTTATTC-CGTTTTGCCCTTCCCCATCA-GAAGGTGTTGTTTAATTTTGT
**
17199 CTTATTCCTGTTTTGCCCTTCCCGGTC-GAAAGGTGTTGTTTAATTTTGT
1 CTTATTCC-GTTTTGCCCTTCCCCATCAG-AAGGTGTTGTTTAATTTTGT
* *
17248 CTTATTCCTGATTTGCCCTTCCCAAT-AGGAAGGTGTT
1 CTTATTCC-GTTTTGCCCTTCCCCATCA-GAAGGTGTT
17285 ATTTTGCCAT
Statistics
Matches: 160, Mismatches: 14, Indels: 18
0.83 0.07 0.09
Matches are distributed among these distances:
47 20 0.12
48 23 0.14
49 115 0.72
50 2 0.01
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.42
Consensus pattern (48 bp):
CTTATTCCGTTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAATTTTGT
Found at i:18942 original size:11 final size:11
Alignment explanation
Indices: 18926--18959 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
18916 GAAGTTCGTG
18926 TTTTGAAGATT
1 TTTTGAAGATT
*
18937 TTTTGAAGATA
1 TTTTGAAGATT
18948 TTTTGAAGATT
1 TTTTGAAGATT
18959 T
1 T
18960 GAAGACAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (11 bp):
TTTTGAAGATT
Found at i:20895 original size:24 final size:24
Alignment explanation
Indices: 20868--20913 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
20858 AAATAAAATC
*
20868 GAATTGTTTTTTTTTCCTTAAACT
1 GAATTGTTTTTTTTCCCTTAAACT
20892 GAATTGTTTTTTTTCCCTTAAA
1 GAATTGTTTTTTTTCCCTTAAA
20914 AAGTATAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.57
Consensus pattern (24 bp):
GAATTGTTTTTTTTCCCTTAAACT
Done.