Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019335.1 Corchorus olitorius cultivar O-4 contig19368, 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: 93040
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:935 original size:3 final size:3
Alignment explanation
Indices: 929--1010 Score: 89
Period size: 3 Copynumber: 27.0 Consensus size: 3
919 TTTCTTTACT
*
929 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TATA CTA TGCTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T--TA TTA
*
976 TTA -TA TTA TTA TTA TTA TTAA TTA -TA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
1011 CTATATAGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
2 6 0.09
3 54 0.79
4 5 0.07
5 3 0.04
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1578 original size:103 final size:103
Alignment explanation
Indices: 1463--1670 Score: 339
Period size: 103 Copynumber: 2.0 Consensus size: 103
1453 AAATTTTAAT
*
1463 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATTAAACTTTT-AAGCTTC
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAA-TAAAATTTTCAAGCTTC
1527 AATATGTAATTTCATTTATCA-ATTAAATTAAATATATTA
65 AATATGTAATTTCATTTAT-ATATTAAATTAAATATATTA
* * * *
1566 TTTAAAATTTTAGTATTTATTTAAAGGGTAAACATGTATTTATCAAATAAAATTTTCAAGGTTTA
1 TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAATTTTCAAGCTTCA
1631 ATATGTAATTTCATTTATATATTAAATTAAATATATTA
66 ATATGTAATTTCATTTATATATTAAATTAAATATATTA
1669 TT
1 TT
1671 ATATTAAAAT
Statistics
Matches: 98, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
102 9 0.09
103 89 0.91
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.46
Consensus pattern (103 bp):
TTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTATCAAATAAAATTTTCAAGCTTCA
ATATGTAATTTCATTTATATATTAAATTAAATATATTA
Found at i:1785 original size:39 final size:40
Alignment explanation
Indices: 1729--1809 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
1719 TTTGATTCCT
*
1729 ATGTAATATATATAATAACTAAAATGCTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* *
1769 ATGTAATA-CTATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1808 AT
1 AT
1810 TCTTAGATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 30 0.79
40 8 0.21
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:2689 original size:36 final size:36
Alignment explanation
Indices: 2642--2711 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
2632 GAGATTTTGG
* *
2642 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
2678 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
2712 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:14850 original size:6 final size:6
Alignment explanation
Indices: 14835--14866 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
14825 TCTAATTCTT
14835 TTTTTC -TTTTC TTTTTC TTTTTC TTTTT- TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTT
14867 GTCCTACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.36
6 16 0.64
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:14857 original size:17 final size:16
Alignment explanation
Indices: 14835--14866 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
14825 TCTAATTCTT
14835 TTTTTCTTTTCTTTTTC
1 TTTTTCTTTT-TTTTTC
14852 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
14867 GTCCTACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTCTTTTTTTTTC
Found at i:22397 original size:16 final size:17
Alignment explanation
Indices: 22369--22404 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
22359 CTTTAACTTC
22369 TTTTACGATTTTGATGT
1 TTTTACGATTTTGATGT
22386 TTTTACGA-TTTGATGT
1 TTTTACGATTTTGATGT
22402 TTT
1 TTT
22405 GCCCTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.17, C:0.06, G:0.17, T:0.61
Consensus pattern (17 bp):
TTTTACGATTTTGATGT
Found at i:22678 original size:29 final size:29
Alignment explanation
Indices: 22637--22699 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
22627 AAATGACTCC
22637 AAATTACAAGTTTAGGAGACAAAACGTTCA
1 AAATTACAAGTTTAGGAGACAAAACG-TCA
*
22667 AAATTA-AAGTTTATGAGACAAAACGTCA
1 AAATTACAAGTTTAGGAGACAAAACGTCA
22695 AAATT
1 AAATT
22700 GTAAAGGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 8 0.25
29 18 0.56
30 6 0.19
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.25
Consensus pattern (29 bp):
AAATTACAAGTTTAGGAGACAAAACGTCA
Found at i:26686 original size:29 final size:29
Alignment explanation
Indices: 26643--26699 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
26633 GCCTTCTCAA
* *
26643 AAAGTTCGGATTCTTATGTGATATTTTTT
1 AAAGTTCGGACTCTTATGTGAAATTTTTT
* *
26672 AAAGTTCGGGCTCTTATTTGAAATTTTT
1 AAAGTTCGGACTCTTATGTGAAATTTTT
26700 GACAAAGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.49
Consensus pattern (29 bp):
AAAGTTCGGACTCTTATGTGAAATTTTTT
Found at i:29837 original size:24 final size:25
Alignment explanation
Indices: 29787--29837 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
29777 TATGTGTAGT
* ** *
29787 CATAGGAACTTTTTTTTTTGGATAA
1 CATAGGAACTATTTTAATTGCATAA
29812 CATAGGAACTATTTTAATTGCA-AA
1 CATAGGAACTATTTTAATTGCATAA
29836 CA
1 CA
29838 CAATTGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (25 bp):
CATAGGAACTATTTTAATTGCATAA
Found at i:35067 original size:39 final size:40
Alignment explanation
Indices: 34987--35069 Score: 123
Period size: 41 Copynumber: 2.1 Consensus size: 40
34977 AACATGTTTG
* *
34987 AAAATCTAATTACAATCAAATATATCTCTCTATATATATTC
1 AAAATCTAATTACAATCAAATATATCTCTC-ACATACATTC
*
35028 AAAATCTAATTACAATTAAATATATCTCTC-CATACATTC
1 AAAATCTAATTACAATCAAATATATCTCTCACATACATTC
35067 AAA
1 AAA
35070 CATCACATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 10 0.26
41 29 0.74
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (40 bp):
AAAATCTAATTACAATCAAATATATCTCTCACATACATTC
Found at i:35969 original size:107 final size:105
Alignment explanation
Indices: 35741--36002 Score: 339
Period size: 107 Copynumber: 2.5 Consensus size: 105
35731 AATTTTTCTA
* ** * * * *
35741 ACCCTTAAAATAAAATTTTAATTTTAATTT-AGGCTAAACTTAATG-CAGTAGTTATATATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* * * *
35804 TTTCTAAAACCCTATAACAATATTCTTAATTATGGAATTT
66 ATTCTAAAACCATATAACAATATTATTAATTATGAAATTT
* * *
35844 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAATTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
* *
35909 ATTCTAAAATCATATAACAATAAATTATTAATTTTGAAATTT
66 ATTCTAAAACCATATAACAAT--ATTATTAATTATGAAATTT
*
35951 ACCCTTAAAATAAAAATAAAATTTTTATTTGGGGCTAAACTTAGTGAAATTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTA
36003 AGGCTAAACT
Statistics
Matches: 137, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
103 27 0.20
104 12 0.09
105 32 0.23
107 66 0.48
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (105 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGGCTAAACTTAGTGAAATTAGTTATATATTTTA
ATTCTAAAACCATATAACAATATTATTAATTATGAAATTT
Found at i:36451 original size:20 final size:20
Alignment explanation
Indices: 36423--36461 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
36413 TTAAAAAAAA
*
36423 TTAATAATTAGTTATTATTT
1 TTAAAAATTAGTTATTATTT
36443 TTAAAAATTAGTTATTATT
1 TTAAAAATTAGTTATTATT
36462 ATTTTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTAAAAATTAGTTATTATTT
Found at i:38045 original size:16 final size:16
Alignment explanation
Indices: 38024--38060 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
38014 GCTTAAAAGC
38024 TTCTTTTTCTTTT-TCT
1 TTCTTTTT-TTTTCTCT
38040 TTCTTTTTTTTTCTCT
1 TTCTTTTTTTTTCTCT
38056 TTCTT
1 TTCTT
38061 GTCTTTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTTTTTTTCTCT
Found at i:38052 original size:20 final size:21
Alignment explanation
Indices: 38027--38066 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
38017 TAAAAGCTTC
*
38027 TTTTTCTTTTTCTT-TCTTTT
1 TTTTTCTCTTTCTTGTCTTTT
38047 TTTTTCTCTTTCTTGTCTTT
1 TTTTTCTCTTTCTTGTCTTT
38067 CATATATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (21 bp):
TTTTTCTCTTTCTTGTCTTTT
Found at i:63588 original size:30 final size:31
Alignment explanation
Indices: 63554--63650 Score: 98
Period size: 30 Copynumber: 3.3 Consensus size: 31
63544 TCGAGACTAT
63554 GCAGCTGCCTTTGTT-GGAGACCTTGCGTAC
1 GCAGCTGCCTTTGTTAGGAGACCTTGCGTAC
* *
63584 GCAGCTGCCCTTGTTGGGAGA-C-T-C--AC
1 GCAGCTGCCTTTGTTAGGAGACCTTGCGTAC
* * *
63610 CCACCATGCCTTTGTTAGGAGACCTTGCGTAT
1 GCAGC-TGCCTTTGTTAGGAGACCTTGCGTAC
63642 GCAGCTGCC
1 GCAGCTGCC
63651 CCTGTTGGGA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
26 5 0.10
27 14 0.27
28 2 0.04
29 2 0.04
30 16 0.31
31 9 0.17
32 4 0.08
ACGTcount: A:0.15, C:0.30, G:0.28, T:0.27
Consensus pattern (31 bp):
GCAGCTGCCTTTGTTAGGAGACCTTGCGTAC
Found at i:63636 original size:58 final size:57
Alignment explanation
Indices: 63559--63668 Score: 193
Period size: 58 Copynumber: 1.9 Consensus size: 57
63549 ACTATGCAGC
*
63559 TGCCTTTGTTGGAGACCTTGCGTACGCAGCTGCCCTTGTTGGGAGACTCACCCACCA
1 TGCCTTTGTTGGAGACCTTGCGTACGCAGCTGCCCCTGTTGGGAGACTCACCCACCA
*
63616 TGCCTTTGTTAGGAGACCTTGCGTATGCAGCTGCCCCTGTTGGGAGACTCACC
1 TGCCTTTGTT-GGAGACCTTGCGTACGCAGCTGCCCCTGTTGGGAGACTCACC
63669 TATCATAACC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 10 0.20
58 40 0.80
ACGTcount: A:0.15, C:0.30, G:0.27, T:0.27
Consensus pattern (57 bp):
TGCCTTTGTTGGAGACCTTGCGTACGCAGCTGCCCCTGTTGGGAGACTCACCCACCA
Found at i:67582 original size:29 final size:28
Alignment explanation
Indices: 67547--67603 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
67537 CAACTTTTCT
* *
67547 TTTGAAAAGAGCTTCTTCTAAGGTTTGC
1 TTTGGAAAGAGCTTCTTCTAAGGCTTGC
*
67575 TTTGGAAAGAGCTTCTTCTATGGCTTGC
1 TTTGGAAAGAGCTTCTTCTAAGGCTTGC
67603 T
1 T
67604 CATCTTCTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (28 bp):
TTTGGAAAGAGCTTCTTCTAAGGCTTGC
Found at i:70348 original size:41 final size:41
Alignment explanation
Indices: 70287--70368 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
70277 AGAGTAGTAG
* *
70287 ATTCTAGTGGTTAGGATTAATATAATCGGAGAAGATTCTTA
1 ATTCTAGTGGTTAGGATTAATATAATCGGAAAAGAATCTTA
*
70328 ATTCTAGTGGTTAGGGTTAATATAATCGGAAAAGAATCTTA
1 ATTCTAGTGGTTAGGATTAATATAATCGGAAAAGAATCTTA
70369 CGTGATAGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.35
Consensus pattern (41 bp):
ATTCTAGTGGTTAGGATTAATATAATCGGAAAAGAATCTTA
Found at i:71603 original size:29 final size:30
Alignment explanation
Indices: 71509--71602 Score: 120
Period size: 29 Copynumber: 3.1 Consensus size: 30
71499 GCTCAAAAAG
*
71509 GCCCCTGAACT-TATACAAAATGGCCAAATAA
1 GCCCCTGAACTCT-TATAAAA-GGCCAAATAA
* * *
71540 GCCCCTGAACTCTAATTACA-GCCAAATAA
1 GCCCCTGAACTCTTATAAAAGGCCAAATAA
71569 GCCCCTGAACTCTTATAAAAGGCCAAATAA
1 GCCCCTGAACTCTTATAAAAGGCCAAATAA
71599 GCCC
1 GCCC
71603 TTTTCTGATG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
29 26 0.48
30 13 0.24
31 14 0.26
32 1 0.02
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (30 bp):
GCCCCTGAACTCTTATAAAAGGCCAAATAA
Found at i:75454 original size:83 final size:83
Alignment explanation
Indices: 75310--75467 Score: 239
Period size: 83 Copynumber: 1.9 Consensus size: 83
75300 ATTAATATAG
*
75310 TTTTATTATACTAAAAACTCTATTTTTATTCAATTAAATCTAATATTTTTATAATAATTTATTTT
1 TTTTATTATACTAAAAACTCTATTTTCATTCAATTAAATCTAATATTTTTATAATAATTTATTTT
75375 TACCATTTTACTATACAA
66 TACCATTTTACTATACAA
* * *
75393 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAAT-TCAATA-TTTTATAATTATTTTATT
1 TTTTATTATACTAAAAACTCTATTTTCATTCAATTAAATCT-AATATTTTTATAA-TAATTTATT
*
75456 TTTACTATTTTA
64 TTTACCATTTTA
75468 ATTTAAAAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
82 9 0.13
83 59 0.87
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.54
Consensus pattern (83 bp):
TTTTATTATACTAAAAACTCTATTTTCATTCAATTAAATCTAATATTTTTATAATAATTTATTTT
TACCATTTTACTATACAA
Found at i:78431 original size:31 final size:31
Alignment explanation
Indices: 78383--78446 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
78373 CATAGGTTTG
*
78383 CTTGATCGCTGTATAGCTACTTGTGGGGATC
1 CTTGATCACTGTATAGCTACTTGTGGGGATC
* * *
78414 CTTGATCACTGTTTAGCTACTTTTGGTGATC
1 CTTGATCACTGTATAGCTACTTGTGGGGATC
78445 CT
1 CT
78447 CATAATATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (31 bp):
CTTGATCACTGTATAGCTACTTGTGGGGATC
Found at i:79002 original size:5 final size:5
Alignment explanation
Indices: 78992--79086 Score: 106
Period size: 5 Copynumber: 19.2 Consensus size: 5
78982 TCTTATCTGG
78992 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT G-TTT -TTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT
* * * * *
79040 GTTTT TTTGTT TTTTT GTTTT TTTGTT TTTTT GTTTT -TTTT TTTTT G
1 GTTTT GTT-TT GTTTT GTTTT GTT-TT GTTTT GTTTT GTTTT GTTTT G
79087 CAACAAGTCT
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
4 10 0.12
5 60 0.75
6 10 0.12
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
GTTTT
Found at i:79039 original size:1 final size:1
Alignment explanation
Indices: 78993--79085 Score: 69
Period size: 1 Copynumber: 93.0 Consensus size: 1
78983 CTTATCTGGG
* * * * * * * * * * *
78993 TTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTGTTTTTTTGTTTTTTTGTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
79058 TTTTTTGTTTTTTTGTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
79086 GCAACAAGTC
Statistics
Matches: 66, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (1 bp):
T
Found at i:79047 original size:16 final size:16
Alignment explanation
Indices: 78998--79085 Score: 119
Period size: 16 Copynumber: 5.7 Consensus size: 16
78988 CTGGGTTTTG
* *
78998 TTTTGTTTTGTT-TTG
1 TTTTGTTTTTTTGTTT
* *
79013 TTTTGTTTTGTT-TTG
1 TTTTGTTTTTTTGTTT
79028 TTTTGTTTTTTTGTTT
1 TTTTGTTTTTTTGTTT
79044 TTTTGTTTTTTTGTTT
1 TTTTGTTTTTTTGTTT
79060 TTTTGTTTTTTTGTTT
1 TTTTGTTTTTTTGTTT
79076 TTTT-TTTTTT
1 TTTTGTTTTTT
79086 GCAACAAGTC
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
15 32 0.46
16 38 0.54
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (16 bp):
TTTTGTTTTTTTGTTT
Found at i:79820 original size:21 final size:23
Alignment explanation
Indices: 79796--79843 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
79786 TTAAACATTG
79796 AATTTCAAAGAT-CAATTGCT-T
1 AATTTCAAAGATACAATTGCTCT
*
79817 AATTTCTAAGATAGCAATTGCTCT
1 AATTTCAAAGATA-CAATTGCTCT
79841 AAT
1 AAT
79844 GGTATATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
23 8 0.35
24 4 0.17
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (23 bp):
AATTTCAAAGATACAATTGCTCT
Found at i:83535 original size:29 final size:28
Alignment explanation
Indices: 83466--83535 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
83456 GCGTTTAGAC
*
83466 GTTTTGCCTCCTAAACTTCAATTTTGGAT
1 GTTTTGCC-CCTAAACTTCAATTTGGGAT
* *
83495 ATTTTGCTCCCTGAACTTCAATCTTGGGAT
1 GTTTTGC-CCCTAAACTTCAAT-TTGGGAT
83525 GTTTTGCCCCT
1 GTTTTGCCCCT
83536 TCAGACTAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (28 bp):
GTTTTGCCCCTAAACTTCAATTTGGGAT
Found at i:89769 original size:2 final size:2
Alignment explanation
Indices: 89762--89807 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
89752 TTTATCGGTG
* *
89762 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89804 TA TA
1 TA TA
89808 ATTTGATGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (2 bp):
TA
Found at i:90707 original size:137 final size:141
Alignment explanation
Indices: 90554--90825 Score: 363
Period size: 137 Copynumber: 2.0 Consensus size: 141
90544 GTCATTTAAG
* * * * * * *
90554 AAATATATTTTAAAAATTCTAATATATCTAAGTTTTTTTAATTAAATTAGTAAAATGATAAAAA-
1 AAATATATTTAAAAAATTATAATATATATAAGTTTTTTAAATGAAAATAGTAAAATGACAAAAAT
* * *
90618 AAAATTGGTATAAGTATATTATAATTAAAT-AA-AAAAATAGAGTTTTTAGTTGAGTAAAA-TAT
66 AAAATAGGTATAAGGATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
*
90680 TAAAACTATAA
131 AAAAACTATAA
* *
90691 AAATATATTTAAAAAATTATAATGTATATAAGTTTTTTAAATGAAAATAGTAAAATGGCAAAAAT
1 AAATATATTTAAAAAATTATAATATATATAAGTTTTTTAAATGAAAATAGTAAAATGACAAAAAT
* * * *
90756 TAAATAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
66 AAAATAGGTATAAGGATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
90821 AAAAA
131 AAAAA
90826 TTTAAATAAT
Statistics
Matches: 114, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
137 55 0.48
138 23 0.20
139 2 0.02
140 27 0.24
141 7 0.06
ACGTcount: A:0.51, C:0.02, G:0.10, T:0.37
Consensus pattern (141 bp):
AAATATATTTAAAAAATTATAATATATATAAGTTTTTTAAATGAAAATAGTAAAATGACAAAAAT
AAAATAGGTATAAGGATATTAGAATTAAATAAATAAAAATAGAGTTTTTAGTTGAGTAAAACTAT
AAAAACTATAA
Found at i:91737 original size:32 final size:32
Alignment explanation
Indices: 91673--91771 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
91663 CAATGATGTC
* *
91673 TACATAAATTAGTATAGTTATAAATACTCTCATG
1 TACATAAATTGGTATAG-T-TAAATACACTCATG
*
91707 TACATAAATTGGTGTAGTTAAATACACTCATG
1 TACATAAATTGGTATAGTTAAATACACTCATG
* * * *
91739 GACATTATTTGGTATAGTTATATACACT-ATG
1 TACATAAATTGGTATAGTTAAATACACTCATG
91770 TA
1 TA
91772 TGGGTAAAGA
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
31 4 0.07
32 36 0.64
33 1 0.02
34 15 0.27
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.38
Consensus pattern (32 bp):
TACATAAATTGGTATAGTTAAATACACTCATG
Found at i:93030 original size:21 final size:20
Alignment explanation
Indices: 92984--93026 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
92974 CTCTCACAAG
* *
92984 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
93004 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
93024 TTT
1 TTT
93027 TCTACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Done.