Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1213
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: 44375
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4702 original size:27 final size:27
Alignment explanation
Indices: 4672--4849 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
4662 ATATTGAGTC
* * * *
4672 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
4699 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
4726 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
4754 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
4781 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
4808 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
4835 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
4850 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:4811 original size:82 final size:81
Alignment explanation
Indices: 4693--4848 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
4683 TGCTATATAA
* *
4693 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
4758 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
4775 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
4839 CACTTAGTGC
65 CACTTAGTGC
4849 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:12887 original size:27 final size:27
Alignment explanation
Indices: 12857--13034 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
12847 ATATTGAGTC
* * * *
12857 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
12884 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
12911 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
12939 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
12966 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
12993 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
13020 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
13035 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:12996 original size:82 final size:81
Alignment explanation
Indices: 12878--13033 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
12868 TGCTATATAA
* *
12878 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
12943 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
12960 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
13024 CACTTAGTGC
65 CACTTAGTGC
13034 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20447 original size:46 final size:46
Alignment explanation
Indices: 20397--20572 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
20387 TGGTTGAGCA
*
20397 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * * *
20443 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
20488 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
20536 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20573 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 13, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
43 4 0.04
45 6 0.06
46 62 0.57
47 28 0.26
48 4 0.04
50 5 0.05
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:20553 original size:93 final size:93
Alignment explanation
Indices: 20394--20565 Score: 292
Period size: 93 Copynumber: 1.8 Consensus size: 93
20384 GGATGGTTGA
* *
20394 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
20459 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
20487 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCC-GAACTCGTTGAG
20551 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
20566 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:26552 original size:46 final size:44
Alignment explanation
Indices: 26502--26676 Score: 192
Period size: 46 Copynumber: 3.8 Consensus size: 44
26492 TGGTTGAGCA
26502 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
* * * *
26548 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAATGTAACTAGGCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT-TATG-GA-T-GGAAG
*
26594 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAA-G
* * *
26640 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
26677 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 98 0.89
47 2 0.02
48 3 0.03
49 1 0.01
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (44 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAAG
Found at i:26656 original size:92 final size:92
Alignment explanation
Indices: 26499--26669 Score: 297
Period size: 92 Copynumber: 1.9 Consensus size: 92
26489 GGATGGTTGA
* *
26499 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
26564 TGAGTCCGAGTTCGTGAATGTAACTAG
66 TGAGTCCGAGTTCGTGAATGTAACTAG
* * *
26591 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
26656 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
26670 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 74 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAATGTAACTAG
Found at i:31941 original size:100 final size:100
Alignment explanation
Indices: 31827--32009 Score: 321
Period size: 100 Copynumber: 1.8 Consensus size: 100
31817 GAAGTTGTCT
* * *
31827 GGTACGCATAGTAGCCTGCACTTAGTACTGCACATGCGACCAATAATCTAGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
*
31892 TGCACTTAGTACTACACACCTGATCACAGTTTTCG
66 TGCACGTAGTACTACACACCTGATCACAGTTTTCG
*
31927 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAGTAGCC
1 GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
31992 TGCACGTAGTACTACACA
66 TGCACGTAGTACTACACA
32010 TGTGACCTCA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 78 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (100 bp):
GGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAATAATCCAGTACACGTAGTAGCC
TGCACGTAGTACTACACACCTGATCACAGTTTTCG
Found at i:32004 original size:49 final size:49
Alignment explanation
Indices: 31835--32016 Score: 213
Period size: 49 Copynumber: 3.7 Consensus size: 49
31825 CTGGTACGCA
* * *
31835 TAGTAGCCTGCACTTAGTACTGCACATGCGACCAATAATCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
* * * ** * *
31884 TAGTAGCCTGCACTTAGTACTACACA-CCTGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACATGC-GA-C-CAATTATCCAGTACACG
*
31935 TAGTAGCCTACACTTAGTACTACACATGCGACCAATTATCCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
* *
31984 TAGTAGCCTGCACGTAGTACTACACATGTGACC
1 TAGTAGCCTGCACTTAGTACTACACATGCGACC
32017 TCACAATAGT
Statistics
Matches: 109, Mismatches: 20, Indels: 8
0.80 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 68 0.62
50 2 0.02
51 37 0.34
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACG
Found at i:33676 original size:45 final size:44
Alignment explanation
Indices: 33565--33869 Score: 296
Period size: 45 Copynumber: 6.8 Consensus size: 44
33555 CATTGGCTTG
* * * * *
33565 GAAAATGAATAAGAACATAGTTGAAAAACAATATGGCATTATAC
1 GAAAATGAATAAGACCATAGTTGAAAGACACTATGGTACTATAC
*
33609 GAAAGTGAATAAGACCATAGTTGAAAGACACTATGGTACTATATC
1 GAAAATGAATAAGACCATAGTTGAAAGACACTATGGTACTATA-C
* **
33654 GGAAATGAATAAGAAAATAGTTGAAAGACACTATGGTACTATACC
1 GAAAATGAATAAGACCATAGTTGAAAGACACTATGGTACTATA-C
*
33699 GAAAATGAATAAGACCATAGTT-AAAGGACACTATGGCAAC-ATGAC
1 GAAAATGAATAAGACCATAGTTGAAA-GACACTATGG-TACTAT-AC
* *
33744 GAAAATGAATAAGACCATAGTTGAAAGACACTATGGCATCT-TGTC
1 GAAAATGAATAAGACCATAGTTGAAAGACACTATGGTA-CTAT-AC
* * * * * *
33789 CAAAATAAATAAGACCATAGTTAAAAGAAACTATGGCA-TCATGTC
1 GAAAATGAATAAGACCATAGTTGAAAGACACTATGGTACT-AT-AC
* * *
33834 GCAAAA-AAATAAAACCATAGTTGAAAGATACTATGG
1 G-AAAATGAATAAGACCATAGTTGAAAGACACTATGG
33870 CATCATATTG
Statistics
Matches: 226, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
43 1 0.00
44 41 0.18
45 174 0.77
46 10 0.04
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (44 bp):
GAAAATGAATAAGACCATAGTTGAAAGACACTATGGTACTATAC
Found at i:33730 original size:90 final size:89
Alignment explanation
Indices: 33565--33871 Score: 340
Period size: 90 Copynumber: 3.4 Consensus size: 89
33555 CATTGGCTTG
* * * *
33565 GAAAATGAATAAGAACATAGTTGAAAAACAATATGGCATTATA-CGAAAGTGAATAAGACCATAG
1 GAAAATGAATAAGAACATAGTTGAAAGACACTATGGCACTATACCGAAAATGAATAAGACCATAG
*
33629 TTGAAAGACACTATGG-TACTAT-ATC
66 TT-AAAGACACTATGGCAAC-ATGA-C
* * *
33654 GGAAATGAATAAGAAAATAGTTGAAAGACACTATGGTACTATACCGAAAATGAATAAGACCATAG
1 GAAAATGAATAAGAACATAGTTGAAAGACACTATGGCACTATACCGAAAATGAATAAGACCATAG
33719 TTAAAGGACACTATGGCAACATGAC
66 TTAAA-GACACTATGGCAACATGAC
* * *
33744 GAAAATGAATAAGACCATAGTTGAAAGACACTATGGCATCT-TGTCC-AAAATAAATAAGACCAT
1 GAAAATGAATAAGAACATAGTTGAAAGACACTATGGCA-CTAT-ACCGAAAATGAATAAGACCAT
* * *
33807 AGTTAAAAGAAACTATGGCATCATGTC
64 AGTT-AAAGACACTATGGCAACATGAC
* *
33834 GCAAAA-AAATAA-AACCATAGTTGAAAGATACTATGGCA
1 G-AAAATGAATAAGAA-CATAGTTGAAAGACACTATGGCA
33872 TCATATTGGA
Statistics
Matches: 189, Mismatches: 20, Indels: 17
0.84 0.09 0.08
Matches are distributed among these distances:
89 41 0.22
90 134 0.71
91 14 0.07
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (89 bp):
GAAAATGAATAAGAACATAGTTGAAAGACACTATGGCACTATACCGAAAATGAATAAGACCATAG
TTAAAGACACTATGGCAACATGAC
Found at i:33845 original size:135 final size:134
Alignment explanation
Indices: 33565--33876 Score: 344
Period size: 135 Copynumber: 2.3 Consensus size: 134
33555 CATTGGCTTG
* * * * ** *
33565 GAAAATGAATAAGAACATAGTTGAAAAACAATATGGCATTATACGAAAGTGAATAAGACCATAGT
1 GAAAATAAATAAGACCATAGTTGAAAGACACTATGGCAACATACGAAAATGAATAAGACCATAGT
* ** * * * *
33630 TGAAAGACACTATGGTACTATATCGGAAATGAATAAGAAAATAGTTGAAAGACACTATGGTACTA
66 TGAAAGACACTATGGCACTATATCCAAAATAAATAAGAAAATAGTTAAAAGAAACTATGGCACTA
33695 TACC
131 TACC
*
33699 GAAAATGAATAAGACCATAGTT-AAAGGACACTATGGCAACATGACGAAAATGAATAAGACCATA
1 GAAAATAAATAAGACCATAGTTGAAA-GACACTATGGCAACAT-ACGAAAATGAATAAGACCATA
* **
33763 GTTGAAAGACACTATGGCATCT-TGTCCAAAATAAATAAGACCATAGTTAAAAGAAACTATGGCA
64 GTTGAAAGACACTATGGCA-CTATATCCAAAATAAATAAGAAAATAGTTAAAAGAAACTATGGCA
**
33827 -TCATGTC
128 CT-ATACC
* * *
33834 GCAAAA-AAATAAAACCATAGTTGAAAGATACTATGGCATCATA
1 G-AAAATAAATAAGACCATAGTTGAAAGACACTATGGCAACATA
33877 TTGGAAGTGT
Statistics
Matches: 150, Mismatches: 22, Indels: 12
0.82 0.12 0.07
Matches are distributed among these distances:
133 3 0.02
134 35 0.23
135 103 0.69
136 9 0.06
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (134 bp):
GAAAATAAATAAGACCATAGTTGAAAGACACTATGGCAACATACGAAAATGAATAAGACCATAGT
TGAAAGACACTATGGCACTATATCCAAAATAAATAAGAAAATAGTTAAAAGAAACTATGGCACTA
TACC
Found at i:34241 original size:13 final size:13
Alignment explanation
Indices: 34223--34252 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
34213 GGAAATAATA
*
34223 ATATAAAGTGTTT
1 ATATAAAATGTTT
34236 ATATAAAATGTTT
1 ATATAAAATGTTT
34249 ATAT
1 ATAT
34253 GAATATTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (13 bp):
ATATAAAATGTTT
Found at i:37920 original size:29 final size:28
Alignment explanation
Indices: 37857--37945 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
37847 CATCTCATTC
* * * *
37857 ATATGGCCCATCAGGCCCAATTC-CATT
1 ATATGGCCCATTAGGCTCAAATCACCTT
*
37884 GATATGGCCTATTAGGC-CTAAATCACCTTT
1 -ATATGGCCCATTAGGCTC-AAATCACC-TT
*
37914 ATATGGCCCGTTAGGCTCAAATCACCTT
1 ATATGGCCCATTAGGCTCAAATCACCTT
37942 ATAT
1 ATAT
37946 TCATGCTCAC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 24 0.47
29 23 0.45
30 3 0.06
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (28 bp):
ATATGGCCCATTAGGCTCAAATCACCTT
Found at i:42299 original size:29 final size:29
Alignment explanation
Indices: 42243--42371 Score: 172
Period size: 29 Copynumber: 4.5 Consensus size: 29
42233 TGGCCCATCT
*
42243 CATTCATAT-GCCCATTAAGCCCAATTCA
1 CATTCATATGGCCCATTAGGCCCAATTCA
* *
42271 CATTCATATGGCCTATCAGGCCCAATTCA
1 CATTCATATGGCCCATTAGGCCCAATTCA
42300 CATTCATATGGCCCATTAGGCCCAATTCA
1 CATTCATATGGCCCATTAGGCCCAATTCA
* * * *
42329 TATTCATATGGCCTATTAGGCCTAAATCA
1 CATTCATATGGCCCATTAGGCCCAATTCA
42358 CCATT-ATATGGCCC
1 -CATTCATATGGCCC
42372 GTTACTCCCA
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
28 9 0.10
29 76 0.86
30 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (29 bp):
CATTCATATGGCCCATTAGGCCCAATTCA
Found at i:42323 original size:58 final size:59
Alignment explanation
Indices: 42243--42371 Score: 192
Period size: 58 Copynumber: 2.2 Consensus size: 59
42233 TGGCCCATCT
*
42243 CATTCATAT-GCCCATTAAGCCCAATTCACATTCATATGGCCTATCAGGCCCAATTCA-
1 CATTCATATGGCCCATTAAGCCCAATTCACATTCATATGGCCTATCAGGCCCAAATCAC
* * * *
42300 CATTCATATGGCCCATTAGGCCCAATTCATATTCATATGGCCTATTAGGCCTAAATCAC
1 CATTCATATGGCCCATTAAGCCCAATTCACATTCATATGGCCTATCAGGCCCAAATCAC
42359 CATT-ATATGGCCC
1 CATTCATATGGCCC
42372 GTTACTCCCA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
57 9 0.14
58 52 0.80
59 4 0.06
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (59 bp):
CATTCATATGGCCCATTAAGCCCAATTCACATTCATATGGCCTATCAGGCCCAAATCAC
Found at i:42382 original size:58 final size:58
Alignment explanation
Indices: 42243--42387 Score: 186
Period size: 58 Copynumber: 2.5 Consensus size: 58
42233 TGGCCCATCT
* *
42243 CATTCATAT-GCCCATTAAGCCCAATTCACATTCATATGGCCTATCAGGCCCAATTCA
1 CATTCATATGGCCCATTACGCCCAATTCACATTCATATGGCCTATCAGGCCCAAATCA
* * * *
42300 CATTCATATGGCCCATTAGGCCCAATTCATATTCATATGGCCTATTAGGCCTAAATCA
1 CATTCATATGGCCCATTACGCCCAATTCACATTCATATGGCCTATCAGGCCCAAATCA
* * *
42358 CCATT-ATATGGCCCGTTACTCCCAAATCAC
1 -CATTCATATGGCCCATTACGCCCAATTCAC
42388 CTTATATTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
57 9 0.12
58 63 0.83
59 4 0.05
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.29
Consensus pattern (58 bp):
CATTCATATGGCCCATTACGCCCAATTCACATTCATATGGCCTATCAGGCCCAAATCA
Found at i:43839 original size:17 final size:16
Alignment explanation
Indices: 43817--43855 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
43807 ACAAAAAAAG
43817 TTTGGGATTTCAGGATT
1 TTTGGGATTTCA-GATT
* *
43834 TTTGGGTTTTGAGATT
1 TTTGGGATTTCAGATT
43850 TTTGGG
1 TTTGGG
43856 GCGTTACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.13, C:0.03, G:0.33, T:0.51
Consensus pattern (16 bp):
TTTGGGATTTCAGATT
Done.