Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012396.1 Corchorus capsularis cultivar CVL-1 contig12417, 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: 30279
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Found at i:1929 original size:16 final size:16
Alignment explanation
Indices: 1910--1952 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
1900 CATAATTTCA
*
1910 TAATTTATTTAGTAAT
1 TAATTTATTTAGGAAT
*
1926 TAATTTATATAGGAAT
1 TAATTTATTTAGGAAT
* *
1942 TGATTTTTTTA
1 TAATTTATTTA
1953 ATAGTTTAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TAATTTATTTAGGAAT
Found at i:2361 original size:14 final size:14
Alignment explanation
Indices: 2337--2402 Score: 62
Period size: 14 Copynumber: 4.4 Consensus size: 14
2327 GTTATTTTCT
2337 TTATCTATCTATTTA
1 TTAT-TATCTATTTA
*
2352 TTATTATCTATCTA
1 TTATTATCTATTTA
2366 TTACTTAGCATCTATTTTA
1 TTA-TT---ATCTA-TTTA
2385 TT-TTATCTATTTA
1 TTATTATCTATTTA
2398 TTATT
1 TTATT
2403 GTATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
13 6 0.14
14 19 0.44
15 6 0.14
17 2 0.05
18 5 0.12
19 5 0.12
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.61
Consensus pattern (14 bp):
TTATTATCTATTTA
Found at i:2378 original size:18 final size:18
Alignment explanation
Indices: 2339--2380 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2329 TATTTTCTTT
**
2339 ATCTATCTATTTATTATT
1 ATCTATCTATTTATTAGC
2357 ATCTATCTA-TTACTTAGC
1 ATCTATCTATTTA-TTAGC
2375 ATCTAT
1 ATCTAT
2381 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.52
Consensus pattern (18 bp):
ATCTATCTATTTATTAGC
Found at i:5462 original size:29 final size:28
Alignment explanation
Indices: 5400--5464 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
5390 AAGTTGTACG
*
5400 ATTTGGATGTTTTGTCCCTTAAATTTCA
1 ATTTGGATGTTTTGTCCCTGAAATTTCA
*
5428 ATTTTGGATGTTTTGTCTCCTGAACTTGT-A
1 A-TTTGGATGTTTTGTC-CCTGAAATT-TCA
5458 ATTTGGA
1 ATTTGGA
5465 GCCATATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 1 0.03
29 21 0.66
30 9 0.28
31 1 0.03
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.49
Consensus pattern (28 bp):
ATTTGGATGTTTTGTCCCTGAAATTTCA
Found at i:12791 original size:2 final size:2
Alignment explanation
Indices: 12784--12817 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12774 TGAAGAAACA
12784 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12818 TTGTCAGTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15755 original size:99 final size:99
Alignment explanation
Indices: 15584--16573 Score: 1497
Period size: 99 Copynumber: 10.0 Consensus size: 99
15574 ACTTAGGTTG
* * *
15584 AATACGAGCTTAGCCGTTCTCACAAAGAGTCCA-GGACTTACGTTCGGCCAACTTAGTTTAGATG
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGG-CTTACGTTCAGCCAACTTAGTTTCGATG
* **
15648 TTCTCACGAAGAGTCTAGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
*
15683 AATACGAACTTAGCCGTTCTTACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
*
15748 TCTCACGATGAGTCTGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * * *
15782 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCCTACGTTCGGCTAACTTAGTTTCGATGC
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
15847 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * * *
15881 ATTACGAACGTT-GTCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGGCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATG
* ** *
15945 TTCTCATGGGGAGTTCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
** *
15980 GTTACGAACGTT-GCCGTTCTCACAAAGAATCCATGGC-TACGTTCAGCCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATG
16043 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * * *
16078 ATTACAAACGTT-GCTGTTTTCACAAAGAGTCCATGGCTTACATTCAGCCAACTTAGTTTCGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATG
16142 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* *
16177 AATACGAACTTAGCCGTTTTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
16242 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
*
16276 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
16341 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * *
16375 AATACGAACTTAGCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCTAACTTAGTTTCGATGT
1 AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
**
16440 TCTCACGGGGAGTCCGGATCGAAATCTAAGGTCA
66 TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
* * * *
16474 ATTACGAACGTT-GCCGTTCTCACAAAGAGTCCAGGGCTTACGTTCGGCCAACTTAGTTTTGATG
1 AATACGAAC-TTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATG
**
16538 TTCTCACGGGGAGTCCGGATCGAAATCTAAGGTCA
65 TTCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
16573 A
1 A
16574 TTTGGAAATT
Statistics
Matches: 832, Mismatches: 54, Indels: 10
0.93 0.06 0.01
Matches are distributed among these distances:
98 89 0.11
99 737 0.89
100 6 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (99 bp):
AATACGAACTTAGCCGTTCTCACAAAGAGTCCATGGCTTACGTTCAGCCAACTTAGTTTCGATGT
TCTCACGATGAGTCCGGATCGAAATCTAAGGTCA
Found at i:16307 original size:51 final size:51
Alignment explanation
Indices: 16240--16406 Score: 143
Period size: 51 Copynumber: 3.3 Consensus size: 51
16230 TAGTTTCGAT
* *
16240 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
** * * * *
16291 GTTCTCACAAAGAGTCC--AT-G-GCT-TACGTTC--A-ACCAACTTAGTTTCGAT
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAG---C--C
* *
16339 GTTCTCACGATGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
1 GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
16390 GTTCTCACAAAGAGTCC
1 GTTCTCACAAAGAGTCC
16407 AGGGCTTACG
Statistics
Matches: 85, Mismatches: 18, Indels: 26
0.66 0.14 0.20
Matches are distributed among these distances:
43 9 0.11
44 1 0.01
46 6 0.07
47 1 0.01
48 16 0.19
49 2 0.02
50 2 0.02
51 31 0.36
52 1 0.01
53 6 0.07
55 1 0.01
56 9 0.11
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.26
Consensus pattern (51 bp):
GTTCTCACAAAGAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAGCC
Found at i:16354 original size:48 final size:48
Alignment explanation
Indices: 16104--16355 Score: 128
Period size: 48 Copynumber: 5.1 Consensus size: 48
16094 TTTTCACAAA
* *
16104 GAGTCCATGGCTTACATTCAGCCAACTTAGTTTCGATGTTCTCACGAT
1 GAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGTTCTCACGAT
** * * * * * *
16152 GAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAG--CCG-T-TT-TCACAAA
1 GAGTCC--AT-G-GCT-TACGTTC--A-ACCAACTTAGTTTCGATGTTCTCACGAT
16203 GAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGTTCTCACGAT
1 GAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGTTCTCACGAT
** * * * * * *
16251 GAGTCCGGATCGAAATCTAAGGTCAAATACGAACTTAG---C--CGTTCTCACAAA
1 GAGTCC--AT-G-GCT-TACGTTC--A-ACCAACTTAGTTTCGATGTTCTCACGAT
16302 GAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGTTCTCACGAT
1 GAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGTTCTCACGAT
16350 GAGTCC
1 GAGTCC
16356 GGATCGAAAT
Statistics
Matches: 144, Mismatches: 34, Indels: 52
0.63 0.15 0.23
Matches are distributed among these distances:
43 18 0.12
44 2 0.01
45 2 0.01
46 12 0.08
47 4 0.03
48 34 0.24
49 4 0.03
50 4 0.03
51 28 0.19
52 4 0.03
53 11 0.08
54 2 0.01
55 2 0.01
56 17 0.12
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (48 bp):
GAGTCCATGGCTTACGTTCAACCAACTTAGTTTCGATGTTCTCACGAT
Found at i:17360 original size:232 final size:233
Alignment explanation
Indices: 16941--17368 Score: 664
Period size: 232 Copynumber: 1.8 Consensus size: 233
16931 CCACATACAG
*** *
16941 CTTCGTGGATCTCCTTCAACACATAGTTGGCTTCATCTGGGTCTACAAACTTCAAAAAAGAAAAG
1 CTTCGTGGATCTCCTTCAACACATAGACAGCTTCATCTGAGTCTACAAACTTCAAAAAAGAAAAG
*
17006 GTGGAGGATTTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTAGC
66 GTGAAGGATTTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTAGC
* * * *
17071 TGCCATGACTTTTGGATCAGATGGAGGATTGATCCCTTTCAAATACTCCATTATCTCGATCATCC
131 TGCCACGACTCTTGGATCAGATGGAGGATCGATCCCTTTCAAATACTCCACTATCTCGATCATCC
17136 ACCTTCGTGGATCAGACTTACATTCAGGGGCTTTCCAC
196 ACCTTCGTGGATCAGACTTACATTCAGGGGCTTTCCAC
* * *
17174 CTTCGTGGATCTCCCTT-AACACATAGACAGCTTCATCT-AGTCTACATACTTCAAAAAAGGAAG
1 CTTCGTGGATCT-CCTTCAACACATAGACAGCTTCATCTGAGTCTACAAACTTCAAAAAAGAAAA
17237 GGTGAAGGATATT-TTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTA
65 GGTGAAGGAT-TTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTA
* * * * *
17301 GCTGTCGCGACTCTTGGATCAGATGGAGGATCGATTCCTTTCAAGTACTTCACTATCTCGATCAT
129 GCTGCCACGACTCTTGGATCAGATGGAGGATCGATCCCTTTCAAATACTCCACTATCTCGATCAT
17366 CCA
194 CCA
17369 GTTAGATCAT
Statistics
Matches: 176, Mismatches: 17, Indels: 5
0.89 0.09 0.03
Matches are distributed among these distances:
232 140 0.80
233 32 0.18
234 4 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (233 bp):
CTTCGTGGATCTCCTTCAACACATAGACAGCTTCATCTGAGTCTACAAACTTCAAAAAAGAAAAG
GTGAAGGATTTCTTATATAGTTCATCATCAATCAACACATACCTTGCCGCTCTTCATGGTCTAGC
TGCCACGACTCTTGGATCAGATGGAGGATCGATCCCTTTCAAATACTCCACTATCTCGATCATCC
ACCTTCGTGGATCAGACTTACATTCAGGGGCTTTCCAC
Found at i:18901 original size:98 final size:99
Alignment explanation
Indices: 18724--18975 Score: 427
Period size: 98 Copynumber: 2.5 Consensus size: 99
18714 TTGTGGGGAA
*
18724 GATCTTCATATCTGACACTTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
1 GATCTCCATATCTGACAC-TCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATC
18789 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAG
65 ACCATCAAACCTTTCAAGCTTGTAACCAACATAAG
*
18824 GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGT-GTTCTTCCATGTTTGGGTTCTATCA
1 GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATCA
* * *
18888 CCATCAGATCTTTCAAGCTTGTAACCAACGTAAG
66 CCATCAAACCTTTCAAGCTTGTAACCAACATAAG
18922 GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTT-TTACCATGTTC
1 GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTT-CCATGTTC
18976 ATGTTCTACG
Statistics
Matches: 144, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
98 96 0.67
99 31 0.22
100 17 0.12
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (99 bp):
GATCTCCATATCTGACACTCTGCCGATCTTCGATGTTGTCGTTCTTCCATGTTCGGGTTCTATCA
CCATCAAACCTTTCAAGCTTGTAACCAACATAAG
Found at i:19028 original size:66 final size:65
Alignment explanation
Indices: 18921--19115 Score: 322
Period size: 66 Copynumber: 3.0 Consensus size: 65
18911 ACCAACGTAA
18921 GGATCTCCATATCTGACAC-TCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
1 GGATCTCCATATC-GACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
18985 G
65 G
*
18986 GGATCTCCATATCGAACACTTCTGTCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
1 GGATCTCCATATCG-ACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTAC
19051 G
65 G
*
19052 GGATCTCCATATCTCG-CACTTCTGCCGATCTTCGATGTTGTCGTTCTACCATGTTCATGTTCTA
1 GGATCTCCATA--TCGACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTA
19116 TCACCATCAA
Statistics
Matches: 123, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
64 1 0.01
65 17 0.14
66 102 0.83
68 3 0.02
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (65 bp):
GGATCTCCATATCGACACTTCTGCCGATCTTCGATGTTGTCGTTTTACCATGTTCATGTTCTACG
Found at i:19435 original size:43 final size:43
Alignment explanation
Indices: 19320--19437 Score: 159
Period size: 43 Copynumber: 2.7 Consensus size: 43
19310 CATATCTGAA
19320 ACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGTTCTTAC
1 ACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGTTCTTAC
*
19363 ACTTCTGCCGATCTTCGAGGTTTCTGTTCTCCTATGTT-TTGAC
1 ACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGTTCTT-AC
* * * *
19406 ATTTCTGCCAATCTACAATGTTGTC-GTTCTCC
1 ACTTCTGCCGATCTTCGATGTT-TCTGTTCTCC
19438 CTTATTCGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 2 0.03
43 63 0.94
44 2 0.03
ACGTcount: A:0.14, C:0.27, G:0.15, T:0.44
Consensus pattern (43 bp):
ACTTCTGCCGATCTTCGATGTTTCTGTTCTCCTATGTTCTTAC
Found at i:20521 original size:34 final size:34
Alignment explanation
Indices: 20483--20587 Score: 162
Period size: 34 Copynumber: 3.2 Consensus size: 34
20473 TAACCCGTTA
20483 GCAGGGTCTTCCAGTTATTTTCACAACCCACTGG
1 GCAGGGTCTTCCAGTTATTTTCACAACCCACTGG
*
20517 GCAGGGTCTTCCAGTTATTATCACAACCCACTGG
1 GCAGGGTCTTCCAGTTATTTTCACAACCCACTGG
* *
20551 GCAGAGTCTTCCAGTTA--TT-ATAACCCACTGG
1 GCAGGGTCTTCCAGTTATTTTCACAACCCACTGG
20582 GCAGGG
1 GCAGGG
20588 CCGATGAAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
31 16 0.24
32 1 0.02
34 49 0.74
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.27
Consensus pattern (34 bp):
GCAGGGTCTTCCAGTTATTTTCACAACCCACTGG
Found at i:20962 original size:20 final size:20
Alignment explanation
Indices: 20919--20962 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
20909 TTACCTGTCT
*
20919 CCAACTAACACGGCCTTTCA
1 CCAACTAACACGGCCTTCCA
* *
20939 CCAACTAATACGGCCTTCCC
1 CCAACTAACACGGCCTTCCA
20959 CCAA
1 CCAA
20963 ATACTTAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.43, G:0.09, T:0.18
Consensus pattern (20 bp):
CCAACTAACACGGCCTTCCA
Found at i:22114 original size:30 final size:30
Alignment explanation
Indices: 22036--22114 Score: 72
Period size: 31 Copynumber: 2.6 Consensus size: 30
22026 AAATGTCTTA
*
22036 GAAGTTTAGGGGGCAAAATGTCCTGAATTTG
1 GAAG-TTAGGGGGCAAAACGTCCTGAATTTG
* * *
22067 GAAATTAAAGGGACAAAACGTCCT-AATTT-
1 GAAGTT-AGGGGGCAAAACGTCCTGAATTTG
22096 GAAGTTCAGGGGGGCAAAA
1 GAAGTT-A-GGGGGCAAAA
22115 AGGCTATAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
29 6 0.16
30 15 0.39
31 17 0.45
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.23
Consensus pattern (30 bp):
GAAGTTAGGGGGCAAAACGTCCTGAATTTG
Found at i:23916 original size:5 final size:6
Alignment explanation
Indices: 23898--23923 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
23888 ATAATTTTTT
23898 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
23924 AGCTCATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:26082 original size:29 final size:30
Alignment explanation
Indices: 26044--26103 Score: 113
Period size: 29 Copynumber: 2.0 Consensus size: 30
26034 GTAATACATA
26044 ATTACAAAACCAAACGCAGGTATCTGAAAT
1 ATTACAAAACCAAACGCAGGTATCTGAAAT
26074 ATTAC-AAACCAAACGCAGGTATCTGAAAT
1 ATTACAAAACCAAACGCAGGTATCTGAAAT
26103 A
1 A
26104 CCCGTCCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 25 0.83
30 5 0.17
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.20
Consensus pattern (30 bp):
ATTACAAAACCAAACGCAGGTATCTGAAAT
Found at i:27312 original size:392 final size:392
Alignment explanation
Indices: 26588--27377 Score: 1580
Period size: 392 Copynumber: 2.0 Consensus size: 392
26578 CTGGTTGAAG
26588 AGTTCAATATAGAGAGCATCAATGCTAGTCAGATTTCGAATGTCGTTCATGGTACTATGAACATG
1 AGTTCAATATAGAGAGCATCAATGCTAGTCAGATTTCGAATGTCGTTCATGGTACTATGAACATG
26653 CTTCCAATCCTTGGAGCTTTCATTGCTGATTCCTACGTAGGGGATTTTGCTGTTGCTGCAATTTC
66 CTTCCAATCCTTGGAGCTTTCATTGCTGATTCCTACGTAGGGGATTTTGCTGTTGCTGCAATTTC
26718 TAGCTTCATCTCTTCTCTGGTAAAATGCATGACTCTCTTGTTTTTGTCTAATCAGTCTAGCGTCA
131 TAGCTTCATCTCTTCTCTGGTAAAATGCATGACTCTCTTGTTTTTGTCTAATCAGTCTAGCGTCA
26783 ATGACATTTTATCTCATAAACTTTAAATCGCGACAACTTGATCCTTGAATTTCCAAATTCAGGAC
196 ATGACATTTTATCTCATAAACTTTAAATCGCGACAACTTGATCCTTGAATTTCCAAATTCAGGAC
26848 AATTGCGTGCTGAACTTTTCAAATTCAAGACAATTTATCCTGACACAATGACAAATTGTCCTGAA
261 AATTGCGTGCTGAACTTTTCAAATTCAAGACAATTTATCCTGACACAATGACAAATTGTCCTGAA
26913 TTTGGAAAATTCATGGAGGAAAATTGTCCTGAAAATAGTTTAGAGAGCAAAGTGTTCTTAGCTTC
326 TTTGGAAAATTCATGGAGGAAAATTGTCCTGAAAATAGTTTAGAGAGCAAAGTGTTCTTAGCTTC
26978 AT
391 AT
26980 AGTTCAATATAGAGAGCATCAATGCTAGTCAGATTTCGAATGTCGTTCATGGTACTATGAACATG
1 AGTTCAATATAGAGAGCATCAATGCTAGTCAGATTTCGAATGTCGTTCATGGTACTATGAACATG
27045 CTTCCAATCCTTGGAGCTTTCATTGCTGATTCCTACGTAGGGGATTTTGCTGTTGCTGCAATTTC
66 CTTCCAATCCTTGGAGCTTTCATTGCTGATTCCTACGTAGGGGATTTTGCTGTTGCTGCAATTTC
27110 TAGCTTCATCTCTTCTCTGGTAAAATGCATGACTCTCTTGTTTTTGTCTAATCAGTCTAGCGTCA
131 TAGCTTCATCTCTTCTCTGGTAAAATGCATGACTCTCTTGTTTTTGTCTAATCAGTCTAGCGTCA
27175 ATGACATTTTATCTCATAAACTTTAAATCGCGACAACTTGATCCTTGAATTTCCAAATTCAGGAC
196 ATGACATTTTATCTCATAAACTTTAAATCGCGACAACTTGATCCTTGAATTTCCAAATTCAGGAC
27240 AATTGCGTGCTGAACTTTTCAAATTCAAGACAATTTATCCTGACACAATGACAAATTGTCCTGAA
261 AATTGCGTGCTGAACTTTTCAAATTCAAGACAATTTATCCTGACACAATGACAAATTGTCCTGAA
27305 TTTGGAAAATTCATGGAGGAAAATTGTCCTGAAAATAGTTTAGAGAGCAAAGTGTTCTTAGCTTC
326 TTTGGAAAATTCATGGAGGAAAATTGTCCTGAAAATAGTTTAGAGAGCAAAGTGTTCTTAGCTTC
27370 AT
391 AT
27372 AGTTCA
1 AGTTCA
27378 GGAGCAAAAA
Statistics
Matches: 398, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
392 398 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (392 bp):
AGTTCAATATAGAGAGCATCAATGCTAGTCAGATTTCGAATGTCGTTCATGGTACTATGAACATG
CTTCCAATCCTTGGAGCTTTCATTGCTGATTCCTACGTAGGGGATTTTGCTGTTGCTGCAATTTC
TAGCTTCATCTCTTCTCTGGTAAAATGCATGACTCTCTTGTTTTTGTCTAATCAGTCTAGCGTCA
ATGACATTTTATCTCATAAACTTTAAATCGCGACAACTTGATCCTTGAATTTCCAAATTCAGGAC
AATTGCGTGCTGAACTTTTCAAATTCAAGACAATTTATCCTGACACAATGACAAATTGTCCTGAA
TTTGGAAAATTCATGGAGGAAAATTGTCCTGAAAATAGTTTAGAGAGCAAAGTGTTCTTAGCTTC
AT
Found at i:27523 original size:147 final size:146
Alignment explanation
Indices: 27249--27526 Score: 362
Period size: 147 Copynumber: 1.9 Consensus size: 146
27239 CAATTGCGTG
* * * *
27249 CTGAACTTTTCAAATTCAAGACAATTTATCCTGACACAATGACAAATTGTCCTGAATTTGGAAAA
1 CTGAACTCTCCAAATTCAAGACAACTTATCCTGACACAAGGACAAATTGTCCTGAATTTGGAAAA
* * * * *
27314 TTCATGGAGGAAAATTGTCCTGAAAATAGTTTAGAGAGCAAAGTGTTCTTAGCTTCATAGTTCAG
66 TT-ATGGAGGAAAATTGTCCCGAAAATAGTTCAGAGAGCAAAGTGTCCTTAGCCTCAGAGTTCAG
27379 GAGCAAAAAATTAGCCC
130 GAGCAAAAAATTAGCCC
* * * *
27396 CTGAACTCTCCAAATTCATGACAACTTATCCTGACGCGAGGGACAAATTGTCCTGAATTTGGGAA
1 CTGAACTCTCCAAATTCAAGACAACTTATCCTGACAC-AAGGACAAATTGTCCTGAATTTGGAAA
* * *
27461 GTT-T-GAGGGCCAAATTGTCCCGAACATAGTTCAGAGAGCAAAGTGTCCTTAGCCTCAGAGTTC
65 ATTATGGA-GG-AAAATTGTCCCGAAAATAGTTCAGAGAGCAAAGTGTCCTTAGCCTCAGAGTTC
27524 AGG
128 AGG
27527 GACATAAAGG
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
145 2 0.02
146 3 0.03
147 81 0.72
148 26 0.23
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (146 bp):
CTGAACTCTCCAAATTCAAGACAACTTATCCTGACACAAGGACAAATTGTCCTGAATTTGGAAAA
TTATGGAGGAAAATTGTCCCGAAAATAGTTCAGAGAGCAAAGTGTCCTTAGCCTCAGAGTTCAGG
AGCAAAAAATTAGCCC
Done.