Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010352.1 Kokia drynarioides strain JFW-HI SEQ_125220, 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: 22081
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.33
Warning! 374 characters in sequence are not A, C, G, or T
Found at i:109 original size:3 final size:3
Alignment explanation
Indices: 101--162 Score: 88
Period size: 3 Copynumber: 20.0 Consensus size: 3
91 ATTAAATATC
* *
101 TAA TAA TAA TAA TAG TAT TAAA TGAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA
148 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
163 ATCGAAAGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 49 0.91
4 5 0.09
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:432 original size:3 final size:3
Alignment explanation
Indices: 424--470 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
414 ATTAAATATC
* *
424 TAA TAA TAA TAA TAG TAT TAAA TGAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TAA TAA TAA TAA TAA
471 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 34 0.87
4 5 0.13
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1551 original size:30 final size:28
Alignment explanation
Indices: 1525--1844 Score: 200
Period size: 30 Copynumber: 10.9 Consensus size: 28
1515 CGAACTTTCT
*
1525 AAAAATTACCATTTTACCCCTAAACTTTC
1 AAAAATTACCATTTTACCCC-AAACTTCC
* * *
1554 AAAAA-TCCCATTTTTGACCTCGAACATTCC
1 AAAAATTACCA-TTTT-ACCCCAAAC-TTCC
*
1584 AAAAATTACCATTTTACCCCTGAACTTCC
1 AAAAATTACCATTTTACCCC-AAACTTCC
*
1613 AAAAA-TCCCATTTTTGACCCCAAACCTTCC
1 AAAAATTACCA-TTTT-ACCCCAAA-CTTCC
* * *
1643 AAAAATCACCATTTTACCCTCGAACTCCC
1 AAAAATTACCATTTTACCC-CAAACTTCC
*
1672 AAAAA-TCCCATTTTTAACCCCAAACCTTCC
1 AAAAATTACCA-TTTT-ACCCCAAA-CTTCC
* * *
1702 AAAAATCACCATTTTACCCCCGAACTCCC
1 AAAAATTACCATTTTA-CCCCAAACTTCC
* **
1731 AAAAA-TCCCATTTTTTACCCCGAGCCTTCC
1 AAAAATTACCA--TTTTACCCC-AAACTTCC
* * *
1761 AAAAATCACCATTTTACCCCCGAACTGCC
1 AAAAATTACCATTTTA-CCCCAAACTTCC
* * * *
1790 AAAAA-TCCCATTTTTTACTCGAACCTTCC
1 AAAAATTACCA--TTTTACCCCAAACTTCC
*
1819 AAAAATCACCATTTTTAACCCCAAAC
1 AAAAATTACCA-TTTT-ACCCCAAAC
1845 ATTACCCCCG
Statistics
Matches: 223, Mismatches: 44, Indels: 47
0.71 0.14 0.15
Matches are distributed among these distances:
28 17 0.08
29 96 0.43
30 97 0.43
31 13 0.06
ACGTcount: A:0.35, C:0.34, G:0.03, T:0.28
Consensus pattern (28 bp):
AAAAATTACCATTTTACCCCAAACTTCC
Found at i:1610 original size:59 final size:59
Alignment explanation
Indices: 1512--1996 Score: 544
Period size: 59 Copynumber: 8.0 Consensus size: 59
1502 CTCCGGAGGT
* * * * *
1512 CCCCGAACTTTCTAAAAATTACCATTTTACCCCTAAACTTTCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATCACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
* * *
1571 CCTCGAACATTCCAAAAATTACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATCACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
* * *
1630 CCCCAAACCTTCCAAAAATCACCATTTTA-CCCTCGAACTCCCAAAAATCCCATTTTTAA
1 CCCCGAACCTTCCAAAAATCACCATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGA
* * * *
1689 CCCCAAACCTTCCAAAAATCACCATTTTACCCCCGAACTCCCAAAAATCCCATTTTTTA
1 CCCCGAACCTTCCAAAAATCACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
* * * *
1748 CCCCGAGCCTTCCAAAAATCACCATTTTACCCCCGAACTGCCAAAAATCCCATTTTTTA
1 CCCCGAACCTTCCAAAAATCACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
* *
1807 -CTCGAACCTTCCAAAAATCACCATTTTTAACCCCAAACATTACCCCCGAACTTCTAAAAATCCC
1 CCCCGAACCTTCCAAAAATCACCA-TTTT-A-CCC---C--T------GAACTTCCAAAAATCCC
*
1871 ATTTTTAA
52 ATTTTTGA
* * *
1879 CCCCAAACTTTCCAAAAATCACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACCTTCCAAAAATCACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
* * * *
1938 CCCCGAACCTTCTAAAAATCACCATTTTA-ACCTCGAACGTCCAAAAATCCTATTTTTGA
1 CCCCGAACCTTCCAAAAATCACCATTTTACCCCT-GAACTTCCAAAAATCCCATTTTTGA
1997 TTTCAAACAT
Statistics
Matches: 373, Mismatches: 35, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
58 27 0.07
59 287 0.77
60 4 0.01
61 3 0.01
64 1 0.00
67 1 0.00
70 3 0.01
71 1 0.00
72 26 0.07
73 20 0.05
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (59 bp):
CCCCGAACCTTCCAAAAATCACCATTTTACCCCTGAACTTCCAAAAATCCCATTTTTGA
Found at i:1791 original size:29 final size:29
Alignment explanation
Indices: 1512--1833 Score: 291
Period size: 29 Copynumber: 10.9 Consensus size: 29
1502 CTCCGGAGGT
* *
1512 CCCCGAACTTTCTAAAAATTACCATTTTAC
1 CCCCGAAC-TTCCAAAAATCACCATTTTAC
** *
1542 CCCTAAACTTTCAAAAATC-CCATTTTTGA-
1 CCCCGAACTTCCAAAAATCACCA-TTTT-AC
* *
1571 CCTCGAACATTCCAAAAATTACCATTTTAC
1 CCCCGAAC-TTCCAAAAATCACCATTTTAC
*
1601 CCCTGAACTTCCAAAAATC-CCATTTTTGA-
1 CCCCGAACTTCCAAAAATCACCA-TTTT-AC
*
1630 CCCCAAACCTTCCAAAAATCACCATTTTAC
1 CCCCGAA-CTTCCAAAAATCACCATTTTAC
* * *
1660 CCTCGAACTCCCAAAAATC-CCATTTTTAA
1 CCCCGAACTTCCAAAAATCACCA-TTTTAC
*
1689 CCCCAAACCTTCCAAAAATCACCATTTTAC
1 CCCCGAA-CTTCCAAAAATCACCATTTTAC
*
1719 CCCCGAACTCCCAAAAATC-CCATTTTTTA-
1 CCCCGAACTTCCAAAAATCACCA--TTTTAC
*
1748 CCCCGAGCCTTCCAAAAATCACCATTTTAC
1 CCCCGA-ACTTCCAAAAATCACCATTTTAC
* **
1778 CCCCGAACTGCCAAAAATC-CCATTTTTT
1 CCCCGAACTTCCAAAAATCACCATTTTAC
* *
1806 ACTCGAACCTTCCAAAAATCACCATTTT
1 CCCCGAA-CTTCCAAAAATCACCATTTT
1834 TAACCCCAAA
Statistics
Matches: 238, Mismatches: 34, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
28 24 0.10
29 103 0.43
30 99 0.42
31 12 0.05
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATCACCATTTTAC
Found at i:1896 original size:30 final size:29
Alignment explanation
Indices: 1850--1994 Score: 168
Period size: 30 Copynumber: 4.9 Consensus size: 29
1840 CAAACATTAC
*
1850 CCCCGAACTTCTAAAAATCCCATTTTTAA
1 CCCCGAACTTCCAAAAATCCCATTTTTAA
* *
1879 CCCCAAACTTTCCAAAAATCACCA-TTTTAC
1 CCCCGAAC-TTCCAAAAATC-CCATTTTTAA
*
1909 CCCCGAACTTCCAAAAATCCCATTTTTGA
1 CCCCGAACTTCCAAAAATCCCATTTTTAA
*
1938 CCCCGAACCTTCTAAAAATCACCA-TTTTAA
1 CCCCGAA-CTTCCAAAAATC-CCATTTTTAA
* * *
1968 CCTCGAACGTCCAAAAATCCTATTTTT
1 CCCCGAACTTCCAAAAATCCCATTTTT
1995 GATTTCAAAC
Statistics
Matches: 98, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
28 5 0.05
29 43 0.44
30 44 0.45
31 6 0.06
ACGTcount: A:0.34, C:0.33, G:0.04, T:0.29
Consensus pattern (29 bp):
CCCCGAACTTCCAAAAATCCCATTTTTAA
Found at i:1966 original size:131 final size:131
Alignment explanation
Indices: 1715--1969 Score: 404
Period size: 131 Copynumber: 1.9 Consensus size: 131
1705 AATCACCATT
* * *
1715 TTACCCCCGAACTCCCAAAAATCCCATTTTTTACCCCGAGCCTTCCAAAAATCACCATTTTACCC
1 TTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC
* *
1780 CCGAACTGCCAAAAATCCCATTTTTTACTCGAACCTTCCAAAAATCACCATTTTTAACCCCAAAC
66 CCGAACTGCCAAAAATCCCATTTTTGACCCGAACCTTCCAAAAATCACCATTTTTAACCCCAAAC
1845 A
131 A
* * *
1846 TTACCCCCGAACTTCTAAAAATCCCATTTTTAACCCCAAACTTTCCAAAAATCACCATTTTACCC
1 TTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC
* *
1911 CCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATCACCA-TTTTAACC
66 CCGAACTGCCAAAAATCCCATTTTTGA-CCCGAACCTTCCAAAAATCACCATTTTTAACC
1970 TCGAACGTCC
Statistics
Matches: 113, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
131 92 0.81
132 21 0.19
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (131 bp):
TTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC
CCGAACTGCCAAAAATCCCATTTTTGACCCGAACCTTCCAAAAATCACCATTTTTAACCCCAAAC
A
Found at i:2022 original size:190 final size:190
Alignment explanation
Indices: 1656--2024 Score: 562
Period size: 190 Copynumber: 1.9 Consensus size: 190
1646 AATCACCATT
*
1656 TTACCCTCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC
1 TTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC
* * *
1721 CCGAACTCCCAAAAATCCCATTTTTTACCCCGAGCCTTCCAAAAATCACCATTTTACCCCCGAAC
66 CCGAACTCCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATCACCATTTTAACCCCGAAC
* * *
1786 TGCCAAAAATCCCATTTTTTACTCGAACCTTCCAAAAATCACCATTTTTAACCCCAAACA
131 TGCCAAAAATCCCATTTTTGACTCAAACATTCCAAAAATCACCATTTTTAACCCCAAACA
* * *
1846 TTACCCCCGAACTTCTAAAAATCCCATTTTTAACCCCAAACTTTCCAAAAATCACCATTTTACCC
1 TTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC
* * *
1911 CCGAACTTCCAAAAATCCCATTTTTGACCCCGAACCTTCTAAAAATCACCATTTTAACCTCGAAC
66 CCGAACTCCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATCACCATTTTAACCCCGAAC
* * *
1976 -GTCCAAAAATCCTATTTTTGATTTCAAACATTCCAAAACT-ACCATTTTT
131 TG-CCAAAAATCCCATTTTTGA-CTCAAACATTCCAAAAATCACCATTTTT
2025 GCCACTTCGT
Statistics
Matches: 161, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
189 1 0.01
190 146 0.91
191 14 0.09
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (190 bp):
TTACCCCCGAACTCCCAAAAATCCCATTTTTAACCCCAAACCTTCCAAAAATCACCATTTTACCC
CCGAACTCCCAAAAATCCCATTTTTGACCCCGAACCTTCCAAAAATCACCATTTTAACCCCGAAC
TGCCAAAAATCCCATTTTTGACTCAAACATTCCAAAAATCACCATTTTTAACCCCAAACA
Found at i:3357 original size:22 final size:22
Alignment explanation
Indices: 3329--3532 Score: 185
Period size: 22 Copynumber: 9.3 Consensus size: 22
3319 CCTATTGTTC
*
3329 TGCACTACGGTGCTTACTGGTT
1 TGCACTACGGTGCTTACTGATT
* * *
3351 TGCACTATGGTGCTTATTGGTT
1 TGCACTACGGTGCTTACTGATT
*
3373 TGCACTACGGTGCCTACTG-TT
1 TGCACTACGGTGCTTACTGATT
* * *
3394 CTGCATTATGGTGCTTATTGATT
1 -TGCACTACGGTGCTTACTGATT
* * *
3417 TGCACTACAGTGCTTATTGACT
1 TGCACTACGGTGCTTACTGATT
* *
3439 TGCATTACGGTGCCTACTGATT
1 TGCACTACGGTGCTTACTGATT
* * *
3461 TGCATTATGGTGCTTATTGATT
1 TGCACTACGGTGCTTACTGATT
* * *
3483 TGCATTACGATGCCTACTGATT
1 TGCACTACGGTGCTTACTGATT
* * * *
3505 TGCATTACAGTACCTACTGATT
1 TGCACTACGGTGCTTACTGATT
3527 TGCACT
1 TGCACT
3533 TCAGTGCCTA
Statistics
Matches: 151, Mismatches: 29, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
21 2 0.01
22 147 0.97
23 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.40
Consensus pattern (22 bp):
TGCACTACGGTGCTTACTGATT
Found at i:3430 original size:66 final size:66
Alignment explanation
Indices: 3319--3486 Score: 230
Period size: 66 Copynumber: 2.5 Consensus size: 66
3309 GGTTATAATA
* * * * * ** **
3319 CCTATTGTTCTGCACTACGGTGCTTACTGGTTTGCACTATGGTGCTTATTGGTTTGCACTACGGT
1 CCTACTGTTCTGCATTATGGTGCTTATTGATTTGCACTACAGTGCTTATTGACTTGCACTACGGT
3384 G
66 G
*
3385 CCTACTGTTCTGCATTATGGTGCTTATTGATTTGCACTACAGTGCTTATTGACTTGCATTACGGT
1 CCTACTGTTCTGCATTATGGTGCTTATTGATTTGCACTACAGTGCTTATTGACTTGCACTACGGT
3450 G
66 G
3451 CCTACTGATT-TGCATTATGGTGCTTATTGATTTGCA
1 CCTACTG-TTCTGCATTATGGTGCTTATTGATTTGCA
3487 TTACGATGCC
Statistics
Matches: 91, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 89 0.98
67 2 0.02
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.41
Consensus pattern (66 bp):
CCTACTGTTCTGCATTATGGTGCTTATTGATTTGCACTACAGTGCTTATTGACTTGCACTACGGT
G
Found at i:3508 original size:66 final size:66
Alignment explanation
Indices: 3337--3530 Score: 230
Period size: 66 Copynumber: 2.9 Consensus size: 66
3327 TCTGCACTAC
* * ** * * * *
3337 GGTGCTTACTGGTTTGCACTATGGTGCTTATTGGTTTGCACTACGGTGCCTACTG-TTCTGCATT
1 GGTGCTTATTGATTTGCACTACAGTGCCTACTGATTTGCATTACGGTGCCTACTGATT-TGCATT
3401 AT
65 AT
* * *
3403 GGTGCTTATTGATTTGCACTACAGTGCTTATTGACTTGCATTACGGTGCCTACTGATTTGCATTA
1 GGTGCTTATTGATTTGCACTACAGTGCCTACTGATTTGCATTACGGTGCCTACTGATTTGCATTA
3468 T
66 T
* * *
3469 GGTGCTTATTGATTTGCATTAC-GATGCCTACTGATTTGCATTACAGTACCTACTGATTTGCA
1 GGTGCTTATTGATTTGCACTACAG-TGCCTACTGATTTGCATTACGGTGCCTACTGATTTGCA
3531 CTTCAGTGCC
Statistics
Matches: 113, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
65 1 0.01
66 110 0.97
67 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (66 bp):
GGTGCTTATTGATTTGCACTACAGTGCCTACTGATTTGCATTACGGTGCCTACTGATTTGCATTA
T
Found at i:3611 original size:40 final size:40
Alignment explanation
Indices: 3567--3653 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
3557 CAATACTTAG
3567 CAGGCTTCATGCTAGTAT-ATCT-ATCGGGCTTAATGCCTAA
1 CAGGCTTCATGCTAGTATAAT-TAAT-GGGCTTAATGCCTAA
* * * *
3607 CAGGCTTCATGTTGGTGTAATTAATGGGCTTAATGCCTAG
1 CAGGCTTCATGCTAGTATAATTAATGGGCTTAATGCCTAA
3647 CAGGCTT
1 CAGGCTT
3654 TGTGTCGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
40 37 0.90
41 4 0.10
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (40 bp):
CAGGCTTCATGCTAGTATAATTAATGGGCTTAATGCCTAA
Found at i:6056 original size:59 final size:58
Alignment explanation
Indices: 5993--6115 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 58
5983 TACTCGGGGG
*
5993 TAAAATGACAATTTTTAAAACTTTC-AGTGTCACAAAT-CAATTTTTTGGAAGTTCGAGGC
1 TAAAATGA-AATTTTTAAAACTTTCGAG-GTCAAAAATGCAA-TTTTTGGAAGTTCGAGGC
** * ** *
6052 TAAAAATGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG
1 T-AAAATGAAATTTTTAAAACTTTCGAGGTCAAAAATGCAATTTTTGGAAGTTCGAGGC
6111 TAAAA
1 TAAAA
6116 ATGGTAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
58 4 0.07
59 40 0.74
60 10 0.19
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (58 bp):
TAAAATGAAATTTTTAAAACTTTCGAGGTCAAAAATGCAATTTTTGGAAGTTCGAGGC
Found at i:6116 original size:59 final size:59
Alignment explanation
Indices: 6034--6391 Score: 261
Period size: 59 Copynumber: 6.1 Consensus size: 59
6024 ACAAATCAAT
* * *
6034 TTTTTGGAAGTTCGAGGCTAAAAATGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGGA
1 TTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA
* ** **
6093 TTTTTGGAAGTTCGAGGGTAAAAATGGTAATTTTGGGAAAATTCGAGGGGAAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA
* ** * * ** * *
6153 ATTTTAAACATTTAG-GGGTAAAAGGGTAA-TTTT-GAGAGTTTCGAGGTCGAAAATGGAG
1 TTTTTGGA-AGTTCGAGGGTAAAAATGTAATTTTTGGA-AGTTTCGAGGTCAAAAATGGAA
* * ** *
6211 TTTTTGGACA-TCCGAGAGT-AAAATGGTAATTTTTAAAAGTTTC-AGTGTTAAAAATGGAA
1 TTTTTGGA-AGTTCGAGGGTAAAAAT-GTAATTTTTGGAAGTTTCGAG-GTCAAAAATGGAA
* * * *
6270 TTTTTGAAAGTTCG-GGGCT-AAAATAG-AATTTTTGGAAGTTTCGGGGTTAAAAAT-GAGT
1 TTTTTGGAAGTTCGAGGG-TAAAAAT-GTAATTTTTGGAAGTTTCGAGGTCAAAAATGGA-A
* * * * * * *
6328 TTTTTAGAGGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTTAG-GGTCAAAAATGGAA
1 TTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA
6386 TTTTTG
1 TTTTTG
6392 TTCAGTTTAG
Statistics
Matches: 232, Mismatches: 51, Indels: 33
0.73 0.16 0.10
Matches are distributed among these distances:
57 9 0.04
58 87 0.38
59 91 0.39
60 41 0.18
61 4 0.02
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (59 bp):
TTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA
Found at i:6141 original size:31 final size:31
Alignment explanation
Indices: 6034--6157 Score: 123
Period size: 30 Copynumber: 4.1 Consensus size: 31
6024 ACAAATCAAT
* *
6034 TTTTTGG-AAGTTCGAGGCTAAAAAT-GAAA
1 TTTTTGGAAAATTCGAGGGTAAAAATGGAAA
** *
6063 TTTTTGGAAGTTTCGA-GGTCAAAAATGG-GA
1 TTTTTGGAAAATTCGAGGGT-AAAAATGGAAA
* *
6093 TTTTTGG-AAGTTCGAGGGTAAAAATGGTAA
1 TTTTTGGAAAATTCGAGGGTAAAAATGGAAA
* *
6123 TTTTGGGAAAATTCGAGGGGAAAAATGGAAA
1 TTTTTGGAAAATTCGAGGGTAAAAATGGAAA
6154 TTTT
1 TTTT
6158 AAACATTTAG
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
29 23 0.29
30 30 0.38
31 25 0.32
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (31 bp):
TTTTTGGAAAATTCGAGGGTAAAAATGGAAA
Found at i:6272 original size:30 final size:30
Alignment explanation
Indices: 6230--6390 Score: 154
Period size: 29 Copynumber: 5.5 Consensus size: 30
6220 ATCCGAGAGT
* * *
6230 AAAATGGTAATTTTTAAAAGTTTCAGTGTTA
1 AAAATGG-AATTTTTAGAAGTTTCGGGGTTA
*
6261 AAAATGGAATTTTT-GAAAG-TTCGGGGCT-
1 AAAATGGAATTTTTAG-AAGTTTCGGGGTTA
* *
6289 AAAATAGAATTTTTGGAAGTTTCGGGGTTA
1 AAAATGGAATTTTTAGAAGTTTCGGGGTTA
* * *
6319 AAAAT-GAGTTTTTTAGAGGTTT-GGGGGTA
1 AAAATGGA-ATTTTTAGAAGTTTCGGGGTTA
* *
6348 AAAATGGAATTTTTAGAAGTTT-AGGGTCA
1 AAAATGGAATTTTTAGAAGTTTCGGGGTTA
6377 AAAATGGAATTTTT
1 AAAATGGAATTTTT
6391 GTTCAGTTTA
Statistics
Matches: 109, Mismatches: 15, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
28 16 0.15
29 58 0.53
30 28 0.26
31 7 0.06
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (30 bp):
AAAATGGAATTTTTAGAAGTTTCGGGGTTA
Found at i:6403 original size:30 final size:28
Alignment explanation
Indices: 6034--6390 Score: 127
Period size: 29 Copynumber: 12.2 Consensus size: 28
6024 ACAAATCAAT
* * * *
6034 TTTTTGGAAGTTCGAGGCTAAAAATGAAA
1 TTTTTAGAAGTT-TAGGGTAAAAATGGAA
* * *
6063 TTTTTGGAAGTTTCGAGGTCAAAAATGGGA
1 TTTTTAGAAGTTTAG-GGT-AAAAATGGAA
* *
6093 TTTTTGGAAGTTCGAGGGTAAAAATGGTAA
1 TTTTTAGAAGTT-TAGGGTAAAAATGG-AA
** * * *
6123 TTTTGGGAAAATTCGAGGGGAAAAATGGAA
1 TTTTTAG-AAGTT-TAGGGTAAAAATGGAA
* * *
6153 ATTTTA-AACATTTAGGGGT-AAAAGGGTAA
1 TTTTTAGAA-GTTTA-GGGTAAAAATGG-AA
* * * *
6182 TTTTGAG-AGTTTCGAGGTCGAAAATGGAG
1 TTTTTAGAAGTTTAG-GGT-AAAAATGGAA
* ** *
6211 TTTTTGGACA-TCCGAGAGT-AAAATGGTAA
1 TTTTTAGA-AGT-TTAGGGTAAAAATGG-AA
* *
6240 TTTTTAAAAGTTTCAGTGTTAAAAATGGAA
1 TTTTTAGAAGTTT-AG-GGTAAAAATGGAA
** *
6270 TTTTT-GAAAGTTCGGGGCT-AAAATAGAA
1 TTTTTAG-AAGTTTAGGG-TAAAAATGGAA
* * *
6298 TTTTTGGAAGTTTCGGGGTTAAAAAT-GAGT
1 TTTTTAGAAGTTT-AGGG-TAAAAATGGA-A
* *
6328 TTTTTAGAGGTTTGGGGGTAAAAATGGAA
1 TTTTTAGAAGTTT-AGGGTAAAAATGGAA
6357 TTTTTAGAAGTTTAGGGTCAAAAATGGAA
1 TTTTTAGAAGTTTAGGGT-AAAAATGGAA
6386 TTTTT
1 TTTTT
6391 GTTCAGTTTA
Statistics
Matches: 250, Mismatches: 50, Indels: 56
0.70 0.14 0.16
Matches are distributed among these distances:
27 1 0.00
28 47 0.19
29 95 0.38
30 79 0.32
31 28 0.11
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (28 bp):
TTTTTAGAAGTTTAGGGTAAAAATGGAA
Found at i:8328 original size:6 final size:6
Alignment explanation
Indices: 8300--8377 Score: 65
Period size: 6 Copynumber: 13.3 Consensus size: 6
8290 TATAATAATC
* * * *
8300 TTAAAT TTAGAAA ATAAAT TTAAAC TTAAA- TTAAAT TTAAAT TCGAAA-
1 TTAAAT TTA-AAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT T-TAAAT
*
8348 -TAAAT TTAAAT TT-AAT ATAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT
8378 CTAAACAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
4 3 0.05
5 9 0.16
6 38 0.67
7 7 0.12
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (6 bp):
TTAAAT
Found at i:8354 original size:34 final size:35
Alignment explanation
Indices: 8300--8409 Score: 125
Period size: 35 Copynumber: 3.1 Consensus size: 35
8290 TATAATAATC
*
8300 TTAAATTTAGAAAATAAATTTAAACTTAAATTAAAT
1 TTAAATTTCG-AAATAAATTTAAACTTAAATTAAAT
*
8336 TTAAA-TTCGAAATAAATTTAAA-TTTAATATAAAT
1 TTAAATTTCGAAATAAATTTAAACTTAAAT-TAAAT
* * ** *
8370 TTAAATTTCTAAACAAATTTATTCTTAAAATAAAT
1 TTAAATTTCGAAATAAATTTAAACTTAAATTAAAT
8405 TTAAA
1 TTAAA
8410 AGGAGTTTGG
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
33 5 0.08
34 23 0.37
35 26 0.41
36 9 0.14
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (35 bp):
TTAAATTTCGAAATAAATTTAAACTTAAATTAAAT
Found at i:8377 original size:17 final size:16
Alignment explanation
Indices: 8282--8409 Score: 98
Period size: 17 Copynumber: 7.4 Consensus size: 16
8272 CCTTATTTAT
8282 TTTAAATTTATAAT-AA
1 TTTAAATTTA-AATAAA
8298 TCTTAAATTTAGAAAATAAA
1 T-TTAAATTT---AAATAAA
*
8318 TTTAAACTTAAATTAAA
1 TTTAAATTTAAA-TAAA
*
8335 TTTAAATTCGAAATAAA
1 TTTAAATT-TAAATAAA
8352 TTTAAATTTAATATAAA
1 TTTAAATTTAA-ATAAA
*
8369 TTTAAATTTCTAAACAAA
1 TTTAAA-TT-TAAATAAA
*
8387 TTT-ATTCTTAAAATAAA
1 TTTAAAT-TT-AAATAAA
8404 TTTAAA
1 TTTAAA
8410 AGGAGTTTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 24
0.74 0.07 0.20
Matches are distributed among these distances:
16 8 0.09
17 53 0.58
18 13 0.14
19 13 0.14
20 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAATAAA
Found at i:9140 original size:206 final size:206
Alignment explanation
Indices: 8744--9304 Score: 691
Period size: 206 Copynumber: 2.7 Consensus size: 206
8734 TCTGGTTTCG
* * * ** * ** **
8744 TTGACTTGGCCTTCTTCTCAGTATCTCATCTGGAAGATGGTCGCATCACTTGTTTTGATCCATTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
*** * * * *
8809 CTCTGTGTTTCATCAGGAAGACGGATTTGGTTCACTTCTCTGTATCTCATCAGGGAGTTAACCAC
66 CTCTGTACCTCATCAGGAAGGCGGATTTGGTTCATTTCTCAGTATCTCATCAGGAAGTTAACCAC
* *
8874 TTTATTGCTTCGACCTGCTTCTTAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTC-ATA
131 TTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGATA
*
8938 TCAGGCGTGAGT
196 TCA-GCGTGAGC
* *
8950 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAA-CTCGCT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATC-CGCT
* * *
9014 TCTTTGTACCTCATCAGGAAGGCGGACTTGGTTCATTTCTCAGTATCTCATCAGGAAGCTAACC-
65 TCTCTGTACCTCATCAGGAAGGCGGATTTGGTTCATTTCTCAGTATCTCATCAGGAAGTTAACCA
* * * *
9078 TTTTATTACTTCGACCTGCTTCTCAGTGTCTTATCAGGAAGCTGGGGTTCGAAGATTTTGCTCGC
130 CTTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGA-TTTGCTCGA
* * *
9143 TTTGAGCGTGGGC
194 TATCAGCGTGAGC
* *
9156 TTGATTTGGTCTTCTTCTTAGTATCTCATCAGGGAGATGACCGCATCGCTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
* *
9221 CTCTGTACCTCATCAGGAAGGCGCATTTGGTTCACTTT-TCCGTATCTCATCAGGAAGTTAA-CA
66 CTCTGTACCTCATCAGGAAGGCGGATTTGGTTCA-TTTCTCAGTATCTCATCAGGAAGTTAACCA
* * * *
9284 GTTTATTGCTCCGATCTGCTT
130 CTTTATTACTTCGACCTGCTT
9305 GAAGCTGGGA
Statistics
Matches: 304, Mismatches: 45, Indels: 12
0.84 0.12 0.03
Matches are distributed among these distances:
205 52 0.17
206 245 0.81
207 7 0.02
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (206 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTT
CTCTGTACCTCATCAGGAAGGCGGATTTGGTTCATTTCTCAGTATCTCATCAGGAAGTTAACCAC
TTTATTACTTCGACCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCGATA
TCAGCGTGAGC
Found at i:9850 original size:27 final size:27
Alignment explanation
Indices: 9820--9879 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
9810 TCAAAATTTT
* * *
9820 TATTAAGAAGAGGATTAAAAGATACAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
*
9847 TATTAAAAAGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAAGAAACAA
9874 TCATTA
1 T-ATTA
9880 GTTGAAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.22
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAAGAAACAA
Found at i:21156 original size:29 final size:29
Alignment explanation
Indices: 21119--21197 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
21109 TTAGTGTCAT
*
21119 AAATAGAATTTTTGGAAGTTCGAGACT-AA
1 AAATGGAATTTTTGGAAGTTCG-GACTCAA
**
21148 AAATGGAATTTTTGGAAGTTTCGGGGTCAA
1 AAATGGAATTTTTGGAAG-TTCGGACTCAA
*
21178 AAATGGGATTTTTGGAAGTT
1 AAATGGAATTTTTGGAAGTT
21198 TGGGGGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 21 0.48
30 23 0.52
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTCGGACTCAA
Found at i:21202 original size:29 final size:29
Alignment explanation
Indices: 21119--21543 Score: 276
Period size: 29 Copynumber: 14.5 Consensus size: 29
21109 TTAGTGTCAT
* **
21119 AAATAGAATTTTTGGAAG-TTCGAGACTAA
1 AAATGGAATTTTTGGAAGTTTCG-GGGTAA
21148 AAATGGAATTTTTGGAAGTTTCGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTCGGGGT-AA
* *
21178 AAATGGGATTTTTGGAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
* * * *
21207 AAATGGTTATTTTGGGAAATTTCGAGGGGAA
1 AAATGG-AATTTTTGGAAGTTTCG-GGGTAA
* * * * **
21238 AAATGAAAATTTT-AAACATTTAAGGGT-A
1 AAATGGAATTTTTGGAA-GTTTCGGGGTAA
* *** *
21266 AAAGGGTAA-TTTT-GAGAGTTTTAAGGTCGA
1 AAATGG-AATTTTTGGA-AGTTTCGGGGT-AA
* *
21296 AAATAGAGTTTTTGGACA--TTCGGGGGT-A
1 AAATGGAATTTTTGGA-AGTTTC-GGGGTAA
** * * *
21324 AAATGGTAATTTTTAAAAGTTTTAGTGTTAA
1 AAATGG-AATTTTTGGAAG-TTTCGGGGTAA
*
21355 AAATGAAATTTTTGGAAG-TTCGGGGCTAA
1 AAATGGAATTTTTGGAAGTTTCGGGG-TAA
* * * *
21384 AAATAGAATTTTTGGAAGTTTTGAGGTCA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
* *
21413 AAATGGGATTTTTGG-AGGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTC-GGGGTAA
* * *
21442 AAATGGAATTCTTGGAAGTTTTGGGGTCA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
* *
21471 AAATGGAATTTTTTGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTCGGGGT-AA
* *
21501 AAATTGAATTTTTGGAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTCGGGGTAA
21530 AAATGGAATTTTTG
1 AAATGGAATTTTTG
21544 TACAGTTTAG
Statistics
Matches: 307, Mismatches: 67, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
28 32 0.10
29 143 0.47
30 111 0.36
31 21 0.07
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTCGGGGTAA
Found at i:21208 original size:59 final size:60
Alignment explanation
Indices: 21080--21543 Score: 355
Period size: 59 Copynumber: 7.9 Consensus size: 60
21070 TTTGGATACC
** * * * *
21080 CGGGGGT-AAAATGGTAATTTTTAAAAGTTTTAGTGTCATAAATAGAATTTTTGGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
* ** * *
21139 CGAGACTAAAAATGG-AATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
* * * * * * * * * *
21198 TGGGGGTAAAAATGGTTATTTTGGGAAATTTCGAGGG-GAAAAATGAAAATTTT-AAACATT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGTTTTG-GGGTCAAAAATGGAATTTTTGGAA-GTT
*** * ** * * *
21258 TAAGGGT-AAAAGGGTAA-TTTT-GAGAGTTTTAAGGTCGAAAATAGAGTTTTTGGACA-TT
1 CGGGGGTAAAAATGGTAATTTTTGGA-AGTTTTGGGGTCAAAAATGGAATTTTTGGA-AGTT
** * * * *
21316 CGGGGGT-AAAATGGTAATTTTTAAAAGTTTTAGTGTTAAAAATGAAATTTTTGGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
* * * * *
21375 CGGGGCTAAAAATAG-AATTTTTGGAAGTTTTGAGGTC-AAAATGGGATTTTTGGAGGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
* *
21433 CGGGGGTAAAAATGG-AATTCTTGGAAGTTTTGGGGTC-AAAATGGAATTTTTTGAAGTT
1 CGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
** * *
21491 TTGGGGTCAAAAATTG-AATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTG
1 CGGGGGT-AAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTG
21544 TACAGTTTAG
Statistics
Matches: 315, Mismatches: 76, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
57 4 0.01
58 107 0.34
59 153 0.49
60 48 0.15
61 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (60 bp):
CGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTT
Found at i:21513 original size:117 final size:118
Alignment explanation
Indices: 21146--21543 Score: 327
Period size: 117 Copynumber: 3.4 Consensus size: 118
21136 GTTCGAGACT
* * *
21146 AAAAATGGAATTTTTGGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAAT
1 AAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT
* * * * ** * * *
21211 GGTTATTTTGGGAAATTTCGAGGGGAAAAAT-GAAAATTTTAAACATTTAAGGGT-
66 GGTAATTTT-GGAAGTTTTG-GGGTAAAAATGGAATTTTTTGAA-GTTTAGGGGTC
* * * *
21265 -AAAAGGGTAA-TTTT-GAGAGTTTTAAGGTCGAAAAT-AGAGTTTTTGGACA-TTCGGGGGT-A
1 AAAAATGG-AATTTTTGGA-AGTTTTGAGGTCAAAAATGGGA-TTTTTGGA-AGTTCGGGGGTAA
** * * * * *
21324 AAATGGTAATTTTTAAAAGTTTTAGTGTTAAAAATGAAATTTTTGGAAG-TTCGGGG-C
62 AAATGGTAA-TTTTGGAAGTTTT-GGGGTAAAAATGGAATTTTTTGAAGTTTAGGGGTC
* *
21381 TAAAAATAGAATTTTTGGAAGTTTTGAGGTC-AAAATGGGATTTTTGGAGGTTCGGGGGTAAAAA
1 -AAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAA
* *
21445 TGG-AATTCTTGGAAGTTTTGGGGTCAAAATGGAATTTTTTGAAGTTTTGGGGTC
65 TGGTAATT-TTGGAAGTTTTGGGGTAAAAATGGAATTTTTTGAAGTTTAGGGGTC
* * * *
21499 AAAAATTGAATTTTTGGAAGTTTAGGGGT-AAAAATGGAATTTTTG
1 AAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTG
21544 TACAGTTTAG
Statistics
Matches: 220, Mismatches: 40, Indels: 40
0.73 0.13 0.13
Matches are distributed among these distances:
116 27 0.12
117 106 0.48
118 82 0.37
119 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (118 bp):
AAAAATGGAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAAT
GGTAATTTTGGAAGTTTTGGGGTAAAAATGGAATTTTTTGAAGTTTAGGGGTC
Done.