Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010318.1 Kokia drynarioides strain JFW-HI SEQ_125180, 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: 25100
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:743 original size:59 final size:59
Alignment explanation
Indices: 651--1050 Score: 536
Period size: 59 Copynumber: 6.8 Consensus size: 59
641 TGAACTTTCC
* * ** * * * *
651 AAAAATCACCATTTTACCCCCGAACTTCCAAAAATATCATTTTTAACCACGAACCTTTT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCT
* * * *
710 AAAAATTACCATTTTATCCTTGAACTTCCAAAAATCCCATTTTTGACC-CTAAACTTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAAC-TTCT
* *
769 AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCT
* * * * *
828 AAAAATTACAATTTTATCCTCGAACTTCCAAAAATCCCATTTTTTACC-CTAAACTTTCC
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAAC-TTCT
* *
887 AAAAATTACCATTTTACCC-CTAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCT
1 AAAAATTACCATTTTACCCTC-GAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCT
* *
946 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGGATCTTCT
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCT
*
1005 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTTGA
1 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGA
1051 TTCCGAACAT
Statistics
Matches: 301, Mismatches: 34, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
58 9 0.03
59 283 0.94
60 9 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCT
Found at i:793 original size:118 final size:118
Alignment explanation
Indices: 643--1050 Score: 629
Period size: 118 Copynumber: 3.5 Consensus size: 118
633 GAGGTCCTTG
* ** * *
643 AACTTTCCAAAAATCACCATTTTACCCCCGAACTTCCAAAAATATCATTTTTAACCACGAACCTT
1 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT
* *
708 TTAAAAATTACCATTTTATCCTTGAACTTCCAAAAATCCCATTTTTGACCCTA
66 CTAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACCCTA
761 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT
1 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT
* *
826 CTAAAAATTACAATTTTATCCTCGAACTTCCAAAAATCCCATTTTTTACCCTA
66 CTAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACCCTA
** *
879 AACTTTCCAAAAATTACCATTTTACCCCTAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTT
1 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT
* **
944 CTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCTCGG
66 CTAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACC-CTA
* * * *
998 ATC-TTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTTGA
1 AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA
1051 TTCCGAACAT
Statistics
Matches: 266, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
118 263 0.99
119 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (118 bp):
AACTTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACCTT
CTAAAAATTACCATTTTATCCTCGAACTTCCAAAAATCCCATTTTTGACCCTA
Found at i:1444 original size:96 final size:96
Alignment explanation
Indices: 1316--1506 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
1306 AAACTTTAAT
* **
1316 ATCGAGGCAATATTCTTTTATTTCGGGTTCCGAAA-ATTTGCGCCTTAACTCACTAGGTGCAATT
1 ATCGAGGCAATATTCTTTTATTTCGGATTCCGAAATA-TTGCGCCTTAACTCACTAGGTGCAACC
* *
1380 TTTCTTTAAATCGA-AGTAATCGAATACCCTTA
65 TTTCTTCAAATCGAGA-TAATCAAATACCCTTA
* *
1412 ATCGAGGCAATGTT-TTCTTATCTTC-GATTCCGAAATATTGCGCCTTAACTTACTAGGTGCAAC
1 ATCGAGGCAATATTCTT-TTAT-TTCGGATTCCGAAATATTGCGCCTTAACTCACTAGGTGCAAC
*
1475 CTTTCTTCAAATCGAGATAATCAAATATCCTT
64 CTTTCTTCAAATCGAGATAATCAAATACCCTT
1507 CTCGCAAAAG
Statistics
Matches: 83, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 2 0.02
96 76 0.92
97 5 0.06
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (96 bp):
ATCGAGGCAATATTCTTTTATTTCGGATTCCGAAATATTGCGCCTTAACTCACTAGGTGCAACCT
TTCTTCAAATCGAGATAATCAAATACCCTTA
Found at i:2422 original size:24 final size:24
Alignment explanation
Indices: 2386--2434 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2376 AACTGCATTG
*
2386 TGTCTTACGAACTGAAAAAGACCA
1 TGTCTTACAAACTGAAAAAGACCA
* *
2410 TGTCTTACAAACTTAAAAAGGCCA
1 TGTCTTACAAACTGAAAAAGACCA
2434 T
1 T
2435 ATTTAACGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
TGTCTTACAAACTGAAAAAGACCA
Found at i:2781 original size:24 final size:23
Alignment explanation
Indices: 2725--2782 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
2715 AAATTGTAAG
*
2725 TTTAAACTTAATTTTTTTATTTAAT
1 TTTAAA-TTAATTTTTTTA-TAAAT
2750 TTTAAATTAATTTTTTTA-AAAT
1 TTTAAATTAATTTTTTTATAAAT
2772 TTT--ATTAATTT
1 TTTAAATTAATTT
2783 AAAGTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.25
22 6 0.19
24 12 0.38
25 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTAAATTAATTTTTTTATAAAT
Found at i:2850 original size:6 final size:6
Alignment explanation
Indices: 2821--2897 Score: 64
Period size: 6 Copynumber: 12.8 Consensus size: 6
2811 TTAAATTTCA
* * * * * * *
2821 TTTAAT TTTCAT TTCAAA TGTAAT TTTAAT TTTAAT TTCAAT TTCAAC
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT
* * *
2869 TTTAAT TTTCAT TTCAAC TTTAAT TTTAA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAA
2898 ACTCTATTAA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAT
Found at i:2852 original size:24 final size:24
Alignment explanation
Indices: 2809--2897 Score: 103
Period size: 24 Copynumber: 3.8 Consensus size: 24
2799 TACAACTTTA
*
2809 ATTT-AAATTTCA-TTTAATTTTC
1 ATTTCAAATTTAATTTTAATTTTC
* *
2831 ATTTCAAATGTAATTTTAATTTTA
1 ATTTCAAATTTAATTTTAATTTTC
*
2855 ATTTC-AATTTCAACTTTAATTTTC
1 ATTTCAAATTT-AATTTTAATTTTC
*
2879 ATTTCAACTTTAATTTTAA
1 ATTTCAAATTTAATTTTAA
2898 ACTCTATTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
22 4 0.07
23 10 0.18
24 37 0.67
25 4 0.07
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.55
Consensus pattern (24 bp):
ATTTCAAATTTAATTTTAATTTTC
Found at i:2863 original size:18 final size:18
Alignment explanation
Indices: 2801--2897 Score: 84
Period size: 18 Copynumber: 5.8 Consensus size: 18
2791 AACTTCATTA
*
2801 CAACTTTAATTTAAATTT
1 CAACTTTAATTTTAATTT
*
2819 C-A-TTTAATTTTCATTT
1 CAACTTTAATTTTAATTT
* *
2835 CAAATGTAATTTTAA--T
1 CAACTTTAATTTTAATTT
*
2851 ----TTTAATTTCAATTT
1 CAACTTTAATTTTAATTT
*
2865 CAACTTTAATTTTCATTT
1 CAACTTTAATTTTAATTT
2883 CAACTTTAATTTTAA
1 CAACTTTAATTTTAA
2898 ACTCTATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
12 9 0.15
14 1 0.02
16 14 0.23
17 2 0.03
18 36 0.58
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.54
Consensus pattern (18 bp):
CAACTTTAATTTTAATTT
Found at i:5849 original size:73 final size:74
Alignment explanation
Indices: 5738--5874 Score: 213
Period size: 73 Copynumber: 1.9 Consensus size: 74
5728 AAGAAAATTA
* * *
5738 TCGAAACCATCTTTTTTGAAAACTATGTATTTCAAAAATTATTTTTAAATTGAAAAATAAGAGTT
1 TCGAAACCATCTTTTTTAAAAACGACGTATTTCAAAAATTATTTTTAAATTGAAAAATAAGAGTT
5803 GCCAAGCTG
66 GCCAAGCTG
* * *
5812 TCGAAACCATC-TTTTTAAAAACGACGTGTTTTAAAAATTATTTTTAAATTGAAAAATAGGAGT
1 TCGAAACCATCTTTTTTAAAAACGACGTATTTCAAAAATTATTTTTAAATTGAAAAATAAGAGT
5875 CACCAGCAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
73 46 0.81
74 11 0.19
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.36
Consensus pattern (74 bp):
TCGAAACCATCTTTTTTAAAAACGACGTATTTCAAAAATTATTTTTAAATTGAAAAATAAGAGTT
GCCAAGCTG
Found at i:6747 original size:59 final size:58
Alignment explanation
Indices: 6683--7149 Score: 394
Period size: 59 Copynumber: 7.9 Consensus size: 58
6673 TCCGAGGGCA
** * *
6683 AAAATGGTAATTTTAGGAAAGTTCGGGGTTAAAAATGAAATTTTGGGAAGTTTTGGGGT
1 AAAATGGTAATTTT-GGAAAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTTTGGGGT
* * * * * *
6742 AAAATGGTAATTTTGAAAAGAATC-AGGATCAAAAATGAATTTTTTTG-AGGTTTAGGGGT
1 AAAATGGTAATTTTGGAAA-AATCGAGG-TTAAAAATGAA-ATTTTGGAAAGTTTTGGGGT
* * * *
6801 AAAATGGTGATTTTGGGAAGAATCAAGGTTAAAAATGGAATTTTGGAAAGTTTTGGGGT
1 AAAATGGTAATTTT-GGAAAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTTTGGGGT
* * ** * **
6860 AAAATGATAATTTGTGGAAAAAATCTG-GGTAAAAAATGAGGTTTTAGAAAGTTTAAGGGT
1 AAAATGGTAATTT-TGG-AAAAATC-GAGGTTAAAAATGAAATTTTGGAAAGTTTTGGGGT
* * * * *
6920 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTGGGAAGTTATGTGGT
1 AAAATGGTAA-TTTTGGAAAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTTTGGGGT
* *
6979 AAAATGGTAATTTTGGAAAAAATCGAGGTTAAAAATGAAAATTTT-GAAAG-TTCGAGTGT
1 AAAATGGTAATTTTGG-AAAAATCGAGGTTAAAAATG-AAATTTTGGAAAGTTTTG-GGGT
* *
7038 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAAT-AGAATTTTGGAAAGTTTGGGGGTT
1 AAAATGGTAA-TTTTGGAAAAATCGAGGTTAAAAATGA-AATTTTGGAAAGTTTTGGGG-T
* * * * *
7098 AACAT-GTAATTTT-CAAAAGTTTGAGGGTTAAAATAT-AATTTTTGGAAAGTTT
1 AAAATGGTAATTTTGGAAAA-ATCGA-GGTTAAAA-ATGAAATTTTGGAAAGTTT
7150 AGGGACCTTT
Statistics
Matches: 330, Mismatches: 56, Indels: 44
0.77 0.13 0.10
Matches are distributed among these distances:
57 5 0.02
58 33 0.10
59 210 0.64
60 79 0.24
61 3 0.01
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTGGAAAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTTTGGGGT
Found at i:6753 original size:29 final size:30
Alignment explanation
Indices: 6682--7148 Score: 122
Period size: 29 Copynumber: 15.8 Consensus size: 30
6672 ATCCGAGGGC
6682 AAAAATGGTAATTTTAGGAAAGTTCGGGGTT
1 AAAAATGGTAATTTT-GGAAAGTTCGGGGTT
* * *
6713 AAAAAT-GAAATTTTGGGAAGTTTTGGGG-T
1 AAAAATGGTAATTTTGGAAAG-TTCGGGGTT
* * * * *
6742 -AAAATGGTAATTTTGAAAAGAATCAGGATC
1 AAAAATGGTAATTTTGGAAAG-TTCGGGGTT
* * *
6772 AAAAAT-G-AATTTTTTTG-AGGTTTAGGGG-T
1 AAAAATGGTAA--TTTTGGAAAG-TTCGGGGTT
* * * **
6801 -AAAATGGTGATTTTGGGAAGAATCAAGGTT
1 AAAAATGGTAATTTTGGAAAG-TTCGGGGTT
*
6831 AAAAATGG-AATTTTGGAAAGTTTTGGGG-T
1 AAAAATGGTAATTTTGGAAAG-TTCGGGGTT
* ** * *
6860 -AAAATGATAATTTGTGGAAAAAATCTGGGTA
1 AAAAATGGTAATTT-TGG-AAAGTTCGGGGTT
* * **
6891 AAAAAT-G-AGGTTTTAGAAAGTTTAAGGG-T
1 AAAAATGGTA-ATTTTGGAAAG-TTCGGGGTT
** * *
6920 -AAAATGGTAATTTTTGGAAAAATCGAGGTC
1 AAAAATGGTAA-TTTTGGAAAGTTCGGGGTT
* * *
6950 AAAAATGG-AATTTTGGGAAGTTATGTGG-T
1 AAAAATGGTAATTTTGGAAAGTT-CGGGGTT
** *
6979 -AAAATGGTAATTTTGGAAAAAATCGAGGTT
1 AAAAATGGTAATTTTGG-AAAGTTCGGGGTT
** *
7009 AAAAATGAAAATTTT-GAAAGTTC-GAGTGT
1 AAAAATGGTAATTTTGGAAAGTTCGGGGT-T
** * *
7038 -AAAATGGTAATTTTTGGAAAAATCGAGGTC
1 AAAAATGGTAA-TTTTGGAAAGTTCGGGGTT
* *
7068 AAAAATAG-AATTTTGGAAAGTTTGGGGGTT
1 AAAAATGGTAATTTTGGAAAG-TTCGGGGTT
* ** *
7098 -AACAT-GTAATTTTCAAAAGTTTGAGGGTT
1 AAAAATGGTAATTTTGGAAAGTTCG-GGGTT
*
7127 -AAAAT-ATAATTTTTGGAAAGTT
1 AAAAATGGTAA-TTTTGGAAAGTT
7149 TAGGGACCTT
Statistics
Matches: 303, Mismatches: 96, Indels: 75
0.64 0.20 0.16
Matches are distributed among these distances:
28 47 0.16
29 106 0.35
30 90 0.30
31 55 0.18
32 5 0.02
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAAATGGTAATTTTGGAAAGTTCGGGGTT
Found at i:6814 original size:118 final size:117
Alignment explanation
Indices: 6683--7110 Score: 452
Period size: 118 Copynumber: 3.6 Consensus size: 117
6673 TCCGAGGGCA
* * *
6683 AAAATGGTAATTTTAGGAAAGTTCGGGGTTAAAAATGAAATTTTGGGAAGTTTTGGGGTAAAATG
1 AAAATGGTAATTTT-GGAAAGATCGAGGTTAAAAATGGAATTTTGGGAAGTTTTGGGGTAAAATG
* ** * * *
6748 GTAATTTT-GAAAAGAATCAGGATCAAAAATGAATTTTTTTG-AGGTTTAGGGGT
65 GTAATTTTGGAAAA-AATCAGG-TAAAAAATGAAGGTTTTAGAAAGTTTAAGGGT
* * * *
6801 AAAATGGTGATTTTGGGAAGAATCAAGGTTAAAAATGGAATTTTGGAAAGTTTTGGGGTAAAATG
1 AAAATGGTAATTTTGGAAAG-ATCGAGGTTAAAAATGGAATTTTGGGAAGTTTTGGGGTAAAATG
* *
6866 ATAATTTGTGGAAAAAATCTGGGTAAAAAATG-AGGTTTTAGAAAGTTTAAGGGT
65 GTAATTT-TGGAAAAAATC-AGGTAAAAAATGAAGGTTTTAGAAAGTTTAAGGGT
* * * *
6920 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATGGAATTTTGGGAAGTTATGTGGTAAAATG
1 AAAATGGTAA-TTTTGGAAAGATCGAGGTTAAAAATGGAATTTTGGGAAGTTTTGGGGTAAAATG
* ** ** *
6985 GTAATTTTGGAAAAAATCGAGGTTAAAAATGAAAATTTT-GAAAGTTCGAGTGT
65 GTAATTTTGGAAAAAATC-AGGTAAAAAATGAAGGTTTTAGAAAGTTTAAGGGT
* * * * * *
7038 AAAATGGTAATTTTTGGAAAAATCGAGGTCAAAAATAGAATTTTGGAAAGTTTGGGGGTTAACAT
1 AAAATGGTAA-TTTTGGAAAGATCGAGGTTAAAAATGGAATTTTGGGAAGTTTTGGGG-TAAAAT
7103 -GTAATTTT
64 GGTAATTTT
7111 CAAAAGTTTG
Statistics
Matches: 264, Mismatches: 38, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
117 5 0.02
118 157 0.59
119 87 0.33
120 15 0.06
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (117 bp):
AAAATGGTAATTTTGGAAAGATCGAGGTTAAAAATGGAATTTTGGGAAGTTTTGGGGTAAAATGG
TAATTTTGGAAAAAATCAGGTAAAAAATGAAGGTTTTAGAAAGTTTAAGGGT
Found at i:7080 original size:30 final size:30
Alignment explanation
Indices: 6920--7086 Score: 136
Period size: 29 Copynumber: 5.7 Consensus size: 30
6910 GTTTAAGGGT
6920 AAAATGGTAATTTTTGGAAAAATCGAGGTCA
1 AAAATGGTAATTTTTGGAAAAATCGAGGT-A
* ** *
6951 AAAATGG-AATTTTGGGAAGTTAT-GTGGT-
1 AAAATGGTAATTTTTGGAA-AAATCGAGGTA
6979 AAAATGGTAA-TTTTGGAAAAAATCGAGGTTA
1 AAAATGGTAATTTTTGG-AAAAATCGAGG-TA
* * **
7010 AAAAT-GAAAATTTT-GAAAGTTCGAGTGT-
1 AAAATGGTAATTTTTGGAAAAATCGAG-GTA
7038 AAAATGGTAATTTTTGGAAAAATCGAGGTCA
1 AAAATGGTAATTTTTGGAAAAATCGAGGT-A
*
7069 AAAATAG-AA-TTTTGGAAA
1 AAAATGGTAATTTTTGGAAA
7087 GTTTGGGGGT
Statistics
Matches: 108, Mismatches: 16, Indels: 26
0.72 0.11 0.17
Matches are distributed among these distances:
28 19 0.18
29 34 0.31
30 31 0.29
31 24 0.22
ACGTcount: A:0.43, C:0.04, G:0.23, T:0.31
Consensus pattern (30 bp):
AAAATGGTAATTTTTGGAAAAATCGAGGTA
Found at i:8307 original size:10 final size:10
Alignment explanation
Indices: 8240--8318 Score: 56
Period size: 10 Copynumber: 7.6 Consensus size: 10
8230 CTTTTTCTTT
8240 TTATTAATTA
1 TTATTAATTA
* *
8250 TTAATAGTTA
1 TTATTAATTA
8260 TTATTAATTA
1 TTATTAATTA
8270 CCGTTATTAA-TA
1 ---TTATTAATTA
8282 CTTATTAA-TA
1 -TTATTAATTA
8292 TTATT-ATTA
1 TTATTAATTA
*
8301 TTAATTATTGTA
1 TT-ATTAAT-TA
8313 TTATTA
1 TTATTA
8319 TTTAATGTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
8 1 0.02
9 9 0.16
10 28 0.50
11 5 0.09
12 6 0.11
13 7 0.12
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (10 bp):
TTATTAATTA
Found at i:8309 original size:13 final size:13
Alignment explanation
Indices: 8240--8309 Score: 56
Period size: 13 Copynumber: 5.4 Consensus size: 13
8230 CTTTTTCTTT
8240 TTATTAATTATTAA
1 TTATT-ATTATTAA
8254 -TAGTTATTATTAA
1 TTA-TTATTATTAA
***
8267 TTACCGTTATTAA
1 TTATTATTATTAA
*
8280 -TACTTATTAAT-A
1 TTA-TTATTATTAA
8292 TTATTATTATTAA
1 TTATTATTATTAA
8305 TTATT
1 TTATT
8310 GTATTATTAT
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
12 10 0.23
13 29 0.67
14 4 0.09
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.56
Consensus pattern (13 bp):
TTATTATTATTAA
Found at i:8332 original size:21 final size:18
Alignment explanation
Indices: 8240--8320 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 18
8230 CTTTTTCTTT
*
8240 TTATTAATTATTAATAGTTA
1 TTATTAATTATT-GTA-TTA
**
8260 TTATTAATTACCGTTATTA
1 TTATTAATTATTG-TATTA
*
8279 ATACTT-ATTAATAT-TATTA
1 TTA-TTAATT-AT-TGTATTA
8298 TTATTAATTATTGTATTA
1 TTATTAATTATTGTATTA
8316 TTATT
1 TTATT
8321 TAATGTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
17 1 0.02
18 14 0.29
19 18 0.38
20 15 0.31
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (18 bp):
TTATTAATTATTGTATTA
Found at i:9062 original size:6 final size:6
Alignment explanation
Indices: 9053--9128 Score: 70
Period size: 6 Copynumber: 13.0 Consensus size: 6
9043 TTATAATATT
** *
9053 TTTAAA TTTAAA TACAAA TTTAAA CTTAAA -TTAAA TTTAAA TTTTAGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTA-AA
*
9102 --TAAA TTTAAA TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
9129 ATGAGTTGAG
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
4 2 0.04
5 11 0.19
6 38 0.67
7 4 0.07
8 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:9066 original size:16 final size:17
Alignment explanation
Indices: 9035--9066 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9025 ATCTTATTCA
9035 TTTTAAATTTATAATAT
1 TTTTAAATTTATAATAT
9052 TTTTAAATTTA-AATA
1 TTTTAAATTTATAATA
9067 CAAATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAATTTATAATAT
Found at i:9076 original size:18 final size:17
Alignment explanation
Indices: 9053--9128 Score: 91
Period size: 18 Copynumber: 4.4 Consensus size: 17
9043 TTATAATATT
*
9053 TTTAAATTTAAATACAAA
1 TTTAAATTTAAAT-TAAA
*
9071 TTTAAACTTAAATTAAA
1 TTTAAATTTAAATTAAA
9088 TTTAAATTTTAGAA-TAAA
1 TTTAAA-TTTA-AATTAAA
*
9106 TTTAAATTTAAAATAAA
1 TTTAAATTTAAATTAAA
9123 TTTAAA
1 TTTAAA
9129 ATGAGTTGAG
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
16 2 0.04
17 23 0.44
18 25 0.48
19 2 0.04
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAATTAAA
Found at i:13343 original size:96 final size:96
Alignment explanation
Indices: 13166--13350 Score: 250
Period size: 96 Copynumber: 1.9 Consensus size: 96
13156 GAAAAGGATG
* *
13166 TTCGATTATCTCAATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCAATTTGAAGAAAGATTGCACCTAGTAAGTTAAAGCGCAAATTTTCAGAATCGA
** *
13231 AGATAAGGAAACATTGCCTTGATTAAGGGTA
66 AGATAAAAAAACATTGCCTCGATTAAGGGTA
* *
13262 TTCGATTATTTCGATTTGAAGAACA-ATTGCACCTAGTAAGTTAAAGCGCAAATTTTC-GAAACT
1 TTCGATTATCTCAATTTGAAGAA-AGATTGCACCTAGTAAGTTAAAGCGCAAATTTTCAG-AA-T
*
13325 CGAA-ATAAAAAAATATTGCCTCGATT
63 CGAAGATAAAAAAACATTGCCTCGATT
13351 TTAAAGTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
95 1 0.01
96 71 0.91
97 6 0.08
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTCAATTTGAAGAAAGATTGCACCTAGTAAGTTAAAGCGCAAATTTTCAGAATCGA
AGATAAAAAAACATTGCCTCGATTAAGGGTA
Found at i:13600 original size:29 final size:27
Alignment explanation
Indices: 13569--13657 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 27
13559 AAATGAGACT
13569 TTTTAGACACCTAGGGGCAAAATGGTAA
1 TTTTAGACA-CTAGGGGCAAAATGGTAA
* * *
13597 TTTTGGACTCTCGGGGGCAAAAATGGTAA
1 TTTTAGACACT-AGGGGC-AAAATGGTAA
* * *
13626 TTTTAGATACTCGAGAGCAAAATGGTAA
1 TTTTAGACACTAG-GGGCAAAATGGTAA
13654 TTTT
1 TTTT
13658 GGGAAAATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
27 2 0.04
28 27 0.54
29 21 0.42
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (27 bp):
TTTTAGACACTAGGGGCAAAATGGTAA
Found at i:13614 original size:28 final size:28
Alignment explanation
Indices: 13582--13659 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 28
13572 TAGACACCTA
13582 GGGGCAAAATGGTAATTTTGGACT-CTCG
1 GGGGCAAAATGGTAATTTTGGA-TACTCG
*
13610 GGGGCAAAAATGGTAATTTTAGATACTCG
1 GGGGC-AAAATGGTAATTTTGGATACTCG
* *
13639 AGAGCAAAATGGTAATTTTGG
1 GGGGCAAAATGGTAATTTTGG
13660 GAAAATTTTG
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 21 0.48
29 23 0.52
ACGTcount: A:0.32, C:0.10, G:0.29, T:0.28
Consensus pattern (28 bp):
GGGGCAAAATGGTAATTTTGGATACTCG
Found at i:13823 original size:29 final size:28
Alignment explanation
Indices: 13791--13982 Score: 145
Period size: 29 Copynumber: 6.5 Consensus size: 28
13781 AAATGTGATC
13791 AAAAATGTAATTTTTGGACA-TATGGGGGT
1 AAAAATGTAATTTTTGGA-AGT-TGGGGGT
* *
13820 -AAAATGGTAATTTTTGCAAGTTTTGGGGT
1 AAAAAT-GTAATTTTTGGAAG-TTGGGGGT
* *
13849 CAAAAATGGAATTTTTGGAAGTTCGAGGGT
1 -AAAAATGTAATTTTTGGAAGTT-GGGGGT
** *
13879 AAAAATGTAATTTTTGGAAGTTTTAAGGTT
1 AAAAATGTAATTTTTGGAAG--TTGGGGGT
* **
13909 AAAAATATAATTTTTGGAAGTTTAAGGGT
1 AAAAATGTAATTTTTGGAAG-TTGGGGGT
**
13938 AAAAATGTAATTTTTAAAAGTTTTGGGGGT
1 AAAAATGTAATTTTTGGAAG--TTGGGGGT
*
13968 CAAAAATATAATTTT
1 -AAAAATGTAATTTT
13983 GGAGGAGTTT
Statistics
Matches: 136, Mismatches: 17, Indels: 18
0.80 0.10 0.11
Matches are distributed among these distances:
28 6 0.04
29 63 0.46
30 47 0.35
31 20 0.15
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAGTTGGGGGT
Found at i:13823 original size:58 final size:58
Alignment explanation
Indices: 13685--13834 Score: 180
Period size: 58 Copynumber: 2.6 Consensus size: 58
13675 AAAAATAGAA
* *
13685 TTTTAGACATATGAGGGTAAAACGGTAATTTTTAGAAAAATCAGTATAAAAAACGAATT
1 TTTTGGACATATGAGGGTAAAATGGTAATTTTTAGAAAAAT-AGTATAAAAAACGAATT
* * * *
13744 TTTTGGACAGT-TGAGAGTAAAATGTTAATTTTTAGAAAAAT-GTGATCAAAAATGTAA-T
1 TTTTGGACA-TATGAGGGTAAAATGGTAATTTTTAGAAAAATAGT-ATAAAAAACG-AATT
*
13802 TTTTGGACATATGGGGGTAAAATGGTAATTTTT
1 TTTTGGACATATGAGGGTAAAATGGTAATTTTT
13835 GCAAGTTTTG
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
57 3 0.04
58 37 0.47
59 37 0.47
60 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.20, T:0.35
Consensus pattern (58 bp):
TTTTGGACATATGAGGGTAAAATGGTAATTTTTAGAAAAATAGTATAAAAAACGAATT
Found at i:13862 original size:30 final size:29
Alignment explanation
Indices: 13791--14016 Score: 183
Period size: 30 Copynumber: 7.6 Consensus size: 29
13781 AAATGTGATC
* *
13791 AAAAATGTAATTTTTGGACA-TATGGGGGT
1 AAAAATGTAATTTTTGGA-AGTTTTGGGGT
*
13820 -AAAATGGTAATTTTTGCAAGTTTTGGGGT
1 AAAAAT-GTAATTTTTGGAAGTTTTGGGGT
* *
13849 CAAAAATGGAATTTTTGGAAG-TTCGAGGGT
1 -AAAAATGTAATTTTTGGAAGTTTTG-GGGT
* *
13879 AAAAATGTAATTTTTGGAAGTTTTAAGGTT
1 AAAAATGTAATTTTTGGAAGTTTT-GGGGT
* **
13909 AAAAATATAATTTTTGGAAGTTTAAGGGT
1 AAAAATGTAATTTTTGGAAGTTTTGGGGT
**
13938 AAAAATGTAATTTTTAAAAGTTTTGGGGGT
1 AAAAATGTAATTTTTGGAAGTTTT-GGGGT
*
13968 CAAAAATATAA-TTTTGGAGGAG-TTTGGGGT
1 -AAAAATGTAATTTTTGGA--AGTTTTGGGGT
* * *
13998 CAAATATATAATTTCTGGA
1 -AAAAATGTAATTTTTGGA
14017 CAATTTAGGG
Statistics
Matches: 162, Mismatches: 23, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.04
29 64 0.40
30 67 0.41
31 23 0.14
32 2 0.01
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTTTGGGGT
Found at i:13862 original size:59 final size:58
Alignment explanation
Indices: 13789--13982 Score: 221
Period size: 59 Copynumber: 3.3 Consensus size: 58
13779 AAAAATGTGA
* *
13789 TCAAAAATGTAATTTTTGGACA-TATGGGGGT-AAAATGGTAATTTTTGCAAGTTTTGGGG
1 TCAAAAATGTAATTTTTGGA-AGT-TGAGGGTAAAAAT-GTAATTTTTGAAAGTTTTGGGG
* * **
13848 TCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTTAAGG
1 TCAAAAATGTAATTTTTGGAAGTT-GAGGGTAAAAATGTAATTTTTGAAAGTTTTGGGG
* * * *
13907 TTAAAAATATAATTTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTAAAAGTTTTGGGGG
1 TCAAAAATGTAATTTTTGGAAG-TTGAGGGTAAAAATGTAATTTTTGAAAGTTTT-GGGG
*
13967 TCAAAAATATAATTTT
1 TCAAAAATGTAATTTT
13983 GGAGGAGTTT
Statistics
Matches: 116, Mismatches: 14, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
58 2 0.02
59 90 0.78
60 24 0.21
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (58 bp):
TCAAAAATGTAATTTTTGGAAGTTGAGGGTAAAAATGTAATTTTTGAAAGTTTTGGGG
Found at i:21382 original size:28 final size:28
Alignment explanation
Indices: 21341--21431 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
21331 AAATGAGACT
* *
21341 TTTTGGACACTCGGGGGCAAAATGATAA
1 TTTTGGACTCTCGGGGGCAAAATGGTAA
* *
21369 TTTTAGACTCTCGGGAGCAAAAATGGTAA
1 TTTTGGACTCTCGGGGGC-AAAATGGTAA
**
21398 TTTTGGACTCTCAAGGGCAAAATGGTAA
1 TTTTGGACTCTCGGGGGCAAAATGGTAA
21426 TTTTGG
1 TTTTGG
21432 GAAAATTTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 31 0.57
29 23 0.43
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (28 bp):
TTTTGGACTCTCGGGGGCAAAATGGTAA
Found at i:21635 original size:30 final size:30
Alignment explanation
Indices: 21593--21744 Score: 175
Period size: 30 Copynumber: 5.1 Consensus size: 30
21583 ATCCGAGGGT
*
21593 AAAATGGTAATTTTTGCAAGTTTTAAGGTCA
1 AAAATGG-AATTTTTGGAAGTTTTAAGGTCA
* * **
21624 AAATTGGAATTTTTGGAAG-TTT-GGGTGT
1 AAAATGGAATTTTTGGAAGTTTTAAGGTCA
** **
21652 AAAATTTAATTTTTGGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAAGGTCA
21682 AAAATGGAATTTTTGGAAGTTTTAAGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAAGGTCA
*
21712 AAAATGGAAATTTTGGAAG-TTTAAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTAA-GGTCA
21742 AAA
1 AAA
21745 GTATAATTTT
Statistics
Matches: 103, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
28 19 0.18
29 11 0.11
30 67 0.65
31 6 0.06
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTAAGGTCA
Found at i:21664 original size:58 final size:59
Alignment explanation
Indices: 21591--21703 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 59
21581 ACATCCGAGG
*
21591 GTAAAATGGTAATTTTTGCAAGTTTTAAGGTCAAAATTGGAATTTTTGGAAGTTTGGGT
1 GTAAAATGGTAATTTTTGCAAGTTTTAAGGTCAAAAATGGAATTTTTGGAAGTTTGGGT
* * **
21650 GTAAAAT-TTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTT
1 GTAAAATGGTAATTTTTGCAAGTTTTAAGGTCAAAAATGGAATTTTTGGAAGTTT
21704 TAAGGTCAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 42 0.86
59 7 0.14
ACGTcount: A:0.31, C:0.03, G:0.25, T:0.42
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGCAAGTTTTAAGGTCAAAAATGGAATTTTTGGAAGTTTGGGT
Found at i:21752 original size:29 final size:30
Alignment explanation
Indices: 21600--21794 Score: 136
Period size: 30 Copynumber: 6.6 Consensus size: 30
21590 GGTAAAATGG
* * *
21600 TAATTTTTGCAAGTTTTAA-GGTCAAAATTG
1 TAATTTTTGGAAG-TTTAAGGGTCAAAAGTA
* * *
21630 GAATTTTTGGAAGTTT--GGGTGTAAAA-TT
1 TAATTTTTGGAAGTTTAAGGGT-CAAAAGTA
** * *
21658 TAATTTTTGGAAGTTTTGGGGTCAAAAATG
1 TAATTTTTGGAAGTTTAAGGGTCAAAAGTA
* * *
21688 GAATTTTTGGAAGTTTTAA-GGTCAAAAATG
1 TAATTTTTGGAAG-TTTAAGGGTCAAAAGTA
* *
21718 GAAATTTTGGAAGTTTAAGGGTCAAAAGTA
1 TAATTTTTGGAAGTTTAAGGGTCAAAAGTA
*
21748 TAA-TTTTGGACAAGTTT-GGGGTC-AAAGTA
1 TAATTTTTGG--AAGTTTAAGGGTCAAAAGTA
21777 TAATTTTTGGACAGTTTA
1 TAATTTTTGGA-AGTTTA
21795 GGGACTTTCA
Statistics
Matches: 138, Mismatches: 15, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
28 20 0.14
29 36 0.26
30 73 0.53
31 9 0.07
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (30 bp):
TAATTTTTGGAAGTTTAAGGGTCAAAAGTA
Found at i:21770 original size:30 final size:30
Alignment explanation
Indices: 21720--21794 Score: 95
Period size: 29 Copynumber: 2.6 Consensus size: 30
21710 CAAAAATGGA
21720 AATTTTGG--AAGTTTAAGGGTCAAAAGTAT
1 AATTTTGGACAAGTTTAAGGGTC-AAAGTAT
*
21749 AATTTTGGACAAGTTT-GGGGTCAAAGTAT
1 AATTTTGGACAAGTTTAAGGGTCAAAGTAT
21778 AATTTTTGGAC-AGTTTA
1 AA-TTTTGGACAAGTTTA
21795 GGGACTTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 22 0.54
30 13 0.32
31 6 0.15
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (30 bp):
AATTTTGGACAAGTTTAAGGGTCAAAGTAT
Done.