Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001886.1 Kokia drynarioides strain JFW-HI SEQ_113659, 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: 100911
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 86 characters in sequence are not A, C, G, or T
Found at i:1591 original size:2 final size:2
Alignment explanation
Indices: 1586--1610 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1576 AAAAAAAAAA
1586 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1611 CACTATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2672 original size:10 final size:11
Alignment explanation
Indices: 2651--2687 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
2641 CCAATTCAAG
*
2651 TTTTTATGAAT
1 TTTTTATAAAT
2662 TTTTTAT-AAT
1 TTTTTATAAAT
2672 TTTTTATAAAT
1 TTTTTATAAAT
2683 TTTTT
1 TTTTT
2688 TTTTTTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (11 bp):
TTTTTATAAAT
Found at i:7295 original size:6 final size:6
Alignment explanation
Indices: 7284--7308 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7274 AATCTTTTAC
7284 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
7309 TAATTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:8548 original size:20 final size:20
Alignment explanation
Indices: 8525--8563 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8515 GTCAACTATC
**
8525 AAAGTCAATGGTCAACGGTT
1 AAAGTCAACAGTCAACGGTT
8545 AAAGTCAACAGTCAACGGT
1 AAAGTCAACAGTCAACGGT
8564 CGATCAACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (20 bp):
AAAGTCAACAGTCAACGGTT
Found at i:8588 original size:18 final size:18
Alignment explanation
Indices: 8527--8589 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
8517 CAACTATCAA
* *
8527 AGTCAATGGTCAACGGTTAA
1 AGTCAACGGTCAACGG-T-C
*
8547 AGTCAACAGTCAACGGTC
1 AGTCAACGGTCAACGGTC
8565 -GATCAACGGTCAACGGTC
1 AG-TCAACGGTCAACGGTC
8583 AGTCAAC
1 AGTCAAC
8590 AATCGGTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
17 1 0.03
18 20 0.54
19 2 0.05
20 14 0.38
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (18 bp):
AGTCAACGGTCAACGGTC
Found at i:9780 original size:40 final size:38
Alignment explanation
Indices: 9712--9846 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
9702 TCCAGAATGG
* *
9712 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
9752 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
9789 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
9830 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
9847 ACTCAAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:9844 original size:41 final size:38
Alignment explanation
Indices: 9744--9847 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
9734 TTCGAAGCAA
* *
9744 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
9781 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
9819 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
9848 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:14897 original size:18 final size:19
Alignment explanation
Indices: 14862--14906 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
14852 TACAAAATGA
14862 TCAAAATAATTTTCAAAAT
1 TCAAAATAATTTTCAAAAT
*
14881 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TCAAAAT
*
14900 TTAAAAT
1 TCAAAAT
14907 TTTGTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
TCAAAATAATTTTCAAAAT
Found at i:14934 original size:25 final size:24
Alignment explanation
Indices: 14887--14933 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
14877 AAATTCAAAA
*
14887 TATTTATAAAAATTTAAAATTTTG
1 TATTTATAAAAAATTAAAATTTTG
* *
14911 TATTTTTAAAAAATTATAATTTT
1 TATTTATAAAAAATTAAAATTTT
14934 TAAAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTTATAAAAAATTAAAATTTTG
Found at i:14961 original size:20 final size:20
Alignment explanation
Indices: 14937--14981 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
14927 TAATTTTTAA
*
14937 AAAAAATCTAAAAATATATAT
1 AAAAATTCTAAAAAT-TATAT
* *
14958 AAAAATTTTAAAAATTTTAT
1 AAAAATTCTAAAAATTATAT
14978 AAAA
1 AAAA
14982 TAATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTCTAAAAATTATAT
Found at i:15940 original size:6 final size:6
Alignment explanation
Indices: 15929--15953 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15919 AATCTTTTAC
15929 AAATAT AAATAT AAATAT AAATAT A
1 AAATAT AAATAT AAATAT AAATAT A
15954 TAATTTTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:17193 original size:20 final size:20
Alignment explanation
Indices: 17170--17208 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17160 GTCAACTATC
**
17170 AAAGTCAATGGTCAACGGTT
1 AAAGTCAACAGTCAACGGTT
17190 AAAGTCAACAGTCAACGGT
1 AAAGTCAACAGTCAACGGT
17209 CGATCAACGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (20 bp):
AAAGTCAACAGTCAACGGTT
Found at i:17233 original size:18 final size:18
Alignment explanation
Indices: 17172--17234 Score: 65
Period size: 18 Copynumber: 3.4 Consensus size: 18
17162 CAACTATCAA
* *
17172 AGTCAATGGTCAACGGTTAA
1 AGTCAACGGTCAACGG-T-C
*
17192 AGTCAACAGTCAACGGTC
1 AGTCAACGGTCAACGGTC
17210 -GATCAACGGTCAACGGTC
1 AG-TCAACGGTCAACGGTC
17228 AGTCAAC
1 AGTCAAC
17235 AATCGGTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
17 1 0.03
18 20 0.54
19 2 0.05
20 14 0.38
ACGTcount: A:0.33, C:0.24, G:0.24, T:0.19
Consensus pattern (18 bp):
AGTCAACGGTCAACGGTC
Found at i:18425 original size:40 final size:38
Alignment explanation
Indices: 18357--18491 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
18347 TCCAGAATGG
* *
18357 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
18397 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
18434 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
18475 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
18492 ACTCAAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:18489 original size:41 final size:38
Alignment explanation
Indices: 18389--18492 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
18379 TTCGAAGCAA
* *
18389 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
18426 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
18464 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
18493 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:23542 original size:18 final size:19
Alignment explanation
Indices: 23507--23551 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
23497 TACAAAATGA
23507 TCAAAATAATTTTCAAAAT
1 TCAAAATAATTTTCAAAAT
*
23526 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TCAAAAT
*
23545 TTAAAAT
1 TCAAAAT
23552 TTTGTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
TCAAAATAATTTTCAAAAT
Found at i:23579 original size:25 final size:24
Alignment explanation
Indices: 23532--23578 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
23522 AAATTCAAAA
*
23532 TATTTATAAAAATTTAAAATTTTG
1 TATTTATAAAAAATTAAAATTTTG
* *
23556 TATTTTTAAAAAATTATAATTTT
1 TATTTATAAAAAATTAAAATTTT
23579 TAAAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTTATAAAAAATTAAAATTTTG
Found at i:23606 original size:20 final size:20
Alignment explanation
Indices: 23582--23626 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
23572 TAATTTTTAA
*
23582 AAAAAATCTAAAAATATATAT
1 AAAAATTCTAAAAAT-TATAT
* *
23603 AAAAATTTTAAAAATTTTAT
1 AAAAATTCTAAAAATTATAT
23623 AAAA
1 AAAA
23627 TAATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTCTAAAAATTATAT
Found at i:23678 original size:109 final size:109
Alignment explanation
Indices: 23558--23778 Score: 424
Period size: 109 Copynumber: 2.0 Consensus size: 109
23548 AAATTTTGTA
*
23558 TTTTTAAAAAATTATAATTTTTAAAAAAAATCTAAAAATATATATAAAAATTTTAAAAATTTTAT
1 TTTTTAAAAAATTATAATTTTTAAAAAAAATCTAAAAAAATATATAAAAATTTTAAAAATTTTAT
23623 AAAATAATAATTTTGGAATCTAAATGAGTGCTTAATGATTCAAG
66 AAAATAATAATTTTGGAATCTAAATGAGTGCTTAATGATTCAAG
*
23667 TTTTTAAAAAATTATAATTTTTTAAAAAAATCTAAAAAAATATATAAAAATTTTAAAAATTTTAT
1 TTTTTAAAAAATTATAATTTTTAAAAAAAATCTAAAAAAATATATAAAAATTTTAAAAATTTTAT
23732 AAAATAATAATTTTGGAATCTAAATGAGTGCTTAATGATTCAAG
66 AAAATAATAATTTTGGAATCTAAATGAGTGCTTAATGATTCAAG
23776 TTT
1 TTT
23779 ATCATACCAA
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 110 1.00
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (109 bp):
TTTTTAAAAAATTATAATTTTTAAAAAAAATCTAAAAAAATATATAAAAATTTTAAAAATTTTAT
AAAATAATAATTTTGGAATCTAAATGAGTGCTTAATGATTCAAG
Found at i:26462 original size:19 final size:19
Alignment explanation
Indices: 26438--26476 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
26428 CAAACGCTTT
26438 AATCCGAGCAATCCAGCAA
1 AATCCGAGCAATCCAGCAA
26457 AATCCGAGCAATCCAGCAA
1 AATCCGAGCAATCCAGCAA
26476 A
1 A
26477 TGCTGCAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.31, G:0.15, T:0.10
Consensus pattern (19 bp):
AATCCGAGCAATCCAGCAA
Found at i:28769 original size:43 final size:43
Alignment explanation
Indices: 28691--28775 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 43
28681 AGGTACAGCG
* *
28691 GACACACAGGCGTGTGCCAGACCGTCTGTGTATACTATTTTGA
1 GACACACAGGCGTGTGCCAGACCGTCTGAGCATACTATTTTGA
* * * *
28734 GACACA-AGGGCGTGTGTCAGGCCGTGTGAGCATACTGTTTTG
1 GACACACA-GGCGTGTGCCAGACCGTCTGAGCATACTATTTTG
28776 CTATTAAAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
42 1 0.03
43 34 0.97
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (43 bp):
GACACACAGGCGTGTGCCAGACCGTCTGAGCATACTATTTTGA
Found at i:34508 original size:42 final size:42
Alignment explanation
Indices: 34445--34529 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
34435 ATTTTAGGCA
*
34445 AGATATTAGCTTTTCACAGTACTCGCCTTCCTTCTTTACATC
1 AGATATTAGCTTTTCACAGTACTCGCCTTCCTCCTTTACATC
* * *
34487 AGATATTGGCTTTTCATAGTACTCGTCTTCCTCCTTTACATC
1 AGATATTAGCTTTTCACAGTACTCGCCTTCCTCCTTTACATC
34529 A
1 A
34530 TCAAGCACGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.41
Consensus pattern (42 bp):
AGATATTAGCTTTTCACAGTACTCGCCTTCCTCCTTTACATC
Found at i:36941 original size:30 final size:28
Alignment explanation
Indices: 36871--36941 Score: 70
Period size: 30 Copynumber: 2.4 Consensus size: 28
36861 AGTAATTTAT
*
36871 ATTTTTATAATTTTTAAAAAATTAAATAAA
1 ATTTTT-T-ATTTTTAAAAAATAAAATAAA
* *
36901 TTTTTATTATTTTTAAAGAATCAAAATATAA
1 ATTTT-TTATTTTTAAAAAAT-AAAATA-AA
36932 ATTTTTTATT
1 ATTTTTTATT
36942 AATTTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 12 0.35
30 15 0.44
31 7 0.21
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
ATTTTTTATTTTTAAAAAATAAAATAAA
Found at i:41776 original size:100 final size:101
Alignment explanation
Indices: 41602--41798 Score: 317
Period size: 100 Copynumber: 2.0 Consensus size: 101
41592 GGAACAGTTT
* *
41602 ACAAGTAGGTTACGTTAAAGAAATTCCATTCTTGATTTATTTCATGAGTTAATGCATGATTGGTA
1 ACAAGTAGGTTACATTAAAGAAATTCCATTCTTGATTTATTTCATGAGTTAATGCATGATTGCTA
* *
41667 CTGAAAAAAAGTTGTAAAGATTATCCTAGGTTCTCC
66 CTGAAAAAAAGATGTAAAGATTATCCAAGGTTCTCC
*
41703 ACAAGTAGGTTACATTAAAG-AATTTCATTCTTGATTTATTTCATGAGTTAATGCA-GTATTGCT
1 ACAAGTAGGTTACATTAAAGAAATTCCATTCTTGATTTATTTCATGAGTTAATGCATG-ATTGCT
*
41766 ATTGAAAAAAAGATGTAAAGATTATCCAAGGTT
65 ACTGAAAAAAAGATGTAAAGATTATCCAAGGTT
41799 TCCCTAGAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
99 1 0.01
100 69 0.78
101 19 0.21
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (101 bp):
ACAAGTAGGTTACATTAAAGAAATTCCATTCTTGATTTATTTCATGAGTTAATGCATGATTGCTA
CTGAAAAAAAGATGTAAAGATTATCCAAGGTTCTCC
Found at i:48160 original size:28 final size:28
Alignment explanation
Indices: 48128--48185 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
48118 AAGATTAGAG
48128 AAATGATTTAAAAGGAAAATGGTTAATT
1 AAATGATTTAAAAGGAAAATGGTTAATT
48156 AAATGATTTAAAAGGAAAATGGTTAATT
1 AAATGATTTAAAAGGAAAATGGTTAATT
48184 AA
1 AA
48186 TTAATTTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (28 bp):
AAATGATTTAAAAGGAAAATGGTTAATT
Found at i:48192 original size:28 final size:28
Alignment explanation
Indices: 48128--48192 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
48118 AAGATTAGAG
*
48128 AAATGATTTAAAAGGAAAATGGTTAATT
1 AAATAATTTAAAAGGAAAATGGTTAATT
*
48156 AAATGATTTAAAAGGAAAATGGTTAATT
1 AAATAATTTAAAAGGAAAATGGTTAATT
*
48184 AATTAATTT
1 AAATAATTT
48193 GCAAGAGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.15, T:0.35
Consensus pattern (28 bp):
AAATAATTTAAAAGGAAAATGGTTAATT
Found at i:50236 original size:18 final size:21
Alignment explanation
Indices: 50215--50253 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
50205 CAATAATATA
50215 ATTT-AATA-ATA-TAAAAAT
1 ATTTAAATATATATTAAAAAT
50233 ATTTAAATATATATTAAAAAT
1 ATTTAAATATATATTAAAAAT
50254 GAAAAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 3 0.17
21 7 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTTAAATATATATTAAAAAT
Found at i:52370 original size:2 final size:2
Alignment explanation
Indices: 52363--52394 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
52353 TTCCTTTCAA
52363 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
52395 TTATTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53963 original size:31 final size:32
Alignment explanation
Indices: 53891--53965 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
53881 GATCCAATTT
* *
53891 GGTACTCAAACTTAACATTTTTTCTTAATTTA
1 GGTACTTAAACTTAACATTTTTTCTTAATGTA
* *
53923 -GTACCTAAACTTGACACTTTTTT-TTAA-GTA
1 GGTACTTAAACTTAACA-TTTTTTCTTAATGTA
53953 GGTACTTAAACTT
1 GGTACTTAAACTT
53966 TTTAAGATCC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 2 0.06
31 28 0.78
32 6 0.17
ACGTcount: A:0.31, C:0.16, G:0.09, T:0.44
Consensus pattern (32 bp):
GGTACTTAAACTTAACATTTTTTCTTAATGTA
Found at i:54173 original size:30 final size:29
Alignment explanation
Indices: 54137--54206 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
54127 TTAATAAATA
*
54137 TAGGTACTAAATTGAATCTAAAAAAAAGTT
1 TAGGTACTAAATTGAAT-AAAAAAAAAGTT
* **
54167 TAGGTACCAAATTGGGTAAAAAAAAAGTT
1 TAGGTACTAAATTGAATAAAAAAAAAGTT
*
54196 TATGTATCTAA
1 TAGGTA-CTAA
54207 TTAAAAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.30
Consensus pattern (29 bp):
TAGGTACTAAATTGAATAAAAAAAAAGTT
Found at i:55835 original size:20 final size:21
Alignment explanation
Indices: 55810--55849 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55800 AAAACGTATA
55810 AAAATAAC-ATCAAAACAACC
1 AAAATAACAATCAAAACAACC
55830 AAAATAACAATCAAAACAAC
1 AAAATAACAATCAAAACAAC
55850 AGTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.68, C:0.23, G:0.00, T:0.10
Consensus pattern (21 bp):
AAAATAACAATCAAAACAACC
Found at i:55883 original size:44 final size:44
Alignment explanation
Indices: 55808--55894 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 44
55798 TAAAAACGTA
* *
55808 TAAAAATAACATCAAAACAACCAAAATAACAATC-AAAACAACAG
1 TAAAAATAACAGCAAAACAACCAAAAAAACAA-CAAAAACAACAG
* *
55852 TAAAAATAATAGCAAAGCAA-CAACAAAAACAACAAAAACAACA
1 TAAAAATAACAGCAAAACAACCAA-AAAAACAACAAAAACAACA
55895 AAATAGCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.68, C:0.20, G:0.03, T:0.09
Consensus pattern (44 bp):
TAAAAATAACAGCAAAACAACCAAAAAAACAACAAAAACAACAG
Found at i:55884 original size:9 final size:9
Alignment explanation
Indices: 55870--55897 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
55860 ATAGCAAAGC
55870 AACAACAAA
1 AACAACAAA
55879 AACAACAAA
1 AACAACAAA
55888 AACAACAAA
1 AACAACAAA
55897 A
1 A
55898 TAGCAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (9 bp):
AACAACAAA
Found at i:55934 original size:20 final size:20
Alignment explanation
Indices: 55911--55964 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 20
55901 CAAAAATAAT
55911 AACAATAAAAACAACACCAA
1 AACAATAAAAACAACACCAA
* *
55931 AACAGTAAAAAAAACAGCACCAA
1 AAC---AATAAAAACAACACCAA
55954 AACAATAAAAA
1 AACAATAAAAA
55965 ATGCATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 10 0.36
23 18 0.64
ACGTcount: A:0.70, C:0.20, G:0.04, T:0.06
Consensus pattern (20 bp):
AACAATAAAAACAACACCAA
Found at i:55951 original size:23 final size:23
Alignment explanation
Indices: 55917--55965 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
55907 TAATAACAAT
*
55917 AAAAACAACACCAAAACAGTAAA
1 AAAAACAACACCAAAACAATAAA
*
55940 AAAAACAGCACCAAAACAATAAA
1 AAAAACAACACCAAAACAATAAA
55963 AAA
1 AAA
55966 TGCATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.71, C:0.20, G:0.04, T:0.04
Consensus pattern (23 bp):
AAAAACAACACCAAAACAATAAA
Found at i:55958 original size:43 final size:42
Alignment explanation
Indices: 55911--56003 Score: 116
Period size: 43 Copynumber: 2.2 Consensus size: 42
55901 CAAAAATAAT
*
55911 AACAATAAAAACA-ACACCAAAACAGTAAAAAAAACAGCACCAA
1 AACAATAAAAA-ATACACCAAAACAGTAAAAAAAA-AGCACAAA
* * * *
55954 AACAATAAAAAATGCATCAAAATAGTAAAAAAAAAGTACAAA
1 AACAATAAAAAATACACCAAAACAGTAAAAAAAAAGCACAAA
55996 AACAATAA
1 AACAATAA
56004 TATAATTTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
42 15 0.34
43 29 0.66
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (42 bp):
AACAATAAAAAATACACCAAAACAGTAAAAAAAAAGCACAAA
Found at i:57058 original size:29 final size:30
Alignment explanation
Indices: 57026--57093 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
57016 TATAGTTTAA
* *
57026 TGTGTAATTGTATATATG-AACTTTGATTT
1 TGTGCAATTGTATACATGAAACTTTGATTT
* *
57055 TGTGCAATTTTATACATGAAATTTTGA-TT
1 TGTGCAATTGTATACATGAAACTTTGATTT
57084 TGATGCAATT
1 TG-TGCAATT
57094 TTTGTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (30 bp):
TGTGCAATTGTATACATGAAACTTTGATTT
Found at i:58129 original size:18 final size:17
Alignment explanation
Indices: 58102--58141 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
58092 GAGGTCGAAA
58102 TTAA-AGTTTATATCATT
1 TTAATAGTTTATAT-ATT
58119 TTAATAGTTTATATATT
1 TTAATAGTTTATATATT
58136 TATAAT
1 T-TAAT
58142 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (17 bp):
TTAATAGTTTATATATT
Found at i:58165 original size:28 final size:30
Alignment explanation
Indices: 58134--58193 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 30
58124 AGTTTATATA
58134 TTTATAATTTTAAAAAA-TAAAATA-AATT
1 TTTATAATTTTAAAAAATTAAAATACAATT
*
58162 TTTATTATTTTAAAAAATTAAAATACAATT
1 TTTATAATTTTAAAAAATTAAAATACAATT
58192 TT
1 TT
58194 ATTATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 16 0.55
29 7 0.24
30 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
TTTATAATTTTAAAAAATTAAAATACAATT
Found at i:58193 original size:29 final size:28
Alignment explanation
Indices: 58134--58203 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 28
58124 AGTTTATATA
*
58134 TTTATAATTTTAAAAAATAAAATAAATT
1 TTTATTATTTTAAAAAATAAAATAAATT
58162 TTTATTATTTTAAAAAATTAAAATACAA-T
1 TTTATTATTTTAAAAAA-TAAAATA-AATT
*
58191 TTTATTATATTAA
1 TTTATTATTTTAA
58204 TTTAGAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 16 0.42
29 20 0.53
30 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTATTATTTTAAAAAATAAAATAAATT
Found at i:59226 original size:3 final size:3
Alignment explanation
Indices: 59218--59260 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
59208 TTACCTTATC
59218 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
59261 TGTTAGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:71209 original size:30 final size:30
Alignment explanation
Indices: 71175--71231 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
71165 GTGGTGGGCT
*
71175 GATGATA-GCTATGGTGAGGGGGGGAGGTTG
1 GATGATATGC-ATGATGAGGGGGGGAGGTTG
*
71205 GATGATATGCATGATGAGGTGGGGAGG
1 GATGATATGCATGATGAGGGGGGGAGG
71232 GGGAACTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.23, C:0.04, G:0.51, T:0.23
Consensus pattern (30 bp):
GATGATATGCATGATGAGGGGGGGAGGTTG
Found at i:78100 original size:3 final size:3
Alignment explanation
Indices: 78092--78119 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
78082 CAATATATTC
78092 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
78120 TAGAATTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:97796 original size:34 final size:34
Alignment explanation
Indices: 97753--97822 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
97743 CAAATTGAAT
97753 AACCAATCTAGCAAGCTCAGGTTATTAAGCATCA
1 AACCAATCTAGCAAGCTCAGGTTATTAAGCATCA
97787 AACCAATCTAGCAAGCTCAGGTTATTAAGCATCA
1 AACCAATCTAGCAAGCTCAGGTTATTAAGCATCA
97821 AA
1 AA
97823 GAATGCGTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.40, C:0.23, G:0.14, T:0.23
Consensus pattern (34 bp):
AACCAATCTAGCAAGCTCAGGTTATTAAGCATCA
Done.