Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012271.1 Kokia drynarioides strain JFW-HI SEQ_127272, 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: 121506
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Warning! 103 characters in sequence are not A, C, G, or T
Found at i:1055 original size:96 final size:96
Alignment explanation
Indices: 871--1062 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
861 TTTTTGGGAA
* ** *
871 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATAATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
936 GAATCGAATATAAGGAAACATTGCCTCGATT
66 GAATCGAATATAAGAAAACATTGCCTAGATT
* *
967 AAGGGTATTCGATAATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATAATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
*
1031 -GAAACTCGAA-ATAA-AATAATATTGCCTAGATT
65 AG-AA-TCGAATATAAGAA-AACATTGCCTAGATT
1063 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 3 0.04
96 75 0.90
97 5 0.06
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATAATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAATATAAGAAAACATTGCCTAGATT
Found at i:1338 original size:30 final size:30
Alignment explanation
Indices: 1303--1677 Score: 272
Period size: 30 Copynumber: 12.7 Consensus size: 30
1293 GCAAAATGAT
*
1303 AATTTTGGGAAAGTTTAGGGTTAAAAATGG
1 AATTTTTGGAAAGTTTAGGGTTAAAAATGG
* * *
1333 AATTTTTAGACA--TTCGAGGTTAAAAATGG
1 AATTTTTGGAAAGTTTAG-GGTTAAAAATGG
*
1362 AATTTTT-GAAAGTTTTAGGGTAAAAAATGG
1 AATTTTTGGAAAG-TTTAGGGTTAAAAATGG
* * * *
1392 AAATGTTGG-AAGTTTTGGGGTCAAAAATGG
1 AATTTTTGGAAAG-TTTAGGGTTAAAAATGG
* * *
1422 AATTTTTAG-AATTTTAGGGGTAAAAATGG
1 AATTTTTGGAAAGTTTAGGGTTAAAAATGG
* * *
1451 AATTTTTTGAAA-TTTCGGGGTCAAAAATGG
1 AATTTTTGGAAAGTTT-AGGGTTAAAAATGG
** * *
1481 AATTTTTGG-AAGCTCGATGG-TAAAAATGA
1 AATTTTTGGAAAG-TTTAGGGTTAAAAATGG
1510 AATTTTTGG-AAGTTTTAGGGTTAAAAATGG
1 AATTTTTGGAAAG-TTTAGGGTTAAAAATGG
* * * *
1540 AACTTTTGG-AAGCTTGGGGGTAAAAATGG
1 AATTTTTGGAAAGTTTAGGGTTAAAAATGG
* * * *
1569 AATTTTTGGAAATTTTGGGGTCAAAAATAG
1 AATTTTTGGAAAGTTTAGGGTTAAAAATGG
* *
1599 AATTTTTGG-AAGTTTCGAGGTTGAAAATGG
1 AATTTTTGGAAAGTTTAG-GGTTAAAAATGG
* * *
1629 AATTTTT-GAAAG-TTCGGGAGTAAAAATAG
1 AATTTTTGGAAAGTTTAGGG-TTAAAAATGG
** *
1658 AATTTTCAGATAGTTTAGGG
1 AATTTTTGGAAAGTTTAGGG
1678 ACCTTCAGGG
Statistics
Matches: 274, Mismatches: 55, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
28 8 0.03
29 115 0.42
30 141 0.51
31 10 0.04
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AATTTTTGGAAAGTTTAGGGTTAAAAATGG
Found at i:1388 original size:59 final size:57
Alignment explanation
Indices: 1311--1677 Score: 299
Period size: 59 Copynumber: 6.2 Consensus size: 57
1301 ATAATTTTGG
* * * *
1311 GAAAGTTTAGGGTTAAAAATGGAATTTTTAGACA-TTCGAGGTTAAAAATGGAATTTTT
1 GAAAGTTTAGGG-TAAAAATGGAATTTTTGGA-ATTTTGGGGTCAAAAATGGAATTTTT
* *
1369 GAAAGTTTTAGGGTAAAAAATGGAAATGTTGGAAGTTTTGGGGTCAAAAATGGAATTTTT
1 GAAAG-TTTAGGGT-AAAAATGGAATTTTTGGAA-TTTTGGGGTCAAAAATGGAATTTTT
* * *
1429 -AGAATTTTAGGGGTAAAAATGGAATTTTTTGAAATTTCGGGGTCAAAAATGGAATTTTT
1 GA-AAGTTTA-GGGTAAAAATGGAA-TTTTTGGAATTTTGGGGTCAAAAATGGAATTTTT
* ** * * * * *
1488 GGAAGCTCGATGGTAAAAATGAAATTTTTGGAAGTTTTAGGGTTAAAAATGGAACTTTT
1 GAAAG-TTTAGGGTAAAAATGGAATTTTTGGAA-TTTTGGGGTCAAAAATGGAATTTTT
* ** *
1547 GGAAGCTTGGGGGTAAAAATGGAATTTTTGGAAATTTTGGGGTCAAAAATAGAATTTTT
1 GAAAG-TTTAGGGTAAAAATGGAATTTTTGG-AATTTTGGGGTCAAAAATGGAATTTTT
* * * * * * * *
1606 GGAAGTTTCGAGGTTGAAAATGGAATTTTTGAAAGTTCGGGAGT-AAAAATAGAATTTTCA
1 GAAAGTTT--AGGGTAAAAATGGAATTTTTGGAATTTTGGG-GTCAAAAATGGAATTTT-T
*
1666 GATAGTTTAGGG
1 GAAAGTTTAGGG
1678 ACCTTCAGGG
Statistics
Matches: 253, Mismatches: 41, Indels: 30
0.78 0.13 0.09
Matches are distributed among these distances:
58 20 0.08
59 170 0.67
60 63 0.25
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (57 bp):
GAAAGTTTAGGGTAAAAATGGAATTTTTGGAATTTTGGGGTCAAAAATGGAATTTTT
Found at i:1428 original size:89 final size:89
Alignment explanation
Indices: 1303--1663 Score: 353
Period size: 89 Copynumber: 4.1 Consensus size: 89
1293 GCAAAATGAT
* * *
1303 AATTTTGGGAAAG-TTTAGGGTTAAAAATGGAATTTTTAGACA-TTCGA-GGTTAAAAATGGAAT
1 AATTTTTGG-AAGTTTTGGGGTCAAAAATGGAATTTTTAGA-AGTTCGAGGGTTAAAAATGGAAT
**
1365 TTTTGAAAGTTTTAGGGTAAAAAATGG
64 TTTTGAAAGTTTCGGGGT-AAAAATGG
* * ** *
1392 AAATGTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAA-TTTTAGGGGTAAAAATGGAATTT
1 AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAGTTCGAGGGTTAAAAATGGAA-TT
1456 TTTGAAA-TTTCGGGGTCAAAAATGG
65 TTTGAAAGTTTCGGGGT-AAAAATGG
* * * * * ** *
1481 AATTTTTGGAAG-CTCGATGGT-AAAAATGAAATTTTTGGAAGTTTTAGGGTTAAAAATGGAACT
1 AATTTTTGGAAGTTTTG-GGGTCAAAAATGGAATTTTTAGAAGTTCGAGGGTTAAAAATGGAATT
* * *
1544 TTTGGAAGCTTGGGGGTAAAAATGG
65 TTTGAAAGTTTCGGGGTAAAAATGG
* * * *
1569 AATTTTTGGAAATTTTGGGGTCAAAAATAGAATTTTTGGAAGTTTCGA-GGTTGAAAATGGAATT
1 AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAG-TTCGAGGGTTAAAAATGGAATT
*
1633 TTTGAAAG-TTCGGGAGTAAAAATAG
65 TTTGAAAGTTTCGGG-GTAAAAATGG
1658 AATTTT
1 AATTTT
1664 CAGATAGTTT
Statistics
Matches: 226, Mismatches: 36, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
88 60 0.27
89 154 0.68
90 12 0.05
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (89 bp):
AATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTAGAAGTTCGAGGGTTAAAAATGGAATTT
TTGAAAGTTTCGGGGTAAAAATGG
Found at i:2693 original size:21 final size:20
Alignment explanation
Indices: 2647--2699 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
2637 TAATAATATT
**
2647 ATTATTATTATTAGTAAGGC
1 ATTATTATTATTAAAAAGGC
*
2667 AGTTATTATTATTAAAAACGTC
1 A-TTATTATTATTAAAAA-GGC
2689 ATTATTATTAT
1 ATTATTATTAT
2700 AGATATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.86
22 3 0.11
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (20 bp):
ATTATTATTATTAAAAAGGC
Found at i:2721 original size:15 final size:15
Alignment explanation
Indices: 2670--2725 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
2660 GTAAGGCAGT
*
2670 TATTATTATTAAAAAC
1 TATTATTATT-AATAC
*
2686 GTCATTATTATT-ATAGA
1 -T-ATTATTATTAATA-C
2703 TATTATTATTAATAC
1 TATTATTATTAATAC
2718 TATTATTA
1 TATTATTA
2726 AATACGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
15 17 0.52
16 6 0.18
17 1 0.03
18 9 0.27
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (15 bp):
TATTATTATTAATAC
Found at i:3399 original size:12 final size:11
Alignment explanation
Indices: 3383--3453 Score: 63
Period size: 11 Copynumber: 6.2 Consensus size: 11
3373 ATAATAAGTT
*
3383 TTAAATATAAA
1 TTAAATTTAAA
3394 TCTAAATTTAAA
1 T-TAAATTTAAA
3406 TTAAATTTAAA
1 TTAAATTTAAA
**
3417 TTTTAAA-ACAAA
1 --TTAAATTTAAA
3429 TTTAAATTTAAA
1 -TTAAATTTAAA
*
3441 ATAAATTTAAA
1 TTAAATTTAAA
3452 TT
1 TT
3454 CAAAATCAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
11 28 0.57
12 16 0.33
13 5 0.10
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:3416 original size:17 final size:17
Alignment explanation
Indices: 3382--3486 Score: 122
Period size: 17 Copynumber: 6.0 Consensus size: 17
3372 TATAATAAGT
*
3382 TTTAAATATAAATCTAAA
1 TTTAAA-ATAAATTTAAA
*
3400 TTTAAATTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
3417 TTTTAAAACAAATTTAAA
1 -TTTAAAATAAATTTAAA
3435 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
3452 TTCAAAATCAATTT-AA
1 TTTAAAATAAATTTAAA
3468 TCTTAAAATAAATCTTAAA
1 T-TTAAAATAAAT-TTAAA
3487 ATGGGTTTAA
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
16 3 0.04
17 46 0.62
18 23 0.31
19 2 0.03
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:3423 original size:7 final size:6
Alignment explanation
Indices: 3382--3453 Score: 69
Period size: 6 Copynumber: 12.3 Consensus size: 6
3372 TATAATAAGT
* * **
3382 TTTAAA TATAAA TCTAAA TTTAAA -TTAAA TTTAAA TTTTAAA -ACAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA
*
3429 TTTAAA TTTAAA -ATAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
3454 CAAAATCAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
5 12 0.23
6 35 0.66
7 6 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:17458 original size:2 final size:2
Alignment explanation
Indices: 17451--17477 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17441 TTGTGCACTG
17451 AT 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 AT A
17478 AAGATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18180 original size:12 final size:12
Alignment explanation
Indices: 18165--18190 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18155 TGGTGGCTAA
18165 AGCGGTGGTCAG
1 AGCGGTGGTCAG
18177 AGCGGTGGTCAG
1 AGCGGTGGTCAG
18189 AG
1 AG
18191 GCTTGGGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.50, T:0.15
Consensus pattern (12 bp):
AGCGGTGGTCAG
Found at i:23390 original size:18 final size:18
Alignment explanation
Indices: 23367--23406 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
23357 AAATCATGCC
23367 AACTACCAGGCAGGCAGG
1 AACTACCAGGCAGGCAGG
23385 AACTACCAGGCAGGCAGG
1 AACTACCAGGCAGGCAGG
23403 AACT
1 AACT
23407 GATGCCTCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.30, T:0.07
Consensus pattern (18 bp):
AACTACCAGGCAGGCAGG
Found at i:29724 original size:16 final size:16
Alignment explanation
Indices: 29703--29739 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
29693 TAAATAATAA
*
29703 AATATTATTATTTATT
1 AATATTATTATTAATT
29719 AATATTATTATTAATT
1 AATATTATTATTAATT
29735 AATAT
1 AATAT
29740 ATCATTTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
AATATTATTATTAATT
Found at i:44153 original size:6 final size:6
Alignment explanation
Indices: 44142--44167 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
44132 TTAGATCTTT
44142 AAGCAA AAGCAA AAGCAA AAGCAA AA
1 AAGCAA AAGCAA AAGCAA AAGCAA AA
44168 ACCACATCTT
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:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGCAA
Found at i:56349 original size:24 final size:25
Alignment explanation
Indices: 56322--56368 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
56312 CAAAATAACT
56322 AAAAAAATAAA-GATAAAATTAATA
1 AAAAAAATAAACGATAAAATTAATA
* *
56346 AAAAATATAAACGTTAAAATTAA
1 AAAAAAATAAACGATAAAATTAA
56369 ATTTATGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAAAAATAAACGATAAAATTAATA
Found at i:56363 original size:25 final size:24
Alignment explanation
Indices: 56313--56368 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 24
56303 AATTGAGAAC
56313 AAAA-TAACTAAAAAAATAAAGAT
1 AAAATTAACTAAAAAAATAAAGAT
*
56336 AAAATTAA-TAAAAAATATAAACGTT
1 AAAATTAACTAAAAAA-ATAAA-GAT
56361 AAAATTAA
1 AAAATTAA
56369 ATTTATGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 11 0.38
24 8 0.28
25 10 0.34
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (24 bp):
AAAATTAACTAAAAAAATAAAGAT
Found at i:56816 original size:41 final size:41
Alignment explanation
Indices: 56672--56938 Score: 150
Period size: 41 Copynumber: 6.5 Consensus size: 41
56662 ATAAACCCCA
* * *
56672 TAAAAGAT-AAAGCAATAGCGGCATTTATAGGAAAAGCGCCGC
1 TAAAAG-TCAAAGCATTAGCGGCGTTTATGGGAAAA-CGCCGC
* * * * * * * *
56714 TAAAGGTTAGAGCATCAGCGGTGTTTATGGGGAAGCGCCAC
1 TAAAAGTCAAAGCATTAGCGGCGTTTATGGGAAAACGCCGC
* * * * * *
56755 TAAAGGTCAGAGAATAAGCGGCGTTTATGGGAAAACACCGT
1 TAAAAGTCAAAGCATTAGCGGCGTTTATGGGAAAACGCCGC
* *
56796 TAAAAGTCAAAGCATTAGCGGCGCTTTCT--AATAAACGCCGC
1 TAAAAGTCAAAGCATTAGCGGCG-TTTATGGGA-AAACGCCGC
* * * * * * * *
56837 TAAAGGTTAAAACATTAGCGACGCTTTCT-AGTAAACGCTGC
1 TAAAAGTCAAAGCATTAGCGGCG-TTTATGGGAAAACGCCGC
* * * *
56878 TAAAGGTCAGAGCATTAGCGGC--TTATGAGAAAGCGCCGC
1 TAAAAGTCAAAGCATTAGCGGCGTTTATGGGAAAACGCCGC
* *
56917 TAAAGGTCAGAGCATTAGCGGC
1 TAAAAGTCAAAGCATTAGCGGC
56939 TCTAGCAACG
Statistics
Matches: 178, Mismatches: 42, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
38 3 0.02
39 31 0.17
40 1 0.01
41 115 0.65
42 28 0.16
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.21
Consensus pattern (41 bp):
TAAAAGTCAAAGCATTAGCGGCGTTTATGGGAAAACGCCGC
Found at i:57673 original size:15 final size:15
Alignment explanation
Indices: 57653--57684 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
57643 TAAAAAAATT
57653 ATTAACATTTCTAAA
1 ATTAACATTTCTAAA
*
57668 ATTAACATTTTTAAA
1 ATTAACATTTCTAAA
57683 AT
1 AT
57685 GGCCCTACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTAACATTTCTAAA
Found at i:60647 original size:21 final size:21
Alignment explanation
Indices: 60617--60657 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
60607 AAATTAAAGC
* * *
60617 GGAGGTAGCAGCGAGGGAAGT
1 GGAGGCAGCAACGAGAGAAGT
60638 GGAGGCAGCAACGAGAGAAG
1 GGAGGCAGCAACGAGAGAAG
60658 CGAGGGAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.49, T:0.05
Consensus pattern (21 bp):
GGAGGCAGCAACGAGAGAAGT
Found at i:61092 original size:54 final size:54
Alignment explanation
Indices: 61017--61120 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
61007 GATCATGTTC
* * *
61017 TTTAGCGGCGTTTGTAAGGAAAGCGCCGTTAAAAACCATGTTCTTTAGTGGTTT
1 TTTAGCGGCGTTTGTAAGGAAAACGCCGCTAAAAACCATGTTATTTAGTGGTTT
* ** * * *
61071 TTTAGTGGCGTTTGTGGGGAAAATGTCGCTAAAGACCATGTTATTTAGTG
1 TTTAGCGGCGTTTGTAAGGAAAACGCCGCTAAAAACCATGTTATTTAGTG
61121 ACGTTTGTGG
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 41 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (54 bp):
TTTAGCGGCGTTTGTAAGGAAAACGCCGCTAAAAACCATGTTATTTAGTGGTTT
Found at i:61143 original size:97 final size:97
Alignment explanation
Indices: 60973--61158 Score: 239
Period size: 97 Copynumber: 1.9 Consensus size: 97
60963 AATCTGTTAA
* * *
60973 TTTTAGTGGCGTTTATGGGAAAAACACCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTAAGGAA
1 TTTTAGTGGCGTTTATGGGAAAAACACCGCTAAAGACCATGTTATTTAGCGACGTTTGTAAGGAA
*
61038 AGCGCCGTTAAAAACCATGTTCTTTAGTGGTT
66 AGCACCGTTAAAAACCATGTTCTTTAGTGGTT
* * *** * *
61070 TTTTAGTGGCGTTTGTGGGGAAAATGTCGCTAAAGACCATGTTATTTAGTGACGTTTGT-GGGAA
1 TTTTAGTGGCGTTTATGGGAAAAACACCGCTAAAGACCATGTTATTTAGCGACGTTTGTAAGG-A
* *
61134 AAGTACCGTTAAAAATCATGTTCTT
65 AAGCACCGTTAAAAACCATGTTCTT
61159 CAGCGGTGTT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
96 2 0.03
97 73 0.97
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.34
Consensus pattern (97 bp):
TTTTAGTGGCGTTTATGGGAAAAACACCGCTAAAGACCATGTTATTTAGCGACGTTTGTAAGGAA
AGCACCGTTAAAAACCATGTTCTTTAGTGGTT
Found at i:61154 original size:43 final size:43
Alignment explanation
Indices: 61071--61255 Score: 142
Period size: 43 Copynumber: 4.3 Consensus size: 43
61061 TTAGTGGTTT
* *
61071 TTTAGTGGCGTTTGTGGGGAAAATGTCGCTAAAGACCATGTTA
1 TTTAGTGACGTTTGTGGGGAAAATGTCGCTAAAAACCATGTTA
* * *
61114 TTTAGTGACGTTTGT-GGGAAAA-GTACCGTTAAAAATCATGTTC
1 TTTAGTGACGTTTGTGGGGAAAATGT--CGCTAAAAACCATGTTA
* * ** * ** * * *
61157 TTCAGCGGTGTTTATGGGGAAAGCGTCGTTAAAGACCATGTTC
1 TTTAGTGACGTTTGTGGGGAAAATGTCGCTAAAAACCATGTTA
* * * *
61200 TTTAGCGACGTTTGTGGGGAAAACG-CTGCTAAAGACCATGTTT
1 TTTAGTGACGTTTGTGGGGAAAATGTC-GCTAAAAACCATGTTA
*
61243 TTTAGCGACGTTT
1 TTTAGTGACGTTT
61256 AATGAAAAGT
Statistics
Matches: 117, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
41 2 0.02
42 8 0.07
43 99 0.85
44 6 0.05
45 2 0.02
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.33
Consensus pattern (43 bp):
TTTAGTGACGTTTGTGGGGAAAATGTCGCTAAAAACCATGTTA
Found at i:61256 original size:86 final size:85
Alignment explanation
Indices: 61067--61256 Score: 211
Period size: 86 Copynumber: 2.2 Consensus size: 85
61057 TTCTTTAGTG
* * * *
61067 GTTTTTTAGTGGCGTTTGTGGGGAAAATGTCGCTAAAGACCATGTTATTTAGTGACGTTTGTGGG
1 GTTTTTTAGCGGCGTTTATGGGGAAAACGTCGCTAAAGACCATGTTATTTAGCGACGTTTGTGGG
* *
61132 AAAAGTACCGTTAAAAATCAT
66 AAAAG-ACCGCTAAAAACCAT
* * * * * *
61153 GTTCTTCAGCGGTGTTTATGGGGAAAGCGTCGTTAAAGACCATGTTCTTTAGCGACGTTTGTGGG
1 GTTTTTTAGCGGCGTTTATGGGGAAAACGTCGCTAAAGACCATGTTATTTAGCGACGTTTGT-GG
* *
61218 GAAAACG-CTGCTAAAGACCAT
65 GAAAA-GACCGCTAAAAACCAT
*
61239 GTTTTTTAGCGACGTTTA
1 GTTTTTTAGCGGCGTTTA
61257 ATGAAAAGTG
Statistics
Matches: 84, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
86 76 0.90
87 7 0.08
88 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.27, T:0.34
Consensus pattern (85 bp):
GTTTTTTAGCGGCGTTTATGGGGAAAACGTCGCTAAAGACCATGTTATTTAGCGACGTTTGTGGG
AAAAGACCGCTAAAAACCAT
Found at i:62382 original size:28 final size:30
Alignment explanation
Indices: 62328--62383 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
62318 TCGTGAGTGG
**
62328 TCACACAACTTTTAAAACTTTTCAATTTCA
1 TCACACAACTTTTAAAACTTTAAAATTTCA
*
62358 TCAC-CAATTTTTAAAA-TTTAAAATTT
1 TCACACAACTTTTAAAACTTTAAAATTT
62384 TAGTCTCTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.35
29 11 0.48
30 4 0.17
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (30 bp):
TCACACAACTTTTAAAACTTTAAAATTTCA
Found at i:70479 original size:21 final size:20
Alignment explanation
Indices: 70433--70488 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 20
70423 CTCAATAATC
*
70433 ATTAATAATAATAA-ATGTT
1 ATTAATAATAATAATATATT
*
70452 -TTCATAATAATAATATTATT
1 ATTAATAATAATAATA-TATT
70472 ATTAATAATAATTAATA
1 ATTAATAATAA-TAATA
70489 AAAAAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 12 0.40
19 1 0.03
20 3 0.10
21 9 0.30
22 5 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
ATTAATAATAATAATATATT
Found at i:71600 original size:30 final size:29
Alignment explanation
Indices: 71544--71716 Score: 188
Period size: 30 Copynumber: 5.8 Consensus size: 29
71534 CCATAAATTG
* *
71544 CATTTTTACCCTCG-AACTTTCGAAAATCC
1 CATTTTTACCC-CGAAACTTCCAAAAATCC
* *
71573 TATTTTTGACCCCGAAACTTCCAAAAATTC
1 CATTTTT-ACCCCGAAACTTCCAAAAATCC
71603 CATTTTTACCCTCG-AACTTCCAAAAATCC
1 CATTTTTACCC-CGAAACTTCCAAAAATCC
*
71632 CATTTTTGACCCCAAAACTTCCAAAAATCC
1 CATTTTT-ACCCCGAAACTTCCAAAAATCC
* * *
71662 CATTTTTTTACCTCGAAACTTTCAAAAATCT
1 CA--TTTTTACCCCGAAACTTCCAAAAATCC
*
71693 CGTTTTTACCCCCGAAACTTCCAA
1 CATTTTTA-CCCCGAAACTTCCAA
71717 GAATTACCAT
Statistics
Matches: 122, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
29 40 0.33
30 58 0.48
31 19 0.16
32 5 0.04
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (29 bp):
CATTTTTACCCCGAAACTTCCAAAAATCC
Found at i:71630 original size:59 final size:59
Alignment explanation
Indices: 71527--71729 Score: 241
Period size: 59 Copynumber: 3.4 Consensus size: 59
71517 AGAGGTCCCT
* * *
71527 AAACTATCCATAAATTGCATTTTTACCCTCGAACTTTCGAAAATCCTATTTTTGACCCCG
1 AAACT-TCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCTATTTTTGACCCCG
* * *
71587 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCTATTTTTGACCCCG
* *
71646 AAACTTCCAAAAATCCCATTTTTTTA-CCTCGAAACTTTCAAAAAT-CTCGTTTTT-ACCCCCG
1 AAACTTCCAAAAATTCCA--TTTTTACCCTCG-AACTTTCAAAAATCCT-ATTTTTGA-CCCCG
*
71707 AAACTTCCAAGAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
71730 GCCCCCGGGT
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
59 65 0.52
60 16 0.13
61 40 0.32
62 3 0.02
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTTCAAAAATCCTATTTTTGACCCCG
Found at i:71736 original size:30 final size:29
Alignment explanation
Indices: 71527--71729 Score: 148
Period size: 30 Copynumber: 6.7 Consensus size: 29
71517 AGAGGTCCCT
*
71527 AAACTATCCATAAATTGCATTTTT-ACCCTCG
1 AAACT-TCCA-AAATTCCATTTTTGACCC-CG
*
71558 -AACTTTCGAAAA-TCCTATTTTTGACCCCG
1 AAAC-TTCCAAAATTCC-ATTTTTGACCCCG
71587 AAACTTCCAAAAATTCCATTTTT-ACCCTCG
1 AAACTTCC-AAAATTCCATTTTTGACCC-CG
* *
71617 -AACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCC-AAAATTCCATTTTTGACCCCG
* * *
71646 AAACTTCCAAAAATCCCATTTTTTTACCTCG
1 AAACTTCC-AAAATTCCA-TTTTTGACCCCG
* * *
71677 AAACTTTCAAAAATCTCGTTTTT-ACCCCCG
1 AAACTTCCAAAATTC-CATTTTTGA-CCCCG
71707 AAACTTCCAAGAATTACCATTTT
1 AAACTTCCAA-AATT-CCATTTT
71730 GCCCCCGGGT
Statistics
Matches: 142, Mismatches: 16, Indels: 28
0.76 0.09 0.15
Matches are distributed among these distances:
28 2 0.01
29 41 0.29
30 69 0.49
31 29 0.20
32 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAATTCCATTTTTGACCCCG
Found at i:79889 original size:17 final size:16
Alignment explanation
Indices: 79866--79926 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
79856 TTAATAAAAT
79866 TTAATATTAAATTTAA
1 TTAATATTAAATTTAA
* *
79882 TCTAATA-TATATCTTGA
1 T-TAATATTAAAT-TTAA
* *
79899 TAAATATTATATTTAA
1 TTAATATTAAATTTAA
79915 TTTAATATTAAA
1 -TTAATATTAAA
79927 GTGAATATGT
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
16 12 0.34
17 23 0.66
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (16 bp):
TTAATATTAAATTTAA
Found at i:80080 original size:25 final size:26
Alignment explanation
Indices: 80030--80081 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
80020 AGTTGTAAAG
*
80030 AGAAAATTCTTTAAAGAGATTATTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
* *
80056 AGAAAATT-TCTAAAGATATTTTTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
80081 A
1 A
80082 TTTATAACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTTT
Found at i:83116 original size:18 final size:18
Alignment explanation
Indices: 83090--83127 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
83080 TAAATTTTCG
83090 AATTCGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
*
83108 AATTTGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
83126 AA
1 AA
83128 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:83356 original size:42 final size:41
Alignment explanation
Indices: 83292--83370 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 41
83282 TATCTTACTC
*
83292 AAATATAATTTCGTTCTTAAAAAAAACTCATAAACTAAACCCA
1 AAATATAATTTCGTTCCT-AAAAAAACTC-TAAACTAAACCCA
*
83335 AAAT-TAATTCTC-TTCCTAAAAAAACTCTAAATTAAA
1 AAATATAATT-TCGTTCCTAAAAAAACTCTAAACTAAA
83371 TAAAAATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
40 8 0.24
41 10 0.30
42 9 0.27
43 6 0.18
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (41 bp):
AAATATAATTTCGTTCCTAAAAAAACTCTAAACTAAACCCA
Found at i:86716 original size:6 final size:6
Alignment explanation
Indices: 86705--86732 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
86695 ACAGAGACAA
86705 GGAGAG GGAGAG GGAGAG GGAGAG GGAG
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAG
86733 CGAAGACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:106525 original size:26 final size:25
Alignment explanation
Indices: 106488--106536 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
106478 ACACCATTAC
*
106488 CCTCTTCCGAGTTCTCAAATATCTTA
1 CCTCTTCCGAGTCCTCAAA-ATCTTA
*
106514 CCTCTTCTGAGTCCTCAAAATCT
1 CCTCTTCCGAGTCCTCAAAATCT
106537 GAATCTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.22, C:0.33, G:0.08, T:0.37
Consensus pattern (25 bp):
CCTCTTCCGAGTCCTCAAAATCTTA
Found at i:118459 original size:20 final size:20
Alignment explanation
Indices: 118434--118473 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
118424 TTATTGAAAA
118434 CTGATTTTTGTTTTTAACTT
1 CTGATTTTTGTTTTTAACTT
118454 CTGATTTTTGTTTTTAACTT
1 CTGATTTTTGTTTTTAACTT
118474 TTACGTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.65
Consensus pattern (20 bp):
CTGATTTTTGTTTTTAACTT
Done.