Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013955.1 Kokia drynarioides strain JFW-HI SEQ_128985, 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: 126830
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2843 original size:46 final size:46
Alignment explanation
Indices: 2767--2865 Score: 153
Period size: 46 Copynumber: 2.2 Consensus size: 46
2757 TCAGTGAACT
*
2767 ATTTCCACCCTTTACACTTGATCACTTTTATATTTCCTACATTTAA
1 ATTTCCACCCTTTACACTTAATCACTTTTATATTTCCTACATTTAA
* * * *
2813 ATTTTCACGCTTTACACTTAATGACTTTTATATTTCCTGCATTTAA
1 ATTTCCACCCTTTACACTTAATCACTTTTATATTTCCTACATTTAA
2859 ATTTCCA
1 ATTTCCA
2866 TTACTCACAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.46
Consensus pattern (46 bp):
ATTTCCACCCTTTACACTTAATCACTTTTATATTTCCTACATTTAA
Found at i:2876 original size:46 final size:46
Alignment explanation
Indices: 2767--2892 Score: 130
Period size: 46 Copynumber: 2.8 Consensus size: 46
2757 TCAGTGAACT
* * *
2767 ATTTCCACCCTTTACACTTGATCACTTTTATATTTCCTACATTTAA
1 ATTTCCACACTTCACACTTAATCACTTTTATATTTCCTACATTTAA
* * * * *
2813 ATTTTCACGCTTTACACTTAATGACTTTTATATTTCCTGCATTTAA
1 ATTTCCACACTTCACACTTAATCACTTTTATATTTCCTACATTTAA
* * *
2859 ATTTCCATTAC-TCACACTCAA-CACTTTTAGATTT
1 ATTTCCA-CACTTCACACTTAATCACTTTTATATTT
2893 ATTTTCAGTA
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
45 11 0.16
46 55 0.82
47 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.04, T:0.45
Consensus pattern (46 bp):
ATTTCCACACTTCACACTTAATCACTTTTATATTTCCTACATTTAA
Found at i:10489 original size:59 final size:59
Alignment explanation
Indices: 10393--10580 Score: 236
Period size: 59 Copynumber: 3.2 Consensus size: 59
10383 ATTTATTTCA
*
10393 AATA-TTTTGTA-AACATTATTTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
1 AATATTTTTGTACAA-ATTAATTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
* * * * *
10451 AATATTTTTGTACAAATTAATATTATATTATTTAATTTAATAAAATAGAAGTTTTTTTT
1 AATATTTTTGTACAAATTAATTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
* * * *
10510 AATATTTTTGTACACATTAGTTTTGGCATATTGTATCATTTAATGAAATAGAAGTTCTTTTG
1 AATATTTTTGTACAAATTAATTTT---ATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
10572 AATATTTTT
1 AATATTTTT
10581 CAACACTCTA
Statistics
Matches: 110, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
58 4 0.04
59 66 0.60
60 2 0.02
62 38 0.35
ACGTcount: A:0.35, C:0.05, G:0.09, T:0.51
Consensus pattern (59 bp):
AATATTTTTGTACAAATTAATTTTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
Found at i:10603 original size:62 final size:60
Alignment explanation
Indices: 10393--10615 Score: 231
Period size: 62 Copynumber: 3.7 Consensus size: 60
10383 ATTTATTTCA
*
10393 AATA-TTTTGTAAACATTATTTT--TATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
1 AATATTTTTGTACAC-TTATTTTGGTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
* * * * * * *
10451 AATATTTTTGTACAAATTAATAT--TATATTATTTAATTTAATAAAATAGAAGTTTTTTTT
1 AATATTTTTGTAC-ACTTATTTTGGTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
* * *
10510 AATATTTTTGTACACATTAGTTTTGGCATATTGTATCATTTAATGAAATAGAAGTTCTTTTG
1 AATATTTTTGTACAC-TTA-TTTTGGTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
** *
10572 AATATTTTTCAACACTCTATTTGTGGTATATTGTTTTATTTAAT
1 AATATTTTTGTACACT-TATTT-TGGTATATTGTTTCATTTAAT
10616 TGAGAACCAA
Statistics
Matches: 134, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
58 5 0.04
59 60 0.45
60 3 0.02
61 4 0.03
62 62 0.46
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (60 bp):
AATATTTTTGTACACTTATTTTGGTATATTGTTTCATTTAATAAAATAGAAGTTCTTTTG
Found at i:22475 original size:25 final size:24
Alignment explanation
Indices: 22430--22478 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
22420 TTTTAAATAA
22430 TTTTAAGAAATTGAAAAATTAATT
1 TTTTAAGAAATTGAAAAATTAATT
*
22454 TTTTAATGAAATAT-AAACATTAATT
1 TTTTAA-GAAAT-TGAAAAATTAATT
22479 ATAAAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 15 0.68
26 1 0.05
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (24 bp):
TTTTAAGAAATTGAAAAATTAATT
Found at i:22922 original size:17 final size:17
Alignment explanation
Indices: 22900--22932 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22890 TTTCAATACC
22900 GTACTAAAATTTTTCAG
1 GTACTAAAATTTTTCAG
*
22917 GTACTAAGATTTTTCA
1 GTACTAAAATTTTTCA
22933 ACCAATATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (17 bp):
GTACTAAAATTTTTCAG
Found at i:26010 original size:18 final size:18
Alignment explanation
Indices: 25987--26033 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
25977 AATCAACCCA
25987 TCATCAATTAGGAAATAG
1 TCATCAATTAGGAAATAG
*
26005 TCATCAATTAGGAATTAG
1 TCATCAATTAGGAAATAG
*
26023 TCGTCAATTAG
1 TCATCAATTAG
26034 AATTTAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (18 bp):
TCATCAATTAGGAAATAG
Found at i:32939 original size:21 final size:21
Alignment explanation
Indices: 32915--32972 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
32905 TAGTGTAGAT
* *
32915 TTCTACCGATACAAGTGACAG
1 TTCTACCAATACAAGTGACAC
* * *
32936 TTCTATCAATAGAAGTGACTC
1 TTCTACCAATACAAGTGACAC
*
32957 CTCTACCAATACAAGT
1 TTCTACCAATACAAGT
32973 TTTGTCTCTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (21 bp):
TTCTACCAATACAAGTGACAC
Found at i:39670 original size:52 final size:52
Alignment explanation
Indices: 39591--39828 Score: 379
Period size: 52 Copynumber: 4.6 Consensus size: 52
39581 GTAAATGAAA
* *
39591 AGGTCTGATGACCAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
39643 AGGTCCGATGACCAAGTGTCATTGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
39695 AGGTCCAATGACTAAGTGTCATCATGAGTATACGAATCCTTTACGGATTATG
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
39747 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
39799 AGGTCCAATGACTATGTGTC-TCGTGAGTAT
1 AGGTCCGATGACTAAGTGTCATCGTGAGTAT
39829 TAAATGAAAC
Statistics
Matches: 173, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
51 10 0.06
52 163 0.94
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (52 bp):
AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:47971 original size:24 final size:24
Alignment explanation
Indices: 47898--47978 Score: 126
Period size: 24 Copynumber: 3.4 Consensus size: 24
47888 TAGACTAATA
* *
47898 AGAGTTTGACTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
* *
47922 AAAATTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
47946 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
47970 AGAGTTTAA
1 AGAGTTTAA
47979 CTGGAAGATT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:54498 original size:22 final size:23
Alignment explanation
Indices: 54457--54499 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
54447 TTATTCTGAA
*
54457 ACAATTTTATATTTTTTTAATGG
1 ACAATTTTATATATTTTTAATGG
54480 ACAATTTT-TATATTTTTAAT
1 ACAATTTTATATATTTTTAAT
54500 AAATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (23 bp):
ACAATTTTATATATTTTTAATGG
Found at i:55428 original size:30 final size:29
Alignment explanation
Indices: 55343--55428 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
55333 AGTTCAGAGG
*
55343 CTAACTTAAACAAAAAAAAAATTC-AGAC
1 CTAACTTAAACAAAAAAAAAATTCAAGAA
** **
55371 CTAA-TGTGAGAACAATTATTAAATTCAAGAA
1 CTAACT-T-A-AACAAAAAAAAAATTCAAGAA
55402 CTAACTTAAACAAAAAAAAAAGTTCAA
1 CTAACTTAAACAAAAAAAAAA-TTCAA
55429 ATCTCAATTT
Statistics
Matches: 43, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
27 1 0.02
28 5 0.12
29 10 0.23
30 18 0.42
31 8 0.19
32 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.22
Consensus pattern (29 bp):
CTAACTTAAACAAAAAAAAAATTCAAGAA
Found at i:58188 original size:13 final size:16
Alignment explanation
Indices: 58158--58195 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
58148 GATAAGAAAA
58158 TATTATTAAATTATTT
1 TATTATTAAATTATTT
58174 TATT-TTAAA-TATTT
1 TATTATTAAATTATTT
*
58188 AATTATTA
1 TATTATTA
58196 TGTTGTCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 8 0.40
16 4 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTATTAAATTATTT
Found at i:63131 original size:36 final size:35
Alignment explanation
Indices: 63084--63182 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 35
63074 TGGTAACAGG
63084 CATGACCTTTGGGTCAACATGGAGTAAAATGAGCAT
1 CATGACCTTTGGGTCAACA-GGAGTAAAATGAGCAT
* * * *
63120 CATGACCTTTGGATCAATAGAGACTAAAATGAGTAT
1 CATGACCTTTGGGTCAACAG-GAGTAAAATGAGCAT
63156 CATGACCTTTGGGTCAACAAGGAGTAA
1 CATGACCTTTGGGTCAAC-AGGAGTAA
63183 GCATGACCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.02
36 51 0.94
37 2 0.04
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.25
Consensus pattern (35 bp):
CATGACCTTTGGGTCAACAGGAGTAAAATGAGCAT
Found at i:69716 original size:20 final size:19
Alignment explanation
Indices: 69683--69720 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
69673 ATTTCAAAAA
*
69683 TAATATTATTTTAATAATT
1 TAATATTATGTTAATAATT
69702 TAATACTTATGTTAATAAT
1 TAATA-TTATGTTAATAAT
69721 ATTTTATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (19 bp):
TAATATTATGTTAATAATT
Found at i:73564 original size:26 final size:26
Alignment explanation
Indices: 73455--73565 Score: 143
Period size: 26 Copynumber: 4.2 Consensus size: 26
73445 TCAAGCCGTT
*
73455 ACAGAAATATAGCTCATT-CGAGCCCAG
1 ACAGAGAT-TAGCTC-TTACGAGCCCAG
* *
73482 AACAGAGATTAGCTTTTACGAGCCTAG
1 -ACAGAGATTAGCTCTTACGAGCCCAG
* *
73509 ACAAAGATTAGCTCTTATGAGCCCAG
1 ACAGAGATTAGCTCTTACGAGCCCAG
73535 ACAGAGATTAGCTCTTACGAGCCCAG
1 ACAGAGATTAGCTCTTACGAGCCCAG
73561 ACAGA
1 ACAGA
73566 TAACACTCAG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 53 0.73
27 13 0.18
28 7 0.10
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (26 bp):
ACAGAGATTAGCTCTTACGAGCCCAG
Found at i:73582 original size:52 final size:52
Alignment explanation
Indices: 73474--73587 Score: 126
Period size: 52 Copynumber: 2.2 Consensus size: 52
73464 TAGCTCATTC
* * * * **
73474 GAGCCCAGAACAGAGATTAGCTTTTACGAGCCTAGACAAAGATTAGCTCTTAT
1 GAGCCCAGAACAGAGATTAGCTCTTACGAGCCCAGAC-AAGATAAACTCAGAT
73527 GAGCCCAG-ACAGAGATTAGCTCTTACGAGCCCAGAC-AGATAACACTCAGATT
1 GAGCCCAGAACAGAGATTAGCTCTTACGAGCCCAGACAAGATAA-ACTCAGA-T
73579 GAG-CCAGAA
1 GAGCCCAGAA
73588 TCCAAAATAT
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
50 5 0.10
51 8 0.15
52 31 0.60
53 8 0.15
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.19
Consensus pattern (52 bp):
GAGCCCAGAACAGAGATTAGCTCTTACGAGCCCAGACAAGATAAACTCAGAT
Found at i:73631 original size:28 final size:28
Alignment explanation
Indices: 73579--73737 Score: 201
Period size: 28 Copynumber: 5.6 Consensus size: 28
73569 CACTCAGATT
* **
73579 GAGCCAGAATCCAAAATATTACTCTTTTC
1 GAGCCAAAAT-CAAAATATCGCTCTTTTC
*
73608 GAGCCAAAATCAAAATATCGCTCTTTTT
1 GAGCCAAAATCAAAATATCGCTCTTTTC
* *
73636 GAGCTAGAATCAAAATATCGCTCTTTTC
1 GAGCCAAAATCAAAATATCGCTCTTTTC
73664 GAGCCAAAATCAAAATATCGCTCTTTTC
1 GAGCCAAAATCAAAATATCGCTCTTTTC
* * * *
73692 GAGCCAAAATTAGAATATCACTCTTTCC
1 GAGCCAAAATCAAAATATCGCTCTTTTC
* *
73720 GAGCCAGAATCAGAATAT
1 GAGCCAAAATCAAAATAT
73738 TTATAAAGCC
Statistics
Matches: 115, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
28 106 0.92
29 9 0.08
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (28 bp):
GAGCCAAAATCAAAATATCGCTCTTTTC
Found at i:73660 original size:56 final size:56
Alignment explanation
Indices: 73577--73737 Score: 223
Period size: 56 Copynumber: 2.9 Consensus size: 56
73567 AACACTCAGA
*
73577 TTGAGCCAGAATCCAAAATATTACTCTTTTCGAGCCAAAATCAAAATATCGCTCTTT
1 TTGAGCCAGAAT-CAAAATATCACTCTTTTCGAGCCAAAATCAAAATATCGCTCTTT
* *
73634 TTGAGCTAGAATCAAAATATCGCTCTTTTCGAGCCAAAATCAAAATATCGCTCTTT
1 TTGAGCCAGAATCAAAATATCACTCTTTTCGAGCCAAAATCAAAATATCGCTCTTT
* * * * * * *
73690 TCGAGCCAAAATTAGAATATCACTCTTTCCGAGCCAGAATCAGAATAT
1 TTGAGCCAGAATCAAAATATCACTCTTTTCGAGCCAAAATCAAAATAT
73738 TTATAAAGCC
Statistics
Matches: 92, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
56 81 0.88
57 11 0.12
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (56 bp):
TTGAGCCAGAATCAAAATATCACTCTTTTCGAGCCAAAATCAAAATATCGCTCTTT
Found at i:75348 original size:14 final size:15
Alignment explanation
Indices: 75329--75363 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
75319 ACTAACTTTT
75329 AATTCAATAATT-AA
1 AATTCAATAATTCAA
*
75343 AATTCACTAATTCAA
1 AATTCAATAATTCAA
75358 AATTCA
1 AATTCA
75364 GTATAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTCAATAATTCAA
Found at i:77166 original size:16 final size:16
Alignment explanation
Indices: 77145--77176 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
77135 ATTGAATTCA
77145 AATGCAAAAACTAAGT
1 AATGCAAAAACTAAGT
77161 AATGCAAAAACTAAGT
1 AATGCAAAAACTAAGT
77177 CTACAAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (16 bp):
AATGCAAAAACTAAGT
Found at i:78691 original size:139 final size:140
Alignment explanation
Indices: 78548--78832 Score: 362
Period size: 140 Copynumber: 2.0 Consensus size: 140
78538 GGAACCTCTT
* * *
78548 ACTCAAA-TATGTAATCACAATTATCTAAT-TATCTAACGAAATGAGCTAATATGTTAAAAATAT
1 ACTCAAAGGATGTAATCACAACTATCT-ATCTATCTAACGAAAT-AACTAATATGTTAAAAA-AT
* * * * *
78611 TAATT-GAAAA-TGAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATGTGACTAGGAAATG
63 TAATTAAAAAATTGAAAAAACTTGAAGCAAAATGAAATAAAAAATACAAATGTAACTAGGAAAAG
*
78674 AATCAAACTCAAG
128 AATCAAACCCAAG
* * *
78687 ACTCAAAGGATGTAATTACAACTATCTATCTATTTAACGAAGTAACTAATATGTTAAAAAATTAA
1 ACTCAAAGGATGTAATCACAACTATCTATCTATCTAACGAAATAACTAATATGTTAAAAAATTAA
* * *
78752 TTAAAAAATTTAAAAAACTTGAAGTAAAATGAAATAAAAAATACAAATGTAAGTAGGAAAAGAAT
66 TTAAAAAATTGAAAAAACTTGAAGCAAAATGAAATAAAAAATACAAATGTAACTAGGAAAAGAAT
* *
78817 CGAACCCGAG
131 CAAACCCAAG
78827 ACTCAA
1 ACTCAA
78833 GGCTAAAAAC
Statistics
Matches: 125, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
138 7 0.06
139 29 0.23
140 89 0.71
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (140 bp):
ACTCAAAGGATGTAATCACAACTATCTATCTATCTAACGAAATAACTAATATGTTAAAAAATTAA
TTAAAAAATTGAAAAAACTTGAAGCAAAATGAAATAAAAAATACAAATGTAACTAGGAAAAGAAT
CAAACCCAAG
Found at i:85409 original size:19 final size:19
Alignment explanation
Indices: 85387--85456 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
85377 AAATTGTAAA
85387 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
*
85406 AAAAATTCAAAATAAATTTT
1 -AAAATTCAAAATAATTTTT
* * *
85426 AAATTTTAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
*
85444 AAATTTTCAAAAT
1 AAA-ATTCAAAAT
85457 TTATATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 7 0.16
19 18 0.42
20 18 0.42
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:85409 original size:20 final size:20
Alignment explanation
Indices: 85386--85428 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
85376 AAAATTGTAA
*
85386 AAAAATTCAAAATAATTTTT
1 AAAAATTCAAAATAAATTTT
85406 AAAAATTCAAAATAAATTTT
1 AAAAATTCAAAATAAATTTT
85426 AAA
1 AAA
85429 TTTTAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTCAAAATAAATTTT
Found at i:85458 original size:17 final size:17
Alignment explanation
Indices: 85419--85478 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
85409 AATTCAAAAT
85419 AAATTT-TAAATTTTAA
1 AAATTTATAAATTTTAA
*
85435 AATATTTATAAATTTTCA
1 AA-ATTTATAAATTTTAA
*
85453 AAATTTAT-ATTTTTAA
1 AAATTTATAAATTTTAA
85469 TAAA-TTATAA
1 -AAATTTATAA
85479 GAAATTCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 12 0.32
17 14 0.38
18 11 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTATAAATTTTAA
Found at i:85467 original size:25 final size:26
Alignment explanation
Indices: 85416--85474 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
85406 AAAAATTCAA
*
85416 AATAAATTTTAAATTTTAAAATATTT
1 AATAAATTTTAAAATTTAAAATATTT
* *
85442 -ATAAATTTTCAAAATTT-ATATTTTT
1 AATAAATTTT-AAAATTTAAAATATTT
85467 AATAAATT
1 AATAAATT
85475 ATAAGAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
AATAAATTTTAAAATTTAAAATATTT
Found at i:85498 original size:21 final size:20
Alignment explanation
Indices: 85465--85512 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
85455 ATTTATATTT
* *
85465 TTAATAAATTATAA-GAAAT
1 TTAAAAAATTATAATGAAAG
85484 TCTAAAAAATATATAATGAAAG
1 T-TAAAAAAT-TATAATGAAAG
85506 TTAAAAA
1 TTAAAAA
85513 TTAAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.04
20 7 0.29
21 11 0.46
22 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.31
Consensus pattern (20 bp):
TTAAAAAATTATAATGAAAG
Found at i:85611 original size:52 final size:51
Alignment explanation
Indices: 85554--85653 Score: 191
Period size: 52 Copynumber: 1.9 Consensus size: 51
85544 ACTTACATAA
85554 GTTAATTAATTATTCAAGTTTATCATACTAAAGTATTTTTTTTTATTTTTCT
1 GTTAATTAATTATTCAAGTTTATCATACTAAAGTA-TTTTTTTTATTTTTCT
85606 GTTAATTAATTATTCAAGTTTATCATACTAAAGTATTTTTTTTATTTT
1 GTTAATTAATTATTCAAGTTTATCATACTAAAGTATTTTTTTTATTTT
85654 GCTTCAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 13 0.27
52 35 0.73
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (51 bp):
GTTAATTAATTATTCAAGTTTATCATACTAAAGTATTTTTTTTATTTTTCT
Found at i:86618 original size:31 final size:31
Alignment explanation
Indices: 86562--86628 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
86552 TTGATACTCG
*
86562 AACTTGACACTTTTTCCTAATTTGGTA-TCTA
1 AACTTGACACTTTTTCCTAAGTTGGTACT-TA
* **
86593 AACTTGACATTTTTTTTTAAGTTGGTACTTA
1 AACTTGACACTTTTTCCTAAGTTGGTACTTA
86624 AACTT
1 AACTT
86629 TTTGGGCTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (31 bp):
AACTTGACACTTTTTCCTAAGTTGGTACTTA
Found at i:96673 original size:27 final size:27
Alignment explanation
Indices: 96635--96689 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
96625 GTTTCACTAG
96635 TCTTTGCAATATTATCTATAAAATCAT
1 TCTTTGCAATATTATCTATAAAATCAT
96662 TCTTTGCAATATTATCTATAAAATCAT
1 TCTTTGCAATATTATCTATAAAATCAT
96689 T
1 T
96690 GCGAAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (27 bp):
TCTTTGCAATATTATCTATAAAATCAT
Found at i:101109 original size:29 final size:29
Alignment explanation
Indices: 101059--101125 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
101049 GAGTCAACAG
* ** *
101059 CCAAGAATTGAAAGTACTAAGAGAGAGCA
1 CCAAGAACTGAAACCACCAAGAGAGAGCA
101088 CCAAGAACTGAAACCACCAAGAGAGAGCA
1 CCAAGAACTGAAACCACCAAGAGAGAGCA
101117 CCAAGAACT
1 CCAAGAACT
101126 AAAAGCAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.48, C:0.22, G:0.21, T:0.09
Consensus pattern (29 bp):
CCAAGAACTGAAACCACCAAGAGAGAGCA
Found at i:101132 original size:16 final size:16
Alignment explanation
Indices: 101084--101132 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
101074 ACTAAGAGAG
101084 AGCACCAAGAACTGAA
1 AGCACCAAGAACTGAA
* *
101100 ACCACCAAG-A--GAG
1 AGCACCAAGAACTGAA
*
101113 AGCACCAAGAACTAAA
1 AGCACCAAGAACTGAA
101129 AGCA
1 AGCA
101133 AAGATTGCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
13 10 0.40
14 1 0.04
15 1 0.04
16 13 0.52
ACGTcount: A:0.51, C:0.27, G:0.18, T:0.04
Consensus pattern (16 bp):
AGCACCAAGAACTGAA
Found at i:105134 original size:51 final size:51
Alignment explanation
Indices: 105058--105198 Score: 219
Period size: 51 Copynumber: 2.8 Consensus size: 51
105048 CTATAAACGA
* *
105058 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT
* * *
105109 AAAGGTTCGATGACTAAGTGTCATCGTGAGTCAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT
* *
105160 AAAGGTCCGATGACTCAGTGTCATCGTGAGTATATGAAT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
105199 TCCTATATGA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 81 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATT
Found at i:107435 original size:38 final size:38
Alignment explanation
Indices: 107383--107458 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
107373 AGGCTTGGAC
107383 CCATCAAGAGCAGGGGTTGAATCTCTAGAAGGTGAAGA
1 CCATCAAGAGCAGGGGTTGAATCTCTAGAAGGTGAAGA
*
107421 CCATCAAGATCAGGGGTTGAATCTCTAGAAGGTGAAGA
1 CCATCAAGAGCAGGGGTTGAATCTCTAGAAGGTGAAGA
107459 AAAATTACTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (38 bp):
CCATCAAGAGCAGGGGTTGAATCTCTAGAAGGTGAAGA
Found at i:121133 original size:17 final size:17
Alignment explanation
Indices: 121113--121166 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
121103 ACTACAATGC
*
121113 AAATGTAATAACAAATA
1 AAATGCAATAACAAATA
* *
121130 AAATGCAGTGACAAATAA
1 AAATGCAATAACAAAT-A
* *
121148 AAATGCAATGACAACTA
1 AAATGCAATAACAAATA
121165 AA
1 AA
121167 TGATATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (17 bp):
AAATGCAATAACAAATA
Found at i:121152 original size:18 final size:18
Alignment explanation
Indices: 121113--121166 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
121103 ACTACAATGC
* *
121113 AAATGTAATAACAAAT-A
1 AAATGCAATGACAAATAA
*
121130 AAATGCAGTGACAAATAA
1 AAATGCAATGACAAATAA
*
121148 AAATGCAATGACAACTAA
1 AAATGCAATGACAAATAA
121166 A
1 A
121167 TGATATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.59, C:0.11, G:0.11, T:0.19
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Done.