Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012542.1 Kokia drynarioides strain JFW-HI SEQ_127551, 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: 50877
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Warning! 60 characters in sequence are not A, C, G, or T
Found at i:12955 original size:30 final size:31
Alignment explanation
Indices: 12901--12959 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
12891 TTAGTAAAAG
*
12901 TAAAATTGTATTTTAATCATTTTAAAAATGA
1 TAAAATTGTAATTTAATCATTTTAAAAATGA
*
12932 TAAAATTTTAATTTAAT-ATTTTAAAAAT
1 TAAAATTGTAATTTAATCATTTTAAAAAT
12960 TATATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (31 bp):
TAAAATTGTAATTTAATCATTTTAAAAATGA
Found at i:14505 original size:59 final size:58
Alignment explanation
Indices: 14431--14806 Score: 429
Period size: 59 Copynumber: 6.4 Consensus size: 58
14421 GTTCGGAATC
14431 AAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAATGTTTGGGGTT
1 AAAAATGGGA-TTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAA-GTTTGGGGTT
* * * *
14491 AAAATTGGGATTTTTGGGAGTTTGGGGGTAAAATGGTAATTTTTAGAAAGTTTGGGGTC
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAG-AAGTTTGGGGTT
*
14550 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAG-AAGTTTGGGGTT
* * * *
14609 AAAAATGGGATTTTT-GAGAGTTTAGAGGGTATAATGGTAATTTTTAGAAGGTTCGGGGTT
1 AAAAATGGGATTTTTGGA-AG-TTCGGGGGTAAAATGGTAATTTTTAGAA-GTTTGGGGTT
* * * * *
14669 AAAAATGAGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGGAGTTTGGGGGT
1 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGTTTGGGGTT
* * * * * *
14727 -AAAATGGTAATTTTAGAAAGTTC-GGGGTCAAAAATGG-GATTTTTGGAAGTTTGGGGGT
1 AAAAATGG-GATTTTTGGAAGTTCGGGGGT--AAAATGGTAATTTTTAGAAGTTTGGGGTT
*
14785 -AAAATGGTAATTTTTGGAAGTT
1 AAAAATGG-GATTTTTGGAAGTT
14807 TAAGGACCTC
Statistics
Matches: 276, Mismatches: 32, Indels: 18
0.85 0.10 0.06
Matches are distributed among these distances:
57 11 0.04
58 60 0.22
59 146 0.53
60 58 0.21
61 1 0.00
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (58 bp):
AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGTTTGGGGTT
Found at i:14560 original size:119 final size:118
Alignment explanation
Indices: 14429--14731 Score: 464
Period size: 119 Copynumber: 2.6 Consensus size: 118
14419 AGGTTCGGAA
*
14429 TCAAAAATGGGATTTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAATGTTTGGGGTTAAA
1 TCAAAAATGGGA-TTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAA-GTTTGGGGTTAAA
* * *
14494 ATTGGGATTTTTGGGAGTTT-GGGGGTAAAATGGTAATTTTTAGAAAGTTTGGGG
64 ATTGGGATTTTTGAGAGTTTAGAGGGTAAAATGGTAATTTTTAGAAAGTTCGGGG
14548 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAAGTTTGGGGTTAAAA
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGG-AAGTTTGGGGTTAAAA
* * *
14613 ATGGGATTTTTGAGAGTTTAGAGGGTATAATGGTAATTTTTAGAAGGTTCGGGG
65 TTGGGATTTTTGAGAGTTTAGAGGGTAAAATGGTAATTTTTAGAAAGTTCGGGG
* * * * *
14667 TTAAAAATGAGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGGAGTTTGGGGGTAAAAT
1 TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTGGGGTTAAAAT
14732 GGTAATTTTA
Statistics
Matches: 169, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
118 80 0.47
119 89 0.53
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (118 bp):
TCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAGTTTGGGGTTAAAAT
TGGGATTTTTGAGAGTTTAGAGGGTAAAATGGTAATTTTTAGAAAGTTCGGGG
Found at i:14807 original size:29 final size:29
Alignment explanation
Indices: 14432--14807 Score: 347
Period size: 29 Copynumber: 12.8 Consensus size: 29
14422 TTCGGAATCA
* * *
14432 AAAATGGGATTTTTTGGAAGTTCGGGGGT
1 AAAATGGTAATTTTTGGAAGTTTGGGGGT
* *
14461 AAAATGGTAATTTTTAGAATGTTTGGGGTT
1 AAAATGGTAATTTTTGGAA-GTTTGGGGGT
* *
14491 AAAATTGG-GATTTTTGGGAGTTTGGGGGT
1 AAAA-TGGTAATTTTTGGAAGTTTGGGGGT
*
14520 AAAATGGTAATTTTTAGAAAGTTT-GGGGT
1 AAAATGGTAATTTTT-GGAAGTTTGGGGGT
* *
14549 CAAAAATGG-GATTTTTGGAAGTTCGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTTGGGGGT
*
14579 AAAATGGTAATTTTTGGAAAGTTTGGGGTT
1 AAAATGGTAATTTTTGG-AAGTTTGGGGGT
* *
14609 AAAAATGG-GATTTTT-GAGAGTTTAGAGGGT
1 -AAAATGGTAATTTTTGGA-AGTTT-GGGGGT
* * * *
14639 ATAATGGTAATTTTTAGAAGGTTCGGGGTT
1 AAAATGGTAATTTTTGGAA-GTTTGGGGGT
* *
14669 AAAAAT-G-AGATTTTTGGGAGTTCGGGGGT
1 -AAAATGGTA-ATTTTTGGAAGTTTGGGGGT
*
14698 AAAATGGTAATTTTTGGGAGTTTGGGGGT
1 AAAATGGTAATTTTTGGAAGTTTGGGGGT
* * *
14727 AAAATGGTAATTTTAGAAAG-TTCGGGGT
1 AAAATGGTAATTTTTGGAAGTTTGGGGGT
*
14755 CAAAAATGG-GATTTTTGGAAGTTTGGGGGT
1 --AAAATGGTAATTTTTGGAAGTTTGGGGGT
14785 AAAATGGTAATTTTTGGAAGTTT
1 AAAATGGTAATTTTTGGAAGTTT
14808 AAGGACCTCC
Statistics
Matches: 284, Mismatches: 40, Indels: 46
0.77 0.11 0.12
Matches are distributed among these distances:
28 30 0.11
29 136 0.48
30 92 0.32
31 26 0.09
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTTGGGGGT
Found at i:15959 original size:7 final size:7
Alignment explanation
Indices: 15949--15973 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
15939 TTTTTTTTAT
15949 TAATTAA
1 TAATTAA
15956 TAATTAA
1 TAATTAA
15963 TAATTAA
1 TAATTAA
15970 TAAT
1 TAAT
15974 ATTATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:16636 original size:15 final size:15
Alignment explanation
Indices: 16572--16620 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
16562 TTTTGGGTAG
16572 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
16587 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
* *
16602 TCTGTAACTGGGCCA
1 TTTGTAATTGGGCCA
16617 TTTG
1 TTTG
16621 GGCCATTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:16690 original size:17 final size:16
Alignment explanation
Indices: 16668--16723 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
16658 TTGGACTTTC
*
16668 TAAATTTAATTTTATAA
1 TAAATTTAAATTTA-AA
16685 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
16702 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
16718 TAAATT
1 TAAATT
16724 CAATTTTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.23
17 26 0.74
18 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:17595 original size:12 final size:12
Alignment explanation
Indices: 17578--17641 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
17568 TTGAAATAAT
*
17578 TTTAAACTTGAA
1 TTTAAACTTAAA
*
17590 TTTAAATTTAAA
1 TTTAAACTTAAA
**
17602 TTTAGTC-TAAA
1 TTTAAACTTAAA
*
17613 TTTGAAA--TAAT
1 TTT-AAACTTAAA
17624 TTTAAACTTAAA
1 TTTAAACTTAAA
17636 TTTAAA
1 TTTAAA
17642 ATCAATTACA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
10 3 0.08
11 13 0.32
12 24 0.60
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (12 bp):
TTTAAACTTAAA
Found at i:19607 original size:29 final size:29
Alignment explanation
Indices: 19531--19717 Score: 146
Period size: 29 Copynumber: 6.4 Consensus size: 29
19521 AAATTACATT
* *
19531 TTTTACCCCCGAACTTCCAAAAATT-CTA
1 TTTTACCCCCAAACTTCCAAAAATTCCAA
*** * **
19559 TTTTAACCTTAAAACATCCAAAAATAACAA
1 TTTT-ACCCCCAAACTTCCAAAAATTCCAA
* *
19589 TTTTACCCCCGAACTTCCAAAAATTCCAT
1 TTTTACCCCCAAACTTCCAAAAATTCCAA
** *
19618 TTTTGACCCTAAAACTTCTAAAAATTACCAA
1 TTTT-ACCCCCAAACTTCCAAAAATT-CCAA
* *
19649 -TTTACCCCTAAACTTCCAAAAATTCCAT
1 TTTTACCCCCAAACTTCCAAAAATTCCAA
* * *
19677 TTTTAACCTCGAAATTTCCAAAAATTACC-A
1 TTTT-ACCCCCAAACTTCCAAAAATT-CCAA
19707 TTTTACCCCCA
1 TTTTACCCCCA
19718 TATGCCCAAA
Statistics
Matches: 122, Mismatches: 30, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
28 7 0.06
29 62 0.51
30 48 0.39
31 5 0.04
ACGTcount: A:0.38, C:0.28, G:0.02, T:0.32
Consensus pattern (29 bp):
TTTTACCCCCAAACTTCCAAAAATTCCAA
Found at i:19663 original size:59 final size:58
Alignment explanation
Indices: 19532--19716 Score: 228
Period size: 59 Copynumber: 3.2 Consensus size: 58
19522 AATTACATTT
* * * * *
19532 TTTACCCCCGAACTTCCAAAAATTCTATTTTAACCTTAAAACATCCAAAAA-TAACAA
1 TTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTACCAA
*
19589 TTTTACCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCTAAAAATTACCAA
1 -TTTACCCCCGAACTTCCAAAAATTCCATTTTT-ACCCTAAAACTTCCAAAAATTACCAA
** * * * *
19649 TTTACCCCTAAACTTCCAAAAATTCCATTTTTAACCTCGAAATTTCCAAAAATTACCAT
1 TTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCT-AAAACTTCCAAAAATTACCAA
19708 TTTACCCCC
1 TTTACCCCC
19717 ATATGCCCAA
Statistics
Matches: 110, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
58 34 0.31
59 71 0.65
60 5 0.05
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (58 bp):
TTTACCCCCGAACTTCCAAAAATTCCATTTTTACCCTAAAACTTCCAAAAATTACCAA
Found at i:30924 original size:18 final size:18
Alignment explanation
Indices: 30898--30933 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
30888 GCATCTAATA
*
30898 TTGTCCCTTGTAATTGTT
1 TTGTCCCTTGTAAATGTT
*
30916 TTGTTCCTTGTAAATGTT
1 TTGTCCCTTGTAAATGTT
30934 CAGAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.14, G:0.17, T:0.56
Consensus pattern (18 bp):
TTGTCCCTTGTAAATGTT
Found at i:32485 original size:201 final size:198
Alignment explanation
Indices: 31918--32553 Score: 813
Period size: 201 Copynumber: 3.2 Consensus size: 198
31908 GATTATCCAC
* * *
31918 AAAC-AGTGAGGCGGTTATCTTCCTGATGAGATACAAAGAAGTATACCAACTCAGGGCTCGATGT
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGT
** *
31982 AGGCAAATCTTTGAACCTCAGCTTCCAGATGAGATACTGAGATGCAGGTCGAAGCAATAAAATGG
66 A-GCAAATCTTTGAACC-CAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGG
*
32047 TTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCTTGATG-AGATACAGAGAAG
129 TTAGCTTCCTGATGAGATAC-GAGAAGTGAACCAAATTCGTCTTCTTGATGAAG-TACAGAGAAG
32111 CAGATTG
192 CAGATTG
* * * *
32118 AAACAAATGACGCGGTCATCTTCCTGATGAGATATAGAGAAGTATACCAACTCAATG--CGA---
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGT
* *
32178 A-CAAATCTTTGAACCCCAGCTTCTTG-TGAGATACTGAGAAGCAGGGCGAAGCAATAAAAAGGT
66 AGCAAATCTTTGAA-CCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGT
* * * * *
32241 TAGCTTCCTGATGAAACATTGAGAAGTGAACCAAATTCGTCTTCTTGATGAAGTACAGAGAAACG
130 TAGCTTCCTGATGAGATA-CGAGAAGTGAACCAAATTCGTCTTCTTGATGAAGTACAGAGAAGCA
32306 GATTG
194 GATTG
*
32311 AAACAAGTGAGGTGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGT
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGT
* * *
32376 GAGCAAATCTTCGAATCCCAGCTTCTTGATGAGATACTAAGAAGCAGGTCGAAGCAATAAAGTGG
66 -AGCAAATCTTTGAA-CCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGG
* * * * ** * *
32441 TCAGCTTCCTGATGAGATACGAAAAAGTGAACCAAATCCGTCTTCCTGATGAAACACGGAGAAGT
129 TTAGCTTCCTGATGAGATACG-AGAAGTGAACCAAATTCGTCTTCTTGATGAAGTACAGAGAAGC
**
32506 AGATCA
193 AGATTG
* * *
32512 AAACAAGTGATGCGGTCGTCTTCCTGATGAGATACTGAGAAG
1 AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAG
32554 AAGGCCAAGT
Statistics
Matches: 375, Mismatches: 48, Indels: 25
0.84 0.11 0.06
Matches are distributed among these distances:
193 146 0.39
194 22 0.06
195 5 0.01
196 1 0.00
199 4 0.01
200 28 0.07
201 169 0.45
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Consensus pattern (198 bp):
AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAAGGCTCGATGT
AGCAAATCTTTGAACCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
AGCTTCCTGATGAGATACGAGAAGTGAACCAAATTCGTCTTCTTGATGAAGTACAGAGAAGCAGA
TTG
Found at i:32965 original size:6 final size:6
Alignment explanation
Indices: 32941--33031 Score: 64
Period size: 6 Copynumber: 15.7 Consensus size: 6
32931 GATTTATTTC
* * * **
32941 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * * *
32988 TAAATT T-AGTC TAAATT TGAAA-- TAATTT TAAACT TAAATT TAAA
1 TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAA
33032 ATCAATTACA
Statistics
Matches: 63, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
4 2 0.03
5 8 0.13
6 50 0.79
7 3 0.05
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.47
Consensus pattern (6 bp):
TAAATT
Found at i:32966 original size:17 final size:18
Alignment explanation
Indices: 32927--32971 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
32917 TTAGATGGGT
* *
32927 TTTAGATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
32945 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
32962 TTTAAATTTA
1 TTTAAATTTA
32972 AATTCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:32991 original size:41 final size:42
Alignment explanation
Indices: 32927--33010 Score: 107
Period size: 41 Copynumber: 2.0 Consensus size: 42
32917 TTAGATGGGT
* * *
32927 TTTAGATTTATTTCTAAAATTAAATTTACTTTAAATTT-AAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTCTAAATTTGAAA
* * *
32968 TTTAAATTCATTTTTAAATTTAAATTTAGTCTAAATTTGAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTCTAAATTTGAAA
33010 T
1 T
33011 AATTTTAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 32 0.89
42 4 0.11
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.51
Consensus pattern (42 bp):
TTTAAATTCATTTCTAAAATTAAATTTACTCTAAATTTGAAA
Found at i:34403 original size:109 final size:109
Alignment explanation
Indices: 34206--34427 Score: 342
Period size: 109 Copynumber: 2.1 Consensus size: 109
34196 AACGGCGGTC
* **
34206 GACAATGCGCTTGGTGGCAACGAGCGACAGACGGCTGGGCTGGGACCGGTCGGAACAGTCGGCCA
1 GACAAGGCGCTTGGTGGCAACGAGCGACAGACGGCTGGGCTGGGACCGGTCAAAACAGTCGGCCA
*
34271 TGGAAGACCTTGAGAGAAAAGAGAGACTTTGAATTTATTTTTTA
66 TGGAAGACCGTGAGAGAAAAGAGAGACTTTGAATTTATTTTTTA
* * * * *
34315 GACAAGGCGGTTGGTGGCGACGAGCGACGGACGGTTGGGCTGGGACCGGTCAAAACAGTCGGGCA
1 GACAAGGCGCTTGGTGGCAACGAGCGACAGACGGCTGGGCTGGGACCGGTCAAAACAGTCGGCCA
34380 TGG-A-ACCGTGAGAGAAAAGAGAGACTTTGAATTTATTTTTTA
66 TGGAAGACCGTGAGAGAAAAGAGAGACTTTGAATTTATTTTTTA
34422 GA-AAGG
1 GACAAGG
34428 AATGAAAAAG
Statistics
Matches: 104, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
106 4 0.04
107 39 0.38
108 1 0.01
109 60 0.58
ACGTcount: A:0.28, C:0.17, G:0.35, T:0.20
Consensus pattern (109 bp):
GACAAGGCGCTTGGTGGCAACGAGCGACAGACGGCTGGGCTGGGACCGGTCAAAACAGTCGGCCA
TGGAAGACCGTGAGAGAAAAGAGAGACTTTGAATTTATTTTTTA
Found at i:34960 original size:30 final size:29
Alignment explanation
Indices: 34924--35133 Score: 144
Period size: 30 Copynumber: 7.1 Consensus size: 29
34914 CCTTGGAGGT
*
34924 CCCTAAACTATTCAAAAATTATATTTTGAC
1 CCCTAAACT-TCCAAAAATTATATTTTGAC
** * *
34954 CCCTAAACTTCTTTAAAATTATATTTTTAA
1 CCCTAAACTTC-CAAAAATTATATTTTGAC
* * *
34984 CCCTAAAACTTCCCAAAATTACATTTTTAC
1 CCCT-AAACTTCCAAAAATTATATTTTGAC
*
35014 CCCAAAACTTCCAAAAATT-TCATTTTGAC
1 CCCTAAACTTCCAAAAATTAT-ATTTTGAC
* * * *
35043 CTCGT-AACATCCGAAAATTACCATTTT-AC
1 C-CCTAAACTTCCAAAAATTA-TATTTTGAC
* *
35072 CACC-AAACTTCTAAAAATTCCAT-TTTTAAC
1 C-CCTAAACTTCCAAAAATT--ATATTTTGAC
*
35102 CCCAAAACTTCCAAAAATTATCATTTT-AC
1 CCCTAAACTTCCAAAAATTAT-ATTTTGAC
35131 CCC
1 CCC
35134 CGAATGTCCA
Statistics
Matches: 142, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
28 2 0.01
29 61 0.43
30 71 0.50
31 8 0.06
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTATATTTTGAC
Found at i:35020 original size:29 final size:29
Alignment explanation
Indices: 34936--35216 Score: 180
Period size: 29 Copynumber: 9.6 Consensus size: 29
34926 CTAAACTATT
* * *
34936 CAAAAATTATATTTTGACCCCTAAACTTC
1 CAAAAATTACATTTTTACCCCAAAACTTC
** * *
34965 TTTAAAATTATATTTTTAACCCTAAAACTTC
1 -CAAAAATTACATTTTT-ACCCCAAAACTTC
*
34996 CCAAAATTACATTTTTACCCCAAAACTTC
1 CAAAAATTACATTTTTACCCCAAAACTTC
* * * ** *
35025 CAAAAATTTCATTTTGACCTCGTAACATC
1 CAAAAATTACATTTTTACCCCAAAACTTC
*
35054 CGAAAATTACCA-TTTTACCACC-AAACTTC
1 CAAAAATTA-CATTTTTACC-CCAAAACTTC
* *
35083 TAAAAATTCCATTTTTAACCCCAAAACTTC
1 CAAAAATTACATTTTT-ACCCCAAAACTTC
**
35113 CAAAAATTATCA-TTTTACCCCCGAA-TGTC
1 CAAAAATTA-CATTTTTACCCCAAAACT-TC
* * * *
35142 CAAAAAACTCCATTTTTTACCCCGAAACTTT
1 C-AAAAATTACA-TTTTTACCCCAAAACTTC
* *
35173 C-AAAATTACCA-TTTTACCCCCAGA-TGTC
1 CAAAAATTA-CATTTTTACCCCAAAACT-TC
*
35201 CAAAAATTCCATTTTT
1 CAAAAATTACATTTTT
35217 GATCCTGATT
Statistics
Matches: 195, Mismatches: 40, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
27 1 0.01
28 18 0.09
29 91 0.47
30 58 0.30
31 26 0.13
32 1 0.01
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (29 bp):
CAAAAATTACATTTTTACCCCAAAACTTC
Found at i:35127 original size:59 final size:58
Alignment explanation
Indices: 34936--35216 Score: 223
Period size: 59 Copynumber: 4.8 Consensus size: 58
34926 CTAAACTATT
* ** ** *
34936 CAAAAATTA-TATTTTGACCCCTAAACTTCTTTAAAATTATATTTTTAACCCTAAAACTTC
1 CAAAAATTACCATTTT-ACCCC-AAACTTC-CAAAAATTCCATTTTTAACCCCAAAACTTC
* * * * ** *
34996 CCAAAATTA-CATTTTTACCCCAAAACTTCCAAAAATTTCA-TTTTGACCTCGTAACATC
1 CAAAAATTACCA-TTTTACCCC-AAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTC
* *
35054 CGAAAATTACCATTTTACCACCAAACTTCTAAAAATTCCATTTTTAACCCCAAAACTTC
1 CAAAAATTACCATTTTACC-CCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTC
* * * * * *
35113 CAAAAATTATCATTTTACCCCCGAA-TGTCCAAAAAACTCCATTTTTTACCCCGAAACTTT
1 CAAAAATTACCATTTTA-CCCCAAACT-TCC-AAAAATTCCATTTTTAACCCCAAAACTTC
*
35173 C-AAAATTACCATTTTACCCCCAGA-TGTCCAAAAATTCCATTTTT
1 CAAAAATTACCATTTTA-CCCCAAACT-TCCAAAAATTCCATTTTT
35217 GATCCTGATT
Statistics
Matches: 181, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
58 58 0.32
59 70 0.39
60 49 0.27
61 4 0.02
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCAAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTC
Found at i:35238 original size:59 final size:59
Alignment explanation
Indices: 35084--35254 Score: 177
Period size: 59 Copynumber: 2.9 Consensus size: 59
35074 CCAAACTTCT
* * * *
35084 AAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTATCATTTTACCCCCGAATGTCCA
1 AAAAACTCCATTTTTGACCCCGAAACTTTC-AAAATTATCATTTTACCCCCGAATGTCCA
* *
35144 AAAAACTCCATTTTTTACCCCGAAACTTTCAAAATTACCATTTTACCCCC-AGATGTCC-
1 AAAAACTCCATTTTTGACCCCGAAACTTTCAAAATTATCATTTTACCCCCGA-ATGTCCA
* * * ** *
35202 AAAAATTCCATTTTTGATCCTG-ATTTTTCTAGAAATTATCATTTTGCCCCCGA
1 AAAAACTCCATTTTTGACCCCGAAACTTTC-A-AAATTATCATTTTACCCCCGA
35255 GAGTAAATTA
Statistics
Matches: 94, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
57 5 0.05
58 20 0.21
59 42 0.45
60 27 0.29
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (59 bp):
AAAAACTCCATTTTTGACCCCGAAACTTTCAAAATTATCATTTTACCCCCGAATGTCCA
Found at i:36912 original size:6 final size:6
Alignment explanation
Indices: 36903--36930 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
36893 CTAAAATTAA
36903 ATATTT ATATTT ATATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATAT
36931 ATGAAATGAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:38444 original size:21 final size:21
Alignment explanation
Indices: 38418--38483 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
38408 TATATTAGAT
38418 TAATATAATTATTTACGTATG
1 TAATATAATTATTTACGTATG
*
38439 TAATAT-TTTATATTA-G-AT-
1 TAATATAATTAT-TTACGTATG
*
38457 TAATATAATTATTTGCGTATG
1 TAATATAATTATTTACGTATG
38478 TAATAT
1 TAATAT
38484 CTCATGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 7 0.19
21 15 0.41
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (21 bp):
TAATATAATTATTTACGTATG
Found at i:38448 original size:39 final size:39
Alignment explanation
Indices: 38403--38483 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
38393 TATGTAAATT
38403 TATTTTATATTAGATTAATATAATTATTTACGTATGTAA
1 TATTTTATATTAGATTAATATAATTATTTACGTATGTAA
*
38442 TATTTTATATTAGATTAATATAATTATTTGCGTATGTAA
1 TATTTTATATTAGATTAATATAATTATTTACGTATGTAA
38481 TAT
1 TAT
38484 CTCATGTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (39 bp):
TATTTTATATTAGATTAATATAATTATTTACGTATGTAA
Found at i:38462 original size:18 final size:18
Alignment explanation
Indices: 38403--38462 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
38393 TATGTAAATT
38403 TATTTTATATTAGATTAA
1 TATTTTATATTAGATTAA
*
38421 TATAATTAT-TTACGTATGTAA
1 TAT-TTTATATTA-G-AT-TAA
38442 TATTTTATATTAGATTAA
1 TATTTTATATTAGATTAA
38460 TAT
1 TAT
38463 AATTATTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
18 12 0.34
19 7 0.20
20 7 0.20
21 9 0.26
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (18 bp):
TATTTTATATTAGATTAA
Found at i:38869 original size:35 final size:35
Alignment explanation
Indices: 38812--38906 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 35
38802 CCAAACTCCC
* *
38812 TTTAAATTTATTTTAAAATTAAATTTGTTTAAAAA
1 TTTAAATTTATTTTAAAATTAAAATTATTTAAAAA
** **
38847 TTTAAATTTATTTTAAGTTTAAAATTATTTTCAAA
1 TTTAAATTTATTTTAAAATTAAAATTATTTAAAAA
* ** *
38882 TTTAAAATTATCATAAATTTAAAAT
1 TTTAAATTTATTTTAAAATTAAAAT
38907 AAATAAAGCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (35 bp):
TTTAAATTTATTTTAAAATTAAAATTATTTAAAAA
Found at i:38901 original size:17 final size:17
Alignment explanation
Indices: 38812--38906 Score: 91
Period size: 17 Copynumber: 5.5 Consensus size: 17
38802 CCAAACTCCC
*
38812 TTTAAATTTATTTTAAA
1 TTTAAAATTATTTTAAA
* * * *
38829 ATTAAATTTGTTTAAAAA
1 TTTAAAATTATTT-TAAA
* *
38847 TTTAAATTTATTTTAAG
1 TTTAAAATTATTTTAAA
38864 TTTAAAATTATTTTCAAA
1 TTTAAAATTATTTT-AAA
**
38882 TTTAAAATTATCATAAA
1 TTTAAAATTATTTTAAA
38899 TTTAAAAT
1 TTTAAAAT
38907 AAATAAAGCC
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
17 37 0.57
18 28 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTAAAATTATTTTAAA
Found at i:40797 original size:30 final size:30
Alignment explanation
Indices: 40729--40931 Score: 216
Period size: 30 Copynumber: 6.8 Consensus size: 30
40719 CCGGAGACAC
*
40729 CGAAACTCCCAAAAATTCCATTTTT-ACCCT
1 CGAAACTTCCAAAAATTCCATTTTTGA-CCT
*
40759 CG-AACTTCTAAAAATTCCATTTTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
** * * *
40788 CGAAACTTCTGAAAATTCAATTTTCGACCC
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
* *
40818 CGAAACTTCCAAAAATTCCATTTCTGACCC
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
*
40848 CAAAACTTCCAAAAATTCCATTTTT-ACCCT
1 CGAAACTTCCAAAAATTCCATTTTTGA-CCT
* * * *
40878 TG-AACATCCAAAATTTCCATTGTTGACCT
1 CGAAACTTCCAAAAATTCCATTTTTGACCT
*
40907 CGAAACTTTCAAAAATTACCATTTT
1 CGAAACTTCCAAAAATT-CCATTTT
40932 GCTCCCGGAT
Statistics
Matches: 143, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
29 49 0.34
30 88 0.62
31 6 0.04
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (30 bp):
CGAAACTTCCAAAAATTCCATTTTTGACCT
Found at i:40805 original size:59 final size:59
Alignment explanation
Indices: 40729--40931 Score: 230
Period size: 59 Copynumber: 3.4 Consensus size: 59
40719 CCGGAGACAC
* * *
40729 CGAAACTCCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCT
1 CGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCT
* * * * *
40788 CGAAACTTCTGAAAATTCAATTTTCGACCC-CGAAACTTCCAAAAATTCCATTTCTGACCC
1 CGAAACTTCTAAAAATTCCATTTT-TACCCTCG-AACTTCCAAAAATTCCATTTTTGACCT
* * * * * *
40848 CAAAACTTCCAAAAATTCCATTTTTACCCTTGAACATCCAAAATTTCCATTGTTGACCT
1 CGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCT
40907 CGAAACTT-TCAAAAATTACCATTTT
1 CGAAACTTCT-AAAAATT-CCATTTT
40932 GCTCCCGGAT
Statistics
Matches: 118, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
59 62 0.53
60 56 0.47
ACGTcount: A:0.34, C:0.28, G:0.06, T:0.33
Consensus pattern (59 bp):
CGAAACTTCTAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCT
Found at i:41066 original size:28 final size:28
Alignment explanation
Indices: 41031--41093 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
41021 CCAAATTTTC
41031 CCAAAATTACCACTTTACCCCCGAGAAT
1 CCAAAATTACCACTTTACCCCCGAGAAT
* *
41059 CCAAAATTACCATTTTACCCCCGAGTAT
1 CCAAAATTACCACTTTACCCCCGAGAAT
41087 CCGAAAA
1 CC-AAAA
41094 GTCTCATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 28 0.88
29 4 0.12
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (28 bp):
CCAAAATTACCACTTTACCCCCGAGAAT
Found at i:41101 original size:29 final size:28
Alignment explanation
Indices: 41031--41103 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
41021 CCAAATTTTC
* *
41031 CCAAAATTACCACTTTACCCCCGAGAAT
1 CCAAAAGTACCATTTTACCCCCGAGAAT
* *
41059 CCAAAATTACCATTTTACCCCCGAGTAT
1 CCAAAAGTACCATTTTACCCCCGAGAAT
41087 CCGAAAAGT-CTCATTTT
1 CC-AAAAGTAC-CATTTT
41104 CAACTCCGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 29 0.73
29 11 0.28
ACGTcount: A:0.33, C:0.32, G:0.08, T:0.27
Consensus pattern (28 bp):
CCAAAAGTACCATTTTACCCCCGAGAAT
Found at i:41404 original size:96 final size:95
Alignment explanation
Indices: 41304--41495 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 95
41294 AAAACTTTAA
* *
41304 AATCGAGGCAA-TATCCTTTTATTTCGAGTT-TCGAAA-ATTCGTGCCTTAACTTACTAGGTGCA
1 AATCGAGGCAAGTATCCTTATATTT-GA-TTCT-GAAATATT-GCGCCTTAACTTACTAGGTGCA
**
41366 ATTTTTCTTCAAATCGAAATAATCGAATACCCTT
62 ACCTTTCTTCAAATCGAAATAATCGAATACCCTT
* *
41400 AATCGAGGCAATGTTTCCTTATCTTTGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACC
1 AATCGAGGCAA-GTATCCTTATATTTGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACC
* *
41465 TTTCTTCAAATCGATATAATCGAATATCCTT
65 TTTCTTCAAATCGAAATAATCGAATACCCTT
41496 TTCCCAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
96 68 0.81
97 6 0.07
98 10 0.12
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (95 bp):
AATCGAGGCAAGTATCCTTATATTTGATTCTGAAATATTGCGCCTTAACTTACTAGGTGCAACCT
TTCTTCAAATCGAAATAATCGAATACCCTT
Done.