Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004241.1 Kokia drynarioides strain JFW-HI SEQ_117511, 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: 29169
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 103 characters in sequence are not A, C, G, or T
Found at i:1828 original size:115 final size:114
Alignment explanation
Indices: 1600--1853 Score: 309
Period size: 115 Copynumber: 2.2 Consensus size: 114
1590 ATACAGTCAT
* * *
1600 CTTCCTGATGAGATACAGAGAAGAATACCAACTCGAGGCTGAATACGAGCAAATCTTCAAATCCT
1 CTTCCTGATGAGATATAGAGAAGTATACCAACTCGAGGCTGAATAC-AGCAAATCTTCAAATCCC
* * * * *
1665 AGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAG
65 AGCTTCTTAATGAGAAACTAAGAAGCAGGGCGAAGCAATAAAATGGTTAG
* * * *
1715 CTTCCTGATGAGATATAGAGAAGTATATCAACTC-AGGGCTCGATGTA-AGCAGATCTTCGAATC
1 CTTCCTGATGAGATATAGAGAAGTATACCAACTCGA-GGCT-GA-ATACAGCAAATCTTCAAATC
1778 CCAGCTTCTTAATGAGACAACTAAGAAGCAGGGCGAAGCAATAAAA-GGTTAG
63 CCAGCTTCTTAATGAGA-AACTAAGAAGCAGGGCGAAGCAATAAAATGGTTAG
*
1830 CTTCTTGATGAGATACT-GAGAAGT
1 CTTCCTGATGAGATA-TAGAGAAGT
1854 GAACCAGATT
Statistics
Matches: 121, Mismatches: 13, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
114 1 0.01
115 91 0.75
116 27 0.22
117 2 0.02
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.24
Consensus pattern (114 bp):
CTTCCTGATGAGATATAGAGAAGTATACCAACTCGAGGCTGAATACAGCAAATCTTCAAATCCCA
GCTTCTTAATGAGAAACTAAGAAGCAGGGCGAAGCAATAAAATGGTTAG
Found at i:2243 original size:207 final size:206
Alignment explanation
Indices: 1753--2354 Score: 682
Period size: 202 Copynumber: 2.9 Consensus size: 206
1743 CAACTCAGGG
* * * * * * * * *
1753 CTCGATGTAAGCAGATCTTCGAATCCCAGCTTCTTAATGAGACAACTAAGAAGCAGGGCGAAGCA
1 CTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGA-AACTGAGAAGCAAGTCGAAGCA
* *
1818 ATAAAA-GGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAGATTCGTTTTCCTGATGAGATA
65 ATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
* * * * * * *
1882 CAGAGAAGCGGATTGAAACAAGCAATGCAGTCATCTTCTTGATGAGATACAGAGAAGAATACCAA
130 CAGAGAAGCGGATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAA
** *
1947 CTCGAGGCTCAA
195 CTCGAAACCCAA
* * *
1959 --C-A--CGAGCAAATCTTCGAACCCCTAACTTCCTGATGAGACACAGAGAAGCAAGTCGAAGCA
1 CTCGATGTGAGCAAATCTTCGAACCCC-AACTTCCTGATGAGAAACTGAGAAGCAAGTCGAAGCA
* * *
2019 ATAAAATGGTTAGCTTCTTGATGGGATACTAAGAAGTGAATCAAATTCGTCTTCCTGATGAGATA
65 ATAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATA
2084 CAGAGAAGCGGATTGAAACCAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCG
130 CAGAGAAGCGGATTGAAA-CAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACC-
2149 AA-TC-AAACCCACA
193 AACTCGAAACCCA-A
* * *
2162 CTCGATGTGAGCAAATTTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAACAA
1 CTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGAAACTGAGAAGCAAGTCGAAGCAA
* ** * * *
2227 TAAAATGGTTAGCTTCTTGATGAAATAC-GAGAAGTGAACCAAAACCATCTTCCTGATGAAAAAC
66 TAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
* ** ** * * * * *
2291 AAAGAAATGGATCAAAACAAGTGATATGGTCGTCTTCCTAATGAGGTACTGAGAAGAAGGCCAA
131 AGAGAAGCGGATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAA
2355 GTCAATGAAA
Statistics
Matches: 335, Mismatches: 51, Indels: 22
0.82 0.12 0.05
Matches are distributed among these distances:
201 39 0.12
202 87 0.26
203 42 0.13
204 5 0.01
205 41 0.12
206 42 0.13
207 61 0.18
208 18 0.05
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (206 bp):
CTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGAAACTGAGAAGCAAGTCGAAGCAA
TAAAATGGTTAGCTTCTTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATAC
AGAGAAGCGGATTGAAACAAGCGATACGGTCATCTTCCTAATGAGATACTGAGAAGAAGACCAAC
TCGAAACCCAA
Found at i:2683 original size:6 final size:6
Alignment explanation
Indices: 2672--2758 Score: 69
Period size: 6 Copynumber: 15.2 Consensus size: 6
2662 GGGCCCAACA
* * * *
2672 AAATTT AAATTT -ATTTT AAAATT AAGTTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
*
2718 --ATTGG AAATTT AAATTT --ATTAT AAATTT AAATTT AAATTT A
1 AAATT-T AAATTT AAATTT AAATT-T AAATTT AAATTT AAATTT A
2759 TTTAAATAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
4 6 0.09
5 9 0.14
6 43 0.67
7 6 0.09
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (6 bp):
AAATTT
Found at i:2701 original size:17 final size:17
Alignment explanation
Indices: 2672--2752 Score: 117
Period size: 17 Copynumber: 4.8 Consensus size: 17
2662 GGGCCCAACA
2672 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
* *
2689 AAAATTAAGTTTATTTT
1 AAATTTAAATTTATTTT
**
2706 AAATTTAAATTTATTGG
1 AAATTTAAATTTATTTT
*
2723 AAATTTAAATTTATTAT
1 AAATTTAAATTTATTTT
2740 AAATTTAAATTTA
1 AAATTTAAATTTA
2753 AATTTATTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:2729 original size:23 final size:21
Alignment explanation
Indices: 2703--2765 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 21
2693 TTAAGTTTAT
2703 TTTAAATTTAAATTTATTGGAAA
1 TTTAAATTTAAATTTATT--AAA
2726 TTTAAATTT--A-TTA-TAAA
1 TTTAAATTTAAATTTATTAAA
2743 TTTAAATTTAAATTTATTTAAA
1 TTTAAATTTAAATTTA-TTAAA
2765 T
1 T
2766 AATGTCCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 12 0.34
19 2 0.06
20 6 0.17
21 1 0.03
22 5 0.14
23 9 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (21 bp):
TTTAAATTTAAATTTATTAAA
Found at i:3433 original size:3 final size:3
Alignment explanation
Indices: 3425--3460 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
3415 TGTAATAGGT
* *
3425 TAA TAA TAA TAA CAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3461 CATTAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:4111 original size:5 final size:5
Alignment explanation
Indices: 4101--4126 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4091 CGGCCCGAAT
4101 CCGAC CCGAC CCGAC CCGAC CCGAC C
1 CCGAC CCGAC CCGAC CCGAC CCGAC C
4127 TAGGATCCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.62, G:0.19, T:0.00
Consensus pattern (5 bp):
CCGAC
Found at i:4567 original size:30 final size:31
Alignment explanation
Indices: 4531--4672 Score: 159
Period size: 30 Copynumber: 4.7 Consensus size: 31
4521 TGTCACCCAC
*
4531 AAACTTCCAAAGATTCCATTTTTAACCTC-G
1 AAACTTCCAAAAATTCCATTTTTAACCTCTG
**
4561 AAACTTCCAAAAATTCCATTTTGGACCT-TG
1 AAACTTCCAAAAATTCCATTTTTAACCTCTG
* *
4591 AAACTTCTAAAAATTCCATTTTT-ACCCCTG
1 AAACTTCCAAAAATTCCATTTTTAACCTCTG
* * *
4621 -AACCTCCAAAATTTCCATTTTTAACC-CTA
1 AAACTTCCAAAAATTCCATTTTTAACCTCTG
*
4650 AAACTTTCAAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
4673 GCCCTCGGAT
Statistics
Matches: 94, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
29 24 0.26
30 63 0.67
31 7 0.07
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (31 bp):
AAACTTCCAAAAATTCCATTTTTAACCTCTG
Found at i:4637 original size:59 final size:60
Alignment explanation
Indices: 4531--4672 Score: 155
Period size: 59 Copynumber: 2.4 Consensus size: 60
4521 TGTCACCCAC
* * * * * *
4531 AAACTTCCAAAGATTCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTGGACCTTG
1 AAACTTCTAAAAATTCCATTTTTAACCTCGAAACCTCCAAAAATTCCATTTTGAACCCTA
* * *
4591 AAACTTCTAAAAATTCCATTTTT-ACCCCTG-AACCTCCAAAATTTCCATTTTTAACCCTA
1 AAACTTCTAAAAATTCCATTTTTAACCTC-GAAACCTCCAAAAATTCCATTTTGAACCCTA
4650 AAACTT-TCAAAAATTACCATTTT
1 AAACTTCT-AAAAATT-CCATTTT
4673 GCCCTCGGAT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.01
59 40 0.57
60 29 0.41
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (60 bp):
AAACTTCTAAAAATTCCATTTTTAACCTCGAAACCTCCAAAAATTCCATTTTGAACCCTA
Found at i:4688 original size:59 final size:57
Alignment explanation
Indices: 4625--4793 Score: 187
Period size: 59 Copynumber: 2.9 Consensus size: 57
4615 CCCCTGAACC
*
4625 TCCAAAATTTCCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTGCCCTCGGATG
1 TCCAAAATTTCCATTTTTAACCCTAAAA-TTTC-AAAATTACCATTTTGCCCTCGAATG
** * * * * *
4684 TCCAAAAACTCCATTTTTAACCTCAAAAATCTCAAAATTACCCTTTTACCCTCTAATG
1 TCCAAAATTTCCATTTTTAACC-CTAAAATTTCAAAATTACCATTTTGCCCTCGAATG
* *
4742 TCTAAAAATTTCC-TTTTTAACCCCAAAATTTCCCAAAATTACCATTTTGCCC
1 TC-CAAAATTTCCATTTTTAACCCTAAAATTT--CAAAATTACCATTTTGCCC
4794 CTAAAAATCC
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
57 7 0.08
58 32 0.35
59 47 0.52
60 5 0.05
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.35
Consensus pattern (57 bp):
TCCAAAATTTCCATTTTTAACCCTAAAATTTCAAAATTACCATTTTGCCCTCGAATG
Found at i:4730 original size:29 final size:29
Alignment explanation
Indices: 4698--4817 Score: 93
Period size: 29 Copynumber: 4.1 Consensus size: 29
4688 AAAACTCCAT
* *
4698 TTTTAACCTCAAAAATCTCAAAATTACCC
1 TTTTAACCCCAAAAATCTCAAAATTACCA
* ** * * *
4727 TTTT-ACCCTCTAATGTCTAAAAATTTCCT
1 TTTTAACCC-CAAAAATCTCAAAATTACCA
* *
4756 TTTTAACCCCAAAATTTCCCAAAATTACCA
1 TTTTAACCCCAAAA-ATCTCAAAATTACCA
*
4786 TTTT-GCCCCTAAAAATC-CAAAATTACCA
1 TTTTAACCCC-AAAAATCTCAAAATTACCA
4814 TTTT
1 TTTT
4818 GCCCCCCGGG
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
28 18 0.25
29 31 0.44
30 22 0.31
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
TTTTAACCCCAAAAATCTCAAAATTACCA
Found at i:4749 original size:58 final size:58
Alignment explanation
Indices: 4628--4797 Score: 175
Period size: 58 Copynumber: 2.9 Consensus size: 58
4618 CTGAACCTCC
* * * **
4628 AAAATTTCCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTGCCCTCGGATGTCCA
1 AAAATCTCCATTTTTAACCC-AAAAATCTC-AAAATTACCATTTTGCCCTCTAATGTCCA
* * *
4688 AAAA-CTCCATTTTTAACCTCAAAAATCTCAAAATTACCCTTTTACCCTCTAATGTCTA
1 AAAATCTCCATTTTTAACC-CAAAAATCTCAAAATTACCATTTTGCCCTCTAATGTCCA
* * *
4746 AAAATTTCC-TTTTTAACCCCAAAATTTCCCAAAATTACCATTTTGCCC-CTAA
1 AAAATCTCCATTTTTAA-CCCAAAA-ATCTCAAAATTACCATTTTGCCCTCTAA
4798 AAATCCAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
58 44 0.47
59 44 0.47
60 5 0.05
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (58 bp):
AAAATCTCCATTTTTAACCCAAAAATCTCAAAATTACCATTTTGCCCTCTAATGTCCA
Found at i:4808 original size:58 final size:58
Alignment explanation
Indices: 4625--4817 Score: 185
Period size: 59 Copynumber: 3.3 Consensus size: 58
4615 CCCCTGAACC
* * **
4625 TCCAAAATTTCCATTTTTAACCCTAAAACTTT-CAAAAATTACCATTTTGCCCTCGGATG
1 TCCAAAATTTCCATTTTTAACCCCAAAA-TTTCCCAAAATTACCATTTTGCCC-CTAATG
** * * * * *
4684 TCCAAAAACTCCATTTTTAACCTCAAAA-ATCTCAAAATTACCCTTTTACCCTCTAATG
1 TCCAAAATTTCCATTTTTAACCCCAAAATTTCCCAAAATTACCATTTTGCCC-CTAATG
* **
4742 TCTAAAAATTTCC-TTTTTAACCCCAAAATTTCCCAAAATTACCATTTTGCCCCTAAAAA
1 TC-CAAAATTTCCATTTTTAACCCCAAAATTTCCCAAAATTACCATTTTGCCCCT-AATG
*
4801 TCCAAAATTACCATTTT
1 TCCAAAATTTCCATTTT
4818 GCCCCCCGGG
Statistics
Matches: 106, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
57 1 0.01
58 47 0.44
59 58 0.55
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
TCCAAAATTTCCATTTTTAACCCCAAAATTTCCCAAAATTACCATTTTGCCCCTAATG
Found at i:9812 original size:20 final size:20
Alignment explanation
Indices: 9789--9850 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
9779 ATTTTTTAAA
9789 ATTTAAAAAAATAAAAAATT
1 ATTTAAAAAAATAAAAAATT
** *
9809 ATTTTTAAAAATGAAAAATT
1 ATTTAAAAAAATAAAAAATT
*
9829 A-TTAAAAAAGTATAAAAATT
1 ATTTAAAAAAATA-AAAAATT
9849 AT
1 AT
9851 AAAATATAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
ATTTAAAAAAATAAAAAATT
Found at i:10758 original size:18 final size:18
Alignment explanation
Indices: 10737--10771 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
10727 AAATTAAATT
*
10737 AATTTGGTTAATTGATCG
1 AATTTGGTTAATCGATCG
10755 AATTTGGTTAATCGATC
1 AATTTGGTTAATCGATC
10772 AGTTAATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (18 bp):
AATTTGGTTAATCGATCG
Found at i:11991 original size:83 final size:83
Alignment explanation
Indices: 11852--12022 Score: 333
Period size: 83 Copynumber: 2.1 Consensus size: 83
11842 TACATTGGAC
11852 TTTGATTATATTTGGAATCTATCTACATCAAACTCTTAAACAGTAGGTAAGCTCCCCTAGCACTG
1 TTTGATTATATTTGGAATCTATCTACATCAAACTCTTAAACAGTAGGTAAGCTCCCCTAGCACTG
11917 GTTTTTCTATTTACAAGA
66 GTTTTTCTATTTACAAGA
*
11935 TTTGATTATATTTGGAATCTATCTAGATCAAACTCTTAAACAGTAGGTAAGCTCCCCTAGCACTG
1 TTTGATTATATTTGGAATCTATCTACATCAAACTCTTAAACAGTAGGTAAGCTCCCCTAGCACTG
12000 GTTTTTCTATTTACAAGA
66 GTTTTTCTATTTACAAGA
12018 TTTGA
1 TTTGA
12023 ATTTAAATTA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 87 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (83 bp):
TTTGATTATATTTGGAATCTATCTACATCAAACTCTTAAACAGTAGGTAAGCTCCCCTAGCACTG
GTTTTTCTATTTACAAGA
Found at i:14220 original size:31 final size:30
Alignment explanation
Indices: 14182--14260 Score: 97
Period size: 30 Copynumber: 2.6 Consensus size: 30
14172 TTTTTGGTCC
*
14182 AATTTGGTACTCAAACTTGACACCGTTTCTT
1 AATTTGGTACTCAAACTTAACACC-TTTCTT
*
14213 AATTTGGTAC-CTAAACTTAACACCTTTTTT
1 AATTTGGTACTC-AAACTTAACACCTTTCTT
* *
14243 AAGTTGGTACTTAAACTT
1 AATTTGGTACTCAAACTT
14261 TTTGGGCTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 21 0.50
31 21 0.50
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (30 bp):
AATTTGGTACTCAAACTTAACACCTTTCTT
Found at i:14557 original size:60 final size:60
Alignment explanation
Indices: 14464--14632 Score: 182
Period size: 60 Copynumber: 2.8 Consensus size: 60
14454 CAATAAATTT
* * * *
14464 AGGTACCAAATTTAATCTAAAAAAAGCTTAGGTACCAAATTAGAAAAAAA-TGCCAAGTTC
1 AGGTACCAAATTGAGTC-AAAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGCCAAGATC
* * *
14524 AGGTATCAAATTGAGTCCAAAAAAGGTTTAGGTACCAAATTA-AAAAAAAGTGTCAAGATC
1 AGGTACCAAATTGAGT-CAAAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGCCAAGATC
** * *
14584 AAATACCAAATTGAGT-AAACAAAAGTTTATGTACTAAATTAAGAAAAAA
1 AGGTACCAAATTGAGTCAAA-AAAAGTTTAGGTACCAAATT-AGAAAAAA
14633 TGTTAAATTC
Statistics
Matches: 91, Mismatches: 13, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
58 3 0.03
59 24 0.26
60 57 0.63
61 7 0.08
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (60 bp):
AGGTACCAAATTGAGTCAAAAAAAGTTTAGGTACCAAATTAGAAAAAAAGTGCCAAGATC
Found at i:14625 original size:59 final size:57
Alignment explanation
Indices: 14481--14654 Score: 188
Period size: 60 Copynumber: 2.9 Consensus size: 57
14471 AAATTTAATC
* * * ** *
14481 TAAAAAAAGCTTAGGTACCAAATTAGAAAAAAATGCCAAGTTCAGGTATCAAATTGAG
1 TAAAAAAAGTTTAGGTACCAAATTA-AAAAAAATGTCAAGATCAAATACCAAATTGAG
*
14539 TCCAAAAAAGGTTTAGGTACCAAATTAAAAAAAAGTGTCAAGATCAAATACCAAATTGAG
1 T--AAAAAAAGTTTAGGTACCAAATTAAAAAAAA-TGTCAAGATCAAATACCAAATTGAG
* * *
14599 TAAACAAAAGTTTATGTACTAAATTAAGAAAAAATGTTAA-ATTCAAATACCAAATT
1 TAAA-AAAAGTTTAGGTACCAAATTAA-AAAAAATGTCAAGA-TCAAATACCAAATT
14655 TATATTAAGA
Statistics
Matches: 99, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
58 5 0.05
59 45 0.45
60 49 0.49
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.25
Consensus pattern (57 bp):
TAAAAAAAGTTTAGGTACCAAATTAAAAAAAATGTCAAGATCAAATACCAAATTGAG
Found at i:16431 original size:16 final size:16
Alignment explanation
Indices: 16387--16436 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
16377 TTTAAAATAG
16387 AAAATTTTAAATTTA-
1 AAAATTTTAAATTTAT
* *
16402 GATATTTTATAATTTAT
1 AAAATTTTA-AATTTAT
*
16419 AAAATTTTAAATTGAT
1 AAAATTTTAAATTTAT
16435 AA
1 AA
16437 TAATAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 7 0.25
16 14 0.50
17 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (16 bp):
AAAATTTTAAATTTAT
Found at i:16455 original size:22 final size:23
Alignment explanation
Indices: 16403--16455 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 23
16393 TTAAATTTAG
*
16403 ATATTTT-ATAATTTATAAAATT
1 ATATTTTGATAATTAATAAAATT
* **
16425 TTAAATTGATAA-TAATAAAATT
1 ATATTTTGATAATTAATAAAATT
16447 ATATTTTGA
1 ATATTTTGA
16456 CTCTTAAAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATATTTTGATAATTAATAAAATT
Found at i:22860 original size:13 final size:13
Alignment explanation
Indices: 22842--22866 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22832 AAATATTAAT
22842 TAATTTATTTATC
1 TAATTTATTTATC
22855 TAATTTATTTAT
1 TAATTTATTTAT
22867 TTTTACAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TAATTTATTTATC
Found at i:24168 original size:18 final size:18
Alignment explanation
Indices: 24145--24207 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 18
24135 GGTTACGGGG
24145 TCTTTGTTTGTTGTTTGT
1 TCTTTGTTTGTTGTTTGT
**
24163 TCTTTGAATG-TGTTGTGT
1 TCTTTGTTTGTTGTT-TGT
*
24181 TCTTTATTGTTTGTTATTTGT
1 TC--T-TTGTTTGTTGTTTGT
24202 TCTTTG
1 TCTTTG
24208 AATGTGATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 4 0.11
18 16 0.46
19 1 0.03
20 1 0.03
21 10 0.29
22 3 0.09
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.67
Consensus pattern (18 bp):
TCTTTGTTTGTTGTTTGT
Found at i:24194 original size:16 final size:18
Alignment explanation
Indices: 24156--24225 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 18
24146 CTTTGTTTGT
24156 TGTT-TGTTCTTTGAATG
1 TGTTGTGTTCTTTGAATG
*
24173 TGTTGTGTTCTTT-ATTG
1 TGTTGTGTTCTTTGAATG
*
24190 TTTGTTATTTGTTCTTTGAATG
1 --TG-T-TGTGTTCTTTGAATG
* *
24212 TGATGAGTTCTTTG
1 TGTTGTGTTCTTTG
24226 TTTACTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
17 7 0.17
18 17 0.41
19 2 0.05
20 3 0.07
21 9 0.22
22 3 0.07
ACGTcount: A:0.11, C:0.06, G:0.23, T:0.60
Consensus pattern (18 bp):
TGTTGTGTTCTTTGAATG
Found at i:24201 original size:39 final size:39
Alignment explanation
Indices: 24148--24224 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
24138 TACGGGGTCT
* * *
24148 TTGTTTGTTGTTTGTTCTTTGAATGTGTTGTGTTCTTTA
1 TTGTTTGTTATTTGTTCTTTGAATGTGATGAGTTCTTTA
24187 TTGTTTGTTATTTGTTCTTTGAATGTGATGAGTTCTTT
1 TTGTTTGTTATTTGTTCTTTGAATGTGATGAGTTCTTT
24225 GTTTACTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.10, C:0.05, G:0.22, T:0.62
Consensus pattern (39 bp):
TTGTTTGTTATTTGTTCTTTGAATGTGATGAGTTCTTTA
Found at i:24227 original size:36 final size:36
Alignment explanation
Indices: 24145--24247 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 36
24135 GGTTACGGGG
* * *
24145 TCTTTGTTTGTTGTTTGTTCTTTGAATGTGTTGTGT
1 TCTTTGTTTGTTATTTGTTCTTTGAATGTGATGAGT
24181 TCTTTATTGTTTGTTATTTGTTCTTTGAATGTGATGAGT
1 TC--T-TTGTTTGTTATTTGTTCTTTGAATGTGATGAGT
** *
24220 TCTTTGTTTACTATTTGTTTTTTGAATG
1 TCTTTGTTTGTTATTTGTTCTTTGAATG
24248 GAGTTGTTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
36 24 0.41
37 1 0.02
38 1 0.02
39 32 0.55
ACGTcount: A:0.12, C:0.06, G:0.20, T:0.62
Consensus pattern (36 bp):
TCTTTGTTTGTTATTTGTTCTTTGAATGTGATGAGT
Found at i:26325 original size:30 final size:30
Alignment explanation
Indices: 26290--26511 Score: 195
Period size: 30 Copynumber: 7.5 Consensus size: 30
26280 AGAATTTGGT
**
26290 GTCAAAATGTAATTTTGGAAAAAATTAGGG
1 GTCAAAATGTAATTTTGGAAAAGTTTAGGG
* *
26320 GTC-AAATATAATTTTAGG-AAA-TTTTGGG
1 GTCAAAATGTAATTTT-GGAAAAGTTTAGGG
* * *
26348 GTTAAAATGTGATTTTGGAAAGGTTT-GGG
1 GTCAAAATGTAATTTTGGAAAAGTTTAGGG
*
26377 GTTCAAAATGTGATTTTGGAAAAGTTTAGGG
1 G-TCAAAATGTAATTTTGGAAAAGTTTAGGG
* * *
26408 GTTAAAATGTGATTTTAGAAAAGTTTAGGG
1 GTCAAAATGTAATTTTGGAAAAGTTTAGGG
* * *
26438 GTTAAAATGTAATTTTAG-AAAGTCTA-GG
1 GTCAAAATGTAATTTTGGAAAAGTTTAGGG
* * ** *
26466 GTTAAAATGCAATTTTAAAAAAGTTTAAGG
1 GTCAAAATGTAATTTTGGAAAAGTTTAGGG
* *
26496 GTTAGAATGTAATTTT
1 GTCAAAATGTAATTTT
26512 TAAATAAAAT
Statistics
Matches: 166, Mismatches: 18, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
28 27 0.16
29 44 0.27
30 91 0.55
31 4 0.02
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (30 bp):
GTCAAAATGTAATTTTGGAAAAGTTTAGGG
Found at i:26355 original size:58 final size:59
Alignment explanation
Indices: 26284--26511 Score: 196
Period size: 58 Copynumber: 3.9 Consensus size: 59
26274 TTTCGAAGAA
* * * *
26284 TTTGGTGTCAAAATGTAATTTTGGAAAAAATTAGGGG-TCAAATATAATTTTAGGAAAT
1 TTTGGGGTTAAAATGTAATTTTGGAAAAGATTAGGGGTTCAAATGTAATTTTAGGAAAT
* * * *
26342 TTTGGGGTTAAAATGTGATTTTGG-AAAGGTTTGGGGTTCAAAATGTGATTTT-GGAAAAGT
1 TTTGGGGTTAAAATGTAATTTTGGAAAAGATTAGGGGTTC-AAATGTAATTTTAGG-AAA-T
* * * * * *
26402 TTAGGGGTTAAAATGTGATTTTAGAAAAGTTTAGGGGTTAAAATGTAATTTTA-GAAAG
1 TTTGGGGTTAAAATGTAATTTTGGAAAAGATTAGGGGTTCAAATGTAATTTTAGGAAAT
* * * ** * *
26460 TCTAGGGTTAAAATGCAATTTTAAAAAAGTTTAAGGGTT-AGAATGTAATTTT
1 TTTGGGGTTAAAATGTAATTTTGGAAAAGATTAGGGGTTCA-AATGTAATTTT
26512 TAAATAAAAT
Statistics
Matches: 141, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
57 10 0.07
58 68 0.48
59 16 0.11
60 35 0.25
61 12 0.09
ACGTcount: A:0.36, C:0.02, G:0.25, T:0.37
Consensus pattern (59 bp):
TTTGGGGTTAAAATGTAATTTTGGAAAAGATTAGGGGTTCAAATGTAATTTTAGGAAAT
Found at i:28422 original size:85 final size:85
Alignment explanation
Indices: 28286--28443 Score: 226
Period size: 85 Copynumber: 1.9 Consensus size: 85
28276 TTCTTGGTCT
** * *
28286 ACTTCTCTGTATCTCATCAGGAAGATAACCACTTCATTGTTTTGATCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAGGAAGATAACCACTTCATTACTTTAACCCACTTCTCTGTATCTCAT
28351 CAGGAAGACAAATTTGGTTC
66 CAGGAAGACAAATTTGGTTC
* * * * * *
28371 ACTTCTTTGTATCTCGTCAGGAAGATGACCATTTTATTACTTTAACCCACTTCTCTGTATCTTAT
1 ACTTCTCTGTATCTCATCAGGAAGATAACCACTTCATTACTTTAACCCACTTCTCTGTATCTCAT
28436 CAGGAAGA
66 CAGGAAGA
28444 TGGGGTTTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 63 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (85 bp):
ACTTCTCTGTATCTCATCAGGAAGATAACCACTTCATTACTTTAACCCACTTCTCTGTATCTCAT
CAGGAAGACAAATTTGGTTC
Found at i:28640 original size:85 final size:85
Alignment explanation
Indices: 28494--28651 Score: 199
Period size: 85 Copynumber: 1.9 Consensus size: 85
28484 GATCTGATCT
* * * *
28494 ACTTCTTTATATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTTTGTATCTCAT
1 ACTTCTTTATATCTCATCAAGAAGATGACCGCCTCATAGTTTCAACCCACTTCTCTATATCTCAT
28559 CAAGAAGACGGATTTGGTCC
66 CAAGAAGACGGATTTGGTCC
* * * * * * **
28579 ACTTCTTTGTATCTCATTAGGAAGATGATCGCTTTATAGTTTTGACCCACTTCTCTATATCTCAT
1 ACTTCTTTATATCTCATCAAGAAGATGACCGCCTCATAGTTTCAACCCACTTCTCTATATCTCAT
*
28644 CAGGAAGA
66 CAAGAAGA
28652 TGTGGTTTGA
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 60 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (85 bp):
ACTTCTTTATATCTCATCAAGAAGATGACCGCCTCATAGTTTCAACCCACTTCTCTATATCTCAT
CAAGAAGACGGATTTGGTCC
Found at i:28648 original size:208 final size:208
Alignment explanation
Indices: 28282--28817 Score: 743
Period size: 208 Copynumber: 2.6 Consensus size: 208
28272 TCATTTCTTG
* * * * *
28282 GTCTACTTCTCTGTATCTCATCAGGAAGATAACCACTTCATTGTTTTGATCCACTTCTCTGTATC
1 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTTTGTATC
* ** * * *
28347 TCATCAGGAAGACAAATTTGGTTCACTTCTTTGTATCTCGTCAGGAAGATGACCATTTTATTACT
66 TCATCAAGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTACT
* *
28412 TTAACCCACTTCTCTGTATCTTATCAGGAAGATGGGGTTTGAAGTCTCATTCATATTGAGCTTCA
131 TTAACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCATATTGAGCTTCA
28477 CCTCATTGATCTGA
196 CCTCATTGAT-TGA
* * * *
28491 -TCTACTTCTTTATATCTCATCAAGAAGATGACCGCCTCATTGTTTCAATCCACTTCTTTGTATC
1 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTTTGTATC
* * * *
28555 TCATCAAGAAGACGGATTTGGTCCACTTCTTTGTATCTCATTAGGAAGATGATCGCTTTA-TAGT
66 TCATCAAGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTA-C
* * *
28619 TTTGACCCACTTCTCTATATCTCATCAGGAAGATGTGGTTTGAAGTCTCATTCGTATTGAGCTTC
130 TTTAACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCATATTGAGCTTC
* * *
28684 GCTTCATTGATTTA
195 ACCTCATTGATTGA
* *
28698 GTCTACTTCTCTGTATCTCATGAGGAAGATGACTGCCTCATTTGTTTTAATCCACTTCTTTGTAT
1 GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCA-TTGTTTTAATCCACTTCTTTGTAT
* * *
28763 CTCATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCAACAAGAAGATGACC
65 CTCATCAAGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACC
28818 TGATAATGCT
Statistics
Matches: 286, Mismatches: 38, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
207 4 0.01
208 209 0.73
209 73 0.26
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (208 bp):
GTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCATTGTTTTAATCCACTTCTTTGTATC
TCATCAAGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTACT
TTAACCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCATATTGAGCTTCA
CCTCATTGATTGA
Done.