Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008264.1 Kokia drynarioides strain JFW-HI SEQ_122929, 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: 57287
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Warning! 8 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--28 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29 TTGTTTAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2663 original size:3 final size:3
Alignment explanation
Indices: 2655--2684 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2645 TGAATGAACT
2655 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
2685 AAATGAAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3967 original size:22 final size:22
Alignment explanation
Indices: 3918--3970 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3908 ACTAAGTCTA
* *
3918 GTCGCAATGGCAAGGGCTCAAC
1 GTCGCGATGGCAAAGGCTCAAC
3940 GTCGCGATGGCAAAGGCT-AGAC
1 GTCGCGATGGCAAAGGCTCA-AC
3962 GTCGCGATG
1 GTCGCGATG
3971 TAACTGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 1 0.04
22 27 0.96
ACGTcount: A:0.25, C:0.25, G:0.36, T:0.15
Consensus pattern (22 bp):
GTCGCGATGGCAAAGGCTCAAC
Found at i:6409 original size:20 final size:19
Alignment explanation
Indices: 6384--6430 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
6374 GAAAATGTAG
*
6384 ACATATATTTAGCAATATCA
1 ACATATATTTAGCAA-AGCA
*
6404 ACATATCA-TTATCAAAGCA
1 ACATAT-ATTTAGCAAAGCA
6423 ACATATAT
1 ACATATAT
6431 ATATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 1 0.04
19 9 0.39
20 12 0.52
21 1 0.04
ACGTcount: A:0.47, C:0.17, G:0.04, T:0.32
Consensus pattern (19 bp):
ACATATATTTAGCAAAGCA
Found at i:10632 original size:15 final size:15
Alignment explanation
Indices: 10563--10659 Score: 74
Period size: 15 Copynumber: 6.3 Consensus size: 15
10553 AAAGAATAAC
10563 AAATAAAT-AAAAAT
1 AAATAAATAAAAAAT
**
10577 AAATAAAAGTAAGAATGT
1 AAAT-AAA-TAA-AAAAT
10595 AAATAACA-AAAAAA-
1 AAATAA-ATAAAAAAT
* * *
10609 AAATGAATAACAAGT
1 AAATAAATAAAAAAT
10624 AAATAAATAATAAAAT
1 AAATAAATAA-AAAAT
*
10640 AAATAAATAAAAATT
1 AAATAAATAAAAAAT
10655 AAATA
1 AAATA
10660 CTAAATAAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
13 1 0.02
14 13 0.20
15 23 0.36
16 16 0.25
17 3 0.05
18 8 0.12
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (15 bp):
AAATAAATAAAAAAT
Found at i:10641 original size:8 final size:9
Alignment explanation
Indices: 10563--10672 Score: 57
Period size: 9 Copynumber: 11.7 Consensus size: 9
10553 AAAGAATAAC
10563 AAATAAATAA
1 AAATAAAT-A
10573 AAATAAATA
1 AAATAAATA
*
10582 AAAGT-AAGA
1 AAA-TAAATA
**
10591 ATGTAAATA
1 AAATAAATA
*
10600 ACAA-AAAAA
1 A-AATAAATA
*
10609 AAATGAATA
1 AAATAAATA
10618 ACAAGTAAAT-
1 A-AA-TAAATA
10628 AAAT-AATA
1 AAATAAATA
10636 AAATAAATA
1 AAATAAATA
*
10645 AATAAAAATTA
1 AA-ATAAA-TA
10656 AATACTAAATA
1 AA-A-TAAATA
10667 AAATAA
1 AAATAA
10673 TGCAAATAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 23
0.69 0.11 0.21
Matches are distributed among these distances:
7 3 0.04
8 8 0.10
9 32 0.42
10 17 0.22
11 14 0.18
12 3 0.04
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (9 bp):
AAATAAATA
Found at i:10658 original size:31 final size:30
Alignment explanation
Indices: 10563--10659 Score: 92
Period size: 31 Copynumber: 3.2 Consensus size: 30
10553 AAAGAATAAC
*
10563 AAATAAAT-AAAAATAAATAAAAGTAAGAATGT
1 AAATAAATAAAAAATAAAT-AAA-TAAAAAT-T
* * *
10595 AAATAACA-AAAAAA-AAATGAATAACAAGT
1 AAATAA-ATAAAAAATAAATAAATAAAAATT
10624 AAATAAATAATAAAATAAATAAATAAAAATT
1 AAATAAATAA-AAAATAAATAAATAAAAATT
10655 AAATA
1 AAATA
10660 CTAAATAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
28 1 0.02
29 9 0.17
30 9 0.17
31 19 0.35
32 10 0.19
33 6 0.11
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (30 bp):
AAATAAATAAAAAATAAATAAATAAAAATT
Found at i:10667 original size:31 final size:31
Alignment explanation
Indices: 10566--10672 Score: 87
Period size: 31 Copynumber: 3.4 Consensus size: 31
10556 GAATAACAAA
*
10566 TAAATAAAAATAAATAAAAGTAAGAATGTAAATAAC
1 TAAAT-AAAATAAAT-AAA-TAAAAAT-TAAAT-AC
* * *
10602 -AAA-AAAA-AAATGAATAACAAGTAAATA-
1 TAAATAAAATAAATAAATAAAAATTAAATAC
*
10629 AATAATAAAATAAATAAATAAAAATTAAATAC
1 TA-AATAAAATAAATAAATAAAAATTAAATAC
10661 TAAATAAAATAA
1 TAAATAAAATAA
10673 TGCAAATAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
28 2 0.03
29 7 0.12
30 9 0.15
31 29 0.49
32 5 0.08
33 4 0.07
35 3 0.05
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.21
Consensus pattern (31 bp):
TAAATAAAATAAATAAATAAAAATTAAATAC
Found at i:17703 original size:18 final size:17
Alignment explanation
Indices: 17682--17727 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
17672 TTTTTAAAAA
17682 TATAAATTTTGGAATTTT
1 TATAAATTTTGGAA-TTT
*
17700 TATAAATATTTTGAATTT
1 TATAAAT-TTTGGAATTT
*
17718 TAAAAATTTT
1 TATAAATTTT
17728 AAAATTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 16 0.64
19 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (17 bp):
TATAAATTTTGGAATTT
Found at i:23775 original size:32 final size:33
Alignment explanation
Indices: 23735--23806 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
23725 AGTTTTCTTG
23735 AAATATTTT-CAAAAAATCT-GTCAAACAATAGA
1 AAATATTTTAC-AAAAATCTAGTCAAACAATAGA
* * * *
23767 AAATATTTTACACAAATTTATTCAAACACTAGA
1 AAATATTTTACAAAAATCTAGTCAAACAATAGA
23800 AAATATT
1 AAATATT
23807 AACTTTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 15 0.44
33 19 0.56
ACGTcount: A:0.51, C:0.12, G:0.04, T:0.32
Consensus pattern (33 bp):
AAATATTTTACAAAAATCTAGTCAAACAATAGA
Found at i:29717 original size:16 final size:16
Alignment explanation
Indices: 29696--29726 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29686 AAAGGTTGAA
29696 AACTTCTCTACACATG
1 AACTTCTCTACACATG
29712 AACTTCTCTACACAT
1 AACTTCTCTACACAT
29727 CCATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.32
Consensus pattern (16 bp):
AACTTCTCTACACATG
Found at i:31709 original size:65 final size:66
Alignment explanation
Indices: 31604--31742 Score: 271
Period size: 65 Copynumber: 2.1 Consensus size: 66
31594 AGATTATAAA
31604 TTCACTAAATCTTGTTCAAACAACCATTAAAATTAAGTAAAACAATCTCACAACACATGTAATTC
1 TTCACTAAATCTTGTTCAAACAACCATTAAAATTAAGTAAAACAATCTCACAACACATGTAATTC
31669 C
66 C
31670 -TCACTAAATCTTGTTCAAACAACCATTAAAATTAAGTAAAACAATCTCACAACACATGTAATTC
1 TTCACTAAATCTTGTTCAAACAACCATTAAAATTAAGTAAAACAATCTCACAACACATGTAATTC
31734 C
66 C
31735 TTCACTAA
1 TTCACTAA
31743 GCATATAATG
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 65 0.90
66 7 0.10
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (66 bp):
TTCACTAAATCTTGTTCAAACAACCATTAAAATTAAGTAAAACAATCTCACAACACATGTAATTC
C
Found at i:33092 original size:80 final size:80
Alignment explanation
Indices: 32955--33112 Score: 221
Period size: 80 Copynumber: 2.0 Consensus size: 80
32945 AATCAAATCC
* * * *
32955 GTCAATTCATGGCACCTAGTGCCTAGCGGATAAATCGCAATAAGTGAGTCCAACTCTAGTTGGAT
1 GTCAATTCATGGCACCCAATGCCTAGCGAATAAATCGCAATAAATGAGTCCAACTCTAGTTGGAT
33020 TAACCAACAATTTCT
66 TAACCAACAATTTCT
* *
33035 GTCAATTCATGGCACCCAATGCCTAGCGAATTAA-CTGCAATAAATGAG-CTCAGCTCTAGTTGG
1 GTCAATTCATGGCACCCAATGCCTAGCGAATAAATC-GCAATAAATGAGTC-CAACTCTAGTTGG
*
33098 ATTAACCAACGATTT
64 ATTAACCAACAATTT
33113 GCGCCCAACG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
79 2 0.03
80 67 0.97
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (80 bp):
GTCAATTCATGGCACCCAATGCCTAGCGAATAAATCGCAATAAATGAGTCCAACTCTAGTTGGAT
TAACCAACAATTTCT
Found at i:37966 original size:14 final size:15
Alignment explanation
Indices: 37942--37971 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
37932 TTGTTTTAAT
37942 TTTATTTTATATTTA
1 TTTATTTTATATTTA
37957 TTTA-TTTATATTTA
1 TTTATTTTATATTTA
37971 T
1 T
37972 AAAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTATATTTA
Found at i:38590 original size:101 final size:101
Alignment explanation
Indices: 38453--38719 Score: 270
Period size: 101 Copynumber: 2.6 Consensus size: 101
38443 TAAATTCAAT
* * * * * *
38453 CCACTGCAACTTCAAGGATATAAGATTTGATGTTGTAGCTTCATCTTGCTCCACTGTAGCTTTAG
1 CCACTGCAACTTCAAGGATATAGGATTTGGTTTTGTAGCTTCATCCTGCTCCACTGCAACTTTAG
* * * * *
38518 GGAGATAAAGATTTGA-TTTCAT-GACTTTAATCTGAC
66 AGAGATAAAGA-TTCACCTTCATAG-CTTCAATCCGAC
* * *
38554 CCACTGCAACTTCAAGGATATAGGATTTGGTTTTGTAGCTTCATCCTGCTCTATTGCAACTTTAT
1 CCACTGCAACTTCAAGGATATAGGATTTGGTTTTGTAGCTTCATCCTGCTCCACTGCAACTTTAG
* * *
38619 AGAGATAATGATTCACCTTCGTAGCTTCAATCCGAT
66 AGAGATAAAGATTCACCTTCATAGCTTCAATCCGAC
* * * * ** *
38655 CGACTGCAACTTTAGGGATATAGGATTTGGTTTTGTAACTTCA-CTCTATTCCACTACAACTTTA
1 CCACTGCAACTTCAAGGATATAGGATTTGGTTTTGTAGCTTCATC-CTGCTCCACTGCAACTTTA
38719 G
65 G
38720 TGGAGATCGA
Statistics
Matches: 136, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
100 4 0.03
101 131 0.96
102 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (101 bp):
CCACTGCAACTTCAAGGATATAGGATTTGGTTTTGTAGCTTCATCCTGCTCCACTGCAACTTTAG
AGAGATAAAGATTCACCTTCATAGCTTCAATCCGAC
Found at i:38612 original size:50 final size:49
Alignment explanation
Indices: 38556--38697 Score: 133
Period size: 51 Copynumber: 2.8 Consensus size: 49
38546 AATCTGACCC
* * *
38556 ACTGCAACTTCAAGGATATAGGATTTGGTTTTGTAGCTTCATCCTGCTCT
1 ACTGCAACTTTAAGGATATAGGATTTGGTTTTGTAGCTTCATCC-GATCG
* * **** *
38606 ATTGCAACTTTATAGAGATA-ATGATTCACCTTCGTAGCTTCAATCCGATCG
1 ACTGCAACTTTA-AG-GATATAGGATTTGGTTTTGTAGCTTC-ATCCGATCG
* *
38657 ACTGCAACTTTAGGGATATAGGATTTGGTTTTGTAACTTCA
1 ACTGCAACTTTAAGGATATAGGATTTGGTTTTGTAGCTTCA
38698 CTCTATTCCA
Statistics
Matches: 69, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
49 5 0.07
50 25 0.36
51 31 0.45
52 8 0.12
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (49 bp):
ACTGCAACTTTAAGGATATAGGATTTGGTTTTGTAGCTTCATCCGATCG
Found at i:38816 original size:51 final size:51
Alignment explanation
Indices: 38747--38926 Score: 160
Period size: 51 Copynumber: 3.5 Consensus size: 51
38737 TACTGTCATT
* *
38747 TTTAATCC-ACCCCTCTACAACTTTAGGGAGATAAATGTTTGCTTTCATGAC
1 TTTAATCCGA-CCCACTACAACTTCAGGGAGATAAATGTTTGCTTTCATGAC
*
38798 TTTAATCCGACCCACTACAACTTCAGGG-GTATAAGAT-TTGATG-TTGCA-G-C
1 TTTAATCCGACCCACTACAACTTCAGGGAG-ATAA-ATGTT--TGCTTTCATGAC
* * ** *
38848 -TTCATCTTG-CTCCACTGTAACTTTAGGGAGATAAATGTTTGCTTTCATGAC
1 TTTAATC-CGAC-CCACTACAACTTCAGGGAGATAAATGTTTGCTTTCATGAC
*
38899 TTTAATTCGACCCACTACAACTTCAGGG
1 TTTAATCCGACCCACTACAACTTCAGGG
38927 GTATGGGATT
Statistics
Matches: 100, Mismatches: 15, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
48 2 0.02
49 12 0.12
50 24 0.24
51 48 0.48
52 12 0.12
53 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (51 bp):
TTTAATCCGACCCACTACAACTTCAGGGAGATAAATGTTTGCTTTCATGAC
Found at i:38966 original size:101 final size:101
Alignment explanation
Indices: 38765--38969 Score: 322
Period size: 101 Copynumber: 2.0 Consensus size: 101
38755 ACCCCTCTAC
38765 AACTTTAGGGAGATAAATGTTTGCTTTCATGACTTTAATCCGACCCACTACAACTTCAGGGGTAT
1 AACTTTAGGGAGATAAATGTTTGCTTTCATGACTTTAATCCGACCCACTACAACTTCAGGGGTAT
* *
38830 AAGATTTGATGTTGCAGCTTCATCTTGCTCCACTGT
66 AAGATTTGATGTTGCAACTTCATCTTACTCCACTGT
*
38866 AACTTTAGGGAGATAAATGTTTGCTTTCATGACTTTAATTCGACCCACTACAACTTCAGGGGTAT
1 AACTTTAGGGAGATAAATGTTTGCTTTCATGACTTTAATCCGACCCACTACAACTTCAGGGGTAT
** * * *
38931 GGGATTTGATGTTGTAACTTC-TCTCTATTCTACTGT
66 AAGATTTGATGTTGCAACTTCATCT-TACTCCACTGT
38967 AAC
1 AAC
38970 CTCAGGGACA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 3 0.03
101 92 0.97
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.36
Consensus pattern (101 bp):
AACTTTAGGGAGATAAATGTTTGCTTTCATGACTTTAATCCGACCCACTACAACTTCAGGGGTAT
AAGATTTGATGTTGCAACTTCATCTTACTCCACTGT
Found at i:39341 original size:49 final size:49
Alignment explanation
Indices: 39250--39461 Score: 244
Period size: 49 Copynumber: 4.3 Consensus size: 49
39240 TGCTTCTCCT
* ** * *
39250 CATCTTTAGGGTATAAGATTCACCGTTACGACTTTAATCTTTCTCTTCA
1 CATCTTTAGGGTATAAGGTTCGTCGTTACGACTTCAATCTTTCCCTTCA
* * * * *
39299 CATCTTTAGGGTATAAGGTTTGTCGTTGCGGCTTCAACCTTTCCCTCCA
1 CATCTTTAGGGTATAAGGTTCGTCGTTACGACTTCAATCTTTCCCTTCA
* * * * *
39348 CATCTCTAGGGTATAAGGTTCGTCATTGCGGCTTCAATCTTTCACTTCA
1 CATCTTTAGGGTATAAGGTTCGTCGTTACGACTTCAATCTTTCCCTTCA
* *
39397 CATCTCTAAGGTATAAGGTTCGTCGTTACGACTTCAATCTTTCCCTTCA
1 CATCTTTAGGGTATAAGGTTCGTCGTTACGACTTCAATCTTTCCCTTCA
**
39446 TGTCTTCTAGGGTATA
1 CATCTT-TAGGGTATA
39462 TGATTCAATA
Statistics
Matches: 137, Mismatches: 25, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
49 129 0.94
50 8 0.06
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (49 bp):
CATCTTTAGGGTATAAGGTTCGTCGTTACGACTTCAATCTTTCCCTTCA
Found at i:40096 original size:112 final size:112
Alignment explanation
Indices: 39889--40104 Score: 326
Period size: 112 Copynumber: 1.9 Consensus size: 112
39879 TATCGTTAGA
* *
39889 CCACTAACCGTCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAAGTGGATAAAATTGATTTT
1 CCACTAACCATCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAAGTGGATAAAATTGAATTT
* *
39954 TATTGGAGACAAATCTCATTTGAATGAAAAGATTAAAAATCATTATT
66 TATTGGAGACAAAGCTCATTTGAATCAAAAGATTAAAAATCATTATT
* * *
40001 CCACTAACCATTATTTCAATGCAAACATGCTTGAACAGGGTTGTAAGGTGGATAAAATTGAATTT
1 CCACTAACCATCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAAGTGGATAAAATTGAATTT
* * *
40066 TGTTGGAGGCAAAGCTCGTTT-ATATCAAAAGATTAAAAA
66 TATTGGAGACAAAGCTCATTTGA-ATCAAAAGATTAAAAA
40105 CGACAAACAT
Statistics
Matches: 93, Mismatches: 10, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
111 1 0.01
112 92 0.99
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (112 bp):
CCACTAACCATCATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAAGTGGATAAAATTGAATTT
TATTGGAGACAAAGCTCATTTGAATCAAAAGATTAAAAATCATTATT
Found at i:40439 original size:19 final size:19
Alignment explanation
Indices: 40416--40498 Score: 66
Period size: 19 Copynumber: 4.4 Consensus size: 19
40406 TTGACCTCTC
40416 CTTTTTC-TTTTTCTTTTT
1 CTTTTTCTTTTTTCTTTTT
* *
40434 CTTTTTTTTTTTTC-TCTT
1 CTTTTTCTTTTTTCTTTTT
*
40452 CTTTCTCTTTTTTTCCTTTTT
1 CTTTTTC-TTTTTT-CTTTTT
*
40473 -TTCTTTATTTTTTCTTTGTT
1 CTT-TTTCTTTTTTCTTT-TT
40493 -TTTTTC
1 CTTTTTC
40499 CTTTGGGTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
18 14 0.27
19 19 0.37
20 13 0.25
21 5 0.10
ACGTcount: A:0.01, C:0.17, G:0.01, T:0.81
Consensus pattern (19 bp):
CTTTTTCTTTTTTCTTTTT
Found at i:40494 original size:11 final size:10
Alignment explanation
Indices: 40418--40496 Score: 65
Period size: 9 Copynumber: 7.9 Consensus size: 10
40408 GACCTCTCCT
40418 TTTTCTTTTTC
1 TTTT-TTTTTC
*
40429 TTTTTCTTT-
1 TTTTTTTTTC
40438 TTTTTTTTTC
1 TTTTTTTTTC
* *
40448 -TCTTCTTTC
1 TTTTTTTTTC
*
40457 TCTTTTTTTC
1 TTTTTTTTTC
*
40467 -CTTTTTTTC
1 TTTTTTTTTC
40476 TTTATTTTTTC
1 TTT-TTTTTTC
40487 TTTGTTTTTT
1 TTT-TTTTTT
40497 TCCTTTGGGT
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
9 24 0.44
10 11 0.20
11 20 0.36
ACGTcount: A:0.01, C:0.15, G:0.01, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:43599 original size:51 final size:51
Alignment explanation
Indices: 43473--43758 Score: 380
Period size: 51 Copynumber: 5.5 Consensus size: 51
43463 TTTCATGTAA
* *
43473 TACTCACGATGACA-TATAGTCATCGGACCCCTTT-GTTCCGT-ATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGA--CCTTTAATT-CGTAAT-GG-ATTCATT
* *
43527 TACTCACGATGACACTAAGTCATCGGACCTTTAATTCGTTATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAATGGATTCATT
*
43578 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAATGGATTCATT
* * *
43629 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCTTT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAATGGATTCATT
* *
43680 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAATGGATTCATT
* * *
43731 TACTTATGATGACACTTAGTTATCGGAC
1 TACTCACGATGACACTTAGTCATCGGAC
43759 TTTTTCGTTT
Statistics
Matches: 216, Mismatches: 13, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
51 177 0.82
52 10 0.05
53 4 0.02
54 24 0.11
55 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATTCGTAATGGATTCATT
Found at i:43756 original size:153 final size:155
Alignment explanation
Indices: 43473--43758 Score: 425
Period size: 153 Copynumber: 1.9 Consensus size: 155
43463 TTTCATGTAA
** *
43473 TACTCACGATGACATATAGTCATCGGACCCCTTTGTTCCGTATAGGAATTCATATACTCACGATG
1 TACTCACGATGACATATAGTCATCGGA-CCCTTTAATCCGTAAAGGAATTCATATACTCACGATG
* * *
43538 ACACTAAGTCATCGGACCTTTAATTCGTTATGGATTCATTTACTCACGATGACACTTAGTCATCG
65 ACACTAAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCG
43603 GACCTTTAATTCGTCATGGATTCATT
130 GACCTTTAATTCGTCATGGATTCATT
* *
43629 TACTCACGATGACACT-TAGTCATCGGA-CCTTTAATCCGTAAAGG-ATTCTTTTACTCACGATG
1 TACTCACGATGACA-TATAGTCATCGGACCCTTTAATCCGTAAAGGAATTCATATACTCACGATG
* * * *
43691 ACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTTATGATGACACTTAGTTATCG
65 ACACTAAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCG
43756 GAC
130 GAC
43759 TTTTTCGTTT
Statistics
Matches: 117, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
153 77 0.66
154 14 0.12
156 25 0.21
157 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (155 bp):
TACTCACGATGACATATAGTCATCGGACCCTTTAATCCGTAAAGGAATTCATATACTCACGATGA
CACTAAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGG
ACCTTTAATTCGTCATGGATTCATT
Found at i:47387 original size:24 final size:24
Alignment explanation
Indices: 47342--47387 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
47332 TTTTTTTTGG
* *
47342 TTAAATTAAAATAAAAATAAAGTT
1 TTAAAGTAAAATAAAAAAAAAGTT
47366 TTAAAGTAAAA-AAATAAAAAAG
1 TTAAAGTAAAATAAA-AAAAAAG
47388 GAAAAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (24 bp):
TTAAAGTAAAATAAAAAAAAAGTT
Found at i:49375 original size:8 final size:9
Alignment explanation
Indices: 49351--49530 Score: 57
Period size: 10 Copynumber: 18.8 Consensus size: 9
49341 AATGATAAAA
*
49351 ATAAAAGTT
1 ATAAAAATT
49360 AT-AAAATT
1 ATAAAAATT
49368 A-AAAAATTTT
1 ATAAAAA--TT
49378 AATAAAAA-T
1 -ATAAAAATT
49387 ATTAAAAAATT
1 A-T-AAAAATT
49398 ATTAAAAATT
1 A-TAAAAATT
*
49408 A-GAAAATT
1 ATAAAAATT
*
49416 GTAAAAAATT
1 AT-AAAAATT
49426 ATAAAAAAATT
1 AT--AAAAATT
*
49437 ATAAAACTTT
1 ATAAAA-ATT
*
49447 ACAAAAATCGT
1 ATAAAAAT--T
*
49458 AAAAAAATT
1 ATAAAAATT
*
49467 ATAAAATTTT
1 ATAAAA-ATT
*
49477 ATAAAGTCATT
1 ATAAA--AATT
*
49488 A-GAAAATT
1 ATAAAAATT
49496 ATAAAAAATT
1 AT-AAAAATT
*
49506 -TAAAGAAAT
1 ATAAA-AATT
*
49515 ATAAAATTT
1 ATAAAAATT
*
49524 GTAAAAA
1 ATAAAAA
49531 AATTATCGTA
Statistics
Matches: 129, Mismatches: 21, Indels: 42
0.67 0.11 0.22
Matches are distributed among these distances:
8 24 0.19
9 26 0.20
10 48 0.37
11 26 0.20
12 5 0.04
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:49413 original size:18 final size:18
Alignment explanation
Indices: 49362--49520 Score: 88
Period size: 19 Copynumber: 8.1 Consensus size: 18
49352 TAAAAGTTAT
49362 AAAATTAAAAAATTTTAATAA
1 AAAATTAAAAAA--TT-ATAA
*
49383 AAATATTAAAAAATTATTA
1 AAA-ATTAAAAAATTATAA
* *
49402 AAAATTAGAAAATTGTAA
1 AAAATTAAAAAATTATAA
49420 AAAATTATAAAAAAATTATAA
1 AAAA-T-T-AAAAAATTATAA
**
49441 AACTTTACAAAAATCGTA-AA
1 AAAATTA-AAAAAT--TATAA
*
49461 AAAATTATAAAATTTTATAA
1 AAAATTA-AAAA-ATTATAA
** *
49481 AGTCATTAGAAAATTATAA
1 A-AAATTAAAAAATTATAA
49500 AAAATTTAAAGAAA-TATAA
1 AAAA-TTAAA-AAATTATAA
49519 AA
1 AA
49521 TTTGTAAAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 26
0.70 0.12 0.17
Matches are distributed among these distances:
18 18 0.17
19 34 0.32
20 24 0.22
21 22 0.21
22 9 0.08
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAATTAAAAAATTATAA
Found at i:49434 original size:11 final size:11
Alignment explanation
Indices: 49368--49472 Score: 57
Period size: 11 Copynumber: 10.3 Consensus size: 11
49358 TTATAAAATT
*
49368 AAAAAATTTTA
1 AAAAAATTATA
*
49379 ATAAAAA-TATT
1 A-AAAAATTATA
49390 AAAAAATTAT-
1 AAAAAATTATA
*
49400 TAAAAA-T-T-
1 AAAAAATTATA
* *
49408 AGAAAATTGT-
1 AAAAAATTATA
49418 AAAAAATTATA
1 AAAAAATTATA
49429 AAAAAATTAT-
1 AAAAAATTATA
*
49439 -AAAACTT-TA
1 AAAAAATTATA
* **
49448 CAAAAATCGTA
1 AAAAAATTATA
49459 AAAAAATTATA
1 AAAAAATTATA
49470 AAA
1 AAA
49473 TTTTATAAAG
Statistics
Matches: 73, Mismatches: 13, Indels: 16
0.72 0.13 0.16
Matches are distributed among these distances:
8 6 0.08
9 8 0.11
10 24 0.33
11 30 0.41
12 5 0.07
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:49461 original size:30 final size:28
Alignment explanation
Indices: 49382--49520 Score: 111
Period size: 30 Copynumber: 4.8 Consensus size: 28
49372 AATTTTAATA
* * *
49382 AAAATATTAAAAAATTAT-TAAAAATTAG
1 AAAAT-TTAAAAAATCATAAAAAAATTAT
*
49410 AAAATTGTAAAAAATTATAAAAAAATTAT
1 AAAATT-TAAAAAATCATAAAAAAATTAT
*
49439 AAAACTTTACAAAAATCGTAAAAAAATTAT
1 AAAA-TTTA-AAAAATCATAAAAAAATTAT
* * * *
49469 AAAATTTTATAAAGTCATTAGAAAATTAT
1 AAAA-TTTAAAAAATCATAAAAAAATTAT
49498 AAAAAATTTAAAGAAAT-ATAAAA
1 --AAAATTTAAA-AAATCATAAAA
49521 TTTGTAAAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.01
28 16 0.18
29 29 0.32
30 37 0.41
31 7 0.08
ACGTcount: A:0.63, C:0.03, G:0.04, T:0.30
Consensus pattern (28 bp):
AAAATTTAAAAAATCATAAAAAAATTAT
Found at i:49723 original size:28 final size:28
Alignment explanation
Indices: 49692--49776 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
49682 TGCTTTTCAT
*
49692 AATTTTTAT-GATTTTTATAAAATTTTAC
1 AATTTTTATAAATTTTT-TAAAATTTTAC
* * *
49720 AATTTTTCTAAATTTTTTACAATTTTAT
1 AATTTTTATAAATTTTTTAAAATTTTAC
*
49748 AATTTGTTTTCAAATTTTTAATAAAATTT
1 AATTT-TTAT-AAATTTTT--TAAAATTT
49777 AAATATATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
28 22 0.48
29 9 0.20
30 8 0.17
32 7 0.15
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (28 bp):
AATTTTTATAAATTTTTTAAAATTTTAC
Found at i:49724 original size:19 final size:20
Alignment explanation
Indices: 49702--49749 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
49692 AATTTTTATG
49702 ATTTTTATAAA-ATTTTACA
1 ATTTTTATAAATATTTTACA
* *
49721 ATTTTTCTAAATTTTTTACA
1 ATTTTTATAAATATTTTACA
49741 A-TTTTATAA
1 ATTTTTATAA
49750 TTTGTTTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTATAAATATTTTACA
Found at i:49757 original size:20 final size:18
Alignment explanation
Indices: 49714--49769 Score: 51
Period size: 20 Copynumber: 2.9 Consensus size: 18
49704 TTTTATAAAA
*
49714 TTTTACAATTTTTCTAAATT
1 TTTTACAA-TTTT-TAATTT
49734 TTTTACAATTTTATAATTT
1 TTTTACAATTTT-TAATTT
49753 GTTTT-CAAATTTTTAAT
1 -TTTTAC-AATTTTTAAT
49770 AAAATTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTACAATTTTTAATTT
Found at i:49826 original size:31 final size:31
Alignment explanation
Indices: 49762--49832 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
49752 TGTTTTCAAA
*
49762 TTTTTAATAAAATTTAAATATATTTTTATAT
1 TTTTTAATAAAATTTAAATATATTTTTAGAT
*
49793 TTTTTATTAAAATTT-AATAATATTTATT-GAT
1 TTTTTAATAAAATTTAAAT-ATATTT-TTAGAT
49824 TTTATTAAT
1 TTT-TTAAT
49833 TTTTATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 3 0.09
31 25 0.74
32 6 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
TTTTTAATAAAATTTAAATATATTTTTAGAT
Found at i:55584 original size:17 final size:17
Alignment explanation
Indices: 55562--55596 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55552 ATGTATTTTT
*
55562 TAAAATAAATGATATAG
1 TAAAATAAATAATATAG
55579 TAAAATAAATAATATAG
1 TAAAATAAATAATATAG
55596 T
1 T
55597 GTATGTTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (17 bp):
TAAAATAAATAATATAG
Found at i:56147 original size:15 final size:15
Alignment explanation
Indices: 56127--56182 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
56117 ATATTTCGGT
56127 TTGAGGATATCCCAA
1 TTGAGGATATCCCAA
56142 TTGAGGAT-TCCTCAA
1 TTGAGGATATCC-CAA
* * *
56157 CTAAAGATATCCCAA
1 TTGAGGATATCCCAA
*
56172 TTGAGGTTATC
1 TTGAGGATATC
56183 TCGATTTGGG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 3 0.09
15 26 0.81
16 3 0.09
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (15 bp):
TTGAGGATATCCCAA
Found at i:56778 original size:73 final size:73
Alignment explanation
Indices: 56659--56805 Score: 285
Period size: 73 Copynumber: 2.0 Consensus size: 73
56649 ATTTAGGATT
*
56659 AAATAGTAATTGCGAGAAATCATGAGGGACTAAATAGCAATTTAATTGAATTATGAGTCATCATG
1 AAATAGTAATTGCGAGAAATCATGAGGGACTAAATAGAAATTTAATTGAATTATGAGTCATCATG
56724 GGATTTAG
66 GGATTTAG
56732 AAATAGTAATTGCGAGAAATCATGAGGGACTAAATAGAAATTTAATTGAATTATGAGTCATCATG
1 AAATAGTAATTGCGAGAAATCATGAGGGACTAAATAGAAATTTAATTGAATTATGAGTCATCATG
56797 GGATTTAG
66 GGATTTAG
56805 A
1 A
56806 TTGATTAAGG
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.30
Consensus pattern (73 bp):
AAATAGTAATTGCGAGAAATCATGAGGGACTAAATAGAAATTTAATTGAATTATGAGTCATCATG
GGATTTAG
Done.