Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012625.1 Kokia drynarioides strain JFW-HI SEQ_127634, 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: 64759
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:1166 original size:6 final size:7
Alignment explanation
Indices: 1143--1193 Score: 57
Period size: 7 Copynumber: 6.7 Consensus size: 7
1133 ATCATAAACT
1143 TTTTATA
1 TTTTATA
1150 TTTTATA
1 TTTTATA
*
1157 TTTTTATT
1 -TTTTATA
1165 TTTTATA
1 TTTTATA
1172 TTTTGAATA
1 TTTT--ATA
1181 TTTTATAA
1 TTTTAT-A
1189 TTTTA
1 TTTTA
1194 AATTATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
7 19 0.50
8 12 0.32
9 7 0.18
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:2056 original size:29 final size:28
Alignment explanation
Indices: 2015--2074 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
2005 TACAAGCTGT
* * *
2015 ATGCACTCAACAAAATCATCATAGCAGC
1 ATGCACTCAACAAAAACATAACAGCAGC
2043 ATGCACTTCAACAAAAACATAACAGCAGC
1 ATGCAC-TCAACAAAAACATAACAGCAGC
2072 ATG
1 ATG
2075 GTTGGCCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.45, C:0.27, G:0.12, T:0.17
Consensus pattern (28 bp):
ATGCACTCAACAAAAACATAACAGCAGC
Found at i:2069 original size:26 final size:27
Alignment explanation
Indices: 2015--2069 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
2005 TACAAGCTGT
*
2015 ATGCACTCAACAAAATCATCATAGCAGC
1 ATGCACTCAACAAAA-CATCATAACAGC
2043 ATGCACTTCAACAAAA-A-CATAACAGC
1 ATGCAC-TCAACAAAACATCATAACAGC
2069 A
1 A
2070 GCATGGTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 9 0.36
27 1 0.04
28 6 0.24
29 9 0.36
ACGTcount: A:0.47, C:0.27, G:0.09, T:0.16
Consensus pattern (27 bp):
ATGCACTCAACAAAACATCATAACAGC
Found at i:7427 original size:2 final size:2
Alignment explanation
Indices: 7422--7448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7412 AACATATATA
7422 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
7449 TGAATTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:9498 original size:29 final size:29
Alignment explanation
Indices: 9452--9520 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
9442 ATTAATTAAT
*
9452 CTAATTAAA-TTAATTAACCTAAAATAAC
1 CTAATGAAATTTAATTAACCTAAAATAAC
* * *
9480 CTAATGGAATTTAATTAACCTAAGATATC
1 CTAATGAAATTTAATTAACCTAAAATAAC
*
9509 GTAATGAAATTT
1 CTAATGAAATTT
9521 CTTATTCCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 7 0.21
29 27 0.79
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (29 bp):
CTAATGAAATTTAATTAACCTAAAATAAC
Found at i:12234 original size:52 final size:52
Alignment explanation
Indices: 12152--12400 Score: 268
Period size: 52 Copynumber: 4.8 Consensus size: 52
12142 GCCATAAACG
* **
12152 AAGAGGTCTGATGTCTAAGTGTCATCATGAGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGAATAAGTGTCATCATGAGTATATGAATCCTTTACGGATT
* * *
12204 AAGAGGTTCGATGAATAAGTGTCATTATGAGTATATGAATCCTTTACGAATT
1 AAGAGGTCCGATGAATAAGTGTCATCATGAGTATATGAATCCTTTACGGATT
* * *
12256 AAGAGGTCCGATGACTAAGTGTCATCGTGTGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGAATAAGTGTCATCATGAGTATATGAATCCTTTACGGATT
* * * * **
12308 AAGAGGGTCCGATGATTCTA-TGTCATCGTGAGTATATGAATCCCTTGTGGATT
1 AAGA-GGTCCGATGAAT-AAGTGTCATCATGAGTATATGAATCCTTTACGGATT
* * ** * *
12361 ATA-AGGTCTGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 A-AGAGGTCCGATGAATAAGTGTCATCATGAGTATATGAAT
12401 GAAGTGAAAT
Statistics
Matches: 169, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
52 125 0.74
53 42 0.25
54 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (52 bp):
AAGAGGTCCGATGAATAAGTGTCATCATGAGTATATGAATCCTTTACGGATT
Found at i:12385 original size:105 final size:104
Alignment explanation
Indices: 12152--12400 Score: 313
Period size: 105 Copynumber: 2.4 Consensus size: 104
12142 GCCATAAACG
* * *
12152 AAGAGGTCTGATGTCTAAGTGTCATCATGAGTATATGAATCCTTTACGGATTAAGAGGTTCGATG
1 AAGAGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATG
* *
12217 AATAAGTGTCATTATGAGTATATGAATCCTTTACGAATT
66 AATAAGTGTCATCATGAGTATATGAATCCCTTACGAATT
* *
12256 AAGAGGTCCGATGACTAAGTGTCATCGTGTGTATATGAATCCTTTACGGATTAAGAGGGTCCGAT
1 AAGAGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGA-GGTCCGAT
* * * ** *
12321 GATTCTA-TGTCATCGTGAGTATATGAATCCCTTGTGGATT
65 GAAT-AAGTGTCATCATGAGTATATGAATCCCTTACGAATT
* * *
12361 ATA-AGGTCTGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 A-AGAGGTCTGATGACTAAGTGTCATCGTGAGTATATGAAT
12401 GAAGTGAAAT
Statistics
Matches: 124, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
104 52 0.42
105 70 0.56
106 2 0.02
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (104 bp):
AAGAGGTCTGATGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCGATG
AATAAGTGTCATCATGAGTATATGAATCCCTTACGAATT
Found at i:16988 original size:120 final size:120
Alignment explanation
Indices: 16846--17088 Score: 486
Period size: 120 Copynumber: 2.0 Consensus size: 120
16836 ATTTGCGAAT
16846 GATAAGTGCAAAAAATAATATGTTTTTAGCTTCATTTTTAATGTGTTTTTGGATGATTATTCGAT
1 GATAAGTGCAAAAAATAATATGTTTTTAGCTTCATTTTTAATGTGTTTTTGGATGATTATTCGAT
16911 ATAAAATGGTGAATTTTGTGCTCCTAATCCTTTAATTTCATGTTTCTATACTTAG
66 ATAAAATGGTGAATTTTGTGCTCCTAATCCTTTAATTTCATGTTTCTATACTTAG
16966 GATAAGTGCAAAAAATAATATGTTTTTAGCTTCATTTTTAATGTGTTTTTGGATGATTATTCGAT
1 GATAAGTGCAAAAAATAATATGTTTTTAGCTTCATTTTTAATGTGTTTTTGGATGATTATTCGAT
17031 ATAAAATGGTGAATTTTGTGCTCCTAATCCTTTAATTTCATGTTTCTATACTTAG
66 ATAAAATGGTGAATTTTGTGCTCCTAATCCTTTAATTTCATGTTTCTATACTTAG
17086 GAT
1 GAT
17089 GTCATTTGGG
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (120 bp):
GATAAGTGCAAAAAATAATATGTTTTTAGCTTCATTTTTAATGTGTTTTTGGATGATTATTCGAT
ATAAAATGGTGAATTTTGTGCTCCTAATCCTTTAATTTCATGTTTCTATACTTAG
Found at i:24509 original size:31 final size:31
Alignment explanation
Indices: 24411--24519 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
24401 GACAAAAGTG
* *
24411 CAAACTTGTAAACTTACTAATAGTTCAATGAT
1 CAAA-TTGTAAACTTACTAATAGTTGAATGAC
* ** *
24443 CAATTTGT-AACTTTTTAA-AATTGAATGAC
1 CAAATTGTAAACTTACTAATAGTTGAATGAC
* *
24472 AAAATTGTAAACTTACTAATAGTTGAGTGAC
1 CAAATTGTAAACTTACTAATAGTTGAATGAC
*
24503 CAAATTGTAAATTTACT
1 CAAATTGTAAACTTACT
24520 CATCCCTATA
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
29 14 0.23
30 16 0.26
31 28 0.46
32 3 0.05
ACGTcount: A:0.40, C:0.12, G:0.11, T:0.37
Consensus pattern (31 bp):
CAAATTGTAAACTTACTAATAGTTGAATGAC
Found at i:28459 original size:18 final size:18
Alignment explanation
Indices: 28432--28476 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
28422 TGTAATGCAA
*
28432 TCTCTCTCTTTCTCTTTC
1 TCTCTCTCTTTCTCATTC
*
28450 TCTTTCTCTTTCTCATTC
1 TCTCTCTCTTTCTCATTC
28468 TCTCTCTCT
1 TCTCTCTCT
28477 CTCTTTTGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTCTCTCTTTCTCATTC
Found at i:28480 original size:6 final size:6
Alignment explanation
Indices: 28436--28476 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
28426 ATGCAATCTC
* *
28436 TCTCTT TCTCTT TCTCTT TCTCTT TCTCAT TCTCTC TCTCT
1 TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCTT TCTCT
28477 CTCTTTTGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (6 bp):
TCTCTT
Found at i:29821 original size:77 final size:75
Alignment explanation
Indices: 29691--29844 Score: 227
Period size: 77 Copynumber: 2.0 Consensus size: 75
29681 TTTTATTTTA
** * * * *
29691 CAAGTGTCGAAACGTTTATTTTTAGAAAACAAACAGGTCTCGAATAATATTTTAAAAATCGAAAT
1 CAAGTGTCGAAACACTTATTTTTAGAAAACAAACAGGCCTCAAACAATATTTTAAAAATCAAAAT
29756 ATGGAGTCGC
66 ATGGAGTCGC
*
29766 CAAGCTGTCGAAACACTTATTTTTGGGAAAACAAACAGGCCTCAAACAATATTTTAAAAATCAAA
1 CAAG-TGTCGAAACACTTATTTTT-AGAAAACAAACAGGCCTCAAACAATATTTTAAAAATCAAA
29831 ATATGGAGTCGC
64 ATATGGAGTCGC
29843 CA
1 CA
29845 CCAAGCTTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
75 4 0.06
76 17 0.24
77 49 0.70
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (75 bp):
CAAGTGTCGAAACACTTATTTTTAGAAAACAAACAGGCCTCAAACAATATTTTAAAAATCAAAAT
ATGGAGTCGC
Found at i:30964 original size:28 final size:30
Alignment explanation
Indices: 30883--30966 Score: 95
Period size: 29 Copynumber: 2.9 Consensus size: 30
30873 CAAAATCGAA
*
30883 ATTTTTGGAAAATTTG-GGGTTAAAAT-TGG
1 ATTTTTGGAAAATTTGAGGG-AAAAATGTGG
**
30912 ATTTTTGGAAAATTTGAGAAAAAAATGT-G
1 ATTTTTGGAAAATTTGAGGGAAAAATGTGG
*
30941 ATTTTT-GAAAATTTGAGGGCAAAATG
1 ATTTTTGGAAAATTTGAGGGAAAAATG
30967 GTAATTTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
28 17 0.36
29 28 0.60
30 2 0.04
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.37
Consensus pattern (30 bp):
ATTTTTGGAAAATTTGAGGGAAAAATGTGG
Found at i:30973 original size:29 final size:29
Alignment explanation
Indices: 30873--31033 Score: 91
Period size: 29 Copynumber: 5.6 Consensus size: 29
30863 ATTTAGGGAT
* *
30873 CAAAATCGAAATTTTTGGAAAATTTG-GGG
1 CAAAATGGTAATTTTT-GAAAATTTGAGGG
* **
30902 TTAAAATTGG--ATTTTTGGAAAATTTGAGAA
1 -CAAAA-TGGTAATTTTT-GAAAATTTGAGGG
* *
30932 AAAAAT-GTGATTTTTGAAAATTTGAGGG
1 CAAAATGGTAATTTTTGAAAATTTGAGGG
* ** **
30960 CAAAATGGTAA-TTTTGGATGTTCAAGGG
1 CAAAATGGTAATTTTTGAAAATTTGAGGG
* **
30988 CGAAATGGTAATTTTT-AGATTTTTGAGGG
1 CAAAATGGTAATTTTTGA-AAATTTGAGGG
*
31017 CAAAATAGTAATTTTTG
1 CAAAATGGTAATTTTTG
31034 GATGTTTAGG
Statistics
Matches: 102, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
27 1 0.01
28 39 0.38
29 55 0.54
30 5 0.05
31 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
CAAAATGGTAATTTTTGAAAATTTGAGGG
Found at i:30974 original size:28 final size:28
Alignment explanation
Indices: 30943--31031 Score: 88
Period size: 28 Copynumber: 3.1 Consensus size: 28
30933 AAAATGTGAT
*
30943 TTTTGAAAATTTGAGGGCAAAATGGTAA
1 TTTTGAATATTTGAGGGCAAAATGGTAA
* * ** *
30971 TTTTGGATGTTCAAGGGCGAAATGGTAA
1 TTTTGAATATTTGAGGGCAAAATGGTAA
* * *
30999 TTTTTAGATTTTTGAGGGCAAAATAGTAA
1 TTTTGA-ATATTTGAGGGCAAAATGGTAA
31028 TTTT
1 TTTT
31032 TGGATGTTTA
Statistics
Matches: 47, Mismatches: 13, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
28 26 0.55
29 21 0.45
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (28 bp):
TTTTGAATATTTGAGGGCAAAATGGTAA
Found at i:31108 original size:30 final size:30
Alignment explanation
Indices: 31047--31176 Score: 156
Period size: 30 Copynumber: 4.4 Consensus size: 30
31037 GTTTAGGGGG
* * *
31047 AATGCAATTTTAGAAAAATTTA-GGGTGAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
*
31076 AATGTGATTTTAGAAAAG-TTAGAGGGTTAA
1 AATGTAATTTTAGAAAAGTTTAG-GGGTTAA
* * *
31106 AATGTAATTTTGGAGAAGTTTAGGGGTCAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
* *
31136 AATGTAATTTTTGGAAAGTTTAGGGGTTAA
1 AATGTAATTTTAGAAAAGTTTAGGGGTTAA
31166 AATGTAATTTT
1 AATGTAATTTT
31177 TAAACCAAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
28 3 0.03
29 15 0.17
30 64 0.74
31 4 0.05
ACGTcount: A:0.38, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
AATGTAATTTTAGAAAAGTTTAGGGGTTAA
Found at i:31177 original size:30 final size:30
Alignment explanation
Indices: 31018--31177 Score: 145
Period size: 30 Copynumber: 5.5 Consensus size: 30
31008 TTTTGAGGGC
*
31018 AAAATAGTAATTTTTGG-ATGTTTAGGGG--
1 AAAAT-GTAATTTTTGGAAAGTTTAGGGGTT
* * * * * *
31046 -GAATGCAATTTTAGAAAAATTTA-GGGTG
1 AAAATGTAATTTTTGGAAAGTTTAGGGGTT
* * *
31074 AAAATGTGATTTTAGAAAAG-TTAGAGGGTT
1 AAAATGTAATTTTTGGAAAGTTTAG-GGGTT
*
31104 AAAATGTAA-TTTTGGAGAAGTTTAGGGGTC
1 AAAATGTAATTTTTGGA-AAGTTTAGGGGTT
31134 AAAATGTAATTTTTGGAAAGTTTAGGGGTT
1 AAAATGTAATTTTTGGAAAGTTTAGGGGTT
31164 AAAATGTAATTTTT
1 AAAATGTAATTTTT
31178 AAACCAAATA
Statistics
Matches: 107, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
26 11 0.10
27 8 0.07
28 3 0.03
29 20 0.19
30 54 0.50
31 11 0.10
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (30 bp):
AAAATGTAATTTTTGGAAAGTTTAGGGGTT
Found at i:33419 original size:29 final size:29
Alignment explanation
Indices: 33387--33697 Score: 95
Period size: 30 Copynumber: 10.5 Consensus size: 29
33377 GCAAAATAGT
*
33387 AATTTTTAGAGGTTCAGGGTTAAAAATGG
1 AATTTTTAGAAGTTCAGGGTTAAAAATGG
* * *
33416 AATTTTTGGACA-TTTAGGG-GAAAAATGG
1 AATTTTTAGA-AGTTCAGGGTTAAAAATGG
* *
33444 AGATTTTTGAAAAGTTCGGGGTTAAAAATGG
1 A-ATTTTT-AGAAGTTCAGGGTTAAAAATGG
* * *
33475 TATTTTTGGATA-TTCTGGAG-T-AAAATGG
1 AATTTTTAGA-AGTTCAGG-GTTAAAAATGG
** * * * *
33503 TTTTTTTTTAGAAAGTT-TGATGTCAAAAATTG
1 --AATTTTTAG-AAGTTCAG-GGTTAAAAATGG
* ** *
33535 AATTTTTTGAAAGTTTGGGGTTAAAAATGA
1 AATTTTTAG-AAGTTCAGGGTTAAAAATGG
* * * *
33565 AATTTTTGGAAATTTAGGGGT-AAAATGG
1 AATTTTTAGAAGTTCAGGGTTAAAAATGG
* * * * *
33593 TAATTTTTGGATAATTTAGGGTTAAAATTAG
1 -AATTTTTAGA-AGTTCAGGGTTAAAAATGG
* *
33624 AATTTTTAGAAATTTAAGGG-T-AAAATGG
1 AATTTTTAG-AAGTTCAGGGTTAAAAATGG
* *
33652 TAATTTTTGAAAAGTTTAGGGGTTAAAATAT-G
1 -AATTTTT-AGAAGTTCA-GGGTTAAAA-ATGG
33684 -ATTTTTAAGAAGTT
1 AATTTTT-AGAAGTT
33698 TGGGGGTCAA
Statistics
Matches: 213, Mismatches: 44, Indels: 49
0.70 0.14 0.16
Matches are distributed among these distances:
28 27 0.13
29 61 0.29
30 94 0.44
31 19 0.09
32 10 0.05
33 2 0.01
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (29 bp):
AATTTTTAGAAGTTCAGGGTTAAAAATGG
Found at i:33482 original size:30 final size:30
Alignment explanation
Indices: 33403--33679 Score: 137
Period size: 30 Copynumber: 9.3 Consensus size: 30
33393 TAGAGGTTCA
* * *
33403 GGGTTAAAAATGGAATTTTTGGACATTTAG
1 GGGTTAAAAATGGAATTTTTGAAAAGTTAG
*
33433 GGG--AAAAATGGAGATTTTTGAAAAGTTCG
1 GGGTTAAAAATGGA-ATTTTTGAAAAGTTAG
* * * *
33462 GGGTTAAAAATGGTATTTTTGGATA-TTCTG
1 GGGTTAAAAATGGAATTTTTGAAAAGTT-AG
* ** * *
33492 GAG-T-AAAATGGTTTTTTTTTAGAAAGTTTG
1 GGGTTAAAAATGG-AATTTTTGA-AAAGTTAG
** * * *
33522 ATGTCAAAAATTGAATTTTTTG-AAAGTTTG
1 GGGTTAAAAATGGAA-TTTTTGAAAAGTTAG
* * *
33552 GGGTTAAAAATGAAATTTTTGGAAATTTAG
1 GGGTTAAAAATGGAATTTTTGAAAAGTTAG
* *
33582 GGG-T-AAAATGGTAATTTTTGGATAATTTA-
1 GGGTTAAAAATGG-AATTTTT-GAAAAGTTAG
* * * *
33611 GGGTTAAAATTAGAATTTTT-AGAAATTTAA
1 GGGTTAAAAATGGAATTTTTGA-AAAGTTAG
33641 GGG-T-AAAATGGTAATTTTTGAAAAGTTTAG
1 GGGTTAAAAATGG-AATTTTTGAAAAG-TTAG
33671 GGGTTAAAA
1 GGGTTAAAA
33680 TATGATTTTT
Statistics
Matches: 188, Mismatches: 37, Indels: 42
0.70 0.14 0.16
Matches are distributed among these distances:
28 28 0.15
29 58 0.31
30 72 0.38
31 16 0.09
32 14 0.07
ACGTcount: A:0.36, C:0.01, G:0.24, T:0.39
Consensus pattern (30 bp):
GGGTTAAAAATGGAATTTTTGAAAAGTTAG
Found at i:33688 original size:59 final size:60
Alignment explanation
Indices: 33538--33690 Score: 203
Period size: 59 Copynumber: 2.6 Consensus size: 60
33528 AAAATTGAAT
* *
33538 TTTTTG-AAAGTTT-GGGGTTAAAA-ATGAAATTTTTGGAAATTTAGGGGTAAAATGGTAA
1 TTTTTGAAAAGTTTAGGGGTTAAAATATG-AATTTTTAGAAATTTAAGGGTAAAATGGTAA
*
33596 TTTTTGGATAA-TTTA-GGGTTAAAAT-TAGAATTTTTAGAAATTTAAGGGTAAAATGGTAA
1 TTTTT-GAAAAGTTTAGGGGTTAAAATAT-GAATTTTTAGAAATTTAAGGGTAAAATGGTAA
33655 TTTTTGAAAAGTTTAGGGGTTAAAATATG-ATTTTTA
1 TTTTTGAAAAGTTTAGGGGTTAAAATATGAATTTTTA
33691 AGAAGTTTGG
Statistics
Matches: 83, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
58 9 0.11
59 59 0.71
60 14 0.17
61 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (60 bp):
TTTTTGAAAAGTTTAGGGGTTAAAATATGAATTTTTAGAAATTTAAGGGTAAAATGGTAA
Found at i:33697 original size:30 final size:30
Alignment explanation
Indices: 33607--33717 Score: 97
Period size: 30 Copynumber: 3.7 Consensus size: 30
33597 TTTTGGATAA
*
33607 TTTA-GGGTTAAAAT-TAGAATTTTT-AGAAA
1 TTTAGGGGTTAAAATAT-G-ATTTTTAAGAAG
* * *
33636 TTTAAGGG-TAAAATGGTAATTTTTGAA-AAG
1 TTTAGGGGTTAAAAT-ATGATTTTT-AAGAAG
33666 TTTAGGGGTTAAAATATGATTTTTAAGAAG
1 TTTAGGGGTTAAAATATGATTTTTAAGAAG
* *
33696 TTTGGGGGTCAAAATATGATTT
1 TTTAGGGGTTAAAATATGATTT
33718 CTGGATAGTG
Statistics
Matches: 68, Mismatches: 7, Indels: 13
0.77 0.08 0.15
Matches are distributed among these distances:
29 18 0.26
30 42 0.62
31 8 0.12
ACGTcount: A:0.37, C:0.01, G:0.23, T:0.40
Consensus pattern (30 bp):
TTTAGGGGTTAAAATATGATTTTTAAGAAG
Found at i:34876 original size:13 final size:13
Alignment explanation
Indices: 34845--34910 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
34835 TTTCTCTTTT
*
34845 TTATTT-TTATTA
1 TTATTTATTAATA
* *
34857 ATATTTATTAATG
1 TTATTTATTAATA
*
34870 TTATTTATTACTA
1 TTATTTATTAATA
*
34883 TTATTTATTATTA
1 TTATTTATTAATA
* *
34896 TT-GTTATTATTA
1 TTATTTATTAATA
34908 TTA
1 TTA
34911 ATTGTTTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
12 16 0.36
13 28 0.64
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (13 bp):
TTATTTATTAATA
Found at i:34893 original size:3 final size:3
Alignment explanation
Indices: 34845--34910 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
34835 TTTCTCTTTT
* * * * *
34845 TTA TTT TTA TTA ATA TTTA TTA ATG TTA TTTA TTA CTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA
*
34893 TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
34911 ATTGTTTTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
3 40 0.83
4 8 0.17
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:35512 original size:6 final size:6
Alignment explanation
Indices: 35493--35546 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
35483 GGACATTATT
* * *
35493 AATTTA AA--TA AATTTA AATTTA AA-ATA AATTTA AAATTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
35537 AATTTA AATT
1 AATTTA AATT
35547 CTGTTGGGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
4 4 0.10
5 8 0.21
6 27 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:35520 original size:17 final size:17
Alignment explanation
Indices: 35493--35546 Score: 92
Period size: 17 Copynumber: 3.2 Consensus size: 17
35483 GGACATTATT
35493 AATTT-AAATAAATTTA
1 AATTTAAAATAAATTTA
35509 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
*
35526 AAATTAAAATAAATTTA
1 AATTTAAAATAAATTTA
35543 AATT
1 AATT
35547 CTGTTGGGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 5 0.14
17 30 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:36252 original size:209 final size:209
Alignment explanation
Indices: 35850--36532 Score: 802
Period size: 209 Copynumber: 3.3 Consensus size: 209
35840 ACCATAGTCT
* * * * * *
35850 TTTGAGTCTGGTTTCATTGATTTAGTCTACTTCTCAATATCTCATCAGGAAGATGACCGTATCAT
1 TTTGAGCCTGATTTCATTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATC-T
* ** * *
35915 -TTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACAGATCTACTTCACTTCTCTA-TATCT
65 CTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTCCACTTCT-AAGTATCT
* * * * *
35978 CATCACGAAGGTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCTTCAGGAAGTTGGGGT
129 CATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGT
36043 TCGAAGATTTGCTCAC
194 TCGAAGATTTGCTCAC
* * * *
36059 TTTGAGCCTGATTTCTTTTATTTGGTCCACTTCTCAGTACCTCATCAGGAAGATGACCGCATCTC
1 TTTGAGCCTGATTTCATTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCTC
* * *
36124 TTGTTTTGATCCACTACTCTGTGCCTCATCAGGAAGACGGATCTGGTCCACTTCTAAGTATTTCA
66 TTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTCCACTTCTAAGTATCTCA
36189 TCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTC
131 TCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTC
* *
36254 GAAGATCTACTCAC
196 GAAGATTTGCTCAC
* * * * * * * *
36268 TTTGAGCCT-AGTTTCATCAAGTTGGTATACTTCTCTGTATCTCATCAGGAAGTTGACCACCTCA
1 TTTGAGCCTGA-TTTCATTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCT
** * * * * *
36332 CTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTC
65 CTTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTCCACTTCTAAGTATCTC
* * * * *
36397 ATTAGGAAGCTGACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATTAAG-AGGTGGGGTT
130 ATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTT
*
36461 CGAAGTTTTGCTCA-
195 CGAAGATTTGCTCAC
** ** * * *
36475 TATTGAGTTTTG-TTTCATCGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGAC
1 T-TTGAG-CCTGATTTCATTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGAC
36533 TGTCTCATTA
Statistics
Matches: 410, Mismatches: 58, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
207 1 0.00
208 72 0.18
209 337 0.82
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.36
Consensus pattern (209 bp):
TTTGAGCCTGATTTCATTAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCTC
TTGTTTTGATCCACTTCTCTGTGTCTCATCAGGAAGACGGATCTGGTCCACTTCTAAGTATCTCA
TCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTC
GAAGATTTGCTCAC
Found at i:47608 original size:29 final size:29
Alignment explanation
Indices: 47576--47771 Score: 89
Period size: 30 Copynumber: 6.7 Consensus size: 29
47566 GTAAAATAGT
*
47576 AATTTTTAGAGGTTCGAGGTCAAAAATGG
1 AATTTTTAGAAGTTCGAGGTCAAAAATGG
* * *
47605 AATTTTTGGACA-TCTGGGGGT--AAAATGG
1 AATTTTTAGA-AGT-TCGAGGTCAAAAATGG
* * * *
47633 TGATTTTTGAAAAGTTTGGGGTCAAAAATGG
1 -AATTTTT-AGAAGTTCGAGGTCAAAAATGG
* * *
47664 AATTTTTGGAAAGTTCAAGGTTAAAAATGG
1 AATTTTTAG-AAGTTCGAGGTCAAAAATGG
* * * * *
47694 AATTTTTGGAAATTCG-GGGCTAAAATGAT
1 AATTTTTAGAAGTTCGAGGTCAAAAATG-G
* * *
47723 AATTTTTAAAAAGATCGGGGGTCAAAATAT-G
1 AATTTTT-AGAAGTTC-GAGGTCAAAA-ATGG
*
47754 -ATTTTAAGAAGTTCGAGG
1 AATTTTTAGAAGTTCGAGG
47772 GTTAAAATAT
Statistics
Matches: 122, Mismatches: 32, Indels: 27
0.67 0.18 0.15
Matches are distributed among these distances:
28 18 0.15
29 41 0.34
30 47 0.39
31 8 0.07
32 6 0.05
33 2 0.02
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (29 bp):
AATTTTTAGAAGTTCGAGGTCAAAAATGG
Found at i:47669 original size:30 final size:30
Alignment explanation
Indices: 47587--47749 Score: 129
Period size: 30 Copynumber: 5.5 Consensus size: 30
47577 ATTTTTAGAG
* *
47587 GTTCGAGGTCAAAAATGGAATTTTTGGACA
1 GTTCGGGGTCAAAAATGGAATTTTTGGAAA
* * *
47617 -TCTGGGGGT--AAAATGGTGATTTTTGAAAA
1 GT-TCGGGGTCAAAAATGG-AATTTTTGGAAA
*
47646 GTTTGGGGTCAAAAATGGAATTTTTGGAAA
1 GTTCGGGGTCAAAAATGGAATTTTTGGAAA
** *
47676 GTTCAAGGTTAAAAATGGAATTTTTGGAAA
1 GTTCGGGGTCAAAAATGGAATTTTTGGAAA
* * **
47706 -TTCGGGG-CTAAAATGATAATTTTTAAAAA
1 GTTCGGGGTCAAAAATG-GAATTTTTGGAAA
*
47735 GATCGGGGGTCAAAA
1 GTTC-GGGGTCAAAA
47750 TATGATTTTA
Statistics
Matches: 103, Mismatches: 21, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
28 13 0.13
29 31 0.30
30 44 0.43
31 11 0.11
32 4 0.04
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (30 bp):
GTTCGGGGTCAAAAATGGAATTTTTGGAAA
Found at i:47758 original size:30 final size:29
Alignment explanation
Indices: 47707--47788 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
47697 TTTTGGAAAT
* *
47707 TCGGGGCTAAAATGATAATTTTTAAAAAGA
1 TCGGGGGTAAAAT-ATGATTTTTAAAAAGA
* *
47737 TCGGGGGTCAAAATATGA-TTTTAAGAAGT
1 TCGGGGGT-AAAATATGATTTTTAAAAAGA
*
47766 TCGAGGGTTAAAATATGATTTTT
1 TCG-GGGGTAAAATATGATTTTT
47789 GGACAGTGTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 21 0.48
30 18 0.41
31 5 0.11
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (29 bp):
TCGGGGGTAAAATATGATTTTTAAAAAGA
Found at i:47758 original size:89 final size:88
Alignment explanation
Indices: 47576--47791 Score: 217
Period size: 89 Copynumber: 2.4 Consensus size: 88
47566 GTAAAATAGT
* * * * * * * *
47576 AATTTTTAGAGGTTCGAGGTCAAAAATGGAATTTTTGGACATCTGGGGGTAAAATGGTGATTTTT
1 AATTTTAAGAAGTTCAAGGTTAAAAATGGAATTTTTGGAAATCTGGGGCTAAAATGATAATTTTT
* **
47641 GAAAAGTTTGGGGTCAAAAATGG
66 AAAAAGTCGGGGGTCAAAAATGG
**
47664 AATTTTTGGAAAGTTCAAGGTTAAAAATGGAATTTTTGGAAAT-TCGGGGCTAAAATGATAATTT
1 AATTTTAAG-AAGTTCAAGGTTAAAAATGGAATTTTTGGAAATCT-GGGGCTAAAATGATAATTT
47728 TTAAAAAGATCGGGGGTCAAAATAT-G
64 TTAAAAAG-TCGGGGGTCAAAA-ATGG
*
47754 -ATTTTAAGAAGTTCGAGGGTTAAAATAT-G-ATTTTTGGA
1 AATTTTAAGAAGTTC-AAGGTTAAAA-ATGGAATTTTTGGA
47792 CAGTGTAGGG
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
88 24 0.22
89 68 0.63
90 14 0.13
91 2 0.02
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (88 bp):
AATTTTAAGAAGTTCAAGGTTAAAAATGGAATTTTTGGAAATCTGGGGCTAAAATGATAATTTTT
AAAAAGTCGGGGGTCAAAAATGG
Found at i:47773 original size:29 final size:29
Alignment explanation
Indices: 47726--47787 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
47716 AAATGATAAT
*
47726 TTTTAAAAAGATCGGGGGTCAAAATATGA
1 TTTTAAAAAGATCGAGGGTCAAAATATGA
* * *
47755 TTTTAAGAAGTTCGAGGGTTAAAATATGA
1 TTTTAAAAAGATCGAGGGTCAAAATATGA
47784 TTTT
1 TTTT
47788 TGGACAGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (29 bp):
TTTTAAAAAGATCGAGGGTCAAAATATGA
Found at i:48939 original size:13 final size:13
Alignment explanation
Indices: 48908--48973 Score: 55
Period size: 13 Copynumber: 5.2 Consensus size: 13
48898 TTTCTCTTTT
*
48908 TTATTT-TTATTA
1 TTATTTATTAATA
* *
48920 ATATTTATTAATG
1 TTATTTATTAATA
*
48933 TTATTTATTACTA
1 TTATTTATTAATA
*
48946 TTATTTATTATTA
1 TTATTTATTAATA
* *
48959 TT-GTTATTATTA
1 TTATTTATTAATA
48971 TTA
1 TTA
48974 ATCATTTTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
12 16 0.36
13 28 0.64
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (13 bp):
TTATTTATTAATA
Found at i:48956 original size:3 final size:3
Alignment explanation
Indices: 48908--48973 Score: 51
Period size: 3 Copynumber: 21.0 Consensus size: 3
48898 TTTCTCTTTT
* * * * *
48908 TTA TTT TTA TTA ATA TTTA TTA ATG TTA TTTA TTA CTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA
*
48956 TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
48974 ATCATTTTTA
Statistics
Matches: 48, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
3 40 0.83
4 8 0.17
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:48980 original size:29 final size:25
Alignment explanation
Indices: 48908--48984 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 25
48898 TTTCTCTTTT
*
48908 TTATTTTTATTAATATTTATTAATG
1 TTATTATTATTAATATTTATTAATG
* *
48933 TTATTTATTACTATTATTTATTATTATTG
1 TTA-TTATTATTAATATTTATTA--A-TG
48962 TTATTATTATTAATCATTT-TTAA
1 TTATTATTATTAAT-ATTTATTAA
48985 AATAAACAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 3 0.07
26 17 0.40
28 13 0.31
29 9 0.21
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (25 bp):
TTATTATTATTAATATTTATTAATG
Found at i:49530 original size:23 final size:22
Alignment explanation
Indices: 49496--49542 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
49486 GAACAATATT
49496 AATTTAAATAAATTTAAACTTA
1 AATTTAAATAAATTTAAACTTA
49518 AATTTATAATAAATTTAAACTTA
1 AATTTA-AATAAATTTAAACTTA
49541 AA
1 AA
49543 ATAAATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTAAATAAATTTAAACTTA
Found at i:49532 original size:11 final size:10
Alignment explanation
Indices: 49496--49536 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
49486 GAACAATATT
49496 AATTTAAATA
1 AATTTAAATA
49506 AATTTAAACTTA
1 AATTTAAA--TA
49518 AATTTATAATA
1 AATTTA-AATA
49529 AATTTAAA
1 AATTTAAA
49537 CTTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.36
11 8 0.29
12 8 0.29
13 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTTAAATA
Found at i:49535 original size:17 final size:17
Alignment explanation
Indices: 49510--49555 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
49500 TAAATAAATT
* *
49510 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
49527 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
49544 TAAATTTAAATT
1 TAAATTTAAATT
49556 CTGTTAGACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:50238 original size:6 final size:6
Alignment explanation
Indices: 50229--50296 Score: 54
Period size: 6 Copynumber: 12.0 Consensus size: 6
50219 TATTTTTGAC
* * * *
50229 ATTTAA ATTTAA A--TGA TTTTAA ACTTAA ATTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
50274 ACTTAA A-ATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA
50297 GTTTCATTTG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
4 2 0.04
5 8 0.17
6 37 0.79
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:50265 original size:23 final size:22
Alignment explanation
Indices: 50231--50280 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
50221 TTTTTGACAT
* *
50231 TTAAATTTAAATGATTTTAAAC
1 TTAAATTTAAATAAATTTAAAC
50253 TTAAATTTAAAATAAATTTAAAC
1 TTAAATTT-AAATAAATTTAAAC
50276 TTAAA
1 TTAAA
50281 ATAAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
TTAAATTTAAATAAATTTAAAC
Found at i:50273 original size:17 final size:17
Alignment explanation
Indices: 50248--50296 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
50238 TAAATGATTT
*
50248 TAAACTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
50265 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
50282 TAAATTTAAATTTAA
1 TAAATTTAAATTTAA
50297 GTTTCATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:50291 original size:23 final size:23
Alignment explanation
Indices: 50246--50296 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
50236 TTTAAATGAT
*
50246 TTTAAACTTAAATTTAAAATAAA
1 TTTAAACTTAAATATAAAATAAA
*
50269 TTTAAACTTAAA-ATAAATTTAAA
1 TTTAAACTTAAATATAAA-ATAAA
50292 TTTAA
1 TTTAA
50297 GTTTCATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAACTTAAATATAAAATAAA
Found at i:51566 original size:17 final size:17
Alignment explanation
Indices: 51544--51585 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
51534 CTCCCTTGAC
*
51544 CTTTAACCTTCCATCTT
1 CTTTAACCTTCCATATT
*
51561 CTTTAACCTTTCATATT
1 CTTTAACCTTCCATATT
51578 CTTGTAAC
1 CTT-TAAC
51586 TACTTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.29, G:0.02, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTCCATATT
Found at i:61190 original size:41 final size:41
Alignment explanation
Indices: 61160--61319 Score: 173
Period size: 41 Copynumber: 3.9 Consensus size: 41
61150 ATTTGTGACG
* * * *
61160 TTTATGAGTAAGTGTCGCTAAAGGTCAGAGCATTAGCGGGA
1 TTTATGAGGAAGCGCCGCTAAAGGTCAGAGCATTAGCGCGA
*
61201 TTTATGAGGAAGCGCCGCTAAAGGTCAGAGCACTAGCGGCG-
1 TTTATGAGGAAGCGCCGCTAAAGGTCAGAGCATTAGC-GCGA
* * * *
61242 CTTATGAGGGAA-CGCCACTAAAAGTGAGAGCATTAGCGACG-
1 TTTATGA-GGAAGCGCCGCTAAAGGTCAGAGCATTAGCG-CGA
* *
61283 CTTATGAGGAAGCGCCGCTAAAGGTTAGAGCATTAGC
1 TTTATGAGGAAGCGCCGCTAAAGGTCAGAGCATTAGC
61320 TAATCTATAT
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
40 5 0.05
41 91 0.89
42 6 0.06
ACGTcount: A:0.30, C:0.18, G:0.31, T:0.21
Consensus pattern (41 bp):
TTTATGAGGAAGCGCCGCTAAAGGTCAGAGCATTAGCGCGA
Found at i:62594 original size:9 final size:9
Alignment explanation
Indices: 62580--62617 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
62570 TTAAAGTATA
62580 AATCAAGGT
1 AATCAAGGT
62589 AATCAAGGT
1 AATCAAGGT
62598 AATCAAGGT
1 AATCAAGGT
*
62607 AATCAATGT
1 AATCAAGGT
62616 AA
1 AA
62618 CATCCGCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (9 bp):
AATCAAGGT
Found at i:63034 original size:11 final size:11
Alignment explanation
Indices: 63018--63048 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
63008 TTCACATTAA
63018 CCACCATTTTT
1 CCACCATTTTT
63029 CCACCATTTTT
1 CCACCATTTTT
*
63040 CCGCCATTT
1 CCACCATTT
63049 CAATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.16, C:0.39, G:0.03, T:0.42
Consensus pattern (11 bp):
CCACCATTTTT
Found at i:64525 original size:6 final size:6
Alignment explanation
Indices: 64514--64558 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
64504 TAATCAAAAT
* *
64514 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGAAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
64559 TATGAATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (6 bp):
TGAAAG
Done.