Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015332.1 Kokia drynarioides strain JFW-HI SEQ_130379, 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: 389104
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 724 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:686 original size:6 final size:6
Alignment explanation
Indices: 614--719 Score: 60
Period size: 6 Copynumber: 18.0 Consensus size: 6
604 ATGGACTTTG
* * * *
614 AATTTA ATTTTAA AATTTA AGCTTTA AAATT- -ATTTCA AATTTA AA-CTA
1 AATTTA AATTT-A AATTTA A-ATTTA AATTTA AATTT-A AATTTA AATTTA
* * ** * *
662 AATTGA AATTTA AA-ATA AATTTA AATTTA AAAATG AATTTA AA-GTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
708 AATTTA AATTTA
1 AATTTA AATTTA
720 GAAATAAATC
Statistics
Matches: 72, Mismatches: 20, Indels: 16
0.67 0.19 0.15
Matches are distributed among these distances:
4 3 0.04
5 12 0.17
6 43 0.60
7 14 0.19
ACGTcount: A:0.51, C:0.03, G:0.04, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:701 original size:29 final size:29
Alignment explanation
Indices: 667--755 Score: 117
Period size: 29 Copynumber: 3.1 Consensus size: 29
657 AACTAAATTG
667 AAATTTAAAATAAATTTAAATTTAAAAAT
1 AAATTTAAAATAAATTTAAATTTAAAAAT
* * *
696 GAATTTAAAGTAAATTTAAATTTAGAAAT
1 AAATTTAAAATAAATTTAAATTTAAAAAT
* * *
725 AAATCTAAAAT-AATTTAAACTCAAAAAT
1 AAATTTAAAATAAATTTAAATTTAAAAAT
753 AAA
1 AAA
756 AATTTGACTC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
28 17 0.33
29 34 0.67
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATTTAAAATAAATTTAAATTTAAAAAT
Found at i:717 original size:17 final size:17
Alignment explanation
Indices: 626--733 Score: 84
Period size: 17 Copynumber: 6.5 Consensus size: 17
616 TTTAATTTTA
*
626 AAATTTAAGCTTTAAAAT
1 AAATTTAA-ATTTAAAAT
* *
644 -TATTTCAAATTTAAACT
1 AAATTT-AAATTTAAAAT
*
661 AAATTGAAATTTAAAAT
1 AAATTTAAATTTAAAAT
678 AAATTTAAATTT--AA-
1 AAATTTAAATTTAAAAT
* *
692 AAA--TGAATTTAAAGT
1 AAATTTAAATTTAAAAT
707 AAATTTAAATTTAGAAAT
1 AAATTTAAATTTA-AAAT
*
725 AAATCTAAA
1 AAATTTAAA
734 ATAATTTAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 16
0.71 0.12 0.16
Matches are distributed among these distances:
12 6 0.09
14 4 0.06
15 5 0.07
17 39 0.56
18 16 0.23
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:7693 original size:29 final size:29
Alignment explanation
Indices: 7651--8144 Score: 198
Period size: 29 Copynumber: 16.8 Consensus size: 29
7641 TTGGACACTC
* *
7651 GGGGCAAAATGGTAATTTTTGGATGTTTG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTG
*
7680 GGGGTAAAATGGTAATTTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGG-AAGTTTG
* **
7709 GGGATAAAAAAT-GTAATTTTTGGACA-TCCG
1 GGGGT--AAAATGGTAATTTTTGGA-AGTTTG
* * * * *
7739 AGGGTAAAATGATAATTTTTTAGACA-CTCG
1 GGGGTAAAATGGTAA-TTTTTGGA-AGTTTG
* * *
7769 AGGGGCAAAATGGTAA-TTTTGGATGTTCG
1 -GGGGTAAAATGGTAATTTTTGGAAGTTTG
*
7798 AGGGGTAAAATGGTAATTTTTGGAAAG-TTC
1 -GGGGTAAAATGGTAATTTTTGG-AAGTTTG
* * * **
7828 AGGTTCAAAAAT-GTGATTTTTTGGACA-TCCG
1 GGGGT--AAAATGGT-AATTTTTGGA-AGTTTG
** ** *
7859 ATGGTAAAATGGTAATTTTT-GAACACTCG
1 GGGGTAAAATGGTAATTTTTGGAA-GTTTG
* * * *
7888 GGGGCAAAATGGTAA-TTTTAGATGTTAG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTG
*
7916 GGGGTAAAATGGTAATTTTTGGAAAG-TTC
1 GGGGTAAAATGGTAATTTTTGG-AAGTTTG
* * *
7945 GGGGTCAAAAAT-GTGATTTTTGGACA-TCTA
1 GGGGT--AAAATGGTAATTTTTGGA-AGTTTG
* * * *
7975 GTGGTAAAATGATAATTTTTGGATGTTCG
1 GGGGTAAAATGGTAATTTTTGGAAGTTTG
* *
8004 GAGGTAAAATGGTAATTTTGGGAAGTTT-
1 GGGGTAAAATGGTAATTTTTGGAAGTTTG
* *
8032 GGGGTCAAAA-GTGCAA-TTTTGGAAAAGTTTT
1 GGGGT-AAAATG-GTAATTTTTGG--AAGTTTG
** *
8063 GGATTAAAACGGTAA-TTTTGGAAGTTTAG
1 GGGGTAAAATGGTAATTTTTGGAAGTTT-G
* * *
8092 AGGGAAAAAT-GTAATTTTTGAGAAGTTTAA
1 GGGGTAAAATGGTAATTTTTG-GAAGTTT-G
*
8122 GGGTTAAAAT-GTAATTTTTGGAA
1 GGGGTAAAATGGTAATTTTTGGAA
8145 AATTTAGGGT
Statistics
Matches: 351, Mismatches: 77, Indels: 74
0.70 0.15 0.15
Matches are distributed among these distances:
27 1 0.00
28 52 0.15
29 151 0.43
30 102 0.29
31 45 0.13
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.34
Consensus pattern (29 bp):
GGGGTAAAATGGTAATTTTTGGAAGTTTG
Found at i:7744 original size:59 final size:58
Alignment explanation
Indices: 7606--7997 Score: 269
Period size: 59 Copynumber: 6.7 Consensus size: 58
7596 GGTAAAACGA
* ** * * *
7606 TAATTTTTGGACACCCGAGGGTAAAACAGTAACTTTTGGACACTCGGG-GCAAAATGG
1 TAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAACTCGGGTGAAAAATGG
** ** * * *
7663 TAATTTTTGGATGTTTGGGGGTAAAATGGTAATTTTTGGAAAGTTCGGGATAAAAAAT-G
1 TAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAA-CTCGGG-TGAAAAATGG
* * * * *
7722 TAATTTTTGGACATCCGAGGGTAAAATGATAATTTTTTAGACACTCGAGGGGCAAAATGG
1 TAATTTTTGGACATCCGAGGGTAAAATGGTAA-TTTTTGGAAACTCG-GGTGAAAAATGG
** * * * *
7782 TAA-TTTTGGATGTTCGAGGGGTAAAATGGTAATTTTTGGAAAGTTCAGGTTCAAAAAT-G
1 TAATTTTTGGACATCCGA-GGGTAAAATGGTAATTTTTGGAAA-CTC-GGGTGAAAAATGG
* * * *
7841 TGATTTTTTGGACATCCGATGGTAAAATGGTAATTTTT-GAACACTCGGGGGCAAAATGG
1 T-AATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAA-ACTCGGGTGAAAAATGG
* ** ** * * *
7900 TAA-TTTTAGATGTTAGGGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAAT-G
1 TAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAA-CTC-GGGTGAAAAATGG
* * *
7958 TGATTTTTGGACAT-CTAGTGGTAAAATGATAATTTTTGGA
1 TAATTTTTGGACATCCGAG-GGTAAAATGGTAATTTTTGGA
7998 TGTTCGGAGG
Statistics
Matches: 251, Mismatches: 66, Indels: 34
0.72 0.19 0.10
Matches are distributed among these distances:
57 59 0.24
58 22 0.09
59 98 0.39
60 60 0.24
61 12 0.05
ACGTcount: A:0.32, C:0.08, G:0.27, T:0.33
Consensus pattern (58 bp):
TAATTTTTGGACATCCGAGGGTAAAATGGTAATTTTTGGAAACTCGGGTGAAAAATGG
Found at i:7747 original size:30 final size:29
Alignment explanation
Indices: 7561--8022 Score: 232
Period size: 29 Copynumber: 15.8 Consensus size: 29
7551 ATTTTGGATG
* * * *
7561 CCGATGGGCAAAACGGTAATTTTTAGACAC
1 CCGA-GGGTAAAATGGTAATTTTTGGACAT
* * *
7591 CCGAGGGTAAAACGATAATTTTTGGACAC
1 CCGAGGGTAAAATGGTAATTTTTGGACAT
** *
7620 CCGAGGGTAAAACAGTAACTTTTGGACA-
1 CCGAGGGTAAAATGGTAATTTTTGGACAT
* **
7648 CTCG-GGGCAAAATGGTAATTTTTGGATGT
1 C-CGAGGGTAAAATGGTAATTTTTGGACAT
** * *
7677 TTGGGGGTAAAATGGTAATTTTTGGAAAGT
1 CCGAGGGTAAAATGGTAATTTTTGGACA-T
* *
7707 TCG-GGATAAAAAAT-GTAATTTTTGGACAT
1 CCGAGGGT--AAAATGGTAATTTTTGGACAT
* *
7736 CCGAGGGTAAAATGATAATTTTTTAGACA-
1 CCGAGGGTAAAATGGTAA-TTTTTGGACAT
* **
7765 CTCGAGGGGCAAAATGGTAA-TTTTGGATGT
1 C-CGA-GGGTAAAATGGTAATTTTTGGACAT
* *
7795 TCGAGGGGTAAAATGGTAATTTTTGGAAAGT
1 CCGA-GGGTAAAATGGTAATTTTTGGACA-T
* * *
7826 TC-AGGTTCAAAAAT-GTGATTTTTTGGACAT
1 CCGAGGGT--AAAATGGT-AATTTTTGGACAT
* *
7856 CCGATGGTAAAATGGTAATTTTTGAACA-
1 CCGAGGGTAAAATGGTAATTTTTGGACAT
* * * **
7884 CTCGGGGGCAAAATGGTAA-TTTTAGATGT
1 C-CGAGGGTAAAATGGTAATTTTTGGACAT
** * *
7913 TAGGGGGTAAAATGGTAATTTTTGGAAAGT
1 CCGAGGGTAAAATGGTAATTTTTGGACA-T
* *
7943 TCG-GGGTCAAAAAT-GTGATTTTTGGACAT
1 CCGAGGGT--AAAATGGTAATTTTTGGACAT
* * **
7972 -CTAGTGGTAAAATGATAATTTTTGGATGT
1 CCGAG-GGTAAAATGGTAATTTTTGGACAT
*
8001 TCG-GAGGTAAAATGGTAATTTT
1 CCGAG-GGTAAAATGGTAATTTT
8023 GGGAAGTTTG
Statistics
Matches: 338, Mismatches: 65, Indels: 59
0.73 0.14 0.13
Matches are distributed among these distances:
28 52 0.15
29 175 0.52
30 68 0.20
31 43 0.13
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (29 bp):
CCGAGGGTAAAATGGTAATTTTTGGACAT
Found at i:8051 original size:87 final size:87
Alignment explanation
Indices: 7893--8051 Score: 221
Period size: 87 Copynumber: 1.8 Consensus size: 87
7883 ACTCGGGGGC
* *
7893 AAAATGGTAATTTTAGATGTTAGGGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATG
1 AAAATGATAATTTTAGATGTTAGGAGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATG
**
7958 TGATTTTTGGACATCTAGTGGT
66 CAATTTTTGGACATCTAGTGGT
* * * * *
7980 AAAATGATAATTTTTGGATGTTCGGAGGTAAAATGGTAA-TTTTGGGAAGTTTGGGGTCAAAAGT
1 AAAATGATAA-TTTTAGATGTTAGGAGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAAT
8044 GCAATTTT
65 GCAATTTT
8052 GGAAAAGTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
87 37 0.60
88 25 0.40
ACGTcount: A:0.31, C:0.04, G:0.28, T:0.36
Consensus pattern (87 bp):
AAAATGATAATTTTAGATGTTAGGAGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATG
CAATTTTTGGACATCTAGTGGT
Found at i:8079 original size:88 final size:85
Alignment explanation
Indices: 7893--8146 Score: 219
Period size: 88 Copynumber: 2.9 Consensus size: 85
7883 ACTCGGGGGC
* * * *
7893 AAAATGGTAATTTTAGATGTTAGGGGGTAAAATGGTAATTTTTGGAAAGTTCGGGGTCAAAAATG
1 AAAATGGTAATTTTGGATGTTAGGAGGTAAAATGGTAATTTTTGGGAAGTTTGGGGTC-AAAA-G
* * *
7958 TGATTTTTGGACATCTAGTGGT
64 TGAATTTTGGAAAACTAGTGGT
* *
7980 AAAATGATAATTTTTGGATGTTCGGAGGTAAAATGGTAA-TTTTGGGAAGTTTGGGGTCAAAAGT
1 AAAATGGTAA-TTTTGGATGTTAGGAGGTAAAATGGTAATTTTTGGGAAGTTTGGGGTCAAAAGT
* **
8044 GCAATTTTGGAAAAGTTTTGGATT
65 G-AATTTTGGAAAACTAGTGG--T
* * * * * *
8068 AAAACGGTAATTTTGGAAGTTTA-GAGGGAAAAAT-GTAATTTTTGAGAAGTTTAAGGGTTAAAA
1 AAAATGGTAATTTTGGATG-TTAGGA-GGTAAAATGGTAATTTTTGGGAAGTTT-GGGGTCAAAA
8131 -TGTAATTTTTGGAAAA
63 GTG-AA-TTTTGGAAAA
8147 TTTAGGGTCA
Statistics
Matches: 137, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
85 3 0.02
86 17 0.12
87 40 0.29
88 59 0.43
89 18 0.13
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.35
Consensus pattern (85 bp):
AAAATGGTAATTTTGGATGTTAGGAGGTAAAATGGTAATTTTTGGGAAGTTTGGGGTCAAAAGTG
AATTTTGGAAAACTAGTGGT
Found at i:8099 original size:28 final size:29
Alignment explanation
Indices: 8068--8141 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 29
8058 GTTTTGGATT
*
8068 AAAACGGTAA-TTTTG-GAAGTTTAGAGGG
1 AAAAAGGTAATTTTTGAGAAGTTTA-AGGG
*
8096 AAAAATGTAATTTTTGAGAAGTTTAAGGG
1 AAAAAGGTAATTTTTGAGAAGTTTAAGGG
* *
8125 TTAAAATGTAATTTTTG
1 -AAAAAGGTAATTTTTG
8142 GAAAATTTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
28 8 0.20
29 9 0.22
30 23 0.57
ACGTcount: A:0.38, C:0.01, G:0.24, T:0.36
Consensus pattern (29 bp):
AAAAAGGTAATTTTTGAGAAGTTTAAGGG
Found at i:8119 original size:30 final size:29
Alignment explanation
Indices: 7917--8177 Score: 107
Period size: 29 Copynumber: 8.9 Consensus size: 29
7907 AGATGTTAGG
**
7917 GGGT-AAAATGGTAATTTTTGGAAAG-TTCG
1 GGGTAAAAAT-GTAATTTTTGG-AAGTTTAA
* *
7946 GGGTCAAAAATGTGATTTTTGGACA-TCT-A
1 GGGT-AAAAATGTAATTTTTGGA-AGTTTAA
* **
7975 GTGGT-AAAATGATAATTTTTGGATG-TTCG
1 G-GGTAAAAATG-TAATTTTTGGAAGTTTAA
* *
8004 GAGGT-AAAATGGTAATTTTGGGAAGTTT-G
1 G-GGTAAAAAT-GTAATTTTTGGAAGTTTAA
* * *
8033 GGGTCAAAAGTGCAA-TTTTGGAAAAGTTT-T
1 GGGT-AAAAATGTAATTTTTGG--AAGTTTAA
* **
8063 GGATTAAAACGGTAA-TTTTGGAAGTTTAGA
1 GG-GTAAAAATGTAATTTTTGGAAGTTTA-A
8093 GGG-AAAAATGTAATTTTTGAGAAGTTTAA
1 GGGTAAAAATGTAATTTTTG-GAAGTTTAA
* *
8122 GGGTTAAAATGTAATTTTTGGAAAATTT-A
1 GGGTAAAAATGTAATTTTTGG-AAGTTTAA
* **
8151 GGGTCAAAATACAATTTTTGGAGAGTT
1 GGGTAAAAATGTAATTTTTGGA-AGTT
8178 CAGGGACCTT
Statistics
Matches: 182, Mismatches: 28, Indels: 44
0.72 0.11 0.17
Matches are distributed among these distances:
28 30 0.16
29 73 0.40
30 73 0.40
31 6 0.03
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTAA
Found at i:8160 original size:59 final size:56
Alignment explanation
Indices: 8008--8170 Score: 155
Period size: 59 Copynumber: 2.8 Consensus size: 56
7998 TGTTCGGAGG
* * *
8008 TAAAATGGTAATTTTGGGAAGTTTGGGGTCAAAAGTGCAATTTTGGAAAAGTTTTGGAT
1 TAAAAT-GTAATTTT-GGAAGTTTAGGGTCAAAA-TGCAATTTTTGAAAAGTTTAGGAT
* ** * * *
8067 TAAAACGGTAATTTTGGAAGTTTAGAGGGAAAAATGTAATTTTTGAGAAGTTTAAGGGT
1 TAAAA-TGTAATTTTGGAAGTTTAG-GGTCAAAATGCAATTTTTGAAAAGTTT-AGGAT
* *
8126 TAAAATGTAATTTTTGGAAAATTTAGGGTCAAAATACAATTTTTG
1 TAAAATGTAA-TTTTGG-AAGTTTAGGGTCAAAATGCAATTTTTG
8171 GAGAGTTCAG
Statistics
Matches: 84, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
58 29 0.35
59 48 0.57
60 7 0.08
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (56 bp):
TAAAATGTAATTTTGGAAGTTTAGGGTCAAAATGCAATTTTTGAAAAGTTTAGGAT
Found at i:9869 original size:96 final size:96
Alignment explanation
Indices: 9692--9876 Score: 277
Period size: 96 Copynumber: 1.9 Consensus size: 96
9682 GAAAAGGATG
**
9692 TTCGATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
**
9757 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAAAAACATTGCCTCGATTAAGGGTA
9788 TTCGATTAT-TTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTC-GAAACT
1 TTCGATTATCTT-GATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-T
*
9851 CGAA-ATAAAAAAATATTGCCTCGATT
63 CGAAGATAAAAAAACATTGCCTCGATT
9877 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
95 3 0.04
96 73 0.90
97 5 0.06
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
TTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
AGATAAAAAAACATTGCCTCGATTAAGGGTA
Found at i:10015 original size:8 final size:8
Alignment explanation
Indices: 9998--10029 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
9988 GTAACCACAA
9998 AAAAAT-C
1 AAAAATAC
10005 AAAAATAC
1 AAAAATAC
10013 AAAAATAC
1 AAAAATAC
10021 -AAAATAC
1 AAAAATAC
10028 AA
1 AA
10030 GTGCATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 13 0.57
8 10 0.43
ACGTcount: A:0.75, C:0.12, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATAC
Found at i:10255 original size:28 final size:28
Alignment explanation
Indices: 10223--10311 Score: 110
Period size: 28 Copynumber: 3.1 Consensus size: 28
10213 AAAACAAAAT
*
10223 TTTTGGACACTCGAGGGTAAAATGGTAA
1 TTTTGGACATTCGAGGGTAAAATGGTAA
**
10251 TTTTGAGAGTTTC-AGGGTCAAAATGG-AA
1 TTTTG-GACATTCGAGGGT-AAAATGGTAA
10279 TTTTTGGACATTCGAGGGTAAAATGGTAA
1 -TTTTGGACATTCGAGGGTAAAATGGTAA
10308 TTTT
1 TTTT
10312 TGAAAGTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
28 28 0.55
29 23 0.45
ACGTcount: A:0.30, C:0.08, G:0.27, T:0.35
Consensus pattern (28 bp):
TTTTGGACATTCGAGGGTAAAATGGTAA
Found at i:10357 original size:59 final size:58
Alignment explanation
Indices: 10237--10546 Score: 329
Period size: 59 Copynumber: 5.3 Consensus size: 58
10227 GGACACTCGA
* * ** *
10237 GGGTAAAATGGTAA-TTTTGAGAGTTTCAGGGTC-AAAATGGAATTTTTGGACATTCGA
1 GGGTAAAAT-GTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAGGTTCGG
* *
10294 GGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAGGTTTGG
1 GGGTAAAAT-GTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAGGTTCGG
* * * * * *
10353 GGGTAAAATTGTAATTTTTGGAAA-CTTCAAGATCAAAAATTGAATTTTTGGAGGTTCGT
1 GGGTAAAA-TGTAATTTTT-GAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAGGTTCGG
* ** *
10412 GGGTAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGGAATTTTTGGAATTTTGG
1 GGGTAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAGGTTCGG
* * * * *
10470 GGGTAAAAATATAATTTTTGGAAGTTTTAGGGTCAAAAATGGATTTTTTGGAAGTTCGA
1 GGGT-AAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAGGTTCGG
* *
10529 GGTTAAAAATATAATTTT
1 GGGT-AAAATGTAATTTT
10547 CGAACAGTGT
Statistics
Matches: 214, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
57 18 0.08
58 55 0.26
59 136 0.64
60 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (58 bp):
GGGTAAAATGTAATTTTTGAAAGTTTTAGGGTCAAAAATGGAATTTTTGGAGGTTCGG
Found at i:10370 original size:28 final size:29
Alignment explanation
Indices: 10235--10546 Score: 143
Period size: 29 Copynumber: 10.7 Consensus size: 29
10225 TTGGACACTC
*
10235 GAGGGTAAAATGGTAA-TTTT-GAGAGTTT
1 GAGGGTAAAATTGTAATTTTTGGAG-GTTT
* * ** *
10263 CAGGGTCAAAA-TGGAATTTTTGGACATTC
1 GAGGGT-AAAATTGTAATTTTTGGAGGTTT
* * *
10292 GAGGGTAAAATGGTAATTTTTGAAAGTTTT
1 GAGGGTAAAATTGTAATTTTTG-GAGGTTT
* *
10322 G-GGGTCAAAAATGGAATTTTTGGAGGTTT
1 GAGGGT-AAAATTGTAATTTTTGGAGGTTT
* ***
10351 GGGGGTAAAATTGTAATTTTTGGAAACTT
1 GAGGGTAAAATTGTAATTTTTGGAGGTTT
* * * *
10380 CAAGATCAAAAATTG-AATTTTTGGAGGTTC
1 GAGGGT--AAAATTGTAATTTTTGGAGGTTT
* * *
10410 GTGGGTAAAA-TGTAATTTTTGAAAGTTTT
1 GAGGGTAAAATTGTAATTTTTG-GAGGTTT
* * **
10439 G-GGGTCAAAAATGGAATTTTTGGAATTTT
1 GAGGGT-AAAATTGTAATTTTTGGAGGTTT
* * * *
10468 GGGGGTAAAAATATAATTTTTGGAAGTTT
1 GAGGGTAAAATTGTAATTTTTGGAGGTTT
* * * * * *
10497 TAGGGTCAAAAATGGATTTTTTGGAAGTTC
1 GAGGGT-AAAATTGTAATTTTTGGAGGTTT
* * *
10527 GAGGTTAAAAATATAATTTT
1 GAGGGTAAAATTGTAATTTT
10547 CGAACAGTGT
Statistics
Matches: 214, Mismatches: 55, Indels: 29
0.72 0.18 0.10
Matches are distributed among these distances:
27 2 0.01
28 28 0.13
29 104 0.49
30 73 0.34
31 7 0.03
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
GAGGGTAAAATTGTAATTTTTGGAGGTTT
Found at i:10426 original size:117 final size:117
Alignment explanation
Indices: 10270--10546 Score: 385
Period size: 117 Copynumber: 2.4 Consensus size: 117
10260 TTTCAGGGTC
10270 AAAATGGAATTTTTGGACA-TTCGAGGGTAAAATGGTAATTTTTGAAAGTTTTGGGGTCAAAAAT
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAT-GTAATTTTTGAAAGTTTTGGGGTCAAAAAT
* * *
10334 GGAATTTTTGGAGGTTTGGGGGTAAAATTGTAATTTTTGGAAACTTCAAGATCA
64 GGAATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTGGAAACTTCAAGATCA
* * *
10388 AAAATTGAATTTTTGGAGGTTCGTGGGTAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGG
* ** * * *
10453 AATTTTTGGAATTTTGGGGGTAAAAATATAATTTTTGGAAGTTTTAGGGTCA
66 AATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTGGAAACTTCAAGATCA
* * *
10505 AAAATGGATTTTTTGGAAGTTCGAGGTTAAAAATATAATTTT
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGTAATTTT
10547 CGAACAGTGT
Statistics
Matches: 139, Mismatches: 18, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
117 98 0.71
118 41 0.29
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (117 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGTAATTTTTGAAAGTTTTGGGGTCAAAAATGG
AATTTTTGGAAGTTTGGGGGTAAAAATATAATTTTTGGAAACTTCAAGATCA
Found at i:10458 original size:29 final size:30
Alignment explanation
Indices: 10241--10525 Score: 173
Period size: 30 Copynumber: 9.7 Consensus size: 30
10231 ACTCGAGGGT
* **
10241 AAAATGGTAA-TTTTGAGAGTTTCAGGGTC-
1 AAAATGG-AATTTTTGAAAGTTTTGGGGTCA
* *
10270 AAAATGGAATTTTTGGACA--TTCGAGGGT--
1 AAAATGGAATTTTT-GAAAGTTTTG-GGGTCA
10298 AAAATGGTAATTTTTGAAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGAAAGTTTTGGGGTCA
* * *
10329 AAAATGGAATTTTTGGAGGTTTGGGGGT-A
1 AAAATGGAATTTTTGAAAGTTTTGGGGTCA
* * * *** *
10358 AAATTGTAATTTTTGGAAA-CTTCAAGATCA
1 AAAATGGAATTTTT-GAAAGTTTTGGGGTCA
* * * *
10388 AAAATTGAATTTTTG-GAGGTTCGTGGGT--
1 AAAATGGAATTTTTGAAAGTTTTG-GGGTCA
*
10416 AAAATGTAATTTTTGAAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGAAAGTTTTGGGGTCA
*
10446 AAAATGGAATTTTTGGAA-TTTTGGGGGT-A
1 AAAATGGAATTTTTGAAAGTTTT-GGGGTCA
** * *
10475 AAAATATAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGAAAGTTTTGGGGTCA
* *
10505 AAAATGGATTTTTTGGAAGTT
1 AAAATGGAATTTTTGAAAGTT
10526 CGAGGTTAAA
Statistics
Matches: 201, Mismatches: 37, Indels: 35
0.74 0.14 0.13
Matches are distributed among these distances:
28 33 0.16
29 77 0.38
30 84 0.42
31 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.26, T:0.38
Consensus pattern (30 bp):
AAAATGGAATTTTTGAAAGTTTTGGGGTCA
Found at i:10536 original size:29 final size:29
Alignment explanation
Indices: 10270--10538 Score: 166
Period size: 29 Copynumber: 9.2 Consensus size: 29
10260 TTTCAGGGTC
* *
10270 AAAATGGAATTTTTGGACA-TTCGAGGGT-
1 AAAATGGAATTTTTGGA-AGTTTGAGGTTA
* * *
10298 AAAATGGTAATTTTTGAAAGTTTTGGGGTCA
1 AAAATGG-AATTTTTGGAAG-TTTGAGGTTA
* * *
10329 AAAATGGAATTTTTGGAGGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGTTA
* * * ** * *
10358 AAATTGTAATTTTTGGAAACTTCAAGATCA
1 AAAATGGAATTTTTGG-AAGTTTGAGGTTA
* * * * *
10388 AAAATTGAATTTTTGGAGGTTCGTGGGT-
1 AAAATGGAATTTTTGGAAGTTTGAGGTTA
* * * *
10416 AAAATGTAATTTTTGAAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAG-TTTGAGGTTA
* * *
10446 AAAATGGAATTTTTGGAATTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGTTA
** * *
10475 AAAATATAATTTTTGGAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTGA-GGTTA
* *
10505 AAAATGGATTTTTTGGAAGTTCGAGGTTA
1 AAAATGGAATTTTTGGAAGTTTGAGGTTA
10534 AAAAT
1 AAAAT
10539 ATAATTTTCG
Statistics
Matches: 178, Mismatches: 55, Indels: 15
0.72 0.22 0.06
Matches are distributed among these distances:
28 23 0.13
29 77 0.43
30 71 0.40
31 7 0.04
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGAGGTTA
Found at i:10546 original size:30 final size:30
Alignment explanation
Indices: 10416--10546 Score: 90
Period size: 30 Copynumber: 4.4 Consensus size: 30
10406 GTTCGTGGGT
* * * *
10416 AAAATGTAA-TTTTTGAAAGTTTTGGGGTCA
1 AAAATATAATTTTTTGGAAG-TTTGAGGTTA
** * * *
10446 AAAATGGAA-TTTTTGGAATTTTGGGGGTA
1 AAAATATAATTTTTTGGAAGTTTGAGGTTA
* *
10475 AAAATATAA-TTTTTGGAAGTTTTAGGGTCA
1 AAAATATAATTTTTTGGAAGTTTGA-GGTTA
** *
10505 AAAAT-GGATTTTTTGGAAGTTCGAGGTTA
1 AAAATATAATTTTTTGGAAGTTTGAGGTTA
10534 AAAATATAATTTT
1 AAAATATAATTTT
10547 CGAACAGTGT
Statistics
Matches: 79, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
29 37 0.47
30 42 0.53
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (30 bp):
AAAATATAATTTTTTGGAAGTTTGAGGTTA
Found at i:12452 original size:6 final size:6
Alignment explanation
Indices: 12443--12535 Score: 81
Period size: 6 Copynumber: 16.2 Consensus size: 6
12433 TTTGAACATT
*
12443 AATTTA AATTTA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AA-TTTA
* * * *
12491 AA--TA AATTTA AACTTA AA-ATA AATTTA ACTTTA AA-ATA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
12535 A
1 A
12536 TTTCTATTGA
Statistics
Matches: 70, Mismatches: 9, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
4 6 0.09
5 10 0.14
6 46 0.66
7 8 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
AATTTA
Found at i:12479 original size:17 final size:17
Alignment explanation
Indices: 12443--12535 Score: 123
Period size: 17 Copynumber: 5.4 Consensus size: 17
12433 TTTGAACATT
*
12443 AATTTAAATTTAAATTTA
1 AATTTAAATTTAAA-ATA
* *
12461 AACTTAAATTTATAATA
1 AATTTAAATTTAAAATA
*
12478 AATTTAAATTTTAAATA
1 AATTTAAATTTAAAATA
*
12495 AATTTAAACTTAAAATA
1 AATTTAAATTTAAAATA
*
12512 AATTTAACTTTAAAATA
1 AATTTAAATTTAAAATA
12529 AATTTAA
1 AATTTAA
12536 TTTCTATTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
17 53 0.82
18 12 0.18
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:12709 original size:56 final size:55
Alignment explanation
Indices: 12646--12756 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 55
12636 CAATAAATAA
*
12646 AAACAAGCAATAATGGTAAATAAATATATATTTATTACCTTGATAACACAATTATT
1 AAACAAGCAATAATGGTAAATAAATATATA-TTATTACCTTGATAACACAACTATT
12702 AAACAAGCAATAATGGTAAATAAATATATATTATTACCTTGATAACACAACTATT
1 AAACAAGCAATAATGGTAAATAAATATATATTATTACCTTGATAACACAACTATT
12757 TGACAATCTT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 24 0.44
56 30 0.56
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (55 bp):
AAACAAGCAATAATGGTAAATAAATATATATTATTACCTTGATAACACAACTATT
Found at i:13222 original size:17 final size:17
Alignment explanation
Indices: 13200--13283 Score: 114
Period size: 17 Copynumber: 4.9 Consensus size: 17
13190 TATTTGAACT
*
13200 TTTAAATTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
13217 TTTAAATTAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
13234 CTTAAAATAAATGTAAA
1 TTTAAAATAAATTTAAA
*
13251 TTTAAAACAAATTTAAA
1 TTTAAAATAAATTTAAA
*
13268 CTTAAAATAAATTTAA
1 TTTAAAATAAATTTAA
13284 CAAATAGGTT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 59 1.00
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:13239 original size:34 final size:34
Alignment explanation
Indices: 13201--13283 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 34
13191 ATTTGAACTT
* **
13201 TTAAATTAAATTTAAATTTAAATTAAATTTAAAC
1 TTAAAATAAATTTAAATTTAAAACAAATTTAAAC
*
13235 TTAAAATAAATGTAAATTTAAAACAAATTTAAAC
1 TTAAAATAAATTTAAATTTAAAACAAATTTAAAC
13269 TTAAAATAAATTTAA
1 TTAAAATAAATTTAA
13284 CAAATAGGTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.39
Consensus pattern (34 bp):
TTAAAATAAATTTAAATTTAAAACAAATTTAAAC
Found at i:17097 original size:2 final size:2
Alignment explanation
Indices: 17090--17124 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17080 ACATACGTAC
*
17090 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17125 AATCTGAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19016 original size:4 final size:4
Alignment explanation
Indices: 19007--19031 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
18997 CATAAATATT
19007 TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA T
19032 GCCATGACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:32527 original size:10 final size:10
Alignment explanation
Indices: 32512--32536 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
32502 CTGTTTTAAA
32512 TTTATAATAT
1 TTTATAATAT
32522 TTTATAATAT
1 TTTATAATAT
32532 TTTAT
1 TTTAT
32537 TTTTATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTATAATAT
Found at i:38608 original size:15 final size:14
Alignment explanation
Indices: 38579--38628 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
38569 TACTTTTAAT
38579 TATTTTAA--ATTA
1 TATTTTAATTATTA
38591 TATTTTAATTATTTA
1 TATTTTAATTA-TTA
* *
38606 TATTTGAAATATTA
1 TATTTTAATTATTA
*
38620 TGTTTTAAT
1 TATTTTAAT
38629 CACTTATGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.27
14 10 0.33
15 12 0.40
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (14 bp):
TATTTTAATTATTA
Found at i:38781 original size:17 final size:17
Alignment explanation
Indices: 38759--38792 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
38749 GAGATGAGAA
*
38759 TAAATTTTTAATTAATT
1 TAAATTTTAAATTAATT
38776 TAAATTTTAAATTAATT
1 TAAATTTTAAATTAATT
38793 ACAACTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATTTTAAATTAATT
Found at i:40205 original size:25 final size:25
Alignment explanation
Indices: 40147--40205 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
40137 AAATTTATGA
*
40147 AATATATTTAAAAATTACTTTGTAT
1 AATATATTTAAAAATTACTTTATAT
*
40172 CAT-TATTTAAAAATTACTTTATACT
1 AATATATTTAAAAATTACTTTATA-T
40197 AATAT-TTTA
1 AATATATTTA
40206 TATACTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 19 0.66
25 9 0.31
26 1 0.03
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (25 bp):
AATATATTTAAAAATTACTTTATAT
Found at i:40459 original size:15 final size:16
Alignment explanation
Indices: 40434--40464 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
40424 TTTGGTACTC
40434 TGTAGATTTTTTTTTT
1 TGTAGATTTTTTTTTT
40450 TGTA-ATTTTTTTTTT
1 TGTAGATTTTTTTTTT
40465 CAAACGCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.13, C:0.00, G:0.10, T:0.77
Consensus pattern (16 bp):
TGTAGATTTTTTTTTT
Found at i:45281 original size:15 final size:17
Alignment explanation
Indices: 45260--45300 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
45250 TAATTTTTTA
45260 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
45276 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
45292 AAAATTATA
1 AAAATTATA
45301 TATTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:45293 original size:24 final size:25
Alignment explanation
Indices: 45231--45309 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 25
45221 TTGACTCTCA
* *
45231 AAAATAATAAAAATTATTTTAATTTTTT
1 AAAATAATAAAAA-TA-TATAA-TTATT
*
45259 AAAAATTATAAAAATATA-AATTATT
1 -AAAATAATAAAAATATATAATTATT
* *
45284 AAAATAATAAAATTATATATTTATT
1 AAAATAATAAAAATATATAATTATT
45309 A
1 A
45310 TCGTAAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 15 0.35
25 11 0.26
26 2 0.05
27 1 0.02
28 2 0.05
29 12 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAATAATAAAAATATATAATTATT
Found at i:45705 original size:20 final size:19
Alignment explanation
Indices: 45667--45705 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
45657 ATATAAATTT
* *
45667 TTTAAAAAGATTTTGGAAA
1 TTTAAAAAAATTTTCGAAA
45686 TTTAATAAAAATTTTCGAAA
1 TTTAA-AAAAATTTTCGAAA
45706 AATATAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (19 bp):
TTTAAAAAAATTTTCGAAA
Found at i:67302 original size:25 final size:25
Alignment explanation
Indices: 67245--67292 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
67235 CATAAAATAG
67245 AAATAATTATATAAAAATTAGAAAA
1 AAATAATTATATAAAAATTAGAAAA
67270 AAATAATTATAT-AAAATTA-AAAA
1 AAATAATTATATAAAAATTAGAAAA
67293 TTCATTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 4 0.17
24 7 0.30
25 12 0.52
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (25 bp):
AAATAATTATATAAAAATTAGAAAA
Found at i:69801 original size:6 final size:6
Alignment explanation
Indices: 69790--69816 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
69780 CGTATCGGTG
69790 GAGACA GAGACA GAGACA GAGACA GAG
1 GAGACA GAGACA GAGACA GAGACA GAG
69817 TTACTCTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.48, C:0.15, G:0.37, T:0.00
Consensus pattern (6 bp):
GAGACA
Found at i:71913 original size:2 final size:2
Alignment explanation
Indices: 71908--71934 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
71898 TTTAAATCTA
71908 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
71935 CTAAAGTAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75682 original size:6 final size:6
Alignment explanation
Indices: 75671--75712 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
75661 AATAAAATAA
75671 CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC
1 CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC CCCATC
75713 TGAATATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.67, G:0.00, T:0.17
Consensus pattern (6 bp):
CCCATC
Found at i:101350 original size:33 final size:34
Alignment explanation
Indices: 101313--101386 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
101303 TGTTTAATCT
*
101313 TTAACCTCCC-TTAACTTTTACCTTAC-ATCTTCC
1 TTAACCTCCCTTTAACTTTAACCTT-CTATCTTCC
*
101346 TTAACCTCCCTTTACCTTTAACCTTCTATCTTCC
1 TTAACCTCCCTTTAACTTTAACCTTCTATCTTCC
101380 TTAACCT
1 TTAACCT
101387 TTCAGATTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 11 0.30
34 26 0.70
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.43
Consensus pattern (34 bp):
TTAACCTCCCTTTAACTTTAACCTTCTATCTTCC
Found at i:106739 original size:17 final size:16
Alignment explanation
Indices: 106717--106775 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 16
106707 ATGTTCAACA
106717 TTTAACCTCCCTTGAC
1 TTTAACCTCCCTTGAC
*
106733 TTTTAACTTTCCATCTTG-C
1 -TTTAAC-CTCC--CTTGAC
106752 -TTAACCTCCCTTGACC
1 TTTAACCTCCCTTGA-C
106768 TTTAACCT
1 TTTAACCT
106776 TCTATCTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 4 0.12
16 4 0.12
17 18 0.53
18 3 0.09
19 1 0.03
20 4 0.12
ACGTcount: A:0.19, C:0.34, G:0.05, T:0.42
Consensus pattern (16 bp):
TTTAACCTCCCTTGAC
Found at i:106761 original size:34 final size:34
Alignment explanation
Indices: 106718--106792 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
106708 TGTTCAACAT
* * *
106718 TTAACCTCCCTTGACTTTTAACTTTCCATCTTGC
1 TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
*
106752 TTAACCTCCCTTGACCTTTAACCTTCTATCTTCC
1 TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
106786 TTAACCT
1 TTAACCT
106793 TTCATATTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.19, C:0.35, G:0.04, T:0.43
Consensus pattern (34 bp):
TTAACCTCCCTTGACCTTTAACCTTCCATCTTCC
Found at i:114179 original size:3 final size:3
Alignment explanation
Indices: 114171--114198 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
114161 GTGGACCATA
114171 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
114199 CCACGACGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:119824 original size:27 final size:26
Alignment explanation
Indices: 119779--119847 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
119769 TTCCGGGTTG
* *
119779 TTTATATAAATGAACCAAA-AAAATTTA
1 TTTACATAAATG-ACCAAATAAAA-ATA
119806 TTTACATAAATGACTCAAATTGAAAAATA
1 TTTACATAAATGAC-CAAA-T-AAAAATA
119835 TTTACATAAATGA
1 TTTACATAAATGA
119848 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
26 2 0.06
27 15 0.42
29 15 0.42
30 4 0.11
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (26 bp):
TTTACATAAATGACCAAATAAAAATA
Found at i:120276 original size:54 final size:53
Alignment explanation
Indices: 120199--120305 Score: 151
Period size: 54 Copynumber: 2.0 Consensus size: 53
120189 TCTACACCGT
* * * * *
120199 CTTTTTCAGATTTAAAAATATTTTTTTTAGTGTTTGCCACCCGATGGCGTACA
1 CTTTTTCAAATTCAAAAATATTTTTTTGAGTGTTTGCCACCCAATGGCCTACA
*
120252 CTTTTCTCAAATTCAAAAATATTTTTTTGATTGTTTGCCACCCAATGGCCTACA
1 CTTTT-TCAAATTCAAAAATATTTTTTTGAGTGTTTGCCACCCAATGGCCTACA
120306 TTACCTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 5 0.11
54 42 0.89
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (53 bp):
CTTTTTCAAATTCAAAAATATTTTTTTGAGTGTTTGCCACCCAATGGCCTACA
Found at i:121438 original size:16 final size:16
Alignment explanation
Indices: 121402--121450 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
121392 GATCAATTTG
* *
121402 TTTTTAAATATATAAT
1 TTTTTATATATATTAT
*
121418 ATTTTATATTATATTAT
1 TTTTTATA-TATATTAT
121435 TTTTTATATATATTAT
1 TTTTTATATATATTAT
121451 ATAATTTATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTTTATATATATTAT
Found at i:141508 original size:17 final size:17
Alignment explanation
Indices: 141486--141519 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
141476 CTAAGGACAA
*
141486 TGCAAAGGCTTCTGTTT
1 TGCAAAGACTTCTGTTT
141503 TGCAAAGACTTCTGTTT
1 TGCAAAGACTTCTGTTT
141520 GTGGTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (17 bp):
TGCAAAGACTTCTGTTT
Found at i:148302 original size:6 final size:6
Alignment explanation
Indices: 148293--148320 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
148283 AAGAAGAAGT
148293 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGA
148321 AGATAACATG
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:151696 original size:3 final size:3
Alignment explanation
Indices: 151675--151710 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
151665 GTAAAAACTC
151675 ATT A-T ATT -TT ATT -TT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
151711 TAGGCGTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.20
3 24 0.80
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:153523 original size:59 final size:56
Alignment explanation
Indices: 153453--153661 Score: 184
Period size: 59 Copynumber: 3.5 Consensus size: 56
153443 GAGTCAAAAC
* * *
153453 GTAATTTTGGAAGAGTTTAGGAGTTAAAATGAGGTTTTAAAAAAGATTATGGGTCAAAT
1 GTAATTTTGGAAAAGTTTAGG-GTTAAAATGA--TTTTAAAAAAGTTTAAGGGTCAAAT
* ** *
153512 GTAATTTTGGAAAAGTTTAGGGATCAAAAATGAAATTTTGGAAAAGTTTAGGGGTCAAGAT
1 GTAATTTTGGAAAAGTTTAGGG-T-TAAAATG--ATTTTAAAAAAGTTTAAGGGTCAA-AT
* * *
153573 GTGATTTTAGAAAAGTTTAAGGGTTAAATATGATTTTAAAAAAGTTTAAGAGTCAAAAT
1 GTAATTTTGGAAAAGTTT-AGGGTTAAA-ATGATTTTAAAAAAGTTTAAGGGTC-AAAT
* ** *
153632 ATAATTTTTAAAAAGTTTGAGGGCTAAAAT
1 GTAATTTTGGAAAAGTTT-AGGGTTAAAAT
153662 ATAGTTTTTA
Statistics
Matches: 123, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
58 3 0.02
59 63 0.51
60 30 0.24
61 22 0.18
62 5 0.04
ACGTcount: A:0.41, C:0.02, G:0.22, T:0.34
Consensus pattern (56 bp):
GTAATTTTGGAAAAGTTTAGGGTTAAAATGATTTTAAAAAAGTTTAAGGGTCAAAT
Found at i:153549 original size:31 final size:30
Alignment explanation
Indices: 153446--153591 Score: 120
Period size: 30 Copynumber: 4.9 Consensus size: 30
153436 GAATTTTGAG
* *
153446 TCAAAACGTAATTTTGGAAGAGTTTA-GGA
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGA
* * ** *
153475 GTTAAAATG-AGGTTTTAAAAAAGATTATGGG-
1 -TCAAAATGTA-ATTTTGGAAAAGTTTA-GGGA
153506 TC-AAATGTAATTTTGGAAAAGTTTAGGGA
1 TCAAAATGTAATTTTGGAAAAGTTTAGGGA
* *
153535 TCAAAAATGAAATTTTGGAAAAGTTTAGGGG
1 TC-AAAATGTAATTTTGGAAAAGTTTAGGGA
* * *
153566 TCAAGATGTGATTTTAGAAAAGTTTA
1 TCAAAATGTAATTTTGGAAAAGTTTA
153592 AGGGTTAAAT
Statistics
Matches: 91, Mismatches: 18, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
28 3 0.03
29 20 0.22
30 39 0.43
31 27 0.30
32 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (30 bp):
TCAAAATGTAATTTTGGAAAAGTTTAGGGA
Found at i:153567 original size:60 final size:59
Alignment explanation
Indices: 153419--153591 Score: 172
Period size: 60 Copynumber: 2.9 Consensus size: 59
153409 AATGAGGTCG
* * * *
153419 AAAAATGAAGTTTTGGAGAA-TTT-TGAGTCAAAACGTAATTTTGGAAGAGTTTAGGAGT
1 AAAAATGAAGTTTTGGAAAAGTTTATGGGTC-AAATGTAATTTTGGAAAAGTTTAGGAGT
* * ** *
153477 TAAAATGAGGTTTTAAAAAAGATTATGGGTCAAATGTAATTTTGGAAAAGTTTAGG-GAT
1 AAAAATGAAGTTTTGGAAAAGTTTATGGGTCAAATGTAATTTTGGAAAAGTTTAGGAG-T
* * * *
153536 CAAAAATGAAATTTTGGAAAAGTTTAGGGGTCAAGATGTGATTTTAGAAAAGTTTA
1 -AAAAATGAAGTTTTGGAAAAGTTTATGGGTCAA-ATGTAATTTTGGAAAAGTTTA
153592 AGGGTTAAAT
Statistics
Matches: 92, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
58 16 0.17
59 26 0.28
60 31 0.34
61 19 0.21
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAAATGAAGTTTTGGAAAAGTTTATGGGTCAAATGTAATTTTGGAAAAGTTTAGGAGT
Found at i:153581 original size:90 final size:90
Alignment explanation
Indices: 153455--153620 Score: 206
Period size: 90 Copynumber: 1.8 Consensus size: 90
153445 GTCAAAACGT
* * * * *
153455 AATTTTGGAAGAGTTTAGGAGTTAAAATGAGGTTTTAAAAAAGATTATGGGTCAAATGTAATTTT
1 AATTTTGGAAAAGTTTAGGAGTCAAAATGAGATTTTAAAAAAGATTAAGGGTCAAATATAATTTT
**
153520 GGAAAAGTTTAGGGATCAAAAATGA
66 AAAAAAGTTTAGGGATCAAAAATGA
* * * * * * *
153545 AATTTTGGAAAAGTTTAGGGGTCAAGATGTGATTTTAGAAAAGTTTAAGGGTTAAATATGATTTT
1 AATTTTGGAAAAGTTTAGGAGTCAAAATGAGATTTTAAAAAAGATTAAGGGTCAAATATAATTTT
153610 AAAAAAGTTTA
66 AAAAAAGTTTA
153621 AGAGTCAAAA
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
90 62 1.00
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.34
Consensus pattern (90 bp):
AATTTTGGAAAAGTTTAGGAGTCAAAATGAGATTTTAAAAAAGATTAAGGGTCAAATATAATTTT
AAAAAAGTTTAGGGATCAAAAATGA
Found at i:153586 original size:30 final size:29
Alignment explanation
Indices: 153487--153654 Score: 131
Period size: 29 Copynumber: 5.6 Consensus size: 29
153477 TAAAATGAGG
* * *
153487 TTTTAAAAAAGATTATGGGTCAAATGTAA
1 TTTTAGAAAAGTTTAGGGGTCAAATGTAA
* * *
153516 TTTTGGAAAAGTTTAGGGATCAAAAATGAAA
1 TTTTAGAAAAGTTTAGGGGTC--AAATGTAA
* *
153547 TTTTGGAAAAGTTTAGGGGTCAAGATGTGA
1 TTTTAGAAAAGTTTAGGGGTCAA-ATGTAA
* * * *
153577 TTTTAGAAAAGTTTAAGGGTTAAATATGA
1 TTTTAGAAAAGTTTAGGGGTCAAATGTAA
* * * *
153606 TTTTAAAAAAGTTTAAGAGTCAAAATATAA
1 TTTTAGAAAAGTTTAGGGGTC-AAATGTAA
153636 TTTTTA-AAAAGTTTGAGGG
1 -TTTTAGAAAAGTTT-AGGG
153655 CTAAAATATA
Statistics
Matches: 114, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
29 41 0.36
30 39 0.34
31 34 0.30
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (29 bp):
TTTTAGAAAAGTTTAGGGGTCAAATGTAA
Found at i:153661 original size:30 final size:29
Alignment explanation
Indices: 153577--153672 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 29
153567 CAAGATGTGA
* *
153577 TTTTAGAAAAGTTTAAGGGTTAAATATGAT
1 TTTTA-AAAAGTTTAAGGGTAAAATATAAT
* *
153607 TTTAAAAAAGTTTAAGAGTCAAAATATAAT
1 TTTTAAAAAGTTTAAGGGT-AAAATATAAT
* *
153637 TTTTAAAAAGTTTGAGGGCTAAAATATAGT
1 TTTTAAAAAGTTTAAGGG-TAAAATATAAT
153667 TTTTAA
1 TTTTAA
153673 TAAAAACATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.23
30 42 0.75
31 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.39
Consensus pattern (29 bp):
TTTTAAAAAGTTTAAGGGTAAAATATAAT
Found at i:177457 original size:12 final size:12
Alignment explanation
Indices: 177442--177474 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
177432 ATAAAAATAA
177442 AAAAAGAAAAAG
1 AAAAAGAAAAAG
*
177454 AAAAATAAAAAG
1 AAAAAGAAAAAG
177466 -AAAAGAAAA
1 AAAAAGAAAA
177475 GCCTCGTCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:182157 original size:2 final size:2
Alignment explanation
Indices: 182152--182176 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
182142 TTAAAATTCA
182152 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
182177 GTTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:183372 original size:42 final size:40
Alignment explanation
Indices: 183325--183405 Score: 94
Period size: 42 Copynumber: 2.0 Consensus size: 40
183315 ATCAAGTAAG
183325 AATATAATTT-TTTTATGTGTCCAT-ACTATATATTATAAAAAT
1 AATAT-ATTTATTTTATGTGT-CATAACT-TAT-TTATAAAAAT
* *
183367 AATATATTTATTTTTTTTGTCATAACTTATTTATAAAAA
1 AATATATTTATTTTATGTGTCATAACTTATTTATAAAAA
183406 AAAAATTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
40 9 0.26
41 10 0.29
42 16 0.46
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (40 bp):
AATATATTTATTTTATGTGTCATAACTTATTTATAAAAAT
Found at i:185562 original size:29 final size:30
Alignment explanation
Indices: 185503--185564 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
185493 ATCTCAAAAT
* *
185503 TATACATGAATTTTGATTTAATGTGCGATTA
1 TATACATGAATTTTAATTTAATGT-CAATTA
*
185534 TATACATGAATTTTAATTTGATGT-AATTA
1 TATACATGAATTTTAATTTAATGTCAATTA
185563 TA
1 TA
185565 CACGTGAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.21
31 22 0.79
ACGTcount: A:0.35, C:0.05, G:0.13, T:0.47
Consensus pattern (30 bp):
TATACATGAATTTTAATTTAATGTCAATTA
Found at i:185572 original size:29 final size:29
Alignment explanation
Indices: 185500--185572 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
185490 TGAATCTCAA
*
185500 AATTATACA-TGAATTTTGATTTAATGTGC
1 AATTATACACTGAATTTTAATTTAATGT-C
* * *
185529 GATTATATACATGAATTTTAATTTGATGT-
1 AATTATACAC-TGAATTTTAATTTAATGTC
185558 AATTATACACGTGAA
1 AATTATACAC-TGAA
185573 ACTCTGATTG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (29 bp):
AATTATACACTGAATTTTAATTTAATGTC
Found at i:188821 original size:23 final size:23
Alignment explanation
Indices: 188794--188837 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
188784 GAACACTGAC
188794 ATGGGCAAAT-GGAAACCGGTACG
1 ATGGGC-AATGGGAAACCGGTACG
188817 ATGGGCAATGGGAAACCGGTA
1 ATGGGCAATGGGAAACCGGTA
188838 TGCCCAAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.34, C:0.16, G:0.36, T:0.14
Consensus pattern (23 bp):
ATGGGCAATGGGAAACCGGTACG
Found at i:194101 original size:2 final size:2
Alignment explanation
Indices: 194094--194121 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
194084 ACTCAAAATA
194094 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
194122 TTTTTTTTTT
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:195248 original size:16 final size:16
Alignment explanation
Indices: 195229--195263 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
195219 GAGTTTCAAA
195229 TTTTTTTATTTTAGGT
1 TTTTTTTATTTTAGGT
* *
195245 TTTTTTTTTTTTTGGT
1 TTTTTTTATTTTAGGT
195261 TTT
1 TTT
195264 AGATTAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.00, G:0.11, T:0.83
Consensus pattern (16 bp):
TTTTTTTATTTTAGGT
Found at i:197598 original size:23 final size:23
Alignment explanation
Indices: 197567--197621 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
197557 TGTTTTATGG
* *
197567 TTTTTAAATATTATTTGATAAA-A
1 TTTTAAAATATT-TTTCATAAATA
197590 TTTTAAAATATTTTTCATAAATA
1 TTTTAAAATATTTTTCATAAATA
197613 TTTTCAAAA
1 TTTT-AAAA
197622 AAATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 8 0.29
23 16 0.57
24 4 0.14
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTTAAAATATTTTTCATAAATA
Found at i:201607 original size:20 final size:19
Alignment explanation
Indices: 201569--201608 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
201559 GTAAAAAAGC
* *
201569 ATAAAAAAATAATATCCAA
1 ATAAAAAAATAACAACCAA
201588 ATAACAAAAATAACAACCAA
1 ATAA-AAAAATAACAACCAA
201608 A
1 A
201609 ACAGTAGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (19 bp):
ATAAAAAAATAACAACCAA
Found at i:201641 original size:22 final size:22
Alignment explanation
Indices: 201616--201674 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
201606 AAAACAGTAG
*
201616 TAAAAATAACAGCAAACAACAT
1 TAAAAATAACAGCAAACAACAA
* * * *
201638 TAAAAACAACA-AAAATAGCAA
1 TAAAAATAACAGCAAACAACAA
201659 TAAAAATAACAGCAAA
1 TAAAAATAACAGCAAA
201675 AATAACACGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 16 0.55
22 13 0.45
ACGTcount: A:0.68, C:0.15, G:0.05, T:0.12
Consensus pattern (22 bp):
TAAAAATAACAGCAAACAACAA
Found at i:201674 original size:24 final size:24
Alignment explanation
Indices: 201593--201678 Score: 65
Period size: 24 Copynumber: 3.8 Consensus size: 24
201583 TCCAAATAAC
* * * *
201593 AAAAATAACAACCAAAACAGTAGT
1 AAAAATAACAACAAAAATAGCAAT
* *
201617 AAAAATAACAGCAAACA-A-C-AT
1 AAAAATAACAACAAAAATAGCAAT
*
201638 -TAAA-AACAACAAAAATAGCAAT
1 AAAAATAACAACAAAAATAGCAAT
*
201660 AAAAATAACAGCAAAAATA
1 AAAAATAACAACAAAAATA
201679 ACACGAAAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
19 9 0.19
20 4 0.09
21 2 0.04
22 2 0.04
23 4 0.09
24 26 0.55
ACGTcount: A:0.67, C:0.15, G:0.06, T:0.12
Consensus pattern (24 bp):
AAAAATAACAACAAAAATAGCAAT
Found at i:201687 original size:24 final size:23
Alignment explanation
Indices: 201642--201699 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
201632 CAACATTAAA
* *
201642 AACAACAAAAATAGCAATAAAAAT
1 AACAACAAAAATAACAA-GAAAAT
* *
201666 AACAGCAAAAATAACACGAAAAT
1 AACAACAAAAATAACAAGAAAAT
201689 AACAATCAAAA
1 AACAA-CAAAA
201700 CAGTAAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 9 0.32
24 19 0.68
ACGTcount: A:0.69, C:0.16, G:0.05, T:0.10
Consensus pattern (23 bp):
AACAACAAAAATAACAAGAAAAT
Found at i:203845 original size:2 final size:2
Alignment explanation
Indices: 203838--203871 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
203828 TCATTTTCAA
203838 AT AT AT 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 AT AT AT
203872 TGCATCGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208412 original size:17 final size:18
Alignment explanation
Indices: 208385--208418 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
208375 GAGTAAGGGA
208385 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
208403 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
208419 TGATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:209862 original size:23 final size:24
Alignment explanation
Indices: 209817--209863 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
209807 ATTCAACATT
**
209817 ATTTATTAGAAAATTACTTAAGTA
1 ATTTATTAGAAAATTACAAAAGTA
*
209841 ATTTATT-TAAAATTACAAAAGTA
1 ATTTATTAGAAAATTACAAAAGTA
209864 TAGTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (24 bp):
ATTTATTAGAAAATTACAAAAGTA
Found at i:214066 original size:16 final size:16
Alignment explanation
Indices: 214028--214066 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
214018 GAATATATTA
*
214028 AAATCTAATATTTTTAT
1 AAAT-TAATATTTTAAT
214045 ACAATTAATATTTTAAT
1 A-AATTAATATTTTAAT
214062 AAATT
1 AAATT
214067 TACTATTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 4 0.20
17 13 0.65
18 3 0.15
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATTAATATTTTAAT
Found at i:231112 original size:18 final size:18
Alignment explanation
Indices: 231072--231114 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
231062 ATTCAAGATG
231072 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
231090 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
231108 TAATTAA
1 TAATTAA
231115 AAATCTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:234817 original size:20 final size:18
Alignment explanation
Indices: 234764--234817 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 18
234754 AATTTATAAG
*
234764 TAATATATT-TATATATC
1 TAATATATTATTTATATC
234781 TAATATATTATGATTATATC
1 TAATATATTAT--TTATATC
234801 AATAATATATTATTTAT
1 --TAATATATTATTTAT
234818 GAATTATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 9 0.29
18 1 0.03
20 10 0.32
22 11 0.35
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATATATTATTTATATC
Found at i:236191 original size:14 final size:15
Alignment explanation
Indices: 236134--236196 Score: 56
Period size: 15 Copynumber: 4.2 Consensus size: 15
236124 TCCCAATTTG
236134 AAAATATAAAAATTA
1 AAAATATAAAAATTA
* *** *
236149 AAATTACCTAATTTGA
1 AAAATATAAAAATT-A
236165 AAAATATAAAAATTA
1 AAAATATAAAAATTA
*
236180 AAAATAT-CAAATTA
1 AAAATATAAAAATTA
236194 AAA
1 AAA
236197 TTCAAGAACT
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
14 9 0.25
15 17 0.47
16 10 0.28
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (15 bp):
AAAATATAAAAATTA
Found at i:249243 original size:18 final size:19
Alignment explanation
Indices: 249220--249257 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
249210 AAAATAATTT
249220 AAAAC-AAT-AATTATGAAA
1 AAAACAAATAAATT-TGAAA
249238 AAAACAAATAAATTTGAAA
1 AAAACAAATAAATTTGAAA
249257 A
1 A
249258 CATTTTTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 9 0.50
20 4 0.22
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAACAAATAAATTTGAAA
Found at i:260360 original size:30 final size:30
Alignment explanation
Indices: 260326--260390 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
260316 ACTTATTTTA
* *
260326 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTCAATATTTTAAAGACAT
* *
260356 TTGTTAATTTTGTCAATATTTTAGAGGCAT
1 TTGTTAATTTTGTCAATATTTTAAAGACAT
260386 TTGTT
1 TTGTT
260391 TGTTAAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.55
Consensus pattern (30 bp):
TTGTTAATTTTGTCAATATTTTAAAGACAT
Found at i:260525 original size:13 final size:13
Alignment explanation
Indices: 260509--260552 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
260499 ATATATATTT
260509 AAAAATAATATAA
1 AAAAATAATATAA
*
260522 AAAAGT-AT-TCAA
1 AAAAATAATAT-AA
260534 AAAAATAATATAA
1 AAAAATAATATAA
260547 AAAAAT
1 AAAAAT
260553 TTAACATAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.04
12 9 0.35
13 15 0.58
14 1 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (13 bp):
AAAAATAATATAA
Found at i:260548 original size:12 final size:12
Alignment explanation
Indices: 260509--260550 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
260499 ATATATATTT
260509 AAAAATAATATA
1 AAAAATAATATA
*
260521 AAAAAGTATTCA-A
1 AAAAA-TAAT-ATA
260534 AAAAATAATATA
1 AAAAATAATATA
260546 AAAAA
1 AAAAA
260551 ATTTAACATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 1 0.04
12 14 0.56
13 9 0.36
14 1 0.04
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (12 bp):
AAAAATAATATA
Found at i:261397 original size:19 final size:20
Alignment explanation
Indices: 261373--261411 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
261363 AACTCATTCA
*
261373 GGATTCGAG-TTTCAAGTTT
1 GGATTCAAGATTTCAAGTTT
*
261392 GGATTCAAGATTTGAAGTTT
1 GGATTCAAGATTTCAAGTTT
261412 AAGGTTCTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.41
Consensus pattern (20 bp):
GGATTCAAGATTTCAAGTTT
Found at i:261694 original size:13 final size:14
Alignment explanation
Indices: 261667--261712 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
261657 TAATTGTTGC
*
261667 ATTAATATGGATAA
1 ATTAATATTGATAA
261681 ATTAAT-TTGATAA
1 ATTAATATTGATAA
*
261694 AGTAATATT-ATTAA
1 ATTAATATTGA-TAA
261708 ATTAA
1 ATTAA
261713 GTATAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (14 bp):
ATTAATATTGATAA
Found at i:272002 original size:11 final size:11
Alignment explanation
Indices: 271986--272014 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
271976 TAAGCTACTC
271986 TCTTCTTCATT
1 TCTTCTTCATT
271997 TCTTCTTCATT
1 TCTTCTTCATT
272008 TCTTCTT
1 TCTTCTT
272015 TTCAAATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (11 bp):
TCTTCTTCATT
Found at i:273097 original size:10 final size:10
Alignment explanation
Indices: 273082--273108 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
273072 CGTTCCCATT
273082 GGGTTTTTGG
1 GGGTTTTTGG
273092 GGGTTTTTGG
1 GGGTTTTTGG
273102 GGGTTTT
1 GGGTTTT
273109 GTCCAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (10 bp):
GGGTTTTTGG
Found at i:273636 original size:12 final size:12
Alignment explanation
Indices: 273619--273644 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
273609 TTTTTTATCC
273619 CTCCCTCCTGGG
1 CTCCCTCCTGGG
273631 CTCCCTCCTGGG
1 CTCCCTCCTGGG
273643 CT
1 CT
273645 ATTTATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.50, G:0.23, T:0.27
Consensus pattern (12 bp):
CTCCCTCCTGGG
Found at i:275286 original size:250 final size:250
Alignment explanation
Indices: 274845--275345 Score: 993
Period size: 250 Copynumber: 2.0 Consensus size: 250
274835 TAGTTTTCCT
*
274845 GTTTAGATCATCTCATCTAGTTGGCATAAGTTTATTCTTCTGGGTATATCTGATTGAATATACCT
1 GTTTAGATCATCTCATCTAGTTGGCATAAGTTTATTCTTCTGAGTATATCTGATTGAATATACCT
274910 GTTTTGAGCTCAAAAGAGAAATATACCCATCCATAAATGTGGTTGAACAAATTGTATAGGCTTTG
66 GTTTTGAGCTCAAAAGAGAAATATACCCATCCATAAATGTGGTTGAACAAATTGTATAGGCTTTG
274975 GAGTGACTTGTCACAAGAATCAGGACTTTCCTAGTCATTTTTGTTATTGATTCACTTGGTTCCAA
131 GAGTGACTTGTCACAAGAATCAGGACTTTCCTAGTCATTTTTGTTATTGATTCACTTGGTTCCAA
275040 CTTGTATGTTACAGCTACACGAAGCAATAGCACGCAAAGAGTCGCAAGAGTTCAA
196 CTTGTATGTTACAGCTACACGAAGCAATAGCACGCAAAGAGTCGCAAGAGTTCAA
275095 GTTTAGATCATCTCATCTAGTTGGCATAAGTTTATTCTTCTGAGTATATCTGATTGAATATACCT
1 GTTTAGATCATCTCATCTAGTTGGCATAAGTTTATTCTTCTGAGTATATCTGATTGAATATACCT
275160 GTTTTGAGCTCAAAAGAGAAATATACCCATCCATAAATGTGGTTGAACAAATTGTATAGGCTTTG
66 GTTTTGAGCTCAAAAGAGAAATATACCCATCCATAAATGTGGTTGAACAAATTGTATAGGCTTTG
275225 GAGTGACTTGTCACAAGAATCAGGACTTTCCTAGTCATTTTTGTTATTGATTCACTTGGTTCCAA
131 GAGTGACTTGTCACAAGAATCAGGACTTTCCTAGTCATTTTTGTTATTGATTCACTTGGTTCCAA
275290 CTTGTATGTTACAGCTACACGAAGCAATAGCACGCAAAGAGTCGCAAGAGTTCAA
196 CTTGTATGTTACAGCTACACGAAGCAATAGCACGCAAAGAGTCGCAAGAGTTCAA
275345 G
1 G
275346 GAAGGGATTA
Statistics
Matches: 250, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
250 250 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (250 bp):
GTTTAGATCATCTCATCTAGTTGGCATAAGTTTATTCTTCTGAGTATATCTGATTGAATATACCT
GTTTTGAGCTCAAAAGAGAAATATACCCATCCATAAATGTGGTTGAACAAATTGTATAGGCTTTG
GAGTGACTTGTCACAAGAATCAGGACTTTCCTAGTCATTTTTGTTATTGATTCACTTGGTTCCAA
CTTGTATGTTACAGCTACACGAAGCAATAGCACGCAAAGAGTCGCAAGAGTTCAA
Found at i:276442 original size:82 final size:82
Alignment explanation
Indices: 276301--276452 Score: 182
Period size: 82 Copynumber: 1.9 Consensus size: 82
276291 TAAATTAATT
* ** * * * *
276301 ATTTTGTTTAAAATTGCATCCGTTTTTAATCAAAAAATGAGTAAATTAATTCCTGTATGTACGAT
1 ATTTTATTTAAAATCACATCCATTTTTAATCAAAAAATGAGTAAATTAATTACTATATGTAAGAT
276366 AAAAAAGCAAAATGATC
66 AAAAAAGCAAAATGATC
* *
276383 ATTTTATTTAAAATCACATCCATTTTTACTTAAAAAATG-GATAAATTAATCTAC-ATATGTAAG
1 ATTTTATTTAAAATCACATCCATTTTTAATCAAAAAATGAG-TAAATTAAT-TACTATATGTAAG
*
276446 ATCAAAA
64 ATAAAAA
276453 TACAATATGC
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
81 1 0.02
82 55 0.95
83 2 0.03
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.36
Consensus pattern (82 bp):
ATTTTATTTAAAATCACATCCATTTTTAATCAAAAAATGAGTAAATTAATTACTATATGTAAGAT
AAAAAAGCAAAATGATC
Found at i:278053 original size:329 final size:329
Alignment explanation
Indices: 277455--278111 Score: 1188
Period size: 329 Copynumber: 2.0 Consensus size: 329
277445 ATTAAACATT
*
277455 GGTTAATTGCCCTTTCTTTTGAGAAAATTCCTTTTCTAATGCAAATCCCAAAGGCAGGTGAATAG
1 GGTTAATTGCCCTTTCTTTTGAGAAAATTCCTTTTCTAATACAAATCCCAAAGGCAGGTGAATAG
* *
277520 TGTGTATAGCACTAAACTCCATTCACCAAATTGCATCTTCCAAGGTCTAAGGCCAAATCATGAGC
66 TGTGTATAGCACTAAACCCCATTCACCAAATTGCATCTTCCAAGGTCTAAGGCCAAATCATAAGC
*
277585 TAACCTGGCCTTGGTTGGGTGTGGAATAAGAAGTCATTTGGATTCAGGACTCTTCATTCAATATA
131 TAACCTGGCCTTGGTTGGGTGTGGAACAAGAAGTCATTTGGATTCAGGACTCTTCATTCAATATA
* * *
277650 TATTCGGACATGAGTACGAAATAATATCCTCAAAATATAACGAAAAACCTAGAATAAGTAAATTC
196 CATTCGGACATGAGTACGAAATAATATCCTCAAAATATAACAAAAAACCTAGAATAAGTAAACTC
*
277715 ATGTCTAGACACATACTCGTATTAAACACTCCTAGTGATGTAGCATATCACCATCACTGAATCAA
261 ATGTCTAGACACATACTCGTATTAAACACTCCAAGTGATGTAGCATATCACCATCACTGAATCAA
277780 TATA
326 TATA
*
277784 GGTTAATTGGCCTTTCTTTTGAGAAAATTCCTTTTCTAATACAAATCCCAAAGGCAGGTGAATAG
1 GGTTAATTGCCCTTTCTTTTGAGAAAATTCCTTTTCTAATACAAATCCCAAAGGCAGGTGAATAG
277849 TGTGTATAGCACTAAACCCCATTCACCAAATTGCATCTTCCAAGGTCTAAGGCCAAATCATAAGC
66 TGTGTATAGCACTAAACCCCATTCACCAAATTGCATCTTCCAAGGTCTAAGGCCAAATCATAAGC
* *
277914 TAACCTGGCCTTGGTTTGGTGTGGAACAAGAAGTCATTTGGATTCTGGACTCTTCATTCAATATA
131 TAACCTGGCCTTGGTTGGGTGTGGAACAAGAAGTCATTTGGATTCAGGACTCTTCATTCAATATA
* * *
277979 CATTCGGACATGAGTATGAAATAATATCCTCAAAATATACCAAAAAACTTAGAATAAGTAAACTC
196 CATTCGGACATGAGTACGAAATAATATCCTCAAAATATAACAAAAAACCTAGAATAAGTAAACTC
278044 ATGTCTAGACACATACTCGTATTAAACACTCCAAGTGATGTAGCATATCACCATCACTGAATCAA
261 ATGTCTAGACACATACTCGTATTAAACACTCCAAGTGATGTAGCATATCACCATCACTGAATCAA
278109 TAT
326 TAT
278112 CTTAGCAGCT
Statistics
Matches: 314, Mismatches: 14, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
329 314 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (329 bp):
GGTTAATTGCCCTTTCTTTTGAGAAAATTCCTTTTCTAATACAAATCCCAAAGGCAGGTGAATAG
TGTGTATAGCACTAAACCCCATTCACCAAATTGCATCTTCCAAGGTCTAAGGCCAAATCATAAGC
TAACCTGGCCTTGGTTGGGTGTGGAACAAGAAGTCATTTGGATTCAGGACTCTTCATTCAATATA
CATTCGGACATGAGTACGAAATAATATCCTCAAAATATAACAAAAAACCTAGAATAAGTAAACTC
ATGTCTAGACACATACTCGTATTAAACACTCCAAGTGATGTAGCATATCACCATCACTGAATCAA
TATA
Found at i:287238 original size:6 final size:6
Alignment explanation
Indices: 287227--287259 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
287217 GAGAGAAGGT
*
287227 TGGTCG TGGTCG TGGTCG TGATCG TGGTCG TGG
1 TGGTCG TGGTCG TGGTCG TGGTCG TGGTCG TGG
287260 GTTTTTGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.15, G:0.48, T:0.33
Consensus pattern (6 bp):
TGGTCG
Found at i:290572 original size:23 final size:24
Alignment explanation
Indices: 290546--290596 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
290536 ATATTATTTT
290546 ATTAATATTTTAAT-AA-TTTAATA
1 ATTAA-ATTTTAATGAATTTTAATA
*
290569 ATTAAATTTTTATGAATTTTTAATA
1 ATTAAATTTTAATGAA-TTTTAATA
290594 ATT
1 ATT
290597 TTTATGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 7 0.29
25 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
ATTAAATTTTAATGAATTTTAATA
Found at i:293304 original size:23 final size:23
Alignment explanation
Indices: 293227--293308 Score: 78
Period size: 23 Copynumber: 3.4 Consensus size: 23
293217 CGAAGTACTT
*
293227 AACAGTAAGCACACAAGTGGTGGGGA
1 AACAGTAAGCACACAA--GGT-GCGA
293253 AACAGTAAGCACACACA-GTGC-A
1 AACAGTAAGCACACA-AGGTGCGA
* *
293275 ATCCAGTAGGCACACAAGGTGCGA
1 A-ACAGTAAGCACACAAGGTGCGA
293299 AACAGTAAGC
1 AACAGTAAGC
293309 GTGCTAGCAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 3 0.06
23 24 0.51
24 4 0.09
26 15 0.32
27 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.27, T:0.11
Consensus pattern (23 bp):
AACAGTAAGCACACAAGGTGCGA
Found at i:300141 original size:38 final size:37
Alignment explanation
Indices: 300090--300165 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 37
300080 TTTTGTCGTT
300090 TTCTTTTAACCAACGTTAACCGTTTAATATTGCTATCC
1 TTCTTTTAACCAACGTTAACCGTTTAATA-TGCTATCC
300128 TTCTTTTAACCAACGTTAACCGTTTAATATGCTATCC
1 TTCTTTTAACCAACGTTAACCGTTTAATATGCTATCC
300165 T
1 T
300166 CTATCTCTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 9 0.24
38 29 0.76
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (37 bp):
TTCTTTTAACCAACGTTAACCGTTTAATATGCTATCC
Found at i:301595 original size:31 final size:30
Alignment explanation
Indices: 301539--301596 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
301529 TTTATTATAA
301539 AATATTTATACTAATTTTAACTAATTGCAT
1 AATATTTATACTAATTTTAACTAATTGCAT
*
301569 AATATTTATTATTAATTATTAA-TAATTG
1 AATATTTA-TACTAATT-TTAACTAATTG
301597 GGCAAAGGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 13 0.52
32 4 0.16
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.50
Consensus pattern (30 bp):
AATATTTATACTAATTTTAACTAATTGCAT
Found at i:315000 original size:3 final size:3
Alignment explanation
Indices: 314992--315022 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
314982 CTGTGTGTTG
*
314992 TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
315023 GATGATAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:315056 original size:9 final size:9
Alignment explanation
Indices: 315009--315055 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
314999 AATAATAATA
*
315009 ATAATAATG
1 ATAATGATG
315018 ATAATGATG
1 ATAATGATG
*
315027 ATAATGACG
1 ATAATGATG
315036 ATAATGATG
1 ATAATGATG
*
315045 ATGATGATG
1 ATAATGATG
315054 AT
1 AT
315056 GCTTTAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (9 bp):
ATAATGATG
Found at i:317364 original size:13 final size:14
Alignment explanation
Indices: 317334--317364 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
317324 TAAAATTAAA
317334 TTAAATTTATTACT
1 TTAAATTTATTACT
317348 TTAAATTTATT-CT
1 TTAAATTTATTACT
317361 TTAA
1 TTAA
317365 TTATTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAAATTTATTACT
Found at i:317381 original size:16 final size:18
Alignment explanation
Indices: 317355--317393 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
317345 ACTTTAAATT
*
317355 TATTCTTTAATT-ATTTC
1 TATTTTTTAATTAATTTC
317372 -ATTTTTTAATTAATTTC
1 TATTTTTTAATTAATTTC
317389 TATTT
1 TATTT
317394 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 10 0.53
17 5 0.26
18 4 0.21
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.67
Consensus pattern (18 bp):
TATTTTTTAATTAATTTC
Found at i:317429 original size:18 final size:17
Alignment explanation
Indices: 317400--317510 Score: 66
Period size: 18 Copynumber: 6.2 Consensus size: 17
317390 ATTTAAAAAA
317400 AAATTAAATTTATTGCTTT
1 AAATT-AATTTATT-CTTT
317419 AAATTAATTTATTATTCTTT
1 AAATTAA--T-TTATTCTTT
*
317439 AAA-T-ATGTAATT-TTT
1 AAATTAAT-TTATTCTTT
* * * *
317454 TAATTAAATTCTTTTTT
1 AAATTAATTTATTCTTT
317471 AAATTTAATTTATTGCTTT
1 AAA-TTAATTTATT-CTTT
* *
317490 AAATTGATTTATTTTTT
1 AAATTAATTTATTCTTT
317507 AAAT
1 AAAT
317511 GTCTTTTTTT
Statistics
Matches: 72, Mismatches: 12, Indels: 18
0.71 0.12 0.18
Matches are distributed among these distances:
15 5 0.07
16 9 0.12
17 13 0.18
18 20 0.28
19 12 0.17
20 8 0.11
21 5 0.07
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (17 bp):
AAATTAATTTATTCTTT
Found at i:317451 original size:41 final size:39
Alignment explanation
Indices: 317406--317643 Score: 107
Period size: 36 Copynumber: 6.6 Consensus size: 39
317396 AAAAAAATTA
317406 AATTTATTGCTTTAAATTAATTTATTATTCTTTAAATATGT
1 AATTTATTG-TTTAAATTAATTTATTATT-TTTAAATATGT
* *
317447 AA--T-TT-TTT-AATTAAATT-CT-TTTTTAAAT-T-T
1 AATTTATTGTTTAAATTAATTTATTATTTTTAAATATGT
*
317477 AATTTATTGCTTTAAATTGATTTA-T-TTTTT-AA-ATGT
1 AATTTATTG-TTTAAATTAATTTATTATTTTTAAATATGT
* * *
317513 --CTT-TT-TTT-AATATAGATTATATT-TTTTAAAAT-TTT
1 AATTTATTGTTTAAAT-TA-ATT-TATTATTTTTAAATATGT
*
317548 AATTTATTGTTTTAAATTGATTTATTATTCTTTAAATATGT
1 AATTTATTG-TTTAAATTAATTTATTATT-TTTAAATATGT
* *
317589 AATTT-TTG--T-AATTAAATT-CTATTTTTAAAT-T-T
1 AATTTATTGTTTAAATTAATTTATTATTTTTAAATATGT
* *
317621 ATTTTATTGCTTTAAATTGATTT
1 AATTTATTG-TTTAAATTAATTT
317644 TTTTAAAATA
Statistics
Matches: 150, Mismatches: 18, Indels: 62
0.65 0.08 0.27
Matches are distributed among these distances:
30 6 0.04
31 5 0.03
32 16 0.11
33 12 0.08
34 15 0.10
35 22 0.15
36 25 0.17
37 10 0.07
38 8 0.05
39 6 0.04
40 13 0.09
41 12 0.08
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (39 bp):
AATTTATTGTTTAAATTAATTTATTATTTTTAAATATGT
Found at i:317456 original size:76 final size:72
Alignment explanation
Indices: 317354--317643 Score: 304
Period size: 71 Copynumber: 4.0 Consensus size: 72
317344 TACTTTAAAT
* * * * *
317354 TTATTCTTTAATTATTTCATTTTTTAATTAATTTCTATTTAAAAAAAAATTAAATTTATTGCTTT
1 TTATTCTTTAAATATGTAATTTTTTAATTAAATTCTATTT----AAAAATTTAATTTATTGCTTT
*
317419 AAATTAATTTA
62 AAATTGATTTA
**
317430 TTATTCTTTAAATATGTAATTTTTTAATTAAATTCT-TTTTTAAATTTAATTTATTGCTTTAAAT
1 TTATTCTTTAAATATGTAATTTTTTAATTAAATTCTATTTAAAAATTTAATTTATTGCTTTAAAT
317494 TGATTTA
66 TGATTTA
** * * * *
317501 -T-TT-TTT-AA-ATGTCTTTTTTTAATATAGATTATATTTTTTAAAATTTTAATTTATTGTTTT
1 TTATTCTTTAAATATGTAATTTTTTAAT-TAAATTCTA---TTTAAAAATTTAATTTATTGCTTT
317561 AAATTGATTTA
62 AAATTGATTTA
** *
317572 TTATTCTTTAAATATGTAATTTTTGTAATTAAATTCTATTTTTAAATTTATTTTATTGCTTTAAA
1 TTATTCTTTAAATATGTAATTTTT-TAATTAAATTCTATTTAAAAATTTAATTTATTGCTTTAAA
317637 TTGATTT
65 TTGATTT
317644 TTTTAAAATA
Statistics
Matches: 178, Mismatches: 25, Indels: 25
0.78 0.11 0.11
Matches are distributed among these distances:
66 13 0.07
67 8 0.04
68 3 0.02
69 2 0.01
70 1 0.01
71 59 0.33
72 1 0.01
73 31 0.17
74 3 0.02
75 5 0.03
76 48 0.27
77 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (72 bp):
TTATTCTTTAAATATGTAATTTTTTAATTAAATTCTATTTAAAAATTTAATTTATTGCTTTAAAT
TGATTTA
Found at i:317500 original size:71 final size:71
Alignment explanation
Indices: 317400--317643 Score: 318
Period size: 71 Copynumber: 3.4 Consensus size: 71
317390 ATTTAAAAAA
* *
317400 AAATTAAATTTATTGCTTTAAATTAATTTATTATTCTTTAAATATGTAATTTTTTAATTAAATTC
1 AAATTTAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGTAATTTTTTAATTAAATTC
317465 TTTTTT
66 TTTTTT
** *
317471 AAATTTAATTTATTGCTTTAAATTGATTTA-T-TT-TTT-AA-ATGTCTTTTTTTAATATAGATT
1 AAATTTAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGTAATTTTTTAAT-TA-AAT
*
317531 ATATTTTTT
64 -TCTTTTTT
*
317540 AAAATTTTAATTTATTGTTTTAAATTGATTTATTATTCTTTAAATATGTAATTTTTGTAATTAAA
1 -AAA-TTTAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGTAATTTTT-TAATTAAA
317605 TTCTATTTTT
63 TTCT-TTTTT
*
317615 AAATTTATTTTATTGCTTTAAATTGATTT
1 AAATTTAATTTATTGCTTTAAATTGATTT
317644 TTTTAAAATA
Statistics
Matches: 148, Mismatches: 13, Indels: 22
0.81 0.07 0.12
Matches are distributed among these distances:
66 13 0.09
67 4 0.03
68 5 0.03
69 9 0.06
70 4 0.03
71 54 0.36
72 1 0.01
73 26 0.18
74 8 0.05
75 9 0.06
76 11 0.07
77 4 0.03
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (71 bp):
AAATTTAATTTATTGCTTTAAATTGATTTATTATTCTTTAAATATGTAATTTTTTAATTAAATTC
TTTTTT
Found at i:317660 original size:142 final size:142
Alignment explanation
Indices: 317406--317661 Score: 426
Period size: 142 Copynumber: 1.8 Consensus size: 142
317396 AAAAAAATTA
317406 AATTTATTGCTTTAAATTAATTTATTATTCTTTAAATATGTAATTTTTTAATTAAATTCTTTTTT
1 AATTTATTGCTTTAAATTAATTTATTATTCTTTAAATATGTAATTTTTTAATTAAATTCTTTTTT
* *
317471 AAATTTAATTTATTGCTTTAAATTGATTTATTTTTTAAATGTCTTTTTTTAATATAGATTATATT
66 AAATTTAATTTATTGCTTTAAATTGATTTATTTTTAAAATATCTTTTTTTAATATAGATTATATT
317536 TTTTAAAATTTT
131 TTTTAAAATTTT
* *
317548 AATTTATTGTTTTAAATTGATTTATTATTCTTTAAATATGTAATTTTTGTAATTAAATTCTATTT
1 AATTTATTGCTTTAAATTAATTTATTATTCTTTAAATATGTAATTTTT-TAATTAAATTCT-TTT
* *
317613 TTAAATTTATTTTATTGCTTTAAATTGA-TT-TTTTTAAAATATGTTTTTT
64 TTAAATTTAATTTATTGCTTTAAATTGATTTATTTTTAAAATATCTTTTTT
317662 AATTTAAACA
Statistics
Matches: 106, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
142 62 0.58
143 14 0.13
144 30 0.28
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (142 bp):
AATTTATTGCTTTAAATTAATTTATTATTCTTTAAATATGTAATTTTTTAATTAAATTCTTTTTT
AAATTTAATTTATTGCTTTAAATTGATTTATTTTTAAAATATCTTTTTTTAATATAGATTATATT
TTTTAAAATTTT
Found at i:317679 original size:20 final size:18
Alignment explanation
Indices: 317645--317685 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
317635 AATTGATTTT
*
317645 TTTAAAATATGTTTTTTAA
1 TTTAAAATAT-ATTTTTAA
317664 TTTAAACATATATTTTTAA
1 TTTAAA-ATATATTTTTAA
317683 TTT
1 TTT
317686 TTGGGTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TTTAAAATATATTTTTAA
Found at i:321569 original size:58 final size:61
Alignment explanation
Indices: 321496--321656 Score: 229
Period size: 62 Copynumber: 2.7 Consensus size: 61
321486 TTATATGCTT
* * * *
321496 TAAATTAATAAATGAATGTTGGGATTAGTCTTTTTAATTACA-CT-CT-ATTTGAAATACG
1 TAAATTAATAAATGAATATTGGGATTAGTCTTTTTCATTACATATACTAATTTAAAATACG
* * *
321554 TACATTCATAAATGAATATTGGGATTAGTCTTTTTCATTACATTATATTAATTTAAAATACG
1 TAAATTAATAAATGAATATTGGGATTAGTCTTTTTCATTACA-TATACTAATTTAAAATACG
321616 TAAATTAATAAATGAATATTGGGATTAGTCTTTTTCATTAC
1 TAAATTAATAAATGAATATTGGGATTAGTCTTTTTCATTAC
321657 CATTTTTTTG
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
58 38 0.42
60 1 0.01
61 1 0.01
62 50 0.56
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (61 bp):
TAAATTAATAAATGAATATTGGGATTAGTCTTTTTCATTACATATACTAATTTAAAATACG
Found at i:323896 original size:2 final size:2
Alignment explanation
Indices: 323889--323917 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
323879 CAAATCTAAA
323889 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
323918 ATGCATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:328748 original size:21 final size:20
Alignment explanation
Indices: 328707--328748 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
328697 TAAAAAAACT
*
328707 AAATTTAAATAAAAATTTTA
1 AAATTTAAATAAAAATATTA
*
328727 AAATTTAAAATAAAAGTATTA
1 AAATTT-AAATAAAAATATTA
328748 A
1 A
328749 TATAACATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
AAATTTAAATAAAAATATTA
Found at i:329587 original size:25 final size:25
Alignment explanation
Indices: 329556--329611 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
329546 TTATTTTAAG
*
329556 TTATTTGTTTTGTTTAATTT-A-ATTT
1 TTATTTGATTTG-TT-ATTTAATATTT
329581 TTATTTGATTTGTTATTTAATATTT
1 TTATTTGATTTGTTATTTAATATTT
329606 TTATTT
1 TTATTT
329612 AGTTGACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 3 0.11
25 21 0.75
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.71
Consensus pattern (25 bp):
TTATTTGATTTGTTATTTAATATTT
Found at i:330357 original size:17 final size:17
Alignment explanation
Indices: 330335--330389 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
330325 AGTTATGGTA
330335 TGATTTAATAAGTGCAT
1 TGATTTAATAAGTGCAT
* * *
330352 TGATTTGAGTTA-TG-GT
1 TGATTT-AATAAGTGCAT
330368 ATGATTTAATAAGTGCAT
1 -TGATTTAATAAGTGCAT
330386 TGAT
1 TGAT
330390 AGAGCGTTGG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.44
Consensus pattern (17 bp):
TGATTTAATAAGTGCAT
Found at i:330364 original size:34 final size:34
Alignment explanation
Indices: 330321--330389 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
330311 TATCCAAAAG
330321 TTTGAGTTATGGTATGATTTAATAAGTGCATTGA
1 TTTGAGTTATGGTATGATTTAATAAGTGCATTGA
330355 TTTGAGTTATGGTATGATTTAATAAGTGCATTGA
1 TTTGAGTTATGGTATGATTTAATAAGTGCATTGA
330389 T
1 T
330390 AGAGCGTTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (34 bp):
TTTGAGTTATGGTATGATTTAATAAGTGCATTGA
Found at i:331857 original size:21 final size:21
Alignment explanation
Indices: 331827--331872 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
331817 ACGAGCTACC
*
331827 GCAATTCTCTACTCCTCCCGG
1 GCAATACTCTACTCCTCCCGG
*
331848 GCAATACTCTACTCCTCCGGG
1 GCAATACTCTACTCCTCCCGG
331869 GCAA
1 GCAA
331873 ATAGACCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (21 bp):
GCAATACTCTACTCCTCCCGG
Found at i:332165 original size:21 final size:20
Alignment explanation
Indices: 332122--332171 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
332112 TCTAAACCTT
* *
332122 AAACCCTAAATCTTAATTCA
1 AAACCCTAAATCTAAACTCA
332142 AAACCCTAAACTCTAAACTCA
1 AAACCCTAAA-TCTAAACTCA
*
332163 AAACTCTAA
1 AAACCCTAA
332172 CCCCTAAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (20 bp):
AAACCCTAAATCTAAACTCA
Found at i:332178 original size:21 final size:21
Alignment explanation
Indices: 332122--332178 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
332112 TCTAAACCTT
* * *
332122 AAACCCTAAA-TCTTAATTCA
1 AAACCCTAAACCCTAAACTCA
*
332142 AAACCCTAAACTCTAAACTCA
1 AAACCCTAAACCCTAAACTCA
* *
332163 AAACTCTAACCCCTAA
1 AAACCCTAAACCCTAA
332179 GCTCTAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACTCA
Found at i:332200 original size:14 final size:14
Alignment explanation
Indices: 332183--332214 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
332173 CCCTAAGCTC
332183 TAAATTCAAAACCT
1 TAAATTCAAAACCT
*
332197 TAAATTTAAAACCT
1 TAAATTCAAAACCT
332211 TAAA
1 TAAA
332215 ACCTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAATTCAAAACCT
Found at i:332229 original size:21 final size:22
Alignment explanation
Indices: 332190--332243 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
332180 CTCTAAATTC
*
332190 AAAACCTTAAATTTAAAACCTT
1 AAAACCTTAAATTTAAAACCCT
332212 AAAACC-TAAATATT-AAACCCT
1 AAAACCTTAAAT-TTAAAACCCT
*
332233 -AAACATTAAAT
1 AAAACCTTAAAT
332244 CATACATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.14
21 16 0.57
22 8 0.29
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAACCTTAAATTTAAAACCCT
Found at i:332281 original size:7 final size:7
Alignment explanation
Indices: 332269--332305 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
332259 CTAAATTTAT
332269 AACCATA
1 AACCATA
332276 AACCATA
1 AACCATA
332283 AACCATA
1 AACCATA
*
332290 AATCATA
1 AACCATA
332297 AACC-TA
1 AACCATA
332303 AAC
1 AAC
332306 AATATATTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.16
Consensus pattern (7 bp):
AACCATA
Found at i:332398 original size:42 final size:42
Alignment explanation
Indices: 332363--332469 Score: 112
Period size: 42 Copynumber: 2.5 Consensus size: 42
332353 ACCTTAAACA
*
332363 TAAAAT-TCAAAACTTTAAACCCTAAATTTAAAACCTCAAAAT
1 TAAAATATC-AAACTTTAAACCCTAAATATAAAACCTCAAAAT
* *
332405 TGAAATATCACACTTTAAACCCTAAATATAAATACCT-AAAAT
1 TAAAATATCAAACTTTAAACCCTAAATATAAA-ACCTCAAAAT
*
332447 TCAAAACA-CTAAACCTTTAAACC
1 T-AAAATATC-AAA-CTTTAAACC
332470 AAAATACAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
42 33 0.61
43 12 0.22
44 9 0.17
ACGTcount: A:0.50, C:0.21, G:0.01, T:0.27
Consensus pattern (42 bp):
TAAAATATCAAACTTTAAACCCTAAATATAAAACCTCAAAAT
Found at i:335277 original size:15 final size:15
Alignment explanation
Indices: 335259--335296 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
335249 ATCTGTTAAA
335259 AATAAATAAAATTTT
1 AATAAATAAAATTTT
335274 AATAAAATAAAATTTT
1 AAT-AAATAAAATTTT
335290 AA-AAATA
1 AATAAATA
335297 TACCCTACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.23
15 3 0.14
16 14 0.64
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAATAAAATTTT
Found at i:335397 original size:13 final size:12
Alignment explanation
Indices: 335371--335401 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
335361 CTAATAAATT
*
335371 AAATAATTTTAA
1 AAATAAATTTAA
335383 AAATAAATTTAA
1 AAATAAATTTAA
335395 AAATAAA
1 AAATAAA
335402 CACAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAAATTTAA
Found at i:335683 original size:19 final size:19
Alignment explanation
Indices: 335643--335684 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
335633 AAAAAATTAC
* *
335643 CTTTCTCTTCTTCTTTTTT
1 CTTTCTCTTCTTCTTCTCT
335662 CTTTCT-TTCTTTCTTCTCT
1 CTTTCTCTTC-TTCTTCTCT
335681 CTTT
1 CTTT
335685 TATTCTCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
CTTTCTCTTCTTCTTCTCT
Found at i:337396 original size:22 final size:20
Alignment explanation
Indices: 337348--337403 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 20
337338 ATTATTTTTC
337348 TAAT-ATTA-TATATTTTAA
1 TAATAATTATTATATTTTAA
** *
337366 TTTTTATTAATTCATATTTTAA
1 TAATAATT-ATT-ATATTTTAA
337388 TAATAATTATTATATT
1 TAATAATTATTATATT
337404 AAAAATGTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 2 0.07
19 3 0.10
20 6 0.21
21 4 0.14
22 14 0.48
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATAATTATTATATTTTAA
Found at i:350873 original size:811 final size:775
Alignment explanation
Indices: 349806--351819 Score: 2258
Period size: 811 Copynumber: 2.6 Consensus size: 775
349796 TCTTCACAAC
* * * * *
349806 TTGAAGCATACGTATGCTGTGTCATTTTTCTTTGACTTTCTATTTAAATGTAATAAATCCTAAAA
1 TTGAAGCATATGTATGCTATGTCATTTTTCTTTGACTCTCTATTTCAATGTAATAAATCCTCAAA
* *
349871 GTATTATATATTTTGGAATTTAAATTTATAAATTTGGATTTAATATTGTTTA-GAGAACTCAAAT
66 GTATTATAGATTTTGGAATTTAAATTTATAAATTTGGATTTAGTATTGTTTAGGA-AACTCAAAT
* * * *
349935 GATAAGTTTGG-AAGATGGAGCGAAAGTTAGAATGGTAATACTTTACGTTTCTTTTTATGATTTT
130 GACAAGTTTGGAAAG-TGGAGTGAAGGTTAGAATGGAAATACTTTACGTTTCTTTTTATGATTTT
* * * *
349999 TAATATAATATCTGACACGTGATATGTAAAAT-GACATTTGGTAAAATAAAATGGATGGAGTTGA
194 TGATATAATATTTGACACATGATATGTAAAATAG-CATTTGGTAAAATAAAATTGATGGAGTTGA
* *
350063 AGATATTTGTTGGTTGAGGTCGAGGGGAGAGAATCACGAGGAGAAATGATCCCTCAACCGATTTT
258 AGATATTTGTTGGTTGAGGTTGAGGGGAGAGAATCACGAGGGGAAATGATCCCTCAACCGATTTT
* *
350128 GCTTGGCTTTTGTGTCTTTCACATCCATTTTTTACGTCAGTATCTGTCTTTTTTTTTTTTTACAC
323 G-TT-G-TTTTGTGT-TTTCACGTCCATTTTTTA-GTCAGTATCTGTC---TTTTTTTTTTATAC
* * * * *
350193 TCTCTACTGATAATTGTTTTAACATCTATACTCGTTTCATCTCTTAATTATTGATATTTTTATTT
380 TCTCTACTGATAATTTTTTTGACATTTATACTCGTTTCATCTCTTATTTATTGATATTTATATTT
* * * *
350258 GTTTTTAAAGATAACGAAA-TCATATTTACACTAAGAATGCG-TAAAACATTTAAATCACTTAAA
445 ATTTTTAAAGAAAAC-AAATTCATATTTACACTAAGAATG-GATAAAACACTTAAATCACTGAAA
* * *
350321 TATCA-ATTATAAAAAATTTGACCATTAAAAAATATTTGTAAACTATATCAATTATAAGAAATAT
508 CATCAGA-CATAAAAAATTTGACCATAAAAAAATATTTGTAAA-T-TA-C-A-TAT--G---TA-
** *
350385 TGTATGTGTTTGATTATATATGAAGAAGTGGAAAAAAACAAATGAAGAGCAAAGATTAAAGAACC
561 -GTA-GTG---G-------A--AA-AA----AAAAAAACAAAACAAGAGCAAAGATAAAAGAACC
* * * *
350450 TGTAGGAACTAGCTAAAAAGAAAATGCTGAGGTCATCACTTCCTTCACAACTCACACAAATCTGT
607 AGTAGAAACTAGCTAAAAAGAAAATGCTGAGGCCATCACTTCCTTCACAACTCACACAAATATGT
* * * *
350515 CTTCAATAATGTC-CCCAAAATTTAATGACTTCTATTTGAATAGGAGAAAGGTTTTATGTCTTAA
672 CTTCAACAATGTCTCCAAAAACTTAATGACTTCTATTTGAATAGGAGAAAGGTCTTATGTCTTAA
* *
350579 TAGGCCATTATAATCATTGTTTATGTCTTAGAGACAGC-A
737 AAGGCCATTATAATCATTGTTTATGTCTTAGAAACA-CTA
* *
350618 -TGAAGTATATGTATGCTATGTCATTTTTCTTTGACTCTCTATTTCAATGTAATAAGTCCTCAAA
1 TTGAAGCATATGTATGCTATGTCATTTTTCTTTGACTCTCTATTTCAATGTAATAAATCCTCAAA
* * * * *
350682 GTATTATAGATTTTGGAATTTAAATTCATAAATTTGGATATCGTATTGTTTAGGAAATTCTAATG
66 GTATTATAGATTTTGGAATTTAAATTTATAAATTTGGATTTAGTATTGTTTAGGAAACTCAAATG
* * * * *
350747 ACAAGTTTGGAAAGTGGCGTGAAGGTTAAAATGGAAATATTTTACGTTTTTTTTTATGATTTCTG
131 ACAAGTTTGGAAAGTGGAGTGAAGGTTAGAATGGAAATACTTTACGTTTCTTTTTATGATTTTTG
* ***
350812 ATATATTATTTGACACATGATATGTAAAATAGCATTTGGTAAAACGTAATTGATGGAGTTGAAGA
196 ATATAATATTTGACACATGATATGTAAAATAGCATTTGGTAAAATAAAATTGATGGAGTTGAAGA
* * * *
350877 TATTTGTTGGTTTAGGTTGAGGAGAGAGAATCACAAGGGGAAATGATCCCTCAACTGATTTTG-T
261 TATTTGTTGGTTGAGGTTGAGGGGAGAGAATCACGAGGGGAAATGATCCCTCAACCGATTTTGTT
* * * * * *
350941 -TTAT-T-TTTT-ATGT-CA----GTA-TCCGTCTCT-TCCTTTTTTTTTTATACTCTCTACTAA
326 GTTTTGTGTTTTCACGTCCATTTTTTAGTCAGTATCTGT-CTTTTTTTTTTATACTCTCTACTGA
*
350995 TAATTTTTTTTGACATTTATACTCGTTTCATCTCTTATTTATTTATATTTATATTTATTTTTAAA
390 TAA-TTTTTTTGACATTTATACTCGTTTCATCTCTTATTTATTGATATTTATATTTATTTTTAAA
* * * * *
351060 GAAAACAAATTTATATTTACATTCATAATGGATGAAACACTTAAATCACTGAAACATCAGACATA
454 GAAAACAAATTCATATTTACACTAAGAATGGATAAAACACTTAAATCACTGAAACATCAGACATA
* *
351125 AGAAATTTGACCATAAAAAAATATTTGTAGATTACATATGTAGTAGTGGAAAAAAAAAAAACAAA
519 AAAAATTTGACCATAAAAAAATATTTGTAAATTACATATGTAGTAGTGGAAAAAAAAAAAACAAA
* * *
351190 ACAAGAGCAAAGATAAAAGAACCAGTAGAAAGTAGCTAGAAAGAGAATGCTGAGGCCATCACTTC
584 ACAAGAGCAAAGATAAAAGAACCAGTAGAAACTAGCTAAAAAGAAAATGCTGAGGCCATCACTTC
* ** * ** * *
351255 CTTCGCTTCTCACGCAAATATGTCTTCAACAATGTCTCCAAAAACTTGGTGACTTCTCTTTGTAT
649 CTTCACAACTCACACAAATATGTCTTCAACAATGTCTCCAAAAACTTAATGACTTCTATTTGAAT
* * *
351320 AGGAGAAATGTCTTATGTCTTAAAAGGGCATTATAATCATTGTTTATGTCTTAGAAATACTA
714 AGGAGAAAGGTCTTATGTCTTAAAAGGCCATTATAATCATTGTTTATGTCTTAGAAACACTA
* * *
351382 TTTGCCTAGCATATGTATGCTATGTCATTTTTCTTTGACTCTCTATTTCAATGCAATAATTCCTC
1 -TTG--AAGCATATGTATGCTATGTCATTTTTCTTTGACTCTCTATTTCAATGTAATAAATCCTC
* *
351447 AAAGTATTATAGATTTTGGAATTTAAATTTATAAATTTAGATTTAGTATTGCTTAGGAAACTCAA
63 AAAGTATTATAGATTTTGGAATTTAAATTTATAAATTTGGATTTAGTATTGTTTAGGAAACTCAA
* * * ** * * *
351512 ATGACTAGTTTGGAAGGTGGAGTGAAGGTTAGAATGGAAATACATTATATGTCTTTTCATTATTT
128 ATGACAAGTTTGGAAAGTGGAGTGAAGGTTAGAATGGAAATACTTTACGTTTCTTTTTATGATTT
* * * *
351577 TTGATATAATATTTGACACGA-GATATGTAAAATAGCATTTGATAAAATACAATTGATGAAGTTA
193 TTGATATAATATTTGACAC-ATGATATGTAAAATAGCATTTGGTAAAATAAAATTGATGGAGTTG
* * * * *
351641 AAAATATTTATTGGTTGACGTTGA-GGAAGAGAATCACGAGGGGAAACGATCCCTCAACCGATTT
257 AAGATATTTGTTGGTTGAGGTTGAGGGGAGAGAATCACGAGGGGAAATGATCCCTCAACCGATTT
* * *
351705 TATTTGATTTTGTGTTTTTCACGTCTATTTTTTATGTCAGTAT-TAGTCTCTTTTTTTTATACTC
322 T-GTTG-TTTTGTG-TTTTCACGTCCATTTTTTA-GTCAGTATCT-GTCTTTTTTTTTTATACTC
* * **
351769 TCAACTGATACTTATTTTTGACATTTATACTAATTTCATCTCTTATTTATT
382 TCTACTGATAATT-TTTTTGACATTTATACTCGTTTCATCTCTTATTTATT
351820 TTTAAAGATA
Statistics
Matches: 1024, Mismatches: 145, Indels: 96
0.81 0.11 0.08
Matches are distributed among these distances:
763 98 0.10
764 76 0.07
766 2 0.00
767 38 0.04
768 242 0.24
769 2 0.00
770 1 0.00
771 3 0.00
772 1 0.00
774 4 0.00
775 3 0.00
776 1 0.00
777 1 0.00
780 5 0.00
781 6 0.01
782 64 0.06
783 3 0.00
786 1 0.00
788 3 0.00
789 1 0.00
790 1 0.00
791 2 0.00
792 30 0.03
793 129 0.13
794 2 0.00
795 8 0.01
797 2 0.00
801 2 0.00
802 2 0.00
803 3 0.00
804 1 0.00
805 1 0.00
806 3 0.00
809 1 0.00
811 276 0.27
812 6 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (775 bp):
TTGAAGCATATGTATGCTATGTCATTTTTCTTTGACTCTCTATTTCAATGTAATAAATCCTCAAA
GTATTATAGATTTTGGAATTTAAATTTATAAATTTGGATTTAGTATTGTTTAGGAAACTCAAATG
ACAAGTTTGGAAAGTGGAGTGAAGGTTAGAATGGAAATACTTTACGTTTCTTTTTATGATTTTTG
ATATAATATTTGACACATGATATGTAAAATAGCATTTGGTAAAATAAAATTGATGGAGTTGAAGA
TATTTGTTGGTTGAGGTTGAGGGGAGAGAATCACGAGGGGAAATGATCCCTCAACCGATTTTGTT
GTTTTGTGTTTTCACGTCCATTTTTTAGTCAGTATCTGTCTTTTTTTTTTATACTCTCTACTGAT
AATTTTTTTGACATTTATACTCGTTTCATCTCTTATTTATTGATATTTATATTTATTTTTAAAGA
AAACAAATTCATATTTACACTAAGAATGGATAAAACACTTAAATCACTGAAACATCAGACATAAA
AAATTTGACCATAAAAAAATATTTGTAAATTACATATGTAGTAGTGGAAAAAAAAAAAACAAAAC
AAGAGCAAAGATAAAAGAACCAGTAGAAACTAGCTAAAAAGAAAATGCTGAGGCCATCACTTCCT
TCACAACTCACACAAATATGTCTTCAACAATGTCTCCAAAAACTTAATGACTTCTATTTGAATAG
GAGAAAGGTCTTATGTCTTAAAAGGCCATTATAATCATTGTTTATGTCTTAGAAACACTA
Done.