Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 8 of 19
Found at i:2676180 original size:69 final size:68
Alignment explanation
Indices: 2676040--2676181 Score: 200
Period size: 68 Copynumber: 2.1 Consensus size: 68
2676030 TTTTAAAAAT
*
2676040 AAAAT-AAAATAAAATATATAATATAAAAAATATATTTAAATAAATATTAAATATAAAATTATAA
1 AAAATAAAAATAAAATATATAATATAAAAAATATATTTAAAAAAATATTAAATATAAAATTATAA
2676104 TAA
66 TAA
* * *
2676107 AAAATAAAAATAAAATATATGATAT-TAAAATATATTTAAGAAATAATATTATATA-AAAATTAA
1 AAAATAAAAATAAAATATATAATATAAAAAATATATTTAA-AAA-AATATTAAATATAAAATT-A
2676170 TAATAA
63 TAATAA
2676176 AAAATA
1 AAAATA
2676182 TAAGTATATT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
67 18 0.27
68 26 0.39
69 23 0.34
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (68 bp):
AAAATAAAAATAAAATATATAATATAAAAAATATATTTAAAAAAATATTAAATATAAAATTATAA
TAA
Found at i:2687108 original size:17 final size:18
Alignment explanation
Indices: 2687088--2687122 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2687078 ACACTGTAGT
2687088 AATGTTTCATA-ATATAA
1 AATGTTTCATATATATAA
*
2687105 AATGTTTTATATATATAA
1 AATGTTTCATATATATAA
2687123 TTGTATAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
AATGTTTCATATATATAA
Found at i:2688178 original size:116 final size:116
Alignment explanation
Indices: 2687974--2688209 Score: 445
Period size: 116 Copynumber: 2.0 Consensus size: 116
2687964 AAAATTAAAG
*
2687974 CACTAAAACGACACTGATGGACATCGTTTCTCTTGACCTGGAACCTTCTTCCAACTTTTAGCTTT
1 CACTAAAACGACACTGATGGACATCGTTTCTCTTGACCTGGAACCTTCTTCCAACCTTTAGCTTT
*
2688039 TGCAGCTGCTCCCTGCCATTCTTCAGCAAATGACTTCTCCAGATTGAGAGT
66 TGCAGCTGCTCCCTGCCATTCTTCAACAAATGACTTCTCCAGATTGAGAGT
*
2688090 CACTAAAACGACACTGATGGACATCGTTTCTCTTGACTTGGAACCTTCTTCCAACCTTTAGCTTT
1 CACTAAAACGACACTGATGGACATCGTTTCTCTTGACCTGGAACCTTCTTCCAACCTTTAGCTTT
2688155 TGCAGCTGCTCCCTGCCATTCTTCAACAAATGACTTCTCCAGATTGAGAGT
66 TGCAGCTGCTCCCTGCCATTCTTCAACAAATGACTTCTCCAGATTGAGAGT
2688206 CACT
1 CACT
2688210 TTCTTAACAC
Statistics
Matches: 117, Mismatches: 3, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
116 117 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (116 bp):
CACTAAAACGACACTGATGGACATCGTTTCTCTTGACCTGGAACCTTCTTCCAACCTTTAGCTTT
TGCAGCTGCTCCCTGCCATTCTTCAACAAATGACTTCTCCAGATTGAGAGT
Found at i:2695371 original size:49 final size:49
Alignment explanation
Indices: 2695318--2695416 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
2695308 ATTTACCAAT
2695318 TTCAAGCCAGACGAAGATTTCAATGTGTATGTGTGTGTACTCGCATGTG
1 TTCAAGCCAGACGAAGATTTCAATGTGTATGTGTGTGTACTCGCATGTG
2695367 TTCAAGCCAGACGAAGATTTCAATGTGTATGTGTGTGTACTCGCATGTG
1 TTCAAGCCAGACGAAGATTTCAATGTGTATGTGTGTGTACTCGCATGTG
2695416 T
1 T
2695417 GTGTGTGCGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (49 bp):
TTCAAGCCAGACGAAGATTTCAATGTGTATGTGTGTGTACTCGCATGTG
Found at i:2708106 original size:26 final size:26
Alignment explanation
Indices: 2708070--2708122 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2708060 TATTACTAGT
2708070 AACTTGTGGTTTATTGATAATATAAA
1 AACTTGTGGTTTATTGATAATATAAA
*
2708096 AACTTGTGGTTTATTGATGATATAAA
1 AACTTGTGGTTTATTGATAATATAAA
2708122 A
1 A
2708123 GTTATACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (26 bp):
AACTTGTGGTTTATTGATAATATAAA
Found at i:2713070 original size:2 final size:2
Alignment explanation
Indices: 2713063--2713095 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2713053 GTGTTGATTT
2713063 TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2713096 GTGTGTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2713085 original size:17 final size:17
Alignment explanation
Indices: 2713063--2713095 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2713053 GTGTTGATTT
*
2713063 TATATATATATTATATA
1 TATATATATATAATATA
2713080 TATATATATATAATAT
1 TATATATATATAATAT
2713096 GTGTGTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATAATATA
Found at i:2733390 original size:13 final size:14
Alignment explanation
Indices: 2733372--2733406 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
2733362 ATATATTTTT
2733372 AATAATTTTTTA-A
1 AATAATTTTTTATA
2733385 AATAATTTTTTATTA
1 AATAATTTTTTA-TA
2733400 AATAATT
1 AATAATT
2733407 AATATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATAATTTTTTATA
Found at i:2737277 original size:2 final size:2
Alignment explanation
Indices: 2737270--2737304 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
2737260 ATATCTTGTA
*
2737270 AT AT AT AT AT AT AT AT AT AT AGT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
2737305 TTGTGTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2737719 original size:2 final size:2
Alignment explanation
Indices: 2737714--2737748 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2737704 TGTGTGTGTG
2737714 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2737749 GACTTTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2738965 original size:13 final size:13
Alignment explanation
Indices: 2738947--2738973 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2738937 TGCCACTCAC
2738947 ATATGTTATCAAA
1 ATATGTTATCAAA
2738960 ATATGTTATCAAA
1 ATATGTTATCAAA
2738973 A
1 A
2738974 GAATTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (13 bp):
ATATGTTATCAAA
Found at i:2741485 original size:8 final size:8
Alignment explanation
Indices: 2741469--2741508 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2741459 CACGTAAATT
*
2741469 CATACATA
1 CATATATA
2741477 CATATATA
1 CATATATA
2741485 CATATATA
1 CATATATA
*
2741493 TATATATA
1 CATATATA
*
2741501 TATATATA
1 CATATATA
2741509 TTTGATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (8 bp):
CATATATA
Found at i:2741487 original size:12 final size:12
Alignment explanation
Indices: 2741470--2741508 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2741460 ACGTAAATTC
*
2741470 ATACATACATAT
1 ATACATATATAT
2741482 ATACATATATAT
1 ATACATATATAT
*
2741494 ATATATATATAT
1 ATACATATATAT
2741506 ATA
1 ATA
2741509 TTTGATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (12 bp):
ATACATATATAT
Found at i:2741491 original size:2 final size:2
Alignment explanation
Indices: 2741478--2741509 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2741468 TCATACATAC
*
2741478 AT AT AT AC 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
2741510 TTGATTATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2750248 original size:40 final size:40
Alignment explanation
Indices: 2750204--2750284 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
2750194 ACTCTTCGAG
*
2750204 ATGTTCCATGTTGGTTAGTCACTTGTCATTTATAAATGAT
1 ATGTTCCATGGTGGTTAGTCACTTGTCATTTATAAATGAT
*
2750244 ATGTTCCATGGTGGTTAGTCACTTGTCATTTGTAAATGAT
1 ATGTTCCATGGTGGTTAGTCACTTGTCATTTATAAATGAT
2750284 A
1 A
2750285 CTATTATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (40 bp):
ATGTTCCATGGTGGTTAGTCACTTGTCATTTATAAATGAT
Found at i:2751404 original size:29 final size:29
Alignment explanation
Indices: 2751372--2751453 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
2751362 GTAGAAGTTA
2751372 AAAAAAAAAAGCTGTACGTGAACAGGTAC
1 AAAAAAAAAAGCTGTACGTGAACAGGTAC
* *
2751401 AAAAGAAAAAGCTGTACATGAACAGGTAC
1 AAAAAAAAAAGCTGTACGTGAACAGGTAC
* * *
2751430 -AAGAGAAAAGCCTGTACGTAAACA
1 AAAAAAAAAAG-CTGTACGTGAACA
2751454 AGAATAAGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.51, C:0.15, G:0.21, T:0.13
Consensus pattern (29 bp):
AAAAAAAAAAGCTGTACGTGAACAGGTAC
Found at i:2752593 original size:26 final size:26
Alignment explanation
Indices: 2752557--2752608 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2752547 ACTGACCATA
2752557 ATGACTCTAATTTTATCAAACAGTTT
1 ATGACTCTAATTTTATCAAACAGTTT
2752583 ATGACTCTAATTTTATCAAACAGTTT
1 ATGACTCTAATTTTATCAAACAGTTT
2752609 GAGGAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (26 bp):
ATGACTCTAATTTTATCAAACAGTTT
Found at i:2753055 original size:10 final size:10
Alignment explanation
Indices: 2753034--2753099 Score: 62
Period size: 10 Copynumber: 6.2 Consensus size: 10
2753024 ATATATGAAT
2753034 AAATAGAATAA
1 AAATA-AATAA
2753045 AAATAAATAA
1 AAATAAATAA
2753055 AAATAAAATAA
1 AAAT-AAATAA
*
2753066 TAATATAAATTGA
1 -AA-ATAAA-TAA
2753079 AAA-AAATAA
1 AAATAAATAA
*
2753088 AAAAAAATAA
1 AAATAAATAA
2753098 AA
1 AA
2753100 TTGAAATCAT
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
9 5 0.10
10 20 0.42
11 12 0.25
12 7 0.15
13 4 0.08
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (10 bp):
AAATAAATAA
Found at i:2758289 original size:10 final size:10
Alignment explanation
Indices: 2758274--2758298 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2758264 TTTAACCATG
2758274 ACCTACCCAA
1 ACCTACCCAA
2758284 ACCTACCCAA
1 ACCTACCCAA
2758294 ACCTA
1 ACCTA
2758299 TTTCCAAAAA
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:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (10 bp):
ACCTACCCAA
Found at i:2760886 original size:57 final size:57
Alignment explanation
Indices: 2760798--2760913 Score: 205
Period size: 57 Copynumber: 2.0 Consensus size: 57
2760788 CAATAAGGAA
2760798 TCAATCAAGCGTATTAATAATTGCTTCATCTCTATTATTGCACCATGTAAACATACC
1 TCAATCAAGCGTATTAATAATTGCTTCATCTCTATTATTGCACCATGTAAACATACC
* **
2760855 TCAATCCAGCGTATTAATTGTTGCTTCATCTCTATTATTGCACCATGTAAACATACC
1 TCAATCAAGCGTATTAATAATTGCTTCATCTCTATTATTGCACCATGTAAACATACC
2760912 TC
1 TC
2760914 CCACCATCAG
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (57 bp):
TCAATCAAGCGTATTAATAATTGCTTCATCTCTATTATTGCACCATGTAAACATACC
Found at i:2769347 original size:23 final size:23
Alignment explanation
Indices: 2769321--2769367 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
2769311 AAATCAAGTA
2769321 TCATACCTAACCTTTGCAGTAAT
1 TCATACCTAACCTTTGCAGTAAT
2769344 TCATACCTAACCTTTGCAGTAAT
1 TCATACCTAACCTTTGCAGTAAT
2769367 T
1 T
2769368 GATGGTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.36
Consensus pattern (23 bp):
TCATACCTAACCTTTGCAGTAAT
Found at i:2771280 original size:2 final size:2
Alignment explanation
Indices: 2771273--2771308 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2771263 CAACAAATAC
*
2771273 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2771309 TAAAAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2773601 original size:21 final size:21
Alignment explanation
Indices: 2773562--2773602 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2773552 TGACGGTTTG
* * *
2773562 TGTGGGTGGGGGTGTGGGGGT
1 TGTGGGGGGGGGGGGGGGGGT
2773583 TGTGGGGGGGGGGGGGGGGG
1 TGTGGGGGGGGGGGGGGGGG
2773603 GGGGGCGGGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.80, T:0.20
Consensus pattern (21 bp):
TGTGGGGGGGGGGGGGGGGGT
Found at i:2773603 original size:23 final size:23
Alignment explanation
Indices: 2773559--2773604 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2773549 TGGTGACGGT
* * * *
2773559 TTGTGTGGGTGGGGGTGTGGGGG
1 TTGTGGGGGGGGGGGGGGGGGGG
2773582 TTGTGGGGGGGGGGGGGGGGGGG
1 TTGTGGGGGGGGGGGGGGGGGGG
2773605 GGGCGGGCCG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.78, T:0.22
Consensus pattern (23 bp):
TTGTGGGGGGGGGGGGGGGGGGG
Found at i:2773631 original size:33 final size:31
Alignment explanation
Indices: 2773586--2773795 Score: 124
Period size: 33 Copynumber: 6.4 Consensus size: 31
2773576 TGGGGGTTGT
2773586 GGGGGG-GGGGGGGGGGGGGGGGCGGGCCGCG
1 GGGGGGCGGGGGGGGGGGGGGGGCGGG-CGCG
*
2773617 GGGGGGCGGTGGGGGGCGGGGGGTG-GGGCGGCG
1 GGGGGGCGG-GGGGGG-GGGGGGGGCGGGC-GCG
* *
2773650 GGGGGCGCGGGGGGTGGGGGGGGGGGGGGGGCG
1 GGGGG-GCGGGGGG-GGGGGGGGGGCGGGCGCG
* * *
2773683 GGGATGGG-GGCGGGGGGAGGTGGGCGGG-G-G
1 GGG--GGGCGGGGGGGGGGGGGGGGCGGGCGCG
* *
2773713 GTGTTGGTGGTGGTGGGGGGGCGGGGGGGCGGGCGTGG
1 G-G--GG-GGCGG-GGGGGGG-GGGGGGGCGGGCG-CG
* **
2773751 GGGGGTGCGCGGGGGGGGGGGCCGCGGGTCGCG
1 GGGGG-GCGGGGGGGGGGGGGGGGCGGG-CGCG
*
2773784 GGGGGGTGGGGG
1 GGGGGGCGGGGG
2773796 CAGGTGTCAC
Statistics
Matches: 141, Mismatches: 17, Indels: 41
0.71 0.09 0.21
Matches are distributed among these distances:
30 2 0.01
31 9 0.06
32 21 0.15
33 57 0.40
34 33 0.23
35 15 0.11
36 1 0.01
37 1 0.01
38 2 0.01
ACGTcount: A:0.01, C:0.11, G:0.81, T:0.07
Consensus pattern (31 bp):
GGGGGGCGGGGGGGGGGGGGGGGCGGGCGCG
Found at i:2773677 original size:79 final size:80
Alignment explanation
Indices: 2773584--2773795 Score: 200
Period size: 86 Copynumber: 2.6 Consensus size: 80
2773574 TGTGGGGGTT
2773584 GTGGGGGGGGGGGGGGGGGGGG-GGCGGGCCGCGGGGGGGCGGTGGGG-GGCGG-GG-GGTGGGG
1 GTGGGGGGGGGGGGGGGGGGGGAGGCGGGCCGCGGGGGGGCGG-GGGGTGGCGGTGGTGGTGGGG
*
2773645 CGGCGGGGGGCGCGGGGG
65 CGGCGGGGGG-GC-GGGC
* * **
2773663 GTGGGGGGGGGGGGGGGGCGGGGATGG-GGGCGGGGGGAGGTGGGCGGGGGGTGTTGGTGGTGGT
1 GTGGGGGGGGGGGGGGGG-GGGGA-GGCGGGC-CGCGG-GG-GGGCGGGGGGTGGCGGTGGTGGT
*
2773727 GGGGGGGCGGGGGGGCGGGC
61 GGGGCGGCGGGGGGGCGGGC
** * *
2773747 GTGGGGGGGTGCGCGGGGGGGGGGGCCGCGGGTCGCGGGGGGGTGGGGG
1 GTGGGGGGG-G-G-GGGGGGGGGGGAGGCGGGCCGCGGGGGGGCGGGGG
2773796 CAGGTGTCAC
Statistics
Matches: 108, Mismatches: 12, Indels: 22
0.76 0.08 0.15
Matches are distributed among these distances:
79 18 0.17
80 4 0.04
81 4 0.04
82 5 0.05
83 14 0.13
84 23 0.21
85 9 0.08
86 24 0.22
87 7 0.06
ACGTcount: A:0.01, C:0.11, G:0.81, T:0.08
Consensus pattern (80 bp):
GTGGGGGGGGGGGGGGGGGGGGAGGCGGGCCGCGGGGGGGCGGGGGGTGGCGGTGGTGGTGGGGC
GGCGGGGGGGCGGGC
Found at i:2773733 original size:1 final size:1
Alignment explanation
Indices: 2773586--2773713 Score: 76
Period size: 1 Copynumber: 128.0 Consensus size: 1
2773576 TGGGGGTTGT
* ** * * * * * * *
2773586 GGGGGGGGGGGGGGGGGGGGGGCGGGCCGCGGGGGGGCGGTGGGGGGCGGGGGGTGGGGCGGCGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
* * * * ** * * * *
2773651 GGGGCGCGGGGGGTGGGGGGGGGGGGGGGGCGGGGATGGGGGCGGGGGGAGGTGGGCGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
2773714 TGTTGGTGGT
Statistics
Matches: 90, Mismatches: 37, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 90 1.00
ACGTcount: A:0.02, C:0.10, G:0.84, T:0.04
Consensus pattern (1 bp):
G
Found at i:2773747 original size:53 final size:48
Alignment explanation
Indices: 2773586--2773771 Score: 171
Period size: 53 Copynumber: 3.8 Consensus size: 48
2773576 TGGGGGTTGT
* * ** * *
2773586 GGGGGGGGGG-GGGGGGGGGGGGCGGGCCGCGGGGGGGCGGTGGGGGGC
1 GGGGGGGGGGCGGGGGGGGTGCGCGGGGGGTGGGGGGG-GGGGGGGGGC
*
2773634 GGGGGGTGGGGCGGCGGGGG-GCGCGGGGGGTGGGGGGGGGGGGGGGGC
1 GGGGGG-GGGGCGGGGGGGGTGCGCGGGGGGTGGGGGGGGGGGGGGGGC
* * * *
2773682 GGGGATGGGGGCGGGGGGAGGTGGGCGGGGGGTGTTGGTGGTGGTGGGGGGGC
1 GGGG-GGGGGGCGGGGGG-GGTGCGCGGGGGGTG--GG-GGGGGGGGGGGGGC
2773735 GGGGGGGCGGGCGTGGGGGGGTGCGCGGGGGG-GGGGG
1 GGGGGGG-GGGCG-GGGGGGGTGCGCGGGGGGTGGGGG
2773772 CCGCGGGTCG
Statistics
Matches: 115, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
48 29 0.25
49 23 0.20
50 20 0.17
52 5 0.04
53 33 0.29
54 5 0.04
ACGTcount: A:0.01, C:0.10, G:0.82, T:0.07
Consensus pattern (48 bp):
GGGGGGGGGGCGGGGGGGGTGCGCGGGGGGTGGGGGGGGGGGGGGGGC
Found at i:2773754 original size:14 final size:12
Alignment explanation
Indices: 2773586--2773772 Score: 148
Period size: 12 Copynumber: 15.0 Consensus size: 12
2773576 TGGGGGTTGT
2773586 GGGGGGGGGGG-
1 GGGGGGGGGGGC
2773597 GGGGGGGGGGGC
1 GGGGGGGGGGGC
2773609 GGGCCGCGGGGGGGC
1 GGG--G-GGGGGGGC
*
2773624 --GGTGGGGGGC
1 GGGGGGGGGGGC
*
2773634 GGGGGGTGGGGC
1 GGGGGGGGGGGC
* *
2773646 GGCGGGGGGCGC
1 GGGGGGGGGGGC
2773658 GGGGGGTGGGGG-
1 GGGGGG-GGGGGC
2773670 GGGGGGGGGGGC
1 GGGGGGGGGGGC
**
2773682 GGGGATGGGGGC
1 GGGGGGGGGGGC
2773694 GGGGGGAGGTGGGC
1 GGGGGG-GG-GGGC
** *
2773708 GGGGGGTGTTGGT
1 GGGGGG-GGGGGC
2773721 GGTGGTGGGGGGGC
1 GG-GG-GGGGGGGC
*
2773735 GGGGGGGCGGGC
1 GGGGGGGGGGGC
*
2773747 GTGGGGGGGTGCGC
1 G-GGGGGGG-GGGC
2773761 GGGGGGGGGGGC
1 GGGGGGGGGGGC
2773773 CGCGGGTCGC
Statistics
Matches: 139, Mismatches: 23, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
10 7 0.05
11 17 0.12
12 56 0.40
13 26 0.19
14 23 0.17
15 10 0.07
ACGTcount: A:0.01, C:0.10, G:0.82, T:0.07
Consensus pattern (12 bp):
GGGGGGGGGGGC
Found at i:2774145 original size:15 final size:14
Alignment explanation
Indices: 2774088--2774144 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
2774078 GTTCCACAAC
2774088 ATTTCCCTCCAAAG
1 ATTTCCCTCCAAAG
* **
2774102 TTTTCAATCCAAAG
1 ATTTCCCTCCAAAG
* *
2774116 TATTCCCCCCCAAAAG
1 -ATTTCCCTCC-AAAG
2774132 ATTTCCCTCCAAA
1 ATTTCCCTCCAAA
2774145 ACATTTGGGA
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
14 14 0.45
15 13 0.42
16 4 0.13
ACGTcount: A:0.32, C:0.35, G:0.05, T:0.28
Consensus pattern (14 bp):
ATTTCCCTCCAAAG
Found at i:2782102 original size:21 final size:21
Alignment explanation
Indices: 2782064--2782104 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2782054 TGATGATGAC
*
2782064 ATAACATGTTAATTTAGTATA
1 ATAACATGTTAATATAGTATA
2782085 ATAACATGATT-ATATAGTAT
1 ATAACATG-TTAATATAGTAT
2782105 TTTTTATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (21 bp):
ATAACATGTTAATATAGTATA
Found at i:2788399 original size:18 final size:19
Alignment explanation
Indices: 2788376--2788420 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
2788366 GTCGAAAATC
2788376 TTTAATTAAAATATTATT-
1 TTTAATTAAAATATTATTA
*
2788394 TTTAA-TAAAATGTTATTA
1 TTTAATTAAAATATTATTA
*
2788412 TTTTATTAA
1 TTTAATTAA
2788421 TGATAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 11 0.48
18 9 0.39
19 3 0.13
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTAATTAAAATATTATTA
Found at i:2796463 original size:2 final size:2
Alignment explanation
Indices: 2796456--2796480 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2796446 TCACAAATGA
2796456 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
2796481 AAATTTCTCA
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:2799719 original size:102 final size:102
Alignment explanation
Indices: 2799541--2799750 Score: 330
Period size: 102 Copynumber: 2.1 Consensus size: 102
2799531 CCATGCATGT
* * *
2799541 ATATGCCAATAATAGATAACATTGCGTCAAAGCAAATTAGACTGGTACTATTAATTGAAAAGTCC
1 ATATGCCAATAATAGATAACATTGCGTCAAAGCAAATAAGACTAGTACAATTAATTGAAAAGTCC
2799606 ATTATTATTGAAAAAGAAAGGGTTACATTGTGTTTTC
66 ATTATTATTGAAAAAGAAAGGGTTACATTGTGTTTTC
* ** * *
2799643 ATATGCCAATAATATATAACATTGCGTCAAAGCAAATAAGGTTAGTACAATTAATTGGAAAGTTC
1 ATATGCCAATAATAGATAACATTGCGTCAAAGCAAATAAGACTAGTACAATTAATTGAAAAGTCC
* *
2799708 ATTATTGTTGAAAAGGAAAGGGTTACATTGTGTTTTC
66 ATTATTATTGAAAAAGAAAGGGTTACATTGTGTTTTC
2799745 ATATGC
1 ATATGC
2799751 TTTTGCCATT
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.33
Consensus pattern (102 bp):
ATATGCCAATAATAGATAACATTGCGTCAAAGCAAATAAGACTAGTACAATTAATTGAAAAGTCC
ATTATTATTGAAAAAGAAAGGGTTACATTGTGTTTTC
Found at i:2800571 original size:17 final size:18
Alignment explanation
Indices: 2800539--2800572 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2800529 CACGGCGTTA
*
2800539 TATTCTCGTTTCTAAATC
1 TATTCTCGTCTCTAAATC
2800557 TATTCTC-TCTCTAAAT
1 TATTCTCGTCTCTAAAT
2800573 TTCCTCCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.24, G:0.03, T:0.50
Consensus pattern (18 bp):
TATTCTCGTCTCTAAATC
Found at i:2814764 original size:6 final size:6
Alignment explanation
Indices: 2814753--2814779 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2814743 TGAACTCCTT
2814753 TCTTTC TCTTTC TCTTTC TCTTTC TCT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCT
2814780 CTCATTTTCT
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:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TCTTTC
Found at i:2820439 original size:2 final size:2
Alignment explanation
Indices: 2820432--2820463 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2820422 TAGAAATCTT
2820432 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2820464 GAGTTTAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2824350 original size:2 final size:2
Alignment explanation
Indices: 2824343--2824376 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2824333 GTTAAAAAGC
2824343 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2824377 TGGGGAGCAA
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2831156 original size:32 final size:33
Alignment explanation
Indices: 2831104--2831171 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
2831094 ATGTTGAGGC
* * *
2831104 ATGATCTCTAAGTGACATGATTAATCCACTTGA
1 ATGATCTCAAAGTGAAATGATTAATCCACTTCA
2831137 ATGATCT-AAAGTGAAATGATTAATCCACTTCA
1 ATGATCTCAAAGTGAAATGATTAATCCACTTCA
2831169 ATG
1 ATG
2831172 GCCAATATTC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
ATGATCTCAAAGTGAAATGATTAATCCACTTCA
Found at i:2834285 original size:27 final size:27
Alignment explanation
Indices: 2834253--2834426 Score: 144
Period size: 27 Copynumber: 6.4 Consensus size: 27
2834243 TATTAATATT
*
2834253 TAAATTATCAATTATTAATATTTAAAA
1 TAAATTATAAATTATTAATATTTAAAA
2834280 TAAATTATAAATTATTAATATTTAAAAA
1 TAAATTATAAATTATTAATATTT-AAAA
** * * *
2834308 TAAA--ATAAATTAAAAAATAATCATAA
1 TAAATTATAAATT-ATTAATATTTAAAA
*
2834334 TAACATT-TAAATTA-TAA-A-TAAAAA
1 TAA-ATTATAAATTATTAATATTTAAAA
* * *
2834358 TTAAATTATCAATTACTAATATTTTAAA
1 -TAAATTATAAATTATTAATATTTAAAA
*
2834386 TAAATTATAAATTATTACTATTTAAAAA
1 TAAATTATAAATTATTAATATTT-AAAA
*
2834414 TTAAATTAAAAAT
1 -TAAATTATAAAT
2834427 CAATGGTCAT
Statistics
Matches: 118, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
24 7 0.06
25 10 0.08
26 18 0.15
27 51 0.43
28 21 0.18
29 11 0.09
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (27 bp):
TAAATTATAAATTATTAATATTTAAAA
Found at i:2834362 original size:106 final size:106
Alignment explanation
Indices: 2834247--2834467 Score: 311
Period size: 106 Copynumber: 2.1 Consensus size: 106
2834237 ATAAAATATT
*
2834247 AATATTTAAATTATCAATTATTAATATTTAAAATAAATTATAAATTATTAATATTTAAAAA-TAA
1 AATA-TTAAATTATCAATTACTAATATTTAAAATAAATTATAAATTATTAATATTTAAAAATTAA
2834311 AATAAATTAAAAAATAATCATAATAACATTTAAATTATAAATAA
65 AATAAA--AAAAAATAATCATAATAACATTTAAATTATAAATAA
* *
2834355 AA-ATTAAATTATCAATTACTAATATTTTAAATAAATTATAAATTATTACTATTTAAAAATTAAA
1 AATATTAAATTATCAATTACTAATATTTAAAATAAATTATAAATTATTAATATTTAAAAATTAAA
* ** ** * *
2834419 TTAAAAATCAATGGTCATAATGATATTTAAATTATAAATAA
66 ATAAAAAAAAATAATCATAATAACATTTAAATTATAAATAA
2834460 AATATTAA
1 AATATTAA
2834468 TATTTTAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
105 32 0.32
106 58 0.57
107 9 0.09
108 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (106 bp):
AATATTAAATTATCAATTACTAATATTTAAAATAAATTATAAATTATTAATATTTAAAAATTAAA
ATAAAAAAAAATAATCATAATAACATTTAAATTATAAATAA
Found at i:2837698 original size:9 final size:9
Alignment explanation
Indices: 2837684--2837715 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
2837674 TACAACTTTG
2837684 ATAAAAAAA
1 ATAAAAAAA
2837693 ATAAAAAAAA
1 AT-AAAAAAA
2837703 ATAAAAAAA
1 ATAAAAAAA
2837712 ATAA
1 ATAA
2837716 TAATAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
ATAAAAAAA
Found at i:2837701 original size:10 final size:10
Alignment explanation
Indices: 2837686--2837712 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2837676 CAACTTTGAT
2837686 AAAAAAAATA
1 AAAAAAAATA
2837696 AAAAAAAATA
1 AAAAAAAATA
2837706 AAAAAAA
1 AAAAAAA
2837713 TAATAATAAT
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:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:2849632 original size:19 final size:19
Alignment explanation
Indices: 2849605--2849684 Score: 54
Period size: 19 Copynumber: 3.9 Consensus size: 19
2849595 ATTATAAATG
*
2849605 ACATCATTTATGAATAGTT
1 ACATAATTTATGAATAGTT
*
2849624 ACATAATTTATAAACGT-GTAAAT
1 ACATAATTTATGAA--TAGT---T
* *
2849647 GACATCATTTACGAATAGTT
1 -ACATAATTTATGAATAGTT
*
2849667 AGATAATTTATGAATAGT
1 ACATAATTTATGAATAGT
2849685 CAGATAATTA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
19 27 0.59
20 3 0.07
21 1 0.02
22 1 0.02
23 3 0.07
24 11 0.24
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (19 bp):
ACATAATTTATGAATAGTT
Found at i:2849689 original size:19 final size:19
Alignment explanation
Indices: 2849653--2849693 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2849643 AAATGACATC
*
2849653 ATTTACGAATAGTTAGATA
1 ATTTACGAATAGTCAGATA
*
2849672 ATTTATGAATAGTCAGATA
1 ATTTACGAATAGTCAGATA
2849691 ATT
1 ATT
2849694 AATAGCGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (19 bp):
ATTTACGAATAGTCAGATA
Found at i:2852749 original size:28 final size:27
Alignment explanation
Indices: 2852709--2852763 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
2852699 GTGTCGTATC
2852709 AATATTATATTTTAAAAAATAAAATATT
1 AATATTATATTTT-AAAAATAAAATATT
* * *
2852737 AATATTTTATTTTTAAAATATAATATT
1 AATATTATATTTTAAAAATAAAATATT
2852764 TTATTAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATATTATATTTTAAAAATAAAATATT
Found at i:2852762 original size:21 final size:22
Alignment explanation
Indices: 2852728--2852768 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
2852718 TTTTAAAAAA
2852728 TAAAATATTAATATTTTATTTT
1 TAAAATATTAATATTTTATTTT
2852750 TAAAATA-TAATATTTTATT
1 TAAAATATTAATATTTTATT
2852769 AATGAGAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAAATATTAATATTTTATTTT
Found at i:2856596 original size:40 final size:40
Alignment explanation
Indices: 2856561--2856639 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
2856551 TCTCAAATGT
2856561 ATCGATAGAAATGCAACAGAATACTTACAGCCTCAAAAAA
1 ATCGATAGAAATGCAACAGAATACTTACAGCCTCAAAAAA
* ** * *
2856601 ATCGATATATTTTCAACAGAATACTTACTGCCTCAAAAA
1 ATCGATAGAAATGCAACAGAATACTTACAGCCTCAAAAA
2856640 TATTTATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (40 bp):
ATCGATAGAAATGCAACAGAATACTTACAGCCTCAAAAAA
Found at i:2861890 original size:20 final size:22
Alignment explanation
Indices: 2861845--2861890 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
2861835 TATTTAACTT
*
2861845 TTTATATTTTAAGTATTATAAT
1 TTTATATTTTAAGTATTATAAG
*
2861867 TTTATA-TTT-AGTATTTTAAG
1 TTTATATTTTAAGTATTATAAG
2861887 TTTA
1 TTTA
2861891 AATAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
21 3 0.14
22 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTATATTTTAAGTATTATAAG
Found at i:2864714 original size:13 final size:13
Alignment explanation
Indices: 2864696--2864720 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2864686 CGCACCTAAG
2864696 GCCGCTTCGCTCA
1 GCCGCTTCGCTCA
2864709 GCCGCTTCGCTC
1 GCCGCTTCGCTC
2864721 GAACCCTCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.48, G:0.24, T:0.24
Consensus pattern (13 bp):
GCCGCTTCGCTCA
Found at i:2869198 original size:39 final size:39
Alignment explanation
Indices: 2869144--2869235 Score: 175
Period size: 39 Copynumber: 2.4 Consensus size: 39
2869134 TATTTCTATT
*
2869144 GCAGCAGCGAGTCTTATAGCTAAGATTATTTCCGTTACA
1 GCAGCAGCTAGTCTTATAGCTAAGATTATTTCCGTTACA
2869183 GCAGCAGCTAGTCTTATAGCTAAGATTATTTCCGTTACA
1 GCAGCAGCTAGTCTTATAGCTAAGATTATTTCCGTTACA
2869222 GCAGCAGCTAGTCT
1 GCAGCAGCTAGTCT
2869236 AATTGCTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (39 bp):
GCAGCAGCTAGTCTTATAGCTAAGATTATTTCCGTTACA
Found at i:2872916 original size:2 final size:2
Alignment explanation
Indices: 2872909--2872942 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2872899 CTTAGTGTTT
* *
2872909 TA TA TA TA TA TA TA TA TA TA TA CA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2872943 CACACCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2873719 original size:2 final size:2
Alignment explanation
Indices: 2873712--2873738 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2873702 AAACTATAAA
2873712 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
2873739 AATCTTCAAA
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:2895462 original size:13 final size:13
Alignment explanation
Indices: 2895436--2895479 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2895426 AATTAAACTG
* *
2895436 AATTTATTTGATA
1 AATTTTTTTTATA
2895449 AATTTTTTTTATA
1 AATTTTTTTTATA
*
2895462 AGTTATTTTTTATA
1 AATT-TTTTTTATA
2895476 AATT
1 AATT
2895480 ATAATTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (13 bp):
AATTTTTTTTATA
Found at i:2895472 original size:14 final size:14
Alignment explanation
Indices: 2895446--2895481 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2895436 AATTTATTTG
2895446 ATAAATT-TTTTTT
1 ATAAATTATTTTTT
*
2895459 ATAAGTTATTTTTT
1 ATAAATTATTTTTT
2895473 ATAAATTAT
1 ATAAATTAT
2895482 AATTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
ATAAATTATTTTTT
Found at i:2895662 original size:18 final size:18
Alignment explanation
Indices: 2895622--2895662 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2895612 TTCGAAAACT
*
2895622 TTTTTTTAAAAAATTTTA
1 TTTTTTTAAAAAATATTA
2895640 TTTTTTTAAAAAA-ATTA
1 TTTTTTTAAAAAATATTA
*
2895657 TCTTTT
1 TTTTTT
2895663 AATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTTTAAAAAATATTA
Found at i:2895662 original size:19 final size:19
Alignment explanation
Indices: 2895620--2895662 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
2895610 TTTTCGAAAA
* *
2895620 CTTTTTTTTAAAAAATTTT
1 CTTTTTTTAAAAAAATTAT
*
2895639 ATTTTTTTAAAAAAATTAT
1 CTTTTTTTAAAAAAATTAT
2895658 CTTTT
1 CTTTT
2895663 AATAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
CTTTTTTTAAAAAAATTAT
Found at i:2898307 original size:8 final size:8
Alignment explanation
Indices: 2898296--2898377 Score: 56
Period size: 8 Copynumber: 9.5 Consensus size: 8
2898286 TTCATACTGA
2898296 ATTTTTTT
1 ATTTTTTT
2898304 ATTTTTTT
1 ATTTTTTT
2898312 ATTAATTTATT
1 ATT--TTT-TT
*
2898323 AATTTTTT
1 ATTTTTTT
*
2898331 ATCATTTTT
1 AT-TTTTTT
2898340 ATTATCTTTT
1 ATT-T-TTTT
*
2898350 ATTTTATT
1 ATTTTTTT
* *
2898358 GTTATTTT
1 ATTTTTTT
*
2898366 ATTTTTTA
1 ATTTTTTT
2898374 ATTT
1 ATTT
2898378 CATAATTATT
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
8 31 0.54
9 12 0.21
10 10 0.18
11 4 0.07
ACGTcount: A:0.22, C:0.02, G:0.01, T:0.74
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2898340 original size:20 final size:20
Alignment explanation
Indices: 2898296--2898343 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2898286 TTCATACTGA
* *
2898296 ATTTTT-TTATTTTTTTATT
1 ATTTTTATTAATTTTTTATC
*
2898315 A-ATTTATTAATTTTTTATC
1 ATTTTTATTAATTTTTTATC
2898334 ATTTTTATTA
1 ATTTTTATTA
2898344 TCTTTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 3 0.13
19 13 0.57
20 7 0.30
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
ATTTTTATTAATTTTTTATC
Found at i:2898349 original size:20 final size:19
Alignment explanation
Indices: 2898296--2898351 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
2898286 TTCATACTGA
2898296 ATTTTT-TTATTTTTT-T-
1 ATTTTTATTATTTTTTATC
2898312 ATTAATTTATTAATTTTTTATC
1 ATT--TTTATT-ATTTTTTATC
*
2898334 ATTTTTATTATCTTTTAT
1 ATTTTTATTATTTTTTAT
2898352 TTTATTGTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
16 3 0.09
18 3 0.09
19 10 0.30
20 13 0.39
21 1 0.03
22 3 0.09
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTTTATTATTTTTTATC
Found at i:2913237 original size:21 final size:21
Alignment explanation
Indices: 2913213--2913253 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2913203 TATTATTAAG
2913213 TAATAGGAGAACTCAAATAAA
1 TAATAGGAGAACTCAAATAAA
2913234 TAATAGGAGAACTCAAATAA
1 TAATAGGAGAACTCAAATAA
2913254 GTATTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (21 bp):
TAATAGGAGAACTCAAATAAA
Found at i:2913442 original size:21 final size:21
Alignment explanation
Indices: 2913418--2913462 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2913408 AAACAGCCAT
**
2913418 TAATCAAATTCTTAATTACTG
1 TAATCAAATAATTAATTACTG
*
2913439 TAATCAAATAATTAATTATTG
1 TAATCAAATAATTAATTACTG
2913460 TAA
1 TAA
2913463 AGTGCAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (21 bp):
TAATCAAATAATTAATTACTG
Found at i:2914520 original size:2 final size:2
Alignment explanation
Indices: 2914513--2914541 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2914503 TTATAATAGA
2914513 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2914542 CTTGGTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2917690 original size:31 final size:31
Alignment explanation
Indices: 2917652--2917713 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2917642 ACTATATATC
*
2917652 AATATGCAGAGCAACCAAACAGAGTATAGCT
1 AATATGCAGAGCAACCAAACAGAGCATAGCT
2917683 AATATGCAGAGCAACCAAACAGAGCATAGCT
1 AATATGCAGAGCAACCAAACAGAGCATAGCT
2917714 TTGTCTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (31 bp):
AATATGCAGAGCAACCAAACAGAGCATAGCT
Found at i:2923305 original size:48 final size:48
Alignment explanation
Indices: 2923234--2923377 Score: 252
Period size: 48 Copynumber: 3.0 Consensus size: 48
2923224 TTCTCAACTG
*
2923234 AAACCACCAATTTCAGGGAGATGGTACAAAGATACACTGAAGTGCCTA
1 AAACCACCAATTTCAGGGAGATGGTACCAAGATACACTGAAGTGCCTA
*
2923282 AAACCACCGATTTCAGGGAGATGGTACCAAGATACACTGAAGTGCCTA
1 AAACCACCAATTTCAGGGAGATGGTACCAAGATACACTGAAGTGCCTA
* *
2923330 AAACCACCAATTTCAGGGAGATGGTACCAAGATATACTGGAGTGCCTA
1 AAACCACCAATTTCAGGGAGATGGTACCAAGATACACTGAAGTGCCTA
2923378 CGAAGGAAGT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 91 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (48 bp):
AAACCACCAATTTCAGGGAGATGGTACCAAGATACACTGAAGTGCCTA
Found at i:2925233 original size:12 final size:11
Alignment explanation
Indices: 2925216--2925243 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
2925206 ATTGATTGGG
2925216 TTTTTTTTTTC
1 TTTTTTTTTTC
2925227 TTTTTTTTTTC
1 TTTTTTTTTTC
2925238 TTTTTT
1 TTTTTT
2925244 ACCTGTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:2925324 original size:15 final size:15
Alignment explanation
Indices: 2925306--2925351 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
2925296 GTGATTACAG
2925306 GTAATATGATTGCAA
1 GTAATATGATTGCAA
2925321 GTAATATGATTGCAA
1 GTAATATGATTGCAA
* *
2925336 GTAATGTGATTACAA
1 GTAATATGATTGCAA
2925351 G
1 G
2925352 GAAAATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (15 bp):
GTAATATGATTGCAA
Found at i:2925592 original size:18 final size:18
Alignment explanation
Indices: 2925566--2925631 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
2925556 AAATGTTAAT
*
2925566 TTTTTATATTTTATTTTA
1 TTTTAATATTTTATTTTA
2925584 TTTTAATA-TTTATTCTTA
1 TTTTAATATTTTATT-TTA
*
2925602 TATTATATATTTTATTTTAA
1 TTTTA-ATATTTTATTTT-A
*
2925622 TTATAATATT
1 TTTTAATATT
2925632 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 6 0.15
18 14 0.35
19 10 0.25
20 10 0.25
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTAATATTTTATTTTA
Found at i:2927466 original size:27 final size:28
Alignment explanation
Indices: 2927409--2927474 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
2927399 TAATAATAAA
* *
2927409 AATACTTTTAATCCACCAGGAGTATATG
1 AATACTTTTAATCCACCAGGAGTAGACG
* * *
2927437 AATACTTTTAATCTATCA-GAGTGGACG
1 AATACTTTTAATCCACCAGGAGTAGACG
*
2927464 AATAATTTTAA
1 AATACTTTTAA
2927475 CCCATAAAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 16 0.50
28 16 0.50
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (28 bp):
AATACTTTTAATCCACCAGGAGTAGACG
Found at i:2927498 original size:31 final size:31
Alignment explanation
Indices: 2927460--2927527 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2927450 TATCAGAGTG
*
2927460 GACGAATAATTTTAACCCA-TAAAGAGTGGAT
1 GACGAATAATTTTAACCCACCAAA-AGTGGAT
* *
2927491 GACGAATACTTTTAACTCACCAAAAGTGGAT
1 GACGAATAATTTTAACCCACCAAAAGTGGAT
2927522 GA-GAAT
1 GACGAAT
2927528 GGATGATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 4 0.12
31 26 0.79
32 3 0.09
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (31 bp):
GACGAATAATTTTAACCCACCAAAAGTGGAT
Found at i:2927565 original size:31 final size:30
Alignment explanation
Indices: 2927527--2927589 Score: 81
Period size: 31 Copynumber: 2.1 Consensus size: 30
2927517 TGGATGAGAA
*
2927527 TGGATGATAAATTCGTTTAACCTACCAAAAG
1 TGGATGATAAATACGTTTAACC-ACCAAAAG
* * *
2927558 TGGATGATGAATACTTTTAACCACCAAGAG
1 TGGATGATAAATACGTTTAACCACCAAAAG
2927588 TG
1 TG
2927590 AATAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.29
Consensus pattern (30 bp):
TGGATGATAAATACGTTTAACCACCAAAAG
Found at i:2936641 original size:15 final size:15
Alignment explanation
Indices: 2936621--2936649 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2936611 TTAGGAGGAT
2936621 TTGGTAGTGAAGGGC
1 TTGGTAGTGAAGGGC
2936636 TTGGTAGTGAAGGG
1 TTGGTAGTGAAGGG
2936650 TTCTTGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.03, G:0.48, T:0.28
Consensus pattern (15 bp):
TTGGTAGTGAAGGGC
Found at i:2936891 original size:27 final size:27
Alignment explanation
Indices: 2936861--2936919 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
2936851 ACATAGTTCT
* *
2936861 CATTACTAGACGATACGACATAAGTCC
1 CATTACCAGACGATACGACATAACTCC
* * * *
2936888 CATTTCCAGACGTTATGACATAACTCT
1 CATTACCAGACGATACGACATAACTCC
2936915 CATTA
1 CATTA
2936920 AGAAACATCC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.34, C:0.25, G:0.12, T:0.29
Consensus pattern (27 bp):
CATTACCAGACGATACGACATAACTCC
Found at i:2942690 original size:90 final size:90
Alignment explanation
Indices: 2942533--2942701 Score: 311
Period size: 90 Copynumber: 1.9 Consensus size: 90
2942523 AGATATACTA
2942533 GGTATGGAACATCTCATCTTCAGCTGACTTAAAGATTTGAATTAGATGAAAGCATCTAAATAACC
1 GGTATGGAACATCTCATCTTCAGCTGACTTAAAGATTTGAATTAGATGAAAGCATCTAAATAACC
2942598 AGTGAGCAATAAAACACAGGTAGTT
66 AGTGAGCAATAAAACACAGGTAGTT
* * *
2942623 GGTATGGAACTTCTCATCTTCAGCTGACTTAGAGATTTGAATTAGATGAAAGCATCTAAATAGCC
1 GGTATGGAACATCTCATCTTCAGCTGACTTAAAGATTTGAATTAGATGAAAGCATCTAAATAACC
2942688 AGTGAGCAATAAAA
66 AGTGAGCAATAAAA
2942702 GCCAATGCAG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 76 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (90 bp):
GGTATGGAACATCTCATCTTCAGCTGACTTAAAGATTTGAATTAGATGAAAGCATCTAAATAACC
AGTGAGCAATAAAACACAGGTAGTT
Found at i:2951002 original size:2 final size:2
Alignment explanation
Indices: 2950995--2951021 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2950985 AATAAAACCA
2950995 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
2951022 AATGAAAGGG
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:2952824 original size:21 final size:21
Alignment explanation
Indices: 2952798--2952838 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2952788 CGATGGTGAT
*
2952798 ATGACATGCTTATATGATATA
1 ATGACATGCTCATATGATATA
2952819 ATGACATGCTCATATGATAT
1 ATGACATGCTCATATGATAT
2952839 TTTTCACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
ATGACATGCTCATATGATATA
Found at i:2962552 original size:33 final size:34
Alignment explanation
Indices: 2962499--2962570 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
2962489 AAAATATATA
* *
2962499 ATATAAGAAATTATATTAAGAAATAAAAATAAACT
1 ATATAAG-AATTATAATAAGAAATAAAAATAAAAT
*
2962534 ATATAAG-ATTATAATAAGAAATGAAAATAAAAT
1 ATATAAGAATTATAATAAGAAATAAAAATAAAAT
2962567 ATAT
1 ATAT
2962571 GACATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 27 0.79
35 7 0.21
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.29
Consensus pattern (34 bp):
ATATAAGAATTATAATAAGAAATAAAAATAAAAT
Found at i:2971142 original size:21 final size:21
Alignment explanation
Indices: 2971118--2971187 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
2971108 AATTTATTAT
2971118 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTGTTTAA
* * * *
2971139 ATTTAAA--TAAGGATGGATTAT
1 ATTTAAATTTAA--TTTGTTTAA
2971160 ATTTAAATTTAATTTGTTTAA
1 ATTTAAATTTAATTTGTTTAA
2971181 ATTTAAA
1 ATTTAAA
2971188 AGAAATGTCC
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 3 0.08
21 31 0.84
23 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (21 bp):
ATTTAAATTTAATTTGTTTAA
Found at i:2971169 original size:57 final size:57
Alignment explanation
Indices: 2971061--2971186 Score: 152
Period size: 57 Copynumber: 2.2 Consensus size: 57
2971051 TATGATGTAA
*
2971061 ATTTATATTTAATTTGTTTAAATTTAAATAAAGACTATTTATGTAATAATTT-ATTAT
1 ATTTAAATTTAATTTGTTTAAATTTAAATAAAGACTATTTATGTAATAATTTAATT-T
* *
2971118 ATTTAAATTTAATTTGTTTAAATTTAAATAAGGA-TGGATTATAT-TTA-AATTTAATTT
1 ATTTAAATTTAATTTGTTTAAATTTAAATAAAGACT--ATT-TATGTAATAATTTAATTT
*
2971175 GTTTAAATTTAA
1 ATTTAAATTTAA
2971187 AAGAAATGTC
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
56 1 0.02
57 49 0.80
58 8 0.13
59 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (57 bp):
ATTTAAATTTAATTTGTTTAAATTTAAATAAAGACTATTTATGTAATAATTTAATTT
Found at i:2971700 original size:34 final size:34
Alignment explanation
Indices: 2971657--2971721 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
2971647 ATATGTTCTA
* *
2971657 TTTTTTATTTGCTTTCTAATGATATATTATACAT
1 TTTTTTATTTCCTTTCAAATGATATATTATACAT
2971691 TTTTTTATTTCCTTTCAAATGATATATTATA
1 TTTTTTATTTCCTTTCAAATGATATATTATA
2971722 AGTATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (34 bp):
TTTTTTATTTCCTTTCAAATGATATATTATACAT
Found at i:2971730 original size:34 final size:34
Alignment explanation
Indices: 2971658--2971732 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
2971648 TATGTTCTAT
* * *
2971658 TTTTTATTTGCTTTCTAATGATATATTATACATT
1 TTTTTATTTCCTTTCAAATGATATATTATACATA
2971692 TTTTTATTTCCTTTCAAATGATATATTATA-AGTA
1 TTTTTATTTCCTTTCAAATGATATATTATACA-TA
2971726 TTTTTAT
1 TTTTTAT
2971733 ATATATCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 1 0.03
34 36 0.97
ACGTcount: A:0.28, C:0.08, G:0.05, T:0.59
Consensus pattern (34 bp):
TTTTTATTTCCTTTCAAATGATATATTATACATA
Found at i:2975681 original size:11 final size:11
Alignment explanation
Indices: 2975665--2975689 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2975655 TAGAATTAGG
2975665 ACAAGCTTTTC
1 ACAAGCTTTTC
2975676 ACAAGCTTTTC
1 ACAAGCTTTTC
2975687 ACA
1 ACA
2975690 TGTTGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (11 bp):
ACAAGCTTTTC
Found at i:2976892 original size:2 final size:2
Alignment explanation
Indices: 2976885--2976910 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2976875 ATCTAGAATC
2976885 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
2976911 TTGGGTGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2978752 original size:29 final size:29
Alignment explanation
Indices: 2978719--2978787 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 29
2978709 TTTTTTTATT
2978719 AAAATTTACAATTTATTTGATTTAAA-ATA
1 AAAATTTA-AATTTATTTGATTTAAATATA
2978748 AAAATTTAAA---ATTTGATTTAAATATA
1 AAAATTTAAATTTATTTGATTTAAATATA
2978774 ATAAA-TTAAATTTA
1 A-AAATTTAAATTTA
2978788 AAAGAGTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
25 12 0.34
26 9 0.26
27 3 0.09
28 2 0.06
29 9 0.26
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
AAAATTTAAATTTATTTGATTTAAATATA
Found at i:2981403 original size:21 final size:21
Alignment explanation
Indices: 2981379--2981433 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
2981369 ATTAACATTT
2981379 ATATAAGTAAATAAAAATAT-A
1 ATATAA-TAAATAAAAATATCA
* *
2981400 ATATAATTAATTAAACATATCA
1 ATATAA-TAAATAAAAATATCA
*
2981422 ATATCATAAATA
1 ATATAATAAATA
2981434 TTTGTACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAATAAATAAAAATATCA
Found at i:2983705 original size:72 final size:72
Alignment explanation
Indices: 2983588--2983732 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 72
2983578 CAATTTTGGG
* * * *
2983588 GATTTGCTTTGATGTCTGATAGAGGAAAAGGGCCTGTGTAGAAATTAAATGAAACTGTTAGAAAA
1 GATTTGCTATGATGTCTGATAAAGGAAAAGGGCCTGTGTAAAAATTAAATGAAACTGTAAGAAAA
2983653 ATATTTT
66 ATATTTT
*** * *
2983660 GATTTGCTATGATGTCCT-ATAAAGGAAAAGGTTTTGTGTAAAAATTAGATGAAGCTGTAAGAAA
1 GATTTGCTATGATGT-CTGATAAAGGAAAAGGGCCTGTGTAAAAATTAAATGAAACTGTAAGAAA
2983724 AATATTTT
65 AATATTTT
2983732 G
1 G
2983733 CAAAACATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
72 61 0.97
73 2 0.03
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (72 bp):
GATTTGCTATGATGTCTGATAAAGGAAAAGGGCCTGTGTAAAAATTAAATGAAACTGTAAGAAAA
ATATTTT
Found at i:2989539 original size:29 final size:29
Alignment explanation
Indices: 2989507--2989571 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
2989497 TAACTAAACT
*
2989507 ATTTTAATTAAAATTTTTTGATCAATTTG
1 ATTTTAATTAAAATTGTTTGATCAATTTG
** *
2989536 ATTTTAA-TAGGATTGTTTGATTAATTTG
1 ATTTTAATTAAAATTGTTTGATCAATTTG
*
2989564 GTTTTAAT
1 ATTTTAAT
2989572 CCAATTATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (29 bp):
ATTTTAATTAAAATTGTTTGATCAATTTG
Found at i:3007856 original size:63 final size:63
Alignment explanation
Indices: 3007673--3007857 Score: 212
Period size: 63 Copynumber: 2.9 Consensus size: 63
3007663 GTTATTGCCA
* * * *
3007673 AGATACATTTTCGACATAATTAATTTAGCCAATTAAATGCACTTAGTTGGTTAAGATATGTTG
1 AGATACATTTTCGACATAATCAATTTAGCCAATTAAATGTACTAAGTTGGTTAAGATGTGTTG
* * * * *
3007736 AGAAACATTTTCAACATAATGAATTTCA-CCAATTAAATATCCTAAGTTGGTTAAGATGTGTTG
1 AGATACATTTTCGACATAATCAATTT-AGCCAATTAAATGTACTAAGTTGGTTAAGATGTGTTG
* ** * *
3007799 AGATGCATTTTCGACATAGCCAATTTAGCCAAATAAATGTAGTAAGTT-GTTGAAGATGT
1 AGATACATTTTCGACATAATCAATTTAGCCAATTAAATGTACTAAGTTGGTT-AAGATGT
3007858 AAAATTAATT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
62 4 0.04
63 96 0.95
64 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (63 bp):
AGATACATTTTCGACATAATCAATTTAGCCAATTAAATGTACTAAGTTGGTTAAGATGTGTTG
Found at i:3008168 original size:50 final size:49
Alignment explanation
Indices: 3008095--3008204 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 49
3008085 AGGGCGAAAG
* *
3008095 GGTTTCAAAATGTGCAGGTTAAAAAGTTCCAGGATTGGTAAGGTT-AAAA
1 GGTTTCAAGATGTGCAGGTTAAAAAGTTCCAGGATTGGTAA-ATTAAAAA
* * **
3008144 GGTTTCGAGATGTGCATGGTTAAAAGGTTTTAGGATTGGTAAATTAAAAA
1 GGTTTCAAGATGTGCA-GGTTAAAAAGTTCCAGGATTGGTAAATTAAAAA
3008194 GGTTTCAAGAT
1 GGTTTCAAGAT
3008205 TGAGAAGCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 16 0.31
50 36 0.69
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (49 bp):
GGTTTCAAGATGTGCAGGTTAAAAAGTTCCAGGATTGGTAAATTAAAAA
Found at i:3008305 original size:36 final size:35
Alignment explanation
Indices: 3008247--3008328 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
3008237 TGCTAAGGTC
* * * * * *
3008247 AAAAGCCTAGAGGATTGAAAAACTGTGTCATGGTTG
1 AAAAGCCTTGAGAATTGAAAAAC-ATGCCAAGATTG
*
3008283 AAAAGCCTTGAGAATTGGAAAACATGCCAAGATTG
1 AAAAGCCTTGAGAATTGAAAAACATGCCAAGATTG
3008318 AAAAGCCTTGA
1 AAAAGCCTTGA
3008329 CGATCAGAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 19 0.49
36 20 0.51
ACGTcount: A:0.40, C:0.13, G:0.24, T:0.22
Consensus pattern (35 bp):
AAAAGCCTTGAGAATTGAAAAACATGCCAAGATTG
Found at i:3008411 original size:61 final size:61
Alignment explanation
Indices: 3008311--3008431 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
3008301 AAAACATGCC
* * * *
3008311 AAGATTGAAAAGCCTTGACGATCAGAAAGCATGTTAGGTTATAAGGTTTAAAGATTGGAGT
1 AAGATTGAAAAGCCTTAACGATCAGAAAGCATGTAAGGTTAGAAGATTTAAAGATTGGAGT
* ** * *
3008372 AAGATTGAAAAGCCTTAAGGATTGGAAAGCTTGTAAGGTTAGAAGATTTTAAGATTGGAG
1 AAGATTGAAAAGCCTTAACGATCAGAAAGCATGTAAGGTTAGAAGATTTAAAGATTGGAG
3008432 AGCATTGTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.28
Consensus pattern (61 bp):
AAGATTGAAAAGCCTTAACGATCAGAAAGCATGTAAGGTTAGAAGATTTAAAGATTGGAGT
Found at i:3008586 original size:34 final size:34
Alignment explanation
Indices: 3008478--3008623 Score: 127
Period size: 34 Copynumber: 4.3 Consensus size: 34
3008468 CTTGTAAGCT
*
3008478 TTTCAAGACAGGAAAGCATTGTAAGGTTAAAAGG
1 TTTCAAGATAGGAAAGCATTGTAAGGTTAAAAGG
* * * * * *
3008512 TGTCATGATGGGAAA-TATGGTTAGAAGGTTAAGAGG
1 TTTCAAGATAGGAAAGCATTG-T--AAGGTTAAAAGG
*
3008548 TTTCAAGATAGGAAAGCATTGTAAGGTTAAAAGA
1 TTTCAAGATAGGAAAGCATTGTAAGGTTAAAAGG
* * *
3008582 TTTCAAGATTGGGAAGC-TTGTGAGG-TAAGAAGG
1 TTTCAAGATAGGAAAGCATTGTAAGGTTAA-AAGG
*
3008615 TTTTAAGAT
1 TTTCAAGAT
3008624 TTAAAAGTTT
Statistics
Matches: 88, Mismatches: 19, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
32 3 0.03
33 21 0.24
34 37 0.42
36 24 0.27
37 3 0.03
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.28
Consensus pattern (34 bp):
TTTCAAGATAGGAAAGCATTGTAAGGTTAAAAGG
Found at i:3015558 original size:3 final size:3
Alignment explanation
Indices: 3015550--3015578 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3015540 GAGTTACTGT
3015550 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3015579 TTCAACTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3021729 original size:13 final size:13
Alignment explanation
Indices: 3021711--3021740 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3021701 TTATGAAAGT
*
3021711 TACTGCTAAAGAG
1 TACTGCTAAAGAA
3021724 TACTGCTAAAGAA
1 TACTGCTAAAGAA
3021737 TACT
1 TACT
3021741 ATCCTTCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (13 bp):
TACTGCTAAAGAA
Found at i:3032982 original size:2 final size:2
Alignment explanation
Indices: 3032975--3033000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3032965 TCCCATTTCC
3032975 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
3033001 TTTCCGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3046841 original size:22 final size:22
Alignment explanation
Indices: 3046807--3046852 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
3046797 TACCACATGA
*
3046807 ATGATTGCAAACACTAATTTAT
1 ATGATTACAAACACTAATTTAT
*
3046829 ATGATTACGAACACTAATTTAT
1 ATGATTACAAACACTAATTTAT
3046851 AT
1 AT
3046853 TTTTCATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (22 bp):
ATGATTACAAACACTAATTTAT
Found at i:3054942 original size:51 final size:51
Alignment explanation
Indices: 3054851--3054953 Score: 134
Period size: 51 Copynumber: 2.0 Consensus size: 51
3054841 AGATAGGAGA
*** *
3054851 GAAGGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGG
1 GAAGGGGGGGGGGGGGGGGGGGGGGAAAAGGGGGGAGGGGGGGGGGGGGGG
* * * *
3054902 GAAGGGGGGGTGGTGGGGGGGGGGTAAAAGGGGTGAGGGGGGGGGGGGGGG
1 GAAGGGGGGGGGGGGGGGGGGGGGGAAAAGGGGGGAGGGGGGGGGGGGGGG
3054953 G
1 G
3054954 GGTATGGAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.10, C:0.00, G:0.86, T:0.04
Consensus pattern (51 bp):
GAAGGGGGGGGGGGGGGGGGGGGGGAAAAGGGGGGAGGGGGGGGGGGGGGG
Found at i:3054945 original size:1 final size:1
Alignment explanation
Indices: 3054854--3054925 Score: 99
Period size: 1 Copynumber: 72.0 Consensus size: 1
3054844 TAGGAGAGAA
* ** * *
3054854 GGGGGGGGGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGAAGGGGGGGTGGTGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
3054919 GGGGGGG
1 GGGGGGG
3054926 TAAAAGGGGT
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.04, C:0.00, G:0.93, T:0.03
Consensus pattern (1 bp):
G
Found at i:3058641 original size:48 final size:48
Alignment explanation
Indices: 3058570--3058665 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
3058560 ATATTATGGA
**
3058570 TAACACATTGACTGGATCCAAATCGGAGAGCAGCAGCGGAGTGCCTGC
1 TAACACATTGACCAGATCCAAATCGGAGAGCAGCAGCGGAGTGCCTGC
3058618 TAACACATTGACCAGATCCAAATCGGAGAGCAGCAGCGGAGTGCCTGC
1 TAACACATTGACCAGATCCAAATCGGAGAGCAGCAGCGGAGTGCCTGC
3058666 CTATATTTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.30, C:0.26, G:0.28, T:0.16
Consensus pattern (48 bp):
TAACACATTGACCAGATCCAAATCGGAGAGCAGCAGCGGAGTGCCTGC
Found at i:3063405 original size:19 final size:19
Alignment explanation
Indices: 3063381--3063417 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3063371 TGTTTATTTC
3063381 AAATTTTACATTA-AAATTA
1 AAATTTTA-ATTATAAATTA
3063400 AAATTTTAATTATAAATT
1 AAATTTTAATTATAAATT
3063418 TTTAATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATTTTAATTATAAATTA
Found at i:3066368 original size:38 final size:37
Alignment explanation
Indices: 3066326--3066399 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
3066316 TTTGTTGTAG
*
3066326 TTATCACTT-TGATGATTATCGATGGTAAATATATAAAA
1 TTATCA-TTCTGACGATTATC-ATGGTAAATATATAAAA
* *
3066364 TTATCATTCTGACGATTATCATGGTGAATATTTAAA
1 TTATCATTCTGACGATTATCATGGTAAATATATAAA
3066400 TTCTATCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 16 0.50
38 16 0.50
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (37 bp):
TTATCATTCTGACGATTATCATGGTAAATATATAAAA
Found at i:3069449 original size:35 final size:35
Alignment explanation
Indices: 3069403--3069478 Score: 152
Period size: 35 Copynumber: 2.2 Consensus size: 35
3069393 AAAGCCAAGT
3069403 ACTTTTATTTCTTTTGTTATCCTGAACTCAGCCTG
1 ACTTTTATTTCTTTTGTTATCCTGAACTCAGCCTG
3069438 ACTTTTATTTCTTTTGTTATCCTGAACTCAGCCTG
1 ACTTTTATTTCTTTTGTTATCCTGAACTCAGCCTG
3069473 ACTTTT
1 ACTTTT
3069479 TCATTCGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.17, C:0.22, G:0.11, T:0.50
Consensus pattern (35 bp):
ACTTTTATTTCTTTTGTTATCCTGAACTCAGCCTG
Found at i:3069654 original size:22 final size:20
Alignment explanation
Indices: 3069613--3069682 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 20
3069603 TATTCAGATG
3069613 TAATTATTTAAAAATAAATA
1 TAATTATTTAAAAATAAATA
* *
3069633 TAATT-TTTTAAAA-AGATA
1 TAATTATTTAAAAATAAATA
*
3069651 -AA-TATTT-ATAATAAATA
1 TAATTATTTAAAAATAAATA
*
3069668 CAATTATTATAAAAA
1 TAATTATT-TAAAAA
3069683 ATAATATAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
16 4 0.10
17 9 0.23
18 6 0.15
19 11 0.28
20 6 0.15
21 3 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
TAATTATTTAAAAATAAATA
Found at i:3070865 original size:41 final size:42
Alignment explanation
Indices: 3070792--3070881 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 42
3070782 GCACTGATCG
** * *
3070792 GGTGCTCC-CCAATGTGGTGTTCCTTGGAGAGCACCGATT-A
1 GGTGCTCCTCCAACATGGTGCTCCTTGGAGAGCACAGATTCA
*
3070832 GGTGCTCCTCCAACATGGTGCTCCTTGGGGAGCACAGATTCA
1 GGTGCTCCTCCAACATGGTGCTCCTTGGAGAGCACAGATTCA
3070874 -GTGCTCCT
1 GGTGCTCCT
3070882 TGAGAAATCC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
40 8 0.19
41 34 0.79
42 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.29, T:0.27
Consensus pattern (42 bp):
GGTGCTCCTCCAACATGGTGCTCCTTGGAGAGCACAGATTCA
Found at i:3076218 original size:126 final size:126
Alignment explanation
Indices: 3076080--3076443 Score: 511
Period size: 124 Copynumber: 2.9 Consensus size: 126
3076070 TATTAGATTT
* * **
3076080 TTTA-AATATTAATAATTAATAATTTAAAATATTAATATTTTATTTTGTTTAAATATTATTATGA
1 TTTATAAT-TTAATCATTAATAATTTAAAATATTAATAATTTATTTAATTTAAATATTATTATGA
*
3076144 TTAATTTTTATTTATTTTATTTTTAAATATTAATAATTGATAATTTAAATATTAATGTTTTA
65 TTAATTTTTATTTATTTTATTTTTAAATATTAATAATTGATAATTTAAATATTAATATTTTA
* *
3076206 TTTATAATTTAATCATTAATATTTTAAAATATTAATAATTTATTAAATTTAAATATTATTATGAT
1 TTTATAATTTAATCATTAATAATTTAAAATATTAATAATTTATTTAATTTAAATATTATTATGAT
* * * **
3076271 CAA-TTAT-TTTATTTTATTGTTAAATATTAATAAAAGATAATTTAAATATTAATATTTTA
66 TAATTTTTATTTATTTTATTTTTAAATATTAATAATTGATAATTTAAATATTAATATTTTA
* * **
3076330 TTTATAATTTAATCATTGAT-ATTTCAAATACCAATAATTTATTTAATTTAAATATTATTATGAT
1 TTTATAATTTAATCATTAATAATTTAAAATATTAATAATTTATTTAATTTAAATATTATTATGAT
3076394 TAATTATTCTATTTTATTTTATTTTTTAAATATTAATAATTGATAATTTA
66 TAATT-TT-TA-TTTATTTTA-TTTTTAAATATTAATAATTGATAATTTA
3076444 TTTTAAATAT
Statistics
Matches: 208, Mismatches: 23, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
123 41 0.20
124 68 0.33
125 4 0.02
126 58 0.28
127 3 0.01
128 9 0.04
129 25 0.12
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (126 bp):
TTTATAATTTAATCATTAATAATTTAAAATATTAATAATTTATTTAATTTAAATATTATTATGAT
TAATTTTTATTTATTTTATTTTTAAATATTAATAATTGATAATTTAAATATTAATATTTTA
Found at i:3076248 original size:42 final size:39
Alignment explanation
Indices: 3076164--3076543 Score: 174
Period size: 42 Copynumber: 9.4 Consensus size: 39
3076154 TTTATTTTAT
* * **
3076164 TTTTAAATATTAATAATTGATAATTTAAATATTAATGTTTTA
1 TTTT-AAT-TTAAT-ATTAATATTTTAAATATTAATAATTTA
3076206 TTTATAATTTAATCATTAATATTTTAAAATATTAATAATTTA
1 TTT-TAATTTAAT-ATTAATATTTT-AAATATTAATAATTTA
* * * * * * *
3076248 -TTAAATTTAAATATTATTATGATCAATTATT-TTATTTTA
1 TTTTAATTT-AATATTAATAT-TTTAAATATTAATAATTTA
** * *
3076287 TTGTTAAATATTAATAAAAGATAATTTAAATATTAATATTTTA
1 TT-TT-AAT-TTAATATTA-ATATTTTAAATATTAATAATTTA
* * **
3076330 TTTATAATTTAATCATTGATATTTCAAATACCAATAATTTA
1 TTT-TAATTTAAT-ATTAATATTTTAAATATTAATAATTTA
* * * * *
3076371 -TTTAATTTAAATATTATTATGATTAATTATT-CTATTTTA
1 TTTTAATTT-AATATTAATAT-TTTAAATATTAATAATTTA
* *
3076410 TTTT-ATTT--T-TTAA-ATATT-AATAATTGATAATTTA
1 TTTTAATTTAATATTAATATTTTAAAT-ATTAATAATTTA
* *
3076444 TTTTAAATATTAATAATTGATCA-TTTAAATATTAATATTTTA
1 TTTT-AAT-TTAAT-ATTAAT-ATTTTAAATATTAATAATTTA
*
3076486 TTTATAATTTAGTCATTAATATTTTAAAATATTAAT-ATTTCA
1 TTT-TAATTTAAT-ATTAATATTTT-AAATATTAATAATTT-A
3076528 -TTTAATTTAAATATTA
1 TTTTAATTT-AATATTA
3076544 TTATGATCAA
Statistics
Matches: 255, Mismatches: 51, Indels: 66
0.69 0.14 0.18
Matches are distributed among these distances:
32 2 0.01
33 6 0.02
34 12 0.05
35 3 0.01
36 3 0.01
37 2 0.01
39 29 0.11
40 43 0.17
41 66 0.26
42 69 0.27
43 20 0.08
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (39 bp):
TTTTAATTTAATATTAATATTTTAAATATTAATAATTTA
Found at i:3076248 original size:85 final size:85
Alignment explanation
Indices: 3076078--3076263 Score: 200
Period size: 85 Copynumber: 2.2 Consensus size: 85
3076068 TTTATTAGAT
* *
3076078 TTTTTAAATATTAATAATTAATAATTTAAAATATTAATATTTTATTTTGTTTAAATATTATTATG
1 TTTTTAAATATTAATAATTAATAATTTAAAATATTAATATTTTATTTTATTTAAATATTAATATG
* * * *
3076143 ATTAATTTTTATTTATTTTA
66 ATTAAATATTATATAATTTA
* *
3076163 TTTTTAAATATTAATAATTGATAATTT-AAATATTAATGTTTTATTTATAATTT-AATCATTAAT
1 TTTTTAAATATTAATAATTAATAATTTAAAATATTAATATTTTATTT-T-ATTTAAAT-ATTAAT
*
3076226 AT-TTTAAAATATTA-ATAATTTA
63 ATGATT-AAATATTATATAATTTA
3076248 TTAAATTTAAATATTA
1 TT---TTTAAATATTA
3076264 TTATGATCAA
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
84 18 0.21
85 40 0.47
86 16 0.19
88 11 0.13
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (85 bp):
TTTTTAAATATTAATAATTAATAATTTAAAATATTAATATTTTATTTTATTTAAATATTAATATG
ATTAAATATTATATAATTTA
Found at i:3076427 original size:75 final size:74
Alignment explanation
Indices: 3076348--3076583 Score: 182
Period size: 75 Copynumber: 3.1 Consensus size: 74
3076338 TTAATCATTG
** *
3076348 ATATTTCAAATACCAATAATTTATTTAATTTAAATATTATTATGATTAATTATTCTATTTTATTT
1 ATATTT-AAATATTAATAATTTATTTAATTTAAATATTATTATGATTAATTATTATATTTTATTT
3076413 TATTTTTTAA
65 TATTTTTTAA
* * *
3076423 ATA-TT-AATAATTGATAATTTATTTTAAATATT-AATA--ATTGATCATTTAAATATTAATATT
1 ATATTTAAAT-ATTAATAATTTA-TTT-AAT-TTAAATATTATT-ATGA-TTAATTATT-ATATT
3076483 TTATTTATAATTTAGTCATT-A
59 TTATTT-T-ATTT--T--TTAA
* *
3076504 ATATTTTAAAATATTAAT-ATTTCATTTAATTTAAATATTATTATGATCAATTATTTTATTTTAT
1 ATA-TTT-AAATATTAATAATTT-ATTTAATTTAAATATTATTATGATTAATTATTATATTTTAT
*
3076568 GTTA-TTTTTAA
63 TTTATTTTTTAA
3076579 ATATT
1 ATATT
3076584 AATAGTTGAT
Statistics
Matches: 127, Mismatches: 12, Indels: 45
0.69 0.07 0.24
Matches are distributed among these distances:
72 3 0.02
73 12 0.09
74 12 0.09
75 22 0.17
76 13 0.10
77 1 0.01
78 6 0.05
79 1 0.01
80 2 0.02
81 15 0.12
82 16 0.13
83 12 0.09
84 9 0.07
85 3 0.02
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (74 bp):
ATATTTAAATATTAATAATTTATTTAATTTAAATATTATTATGATTAATTATTATATTTTATTTT
ATTTTTTAA
Found at i:3076455 original size:27 final size:27
Alignment explanation
Indices: 3076417--3076470 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
3076407 TTATTTTATT
3076417 TTTTAAATATTAATAATTGATAATTTA
1 TTTTAAATATTAATAATTGATAATTTA
*
3076444 TTTTAAATATTAATAATTGATCATTTA
1 TTTTAAATATTAATAATTGATAATTTA
3076471 AATATTAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.52
Consensus pattern (27 bp):
TTTTAAATATTAATAATTGATAATTTA
Found at i:3076460 original size:280 final size:271
Alignment explanation
Indices: 3076159--3076770 Score: 840
Period size: 280 Copynumber: 2.2 Consensus size: 271
3076149 TTTTATTTAT
*
3076159 TTTATTTTTAAATATTAATAATTGATAATTTAAATATTAATGTTTTATTTATAATTTAATCATTA
1 TTTA-TTTTAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTA
3076224 ATATTTTAAAATATTAATAATTT-ATTAAATTTAAATATTATTATGATCAATTATTTTATTTTAT
65 ATATTTTAAAATATTAAT-ATTTCATTAAATTTAAATATTATTATGATCAATTATTTTATTTTA-
* * * *
3076288 TGTTAAATATTAATAAAAGATAATTTAAATA-TTAATAT-TTTATTTATAAT-TTAATCATTGAT
128 TGTT--AT-TT--T-AAA-AT-A-TT-AATAGTTAAT-TGCTTATTTAAAATATTAATAATAGAT
*
3076350 -ATTTCAAATACCAATAATTTATTTAATTTAAATATTATTATGATTAA-TTATTCTATTTTATTT
182 AATTT-AAATACCAATAATTTATTTAATTTAAATATTATTATGATAAATTTATTCTA-TTTATTT
3076413 TATTTTTTAAATATTAATAATTGATAA
245 TATTTTTTAAATATTAATAATTGATAA
* *
3076440 TTTATTTTAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTTAGTCATTAA
1 TTTATTTTAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAA
*
3076505 TATTTTAAAATATTAATATTTCATTTAATTTAAATATTATTATGATCAATTATTTTATTTTATGT
66 TATTTTAAAATATTAATATTTCATTAAATTTAAATATTATTATGATCAATTATTTTATTTTATGT
* * **
3076570 TATTTTTAAATATTAATAGTTGATTGCTTATTTAAAATATTAATAATAGATAATTTAAATATTAA
131 TATTTTAAAATATTAATAGTTAATTGCTTATTTAAAATATTAATAATAGATAATTTAAATACCAA
* *
3076635 TATTTTATTTAATTTAAATATTATTATGATAAATTTTTATTTTATTTATTTTATTTTTTAAATAT
196 TAATTTATTTAATTTAAATATTATTATGATAAA--TTTATTCTATTTATTTTATTTTTTAAATAT
*
3076700 TAATAATTGGTAA
259 TAATAATTGATAA
* * * *
3076713 TTTATTTAAAATATTAATAATTGATGATTTAATTATTAATATTTTATATATAATTTAA
1 TTTATTTTAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAA
3076771 ATGATATTAT
Statistics
Matches: 302, Mismatches: 21, Indels: 24
0.87 0.06 0.07
Matches are distributed among these distances:
269 5 0.02
270 16 0.05
271 49 0.16
272 6 0.02
273 88 0.29
274 8 0.03
276 2 0.01
277 2 0.01
279 8 0.03
280 114 0.38
281 4 0.01
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (271 bp):
TTTATTTTAAATATTAATAATTGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAA
TATTTTAAAATATTAATATTTCATTAAATTTAAATATTATTATGATCAATTATTTTATTTTATGT
TATTTTAAAATATTAATAGTTAATTGCTTATTTAAAATATTAATAATAGATAATTTAAATACCAA
TAATTTATTTAATTTAAATATTATTATGATAAATTTATTCTATTTATTTTATTTTTTAAATATTA
ATAATTGATAA
Found at i:3076470 original size:156 final size:156
Alignment explanation
Indices: 3076283--3076645 Score: 541
Period size: 156 Copynumber: 2.3 Consensus size: 156
3076273 ATTATTTTAT
* *
3076283 TTTATTGTTAAATATTAATAAAAGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTG
1 TTTATT-TTAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTA
* *
3076348 ATA-TTTCAAATACCAATAATTT-ATTTAATTTAAATATTATTATGATTAATTATTCTATTTTAT
65 ATATTTTAAAATACCAAT-ATTTCATTTAATTTAAATATTATTATGATCAATTATTCTATTTTAT
*
3076411 TTTATTTTTTAAATATTAATAATTGATAA
129 GTTA-TTTTTAAATATTAATAATTGATAA
* * *
3076440 TTTATTTTAAATATTAATAATTGATCATTTAAATATTAATATTTTATTTATAATTTAGTCATTAA
1 TTTATTTTAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAA
** *
3076505 TATTTTAAAATATTAATATTTCATTTAATTTAAATATTATTATGATCAATTATTTTATTTTATGT
66 TATTTTAAAATACCAATATTTCATTTAATTTAAATATTATTATGATCAATTATTCTATTTTATGT
* **
3076570 TATTTTTAAATATTAATAGTTGATTG
131 TATTTTTAAATATTAATAATTGATAA
* *
3076596 CTTATTTAAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTA
1 TTTATTTTAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTA
3076646 ATTTAAATAT
Statistics
Matches: 186, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
156 127 0.68
157 59 0.32
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (156 bp):
TTTATTTTAAATATTAATAATAGATAATTTAAATATTAATATTTTATTTATAATTTAATCATTAA
TATTTTAAAATACCAATATTTCATTTAATTTAAATATTATTATGATCAATTATTCTATTTTATGT
TATTTTTAAATATTAATAATTGATAA
Found at i:3076541 original size:24 final size:23
Alignment explanation
Indices: 3076366--3076543 Score: 57
Period size: 22 Copynumber: 7.9 Consensus size: 23
3076356 AATACCAATA
*
3076366 ATTTATTTAATTTAAATATTATT
1 ATTTATTTAATTTAAATATTAAT
* *
3076389 ATGATTAATT-ATTCT--AT-TTTAT
1 AT--TTATTTAATT-TAAATATTAAT
3076411 -TTTATTT--TTTAAATATTAAT
1 ATTTATTTAATTTAAATATTAAT
*
3076431 AATTGATAATTTATTTTAAATATTAAT
1 -ATT--T-ATTTAATTTAAATATTAAT
* *
3076458 AATTGA--TCATTTAAATATTAAT
1 -ATTTATTTAATTTAAATATTAAT
*
3076480 ATTTTATTTATAATTT-AGTCATTAAT
1 A-TTTA-TT-TAATTTAAAT-ATTAAT
3076506 A--T-TTT-A---AAATATTAAT
1 ATTTATTTAATTTAAATATTAAT
3076522 ATTTCATTTAATTTAAATATTA
1 ATTT-ATTTAATTTAAATATTA
3076544 TTATGATCAA
Statistics
Matches: 115, Mismatches: 12, Indels: 55
0.63 0.07 0.30
Matches are distributed among these distances:
16 7 0.06
17 3 0.03
18 3 0.03
19 8 0.07
20 8 0.07
21 5 0.04
22 22 0.19
23 5 0.04
24 13 0.11
25 12 0.10
26 12 0.10
27 17 0.15
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTATTTAATTTAAATATTAAT
Found at i:3076561 original size:25 final size:24
Alignment explanation
Indices: 3076505--3076561 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
3076495 TAGTCATTAA
* *
3076505 TATTTTAAAATATTAATATTTCATT
1 TATTTT-AAATATTAATATATCAAT
* *
3076530 TAATTTAAATATTATTATGATCAAT
1 TATTTTAAATATTAATAT-ATCAAT
3076555 TATTTTA
1 TATTTTA
3076562 TTTTATGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (24 bp):
TATTTTAAATATTAATATATCAAT
Found at i:3076718 original size:117 final size:115
Alignment explanation
Indices: 3076512--3076874 Score: 420
Period size: 117 Copynumber: 3.2 Consensus size: 115
3076502 TAATATTTTA
* *
3076512 AAATATTAATATTTCATTTAATTTAAATATTATTATGATCAA---TTATTTTATTTTATGTTATT
1 AAATATTAATATTTTATTTAATTTAAATATTATTATGAT-AATTTTTATTTTA-TTTATTTTATT
* *** *
3076574 TTTAAATATTAATAGTTGATTGCTTATTTAAAATATTAATAATAGATAATTT
64 TTTAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATTT
3076626 AAATATTAATATTTTATTTAATTTAAATATTATTATGATAAATTTTTATTTTATTTATTTTATTT
1 AAATATTAATATTTTATTTAATTTAAATATTATTATGAT-AATTTTTATTTTATTTATTTTA-TT
* *
3076691 TTTAAATATTAATAATTGGTAATTTATTTAAAATATTAATAATTGATGATTT
64 TTTAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATTT
* * * * *
3076743 AATTATTAATATTTTATATATAATTTAAATGA-TATTATGCTTATTTAT-TTTTATTTATTTTGT
1 AAATATTAATATTTTAT-T-TAATTTAAAT-ATTATTATGATAATTTTTATTTTATTTATTTTAT
* ** * *
3076806 TGTTAAATAGGAGTAATTTATAATTTATTT----TATTAATAATTGATAATTT
63 TTTTAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATTT
*
3076855 AAATGTTAATATTTTATTTA
1 AAATATTAATATTTTATTTA
3076875 TAACTTAATA
Statistics
Matches: 218, Mismatches: 24, Indels: 18
0.84 0.09 0.07
Matches are distributed among these distances:
110 2 0.01
111 1 0.00
112 33 0.15
114 40 0.18
116 33 0.15
117 84 0.39
118 6 0.03
119 18 0.08
120 1 0.00
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (115 bp):
AAATATTAATATTTTATTTAATTTAAATATTATTATGATAATTTTTATTTTATTTATTTTATTTT
TAAATATTAATAATTGATAATTTATTTAAAATATTAATAATTGATAATTT
Found at i:3076743 original size:27 final size:26
Alignment explanation
Indices: 3076574--3076626 Score: 52
Period size: 27 Copynumber: 2.0 Consensus size: 26
3076564 TTATGTTATT
* ***
3076574 TTTAAATATTAATAGTTGATTGCTTA
1 TTTAAATATTAATAATTGATAATTTA
*
3076600 TTTAAAATATTAATAATAGATAATTTA
1 TTT-AAATATTAATAATTGATAATTTA
3076627 AATATTAATA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
26 3 0.14
27 18 0.86
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTAAATATTAATAATTGATAATTTA
Found at i:3076902 original size:16 final size:16
Alignment explanation
Indices: 3076881--3076911 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3076871 TTTATAACTT
*
3076881 AATATTAATATTTTAA
1 AATATTAACATTTTAA
3076897 AATATTAACATTTTA
1 AATATTAACATTTTA
3076912 TTAAAATTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTAACATTTTAA
Found at i:3093428 original size:21 final size:21
Alignment explanation
Indices: 3093402--3093452 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3093392 TGAACCCAGG
*
3093402 GCTTGTTGTAGATTGGTTAAT
1 GCTTGTTGCAGATTGGTTAAT
3093423 GCTTGTTGCAGATTGGTTAAT
1 GCTTGTTGCAGATTGGTTAAT
3093444 GCTTGTTGC
1 GCTTGTTGC
3093453 TGTTGGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.16, C:0.10, G:0.29, T:0.45
Consensus pattern (21 bp):
GCTTGTTGCAGATTGGTTAAT
Found at i:3101697 original size:2 final size:2
Alignment explanation
Indices: 3101690--3101721 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3101680 ATTAAGTGCT
3101690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3101722 CTTAATTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3109737 original size:17 final size:17
Alignment explanation
Indices: 3109703--3109740 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3109693 CTCTCTCATT
*
3109703 AAATTAAAATAAATTTA
1 AAATTAAAATAAAATTA
3109720 AAATATAAAA-AAAATTA
1 AAAT-TAAAATAAAATTA
3109737 AAAT
1 AAAT
3109741 GAGTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATTAAAATAAAATTA
Found at i:3109747 original size:28 final size:27
Alignment explanation
Indices: 3109703--3109758 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 27
3109693 CTCTCTCATT
3109703 AAATTAAAATAAATTTAAAATATAAAAA
1 AAATTAAAATAAATTTAAAATA-AAAAA
* *
3109731 AAATTAAAATGAGTTTAAAATAAAAAA
1 AAATTAAAATAAATTTAAAATAAAAAA
3109758 A
1 A
3109759 TTAAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (27 bp):
AAATTAAAATAAATTTAAAATAAAAAA
Done.