Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 16 of 117
Found at i:1691628 original size:14 final size:17
Alignment explanation
Indices: 1691611--1691647 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
1691601 TATATATATA
1691611 TATTTTA-TC-TTTTT-
1 TATTTTATTCATTTTTG
1691625 TATTTTATTCATTTTTG
1 TATTTTATTCATTTTTG
1691642 TATTTT
1 TATTTT
1691648 TACTTATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
16 5 0.25
17 6 0.30
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (17 bp):
TATTTTATTCATTTTTG
Found at i:1692062 original size:26 final size:25
Alignment explanation
Indices: 1692019--1692073 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
1692009 TCTGGGAGTA
1692019 AGAAAAATTTTTTAGAAATTTTTGG
1 AGAAAAATTTTTTAGAAATTTTTGG
* *
1692044 AGAAAATTTTTTCTGGAAATTTTTGG
1 AGAAAAATTTTT-TAGAAATTTTTGG
1692070 -GAAA
1 AGAAA
1692074 TTTCCAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 15 0.56
26 12 0.44
ACGTcount: A:0.38, C:0.02, G:0.18, T:0.42
Consensus pattern (25 bp):
AGAAAAATTTTTTAGAAATTTTTGG
Found at i:1692794 original size:57 final size:57
Alignment explanation
Indices: 1692713--1693112 Score: 534
Period size: 57 Copynumber: 6.7 Consensus size: 57
1692703 AAATTCCAAA
*
1692713 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1 AAAAA-ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
1692771 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAATTTCC
*
1692828 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC
* * *
1692890 AAAAAAAATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCAAA
1 --AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT--AAATTTC--C
*
1692953 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAA
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA-TTTC-C
* * *
1693012 AAAAAAGAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCGAAATTTTC
1 AAAAAATA-TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCC
1693072 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1693113 CTAAAAAAAA
Statistics
Matches: 311, Mismatches: 13, Indels: 35
0.87 0.04 0.10
Matches are distributed among these distances:
56 1 0.00
57 91 0.29
58 5 0.02
59 49 0.16
60 50 0.16
61 58 0.19
62 14 0.05
63 1 0.00
64 42 0.14
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (57 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC
Found at i:1692931 original size:121 final size:116
Alignment explanation
Indices: 1692713--1693112 Score: 581
Period size: 121 Copynumber: 3.4 Consensus size: 116
1692703 AAATTCCAAA
1692713 AAAAATATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC--AAAAA
1 AAAAA-ATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAA
*
1692776 ATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAAT-AAATTTCC
65 ATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATCAAATTTCC
1692828 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCCAAA
*
1692893 AAAAATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCAAA
61 AAAAATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATC-AAATTTC--C
* *
1692953 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTTCAAAAAAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAAA
* * *
1693018 GAGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCGAAATTTTC
66 TATTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTT-AAAATC-AAATTTCC
*
1693072 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
1693113 CTAAAAAAAA
Statistics
Matches: 262, Mismatches: 10, Indels: 22
0.89 0.03 0.07
Matches are distributed among these distances:
114 38 0.15
115 5 0.02
117 2 0.01
119 53 0.20
120 26 0.10
121 85 0.32
122 4 0.02
123 7 0.03
125 42 0.16
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (116 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAAAAAA
TATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAATCAAATTTCC
Found at i:1695203 original size:22 final size:23
Alignment explanation
Indices: 1695177--1695231 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
1695167 TCACTACCAC
*
1695177 CTTCT-ATATTTTACTTTGCTTT
1 CTTCTCATATTTTACTTTGCTCT
* *
1695199 CTTCTCGATCTTTTACTTTTCTCT
1 CTTCTC-ATATTTTACTTTGCTCT
*
1695223 CTTCCCATA
1 CTTCTCATA
1695232 CACTTACTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 5 0.19
23 2 0.08
24 19 0.73
ACGTcount: A:0.13, C:0.27, G:0.04, T:0.56
Consensus pattern (23 bp):
CTTCTCATATTTTACTTTGCTCT
Found at i:1695542 original size:129 final size:129
Alignment explanation
Indices: 1695312--1695569 Score: 516
Period size: 129 Copynumber: 2.0 Consensus size: 129
1695302 CCTTGACTAG
1695312 TCTGACATACTTTCTAGTCAGCTCCTATAAGCTCCTCCATCACCAGATCAGAAATTATATCAACA
1 TCTGACATACTTTCTAGTCAGCTCCTATAAGCTCCTCCATCACCAGATCAGAAATTATATCAACA
1695377 TACCTTTATTTAAGTTCTAAATATTGAATTTTTCTGCATGCATGAAAACTTATGATGTGTTAGA
66 TACCTTTATTTAAGTTCTAAATATTGAATTTTTCTGCATGCATGAAAACTTATGATGTGTTAGA
1695441 TCTGACATACTTTCTAGTCAGCTCCTATAAGCTCCTCCATCACCAGATCAGAAATTATATCAACA
1 TCTGACATACTTTCTAGTCAGCTCCTATAAGCTCCTCCATCACCAGATCAGAAATTATATCAACA
1695506 TACCTTTATTTAAGTTCTAAATATTGAATTTTTCTGCATGCATGAAAACTTATGATGTGTTAGA
66 TACCTTTATTTAAGTTCTAAATATTGAATTTTTCTGCATGCATGAAAACTTATGATGTGTTAGA
1695570 CTACAAAAAT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 129 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (129 bp):
TCTGACATACTTTCTAGTCAGCTCCTATAAGCTCCTCCATCACCAGATCAGAAATTATATCAACA
TACCTTTATTTAAGTTCTAAATATTGAATTTTTCTGCATGCATGAAAACTTATGATGTGTTAGA
Found at i:1699429 original size:29 final size:25
Alignment explanation
Indices: 1699348--1699437 Score: 85
Period size: 26 Copynumber: 3.4 Consensus size: 25
1699338 TTAGTTTTTA
*
1699348 TTATATATAATTA-ATTATTAATAAT
1 TTATAT-TAATAATATTATTAATAAT
* *
1699373 ATCATATTAATAATATTATT-ATCAT
1 -TTATATTAATAATATTATTAATAAT
1699398 TTATATTAATCAATTATAATATTAATAAT
1 TTATATTAAT-AA-TAT--TATTAATAAT
1699427 TTATATTAATA
1 TTATATTAATA
1699438 TATCAAAGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
24 9 0.17
25 11 0.21
26 14 0.26
28 5 0.09
29 14 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (25 bp):
TTATATTAATAATATTATTAATAAT
Found at i:1699613 original size:17 final size:17
Alignment explanation
Indices: 1699591--1699625 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1699581 AAATTAATTT
1699591 AGTAAAAATATATTAAA
1 AGTAAAAATATATTAAA
*
1699608 AGTAAAAATTTATTAAA
1 AGTAAAAATATATTAAA
1699625 A
1 A
1699626 ATAATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (17 bp):
AGTAAAAATATATTAAA
Found at i:1699695 original size:12 final size:13
Alignment explanation
Indices: 1699668--1699700 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1699658 TAAACACATT
*
1699668 AAATATTTTTTGA
1 AAATAATTTTTGA
1699681 AAATAATTTTT-A
1 AAATAATTTTTGA
1699693 AAATAATT
1 AAATAATT
1699701 AAAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
AAATAATTTTTGA
Found at i:1700138 original size:17 final size:17
Alignment explanation
Indices: 1700116--1700148 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1700106 CACAAAATGT
1700116 GAAAATTTCTTAATTAA
1 GAAAATTTCTTAATTAA
*
1700133 GAAAATTTTTTAATTA
1 GAAAATTTCTTAATTA
1700149 TTTTAAAAAT
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:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (17 bp):
GAAAATTTCTTAATTAA
Found at i:1700262 original size:19 final size:19
Alignment explanation
Indices: 1700219--1700255 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1700209 TTATGTTATT
1700219 TTTAATAAATTTTTATTAC
1 TTTAATAAATTTTTATTAC
*
1700238 TTTAATATATTTTTATTA
1 TTTAATAAATTTTTATTA
1700256 TATTAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTAATAAATTTTTATTAC
Found at i:1700443 original size:16 final size:14
Alignment explanation
Indices: 1700408--1700448 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 14
1700398 AATTTTGATA
1700408 TATTAAT-TTAAAT
1 TATTAATATTAAAT
1700421 TATTAATATTATAAT
1 TATTAATATTA-AAT
1700436 TGATTAATATTAA
1 T-ATTAATATTAA
1700449 TGATAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 7 0.28
14 3 0.12
15 5 0.20
16 10 0.40
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:1702515 original size:18 final size:18
Alignment explanation
Indices: 1702487--1702523 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
1702477 ATAGATTATG
1702487 ATTATAAAATA-AAAAAA
1 ATTATAAAATACAAAAAA
1702504 ATTATGAAAATACAAAAAA
1 ATTAT-AAAATACAAAAAA
1702523 A
1 A
1702524 ATAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.28
18 6 0.33
19 7 0.39
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.22
Consensus pattern (18 bp):
ATTATAAAATACAAAAAA
Found at i:1706236 original size:60 final size:60
Alignment explanation
Indices: 1706161--1706333 Score: 206
Period size: 60 Copynumber: 2.9 Consensus size: 60
1706151 AATGCTTTTA
* * * * * *
1706161 TTCAAGAAAATTTGATACTTTCAACTTTTTCTT-AAAAAATATTTTTTTGAAATTTTTATT
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAAATA-TCTTTTGAAAATTTCATC
*
1706221 TTCAAGAAAAATTGATA-TTCTCAACTTTTCCTCCAAAAAAATATCTTTTGAAAATTTCATC
1 TTCAAGAAAAATTGATACTT-TCAACTTTTCCT-TAAAAAAATATCTTTTGAAAATTTCATC
* * * *
1706282 TTCAAGAAAAATTGATACCTTCAACTTTTCCTTAAAAACATTTCTTGTGAAA
1 TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAAATATCTTTTGAAA
1706334 TATATTTTTT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.02
60 43 0.44
61 43 0.44
62 9 0.09
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (60 bp):
TTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAAAATATCTTTTGAAAATTTCATC
Found at i:1706273 original size:61 final size:62
Alignment explanation
Indices: 1706161--1706313 Score: 181
Period size: 61 Copynumber: 2.5 Consensus size: 62
1706151 AATGCTTTTA
* ** * * * *
1706161 TTCAAGAAAATTTGATACTT-TCAACTTTT--TCTTAAAAAATATTTTTTTGAAATTTTTATT
1 TTCAAGAAAAATTGATA-TTCTCAACTTTTCCTCCAAAAAAATATTCTTTTGAAAATTTCATC
1706221 TTCAAGAAAAATTGATATTCTCAACTTTTCCTCCAAAAAAATA-TCTTTTGAAAATTTCATC
1 TTCAAGAAAAATTGATATTCTCAACTTTTCCTCCAAAAAAATATTCTTTTGAAAATTTCATC
*
1706282 TTCAAGAAAAATTGATA-CCTTCAACTTTTCCT
1 TTCAAGAAAAATTGATATTC-TCAACTTTTCCT
1706314 TAAAAACATT
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
59 2 0.02
60 26 0.32
61 43 0.53
62 10 0.12
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (62 bp):
TTCAAGAAAAATTGATATTCTCAACTTTTCCTCCAAAAAAATATTCTTTTGAAAATTTCATC
Found at i:1706639 original size:60 final size:59
Alignment explanation
Indices: 1706565--1706771 Score: 196
Period size: 60 Copynumber: 3.5 Consensus size: 59
1706555 TTGAAAGATT
* *
1706565 TTTTTGAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTGAAATTTTATTC
1 TTTTT-AA-GAAAATTGATACTTTCAACTTTTCATAAAAAAATATTTTTGAAATTTTATTC
* * * * *
1706626 TTTTTATGAAAAATTGATACTTTCAATTTTTTATTAAAAAA-A---TTAAAATTTT-TATC
1 TTTTTAAG-AAAATTGATACTTTCAACTTTTCATAAAAAAATATTTTTGAAATTTTAT-TC
* * * *
1706682 --TTCAAGGAAAATTGATACTTTCAACTTTTCTTTAAAACAAATTTTTTTGAACTTTTATT-
1 TTTTTAA-GAAAATTGATACTTTCAACTTTTC-ATAAAA-AAATATTTTTGAAATTTTATTC
1706741 TTTTTAAGAAAATTGATACTTTCAACTTTTC
1 TTTTTAAGAAAATTGATACTTTCAACTTTTC
1706772 GAAAGAATAT
Statistics
Matches: 118, Mismatches: 16, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
54 24 0.20
55 6 0.05
56 14 0.12
59 2 0.02
60 62 0.53
61 10 0.08
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.48
Consensus pattern (59 bp):
TTTTTAAGAAAATTGATACTTTCAACTTTTCATAAAAAAATATTTTTGAAATTTTATTC
Found at i:1707046 original size:21 final size:20
Alignment explanation
Indices: 1707020--1707065 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1707010 GAAAAATAAG
1707020 CAAATA-AATAAAGAAGAGAAA
1 CAAATAGAA-AAAGAAGA-AAA
1707041 CAAATAGAAAAAGAAGAAAA
1 CAAATAGAAAAAGAAGAAAA
1707061 -AAATA
1 CAAATA
1707066 CCTTTGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.21
20 3 0.12
21 14 0.58
22 2 0.08
ACGTcount: A:0.74, C:0.04, G:0.13, T:0.09
Consensus pattern (20 bp):
CAAATAGAAAAAGAAGAAAA
Found at i:1707873 original size:13 final size:14
Alignment explanation
Indices: 1707848--1707877 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1707838 AAACTTTTGG
1707848 TTTTAATTATTATT
1 TTTTAATTATTATT
1707862 TTTTAATT-TTATT
1 TTTTAATTATTATT
1707875 TTT
1 TTT
1707878 CTTATCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTAATTATTATT
Found at i:1708258 original size:85 final size:83
Alignment explanation
Indices: 1708150--1708697 Score: 294
Period size: 85 Copynumber: 6.4 Consensus size: 83
1708140 CAAACCAGAA
* * *
1708150 TCTAAAATAAATAACTTGGACTAAGTCGAAGAAGGATTTGACATAGGCCAAAATTCAAAACAAAA
1 TCTAAAATAAATAACTTGGACTAA-CCAAAGAA-GATATGACATAGGCCAAAATTCAAAACAAAA
*
1708215 TGACTTAGATGGAACTGAAG
64 TGACATAGATGGAACTGAAG
* * *** * *
1708235 TCTAACATAAATAACTTGAACTAAACCAAAGATAGATATGGTGTAGGTCGAAATTCAAAAC-AAA
1 TCTAAAATAAATAACTTGGACT-AACCAAAGA-AGATATGACATAGGCCAAAATTCAAAACAAAA
**
1708299 TGACATAGATGGAACCAAAG
64 TGACATAGATGGAACTGAAG
* * * * *
1708319 TCTAAAATAAGTAACTTGGATTGAACCAAAAAAAGATCTGACATAGGCCAAAATCCAAAACAAAA
1 TCTAAAATAAATAACTTGGACT-AACC-AAAGAAGATATGACATAGGCCAAAATTCAAAACAAAA
* * *
1708384 TGACATGGATGAAATTGAAG
64 TGACATAGATGGAACTGAAG
* * * * * ** * * * *
1708404 TCTAAAATAAGTTACCTAGACCGAACTGAAGAAGGATTTGGCACAGGCCATAAGTTAAAATCTAA
1 TCTAAAATAAATAACTTGGA-CTAACCAAAGAA-GATATGACATAGGCC---A---AAATTC-AA
* * *
1708469 AACAAAATGACCTAGATAGAA-TCAAAG
57 AACAAAATGACATAGATGGAACT-GAAG
* * * * * * * * ** *
1708496 TTTAAAATAAGTAACCTGGACTGACCTAAGGATGGATCTGGCATAGGTTAAAATCCAAAACAAAA
1 TCTAAAATAAATAACTTGGACTAACC-AAAGA-AGATATGACATAGGCCAAAATTCAAAACAAAA
* * *
1708561 TGACCTAGAGGGAA-TCAAAG
64 TGACATAGATGGAACT-GAAG
* * * * ***
1708581 TCTAAAATAAGTAACTTGGACTAAACCAAAGAAGGATCT-AGCATAGGCTAAAATCCAAAATTTA
1 TCTAAAATAAATAACTTGGACT-AACCAAAGAA-GATATGA-CATAGGCCAAAATTCAAAACAAA
* * *
1708645 ATGACCTGGATGGAACCGAAG
63 ATGACATAGATGGAACTGAAG
* * *
1708666 TCTACAAGTAAACAATTTGGACTAAGCCAAAG
1 TCTA-AAATAAATAACTTGGACTAA-CCAAAG
1708698 TACATTGGTA
Statistics
Matches: 357, Mismatches: 84, Indels: 43
0.74 0.17 0.09
Matches are distributed among these distances:
84 67 0.19
85 197 0.55
86 30 0.08
88 1 0.00
89 1 0.00
91 8 0.02
92 53 0.15
ACGTcount: A:0.46, C:0.15, G:0.18, T:0.21
Consensus pattern (83 bp):
TCTAAAATAAATAACTTGGACTAACCAAAGAAGATATGACATAGGCCAAAATTCAAAACAAAATG
ACATAGATGGAACTGAAG
Found at i:1708615 original size:177 final size:176
Alignment explanation
Indices: 1708291--1708617 Score: 395
Period size: 177 Copynumber: 1.9 Consensus size: 176
1708281 GTCGAAATTC
* * *
1708291 AAAACAAATGACATAGATGGAACCAAAGTCTAAAATAAGTAACTTGGATTGAACCAAAAAAAGAT
1 AAAACAAATGACATAGATAGAACCAAAGTCTAAAATAAGTAACCTGGACTGAACCAAAAAAAGAT
* * ** *
1708356 CTGACATAGGCCAAAATCCAAAACAAAATGACATGGATGAAATTGAAGTCTAAAATAAGTTACCT
66 CTGACATAGGCCAAAATCCAAAACAAAATGACATAGAGGAAATCAAAGTCTAAAATAAGTAACCT
* **
1708421 AGACCGAACTGAAGAAGGATTTGGCACAGGCCATAAGTTAAAATCT
131 AGACCAAACCAAAGAAGGATTTGGCACAGGCCATAAGTTAAAATCT
* * * ** **
1708467 AAAACAAAATGACCTAGATAGAATCAAAGTTTAAAATAAGTAACCTGGACTG-ACCTAAGGATGG
1 AAAAC-AAATGACATAGATAGAACCAAAGTCTAAAATAAGTAACCTGGACTGAACC-AAAAAAAG
* ** * *
1708531 ATCTGGCATAGGTTAAAATCCAAAACAAAATGACCTAGAGGGAATCAAAGTCTAAAATAAGTAAC
64 ATCTGACATAGGCCAAAATCCAAAACAAAATGACATAGAGGAAATCAAAGTCTAAAATAAGTAAC
* * *
1708596 TTGGACTAAACCAAAGAAGGAT
129 CTAGACCAAACCAAAGAAGGAT
1708618 CTAGCATAGG
Statistics
Matches: 123, Mismatches: 26, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
176 8 0.07
177 115 0.93
ACGTcount: A:0.47, C:0.15, G:0.18, T:0.20
Consensus pattern (176 bp):
AAAACAAATGACATAGATAGAACCAAAGTCTAAAATAAGTAACCTGGACTGAACCAAAAAAAGAT
CTGACATAGGCCAAAATCCAAAACAAAATGACATAGAGGAAATCAAAGTCTAAAATAAGTAACCT
AGACCAAACCAAAGAAGGATTTGGCACAGGCCATAAGTTAAAATCT
Found at i:1711149 original size:186 final size:184
Alignment explanation
Indices: 1710944--1711345 Score: 436
Period size: 186 Copynumber: 2.2 Consensus size: 184
1710934 TTCGTAAAGC
** * * * * * * * *
1710944 ATCACTACTTGGGTACTTTTAGAATCCCGTGATCGGGTAAAATTTT-TTTTCTCCCTTTTTTATC
1 ATCACTACTTGAATACTTTTAGAATCCCATCATCAGATAAAATTTTCTTTTCTACATTCTTTATA
** * * * *
1711008 ACTTTATT-TTTAGTTTTATAACAAAAAAGAAACATTTTTATTATATTGAAAATTTTTTATGAAT
66 ACTTTATTAAATA-TTTTATAAC-AAAAAGAAA-ATTTTTATTATATTAAAAACTTTTGATAAAT
*
1711072 ACTCCAATATATTGATAGTATTTTAAAAAAAAAA-TTTCACCTAGAGATTTCTTAGAT
128 ACTCCAATATATTGATAGTA-TTTAAAAAAAAAATTTTCACCTAGAGATTTCATAGAT
* * * *
1711129 ATCACTACTTGAAATACTTTTA-AATCTCATCTTTAGATAAAATTTTCTTTTTTACATTCTTTAT
1 ATCACTACTTG-AATACTTTTAGAATCCCATCATCAGATAAAATTTTCTTTTCTACATTCTTTAT
* * *
1711193 AATTTTATTAAATATTTTATAACAAAAAGAAAATTTTTATTCTATTAAAAACTTTTGGTAAATAC
65 AACTTTATTAAATATTTTATAACAAAAAGAAAATTTTTATTATATTAAAAACTTTTGATAAATAC
* * *
1711258 TCCAATATGTTGGTAGTATTTAAAAAAAAAATCTTTTCACCTAGAGATTTCATAGGT
130 TCCAATATATTGATAGTATTTAAAAAAAAAA--TTTTCACCTAGAGATTTCATAGAT
* *
1711315 ATCACTACTTGGAATACCTTT-GAATCTCATC
1 ATCACTACTT-GAATACTTTTAGAATCCCATC
1711346 TAAGGATAAA
Statistics
Matches: 181, Mismatches: 28, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
183 13 0.07
184 43 0.24
185 37 0.20
186 85 0.47
187 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (184 bp):
ATCACTACTTGAATACTTTTAGAATCCCATCATCAGATAAAATTTTCTTTTCTACATTCTTTATA
ACTTTATTAAATATTTTATAACAAAAAGAAAATTTTTATTATATTAAAAACTTTTGATAAATACT
CCAATATATTGATAGTATTTAAAAAAAAAATTTTCACCTAGAGATTTCATAGAT
Found at i:1711346 original size:186 final size:188
Alignment explanation
Indices: 1711021--1711391 Score: 493
Period size: 186 Copynumber: 2.0 Consensus size: 188
1711011 TTATTTTTAG
* * * *
1711021 TTTTATAACAAAAAAGAAACATTTTTATTATATTGAAAATTTTTTATGAATACTCCAATATATTG
1 TTTTATAACAAAAAAGAAACATTTTTATTATATTAAAAACTTTTGATAAATACTCCAATATATTG
* *
1711086 ATAGTATTTTAAAAAAAAAATTTCACCTAGAGATTTCTTAGATATCACTACTTGAAATACTTTTA
66 ATAGTATTTTAAAAAAAAAATTTCACCTAGAGATTTCATAGATATCACTACTTGAAATACCTTTA
* *
1711151 AATCTCATCTTTA-GAT-AAAATTTTCTT-TTTTACATTCTTTATAATTTTATTAAATA
131 AATCTCATC-TAAGGATAAAAATTTCCTTCTTTTACATTCTTTATAATTTTATTAAATA
* * *
1711207 TTTTATAAC-AAAAAGAAA-ATTTTTATTCTATTAAAAACTTTTGGTAAATACTCCAATATGTTG
1 TTTTATAACAAAAAAGAAACATTTTTATTATATTAAAAACTTTTGATAAATACTCCAATATATTG
* * *
1711270 GTAGTA-TTTAAAAAAAAAATCTTTTCACCTAGAGATTTCATAGGTATCACTACTTGGAATACCT
66 ATAGTATTTTAAAAAAAAAA---TTTCACCTAGAGATTTCATAGATATCACTACTTGAAATACCT
* * * *
1711334 TTGAATCTCATCTAAGGATAAAAAATTTCCTTCTTTTATATTTTTTATTATTTTATTA
128 TTAAATCTCATCTAAGGAT-AAAAATTTCCTTCTTTTACATTCTTTATAATTTTATTA
1711392 TTATTCATTT
Statistics
Matches: 160, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
183 13 0.08
184 43 0.27
185 11 0.07
186 61 0.38
188 10 0.06
189 22 0.14
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (188 bp):
TTTTATAACAAAAAAGAAACATTTTTATTATATTAAAAACTTTTGATAAATACTCCAATATATTG
ATAGTATTTTAAAAAAAAAATTTCACCTAGAGATTTCATAGATATCACTACTTGAAATACCTTTA
AATCTCATCTAAGGATAAAAATTTCCTTCTTTTACATTCTTTATAATTTTATTAAATA
Found at i:1711419 original size:18 final size:17
Alignment explanation
Indices: 1711367--1711420 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
1711357 AATTTCCTTC
1711367 TTTTA-TATTTTTTATT
1 TTTTATTATTTTTTATT
* *
1711383 ATTTTATTATTATTCATT
1 -TTTTATTATTTTTTATT
1711401 TTTTAGTTATTTTTTATT
1 TTTTA-TTATTTTTTATT
1711419 TT
1 TT
1711421 AAAAATTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 10 0.32
18 21 0.68
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTATTATTTTTTATT
Found at i:1726078 original size:18 final size:18
Alignment explanation
Indices: 1726055--1726097 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1726045 TTTTTCATTT
*
1726055 TTTATTACTT-ATTCTTAA
1 TTTATTAATTAATT-TTAA
*
1726073 TTTATTAATTAATTTTTA
1 TTTATTAATTAATTTTAA
1726091 TTTATTA
1 TTTATTA
1726098 TTTTATAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATTAATTAATTTTAA
Found at i:1726303 original size:6 final size:6
Alignment explanation
Indices: 1726292--1726344 Score: 54
Period size: 6 Copynumber: 8.2 Consensus size: 6
1726282 TATTAAAAAG
1726292 TTTTAT TTTTAT TTTTAT TATTT-T ATTTTAT TTTATCAT TTTTAT TTATTAT
1 TTTTAT TTTTAT TTTTAT T-TTTAT -TTTTAT TTT-T-AT TTTTAT TT-TTAT
1726344 T
1 T
1726345 ACTAAAGTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
6 24 0.59
7 12 0.29
8 5 0.12
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTAT
Found at i:1726317 original size:14 final size:13
Alignment explanation
Indices: 1726292--1726344 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
1726282 TATTAAAAAG
1726292 TTTTA-TTTTTAT
1 TTTTATTTTTTAT
1726304 TTTTATTATTTTA-
1 TTTTATT-TTTTAT
*
1726317 TTTTATTTTATCAT
1 TTTTATTTT-TTAT
*
1726331 TTTTATTTATTAT
1 TTTTATTTTTTAT
1726344 T
1 T
1726345 ACTAAAGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 7 0.21
13 14 0.41
14 13 0.38
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTTTTTAT
Found at i:1726320 original size:19 final size:19
Alignment explanation
Indices: 1726292--1726338 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
1726282 TATTAAAAAG
*
1726292 TTTTATTTTTATTTTTATTA-
1 TTTTA-TTTTA-TTTTATCAT
1726312 TTTTATTTTATTTTATCAT
1 TTTTATTTTATTTTATCAT
1726331 TTTTATTT
1 TTTTATTT
1726339 ATTATTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 13 0.52
20 5 0.20
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTTTATTTTATCAT
Found at i:1726451 original size:23 final size:20
Alignment explanation
Indices: 1726424--1726473 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
1726414 TTAAATATTT
1726424 AAATATACATAAATATTATAAA
1 AAATATACAT-AA-ATTATAAA
*
1726446 ACAATATATATAAATTATAAA
1 A-AATATACATAAATTATAAA
1726467 AAATATA
1 AAATATA
1726474 AAAAATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 3 0.12
23 8 0.31
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATATACATAAATTATAAA
Found at i:1728897 original size:21 final size:21
Alignment explanation
Indices: 1728859--1728898 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1728849 GCTAAAAAGG
*
1728859 TTTTGATCTCGTCTACTTTTC
1 TTTTGATCTAGTCTACTTTTC
1728880 TTTTGATCTAG-CTCACTTT
1 TTTTGATCTAGTCT-ACTTT
1728899 ATCATGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.12, C:0.23, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTTGATCTAGTCTACTTTTC
Found at i:1732861 original size:19 final size:20
Alignment explanation
Indices: 1732837--1732902 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
1732827 TCTTATTTAT
**
1732837 TTATTTATTGCTAT-TATTA
1 TTATTTATTAATATATATTA
1732856 TTATTTATTAATATATATT-
1 TTATTTATTAATATATATTA
*
1732875 TTATCTATTAATATATATTA
1 TTATTTATTAATATATATTA
1732895 TTATTTAT
1 TTATTTAT
1732903 CTATTAATGT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (20 bp):
TTATTTATTAATATATATTA
Found at i:1732863 original size:10 final size:10
Alignment explanation
Indices: 1732829--1732947 Score: 61
Period size: 10 Copynumber: 12.2 Consensus size: 10
1732819 ATTTTGTATC
1732829 TTATTTA-T-
1 TTATTTATTA
*
1732837 TTATTTATTG
1 TTATTTATTA
*
1732847 CTA-TTATTA
1 TTATTTATTA
1732856 TTATTTATTA
1 TTATTTATTA
* *
1732866 ATATATATT-
1 TTATTTATTA
*
1732875 TTATCTATTA
1 TTATTTATTA
* *
1732885 ATATATATTA
1 TTATTTATTA
1732895 TTATTTATCTA
1 TTATTTAT-TA
*
1732906 TTAATGTA-TA
1 TT-ATTTATTA
*
1732916 TAAATTT-TTA
1 T-TATTTATTA
* *
1732926 TTATTAACTA
1 TTATTTATTA
*
1732936 TTATCTATTA
1 TTATTTATTA
1732946 TT
1 TT
1732948 TATCTTTTTT
Statistics
Matches: 82, Mismatches: 20, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
8 7 0.09
9 18 0.22
10 49 0.60
11 4 0.05
12 4 0.05
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (10 bp):
TTATTTATTA
Found at i:1732926 original size:28 final size:24
Alignment explanation
Indices: 1732848--1732952 Score: 93
Period size: 24 Copynumber: 4.6 Consensus size: 24
1732838 TATTTATTGC
*
1732848 TATTATTA-TTATTTATT-A-ATA
1 TATTATTATTTATCTATTAATATA
1732869 TA-TA-T-TTTATCTATTAATATA
1 TATTATTATTTATCTATTAATATA
*
1732890 TATTATTATTTATCTATTAATGTA
1 TATTATTATTTATCTATTAATATA
*
1732914 TATAAATT-TTTAT-TATTAACTAT-
1 TAT-TATTATTTATCTATTAA-TATA
1732937 TATCTATTATTTATCT
1 TAT-TATTATTTATCT
1732953 TTTTTTTGGT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
19 9 0.13
20 3 0.04
21 7 0.10
22 2 0.03
23 13 0.19
24 30 0.44
25 4 0.06
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.59
Consensus pattern (24 bp):
TATTATTATTTATCTATTAATATA
Found at i:1733699 original size:3 final size:3
Alignment explanation
Indices: 1733693--1733732 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
1733683 TTTTCTCATT
1733693 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
1733733 GATTAGAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1733894 original size:55 final size:56
Alignment explanation
Indices: 1733823--1733929 Score: 189
Period size: 55 Copynumber: 1.9 Consensus size: 56
1733813 TTAAAAATAT
*
1733823 TTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCCAAAAACA
1 TTTTAGAGAAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCCAAAAACA
*
1733879 TTTTAGAG-AAAGTTGAAAGTATCAATTTCCCTTGAAAATAAAATTTCCAAA
1 TTTTAGAGAAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCCAAA
1733930 TGCTTTAAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
55 41 0.84
56 8 0.16
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (56 bp):
TTTTAGAGAAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCCAAAAACA
Found at i:1733949 original size:82 final size:82
Alignment explanation
Indices: 1733858--1734025 Score: 318
Period size: 82 Copynumber: 2.0 Consensus size: 82
1733848 ATTTTCCTTA
*
1733858 AAAATAAAATTTCCAAAAACATTTTAGAGAAAGTTGAAAGTATCAATTTCCCTTGAAAATAAAAT
1 AAAATAAAATTTCCAAAAACATTTTAGAGAAAGTTAAAAGTATCAATTTCCCTTGAAAATAAAAT
1733923 TTCCAAATGCTTTAAGG
66 TTCCAAATGCTTTAAGG
*
1733940 AAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTAAAAGTATCAATTTCCCTTGAAAATAAAAT
1 AAAATAAAATTTCCAAAAACATTTTAGAGAAAGTTAAAAGTATCAATTTCCCTTGAAAATAAAAT
1734005 TTCCAAATGCTTTAAGG
66 TTCCAAATGCTTTAAGG
1734022 AAAA
1 AAAA
1734026 GTTGAAAGTA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 84 1.00
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.30
Consensus pattern (82 bp):
AAAATAAAATTTCCAAAAACATTTTAGAGAAAGTTAAAAGTATCAATTTCCCTTGAAAATAAAAT
TTCCAAATGCTTTAAGG
Found at i:1734041 original size:54 final size:55
Alignment explanation
Indices: 1733939--1734123 Score: 282
Period size: 54 Copynumber: 3.4 Consensus size: 55
1733929 ATGCTTTAAG
*
1733939 GAAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTAAAAGTATCAATTTCCCTT
1 GAAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTGAAAGTATCAATTTCCCTT
** * * *
1733994 GAAAATAAAATTTCCAAATGC-TTTAAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 GAAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTGAAAGTATCAATTTCCCTT
*
1734048 AAAAATAAAATTTCCAAAAAACATTTTAGGGAAAGTTGAAAGTATCAATTTCCCTT
1 GAAAATAAAATTTCC-AAAAACATTTTAGGGAAAGTTGAAAGTATCAATTTCCCTT
*
1734104 GAAAATAAAATTTTCAAAAA
1 GAAAATAAAATTTCCAAAAA
1734124 ATATATATAT
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
54 43 0.38
55 28 0.25
56 43 0.38
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (55 bp):
GAAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTGAAAGTATCAATTTCCCTT
Found at i:1734206 original size:55 final size:55
Alignment explanation
Indices: 1734138--1734281 Score: 172
Period size: 55 Copynumber: 2.7 Consensus size: 55
1734128 ATATATATAT
1734138 ATTTT-GAGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAAACTTCCAAAAAC
1 ATTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAA-AATAAAACTTCCAAAAAC
** **
1734193 ATTTTAGAG-AAAGTTGAAAGTATCAA-TTTCTCTTGAAAATAAATTTTCCAAATGC
1 ATTTTAGAGAAAAGTTGAAAGTATCAATTTTC-CTT-AAAATAAAACTTCCAAAAAC
* *
1734248 -GTTAAG-GAAAAGTTGAAAGTATCAATTTTCCTTA
1 ATTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTA
1734282 TATAAAAGCA
Statistics
Matches: 78, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
53 2 0.03
54 28 0.36
55 43 0.55
56 5 0.06
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (55 bp):
ATTTTAGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAATAAAACTTCCAAAAAC
Found at i:1744753 original size:22 final size:21
Alignment explanation
Indices: 1744722--1744770 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
1744712 TACTATGCTT
* *
1744722 AAAAGAAAAAGGTAAAAAGAA
1 AAAAAAAAAAGGAAAAAAGAA
*
1744743 AGAAAAAAAAAGGAAAAAAGGA
1 A-AAAAAAAAAGGAAAAAAGAA
1744765 AAAAAA
1 AAAAAA
1744771 GAATGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.25
22 18 0.75
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAGGAAAAAAGAA
Found at i:1745840 original size:44 final size:42
Alignment explanation
Indices: 1745790--1745998 Score: 131
Period size: 44 Copynumber: 5.1 Consensus size: 42
1745780 GAGCATTTAC
1745790 TTTCAAAGTTATGATGCCTCTGATTAGAGGAGCCTTGTTTATTT
1 TTTCAAAGTTATGA-GCCTCTGATTAGAGGAGCCTTGTTTA-TT
* *
1745834 TTTCAAAGTCGT-TGAGCCTCTGTTTAGAGAAG-C---TTTA--
1 TTTCAAAGT--TATGAGCCTCTGATTAGAGGAGCCTTGTTTATT
* *
1745871 TTT--AAGTCGT-TGAGCCTCT-ATTTAGAAGAGCTTTGTTTATT
1 TTTCAAAGT--TATGAGCCTCTGA-TTAGAGGAGCCTTGTTTATT
* *
1745912 TTTCAAAAGTCATTGAGCCTCTGATTAGAGGAGCC--ATTTATT
1 TTTC-AAAGTTA-TGAGCCTCTGATTAGAGGAGCCTTGTTTATT
* * * * *
1745954 TTT-AAGGTCATGAAGCCTTTGTTTAGAGGAGCTTTGTTTATT
1 TTTCAAAGTTATG-AGCCTCTGATTAGAGGAGCCTTGTTTATT
1745996 TTT
1 TTT
1745999 TTTAAAGTCG
Statistics
Matches: 132, Mismatches: 15, Indels: 38
0.71 0.08 0.21
Matches are distributed among these distances:
35 23 0.17
37 3 0.02
39 6 0.05
40 27 0.20
41 3 0.02
42 18 0.14
43 1 0.01
44 46 0.35
45 4 0.03
46 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.43
Consensus pattern (42 bp):
TTTCAAAGTTATGAGCCTCTGATTAGAGGAGCCTTGTTTATT
Found at i:1745885 original size:35 final size:35
Alignment explanation
Indices: 1745839--1745909 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 35
1745829 TATTTTTTCA
*
1745839 AAGTCGTTGAGCCTCTGTTTAG-AGAAGCTTTATTT
1 AAGTCGTTGAGCCTCTATTTAGAAG-AGCTTTATTT
*
1745874 AAGTCGTTGAGCCTCTATTTAGAAGAGCTTTGTTT
1 AAGTCGTTGAGCCTCTATTTAGAAGAGCTTTATTT
1745909 A
1 A
1745910 TTTTTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 31 0.94
36 2 0.06
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.39
Consensus pattern (35 bp):
AAGTCGTTGAGCCTCTATTTAGAAGAGCTTTATTT
Found at i:1745908 original size:79 final size:83
Alignment explanation
Indices: 1745800--1746014 Score: 246
Period size: 79 Copynumber: 2.6 Consensus size: 83
1745790 TTTCAAAGTT
* * *
1745800 ATGATGCCTCTGA-TTAGAGGAGCCTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGA
1 ATGAAGCCTCT-ATTTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGA
1745864 AG-C-TTTA-TTTAA-GTC
65 AGCCATTTATTTTAAGGTC
* * *
1745879 GTTG-AGCCTCTATTTAGAAGAGCTTTGTTTA-TTTTTCAAAAGTCATTGAGCCTCTGATTAGAG
1 -ATGAAGCCTCTATTTAGAGGAGCTTTGTTTATTTTTTC-AAAGTCGTTGAGCCTCTGATTAGAG
*
1745942 GAGCCATTTATTTTTAAGGTC
64 AAGCCATTTA-TTTTAAGGTC
* * *
1745963 ATGAAGCCTTTGTTTAGAGGAGCTTTGTTTATTTTTTTTAAAGTCGTTGAGC
1 ATGAAGCCTCTATTTAGAGGAGCTTTGTTTA-TTTTTTCAAAGTCGTTGAGC
1746015 TTCAGCTTAG
Statistics
Matches: 112, Mismatches: 13, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
78 7 0.06
79 47 0.42
80 3 0.03
81 4 0.04
83 7 0.06
84 27 0.24
85 12 0.11
86 5 0.04
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.42
Consensus pattern (83 bp):
ATGAAGCCTCTATTTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGAGAA
GCCATTTATTTTAAGGTC
Found at i:1745994 original size:42 final size:43
Alignment explanation
Indices: 1745874--1746034 Score: 132
Period size: 44 Copynumber: 3.7 Consensus size: 43
1745864 AGCTTTATTT
* * *
1745874 AAGTCGTTGAGCCTCTATTTAGAAGAGCTTTGTTTATTTTTCAA
1 AAGTCATTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTT-AA
* **
1745918 AAGTCATTGAGCCTCTGATTAGAGGAGC--CATTTATTTTT-A
1 AAGTCATTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTAA
* * *
1745958 AGGTCA-TGAAGCCTTTGTTTAGAGGAGCTTTGTTTATTTTTTTTA
1 AAGTCATTG-AGCCTCTGTTTAGAGGAGCTTTGTTTA--TTTTTAA
* * * * *
1746003 AAGTCGTTGAGCTTCAGCTTAGGGGAGCTTTG
1 AAGTCATTGAGCCTCTGTTTAGAGGAGCTTTG
1746035 ATCAAACTTT
Statistics
Matches: 92, Mismatches: 18, Indels: 13
0.75 0.15 0.11
Matches are distributed among these distances:
39 2 0.02
40 23 0.25
42 13 0.14
44 29 0.32
45 23 0.25
46 2 0.02
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (43 bp):
AAGTCATTGAGCCTCTGTTTAGAGGAGCTTTGTTTATTTTTAA
Found at i:1746250 original size:20 final size:20
Alignment explanation
Indices: 1746231--1746297 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1746221 TGTATCTTAT
**
1746231 TTATTTATTGCTAT-TATTA
1 TTATTTATTAATATATATTA
*
1746250 TTATTTATTAATATATATTT
1 TTATTTATTAATATATATTA
*
1746270 TTATCTATTAATATATATTA
1 TTATTTATTAATATATATTA
1746290 TTATTTAT
1 TTATTTAT
1746298 CTATTAATGT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.63
Consensus pattern (20 bp):
TTATTTATTAATATATATTA
Found at i:1746257 original size:10 final size:10
Alignment explanation
Indices: 1746231--1746303 Score: 58
Period size: 10 Copynumber: 7.3 Consensus size: 10
1746221 TGTATCTTAT
*
1746231 TTATTTATTG
1 TTATTTATTA
*
1746241 CTA-TTATTA
1 TTATTTATTA
1746250 TTATTTATTA
1 TTATTTATTA
* * *
1746260 ATATATATTT
1 TTATTTATTA
*
1746270 TTATCTATTA
1 TTATTTATTA
* *
1746280 ATATATATTA
1 TTATTTATTA
1746290 TTATTTATCTA
1 TTATTTAT-TA
1746301 TTA
1 TTA
1746304 ATGTATATAA
Statistics
Matches: 48, Mismatches: 13, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
9 7 0.15
10 36 0.75
11 5 0.10
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.62
Consensus pattern (10 bp):
TTATTTATTA
Found at i:1746287 original size:24 final size:25
Alignment explanation
Indices: 1746260--1746347 Score: 96
Period size: 24 Copynumber: 3.6 Consensus size: 25
1746250 TTATTTATTA
1746260 ATATATATT-TTTATCTATTAATAT
1 ATATATATTATTTATCTATTAATAT
*
1746284 ATAT-TATTATTTATCTATTAATGT
1 ATATATATTATTTATCTATTAATAT
*
1746308 ATATAAACTT-TTTAT-TATTAACTAT
1 ATATATA-TTATTTATCTATTAA-TAT
*
1746333 -TATCTATTATTTATC
1 ATATATATTATTTATC
1746348 CTTTTTTTGC
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
23 6 0.11
24 37 0.70
25 8 0.15
26 2 0.04
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (25 bp):
ATATATATTATTTATCTATTAATAT
Found at i:1747386 original size:56 final size:55
Alignment explanation
Indices: 1747193--1747411 Score: 287
Period size: 55 Copynumber: 3.9 Consensus size: 55
1747183 AAAATATTAT
* * *
1747193 TTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCCAAAAATA
1 TTTTAGGG-AAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCCAAAAACA
* * * **
1747249 TTTTAGGGAAAGTTAAAAGTATCAATTTCCCTTGAAAATAAAATTTTCAAATGC-
1 TTTTAGGGAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCCAAAAACA
* * * *
1747303 TTTAAGGAAAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAAATTTCCAAAAAACA
1 TTTTAGG-GAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCC-AAAAACA
*
1747360 TTTTAGGGAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTTCAAAA
1 TTTTAGGGAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCCAAAA
1747412 CAAATATATA
Statistics
Matches: 138, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
54 6 0.04
55 78 0.57
56 48 0.35
57 6 0.04
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (55 bp):
TTTTAGGGAAAGTTGAAAGTATCAATTTCCCTTAAAAATAAAATTTCCAAAAACA
Found at i:1747400 original size:111 final size:110
Alignment explanation
Indices: 1747201--1747557 Score: 380
Period size: 110 Copynumber: 3.2 Consensus size: 110
1747191 ATTTTTGGGG
*
1747201 AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCCAAAAATATTTTAGGGAAAGTTAAA
1 AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTAAA
*
1747266 AGTATCAATTTCCCTTGAAAATAAAATTTTCAAATGCTTTAAGGA
66 AGTATCAATTTCCCTTAAAAATAAAATTTTCAAATGCTTTAAGGA
* *
1747311 AAAAGTTGAAAGTATCAATTTTCTTTAAAAATAAAATTTCCAAAAAACATTTTAGGGAAAGTTGA
1 AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCC-AAAAACATTTTAGGGAAAGTTAA
*
1747376 AAGTATCAATTTCCCTTAAAAATAAAATTTTCAAA-ACAAATATATATATTCTTGGGA
65 AAGTATCAATTTCCCTTAAAAATAAAATTTTCAAATGC---T-T-TA-A------GGA
* * * * * * *
1747433 AAAATTTGAAAGCATCAATTTTTCTTAAAAATTAAACTT-C-----CA----A-GGAAAATTGAA
1 AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTAAA
* *
1747487 AGTATCAATTTCCCTTGAAAATAAAATTTCCAAATGCTTTAAGG-
66 AGTATCAATTTCCCTTAAAAATAAAATTTTCAAATGCTTTAAGGA
1747531 AAAAGTTGAAAGTATCAATTTTCCTTA
1 AAAAGTTGAAAGTATCAATTTTCCTTA
1747558 TGTAAAAGCA
Statistics
Matches: 215, Mismatches: 18, Indels: 40
0.79 0.07 0.15
Matches are distributed among these distances:
98 24 0.11
99 2 0.01
105 1 0.00
106 2 0.01
107 1 0.00
108 1 0.00
110 83 0.39
111 57 0.27
113 1 0.00
114 1 0.00
115 4 0.02
116 1 0.00
121 1 0.00
122 36 0.17
ACGTcount: A:0.45, C:0.11, G:0.10, T:0.34
Consensus pattern (110 bp):
AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCCAAAAACATTTTAGGGAAAGTTAAA
AGTATCAATTTCCCTTAAAAATAAAATTTTCAAATGCTTTAAGGA
Found at i:1747508 original size:44 final size:45
Alignment explanation
Indices: 1747433--1747519 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 45
1747423 ATTCTTGGGA
** *
1747433 AAAATTTGAAAGCATCAATTTTTCTTAAAAATTAAACTTCCAAGG
1 AAAATTTGAAAGCATCAATTTCCCTTAAAAATAAAACTTCCAAGG
* * *
1747478 AAAA-TTGAAAGTATCAATTTCCCTTGAAAATAAAATTTCCAA
1 AAAATTTGAAAGCATCAATTTCCCTTAAAAATAAAACTTCCAA
1747520 ATGCTTTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 32 0.89
45 4 0.11
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (45 bp):
AAAATTTGAAAGCATCAATTTCCCTTAAAAATAAAACTTCCAAGG
Found at i:1749300 original size:60 final size:60
Alignment explanation
Indices: 1749219--1749429 Score: 244
Period size: 60 Copynumber: 3.4 Consensus size: 60
1749209 GACTTTATTC
* * * *
1749219 AAGAAAATTTGATACTTTCAACTTTTCCTTAAAAAAACATTTTTTGAAATTTTTATTTTTG
1 AAGAAAA-TTGATACTTTCAACTTTTCCTAAAAAAAATATTTTTTGAAATTTTTATTCTTA
* * *
1749280 AAGAAAATTGATACTCTCAACTTTTTCTCCAAAAAAAAATATCTTTTTTGAAAATTTTA-TCTTC
1 AAGAAAATTGATACTTTCAAC--TTT-TCCTAAAAAAAATA--TTTTTTGAAATTTTTATTCTT-
1749344 A
60 A
* **
1749345 AGGAAAATTGATACTTTCAACTTTTCCTAAAAAAAATATTTTTTGAAATTTTTATTCCCA
1 AAGAAAATTGATACTTTCAACTTTTCCTAAAAAAAATATTTTTTGAAATTTTTATTCTTA
* *
1749405 AAGAAAATTGATACTTCCAATTTTT
1 AAGAAAATTGATACTTTCAACTTTT
1749430 TTTTAAAACC
Statistics
Matches: 127, Mismatches: 16, Indels: 15
0.80 0.10 0.09
Matches are distributed among these distances:
60 51 0.40
61 9 0.07
62 16 0.13
63 14 0.11
64 3 0.02
65 34 0.27
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (60 bp):
AAGAAAATTGATACTTTCAACTTTTCCTAAAAAAAATATTTTTTGAAATTTTTATTCTTA
Found at i:1749727 original size:59 final size:57
Alignment explanation
Indices: 1749664--1749942 Score: 171
Period size: 59 Copynumber: 4.7 Consensus size: 57
1749654 TTTTAATATT
*
1749664 ATATTTTTTGAAAGATTTTTTTTGAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAA
1 ATATTTTTTGAAA-ATTTTTTTTCAAGGAAAATTGATACTTTCAACTTTTTCT-AAAAA
* * *
1749723 ATA-TTTTTG-AAATTTTTATTCTCTTTAAAGAAAATTAATACTTTCAAATTTTTCTAAAAA
1 ATATTTTTTGAAAATTTTT-TT-TC---AAGGAAAATTGATACTTTCAACTTTTTCTAAAAA
*** * ** * * *
1749783 A-A-AAATT-AAAATTTTTACCTTCAATAAAAATTGATACTTTTAACTTTTCCTTAAAAC
1 ATATTTTTTGAAAATTTTT--TTTCAAGGAAAATTGATACTTTCAACTTTTTC-TAAAAA
* * *
1749840 ATATTTTTT-AAACTTTTATTTTTTTAA-GAAAATTGACACTTTCAACTTTTT-TGAAAGAA
1 ATATTTTTTGAAA--ATT-TTTTTTCAAGGAAAATTGATACTTTCAACTTTTTCT-AAA-AA
*
1749899 TATATGTTTTTCTGAAAA-TTTTTTTCAAGGAAGATTGATACTTT
1 -ATA--TTTTT-TGAAAATTTTTTTTCAAGGAAAATTGATACTTT
1749943 AATTTCTCCT
Statistics
Matches: 168, Mismatches: 31, Indels: 40
0.70 0.13 0.17
Matches are distributed among these distances:
56 28 0.17
57 11 0.07
58 11 0.07
59 42 0.25
60 22 0.13
61 42 0.25
62 8 0.05
63 1 0.01
64 3 0.02
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (57 bp):
ATATTTTTTGAAAATTTTTTTTCAAGGAAAATTGATACTTTCAACTTTTTCTAAAAA
Found at i:1750614 original size:20 final size:20
Alignment explanation
Indices: 1750576--1750614 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1750566 ACCAAAAAAC
**
1750576 TCACCAAAAATTTTGAATTT
1 TCACCAAAAATTTCAAATTT
1750596 TCACCAAAAATTTCAAATT
1 TCACCAAAAATTTCAAATT
1750615 AATTTTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (20 bp):
TCACCAAAAATTTCAAATTT
Found at i:1755335 original size:12 final size:12
Alignment explanation
Indices: 1755315--1755344 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1755305 ATTTGGAAAT
*
1755315 GATGTTGATGCC
1 GATGCTGATGCC
1755327 GATGCTGATGCC
1 GATGCTGATGCC
1755339 GATGCT
1 GATGCT
1755345 AATGACAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (12 bp):
GATGCTGATGCC
Found at i:1757734 original size:72 final size:72
Alignment explanation
Indices: 1757638--1757807 Score: 268
Period size: 72 Copynumber: 2.4 Consensus size: 72
1757628 CACAAGCTTC
* * * * *
1757638 GTCATGTTTCCAATTGAAGCAGGGATTGAACCAGAGAACATATTTTGATCAAGGTCGAGAGTAGA
1 GTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAAAACATATTTTGATCAAGGTAGAGAGTAGA
1757703 TAAGCTG
66 TAAGCTG
* * *
1757710 GTCAATTTTCCTATGGAAGCAGGGATTGAACCATAAAACATATTTTGATGAAGGTAGAGAGTAGA
1 GTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAAAACATATTTTGATCAAGGTAGAGAGTAGA
1757775 TAAGCTG
66 TAAGCTG
1757782 GTCAAGTTTCCTATGGAAGCAGGGAT
1 GTCAAGTTTCCTATGGAAGCAGGGAT
1757808 GACACCGGTG
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 89 1.00
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (72 bp):
GTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAAAACATATTTTGATCAAGGTAGAGAGTAGA
TAAGCTG
Found at i:1760927 original size:26 final size:28
Alignment explanation
Indices: 1760862--1760927 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 28
1760852 GTTTTTTCAT
1760862 AATATATTC-TTATGTTATTTTATTTAAA
1 AATATATTCTTTATGTTA-TTTATTTAAA
* *
1760890 AATA-ATTTTTTAT-TTA-TTATTTGAA
1 AATATATTCTTTATGTTATTTATTTAAA
1760915 AATATATTCTTTA
1 AATATATTCTTTA
1760928 ATTTGTAAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 12 0.36
26 7 0.21
27 6 0.18
28 8 0.24
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (28 bp):
AATATATTCTTTATGTTATTTATTTAAA
Found at i:1762189 original size:25 final size:25
Alignment explanation
Indices: 1762125--1762189 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
1762115 GTACATAGAG
* *
1762125 AAATTAACAAATTAAATTTTATATA
1 AAATTAAAAAATTAAATTTTATAAA
* **
1762150 ATA-TAAAATTTTTAAATTTTATAAA
1 AAATTAAAA-AATTAAATTTTATAAA
1762175 AAATTAAAAAATTAA
1 AAATTAAAAAATTAA
1762190 CATGTATTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
24 4 0.13
25 21 0.70
26 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
AAATTAAAAAATTAAATTTTATAAA
Found at i:1762587 original size:18 final size:17
Alignment explanation
Indices: 1762566--1762665 Score: 73
Period size: 18 Copynumber: 5.8 Consensus size: 17
1762556 TAGCATACCC
1762566 TATTCTTATATTATAGTA
1 TATT-TTATATTATAGTA
*
1762584 TATTATTATAGTATAGTA
1 TATT-TTATATTATAGTA
*
1762602 TATTGTTATAATATA-T-
1 TATT-TTATATTATAGTA
*
1762618 TATTATATTATTATAGTA
1 TATTTTA-TATTATAGTA
* * *
1762636 TAATATATTATTATGGTA
1 TATTTTA-TATTATAGTA
1762654 TA--TTATATTATA
1 TATTTTATATTATA
1762666 TTCTATTCTA
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
15 8 0.12
16 12 0.17
17 2 0.03
18 47 0.68
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (17 bp):
TATTTTATATTATAGTA
Found at i:1762592 original size:13 final size:13
Alignment explanation
Indices: 1762574--1762659 Score: 68
Period size: 13 Copynumber: 6.2 Consensus size: 13
1762564 CCTATTCTTA
1762574 TATTATAGTATAT
1 TATTATAGTATAT
1762587 TATTATAGTATAGT
1 TATTATAGTATA-T
*
1762601 ATATTGTTATAATATAT
1 -TA---TTATAGTATAT
1762618 TATTATA-T-TAT
1 TATTATAGTATAT
*
1762629 TATAGTATAATATAT
1 TAT--TATAGTATAT
*
1762644 TATTATGGTATAT
1 TATTATAGTATAT
1762657 TAT
1 TAT
1762660 ATTATATTCT
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
11 6 0.10
12 1 0.02
13 32 0.52
14 2 0.03
15 8 0.13
16 2 0.03
17 1 0.02
18 9 0.15
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.53
Consensus pattern (13 bp):
TATTATAGTATAT
Found at i:1762611 original size:36 final size:36
Alignment explanation
Indices: 1762536--1762664 Score: 123
Period size: 36 Copynumber: 3.4 Consensus size: 36
1762526 TTTGTAGTAT
* *** *
1762536 TATTATTATTATTATTATTATAGCATACCCTATTCTTA
1 TATTA-TATTA-TATTATTATAGTATAATATATTATTA
* * *
1762574 TATTATAGTATATTATTATAGTATAGTATATTGTTA
1 TATTATATTATATTATTATAGTATAATATATTATTA
1762610 TAATATATTATTATATTATTATAGTATAATATATTATTA
1 T-AT-TA-TATTATATTATTATAGTATAATATATTATTA
**
1762649 TGGTATATTATATTAT
1 TATTATATTATATTAT
1762665 ATTCTATTCT
Statistics
Matches: 77, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
36 33 0.43
37 8 0.10
38 7 0.09
39 29 0.38
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (36 bp):
TATTATATTATATTATTATAGTATAATATATTATTA
Found at i:1762624 original size:26 final size:25
Alignment explanation
Indices: 1762595--1762666 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
1762585 ATTATTATAG
1762595 TATAGTATATTGTTATAATATATTAT
1 TATAGTATATTG-TATAATATATTAT
* *
1762621 TATATTATTATAGTATAATATATTAT
1 TATAGTA-TATTGTATAATATATTAT
* * *
1762647 TATGGTATATTATATTATAT
1 TATAGTATATTGTATAATAT
1762667 TCTATTCTAT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
25 10 0.26
26 24 0.63
27 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (25 bp):
TATAGTATATTGTATAATATATTAT
Found at i:1762625 original size:39 final size:38
Alignment explanation
Indices: 1762539--1762659 Score: 120
Period size: 39 Copynumber: 3.2 Consensus size: 38
1762529 GTAGTATTAT
* *** *
1762539 TATTATTATTATTATTATAGCATACCCTATTCTTATAT-
1 TATTATTA-TATTATTATAGTATAATATATTATTATATA
* * *
1762577 TA-TAGTATATTATTATAGTATAGTATATTGTTATAATA
1 TATTATTATATTATTATAGTATAATATATTATTAT-ATA
*
1762615 TATTATTATATTATTATAGTATAATATATTATTATGGTA
1 TATTATTATATTATTATAGTATAATATATTATTAT-ATA
1762654 TATTAT
1 TATTAT
1762660 ATTATATTCT
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
36 22 0.32
37 6 0.09
38 4 0.06
39 37 0.54
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.53
Consensus pattern (38 bp):
TATTATTATATTATTATAGTATAATATATTATTATATA
Found at i:1762660 original size:5 final size:5
Alignment explanation
Indices: 1762571--1762677 Score: 53
Period size: 5 Copynumber: 21.4 Consensus size: 5
1762561 TACCCTATTC
* * * * *
1762571 TTATA TTATA GTATA -T-TA TTATA GTATA GTATA -T-TG TTATA ATATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
* *
1762617 TTAT- TATATTA TTATA GTATA ATATA TTATTA TGGTATA TTATA TTATA
1 TTATA T-TA-TA TTATA TTATA TTATA TTA-TA T--TATA TTATA TTATA
* *
1762666 TTCTA TTCTA TT
1 TTATA TTATA TT
1762678 TTTTTTTTAT
Statistics
Matches: 82, Mismatches: 10, Indels: 20
0.73 0.09 0.18
Matches are distributed among these distances:
3 3 0.04
4 5 0.06
5 62 0.76
6 6 0.07
7 4 0.05
8 2 0.02
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (5 bp):
TTATA
Found at i:1763674 original size:17 final size:17
Alignment explanation
Indices: 1763652--1763685 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1763642 TTTTATTTTT
*
1763652 GGAAAATAATAAAATAA
1 GGAAAAAAATAAAATAA
1763669 GGAAAAAAATAAAATAA
1 GGAAAAAAATAAAATAA
1763686 AAATTTTTTT
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:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (17 bp):
GGAAAAAAATAAAATAA
Found at i:1766597 original size:17 final size:16
Alignment explanation
Indices: 1766551--1766599 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
1766541 ATGTGGCATT
1766551 ATAAT-TTTTTATTTA
1 ATAATATTTTTATTTA
* *
1766566 ATGATTTTTTATATTTA
1 ATAATATTTT-TATTTA
1766583 ATAAATATTTTTATTTA
1 AT-AATATTTTTATTTA
1766600 TTTTTTTACG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 4 0.14
16 4 0.14
17 14 0.50
18 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
ATAATATTTTTATTTA
Found at i:1767904 original size:29 final size:30
Alignment explanation
Indices: 1767865--1767932 Score: 122
Period size: 29 Copynumber: 2.3 Consensus size: 30
1767855 AGACACAAAG
1767865 AAAAAT-ACAAAAATAGAGAACTCG-AAAA
1 AAAAATCACAAAAATAGAGAACTCGAAAAA
1767893 AAAAATCACAAAAATAGAGAACTCGAAAAA
1 AAAAATCACAAAAATAGAGAACTCGAAAAA
1767923 AAAAATCACA
1 AAAAATCACA
1767933 TGCAAAAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 6 0.16
29 18 0.47
30 14 0.37
ACGTcount: A:0.68, C:0.13, G:0.09, T:0.10
Consensus pattern (30 bp):
AAAAATCACAAAAATAGAGAACTCGAAAAA
Found at i:1768481 original size:17 final size:18
Alignment explanation
Indices: 1768442--1768484 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
1768432 ATGTTGTTTC
*
1768442 TATTTT-TTTGTATTTTG
1 TATTTTATTTGTATTTAG
1768459 TA-TTTATTT-TATTTAG
1 TATTTTATTTGTATTTAG
1768475 TATTTTATTT
1 TATTTTATTT
1768485 ATGTGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.19, C:0.00, G:0.07, T:0.74
Consensus pattern (18 bp):
TATTTTATTTGTATTTAG
Found at i:1770649 original size:19 final size:20
Alignment explanation
Indices: 1770613--1770650 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1770603 ATTATTTAAT
*
1770613 ATTTATAAAATTAATAAATA
1 ATTTATAAAATCAATAAATA
*
1770633 ATTTA-AAAATCAGTAAAT
1 ATTTATAAAATCAATAAAT
1770651 TTTTTTATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTTATAAAATCAATAAATA
Found at i:1775389 original size:16 final size:15
Alignment explanation
Indices: 1775345--1775400 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
1775335 TTAAAATTCT
1775345 TTTAATTATTTAAAA
1 TTTAATTATTTAAAA
* *
1775360 TTAAAATATATTAAACA
1 TTTAATTAT-TTAAA-A
1775377 TTTAATTATTT-AAA
1 TTTAATTATTTAAAA
1775391 TTT-ATTATTT
1 TTTAATTATTT
1775401 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 7 0.20
14 4 0.11
15 9 0.26
16 7 0.20
17 8 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTAATTATTTAAAA
Found at i:1775435 original size:18 final size:16
Alignment explanation
Indices: 1775402--1775439 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
1775392 TTATTATTTT
1775402 ATTTTTAAAATAATTA
1 ATTTTTAAAATAATTA
1775418 ATTTTTAATAATTAATTA
1 ATTTTTAA-AA-TAATTA
1775436 ATTT
1 ATTT
1775440 AATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTTTAAAATAATTA
Found at i:1776922 original size:60 final size:62
Alignment explanation
Indices: 1776846--1776960 Score: 198
Period size: 60 Copynumber: 1.9 Consensus size: 62
1776836 ATAATTAACA
*
1776846 AAATATATATTCCTTTGAACTATCCAAATCATGGCTTTTTTCTT-ATAT-ATTCCTTTGAAC
1 AAATATATATTCCTTTGAACTATCCAAATCATGGCTTCTTTCTTAATATCATTCCTTTGAAC
*
1776906 AAATATATATTCCTTTGAACTATCCAAATTATGGCTTCTTTCTTAATATCATTCC
1 AAATATATATTCCTTTGAACTATCCAAATCATGGCTTCTTTCTTAATATCATTCC
1776961 AAGTCTTGTT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 42 0.82
61 4 0.08
62 5 0.10
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.44
Consensus pattern (62 bp):
AAATATATATTCCTTTGAACTATCCAAATCATGGCTTCTTTCTTAATATCATTCCTTTGAAC
Found at i:1779720 original size:50 final size:50
Alignment explanation
Indices: 1779615--1779720 Score: 133
Period size: 50 Copynumber: 2.1 Consensus size: 50
1779605 TCCATAATTG
* * * *
1779615 ATTCAACCATTAAACCATAGAATCGAATCTTGGATTCTCAAAATTGAGAT
1 ATTCAACCACTAAACCATAAAATCAAATCTTGGATTCTCAAAATTAAGAT
* **
1779665 CTTCAACCACTAAACCATAAAATCAAATCATT-GATTCTCTGAATTAAGAT
1 ATTCAACCACTAAACCATAAAATCAAATC-TTGGATTCTCAAAATTAAGAT
1779715 ATTCAA
1 ATTCAA
1779721 ATTCCCACAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 45 0.96
51 2 0.04
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.30
Consensus pattern (50 bp):
ATTCAACCACTAAACCATAAAATCAAATCTTGGATTCTCAAAATTAAGAT
Found at i:1780481 original size:84 final size:85
Alignment explanation
Indices: 1780364--1780552 Score: 229
Period size: 85 Copynumber: 2.2 Consensus size: 85
1780354 ATCATGCCCA
* * * * * * * *
1780364 AAAAACTTGGAGACTACGCTTAGAGGTCTTACAAATCTCAACT-TTAAAACAGATTTAGCTCAGA
1 AAAAACTTAGAGATTATGCCTAAAGGTCTTACAAATCTCAACTCTAAAAACAGATTTAGCTAAAA
* * *
1780428 AGACTTACGAATCTTGC-CTG
66 AAACTTACAAATCTTACTC-G
*
1780448 AAAAACTTAGAGATTATGCCTAAAGGTCTTACAAATCTCAACTCTAAAAATAGATTTAGCTAAAA
1 AAAAACTTAGAGATTATGCCTAAAGGTCTTACAAATCTCAACTCTAAAAACAGATTTAGCTAAAA
1780513 AAACTTACAAATCTTACTCG
66 AAACTTACAAATCTTACTCG
**
1780533 AAGGACTTAGAGATTATGCC
1 AAAAACTTAGAGATTATGCC
1780553 ATGACGTCTT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
84 38 0.43
85 50 0.56
86 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (85 bp):
AAAAACTTAGAGATTATGCCTAAAGGTCTTACAAATCTCAACTCTAAAAACAGATTTAGCTAAAA
AAACTTACAAATCTTACTCG
Found at i:1781311 original size:121 final size:116
Alignment explanation
Indices: 1781161--1781389 Score: 395
Period size: 116 Copynumber: 1.9 Consensus size: 116
1781151 TTTTGTTCAG
1781161 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTCTTTTAAGGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTA--TTTC---TAAGGA
*
1781226 AAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGA
61 AAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTTATTTCTGA
1781282 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATT
*
1781347 GATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGGAATTT
66 GATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTT
1781390 TTTATTTTTA
Statistics
Matches: 106, Mismatches: 2, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
116 52 0.49
119 4 0.04
121 50 0.47
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (116 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATT
GATACTTTCAACTTTTCCCTAAAAATATATTTTTTTGAAATTTATTTCTGA
Found at i:1781348 original size:57 final size:57
Alignment explanation
Indices: 1781161--1781380 Score: 332
Period size: 57 Copynumber: 3.7 Consensus size: 57
1781151 TTTTGTTCAG
1781161 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTA--TTTC---TAA
* * *
1781223 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTGGAAATTTATTTCTAA
1781282 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
*
1781339 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATAT-TTTTT
1781381 TTGGAATTTT
Statistics
Matches: 148, Mismatches: 7, Indels: 10
0.90 0.04 0.06
Matches are distributed among these distances:
57 55 0.37
58 5 0.03
59 36 0.24
62 38 0.26
64 14 0.09
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:1781478 original size:12 final size:11
Alignment explanation
Indices: 1781458--1781518 Score: 68
Period size: 11 Copynumber: 5.2 Consensus size: 11
1781448 AACCTAATCT
*
1781458 AATAAATAAAA
1 AATAAAAAAAA
1781469 AATAAAATAAACA
1 AATAAAA-AAA-A
*
1781482 AATAAACAAAGA
1 AATAAA-AAAAA
1781494 AATAAAAAAAAA
1 AAT-AAAAAAAA
1781506 AATAAAAAAAA
1 AATAAAAAAAA
1781517 AA
1 AA
1781519 CAACCTGGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
11 16 0.37
12 14 0.33
13 12 0.28
14 1 0.02
ACGTcount: A:0.84, C:0.03, G:0.02, T:0.11
Consensus pattern (11 bp):
AATAAAAAAAA
Found at i:1781502 original size:32 final size:31
Alignment explanation
Indices: 1781461--1781521 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
1781451 CTAATCTAAT
* *
1781461 AAATAAAAAATAAAATAAACAAATAAACAAAG
1 AAATAAAAAAAAAAATAAA-AAAAAAACAAAG
1781493 AAATAAAAAAAAAAATAAAAAAAAAACAA
1 AAATAAAAAAAAAAATAAAAAAAAAACAA
1781522 CCTGGAGCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.84, C:0.05, G:0.02, T:0.10
Consensus pattern (31 bp):
AAATAAAAAAAAAAATAAAAAAAAAACAAAG
Found at i:1781869 original size:20 final size:20
Alignment explanation
Indices: 1781844--1781881 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1781834 GAACACCGGT
*
1781844 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
1781864 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
1781882 CATCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:1781964 original size:19 final size:19
Alignment explanation
Indices: 1781922--1781969 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1781912 TCTGGGATTC
* *
1781922 TTCGCCGGAAACTGGACTG
1 TTCGCCGGAAACTGCAATG
* *
1781941 GTCGCCGGAAACTTCAATG
1 TTCGCCGGAAACTGCAATG
1781960 TTCGCCGGAA
1 TTCGCCGGAA
1781970 TTGTTGCCGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.21
Consensus pattern (19 bp):
TTCGCCGGAAACTGCAATG
Found at i:1781982 original size:31 final size:31
Alignment explanation
Indices: 1781942--1782011 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1781932 ACTGGACTGG
* *
1781942 TCGCCGGAAACTTC-AATGTTCGCCGGAATTGT
1 TCGCCGGAAAATTCAAAT-TTCGCCGAAATT-T
1781974 T-GCCGGAAAATTCAAATTTCGCCGAAATTT
1 TCGCCGGAAAATTCAAATTTCGCCGAAATTT
1782004 TCGCCGGA
1 TCGCCGGA
1782012 TTCTGGAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 2 0.06
31 28 0.82
32 4 0.12
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (31 bp):
TCGCCGGAAAATTCAAATTTCGCCGAAATTT
Found at i:1789359 original size:17 final size:18
Alignment explanation
Indices: 1789339--1789373 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1789329 TTTTTTTTTT
1789339 AAAAATT-TATTTTCAAG
1 AAAAATTATATTTTCAAG
1789356 AAAAATTGATATTTTCAA
1 AAAAATT-ATATTTTCAA
1789374 CTTTTCCTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAAATTATATTTTCAAG
Found at i:1789576 original size:60 final size:60
Alignment explanation
Indices: 1789223--1789584 Score: 310
Period size: 60 Copynumber: 5.8 Consensus size: 60
1789213 TTATTTTTCA
* * ** *
1789223 TATTTTCTTAAGGAAAATTGATACTTTCAACTTTTCCT-TAAAATGCCTTTTTTTTAGAA-TTT
1 TATTTTC--AAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-AC-TTTTTCAAAAATTTT
* * * *
1789285 TATTTTTAAGGAAAATTGGTA-TTTCCAACTTTTCCTC-AAAATGCTTTTTTTTTTAAAAA--TT
1 TATTTTCAAGGAAAATTGATACTTT-CAACTTTTCCTCAAAAATAC----TTTTTCAAAAATTTT
* *
1789346 TATTTTCAAGAAAAATTGATATTTTCAACTTTTCCTCAAAAATATATATCTTTTT-AAAATTTTT
1 TATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTC--AAA-A-ATA-CTTTTTCAAAA-----
1789410 ATTTTT
56 A-TTTT
* * **
1789416 TATCTTCAA-GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAATTTT
1 TATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTCAAAAATTTT
*
1789475 TATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATGCTTTTTCAAAAATTTT
1 TATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTCAAAAATTTT
* *
1789535 TATTTTCAAGGAAAATTCATACTTTCAACTTTGT-CTCAAAAATATTTTTT
1 TATTTTCAAGGAAAATTGATACTTTCAACTTT-TCCTCAAAAATACTTTTT
1789585 TAATTTTGTT
Statistics
Matches: 255, Mismatches: 22, Indels: 48
0.78 0.07 0.15
Matches are distributed among these distances:
59 16 0.06
60 121 0.47
61 33 0.13
62 23 0.09
63 5 0.02
64 7 0.03
65 7 0.03
66 3 0.01
67 5 0.02
69 25 0.10
70 10 0.04
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (60 bp):
TATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATACTTTTTCAAAAATTTT
Found at i:1791081 original size:42 final size:42
Alignment explanation
Indices: 1791058--1791335 Score: 326
Period size: 42 Copynumber: 6.6 Consensus size: 42
1791048 AGGCTCAATG
* *
1791058 ACTTTCAAAAATAAAAATGCTCCTCTAAACAGAGGC-ACCACA
1 ACTTTGAAAAAT-AAAATGCTCCTCTAAATAGAGGCAACCACA
* * * * * * **
1791100 ACTTTGGAAAGTAAATTGCTTCTCTAAACAGAGG-TACCATG
1 ACTTTGAAAAATAAAATGCTCCTCTAAATAGAGGCAACCACA
* * *
1791141 ACTTTAGAAAAATAAATTGCTCCTCCAAATAGAGGCAACCACG
1 ACTTT-GAAAAATAAAATGCTCCTCTAAATAGAGGCAACCACA
* *
1791184 ACTTTGAAAAATAAATTACTCCTCTAAATAGAGGCAACCACA
1 ACTTTGAAAAATAAAATGCTCCTCTAAATAGAGGCAACCACA
* *
1791226 ACTTTGAAAAATAAAATGCTCTTCTAAATAGAGGCAACCATA
1 ACTTTGAAAAATAAAATGCTCCTCTAAATAGAGGCAACCACA
* *
1791268 ACTTTGAAAAATAAAATGCCCCTCTAAATAGAGGCAACCATA
1 ACTTTGAAAAATAAAATGCTCCTCTAAATAGAGGCAACCACA
*
1791310 ACTTTAGAAAAAATAAAAGGCTCCTC
1 ACTTT-G-AAAAATAAAATGCTCCTC
1791336 AATAATCATG
Statistics
Matches: 206, Mismatches: 25, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
41 29 0.14
42 150 0.73
43 11 0.05
44 16 0.08
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.23
Consensus pattern (42 bp):
ACTTTGAAAAATAAAATGCTCCTCTAAATAGAGGCAACCACA
Found at i:1791563 original size:41 final size:41
Alignment explanation
Indices: 1791440--1791565 Score: 189
Period size: 41 Copynumber: 3.0 Consensus size: 41
1791430 ACCTTTCAGC
* *
1791440 TTTGCCTAAAATTCATTGAAATTTGATTCTCAAAATTTTAGC
1 TTTGCC-AAAATTCACTGAAATTTGATTCTCAAAATTTTAGT
* * * *
1791482 TTTGCTAGAATTCACTGAAATTTGATTTTTAAAATTTTAGT
1 TTTGCCAAAATTCACTGAAATTTGATTCTCAAAATTTTAGT
1791523 TTTGCCAAAATTCACTGAAATTTGATTCTCAAAATTTTAGT
1 TTTGCCAAAATTCACTGAAATTTGATTCTCAAAATTTTAGT
1791564 TT
1 TT
1791566 CTCAATATTC
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 69 0.93
42 5 0.07
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (41 bp):
TTTGCCAAAATTCACTGAAATTTGATTCTCAAAATTTTAGT
Found at i:1791823 original size:21 final size:21
Alignment explanation
Indices: 1791797--1791858 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1791787 GGTTTCACAT
1791797 CTCAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
*
1791818 CTCAAAGATTCTCATTTG-AG
1 CTCAAAGATTCTCATTTGAAA
* *
1791838 TTGAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
1791859 TCAGGACTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:1791846 original size:20 final size:20
Alignment explanation
Indices: 1791797--1791857 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1791787 GGTTTCACAT
1791797 CTCAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTG-AA
*
1791818 CTCAAAGATTCTCATTTGAG
1 CTCAAAGATTCTCATTTGAA
* *
1791838 TTGAAAGATTCTCATTTGAA
1 CTCAAAGATTCTCATTTGAA
1791858 ATCAGGACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (20 bp):
CTCAAAGATTCTCATTTGAA
Found at i:1797276 original size:59 final size:60
Alignment explanation
Indices: 1797167--1797514 Score: 217
Period size: 60 Copynumber: 5.5 Consensus size: 60
1797157 TTTATACAAG
* * *
1797167 AAAAATTGATACTTTCAACTTTTCTTTAAAGCATTTTAAGGTTTTATTTTTCATA-TTT-TTTTT
1 AAAAATTGATACTTTCAACTTTTCCTCAAA--A-TTT---GTTTT-TTTTTCAAATTTTATTTTT
1797230 AA
59 AA
* *
1797232 AAAAACTTGATACTTTCAACTTTTCCTTAAAATTTGTTTTTTTTTTAGAATTTTATTTTTAA
1 AAAAA-TTGATACTTTCAACTTTTCCTCAAAATTTGTTTTTTTTTCA-AATTTTATTTTTAA
* * * * **
1797294 GGAAAATTGGTATTTTCAACATTTCCTCAAAA--TGCTTTTTTTTGGAAATTTTATTTTTAA
1 -AAAAATTGATACTTTCAACTTTTCCTCAAAATTTG-TTTTTTTTTCAAATTTTATTTTTAA
* * * * * *
1797354 AAAAATTGATATTTTCTAA-TTTTCCTCAAAAATATATATCTTTTTAAAATTTTTATTTTTTATC
1 AAAAATTGATACTTTC-AACTTTTCCTC-AAAATTTGTTTTTTTTTCAAA-TTTTA-TTTTTA--
1797418 CTCA
60 ---A
* ** * *
1797422 AGGAAAATTGATACTTTCAACTTTTCCTCAAAA-ATG-TTTTTTTAAAAATTTTTATTTTCACG
1 A--AAAATTGATACTTTCAACTTTTCCTCAAAATTTGTTTTTTTTTCAAA-TTTTATTTTTA-A
1797484 AAAAATTGATACTTTCAAC-TTTCTCTCAAAA
1 AAAAATTGATACTTTCAACTTTTC-CTCAAAA
1797515 ATATTTTTTT
Statistics
Matches: 237, Mismatches: 25, Indels: 47
0.77 0.08 0.15
Matches are distributed among these distances:
59 31 0.13
60 53 0.22
61 21 0.09
62 37 0.16
63 13 0.05
64 1 0.00
65 5 0.02
66 29 0.12
67 15 0.06
68 4 0.02
69 6 0.03
70 22 0.09
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.49
Consensus pattern (60 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAATTTGTTTTTTTTTCAAATTTTATTTTTAA
Found at i:1810102 original size:66 final size:66
Alignment explanation
Indices: 1810002--1810237 Score: 193
Period size: 58 Copynumber: 3.8 Consensus size: 66
1809992 TTTTTTAAAA
* * *
1810002 TTTATTTTCAAGAAAAATTGATATTTTCAACTTTT-C-AAAAATATATATCTTTTTAAAATTTTT
1 TTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAA-ATAT-T-TTTTGAAAATTTTT
1810065 ATTT
63 ATTT
*
1810069 TTTATCTTCAAG-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTTTA--
1 TTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTGAAAATTTTTATT
1810131 -
66 T
* * ** *
1810131 --T-T-TTCAAGGAAAATT-ATACTTTCAACTTTTCCTCAAAAATGCTTTTTCAAAA-----A-T
1 TTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTGAAAATTTTTATT
1810185 T
66 T
* * * *
1810186 TTTATTTTCAAGGAAAATTCATACTTTCAACTTTGT-CTCAAAAATATTTTTT
1 TTTATCTTCAAGAAAAATTGATACTTTCAACTTT-TCCTAAAAAATATTTTTT
1810238 TAATTTTGTT
Statistics
Matches: 149, Mismatches: 9, Indels: 29
0.80 0.05 0.16
Matches are distributed among these distances:
53 1 0.01
57 1 0.01
58 41 0.28
59 20 0.13
60 29 0.19
61 1 0.01
65 14 0.09
66 22 0.15
67 16 0.11
68 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (66 bp):
TTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATATTTTTTGAAAATTTTTATT
T
Found at i:1810128 original size:59 final size:59
Alignment explanation
Indices: 1810067--1810240 Score: 255
Period size: 59 Copynumber: 3.0 Consensus size: 59
1810057 AAATTTTTAT
* *
1810067 TTTTTATCTTCAA-GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAA
1 TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAA
* **
1810125 TTTTTATTTTCAAGGAAAATT-ATACTTTCAACTTTTCCTCAAAAATGCTTTTTCAAAAA
1 TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTAAAA
*
1810184 TTTTTATTTTCAAGGAAAATTCATACTTTCAACTTTGT-CTCAAAAATATTTTTTTAA
1 TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTT-TCCTCAAAAATATTTTTTTAA
1810241 TTTTGTTTCA
Statistics
Matches: 105, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
58 37 0.35
59 44 0.42
60 23 0.22
61 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (59 bp):
TTTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAA
Found at i:1810129 original size:58 final size:58
Alignment explanation
Indices: 1809882--1810237 Score: 278
Period size: 60 Copynumber: 5.8 Consensus size: 58
1809872 TTATTTTTCA
* * * *
1809882 TATTTTCTTAAGGAAAATTGATACTTTCAACTTTTCCT-TAAAATGCCTTTTTTTTAGAA-TTT
1 TATTTTC--AAGGAAAATT-ATACTTTCAACTTTTCCTCAAAAAT---ATTTTTTAAAAATTTT
* * * * *
1809944 TATTTTTAAGGAAAATTGGTA-TTTCCAACTTTTCCTCAAAATGCTTTTTTTTTTAAAA--TT
1 TATTTTCAAGGAAAATT-ATACTTT-CAACTTTTCCTCAAAA---ATATTTTTTAAAAATTTT
* * **
1810004 TATTTTCAAGAAAAATTGATATTTTCAACTTTT-CAAAAATATATATCTTTTTAAAATTTTTATT
1 TATTTTCAAGGAAAATT-ATACTTTCAACTTTTCCTCAAA-A-ATAT-TTTTTAAAA-----A-T
1810068 TTT
56 TTT
* *
1810071 TATCTTCAA-GAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAATTTT
1 TATTTTCAAGGAAAATT-ATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAATTTT
* *
1810129 TATTTTCAAGGAAAATTATACTTTCAACTTTTCCTCAAAAATGCTTTTTCAAAAATTTT
1 TATTTTCAAGGAAAATTATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTAAAAATTTT
1810188 TATTTTCAAGGAAAATTCATACTTTCAACTTTGT-CTCAAAAATATTTTTT
1 TATTTTCAAGGAAAATT-ATACTTTCAACTTT-TCCTCAAAAATATTTTTT
1810238 TAATTTTGTT
Statistics
Matches: 247, Mismatches: 26, Indels: 45
0.78 0.08 0.14
Matches are distributed among these distances:
58 39 0.16
59 58 0.23
60 76 0.31
61 18 0.07
62 6 0.02
64 10 0.04
65 4 0.02
66 22 0.09
67 14 0.06
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (58 bp):
TATTTTCAAGGAAAATTATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAATTTT
Found at i:1811722 original size:42 final size:41
Alignment explanation
Indices: 1811675--1811978 Score: 257
Period size: 42 Copynumber: 7.2 Consensus size: 41
1811665 AGTAAACAAA
* * * * *
1811675 GCTCCTCTAAACAGAGGCTCAATGACTTTCAAAAATAAAAAT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAT-AAATT
* * *
1811717 GCTCCTCTAAACAGAGGCACCACAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
* * *
1811758 GCTTCTCTAAACAGAGGTACCATGACTTTAGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAATAAATT
* *
1811800 GCTCCTCCAAATAGAGGCAACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGC-ACCACGACTTTGAAAAATAAATT
* * * *
1811842 ACTCCTCTAAATAGAGGCAACCACAACTTTGGGAAAAATAAAAT
1 GCTCCTCTAAACAGAGGC-ACCACGACTTT--GAAAAATAAATT
* * ** *
1811886 GCTCTTCTAAATAGAGGCAACCATAACTTTGAAAAATAAAAT
1 GCTCCTCTAAACAGAGGC-ACCACGACTTTGAAAAATAAATT
* * * ** **
1811928 ACCCCTCTAAATAGAGGCAACCATAACTTTAGAAAAAATAAAAG
1 GCTCCTCTAAACAGAGGC-ACCACGACTTT-G-AAAAATAAATT
1811972 GCTCCTC
1 GCTCCTC
1811979 AATAATCATG
Statistics
Matches: 224, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
41 29 0.13
42 131 0.58
43 11 0.05
44 53 0.24
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAATAAATT
Found at i:1811907 original size:86 final size:85
Alignment explanation
Indices: 1811705--1811978 Score: 336
Period size: 86 Copynumber: 3.2 Consensus size: 85
1811695 AATGACTTTC
* * * * *
1811705 AAAAATAAAAATGCTCCTCTAAACAGAGGC-ACCACAACTTTGGAAAGTAAATTGCTTCTCTAAA
1 AAAAAT-AAAATGCTCCTCTAAATAGAGGCAACCACAACTTTGAAAAATAAATTACTCCTCTAAA
* * * *
1811769 CAGAGG-TACCATGACTTTAG
65 TAGAGGCAACCATAACTTTGG
* * *
1811789 AAAAATAAATTGCTCCTCCAAATAGAGGCAACCACGACTTTGAAAAATAAATTACTCCTCTAAAT
1 AAAAATAAAATGCTCCTCTAAATAGAGGCAACCACAACTTTGAAAAATAAATTACTCCTCTAAAT
*
1811854 AGAGGCAACCACAACTTTGGG
66 AGAGGCAACCATAACTTT-GG
* * * *
1811875 AAAAATAAAATGCTCTTCTAAATAGAGGCAACCATAACTTTGAAAAATAAAATACCCCTCTAAAT
1 AAAAATAAAATGCTCCTCTAAATAGAGGCAACCACAACTTTGAAAAATAAATTACTCCTCTAAAT
*
1811940 AGAGGCAACCATAACTTTAGA
66 AGAGGCAACCATAACTTT-GG
*
1811961 AAAAATAAAAGGCTCCTC
1 AAAAATAAAATGCTCCTC
1811979 AATAATCATG
Statistics
Matches: 162, Mismatches: 25, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
83 20 0.12
84 40 0.25
85 9 0.06
86 93 0.57
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (85 bp):
AAAAATAAAATGCTCCTCTAAATAGAGGCAACCACAACTTTGAAAAATAAATTACTCCTCTAAAT
AGAGGCAACCATAACTTTGG
Found at i:1811942 original size:128 final size:125
Alignment explanation
Indices: 1811698--1811970 Score: 325
Period size: 128 Copynumber: 2.1 Consensus size: 125
1811688 GAGGCTCAAT
* * * *
1811698 GACTTTCAAAAATAAAAATGCTCCTCTAAACAGAGGCACCACAACTTTGGAAAGTAAATTGCTTC
1 GACTTTGAAAAAT-AAAATACTCCTCTAAACAGAGGCACCACAACTTTGGAAAATAAAATGCTTC
* * * * *
1811763 TCTAAACAGAGGTACCATGACTTTAGAAAAATAAATTGCTCCTCCAAATAGAGGCAACCAC
65 TCTAAACAGAGGAACCATAACTTTAGAAAAATAAAATACCCCTCCAAATAGAGGCAACCAC
* *
1811824 GACTTTGAAAAATAAATTACTCCTCTAAATAGAGGCAACCACAACTTTGGGAAAAATAAAATGC-
1 GACTTTGAAAAATAAAATACTCCTCTAAACAGAGGC-ACCACAACTTT-GG-AAAATAAAATGCT
* * *
1811888 TCTTCTAAATAGAGGCAACCATAACTTT-GAAAAATAAAATACCCCTCTAAATAGAGGCAACCAT
63 TC-TCTAAACAGAGG-AACCATAACTTTAGAAAAATAAAATACCCCTCCAAATAGAGGCAACCAC
*
1811952 AACTTTAGAAAAAATAAAA
1 GACTTT-G-AAAAATAAAA
1811971 GGCTCCTCAA
Statistics
Matches: 124, Mismatches: 16, Indels: 10
0.83 0.11 0.07
Matches are distributed among these distances:
125 20 0.16
126 23 0.19
127 4 0.03
128 57 0.46
129 11 0.09
130 9 0.07
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (125 bp):
GACTTTGAAAAATAAAATACTCCTCTAAACAGAGGCACCACAACTTTGGAAAATAAAATGCTTCT
CTAAACAGAGGAACCATAACTTTAGAAAAATAAAATACCCCTCCAAATAGAGGCAACCAC
Found at i:1812144 original size:41 final size:41
Alignment explanation
Indices: 1812075--1812205 Score: 190
Period size: 41 Copynumber: 3.2 Consensus size: 41
1812065 TCATAAGAAC
* *
1812075 ATTTCAGCTTTGCCTAAAATTCATTGAAATTTGATTCTCAAA
1 ATTTTAGCTTTG-CTAAAATTCACTGAAATTTGATTCTCAAA
* * *
1812117 ATTTTAGCTTTGCTAGAATTCACTGAAATTTGATTTTTAAA
1 ATTTTAGCTTTGCTAAAATTCACTGAAATTTGATTCTCAAA
* *
1812158 ATTTTAGTTTTGCCAAAATTCACTGAAATTTGATTCTCAAA
1 ATTTTAGCTTTGCTAAAATTCACTGAAATTTGATTCTCAAA
1812199 ATTTTAG
1 ATTTTAG
1812206 TTTCTCAATA
Statistics
Matches: 79, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 68 0.86
42 11 0.14
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.44
Consensus pattern (41 bp):
ATTTTAGCTTTGCTAAAATTCACTGAAATTTGATTCTCAAA
Found at i:1812466 original size:21 final size:21
Alignment explanation
Indices: 1812440--1812501 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1812430 GGTTTCACAT
1812440 CTCAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
*
1812461 CTCAAAGATTCTCATTTG-AG
1 CTCAAAGATTCTCATTTGAAA
* *
1812481 TTGAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTGAAA
1812502 TCAGGACTCC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:1812489 original size:20 final size:20
Alignment explanation
Indices: 1812440--1812500 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
1812430 GGTTTCACAT
1812440 CTCAAAGATTCTCATTTGAAA
1 CTCAAAGATTCTCATTTG-AA
*
1812461 CTCAAAGATTCTCATTTGAG
1 CTCAAAGATTCTCATTTGAA
* *
1812481 TTGAAAGATTCTCATTTGAA
1 CTCAAAGATTCTCATTTGAA
1812501 ATCAGGACTC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.36
Consensus pattern (20 bp):
CTCAAAGATTCTCATTTGAA
Found at i:1817923 original size:60 final size:59
Alignment explanation
Indices: 1817813--1818162 Score: 186
Period size: 60 Copynumber: 5.5 Consensus size: 59
1817803 TTTATACAAG
* * * *
1817813 AAAAATTGATACTTTCAACTTTTCTTTAAAGCATTTTAAGGTTTTATTTTTCATATTTTTTTTAA
1 AAAAATTGATACTTTCAACTTTTCCTCAAA--A-TTT---GTTTT-TTTTTAAAATTTTTTTTAA
1817878 A
59 A
* * *
1817879 AAAAACTTGATACTTTCAACTTTTCCTTAAAATTTGTTTTTTTTTTAGAATTTTATTTTTAAG
1 AAAAA-TTGATACTTTCAACTTTTCCTCAAAATTTG-TTTTTTTTTA-AAATTT-TTTTTAAA
* * * * *** *
1817942 GAAAATTGGTATTTTCAACCTTTCCTCAAAATGCCTTTTTTTTTAAAATTTTATTTTTAA
1 AAAAATTGATACTTTCAACTTTTCCTCAAAATTTGTTTTTTTTTAAAATTTT-TTTTAAA
* * * * *
1818002 AAAAATTGATATTTTCTAA-TTTTCCTCAAAAATATATATCTTTTTAAAATTTTTATTTTTTATC
1 AAAAATTGATACTTTC-AACTTTTCCTC-AAAATTTGTTTTTTTTTAAAA---TT-TTTTTTA--
1818066 CTCAA
58 ---AA
* * * * **
1818071 GGAAAATTGATACTTTCAACTTTTCCTCAAAA-ATG-CTTTTTTAAAAATTTTTATTTTCACG
1 -AAAAATTGATACTTTCAACTTTTCCTCAAAATTTGTTTTTTTTTAAAA-TTTT-TTTT-AAA
1818132 AAAAATTGATACTTTCAAC-TTTCTCTCAAAA
1 AAAAATTGATACTTTCAACTTTTC-CTCAAAA
1818163 ATATTTTTTT
Statistics
Matches: 229, Mismatches: 34, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
59 5 0.02
60 56 0.24
61 34 0.15
62 31 0.14
63 11 0.05
64 11 0.05
65 10 0.04
66 6 0.03
67 33 0.14
68 2 0.01
69 8 0.03
70 22 0.10
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.49
Consensus pattern (59 bp):
AAAAATTGATACTTTCAACTTTTCCTCAAAATTTGTTTTTTTTTAAAATTTTTTTTAAA
Found at i:1825480 original size:3 final size:3
Alignment explanation
Indices: 1825472--1825545 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
1825462 TTCATCTTAA
1825472 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1825520 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
1825546 TAATAATAAT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1825550 original size:3 final size:3
Alignment explanation
Indices: 1825544--1825587 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1825534 CAACAACAAC
1825544 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1825588 ATCTATGTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1834350 original size:72 final size:72
Alignment explanation
Indices: 1834272--1834783 Score: 164
Period size: 72 Copynumber: 7.1 Consensus size: 72
1834262 CCAAAGAAAT
1834272 TATTTTGACTCAAAGAAAAGTCAGAGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1 TATTTTGACTCAAAGAAAAGTCAGAGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1834337 GAAAACA
66 GAAAACA
* * * * ** * * ** **** * *
1834344 TATTTTGA-T-AAAGGTAGAGAGT-GGATAAACGGGTCAAG-TTTACTAT-GGAAGCAGGGATTG
1 TATTTTGACTCAAA-G-A-AAAGTCAGAGAGA-GATTTAAGCATCCCTATCTCTTG-AGGTATCG
* *
1834404 AACCAGAGAAA-T
61 ACCCAGA-AAACA
*** *
1834416 TATTTTGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1 TATTTTGACTCAAAGAAAAGTCAGAGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1834481 GAAAACA
66 GAAAACA
* * * * **** *
1834488 TATTTTGA-T-AAAGGTAGAGAGT--G-GATAGACTGGTCAAG-TTCCCTAT-GGAAGCAGGGAT
1 TATTTTGACTCAAA-G-A-AAAGTCAGAGAGAGA-T--TTAAGCATCCCTATCTCTTG-AGGTAT
* * *
1834546 TGAACCAGAGAAA-T
59 CGACCCAGA-AAACA
** * * * *
1834560 TATTTTGACTCATCGCAAAGTCAGTGAGAGATTTAAGCATGCCAATCTCTTGAGGTATCGACCCA
1 TATTTTGACTCAAAGAAAAGTCAGAGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
1834625 GAAAACA
66 GAAAACA
* * * * * * * * * **** * *
1834632 TATTTTGA-TCAAGGTAGAGAACAGATAG-GCTGATCAAG-TTTCCTAT-GGAAGCAGGGATTGA
1 TATTTTGACTCAAAGAAAAG-TCAGAGAGAGAT--TTAAGCATCCCTATCTCTTG-AGGTATCGA
* *
1834693 ACCAGAGAAA-T
62 CCCAGA-AAACA
** *
1834704 TATTTTGACTCAAATCAAAGTCAGTA-AGAGATTTAAGCATGCCTATCTCTTGAGGTATCGACCC
1 TATTTTGACTCAAAGAAAAGTCAG-AGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCC
1834768 AGAAAACA
65 AGAAAACA
1834776 TATTTTGA
1 TATTTTGA
1834784 TAAAGGTAGA
Statistics
Matches: 292, Mismatches: 109, Indels: 78
0.61 0.23 0.16
Matches are distributed among these distances:
70 10 0.03
71 47 0.16
72 179 0.61
73 48 0.16
74 8 0.03
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.27
Consensus pattern (72 bp):
TATTTTGACTCAAAGAAAAGTCAGAGAGAGATTTAAGCATCCCTATCTCTTGAGGTATCGACCCA
GAAAACA
Found at i:1834450 original size:144 final size:144
Alignment explanation
Indices: 1834190--1835113 Score: 1528
Period size: 144 Copynumber: 6.4 Consensus size: 144
1834180 AGGGATTGAA
* * *
1834190 CCAGAGAACATATTTTGATGAAGATAGAGAGTGGATA-AGCTGGTCAAGTTTCCTATGGAAGCAG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGA-CTGGTCAAGTTTCCTATGGAAGCAG
* * * *
1834254 GGATTGAACCAAAGAAATTATTTTGACTCAAAGAAAAGTCAGAGAGAGATTTAAGCATCCCTATC
65 GGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATCCCTATC
1834319 TCTTGAGGTATCGAC
130 TCTTGAGGTATCGAC
* * *
1834334 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAAACGGGTCAAGTTTACTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
*
1834399 GATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATTTAAGCATCCCTATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATCCCTATCT
1834464 CTTGAGGTATCGAC
131 CTTGAGGTATCGAC
*
1834478 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTCCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
* * *
1834543 GATTGAACCAGAGAAATTATTTTGACTCATCGCAAAGTCAGTGAGAGATTTAAGCATGCCAATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATCCCTATCT
1834608 CTTGAGGTATCGAC
131 CTTGAGGTATCGAC
* *** * *
1834622 CCAGAAAACATATTTTGATCAAGGTAGAGAACAGATAGGCTGATCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
** * *
1834687 GATTGAACCAGAGAAATTATTTTGACTCAAATCAAAGTCAGTAAGAGATTTAAGCATGCCTATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATCCCTATCT
1834752 CTTGAGGTATCGAC
131 CTTGAGGTATCGAC
1834766 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
* *
1834831 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTTAAGCATGCCTATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATCCCTATCT
1834896 CTTGAGGTATCGAC
131 CTTGAGGTATCGAC
* *
1834910 CCAGAAAACATATTTTGATGAAGGTAGAGACTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
*
1834975 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCC-ATC
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCAT-CCCTATC
*
1835039 TCTTGACGTATCGAC
130 TCTTGAGGTATCGAC
*
1835054 CCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAA
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAA
1835114 ATTATTTTGA
Statistics
Matches: 729, Mismatches: 49, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
144 726 1.00
145 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (144 bp):
CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATCCCTATCT
CTTGAGGTATCGAC
Found at i:1834712 original size:288 final size:288
Alignment explanation
Indices: 1834190--1835684 Score: 2431
Period size: 288 Copynumber: 5.3 Consensus size: 288
1834180 AGGGATTGAA
* * *
1834190 CCAGAGAACATATTTTGATGAAGATAGAGAGTGGATA-AGCTGGTCAAGTTTCCTATGGAAGCAG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGA-CTGGTCAAGTTTCCTATGGAAGCAG
* * * * *
1834254 GGATTGAACCAAAGAAATTATTTTGACTCAAAGAAAAGTCAGAGAGAGATTTAAGCATCCCTATC
65 GGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATGCCTATC
* *
1834319 TCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAAACGGGTCAAGTT
130 TCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTT
*
1834384 TACTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATT
195 TCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATT
1834449 TAAGCAT-CCCTATCTCTTGAGGTATCGAC
260 TAAGCATGCCC-ATCTCTTGAGGTATCGAC
*
1834478 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTCCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
* *
1834543 GATTGAACCAGAGAAATTATTTTGACTCATCGCAAAGTCAGTGAGAGATTTAAGCATGCCAATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATGCCTATCT
* *** * *
1834608 CTTGAGGTATCGACCCAGAAAACATATTTTGATCAAGGTAGAGAACAGATAGGCTGATCAAGTTT
131 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
* *
1834673 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAAATCAAAGTCAGTAAGAGATTT
196 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATTT
*
1834738 AAGCATGCCTATCTCTTGAGGTATCGAC
261 AAGCATGCCCATCTCTTGAGGTATCGAC
1834766 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
*
1834831 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTTAAGCATGCCTATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATGCCTATCT
* *
1834896 CTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGACTGGATAGACTGGTCAAGTTT
131 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
* *
1834961 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTT
196 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATTT
*
1835026 AAGCATGCCCATCTCTTGACGTATCGAC
261 AAGCATGCCCATCTCTTGAGGTATCGAC
*
1835054 CCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCC--T---------
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
* *
1835108 -A-T------G-GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATGCCTATCT
* *
1835164 CTTGAGGCATCGACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTT
131 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
* *
1835229 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTT
196 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATTT
1835294 AAGCATGCCCATCTCTTGAGGTATCGAC
261 AAGCATGCCCATCTCTTGAGGTATCGAC
* *
1835322 CCAGAAAACAAATTTTGATAAAGGTAGAGAGTGGATAAACTGGTCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
* * *
1835387 GATTGAACCAGAGAAATTATTTTGACTCAACTCAAAATCTGTGAGAGATTTAAGCATGCCTATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATGCCTATCT
1835452 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
131 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
*
1835517 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAATCAGTGAGAGATTT
196 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATTT
1835582 AAGCATGCCCATCTCTTGAGGTATCGAC
261 AAGCATGCCCATCTCTTGAGGTATCGAC
1835610 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
*
1835675 GATAGAACCA
66 GATTGAACCA
1835685 CGTAGATAGT
Statistics
Matches: 1121, Mismatches: 64, Indels: 44
0.91 0.05 0.04
Matches are distributed among these distances:
268 251 0.22
269 1 0.00
270 1 0.00
275 1 0.00
276 1 0.00
280 1 0.00
281 1 0.00
286 1 0.00
287 1 0.00
288 859 0.77
289 3 0.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (288 bp):
CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
GATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCAGTGAGAGATTTAAGCATGCCTATCT
CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAGATTT
AAGCATGCCCATCTCTTGAGGTATCGAC
Found at i:1834999 original size:432 final size:432
Alignment explanation
Indices: 1834190--1835684 Score: 2417
Period size: 432 Copynumber: 3.5 Consensus size: 432
1834180 AGGGATTGAA
* * *
1834190 CCAGAGAACATATTTTGATGAAGATAGAGAGTGGATA-AGCTGGTCAAGTTTCCTATGGAAGCAG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGA-CTGGTCAAGTTTCCTATGGAAGCAG
*
1834254 GGATTGAACCAAAGAAATTATTTTGACTCAAAG-AAAAGTCAG-AGAGAGATTTAAGCAT-CCCT
65 GGATTGAACCAGAGAAATTATTTTGACTCAAAGCAAAA-TCAGTA-AGAGATTTAAGCATGCCC-
* *
1834316 ATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAAACGGGTCAA
127 ATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAA
* * *
1834381 GTTTACTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAGTCAGTGAGAG
192 GTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAG
*
1834446 ATTTAAGCATCCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTG
257 ATTTAAGCATGCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTG
* *
1834511 GATAGACTGGTCAAGTTCCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCATCGC
322 GATAGACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGC
*
1834576 AAAGTCAGTGAGAGATTTAAGCATGCCAATCTCTTGAGGTATCGAC
387 AAAATCAGTGAGAGATTTAAGCATGCCAATCTCTTGAGGTATCGAC
* *** * *
1834622 CCAGAAAACATATTTTGATCAAGGTAGAGAACAGATAGGCTGATCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
* * *
1834687 GATTGAACCAGAGAAATTATTTTGACTCAAATCAAAGTCAGTAAGAGATTTAAGCATGCCTATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAAAGCAAAATCAGTAAGAGATTTAAGCATGCCCATCT
1834752 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
131 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
1834817 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTT
196 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTT
* *
1834882 AAGCATGCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATGAAGGTAGAGACTGGATA
261 AAGCATGCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATA
1834947 GACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAA
326 GACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAA
* *
1835012 TCAGTGAGAGATTTAAGCATGCCCATCTCTTGACGTATCGAC
391 TCAGTGAGAGATTTAAGCATGCCAATCTCTTGAGGTATCGAC
*
1835054 CCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCC--T---------
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
* *
1835108 -A-T------G-GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAAAGCAAAATCAGTAAGAGATTTAAGCATGCCCATCT
* *
1835164 CTTGAGGCATCGACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTT
131 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
1835229 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTT
196 CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTT
* *
1835294 AAGCATGCCCATCTCTTGAGGTATCGACCCAGAAAACAAATTTTGATAAAGGTAGAGAGTGGATA
261 AAGCATGCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATA
* *
1835359 AACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACTCAAAA
326 GACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAA
* *
1835424 TCTGTGAGAGATTTAAGCATGCCTATCTCTTGAGGTATCGAC
391 TCAGTGAGAGATTTAAGCATGCCAATCTCTTGAGGTATCGAC
1835466 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
1 CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
** *
1835531 GATTGAACCAGAGAAATTATTTTGACTCAACTCAAAATCAGTGAGAGATTTAAGCATGCCCATCT
66 GATTGAACCAGAGAAATTATTTTGACTCAAAGCAAAATCAGTAAGAGATTTAAGCATGCCCATCT
1835596 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
131 CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
*
1835661 CCTATGGAAGCAGGGATAGAACCA
196 CCTATGGAAGCAGGGATTGAACCA
1835685 CGTAGATAGT
Statistics
Matches: 986, Mismatches: 53, Indels: 48
0.91 0.05 0.04
Matches are distributed among these distances:
412 391 0.40
413 1 0.00
414 1 0.00
419 1 0.00
420 1 0.00
424 1 0.00
425 1 0.00
430 1 0.00
431 1 0.00
432 581 0.59
433 6 0.01
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (432 bp):
CCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGG
GATTGAACCAGAGAAATTATTTTGACTCAAAGCAAAATCAGTAAGAGATTTAAGCATGCCCATCT
CTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTT
CCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTT
AAGCATGCCTATCTCTTGAGGTATCGACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATA
GACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCAGAGAAATTATTTTGACTCAACGCAAAA
TCAGTGAGAGATTTAAGCATGCCAATCTCTTGAGGTATCGAC
Found at i:1835207 original size:124 final size:124
Alignment explanation
Indices: 1834987--1835237 Score: 484
Period size: 124 Copynumber: 2.0 Consensus size: 124
1834977 TTGAACCAGA
*
1834987 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGACGTATCG
1 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGACGCATCG
1835052 ACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATG
66 ACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATG
*
1835111 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGCATCG
1 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGACGCATCG
1835176 ACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATG
66 ACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATG
1835235 GAA
1 GAA
1835238 GCAGGGATTG
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.27
Consensus pattern (124 bp):
GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGACGCATCG
ACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATG
Found at i:1835266 original size:72 final size:72
Alignment explanation
Indices: 1835188--1835555 Score: 195
Period size: 72 Copynumber: 5.1 Consensus size: 72
1835178 CCAGAAAACA
*
1835188 TATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCA
1 TATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCA
1835253 GAGAAAT
66 GAGAAAT
* * * * * * * * * * **** * *
1835260 TATTTTGACTCAACGCAAAGTCACT-GAGAGA-T--TTAAGCATGCCCATCTCTTG-AGGTATCG
1 TATTTTGA-TAAAGGTAGAG--AGTGGATAGACTGGTCAAG-TTTCCTAT-GGAAGCAGGGATTG
* *
1835320 ACCCAGA-AAACA
61 AACCAGAGAAA-T
* *
1835332 AATTTTGATAAAGGTAGAGAGTGGATAAACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCA
1 TATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCA
1835397 GAGAAAT
66 GAGAAAT
* * * * * * * * **** * *
1835404 TATTTTGACTCAA-CTCA-AAATCTGTGAGAGA-T--TTAAGCATGCCTATCTCTTG-AGGTATC
1 TATTTTGA-TAAAGGT-AGAGA-GTG-GATAGACTGGTCAAG-TTTCCTAT-GGAAGCAGGGATT
* *
1835463 GACCCAGA-AAACA
60 GAACCAGAGAAA-T
1835476 TATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCA
1 TATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCA
1835541 GAGAAAT
66 GAGAAAT
1835548 TATTTTGA
1 TATTTTGA
1835556 CTCAACTCAA
Statistics
Matches: 197, Mismatches: 73, Indels: 52
0.61 0.23 0.16
Matches are distributed among these distances:
69 2 0.01
70 9 0.05
71 31 0.16
72 114 0.58
73 30 0.15
74 9 0.05
75 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.27
Consensus pattern (72 bp):
TATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCAGGGATTGAACCA
GAGAAAT
Found at i:1835371 original size:144 final size:144
Alignment explanation
Indices: 1835111--1835684 Score: 1049
Period size: 144 Copynumber: 4.0 Consensus size: 144
1835101 GTTTCCTATG
*
1835111 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGCATCG
1 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCG
*
1835176 ACCCAGAAAACATATTTTGATAAAGGTGGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
66 ACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
1835241 GGGATTGAACCAGA
131 GGGATTGAACCAGA
* *
1835255 GAAATTATTTTGACTCAACGCAAAGTCACTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCG
1 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCG
* *
1835320 ACCCAGAAAACAAATTTTGATAAAGGTAGAGAGTGGATAAACTGGTCAAGTTTCCTATGGAAGCA
66 ACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
1835385 GGGATTGAACCAGA
131 GGGATTGAACCAGA
* * *
1835399 GAAATTATTTTGACTCAACTCAAAATCTGTGAGAGATTTAAGCATGCCTATCTCTTGAGGTATCG
1 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCG
1835464 ACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
66 ACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
1835529 GGGATTGAACCAGA
131 GGGATTGAACCAGA
*
1835543 GAAATTATTTTGACTCAACTCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCG
1 GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCG
1835608 ACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
66 ACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
*
1835673 GGGATAGAACCA
131 GGGATTGAACCA
1835685 CGTAGATAGT
Statistics
Matches: 414, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 414 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (144 bp):
GAAATTATTTTGACTCAACGCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCG
ACCCAGAAAACATATTTTGATAAAGGTAGAGAGTGGATAGACTGGTCAAGTTTCCTATGGAAGCA
GGGATTGAACCAGA
Found at i:1835626 original size:72 final size:72
Alignment explanation
Indices: 1835404--1835627 Score: 174
Period size: 72 Copynumber: 3.1 Consensus size: 72
1835394 CCAGAGAAAT
*
1835404 TATTTTGACTCAACTCAAAATCTGTGAGAGATTTAAGCATGCCTATCTCTTGAGGTATCGACCCA
1 TATTTTGACTCAACTCAAAATCAGTGAGAGATTTAAGCATGCCTATCTCTTGAGGTATCGACCCA
1835469 GAAAACA
66 GAAAACA
* * * * * * * * **** * *
1835476 TATTTTGA-TAAAGGT--AGA-GAGTGGATAGACTGGTCAAG-TTTCCTAT-GGAAGCAGGGATT
1 TATTTTGACTCAA-CTCAAAATCAGT-GAGAGA-T--TTAAGCATGCCTATCTCTTG-AGGTATC
* *
1835535 GAACCAGAGAAA-T
60 GACCCAGA-AAACA
*
1835548 TATTTTGACTCAACTCAAAATCAGTGAGAGATTTAAGCATGCCCATCTCTTGAGGTATCGACCCA
1 TATTTTGACTCAACTCAAAATCAGTGAGAGATTTAAGCATGCCTATCTCTTGAGGTATCGACCCA
1835613 GAAAACA
66 GAAAACA
1835620 TATTTTGA
1 TATTTTGA
1835628 TAAAGGTAGA
Statistics
Matches: 104, Mismatches: 34, Indels: 28
0.63 0.20 0.17
Matches are distributed among these distances:
69 2 0.02
70 7 0.07
71 12 0.12
72 61 0.59
73 12 0.12
74 7 0.07
75 3 0.03
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.29
Consensus pattern (72 bp):
TATTTTGACTCAACTCAAAATCAGTGAGAGATTTAAGCATGCCTATCTCTTGAGGTATCGACCCA
GAAAACA
Found at i:1837431 original size:15 final size:16
Alignment explanation
Indices: 1837406--1837447 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1837396 TGTTGGTAAT
*
1837406 TTATAAAATAAAATTA
1 TTATTAAATAAAATTA
*
1837422 -TATTAAATAAATTTA
1 TTATTAAATAAAATTA
1837437 TTTATTAAATA
1 -TTATTAAATA
1837448 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTAAATAAAATTA
Found at i:1838593 original size:20 final size:20
Alignment explanation
Indices: 1838568--1838606 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1838558 GAAATTTTTT
*
1838568 ATTAAAAATATTAAATTAAA
1 ATTAAAAATAATAAATTAAA
*
1838588 ATTAAAATTAATAAATTAA
1 ATTAAAAATAATAAATTAA
1838607 TAAATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATTAAAAATAATAAATTAAA
Found at i:1839520 original size:50 final size:50
Alignment explanation
Indices: 1839423--1839520 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
1839413 CAAAAACATT
* * * *
1839423 TTGAATAATCTCCAATAAAAATTAGAAATGATTATTTAAGGCATTTTTTA
1 TTGAATAATCCCCAATAAAAAATAGAAATGATTATTCAAGACATTTTTTA
*
1839473 TTGAATAATCCCCAATAAAAAAT-GAAATGGATTATTCAAGACGTTTTT
1 TTGAATAATCCCCAATAAAAAATAGAAAT-GATTATTCAAGACATTTTT
1839521 AGCCAAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
49 5 0.12
50 37 0.88
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (50 bp):
TTGAATAATCCCCAATAAAAAATAGAAATGATTATTCAAGACATTTTTTA
Found at i:1839571 original size:60 final size:62
Alignment explanation
Indices: 1839501--1839619 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 62
1839491 AAAATGAAAT
1839501 GGATTATTCAAGACGTTTT-TAGCCAAAAATGACTTGAATAA-CCCATTTAATTTTTTTAAG
1 GGATTATTCAAGACGTTTTCTAGCCAAAAATGACTTGAATAATCCCATTTAATTTTTTTAAG
* * * * *
1839561 GGATTATTCAAGGCGTTTTCTAGCTAAAAATGCCTTGAATAATCCCTTTTTATTTTTTT
1 GGATTATTCAAGACGTTTTCTAGCCAAAAATGACTTGAATAATCCCATTTAATTTTTTT
1839620 TATTATTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 18 0.35
61 20 0.38
62 14 0.27
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.42
Consensus pattern (62 bp):
GGATTATTCAAGACGTTTTCTAGCCAAAAATGACTTGAATAATCCCATTTAATTTTTTTAAG
Found at i:1839922 original size:60 final size:58
Alignment explanation
Indices: 1839832--1840123 Score: 235
Period size: 60 Copynumber: 4.8 Consensus size: 58
1839822 AATTTTTTGT
* * ** *
1839832 AAGGGATTATTCCAGGCATTTTTTGGCTAGAAATGCCTTGAATAATCCCAAAAAAATGG
1 AAGGGATTATTCAAGGCA-TTTTTGACTAGAAACACCTTGAATAATCCAAAAAAAATGG
* *
1839891 AAGGAGATTATTCAAGGCATTTTTTTACTAGAAACACCTTGAATAATCTACAAAAAAAATTAG
1 AAGG-GATTATTCAAGGCA-TTTTTGACTAGAAACACCTTGAATAATC--CAAAAAAAA-TGG
* * * * * * *
1839954 AGGGGATTATTGAAGGTATTTTTAACCAAAAATACCTTGAATAATCCAAAAAAAATTGG
1 AAGGGATTATTCAAGGCATTTTTGACTAGAAACACCTTGAATAATCCAAAAAAAA-TGG
* * * ***** *
1840013 AATGGGATTATTCAAGGTATTTTTGGCTAGAAACGCCTTGAATAAATCCATTCAATTTTTTGT
1 AA-GGGATTATTCAAGGCATTTTTGACTAGAAACACCTTGAAT-AATCCA---AAAAAAATGG
*
1840076 AAGGGATTATTCAAGGCATTTTTGAGCCA-AAATCACCTTGAATAATCC
1 AAGGGATTATTCAAGGCATTTTTGA-CTAGAAA-CACCTTGAATAATCC
1840124 CTCAAAAAAT
Statistics
Matches: 189, Mismatches: 33, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
59 17 0.09
60 71 0.38
61 30 0.16
62 49 0.26
63 20 0.11
64 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (58 bp):
AAGGGATTATTCAAGGCATTTTTGACTAGAAACACCTTGAATAATCCAAAAAAAATGG
Found at i:1839963 original size:122 final size:121
Alignment explanation
Indices: 1839834--1840057 Score: 290
Period size: 121 Copynumber: 1.8 Consensus size: 121
1839824 TTTTTTGTAA
* ** * * * *
1839834 GGGATTATTCCAGGCATTTTTTGGCTAGAAATGCCTTGAATAATCCCAAAAAAA-TGGAA-GGAG
1 GGGATTATTCAAGGCA-TTTTTAACCAAAAATACCTTGAATAATCCAAAAAAAATTGGAATGG-G
*
1839897 ATTATTCAAGGCATTTTTTTACTAGAAACACCTTGAATAATCTACAAAAAAAATTAGAG
64 ATTATTCAAGGCA-TTTTTGACTAGAAACACCTTGAATAATCTACAAAAAAAATTAGAG
* *
1839956 GGGATTATTGAAGGTATTTTTAACCAAAAATACCTTGAATAATCCAAAAAAAATTGGAATGGGAT
1 GGGATTATTCAAGGCATTTTTAACCAAAAATACCTTGAATAATCCAAAAAAAATTGGAATGGGAT
* * *
1840021 TATTCAAGGTATTTTTGGCTAGAAACGCCTTGAATAA
66 TATTCAAGGCATTTTTGACTAGAAACACCTTGAATAA
1840058 ATCCATTCAA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
121 54 0.62
122 31 0.36
123 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (121 bp):
GGGATTATTCAAGGCATTTTTAACCAAAAATACCTTGAATAATCCAAAAAAAATTGGAATGGGAT
TATTCAAGGCATTTTTGACTAGAAACACCTTGAATAATCTACAAAAAAAATTAGAG
Found at i:1840044 original size:244 final size:242
Alignment explanation
Indices: 1839736--1840185 Score: 554
Period size: 244 Copynumber: 1.9 Consensus size: 242
1839726 CCTTTGATAG
* * *
1839736 CCAAAAATATCTTGAATAATTCTCTAAAAAATGAAAGAGATTATTTAAGATATTTTTAGCTAGAA
1 CCAAAAATACCTTGAATAATTCTCAAAAAAATGAAAGAGATTATTCAAGATATTTTTAGCTAGAA
** * * *
1839801 ACATTTTGAAT-AACCCTATTTAATTTTTTGTAAGGGATTATTCCAGGCATTTTTTG-GCTAGAA
66 ACACCTTGAATAAACCC-ATTCAATTTTTTGTAAGGGATTATTCAAGGCA-TTTTTGAGCCA-AA
* * * * *
1839864 AT-GCCTTGAATAATCCC-AAAAAAATGGAAGGAGATTATTCAAGGCATTTTTTTA-CTAGAAAC
128 ATCACCTTGAATAATCCCTAAAAAAATGAAAGGAGATTATTAAAGG--TGTTTTTAGCTAAAAAC
*
1839926 ACCTTGAATAATCTACAAAAAAAATTAGAGGGGATTATTGAAGGTATTTTTAA
191 ACCTTCAATAAT-TACAAAAAAAATTAGAGGGGATTATTGAAGGTATTTTTAA
* * * *
1839979 CCAAAAATACCTTGAATAA-TC-CAAAAAAAATTGGAATGGGATTATTCAAGGTATTTTTGGCTA
1 CCAAAAATACCTTGAATAATTCTC-AAAAAAA-T-GAAAGAGATTATTCAAGATATTTTTAGCTA
* *
1840042 GAAACGCCTTGAATAAATCCATTCAATTTTTTGTAAGGGATTATTCAAGGCATTTTTGAGCCAAA
63 GAAACACCTTGAATAAACCCATTCAATTTTTTGTAAGGGATTATTCAAGGCATTTTTGAGCCAAA
* * * *
1840107 ATCACCTTGAATAATCCCTCAAAAAATTAAAGGGGATTATTAAAGGTGTTTTTAGCTAAAAACGC
128 ATCACCTTGAATAATCCCTAAAAAAATGAAAGGAGATTATTAAAGGTGTTTTTAGCTAAAAACAC
1840172 CTTCAATAATTACA
193 CTTCAATAATTACA
1840186 CTTTCCGTTG
Statistics
Matches: 175, Mismatches: 24, Indels: 16
0.81 0.11 0.07
Matches are distributed among these distances:
241 1 0.01
242 8 0.05
243 40 0.23
244 100 0.57
245 26 0.15
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (242 bp):
CCAAAAATACCTTGAATAATTCTCAAAAAAATGAAAGAGATTATTCAAGATATTTTTAGCTAGAA
ACACCTTGAATAAACCCATTCAATTTTTTGTAAGGGATTATTCAAGGCATTTTTGAGCCAAAATC
ACCTTGAATAATCCCTAAAAAAATGAAAGGAGATTATTAAAGGTGTTTTTAGCTAAAAACACCTT
CAATAATTACAAAAAAAATTAGAGGGGATTATTGAAGGTATTTTTAA
Found at i:1840082 original size:122 final size:117
Alignment explanation
Indices: 1839733--1840181 Score: 357
Period size: 122 Copynumber: 3.7 Consensus size: 117
1839723 TCCCCTTTGA
* * * * *
1839733 TAGCCAAAAATATCTTGAATAATTCTCTAAAAAATGAAAGAGATTATTTAAGATATTTTTAGCTA
1 TAGCCAAAAATACCTTGAATAA-TC-CAAAAAAATG-AAGGGATTATTCAAGGTATTTTTAGCTA
** * * *
1839798 GAAACATTTTGAATAACCCTATTTAATTTTTTGTAAGGGATTATTCCAGGCATTTTT
63 GAAACACCTTGAATAATCC-ATTAAATTTTTTGTAAGGGATTATTCAAGGCA-TTTT
* * * * *
1839855 TGGCTAGAAATGCCTTGAATAATCCCAAAAAAATGGAAGGAGATTATTCAAGGCATTTTTTTA-C
1 TAGCCAAAAATACCTTGAATAAT-CCAAAAAAAT-GAAGG-GATTATTCAAGG--TATTTTTAGC
* *** * * * *
1839919 TAGAAACACCTTGAATAATCTACA-AAAAAAATTAG-AGGGGATTATTGAAGGTATTTT
61 TAGAAACACCTTGAATAATC--CATTAAATTTTTTGTAAGGGATTATTCAAGGCATTTT
* *
1839976 TAACCAAAAATACCTTGAATAATCCAAAAAAAATTGGAATGGGATTATTCAAGGTATTTTTGGCT
1 TAGCCAAAAATACCTTGAATAATCC-AAAAAAA-T-GAA-GGGATTATTCAAGGTATTTTTAGCT
* *
1840041 AGAAACGCCTTGAATAAATCCATTCAATTTTTTGTAAGGGATTATTCAAGGCATTTT
62 AGAAACACCTTGAAT-AATCCATTAAATTTTTTGTAAGGGATTATTCAAGGCATTTT
* * * *
1840098 TGAGCC-AAAATCACCTTGAATAATCCCTCAAAAAATTAAAGGGGATTATTAAAGGTGTTTTTAG
1 T-AGCCAAAAAT-ACCTTGAATAAT--C-CAAAAAAATGAA-GGGATTATTCAAGGTATTTTTAG
* * *
1840162 CTAAAAACGCCTTCAATAAT
60 CTAGAAACACCTTGAATAAT
1840182 TACACTTTCC
Statistics
Matches: 259, Mismatches: 49, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
120 10 0.04
121 62 0.24
122 92 0.36
123 77 0.30
124 9 0.03
125 8 0.03
126 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (117 bp):
TAGCCAAAAATACCTTGAATAATCCAAAAAAATGAAGGGATTATTCAAGGTATTTTTAGCTAGAA
ACACCTTGAATAATCCATTAAATTTTTTGTAAGGGATTATTCAAGGCATTTT
Found at i:1840159 original size:61 final size:61
Alignment explanation
Indices: 1839867--1840181 Score: 211
Period size: 60 Copynumber: 5.2 Consensus size: 61
1839857 GCTAGAAATG
* * * *
1839867 CCTTGAATAATCCC-AAAAAAA-TGGAAGGAGATTATTCAAGGCATTTTTTTA-CTAGAAA-CA
1 CCTTGAATAATCCCAAAAAAAATTGAAAGGGGATTATTCAAGG--TATTTTTAGCCA-AAATCA
* * * *
1839927 CCTTGAATAATCTACAAAAAAAATT-AGAGGGGATTATTGAAGGTATTTTTAACCAAAAAT-A
1 CCTTGAATAATC-CCAAAAAAAATTGAAAGGGGATTATTCAAGGTATTTTTAGCC-AAAATCA
* * * * *
1839988 CCTTGAATAAT-CCAAAAAAAATTGGAATGGGATTATTCAAGGTATTTTTGGCTAGAAA-CG
1 CCTTGAATAATCCCAAAAAAAATTGAAAGGGGATTATTCAAGGTATTTTTAGCCA-AAATCA
* **** * *
1840048 CCTTGAATAAAT-CCATTCAATTTTTTGTAA-GGGATTATTCAAGGCATTTTTGAGCCAAAATCA
1 CCTTGAAT-AATCCCA--AAAAAAATTGAAAGGGGATTATTCAAGGTATTTTT-AGCCAAAATCA
** * * * * *
1840111 CCTTGAATAATCCCTCAAAAAATT-AAAGGGGATTATTAAAGGTGTTTTTAGCTAAAAACG
1 CCTTGAATAATCCCAAAAAAAATTGAAAGGGGATTATTCAAGGTATTTTTAGCCAAAATCA
*
1840171 CCTTCAATAAT
1 CCTTGAATAAT
1840182 TACACTTTCC
Statistics
Matches: 200, Mismatches: 39, Indels: 32
0.74 0.14 0.12
Matches are distributed among these distances:
59 12 0.06
60 72 0.36
61 46 0.23
62 48 0.24
63 22 0.11
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (61 bp):
CCTTGAATAATCCCAAAAAAAATTGAAAGGGGATTATTCAAGGTATTTTTAGCCAAAATCA
Found at i:1841322 original size:34 final size:34
Alignment explanation
Indices: 1841265--1841335 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
1841255 GTAGCAGCGC
*
1841265 TTTCTACTATAAACGTCACTAAATTTAGTGGCAT
1 TTTCTACTATAAACGTCACTAAATTTAGAGGCAT
** *
1841299 TTTCTACTATAAAC-TCTTTTAAATTTAGAGGCGT
1 TTTCTACTATAAACGTC-ACTAAATTTAGAGGCAT
1841333 TTT
1 TTT
1841336 ATGATAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 2 0.06
34 30 0.94
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (34 bp):
TTTCTACTATAAACGTCACTAAATTTAGAGGCAT
Found at i:1842304 original size:14 final size:14
Alignment explanation
Indices: 1842264--1842309 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
1842254 ATCAATTTTG
1842264 ATTTTTAATTTTA--
1 ATTTTT-ATTTTATC
* *
1842277 ATTTTAATTGTATC
1 ATTTTTATTTTATC
1842291 ATTTTTATTTTATC
1 ATTTTTATTTTATC
1842305 ATTTT
1 ATTTT
1842310 GAAATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 5 0.19
13 5 0.19
14 17 0.63
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (14 bp):
ATTTTTATTTTATC
Found at i:1842943 original size:18 final size:18
Alignment explanation
Indices: 1842916--1842950 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1842906 TATTTTATAA
*
1842916 TAATATATTTATAAAAAT
1 TAATAAATTTATAAAAAT
*
1842934 TAATAAATTTTTAAAAA
1 TAATAAATTTATAAAAA
1842951 CTTTATGATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAAATTTATAAAAAT
Found at i:1843513 original size:15 final size:16
Alignment explanation
Indices: 1843476--1843509 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
1843466 ATTTTAATTT
1843476 TATTAAATATTTAAAG
1 TATTAAATATTTAAAG
1843492 TATTAAA-ATTT-AAG
1 TATTAAATATTTAAAG
1843506 TATT
1 TATT
1843510 TAAAGATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 4 0.22
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (16 bp):
TATTAAATATTTAAAG
Found at i:1843592 original size:20 final size:21
Alignment explanation
Indices: 1843547--1843592 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1843537 GAGTAGAAAT
* *
1843547 ATAATATTATTTTTAATTTTA
1 ATAAAATTATTTTTAATCTTA
*
1843568 TTAAAATTA-TTTTAATCTTA
1 ATAAAATTATTTTTAATCTTA
1843588 ATAAA
1 ATAAA
1843593 CTTTTAAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
ATAAAATTATTTTTAATCTTA
Found at i:1850060 original size:40 final size:42
Alignment explanation
Indices: 1849974--1850060 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 42
1849964 AATAATTACG
* * * *
1849974 GTTTTTTTACTATTAGATTACGATTTTTTTTAAAAGTTATAA
1 GTTTTTTTACTATTAGACTACGATTTTTTTCAAAAATCATAA
* *
1850016 -TTTTTTTA-TGTTAGACTATGATTTTTTTCAAAAATCA-AA
1 GTTTTTTTACTATTAGACTACGATTTTTTTCAAAAATCATAA
1850055 GTTTTT
1 GTTTTT
1850061 AGGTATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
39 2 0.05
40 28 0.74
41 8 0.21
ACGTcount: A:0.30, C:0.06, G:0.09, T:0.55
Consensus pattern (42 bp):
GTTTTTTTACTATTAGACTACGATTTTTTTCAAAAATCATAA
Done.