Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007832.1 Hibiscus syriacus cultivar Beakdansim tig00110174_pilon, 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: 4020056
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 21
Found at i:2268826 original size:26 final size:26
Alignment explanation
Indices: 2268743--2268827 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
2268733 GGTGAGAACA
* *
2268743 AGTATTTAATTTAAACTAAACGACTT
1 AGTAGTTAATTTAAACTAAACTACTT
* * *
2268769 AGTAGTT-ATCCTTATA-T-AACTTTCTA
1 AGTAGTTAAT--TTAAACTAAAC-TACTT
2268795 AG-AGTTAATTTAAACTAAACTACTT
1 AGTAGTTAATTTAAACTAAACTACTT
2268820 AGTAGTTA
1 AGTAGTTA
2268828 TCTTTATCTA
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
24 4 0.09
25 15 0.34
26 21 0.48
27 4 0.09
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (26 bp):
AGTAGTTAATTTAAACTAAACTACTT
Found at i:2268838 original size:26 final size:26
Alignment explanation
Indices: 2268758--2268838 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 26
2268748 TTAATTTAAA
* *
2268758 CTAAACGACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTATCTTTAT
* * * * *
2268784 AT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTTTAT
2268809 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATCTTTAT
2268835 CTAA
1 CTAA
2268839 CTTTCTAAGA
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
25 17 0.45
26 21 0.55
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.41
Consensus pattern (26 bp):
CTAAACTACTTAGTAGTTATCTTTAT
Found at i:2268851 original size:25 final size:25
Alignment explanation
Indices: 2268772--2268851 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
2268762 ACGACTTAGT
* *
2268772 AGTTATCCTTATATAACTTTCTAAG
1 AGTTATCTTTATCTAACTTTCTAAG
* * * *
2268797 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTTTATCT-AACTTTCTAAG
2268822 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATCTTTATCTAACTTTCTAAG
2268848 AGTT
1 AGTT
2268852 GGTGTTATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
25 21 0.52
26 19 0.47
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.44
Consensus pattern (25 bp):
AGTTATCTTTATCTAACTTTCTAAG
Found at i:2273025 original size:26 final size:25
Alignment explanation
Indices: 2272996--2273076 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 25
2272986 TTAATTTAAA
2272996 CTAAACTACTTAGTAGTTATCCTTAT
1 CTAAACTACTTAGTAGTTAT-CTTAT
* * *
2273022 CT-AACTTTCTAAG-AGTTAAT-TTAAA
1 CTAAAC-TACTTAGTAGTT-ATCTT-AT
2273047 CTAAACTACTTAGTAGTTATCTTTAT
1 CTAAACTACTTAGTAGTTATC-TTAT
2273073 CTAA
1 CTAA
2273077 CTTTCTAAGA
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.40
26 21 0.50
27 2 0.05
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (25 bp):
CTAAACTACTTAGTAGTTATCTTAT
Found at i:2273038 original size:25 final size:24
Alignment explanation
Indices: 2273010--2273090 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 24
2273000 ACTACTTAGT
2273010 AGTTATCCTTATCTAACTTTCTAAG
1 AGTTAT-CTTATCTAACTTTCTAAG
* * *
2273035 AGTTAAT-TTAAACTAAAC-TACTTAG
1 AGTT-ATCTT-ATCT-AACTTTCTAAG
2273060 TAGTTATCTTTATCTAACTTTCTAAG
1 -AGTTATC-TTATCTAACTTTCTAAG
2273086 AGTTA
1 AGTTA
2273091 GTGTTATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
24 2 0.05
25 22 0.51
26 17 0.40
27 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (24 bp):
AGTTATCTTATCTAACTTTCTAAG
Found at i:2273062 original size:51 final size:51
Alignment explanation
Indices: 2272986--2273127 Score: 203
Period size: 51 Copynumber: 2.8 Consensus size: 51
2272976 GAACAAGTAT
2272986 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
*
2273037 TTAATTTAAACTAAACTACTTAGTAGTTATCTTTATCTAACTTTCTAAGAG
1 TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
* * * * * * *
2273088 TTAGTGTTATATTAAAATACTAATTAATTATCCTTATCTA
1 TTAAT-TTAAACTAAACTACTTAGTAGTTATCCTTATCTA
2273128 TCGAGTAACC
Statistics
Matches: 81, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
51 54 0.67
52 27 0.33
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (51 bp):
TTAATTTAAACTAAACTACTTAGTAGTTATCCTTATCTAACTTTCTAAGAG
Found at i:2282423 original size:31 final size:30
Alignment explanation
Indices: 2282412--2282478 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
2282402 GTTAGAGTGA
*
2282412 TTTAGGGTTAGGATTTTTATGTTAGAATAG
1 TTTAGGGTTAGGGTTTTTATGTTAGAATAG
* *
2282442 TTTAGGGTTATGGTTTTTATGTTATAA-AGG
1 TTTAGGGTTAGGGTTTTTATGTTAGAATA-G
2282472 TTTAGGG
1 TTTAGGG
2282479 GTCTTAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (30 bp):
TTTAGGGTTAGGGTTTTTATGTTAGAATAG
Found at i:2282429 original size:30 final size:30
Alignment explanation
Indices: 2282395--2282478 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
2282385 CGTTTAGGGT
* *
2282395 TTTTTGGGTTAGAGT-GATTTAGGGTTA-GG
1 TTTTTAGGTTAGAATAG-TTTAGGGTTATGG
*
2282424 ATTTTTATGTTAGAATAGTTTAGGGTTATGG
1 -TTTTTAGGTTAGAATAGTTTAGGGTTATGG
* *
2282455 TTTTTATGTTATAA-AGGTTTAGGG
1 TTTTTAGGTTAGAATA-GTTTAGGG
2282479 GTCTTAAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 1 0.02
30 43 0.91
31 3 0.06
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.48
Consensus pattern (30 bp):
TTTTTAGGTTAGAATAGTTTAGGGTTATGG
Found at i:2284208 original size:29 final size:29
Alignment explanation
Indices: 2284149--2284209 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
2284139 TGTGTAGCTC
* *
2284149 GTTGTAAGATAAATCCCACTCATTGTATA
1 GTTGTAACATAAATCCCACTCATTATATA
* *
2284178 GTTGTAACATAAATCCCACTCGTTATGTA
1 GTTGTAACATAAATCCCACTCATTATATA
2284207 GTT
1 GTT
2284210 TTATAATGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (29 bp):
GTTGTAACATAAATCCCACTCATTATATA
Found at i:2288822 original size:21 final size:23
Alignment explanation
Indices: 2288771--2288822 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2288761 GATTCCCCTG
2288771 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
2288794 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
2288815 TGGGGGGA
1 TGGGGGGA
2288823 TCAATTCCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:2292678 original size:22 final size:21
Alignment explanation
Indices: 2292636--2292675 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2292626 GAGTTTATTT
*
2292636 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2292657 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2292676 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2295284 original size:8 final size:8
Alignment explanation
Indices: 2295270--2295354 Score: 77
Period size: 8 Copynumber: 10.6 Consensus size: 8
2295260 TACGAGCCAC
2295270 TTTGAGA-
1 TTTGAGAG
2295277 TATTGAGAG
1 T-TTGAGAG
2295286 TTTGAGAG
1 TTTGAGAG
*
2295294 TTTCAGA-
1 TTTGAGAG
2295301 TATTGAGAG
1 T-TTGAGAG
*
2295310 TTTGAAAG
1 TTTGAGAG
*
2295318 TTTGAGAA
1 TTTGAGAG
2295326 TTTGAGAG
1 TTTGAGAG
*
2295334 TTTAAGAG
1 TTTGAGAG
*
2295342 -ATGCAGAG
1 TTTG-AGAG
2295350 TTTGA
1 TTTGA
2295355 TAATTTTAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
7 3 0.05
8 55 0.89
9 4 0.06
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.36
Consensus pattern (8 bp):
TTTGAGAG
Found at i:2295306 original size:24 final size:24
Alignment explanation
Indices: 2295274--2295341 Score: 93
Period size: 24 Copynumber: 2.8 Consensus size: 24
2295264 AGCCACTTTG
2295274 AGATATTGAGAGTTTGAGAGTTTC
1 AGATATTGAGAGTTTGAGAGTTTC
* *
2295298 AGATATTGAGAGTTTGAAAGTTTG
1 AGATATTGAGAGTTTGAGAGTTTC
*
2295322 AGA-ATTTGAGAGTTTAAGAG
1 AGATA-TTGAGAGTTTGAGAG
2295342 ATGCAGAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.03
24 38 0.97
ACGTcount: A:0.34, C:0.01, G:0.29, T:0.35
Consensus pattern (24 bp):
AGATATTGAGAGTTTGAGAGTTTC
Found at i:2296261 original size:26 final size:26
Alignment explanation
Indices: 2296225--2296274 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
2296215 AAAAAATATA
*
2296225 TATGATGTATGTACATATGTATGATG
1 TATGATGTATGTACATAAGTATGATG
*
2296251 TATGATGTATGTATATAAGTATGA
1 TATGATGTATGTACATAAGTATGA
2296275 ATATAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (26 bp):
TATGATGTATGTACATAAGTATGATG
Found at i:2296606 original size:14 final size:14
Alignment explanation
Indices: 2296561--2296607 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2296551 ACTTTATAAG
2296561 TATAAAGTATA-ATA
1 TATAAA-TATATATA
* *
2296575 TATAAGTATATGTA
1 TATAAATATATATA
*
2296589 TATAAATATATATG
1 TATAAATATATATA
2296603 TATAA
1 TATAA
2296608 TGTATGCGCG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 4 0.15
14 23 0.85
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (14 bp):
TATAAATATATATA
Found at i:2297530 original size:16 final size:16
Alignment explanation
Indices: 2297511--2297544 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2297501 TGTAACTTAT
*
2297511 AAGTAAGGTAAGTATC
1 AAGTAAGGTAAATATC
*
2297527 AAGTCAGGTAAATATC
1 AAGTAAGGTAAATATC
2297543 AA
1 AA
2297545 ACCAATTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (16 bp):
AAGTAAGGTAAATATC
Found at i:2299002 original size:16 final size:18
Alignment explanation
Indices: 2298967--2299004 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
2298957 TAAAATTTCA
*
2298967 AAAATTATTTAAATAAAT
1 AAAATTATTCAAATAAAT
2298985 AAAA-TATTCAAA-AAAT
1 AAAATTATTCAAATAAAT
2299001 AAAA
1 AAAA
2299005 AATAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 7 0.37
18 4 0.21
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAATTATTCAAATAAAT
Found at i:2299005 original size:17 final size:19
Alignment explanation
Indices: 2298966--2299005 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
2298956 ATAAAATTTC
*
2298966 AAAAATTATTTAAATAAAT
1 AAAAATTATTCAAATAAAT
2298985 -AAAA-TATTCAAA-AAAT
1 AAAAATTATTCAAATAAAT
2299001 AAAAA
1 AAAAA
2299006 ATAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATTATTCAAATAAAT
Found at i:2299007 original size:27 final size:27
Alignment explanation
Indices: 2298954--2299019 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
2298944 TTAAAATTTA
* **
2298954 AAATAAAATTTCAAAAATTATTTAAAT
1 AAATAAAATTTCAAAAAATATAAAAAT
2298981 AAATAAAATATTCAAAAAATA-AAAAAT
1 AAATAAAAT-TTCAAAAAATATAAAAAT
*
2299008 -AATATAATTTCA
1 AAATAAAATTTCA
2299020 TATTCTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 4 0.12
26 7 0.21
27 13 0.38
28 10 0.29
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATAAAATTTCAAAAAATATAAAAAT
Found at i:2304517 original size:21 final size:21
Alignment explanation
Indices: 2304491--2304540 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
2304481 ATAATCTCTT
2304491 GCATGTCAGAGCCTACAACGA
1 GCATGTCAGAGCCTACAACGA
*
2304512 GCATGTCAGAGCCTGCAACGA
1 GCATGTCAGAGCCTACAACGA
2304533 GCATGTCA
1 GCATGTCA
2304541 TCAACGTACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
GCATGTCAGAGCCTACAACGA
Found at i:2319023 original size:32 final size:32
Alignment explanation
Indices: 2318987--2319060 Score: 112
Period size: 32 Copynumber: 2.3 Consensus size: 32
2318977 GATAAGTTAT
*
2318987 TTTTTGGTTCGAATCAATATCAGATCGGTTGA
1 TTTTTGGGTCGAATCAATATCAGATCGGTTGA
** *
2319019 TTTTTGGGTCGGGTTAATATCAGATCGGTTGA
1 TTTTTGGGTCGAATCAATATCAGATCGGTTGA
2319051 TTTTTGGGTC
1 TTTTTGGGTC
2319061 CGATTAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.19, C:0.11, G:0.27, T:0.43
Consensus pattern (32 bp):
TTTTTGGGTCGAATCAATATCAGATCGGTTGA
Found at i:2319068 original size:32 final size:32
Alignment explanation
Indices: 2319002--2319076 Score: 123
Period size: 32 Copynumber: 2.3 Consensus size: 32
2318992 GGTTCGAATC
* *
2319002 AATATCAGATCGGTTGATTTTTGGGTCGGGTT
1 AATATCAGATCGGTTGATTTTTGGGTCCGATT
2319034 AATATCAGATCGGTTGATTTTTGGGTCCGATT
1 AATATCAGATCGGTTGATTTTTGGGTCCGATT
*
2319066 AATACCAGATC
1 AATATCAGATC
2319077 AATTATATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.37
Consensus pattern (32 bp):
AATATCAGATCGGTTGATTTTTGGGTCCGATT
Found at i:2319075 original size:64 final size:64
Alignment explanation
Indices: 2318954--2319076 Score: 149
Period size: 64 Copynumber: 1.9 Consensus size: 64
2318944 GGTCGAGTTA
* * * * *
2318954 ATTTTTGGGTTGGGTGATTATCAGATAAGTTATTTTTTGGTTCGAATCAATATCAGATCGGTTG
1 ATTTTTGGGTCGGGTGAATATCAGATAAGTTATTTTTGGGTCCGAATCAATACCAGATCGGTTG
* ** *
2319018 ATTTTTGGGTCGGGTTAATATCAGATCGGTTGATTTTTGGGTCCG-ATTAATACCAGATC
1 ATTTTTGGGTCGGGTGAATATCAGATAAGTT-ATTTTTGGGTCCGAATCAATACCAGATC
2319077 AATTATATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 38 0.78
65 11 0.22
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (64 bp):
ATTTTTGGGTCGGGTGAATATCAGATAAGTTATTTTTGGGTCCGAATCAATACCAGATCGGTTG
Found at i:2322372 original size:12 final size:12
Alignment explanation
Indices: 2322355--2322385 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2322345 AACATATTCC
2322355 AAATGACCATGA
1 AAATGACCATGA
2322367 AAATGACCATGA
1 AAATGACCATGA
2322379 AAATGAC
1 AAATGAC
2322386 AATGTGAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (12 bp):
AAATGACCATGA
Found at i:2329206 original size:28 final size:28
Alignment explanation
Indices: 2329166--2329220 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
2329156 ATATCTAAAG
2329166 ATTAACCTTAATTATTG-TAAAAAAAAAT
1 ATTAACCTTAATT-TTGATAAAAAAAAAT
*
2329194 ATTAACCTTAATTTTGATAAAATAAAA
1 ATTAACCTTAATTTTGATAAAAAAAAA
2329221 GTATCAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (28 bp):
ATTAACCTTAATTTTGATAAAAAAAAAT
Found at i:2330198 original size:22 final size:22
Alignment explanation
Indices: 2330166--2330214 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
2330156 TTTGGCCCTA
*
2330166 CTCCCCGCTGCATGCTCGCCTG
1 CTCCCCACTGCATGCTCGCCTG
2330188 CTCCCCACTGCATGCTCGCCTG
1 CTCCCCACTGCATGCTCGCCTG
2330210 CTCCC
1 CTCCC
2330215 GCTGCTCCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.06, C:0.53, G:0.18, T:0.22
Consensus pattern (22 bp):
CTCCCCACTGCATGCTCGCCTG
Found at i:2330716 original size:30 final size:30
Alignment explanation
Indices: 2330656--2330761 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
2330646 TTTAGTTAAT
*
2330656 TAGTTTTTTAGTAGTGAA-TTATACTTAAAAAA
1 TAGTTTATTAGT--TGAAGTTATA-TTAAAAAA
* *
2330688 TCGTTTATTAGTTTAAGTTATATTAAAAAA
1 TAGTTTATTAGTTGAAGTTATATTAAAAAA
*
2330718 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAAAA
2330748 TAGTTTATTAGTTG
1 TAGTTTATTAGTTG
2330762 TTTAAAGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.78
31 5 0.07
32 10 0.15
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAAAA
Found at i:2330842 original size:15 final size:16
Alignment explanation
Indices: 2330814--2330847 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
2330804 GTTTGTTACT
2330814 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
2330830 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
2330845 TTA
1 TTA
2330848 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:2333294 original size:59 final size:58
Alignment explanation
Indices: 2333160--2333278 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 58
2333150 AAATATACAT
*
2333160 TAAATAAT-ATT-TTAAATCATTAGTATCAAATAATTAAATATTAATAATAAATCATTA
1 TAAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATT-ATAATAAATCATTA
* *
2333217 TTAATAATAATTAGTAAATCATTAGTATCAAATCATTAAATATT-TAA-AAATCATTAA
1 TAAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATT-A
2333274 TAAAT
1 TAAAT
2333279 TTGACTATGT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
56 8 0.15
57 15 0.27
58 3 0.05
59 29 0.53
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (58 bp):
TAAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTATAATAAATCATTA
Found at i:2333453 original size:26 final size:26
Alignment explanation
Indices: 2333344--2333692 Score: 353
Period size: 26 Copynumber: 13.7 Consensus size: 26
2333334 TTATTCTATA
* * *
2333344 ATTATTAGT-AATAATTATTA-AATC
1 ATTATTATTAAATCATTATTATAATG
* *
2333368 ATTAGTATTAAATCATTATTATAA-A
1 ATTATTATTAAATCATTATTATAATG
* * * * *
2333393 ATCATTACTAAATAATTACTA-AATA
1 ATTATTATTAAATCATTATTATAATG
* *
2333418 ATTACTATTAAATCATTATTATCATCATT
1 ATTATTATTAAATCATTATTAT-A--ATG
2333447 ATTATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
2333473 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
2333499 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* * *
2333525 ATTATTATCAAATCATTACTA-AATC
1 ATTATTATTAAATCATTATTATAATG
*
2333550 ATCAAATTATT-AA--A-TATT-TAA--
1 AT--TATTATTAAATCATTATTATAATG
*
2333571 ATCATTATTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
2333597 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
2333623 ATTATTACTAAATCATTATTATAATG
1 ATTATTATTAAATCATTATTATAATG
* *
2333649 ATTATTATCAAATCATTACTATAATG
1 ATTATTATTAAATCATTATTATAATG
*
2333675 ATTATTATCAAATCATTA
1 ATTATTATTAAATCATTA
2333693 CTAAATCATC
Statistics
Matches: 277, Mismatches: 31, Indels: 32
0.81 0.09 0.09
Matches are distributed among these distances:
19 6 0.02
20 2 0.01
21 2 0.01
22 1 0.00
23 9 0.03
24 13 0.05
25 48 0.17
26 166 0.60
27 6 0.02
28 1 0.00
29 23 0.08
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.45
Consensus pattern (26 bp):
ATTATTATTAAATCATTATTATAATG
Found at i:2333476 original size:20 final size:20
Alignment explanation
Indices: 2333438--2333476 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2333428 AATCATTATT
* *
2333438 ATCATCATTATTATTATTAA
1 ATCATCATTATAATGATTAA
*
2333458 ATCATTATTATAATGATTA
1 ATCATCATTATAATGATTA
2333477 TTACTAAATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (20 bp):
ATCATCATTATAATGATTAA
Found at i:2333622 original size:150 final size:152
Alignment explanation
Indices: 2333423--2333706 Score: 502
Period size: 150 Copynumber: 1.9 Consensus size: 152
2333413 AAATAATTAC
* *
2333423 TATTAAATCATTATTATCATCATTATTATTATTAAATCATTATTATAATGATTATTACTAAATCA
1 TATTAAATCATTATTATCA-CATGATTATTACTAAATCATTATTATAATGATTATTACTAAATCA
*
2333488 TTATTATAATGATTATTA-CTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT
65 TTATTATAATGATTATTATC-AAATCATTACTATAATGATTATTATCAAATCATTACTAAATCAT
2333552 CAAATTATTAAATATTTAAATCAT
129 CAAATTATTAAATATTTAAATCAT
2333576 TATTAAATCATTATTAT-A-ATGATTATTACTAAATCATTATTATAATGATTATTACTAAATCAT
1 TATTAAATCATTATTATCACATGATTATTACTAAATCATTATTATAATGATTATTACTAAATCAT
2333639 TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
66 TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
2333704 AAT
131 AAT
2333707 CTATCATAAT
Statistics
Matches: 127, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
150 108 0.85
151 1 0.01
152 1 0.01
153 17 0.13
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (152 bp):
TATTAAATCATTATTATCACATGATTATTACTAAATCATTATTATAATGATTATTACTAAATCAT
TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
AATTATTAAATATTTAAATCAT
Found at i:2333703 original size:14 final size:13
Alignment explanation
Indices: 2333357--2333692 Score: 226
Period size: 14 Copynumber: 26.1 Consensus size: 13
2333347 ATTAGTAATA
2333357 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
2333371 AGTATTAAATCATT
1 ATTA-TAAATCATT
2333385 ATTATAAAATCATT
1 ATTAT-AAATCATT
*
2333399 A--CTAAAT-A--
1 ATTATAAATCATT
*
2333407 ATTACTAAATAATT
1 ATTA-TAAATCATT
*
2333421 ACTATTAAATCATT
1 ATTA-TAAATCATT
* *
2333435 ATTATCATCATTATT
1 ATTAT-A-AATCATT
2333450 ATTATTAAATCATT
1 ATTA-TAAATCATT
*
2333464 ATTAT-AATGATT
1 ATTATAAATCATT
2333476 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2333490 ATTAT-AATGATT
1 ATTATAAATCATT
2333502 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2333516 ATTAT-AATGATT
1 ATTATAAATCATT
2333528 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2333542 A--CTAAATCATCAA
1 ATTATAAATCAT--T
*
2333555 ATTATTAA--A-T
1 ATTATAAATCATT
2333565 ATT-TAAATCATT
1 ATTATAAATCATT
2333577 A-T-TAAATCATT
1 ATTATAAATCATT
*
2333588 ATTAT-AATGATT
1 ATTATAAATCATT
2333600 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2333614 ATTAT-AATGATT
1 ATTATAAATCATT
2333626 ATTACTAAATCATT
1 ATTA-TAAATCATT
*
2333640 ATTAT-AATGATT
1 ATTATAAATCATT
2333652 ATTATCAAATCATT
1 ATTAT-AAATCATT
* *
2333666 ACTAT-AATGATT
1 ATTATAAATCATT
2333678 ATTATCAAATCATT
1 ATTAT-AAATCATT
2333692 A
1 A
2333693 CTAAATCATC
Statistics
Matches: 255, Mismatches: 34, Indels: 66
0.72 0.10 0.19
Matches are distributed among these distances:
8 1 0.00
9 3 0.01
10 4 0.02
11 28 0.11
12 78 0.31
13 14 0.05
14 113 0.44
15 13 0.05
16 1 0.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (13 bp):
ATTATAAATCATT
Found at i:2333742 original size:150 final size:150
Alignment explanation
Indices: 2333447--2333743 Score: 438
Period size: 150 Copynumber: 2.0 Consensus size: 150
2333437 TATCATCATT
*
2333447 ATTATTATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTACTAAAT
1 ATTATTACTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTACTAAAT
* * * **
2333512 CATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATTATTAAATATTTAAATCATT
66 CATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATTATTAAATAATCAAATCAAA
* *
2333577 ATTAAATCATTATTATAATG
131 ATTAAACCATAATTATAATG
2333597 ATTATTACTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTA-TCAAA
1 ATTATTACTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTACT-AAA
* *
2333661 TCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATCTA-T-CATAATCGAATCA
65 TCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAAT-TATTAAATAATCAAATCA
* *
2333724 AAATGTCAACCCTAATTATA
129 AAAT-TAAACCATAATTATA
2333744 TAGTATTTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
149 12 0.09
150 118 0.89
151 2 0.02
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (150 bp):
ATTATTACTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTACTAAAT
CATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATTATTAAATAATCAAATCAAA
ATTAAACCATAATTATAATG
Found at i:2333998 original size:12 final size:12
Alignment explanation
Indices: 2333981--2334039 Score: 88
Period size: 12 Copynumber: 5.1 Consensus size: 12
2333971 GTTCATTAAA
2333981 TATTAAATTCAT
1 TATTAAATTCAT
2333993 TATTAAATTCAT
1 TATTAAATTCAT
2334005 TATTAAA-TCAT
1 TATTAAATTCAT
2334016 TATTTAAATT-AT
1 TA-TTAAATTCAT
2334028 TATTAAA-TCAT
1 TATTAAATTCAT
2334039 T
1 T
2334040 TTTATGGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.02
11 14 0.32
12 28 0.64
13 1 0.02
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:2334019 original size:23 final size:23
Alignment explanation
Indices: 2333981--2334043 Score: 94
Period size: 23 Copynumber: 2.7 Consensus size: 23
2333971 GTTCATTAAA
2333981 TATTAAATTCATTA-TTAAATTCAT
1 TATTAAA-TCATTATTTAAATT-AT
2334005 TATTAAATCATTATTTAAATTAT
1 TATTAAATCATTATTTAAATTAT
2334028 TATTAAATCATT-TTTA
1 TATTAAATCATTATTTA
2334044 TGGTTAATTG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.11
23 20 0.53
24 14 0.37
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTAAATCATTATTTAAATTAT
Found at i:2334251 original size:49 final size:49
Alignment explanation
Indices: 2334183--2334417 Score: 436
Period size: 49 Copynumber: 4.8 Consensus size: 49
2334173 TTAAATCATT
*
2334183 ATTATTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
2334232 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
2334281 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
2334330 ATTACTATCAAATCATTAAATATTAATAATAATTT-ATTATTACTAATC
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
*
2334378 ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTA
1 ATTACTATCAAATCATTAAATATTAATAATAATTTCATTA
2334418 ATATTAGTTA
Statistics
Matches: 181, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
48 47 0.26
49 134 0.74
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
Found at i:2334269 original size:22 final size:22
Alignment explanation
Indices: 2334195--2334271 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
2334185 TATTATCAAA
2334195 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
* *
2334217 TCATTATTACTAATCATTACT-ATCAA-A
1 TC---ATTA--AAT-ATTAATAAT-AATT
2334244 TCATTAAATATTAATAATAATT
1 TCATTAAATATTAATAATAATT
2334266 TCATTA
1 TCATTA
2334272 TTACTAATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 18
0.66 0.06 0.28
Matches are distributed among these distances:
21 7 0.17
22 13 0.31
24 4 0.10
25 4 0.10
27 7 0.17
28 7 0.17
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.44
Consensus pattern (22 bp):
TCATTAAATATTAATAATAATT
Found at i:2338087 original size:21 final size:21
Alignment explanation
Indices: 2338061--2338100 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2338051 CAGAACCCCA
*
2338061 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2338082 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2338101 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2338132 original size:21 final size:23
Alignment explanation
Indices: 2338082--2338141 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
2338072 ATTCCCCTGT
2338082 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
* *
2338105 AGGGGGAATTGGTT-CCC-TC-A
1 GGGGGGAATCGGTTCCCCTTCAA
* *
2338125 GGGGGGGATCGATTCCC
1 GGGGGGAATCGGTTCCC
2338142 TCTGCACCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 11 0.37
21 4 0.13
22 3 0.10
23 12 0.40
ACGTcount: A:0.17, C:0.23, G:0.38, T:0.22
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:2346628 original size:10 final size:10
Alignment explanation
Indices: 2346613--2346654 Score: 75
Period size: 10 Copynumber: 4.2 Consensus size: 10
2346603 AAGTTGTTGC
2346613 TCATTTCCTT
1 TCATTTCCTT
2346623 TCATTTCCTT
1 TCATTTCCTT
2346633 TCATTTCCTT
1 TCATTTCCTT
*
2346643 TCCTTTCCTT
1 TCATTTCCTT
2346653 TC
1 TC
2346655 TTGTTTCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.60
Consensus pattern (10 bp):
TCATTTCCTT
Found at i:2346629 original size:5 final size:5
Alignment explanation
Indices: 2346616--2346654 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
2346606 TTGTTGCTCA
* *
2346616 TTTCC TTTCA TTTCC TTTCA TTTCC TTTCC TTTCC TTTC
1 TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTCC TTTC
2346655 TTGTTTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTCC
Found at i:2347034 original size:28 final size:28
Alignment explanation
Indices: 2347000--2347053 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
2346990 ATAATCTAAT
*
2347000 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
2347028 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
2347054 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:2347060 original size:28 final size:28
Alignment explanation
Indices: 2346996--2347060 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
2346986 TTATATAATC
*
2346996 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
2347024 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
2347052 TAATTTATA
1 TAATATATA
2347061 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:2347063 original size:21 final size:21
Alignment explanation
Indices: 2347030--2347078 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2347020 TTAATATAAT
2347030 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
2347051 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
2347072 ATTAACT
1 A-TAACT
2347079 AAATTTATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:2347837 original size:29 final size:29
Alignment explanation
Indices: 2347759--2347865 Score: 128
Period size: 29 Copynumber: 3.7 Consensus size: 29
2347749 GTTGGACGTC
** *
2347759 GGGCGTGCATGGCGACCTATAAGGTCGCT
1 GGGCGTGCATGGCGACCTACCATGTCGCT
2347788 GGGCGTGCATGGCGACCTACCATGTCGCCT
1 GGGCGTGCATGGCGACCTACCATGTCG-CT
*
2347818 -GGCGTGCATGGCGACCTACCATGTCGTT
1 GGGCGTGCATGGCGACCTACCATGTCGCT
* *
2347846 GGG-ATGCCCTGGCGACCTAC
1 GGGCGTG-CATGGCGACCTAC
2347866 GGCAACACTG
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
28 3 0.04
29 64 0.93
30 2 0.03
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.21
Consensus pattern (29 bp):
GGGCGTGCATGGCGACCTACCATGTCGCT
Found at i:2348503 original size:14 final size:16
Alignment explanation
Indices: 2348484--2348522 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
2348474 ATAGTAGCAA
2348484 AATTTTTTTAA-ATT-
1 AATTTTTTTAATATTG
2348498 AATTTTATTTAATATTG
1 AATTTT-TTTAATATTG
2348515 AATTTTTT
1 AATTTTTT
2348523 AAAGTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.27
15 5 0.23
16 5 0.23
17 6 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
AATTTTTTTAATATTG
Found at i:2348756 original size:18 final size:17
Alignment explanation
Indices: 2348725--2348763 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2348715 AAAAAATATG
* *
2348725 AAAATAAAATTATTTTT
1 AAAATAAAAATATTTTC
2348742 AAAATTAAAAATATTTTC
1 AAAA-TAAAAATATTTTC
2348760 AAAA
1 AAAA
2348764 AATTTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
AAAATAAAAATATTTTC
Found at i:2352425 original size:2 final size:2
Alignment explanation
Indices: 2352418--2352450 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2352408 TGTTGTTTCC
*
2352418 AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2352451 AGATTGAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2357807 original size:20 final size:20
Alignment explanation
Indices: 2357782--2357832 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2357772 GATTAAAGTA
*
2357782 GTATCGATACTAATGTGT-AG
1 GTATCGATACTAA-GGGTAAG
* *
2357802 GTATCGACACCAAGGGTAAG
1 GTATCGATACTAAGGGTAAG
2357822 GTATCGATACT
1 GTATCGATACT
2357833 GTAATTCAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (20 bp):
GTATCGATACTAAGGGTAAG
Found at i:2363423 original size:22 final size:21
Alignment explanation
Indices: 2363383--2363423 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2363373 TATATAATTC
* *
2363383 AATCAAAAACAACACTTTTAA
1 AATCAAAAACAAAAATTTTAA
2363404 AATCAAAAACAAAATATTTT
1 AATCAAAAACAAAA-ATTTT
2363424 TTATTTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.27
Consensus pattern (21 bp):
AATCAAAAACAAAAATTTTAA
Found at i:2363903 original size:21 final size:21
Alignment explanation
Indices: 2363839--2363904 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
2363829 CGGTACACTA
2363839 CATAGTGTATCGATGCACATT
1 CATAGTGTATCGATGCACATT
* *
2363860 CA-ACGATGCATCAATGCACATT
1 CATA-G-TGTATCGATGCACATT
*
2363882 CATAGTGTATCGATGCATATT
1 CATAGTGTATCGATGCACATT
2363903 CA
1 CA
2363905 AGGAATGCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 18 0.49
22 17 0.46
23 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (21 bp):
CATAGTGTATCGATGCACATT
Found at i:2363904 original size:43 final size:44
Alignment explanation
Indices: 2363839--2363942 Score: 140
Period size: 43 Copynumber: 2.4 Consensus size: 44
2363829 CGGTACACTA
*
2363839 CATAGTGTATCGATGCACATTCAACG-ATGCATCAATGCACATT
1 CATAGTGTATCGATGCACATTCAACGAATGCATCAATACACATT
* * ** *
2363882 CATAGTGTATCGATGCATATTCAAGGAATGCATCGGTACACTTT
1 CATAGTGTATCGATGCACATTCAACGAATGCATCAATACACATT
2363926 C-TAGTGTATCGATGCAC
1 CATAGTGTATCGATGCAC
2363943 TTTGCACAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
43 39 0.74
44 14 0.26
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAACGAATGCATCAATACACATT
Found at i:2371853 original size:17 final size:18
Alignment explanation
Indices: 2371810--2371854 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
2371800 TAAATTTCAA
2371810 AATATATT-A-TAATTAT
1 AATATATTAATTAATTAT
2371826 AATATGATTAATTAATTAT
1 AATAT-ATTAATTAATTAT
*
2371845 TATAT-TTAAT
1 AATATATTAAT
2371855 ATTTTACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 5 0.20
17 8 0.32
18 1 0.04
19 11 0.44
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
AATATATTAATTAATTAT
Found at i:2371964 original size:30 final size:32
Alignment explanation
Indices: 2371922--2371986 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
2371912 TTTTATAAAA
*
2371922 TATATATTTTAATTACTA-TATT-TATATATT
1 TATATATTTTAATTAATATTATTATATATATT
*
2371952 TATAT-TTATTAATTAATATTATTATATTTATT
1 TATATATT-TTAATTAATATTATTATATATATT
2371984 TAT
1 TAT
2371987 TATAATCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 2 0.07
30 14 0.47
31 4 0.13
32 10 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (32 bp):
TATATATTTTAATTAATATTATTATATATATT
Found at i:2371970 original size:22 final size:22
Alignment explanation
Indices: 2371923--2371988 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2371913 TTTATAAAAT
* * *
2371923 ATATATTT-TAATTACTATATTT
1 ATATATTTATATTTATTA-ATTA
2371945 ATATATTTATATTTATTAATTA
1 ATATATTTATATTTATTAATTA
*
2371967 ATAT-TATTATATTTATTTATTA
1 ATATAT-TTATATTTATTAATTA
2371989 TAATCATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.79
23 7 0.18
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATATTTATATTTATTAATTA
Found at i:2371975 original size:13 final size:13
Alignment explanation
Indices: 2371941--2371990 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
2371931 TAATTACTAT
2371941 ATTTA-TATATTTA
1 ATTTATTATA-TTA
2371954 TATTTATTA-ATTA
1 -ATTTATTATATTA
*
2371967 ATATTATTATATTT
1 AT-TTATTATATTA
2371981 ATTTATTATA
1 ATTTATTATA
2371991 ATCATTTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 2 0.06
13 17 0.53
14 11 0.34
15 2 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTATTATATTA
Found at i:2372000 original size:36 final size:36
Alignment explanation
Indices: 2371933--2372001 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
2371923 ATATATTTTA
* *
2371933 ATTACTATATTTATATATTTATATTTATTAATTAAT
1 ATTACTATATTTATATATTTATAATCATTAATTAAT
* *
2371969 ATTATTATATTTATTTA-TTATAATCATTTAATT
1 ATTACTATATTTATATATTTATAATCA-TTAATT
2372002 TCTACGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 7 0.25
36 21 0.75
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (36 bp):
ATTACTATATTTATATATTTATAATCATTAATTAAT
Found at i:2372771 original size:26 final size:24
Alignment explanation
Indices: 2372709--2372771 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
2372699 CATTTTAATC
2372709 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
2372733 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
2372756 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
2372772 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:2372773 original size:22 final size:23
Alignment explanation
Indices: 2372743--2372789 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2372733 AAAATATATT
2372743 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
2372766 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
2372788 TA
1 TA
2372790 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:2372803 original size:32 final size:32
Alignment explanation
Indices: 2372737--2372816 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
2372727 ATATTTAAAA
* *
2372737 TATATTTATTAATATTTCTAATAATATAATAT
1 TATATTTATTAATATTTATAATAAAATAATAT
2372769 TATATTT-TTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT--AT
*
2372801 TATATTATAATAATAT
1 TATATT-TATTAATAT
2372817 AAGATATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
30 13 0.32
31 6 0.15
32 15 0.38
33 1 0.03
34 5 0.12
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (32 bp):
TATATTTATTAATATTTATAATAAAATAATAT
Found at i:2372828 original size:23 final size:22
Alignment explanation
Indices: 2372777--2372849 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
2372767 ATTATATTTT
*
2372777 TAATATTATAATAAAAT-AATCAA
1 TAATATTATAATAATATAAAT--A
*
2372800 TTATATTATAATAATATAAGATA
1 TAATATTATAATAATATAA-ATA
*
2372823 TAATATTTTTAA-AATAT-AATA
1 TAATA-TTATAATAATATAAATA
2372844 TAATAT
1 TAATAT
2372850 AACACTATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 1 0.02
21 8 0.19
22 1 0.02
23 25 0.58
24 6 0.14
25 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (22 bp):
TAATATTATAATAATATAAATA
Found at i:2372849 original size:26 final size:26
Alignment explanation
Indices: 2372757--2372851 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 26
2372747 AATATTTCTA
* *
2372757 ATAATATAATATTATATTTTTAATATT
1 ATAATATAATATAATATTTTTAA-AAT
* * **
2372784 ATAATA-AA-ATAATCAATTATATTAT
1 ATAATATAATATAAT-ATTTTTAAAAT
2372809 AATAATATAAGATATAATATTTTTAAAAT
1 -ATAATAT-A-ATATAATATTTTTAAAAT
2372838 ATAATATAATATAA
1 ATAATATAATATAA
2372852 CACTATTACT
Statistics
Matches: 52, Mismatches: 10, Indels: 13
0.69 0.13 0.17
Matches are distributed among these distances:
25 5 0.10
26 19 0.37
27 7 0.13
28 8 0.15
29 8 0.15
30 5 0.10
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
ATAATATAATATAATATTTTTAAAAT
Found at i:2372982 original size:28 final size:28
Alignment explanation
Indices: 2372950--2373003 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
2372940 TTATAAAAAA
*
2372950 TAATATTTTAATAATAAATAA-ATTAATT
1 TAATATTTTAAAAAT-AATAATATTAATT
2372978 TAATATTTTAAAAATAATAATATTAA
1 TAATATTTTAAAAATAATAATATTAA
2373004 ATTTTATGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATATTTTAAAAATAATAATATTAATT
Found at i:2377344 original size:209 final size:208
Alignment explanation
Indices: 2376984--2377400 Score: 780
Period size: 209 Copynumber: 2.0 Consensus size: 208
2376974 ATATTAAACA
2376984 TAGGGTCAAGGCTTTAGACCTTAAGAATTTGTCTGAAGAATATAAACAAGCAAAGCTCTATGAAC
1 TAGGGTCAAGGCTTTAGACCTTAAGAATTTGTCTGAAGAATATAAACAAGCAAAGCTCTATGAAC
*
2377049 TGTCAGTGGAGTTTGAAAATAGAAGATTGAAGTCTTCTTTTAAAATCCCACCCTACCCAAACCCC
66 TATCAGTGGAGTTTGAAAATAGAAGATTGAAGTCTTCTTTTAAAATCCCACCCTACCCAAACCCC
*
2377114 ATATCTACATCTAAGACAACTGCACTACCAGTAACTACAAAGCTTTCTTCAATACCAAATCCAAA
131 ATATCTACATCTAAGACAACTGCACTACCAGTAACTACAAAGCTTACTTCAATACCAAATCCAAA
2377179 ACAAAATCTTATGG
196 ACAAAA-CTTATGG
* *
2377193 TAGGGTCAAGGCTTTAGACCTTAAGAATTTGTCTGAAGCATGTAAACAAGCAAAGCTCTATGAAC
1 TAGGGTCAAGGCTTTAGACCTTAAGAATTTGTCTGAAGAATATAAACAAGCAAAGCTCTATGAAC
*
2377258 TATCAGTGGAGTTTGAAAATAGAAGATTGAAGTCTTCTTTTAAAATCGCACCCTACCCAAACCCC
66 TATCAGTGGAGTTTGAAAATAGAAGATTGAAGTCTTCTTTTAAAATCCCACCCTACCCAAACCCC
2377323 ATATCTACATCTAAGACAACTGCACTACCAGTAACTACAAAGCTTACTTCAATACCAAATCCAAA
131 ATATCTACATCTAAGACAACTGCACTACCAGTAACTACAAAGCTTACTTCAATACCAAATCCAAA
2377388 ACAAAACTTATGG
196 ACAAAACTTATGG
2377401 ATTATAGAAG
Statistics
Matches: 203, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
208 7 0.03
209 196 0.97
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (208 bp):
TAGGGTCAAGGCTTTAGACCTTAAGAATTTGTCTGAAGAATATAAACAAGCAAAGCTCTATGAAC
TATCAGTGGAGTTTGAAAATAGAAGATTGAAGTCTTCTTTTAAAATCCCACCCTACCCAAACCCC
ATATCTACATCTAAGACAACTGCACTACCAGTAACTACAAAGCTTACTTCAATACCAAATCCAAA
ACAAAACTTATGG
Found at i:2385657 original size:16 final size:16
Alignment explanation
Indices: 2385636--2385668 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2385626 TAATAAATAA
2385636 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2385652 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2385668 A
1 A
2385669 AATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2385758 original size:16 final size:16
Alignment explanation
Indices: 2385737--2385797 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
2385727 TAATAAATAA
2385737 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
2385753 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
2385769 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
2385785 ACGAACATCAACG
1 ACGAACATAAACG
2385798 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.54, C:0.23, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2386804 original size:24 final size:24
Alignment explanation
Indices: 2386776--2386850 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
2386766 GATTGGGTTA
*
2386776 AACATAAATGAAAGAACATAAACG
1 AACATAAATGAACGAACATAAACG
2386800 AACAT-AATCGAACGAACATAAACG
1 AACATAAAT-GAACGAACATAAACG
** *
2386824 AACATAACCGAACGAACATAATCG
1 AACATAAATGAACGAACATAAACG
2386848 AAC
1 AAC
2386851 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.07
24 41 0.91
25 1 0.02
ACGTcount: A:0.56, C:0.20, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:2386813 original size:14 final size:14
Alignment explanation
Indices: 2386796--2386851 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
2386786 AAAGAACATA
2386796 AACGAACATAATCG
1 AACGAACATAATCG
2386810 AACGAACAT-A---
1 AACGAACATAATCG
*
2386820 AACGAACATAACCG
1 AACGAACATAATCG
2386834 AACGAACATAATCG
1 AACGAACATAATCG
2386848 AACG
1 AACG
2386852 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:2386850 original size:10 final size:10
Alignment explanation
Indices: 2386789--2386836 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
2386779 ATAAATGAAA
2386789 GAACATAAAC
1 GAACATAAAC
2386799 GAACATAATCGAAC
1 GAACAT-A---AAC
2386813 GAACATAAAC
1 GAACATAAAC
*
2386823 GAACATAACC
1 GAACATAAAC
2386833 GAAC
1 GAAC
2386837 GAACATAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:2386861 original size:24 final size:24
Alignment explanation
Indices: 2386789--2386850 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
2386779 ATAAATGAAA
*
2386789 GAACATAAACGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
2386813 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
*
2386837 GAACATAATCGAAC
1 GAACATAAACGAAC
2386851 GTTCACGAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.23, G:0.13, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:2387581 original size:60 final size:59
Alignment explanation
Indices: 2387456--2387615 Score: 162
Period size: 60 Copynumber: 2.6 Consensus size: 59
2387446 CATCCTCGTT
* ** *
2387456 CTAAATTAGTCCCTAAACTTTTAAACATTTCAATTTTATCCTTAAACTATAACAATTATT
1 CTAAATTAGTCCC-AAACTTTTGAACATTTCAATTTTATCCCCAAACTATAACAATTATC
* * * *
2387516 TTAAATTAGTCCTCAAACTTTTGAACATTTC-ATTTTCATCCCCAAGCTATGA-TATTCATC
1 CTAAATTAGTCC-CAAACTTTTGAACATTTCAATTTT-ATCCCCAAACTATAACAATT-ATC
* *
2387576 CTAAATTGGTCCCCAAACTTTTTGAATATTTCAATTTTAT
1 CTAAATTAGT-CCCAAAC-TTTTGAACATTTCAATTTTAT
2387616 TCTAAATTAT
Statistics
Matches: 83, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
59 8 0.10
60 53 0.64
61 17 0.20
62 5 0.06
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (59 bp):
CTAAATTAGTCCCAAACTTTTGAACATTTCAATTTTATCCCCAAACTATAACAATTATC
Found at i:2390023 original size:19 final size:20
Alignment explanation
Indices: 2389987--2390034 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
2389977 TCTAAATCCT
* *
2389987 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATTCCATTTTAG
2390007 TTTTCAAAA-TCCATTTTAG
1 TTTTCAAAATTCCATTTTAG
*
2390026 CTTTCAAAA
1 TTTTCAAAA
2390035 GAAAATCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.31, C:0.15, G:0.06, T:0.48
Consensus pattern (20 bp):
TTTTCAAAATTCCATTTTAG
Found at i:2391795 original size:48 final size:48
Alignment explanation
Indices: 2391727--2391821 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 48
2391717 ACCTGAATTG
*
2391727 ACCCAACTTACTATAAACTCAAATAAAA-CTGAAACTCGAAATGACCCA
1 ACCCAACTTACTATAAACTCAAATAAAATC-GAAACTCGAAATAACCCA
* *
2391775 ACCCGACTTACTATAGACTCAAATAAAATCGAAACTCGAAATAACCC
1 ACCCAACTTACTATAAACTCAAATAAAATCGAAACTCGAAATAACCC
2391822 GACTCGACCC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 42 0.98
49 1 0.02
ACGTcount: A:0.46, C:0.27, G:0.07, T:0.19
Consensus pattern (48 bp):
ACCCAACTTACTATAAACTCAAATAAAATCGAAACTCGAAATAACCCA
Found at i:2393842 original size:21 final size:21
Alignment explanation
Indices: 2393818--2393907 Score: 56
Period size: 21 Copynumber: 4.3 Consensus size: 21
2393808 AGAGGTTAAG
2393818 ACCTTTCGATGAAATGACTTA
1 ACCTTTCGATGAAATGACTTA
** * * *
2393839 ACCTTTTAATTAAAAGACTTC
1 ACCTTTCGATGAAATGACTTA
* * * **
2393860 TCCTTTTGATGAAAGGGTTTA
1 ACCTTTCGATGAAATGACTTA
*
2393881 ACCTTTTC-ATGAAATGATTTA
1 ACC-TTTCGATGAAATGACTTA
*
2393902 ATCTTT
1 ACCTTT
2393908 TCATGAAGAG
Statistics
Matches: 51, Mismatches: 17, Indels: 3
0.72 0.24 0.04
Matches are distributed among these distances:
20 3 0.06
21 45 0.88
22 3 0.06
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
ACCTTTCGATGAAATGACTTA
Found at i:2393908 original size:21 final size:21
Alignment explanation
Indices: 2393861--2393914 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
2393851 AAAGACTTCT
* *
2393861 CCTTTTGATGAAAGGGTTTAA
1 CCTTTTCATGAAAGGATTTAA
*
2393882 CCTTTTCATGAAATGATTTAA
1 CCTTTTCATGAAAGGATTTAA
*
2393903 TCTTTTCATGAA
1 CCTTTTCATGAA
2393915 GAGAATTGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (21 bp):
CCTTTTCATGAAAGGATTTAA
Found at i:2404662 original size:5 final size:5
Alignment explanation
Indices: 2404643--2404686 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
2404633 AACTTGTAAC
2404643 TTGTG -TGTG -TGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG T
1 TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG TTGTG T
2404687 CTTGTAACTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 8 0.21
5 30 0.79
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (5 bp):
TTGTG
Found at i:2404786 original size:21 final size:21
Alignment explanation
Indices: 2404762--2404857 Score: 86
Period size: 21 Copynumber: 4.6 Consensus size: 21
2404752 AGAGGTTAAG
*
2404762 ACCTTTCGATGAAAGGACTTA
1 ACCTTTTGATGAAAGGACTTA
* *
2404783 ACCTTTTGATTAAAAGACTT-
1 ACCTTTTGATGAAAGGACTTA
**
2404803 TTCTTTTGATGAAAGGACTTA
1 ACCTTTTGATGAAAGGACTTA
* * * *
2404824 ACATTTTCATGAAATGATTTA
1 ACCTTTTGATGAAAGGACTTA
* *
2404845 ATCTTTTCATGAA
1 ACCTTTTGATGAA
2404858 GAGAATTGTT
Statistics
Matches: 59, Mismatches: 15, Indels: 2
0.78 0.20 0.03
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (21 bp):
ACCTTTTGATGAAAGGACTTA
Found at i:2404810 original size:20 final size:20
Alignment explanation
Indices: 2404785--2404822 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2404775 AGGACTTAAC
*
2404785 CTTTTGATTAAAAGACTTTT
1 CTTTTGATGAAAAGACTTTT
*
2404805 CTTTTGATGAAAGGACTT
1 CTTTTGATGAAAAGACTT
2404823 AACATTTTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.45
Consensus pattern (20 bp):
CTTTTGATGAAAAGACTTTT
Found at i:2405202 original size:12 final size:12
Alignment explanation
Indices: 2405187--2405314 Score: 70
Period size: 12 Copynumber: 10.3 Consensus size: 12
2405177 TTTGGTTTTT
2405187 TTATATATTATA
1 TTATATATTATA
*
2405199 TTATATTTTCATA
1 TTATATATT-ATA
*
2405212 TTACTATTATTATTG
1 TTA-TA-TATTA-TA
2405227 TTATGATTATTAT-
1 TTAT-A-TATTATA
* * *
2405240 TTTTCTATTTTA
1 TTATATATTATA
*
2405252 CTCATATA-TATA
1 -TTATATATTATA
2405264 -TATATA-TATA
1 TTATATATTATA
2405274 TATATATATATATA
1 T-TATATAT-TATA
2405288 TATATATATTAT-
1 T-TATATATTATA
2405300 TTAT-TATTATA
1 TTATATATTATA
2405311 TTAT
1 TTAT
2405315 TTTTTTTTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
10 15 0.16
11 12 0.13
12 18 0.19
13 16 0.17
14 18 0.19
15 14 0.15
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATATATTATA
Found at i:2405262 original size:2 final size:2
Alignment explanation
Indices: 2405255--2405296 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2405245 TATTTTACTC
2405255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2405297 TATTTATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2405312 original size:15 final size:15
Alignment explanation
Indices: 2405292--2405330 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2405282 TATATATATA
2405292 TATATTATTTATTAT
1 TATATTATTTATTAT
* *
2405307 TATATTATTTTTTTT
1 TATATTATTTATTAT
2405322 TAT-TTATTT
1 TATATTATTT
2405331 TACTTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATATTATTTATTAT
Found at i:2405328 original size:19 final size:19
Alignment explanation
Indices: 2405288--2405344 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
2405278 TATATATATA
* *
2405288 TATATATATTATTTATTA-T
1 TATAT-TATTTTTTTTTATT
2405307 TATATTATTTTTTTTTATT
1 TATATTATTTTTTTTTATT
* * *
2405326 TATTTTACTTATTTTTATT
1 TATATTATTTTTTTTTATT
2405345 CTTCATTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 10 0.31
19 22 0.69
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TATATTATTTTTTTTTATT
Found at i:2408616 original size:8 final size:8
Alignment explanation
Indices: 2408603--2408638 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
2408593 GAACATTTCA
*
2408603 TGCATTCT
1 TGCATTTT
2408611 TGCA-TTT
1 TGCATTTT
2408618 TGCATTTT
1 TGCATTTT
2408626 TGCATTTT
1 TGCATTTT
2408634 TGCAT
1 TGCAT
2408639 CTTCATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (8 bp):
TGCATTTT
Found at i:2408623 original size:15 final size:16
Alignment explanation
Indices: 2408603--2408638 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2408593 GAACATTTCA
2408603 TGCATTCTTGCA-TTT
1 TGCATTCTTGCATTTT
*
2408618 TGCATTTTTGCATTTT
1 TGCATTCTTGCATTTT
2408634 TGCAT
1 TGCAT
2408639 CTTCATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (16 bp):
TGCATTCTTGCATTTT
Found at i:2409768 original size:15 final size:14
Alignment explanation
Indices: 2409757--2409829 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
2409747 AACAAAAATG
2409757 AAAAGAAAAAAAAC
1 AAAAGAAAAAAAAC
*
2409771 AAAACAAAAAAAA-
1 AAAAGAAAAAAAAC
* * *
2409784 AAGAGAAACAAAAG
1 AAAAGAAAAAAAAC
2409798 AAAA-AAAGAAAGAAC
1 AAAAGAAA-AAA-AAC
* *
2409813 AAAA-ATAAAAAAG
1 AAAAGAAAAAAAAC
2409826 AAAA
1 AAAA
2409830 AGGGACAAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
13 19 0.40
14 20 0.43
15 8 0.17
ACGTcount: A:0.84, C:0.05, G:0.10, T:0.01
Consensus pattern (14 bp):
AAAAGAAAAAAAAC
Found at i:2409780 original size:20 final size:20
Alignment explanation
Indices: 2409747--2409830 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 20
2409737 TCCAATCAAG
*
2409747 AACAAAAATGAAAAGAAAAAA
1 AACAAAAA-AAAAAGAAAAAA
2409768 AACAAAACAAAAAA-AAAAGAGA
1 AACAAAA-AAAAAAGAAAA-A-A
*
2409790 AACAAAAGAAAAAAAGAAAGAAC
1 AAC-AAA-AAAAAAAGAAA-AAA
*
2409813 AA-AAATAAAAAAGAAAAA
1 AACAAAAAAAAAAGAAAAA
2409831 GGGACAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
19 2 0.04
20 14 0.26
21 15 0.28
22 5 0.09
23 11 0.21
24 5 0.09
25 1 0.02
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (20 bp):
AACAAAAAAAAAAGAAAAAA
Found at i:2409784 original size:17 final size:16
Alignment explanation
Indices: 2409762--2409830 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
2409752 AAATGAAAAG
*
2409762 AAAAAAAACAAAACAA
1 AAAAAAAAAAAAACAA
*
2409778 AAAAAAAAGAGAAACAA
1 AAAAAAAA-AAAAACAA
* *
2409795 AAGAAAAAAAGAAAGAA
1 AA-AAAAAAAAAAACAA
* * *
2409812 CAAAAATAAAAAAGAA
1 AAAAAAAAAAAAACAA
2409828 AAA
1 AAA
2409831 GGGACAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
16 22 0.50
17 16 0.36
18 6 0.14
ACGTcount: A:0.84, C:0.06, G:0.09, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAAAAACAA
Found at i:2409790 original size:27 final size:26
Alignment explanation
Indices: 2409747--2409801 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
2409737 TCCAATCAAG
**
2409747 AACAAAAATGAAAAGAAAAAAAACAA
1 AACAAAAAAAAAAAGAAAAAAAACAA
* *
2409773 AACAAAAAAAAAAGAGAAACAAAAGAA
1 AACAAAAAAAAAA-AGAAAAAAAACAA
2409800 AA
1 AA
2409802 AAAGAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.82, C:0.07, G:0.09, T:0.02
Consensus pattern (26 bp):
AACAAAAAAAAAAAGAAAAAAAACAA
Found at i:2409814 original size:37 final size:36
Alignment explanation
Indices: 2409757--2409828 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
2409747 AACAAAAATG
2409757 AAAAGAAAAAAAACAAAACAAAAA-AAAAAGAGAAAC
1 AAAAGAAAAAAAACAAAACAAAAATAAAAA-AGAAAC
2409793 AAAAGAAAAAAAGA-AAGAACAAAAATAAAAAAGAAA
1 AAAAGAAAAAAA-ACAA-AACAAAAATAAAAAAGAAA
2409829 AAGGGACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
36 14 0.42
37 14 0.42
38 5 0.15
ACGTcount: A:0.83, C:0.06, G:0.10, T:0.01
Consensus pattern (36 bp):
AAAAGAAAAAAAACAAAACAAAAATAAAAAAGAAAC
Found at i:2409823 original size:21 final size:20
Alignment explanation
Indices: 2409744--2409829 Score: 79
Period size: 22 Copynumber: 4.1 Consensus size: 20
2409734 AGATCCAATC
2409744 AAGAACAAAAATGAAAAGAAAA
1 AAGAACAAAAAT-AAAA-AAAA
2409766 AA-AACAAAACA-AAAAAAAA
1 AAGAACAAAA-ATAAAAAAAA
*
2409785 AGAGAAACAAAAGA-AAAAAAGA
1 A-AG-AACAAAA-ATAAAAAAAA
2409807 AAGAACAAAAATAAAAAAGAA
1 AAGAACAAAAATAAAAAA-AA
2409828 AA
1 AA
2409830 AGGGACAAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
19 6 0.11
20 18 0.33
21 12 0.22
22 19 0.35
ACGTcount: A:0.81, C:0.06, G:0.10, T:0.02
Consensus pattern (20 bp):
AAGAACAAAAATAAAAAAAA
Found at i:2411507 original size:106 final size:106
Alignment explanation
Indices: 2411384--2412429 Score: 1517
Period size: 106 Copynumber: 10.0 Consensus size: 106
2411374 GCCACTCGAC
* * *
2411384 ACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAAGTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
**
2411449 GAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* *
2411490 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
2411555 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
2411596 ACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
2411661 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
2411702 ACAACGCAAGTTCAACTTCACGATGATGGGACCGCTGGTTGTCAATAAAC---TTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
*
2411764 GAGCCAATTTCAACTTAACAGCGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * * *
2411805 ACAACGTAAGTTCAACTTCACGACGAAGAGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
* *
2411870 GAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCAAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* *
2411911 ACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAAC-AACAATTTCCCAATTTC
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAATTTC
*
2411974 AGAGCCAATTTCAACTTCGCAGCGAAGGATATTGGACTCCAG
65 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
*
2412016 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
**
2412081 GAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * *
2412122 ACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
* *
2412187 GAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AG
* ** * * *
2412228 ACAACACAAGCCCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AATTT--C-A-TTCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
* * *
2412287 GAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAG
66 GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
* * * **** *
2412328 ACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTT-TTGGTTGCA
1 ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
* *
2412392 GAGCCAATTTCAACTTCAC-GACGGAGGATATTAGACTC
66 GAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
2412430 GGAACAATGC
Statistics
Matches: 859, Mismatches: 67, Indels: 29
0.90 0.07 0.03
Matches are distributed among these distances:
100 79 0.09
101 4 0.00
102 6 0.01
103 97 0.11
104 5 0.01
105 137 0.16
106 531 0.62
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
ACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCA
GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAG
Found at i:2413170 original size:37 final size:37
Alignment explanation
Indices: 2413120--2413216 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
2413110 TCCTACTTGA
* *
2413120 ATTCAAACTCCTAAAAATAGGATAGAATTTTGCTAGG
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTACTAGG
* *
2413157 ATTCAAACTCCTAAAAATAGGATAGAGTTCTACTATG
1 ATTCAAACTCCTAAAAATAGGATAGAATTCTACTAGG
* *
2413194 ATTTAAACTCCTAAAGATAGGAT
1 ATTCAAACTCCTAAAAATAGGAT
2413217 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
ATTCAAACTCCTAAAAATAGGATAGAATTCTACTAGG
Found at i:2413767 original size:19 final size:19
Alignment explanation
Indices: 2413686--2413776 Score: 60
Period size: 19 Copynumber: 4.5 Consensus size: 19
2413676 TTTTTTACAC
*
2413686 TATATACTA-TTATTATATA
1 TATATA-TATTTATTATTTA
* *
2413705 TACATATATTTTTTATTTA
1 TATATATATTTATTATTTA
*
2413724 T-TCATATTCATTTGATTATTTTT
1 TAT-ATA-T-ATTT-ATTA-TTTA
2413747 TAATACTATATTTATTATTTA
1 T-ATA-TATATTTATTATTTA
2413768 TATATATAT
1 TATATATAT
2413777 ATACTTTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 18
0.69 0.09 0.22
Matches are distributed among these distances:
18 2 0.04
19 22 0.39
20 4 0.07
21 8 0.14
22 7 0.12
23 8 0.14
24 2 0.04
25 3 0.05
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.59
Consensus pattern (19 bp):
TATATATATTTATTATTTA
Found at i:2414002 original size:18 final size:19
Alignment explanation
Indices: 2413981--2414031 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
2413971 TTTTGATTTT
2413981 TTTTTATATTATATTA-TA
1 TTTTTATATTATATTATTA
*
2413999 TTTTCATATTACTATTATTA
1 TTTTTATATTA-TATTATTA
*
2414019 TTGTTATGATTAT
1 TTTTTAT-ATTAT
2414032 TACTTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.37
19 5 0.19
20 8 0.30
21 4 0.15
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTATATTATATTATTA
Found at i:2414080 original size:4 final size:4
Alignment explanation
Indices: 2414067--2414104 Score: 67
Period size: 4 Copynumber: 9.2 Consensus size: 4
2414057 TATATATTAA
2414067 TATT TCATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT T-ATT TATT TATT TATT TATT TATT TATT TATT T
2414105 TTCCTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2414113 original size:16 final size:16
Alignment explanation
Indices: 2414094--2414134 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2414084 TATTTATTTA
*
2414094 TTTATTTATTTTTCCT
1 TTTATTTATTTTTACT
2414110 TTTATTT-TTTTTACT
1 TTTATTTATTTTTACT
2414125 TATT-TTTATT
1 T-TTATTTATT
2414135 CTTCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTATTTTTACT
Found at i:2417424 original size:8 final size:8
Alignment explanation
Indices: 2417411--2417446 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
2417401 GAACATTTCA
*
2417411 TGCATTCT
1 TGCATTTT
2417419 TGCA-TTT
1 TGCATTTT
2417426 TGCATTTT
1 TGCATTTT
2417434 TGCATTTT
1 TGCATTTT
2417442 TGCAT
1 TGCAT
2417447 CTTCATCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 6 0.23
8 20 0.77
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (8 bp):
TGCATTTT
Found at i:2417431 original size:15 final size:16
Alignment explanation
Indices: 2417411--2417446 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2417401 GAACATTTCA
2417411 TGCATTCTTGCA-TTT
1 TGCATTCTTGCATTTT
*
2417426 TGCATTTTTGCATTTT
1 TGCATTCTTGCATTTT
2417442 TGCAT
1 TGCAT
2417447 CTTCATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.56
Consensus pattern (16 bp):
TGCATTCTTGCATTTT
Found at i:2418639 original size:18 final size:17
Alignment explanation
Indices: 2418606--2418655 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
2418596 AACAAAAAAG
*
2418606 AAAAGAAGAAAA-AAAC
1 AAAAGAAAAAAAGAAAC
*
2418622 CAAAGAAAAAAGAGAAAC
1 AAAAGAAAAAA-AGAAAC
2418640 AAAAGAAAAAAAGAAA
1 AAAAGAAAAAAAGAAA
2418656 AAACAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 9 0.31
17 6 0.21
18 14 0.48
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAAGAAAC
Found at i:2418649 original size:30 final size:31
Alignment explanation
Indices: 2418593--2418664 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
2418583 AGATCCAATC
*
2418593 AAGAACAAAAAAGAAAAGAAGAAAAAAACCA
1 AAGAACAAAAAAGAAAAAAAGAAAAAAACCA
* *
2418624 AAGAA-AAAAGAGAAACAAAAGAAAAAAA-GA
1 AAGAACAAAAAAGAAA-AAAAGAAAAAAACCA
*
2418654 AAAAACAAAAA
1 AAGAACAAAAA
2418665 TCAAAAAGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (31 bp):
AAGAACAAAAAAGAAAAAAAGAAAAAAACCA
Found at i:2418656 original size:13 final size:12
Alignment explanation
Indices: 2418600--2418678 Score: 50
Period size: 13 Copynumber: 6.0 Consensus size: 12
2418590 ATCAAGAACA
2418600 AAAAAGAAAAGAAG
1 AAAAA-AAAA-AAG
*
2418614 AAAAAAACCAAAG
1 AAAAAAA-AAAAG
* *
2418627 AAAAAAGAGAAAC
1 AAAAAA-AAAAAG
2418640 AAAAGAAAAAAAG
1 AAAA-AAAAAAAG
*
2418653 AAAAAACAAAAATC
1 AAAAAA-AAAAA-G
*
2418667 AAAAAGAAAAAG
1 AAAAAAAAAAAG
2418679 GGACAAAAAG
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
12 2 0.04
13 36 0.69
14 14 0.27
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:2418657 original size:8 final size:8
Alignment explanation
Indices: 2418593--2418658 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
2418583 AGATCCAATC
*
2418593 AAGAACAA
1 AAGAAAAA
*
2418601 AA-AAGAA
1 AAGAAAAA
2418608 AAGAAGAAA
1 AAGAA-AAA
**
2418617 AA-AACCA
1 AAGAAAAA
2418624 AAGAAAAA
1 AAGAAAAA
2418632 AGAGAAACAA
1 A-AGAAA-AA
2418642 AAGAAAAA
1 AAGAAAAA
2418650 AAGAAAAA
1 AAGAAAAA
2418658 A
1 A
2418659 CAAAAATCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
7 9 0.19
8 21 0.45
9 14 0.30
10 3 0.06
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:2418659 original size:20 final size:20
Alignment explanation
Indices: 2418601--2418677 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
2418591 TCAAGAACAA
*
2418601 AAAAGAAAAGAAGAAAAAAAC
1 AAAAGAAAAAAAG-AAAAAAC
* *
2418622 CAAAG-AAAAAAG-AGAAAC
1 AAAAGAAAAAAAGAAAAAAC
2418640 AAAAGAAAAAAAGAAAAAAC
1 AAAAGAAAAAAAGAAAAAAC
*
2418660 AAAA-ATCAAAAAGAAAAA
1 AAAAGA-AAAAAAGAAAAA
2418678 GGGACAAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.19
19 8 0.17
20 26 0.55
21 4 0.09
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (20 bp):
AAAAGAAAAAAAGAAAAAAC
Found at i:2418678 original size:26 final size:26
Alignment explanation
Indices: 2418623--2418677 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
2418613 GAAAAAAACC
* *
2418623 AAAGAAAAAAGAGAAACAAAAGAAAA
1 AAAGAAAAAACAAAAACAAAAGAAAA
2418649 AAAGAAAAAACAAAAATCAAAAAGAAAA
1 AAAGAAAAAACAAAAA-C-AAAAGAAAA
2418677 A
1 A
2418678 GGGACAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.56
27 1 0.04
28 10 0.40
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (26 bp):
AAAGAAAAAACAAAAACAAAAGAAAA
Found at i:2420391 original size:106 final size:106
Alignment explanation
Indices: 2420206--2420723 Score: 808
Period size: 106 Copynumber: 4.9 Consensus size: 106
2420196 TCACGACGAA
* * * *
2420206 TGTCAACAAACAAGTTCCCAATTTCAGAGCCAATTTCAATTTCACAGCGAAGAATATTAGACTCC
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
2420271 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * *
2420312 TGTCAAGAAACAATTTCCAAATTTCATAGCCAATTTCAACATCACAGCGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
2420377 AGACAA-AGCAAGTTCAACTTCACGACGAA--GACCGCTGGT
66 AGACAACA-CAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
2420416 TGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
2420481 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGT
66 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
2420522 TGTCAATAAACAACTTCCCAATTTCAGAGCCAAATTCAACTTCATAGCGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
2420587 AGACAACACAAGTTCAACTTCATGACGAAGGGACCGCTGGT
66 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
2420628 TGTCAACAAACAACTTCTCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
2420693 AGACAACACAAGTTCAACTTCACAACGAAGG
66 AGACAACACAAGTTCAACTTCACGACGAAGG
2420724 ATATTGGACT
Statistics
Matches: 379, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
104 97 0.26
105 1 0.00
106 281 0.74
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (106 bp):
TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:2420450 original size:210 final size:211
Alignment explanation
Indices: 2420206--2420723 Score: 815
Period size: 210 Copynumber: 2.5 Consensus size: 211
2420196 TCACGACGAA
* * * *
2420206 TGTCAACAAACAAGTTCCCAATTTCAGAGCCAATTTCAATTTCACAGCGAAGAATATTAGACTCC
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* * *
2420271 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAGAAACAATTTCCAAATTT
66 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAAGAAACAACTTCCAAATTT
* *
2420336 CATAGCCAATTTCAACATCACAGCGAAGGATATTGGACTCCAGACAA-AGCAAGTTCAACTTCAC
131 CAGAGCCAAATTCAACATCACAGCGAAGGATATTGGACTCCAGACAACA-CAAGTTCAACTTCAC
2420400 GACGAA-GACCGCTGGT
195 GACGAAGGACCGCTGGT
* * *
2420416 TGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
* *
2420481 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAACTTCCCAATTT
66 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAAGAAACAACTTCCAAATTT
* * *
2420546 CAGAGCCAAATTCAACTTCATAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATG
131 CAGAGCCAAATTCAACATCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
2420611 ACGAAGGGACCGCTGGT
196 ACGAA-GGACCGCTGGT
* * *
2420628 TGTCAACAAACAACTTCTCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCA
1 TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
*
2420693 AGACAACACAAGTTCAACTTCACAACGAAGG
66 AGACAACACAAGTTCAACTTCACGACGAAGG
2420724 ATATTGGACT
Statistics
Matches: 282, Mismatches: 23, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
210 182 0.65
211 1 0.00
212 99 0.35
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (211 bp):
TGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAAGAAACAACTTCCAAATTT
CAGAGCCAAATTCAACATCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
ACGAAGGACCGCTGGT
Found at i:2420710 original size:43 final size:43
Alignment explanation
Indices: 2420662--2420758 Score: 167
Period size: 43 Copynumber: 2.3 Consensus size: 43
2420652 CAGAGCCAAT
*
2420662 TTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAG
* *
2420705 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
1 TTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAG
2420748 TTCAACTTCAC
1 TTCAACTTCAC
2420759 GATGAAGGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAG
Found at i:2420748 original size:149 final size:149
Alignment explanation
Indices: 2420556--2420872 Score: 499
Period size: 149 Copynumber: 2.1 Consensus size: 149
2420546 CAGAGCCAAA
* * *
2420556 TTCAACTTCATAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATGACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
*
2420621 CGCTGGTTGTCAACAAACAACTTCTCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
66 CGCTGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
* *
2420686 GGACTCAAGACAACACAAG
131 GGACCCAACACAACACAAG
* *
2420705 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
* * * *
2420770 CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTT
66 CGCTGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
2420835 GGACCCAACACAACACAAG
131 GGACCCAACACAACACAAG
** *
2420854 CCCAACTTCACGACGAAGG
1 TTCAACTTCACAACGAAGG
2420873 GGCGGTTGAT
Statistics
Matches: 153, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (149 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
CGCTGGTTGTCAACAAACAACTTCCCAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATT
GGACCCAACACAACACAAG
Found at i:2420816 original size:106 final size:103
Alignment explanation
Indices: 2420705--2421045 Score: 359
Period size: 106 Copynumber: 3.3 Consensus size: 103
2420695 ACAACACAAG
* *
2420705 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
*
2420770 CGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCAAT
66 AGCTGGTTGTCAA-AAACAA-TTCCC-ATTTCAGAGCCAAT
* * * * ** *
2420811 TTCAACTTCTCAGCGAAGGATCTTGGAC-CCAACACAACACAAGCCCAACTTCACGACGAAGGGG
1 TTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACACAAGTTCAACTTCACGACGAAGGGA
* * * * * *
2420875 CGGTTGATTGTCAACAA-AATT-TCA-TTCAGAGTCAA-
65 CAGCTGGTTGTCAAAAACAATTCCCATTTCAGAGCCAAT
** * * *
2420910 TTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACATAAGTTCAACTTCACAACGAAGGGAC
1 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
* *
2420975 AGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAAT
66 AGCTGGTTGTCAA-AAACAA-TTCCC-ATTTCAGAGCCAAT
* *
2421016 TTCAACTTCACGACGGAGGATATTGGACTC
1 TTCAACTTCACAACGAAGGATATTGGACTC
2421046 GAAACAATGC
Statistics
Matches: 189, Mismatches: 37, Indels: 18
0.77 0.15 0.07
Matches are distributed among these distances:
99 63 0.33
100 13 0.07
101 3 0.02
102 3 0.02
103 3 0.02
104 2 0.01
105 13 0.07
106 89 0.47
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (103 bp):
TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGAC
AGCTGGTTGTCAAAAACAATTCCCATTTCAGAGCCAAT
Found at i:2421835 original size:36 final size:37
Alignment explanation
Indices: 2421734--2421837 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
2421724 CCTTTTCGTC
* *
2421734 CTACTAGAATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2421771 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
2421808 CTACTATGATT-TAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
2421838 CCAAAAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
36 17 0.30
37 40 0.70
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:2422299 original size:22 final size:23
Alignment explanation
Indices: 2422274--2422320 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
2422264 ATTGATTCTT
2422274 TACATATATATATTA-TTATTTA
1 TACATATATATATTATTTATTTA
* *
2422296 TACATATATTTTTTATTTATTTA
1 TACATATATATATTATTTATTTA
2422319 TA
1 TA
2422321 TTCATTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TACATATATATATTATTTATTTA
Found at i:2422321 original size:19 final size:20
Alignment explanation
Indices: 2422272--2422321 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
2422262 CAATTGATTC
*
2422272 TTTACATATATATATTATTA
1 TTTATATATATATATTATTA
* *
2422292 TTTATACATATAT-TTTTTA
1 TTTATATATATATATTATTA
*
2422311 TTTATTTATAT
1 TTTATATATAT
2422322 TCATTTGGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATATATATATTATTA
Found at i:2422626 original size:2 final size:2
Alignment explanation
Indices: 2422621--2422676 Score: 91
Period size: 2 Copynumber: 29.5 Consensus size: 2
2422611 TTTTCTCATT
2422621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2422662 T- TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA T
2422677 TTCATTTATT
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 48 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2428789 original size:39 final size:39
Alignment explanation
Indices: 2428693--2428827 Score: 153
Period size: 39 Copynumber: 3.4 Consensus size: 39
2428683 TATTTGAGTC
* * * * * *
2428693 GCACCAAAGTGCTTACGCATAAGGTTACGTCGACCCTTTTT
1 GCACCGAAGTGCTTACGCATAAGGATGCATCTATCC--TTT
* ** *
2428734 TCACCGAAGTGCTTACGCATAAGGATGTGTTTATCCTTT
1 GCACCGAAGTGCTTACGCATAAGGATGCATCTATCCTTT
*
2428773 GCACCGAAGTGCTTACGCATAAGGCTGCATCTATCCTTT
1 GCACCGAAGTGCTTACGCATAAGGATGCATCTATCCTTT
2428812 GCACCGAAGTGCTTAC
1 GCACCGAAGTGCTTAC
2428828 CCAATATGTA
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 53 0.65
41 28 0.35
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.30
Consensus pattern (39 bp):
GCACCGAAGTGCTTACGCATAAGGATGCATCTATCCTTT
Found at i:2433450 original size:23 final size:23
Alignment explanation
Indices: 2433424--2433471 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
2433414 ATAAAGTACA
*
2433424 ATAACATACTAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
** *
2433447 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
2433470 AT
1 AT
2433472 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:2434220 original size:18 final size:18
Alignment explanation
Indices: 2434197--2434233 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2434187 CGAAATATAT
2434197 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2434215 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2434233 A
1 A
2434234 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2434462 original size:22 final size:23
Alignment explanation
Indices: 2434437--2434500 Score: 94
Period size: 22 Copynumber: 2.8 Consensus size: 23
2434427 ATGCGAGATA
2434437 GATACCTATTACATTATATAA-C
1 GATACCTATTACATTATATAAGC
*
2434459 GATACCTATTACATTATATAAGG
1 GATACCTATTACATTATATAAGC
* *
2434482 GCTACCTATTACATCATAT
1 GATACCTATTACATTATAT
2434501 GTTTACCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
22 21 0.55
23 17 0.45
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (23 bp):
GATACCTATTACATTATATAAGC
Found at i:2434880 original size:20 final size:20
Alignment explanation
Indices: 2434851--2434903 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
2434841 GATAGACACT
*
2434851 TTACAATATAACCATACCTA
1 TTACATTATAACCATACCTA
*
2434871 TTACATTATATAAACGATACCTA
1 TTACA-T-TAT-AACCATACCTA
2434894 -TACATTATAA
1 TTACATTATAA
2434904 GGGCTACCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.07
20 8 0.29
21 1 0.04
22 7 0.25
23 10 0.36
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (20 bp):
TTACATTATAACCATACCTA
Found at i:2434897 original size:22 final size:22
Alignment explanation
Indices: 2434856--2434902 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
2434846 ACACTTTACA
2434856 ATATAACCATACCTATTACATT
1 ATATAACCATACCTATTACATT
*
2434878 ATATAAACGATACCTA-TACATT
1 ATAT-AACCATACCTATTACATT
2434900 ATA
1 ATA
2434903 AGGGCTACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 10 0.43
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (22 bp):
ATATAACCATACCTATTACATT
Done.